[go: up one dir, main page]

WO2024227447A1 - Compositions et méthodes d'analyse d'un échantillon pour des cellules immunitaires spécifiques d'un antigène - Google Patents

Compositions et méthodes d'analyse d'un échantillon pour des cellules immunitaires spécifiques d'un antigène Download PDF

Info

Publication number
WO2024227447A1
WO2024227447A1 PCT/CN2024/091080 CN2024091080W WO2024227447A1 WO 2024227447 A1 WO2024227447 A1 WO 2024227447A1 CN 2024091080 W CN2024091080 W CN 2024091080W WO 2024227447 A1 WO2024227447 A1 WO 2024227447A1
Authority
WO
WIPO (PCT)
Prior art keywords
mhc
hla
immune cells
peptide
display
Prior art date
Application number
PCT/CN2024/091080
Other languages
English (en)
Inventor
Yujiang Geno SHI
Gang Song
Original Assignee
Immunoracle Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Immunoracle Inc. filed Critical Immunoracle Inc.
Publication of WO2024227447A1 publication Critical patent/WO2024227447A1/fr

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56966—Animal cells
    • G01N33/56972—White blood cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70539—MHC-molecules, e.g. HLA-molecules
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56966—Animal cells
    • G01N33/56977—HLA or MHC typing
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54313—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals the carrier being characterised by its particulate form

