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WO2024218318A1 - Marqueurs pour prédiction de l'efficacité thérapeutique d'une cellule tique d'une cellule t - Google Patents

Marqueurs pour prédiction de l'efficacité thérapeutique d'une cellule tique d'une cellule t Download PDF

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Publication number
WO2024218318A1
WO2024218318A1 PCT/EP2024/060760 EP2024060760W WO2024218318A1 WO 2024218318 A1 WO2024218318 A1 WO 2024218318A1 EP 2024060760 W EP2024060760 W EP 2024060760W WO 2024218318 A1 WO2024218318 A1 WO 2024218318A1
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WIPO (PCT)
Prior art keywords
cells
cell
car
cd45ra
cell population
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PCT/EP2024/060760
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English (en)
Inventor
Simon Haas
Schayan YOUSEFIAN
Dominik VONFICHT
Michael Schmitt
Maria-Luisa SCHUBERT
Andreas Trumpp
Original Assignee
Charité - Universitätsmedizin Berlin
Universität Heidelberg
Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts
Hi-Stem Ggmbh
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Publication of WO2024218318A1 publication Critical patent/WO2024218318A1/fr

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    • 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
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
    • G01N33/5047—Cells of the immune system
    • G01N33/505—Cells of the immune system involving T-cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/31—Chimeric antigen receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
    • A61K40/421—Immunoglobulin superfamily
    • A61K40/4211—CD19 or B4
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/38—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the cancer treated
    • A61K2239/48—Blood cells, e.g. leukemia or lymphoma
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/70503—Immunoglobulin superfamily, e.g. VCAMs, PECAM, LFA-3
    • G01N2333/70539—MHC-molecules, e.g. HLA-molecules
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30 CD40 or CD95
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/70589—CD45
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/70596—Molecules with a "CD"-designation not provided for elsewhere in G01N2333/705
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the invention relates to the field of biology and medicine, in particular to the field of genetically modified therapeutic cell products and methods for generating such cells and cell products.
  • the invention relates to a method for assessing a therapeutic efficacy of a T cell.
  • the method comprises providing a sample comprising one or more T cells, and determining for the one or more T cells an expression level of at least CD39, wherein said expression level is indicative of therapeutic efficacy.
  • the invention further relates to a method for the prognosis, prediction, risk assessment and/or risk stratification of responsiveness of a subject having or suspected of having a cancer to a treatment with a therapeutic T cell population.
  • the method comprises assessing the therapeutic efficacy of a T-cell, wherein the therapeutic efficacy of the T cell is indicative of the responsiveness of the subject to a treatment with said T cell or a T cell population produced from said T cell.
  • the present invention further relates to a method for enhancing a therapeutic efficacy of, or for selecting T cells to produce a therapeutically effective T cell population.
  • the method comprises providing a sample comprising one or more T cells, determining for the T cells an expression level of CD39, and optionally CD27, CD45RA and/or HLADR, and selecting T cells for a therapeutic product based on said expression levels, optionally comprising selectively enriching and/or expanding said selected T cells to produce a therapeutically effective T cell population, and/or optionally comprising adding an inhibitor of CD39 during cultivation and/or expansion of said cells and/or upon administration of said therapeutically effective T cell population to a subject.
  • the invention further relates to a T cell population obtainable from the method according to the present invention.
  • the invention further relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 40% (by cell number) CD39- T-cells, preferably at least 50% CD39- T cells, more preferably at least 60% CD39- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention further relates to pharmaceutical composition comprising a T cell population according to the present invention.
  • the invention further relates to a kit for carrying out the method, comprising detection reagents for determining an expression level of CD39 and/or CD27, and optionally additionally for CD45RA and/or HLADR, for one or more T cells, and reference data, or means to obtain reference data, for assessing the therapeutic efficacy of a T cell.
  • BACKGROUND OF THE INVENTION Chimeric antigen receptor (CAR) T-cells which combine the antigen-binding properties of antibodies with the effector functions of T cells, have revolutionized the treatment of cancerous diseases, in particular lymphoid hematological diseases since their first approval in 2017 in the US and 2018 in the EU.
  • the basis of this treatment method is the patient's own (autologous) T cells, which, after isolation from the patient, are genetically modified to present a chimeric antigen receptor (CAR) on their surface that targets cancer associated antigens, are expanded over usually two or more weeks and are subsequently intravenously administered to the patient. Cells presenting the corresponding antigen on their surface are then recognized and killed by the administered CAR T cells.
  • CAR-T cell products approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA) that target various malignant hematologic diseases and different surface proteins (e.g., CD19 and BCMA). Further, a large number of CAR-T cell therapies is in clinical development.
  • CAR-T cell products for the treatment of B-cell malignancies e.g., anti-CD19 CAR expressing T cells
  • methods for dosing thereof are disclosed in WO2020/102770A1.
  • the production of CAR-T cells is a time-consuming process (several weeks to months) and the cost of this individualized therapy are high with at least 275,000 to 350,000 Euros per administration.
  • CAR-T cell therapies especially in the treatment of malignancies of the lymphatic system and most recently in the treatment of autoimmune diseases, recurrences relapses or progression of disease after CAR-T cell therapy are frequent (Mackensen et al., 2022).
  • Ineffective therapies further cause many patients to lose valuable lifespan and may subsequently subject patients to be ineligible for further therapy.
  • WO2019/232510A1 discloses a method for predicting the clinical outcome in response to CAR-T cancer treatments.
  • CAR-T cell products there are only few strategies for evaluation of CAR-T cell products known in the prior art, which include the readout of surface markers (Locke et al., 2020, Caballero et al., 2022), T cell subtypes/differentiation stages (Chen et al., 2022, Haradhvala et al., 2022), or patient-specific genetic alterations (Shouval et al., 2021).
  • WO2016/061456A1 discloses CD39 for the characterization of exhausted T-cells such as CD8+ T cells. High CD39 expression identifies terminally exhausted T cells and may distinguish between reversible and irreversible T cell exhaustion.
  • determination of CD39 may be used for determination of T cell function during chronic immune disorders such as chronic viral infections, and to determine whether a chronic immune disorder is likely to respond to anti-CD39 therapy.
  • High expression of CD39 in tumor infiltrating CD8+ T cells was associated with features of exhaustion such as reduced production of TNF and PL2 and expression of coinhibitory receptors.
  • the frequency of CD8+ T cells highly expressing CD39 within the tumor microenvironment increased with tumor growth.
  • these documents do not disclose the evaluation of CAR T cell products to ensure or increase the chances of responsiveness of the patient to the therapy.
  • DLBCL large B cell lymphoma
  • high expression of CD27 in a T cell population CCR7+/CD27+ CD8, central memory T cells
  • Goldberg et al (2022) characterized immune cell populations from CAR-T cell products compared to leukapheresis samples and demonstrated upregulation of many trafficking and activation molecules such as integrin- ⁇ 7, CD11a or CD25 in the transduced T cell within the CAR-T cell product.
  • AU2022203932A1 further describes several surface markers for the characterization of CAR T cell products correlating with patient responsiveness.
  • CD27 expression is described in combination with other proteins, with higher numbers of CD27+ immune effector cells correlating with patient response to CD19 CAR therapy.
  • WO2019/213282A1 similarly discloses several surface markers to evaluate or monitor the effectiveness of CAR-expressing cell populations such as CAR T cells.
  • CD27 expression is described in combination with other markers and a higher percentage of CD27+ CAR-expressing cells is observed in a patient responding to therapy with said CAR-expressing cell product (responder) in comparison to a patient not responding to said therapy (non-responder).
  • WO2022/055946A1 discloses methods for obtaining a cell population enriched for T cells with a CD3+CD39-CD69- phenotype from a patient, which may be expanded and reinfused back to the patient for immunotherapy.
  • the T cells may be further modified to induce expression of further markers such as CD27+, or inhibiting expression of further markers such as CD38+.
  • US2021/0130438A1 discloses CD8+ T cells that were modified ex vivo to have an increased expression of CXCR6.
  • the T cells may be further treated to show modulated expression, activity or function of various genes, to avoid dysfunctional gene expression signatures.
  • the above approaches have so far only considered individual aspects of T cell biology, thereby not considering the complexity of the holistic T cell compartment, resulting in reduced accuracy and statistical robustness of quality evaluation and prediction of the responsiveness of a patient to the CAR- T cell product.
  • T cell therapies in particular CAR-T cell therapies
  • CAR-T cell therapies there is an urgent need for accurate and easily determinable quality criteria and measures for responsiveness of a patient to any given therapeutic T cell product to enable optimization, improved and cost effective clinical application of these T cell products, and reduction of ineffective therapeutic approaches that may involve toxic side effects (e.g., cytopenia, neurotoxicity, cytokine release syndrome) potentially resulting in loss of lifespan or ineligibility for further therapies.
  • toxic side effects e.g., cytopenia, neurotoxicity, cytokine release syndrome
  • the technical problem underlying the present invention is to provide improved and/or alternative means for immunotherapy with a therapeutic T cell, such as CAR-T cells, that overcome the disadvantages of the prior art.
  • One object of the present invention is to provide straightforward and reliable methods to determine, improve and/or enhance the therapeutic efficacy of T cells and therapeutic T cell products, such as CAR T cell products.
  • a further problem underlying the invention is to provide improved or alternative means for prognosis and/or prediction of the responsiveness of a subject to a therapy with therapeutic T cell populations, in order to enable optimization of therapeutic T cell populations.
  • a further object of the invention is to provide means for assessing the therapeutic efficacy of T cells and the responsiveness of a subject to therapy with the therapeutic T cells.
  • a further object of the invention is to provide means for assessing and optimizing the dosage or cell number of therapeutic T cells or T cell products administered to a subject, that result in responsiveness of a subject to therapy with the therapeutic T cells or T cells product.
  • a further object of the invention is to provide straightforward, simple and reliable means for assessing therapeutic efficacy of “out-of-specification” T cells and T cell products and the responsiveness of a subject thereto.
  • a further object of the invention is to provide simple and reliable means for optimizing the manufacture and production of therapeutic T cells and T cell products that shown high therapeutic efficacy and responsiveness in a subject.
  • the invention relates to a method for assessing a therapeutic efficacy of a T cell, comprising: - providing a sample comprising one or more T cells, and - determining for the one or more T cells an expression level of at least CD39, - wherein said expression level is indicative of therapeutic efficacy.
  • the method additionally comprises determining an expression level of CD27, CD45RA and/or HLADR for the one or more T cells.
  • the method comprises determining an expression level of CD39 and CD27, and optionally additionally CD45RA and/or HLADR, for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy.
  • the method comprises determining an expression level of CD39 and CD45RA and optionally additionally CD27 and/or HLADR, for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy. In one embodiment, the method comprises determining an expression level of CD39 and HLADR and optionally additionally CD27 and/or CD45RA, for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy. In one embodiment, the method comprises determining an expression level of CD39, CD27 and HLADR, for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy.
  • the method comprises determining an expression level of CD39, CD27 and CD45RA for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy.
  • the invention relates to a method for assessing a therapeutic efficacy of a T cell, comprising: - providing a sample comprising one or more T cells, and - determining for the one or more T cells an expression level of at least CD27, - wherein said expression level is indicative of therapeutic efficacy.
  • the method additionally comprises determining an expression level of CD39, CD45RA and/or HLADR for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy.
  • the method comprises determining an expression level of CD27 and CD45RA and optionally additionally CD39 and HLADR. In one embodiment, the method comprises determining an expression level of CD27 and HLADR and optionally additionally CD39 and CD45RA. In one embodiment, the determined expression level of CD39 and optionally CD27 and/or CD45RA is compared to a reference level, preferably a reference expression level of CD39 and optionally of CD27 and/or CD45RA for a T cell having no therapeutic efficacy, wherein an expression level below the reference level (preferably defining CD39- and optionally CD27- T and/or CD45RA- cells) is indicative of a therapeutic efficacy of said T cell.
  • a reference level preferably a reference expression level of CD39 and optionally of CD27 and/or CD45RA for a T cell having no therapeutic efficacy
  • the determined expression level of CD27 and optionally CD39 and/or CD45RA is compared to a reference level, preferably a reference expression level of CD27 and optionally of CD39 and/or CD45RA for a T cell having no therapeutic efficacy, wherein an expression level below the reference level (preferably defining CD27- and optionally CD39- T and/or CD45RA- cells) is indicative of a therapeutic efficacy of said T cell.
  • the determined expression level of HLADR is compared to a reference level, preferably a reference expression level of HLADR for a T cell having no therapeutic efficacy, wherein an expression level above the reference level (preferably defining HLADR+ cells) is indicative of therapeutic efficacy.
  • the method comprises determining an expression level of CD39 and CD27 for the one or more T cells, wherein said expression levels are indicative of therapeutic efficacy.
  • low or negligible levels of CD39 and CD27 expression are determined in the T cells, preferably as CD27- and CD39- T cells, which indicates a therapeutic efficacy of said cells.
  • the method of the present invention provides a straightforward method to reliably assess the therapeutic efficacy of a T cell in a standardized manner by determining the expression level of CD39, CD27, CD45RA and/or HLADR on the surface of T cells.
  • assessing the therapeutic efficacy of T cells according to the present invention further allows to enhance the therapeutic efficacy, optimize the production of therapeutic T cell populations from such therapeutically effective T cells, such as CAR-T cell products, and to predict the responsiveness of a subject treated with such therapeutic T cells.
  • T cell therapy such as CAR -T cell therapy
  • the ineffectiveness of T cell products and non-responsiveness of patients to T cell therapy, such as CAR -T cell therapy, is one of the major hurdles resulting in unnecessary therapeutic approaches that may involve toxic side effects with potential resulting in a loss of lifespan or ineligibility for further therapies and high costs for healthcare systems.
  • only few methods are known in the prior art for characterization of T cell products allowing evaluation of therapeutic efficiency of T cells and T cell products.
  • the method of the present invention allows the reliable prediction of therapeutic efficacy and responsiveness for various cell types, e.g., CD4+ and CD8+ T cells, present in therapeutic T cell products.
  • the method was developed by analyzing the expression of markers on the surface of T cells by using spectral flow cytometry, which unlike conventional flow cytometry, enables the readout of more than 30 surface markers in millions of cells within a few minutes, allowing to take into account key aspects of the complex T cell biology, such as activation states, cell stages, and cell subtypes, at the single cell level.
