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WO2014193625A1 - Fully human antibodies against human receptor integrin alpha-4 - Google Patents

Fully human antibodies against human receptor integrin alpha-4 Download PDF

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Publication number
WO2014193625A1
WO2014193625A1 PCT/US2014/037325 US2014037325W WO2014193625A1 WO 2014193625 A1 WO2014193625 A1 WO 2014193625A1 US 2014037325 W US2014037325 W US 2014037325W WO 2014193625 A1 WO2014193625 A1 WO 2014193625A1
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WO
WIPO (PCT)
Prior art keywords
antibody
seq
integrin alpha
variable region
sequence
Prior art date
Application number
PCT/US2014/037325
Other languages
French (fr)
Inventor
Ilya ALEXANDROV
Tajib Mirzabekov
Roman MIKHAILOV
Khikmet SADYKOV
Anton CHESTUKHIN
Alexey REPIK
Vasily IGNATIEV
Yan Lavrovsky
Original Assignee
R-Pharm Overseas, Inc.
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Filing date
Publication date
Application filed by R-Pharm Overseas, Inc. filed Critical R-Pharm Overseas, Inc.
Publication of WO2014193625A1 publication Critical patent/WO2014193625A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2839—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the integrin superfamily
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance

Definitions

  • the invention generally relates to the field of molecular biology, immunology, autoimmune and inflammatory diseases and oncology. More specifically, the invention relates to antibodies that bind to human receptor integrin alpha-4.
  • BACKGROUND Alpha4 integrin is among 24 integrin families of cell-adhesion molecules containing noncovalently-associated alpha and beta subunits. Eighteen different integrin alpha subunits and eight different beta subunits have been reported to date in vertebrates, forming at least 24 alpha/beta heterodimers. These varied formations suggest that integrins constitute the most structurally and functionally diverse family of cell-adhesion molecules yet known. Integrins mediate cell-cell and cell extracellular matrix interactions over a wide range of biological contexts. Integrins support force-resistant stable firm adhesion as well as the dynamic adhesive interactions observed in cellular polarization and cell migration. Integrins play a crucial role in many physiological processes, including tissue morphogenesis, inflammation, wound healing, and regulation of cell growth and differentiation.
  • Alpha4 integrin plays a critical role in their adhesive interactions with endothelial cells during migration to lymphoid organs and extravasation to sites of inflammation.
  • Alpha4-betal binds to a major endothelial ligand vascular cell adhesion molecule (VCAM-1), and an extracellular matrix ligand fibronectin (FN) deposited in inflamed tissues, while alpha4-beta7 binds to MAdCAM-1 preferentially expressed in the gut.
  • VCAM-1 major endothelial ligand vascular cell adhesion molecule
  • FN extracellular matrix ligand fibronectin
  • Alpha4 integrins are known to play crucial roles in tissue-specific leukocyte trafficking to the inflamed brain (alpha4- betal) and to the inflamed gut (alpha4-beta7).
  • Alpha4 integrins are also known to regulate hematopoietic stem cell trafficking and retention in the bone marrow.
  • Persistent accumulation of leukocytes is a hallmark of the chronic inflammation observed in the affected tissues of autoimmune diseases such as Multiple sclerosis (MS) and Crohn's disease.
  • MS Multiple sclerosis
  • the leukocyte-endothelial interactions leading to extravasation are regulated by a sequence of multiple steps involving adhesion molecules and chemokine signaling.
  • circulating leukocytes that flow in blood vessels start to tether and roll along endothelial cells via selectins and their ligands.
  • This rolling interaction serves to slow down leukocytes and place them in proximity to the inflamed endothelial cells, thereby enabling these cells to efficiently scan the endothelial surface for available chemokines.
  • leukocytes encounter chemokines and become activated via chemokine receptors present on the leukocytes.
  • Chemokine signaling elicits an intracellular signaling cascade that eventually impinges on integrin cytoplasmic domains, thereby triggering integrin activation.