Definitions

  • the application relates to compositions and methods of analyzing a sample for antigen-specific immune cells.
  • MHC peptide-major histocompatibility complex
  • T cells e.g., T cells
  • MHC multimers have been prepared using antibody dimerization or tetravalent binding of biotin-streptavidin, and these MHC dimers or tetramers show increased avidity for their cognate TCR. To date, MHC multimers have been successfully used to visualize antigen-specific CD8 T cells ex vivo by flow cytometry.
  • MHC tetramers are constructed by tetramerization of C-terminal biotinylated pMHC monomers with streptavidin molecules. MHC tetramers have been proven to be versatile and useful for detecting ⁇ T cells through flow cytometry and in situ staining. The well-established characteristics of MHC tetramers and their public and commercial availability have led to their widespread usage in T-cell research. MHC tetramer-staining technology has been expanding to include new research areas such as enrichment of rare T cells, construction of large libraries and high-throughput epitope screening, cytometry by time-of-flight mass spectrometry (CyTOF) , and combinatorial staining for multiple detection.
  • CDTOF time-of-flight mass spectrometry
  • An MHC pentamer consisting of five pMHC complexes arranged in a planar configuration is commercially produced and has increased sensitivity for staining T cells with the low-affinity TCR because of its higher valency than that of dimers or tetramers. More recently, another commercially available pMHC complex linked to a dextran backbone, a pMHC dextramer, has also been found to be useful for the detection of T cells with low-affinity TCRs because of its increased valency. See e.g., Mol Cells. 2021 May 31; 44 (5) : 328–334.
  • immune cell e.g., T cell
  • assays can be used to characterize immune cell (e.g., T cell) responses in order to determine the state and capability of the immune system.
  • immune cell e.g., T cell
  • Such studies can reveal fundamental mechanisms underlying immunity aid the design of clinical diagnostics, help develop intervention therapies, and determine signatures of effective immune responses.
  • antigen-specific immune cells are often a very small percentage of the cells that can be obtained from a sample (e.g., a blood sample) , effective detection and analysis of such cells could be challenging.
  • the present application in one aspect provides methods of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, the method comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization. In some embodiments, the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the present application in another aspect provides methods of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, the method comprising: a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the method further comprises determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived.
  • the present application in another aspect provides methods of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, comprising: a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived.
  • the immune cells comprise T cells, optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are selected from the group consisting of: a cytotoxic T cell, a memory T cell, and a tumor infiltrating T cell.
  • the immune cells comprise B cells.
  • the method further comprises removing unbound display moiety following contacting the immune cells with the agent recognizing the display moiety and prior to detecting the immune cells bound to the display moiety.
  • the antigenic peptide is associated with a cancer or tumor antigen, optionally wherein the antigenic peptide is a neoantigen peptide.
  • the sample is obtained from one or more individuals exhibiting no pathological symptom of a cancer.
  • the antigenic peptide is associated with a pathogen antigen, optionally wherein the antigenic peptide is associated with a virus, a bacteria, or a fungus antigen.
  • the antigenic is an autoantigenic peptide associated with an autoantigen.
  • the immune cells are immobilized on the solid substrate such as a bead.
  • the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the display moiety comprises a library of antigenic peptides for a mutation associated with a cancer or tumor, wherein the library comprises at least about 5, 10, 12, 15, 18 or 20 distinct neoantigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide is a neoantigenic peptide comprising a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer. In some embodiments, the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-Amolecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the antigenic peptide is about 8 to about 10 amino acids long.
  • the MHC comprises a MHC class II molecule.
  • the MHC class II molecule is selected from the group consisting of HLA-DQ and HLA-DR.
  • the antigenic peptide is about 10 to about 20 amino acids long.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises a particle.
  • the particle in the display moiety is selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer.
  • the particle in the display moiety is a dextran particle.
  • the particle in the display moiety is a magnetic nanoparticle or polystyrene nanoparticle.
  • the particle in the display moiety is an agarose bead or a sepharose bead.
  • the antigenic peptide or MHC is directly attached to the particle in the display moiety.
  • the antigenic peptide or MHC is attached to the particle in the display moiety via a binding pair comprising a first binding component attached to the antigenic peptide and a second binding component bound to the particle.
  • the display moiety comprises a cell.
  • the cell comprises a polynucleotide encoding the antigenic peptide.
  • the polynucleotide encodes a plurality of antigenic peptides.
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • the method further comprises phenotyping immune cells bound to the display moiety.
  • the method further comprises sequencing one or more nucleic acids in immune cells bound to the display moiety, optionally wherein the method further comprises analyzing the sequences of the one or more nucleic acids, optionally wherein the one or more nucleic acids is a TCR, CD8, CD45 sequences or any specific sequence that is characteristic of the captured immune cells, optionally wherein analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing and/or RNAseq sequencing, alternatively, by a array of primer sequence-specific q-PCR, and/or RT-PCR.
  • the method further comprises subjecting the immune cell bound to the display moiety to mass spectrometry analysis.
  • the method further comprises identifying one or more epigenetic modifications in the immune cell, optionally wherein the more or more epigenetic modifications comprises DNA methylation and/or histone glycosylation.
  • the individual is a human. In some embodiments, the individual is at least about 50 years old.
  • the individual a) has not previously been diagnosed as having a cancer, optionally wherein the individual is at risk of having cancer, or b) the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the individual a) has not been diagnosed as having an infection by a pathogen, optionally wherein the individual is at risk of having the infection, and/or b) exhibits no pathological symptom of an infection by a pathogen, optionally exhibits no pathological symptom of an infection by the pathogen.
  • the individual a) has not been diagnosed as having an immune response against the autoantigen, optionally wherein the individual is at risk of developing the immune response against the autoantigen, and/or b) exhibits no pathological symptom of an immune response (e.g., an autoimmune disease or disorder) , optionally exhibits no pathological symptom of an immune response against the autoantigen.
  • an immune response e.g., an autoimmune disease or disorder
  • the sample is selected from the group consisting of: blood, plasma, and a peripheral blood mononuclear cell (PBMC) sample.
  • PBMC peripheral blood mononuclear cell
  • the bait composition comprises a plurality of different display moieties.
  • the each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide.
  • the plurality of different display moieties in the bait composition comprises at least two different display moieties, each comprising a different MHC molecule.
  • the plurality of different display moieties in the bait composition comprises at least four different display moieties, each comprising a different MHC molecule.
  • the plurality of different display moieties in the bait composition comprises at least 100 different display moieties, each comprising a different MHC molecule.
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label.
  • the different detectable labels comprise fluorophore (s) .
  • the agent comprises an antibody that binds to the display moiety.
  • the present application provides methods of detecting antigen-specific immune cells in an individual, comprising: analyzing a sample from the individual according to any of the methods described above, wherein a predetermined characteristic of the immune cells is indicative of a disease or a disorder in the individual.
  • the predetermined characteristic of the immune cell comprises the presence of the immune cells.
  • the presence of immune cells specifically binds to a bait composition comprising one or more neoantigens is indicative of the presence of a cancer.
  • the presence of immune cells specifically binds to a bait composition comprising one or more antigens of a pathogen (e.g., virus, bacteria, fungus) is indicative of the presence of an infection of the pathogen.
  • a pathogen e.g., virus, bacteria, fungus
  • the presence of immune cells specifically binds to a bait composition comprising one or more autoantigens associated with an autoimmune disease or disorder is indicative of the presence of the immune disease or disorder.
  • the predetermined characteristic of the immune cell comprises a quantity of the immune cell above a threshold level.
  • the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature.
  • the signature epigenetic modification comprises a DNA or RNA methylation, hydroxylation signature and a histone acetylation, methylation and/or glycosylation signature.
  • the present application in another aspect provides methods of detecting residual cancer in an individual, wherein the individual has been previously treated with an anti-cancer therapy and exhibits no pathological symptom of cancer after treatment, the method comprising analyzing a post-treatment sample from the individual according to any of the methods describe above, wherein a predetermined characteristic of the immune cell from the post-treatment sample is indicative of residual cancer in the individual.
  • the method comprises: a) analyzing a pre-treatment sample from the individual prior to anti-cancer therapy and a post-treatment sample from the individual according to the method of any of the methods described above, and b) comparing the characteristics of the immune cells from the pre-treatment sample and immune cells from the post-treatment sample; wherein a predetermined difference in characteristics of the immune cell from the pre-treatment sample and the immune cell from the post-treatment sample is indicative of residual cancer in the individual.
  • the present application in another aspect provides methods of treating a cancer in an individual, comprising a) diagnosing the individual as having cancer according to the method of some of the methods described above; and b) subjecting the individual to an anti-cancer therapy.
  • the anti-cancer therapy is not an immunotherapy.
  • the cancer is a solid tumor.
  • the present application in another aspect provides methods of treating an infection in an individual, comprising a) diagnosing the individual as having an infection by a pathogen according to some of the methods described above; and b) subjecting the individual to a therapy for the pathogen.
  • the present application in another aspect provides methods of treating an autoimmune disease or disorder in an individual, comprising a) diagnosing the individual as having an autoimmune disease or disorder according to some of the methods described above; and b) subjecting the individual to a therapy for the disease or disorder.
  • the present application in another aspect provides a composition comprising one or more display moieties comprising a particle associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises no less than or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises at least one MHC molecule complexed with a peptide, wherein at least two or more of the MHC-peptide complexes are different.
  • the one or more of the plurality of MHC-peptide complexes is an MHC-peptide monomer, MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • each of the plurality of MHC-peptide complex is an MHC-peptide monomer, an MHC-peptide dimer or an MHC-peptide trimer.
  • At least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the plurality of MHC-peptide complexes on the particle comprise at least 20 MHC-peptide complexes, such as at least 50 or 100 MHC-peptide complexes.
  • the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin.
  • the second binding component comprises a biotin
  • the first binding component comprises streptavidin.
  • the particle is solid.
  • the particle has a diameter of at least 0.1, 0.2, 0.25, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1 ⁇ m. In some embodiments, the particle has a diameter of about 0.5 ⁇ m to about 20 ⁇ m, such as about 0.5 ⁇ m to about 10 ⁇ m, or about 1 ⁇ m.
  • the particle has a surface area of about 1 ⁇ m 2 to about 20 ⁇ m 2 .
  • the particle has about 10 to about 10000 second binding component associated with it.
  • the particle is spherical. In some embodiments, the particle is a bead.
  • the particle is magnetic
  • the display moiety comprises at least two different MHC molecules.
  • the at least two different MHC molecules comprise two different MHC class I molecules.
  • the at least two different MHC molecules comprise two different MHC class II molecules.
  • the at least two different MHC molecules comprise both an MHC class I molecule and an MHC class II molecule.
  • the display moiety comprises an HLA-A molecule.
  • the HLA-A molecule comprises a mutation that reduces its binding to CD8.
  • the HLA-Amolecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DQ and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen. In some embodiments, the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two distinct peptides. In some embodiments, the display moiety comprises at least five distinct peptides. In some embodiments, the display moiety comprises at least 10, 20, or 50 distinct peptides. In some embodiments, the at least two distinct peptides in the display moiety do not overlap. In some embodiments, the at least two distinct peptides in the display moiety overlaps. In some embodiments, the at least two distinct peptides are associated with (e.g., derived from) two different antigens. In some embodiments, the two distinct antigens comprise two distinct mutations of one or more genes associated with a disease. In some embodiments, the disease is a cancer, the gene is a oncogene. In some embodiments, the disease is not a cancer or tumor (e.g., an infection, e.g., an autoimmune disease) .
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application in another aspect provides bait compositions comprising one or more display moiety described above.
  • the bait composition comprises a plurality of the display moieties described above.
  • the bait composition comprises at least two different display moieties.
  • the bait composition comprises an HLA-A molecule, an HLA-B molecule, and an HLA-C molecule.
  • the bait composition comprises HLA-A*24: 02, HLA-A*11: 01, HLA- A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the bait composition comprises at least 25, 50, 100, 150, 200, or 250 different peptides. In some embodiments, the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens. In some embodiments, the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene. In some embodiments, the gene is an oncogene. In some embodiments, the peptides in the bait composition are associated with mutations in at least two, three, four, five or six genes. In some embodiments, the genes are oncogenes. In some embodiments, the bait composition does not comprise a fluorochrome or fluorophore.
  • the present application in another aspect provides methods of analyzing immune cells in a sample from an individual, comprising a) contacting a plurality of immune cells with one or more of the display moieties or any of the bait compositions described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties.
  • the immune cells comprise T cells.
  • the immune cells are selected from the group consisting of: cytotoxic T cells, memory T cells, and tumor infiltrating T cells.
  • the T cells are CD4+ T cells and/or CD8+ T cells.
  • the immune cells comprise B cells.
  • the immune cells comprise a mixture of immune cells comprising T cells, B cells, macrophage cells, or dendritic cells, or combinations thereof.
  • the sample is selected from the group consisting of: blood, plasma, and a peripheral blood mononuclear cell (PMBC) sample.
  • the sample is obtained from a diseased tissue.
  • the diseased tissue is a cancer tissue or tumor tissue.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • the individual is a human. In some embodiments, the individual has no indication of a disease.
  • detecting or analyzing the immune cells that bind to one or more display moieties comprises observing the agglutination of immune cells and MHC-multimer units. In some embodiments, detecting or analyzing the immune cells that bind to one or more display moieties comprises 1) immobilizing immune cells on a solid substrate prior to or after step a) , 2) contacting the immobilized immune cells with a detection agent recognizing the display moieties under a condition sufficient for the agent to bind to the display moieties; and 3) detecting the detection agent, thereby detecting the immune cells bound to the display moieties.
  • FIG. 1 exemplifies newly predicated Kras neoantigens (SEQ ID NOs: 57-76) originated from the six most common Kras mutation (Kras G12V, Kras G12D, Kras G12R, Kras G12C, Kras G12I, Kras G12A) .
  • FIG. 2 shows that four most common HLA-A, including HLA-A: 0201, HLA-A: 2402, HLA-A: 0301, HLA-A: 1101, and ⁇ 2m were expressed and purified from Ecoli.
  • the target proteins were expressed in insoluble inclusion body (DPE) .
  • DPE insoluble inclusion body
  • FIG. 3 shows that the assembly of five common mutant Kras neoantigen library.
  • HLA-A 0201, HLA-A: 2402, HLA-A: 0301, HLA-A: 1101) and four most common Kras mutation (Kras G12V, Kras G12D, Kras G12R, Kras G12C) .
  • the figure only presented part of the results of Kras G12V mutation.
  • FIG. 4 demonstrates the confirmation of luciferase intensity in constructed pancreatic tumor cell lines. D-luciferin was used as substrate. The signal was captured 15min later after D-luciferin intraperitoneal injection.
  • FIG. 5 depicts tumor sizes 12 days post inoculation of 1 ⁇ 10 5 or 1 ⁇ 10 6 Pano2-Luc-GFP tumor cells (panel A) and tumor growth curve of Pano2-Luc-GFP tumor in C57BL/6J mice after 1 ⁇ 10 6 tumor cells were subcutaneously challenged as measured by tumor volume (panel B) .
  • FIG. 6 depicts construction of plasmid overexpression five common Kras mutation.
  • the band size was about 750bp. Two replicates were loaded, and the bands less than 50bp were non-specific bands.
  • FIGs. 7A and 7B depicts the detection of Kras mutation neoantigen specific CD8 + T cells in peripheral blood of mice as early as Day 4 after intravenous tumor cell challenge of 4 ⁇ 10 5 or 1 ⁇ 10 6 cells.
  • FIG. 8 depicts the detection of Kras mutation neoantigen specific CD8 + T cells in peripheral blood of mice as early as Day 4 after intravenous tumor cell challenge of 1 ⁇ 10 4 or 1 ⁇ 10 5 cells.
  • FIGs. 9A and 9B depicts the detection of Kras mutation neoantigen specific CD8 + T cells in peripheral blood of mice as early as Day 4 after subcutaneous tumor challenge of 4 ⁇ 10 5 cells.
  • the Tetramer + CD8 + T cells population (ranged from 0.042%to 0.22, median: 0.0866%) was detectable in mice challenged with Pan02-n peptide, but no Tetramer + CD8 + T cells were detectable in mice challenge with Pan02-EV cells.
  • FIGs. 10A and 10B depicts the tumor growth curve of mice inoculated with 4 ⁇ 10 5 cells Pan02-EV (without neoantigen expressing Kras mutation) and Pan02-n (with neoantigen expressing Kras mutation) tumor cells as assessed via bioluminescence (FIG. 9A) and the picture of mice at day 4 post tumor challenge evidencing no observation of tumor at the site of inoculation (red circle) (FIG. 9B) .
  • FIGs. 11A-11C depict the presence or absence of Kras mutation neoantigen specific CD8 + T cells with Kras mutation specific Tetramer library in peripheral blood of pancreatic cancer patients (Patient #1-13) .
  • FIG. 12 depicts of a summary of the presence or absence of CD8 + T cells in thirteen confirmed pancreatic patients with a presence or absence of a Kras mutation and a specific HLA-A phenotype.
  • twenty G12D neoantigen peptides associated MHC tetramers were included in the bait composition but only four G12R neoantigen peptides associated tetramers were included.
  • FIG. 13 depicts schematic and process of MHC Class I Tetramer (MHC-Tetramer) synthesis.
  • MHC-Tetramer MHC Class I Tetramer
  • A The components and assembly of MHC peptide monomer.
  • B Schematic of MHC-Tetramer and targeting strategies for the MHC-Tetramer which binds with the specific CD8+ T cells in cancer patients blood.
  • the exemplary targets are B2M, Streptavidin, Biotin and any labelled tags such as PE, APC or His.
  • FIG. 14 depicts the main process for a sandwich ELISA.
  • the method is stepwise in the order shown.
  • the 1st step is to coat the ELISA plate with capture antibody.
  • any antigen in the sample e.g. blood, or cell supernatant
  • the detection antibody which is labelled with horse radish peroxidase or alkaline phosphatase will be added and binds to any target antigen already bound to the capture antibody.
  • a substrate is added to the plate such as the chromogenic to convert the substrate (e.g. TMB or ABTS) into a colored product which can be measured using a plate reader.
  • the detailed protocol for a ELISA is outlined in the figure.
  • C Exemplary methods.
  • the MHC-tetramer bind to the specific TCR in the CD8+ T cells in patient blood or cells and then the CD8+ cells are captured by the CD8 antibody coated to plate or conjugated to magnetic beads.
  • the HRP-detection antibody can identify the captured CD8 antibody using a plate reader.
  • the cells are incubated with CD8 antibody coated to plate or conjugated to magnetic beads and then the MHC-tetramer are added in the resulted cells. Then the HRP-detection antibody (mainly targeting the components of MHC-Tetramer) are added and the MHC-Tetramer binding CD8+ T cells can be detected.
  • FIG. 15 depicts schematic and process of exemplary method to capture the specific MHG-Tetramer binding CD8+ T cells.
  • A-B For example, the MHC-Tetramers with different tags are added to the immune cells first. Then the magnetic beads are added as indicated in the step 2. The presence of MHC-Tetramers binding CD8+T cells will be identified by the HRP antibodies in step 3.
  • C The CD8 antibody conjugated magnetic beads are added to the immune cells first. The MHC-Tetramers with different tags are then added as indicated in the step 2. The presence of MHC-Tetramers binding CD8+T cells will be identified by the HRP antibodies in step 3.
  • FIG. 16 depicts strategy of clinical sample collection and tumor neoantigen specific CD8+ T cells identification by ELISA.
  • FIG. 17 depicts the main process and result for the detection of MHC-Tetramers binding CD8+ T cells by HRP- ⁇ 2-microglobulin antibody.
  • A The main method is shown stepwise. The cells were mixed with MHC-Tetramer and then incubated with CD8 antibody conjugated magnetic beads. HRP- ⁇ 2-microglobulin antibody was the detection antibody used to identify MHC-Tetramers binding CD8+T cells.
  • B The result using the method described in (A) to detect the MHC-Tetramers binding CD8+T cells.
  • FIG. 18 depicts the main process and result for the detection of MHC-Tetramers binding CD8+ T cells by HRP-PE antibody.
  • A The main method is shown stepwise. The cells were mixed with CD8 antibody conjugated magnetic beads firstly then incubated with MHC-Tetramers. HRP-PE antibody was the detection antibody used to identify MHC-Tetramers binding CD8+T cells.
  • B The result according to method shown in (A) .
  • FIG. 19 depicts the main process and result for the detection of MHC-Tetramers binding CD8+ T cells by HRP-PE antibody.
  • A The modified method to capture the MHC-Tetramers binding CD8+ T cells by HRP-PE antibody. In this protocol, the tubes were changed to new tubes after MHC-Tetramer washing step. The tube change can also be done when CD8 conjugated bead washing step.
  • B The result from this modified method shown in (A) . There’s a 3-fold difference between Group 1 and 4. The presentative photo for result (B) . in duplicates.
  • FIG. 20 depicts a scheme of the exemplary method.
  • FIG. 21 depicts a scheme of high throughput identification of pancreatic neoantigen specific immune cells (e.g., CD 8+ T Cells) in population.
  • pancreatic neoantigen specific immune cells e.g., CD 8+ T Cells
  • FIG. 22 depicts exemplary list of HLA subtype and high frequency tumor mutations employed in Tetramer library construction for the analysis of early pancreatic cancer
  • FIG. 23 depicts a scheme of DNA barcoded antibody for CD45 or CD8 specific T cells.
  • FIG. 24 depicts a scheme of exemplary methods for DNA barcoded CD8+ T cells identification from multiple pancreatic cancer patients by ELISA.
  • FIG. 25 depicts a scheme of another exemplary methods for antigen specific immune cells (e.g., neoantigen specific CD8+ T cells) capture by magnetic beads and DNA barcode based ELISA assay.
  • antigen specific immune cells e.g., neoantigen specific CD8+ T cells
  • FIG. 26 depicts a scheme of another exemplary methods for antigen specific immune cells (e.g., neoantigen specific CD8+ T cells) capture by tetramer-beads and DNA barcode based ELISA assay.
  • antigen specific immune cells e.g., neoantigen specific CD8+ T cells
  • FIG. 27A depicts a scheme of another exemplary methods for antigen specific immune cells (e.g., neoantigen specific CD8+ T cells) capture by MHC-tetramer-beads bound with multiple antigenic peptides and DNA barcode based ELISA assay.
  • antigen specific immune cells e.g., neoantigen specific CD8+ T cells
  • FIG. 27B depicts a scheme of another exemplary methods for antigen specific immune cells (e.g., neoantigen specific CD8+ T cells) capture by MHC-tetramers bound with multiple antigenic peptides and DNA barcode based ELISA assay.
  • antigen specific immune cells e.g., neoantigen specific CD8+ T cells
  • FIG. 27C exemplifies Kras neoantigens (SEQ ID NOs: xx-xx) originated from Kras mutations (Kras G12V, Kras G12D, Kras G12R) .
  • FIG. 28A depicts the characterization of MHC-tetramer and MHC-tetramer-bead on PAGE.
  • FIG. 28B depicts the detection of Kras mutation neoantigen specific CD8 + T cells in peripheral blood of mice by MHC-tetramer-beads in an agglutination assay.
  • FIG. 28C depicts the results of Kras mutation neoantigen specific CD8 + T cells in peripheral blood of mice by MHC-tetramer-beads in an agglutination assay.
  • FIG. 28D depicts the detection of Kras mutation neoantigen specific CD8 + T cells in mice spleen by MHC-tetramer-beads in an agglutination assay.
  • FIG. 28E depicts the results of Kras mutation neoantigen specific CD8 + T cells in mice spleen by MHC-tetramer-beads in an agglutination assay.
  • FIG. 29A depicts the characterization of MHC- ⁇ -galactosidase-beads and Kras G12D MHC-monomer on PAGE.
  • FIG. 29B depicts the characterization of MHC- ⁇ -galactosidase-beads and Kras G12D MHC-monomer and MHC-tetramer on PAGE.
  • FIG. 29C depicts the detection of Kras G12D neoantigen specific CD8 + T cells in peripheral blood of mice by MHC-tetramer-beads in an agglutination assay.
  • FIG. 29D-29E depict the detection of Kras G12D neoantigen specific CD8 + T cells in mice spleen by MHC-tetramer-beads in an agglutination assay.
  • FIG. 30A depicts the characterization of MHC-monomer bound with multiple antigenic peptides on PAGE.
  • FIG. 30B depicts the characterization of MHC-tetramer bound with multiple antigenic peptides on PAGE.
  • FIG. 30C depicts the peptide standards in LC-MS/MS detection.
  • FIG. 30D depicts the detection of antigenic peptides from PAGE.
  • FIG. 30E depicts the characterization of MHC-tetramer bound with multiple antigenic peptides in LC-MS/MS detection.
  • FIG. 30F depicts the characterization of MHC-monomer and MHC-tetramer on PAGE.
  • FIG. 31A depicts the detection of Kras G12V neoantigen specific CD8 + T cells in mice spleen by MHC-monomer-beads.
  • FIG. 31B depicts the detection of Kras G12D neoantigen specific CD8 + T cells in human peripheral blood by MHC-monomer-beads.
  • FIG. 31C depict the detection of Kras multiple specific CD8 + T cells in human peripheral blood by MHC-monomer-beads with multiple antigenic peptides.
  • FIG. 31D-FIG. 31E depict the detection of stimulated Kras multiple specific CD8 + T cells in human peripheral blood by MHC-monomer-beads with multiple antigenic peptides.
  • the present application provides methods of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide.
  • the presence such immune cells are indicative of the presence of a disease or condition in the individual.
  • the application is at least partly based on inventors’ unique insight that immune cells activated by specific antigens (such as tumor neoantigens) can be detectable in an individual even before any pathological symptoms of disease or condition (e.g., cancer) are exhibited, thus serving as useful markers for detection of such disease or condition at early stage.
  • exemplary Kras mutation associated neoantigen-specific T cells were successfully detected in mice intravenously or subcutaneously inoculated with tumor cells (of as low as 10 4 cells, see, e.g., FIG. 8) expressing Kras mutation associated neoantigens and as early as day 4 after inoculation (see e.g., FIG. 9A-9B) , which is prior to the any detection via bioluminescence (see e.g., FIG. 10A-10B) , or in pancreatic cancer patients harboring Kras mutations (e.g., see FIG. 11A-11C and 12) .
  • These data demonstrated that the provided methods can be successfully used for cancer detection including both early cancer detection as well as for monitoring cancer cells in individuals who may have residual minimal cancer cells.
  • the present application also provides innovative methods that exploit immunoassays such as ELISA for effectively, economically, and efficiently detect the presence of antigen-specific immune cells even when they are in a very low abundance in a sample (e.g., less than 1%) .
  • the methods of the present application have been demonstrated to successfully detect neoantigen-specific immune cells in cancer patients and detecting pathogen-specific immune cells in patients infected with the pathogen. Some embodiments of the methods demonstrate surprisingly high sensitivity.
  • the methods enable a high throughput analysis of a mixed sample that has immune cells derived from a plurality of individuals (e.g., 10-30 individuals) by associating a unique barcode with the immune cells from each individuals. See e.g., Examples 3 and 4.
  • the present application in one aspect provides methods of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, the method comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety.
  • the present application in another aspect provides methods of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, the method comprising: a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety.
  • the present application in another aspect provides methods of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, comprising: a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived.
  • Methods of detecting antigen-specific immune cells in an individual, methods of detecting residual cancer, methods of treating a cancer, infection or an autoimmune disease are also provided.
  • compositions comprising display moieties comprising a particle associated with a plurality of MHC-peptide complexes.
  • the plurality of MHC-peptide complexes comprises more than 2, 3, 4, 5, 6, 8, 9, 10 or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises at least one MHC molecule complexed with a peptide, wherein at least two or more of the MHC-peptide complexes are different.
  • the MHC-peptide complex is an MHC-peptide monomer.
  • the particle is solid.
  • the plurality of MHC-peptide complexes comprises at least 20, 50, or 100 MHC-peptide complexes.
  • the display moieties described herein are a powerful tool that can be used to simultaneously screen antigen-specific immune cells from an individual that specifically recognize a plurality of peptides (e.g., neoantigen peptides) with high sensitivity.
  • These display moieties by having a plurality of heterogenous MHC-peptide complexes associated with a particle, enable aggregation of antigen-specific immune cells that can be conveniently observed under microscope or bare eyes. Accordingly, it provides powerful, sensitive, cost-effective and convenient platform technology for screening, detecting and analyzing antigen-specific immune cells in different contexts (e.g., cancers, autoimmune diseases, infections) .
  • Bait compositions comprising the display moieties, methods of analyzing or detecting antigen-specific immune cells by using the display moieties or bait compositions (such as those described above) , and methods of treating patients that involve using methods of detecting antigen-specific immune cells as described herein are also provided in the application.
  • the term "antigen" is a substance that induces an immune response.
  • neoantigen is an antigen that has at least one alteration that makes it distinct from the corresponding wild-type, parental antigen, e.g., via mutation in a tumor cell or post-translational modification specific to a tumor cell.
  • a neoantigen can include a polypeptide sequence.
  • a mutation that results in a neoantigen can include a frameshift or non-frameshift indel, missense or nonsense substitution, splice site alteration, genomic rearrangement or gene fusion, or any genomic or expression alteration giving rise to a neoORF.
  • a mutations can also include a splice variant.
  • Post-translational modifications specific to a tumor cell can include aberrant phosphorylation.