  • the inventors analyzed CAR-T cell products from patients enrolled in a phase I/II CAR-T cell clinical trial the expression of 34 surface markers was detected by spectral flow cytometry and analyzed by non-supervised clustering algorithms. Based on this single cell analysis, the surface markers CD39, CD27, CD45RA and HLADR were identified, the expression level of which significantly correlates with the therapeutic efficacy of T cells in the clinical trial, and thus allows reliable prediction of therapeutic efficacy of the cell product and thus the responsiveness of a patient.
  • This approach systematically determined biomarkers and biomarker combinations using conventional cytometry that predict CAR-T cell therapy response in patients, by way of example in patients with acute lymphoblastic leukemia.
  • the surface markers CD39, CD27, CD45RA and HLADR allow a statistically significant and robust assessment of therapeutic efficacy of T cells.
  • determining the expression level of the surface markers CD39 and CD27 is particularly advantageous to assess the therapeutic efficacy of a therapeutic T cell and T cell products.
  • the method of the present invention advantageously enables a fast and cost-efficient assessment with standard laboratory equipment present in clinical, research and industrial labs, e.g., by determining the expression of the surface markers by using immunoassays such as ELISA or conventional flow or mass cytometry.
  • T cell products such as CAR T cell products, which after manufacturing do not meet the specific quality criteria defined upon clinical approval, e.g., due to a number of CAR T cells below a threshold within the cell product, low cell viability or a low number of immature T cells, can be assessed for their therapeutic efficacy.
  • the one or more T cells are used to produce a therapeutic T cell population, preferably a CAR-T cell population, the production of the therapeutic T cell population comprising, i.
  • the one or more T cells identified using the biomarker analysis described herein are subsequently modified to express a CAR and thereafter expanded to generate a therapeutic cell product.
  • a genetically modified CAR-T cell population may be assessed using the biomarker analysis described herein to assess efficacy prior to administration.
  • Either procedure enables selection of an efficacious cell product or subsequent increasing of efficacy of a cell product by increasing the proportion of desirable - defined by the biomarker expression levels described herein - cells prior to administration.
  • - the expression level of CD39 and optionally of CD27, CD45RA and/or HLADR is determined prior to genetic modification of the T cells
  • - The expression level of CD39 and optionally of CD27, CD45RA and/or HLADR is determined after genetic modification and prior to expansion of the T cells
  • - the expression level of CD39 and optionally of CD27, CD45RA and/or HLADR is determined after genetic modification and expansion of the T cells.
  • the expression level of CD27 and optionally of CD39, CD45RA and/or HLADR is determined prior to genetic modification of the T cells
  • - The expression level of CD27 and optionally of CD39, CD45RA and/or HLADR is determined after genetic modification and prior to expansion of the T cells
  • - the expression level of CD27 and optionally of CD39, CD45RA and/or HLADR is determined after genetic modification and expansion of the T cells.
  • the expression level of CD39 and CD27 and optionally CD45RA and/or HLADR is determined prior to genetic modification of the T cells
  • - The expression level of CD39 and CD27 and optionally CD45RA and/or HLADR is determined after genetic modification and prior to expansion of the T cells
  • - the expression level of CD39 and CD27 and optionally CD45RA and/or HLADR is determined after genetic modification and expansion of the T cells.
  • the method of the present invention allows determination of the therapeutic efficacy of unmodified and genetically modified T cells and thus assessment of efficacy at any stage of the production of a therapeutic T cell population.
  • the method of the present invention can be performed with standard equipment present in clinical, research and industrial labs in a simple, fast and cost-efficient manner which is advantageous for quality assessment and monitoring of the manufacturing process and therapy responsiveness in a patient.
  • the expression level of CD39 and optionally CD27, CD45RA and/or HLADR is determined by flow cytometry, microscopy, an immunoassay, such as ELISA, mass spectrometry and/or mass cytometry. In one embodiment, the expression level of CD27 and optionally CD39, CD45RA and/or HLADR is determined by flow cytometry, microscopy, an immunoassay, such as ELISA, mass spectrometry and/or mass cytometry. In one embodiment, the expression level of CD39 and CD27 and optionally CD45RA and/or HLADR is determined by flow cytometry, microscopy, an immunoassay, such as ELISA, mass spectrometry and/or mass cytometry.
  • the T cell-containing sample was isolated from peripheral blood of a subject by leukapheresis.
  • the one or more T cells are autologous with respect to a subject receiving the T cells.
  • the one or more T cells are allogenic with respect to a subject receiving the T cells.
  • the sample is isolated from a subject after administration of a therapeutic T cell population to the subject. The invention therefore enables post-administration assessment of T cell efficacy, to provide e.g., an assessment and/or understanding of whether the T cells after administration maintained or no longer exhibit an efficacious biomarker expression pattern, using the biomarker expression as described herein.
  • the one or more T-cells are CD4+ and/or CD8+ T cells.
  • the method of the present invention allows determination of an efficacious biomarker expression pattern in various T cell populations, in particular in CD4+ and in CD8+ populations. Considering these two T cell populations are frequently employed and highly relevant for various therapeutic T cell products, the present invention is of great relevance to assessing T cell therapy success.
  • the invention relates to a method for the prognosis, prediction, risk assessment and/or risk stratification of responsiveness of a subject having or suspected of having a cancer to a treatment with a therapeutic T cell population, the method comprising: - assessing the therapeutic efficacy of a T-cell, - wherein the therapeutic efficacy of the T cell is indicative of the responsiveness of the subject to a treatment with said T cell or a T cell population produced from said T cell. Prediction of therapy response to a T cell population or product is particularly important to avoid ineffective and thus unnecessary therapies, potentially resulting in side effects, loss of time for the patient and high costs.
  • the method of the present invention based on the determination of the expression of the surface markers CD39, CD27, CD45RA and HLADR, considers multiple aspects of T cell biology and thus advantageously enables robust and rapid prediction of a patient's response to therapy.
  • the invention relates to a method for enhancing a therapeutic efficacy of, or for selecting T cells to produce a therapeutically effective T cell population.
  • the method for enhancing a therapeutic efficacy of a T cell population, or for selecting T cells to produce a therapeutically effective T cell population comprises: - providing a sample comprising one or more T cells, - determining for the T cells an expression level of CD39, and optionally CD27, CD45RA and/or HLADR, and - selecting T cells for a therapeutic product based on said expression levels, - optionally comprising selectively enriching and/or expanding said selected T cells to produce a therapeutically effective T cell population, and/or - optionally comprising adding an inhibitor of CD39 during cultivation and/or expansion of said cells and/or upon administration of said therapeutically effective T cell population to a subject.
  • the method comprises adding an inhibitor of CD39 during cultivation and/or expansion of the T cells, prior to administration of said therapeutically effective T cell population to a subject and/or upon administration of said therapeutically effective T cell population to a subject.
  • the invention further relates to a method for enhancing a therapeutic efficacy of, or for selecting CAR T cells to produce a therapeutically effective CAR T cell population.
  • the method for enhancing a therapeutic efficacy of a CAR T cell population, or for selecting CAR T cells to produce a therapeutically effective CAR T cell population comprises: - providing a sample comprising one or more CAR T cells, - determining for the T cells an expression level of CD39, and optionally CD27, CD45RA and/or HLADR, and - selecting CAR T cells for a therapeutic product based on said expression levels, - optionally comprising selectively enriching and/or expanding said selected CAR T cells to produce a therapeutically effective CAR T cell population, and/or - optionally comprising adding an inhibitor of CD39 during cultivation and/or expansion of said cells and/or upon administration of said therapeutically effective CAR T cell population to a subject.
  • the method comprises adding an inhibitor of CD39 during cultivation and/or expansion of the CAR T cells and/or upon administration of said therapeutically effective CAR T cell population to a subject. In preferred embodiments the method comprises adding an inhibitor of CD39 during cultivation and/or expansion of the CAR T cells, prior to administration of said therapeutically effective CAR T cell population to a subject and/or upon administration of said therapeutically effective CAR T cell population to a subject.
  • the invention relates to a method for enhancing a therapeutic efficacy of, or for selecting T cells to produce, a therapeutically effective T cell population, comprising: - providing a sample comprising one or more T cells, - determining for the T cells an expression level of CD27, and optionally CD39, CD45RA and/or HLADR, and - selecting T cells for a therapeutic product based on said expression levels, - optionally comprising selectively enriching and/or expanding said selected T cells to produce a therapeutically effective T cell population, and/or - optionally comprising adding an inhibitor of CD27 during cultivation and/or expansion of said cells and/or upon administration of said therapeutically effective T cell population to a subject.
  • the method comprises adding an inhibitor of CD27 during cultivation and/or expansion of the T cells, prior to administration of said therapeutically effective T cell population to a subject and/or upon administration of said therapeutically effective T cell population to a subject.
  • the method of the present invention based on the determination of the expression of the surface markers CD39, CD27, CD45RA and/or HLADR, enables identifying the potential efficacy of a therapeutic cell, cell population or cell product.
  • the method comprises optionally selecting or enriching the desired cells to enhance efficacy. Means for such selecting or enriching the relevant cell group are known to a person skilled in the art.
  • Cells may be sorted and selected based on biomarker expression, for example using established cell sorting cytometry techniques.
  • cell culture conditions may be adjusted to select for the desired cell population during expansion, while preparing a therapeutic cell product.
  • a method of enhancing the therapeutic efficacy of a T cell population may involve actively treating the cells during cultivation or expansion in order to obtain a desired population, as defined by the biomarkers described in detail herein.
  • inhibitors of a relevant biomarker, such as CD39 or CD27 may be administered to cells, at any given stage or cell processing, in order to enhance the cell population with respect to obtaining an efficacious population of T cells.
  • an inhibitor of CD39 and/or an inhibitor of CD27 may be added to the cells during cultivation to reduce expression and/or activity of these markers, thereby achieving a cell population with the desired characteristics.
  • the addition of a CD39 inhibitor during cultivation and expansion of the therapeutic T cells allows to selectively produce a T cell product enriched in CD39- negative cells in a simple and cost-effective manner.
  • highly efficient therapeutic T cell populations and products can be obtained, avoiding manufacturing of inactive T cell products and thus significant financial loss and loss of time for the patient.
  • the addition of a CD39 inhibitor to the T cell population prior to or upon administration surprisingly allows control over the number of CD39- T cells administered to the patient and their expansion within the subject, thus ensuring a therapeutic efficacy of the product.
  • the inhibitor of CD39 is POM 1, ARL 67156 trisodium salt, PSB 06126, PSB 069 (CAS 78510-31-3) or mixtures thereof.
  • the invention relates to a T cell population obtainable from a method as described herein.
  • the T cell population may be defined by the biomarker expression levels and/or presence of particular cell types, without explicit reference to any one of the methods described herein.
  • the T cell population as such may, in embodiments, be obtained by any one or more of the methods disclosed herein, such as a method for determining a therapeutic efficacy of a T cell, a method for enhancing a therapeutic efficacy, or for selecting T cells according to the desired characteristics, in order to produce a therapeutically effective T cell population according to the present invention.
  • the invention therefore provides multiple means for obtaining a desired T cell population, which exhibits the therapeutic efficacy as may be required in any given clinical setting.
  • the invention also relates to the T cell populations as such, which may be processed and/or produced using one or more of the methods described herein.
  • a therapeutic T cell product derived by the methods of the invention comprises a higher percentage or proportion of therapeutically effective T cells, resulting in higher responsiveness of patients to such products and more sustainable clinical success, thereby saving time and costs.
  • such a higher percentage or proportion of the desired T cells may be determined in reference to a control population, for example a T cell population that has not undergone selection or enhancement of the desirable marker expression profiles as described herein.
  • Other reference T cell populations of the prior art may also be considered.
  • the T cell populations described herein comprise greater numbers (or percentages or proportions) of T cells with the desired marker expression levels compared to those T cell populations of the prior art.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 40% (by cell number) CD39- T-cells, preferably at least 50% CD39- T cells, more preferably at least 60% CD39- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ CAR-T cells, wherein said T cell population comprises at least 56% (by cell number) CD4+ CD39- T-cells, preferably at least 60% CD4+ CD39-T cells, more preferably at least 87.5% CD4+ CD39- T cells, even more preferably at least or about 95% CD4+CD39- T cells.
  • the invention relates to a T cell population comprising therapeutic CD8+ CAR-T cells, wherein said T cell population comprises at least 40% (by cell number) CD8+CD39- T-cells, preferably at least 50% CD8+ CD39-T cells, more preferably at least 79.2% CD8+CD39- T cells, even more preferably at least or about 91.50% CD8+CD39- T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 55% (by cell number) CD27- T-cells, preferably at least 60% CD27- T cells, more preferably at least 70% CD27- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ CAR-T cells, wherein said T cell population comprises at least 54% (by cell number) CD4+ CD27- T-cells, preferably at least 60% CD4+CD27- T cells, more preferably at least 79.70% CD4+ CD27- T cells, even more preferably at least or about 81.30% CD4+ CD27- T cells.
  • the invention relates to a T cell population comprising therapeutic CD8+ CAR-T cells, wherein said T cell population comprises at least 64% (by cell number) CD8+ CD27- T-cells, preferably at least 70% CD8+ CD27-T cells, more preferably at least 90.50% CD8+ CD27- T cells, even more preferably at least or about 91.30% CD8+ CD27- T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 30% (by cell number) CD39-CD27- T-cells, preferably at least 40% CD39-CD27- T cells, more preferably at least 50% CD39-CD27- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ CAR-T cells, wherein said T cell population comprises at least 28% (by cell number) CD4+CD39- CD27- T-cells, preferably at least 50% CD4+CD39- CD27- T cells, more preferably at least 71.30% CD4+CD39-CD27- T cells, even more preferably at least or about 74.20% CD4+CD39- CD27- T cells.
  • the invention relates to a T cell population comprising therapeutic CD8+ CAR-T cells, wherein said T cell population comprises at least 27% (by cell number) CD8+CD39- CD27- T-cells, preferably at least 50% CD8+CD39- CD27- T cells, more preferably at least 71.90% CD8+CD39- CD27- T cells, even more preferably at least or about 84.20% CD8+CD39- CD27- T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 45% (by cell number) CD39-CD45RA- T-cells, preferably at least 50% CD39-CD45RA- T cells, more preferably at least 60% CD39-CD45RA- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ CAR-T cells, wherein said T cell population comprises at least 43% (by cell number) CD4+CD39- CD45RA- T-cells, preferably at least 60% CD4+CD39-CD45RA-T cells, more preferably at least 78.60% CD4+CD39-CD45RA- T cells, even more preferably at least or about 88.90% CD4+CD39-CD45RA- T cells.