  • global conformational changes occur that rapidly convert a low-affinity latent integrin into a high-affinity ligand-competent state. In this way, the high-affinity integrin mediates the rapid arrest of rolling leukocytes and shear-resistant firm adhesion at inflamed endothelial cells.
  • the cascade of leukocyte-endothelial cell interactions was originally thought to contain three steps (i.e., rolling by selectins, activation by chemokines, and upregulation of integrin affinity) before transmigration of leukocytes across the endothelial barrier could occur.
  • a crawling step has recently been added to this cascade. Specifically, leukocytes crawl along the endothelial surface from the point of arrest to that of transmigration.
  • the dynamic regulation of integrin affinity plays a critical role in supporting such leukocyte crawling.
  • leukocytes During transendothelial migration (TEM), leukocytes proceed through endothelial cells via two distinct routes, either paracellular or transcellular. In the former, leukocytes transmigrate in between adjacent endothelial cells, which usually form tightly sealed junctions, thereby leaving no space between them.
  • paracellular TEM the junctions between endothelial cells are dynamically disassembled, thereby creating a gap for a leukocyte to pass through. This gap is closed as soon as the trailing edge of the leukocyte passes beyond it.
  • transcellular TEM a leukocyte transmigrates through a single endothelial cell. A pore is formed for a leukocyte to move through.
  • the pore formation that develops during transcellular TEM is thought to be mediated by a dynamic remodeling of the endothelial cell-rich plasma membrane that involves vimentin as well as caveolae or vesiculovacuolar organelles.
  • Organ-specific homing of leukocytes is made possible primarily by unique combinations of cell-adhesionmolecules and chemokine receptors.
  • Naive lymphocytes recirculate between the blood stream and peripheral lymphoid tissues, thereby patrolling the body for microorganisms and transformed cells.
  • Gut-tropic effector T cells which play a pathogenic role in inflammatory bowel diseases, upregulate in integrin alpha-4-beta7 and the chemokine receptor CCR9.
  • Brain-tropic effector T cells which are responsible for the pathogenesis of multiple sclerosis, upregulate in integrin alpha-4-betal .
  • CNS central nervous system
  • integrin ligands chemoattractants and integrin ligands. Prolonged selectin-mediated rolling of neutrophils and lymphocytes may also lead to integrin activation. Once firmly arrested, integrins serve for leukocytes to bind to other blood-borne leukocytes and platelets. VLA-4 have been shown to facilitate leukocyte migration across the basement membrane of blood vessels, as well as across extracellular matrix (ECM). The interaction of these integrins with ECM may propagate leukocyte immobilization, or bridging between cells. Eventually, VLA-4 integration leads to extravasation of neutrophils and lymphocytes into peripheral tissues and CNS. Thus antibodies that inhibit the interaction between integrin alpha-4 and it's ligand VCAM1 may serve as a therapy for MS and Crohn's disease.
  • ECM extracellular matrix
  • MS is an inflammatory demyelinating disorder of CNS. Histopatho logically, most acute active MS lesions are characterized by monocytes and lymphocytes infiltration in to the brain. This is considered a critical event in the pathogenesis of MS. Cell adhesion of leukocytes to the endothelial wall has been a major target of drug development against MS.
  • Antibodies against integrin alpha-4 (VLA-4) were the first pharmacological agents that were successfully brought to clinical trials and approved for the treatment of relapsing-remitting MS (RR-MS).
  • Natalizumab is a humanized anti-integrin alpha-4 monoclonal antibody which under the trade name TYSABRI was approved by the U.S.
  • FDA Food and Drug Administration
  • natalizumab is regarded as the most potent treatment for RR-MS.
  • the scientific rationale for the therapy with antibodies that block integrin alpha-4 is the reduction of leukocyte extravasations into the peripheral tissues, including the brain and the spinal cord by interfering with the physical interaction of VLA-4 with its natural ligands, VCAM-1 and FN.
  • the invention is based, in part, upon the discovery of antibodies that specifically bind to human integrin alpha-4 blocking the VCAM-1 /integrin alpha-4 interactions.
  • Series of antibodies were isolated from antibody libraries that contained fully human antibody frames.