  • Post-translational modifications specific to a tumor cell can also include a proteasome-generated spliced antigen. See Liepe et al., A large fraction of HLA class I ligands are proteasome-generated spliced peptides; Science. 2016 Oct 21; 354 (6310) : 354-358.
  • tumor neoantigen or “cancer neoantigen” is a neoantigen present in a subject's tumor cell or tissue but not in the subject's corresponding normal cell or tissue.
  • missense mutation is a mutation causing a substitution from one amino acid to another.
  • nonsense mutation is a mutation causing a substitution from an amino acid to a stop codon.
  • frameshift mutation is a mutation causing a change in the frame of the protein.
  • the term “indel” is an insertion or deletion of one or more nucleic acids.
  • the percent “identity” can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.
  • sequence comparison typically one sequence acts as a reference sequence to which test sequences are compared.
  • test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
  • sequence comparison algorithm then calculates the percent sequence identity for the test sequence (s) relative to the reference sequence, based on the designated program parameters.
  • sequence similarity or dissimilarity can be established by the combined presence or absence of particular nucleotides, or, for translated sequences, amino acids at selected sequence positions (e.g., sequence motifs) .
  • epitopope is the specific portion of an antigen typically bound by an antibody or T-cell receptor.
  • immunogenic is the ability to elicit an immune response, e.g., via T-cells, B cells, or both.
  • HLA binding affinity means affinity of binding between a specific antigen and a specific MHC allele.
  • the term "bait composition” is a composition comprising a molecule (e.g., an antigenic peptide) used to enrich a cell that specifically binds to the bait from a sample.
  • a molecule e.g., an antigenic peptide
  • antigenic peptide described herein is not limited to peptides that are capable of inducing an immune response. It is exchangeable to “peptide” and includes any peptide that can be presented by an MHC molecule.
  • variable is a difference between a subject's nucleic acids and the reference human genome used as a control.
  • allele is a version of a gene or a version of a genetic sequence or a version of a protein.
  • HLA type is the complement of HLA gene alleles.
  • exome is a subset of the genome that codes for proteins.
  • An exome can be the collective exons of a genome.
  • proteome is the set of all proteins expressed and/or translated by a cell, group of cells, or individual.
  • extract is a dextran-based peptide-MHC multimers used for antigen-specific immune-cell staining in flow cytometry.
  • MHC multimers is a peptide-MHC complex comprising multiple peptide-MHC monomer units.
  • MHC tetramers is a peptide-MHC complex comprising four peptide-MHC monomer units.
  • MHC monomers is a peptide-MHC complex comprising one peptide-MHC monomer units.
  • MHC dimers is a peptide-MHC complex comprising two peptide-MHC monomer units.
  • MHC trimers is a peptide-MHC complex comprising three peptide-MHC monomer units.
  • the term “Latex Agglutination Test (LAT) ” refers to a class of bioanalytical methods used to detect the presence (qualitive) and sometimes the amount of a substance (quantitative) in a sample. In the presence of a specific substance (e.g. antigen, antibody, or cell) , the latex particles agglomerate, forming clumps or aggregations of particles.
  • LAT Latex Agglutination Test
  • Latex Beads refers to spherical particles, e.g. polystyrene, poly (methyl methacrylate) , polyacrylates, or other similar types of polymers. These Latex beads can vary in size, typically ranging from nanometers to micrometers in diameter. Their surface may be functionalized or modified to allow for the attachment of biological molecules, chemical compounds, or other substances. Latex beads can be used in a range of applications including, but not limited to, diagnostic assays, bioseparation, drug delivery, and as standards or controls in various analytical techniques.
  • sample refers to an aliquot of body fluid or a tissue obtained from a subject which contains an immune cell.
  • mammal encompasses both humans and non-humans and includes but is not limited to humans, non-human primates, canines, felines, murines, bovines, equines, and porcines.
  • treatment is an approach for obtaining beneficial or desired results, including clinical results.
  • beneficial or desired clinical results include, but are not limited to, one or more of the following: alleviating one or more symptoms resulting from the disease, diminishing the extent of the disease, stabilizing the disease (e.g., preventing or delaying the worsening of the disease) , preventing or delaying the spread (e.g., metastasis) of the disease, preventing or delaying the recurrence of the disease, delaying or slowing the progression of the disease, ameliorating the disease state, providing a remission (partial or total) of the disease, decreasing the dose of one or more other medications required to treat the disease, delaying the progression of the disease, increasing or improving the quality of life, increasing weight gain, and/or prolonging survival.
  • treatment is a reduction of pathological consequence of cancer (such as, for example, tumor volume) .
  • the methods of the application contemplate any one or more of these aspects
  • a “reference” as used herein, refers to any sample, standard, or level that is used for comparison purposes.
  • a reference may be obtained from a healthy and/or non-diseased sample.
  • a reference may be obtained from an untreated sample.
  • a reference is obtained from a non-diseased or non-treated sample of an individual.
  • a reference is obtained from one or more healthy individuals who are not the individual or patient.
  • subject “individual, ” and “patient” are used interchangeably herein to refer to a mammal, including, but not limited to, human, bovine, horse, feline, canine, rodent, or primate. In some embodiments, the individual is a human.
  • references to “about” a value or parameter herein includes (and describes) variations that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X” .
  • reference to “not” a value or parameter generally means and describes “other than” a value or parameter.
  • the method is not used to treat cancer of type X means the method is used to treat cancer of types other than X.
  • the present application provides methods of analyzing a sample from one or more individuals, e.g., for the presence or absence of immune cells capable of binding to an antigenic peptide. Such methods can be further used for e.g., diagnosis of a disease or condition (e.g., a cancer, e.g., an infection, e.g., an autoimmune cells) .
  • a disease or condition e.g., a cancer, e.g., an infection, e.g., an autoimmune cells
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic peptide is associated with a cancer or tumor antigen, optionally wherein the antigenic peptide
  • the sample is obtained from one or more individuals exhibiting no pathological symptom of a cancer.
  • the individual a) has not previously been diagnosed as having a cancer, optionally wherein the individual is at risk of having cancer, or b) the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the neoantigenic peptide comprising a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other, e.g., by washing the immune cells for at least 1, 2, or 3 times.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic peptide is associated with a pathogen antigen, optionally wherein the antigenic
  • the individual a) has not been diagnosed as having an infection by a pathogen, optionally wherein the individual is at risk of having the infection, and/or b) exhibits no pathological symptom of an infection by a pathogen, optionally exhibits no pathological symptom of an infection by the pathogen.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic is an autoantigenic peptide associated with an autoantigen.
  • the individual a) has not been diagnosed as having an immune response against the autoantigen, optionally wherein the individual is at risk of developing the immune response against the autoantigen, and/or b) exhibits no pathological symptom of an immune response (e.g., an autoimmune disease or disorder) , optionally exhibits no pathological symptom of an immune response against the autoantigen.
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the immune cells are immobilized on the solid substrate such as a bead, and optionally where
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual. In some embodiments, prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) . In some embodiments, the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the display moiety comprises a library of antigenic peptides for a mutation associated with a
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual. In some embodiments, prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) . In some embodiments, the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer. In some embodiments, the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic peptide 1) has one or more of the following characteristics: a) having a binding
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual. In some embodiments, prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) . In some embodiments, the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-Amolecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immobilized immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; and c) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the display moiety further comprises a detectable label (e.g., a fluorophor
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual. In some embodiments, prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) . In some embodiments, the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic peptide is associated with a cancer or tumor antigen, optionally wherein the antigenic peptide is a neoantigen peptide.
  • the sample is obtained from one or more individuals exhibiting no pathological symptom of a cancer.
  • the individual a) has not previously been diagnosed as having a cancer, optionally wherein the individual is at risk of having cancer, or b) the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the neoantigenic peptide comprising a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-Amolecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic peptide is associated with a pathogen antigen, optionally wherein the antigenic peptide is associated with a virus, a bacteria, or a fungus antigen.
  • the individual a) has not been diagnosed as having an infection by a pathogen, optionally wherein the individual is at risk of having the infection, and/or b) exhibits no pathological symptom of an infection by a pathogen, optionally exhibits no pathological symptom of an infection by the pathogen.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic is an autoantigenic peptide associated with an autoantigen.
  • the individual a) has not been diagnosed as having an immune response against the autoantigen, optionally wherein the individual is at risk of developing the immune response against the autoantigen, and/or b) exhibits no pathological symptom of an immune response (e.g., an autoimmune disease or disorder) , optionally exhibits no pathological symptom of an immune response against the autoantigen.
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA- A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the immune cells are immobilized on the solid substrate such as a bead, and optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-Amolecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the display moiety comprises a library of antigenic peptides for a mutation associated with a cancer or tumor, a pathogen, or an autoantigen, wherein the library comprises at least about 5, 10, 12, 15, 18 or 20 distinct antigenic peptides (e.g., neoantigenic) .
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer. In some embodiments, the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the antigenic peptide 1) has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-Amolecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and d) detecting the detection agent, thereby detecting the immune cells bound to the display moiety, wherein the display moiety further comprises a detectable label (e.g., a fluorophore, e.g., a PE or APC) , wherein the detection agent binds to the detectable label.
  • a detectable label e.g., a fluorophore, e.g., a PE or APC
  • the sample is obtained from a single individual.
  • the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-Amolecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the antigenic peptide is associated with a cancer or tumor antigen, optionally wherein the antigenic peptide is a neoantigen peptide.
  • the sample is obtained from one or more individuals exhibiting no pathological symptom of a cancer.
  • the individual a) has not previously been diagnosed as having a cancer, optionally wherein the individual is at risk of having cancer, or b) the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the neoantigenic peptide comprising a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the antigenic peptide is associated with a pathogen antigen, optionally wherein the antigenic peptide is associated with a virus, a bacteria, or a fung
  • the individual a) has not been diagnosed as having an infection by a pathogen, optionally wherein the individual is at risk of having the infection, and/or b) exhibits no pathological symptom of an infection by a pathogen, optionally exhibits no pathological symptom of an infection by the pathogen.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the antigenic is an autoantigenic peptide associated with an autoantigen.
  • the individual a) has not been diagnosed as having an immune response against the autoantigen, optionally wherein the individual is at risk of developing the immune response against the autoantigen, and/or b) exhibits no pathological symptom of an immune response (e.g., an autoimmune disease or disorder) , optionally exhibits no pathological symptom of an immune response against the autoantigen.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the immune cells are immobilized on the solid substrate such as a bead, optionally wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the immune cells are immobilized on a solid substrate (e.g., via a bead) , and optionally wherein the bead is associated with an antibody
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the display moiety comprises a library of antigenic peptides for a mutation associated with a cancer or tumor, a pathogen, or an autoantigen, wherein the library
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) is hydrophobic; and d) has high content of aromatic residues.
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer. In some embodiments, the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the antigenic peptide 1) has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM to an MHC
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety further comprises a detectable label (e.g., a fluorophore) .
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • a method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide comprising a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture, d) detecting immune cells bound to the display moiety in the bait-sample mixture; and e) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, wherein the display moiety further comprises a detectable label (e.g., a fluorophore, e.g., a PE or APC) , wherein
  • a detectable label
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • the sample is a blood sample (e.g., PBMC sample) .
  • the immune cells comprise T cells (e.g., CD8 T cells) , optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • the MHC molecule comprises a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-Amolecule, further optionally wherein the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • the “condition” in the term “under a condition sufficient for an immune cell to bind to the display moiety” refers to conditions in which specific binding between the immune cells and the display moiety happen. In some embodiments, it refers to conditions that involve about or at least about 5, 10, 15, 20, 25, or 30 minutes of incubation of the immune cells and display moiety (e.g., at room temperature in a medium) . In some embodiments, it refers to conditions under at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%of the maximum binding between the immune cells and the display moiety happen. Maximum binding can be assessed by, e.g., contacting immune cells with display moiety for adequate time (e.g., 30 minutes) under a proper condition (e.g., room temperature) .
  • the immune cells are immobilized to a solid substrate, e.g., via an agent binding to the immune cells that is coated to or conjugated with the solid substrate.
  • the agent is an antibody that specifically recognizes a surface marker of the immune cells.
  • the agent is an anti-CD8 antibody and the immune cells are CD8 T cells.
  • the agent is an anti-CD4 antibody and the immune cells are CD4 T cells.
  • the agent is an anti-CD3 antibody and the immune cells are T cells.
  • the immobilization can be carried out by mixing immune cells with the agent (or incubating the immune cells with the agent) that specifically binds to the immune cells.
  • the agent is already coated or conjugated on a solid substrate, such as a plate or magnetic bead.
  • a washing step can be applied to remove the cells not bound to the agent (e.g., using a magnet) . See e.g., Example 2-4.
  • the solid support (or “solid substrate” which can be used interchangeably) comprises a plate or a surface of a particle (such as a surface of a particle, such as an inner surface of a porous particle) .
  • the solid support comprises any of beads (e.g., magnetic beads) , porous beads, porous matrices, arrays, glass surfaces, silicon surfaces, plastic surfaces, filters, membranes, nylons, silicon wafer chips, flow-through chips.
  • the solid support comprises any of a biochip containing electronics, a microtiter well, an ELISA plate, a spin interference disc, a nitrocellulose membrane, a nitrocellulose-based polymer surface, a nanoparticle, or a microsphere.
  • the sample is a mixture a plurality of individual samples. In some embodiments, the plurality of individual samples are from a single individual. In some embodiments, the plurality of individual samples are from a plurality of individuals.
  • the sample is a mixture a plurality of individual samples and each of the plurality of individual samples is obtained from a different individual.
  • the method comprises prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the association can be achieved by e.g., mixing immune cells with a molecule (e.g., an antibody that binds to the immune cells, e.g., a CD45 antibody) that comprises the unique barcode and binds to the immune cells for them to bind to each other.
  • a molecule e.g., an antibody that binds to the immune cells, e.g., a CD45 antibody
  • unique barcode can be associated to cells via e.g., an antibody conjugated or fused with the barcode that specifically binds to the cells.
  • the barcode is a nucleic acid barcode (e.g., DNA barcode) .
  • the unique DNA barcode is randomized barcode with a length of about 10-20 nucleic acids (e.g., 12-18 nucleic acids) .
  • the barcode is a peptide barcode.
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least 1, 2, or 3 times.
  • the method further comprises determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived.
  • nucleic acids can be purified, and sequencing can used to identify the immune cells with which a unique DNA barcode is associated with. See e.g., Example 4.
  • the particle described herein is a dextran particle.
  • the particle is a magnetic nanoparticle or polystyrene nanoparticle.
  • the particle is an agarose bead or a sepharose bead.
  • the antigenic peptide or MHC is directly attached to the particle.
  • the antigenic peptide or MHC is attached to the particle via a binding pair comprising a first binding component attached to the antigenic peptide and a second binding component bound to the particle.
  • the display moiety comprises a cell.
  • the cell comprises a polynucleotide encoding the antigenic peptide.
  • the polynucleotide encodes a plurality of antigenic peptides.
  • the individual is a human. In some embodiments, the individual is at least about 50 years old (e.g., at least 50, 60, 70, or 80 years old) .
  • the sample described herein can be any sample from the individual.
  • the sample described herein is a blood sample.
  • the sample described herein is a plasma sample.
  • the sample described herein comprises peripheral blood mononuclear cell (PMBC) .
  • the sample described herein is a sample (e.g., a biopsy sample) obtained from a tissue or organ of the individual.
  • the sample is obtained from a lymph node of the individual.
  • the methods described herein have high specificity and sensitivity and enable it to detect antigen-specific immune cells even when they are rare in the sample (e.g., less than 1%) .
  • Sensitivity is calculated as the %of the true positive/ (true positive +false negative) .
  • Specificity is calculated as the %of the true negative/ (true negative + false positive) .
  • the method described herein demonstrated a specificity of more than about 50%, 60%, 70%, 80%, 90%, 95%, or 100%.
  • the method described herein demonstrated a sensitivity of more than about 50%, 55%, 60%, 65%, 70%, 75%or 80%.
  • the sample comprises PBMC and the immune cells comprise or are T cells or B cells contained in the PBMC.
  • the immune cells are not subject to an enrichment step for the immune cells in general or immune cells that specifically binds to the antigenic peptide prior to contacting with the bait composition.
  • the immune cells are not subject to an enrichment step for the immune cells in general or immune cells that specifically binds to the antigenic peptide throughout this methods.
  • the sample comprise no more than 1x10 8 , 5x10 7 , 2x10 7 , 1x10 7 , 5x10 6 , 2x10 6 , or 1x10 6 PBMCs.
  • the sample comprise no more than 1x10 6 , 5x10 5 , 2x10 5 , 1x10 5 , 5x10 4 , 2x10 4 , 1x10 4 , 7x10 3 , 5x10 3 , 2x10 3 , 1x10 3 , 5x10 2 , 2x10 2 , or 1x10 2 immune cells (e.g., CD8 T cells, e.g., immune cells that bind to antigenic peptide (s) in the bait composition, e.g., CD4 or CD8 T cells that bind to antigenic peptide (s) in the bait composition) .
  • CD8 T cells e.g., immune cells that bind to antigenic peptide (s) in the bait composition
  • CD4 or CD8 T cells that bind to antigenic peptide (s) in the bait composition
  • the present application further comprises methods of analyzing immune cells in a sample from an individual, comprising a) contacting a plurality of immune cells with the one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual does not exhibit a pathological symptom of a cancer, infection or autoimmune disease.
  • a sample e.g., PBMCs
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least more than 12 MHC-peptide complexes, wherein each of the MHC-peptide complex is an MHC-peptide monomer comprising an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different.
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-Amolecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual does not exhibit a pathological symptom of a cancer, infection or autoimmune disease.
  • a sample e.g., PBMCs
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprises at least 20, 50, 100, 500, 1,000, 5,000, 10,000, 20,000, 50,000, 10,0000, 15,000, 20,0000 MHC-peptide complexes.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-Amolecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual does not exhibit a pathological symptom of a cancer, infection or autoimmune disease.
  • a sample e.g., PBMCs
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least 0.5 ⁇ m.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-Amolecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual does not exhibit a pathological symptom of a cancer, infection or autoimmune disease.
  • a sample e.g., PBMCs
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprise a) at least two different MHC molecules, and b) at least two different peptides.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4,
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual does not exhibit a pathological symptom of a cancer, infection or autoimmune disease.
  • a sample e.g., PBMCs
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class I molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-Amolecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual does not exhibit a pathological symptom of a cancer, infection or autoimmune disease.
  • a sample e.g., PBMCs
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class II molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-Amolecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-Amolecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule. In some embodiments, the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule. In some embodiments, the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens. In some embodiments, the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene. In some embodiments, the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex is an MHC-peptide monomer comprising an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different.
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-Amolecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprises at least 20, 50, 100, 500, 1,000, 5,000, 10,000, 20,000, 50,000, 10,0000, 15,000, 20,0000 MHC-peptide complexes.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least 0.5 ⁇ m.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprise a) at least two different MHC molecules, and b) at least two different peptides.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4,
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-Amolecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC- peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class I molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual is at risk of developing a disease or condition, such as cancer, infection or autoimmune disease or disorder, e.g., an individual who has a family history of such disease or has been exposed to a pathogen, but has not been treated for the disease or condition.
  • a disease or condition such as cancer, infection or autoimmune disease or disorder
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class II molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties or a bait composition described herein, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the minimal residual disease is too minimal to be detected by imaging instruments (e.g., a routinely used or standard imaging instrument used for detection of the cancer) .
  • the location of the minimal residual disease is diverse.
  • the minimal residual cancer is a result of immune escape or resistance to treatment.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample e.g., PBMCs
  • the number of cells in the sample is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex is an MHC-peptide monomer comprising an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different.
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprises at least 20, 50, 100, 500, 1,000, 5,000, 10,000, 20,000, 50,000, 10,0000, 15,000, 20,0000 MHC-peptide complexes.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA- DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least 0.5 ⁇ m.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprise a) at least two different MHC molecules, and b) at least two different peptides.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4,
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-Amolecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class I molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA- DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • a methods of analyzing immune cells in a sample from an individual comprising a) contacting a plurality of immune cells with one or more display moieties, and b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties, wherein the immune cells are obtained from a sample (e.g., PBMCs) of an individual, wherein the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the number of cells in the sample (e.g., PBMCs) is no more than about 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • each of the one or more display moieties comprises a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class II molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • the one or more display moieties are comprised in a bait composition.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the display moieties or the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • the immune cells are T cells (e.g., CD8+ T cells or CD4+ T cells) .
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the immune cells are immobilized to a solid substrate, e.g., via an agent binding to the immune cells that is coated to or conjugated with the solid substrate.
  • the agent is an antibody that specifically recognizes a surface marker of the immune cells.
  • the agent is an anti-CD8 antibody and the immune cells are CD8 T cells.
  • the agent is an anti-CD4 antibody and the immune cells are CD4 T cells.
  • the agent is an anti-CD3 antibody and the immune cells are T cells.
  • the immobilization can be carried out by mixing immune cells with the agent (or incubating the immune cells with the agent) that specifically binds to the immune cells.
  • the agent is already coated or conjugated on a solid substrate, such as a plate or magnetic bead.
  • a washing step can be applied to remove the cells not bound to the agent (e.g., using a magnet) . See e.g., Examples.
  • the number of immune cells is no more than about 10 8 , 5x10 7 , 10 7 , 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • the solid substrate comprises a plate or a surface of a particle (such as a surface of a particle which is different from the particle used as support in display moieties, such as an inner surface of a porous particle) .
  • the solid substrate comprises any of beads (e.g., magnetic beads) , porous beads, porous matrices, arrays, glass surfaces, silicon surfaces, plastic surfaces, filters, membranes, nylons, silicon wafer chips, flow-through chips.
  • the solid substrate comprises any of a biochip containing electronics, a microtiter well, an ELISA plate, a spin interference disc, a nitrocellulose membrane, a nitrocellulose-based polymer surface, a nanoparticle, or a microsphere.
  • contacting a plurality of immune cells with the display moiety or a bait composition is conducted under a condition sufficient for an immune cell to bind to the display moieties.
  • the “condition” in the term “under a condition sufficient for an immune cell to bind to the display moieties” refers to conditions in which specific binding between the immune cells and the display moieties happen. In some embodiments, it refers to conditions that involve about or at least about 5, 10, 15, 20, 25, or 30 minutes of incubation of the immune cells and display moieties (e.g., at room temperature in a medium) .
  • it refers to conditions under at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%of the maximum binding between the immune cells and the display moieties happen.
  • Maximum binding can be assessed by, e.g., contacting immune cells with display moieties for adequate time (e.g., 30 minutes) under a proper condition (e.g., room temperature) .
  • the sample is a mixture a plurality of individual samples. In some embodiments, the plurality of individual samples are from a single individual. In some embodiments, the plurality of individual samples are from a plurality of individuals.
  • the sample is a mixture a plurality of individual samples and each of the plurality of individual samples is obtained from a different individual.
  • the method comprises prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the association can be achieved by e.g., mixing immune cells with a molecule (e.g., an antibody that binds to the immune cells, e.g., a CD45 antibody) that comprises the unique barcode and binds to the immune cells for them to bind to each other.
  • a molecule e.g., an antibody that binds to the immune cells, e.g., a CD45 antibody
  • unique barcode can be associated to cells via e.g., an antibody conjugated or fused with the barcode that specifically binds to the cells.
  • the barcode is a nucleic acid barcode (e.g., DNA barcode) .
  • the unique DNA barcode is randomized barcode with a length of about 10-20 nucleic acids (e.g., 12-18 nucleic acids) .
  • the barcode is a peptide barcode.
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least 1, 2, or 3 times.
  • the method further comprises determining the unique barcode associated with the immune cells bound to the display moieties, thereby identifying the sample from which the immune cells are derived.
  • nucleic acids can be purified, and sequencing can used to identify the immune cells with which a unique DNA barcode is associated with.
  • the individual is a human. In some embodiments, the individual is at least about 50 years old (e.g., at least 50, 60, 70, or 80 years old) .
  • the sample described herein can be any sample from the individual.
  • the sample described herein is a blood sample.
  • the sample described herein is a plasma sample.
  • the sample described herein comprises peripheral blood mononuclear cell (PMBC) .
  • the number of PBMCs is no more than about 10 8 , 5x10 7 , 10 7 , 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • the sample described herein is a sample (e.g., a biopsy sample) obtained from a tissue or organ of the individual.
  • the sample is obtained from a lymph node of the individual.
  • the methods described herein have high specificity and sensitivity that enable it to detect antigen-specific immune cells even when they are rare in the sample (e.g., less than 1%) .
  • the sample comprises PBMC and the immune cells comprise or are T cells or B cells contained in the PBMC.
  • the immune cells are not subject to an enrichment step for the immune cells in general or immune cells that specifically binds to the peptide prior to contacting with the bait composition. In some embodiments, the immune cells are not subject to an enrichment step for the immune cells in general or immune cells that specifically binds to the peptide throughout this methods.