  • the invention relates to a T cell population comprising therapeutic CD8+ CAR-T cells, wherein said T cell population comprises at least 24% (by cell number) CD8+CD39- CD45RA- T-cells, preferably at least 50% CD8+CD39-CD45RA- T cells, more preferably at least 69% CD8+CD39-CD45RA- T cells, even more preferably at least or about 79.50% CD8+CD39- CD45RA- T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 30% (by cell number) CD39-CD27- CD45RA- T-cells, preferably at least 40% CD39-CD27- CD45RA- T cells, more preferably at least 50% CD39-CD27- CD45RA- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ CAR-T cells, wherein said T cell population comprises at least 26% (by cell number) CD4+CD39- CD27-CD45RA- T-cells, preferably at least 50% CD4+CD39-CD27-CD45RA-T cells, more preferably at least 68.90% CD4+CD39-CD27-CD45RA- T cells, even more preferably at least or about 73.60% CD4+CD39-CD27-CD45RA- T cells.
  • the invention relates to a T cell population comprising therapeutic CD8+ CAR-T cells, wherein said T cell population comprises at least 22% (by cell number) CD8+CD39- CD27-CD45RA- T-cells, preferably at least 50% CD8+CD39-CD27-CD45RA- T cells, more preferably at least 67.90% CD8+CD39-CD27-CD45RA- T cells, even more preferably at least or about 81.60% CD8+CD39-CD27-CD45RA- T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 25% (by cell number) CD39-CD27- HLADR+ T-cells, preferably at least 30% CD39-CD27- HLADR+ T cells, more preferably at least 40% CD39-CD27- HLADR+ T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ CAR-T cells, wherein said T cell population comprises at least 20% (by cell number) CD4+CD39- CD27-HLADR+ T-cells, preferably at least 40% CD4+CD39-CD27-HLADR+T cells, more preferably at least 53% CD4+CD39-CD27-HLADR+ T cells, even more preferably at least or about 61.50% CD4+CD39-CD27-HLADR+ T cells.
  • the invention relates to a T cell population comprising therapeutic CD8+ CAR-T cells, wherein said T cell population comprises at least 25% (by cell number) CD8+CD39- CD27-HLADR+ T-cells, preferably at least 50% CD8+CD39-CD27-HLADR+ T cells, more preferably at least 68.20% CD8+CD39-CD27-HLADR+ T cells, even more preferably at least or about 80.10% CD8+CD39-CD27-HLADR+ T cells.
  • the features of the embodiments above regarding the T cell populations may be combined.
  • the T cell population comprising at least 25% CD39-CD27- HLADR+ T- cells, may also comprise at least 30% CD39-CD27- CD45RA- T-cells.
  • each cell may be characterized by multiple marker expression levels, the above cell populations may, in embodiments, overlap with each other.
  • Each of the above cell populations is therefore not considered mutually exclusive of each other.
  • Each of the marker combinations disclosed herein represents therefore a preferred and beneficial combination of marker expression levels that can be used to identify a cell population of the invention accurately and unambiguously.
  • T cell populations with such beneficial numbers or proportions of such cells are an aspect of the invention.
  • Beneficial quantities of each relevant cell type, as defined by one or more various markers disclosed herein, may be derived from the examples, for example the data presented in tables 5-16 and Figure 9.
  • the population may be defined by the number (or percentage or proportion) of T cells in the population that exhibit the CD39-, CD27- CD45RA- and/or HLADR+ phenotypes. This phenotype may be measured with respect to the total number of T cells in the cell population, with respect to the total number of CD4+ T cells in the population, with respect to the total number of CD8+ T cells in the population, or with respect to the number of CAR-T cells, or CD4+ CAR-T cells and/or CD8+ CAR-T cells in the population.
  • a T cell population may comprise a mixture of CD4+, CD8+ and/or CAR-expressing cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 40% (by cell number) CD39- T-cells, preferably at least 50% CD39- T cells, more preferably at least 60% CD39- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells.
  • the T cell population may comprise CD4+ and/or CD8+ CAR-T cells in an undefined amount.
  • the T cell population comprises at least 40% (by cell number) CD39- T-cells, with respect to the total number of T cells in the population.
  • the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, with respect to the total number of T cells in the population.
  • the percentage of CAR-T cells is presented optionally, as the beneficial proportion of T cells defined as CD39- may be determined before or after genetic modification to the T cells to express a CAR. Nevertheless, the T cell with these beneficial proportions of CD39- cells is an advantageous cell population for subsequent CAR modification to prepare a CAR-T cell.
  • the proportion of T cells defined as CD39- may be determined in a CAR-T cell population, whereby not necessarily all T cells are CAR-T cells. As is known to a skilled person, some T cells may be present in a CAR T cell population in which a CAR is not expressed.
  • the T cell population comprises: - at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, and - wherein said T cell population comprises at least 40% (by cell number) CD39- CD27- T- cells, preferably at least 50% CD39- CD27- T cells, more preferably at least 60% CD39- CD27- T cells, and/or - wherein said T cell population comprises at least 45% (by cell number) CD39-CD45RA- T-cells, preferably at least 50% CD39-CD45RA- T cells, more preferably at least 60% CD39-CD45RA- T cells.
  • the T cell population comprises: - at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, and - wherein said T cell population comprises at least 30% (by cell number) CD39-CD27- CD45RA- T-cells, preferably at least 40% CD39-CD27-CD45RA- T cells, more preferably at least 50% CD39-CD27-CD45RA- T cells, and/or - wherein said T cell population comprises at least 25% (by cell number) CD39-CD27- HLADR+ T-cells, preferably at least 30% CD39-CD27- HLADR+ T cells, more preferably at least 40% CD39-CD27- HLADR+ T cells.
  • the T cell population comprises: - CD4+ and/or CD8+ CAR-T cells, preferably at least 40% (by cell number), and - wherein said CD4+ CAR-T cells comprise at least 56% (by cell number) CD39- T-cells, preferably at least 60% CD39- T cells, more preferably at least 87.50% CD39- T cells, even more preferably at least or about 95% CD39- T cells, and/or - wherein said CD8+ CAR-T cells comprise at least 40% (by cell number) CD39- T-cells, preferably at least 50% CD39- T cells, more preferably at least 79.20% CD39- T cells, even more preferably at least or about 91.50% CD39- T cells.
  • the T cell population comprises: - CD4+ and/or CD8+ CAR-T cells, preferably at least 40 % (by cell number) and - wherein said CD4+ CAR-T cells comprise at least 54% (by cell number) CD27- T-cells, preferably at least 60% CD27- T cells, more preferably at least 79.70% CD27- T cells, even more preferably at least or about 81.30% CD27- T cells, and/or - wherein said CD8+ CAR-T cells comprise at least 64% (by cell number) CD27- T-cells, preferably at least 70% CD27- T cells, more preferably at least 90.50% CD27- T cells, even more preferably at least or about 91.30% CD27- T cells.
  • the T cell population comprises: - CD4+ and/or CD8+ CAR-T cells, preferably at least 40% (by cell number) and - wherein said CD4+ CAR-T cells comprise at least 28% (by cell number) CD39- CD27- T- cells, preferably at least 50% CD39- CD27- T cells, more preferably at least 71.30% CD39- CD27- T cells, even more preferably at least or about 74.20% CD39- CD27- T cells and/or - wherein said CD8+ CAR-T cells comprise at least 27% (by cell number) CD39- CD27- T- cells, preferably at least 50% CD39- CD27- T cells, more preferably at least 71.90% CD39- CD27- T cells, even more preferably at least or about 84.20% CD39- CD27- T cells.
  • the T cell population comprises: - CD4+ and/or CD8+ CAR-T cells, preferably at least 40% (by cell number) and - wherein said CD4+ CAR-T cells comprise at least 43% (by cell number) CD39- CD45RA- T-cells, preferably at least 60% CD39- CD45RA- T cells, more preferably at least 78.60% CD39- CD45RA- T cells, even more preferably at least or about 88.90% CD39- CD45RA- T cells, and/or - wherein said CD8+ CAR-T cells comprise at least 24% (by cell number) CD39- CD45RA- T-cells, preferably at least 50% CD39- CD45RA- T cells, more preferably at least 69% CD39- CD45RA- T cells, even more preferably at least or about 79.50% CD39- CD45RA- T cells.
  • the T cell population comprises: - CD4+ and/or CD8+ CAR-T cells, preferably at least 40% (by cell number) and - wherein said CD4+ CAR-T cells comprise at least 26% (by cell number) CD39-CD27- CD45RA- T-cells, preferably at least 50% CD39-CD27-CD45RA- T cells, more preferably at least 68.90% CD39-CD27-CD45RA- T cells, even more preferably at least or about 73.60% CD39-CD27-CD45RA- T cells, and/or - wherein said CD8+ CAR-T cells comprise at least 22% (by cell number) CD39-CD27- CD45RA- T-cells, preferably at least 50% CD39-CD27-CD45RA- T cells, more preferably at least 67.90% CD39-CD27-CD45RA- T cells, even more preferably at least or about 81.60% CD39-CD27-CD45RA- T cells.
  • the T cell population comprises: - CD4+ and/or CD8+ CAR-T cells, preferably at least 40% (by cell number) and - wherein said CD4+ CAR-T cells comprise at least 20% (by cell number) CD39-CD27- HLADR+ T-cells, preferably at least 40% CD39-CD27- HLADR+ T cells, more preferably at least 53% CD39-CD27- HLADR+ T cells, even more preferably at least or about 61.50% CD39-CD27- HLADR+ T cells and/or - wherein said CD8+ CAR-T cells comprise at least 25% (by cell number) CD39-CD27- HLADR+ T-cells, preferably at least 50% CD39-CD27- HLADR+ T cells, more preferably at least 68.2% CD39-CD27- HLADR+ T cells, even more preferably at least or about 80.1% CD39-CD27- HLADR+ T cells.
  • the features of the embodiments above regarding the T cell populations may be combined.
  • the T cell population comprising at least 25% CD39-CD27- HLADR+ T- cells may also comprise at least 30% CD39-CD27- CD45RA- T-cells.
  • each cell may be characterized by multiple marker expression levels
  • the above cell populations may, in embodiments, overlap with each other.
  • Each of the above cell populations is therefore not considered mutually exclusive of each other.
  • Each of the marker combinations disclosed herein represents therefore a preferred and beneficial combination of marker expression levels that can be used to identify a cell population of the invention accurately and unambiguously.
  • any one or more features above represented as “at least a given % (by cell number)” may include any % value above the given value up to 100%.
  • any one or more features above represented as “at least 40% (by cell number)” may comprise at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% (by cell number).
  • any one or more features above represented as “at least 50% (by cell number)” may comprise at least 50%, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% (by cell number).
  • any one or more features above represented as “at least 60% (by cell number)” may comprise at least 60%, 65, 70, 75, 80, 85, 90, or at least 95% (by cell number).
  • the T cell population comprises: - at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells, and - wherein said T cell population comprises at least 30% (by cell number) CD39- CD27- T- cells, therefore at least 30%, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 or at least 95% CD39- CD27- T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 40% (by cell number) CD39- T-cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD39- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 55% (by cell number) CD27- T-cells, therefore at least 55%, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD27- T cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 30% (by cell number) CD39-CD27- T-cells, therefore at least 30%, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD39-CD27- T-cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 45% (by cell number) CD39-CD45RA- T-cells, therefore at least 45%, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD39-CD27- T-cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 26% (by cell number) CD39-CD27-CD45RA- T-cells, therefore at least 30%, 35, 40.45, 50, 55, 60, 65, 70, 75, 80, 85, 90 or at least 95% CD39-CD27- T-cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 56% (by cell number) CD39-CD27-HLADR+ T-cells, therefore at least 25%, 30, 35, 40. 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 or at least 95% CD39-CD27- T-cells, wherein preferably the T cell population comprises at least 40% (by cell number) CD4+ and/or CD8+ CAR-T cells, therefore at least 40%, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or at least 95% CD4+ and/or CD8+ CAR-T cells.
  • the population may be defined by the number of T cells in the population that exhibit the CD39- and CD27- phenotype. This phenotype may be measured with respect to the total number of T cells in the cell population, with respect to the total number of CD4+ T cells in the population, with respect to the total number of CD8+ T cells in the population, or with respect to the number of CAR-T cells, or CD4+ CAR-T cells and/or CD8+ CAR-T cells in the population.
  • a T cell population may comprise a mixture of CD4+, CD8+ and/or CAR-expressing cells.
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 0.215*10 6 CD39- CD27- CAR T-cells per kg body weight of a patient the T cell population is administered to, preferably at least 0.23*10 6 CD39-CD27- CAR T cells per kg body weight of a patient the T cell population is administered to, more preferably at least 0.25*10 6 CD39-CD27- CAR T cells per kg body weight of a patient the T cell population is administered to.
  • the total cells for administration to a patient are present in a single dosage unit, administration unit or preparation.
  • each of the above-mentioned cell numbers may vary with respect to the actual cell number in a T cell population, for example, variations in these values of ⁇ 0.01*10 6 to 0.15*10 6 is contemplated, such as ⁇ 0.01*10 6 , 0.02*10 6, 0.03*10 6 , 0.04*10 6 , 0.05*10 6 , 0.06*10 6 , 0.07*10 6 , 0.08*10 6 , 0.09*10 6 , 0.1*10 6 , 0.11*10 6 , 0.12*10 6 , 0.13*10 6 , 0.14*10 6 or 0.15*10 6 .
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 0.95*10 7 CD39- CD27- CAR T-cells per m2 of the body surface of a patient the T cell population is administered to, preferably at least 0.98*10 7 CD39-CD27- CAR T cells per m 2 of the body surface of a patient the T cell population is administered to, more preferably at least 1.00 *10 7 CD39-CD27- CAR T cells per m2 of the body surface of a patient the T cell population is administered to.
  • the total cells for administration to a patient are present in a single dosage unit, administration unit or preparation.