  • the CDRs (Complementarity Determining Regions) of integrin alpha-4 -specific antibodies differ from each other, consistent with the design of the antibody libraries used.
  • CDRl and CDR2 of the antibody heavy chain were randomized to provide limited number of variation and CDR3 of the heavy chain was randomized to include all possible amino acid combinations.
  • CDRl and CDR2 were invariant and CDR3 was randomized completely. Since the frameworks for both heavy and light chain of antibodies were corresponding to human sequences, the antibodies described herein could be administered to humans without additional modifications such as a "humanization" process.
  • the antibodies could also be used as diagnostics and for research purposes.
  • the monoclonal antibodies disclosed herein are applicable for integrin alpha-4 /VCAM-1 signaling cascade targeting in drug development for cancer and immunological disorders, such as Crohn's and MS, and others.
  • the invention provides for an isolated antibody (IN8), or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor.
  • the antibody comprises an immunoglobulin light chain of SEQ. ID NO. 90, and an immunoglobulin heavy chain of SEQ. ID NO. 82.
  • the antibody can be a monoclonal antibody.
  • the invention further provides for an isolated antibody (integrin IN9A), or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor.
  • the antibody comprises an immunoglobulin light chain of SEQ. ID NO. 92, and an immunoglobulin heavy chain of SEQ. ID NO. 84.
  • the antibody can be a monoclonal antibody.
  • the invention even further provides for an isolated antibody (IN 10), or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor.
  • the antibody comprises an immunoglobulin light chain of SEQ. ID NO. 94, and an immunoglobulin heavy chain of SEQ. ID NO. 86.
  • the antibody can be a monoclonal antibody.
  • the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4.
  • the antibody comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 57, a CDRL2 comprising the sequence of SEQ. ID NO. 58, and a CDRL3 comprising the sequence of SEQ. ID NO. 59.
  • the antibody further comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the sequence of SEQ. ID NO. 17, a CDRH2 comprising the sequence of SEQ. ID NO. 18, and a CDRH3 comprising the sequence of SEQ. ID NO. 19.
  • the CDR sequences of the antibody can be interposed between human or humanized framework sequences.
  • the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4.
  • the antibody comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 58, a CDRL2 comprising the sequence of SEQ. ID NO. 59, and a CDRL3 comprising the sequence of SEQ. ID NO. 61.
  • the antibody further comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the sequence of SEQ. ID NO. 23, a CDRH2 comprising the sequence of SEQ. ID NO. 24, and a CDRH3 comprising the sequence of SEQ. ID NO. 25.
  • the CDR sequences of the antibody can be interposed between human or humanized framework sequences.
  • the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4.
  • the antibody comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 58, a CDRL2 comprising the sequence of SEQ. ID NO. 59, and a CDRL3 comprising the sequence of SEQ. ID NO. 63.
  • the antibody further comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the sequence of SEQ. ID NO. 29, a CDRH2 comprising the sequence of SEQ. ID NO. 30, and a CDRH3 comprising the sequence of SEQ. ID NO. 31.
  • the CDR sequences of the antibody can be interposed between human or humanized framework sequences.
  • the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4.
  • the antibody comprises an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ. ID NO. 41, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ. ID NO. 01.
  • the antibody can be a monoclonal antibody.
  • the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4.
  • the antibody comprises an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ. ID NO. 45, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ. ID NO. 05.
  • the antibody can be a monoclonal antibody.
  • the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor.
  • the antibody comprises an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ. ID NO. 49, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ. ID NO. 09.
  • the antibody can be a monoclonal antibody.
  • Figure 1 schematically shows representation of a typical antibody. Gray areas on the scheme depict Constant Regions of both antibody light and heavy chains, black areas depict Variable
  • Regions of the antibody light chain depict Variable Regions of the antibody heavy chain.