  • the sample comprise no more than 1x10 8 , 5x10 7 , 2x10 7 , 1x10 7 , 5x10 6 , 2x10 6 , or 1x10 6 PBMCs. In some embodiments, the sample comprise no more than 1x10 6 , 5x10 5 , 2x10 5 , 1x10 5 , 5x10 4 , 2x10 4 , 1x10 4 , 7x10 3 , 5x10 3 , 2x10 3 , 1x10 3 , 5x10 2 , 2x10 2 , or 1x10 2 immune cells (e.g., CD8 T cells, e.g., immune cells that bind to peptide (s) in the bait composition, e.g., CD4 or CD8 T cells that bind to peptide (s) in the bait composition) .
  • immune cells e.g., CD8 T cells, e.g., immune cells that bind to peptide (s) in the bait composition, e.g
  • a method of detecting antigen-specific immune cells in an individual comprising: analyzing a sample from the individual according to any of the methods described herein, wherein a predetermined characteristic of the immune cells is indicative of a disease or a disorder in the individual.
  • the predetermined characteristic of the immune cell comprises the presence of the immune cells.
  • the presence of immune cells specifically binds to a bait composition comprising one or more neoantigens is indicative of the presence of a cancer.
  • the presence of immune cells specifically binds to a bait composition comprising one or more antigens of a pathogen (e.g., virus, bacteria, fungus) is indicative of the presence of an infection of the pathogen.
  • the presence of immune cells specifically binds to a bait composition comprising one or more autoantigens associated with an autoimmune disease or disorder is indicative of the presence of the immune disease or disorder.
  • the predetermined characteristic of the immune cell comprises a quantity of the immune cell above a threshold level. In some embodiments, the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature. In some embodiments, the signature epigenetic modification comprises a DNA methylation signature and a histone glycosylation signature.
  • a method of detecting antigen-specific immune cells in an individual comprising: a) immobilizing immune cells from the sample on a solid support, wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptid
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual. In some embodiments, prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) . In some embodiments, the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization. In some embodiments, the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • a method of detecting antigen-specific immune cells in an individual comprising: a) contacting the immune cells with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; b) contacting the immune cells with a detection agent recognizing the display moiety under a condition sufficient for the agent to bind to the display moiety; c) immobilizing the immune cells from the sample on a solid support, and
  • the sample is obtained from a single individual. In some embodiments, the sample is a mixture a plurality of individual samples, each obtained from a different individual. In some embodiments, prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode.
  • a method of detecting antigen-specific immune cells in a plurality of individuals comprising: a) separately processing each of the plurality of individual samples such that immune cells contained therein are associated with a unique sample barcode, b) combining the plurality of processed samples to form a sample mixture, c) contacting the sample mixture with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample
  • a method of detecting antigen-specific immune cells in an individual comprising: a) contacting the sample with a bait composition comprising an display moiety comprising an antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; b) isolating an immune cell associated with the
  • the predetermined characteristic of the immune cell further comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and a histone glycosylation signature) .
  • the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydrophobic; and e) has high content of aromatic residues.
  • a binding affinity of about 1 nM to about 5000 nM e.g., about 1 nM to about 50 nM, about 50 n
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the cancer status in the individual.
  • the information about cancer status comprises: classification of cancer; type of cancer; nature of cancer; origin of cancer; stage of cancer; likelihood of cancer progression; likelihood of developing one or more cancer symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • a method of detecting antigen-specific immune cells in an individual comprising: a) contacting the sample with a bait composition comprising an display moiety comprising an antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; b) isolating an immune cell associated with the
  • the predetermined characteristic of the immune cell further comprises a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and a histone glycosylation signature) .
  • the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydrophobic; and e) has high content of aromatic residues.
  • a binding affinity of about 1 nM to about 5000 nM e.g., about 1 nM to about 50 nM, about 50 n
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises detecting and/or quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the cancer status in the individual.
  • the information about cancer status comprises: classification of cancer; type of cancer; nature of cancer; origin of cancer; stage of cancer; likelihood of cancer progression; likelihood of developing one or more cancer symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • a method of detecting cancer in an individual comprising: a) contacting the sample with a bait composition comprising an display moiety comprising a cancer antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; b) isolating an immune cell associated with the display moiety; and c) analyzing the immune cell, wherein a predetermined characteristic of the immune cell is indicative of cancer in the individual, and wherein the predetermined characteristic of the immune cell comprises a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and a
  • the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same. In some embodiments, the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydro
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises detecting and/or quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the cancer status in the individual.
  • the information about cancer status comprises: classification of cancer; type of cancer; nature of cancer; origin of cancer; stage of cancer; likelihood of cancer progression; likelihood of developing one or more cancer symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • a method of detecting residual cancer in an individual comprising analyzing a post-treatment sample from the individual.
  • the method further comprises a) analyzing a pre-treatment sample from the individual prior to anti-cancer therapy and a post-treatment sample from the individual according to any of the methods described herein, and b) comparing the characteristics of the immune cells from the pre-treatment sample and isolated immune cells from the post-treatment sample.
  • a predetermined difference in characteristics of the immune cell from the pre-treatment sample and the immune cell from the post-treatment sample is indicative of residual cancer in the individual.
  • the predetermined characteristic of the immune cell comprises the presence of the immune cell, optionally further comprising a quantity of the immune cell above a threshold level.
  • the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and/or a histone glycosylation signature) .
  • the method comprises: a) contacting the pre-treatment and/or post-treatment sample with a bait composition comprising an display moiety comprising a cancer antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; b) isolating an immune cell associated with the display moiety; and c) analyzing the immune cell.
  • the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydrophobic; and e) has high content of aromatic residues.
  • a binding affinity of about 1 nM to about 5000 nM e.g., about 1 nM to about 50 nM, about 50 n
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises detecting and/or quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the cancer status in the individual.
  • the information about cancer status comprises: classification of cancer; type of cancer; nature of cancer; origin of cancer; stage of cancer; likelihood of cancer progression; likelihood of developing one or more cancer symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • the methods described herein involve (e.g., comprises) conducting an agglutination test.
  • the agglutination test comprises observing the agglutination of cells under a microscope or bare eyes.
  • the number of immune cells is no more than about 10 8 , 5x10 7 , 10 7 , 5x10 6 , 2x10 6 , 10 6 , 5x10 5 , 2x10 5 , 10 5 , 5x10 4 , 4x10 4 , 2x10 4 , or 10 4 cells.
  • Agglutination tests are a class of bioanalytical methods used to detect the presence (qualitive) and sometimes the amount of a substance (quantitative) in a sample.
  • the process generally involves the clumping or aggregation of particles in response to a specific substance, such as an antigen, antibody, or cell.
  • the agglutination reaction occurs with specially designed particles and is often utilized in various diagnostic applications, including blood typing, pathogen detection, and measuring antibody levels.
  • antibodies or other binding agents are mixed with a sample containing potential target antigens. If the antigens are present, they bind to the antibodies, causing the particles to clump together, or agglutinate. This clumping can be observed directly or quantified using various detection methods.
  • the reaction is controlled to avoid non-specific agglutination, which can lead to false-positive results.
  • various buffers and additives may be used to achieve the desired reaction conditions, including pH, ionic strength, and temperature.
  • the test may be performed in various formats, such as slide agglutination, tube agglutination, or microplate agglutination, depending on the sample type, target concentration, and required throughput.
  • a latex beads-based agglutination test is utilized to employ latex beads as the carrier particles for the binding agents.
  • these latex beads offer several advantages, including uniform size, shape, and surface properties, which can be precisely controlled to optimize the test’s performance.
  • the latex beads can be functionalized with various chemical groups and conjugated to appropriate reagents such as antibodies or antigens, or they can passively bind to these reagents.
  • the LBAT comprises bead functionalization.
  • the latex beads are functionalized with the required binding agents. This may involve chemical activation, coupling chemistry, and purification steps.
  • the LBAT comprises sample preparation. The sample is prepared according to the specific requirements of the test, which may include dilution, filtration, or other preprocessing steps.
  • the LBAT comprises reaction mixing: The functionalized beads are mixed with the sample in a controlled environment. Buffer solutions, stabilizers, or other additives may be used to ensure optimal reaction conditions.
  • the LBAT comprises incubation. The reaction mixture is incubated to allow time for the agglutination to occur.
  • the temperature, time, and agitation may be adjusted to achieve the desired reaction kinetics.
  • the LBAT comprises detection.
  • the agglutination is observed or quantified using appropriate detection methods. This may include visual inspection, microscopy, or instrumental analysis, such as spectrophotometry.
  • the use of latex beads in agglutination tests allows for the customization of the beads to meet the unique requirements of different applications, including infectious disease diagnosis, immunological research, food testing, etc.
  • Latex beads colloquial particles developed in the mid-20th century, play a significant role in advancing diagnostics and molecular biology.
  • these beads are synthesized through emulsion polymerization, where monomers are polymerized in an aqueous phase to form polymer beads.
  • this process often involves the use of stabilizers and surfactants to control the size and shape of the particles.
  • subsequent refinements in synthesis techniques have allowed for greater uniformity and control over the physical properties of the particles, such as size, shape, and surface charge.
  • Latex beads have a core made of synthetic polymers, with polystyrene being the most common core material. In some embodiments, it is best known for its structural strength and for being chemically and physically inert when interacting with biological systems. In some embodiments, other variants of latex beads have been synthesized using polymers such as poly (methyl methacrylate) (PMMA) and poly (lactic-co-glycolic acid) (PLGA) , a biodegradable polymer known for its use in drug delivery applications. In some embodiments, the size of latex beads can be finely controlled and typically ranges from about 20 nanometers to about 100 micrometers in diameter.
  • the core of the beads often incorporates a crosslinking agent, such as divinylbenzene (DVB) .
  • a crosslinking agent such as divinylbenzene (DVB)
  • crosslinking imparts a three-dimensional network within the polymer, greatly enhancing the structural integrity and solvent resistance of the beads.
  • the latex beads have a diameter of about at least 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1 ⁇ m. In some embodiments, the latex beads have a diameter of about 0.01 to about 150 ⁇ m, or 0.1 to about 100 ⁇ m (such as about 0.1 to about 50 ⁇ m, such as about 0.5 ⁇ m to about 20 ⁇ m, such as about 0.5 ⁇ m to about 10 ⁇ m, such as about 0.5 ⁇ m to about 5 ⁇ m, such as about 0.5 ⁇ m to about 2.5 ⁇ m) . In some embodiments, the latex beads have a diameter of about 0.1 to about 10 ⁇ m. In some embodiments, the latex beads have a diameter of about 0.5 to about 2 ⁇ m. In some embodiments, the latex beads have a diameter of about 1 ⁇ m.
  • the surface modification of latex beads is central to their utility in various applications, as it allows them to be tailored to specific test requirements.
  • the beads can be designed to conjugate various biological targets such as antibodies, proteins, carbohydrates, DNA, or RNA by introducing different surface functional groups.
  • carboxylated beads for instance, provide a reactive surface for covalent conjugation of biomolecules, making them ideal for immobilizing proteins or antibodies through carbodiimide chemistry.
  • amine-functionalized beads contain primary amine groups that can react with various target molecules, and are commonly utilized for oligonucleotide and peptide conjugation.
  • aldehyde-functionalized beads have the capacity to react with amine groups to form Schiff bases, making them suitable for protein coupling, while hydroxyl beads can be used for additional modifications or as blank controls.
  • specialized functionalization options include magnetic beads, fluorescently-labeled beads, and biotinylated beads that can bind to streptavidin or avidin, enhancing the flexibility and adaptability of latex beads across a broad range of applications.
  • a method of treating a cancer in an individual comprising a) diagnosing the individual as having cancer according to the methods described herein; and b) subjecting the individual to an anti-cancer therapy.
  • diagnosing the individual comprises a) obtaining a sample from the individual, b) contacting the sample with a bait composition comprising an display moiety comprising a cancer antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; c) isolating an immune cell associated with the display moiety; and d) analyzing the immune cell, wherein a predetermined characteristic of the immune cell is indicative of cancer in the individual.
  • the predetermined characteristic of the immune cell comprises the presence of the immune cell.
  • the predetermined characteristic of the immune cell comprises a quantity of the immune cell above a threshold level. In some embodiments, the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and/or a histone glycosylation signature) . In some embodiments, the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydrophobic; and e) has high content of aromatic residues.
  • a binding affinity of about 1 nM to about 5000 nM e.g., about 1 nM to about 50 nM, about 50 n
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises detecting and/or quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the cancer status in the individual.
  • the information about cancer status comprises: classification of cancer; type of cancer; nature of cancer; origin of cancer; stage of cancer; likelihood of cancer progression; likelihood of developing one or more cancer symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • the anti-cancer therapy is a standard or commonly used agent or therapy for treating cancer (e.g., a specific cancer) .
  • the anti-cancer therapy comprises a chemotherapeutic agent.
  • the anti-cancer therapy comprises a surgery.
  • the anti-cancer therapy comprises a radiation therapy.
  • the anti-cancer therapy comprises an immunotherapy.
  • the anti-cancer therapy comprises a cell therapy (such as a cell therapy comprising an immune cell (e.g., CAR T cell) ) .
  • the anti-cancer therapy comprises an angiogenesis inhibitor.
  • the anti-cancer therapy is not an immunotherapy.
  • the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the minimal residual disease is too minimal to be detected by imaging instruments (e.g., a routinely used or standard imaging instrument used for detection of the cancer) .
  • the location of the minimal residual disease is diverse.
  • the minimal residual cancer is a result of immune escape or resistance to treatment.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • a method of treating an infection in an individual comprising a) diagnosing the individual as having infection according to the methods described herein; and b) subjecting the individual to an anti-infection therapy.
  • diagnosing the individual comprises a) obtaining a sample from the individual, b) contacting the sample with a bait composition comprising an display moiety comprising an infection antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; c) isolating an immune cell associated with the display moiety; and d) analyzing the immune cell, wherein a predetermined characteristic of the immune cell is indicative of infection in the individual.
  • the predetermined characteristic of the immune cell comprises the presence of the immune cell.
  • the predetermined characteristic of the immune cell comprises a quantity of the immune cell above a threshold level. In some embodiments, the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and/or a histone glycosylation signature) . In some embodiments, the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydrophobic; and e) has high content of aromatic residues.
  • a binding affinity of about 1 nM to about 5000 nM e.g., about 1 nM to about 50 nM, about 50 n
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises detecting and/or quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the infection status in the individual.
  • the information about infection status comprises: classification of infection; type of infection; nature of infection; origin of infection; stage of infection; likelihood of infection progression; likelihood of developing one or more infection symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • a method of treating an autoimmune disease or condition in an individual comprising a) diagnosing the individual as having autoimmune disease or condition according to the methods described herein; and b) subjecting the individual to an anti-autoimmune disease or condition therapy.
  • diagnosing the individual comprises a) obtaining a sample from the individual, b) contacting the sample with a bait composition comprising an display moiety comprising an autoimmune disease or condition antigenic peptide under a condition sufficient for an immune cell (e.g., a T cell, a cytotoxic T cell, a helper T cell, a memory T cell, and/or a tumor infiltrating T cell) to bind to the display moiety; c) isolating an immune cell associated with the display moiety; and d) analyzing the immune cell, wherein a predetermined characteristic of the immune cell is indicative of autoimmune disease or condition in the individual.
  • the predetermined characteristic of the immune cell comprises the presence of the immune cell.
  • the predetermined characteristic of the immune cell comprises a quantity of the immune cell above a threshold level. In some embodiments, the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature (e.g., a DNA methylation signature and/or a histone glycosylation signature) . In some embodiments, the display moiety comprises two or more (e.g., four) antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same.
  • the antigenic peptide has one or more of the following characteristics: a) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule; b) having a binding affinity of about 1 nM to about 5000 nM (e.g., about 1 nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule; c) having a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) is hydrophobic; and e) has high content of aromatic residues.
  • a binding affinity of about 1 nM to about 5000 nM e.g., about 1 nM to about 50 nM, about 50 n
  • the antigenic peptide has low immunogenicity.
  • the display moiety comprises an MHC molecule complexed with the antigenic peptide.
  • the MHC molecule is a MHC class I molecule and/or a MHC class II molecule.
  • the immune cell is an isolated single immune cell.
  • the immune cell is in a mixture of immune cells.
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • further analyzing the immune cell comprises detecting and/or quantifying the immune cell.
  • further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell, optionally further comprising analyzing the sequences of the one or more nucleic acids (e.g., a TCR related sequence) .
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications (e.g., DNA or RNA methylation, hydroxymethylation, and/or histone modifications such as acetylation, methylation, glycosylation) in the immune cell.
  • the method further comprises generating a report comprising information about the autoimmune disease or condition status in the individual.
  • the information about autoimmune disease or condition status comprises: classification of autoimmune disease or condition; type of autoimmune disease or condition; nature of autoimmune disease or condition; origin of autoimmune disease or condition; stage of autoimmune disease or condition; likelihood of autoimmune disease or condition progression; likelihood of developing one or more autoimmune disease or condition symptoms; molecular diagnosis; NGS pathology; and/or treatment options for the individual.
  • the bait composition comprises a plurality of different display moieties.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide (e.g., at least about two, four, 10, 25, 50, 75, or 100 different display moieties, each comprising a different MHC molecule) .
  • each of the different display moieties comprising different MHC molecules comprises a different detectable label (e.g., a fluorophore) .
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) , and/or separating immune cells associated with each of the different display moieties comprising different MHC molecules into different populations, optionally further comprises contacting each of a plurality of different display moieties with a sample from the individual separately and isolating the immune cell associated with each of the different display moiety.
  • the method further comprises culturing the immune cell prior to the analyzing step.
  • the display moiety comprises a particle (e.g., a particle selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer) .
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing, RNAseq sequencing, and/or subjecting the immune cell to mass spectrometry analysis.
  • Bait compositions display moieties, MHC-peptide complexes, and antigenic peptides
  • the present application provides a composition comprising one or more display moieties or bait compositions.
  • Bait compositions described herein comprise one or more display moieties comprising one or more antigenic peptides (e.g., comprising one or more MHC-peptide complexes) , wherein an immune cell (such as a T cell) binds (e.g., cognately binds) to the display moiety and/or antigenic peptide.
  • an immune cell such as a T cell
  • Any of these bait compositions, display moieties can be used in the methods of analyzing a sample, methods of detecting antigen-specific immune cells and methods of treatment described herein.
  • the display moiety described herein comprises an MHC molecule complexed with an antigenic peptide (e.g. a neoantigenic peptide, e.g., a truncal neoantigenic peptide) .
  • an antigenic peptide e.g. a neoantigenic peptide, e.g., a truncal neoantigenic peptide
  • the present application in one aspect provides display moieties that comprise a support (e.g., a particle) associated with a plurality of MHC-peptide complexes (e.g., MHC-peptide monomers) , wherein at least two of the MHC-peptide complexes are different.
  • a support e.g., a particle
  • MHC-peptide complexes e.g., MHC-peptide monomers
  • the display moiety comprises a support (such as a particle) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises no less than or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises at least one MHC molecule complexed with a peptide, wherein at least two or more of the MHC-peptide complexes are different.
  • a support such as a particle associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises no less than or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises at least one MHC molecule complexed with a peptide, wherein at least two or more of the MHC-peptide complexes are different.
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application provides a display moiety comprising a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex is an MHC-peptide monomer comprising an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes
  • each of the MHC-peptide complex is an M
  • the plurality of MHC-peptide complexes comprise at least 20 MHC-peptide complexes. In some embodiments, the plurality of MHC-peptide complexes 20, 50, 100, 500, 1,000, 5,000, 10,000, 20,000, 50,000, 10,0000, 15,000, 20,0000 MHC-peptide complexes. In some embodiments, the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle. In some embodiments, the first binding component comprises a biotin, and the second binding component comprises streptavidin.
  • the particle has a diameter of at least 0.5 ⁇ m (e.g., at least 1 ⁇ m) . In some embodiments, the particle has a diameter of about 0.01 ⁇ m to about 100 ⁇ m (e.g., 0.5 ⁇ m to about 100 ⁇ m, e.g., 0.5 ⁇ m to about 20 ⁇ m) . In some embodiments, the particle has a diameter of about 0.5 ⁇ m to about 10 ⁇ m.In some embodiments, the particle has a diameter of about 1 ⁇ m.
  • the particle has a surface area of about 0.01 ⁇ m 2 to about 1000 ⁇ m 2 (e.g., about 0.1 ⁇ m 2 to about 100 ⁇ m 2 , about 1 ⁇ m 2 to about 20 ⁇ m 2 ) . In some embodiments, the particle has a number of about 10 to about 200,000 (e.g., about 100 to about 20000, e.g., about 10 to about 10000) second binding component associated with it. In some embodiments, the display moiety comprises at least two different MHC class I molecules. In some embodiments, wherein the display moiety comprises at least two different MHC class II molecules. In some embodiments, wherein the display moiety comprises at least one MHC class I molecule and at least one MHC class II molecule.
  • the display moiety comprises an HLA-A molecule. In some embodiments, . In some embodiments, the HLA-A molecule comprises a mutation that reduces its binding to CD8. In some embodiments, the HLA-Amolecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen.
  • the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two different peptides (e.g., at least 2, 5, 10, 20, 30, 40, 50, 100, 200, 500, or 1000 different peptides) .
  • the at least two distinct peptides are associated with two different antigens.
  • the two distinct antigens comprise two distinct mutations of one or more genes (e.g., oncogenes) associated with a disease (e.g., a cancer) .
  • the oncogene has a driven mutation.
  • the oncogene comprises one or more of KRAS, EGFR, POLE, TP53, SMAD, BRCA1, CDKN2A, TNN, MUC16, BRAF and ALK.
  • the oncogene comprises TP53, KRAS, MUC16, SMAD, CDKN2A and TNN.
  • the at least two different peptides overlap (e.g., overlap for at least 2, 3, 4, 5, or 6 amino acids) . In some embodiments, the at least two different peptides do not overlap. In some embodiments, the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application provides a display moiety comprising a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprises at least 20, 50, 100, 500, 1,000, 5,000, 10,000, 20,000, 50,000, 10,0000, 15,000, 20,000, 50,000, 100,000, 200,000, 500,000, or 1,000,000 MHC-peptide complexes.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin, or vice versa.
  • the particle has a diameter of at least 0.5 ⁇ m (e.g., at least 1 ⁇ m) .
  • the particle has a diameter of about 0.01 ⁇ m to about 100 ⁇ m (e.g., 0.5 ⁇ m to about 100 ⁇ m, e.g., 0.5 ⁇ m to about 20 ⁇ m) . In some embodiments, the particle has a diameter of about 0.5 ⁇ m to about 10 ⁇ m.In some embodiments, the particle has a diameter of about 1 ⁇ m. In some embodiments, the particle has a surface area of about 0.01 ⁇ m 2 to about 1000 ⁇ m 2 (e.g., about 0.1 ⁇ m 2 to about 100 ⁇ m 2 , about 1 ⁇ m 2 to about 20 ⁇ m 2 ) .
  • the particle has a number of about 10 to about 200,000 (e.g., about 100 to about 20000, e.g., about 10 to about 10000) second binding component associated with it.
  • the display moiety comprises at least two different MHC class I molecules. In some embodiments, wherein the display moiety comprises at least two different MHC class II molecules. In some embodiments, wherein the display moiety comprises at least one MHC class I molecule and at least one MHC class II molecule. In some embodiments, the display moiety comprises an HLA-A molecule. In some embodiments, the HLA-A molecule comprises a mutation that reduces its binding to CD8.
  • the HLA-A molecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen.
  • the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two different peptides (e.g., at least 2, 5, 10, 20, 30, 40, 50, 100, 200, 500, or 1000 different peptides) .
  • the at least two distinct peptides are associated with two different antigens.
  • the two distinct antigens comprise two distinct mutations of one or more genes (e.g., oncogenes) associated with a disease (e.g., a cancer) .
  • the oncogene has a driven mutation.
  • the oncogene comprises one or more of KRAS, EGFR, POLE, TP53, SMAD, BRCA1, CDKN2A, TNN, MUC16, BRAF and ALK.
  • the oncogene comprises TP53, KRAS, MUC16, SMAD, CDKN2A and TNN.
  • the at least two different peptides overlap.
  • the at least two different peptides do not overlap.
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application provides a display moiety comprising a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least 0.5 ⁇ m.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the particle has a surface area of at least about 1 ⁇ m 2 , or has a diameter of at least
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin.
  • the particle has a diameter of about 0.5 ⁇ m to about 100 ⁇ m (e.g., 0.5 ⁇ m to about 100 ⁇ m, e.g., 1 ⁇ m to about 20 ⁇ m) . In some embodiments, the particle has a diameter of about 1 ⁇ m to about 10 ⁇ m.
  • the particle has a diameter of about 1 ⁇ m. In some embodiments, the particle has a surface area of about 1 ⁇ m 2 to about 1000 ⁇ m 2 (e.g., about 1 ⁇ m 2 to about 100 ⁇ m 2 , about 1 ⁇ m 2 to about 20 ⁇ m 2 ) . In some embodiments, the particle has a number of about 10 to about 200,000 (e.g., about 100 to about 20000, e.g., about 10 to about 10000) second binding component associated with it. In some embodiments, the display moiety comprises at least two different MHC class I molecules. In some embodiments, wherein the display moiety comprises at least two different MHC class II molecules.
  • the display moiety comprises at least one MHC class I molecule and at least one MHC class II molecule.
  • the display moiety comprises an HLA-A molecule.
  • the HLA-A molecule comprises a mutation that reduces its binding to CD8.
  • the HLA-Amolecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen.
  • the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two different peptides (e.g., at least 2, 5, 10, 20, 30, 40, 50, 100, 200, 500, or 1000 different peptides) .
  • the at least two distinct peptides are associated with two different antigens.
  • the two distinct antigens comprise two distinct mutations of one or more genes (e.g., oncogenes) associated with a disease (e.g., a cancer) .
  • the oncogene has a driven mutation.
  • the oncogene comprises one or more of KRAS, EGFR, POLE, TP53, SMAD, BRCA1, CDKN2A, TNN, MUC16, BRAF and ALK.
  • the oncogene comprises TP53, KRAS, MUC16, SMAD, CDKN2A and TNN.
  • the at least two different peptides overlap.
  • the at least two different peptides do not overlap.
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application provides a display moiety comprising a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the plurality of MHC-peptide complexes comprise a) at least two different MHC molecules, and b) at least two different peptides.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4,
  • one or more of the plurality of MHC-peptide complexes is an MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin.
  • the particle has a diameter of at least 0.5 ⁇ m (e.g., at least 1 ⁇ m) .
  • the particle has a diameter of about 0.01 ⁇ m to about 100 ⁇ m (e.g., 0.5 ⁇ m to about 100 ⁇ m, e.g., 0.5 ⁇ m to about 20 ⁇ m) .
  • the particle has a diameter of about 0.5 ⁇ m to about 10 ⁇ m. In some embodiments, the particle has a diameter of about 1 ⁇ m. In some embodiments, the particle has a surface area of about 0.01 ⁇ m 2 to about 1000 ⁇ m 2 (e.g., about 0.1 ⁇ m 2 to about 100 ⁇ m 2 , about 1 ⁇ m 2 to about 20 ⁇ m 2 ) . In some embodiments, the particle has a number of about 10 to about 200,000 (e.g., about 100 to about 20000, e.g., about 10 to about 10000) second binding component associated with it. In some embodiments, the display moiety comprises at least two different MHC class I molecules.
  • the display moiety comprises at least two different MHC class II molecules. In some embodiments, wherein the display moiety comprises at least one MHC class I molecule and at least one MHC class II molecule. In some embodiments, the display moiety comprises an HLA-A molecule. In some embodiments, the HLA-A molecule comprises a mutation that reduces its binding to CD8. In some embodiments, the HLA-A molecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen.