  • each of the above-mentioned cell numbers may vary with respect to the actual cell number in a T cell population, for example, variations in these values of ⁇ 0.01 to 0.3*10 7 is contemplated, such as ⁇ 0.01*10 7 , 0.02*10 7 , 0.03*10 7 , 0.04*10 7 , 0.05*10 7 , 0.06*10 7 , 0.07*10 7 , 0.08*10 7 , 0.09*10 7 , 0.1*10 7 , 0.11*10 7 , 0.12*10 7 , 0.13*10 7 , 0.14*107, 0.15*107, 0.16*107, 0.17*107, 0.18*107, 0.19*107, 0.2*107, 0.21*107, 0.22*107, 0.23*107, 0.24*10 7 , 0.25*10 7 , 0.26*10 7 , 0.27*107, 0.28*10 7 , 0.29*10 7 or 0.3*10 7 .
  • the invention relates to a T cell population comprising therapeutic CD4+ and/or CD8+ CAR-T cells, wherein said T cell population comprises at least 2.05*10 7 CD39- CD27- CAR T-cells, suitable for administration to a single patient, preferably at least 2.10*10 7 CD39-CD27- CAR T cells, more preferably at least 2.15*10 7 CD39-CD27- CAR T cells.
  • the total cells for administration to a patient are present in a single dosage unit, administration unit or preparation.
  • each of the above-mentioned cell numbers may vary with respect to the actual cell number in a T cell population, for example, variations in these values of ⁇ 0.01 to 0.3*10 7 is contemplated, such as ⁇ 0.01*10 7 , 0.02*10 7 , 0.03*10 7 , 0.04*10 7 , 0.05*10 7 , 0.06*10 7 , 0.07*10 7 , 0.08*10 7 , 0.09*10 7 , 0.1*10 7 , 0.11*10 7 , 0.12*10 7 , 0.13*10 7 , 0.14*10 7 , 0.15*10 7 , 0.16*10 7 , 0.17*10 7 , 0.18*10 7 , 0.19*10 7, 0.2*10 7 , 0.21*107, 0.22*10 7 , 0.23*107, 0.24*10 7 , 0.25*10 7 , 0.26*10 7 , 0.27*107, 0.28*10 7 , 0.29*10 7 or 0.3*
  • a person skilled in the art is able to convert the above-mentioned units and reference values for the number of T cells, for example on the basis of body weight or body surface area of a patient intended to receive treatment.
  • a single dosage unit, single administration unit or preparation comprises all cells for a single administration to a patient.
  • the absolute number of CD39-CD27- CAR T cells in a T cell population can be determined.
  • the above disclosed values for the preferred minimal number of cells associated with the therapeutic efficacy of the T cell product represent possible embodiments of the invention.
  • a person skilled in the art is able to determine further values and thresholds for therapeutic T cell products, such as “out-of-specification” CAR T cell products, dependent on the respective quality criteria of the product and the disclosures of the present invention by using the method of the present invention.
  • the number of CAR+CD39-CD27- T cells per kg bodyweight, per m 2 body surface or per patient
  • responders R
  • non-responders NR
  • T cell populations with such absolute numbers of therapeutically effective T cells are an aspect of the invention.
  • Beneficial quantities of CAR+CD39-CD27- T cells may be derived from the examples, for example the data presented in tables 18 and 19 and Figure 10.
  • Based on the absolute cell numbers e.g., per kg, m2 body surface or per patient
  • advantageously also “out-of-specification” CAR T cells products, which do not meet the quality criteria e.g., have a total number of CAR T cells below a threshold within the cell product can be assessed for their therapeutic efficacy.
  • thresholds is advantageously possible to determine whether these “out-of-specification products” comprise a sufficient absolute number of therapeutically effective CAR T and are thus therapeutically effective despite not meeting the quality criteria.
  • the invention relates to a T cell population as described herein for use as a medicament in the treatment of a cancer, such as a solid, lymphatic, or hematologic cancer, preferably a lymphatic or hematologic cancer, such as acute lymphoblastic leukemia (ALL).
  • a cancer such as a solid, lymphatic, or hematologic cancer, preferably a lymphatic or hematologic cancer, such as acute lymphoblastic leukemia (ALL).
  • ALL acute lymphoblastic leukemia
  • the invention relates to a kit for carrying out a method of the invention, comprising: - detection reagents for determining an expression level of CD39, and optionally additionally for CD27, CD45RA and/or HLADR, for one or more T cells, and - reference data, or means to obtain reference data, for assessing the therapeutic efficacy of a T cell, wherein the reference data comprises reference levels for the expression level of CD39, and optionally additionally for CD27, CD45RA and/or HLADR, that indicate therapeutic efficacy, - preferably wherein said reference data is stored on a computer readable medium and/or employed in the form of a computer executable code, such as an algorithm, configured for comparing the determined expression levels of CD39, and optionally additionally for CD27, CD45RA and/or HLADR, with the reference levels.
  • the invention relates to a kit for carrying out a method of the invention, comprising: - detection reagents for determining an expression level of CD27, and optionally additionally for CD39, CD45RA and/or HLADR, for one or more T cells, and - reference data, or means to obtain reference data, for assessing the therapeutic efficacy of a T cell, wherein the reference data comprises reference levels for the expression level of CD27, and optionally additionally for CD39, CD45RA and/or HLADR, that indicate therapeutic efficacy, - preferably wherein said reference data is stored on a computer readable medium and/or employed in the form of a computer executable code, such as an algorithm, configured for comparing the determined expression levels of CD27, and optionally additionally for CD39, CD45RA and/or HLADR, with the reference levels.
  • the invention relates to a kit for carrying out a method of the invention, comprising: - detection reagents for determining an expression level of CD39 and CD27, and optionally additionally for CD45RA and/or HLADR, for one or more T cells, and - reference data, or means to obtain reference data, for assessing the therapeutic efficacy of a T cell, wherein the reference data comprises reference levels for the expression level of CD39 and CD27, and optionally additionally for CD45RA and/or HLADR, that indicate therapeutic efficacy, - preferably wherein said reference data is stored on a computer readable medium and/or employed in the form of a computer executable code, such as an algorithm, configured for comparing the determined expression levels of CD39 and CD27, and optionally additionally for CD45RA and/or HLADR, with the reference levels.
  • features used to describe a method for assessing therapeutic efficacy of a T cell may be used to describe a method for prognosis of responsiveness of a subject to a treatment with a therapeutic T cell population, a method for enhancing therapeutic efficacy of a T cell population, or for producing a therapeutically effective T cell population, or vice versa.
  • Any feature describing a T cell population for example those obtained by a method or a kit of the invention, may be used to define a method of the invention, and vice versa.
  • features used to describe the methods of the invention may be used to describe the cells or kit.
  • T cell also termed "T lymphocyte” is an immune cell belonging to the group of lymphocytes.
  • a T cell can be a thymocyte, immature T lymphocyte, mature T lymphocyte, resting T lymphocyte, cytokine-induced killer cell (CIK cell) or activated T lymphocyte.
  • T cells originate from the bone marrow and migrate via the blood stream to the thymus, where they generate T cell receptors (TCR) and undergo a positive and negative selection in which the cells that show high affinity to endogenous proteins are degraded.
  • T cells may be a T helper (Th; CD4+ T cell) cell, for example a T helper (Th) cell, such as a TH1, TH2, TH3, TH17, TH9 or TFH cell.
  • Th T helper
  • the T cell can be a cytotoxic T cell (CTL; CD8+ T cell), CD4+CD8+ T cell, CD4 CD8 T cell, or a regulatory T cell (Treg) or any other subset of T cells such as a cytokine-induced killer (CIK) cell which is typically a CD3- and CD56-positive, non-major histocompatibility complex (MHC)- restricted, natural killer (NK)-like T lymphocyte.
  • CIK cytokine-induced killer
  • MHC non-major histocompatibility complex
  • NK natural killer
  • the T cell can be a naive, effector, memory, effector storage, central storage, memory stem T cell.
  • the T cell can be an umbilical cord blood cell.
  • the T cell can be a peripheral lymphocyte.
  • a T-cell can be derived and expanded from peripheral mononuclear blood cells (PBMCs).
  • the T-cell may be autologous with respect to an individual to whom it is to be administered.
  • the T-cell may be allogeneic with respect to an individual to whom it is to be administered.
  • therapeutic efficacy refers to the extent to which a drug or other therapeutic intervention, such as the treatment with a therapeutic T cell population, is capable of modifying the course of a disease, e.g. to cause remission of a disease.
  • remission or “tumor regression” refers to a stop of tumor growth and/or expansion of tumor cells, a reduction of tumors size and/or amount tumor cells or elimination of cancer cells from the body of a subject.
  • complete remission refers to elimination of cancer cells from the body of a subject, meaning that no cancer cells and/or markers therefore are detectable e.g., by physical exam, detection of markers in a blood sample and/or imaging.
  • partial remission refers to a decrease of tumor size and/or amount of tumor cells or a stop of the growth of the tumor and/or expansion of tumor cells.
  • remission rate refers to the percentage of a group of patients with a comparable disease in showing remission after a specific treatment, e.g., with a therapeutic T cell population.
  • the invention therefore represents a prognosis, or advanced determination or assessment, of potential efficacy of a T cell population, prior to administration to a patient.
  • responsiveness or “responsiveness to a treatment with a therapeutic T cell population” refers to the patient’s response to treatment, in particular regarding a therapeutic effect of the T cell population being achieved in the subject, for example by assessing or prognosing remission of a disease (e.g., a cancerous disease) after treatment with a therapeutic T cell population.
  • a disease e.g., a cancerous disease
  • non responder refers to a subject showing no remission after treatment with a therapeutic T cell population such as a CAR-T cell population.
  • non responder refers to a subject showing only partial remission after treatment with a therapeutic T cell population. In embodiments the term “non responder” refers to a subject showing minimal residual disease after treatment with a therapeutic T cell population. In embodiments the term “responder” refers to a subject showing remission after treatment with a therapeutic T cell population such as a CAR-T cell population. In embodiments the term “responder” refers to a subject showing full remission after treatment with a therapeutic T cell population such as a CAR-T cell population.
  • surface marker refers to molecules used to characterize a cell type, and preferably refer to a protein presented (expressed) on the surface of a cell, or in some cases to other cell surface molecules, such as carbohydrates attached to a cell membrane. Surface markers are often specific for certain cell types. The most common cell surface markers are cluster of differentiation (CD) molecules. CD molecules are mostly membrane-bound glycoproteins, some of which are expressed in a cell-specific manner, e.g., CD3, CD4, CD8 and CD25 are commonly used to identify T cells. CD molecules can have a wide variety of functions including without limitation receptor or signaling functions, enzymatic activity and intercellular communication.
  • expression of a surface marker refers to the process wherein a gene is transcribed into RNA and/or translated into protein, e.g., a surface marker.
  • expression or “expression level” relates to the presence or absence of a surface marker on the surface of a cell.
  • a cell showing expression (+) also termed “positive expression” or “positive expression level” has a detectable amount of the respective surface marker on its surface and a cell showing no expression (-) also termed “negative expression” or “negative expression level” has no or only negligible amounts of the surface marker on its surface.
  • the term CD39- refers to cells having no or only negligible amounts of CD39 on their surface
  • the term CD39-CD27- refers to cells having no or only negligible amounts of CD39 and CD27 on their surface
  • CD39- CD27- HLADR+ refers to cells having no or only negligible amounts of CD39 and CD27 and a detectable amount of HLADR on their surface.
  • a negative expression level of CD39 on the surface of a T cell is indicative of therapeutic efficacy of the T cell.
  • a negative expression level of CD27 on the surface of a T cell is indicative of therapeutic efficacy of the T cell.
  • a negative expression level of CD39 and CD27 on the surface of a T cell is indicative of therapeutic efficacy of the T cell.
  • a negative expression level of CD39 and CD45RA on the surface of a T cell is indicative of therapeutic efficacy of the T cell.
  • a negative expression level of CD39, CD27 and CD45 on the surface of a T cell is indicative of therapeutic efficacy of the T cell.
  • a negative expression level of CD39 and CD27 and a positive expression level of HLADR on the surface of a T cell is indicative of therapeutic efficacy of the T cell.
  • the expression level of surface markers such as CD molecules on the surface of a cell can be determined by methods known to a person skilled in the art including, without limitation, flow cytometry, spectral flow cytometry, mass cytometry, microscopy methods such as immunofluorescence and immunohistochemistry, immunoassays such as ELISA, mass spectrometry and next generation RNA sequencing.
  • a person skilled in the art is capable of selecting a suitable method for the determination of the expression level of surface markers.
  • the term “reference level” refers to a value or number capable of comparison to a determined level, preferably derived from a reference sample.
  • the reference level is an expression level of a surface marker indicative of therapeutic efficacy of a T cell, preferably CD39, CD27, CD45RA and/or HLADR.
  • a reference sample includes any sample, standard, or level that is used for comparison purposes.
  • a reference sample preferably comprises T cells having no therapeutic efficacy, e.g., a sample taken from a subject showing no responsiveness to a therapy with a therapeutic T cell population.
  • a reference sample preferably comprises CD39-, CD39-CD27-, CD39-CD27-CD45RA-, CD39-CD45RA- and/or CD39-CD27-HLADR+ T cells.
  • CD39 also termed “ectonucleoside triphosphate diphosphohydrolase-1” or “NTPDase-1” is a cell surface marker with enzymatic activity, which has its catalytic site on the extracellular site. CD39 hydrolyzes ATP to AMP, which is degraded by dephosphorylation by the ecto-5’-nucleotidase CD73 to the immunosuppressive molecule adenosine. It is involved in control of the extracellular nucleoside triphosphate pool (NTP), suppression of inflammation and control of platelet activation. Ectonucleotidases are found on tumor cells themselves, but also on T-cells or other immune cells.
  • CD8+ T- cell populations showing high expression of CD39 represent a marker of T cell exhaustion and dysfunction, particularly tumor-infiltrating T cells (Gupta et al., 2015, Canale et al., 2018). Dysfunctional status is associated with suppression of (CAR) T cell activation and effector functions.
  • a C39- or CD39 negative cell is a cell lacking CD39 on its surface, or expressing only negligible levels of CD39, on its surface.
  • CD27 is a cell surface marker and a member of the tumor necrosis factor receptor superfamily. CD27 is expressed on both na ⁇ ve and activated effector T cells as well as NK cells and activated B cells.