  • VH - Variable Regions of the antibody heavy chain VL - Variable Regions of the antibody light chain
  • CL Constant Region of the antibody light chain. Links between heavy and light chains and between two heavy chains depict intermolecular disulfide bridges;
  • Figure 2 schematically shows the amino acid sequences defining a complete immunoglobulin Heavy Chain Variable Region of the antibodies assigned as IN8, IN9, IN9A, IN9B, INIO, IN20,
  • amino acid sequences are aligned relative to each other where the regions defining CDR1, CDR2 and CDR3 respectively are identified in boxes; the unboxed sequences represent immunoglobulin framework; the length of shorter CDRs is adjusted for the alignment purpose by introducing dashes (-);
  • FIG 3 schematically shows amino acid sequences of CDR1, CDR2 and CDR3 for each immunoglobulin Heavy Chain Variable Region shown in Figure 2;
  • Figure 4 schematically shows the amino acid sequences defining a complete immunoglobulin
  • amino acid sequences are aligned relative to each other where the regions defining CDR1, CDR2 and CDR3 respectively are identified in boxes; the unboxed sequences represent immunoglobulin framework; the length of shorter CDRs is adjusted for the alignment purpose by introducing dashes (-);
  • FIG. 5 schematically shows amino acid sequences of CDR1, CDR2 and CDR3 for each immunoglobulin Light Chain (Kappa) Variable Region shown in Figure 4;
  • Figure 6 A show a graphic representation of VCAM-1 adhesion assay results performed with
  • Figure 7 shows the distribution of hydrodymanic sizes of antibodies IN8 (top peak), IN9A (middle peak), and IN 10 (lower peak) on freshly isolated (top panel a) and stored at 37°C for 8 days (bottom panel b) preparations, the table insert in top panel a) shows the average diameters of antibody molecules in solution after incubation, the graph for Tysabri is not shown but in also appears with a hydrodinamyc diameter of around 12.55 nM, all measurements have been carried out at a final protein concentartions of 2 mg/ml;
  • Figure 8 shows a graphic representation of specific heat capacity (Cp) measurements of antibodies IN8 (dot line), IN9A (dashed line), and IN 10 (solid line), derived from DSC data; and
  • Figure 9 shows a graphic representation of far-UV circular dichroism (CD) data for antibodies IN8, IN9A and IN10, alongside with Tysabri, while the curves are virtually
  • the invention is based, in part, upon the discovery of antibodies that specifically bind to human integrin alpha-4 (UniProtKB/Swiss-Prot: P13612) and block interactions with its cognate ligand VCAM-1 (UniProtKB/Swiss-Prot: PI 9320).
  • the antibodies could be used for a variety of diagnostic and therapeutic applications and as research tools.
  • the antibodies were selected for their ability to bind to human integrin alpha-4 with high affinity, specificity and selectivity.
  • the antibodies described herein are engineered on the basis of human sequences, all of them could be administered to humans directly. Depending on a particular application, the described antibodies could be used as targeting moieties for various payloads such as
  • the invention provides for an isolated antibody that specifically binds to human integrin alpha-4.
  • the antibody is comprised of (1) an immunoglobulin light chain variable region comprised of three CDRs and (2) an immunoglobulin heavy chain variable region comprised of three other CDRs.
  • the CDRs are embedded into the immunoglobulin framework generated by less variable FR domains.
  • the CDRs of the immunoglobulin light and heavy chain brought together in immunoglobulin molecule define a unique binding site that specifically binds to a native conformation of integrin alpha-4.
  • the terms "binds specifically” or “specifically binds” are interchangeable and mean that binding affinities (EC50 values) of the antibodies described herein are below 50 nM (5* 10 ⁇ 8 M).
  • the antibodies can comprise both immunoglobulin heavy and light chain sequences of fragments thereof, such as Fab or Fab 2 fragments. It is understood that specific binding and functional properties can be displayed by a full-length intact immunoglobulin or antigen binding fragment thereof or biosynthetic antibody site.
  • each of the antibody molecules can be an intact antibody, for example, a monoclonal antibody.
  • the antigen binding could be displayed by an antigen binding fragment of an antibody or can be a biosynthetic antibody binding site.
  • Antibody fragments include Fab, Fab 2 or Fv fragments. Techniques for making such antibody fragments are known to those skilled in the art.