  • the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two different peptides (e.g., at least 2, 5, 10, 20, 30, 40, 50, 100, 200, 500, or 1000 different peptides) .
  • the at least two distinct peptides are associated with two different antigens.
  • the two distinct antigens comprise two distinct mutations of one or more genes (e.g., oncogenes) associated with a disease (e.g., a cancer) .
  • the oncogene has a driven mutation.
  • the oncogene comprises one or more of KRAS, EGFR, POLE, TP53, SMAD, BRCA1, CDKN2A, TNN, MUC16, BRAF and ALK.
  • the oncogene comprises TP53, KRAS, MUC16, SMAD, CDKN2A and TNN.
  • the at least two different peptides overlap.
  • the at least two different peptides do not overlap.
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application provides a display moiety comprising a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class I molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the display moiety comprises at least two different MHC class I molecules.
  • At least one or each of the plurality of MHC-peptide complexes is an MHC-peptide monomer, MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin.
  • the particle has a diameter of about 0.5 ⁇ m to about 100 ⁇ m (e.g., 0.5 ⁇ m to about 100 ⁇ m, e.g., 1 ⁇ m to about 20 ⁇ m) . In some embodiments, the particle has a diameter of about 1 ⁇ m to about 10 ⁇ m.
  • the particle has a diameter of about 1 ⁇ m. In some embodiments, the particle has a surface area of about 1 ⁇ m 2 to about 1000 ⁇ m 2 (e.g., about 1 ⁇ m 2 to about 100 ⁇ m 2 , about 1 ⁇ m 2 to about 20 ⁇ m 2 ) . In some embodiments, the particle has a number of about 10 to about 200,000 (e.g., about 100 to about 20000, e.g., about 10 to about 10000) second binding component associated with it. In some embodiments, wherein the display moiety comprises at least two different MHC class II molecules. In some embodiments, wherein the display moiety comprises at least one MHC class I molecule and at least one MHC class II molecule.
  • the display moiety comprises an HLA-A molecule.
  • the HLA-A molecule comprises a mutation that reduces its binding to CD8.
  • the HLA-A molecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen.
  • the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two different peptides (e.g., at least 2, 5, 10, 20, 30, 40, 50, 100, 200, 500, or 1000 different peptides) .
  • the at least two distinct peptides are associated with two different antigens.
  • the two distinct antigens comprise two distinct mutations of one or more genes (e.g., oncogenes) associated with a disease (e.g., a cancer) .
  • the oncogene has a driven mutation.
  • the oncogene comprises one or more of KRAS, EGFR, POLE, TP53, SMAD, BRCA1, CDKN2A, TNN, MUC16, BRAF and ALK.
  • the oncogene comprises TP53, KRAS, MUC16, SMAD, CDKN2A and TNN.
  • the at least two different peptides overlap.
  • the at least two different peptides do not overlap.
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • the present application provides a display moiety comprising a particle (e.g., a spherical particle, e.g., a solid particle, e.g., a bead) associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises at least or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises an MHC molecule complexed with a peptide, wherein at least two MHC-peptide complexes are different, wherein the display moiety comprises at least two different MHC class II molecules.
  • a particle e.g., a spherical particle, e.g., a solid particle, e.g., a bead
  • the display moiety comprises at least two different MHC class II molecules.
  • At least one or each of the plurality of MHC-peptide complexes is an MHC-peptide monomer, MHC-peptide dimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer.
  • at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin.
  • the particle has a diameter of about 0.5 ⁇ m to about 100 ⁇ m (e.g., 0.5 ⁇ m to about 100 ⁇ m, e.g., 1 ⁇ m to about 20 ⁇ m) . In some embodiments, the particle has a diameter of about 1 ⁇ m to about 10 ⁇ m.
  • the particle has a diameter of about 1 ⁇ m. In some embodiments, the particle has a surface area of about 1 ⁇ m 2 to about 1000 ⁇ m 2 (e.g., about 1 ⁇ m 2 to about 100 ⁇ m 2 , about 1 ⁇ m 2 to about 20 ⁇ m 2 ) . In some embodiments, the particle has a number of about 10 to about 200,000 (e.g., about 100 to about 20000, e.g., about 10 to about 10000) second binding component associated with it. In some embodiments, wherein the display moiety comprises at least one MHC class I molecule. In some embodiments, the display moiety comprises an HLA-A molecule.
  • the HLA-A molecule comprises a mutation that reduces its binding to CD8. In some embodiments, the HLA-A molecule comprises an HLA A2 heavy chain with a A245V mutation. In some embodiments, the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
  • the peptide is associated with a cancer or tumor antigen.
  • the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • the display moiety comprises at least two different peptides (e.g., at least 2, 5, 10, 20, 30, 40, 50, 100, 200, 500, or 1000 different peptides) .
  • the at least two distinct peptides are associated with two different antigens.
  • the two distinct antigens comprise two distinct mutations of one or more genes (e.g., oncogenes) associated with a disease (e.g., a cancer) .
  • the oncogene has a driven mutation.
  • the oncogene comprises one or more of KRAS, EGFR, POLE, TP53, SMAD, BRCA1, CDKN2A, TNN, MUC16, BRAF and ALK.
  • the oncogene comprises TP53, KRAS, MUC16, SMAD, CDKN2A and TNN.
  • the at least two different peptides overlap.
  • the at least two different peptides do not overlap.
  • the display moiety does not comprise a fluorochrome or fluorophore.
  • Support e.g., particle
  • the support such as particles described herein can be any medium that provide a support for association with the MHC-peptide complexes described herein.
  • the particle is solid. In some embodiments, the particle is not solid (e.g., hollow in the middle, e.g., having a dextran or polymer backbone) . See e.g., J Immunol Methods. 2006 Mar 20; 310 (1-2) : 136-48.
  • the particle is spherical (e.g., a bead) .
  • the diameter refers to minimum diagonal length; in some embodiments, diameter refers to the maximum diagonal length; in some embodiments, diameter refers to the average diagonal length.
  • the particle has a diameter of at least 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1 ⁇ m. In some embodiments, the particle has a diameter of about 0.01 to about 150 ⁇ m, or 0.01 to about 100 ⁇ m (such as about 0.1 to about 50 ⁇ m, such as about 0.5 ⁇ m to about 20 ⁇ m, such as about 0.5 ⁇ m to about 10 ⁇ m, such as about 0.5 ⁇ m to about 5 ⁇ m, such as about 0.5 ⁇ m to about 2.5 ⁇ m) . In some embodiments, the particle has a diameter of about 0.1 to about 10 ⁇ m. In some embodiments, the particle has a diameter of about 0.5 to about 2 ⁇ m. In some embodiments, the particle has a diameter of about 1 ⁇ m.
  • the particle has a surface area of about 0.01 ⁇ m 2 to about 400 ⁇ m 2 (such as about 0.1 ⁇ m 2 to about 20 ⁇ m 2 , about 0.1 ⁇ m 2 to about 10 ⁇ m 2 , or about 1 ⁇ m 2 to about 10 ⁇ m 2 ) . In some embodiments, the particle has a surface area of at least about 0.01 ⁇ m 2 , about 0.1 ⁇ m 2 , or about 1 ⁇ m 2 .
  • the particle has a number of at least about 2, 4, 5, 10, 12, 20, 50, 100, 200, 500, or 1000 binding component (e.g., second binding component as discussed above) . In some embodiments, the particle has a number of about 2 to about 100000 (such as 13-100000, 20-100000, 50-100000, 100-10000) binding component associated with it. In some embodiments, the binding component (e.g., streptavidin) is directly conjugated to the particle.
  • binding component e.g., streptavidin
  • the particle is magnetic
  • the one or more of the plurality of MHC-peptide complexes are MHC-peptide monomers. In some embodiments, the one or more of the plurality of MHC-peptide complexes are MHC-peptide dimers. In some embodiments, the one or more of the plurality of MHC-peptide complexes are MHC-peptide trimers. In some embodiments, the one or more of the plurality of MHC-peptide complexes consist of MHC-peptide monomers, dimers and/or trimers. In some embodiments, the one or more of the plurality of MHC-peptide complexes are MHC-peptide tetramers.
  • the one or more of the plurality of MHC-peptide complexes are MHC-peptide pentamers. In some embodiments, the one or more of the plurality of MHC-peptide complexes are MHC-peptide octamers. In some embodiments, the one or more of the plurality of MHC-peptide complexes are MHC-peptide dextramers. In some embodiments, the one or more of the plurality of MHC-peptide complexes are MHC-peptide dodecamer. In some embodiments, at least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers. In some embodiments, the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the one or more of the plurality of MHC-peptide complexes comprise a mixture of one or more of MHC-peptide monomers, one or more of MHC-peptide tetramers, one or more of MHC-peptide dimers, one or more of MHC-peptide pentamers, one or more of MHC-peptide octamers, one or more of MHC-peptide dextramers, and/or one or more of MHC-peptide dodecamers.
  • the one or more of the plurality of MHC-peptide complexes comprise a mixture of one or more of MHC-peptide monomers and one or more of MHC-peptide tetramers.
  • At least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • the plurality of MHC-peptide complexes comprise at least 20 MHC-peptide complexes. In some embodiments, the plurality of MHC-peptide complexes comprise at least 50 MHC-peptide complexes. In some embodiments, the plurality of MHC-peptide complexes comprise at least 100 MHC-peptide complexes. In some embodiments, the plurality of MHC-peptide complexes comprise at least 500 MHC-peptide complexes. In some embodiments, the plurality of MHC-peptide complexes comprise at least 1000 MHC-peptide complexes. In some embodiments, the plurality of MHC-peptide complexes comprise about 10-100000 (such as 20-100000, 50-10000, 100-10000) MHC-peptide complexes.
  • one or more, or each of the plurality of the MHC-peptide complex is attached to the support (e.g., the particle) directly (i.e., no intermediate sperate molecule in between) .
  • one or more, or each of the plurality of the MHC-peptide complex is attached to the support (e.g., the particle) via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • Exemplary binding pairs comprise any binding pairs that selectively bind to each other.
  • the binding components are solely for promoting the binding between the MHC-peptide complex and the support (e.g., the particle) .
  • the first binding component comprises biotin or a synthetic mimic of biotin (e.g., 2-iminobiotin)
  • the second binding component comprises streptavidin or a synthetic mimic of streptavidin, or vice versa. See e.g., Chem Soc Rev. 2017 May 9; 46 (9) : 2391–2403.
  • the first binding component comprises a biotin
  • the second binding component comprises streptavidin.
  • the binding components are any suitable moieties known in the art (such as, thiol, maleimide, cyclodextrin, amine, adamantine, carboxy, azide, and alkyne) .
  • the two binding components comprise a binding pair that reacts via a click chemistry reaction.
  • Exemplary reactions include: Strain-promoted azido-alkyne cycloaddition (SPAAC) , Cu-mediated azido-alkyne cycloaddition (CuAAC) , Staudinger ligation, Boronic acid-mediated facile assembly involving aromatic aminothiols, Boronic acid-mediated facile assembly involving amines or oximes, Boronic acid-mediated facile assembly involving hydrazides, Boronic acid-mediated facile assembly involving ⁇ -aminothiols, Boronic acid-mediated facile assembly involving amines, Strained alkyne-tetrazine cycloaddition, Strain-promoted alkyne-nitrone cycloaddition (SPANC) , Strain-promoted alkyne-tetrazole cycloaddition, Sydnone-strained alkyne reaction. See e.g., Acta Pharm Sin B. 2023 May; 13 (5) : 1990-2016.
  • MHC I and II molecules present protein fragments to CD8+ and CD4+ T cells, respectively. These molecules are essential for cell-mediated immunity and therefore appeared at the inception of the adaptive immune system. For their construction they used two Ig-domains topped by two parallel alpha helixes resting on a platform of beta-pleated sheets. This capital structure generated a peptide-binding groove between the alpha helixes, which is ‘evolutionarily speaking’ likely borrowed from earlier chaperone structures. Yet MHC I and MHC II molecules are unique in the proteome because of their extreme polymorphism (>10,000 different alleles of MHC I molecules have been identified thus far) . This has interesting consequences.
  • Polymorphic residues on the top alpha helixes interact with the TCR and are the basis for the specificity of TCRs for both an antigen peptide plus a particular allelic form of an MHC molecule (a phenomenon called MHC restriction) .
  • Polymorphic residues in the MHC peptide binding groove change the nature and location of so-called pockets. These variable pockets are filled by complementary variable amino acid side chains of peptides (so-called anchor residues) , with the effect that different fragments from a defined antigen are presented by different polymorphic MHC molecules.
  • anchor residues complementary variable amino acid side chains of peptides
  • most other amino acids in a peptide fill a free space and can be (almost) any of the 20 amino acids.
  • each kind of MHC molecules can present a very large repertoire of peptides.
  • 3 to 6 different MHC I as well as 3 to 12 different MHC II molecules the exact number depending on how many different MHC alleles were inherited from one’s parents and how the MHC II subunits paired
  • cells can present a large fraction of the universe of peptides, although not all sequences. See e.g., Trends Immunol. 2016 Nov; 37 (11) : 724–737.
  • MHC I molecules can present a peptidome of around 6 ⁇ 20 (6–7) different peptides, and MHC II ca display up to 12 ⁇ 20 (10) peptides.
  • MHC II ca display up to 12 ⁇ 20 (10) peptides.
  • such a large array of peptides cannot all be presented because there are only around 200,000 MHC I and 20,000 MHC II molecules on cells such as B and T cells per cell.
  • the real number of different peptides presented by one cell is likely less than 10,000.
  • MHC polymorphism is good for the survival of the population and not necessarily the individual. See e.g., Trends Immunol. 2016 Nov; 37 (11) : 724–737.
  • the MHC molecules described herein can be any MHC molecules. See e.g., Cell Mol Immunol. 2015 Mar; 12 (2) : 139-53.
  • the MHC molecule is a MHC class I molecule.
  • the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, HLA-C, and HLA-D. In some embodiments, the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C. In some embodiments, MHC class I molecule comprises a HLA-A molecule. In some embodiments, the HLA-A molecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation. It was found that this mutation does not result in loss of reactivity towards some of the specific T cells, but in fact with result in a decreased the background staining.
  • the MHC class I molecule is selected from the group consisting HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the MHC class I molecule comprises multiple kinds of MHC class I molecules comprising HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the MHC class I molecule comprises multiple kinds of MHC class I molecules comprising HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the HLA molecule has a His-tag fused to the C-terminus.
  • the HLA molecule has a polypeptide (e.g., a GS linker, e.g., a G4S linker) that has a length of about 5-15, 7-13, 8-12, 9-11 or 10 amino acids fused to the C-terminus.
  • the antigenic peptide complexed with MHC I molecule is about 8 to about 10 amino acids long. In some embodiments, the antigenic peptide is at least 8 (e.g., 8, 9, or 10) amino acids long.
  • the MHC molecule is a recombinant MHC I molecule.
  • the MHC molecule is a MHC class II molecule.
  • the MHC class II molecule is selected from the group consisting of HLA-DR, HLA-DQ, and HLA-DF. In some embodiments, the MHC class II molecule is selected from the group consisting of HLA-DQ and HLA-DR.
  • the antigenic peptide that complexed with a MHC class II molecule is about 10 to about 20 amino acids long. In some embodiments, the antigenic peptide is at least 10 (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) amino acids long.
  • the MHC molecule is a recombinant MHC II molecule.
  • the MHC molecule comprise both an MHC I molecule and an MHC II molecule.
  • the MHC molecule matches with at least one HLA type of the individual from where the sample is obtained.
  • a MHC I molecule comprising HLA-A*24: 02 or HLA-A*11: 01 is used when the individual has both HLA-A*24: 02 and HLA-A*11: 01.
  • Patient-specific NGS data from WGS, WES, or RNA-seq can be used to predict HLA types with computational tools such as Optiptype and Polysolver (polymorphic loci resolver) . See e.g., Szolet et al., Bioinformatics 30, 3310–3316, e.g., Shukla et al., Nat. Biotechnol.
  • Reads can be selected from the NGS data that potentially derived from the HLA region and then they can be fully aligned to a full-length genomic library of all known HLA alleles. See e.g., Nucleic Acids Res. 41, D1222–D1227.
  • the MHC molecule is coupled with a chaperon molecule prior to being complexed to the antigenic peptide. See e.g., Overall et al., Nat Commun. 2020 Apr 20; 11 (1) : 1909.
  • the display moiety comprises an HLA-A molecule, an HLA-B molecule and/or an HLA-C molecule. In some embodiments, the display moiety comprises an HLA-A molecule. In some embodiments, the HLA-A molecule comprises a mutation that reduces its binding to CD8. In some embodiments, the HLA-A molecule comprises an HLA A2 heavy chain with a A245V mutation.
  • the display moiety comprises an MHC class II molecule.
  • the MHC class II molecule is selected from the group consisting of an HLA-DO molecule, an HLA-DM molecule, an HLA-DP molecule, an HLA-DQ molecule and an HLA-DR molecule.
  • the MHC class II molecule is selected from the group consisting of an HLA-DP molecule, an HLA-DQ molecule and an HLA-DR molecule.
  • the display moiety comprises an MHC class II molecule selected from the group consisting of an HLA-DQ molecule and an HLA-DR molecule.
  • the display moiety described herein comprises at least two different MHC molecules.
  • the at least two different MHC molecules comprises two different MHC class I molecules.
  • the two different MHC class I molecules comprise an HLA-A molecule and at least one of an HLA-B molecule and an HLA-C molecule.
  • the two different MHC class I molecules comprise an HLA-A molecule and an HLA-B molecule.
  • the two different MHC class I molecules comprise an HLA-A molecule and an HLA-C molecule.
  • the two different MHC class I molecules comprise an HLA-B molecule and an HLA-C molecule.
  • the two different MHC class I molecules comprise a) an HLA-A molecule, b) an HLA-B molecule and c) an HLA-C molecule.
  • the MHC multimer comprises at least two MHC class I molecules that are at least two different HLA-A molecules.
  • the at least two different HLA-A molecules are selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • the at least two different MHC molecules comprises two different MHC class II molecules.
  • the two different MHC class II molecules comprise at least two MHC class molecules selected from the group consisting of an HLA-DP molecule, an HLA-DQ molecule and an HLA-DR molecule.
  • the two different MHC class II molecules comprise an HLA-DP molecule and an HLA-DQ molecule.
  • the two different MHC class II molecules comprise an HLA-DP molecule and an HLA-DR molecule.
  • the two different MHC class II molecules comprise an HLA-DR molecule and an HLA-DQ molecule.
  • the two different MHC class II molecules comprise an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the at least two different MHC molecules comprises both an MHC class I molecule and an MHC class II molecule. In some embodiments the at least two different MHC molecules comprise a) an HLA-A molecule and b) an MHC class II molecule selected from the group consisting of an HLA-DP molecule, an HLA-DQ molecule and an HLA-DR molecule. In some embodiments the at least two different MHC molecules comprise a) an HLA-A molecule and b) an HLA-DP molecule. In some embodiments the at least two different MHC molecules comprise a) an HLA-A molecule and b) an HLA-DQ molecule. In some embodiments the at least two different MHC molecules comprise a) an HLA-A molecule and b) an HLA-DR molecule.
  • the display moiety comprises two or more (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1000, 10,000, or 100,000) antigenic peptides. In some embodiments, the display moiety comprises four antigenic peptides. In some embodiments, the two or more antigenic peptides in the display moiety are the same or similar. In some embodiments, the two or more antigenic peptides in the display moiety are distinct. In some embodiments, at least one of the two or more antigenic peptides is a truncal antigenic peptide.
  • the display moiety comprises an MHC/peptide monomer, dimer, trimer, and/or tetramer.
  • MHC/peptide complexes are assembled into monomers, dimers, trimers, and/or tetramers, comprising 1, 2, 3, or 4 MHC/peptide complexes bound to a display moiety.
  • the MHC/peptide complex further comprises a detectable label.
  • the detectable label is a fluorophore, such as phycoerythrin (PE) , allophycocyanin (APC) or any fluorophore known in the art.
  • the MHC/peptide complex does not comprise a detectable label.
  • the MHC/peptide complex is assembled into a multimer (such as, dimer, trimer, tetramer, pentamer, hexamer, or high order multimer) .
  • the multimer can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 MHC/peptide complexes.
  • a high throughput peptide-MHC (pMHC) tetramer library is constructed. See e.g., Overall et al., Nat Commun. 2020 Apr 20; 11 (1) : 1909.
  • the display moiety further comprises a barcode (e.g., a DNA barcode) .
  • each of the one or more display moieties comprises a unique barcode (e.g., a unique DNA barcode) . See e.g., Overall et al., Nat Commun. 2020 Apr 20; 11 (1) : 1909.
  • the display moiety comprises a particle.
  • the particle is selected from the group consisting of a surface, a nanoparticle, a bead, and a polymer.
  • the particle is a magnetic nanoparticle, e.g. for isolation using a magnet. See e.g., Peng et al., Cell Rep. 2019 Sep 3; 28 (10) : 2728-2738. e7.
  • the magnetic particle comprises magnetic iron oxide.
  • the particle is a polystyrene nanoparticle, e.g., for isolation by gravity.
  • the particle is an agarose bead.
  • the particle is a sepharose bead.
  • the particle is a dextran particle. In some embodiments, the particle is a biotinylated dextran or a streptavidin-coated dextran.
  • the particle in the display moiety is not the same as the solid support or substrate used to immobilize the immune cells as described herein.
  • the particle is detectable. In some embodiments, the particle is fluorescent. In some embodiments, the particle is attached directly or indirectly to a fluorophore. In some embodiments, the particle is modified with an attachment moiety for attaching additional molecules.
  • the antigenic peptide or MHC is directly attached to the particle. In some embodiments, the antigenic peptide or MHC is attached to the particle via a binding pair comprising a first binding component attached to the antigenic peptide and a second binding component bound to the particle.
  • the binding components are any suitable moieties known in the art (such as, thiol, maleimide, cyclodextrin, amine, adamantine, carboxy, azide, and alkyne) .
  • multiple display moieties e.g., MHC/peptide complexes
  • MHC/peptide complexes are attached to a single particle.
  • the display moiety comprises a cell (e.g., an antigen presenting cell, e.g., a dendritic cell, e.g., a macrophage) .
  • the cell comprises a polynucleotide encoding the antigenic peptide (e.g., a truncal antigenic peptide) .
  • the polynucleotide encodes a plurality of antigenic peptides.
  • the plurality of antigenic peptides are displayed on the surface of the cell (e.g., antigen presenting cells) .
  • the cells used for display antigenic peptides are different from the immune cells in the sample described herein.
  • the plurality of antigenic peptides are displayed on the surface of the cell in complex with an MHC molecule.
  • the cell is obtained from the individual. In some embodiments, the cell has at least one (or two) same HLA type as that of the individual. For example, if the individual has HLA-A*24: 02, the cell in the display moiety also has HLA-A*24: 02.
  • the display moiety further comprises a detectable label.
  • the detectable label is a fluorophore.
  • the display moiety is itself fluorescent or is attached to a fluorophore directly or indirectly.
  • the fluorophore is a phycoerythrin (PE) , allophycocyanin (APC) or any fluorophore known in the art.
  • Antigenic peptides i.e., peptides
  • Peptides described herein can be derived from exogenous antigens (e.g., an antigen from a pathogen) or endogenous antigens (e.g., an antigen associated with a cancer cell, e.g., a neoantigen, e.g., an autoantigen) .
  • exogenous antigens e.g., an antigen from a pathogen
  • endogenous antigens e.g., an antigen associated with a cancer cell, e.g., a neoantigen, e.g., an autoantigen
  • the size of a antigenic peptide can comprise, but is not limited to, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120 or greater amino molecule residues, and any range derivable therein.
  • the antigenic peptide molecules are equal to or less than 50 amino acids.
  • the antigenic peptide complexed with a MHC Class I molecule has 15 residues or less in length and usually consist of between about 8 and about 11 residues, particularly 9 or 10 residues. In some embodiments, the antigenic peptides complexed with a MHC Class II molecule has 6-30 residues.
  • a longer peptide can be designed in several ways. For example, when presentation likelihoods of peptides on HLA alleles are predicted or known, a longer peptide could consist of either: (1) individual presented peptides with an extensions of 2-5 amino acids toward the N-and C-terminus of each corresponding gene product; (2) a concatenation of some or all of the presented peptides with extended sequences for each.
  • the one or more antigenic peptides are about 8-50 amino acids in length. In some embodiments, it is about 8-10 amino acids in length. In some embodiments, it is greater than 10 amino acids in length, greater than 15 amino acids in length, greater than 20 amino acids in length, or greater than 30 amino acids in length. In some embodiments, it is about 24-40 amino acids in length.
  • the one or more antigenic peptides used in the bait compositions described herein are further optimized based upon one or more selection criteria.
  • the antigenic peptides are further selected based on their likelihood to be processed and/or presented on the cell surface HLA molecules.
  • in silico prediction algorithms such as any of the algorithms described herein
  • immunopeptidomics analysis is used as the basis for the selection.
  • the one or more antigenic peptides are selected based upon its binding affinity to a) an MHC molecule and/or b) a cognate TCR molecule.
  • the antigenic peptide has a binding affinity that is less than 5000 nM (IC50) to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity of about 500 nM to 5000 nM (IC50) to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity that is less than 500 nM (IC50) to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity of about 250 nM to 500 nM IC50 to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity that is less than 250 nM (IC50) to an MHC molecule.
  • the antigenic peptide has a binding affinity that is less than 100 nM (IC50) to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity of about 50 nM to 500 nM IC50 to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity that is less than 50 nM (IC50) to an MHC molecule. In some embodiments, the antigenic peptide has a binding affinity of about 1 nM to 50 nM IC50 to an MHC molecule.
  • the antigenic peptide has a binding affinity that is less than 5000 nM (IC50) to a cognate TCR molecule. In some embodiments, the antigenic peptide has a binding affinity of about 500 nM to 5000 nM (IC50) to a cognate TCR molecule. In some embodiments, the antigenic peptide has a binding affinity of about 50 nM to 500 nM IC50 to a cognate TCR molecule. In some embodiments, the antigenic peptide has a binding affinity of about 1 nM to 50 nM IC50 to a cognate TCR molecule.
  • the antigenic peptide is selected based upon its hydrophobic status. In some embodiments, the antigenic peptide is hydrophobic. In some embodiments, the antigenic peptide has a high content of aromatic residues. In some embodiments, the antigenic peptide has at least about 10%, 20%, 30%, or 40%aromatic residues.
  • the antigenic peptide has a binding affinity of about 1nM to about 5000 nM (e.g., about 1nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to an MHC molecule, a binding affinity of about 1nM to about 5000 nM (e.g., about 1nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM) to a cognate TCR molecule, a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus, is hydrophobic, and has high content of aromatic residues.
  • a binding affinity of about 1nM to about 5000 nM e.g., about 1nM to about 50 nM, about 50 nM to about 500 nM, about 500 nM to about 5000 nM
  • an MHC molecule e.g.
  • the antigenic peptide has low immunogenicity. Immunogenicity of the antigenic peptide can be predicted by algorithm developed for this purpose. See e.g., Riley et al., Front Immunol. 2019 Aug 28; 10: 2047; e.g., Schmidt et al., Cell Rep Med. 2021 Feb 6; 2 (2) : 100194.
  • the antigenic peptide may be flanked by universal sequences or portions thereof.
  • the universal sequences or portions allow for rapid, high throughput methods for replacing or inserting the antigenic peptide encoding nucleotide in the polynucleotide MHC template.
  • the antigenic peptides further comprise a unique defined barcode sequence operably associated with the identity of each distinct polypeptide.
  • the unique defined barcodes provide an antigen-specific sequence for identification during the analysis of the immune cell. See e.g., Peng et al., Cell Rep. 2019 Sep 3; 28 (10) : 2728-2738. e7.
  • the peptide is associated with a cancer or tumor antigen. In some embodiments, the peptide is associated with a neoantigen.
  • the peptide is associated with an antigen of a pathogen.
  • the pathogen is a virus, bacteria of fungus.
  • the peptide is associated with an autoantigen.
  • Neoantigenic peptides
  • Neoantigens can be formed via various mechanisms. Non-synonymous somatic mutations, which can alter amino acid coding sequences, are the main cause of neo-epitopes. Except for somatic non-synonymous protein-altering mutations, tumor neoantigens can be generated from alternative splicing variations. Multiple computational methods and databases have been developed to identify alternative splicing events from RNA-seq data, such as SplAdder and CancerSplicingQTL2. See e.g., Kahles et al., Bioinformatics 32 1840–1847; Tian et al., Nucleic Acids Res. 47 D909–D916.
  • Sandwich immunoassays in the miniaturized system could successfully identify tumor antigens in sera samples extracted from patients. See e.g., Pollard et al., Proteomics Clin. Appl. 1 934–952 (2007) ; Yang et al., Biosens. Bioelectron. 40 385–392 (2013) .
  • Serologic Proteome analysis (SERPA) or 2-D western blots consists of the isoelectric focusing (IEF) gel run in the first dimension and SDS-PAGE gel run in the second dimension.
  • SERPA separates the proteins in the gel by their isoelectric point (IP) and molecular mass and then transfers the proteins from the gel to a carrier membrane to screen antibodies. Finally, the antigenic protein spots can be identified by MS. See e.g., Tjalsma et al., Proteomics Clin. Appl. 2 167–180 (2008) . This approach has been used to identify antigens in different tumor types. Serological analysis of recombinant cDNA expression libraries (SEREX) , which combines serological analysis with antigen cloning techniques, is a widely used technique to explore tumors’ antigen repertoire.
  • SEEEX Serological analysis of recombinant cDNA expression libraries
  • SEREX first construct a cDNA library from cancer cell lines or fresh tumor samples, then screen the cDNA library with autologous sera of cancer patients, and finally sequence the immune-reactive clones.
  • SEREX have identified a variety of tumor antigens including CTAs, differentiation antigens, mutational antigens, splice-variant antigens and overexpressed antigens. See e.g., Chen et al., Proc. Natl. Acad. Sci. U.S.A. 94 1914–1918 (1997) .
  • MAPPing Multiple Affinity Protein Profiling
  • nanoplasmonic biosensor have also been developed to identify tumor antigens. See e.g., Lee et al., Biosens. Bioelectron. 74 341–346 (2015) .
  • the one or more neoantigenic peptides described herein are obtained from a neoantigenic database (such as any of the neoantigenic databases described herein) .
  • a neoantigenic database such as any of the neoantigenic databases described herein.
  • Tan et al constructed a manually curated database ( “dbPepNeo” ) for human tumor neoantigen peptides based upon the four criterias as below: (i) peptides were isolated from human tumor tissues or cell lines, (ii) peptides contained non-synonymous mutations in amino acid sequence, (iii) Peptides can be bound by HLA-I molecules, (iv) Peptides can induce CD8+ T cell responses.
  • Xia et al constructed another database, NEPdb, which provides pan-cancer level predicted HLA-I neoepitopes derived from 16, 745 shared cancer somatic mutations, using state-of-the-art predictors. See Xia et al., Front Immunol. 2021; 12: 644637. Wu et al.
  • TSNAdb v1.0 tumor-specific neoantigen database
  • HLA human leukocyte antigen
  • the one or more neoantigenic peptides are obtained from analyzing the biological information of the individual (such as a patient who had a cancer) .
  • the neoantigenic peptides are obtained from a computational analysis of a cancer patient’s tumor genome. See e.g., Roudko et al. Front Immunol. 2020; 11: 27.
  • the neoantigenic peptides are obtained from a computational analysis of a cancer patient’s transcriptome. See e.g., Caushi et al., Nature. 2021 Aug; 596 (7870) : 126-132.
  • the neoantigenic peptides are obtained from a computational analysis of a cancer patient’s proteome. See e.g., Wen et al. Nat Commun. 2020 Apr 9; 11 (1) : 1759.