  • CD27 is required for generation and long-term maintenance of T cell immunity. It binds to ligand CD70, leading to differentiation and clonal expansion of T cells, improved survival and memory of cytotoxic T cells and increased production of cytokines. CD27 further plays a key role in regulating B-cell activation and immunoglobulin synthesis.
  • a C27- or CD27 negative cell is a cell lacking CD27 on its surface, or expressing only negligible levels of CD27, on its surface.
  • CD45 also termed “Protein tyrosine phosphatase, receptor type, C” or “PTPRC” is a cell surface marker and a protein tyrosine phosphatase that regulates a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation and is an essential regulator of T- and B-cell antigen receptor signaling.
  • CD45 is a transmembrane protein present in various isoforms and on all differentiated hematopoietic cells (except erythrocytes and plasma cells).
  • the gene encoding for the CD45 protein family comprises 34 exons, whereby in particular exons 4, 5 and 6 are alternatively spliced, generating different protein products also termed “isoforms of CD45”, which can be further modified in their extracellular domain, e.g., by glycosylation.
  • isoforms include without limitation CD45RA, CD45RO and CD45R, which are expressed on different cell types.
  • CD45RA is typically expressed on na ⁇ ve T lymphocytes, whereas activated and memory T cells express CD45RO.
  • a C45RA- or CD45RA negative cell is a cell lacking CD45RA on its surface, or expressing only negligible levels of CD45RA, on its surface.
  • HLA-DR Human Leukocyte Antigen - DR isotype
  • HLA-DR Human Leukocyte Antigen - DR isotype
  • MHC major histocompatibility complex
  • HLAs also termed MHC molecules, are glycoproteins anchored in the cell membrane and are classified as immunoglobulins. HLAs are classified into class I MHC molecules and class II MHC molecules. Class I includes HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G and 35 subgroups thereof. Class II includes HLA-DP, HLA-DQ, HLA-DR and subgroups thereof. Class I MHC molecules are located as transmembrane glycoproteins on the surface of all nucleated cells.
  • Class II MHC molecules including HLADR are typically found on antigen presenting cells (APCs), such as B cells, phagocytosing cells (e.g., macrophages), and dendritic cells, but also on other cells such as activated T cells.
  • APCs antigen presenting cells
  • B cells such as B cells, phagocytosing cells (e.g., macrophages), and dendritic cells
  • both classes of HLA molecules serve to bind peptides and present them on the cell surface to the cells of the immune system.
  • APCs and activated T cells HLA-DR forms a complex with potentially foreign peptide antigens, which are generally between 9 and 30 amino acids long, thereby constituting a ligand for the T cell receptor (TCR) of T cells.
  • TCR T cell receptor
  • a HLADR+ or HLADR positive cell is a cell expressing HLADR its surface.
  • Immunotherapy in the context of the present invention is to be understood to comprise any therapeutic agent employing the immune system for treatment of an unwanted (pathogenic) condition, such as an immune reaction prior to and/or after allogenic transplantation, an autoimmune disease or a cancerous disease.
  • an unwanted (pathogenic) condition such as an immune reaction prior to and/or after allogenic transplantation, an autoimmune disease or a cancerous disease.
  • cancer immunotherapy this approach takes advantage of the fact that cancer cells have subtly different molecules on their surface, which can be recognized by the immune system.
  • Immunotherapy encompasses, without limitation, cellular and antibody therapy.
  • Cellular therapies according to the present invention involve the administration of T cells or therapeutic T cell populations.
  • terapéutica T cell population refers to a population of T cells which are produced from a T cell by genetically modifying the T cell, preferably to express a CAR or other targeting moiety, such as any other naturally occurring or synthetic construct providing antigen-specific targeting, including chimeric antigens (CARs) or T cell receptors (TCRs), and expanding said genetically modified T cells.
  • CARs chimeric antigens
  • TCRs T cell receptors
  • Chimeric antigen receptors are molecules that combine antibody-based specificity for a desired antigen (e.g., CD19) with a T cell receptor-activating intracellular domain to generate a chimeric protein that exhibits a specific (e.g., against cells expressing CD19) cellular immune activity.
  • a chimeric antigen receptor comprises an intracellular domain, a transmembrane domain, and an extracellular antigen-binding domain, comprising an antibody or antibody fragment that binds a target antigen such as a cancer antigen.
  • CARs are typically described as comprising an extracellular ectodomain (antigen-binding domain) derived from an antibody or fragment thereof and an endodomain, comprising signaling modules originally derived from T cell signaling proteins.
  • the ectodomain preferably comprises variable regions from the heavy and light chains of an immunoglobulin configured as a single-chain variable fragment (scFv).
  • the scFv is preferably attached to a hinge region that provides flexibility and transduces signals through an anchoring transmembrane moiety to an intracellular signaling domain.
  • the transmembrane domains originate preferably from either CD8a or CD28.
  • the signaling domain consists of the zeta chain of the TCR complex.
  • generation refers to the structure of the intracellular signaling domains.
  • Second generation CARs are equipped with a single costimulatory domain originated from CD28 or 4-1 BB.
  • Third generation CARs already include two costimulatory domains, e.g. CD28, 4-1 BB, ICOS or OX40.
  • Fourth generation CARs additionally deliver immune stimulatory proteins and/or checkpoint regulatory proteins.
  • the fifth CAR generation incorporates control elements for the regulation of CAR expression, which allows to induce and/or completely switch off the CAR expression or CAR expressing cells, e.g., by suicide genes.
  • the present invention preferably relates to a second, third, fourth or fifth generation CAR.
  • CARs comprise an intracellular domain or an intracellular signaling domain, and an transmembrane domain, and an extracellular domain (also referred to as a binding domain or antigen-binding domain) that binds to a preferred target protein.
  • the ligand or extracellular ligand binding domain is selected so that the cell expressing the CAR is targeted to a cancer cell or tumor.
  • Any cancer antigen can be a tumor antigen and any tumor antigen can be a caner antigen.
  • the extracellular antigen-binding domain of a CAR is usually derived from a monoclonal antibody (mAb) or from receptors or their ligands.
  • the CAR comprises an extracellular antigen-binding domain, comprising for example an antibody or antibody fragment that binds CD19.
  • Antibodies or antibody fragments of the invention therefore include, but are not limited to polyclonal, monoclonal, bispecific, human, humanized or chimeric antibodies, single chain fragments (scFv), single variable fragments (ssFv), single domain antibodies (such as VHH fragments from nanobodies), Fab fragments, F(ab')2 fragments, fragments produced by a Fab expression library, anti-idiotypic antibodies and epitope-binding fragments or combinations thereof of any of the above, provided that they retain similar binding properties of the CAR described herein, preferably comprising the corresponding CDRs, or VH and VL regions as described herein.
  • mini-antibodies and multivalent antibodies such as diabodies, triabodies, tetravalent antibodies and peptabodies can be used in a method of the invention.
  • the immunoglobulin molecules of the invention can be of any class (i.e., IgG, IgE, IgM, IgD and IgA) or subclass of immunoglobulin molecules.
  • the term antibody as used herein, also includes antibodies and antibody fragments, either produced by the modification of whole antibodies or synthesized de novo using recombinant DNA methodologies.
  • an "antibody” generally refers to a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes or fragments of immunoglobulin genes.
  • the term “antibody” may also be considered to be referred to.
  • the recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes.
  • Light chains are classified as either kappa or lambda.
  • Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD, and IgE, respectively.
  • the basic immunoglobulin (antibody) structural unit is known to comprise a tetramer or dimer.
  • Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light” (L) (about 25 kD) and one "heavy” (H) chain (about 50-70 kD).
  • the N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids, primarily responsible for antigen recognition.
  • the terms "variable light chain” and “variable heavy chain” refer to these variable regions of the light and heavy chains, respectively.
  • the antibody or the immunological portion of the antibody can be chemically conjugated to, or expressed as, a fusion protein with other proteins.
  • Single-chain Fv or “scFv” antibody fragments comprise the VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain and in either orientation (e.g., VL-VH or VH-VL).
  • the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding.
  • a CAR contemplated herein comprises an antigen-specific binding domain that is a scFv and may be a murine, human or humanized scFv.
  • Single chain antibodies may be cloned from the V region genes of a hybridoma specific for a desired target.
  • the CARs of the invention are intended to bind against mammalian, in particular human, protein targets.
  • the use of protein names may correspond to either mouse or human versions of a protein.
  • Affinities of binding domain polypeptides and CAR proteins can be readily determined using conventional techniques, e.g., by competitive ELISA (enzyme-linked immunosorbent assay), or by binding association, or displacement assays using labeled ligands, or using a surface-plasmon resonance device such as the Biacore.
  • Specific binding is to be understood as via one skilled in the art, whereby the skilled person is clearly aware of various experimental procedures that can be used to test binding and binding specificity. Methods for determining equilibrium association or equilibrium dissociation constants are known in the art. Some cross-reaction or background binding may be inevitable in many protein- protein interactions; this is not to detract from the "specificity" of the binding between CAR and epitope.
  • specific binding describes binding of an e.g., anti-CD19 antibody or antigen binding fragment thereof (or a CAR comprising the same) to CD19 at greater binding affinity than background binding.
  • the term “directed against” is also applicable when considering the term “specificity” in understanding the interaction between antibody and epitope.
  • an "antigen (Ag)” refers to a compound, composition, or substance that can bind to an antibody.
  • An antigen stimulating an “immune response” or “immune reaction” such as the production antibodies or a T cell response in an animal or human subject is also referred to as “immunogen”.
  • Antigens and/or immunogens usually comprise protein, lipid and/or carbohydrate structures.
  • An antigen usually has several antigenic substructures, which are the region of an antigen to which a binding agent binds, and which are referred to as “determinants” or “epitopes”.
  • the target antigen is a cancer antigen.
  • Any suitable antigen can be selected depending on the type of cancer.
  • a “cancer antigen”, “Cancer-associated antigen”, “tumor antigen” or “tumor-associated antigen” is expressed interchangeably on the surface of cancer cells, either completely or as a fragment (e.g., MHC / peptide).
  • Tumor antigens are either specifically expressed on tumor cells and not found on non-pathogenic cells or abnormally expressed, e.g., at least twice above the level found in non-pathogenic cells.
  • a tumor antigen is a cell surface molecule that is inadequately synthesized in cancer cells, e.g., a molecule that contains deletions, additions or mutations compared to a molecule expressed in normal cells. Antigens, specifically found on tumor cells, may appear foreign to the immune system and their presence may cause the immune cells to attack the transformed tumor cells. Tumor antigen refers to an antigen that is commonly found in a specific hyperproliferative disease.
  • the antigen of hyperproliferative disease of the present invention is a primary or metastatic melanoma, thymoma, lymphoma, sarcoma, lung cancer, liver cancer, non-Hodgkin's lymphoma, Hodgkin's lymphoma, leukemia, uterine cancer, cervical cancer, bladder cancer, derived from cancers such as kidney and breast cancer, prostate cancer, ovarian cancer, adenocarcinoma such as pancreatic cancer and the like.
  • Cancer associated antigen include without limitation CD19, BCMA; APRIL/TNFSF13, Mic A/B, T cell associated antigens: CD3, CD5, CD7, Folate receptor alpha (FRa), ERBB2 (HER2/neu), EphA2, IL-13Ra2, epidermal growth factor receptor (EGFR), Mesothelin, TSHR, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, prostate specific membrane antigen (PSMA), ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, interleukin-11 receptor a (IL-11Ra), PSCA, PRSS21, VEGFR2, LewisY, CD24, platelet-derived growth factor receptor-beta (PDGFR-beta), SSEA-4, CD20, MUC1, NCAM, Prostase, PAP, ELF2M, Ephrin
  • Cancer is a disease characterized by the uncontrolled growth of abnormal cells. Cancer refers to any type of cancerous growth or carcinogenic process, metastatic tissue or malignant transformed cells, tissues or organs, regardless of histopathological type or invasive stage. Cancer cells can spread locally or to other parts of the body via the bloodstream and lymphatic system. Cancer cells spreading to other parts to the body are termed “metastatic cells” or “metastatic tumor cells”.
  • tumor cells and cancer, used herein, are utilized interchangeably, e.g., both terms include solid and liquid, e.g. general or circulating tumors, premalignant and malignant cancers and tumors.
  • liquid cancers include, but not limited to, acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), acute myeloid Leukemia (acute myelogenous leukemia (AML), chronic bone marrow cancer, chronic myelogenous leukemia (CML), Hodgkin lymphoma, non-Hodgkin lymphoma, and myeloma.
  • ALL acute lymphocytic leukemia
  • CLL chronic lymphocytic leukemia
  • AML acute myeloid Leukemia
  • CML chronic bone marrow cancer
  • Hodgkin lymphoma e.g. colon
  • urogenital organs e.g. kidney, urothelial cells
  • prostate and throat malignant organ systems including tumors such as sarcomas, adenocarcinomas and cancer.
  • breast cancer examples include ductal carcinoma in situ (DCIS), lobular carcinoma in situ (LCIS), invasive ductal carcinoma (IDC), invasive ductal carcinoma including tubular, medullary, mucinous, papillary, and cribriform carcinomas, invasive lobular carcinoma (ILC), inflammatory breast cancer, male breast cancer, Paget’s Disease of the nipple, phyllodes tumors of the breast, recurrent and/or metastatic breast cancer.
  • Adenocarcinoma includes most malignant tumors such as colon cancer, rectal cancer, renal cell cancer, liver cancer, non-small cell lung cancer, small intestine cancer and esophageal cancer.
  • the cancer is a melanoma, e.g. an advanced stage melanoma.
  • Metastatic lesions of the cancer can also be treated or prevented with the methods and compositions of the invention.
  • Examples of other types of cancer that can be treated are bone cancer, pancreatic cancer, skin cancer, head and neck cancer, skin or intraocular melanoma, uterine cancer, ovarian cancer, rectal cancer, anal cancer, stomach cancer, testicular cancer, faropius duct cancer, Endometrial cancer, cervical cancer, vaginal cancer, vulvar cancer, Hodgkin's disease, non-Hodgkin's lymphoma, esophageal cancer, small intestine cancer, endocrine cancer, thyroid cancer, parathyroid cancer, adrenal cancer, soft tissue sarcoma, urethral cancer, penile cancer, acute myeloid leukemia, chronic myelocytic leukemia, acute lymphoblastic leukemia, chronic or acute leukemia including chronic lymphatic leukemia, solid
  • T cells genetically modified to express a CAR for use as a medicament in the treatment of a cancer.