  • a number of biosynthetic antibody binding sites are known in the art and include single Fv or sFv molecules, for example as described in US Patent # 5,476,786.
  • Other biosynthetic antibody binding sites include bi-specific or bi-functional antibodies that bind to at least two different target molecules.
  • a bi-specific antibody can bind to human integrin alpha-4 and to another antigen of interest. Methods for making bi-specific antibodies are known in art and include fusing hybridomas or linking Fab fragment together.
  • Antibodies described in this invention can be produced in different ways utilizing previously developed approaches.
  • DNA encoding variable regions of light and heavy chains can be synthesized chemically using commercially available services and sequence information provided in this invention.
  • the DNA encoding variable regions of heavy and light chains can be amplified by Polymerase Chain Reaction (PCR) using the original clones of Fab fragments of the antibodies described herein, as templates.
  • Synthetic or PCR-amplified DNA fragments can be genetically fused with appropriate nucleotide sequences to generate full-size antibodies or fragments thereof.
  • Antibody expression constructs can be generated by including immunoglobulin constant region coding sequences, sequences providing expression control and other standard elements of expression systems. Generation of specific gene expression constructs is within ordinary skill in the art.
  • DNA sequences encoding antibodies of interest can be genetically inserted into expression vectors that can be introduced into host cells using standard transfection of
  • E. coli bacterial expression
  • mammalian expression Choinese Hamster Ovary (CHO) cells, HeLa cells, Baby Hamster Kidney (BHK) cells, monkey kidney (COS) cells, Human Embryo Kidney (HEK- 293) cells and myeloma cells that do not produce endogenous immunoglobulins.
  • Transfected or transformed host cells can be propagated under conditions providing expression of genes of interest, such as immunoglobulin light and heavy chains and fragments thereof.
  • the expressed proteins can be harvested using common techniques known in the art.
  • E. co/z ' -based expression system is particularly suitable for production of Fab, Fab 2 or sFv antibody fragments.
  • the engineered antibody gene is cloned into a vector suitable for bacterial expression downstream from a commonly used bacterial promoters, e.g. T5 of Lac. Genetic fusion of a signal sequence providing targeting on the expressed protein into the periplasm may enable production and accumulation of soluble forms of antibody fragments into the periplasm of bacterial cells. Extraction of proteins of interest and, specifically, of antibody fragments from the periplasm of bacteria is a well-established array of standard methods known in the art.
  • DNA coding sequences must be inserted into appropriate expression vectors containing adequate eukaryotic promoter, signal peptide for secretion from the cells and other genetic elements known in the arts.
  • Mammalian expression systems are particularly suitable for production of full-size
  • immunoglobulins One of the approaches for antibody production is transient co-expression of heavy (variable + constant) and light (variable + constant) chains of immunoglobulin genetically introduced into two separate expression vectors. Another approach for antibody production is expression on both heavy and light chains from a single bi-cistronic vector. Alternatively, stable cell lines constitutively expressing both heavy and light chains can be generated using single vector approach or utilizing two-vector systems.
  • epitope or purification tags or peptide and protein toxins can be genetically fused to the expression constructs encoding heavy chain, light chain or combination of both immunoglobulin chains.
  • the antibodies disclosed herein can be modified to improve performance which largely depends on the intended use.
  • the antibody can be genetically modified to reduce its immunogenicity in the intended recipient.
  • the antibody can be genetically fused or coupled to another peptide or protein, such as epitope tag, purification tag, a growth factor, cytokine or natural or modified toxin.
  • integrin alpha-4 -specific antibodies described herein can be used as therapeutic and diagnostic agents or as reagents for basic and applied research and development.
  • the antibodies in the invention specifically bind to human integrin alpha-4 and block interactions with its cognate ligand VCAM-1, they can be utilized in a variety of therapeutic applications. It is contemplated that the antibodies of the invention can be used for the treatment of a variety of disorders in which integrin alpha-4 mediated signaling is involved. This includes Multiple Sclerosis, Crohn's desease and alike, as well as various types of cancers.
  • the antibodies are typically modified directly or indirectly with a detection moiety.