  • the neoantigenic peptides are selected from patient data.
  • the patient data is derived from data from a group of patients having a particular type of cancer (e.g., any of the cancers described here) .
  • the patient data is derived from data from a group of patients having any cancer.
  • the group of patients are from the same sex (e.g., male or female) .
  • the group of patients are from the same ethnicity.
  • the group of patients bear one or more biomarkers (e.g., an aberration in a particular gene, e.g., KRAS, e.g., PTEN) .
  • the one or more neoantigenic peptides are derived from any polypeptide known to or have been found to contain a tumor specific mutation. Suitable polypeptides from which the neoantigenic peptides can be derived can be found for example in various databases available in the field (e.g., COSMIC database) . These databases curate comprehensive information on somatic mutations in human cancer.
  • the peptide contains a tumor specific mutation.
  • the tumor specific mutation is a driver mutation for a particular cancer type.
  • the neoantigenic peptide is selected based upon its mutational status. In some embodiments, the neoantigenic peptide has a mutation at the third amino acid position counting from the N-terminus, relative to a wildtype peptide. In some embodiments, the neoantigenic peptides may comprise two or more (such as at least 2, 3, 4, or 5) somatic mutations.
  • a library of tumor specific neoantigenic peptides are synthesized (e.g., based upon one or a group of patients as described above) .
  • the neoantigenic peptides are obtained by exome high throughput sequencing and prescreened with epitope prediction algorithms.
  • the methods involve constructing a plurality of neoantigen peptide peptides (e.g., building a library, such as in Example 1 and FIG. 1) .
  • the pluralirty of neoantigen peptides are based upon a known mutation (e.g., Kras mutation) .
  • the plurality of neoantigen peptides based upon one known mutation e.g., a point mutation, e.g., Kras G12D, G12V, G12C, G12R, G12A, or G12I
  • the plurality of neoantigen peptides based upon one known mutation comprise at least about 5, 10, 12, 15, 18 or 20 distinct neoantigen peptides that a) have a binding affinity of about 1 nM to about 5000 nM to an MHC molecule; b) have a binding affinity of about 1 nM to about 5000 nM to a cognate TCR molecule; c) have a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus; d) are hydrophobic; and/or e) have high content of aromatic residues.
  • the display moiety comprises at least two distinct peptides (e.g., at least 3, 4, 5, 10, 12, 15, 20, 50, or 100 distinct peptides) . In some embodiments, the display moiety comprises at least five distinct peptides. In some embodiments, the display moiety comprises at least 10 distinct peptides. In some embodiments, the at least two distinct peptides in the display moiety do not overlap. In some embodiments, the at least two distinct peptides in the display moiety overlaps.
  • the at least two distinct peptides are associated with two different antigens. In some embodiments, the at least two distinct peptides are associated with at least three, four, five, six, ten, or twelve different antigens. In some embodiments, the at least two distinct peptides are associated with at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 different antigens.
  • the at least two distinct antigens comprise two distinct mutations of one or more genes associated with a disease. In some embodiments, the at least two distinct antigens comprise 3, 4, 5, 6, 10, 12, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 distinct mutations of one or more genes associated with a disease.
  • the disease is a cancer. In some embodiments, the gene is an oncogene. In some embodiments, the disease is not a cancer or tumor (e.g., an infection associated with a pathogen, e.g., an autoimmune disease) .
  • the present application also provides bait compositions that comprise a plurality of the display moieties described here.
  • the bait composition comprises at least two different display moieties.
  • the bait composition comprises at least about 20, 50, 100, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000 different MHC-peptide complexes.
  • the bait composition comprises a) at least two different MHC molecules (such as at least three, four, five, or six) different MHC molecules, and b) at least about 20, 50, 100, 150, 200, 250, 300, 400, 500, 750, or 1000 different peptides.
  • the bait composition comprises a) at least two different (or at least three different) different MHC I molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the at least two or three different MHC molecules comprise an HLA-A molecule and at least one of an HLA-B molecule and an HLA-C molecule.
  • the at least two or three different MHC molecules comprise an HLA-A molecule, an HLA-B molecule, and an HLA-C molecule.
  • the at least two or three different MHC molecules comprise two or more different HLA molecules.
  • the bait composition comprises HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, or HLA-A*03: 01. In some embodiments, the bait composition comprises HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two, three, or four HLA-A molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides, wherein the two, three or four HLA-A molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • the bait composition comprises a) at least two different (or at least three different) different MHC II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the bait composition comprises a) at least one MHC class I molecule and at least one MHC class II molecule, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides. In some embodiments, the bait composition comprises a) at least two different MHC class I molecules and at least one MHC class II molecule, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides. In some embodiments, the bait composition comprises a) at least one MHC class I molecule and at least two different MHC class II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the bait composition comprises a) at least two different MHC class I molecules and at least two MHC class II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the MHC class I molecule or molecules comprise an HLA-A molecule, an HLA-B molecule and/or an HLA-C molecule.
  • the MHC class I molecule or molecules comprise an HLA-A molecule, an HLA-B molecule and an HLA-C molecule.
  • the MHC class I molecule or molecules comprise two or more different HLA-A molecules.
  • the bait composition comprises HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, or HLA-A*03: 01.
  • the one or more MHC class II molecules comprise an HLA-DM molecule, an HLA-DO molecule, an HLA-DP molecule, an HLA-DQ molecule, or an HLA-DR molecule.
  • the one or more MHC class II molecules comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the bait composition comprises a) at least three MHC class I molecules and at least one MHC class II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides. In some embodiments, the bait composition comprises a) at least one MHC class I molecule and at least three MHC class II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides. In some embodiments, the bait composition comprises a) at least three MHC class I molecules and at least three MHC class II molecules, and b) at least about 20, 50, 100, 150, 200, or 250 different peptides.
  • the at least three MHC class I molecules comprise an HLA-A molecule and at least one of an HLA-B molecule and an HLA-C molecule. In some embodiments, the at least three MHC class I molecules comprise an HLA-A molecule, an HLA-B molecule and an HLA-C molecule. In some embodiments, the at least three MHC class I molecules comprise two or three or more different HLA-A molecules. In some embodiments, the bait composition comprises HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, or HLA-A*03: 01. In some embodiments, the three or more MHC class II molecules comprise an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene.
  • the gene is an oncogene.
  • the peptides in the bait composition are associated with mutations in at least two, three, four, five or six genes.
  • the genes are oncogenes.
  • the bait composition does not comprise a fluorochrome or fluorophore.
  • the MHC molecules match with at least one, two, three, four, five or six HLA type of the individual from where the sample is obtained.
  • MHC I molecules comprising HLA-A*24: 02 and HLA-A*11: 01 is used when the individual has both HLA-A*24: 02 and HLA-A*11: 01.
  • MHC I molecules comprising at least one specific HLA-A molecule, one specific HLA-B molecule and one specific HLA-C molecule are used when the individual has the specific HLA-A, HLA-B, and HLA-C molecules.
  • Patient-specific NGS data from WGS, WES, or RNA-seq can be used to predict HLA types with computational tools such as Optiptype and Polysolver (polymorphic loci resolver) .
  • computational tools such as Optiptype and Polysolver (polymorphic loci resolver) .
  • Optiptype and Polysolver polymorphic loci resolver
  • Reads can be selected from the NGS data that potentially derived from the HLA region and then they can be fully aligned to a full-length genomic library of all known HLA alleles. See e.g., Nucleic Acids Res. 41, D1222–D1227.
  • the MHC molecule is coupled with a chaperon molecule prior to being complexed to the peptide. See e.g., Overall et al., Nat Commun. 2020 Apr 20; 11 (1) : 1909.
  • a high throughput peptide-MHC (pMHC) tetramer library is constructed. See e.g., Overall et al., Nat Commun. 2020 Apr 20; 11 (1) : 1909.
  • the bait composition comprises a plurality of different display moieties.
  • Use of the plurality of different display moieties can facilitate or promote identification of heterogeneous antigenic specific immune cells (e.g., T cells) .
  • multiple display moieties comprise at least 2, 3, or 4 kinds of MHC molecules.
  • multiple display moieties comprise at least two (e.g., 2, or 3, or 4) different kinds of MHC class I molecules, optionally the at least two (e.g., 2, 3, or 4) different kinds of MHC class I molecules are selected from the group consisting of HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • multiple display moieties comprise HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • At least two of the plurality of different display moieties in the bait composition comprise different antigenic peptides.
  • each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide.
  • the plurality of different display moieties comprise a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of different antigenic peptides.
  • at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%of antigenic peptides for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • At least 30%, 40%, 50%, 60%, 70%, 80%, or 90%of antigenic peptides for a specific kind of MHC molecule e.g., HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, or HLA-A*03: 01
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties comprise at least one kind of MHC molecule that is HLA-A*24: 02, wherein HLA-A*24: 02 is complexed with at least two different antigenic peptides.
  • HLA-A*24: 02 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • the plurality of different display moieties further comprises HLA-A*11: 01, optionally wherein HLA-A*11: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*11: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*11: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties further comprises HLA-A*02: 01, optionally wherein HLA-A*02: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*02: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*02: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties further comprises HLA-A*03: 01, optionally wherein HLA-A*03: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*03: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*03: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties comprise at least one kind of MHC molecule that is HLA-A*11: 01, wherein HLA-A*11: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*11: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*11: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties further comprises HLA-A*02: 01, optionally wherein HLA-A*02: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*02: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*02: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties further comprises HLA-A*03: 01, optionally wherein HLA-A*03: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*03: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*03: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties comprise at least one kind of MHC molecule that is HLA-A*02: 01, wherein HLA-A*02: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*02: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*02: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties further comprises HLA-A*03: 01, optionally wherein HLA-A*03: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*03: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*03: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties comprise at least one kind of MHC molecule that is HLA-A*03: 01, wherein HLA-A*03: 01 is complexed with at least two different antigenic peptides.
  • HLA-A*03: 01 is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for HLA-A*03: 01 for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a cancer e.g., a specific cancer
  • the plurality of different display moieties comprise at least four kinds of MHC molecules, wherein the at least four kinds of MHC molecules comprise HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • each kind of the MHC molecules (HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01) are complexed with at least two different antigenic peptides.
  • each kind of the MHC molecule is complexed with a number (e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100) of antigenic peptides, optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for the specific MHC molecule for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • a number e.g., about 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100
  • antigenic peptides optionally wherein at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%antigenic peptides for the specific MHC molecule for a cancer (e.g., a specific cancer) in a neoantigen database are included in the number of different antigenic peptides.
  • the method comprises separately contacting each of a plurality of different display moieties with a sample from the individual separately and separately isolating the immune cell associated with each of the different display moiety.
  • different display moieties may comprise display moieties with antigenic peptides associated with different antigens (e.g., different neoantigens, e.g., KRAS-12D, KRAS-12G, KRAS-12C) .
  • the method comprises contacting the plurality of different display moieties with a sample from the individual, and analyzing the pool of immune cells.
  • a sample from the individual For example, use of multi-color-labeled MHC tetramers for multiplex flow cytometry, pMHC tetramers labeled for mass cytometry analysis, and DNA-labeled tetramers designed for sequencing analysis have also been reported. See e.g., Andersen et al. Nat Protoc. 2012 Apr 12; 7 (5) : 891-902.
  • the one or more neoantigenic peptides are selected through one or more steps as described below.
  • the one or more neoantigenic peptides comprise a truncal peptide.
  • Truncal peptides described herein refer to those presented by all or most tumor subclones, is prioritized for inclusion into the bait composition.
  • truncal peptides predicted to be presented with high probability or if the number of truncal peptides predicted to be presented with high probability is small enough that additional non-truncal peptides can be included in the display moiety, then further peptides can be prioritized by estimating the number and identity of tumor subclones and choosing peptides so as to maximize the number of tumor subclones covered.
  • Neoantigenic peptides can be selected via various methods or processes.
  • an integrated multi-dimensional model described below is applied that places candidate neoantigens in a space with at least one or more of the following axes and optimizes selection using an integrative approach. See e.g., WO2019050994A.
  • Probability of sequencing artifact (lower probability of artifact is typically preferred) .
  • Probability of presentation (higher probability of presentation is typically preferred) .
  • HLA genes large number of HLA molecules involved in the presentation of a set of neoantigens is typically preferred.
  • Exemplary bait compositions, display moieties and neoantigens e.g., for analyzing immune cells from an individual for the presence of a lung cancer (e.g., NSCLC) )
  • Exemplary bait compositions were determined using the methodology described herein.
  • the one or more neoantigenic peptides comprise one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50) sequences selected from the group consisting of SEQ ID NOs: 1-56.
  • the one or more neoantigenic peptides comprise the amino acid sequences set forth in SEQ ID NOs: 1-5. In some embodiments, the one or more neoantigenic peptides further comprise one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, or 40) sequences selected from the group consisting of SEQ ID NOs: 6-50 and/or one or more (e.g., 1, 2, 3, 4, 5 or 6) sequences selected from the group consisting of SEQ ID NOs: 51-56.
  • the one or more neoantigenic peptides comprise one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, or 40) sequences selected from the group consisting of SEQ ID NOs: 6-50. In some embodiments, the one or more neoantigenic peptides comprise the amino acid sequences set forth in SEQ ID NOs: 6-50. In some embodiments, the one or more neoantigenic peptides further comprise one or more (e.g., 1, 2, 3, 4, or 5) sequences selected from the group consisting of SEQ ID NOs: 1-5 and/or one or more (e.g., 1, 2, 3, 4, 5 or 6) sequences selected from the group consisting of SEQ ID NOs: 51-56.
  • one or more neoantigenic peptides comprise one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, or 40) sequences selected from the group consisting of SEQ ID NOs: 6-50. In some embodiments, the one or more n
  • the one or more neoantigenic peptides comprise the amino acid sequences set forth in SEQ ID NOs: 51-56. In some embodiments, the one or more neoantigenic peptides further comprise one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, or 40) sequences selected from the group consisting of SEQ ID NOs: 6-50 and/or one or more one or more (e.g., 1, 2, 3, 4, or 5) sequences selected from the group consisting of SEQ ID NOs: 1-5.
  • the one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) neoantigenic peptides comprise the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 6, 23, 25, 27, 35-37, 40, and 48.
  • the one or more (e.g., 5, 10, 15, 20, 25, or 30) neoantigenic peptides comprise the amino acid sequences selected from the group consisting of SEQ ID NOs: 9-13, 15, 16, 18, 19, 22, 24, 26, 28-34, 38, 39, 41-47, 49, and 50.
  • the one or more (e.g., 1, 2, 3, or 4) neoantigenic peptides comprise the amino acid sequences selected from the group consisting of SEQ ID NOs: 2, 4, 5, and 8.
  • the one or more (e.g., 1, 2, 3, 4, or 5) neoantigenic peptides comprise the amino acid sequences selected from the group consisting of SEQ ID NOs: 3, 14, 17, 20, and 21.
  • the one or more (e.g., 1, 2, 3, or 4) neoantigenic peptides comprise the amino acid sequences selected from the group consisting of SEQ ID NOs: 53, 55, 51, and 52.
  • the one or more (e.g., 1 or 2) neoantigenic peptides comprise the amino acid sequences selected from the group consisting of SEQ ID NOs: 54 and 56.
  • the one or more neoantigenic peptides comprise amino acid sequences set forth in SEQ ID NOs: 1-56.
  • the bait composition comprises one or more display moieties comprising one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50) MHC-peptide complexes (i.e., pMHC) paired as shown in Table 1.
  • the bait composition comprises one or more display moieties comprising pMHC comprising one or more neoantigenic peptides set forth in SEQ ID NOs 1-5 complexed with a MHC molecule according to Table 1.
  • the bait composition comprises one or more display moieties comprising pMHC comprising one or more (e.g., at least 2, 5, 10, 15, 20, 25, 30, 35, or 40) neoantigenic peptides comprising amino acids selected from the group consisting of SEQ ID NOs: 6-50 complexed with a MHC molecule according to Table 1.
  • the bait composition comprises one or more display moieties comprising pMHC comprising one or more (e.g., 1, 2, 3, 4, 5 or 6) neoantigenic peptides comprising amino acids selected from the group consisting of SEQ ID NOs: 51-56 complexed with a MHC molecule according to Table 1.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 6, 23, 25, 27, 35-37, 40, and 48, wherein the MHC molecule is HLA-A*24: 02.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NOs: 1, 6, 23, 25, 27, 35-37, 40, and 48, wherein the MHC molecule is HLA-A*24: 02.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising (e.g., 5, 10, 15, 20, 25, or 30) amino acid sequences selected from the group consisting of SEQ ID NOs: 9-13, 15, 16, 18, 19, 22, 24, 26, 28-34, 38, 39, 41-47, 49, and 50, wherein the MHC molecule is HLA-A*11: 01.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NOs: 9-13, 15, 16, 18, 19, 22, 24, 26, 28-34, 38, 39, 41-47, 49, and 50, wherein the MHC molecule is HLA-A*11: 01.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising one or more (e.g., 1, 2, 3, or 4) amino acid sequences selected from the group consisting of SEQ ID NOs: 2, 4, 5, and 8, wherein the MHC molecule is HLA-A*02: 01.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NOs: 2, 4, 5, and 8, wherein the MHC molecule is HLA-A*02: 01.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising one or more (e.g., 1, 2, 3, 4 or 5) amino acid sequences selected from the group consisting of SEQ ID NOs: 3, 14, 17, 20, and 21, wherein the MHC molecule is HLA-A*03: 01.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NOs: 3, 14, 17, 20, and 21, wherein the MHC molecule is HLA-A*03: 01.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising one or more (e.g., 1, 2, 3, or 4) amino acid sequences selected from the group consisting of SEQ ID NOs: 53, 55, 51, and 52, wherein the MHC molecule is HLA-B molecule.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NOs: 53, 55, 51, and 52, wherein the MHC molecule is HLA-B molecule.
  • the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 54 and 56, wherein the MHC molecule is HLA-C molecule. In some embodiments, the display moieties comprise one or more MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NOs: 54 and 56, wherein the MHC molecule is HLA-C molecule.
  • the display moieties comprise MHC-peptide complexes comprising neoantigenic peptides comprising amino acid sequences set forth in SEQ ID NO: 1-56, wherein each of the neoantigen peptides is complexed with a MHC molecule according to Table 1.
  • Neoantigenic peptides having a desired activity or property can be modified to provide certain desired attributes, while increasing or at least retaining substantially all of the biological activity of the unmodified peptide to bind the desired MHC molecule and activate the appropriate immune cell (e.g., a T cell) .
  • neoantigenic peptide described herein can be subject to various changes, such as substitutions, either conservative or non-conservative, where such changes might provide for certain advantages in their use, such as improved MHC binding, stability or presentation.
  • conservative substitutions is meant replacing an amino acid residue with another which is biologically and/or chemically similar, e.g., one hydrophobic residue for another, or one polar residue for another.
  • substitutions include combinations such as Gly, Ala; Val, Ile, Leu, Met; Asp, Glu; Asn, Gin; Ser, Thr; Lys, Arg; and Phe, Tyr.
  • the effect of single amino acid substitutions may also be probed using D-amino acids.
  • Such modifications can be made using well known peptide synthesis procedures, as described in e.g., Merrifield, Science 232: 341-347 (1986) , Barany &Merrifield, The Peptides, Gross &Meienhofer, eds. (N.Y., Academic Press) , pp. 1-284 (1979) ; and Stewart &Young, Solid Phase Peptide Synthesis, (Rockford, 111., Pierce) , 2d Ed. (1984) .
  • Proteins or peptides described herein can be made by any technique known to those of skill in the art, including the expression of proteins, polypeptides or peptides through standard molecular biological techniques, the isolation of proteins or peptides from natural sources, or the chemical synthesis of proteins or peptides.
  • the nucleotide and protein, polypeptide and peptide sequences corresponding to various genes have been previously disclosed, and can be found at computerized databases known to those of ordinary skill in the art.
  • One such database is the National Center for Biotechnology Information's Genbank and GenPept databases located at the National Institutes of Health website.
  • the coding regions for known genes can be amplified and/or expressed using the techniques disclosed herein or as would be known to those of ordinary skill in the art.
  • various commercial preparations of proteins, polypeptides and peptides are known to those of skill in the art.
  • Bait compositions comprising antigenic peptides associated with a pathogen or autoimmune disease can be similarly designed and/or selected.
  • the methods described herein comprise isolating an immune cell associated with the display moiety. In some embodiments, the methods comprise isolating immune cells prior to detecting immune cells binding to bait composition. In some embodiments, the methods comprise isolating immune cells following detecting immune cells binding to bait composition.
  • the method does not comprise isolating immune cells prior to detecting immune cells binding to bait composition.
  • the methods described herein comprise further analysis of the antigen-specific immune cells. In some embodiments, the method comprises demobilization of the immune cells or releasing the immune cells from the solid substrate for further analysis.
  • the methods described herein further provides culturing the immune cell following the detecting immune cells binding to bait composition and/or prior to further analysis. In some embodiments, the methods described herein does not comprise a step of culturing the immune cell prior to further analysis.
  • the isolating step comprises separating immune cells associated with the display moiety from the rest of the sample prior to detecting the immune cells associated with the display moiety.
  • the isolating step comprises using fluorescence-activated cell sorting (FACS) .
  • FACS fluorescence-activated cell sorting
  • the display moiety may be attached to one or more fluorescent attachment moieties, such as a streptavidin core attached or bound to a fluorescent molecule.
  • the display moiety is fluorescent or conjugated to a fluorophore directly.
  • multiple elements within the display moiety can be fluorescent, including each comprising a different fluorophore.
  • the display moiety used is magnetic or non-magnetic.
  • magnetic separation methods can be used in conjunction with FACS (e.g., before, after, or before and after FACS) .
  • FACS e.g., before, after, or before and after FACS
  • magnetic activated cell sorting, affinity chromatography, or any of the methods of cell sorting known in the art are used.
  • the immune cell is selected from the group consisting of: a cytotoxic T cell (e.g., a CD8+ T cell) , a helper T cell (e.g., a CD4+ T cell) , a memory T cell, and a tumor infiltrating T cell.
  • a cytotoxic T cell e.g., a CD8+ T cell
  • a helper T cell e.g., a CD4+ T cell
  • the immune cell is a helper T cell.
  • the immune cell is a B cell. In some embodiments, the B cell is a memory B cell.
  • the immune cell is an isolated single immune cell. In some embodiments, the immune cell is in a mixture of immune cells.
  • the immune cell e.g., a T cell
  • the mixture of immune cells e.g., a mixture containing both T cells and antigen presenting cells
  • the mixture of immune cells is a mixture comprising T cells, memory T cells, macrophage cells, or dendritic cells, or combinations thereof.
  • culturing the immune cell comprises incubating the immune cell (such as a T cell) with one or more antigenic peptides described herein. In some embodiments, culturing the immune cell (such as a T cell) comprising incubating the immune cell (such as a T cell) with one or more antigenic peptides described herein for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 days. In some embodiments, culturing the immune cell (such as a T cell) comprising incubating the immune cell (such as a T cell) with one or more antigenic peptides described herein for less than 5, 4, 3, 2, or 1 day. In some embodiments, culturing the immune cell comprises incubating the immune cell (such as a T cell) with one or more cytokines (e.g., IL-2, IL-7, IL-15) .
  • cytokines e.g., IL-2, IL-7, IL-15
  • further analyzing the immune cell comprises quantifying the immune cell. In some embodiments, further analyzing the immune cell comprises sequencing one or more nucleic acids in the immune cell. In some embodiments, further analyzing the immune cell further comprises analyzing the sequences of the one or more nucleic acids. In some embodiments, the one or more nucleic acids comprises a nucleic acid sequence selected from the group consisting of a TCR sequence. In some embodiments, analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing. In some embodiments, analyzing the sequences of the one or more nucleic acids comprises RNA sequencing. In some embodiments, analyzing the sequences of the one or more nucleic acids comprises single cell sequencing (such as scRNAseq) .
  • analyzing the sequences of the one or more nucleic acids comprises decoding the barcode sequences. In some embodiments, analyzing the sequences of the one or more nucleic acids comprises identifying the rearranged genes on the tumor specific neoantigen activated immune cells. In some embodiments, analyzing the sequences of the one or more nucleic acids comprises identifying the rearranged T cell receptor (TCR) genes.
  • TCR T cell receptor
  • further analyzing the immune cell comprises counting number or percentage of immune cells that bind to the bait composition and determining if the number or percentage of immune cells is above a threshold level, wherein the number or percentage of immune cells above a threshold level is indicative of cancer in the individual.
  • the immune cells are T cells (e.g., total T cells) .
  • the immune cells are CD8+ T cells.
  • the immune cells are CD4+ T cells.
  • the immune cells are memory T cells.
  • the threshold is at least about 10, 20, 30, 40, 50, 75, 100, 150, 200, 250, 500, 1000, 2000, 3000, 4000, or 5000 immune cells that bind to the bait composition within a total of about 1x10 5 , 5x10 5 , 1x10 6 , 2x10 6 , 6x10 6 , 1x10 7 , 2x10 7 , 5x10 7 , or 1x10 8 cells (e.g., immune cells) obtained in the sample (e.g., blood) from the individual.
  • the sample e.g., blood
  • At least about 1x10 5 CD8 cells are analyzed, and cut-offs are set to more than 0.001% (such as more than about 0.001%, 0.002%, 0.003%, 0.004%, or 0.005%of CD8 cells and more than at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 events. In some embodiments, at least about 1x10 5 CD8 cells are analyzed, and cut-offs are set to more than 0.005%of CD8 cells and more than at least about 10 events.
  • Analysis of the immune repertoire usually involves one or more diversity indexes, such as Shannon entropy, clonality, and high ⁇ expanded clone (HEC) ratio, which are used to evaluate the amplification status of different TCR sequences and determine whether there is a high expansion of a few T ⁇ cell clones.
  • diversity indexes such as Shannon entropy, clonality, and high ⁇ expanded clone (HEC) ratio
  • analyzing immune cells comprises analyzing repertoire diversity (e.g., Shannon diversity) of T cells obtained from the individual.
  • analyzing repertoire diversity comprises comparing the repertoire diversity of T cells obtained from the individual to that of T cells from a reference individual (such as a healthy individual, or a group of healthy individuals) and determine if the repertoire diversity is below a threshold, wherein the repertoire diversity (e.g., Shannon diversity) being below a threshold diversity is indicative of cancer in the individual.
  • the threshold is a Shannon diversity that is lower (e.g., at least about 5%, 10%, 15%, 20%, 25%or 30%) lower than that of T cells from a reference individual, it is indicative of cancer in the individual.
  • further analyzing the immune cell comprises generating a signature profile.
  • the signature profile is associated with a specific cancer.
  • the cancer is hepatocellular carcinoma (HCC)
  • the signature profile comprises a three gene signature, wherein the three genes are CXCR2, CCR2 and EP400. See e.g., Shi et al., Eur J Cancer. 2014 Mar; 50 (5) : 928-36.
  • further analyzing the immune cell comprises generating a CD8 and/or CD4 T cell signature profile (e.g., gene expression profile (RNA-seq) , gene rearrangement, 5mC, 5hmC or 5caC profile) .
  • a CD8 and/or CD4 T cell signature profile e.g., gene expression profile (RNA-seq) , gene rearrangement, 5mC, 5hmC or 5caC profile
  • further analyzing the immune cell comprises sequencing one or more nucleic acids and generating a library.
  • the one or more nucleic acids are repertoire related nucleic acids (e.g., VDJ gene-related DNA or RNA) .
  • analyzing the isolating immune cells further comprises analyzing repertoire of the T cells as described above.
  • analyzing the sequences of the one or more nucleic acids comprises a) obtaining an enriched sample from the immune cell, wherein the enriched sample is enriched for the one or more nucleic acids and b) sequencing the one or more nucleic acids in the enriched sample.
  • further analyzing the immune cell further comprises subjecting the immune cell to mass spectrometry analysis. In some embodiments, further analyzing the immune cell further comprises subjecting the immune cell to Assay for Transposase-Accessible Chromatin using sequencing (ATAC) -sequencing. In some embodiments, further analyzing the immune cell further comprises subjecting the immune cell to chromatin immunoprecipitation (ChIP) -sequencing.
  • ATC Transposase-Accessible Chromatin using sequencing
  • ChIP chromatin immunoprecipitation
  • T cells tumor specific immune cells
  • CD8+ T cells tumor specific immune cells
  • further analyzing the immune cell further comprises identifying one or more epigenetic modifications in the T cell receptor genes of the immune cell.