  • the invention contemplates T cells genetically modified to express a CAR, for use as a medicament in the treatment of a solid, lymphatic, or hematologic cancer.
  • the term "genetically engineered” or “genetically modified” refers to the addition of genetic material, preferably in the form of DNA or RNA, into the total genetic material in a cell.
  • genetic modifications can be carried out selectively, or not, at a specific location in the genome of a cell.
  • genetically modified cells refers to the introduction-permanently or transiently- of extra genetic material in the form of DNA or RNA into the total genetic material in a cell that restores, corrects, or modifies expression of a gene, or for the purpose of expressing a therapeutic polypeptide, e.g., a CAR.
  • the CARs contemplated herein are introduced and expressed in T cells so as to redirect their specificity to a target antigen of interest, e.g., a CD19 polypeptide.
  • the invention provides methods for producing a therapeutic T cell population expressing a CAR.
  • the method comprises transfecting or transducing one or more T cells isolated from an individual such that the T cell expresses a CAR.
  • the one or more T cells are isolated from an individual and genetically modified without further manipulation in vitro. Such cells can then be directly re-administered into the individual.
  • the one or more T cells are first activated and stimulated to proliferate in vitro prior to being genetically modified to express a CAR.
  • the T cells may be cultured before and/or after being genetically modified (i.e., transduced or transfected to express a CAR).
  • the T cells are expanded after being genetically modified (i.e., transduced or transfected to express a CAR).
  • Manufacturing of CAR T cell products is usually conducted over approx.8 to 12 days in an approved current Good Manufacturing Practice (cGMP) clean room facility in a closed or functionally closed system to reduce the risk of product contamination (Roddie et al.2019; Schubert et al.2019; Castellá et al.2020).
  • Starting material for CAR-T is usually derived from non-mobilized leukapheresis.
  • Leukapheresis material may be cryopreserved prior to manufacture.
  • CAR T manufacture from the leukapheresis material usually includes the following steps: 1) Step 1 (Day 1): Optionally T cell enrichment post-leukapheresis. This step may for example be performed by Ficoll density gradient centrifugation, elutriation or immune magnetic bead separation. 2) Step 2 (Days 1 and 2): T cell activation using synthetic antigen presenting technologies (CD3 +/ ⁇ CD28).
  • Step 3 (From Day 1 onwards): T cell stimulation. This step may for example be performed by addition of IL-2, IL-7, and IL-15 in the culture medium (as per protocol) (Hoffmann et al.2018; Gong et al.2019). 4) Step 4 (Days 2 and 3): Gene delivery/transduction, for example with a retroviral or lentiviral CAR vector. This step may for example be performed by optionally using, retronectin or Vectofusin® to enhance transduction.
  • Step 5 (Days 3, 4 and onwards): T cell expansion. This step may for example be performed by using T-fasks, plates or culture bags; bioreactors, e.g., G-RexTM fask (Wilson Wolf Manufacturing); Xuri WAVETM Bioreactor (GE Life Systems) and CliniMACS ProdigyTM (Miltenyi BioTec). 6) Step 6 (Day 8 onwards): T cell harvest and cryopreservation. The cryopreservation methodology often mirrors processes defined for haematopoietic cells. Methods include without limitation passive freezing ( ⁇ 80 °C freezer) and controlled-rate freezing. 7) Step 7 (Day 8 onwards): CAR-T cell quality assurance control and release testing.
  • T cell products such as CAR-T cell products have to comply with quality control/end-product specifications stipulated in the certificate of analysis.
  • Quality parameters and criteria may vary according to the regulatory documents of said product. These criteria may without limitation for example include the following criteria regarding immunophenotype, functionality and sterility which may be assessed by the exemplary method outlined below: Parameter Method Acceptance criteria Appearance Visual inspection Cloudy liquid solution CAR+ cells (%) Flow Cytometry >20% CD3+ cells (%) Flow cytometry >70% Cell viability (%) Neubauer cell counting with >70% trypan blue exclusion Sterility Microbial growth E.
  • Ph.2.6.1 Sterile from bacteria/fungi Mycoplasma PCR, Serology Absent Endotoxin Chromogenic assay ⁇ 0.5 EU/mL CAR/CD45RA/CCR7 Flow Cytometry A high proportion of immature For detection of TE/ T cells is desirable for a long- TEM/TEMRA/TCM/TN lasting CAR-T cell effect in subpopulations the patient Cytotoxic potency Cr-51 release assays in >40% killing at an tumour CAR-T cell co-culture, effector/target ratio of 10:1 (or assessed by fow cytometry higher ratio) in a 4-h assay; Integrationitious viruses PCR Absent Number of transgene Real-time PCR (Kunz et al.
  • OOS Out of specification
  • T cell products such as CAR-T cell products
  • OOS In of specification
  • T cell products preferably for T cell products such as CAR-T cell products, refers to any discrepancy or non-conformance of a test result or quality inspection from the established acceptance criteria or qualification criteria or specifications set forth by the regulatory documents, official standards or by the manufacturer. These criteria or specifications typically include aspects such as cell numbers, numbers of therapeutically active cells, purity, identity, potency, safety and other relevant quality attributes of the product, such as the immunophenotypic, functional and sterility criteria outlined above.
  • Out of specification CAR T cell product refers to preparations of T cells, such as T cells genetically modified with a CAR (CAR T cells) that do not meet or do not conform to pre-defined acceptable limits or performance standards during quality control and testing, such as the immunophenotypic, functional and sterility criteria outlined above.
  • This non-conformity may without limitation be due to deviations in total cell counts, biological activities, physico-chemical properties, cell counts of immunogenic T lymphocytes, contamination or other critical quality attributes that are essential for the safety and efficacy of the product.
  • Out-of-specification (OOS) products cannot be released in the usual way, and its clinical use is at the discretion of the treating physician in concert with the regulatory authorities, informed through an OOS report.
  • OOS Out-of-specification
  • SF serum-free
  • XF xenogeneic-free
  • ACF Animal component free
  • CD chemically defined
  • GMP good manufacturing practices
  • Conventional bioreactor platform technologies developed for large scale mammalian cell expansion are effective in the present invention, and are capable of delivering nutrients and oxygen to an expanding cell population. These systems often utilize mechanisms to enhance oxygen delivery, such as stirring, rocking, or perfusion. For most cell therapies, cell expansion is required to reach the clinical dose required. There are several platforms available that enable expansion of the cells. For immunotherapies, the most commonly used systems are static gas permeable culture bags, G35 Rex bioreactors, wave-mixed bioreactors, and the Miltenyi Prodigy system.
  • GPB gas permeable bags
  • VueLife Saint Gobain
  • Charter Medical and OriGen gas permeable bags
  • GPB are designed to enable a high rate of gas transfer to the cells while maintaining low water permeability enabling culturing of cells in a closed system, unlikely conventional tissue culture flasks, and several groups have demonstrated growth of T cells in these bags.
  • G-Rex bioreactors Wang Wolf
  • the G-Rex bioreactors allow expansion of cells from a low seeding density and don't necessarily require a media exchange as the design has a large enough reservoir of media to enable cell culture for 8–10 days. As they mimic the format and handling of tissue culture flasks, they can represent a simple and cost- effective way to initially transfer a process from a preclinical to early clinical setting.
  • closed-system bioreactors are employed.
  • the G-Rex cell culture platform is based on a gas-permeable membrane technology that provides advantages over other systems. Closed-system bioreactors, such as gas-permeable membrane-based bioreactors, provide a physiological environment and avoid the risk and cost associated with more complex systems.
  • Wave-mixed bioreactors use the rocking wave motion to enable efficient mixing and oxygen transfer within the reactor in a low shear side-to-side motion and have become a common platform for commercial scale-up of T-cell immunotherapies.
  • wave-mixed bioreactors There are several wave-mixed bioreactors on the market including the SmartRocker (Finesse), Allegro (Pall), Biostat RM (Sartorius), and Xuri Cell Expansion System (GE Healthcare), among others.
  • Wave-mixed bioreactors are functionally closed-system bioreactors, and reduce the amount of manual labor in the cell expansion phase of the culture due to their built-in automation features.
  • the CliniMACS Prodigy (Miltenyi Biotec) is an all-in-one solution that not only enables immune cell expansion, but several other steps within the immunotherapy workflow including cell selection through magnetic separation, cell washing, and final product formulation in a closed system.
  • the CliniMACS Prodigy supports a culture volume of up to 400 mL (300 mL working volume).
  • Stirred tank reactors (STRs) are commonly used in monoclonal antibody production and have a scale ranging from hundreds of milliliters (e.g., spinner flasks) to thousands of liters.
  • T cells of the invention can be autologous/autogeneic ("self”) or non-autologous ("non- self,” e.g., allogeneic, syngeneic or xenogeneic).
  • autologous refers to cells from the same subject, and represent a preferred embodiment of the invention.
  • Allogeneic refers to cells of the same species that differ genetically to the cell in comparison.
  • Syngeneic refers to cells of a different subject that are genetically identical to the cell in comparison.
  • Xenogeneic refers to cells of a different species to the cell in comparison.
  • the cells of the invention are autologous or allogeneic.
  • the T cells of the invention are autologous or allogeneic.
  • the present invention further provides methods for enhancing the therapeutic efficacy of T cells and for selecting T cells to produce a therapeutic T cell population.
  • the method comprises determining the therapeutic efficacy of the T cells and selecting T cells for a therapeutic product based on the expression levels of CD39, CD27, CD45RA and/or HLADR.
  • Methods for selecting T cells based on their surface marker expression include positive or negative selection techniques such as cell sorting and/or selection via negative magnetic immunoadherence (e.g., magnetic-Activated Cell Sorting (MACS) using antibodies conjugated to magnetic beads) or flow cytometry (e.g., Fluorescence Activated Cell Sorting (FACS)) that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected.
  • MACS systems are commercially available from Miltenyi Biotec and ThermoFisher, which have developed closed system magnetic cell selection technologies (CliniMACS Prodigy and CTS Dynamag, respectively) along with corresponding reagents that enable isolation of specific cell populations.
  • the invention further comprises an enriching step of the selected T cells prior and/or during expansion of said T cells.
  • culture conditions are adapted to promote expansion of said selected populations and/or hinder expansion of other T cell populations, e.g., by addition of one or more enhancers or inhibitors of certain surface markers such as an inhibitor of CD39 and/or CD27.
  • Inhibitors of CD39 are well known and include without limitation POM 1 (CAS 12141-67-2), ARL 67156 trisodium salt (CAS 160928-38-1), PSB 06126 (CAS 1052089-16-3), PSB 069 (CAS 78510-31-3) and inhibitors disclosed in Yunshuo et al.
  • the source of cells is obtained from a subject.
  • T cells can be obtained from a number of sources including, but not limited to, peripheral blood mononuclear cells, bone marrow, lymph nodes tissue, cord blood, thymus issue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
  • T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled person, such as sedimentation, e.g., FICOLLTM separation, antibody-conjugated bead- based methods such as MACSTM separation (Miltenyi).
  • cells from the circulating blood of an individual are obtained by apheresis, preferably leukapheresis.
  • the apheresis product typically contains lymphocytes, including T cells, monocytes, granulocyte, B cells, other nucleated white blood cells, red blood cells, and platelets.
  • the cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing.
  • the cells can be washed with phosphate buffered saline (PBS) or with another suitable solution that lacks calcium, magnesium, and most, if not all other, divalent cations.
  • PBS phosphate buffered saline
  • a washing step may be accomplished by methods known to those in the art, such as by using a semiautomated flow through centrifuge.
  • a semiautomated flow through centrifuge For example, the Cobe 2991 cell processor, the Baxter CytoMate, or the like.
  • the cells may be resuspended in a variety of biocompatible buffers or other saline solution with or without buffer.
  • the undesirable components of the leukapheresis sample may be removed in the cell directly resuspended culture media.
  • T cells are isolated by leukapheresis, comprising additionally lysing of the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLLTM gradient.
  • a specific subpopulation of T cells can be further isolated by positive or negative selection techniques.
  • One method for use herein is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected.
  • T lymphocytes can be further isolated and, both cytotoxic and helper T lymphocytes, can be sorted into naive, memory, and effector T cell subpopulations either before or after genetic modification and/or expansion.
  • the T cells can be genetically modified following isolation and optionally sorting using known methods, or the T cells can be activated, enriched and/or expanded (or differentiated in the case of progenitors such as peripheral blood mononuclear cells (PBMCs)) in vitro prior to being genetically modified.
  • T cells can be activated and expanded before or after genetic modification to express a CAR, using methods as described, for example, in U.S.
  • activation of PBMCs requires stimulation via with anti-CD3 and anti-CD28 antibodies.
  • IL-7 and IL-15 are added as growth factor for expansion of activated PBMCs.
  • the invention provides a method of storing the therapeutic T cells and therapeutic T cell populations, comprising cryopreserving the T cells or T cell populations such that the cells remain viable upon thawing.
  • a fraction of the therapeutic T cells or therapeutic T cell populations can be cryopreserved by methods known in the art to provide a permanent source of such cells for the future administration to a subject, such as for the treatment of a cancerous disease.
  • the cryopreserved T cells can be thawed, grown and expanded for more such cells.
  • a "pharmaceutical composition” refers to a composition formulated in pharmaceutically acceptable or physiologically acceptable solutions for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy.
  • compositions comprising the cells activated and expanded as described herein may be utilized in the treatment of a cancerous disease.
  • the T cells and T cell populations of the present invention may be administered either alone, or as a pharmaceutical composition in combination with carriers, diluents, excipients, and/or with other components such as cytokines, growth factors, hormones, small molecules chemotherapeutics, pro-drugs, drugs such as inhibitors of CD39, CD27 or CD45RA, antibodies, other various pharmaceutically-active agents or cell populations.
  • pharmaceutical compositions contemplated herein comprise an amount of T cells, in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients.
  • compositions there is virtually no limit to other components that may also be included in the compositions, provided that the additional agents do not adversely affect the ability of the composition to deliver the intended therapy.
  • pharmaceutically acceptable is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • pharmaceutically acceptable carrier includes without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye/colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, surfactant, or emulsifier which has been approved by the United States Food and Drug Administration and/or European Medicines Agency (EMA) as being acceptable for use in humans or domestic animals.
  • EMA European Medicines Agency
  • compositions of the present invention comprising T cells or T cell populations, may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives.