  • the detection moiety is a functional addition to the antibody that can be detected either directly or indirectly or is capable of generating a detectable signal.
  • the detectable moiety can be a
  • radionuclide Iodine, Phosphorus, Carbon or others
  • fluorescent or chemiluminescent compound such as fluorescein, rhodamine or luciferine.
  • Enzyme moieties include alkaline phosphatase, horse radish peroxidase, beta-galactozidase and others. Methods for conjugation of the detection moieties largely depend on the nature of the moiety and routinely can be reproduced by those experienced in the art.
  • the antibodies of the invention can be used in a broad range of immunological techniques know in the art. Examples of such techniques include sandwich immunoassays (ELISA), competitive immunoassays, cell surface staining procedures combined with FACS analysis, immunocyto- and immunohistochemical procedures. Protocols and method all of these procedures and assays are well-established and can be routinely carried out by those skilled in the art. EXAMPLES
  • Example 1 Generation of Magnetic Proteo liposomes as antigen presenting platforms.
  • integrin alpha-4 Isolation of antibodies that recognize native conformations of integrin alpha-4 is absolutely critical for the development of such antibodies as therapeutics. In the human body and tissues integrin alpha-4 is present in its native form, therefore only the antibodies that bind to the native receptor have practical utility. Preparation of antigen-presenting platforms that provide oriented and functional receptor in its native conformation is far from being trivial. Many methods of antibody generation, for example generation of antibodies against peptide epitopes or receptor fragments, usually are not successful for complex targets such as integrin alpha-4.
  • Previously patented technology that relies on the generation of magnetic proteoliposomes (MPLs) (Sodroski, J.G. and T. Mirzabekov, Proteoliposomes containing an integral membrane protein having one or more transmembrane domains; US Patent 6,761,902;) has been used for isolation of antibodies against integrin alpha-4.
  • MPLs magnetic proteoliposomes
  • the main advantage of the core technology that relies on usage of MPLs is the ability to present highly purified and concentrated antigen (human integrin alpha-4 in this invention) properly oriented and, most importantly, in its native conformation and functional state.
  • highly purified and concentrated antigen human integrin alpha-4 in this invention
  • US Patent 6,761,902 can be applied to a variety of complex membrane proteins, each target requires extensive optimization of protein extraction and MPL formation conditions.
  • a stable cell line Prior to preparing MPL particles, a stable cell line was prepared, utilizing established protocols, overexpressing human recombinant integrin alpha-4. The condition for extraction of human integrin alpha-4 were tested and optimized prior to the initiation of the antibody selection procedure. An extensive matrix of combinations of various detergents, salts and buffer components was analyzed to identify conditions providing a balance between effective extraction of the integrin alpha-4 and retaining of its function and native conformation. The integrin alpha-4 functionality was tested by assaying binding of its ligand, VCAM-1, to the integrin alpha-4 immobilized on the surface of the MPLs.
  • Example 2 Antibody libraries and selection of anti-integrin alpha-4 antibodies.
  • phage display library represents a collection of individual phage particles that express only a certain type of a genetic fusion of an individual Fab antibody fragment with a surface protein intrinsic for this particular type of phage.
  • a fraction of the phage display library usually containing 10 12 -10 13 phage particles is used as a primary source of the antibody variety.
  • a fraction of the phage display library (10 12 -10 13 phage particles) was incubated with MPL preparations containing functional integrin alpha-4 in its native conformation.
  • the phage particles that did not bind to the integrin alpha-4-MPLs were removed by a series of subsequent washes under conditions providing retention of the native conformation of integrin alpha-4.
  • the pool of phage particles that was bound to integrin alpha-4-MPLs was removed by acidic elution.
  • the deconvo luted phage output (usually 10 6 -10 8 phage particles) was harvested and further amplified by propagation in E. coli.
  • the pool of the amplified phage is then used further for the second selection round as described for the first round above.
  • a minimum of 2 and maximum of 4 selection rounds are carried out for a standard selection procedure.
  • This example describes a procedure for screening antibodies specific against native conformations of integrin alpha-4 receptor.