  • the one or more epigenetic modifications comprises histone acetylation, histone ubiquitination, and/or histone methylation.
  • the one or more epigenetic modifications comprises DNA or RNA methylation, hydroxylation and/or histone glycosylation.
  • the individual described herein is a mammal (such as a human, dog, cat, or horse) . In some embodiments, the individual is a human.
  • the individual has not previously been diagnosed as having a cancer (e.g. any cancer or a specific type of cancer) .
  • a cancer e.g. any cancer or a specific type of cancer
  • the individual has previously been diagnosed as having a cancer.
  • the individual has minimal residual disease (MRD) .
  • the individual has minimal residual cancer.
  • the minimal residual cancer is seen after the cancer was surgical resected or cured.
  • the minimal residual disease is too minimal to be detected by imaging instruments (e.g., a routinely used or standard imaging instrument used for detection of the cancer) .
  • the location of the minimal residual disease is diverse.
  • the minimal residual cancer is a result of immune escape or resistance to treatment.
  • the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • the individual is at risk of developing cancer.
  • the risk of having cancer is based on any one or more factors selected from the group consisting of family history, mutations, environmental factors, and age.
  • the individual is predicted by a doctor to have a risk of at least 20%, 30%, 40%, or 50%to develop a cancer (such as any specific kind of cancer) based upon any one or more factors selected from the group consisting of family history, mutations, environmental factors, and age.
  • the individual is a human and is at least about 50 years old (e.g., such as at least about 50, 60, 70, or 80 years old) .
  • the individual is no more than 14 years old.
  • the individual is a male. In some embodiments, the individual is a female.
  • the cancer described herein can be a cancer in general, or any type of cancer.
  • the cancer is a solid tumor.
  • the cancer is a liquid cancer.
  • the cancer is a carcinoma, a sarcoma, a myeloma, a leukemia, a lymphoma, a blastoma, a germ cell tumor, or any combination thereof. In some embodiments, the cancer is a squamous cell carcinoma or an adenocarcinoma.
  • the cancer is selected from the group consisting of: small cell lung cancer, non-small-cell lung cancer, nasopharyngeal cancer, colorectal cancer, anal cancer, liver cancer, bladder cancer, testicular cancer, cervical cancer, ovarian cancer, gastric cancer, esophageal cancer, head-and-neck cancer, pancreatic cancer, prostate cancer, renal cancer, thyroid cancer, melanoma cancer, and breast cancer.
  • the cancer is a recurrent cancer.
  • the method of analyzing a sample of an individual further comprises generating a report comprising information about the disease or condition status (such as cancer status) in the individual.
  • the information about disease or condition (e.g., cancer) status comprises likelihood of the presence of a disease or condition (e.g., cancer) , classification of disease or condition (e.g., cancer) , type of disease or condition (e.g., cancer) , nature of disease or condition (e.g., cancer) , origin of disease or condition (e.g., cancer) , stage of disease or condition (e.g., cancer) , likelihood of disease or condition (e.g., cancer) progression, likelihood of developing one or more disease or condition (e.g., cancer) symptoms, and/or treatment options for the individual.
  • a disease or condition e.g., cancer
  • classification of disease or condition e.g., cancer
  • type of disease or condition e.g., cancer
  • nature of disease or condition e.g., cancer
  • origin of disease or condition e.g., cancer
  • stage of disease or condition e.g., cancer
  • likelihood of disease or condition (e.g., cancer) progression
  • the information about the disease or condition (e.g., cancer) status is based upon the results gathered from analyzing the immune cells that bind to the bait composition as discussed above.
  • the likelihood of the presence of a disease or condition (e.g., cancer) is wholly or at least partly based upon the number and/or percentage of immune cells (e.g., T cells) that bind to the bait composition.
  • the generated report comprises the information that the disease or condition (e.g., cancer) is present in the individual.
  • the generated report comprises the information that there is a median or high likelihood of the presence of the disease or condition (e.g., cancer) .
  • the likelihood of the presence of a disease or condition is wholly or at least partly based upon the repertoire diversity of T cells that bind to the bait composition.
  • the repertoire diversity e.g., Shannon diversity
  • the generated report comprises the information that the disease or condition (e.g., cancer) is present in the individual.
  • the generated report comprises the information that there is a median or high likelihood of the presence of the disease or condition (e.g., cancer) .
  • the information about disease or condition (e.g., cancer) status comprises gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature.
  • the signature epigenetic modification comprises a DNA methylation signature and a histone glycosylation signature.
  • Embodiment 1 A method of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, the method comprising:
  • a) immobilizing immune cells from the sample on a solid support wherein the immune cells: 1) prior to immobilization, have been contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety; or 2) after the immobilization, are contacted with a bait composition comprising a display moiety comprising the antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety;
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other prior to step c) .
  • Embodiment 2 A method of analyzing a sample from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, the method comprising:
  • the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other prior to step d) .
  • Embodiment 3 The method of embodiment 1 or embodiment 2, wherein the sample is obtained from a single individual.
  • Embodiment 4 The method of embodiment 1 or embodiment 2, wherein the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • Embodiment 5 The method of embodiment 4, wherein prior to being combined to form the mixture each of the plurality of individual samples is separately processed such that the immune cells contained therein are associated with a unique sample barcode (e.g., via mixing the immune cells with a molecule comprising the unique sample barcode) .
  • the method further comprises removing unbound molecule comprising the barcode (molecules not bound by the immune cells) e.g., via washing the immune cells for at least one time.
  • Embodiment 6 The method of embodiment 5, wherein the method further comprises determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived.
  • Embodiment 7 The method of any one of embodiments 1 and 3-6, wherein the immune cells have been contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety prior to the immobilization.
  • Embodiment 8 The method of any one of embodiments 1 and 3-6, wherein the immune cells are contacted with a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety following the immobilization.
  • Embodiment 9 A method of analyzing a plurality of samples from one or more individuals for the presence or absence of immune cells capable of binding to an antigenic peptide, comprising:
  • a bait composition comprising a display moiety comprising an antigenic peptide under a condition sufficient for an immune cell to bind to the display moiety, thereby forming a bait-sample mixture
  • step d) determining the unique barcode associated with the immune cells bound to the display moiety, thereby identifying the sample from which the immune cells are derived, optionally wherein the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other prior to step d) .
  • Embodiment 10 The method of any one of embodiments 1-9, wherein the immune cells comprise T cells, optionally the immune cells comprise no more than about 10%, 5%, 4%, 3%, 2%or 1%T cells specifically binding to antigenic peptide in the bait composition.
  • Embodiment 11 The method of embodiment 10, wherein the immune cells are selected from the group consisting of: a cytotoxic T cell, a memory T cell, and a tumor infiltrating T cell.
  • Embodiment 12 The method of any one of embodiments 1-9, wherein the immune cells comprise B cells.
  • Embodiment 13 The method of any one of embodiments 1-12, wherein the method further comprises removing unbound display moiety following contacting the immune cells with the agent recognizing the display moiety and prior to detecting the immune cells bound to the display moiety.
  • Embodiment 14 The method of any one of embodiments 1-13, wherein the antigenic peptide is associated with a cancer or tumor antigen, optionally wherein the antigenic peptide is a neoantigen peptide.
  • Embodiment 15 The method of embodiment 14, wherein the sample is obtained from one or more individuals exhibiting no pathological symptom of a cancer.
  • Embodiment 16 The method of any one of embodiments 1-13, wherein the antigenic peptide is associated with a pathogen antigen, optionally wherein the antigenic peptide is associated with a virus, a bacteria, or a fungus antigen.
  • Embodiment 17 The method of any one of embodiments 1-13, wherein the antigenic is an autoantigenic peptide associated with an autoantigen.
  • Embodiment 18 The method of any one of embodiments 1-8 and 10-17, wherein the immune cells are immobilized on the solid substrate such as a bead.
  • Embodiment 19 The method of embodiment 18, wherein the bead is associated with an antibody recognizing the immune cells, optionally wherein the antibody is a CD8 antibody.
  • Embodiment 20 The method of any one of embodiments 1-19, wherein the display moiety comprises two or more antigenic peptides, optionally wherein the display moiety comprises four antigenic peptides.
  • Embodiment 21 The method of embodiment 20, wherein the two or more antigenic peptides in the display moiety are the same.
  • Embodiment 22 The method of embodiments 14-15 and 18-21, wherein the display moiety comprises a library of antigenic peptides for a mutation associated with a cancer or tumor, wherein the library comprises at least about 5, 10, 12, 15, 18 or 20 distinct neoantigenic peptides.
  • Embodiment 23 The method of any one of embodiments 1-22, wherein the antigenic peptide has one or more of the following characteristics:
  • c) is hydrophobic
  • Embodiment 24 The method of any one of embodiments 14-15 and 18-23, wherein the antigenic peptide is a neoantigenic peptide comprising a mutation relative to a wildtype peptide, optionally at the third amino acid position counting from the N-terminus.
  • Embodiment 25 The method of any one of embodiments 1-24, wherein the antigenic peptide has low immunogenicity.
  • Embodiment 26 The method of any one of embodiments 1-25, wherein the display moiety comprises an MHC molecule complexed with the antigenic peptide, optionally wherein the MHC molecule comprises a MHC multimer, further optionally the MHC multimer is a MHC tetramer or a MHC dextramer.
  • Embodiment 27 The method of embodiment 26, wherein the MHC molecule comprises a MHC class I molecule.
  • Embodiment 28 The method of embodiment 27, wherein the MHC class I molecule is selected from the group consisting of HLA-A, HLA-B, and HLA-C, optionally wherein MHC class I molecule comprises a HLA-A molecule, further optionally wherein the HLA-Amolecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises a HLA A2 heavy chain with a A245V mutation.
  • Embodiment 29 The method of embodiment 27 or 28, wherein the antigenic peptide is about 8 to about 10 amino acids long.
  • Embodiment 30 The method of embodiment 26, wherein the MHC comprises a MHC class II molecule.
  • Embodiment 31 The method of embodiment 30, wherein the MHC class II molecule is selected from the group consisting of HLA-DQ and HLA-DR.
  • Embodiment 32 The method of embodiment 30 or 31, wherein the antigenic peptide is about 10 to about 20 amino acids long.
  • Embodiment 33 The method of any one of embodiments 26-32, wherein the display moiety comprises two or more different kinds of MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • Embodiment 34 The method of any one of embodiments 1-33, wherein the display moiety comprises a particle.
  • Embodiment 35 The method of embodiment 34, wherein the particle in the display moiety is selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer.
  • Embodiment 36 The method of embodiment 34 or 35, wherein the particle in the display moiety is a dextran particle.
  • Embodiment 37 The method of embodiment 34 or 35, wherein the particle in the display moiety is a magnetic nanoparticle or polystyrene nanoparticle.
  • Embodiment 38 The method of embodiment 34 or 35, wherein the particle in the display moiety is an agarose bead or a sepharose bead.
  • Embodiment 39 The method of any one of embodiments 34-38, wherein the antigenic peptide or MHC is directly attached to the particle in the display moiety.
  • Embodiment 40 The method of any one of embodiments 34-38, wherein the antigenic peptide or MHC is attached to the particle in the display moiety via a binding pair comprising a first binding component attached to the antigenic peptide and a second binding component bound to the particle.
  • Embodiment 41 The method of any one of embodiments 1-40, wherein the display moiety comprises a cell.
  • Embodiment 42 The method of embodiment 41, wherein the cell comprises a polynucleotide encoding the antigenic peptide.
  • Embodiment 43 The method of embodiment 42, wherein the polynucleotide encodes a plurality of antigenic peptides.
  • Embodiment 44 The method of any one of embodiments 1-43, wherein the display moiety further comprises a detectable label.
  • Embodiment 45 The method of embodiment 44, wherein the detectable label is a fluorophore.
  • Embodiment 46 The method of any one of embodiments 1-45, wherein the method further comprises isolating immune cells bound to the display moiety or removing the display moiety or immune cells not bound to each other.
  • Embodiment 47 The method of any one of embodiments 1-46, wherein the method further comprises phenotyping immune cells bound to the display moiety.
  • Embodiment 48 The method of any one of embodiments 1-47, wherein the method further comprises sequencing one or more nucleic acids in immune cells bound to the display moiety, optionally wherein the method further comprises analyzing the sequences of the one or more nucleic acids, optionally wherein the one or more nucleic acids is a TCR, CD8, CD45 sequences or any specific sequence that is characteristic of the captured immune cells, optionally wherein analyzing the sequences of the one or more nucleic acids comprises whole genome sequencing and/or RNAseq sequencing, alternatively, by a array of primer sequence-specific q-PCR, and/or RT-PCR.
  • Embodiment 49 The method of any one of embodiments 1-48, wherein the method further comprises subjecting the immune cell bound to the display moiety to mass spectrometry analysis.
  • Embodiment 50 The method of any one of embodiments 1-49, wherein the method further comprises identifying one or more epigenetic modifications in the immune cell, optionally wherein the more or more epigenetic modifications comprises DNA methylation and/or histone glycosylation.
  • Embodiment 51 The method of any one of embodiments 1-50, wherein the individual is a human.
  • Embodiment 52 The method of embodiment 51, wherein the individual is at least about 50 years old.
  • Embodiment 53 The method of any one of embodiments 14-15 and 18-52, wherein the individual a) has not previously been diagnosed as having a cancer, optionally wherein the individual is at risk of having cancer, or b) the individual has been previously treated for cancer and exhibits no pathological symptom of a cancer after the treatment.
  • Embodiment 54 The method of any one of embodiments 16 and 18-54, wherein the individual a) has not been diagnosed as having an infection by a pathogen, optionally wherein the individual is at risk of having the infection, and/or b) exhibits no pathological symptom of an infection by a pathogen, optionally exhibits no pathological symptom of an infection by the pathogen.
  • Embodiment 55 The method of any one of embodiments 17 and 18-54, wherein the individual a) has not been diagnosed as having an immune response against the autoantigen, optionally wherein the individual is at risk of developing the immune response against the autoantigen, and/or b) exhibits no pathological symptom of an immune response (e.g., an autoimmune disease or disorder) , optionally exhibits no pathological symptom of an immune response against the autoantigen.
  • an immune response e.g., an autoimmune disease or disorder
  • Embodiment 56 The method of any one of embodiments 1-55, wherein the sample is selected from the group consisting of: blood, plasma, and a peripheral blood mononuclear cell (PBMC) sample.
  • PBMC peripheral blood mononuclear cell
  • Embodiment 57 The method of any one of embodiments 1-57, wherein the bait composition comprises a plurality of different display moieties.
  • Embodiment 58 The method of embodiment 57, wherein the each of the plurality of different display moieties in the bait composition comprises a different antigenic peptide.
  • Embodiment 59 The method of embodiment 57 or 58, wherein the plurality of different display moieties in the bait composition comprises at least two different display moieties, each comprising a different MHC molecule.
  • Embodiment 60 The method of embodiment 59, wherein the plurality of different display moieties in the bait composition comprises at least four different display moieties, each comprising a different MHC molecule.
  • Embodiment 61 The method of embodiment 60, wherein the plurality of different display moieties in the bait composition comprises at least 100 different display moieties, each comprising a different MHC molecule.
  • Embodiment 62 The method of any one of embodiments 59-61, wherein each of the different display moieties comprising different MHC molecules comprises a different detectable label.
  • Embodiment 63 The method of embodiment 62, wherein the different detectable labels comprise fluorophore (s) .
  • Embodiment 64 The method of any one of embodiments 1-6 and 10-63, wherein the agent comprises an antibody that binds to the display moiety.
  • Embodiment 65 A method of detecting antigen-specific immune cells in an individual, comprising: analyzing a sample from the individual according to any one of embodiments 1-64, wherein a predetermined characteristic of the immune cells is indicative of a disease or a disorder in the individual.
  • Embodiment 66 The method of embodiment 65, wherein the predetermined characteristic of the immune cell comprises the presence of the immune cells.
  • Embodiment 67 The method of embodiment 66, wherein the presence of immune cells specifically binds to a bait composition comprising one or more neoantigens is indicative of the presence of a cancer.
  • Embodiment 68 The method of embodiment 66, wherein the presence of immune cells specifically binds to a bait composition comprising one or more antigens of a pathogen (e.g., virus, bacteria, fungus) is indicative of the presence of an infection of the pathogen.
  • a pathogen e.g., virus, bacteria, fungus
  • Embodiment 69 The method of embodiment 66, wherein the presence of immune cells specifically binds to a bait composition comprising one or more autoantigens associated with an autoimmune disease or disorder is indicative of the presence of the immune disease or disorder.
  • Embodiment 70 The method of any one of embodiments 66-69, wherein the predetermined characteristic of the immune cell comprises a quantity of the immune cell above a threshold level.
  • Embodiment 71 The method of any one of embodiments 65-70, wherein the predetermined characteristic of the immune cell comprises a gene expression profile signature, a gene mutation profile signature, and/or an epigenetic modification signature.
  • Embodiment 72 The method of embodiment 71, wherein the signature epigenetic modification comprises a DNA or RNA methylation, hydroxylation signature and a histone acetylation, methylation and/or glycosylation signature.
  • Embodiment 73 A method of detecting residual cancer in an individual, wherein the individual has been previously treated with an anti-cancer therapy and exhibits no pathological symptom of cancer after treatment, the method comprising analyzing a post-treatment sample from the individual according to the method of any one of embodiments 14-15, 18-53 and 56-64, wherein a predetermined characteristic of the immune cell from the post-treatment sample is indicative of residual cancer in the individual.
  • Embodiment 74 The method of embodiment 73, wherein the method comprises: a) analyzing a pre-treatment sample from the individual prior to anti-cancer therapy and a post-treatment sample from the individual according to the method of any one of embodiments 14-15, 18-53 and 56-64, and b) comparing the characteristics of the immune cells from the pre-treatment sample and immune cells from the post-treatment sample; wherein a predetermined difference in characteristics of the immune cell from the pre-treatment sample and the immune cell from the post-treatment sample is indicative of residual cancer in the individual.
  • Embodiment 75 A method of treating a cancer in an individual, comprising a) diagnosing the individual as having cancer according to the method of any one of embodiments 67 and 70-72; and b) subjecting the individual to an anti-cancer therapy.
  • Embodiment 76 The method of embodiment 75, wherein the anti-cancer therapy is not an immunotherapy.
  • Embodiment 77 The method of any one of embodiments 1-76, wherein the cancer is a solid tumor.
  • Embodiment 78 A method of treating an infection in an individual, comprising a) diagnosing the individual as having an infection by a pathogen according to the method of any one of embodiments 68 and 70-72; and b) subjecting the individual to a therapy for the pathogen.
  • Embodiment 79 A method of treating an autoimmune disease or disorder in an individual, comprising a) diagnosing the individual as having an autoimmune disease or disorder according to the method of any one of embodiments 69-72; and b) subjecting the individual to a therapy for the disease or disorder.
  • Embodiment 80 A display moiety comprising a particle associated with a plurality of MHC-peptide complexes, wherein the plurality of MHC-peptide complexes comprises no less than or more than 2, 3, 4, 5, 6, 8, 9, 10, or 12 MHC-peptide complexes, wherein each of the MHC-peptide complex comprises at least one MHC molecule complexed with a peptide, wherein at least two or more of the MHC-peptide complexes are different.
  • Embodiment 81 The display moiety of embodiment 80, wherein one or more of the plurality of MHC-peptide complexes is an MHC-peptide monomer, an MHC-peptide dimer, an MHC-peptide trimer, an MHC-peptide tetramer, an MHC-peptide pentamer, an MHC-peptide octamer, an MHC-peptide dextramer, or an MHC-peptide dodecamer, optionally wherein each of the plurality of MHC-peptide complex is an MHC-peptide monomer, an MHC-peptide dimer or an MHC-peptide trimer.
  • At least one MHC-peptide complex in the plurality of MHC-peptide complexes has two distinct MHC-peptide monomers.
  • the at least one MHC complex is an MHC-peptide dimer, an MHC-peptide trimer, or an MHC-peptide tetramer.
  • Embodiment 82 The display moiety of embodiment 80 or embodiment 81, wherein the plurality of MHC-peptide complexes comprises at least 20 MHC-peptide complexes, optionally wherein the plurality of MHC-peptide complexes comprise at least 50 or 100 MHC-peptide complexes.
  • Embodiment 83 The display moiety of any one of embodiments 80-82, wherein the MHC-peptide complex is attached to the particle via a binding pair comprising a first binding component attached to MHC-peptide complex or a unit thereof (i.e., a MHC-peptide monomer) and a second binding component bound to the particle.
  • Embodiment 84 The display moiety of embodiment 83, wherein the first binding component comprises a biotin, and the second binding component comprises streptavidin.
  • Embodiment 85 The display moiety of any one of embodiments 80-84, wherein the particle is solid.
  • Embodiment 86 The display moiety of any one of embodiments 80-85, wherein the particle has a diameter of about 0.1 ⁇ m to about 150 ⁇ m or 0.1 ⁇ m to about 50 ⁇ m (e.g., at least about 0.1 ⁇ m, 0.2 ⁇ m, 0.25 ⁇ m, 0.5 ⁇ m, 0.75 ⁇ m, or 1 ⁇ m) .
  • Embodiment 87 The display moiety of embodiment 86, wherein the particle has a diameter of about 0.5 ⁇ m to about 20 ⁇ m, optionally wherein the particle has a diameter of about 0.5 ⁇ m to about 10 ⁇ m, further optionally wherein the particle has a diameter of about 1 ⁇ m.
  • Embodiment 88 The display moiety of any one of embodiments 80-87, wherein the particle has a surface area of about 1 ⁇ m 2 to about 20 ⁇ m 2 .
  • Embodiment 89 The display moiety of any one of embodiments 80-88, wherein the particle has a number of about 10 to about 10000 second binding component associated with it.
  • Embodiment 90 The display moiety of any one of embodiments 80-89, wherein the particle is spherical, optionally wherein the particle is a bead.
  • Embodiment 91 The display moiety of any one of embodiments 80-90, wherein the particle is magnetic.
  • Embodiment 92 The display moiety of any one of embodiments 80-91, wherein display moiety comprises at least two different MHC molecules.
  • Embodiment 93 The display moiety of embodiment 92, wherein the at least two different MHC molecules comprises two different MHC class I molecules.
  • Embodiment 94 The display moiety of embodiment 92 or embodiment 93, wherein the at least two different MHC molecules comprises two different MHC class II molecules.
  • Embodiment 95 The display moiety of any one of embodiments 92-94, wherein the at least two different MHC molecules comprises both an MHC class I molecule and an MHC class II molecule.
  • Embodiment 96 The display moiety of any one of embodiments 80-95, wherein the display moiety comprises an HLA-A molecule, further optionally wherein the HLA-Amolecule comprises a mutation that reduces its binding to CD8, further optionally where the HLA-A molecule comprises an HLA A2 heavy chain with a A245V mutation.
  • Embodiment 97 The display moiety of any one of embodiments 80-96, wherein the display moiety comprises at least two MHC class I molecules selected from the group consisting of a) HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01, or b) HLA-A*69: 01, HLA-A*31: 01, HLA-A*29: 01HLA-A*33: 02, HLA-A*02: 06, HLA-A*02: 07, HLA-A*30: 01, HLA-A*01: 01, HLA-A*02: 03, HLA-A*33: 03.
  • Embodiment 98 The display moiety of any one of embodiments 80-97, wherein the display moiety comprises an MHC class II molecule selected from the group consisting of HLA-DQ and HLA-DR.
  • Embodiment 99 The display moiety of any one of embodiments 80-98, wherein the peptide is associated with a cancer or tumor antigen, optionally wherein the peptide is associated with a neoantigen.
  • Embodiment 100 The display moiety of any one of embodiments 80-99, wherein the peptide is associated with an antigen of a pathogen, optionally wherein the pathogen is a virus, bacteria of fungus.
  • Embodiment 101 The display moiety of any one of embodiments 80-100, wherein the peptide is associated with an autoantigen.
  • Embodiment 102 The display moiety of any one of embodiments 80-101, wherein the display moiety comprises at least two distinct peptides.
  • Embodiment 103 The display moiety of embodiment 102, wherein the display moiety comprises at least five distinct peptides, optionally wherein the display moiety comprises at least 10 distinct peptides.
  • Embodiment 104 The display moiety of embodiment 102 or embodiment 103, wherein at least two distinct peptides in the display moiety do not overlap.
  • Embodiment 105 The display moiety of any one of embodiments 102-104, wherein at least two distinct peptides in the display moiety overlaps.
  • Embodiment 106 The display moiety of any one of embodiments 102-105 wherein the at least two distinct peptides are associated with two different antigens.
  • Embodiment 107 The display moiety of any one of embodiments 102-106, wherein the two distinct antigens comprise two distinct mutations of one or more genes associated with a disease, optionally 1) wherein the disease is a cancer, the gene is a oncogene, or 2) wherein the disease is not a cancer or tumor.
  • Embodiment 108 The display moiety of any one of embodiments 80-107, wherein the display moiety does not comprise a fluorochrome or fluorophore.
  • Embodiment 109 A bait composition comprising the display moiety of any one of embodiments 80-108.
  • Embodiment 110 The bait composition of embodiment 109, wherein the bait composition comprises at least two different display moieties.
  • Embodiment 111 The bait composition of embodiment 109 or embodiment 110, wherein the bait composition comprises an HLA-A molecule, an HLA-B molecule, and an HLA-C molecule.
  • Embodiment 112 The bait composition of any one of embodiments 109-111, wherein the bait composition comprises HLA-A*24: 02, HLA-A*11: 01, HLA-A*02: 01, and HLA-A*03: 01.
  • Embodiment 113 The bait composition of any one of embodiments 109-112, wherein the bait composition comprises an HLA-DP molecule, an HLA-DQ molecule, and an HLA-DR molecule.
  • Embodiment 114 The bait composition of any one of embodiments 109-113, wherein the bait composition comprises at least 25, 50, 100, 150, 200, or 250 different peptides.
  • Embodiment 115 The bait composition of any one of embodiments 109-114, wherein the peptides in the bait composition are associated with at least 25, 50, 75, 100, 125, 150, 175, 200, 225, or 250 different antigens.
  • Embodiment 116 The bait composition of any one of embodiments 109-115, wherein the bait composition comprises at least 2, 3, 4, 5, 6, or 7 different overlapping peptides associated a mutation in a gene, optionally wherein the gene is an oncogene.
  • Embodiment 117 The bait composition of any one of embodiments 109-116, wherein the peptides in the bait composition are associated with mutations in at least two, three, four, five or six genes, optionally wherein the genes are oncogenes.
  • Embodiment 118 The bait composition of any one of embodiments 109-117, wherein the bait composition does not comprise a fluorochrome or fluorophore.
  • Embodiment 119 A method of analyzing immune cells in a sample from an individual, comprising a) contacting a plurality of immune cells with the display moiety of any one of embodiments 80-108 or a bait composition of any one of embodiments 109-118, b) detecting or analyzing the one or more immune cells that bind to one or more of the display moieties.
  • Embodiment 120 The method of embodiment 119, wherein the immune cells comprise T cells.
  • Embodiment 121 The method of embodiment 119 or embodiment 120, wherein the immune cells are selected from the group consisting of: cytotoxic T cells, memory T cells, and tumor infiltrating T cells, optionally wherein the T cells are CD4+ T cells and/or CD8+ T cells.
  • Embodiment 122 The method of any one of embodiments 119-121, wherein the immune cells comprise B cells.
  • Embodiment 123 The method of any one of embodiments 119-122, wherein the immune cells comprise a mixture of immune cells comprising T cells, B cells, macrophage cells, or dendritic cells, or combinations thereof.
  • Embodiment 124 The method of any one of embodiments 119-123, wherein the sample is selected from the group consisting of: blood, plasma, and a peripheral blood mononuclear cell (PMBC) sample.
  • the sample is selected from the group consisting of: blood, plasma, and a peripheral blood mononuclear cell (PMBC) sample.
  • PMBC peripheral blood mononuclear cell
  • Embodiment 125 The method of any one of embodiments 119-124, wherein the sample is obtained from a diseased tissue, optionally wherein the diseased tissue is a cancer tissue or tumor tissue.
  • Embodiment 126 The method of any one of embodiments 119-125, wherein the sample is obtained from a single individual.
  • Embodiment 127 The method of any one of embodiments 119-125, wherein the sample is a mixture a plurality of individual samples, each obtained from a different individual.
  • Embodiment 128 The method of any one of embodiments 119-127, wherein the individual is a human.
  • Embodiment 129 The method of any one of embodiments 119-128, wherein the individual has no indication of a disease, optionally wherein the disease is a cancer.
  • Embodiment 130 The method of any one of embodiments 119-129, wherein detecting or analyzing the immune cells that bind to one or more display moieties comprises observing the agglutination of immune cells and MHC-multimer units.
  • Embodiment 131 The method of any one of embodiments 119-130, wherein detecting or analyzing the immune cells that bind to one or more display moieties comprises 1) immobilizing immune cells on a solid substrate prior to or after step a) , 2) contacting the immobilized immune cells with a detection agent recognizing the display moieties under a condition sufficient for the agent to bind to the display moieties; and 3) detecting the detection agent, thereby detecting the immune cells bound to the display moieties.
  • HLA-A: 02: 01, HLA-A: 24: 02, HLA-A: 11: 01, HLA-A: 03: 01, and ⁇ -2M were expressed in Escherichia coli.
  • the purified subunits were confirmed by Coomassie blue staining. See e.g., FIG. 2.
  • Neoantigens comprising one of the four most common Kras mutations, including Kras G12V, Kras G12D, Kras G12R, Kras G12C were selected for building the exemplified neoantigen library. Twenty predicated neoantigens for each mutation were designed according to the features of neoantigens. These features include binding affinity with MHC molecules and/or T cells, binding stability, mutation sequence, and public neoantigens library. See e.g., FIG. 1.
  • the neoantigen library was synthesized by Nanjing Peptide Biotech Ltd. The purity of peptide was above 95%.
  • Tetramers for specific neoantigens were assembly in vitro. The brief procedure was as following.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Cell Biology (AREA)
  • Hematology (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • General Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Organic Chemistry (AREA)
  • Microbiology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Virology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Food Science & Technology (AREA)
  • Toxicology (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