  • Compositions of the present invention are preferably formulated for parenteral administration, e.g., intravascular (intravenous or intraarterial), intraperitoneal or intramuscular administration.
  • the liquid pharmaceutical compositions may include one or more of the following: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose.
  • sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride
  • fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending
  • compositions contemplated herein comprise an effective amount of T cells, alone or in combination with one or more therapeutic agents.
  • T cell compositions may be administered alone or in combination with other known cancer treatments, such as radiation therapy, chemotherapy, transplantation, immunotherapy, hormone therapy, photodynamic therapy, etc.
  • the compositions may also be administered in combination with antibiotics.
  • Such therapeutic agents may be accepted in the art as a standard treatment for a particular disease state as described herein, such as a particular cancer.
  • Exemplary therapeutic agents contemplated include cytokines, growth factors, steroids, NSAIDs, DMARDs, anti- inflammatories, chemotherapeutics, radiotherapeutics, therapeutic antibodies, or other active and ancillary agents.
  • a chemotherapeutic agent prior to administration of the T cell composition to a subject, may be administered to the subject for lymphodepletion.
  • the chemotherapeutic agent may be administered 7, 6, 5, 4, 3, 2, and/or 1 day prior to administration of the T cell composition to the subject.
  • Lymphodepletion refers to a method to decrease the number of leucocytes and to stimulate cytokine production to support cell expansion of the therapeutic T cell population subsequently administered to the subject.
  • compositions of the present invention comprise an amount of T cells contemplated herein.
  • amount refers to "an amount effective” or “an effective amount” of a T cell, to achieve a beneficial or desired prophylactic or therapeutic result, including clinical results.
  • a “therapeutically effective amount” of a genetically modified T cell may vary according to factors such as the disease state, age, sex, and weight of the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of T cells are outweighed by the therapeutically beneficial effects.
  • terapéuticaally effective amount includes an amount that is effective to "treat" a subject (e.g., a patient).
  • a therapeutic amount is indicated, the precise amount of the compositions of the present invention to be administered can be determined by a physician with consideration of individual differences in age, weight, stage of the medical condition, and condition of the patient (subject). It can generally be stated that a pharmaceutical composition comprising the T cells or therapeutic T cell population described herein may be administered at a dosage of 10 2 to 10 10 cells/kg body weight, preferably 10 5 to 10 6 cells/kg body weight, including all integer values within those ranges.
  • a pharmaceutical composition comprising the T cells or therapeutic T cell population described herein may be administered at a dosage of 10 2 to 10 10 cells/m 2 , preferably 10 6 to 10 8 cells/m 2 , more preferably 1 ⁇ 10 6 to 20 ⁇ 10 7 cells/m 2 , including all integer values within those ranges.
  • the number of cells will depend upon the ultimate use for which the composition is intended as will the type of cells included therein.
  • the cells are generally in a volume of a liter or less, can be 500 mL or less, even 250 mL or 100 mL or less.
  • the density of the desired cells is typically greater than 10 6 cells/ml and generally is greater than 10 7 cells/ml, generally 10 8 cells/ml or greater.
  • the clinically relevant number of immune cells can be apportioned into multiple infusions that cumulatively equal or exceed 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , or 10 12 cells.
  • lower numbers of cells may be administered.
  • T cell compositions may be administered multiple times at dosages within these ranges.
  • the T cells may be allogeneic, syngeneic, xenogeneic, or autologous to the patient undergoing therapy.
  • a subject, patient or host may be an organism, a cell culture of patient cells or cell lines, an animal, or a cell culture of animal cells or cell lines.
  • a subject or patient refers preferably to a species from which a sample is taken, and/or whose biological material makes up the majority of the biological material of a sample.
  • a subject or patient can be selected from the group comprising vertebrae, animals, livestock, mammals, humans, preferably mammal or human.
  • treatment or “treating” includes any beneficial or desirable effect on the symptoms or pathology of a disease or pathological condition, and may include even minimal reductions in one or more measurable markers of the disease or condition being treated.
  • Treatment can involve optionally either the reduction or amelioration of symptoms of the disease or condition, or the delaying of the progression of the disease or condition. "Treatment” does not necessarily indicate complete eradication or cure of the disease or condition, or associated symptoms thereof.
  • a method of treating a cancerous disease in a subject in need thereof comprises administering an effective amount, e.g., therapeutically effective amount of a composition comprising the T cells contemplated herein.
  • the quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined by clinical trials.
  • compositions contemplated herein may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation.
  • compositions are administered parenterally.
  • parenteral administration and “administered parenterally” as used herein refers to modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravascular, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intratumoral, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.
  • compositions contemplated herein are administered to a subject by direct injection into a tumor, lymph node, or site of infection.
  • the invention further relates to kits, the use of the kits and methods wherein such kits are used.
  • the invention relates to kits for carrying out the herein above and below provided methods.
  • the herein provided definitions, e.g., provided in relation to the methods, also apply to the kits of the invention.
  • the kits can be part of a medical device which also contains calibrators, controls, buffer reagents and can be used in connection with a diagnostic instrument and/or software.
  • the invention relates to kits for assessing a therapeutic efficacy of a T cell and/or the prognosis, prediction, risk assessment and/or risk stratification of responsiveness of a subject having or suspected of having a cancer to a treatment with a therapeutic T cell population.
  • the “detection reagent” or the like are reagents that are suitable to determine the expression level of the herein described marker(s), e.g., of CD39, CD27, CD45RA and/or HLADR.
  • detection reagents are, for example, ligands, e.g., antibodies or fragments thereof, which specifically bind to the peptide or epitopes of the herein described marker(s).
  • Such ligands might be used e.g., in immunoassays (e.g., luminescence immunoassay (LIA), radioimmunoassay (RIA), chemiluminescence- and fluorescence- immunoassays, enzyme immunoassay (EIA), Enzyme-linked immunoassays (ELISA), luminescence-based bead arrays, magnetic beads-based arrays, protein microarray assays, rapid test formats and rare cryptate assay), flow cytometry, FACS, mass cytometry, mass spectroscopy, immunohistochemistry and microscopy.
  • immunoassays e.g., luminescence immunoassay (LIA), radioimmunoassay (RIA), chemiluminescence- and fluorescence- immunoassays, enzyme immunoassay (EIA), Enzyme-linked immunoassays (ELISA), luminescence-based bead arrays, magnetic beads-based arrays, protein microarray
  • detection reagents that are employed to determine the level of the marker(s) may also be comprised in the kit and are herein considered as detection reagents.
  • detection reagent can thus also be reagents, e.g., enzymes, chemicals and buffers, that are used to prepare the sample for the analysis.
  • Detection reagents according to the invention can also be calibration solution(s), e.g., which can be employed to determine and compare the level of the marker(s).
  • the antibodies may be monoclonal as well as polyclonal antibodies. Particularly, antibodies that are specifically binding to CD39, CD27, CD45RA or HLADR or fragments thereof are used.
  • An antibody is typically considered to be specific, if its affinity towards the molecule of interest, e.g., CD39, or the fragment thereof is at least 50-fold higher, preferably 100-fold higher, most preferably at least 1000-fold higher than towards other molecules comprised in a sample containing the molecule of interest. It is well known in the art how to develop and to select antibodies with a given specificity. In the context of the invention, monoclonal antibodies as detection reagent are preferred. The antibody or the antibody binding fragment binds specifically to the herein defined surface markers or fragments thereof. Alternatively, instead of antibodies, other capture molecules or molecular scaffolds that specifically and/or selectively recognize CD39, CD27, CD45RA or HLADR may be encompassed by the scope of the present invention.
  • capture molecules or “molecular scaffolds” comprises molecules which may be used to bind target molecules or molecules of interest, i.e., analytes (e.g., CD39 or CD27), from a sample.
  • Capture molecules must thus be shaped adequately, both spatially and in terms of surface features, such as surface charge, hydrophobicity, hydrophilicity, presence or absence of lewis donors and/or acceptors, to specifically bind the target molecules or molecules of interest.
  • the binding may, for instance, be mediated by ionic, van-der-Waals, pi-pi, sigma-pi, hydrophobic or hydrogen bond interactions or a combination of two or more of the aforementioned interactions or covalent interactions between the capture molecules or molecular scaffold and the target molecules or molecules of interest.
  • capture molecules or molecular scaffolds may for instance be selected from the group consisting of a nucleic acid molecule, a carbohydrate molecule, a PNA molecule, a protein, a peptide and a glycoprotein.
  • Capture molecules or molecular scaffolds include, for example, aptamers, DARpins (Designed Ankyrin Repeat Proteins). Affimers and the like are included.
  • reference data comprise reference expression level(s) of CD39 and optionally CD27, CD45RA and/or HLADR.
  • the levels of CD39 and optionally CD27, CD45RA and/or HLADR in the sample comprising one or more T cells can be compared to the reference levels comprised in the reference data of the kit.
  • the reference data can also include a reference sample to which the level of CD39, CD27, CD45RA and/or HLADR is compared.
  • the reference data can also include an instruction manual how to use the kits of the invention.
  • Fig.1 HD-CAR-1 study profile.
  • Fig.2 Efficacy of HD-CAR-1 treatment and patient outcome.
  • Fig.3 Expansion of HD-CAR-1 CARTs.
  • Fig.5 Additional data on the cellular composition of CART products and of corresponding PB samples.
  • Fig.6 Hematologic toxicity of HD-CAR-1 treatment.
  • Fig.7 CD39 and CD27 in CAR-T products are predictive markers for therapy response.
  • Fig.8 Comparison of the inventive approach with previous approaches employed in the prior art
  • Fig.9 CD39, CD27, CD45RA and HLADR in CAR-T products are predictive markers for therapy response.
  • Fig.10 CD39 and CD27 in CAR-T products are predictive markers for therapy response independent of the dosis level.
  • Fig.1 Fifteen patients with relapsed and/or refractory (r/r) acute lymphoblastic leukemia (ALL) after at least two prior therapy lines were screened and enrolled into HD-CAR-1. For all patients, leukapheresis and manufacturing of CARTs was feasible. Two patients did not receive the HD- CAR-1 CART product due to progressive disease (PD).
  • PD progressive disease
  • E Swimmer plot depicting the course of individual HD-CAR-1 patients.
  • PB peripheral blood
  • SCG-DP-PCR single copy gene duplex quantitative PCR
  • C Maximum CART copies (cmax) within 28 days after CART administration and clinical response at EOS (data of UPN#8 not shown due to progressive disease on day 23 after CARTs). Median (cmax) 22.350 CART/ ⁇ g DNA PBMC.
  • UMAP Uniform manifold approximation and projection
  • CD8+ and CD4+ T cells from the PBMC samples were extracted and fluorescence intensity levels of CD8/CD4 expression were plotted against the fluorescence intensity of the CAR targeting antibody.
  • CAR+ cells were determined by setting a CD8+/CD4+ T cell specific cutoff for downstream analysis.
  • CAR+ cells were identified as displayed in Figure 4.J and as described in the material and methods section.
  • CM central memory T-cells
  • cDC conventional dendritic cells
  • EM effector memory T-cells
  • hi , TCR: T-cell receptor
  • NK natural killer
  • NKT natural killer T-cells
  • pDC plasmacytoid dendritic cells
  • SCM memory stem cell-like T-cells.
  • Fig.5 (A) Boxplots indicate differential abundances of cell populations within the CART product (displayed in 4.A) between responders and non-responders. Positive log2 fold changes indicate that a respective population is more abundant in responders, whereas negative log2 fold changes indicate that the population is more abundant in non-responders.
  • Fig.7 A) UMAP representation of a subset of the CD8+ CAR-T product from 10 patients.
  • CD39 and CD27 in CAR-T products are predictive markers for therapy response independent of dose.
  • AE adverse event
  • ALL acute lymphoblastic leukemia
  • alloSCT allogeneic stem cell transplantation
  • ASTCT American Society for Transplantation and Cellular Therapy
  • BM bone marrow
  • CAR chimeric antigen receptor
  • CART chimeric antigen receptor T cells
  • CD cluster of differentiation
  • cmax maximal concentration
  • CR complete re- mission
  • CRS cytokine release syndrome
  • CTCAE Common Terminology Criteria for Adverse Events
  • DIC disseminated intravascular coagulation
  • DL dose level
  • DLT dose-limiting toxicity
  • EC ethics committee
  • EFS event-free survival
  • EOS end-of- study
  • GI gastrointestinal
  • GMP Good Manufacturing Practice
  • GvHD graft-versus- host disease
  • HD-CAR-1 Heidelberg CAR trial 1
  • ICANS immune effector cell-associated neurotoxicity syndrome
  • IIT investigator-initiated trial
  • IL interleukin
  • MRD minimal residual disease
  • Example 1 Methods employed Study design - Treatment of adult ALL patients with third-generation CD19-directed CAR T cells
  • Endpoints included feasibility of manufacturing and treatment- safety, clinical efficacy and survival. Patients were evaluated as outlined in the study calendar (Schubert et al., 2019). Written informed consent was obtained from all patients prior to treatment.
  • PBMCs peripheral blood mononuclear cells
  • IL-7 interleukin-7 (10 ng/mL) and IL-15 (5 ng/mL)
  • CellGenix CART treatment and follow-up, evaluation of toxicity and outcome Patients received the respective dose of HD-CAR-1 CARTs on day 0 after lymphodepletion (fludarabine 90 mg/m2 and cyclophosphamide 1500 mg/m 2 ).
  • Cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) were graded according to the consensus guidelines of the American Society for Transplantation and Cellular Therapy (ASCTC) (Lee et al., 2019) and managed according to institutional guidelines and as published (Schubert et al., 2021).
  • TLS Tumor lysis syndrome
  • AEs Adverse events
  • CCAE National Cancer Institute Common Terminology Criteria for Adverse Events
  • Lymphodepletion, CART administration, and safety monitoring were per- formed as inpatient procedures with mandatory hospitalization from day -6 through day +14. Following patient discharge, patients presented in the outpatient department ac- cording to the study visit schedule (Schubert et al., 2019).