  • the screening procedure is based on the usage of live cells expressing human integrin alpha- 4 receptor on their surface. Generation of stable cell lines expressing integrin alpha-4 is described in Example 6 below. R1610 cells expressing integrin alpha-4 were used for screening.
  • Phage outputs from 3 rd or 4 th selection rounds represented pools of page particles that were used to infect E. coli to produce phagemid DNA.
  • the phagemid DNA was digested with Nhel and BstEII to excise the entire Fab fragment and further introduced (ligated) into pQE3-Kan expression vector (Quiagen) digested with the same restriction enzymes, Nhel-BstEII.
  • the resulting genetic construct was suitable for expression of Fab antibody fragment in bacteria under control of T5 promoter.
  • the cells expressing human integrin alpha-4 were mixed with individual Fab preparations and allowed to interact for 30 min at 4°C. Unbound material was removed by pelleting the cells and by aspirating the supernatant. Binding the Fab antibody fragments to the cells was analyzed by secondary antibodies conjugated to phycoerythrin. The antibody binding was quantified by FACS analysis using 96-well plate compatible Guava flow cytometer. Clones that gave increase of the signal >5 fold over the background were scored as positive and kept for further analysis.
  • the antibody clones that bound to integrin alpha-4 were re-tested for their ability to interact with parental cells that did not express integrin alpha-4 in order to identify specific integrin alpha- 4 binders.
  • the test was performed as described above and the final candidates from the screening had the following properties: they bind to the integrin alpha-4-expressing cells but not the integrin alpha-4-negative parental cells.
  • Example 4 Sequencing of anti-integrin alpha-4 antibodies.
  • Example 3 The candidate Fab antibody clones identified in Example 3 were subjected to a sequencing analysis to identify independent clones. Bacterial cultures were submitted to Beckman Genomics automated sequencing facility.
  • the experimental sequencing data were analyzed by appropriate software, specifically the nucleic acid sequences were aligned to identify identical clones and to determine the differences in the deduced protein sequences.
  • variable regions can be identified using IMGT ACQUEST webserver-based software at http:// ⁇ vw.imgi org/IMGT_ y q3 ⁇ 4est/share/textes/.
  • the sequencing analysis enabled detection of clones with identical sequences and only clones with unique and distinct DNA and protein sequences were kept for further evaluation.
  • variable region of the sequences shown below are combined with the corresponding constant region sequences.
  • Signal peptides are not presented in the sequence; each sequence starts from the actual beginning of the antibody molecule according to Kabat numbering system.
  • nucleotide sequence (Seq. ID NO. 78) 1 GCTAGCACCA AGGGCCCATC GGTCTTCCCC CTGGCACCCT CCTCCAAGAG CACCTCTGGG
  • AAATCTTGTG ACAAAACTCA CACATGCCCA CCGTGCCCAG CACCTGAACT CCTGGGGGGA
  • EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP 61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QSYASPFTFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL 181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
  • EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP 61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYYDYPVTFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL 181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
  • EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP 61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QSYDDPITFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL 181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
  • This Example describes design and generation of expression constructs for inducible expression of human integrin alpha-4 receptor.
  • this example describes epitope and purification tags genetically fused to the nucleic acid sequences encoding integrin alpha-4 and its orthologs.
  • Human integrin alpha-4 receptor (NCBI Reference Sequence: NM_000885.4) was amplified by PCR using Clone ID HsCD00446160 (DNASU Plasmid Repository) as a template.
  • Clone ID HsCD00446160 DNASU Plasmid Repository
  • the endogenous native Stop codon of integrin alpha-4 was removed using IA-004 Reverse primer to provide in- frame genetic fusion with Strep-tag (h.ttp://www.iba-go.de/prottoojs/prot_stT ptag.html..