Abstract

L'invention concerne des méthodes d'analyse d'un échantillon provenant d'un ou de plusieurs individus pour la présence ou l'absence de cellules immunitaires capables de se lier à un peptide antigénique. L'invention concerne également des méthodes de détection ou de traitement d'un cancer ou d'une tumeur, d'une infection pathogène ou de maladies auto-immunes. L'invention concerne également des fractions exposées qui ont une particule associée à une pluralité de complexes peptide/CMH dans lesquels au moins deux complexes peptide/CMH sont différents. L'invention concerne également des compositions d'appât qui ont une pluralité de fractions exposées et des méthodes d'analyse de cellules immunitaires à l'aide des fractions exposées ou des compositions d'appât en tant qu'outil de criblage.
PCT/CN2024/091080 2023-05-03 2024-05-03 Compositions et méthodes d'analyse d'un échantillon pour des cellules immunitaires spécifiques d'un antigène WO2024227447A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202363463886P 2023-05-03 2023-05-03
US63/463,886 2023-05-03

Publications (1)

Publication Number Publication Date
WO2024227447A1 true WO2024227447A1 (fr) 2024-11-07

Family

ID=93332790

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/CN2024/091080 WO2024227447A1 (fr) 2023-05-03 2024-05-03 Compositions et méthodes d'analyse d'un échantillon pour des cellules immunitaires spécifiques d'un antigène

Country Status (1)

Country Link
WO (1) WO2024227447A1 (fr)

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR20050021287A (ko) * 2003-08-25 2005-03-07 가부시키가이샤 메디넷 ＣＴＬ(세포상해성 Ｔ임파구:ｃｙｔｏｔｏｘｉｃ Ｔｌｙｍｐｈｏｃｙｔｅ)의 유도방법
JP2005245430A (ja) * 2003-08-25 2005-09-15 Medeinetto:Kk Ｃｔｌの誘導方法
CN1877336A (zh) * 2005-04-20 2006-12-13 弗·哈夫曼-拉罗切有限公司 鉴定生物药物中与免疫原性相关表位的方法
CN101935636A (zh) * 2002-11-09 2011-01-05 英美偌科有限公司 T细胞受体展示
CN104812396A (zh) * 2012-04-30 2015-07-29 生物治疗公司 β-葡聚糖免疫治疗方法
CN104877008A (zh) * 2005-08-09 2015-09-02 肿瘤疗法·科学股份有限公司 用于hla-a2阳性人群的来自gpc3的癌症排斥抗原肽以及含有该肽的药物
CN114591404A (zh) * 2022-03-23 2022-06-07 成都朗谷生物科技股份有限公司 适用于白细胞抗原单倍型为hla-a2个体的乙型肝炎病毒抗原肽及其应用
CN115508550A (zh) * 2017-04-11 2022-12-23 希森美康株式会社 免疫细胞免疫刺激应答性的测定、免疫细胞免疫突触形成能力的判定、以及细胞分析装置

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101935636A (zh) * 2002-11-09 2011-01-05 英美偌科有限公司 T细胞受体展示
KR20050021287A (ko) * 2003-08-25 2005-03-07 가부시키가이샤 메디넷 ＣＴＬ(세포상해성 Ｔ임파구:ｃｙｔｏｔｏｘｉｃ Ｔｌｙｍｐｈｏｃｙｔｅ)의 유도방법
JP2005245430A (ja) * 2003-08-25 2005-09-15 Medeinetto:Kk Ｃｔｌの誘導方法
CN1877336A (zh) * 2005-04-20 2006-12-13 弗·哈夫曼-拉罗切有限公司 鉴定生物药物中与免疫原性相关表位的方法
CN104877008A (zh) * 2005-08-09 2015-09-02 肿瘤疗法·科学股份有限公司 用于hla-a2阳性人群的来自gpc3的癌症排斥抗原肽以及含有该肽的药物
CN104812396A (zh) * 2012-04-30 2015-07-29 生物治疗公司 β-葡聚糖免疫治疗方法
CN115508550A (zh) * 2017-04-11 2022-12-23 希森美康株式会社 免疫细胞免疫刺激应答性的测定、免疫细胞免疫突触形成能力的判定、以及细胞分析装置
CN114591404A (zh) * 2022-03-23 2022-06-07 成都朗谷生物科技股份有限公司 适用于白细胞抗原单倍型为hla-a2个体的乙型肝炎病毒抗原肽及其应用

Similar Documents

Publication Publication Date Title
US11668705B2 (en) General detection and isolation of specific cells by binding of labeled molecules
JP7531009B2 (ja) Ｈｌａクラスｉｉ特異的エピトープの予測およびｃｄ４＋ ｔ細胞の特徴付けのための方法およびシステム
Peng et al. Sensitive detection and analysis of neoantigen-specific T cell populations from tumors and blood
Pritchard et al. Exome sequencing to predict neoantigens in melanoma
Border et al. Affinity-enhanced T-cell receptors for adoptive T-cell therapy targeting MAGE-A10: strategy for selection of an optimal candidate
CN111233978B (zh) 用于检测肽/mhc/tcr结合的方法
KR101602010B1 (ko) 암, 자가면역 및 감염 질환 면역요법 개발을 위한 자연적으로 가공된 hla-제한 펩티드의 차별 정량법
US10545154B2 (en) Method for the absolute quantification of naturally processed HLA-restricted cancer peptides
US11300574B2 (en) Methods for treating breast cancer and for identifying breast cancer antigens
KR20180014769A (ko) 특정 집단에 대한 항원으로 t 세포를 스크리닝하기 위한 조성물 및 방법
WO2012031122A2 (fr) Méthodes et compositions pour le diagnostic et le traitement du cancer et des troubles auto-immuns
CN113891935A (zh) 肽文库及其使用方法
JP7145980B2 (ja) 腫瘍浸潤リンパ球にて発現するｔ細胞受容体により認識される抗原を識別するためのシステム
WO2024227447A1 (fr) Compositions et méthodes d'analyse d'un échantillon pour des cellules immunitaires spécifiques d'un antigène
JP5172657B2 (ja) 顆粒球抗体の検出に用いられるパネル細胞
US20250044288A1 (en) Cellular assays and methods to assess mhc-peptide-tcr interactions and kinetics
US20250123278A1 (en) Methods of analyzing a sample for cancer-specific immune cells
RU2826261C2 (ru) Способ и системы для прогнозирования специфических для hla класса ii эпитопов и охарактеризации cd4+ t-клеток
EP4550335A1 (fr) Procédés de criblage de récepteurs de lymphocytes t
CN118355277A (zh) 评定mhc-肽-tcr相互作用和动力学的细胞测定和方法
WO2024153619A1 (fr) Protéines et procédés d'isolement de nucléosomes circulants
JP2015203683A (ja) 生体試料中の個別多種及び／又は混合多種の疾患関連自己抗体の検出方法、キット及び検出装置

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 24799903

Country of ref document: EP

Kind code of ref document: A1