  • HD-CAR-1 Clinical efficacy of HD-CAR-1 treatment was assessed according to response criteria defined for ALL (Appelbaum et al., 2007; Cheson et al., 2007), i.e., bone marrow (BM) aspiration and/or radiologic imaging in case of extramedullary disease Assessment of CART frequencies
  • HD-CAR-1 CART frequencies were quantified by single copy gene (SCG)-based duplex quantitative PCR (SCG-DP-PCR) amplifying simultaneously the human SCG ribonuclease (RNase) P RNA component H1 (RPPH1) and the FMC63 domain of the CAR transgene as described (Kunz et al., 2020).
  • Table 1 Antibodies used for assessment of cellular composition of CART products and of PB samples of patients after CART treatment
  • Antibodies vendor Cat.no Staining number CD19-BUV496 BD 612938 1 CAR T detection reagent Miltenyi 130-129-550 2 CD16-BUV395 BD 563784 3 CD33 BUV563 BD 741369 3 CD314 BUV615 BD 751305 3 CD27 BUV661 BD 741609 3 CD8 BUV737 BD 741850 3 CD45 BUV805 BD 612891 3 CD141 BV421 Biolegend 344114 3 IgD Pacific Blue Biolegend 348223 3 CD45RO BV570 Biolegend 304225 3 CD11c BV605 Biolegend 301635 3 CD279 BV650 BD 564104 3 CD56 BV711 Biolegend 318336 3 TCRab BV750 BD 747180 3 CD45RA BV785 BD 564552 3 CD11b
  • the cells are washed, centrifuged at 350g for 5 min, and then transferred to 96-well V-plates. After repeated washing and centrifugation (see above), cells are first labeled with CART detection reagent (Miltenyi) and incubated for 20 min at 4°C. Cells are then washed with 150 ⁇ l PBS 2%FCS, centrifuged and labeled with streptavidin-PE, CD3 BV711, CD27-APC, CD8-FITC, CD4 APC-Cy7 and CD39-BV421 and incubated for 20 min at 4°C. The cells are then washed one more time and are resuspended in 200 ⁇ l of PBS 2%FSC.
  • CART detection reagent Miltenyi
  • CD3+ T cells are gated and then CD4+ and CD8+ positive cells are distinguished. Subsequently, it is determined in the respective populations which of the cells expresses the CART receptor.
  • CD39 vs. CD27 is then plotted on all CD3+ CD4+ CART+ and CD3+ CD8+ CART+ cells in a scatterplot and gated on CD39-CD27 cells. These are subsequently quantified.
  • Computational analysis Spectral unmixing of obtained data was performed using SpectroFlow (Cytek Biosciences).
  • the R packages Spectre (19), CATALYST(20) and diffcyt were used.
  • CART product and PBMC data were merged into a single data table, with keywords denoting the sample, group, and other metadata added to each row (cell). Since data were acquired over the course of two days, batch alignment was performed by computing quantile conversions using reference samples recorded with each batch, and then applied to the samples in each batch using CytoNorm (VanGassen et al., 2020) in Spectre. The batch-corrected values were used for all downstream computations including clustering and differential expression analyses.
  • T cells For detailed clustering and subset annotation of individual T cell populations (CD4+ and CD8+ T cells), the cluster function from the CATALYST package (Nowicka et al., 2017) (version 1.18.1) was used, which performs a FlowSOM clustering and Con- sensusClusterPlus metaclustering. Markers that were included for clustering were specified and were dependent on the respective T cell population excluding cells ex- pressing the CAR. For cellular visualizations, the dimensionality reduction algorithm Uniform manifold ap- proximation and projection (UMAP) (McInnes et al., 2018) was used on downsampled data, taking sur- face expression of used markers into consideration.
  • UMAP Uniform manifold ap- proximation and projection
  • CAR T cells For analysis of CD4+ or CD8+ CARTs, the CD4+ and CD8+ T cell clusters were selected and the surface expression of the CAR detection marker was used to gate CAR+ T cells. Within the CD4+ or CD8+ T cell compartments, cells were gated using the same cutoffs for every sample. Due to spectral spillover, different cutoffs for the CD4+ and CD8+ compartment were applied.
  • PCA principal component analysis
  • the cell type frequencies for each sample were used as input. Cell type frequencies were calculated sample-wise by dividing the number of cells of per population by the total number of cells within that sample.
  • the diffcyt package (Weber et al., 2019) (version 1.14.0) was used.
  • the models and contrast matrices were set up with the createFormula and createContrast functions from the diffcyt package.
  • a Generalized Linear Mixed Model (GLMM) was used and adjusted p-values (based on Benjamini- Hochberg (Benjamini et al., 1995) method) were returned.
  • a Linear Mixed Model (LMM) was applied and the unadjusted p-value was reported.
  • Differential abundance analyses were performed by calculating the frequency of cells per population out of the total CD45+ cells per sample or the frequency of cells per CD4+ or CD8+ T cell subset out of all CD3+ TCRab+ T cells respectively.
  • the mean frequency for every population in non-responders was calculated. Then, frequencies for every population in responders were divided by the corresponding mean frequency from non-responders as determined in the step before.
  • the mean frequency for every population in healthy donors was calculated. Then, frequencies for every population in CAR recipients were divided by the corresponding mean frequency from non-responders as determined in the step before.
  • Sample specific fold-changes were log2 transformed and visualized as boxplots.
  • Statistical analysis Statistics were calculated using Prism Software (Graphpad Software Inc., version 8.2.2).
  • Progression-free survival was calculated from the date of CART administration until the date of clinical progression, relapse or death, respectively.Differences between survival curves were descriptively calculated by log-rank testing. A p-value ⁇ 0.05 was considered statistically significant.
  • Results and Discussion Patient characteristics Between September 2018 and January 2022, 15 patients with r/r ALL were enrolled ( Figure 1). The patient baseline characteristics are detailed in Table 2. Median age of patients was 41 (range 21 to 67) years. Median time from initial diagnosis to CART administration was 22 (range 5 to 117) months and patients had received a median of 4 (range 2 to 9) prior treatment lines, including allogeneic stem cell transplantation (alloSCT) in 12 patients (80%).
  • alloSCT allogeneic stem cell transplantation
  • Table 2 Patient characteristics ALL: acute lymphoblastic leukemia; alloSCT: allogeneic stem cell transplantation; BM: bone marrow; c-ALL: common B-cell leukemia; CART: chimeric antigen receptor T cells; CNS: central nervous system; CR: complete remission; CSF: cerebrospinal fluid; F: female; LD: lymphodepletion; M: male; MPAL: mixed-phenotype acute leukemia; MRD: minimal residual disease; PR: partial remission; pre-ALL: precursor B-cell acute lymphoblastic leukemia; PD: progressive disease; SD: stable disease; tx: therapy; UPN: unique patient number. ⁇ patient #14 and #15 did not receive HD-CAR-1 CARTs due to progressive disease.
  • CD4 clone SK3
  • CD8 clone SK1
  • CD14 clone MOP9
  • CD34 clone 8G12
  • CD4 clone SK3
  • CD8 clone SK1
  • CD14 clone MOP9
  • CD34 clone 8G12
  • CD19-directed CAR specific cells the biotinylated CD19 CAR Detection Reagent and the Anti- Biotin antibody (both Miltenyi Biotec) were used. Staining was performed according to the manufacturer’s instruction. After staining, the cells were fixed with 4% paraformaldehyde (PFA) (Morphisto) and stored at 4°C until measurement.
  • PFA paraformaldehyde
  • CD45 vs. CD3 was used to gate for CD3 T cells from which CD19 CARTs were selected.
  • Cell counting was performed with the automated cell counting system LunaFL (Logos Biosystems). In the final product no B cells or CD34-positive stem cells were detected.
  • CART administration Of 15 patients, six patients received bridging therapy between leukapheresis and lymphodepleting therapy. Thirteen patients received HD-CAR-1 CARTs (UPN#14 and UPN#15 did not receive CARTs due to progressive disease (PD) during CART manufacturing).
  • PD progressive disease
  • ALL acute lymphoblastic leukemia
  • BM bone marrow
  • c-ALL common B-cell leuke- mia
  • CART chimeric antigen receptor T cells
  • CR complete remission
  • CRS cytokine release syndrome
  • CSF cerebro spinal fluid
  • EOS end-of-study on day 90 after HD-CAR-1 treatment
  • F female; M: male; MPAL: mixed-phenotype acute leukemia; MOV: multi organ failure; MRD: minimal residual disease; n.r.: not reached;
  • pre-ALL precursor B-cell acute lymphoblastic leukemia
  • PD progressive disease
  • RSV respiratory syncytial virus
  • SD stable disease
  • TRM treatment-related mortality
  • UPN unique patient number. ⁇ patient died before reaching EOS. *no pathogen identified.
  • the CART product of analyzed patients contained mostly CD4+ and CD8+ T-cells. Also, minor fractions of ⁇ -T cells and natural killer (NK) cells were identified ( Figure 4 A, Figure 5 A). All CART products contained CAR-positive T-cells (Table 3). Unsupervised clustering and dimensionality reduction of the CD4+ and CD8+ T-cell compartments revealed differences in the cellular composition of the CART product in responders and non-responders ( Figure 4 B, 4 C): in responders, higher frequencies of CD39-negative effector memory-like CD4+ and CD8+ T-cells were observed, whereas non-responders displayed higher levels of CD39-positive effector memory like T-cells ( Figure 4 C, 4 D, 4 G).
  • CD39 is expressed on T cell subsets (Borsellino et al., 2007; Deaglio et al., 2007) and its expression on CD8 positive T cells has been associated with T cell exhaustion (Gupta et al., 2015; Qi et al., 2015).
  • CARTs with a less differentiated phenotype e.g., central memory or na ⁇ ve CARTs
  • mediate better expansion, persistence and antitumor activity Fraietta et al., 2018; Frigault et al., 2015
  • T cell exhaustion is as- sociated with inferior response (Bai et al., 2022; Deng et al., 2020).
  • CD39 expression on CARTs has been linked to reduced CART expansion (Myers et al., 2022; Roselli et al., 2021).
  • CD39 within the CART product is highly relevant to predict responsiveness and therapeutic outcome in CART patients.
  • CD39 is a highly specific marker for the therapeutic efficacy of T cells and thus responsiveness in a subject treated with such T cells.
  • CD39, CD27, CD45RA and HLADR in CAR-T product are predictive markers for therapy response
  • composition of CAR-T products comprising CD8+ and CD4+ T cells from 10 patients was evaluated high dimensional flow cytometry.
  • Figure 7 A shows an UMAP representation of a subset of the CD8+ CAR-T product from 10 patients
  • Figure 7 B Highlights the cell density within the CD8+ CAR-T product between non-responsive (NonRes) and responsive (Res) patients.
  • Expression of CD27 and CD39 in the CD8+ CAR-T product is shown in Figure 7 C and Frequency of CD39-CD27- cells within the CD8+, CAR+ (CAR-T cell receptor) compartment in Figure 7 D.
  • Figure 7 E shows an UMAP representation of a subset of the CD4+ CAR-T product from 10 patients
  • Figure 7 F highlights cell density within the CD4+ CAR-T product between non-responsive (NonRes) and responsive (Res) patients.
  • FIG 7 G Expression of CD27 and CD39 in the CD4+ CAR-T product is shown in Figure 7 G and frequency of CD39-CD27- cells within the CD4+, CAR+ (CAR-T cell receptor) compartment. Is shown in Figure 7 H. The frequency of CD39-CD27 T cells, each within the CD4+ and CD8+ T cell compartments, correlates significantly with the patient's response to CAR T cell therapy.
  • Figure 9 A)-F) shows the frequency of CD39-, CD27-, CD39-CD27-, CD39-CD27-CD45RA-, CD39-CD27-HLADR+ and CD39-CD45RA- cells in the CD4+ or CD8+ CAR- or CAR+ compartment of responders (R) and non-responders (NR).
  • Figure 8 D)-F) Biomarker combination in the CD4+CAR+ CAR-T cell product (cells from 10 patients, evaluated high dimensional flow cytometry) between the inventive biomarker combination in comparison to approaches of the prior art (Locke et al., 2020; Caballero et al., 2022) employing other biomarker combinations.
  • the frequency of CD39-CD27- cells is significantly higher in CAR-T cell therapy responding patients ( Figure 8 D). No significant differences were detected with the approach of Lock et al, 2020 between responders and non- responders ( Figure 8 E). No significant differences were found in the CD4+CAR+ compartment with the combination of Caballero between responders and non-responders ( Figure 8 F).
  • Example 2 Methods: The methods described within example 1 (e.g., HD-CAR-1 CART manufacturing, CART treatment and follow-up, evaluation of toxicity and outcome, Assessment of CART frequencies, Assessment of cellular composition of CART products and patient samples by Flow cytometry, Computational analysis and Statistical analysis) were similarly employed within example 2.
  • Table 17 Dosage levels administered within the dose escalation study Dosage level Number of cells infused per m 2 body surface area I (low) 1 million II (low) 5 million III (low) 20 million IV (low) 50 million V (high) 100 million VI (high) 200 million Results and Discussion
  • Figure 10 A)-D shows absolute number (calculated per m 2 body surface area, per patient (absolute numbers infused) and kg body weight, Fig.10 A to C) and relative frequency (Fig.10 D) of CD39-CD27-CAR+ cells in responders (R) and non-responders (NR) within all dose levels (high and low). The results are further presented in Tables 18 and 19. Table 18: Patient characteristics No.

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Abstract

L'invention concerne une méthode d'évaluation de l'efficacité thérapeutique d'une cellule T. Dans certains modes de réalisation, la méthode consiste à fournir un échantillon comprenant une ou plusieurs cellules T, et à déterminer pour la ou les cellules T un niveau d'expression d'au moins CD39, ledit niveau d'expression indiquant une efficacité thérapeutique. L'invention concerne également une méthode de pronostic, de prédiction, d'évaluation du risque et/ou de stratification du risque de réactivité d'un sujet atteint ou suspecté d'être atteint d'un cancer à un traitement par une population de cellules T thérapeutiques. L'invention concerne en outre une méthode d'amélioration de l'efficacité thérapeutique ou de sélection des cellules T pour produire une population de cellules T efficace sur le plan thérapeutique. Les niveaux d'expression de CD39, et éventuellement de CD27, CD45RA et/ou HLADR sont privilégiés. L'invention concerne par ailleurs une population de cellules T comprenant des cellules CAR-T CD4+ et/ou CD8+ thérapeutiques, définies par des pourcentages de cellules présentant lesdits profils de marqueurs. L'invention concerne enfin une trousse pour la mise en œuvre de ladite méthode.
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