  • IA-003 direct primer (Seq. ID NO. 67)
  • AC-001 direct 'structural' primer (Seq. ID NO. 69) 5' - AGCGGGTCCTCTGGAGGGGGAGACTATAAGGATGACGATGACAAGAGTA TGGATGAGAAAACGACAGGTTGGCGCGGCGGGCATGTCGTT -3' AC-002 reverse 'structural' primer (Seq. ID NO. 70)
  • AGCTCACCGGCCAGTCCTTCAACGACATGCCCGCCGCGCC -3' AC-003 direct PCR primer (Seq. ID NO. 71)
  • Example 6 Generation of stable cell lines expressing recombinant integrin alpha-4.
  • the expression constructs encoding human integrin alpha-4 receptor described in Example 5 were used for generation of stable cell lines.
  • Commercially available cell lines, R1610, Cf2Th and HEK-293 (ATCC) were used.
  • the expression constructs were verified for the expression of the protein of interest in a transient transfection experiment and then the cells were propagated on a medium containing Zeocin to select for stable cell lines harboring the gene of interest.
  • Expression of the integrin alpha-4 was verified by Western blot and by FACS analysis to ensure that the expressed protein was translocated to the plasma membrane. For both techniques, commercially available antibodies were used.
  • Example 7 Conversion of the Fab antibody fragments into immunoglobulins and their production. This Example provides description an approach for subcloning of Fab fragments into mammalian expression vectors for production of fully functional immunoglobulins. A protein production approach is also provided herein.
  • the candidate Fab antibody Heavy Chain variable region fragments described in the foregoing Examples 2-4 were converted into full size immunoglobulins of IgGl framework.
  • Variable region of the heavy chain was fused to the constant region of human IgGl isotype using expression vector pTT-5 (NRC Biotechnology Research Institute, National Research Council of Canada) modified by introducing the constant region of human IgGl from pFUSE-CHIg-hGl expression vector (Invivogen) resulting in pTT-IgGl-HC vector.
  • the signal peptide from immunoglobulin kappa light chain variable region (Mus musculus, gb
  • Immunoglobulin 20-amino acid signal peptide sequence where starting methionine is underlined (Seq. ID NO. 73)
  • variable regions of the heavy chain were amplified by PCR to introduce into the following cloning sites: 5 '-end cloning restriction site is Sail, 3 '-end restriction site is Nhel.
  • the resulting PCR fragment was digested with Sail -Nhel restriction enzymes and then introduced into pTT-IgGl-HC vector digested with the same enzymes.
  • A-370 direct PCR primer for amplification of Heavy Chain Variable Region (Sail restriction site is underlined) (Seq. ID NO. 74)
  • Region of light chain was fused to the constant region of human light chain kappa using expression vector pTT-5 (NRC Biotechnology Research Institute, National Research Council of Canada) modified by introduction of the constant region of human light chain fragmen from pFUSE2- CLIg-hk expression vector (Invivogen) resulting in pTT-LC-Kappa.
  • the signal peptide from immunoglobulin kappa light chain variable region (Mus musculus, gb
  • variable regions of the light chain were amplified by PCR to introduce for the following cloning sites: 5 '-end cloning restriction site is Sail, 3 '-end restriction site is BsiWI.
  • the resulting PCR fragment was digested with Sall-BsiWI restriction enzymes and then introduced into pTT-LC-Kappa vector digested with the same enzymes.
  • A-340 direct PCR primer for amplification of Light Chain Kappa Variable Region (Sail restriction site is underlined) (Seq. ID NO. 76)
  • the antibodies in a format of human IgGl framework were produced using a protocol for transfection of CHO-3E7 cells using LPEI MAX in shake flask cultures.
  • CHO-3E7 cells provided by NRC Biotechnology Research Institute, National Research Council of Canada, were diluted to 0.8 xlO 6 cells/ml 24 h before transfection.
  • On the day of transfection cell density was adjusted to 2.0 to 2.2xl0 6 cells/ml using complete FreeStyleTM CHO medium and cell viability was greater than 97%.
  • PEI Polyethylenimine
  • Polyethylenimine ' 'MAX' ' linear, MW 25 kDa (40 kDa nominal), 3 mg/ml stock solution in water, pH 7.0 (Polysciences Inc. cat# 24765-2) was mixed with purified and quantified plasmid DNA of interest.
  • A260/A280 ratio (use 50 mM Tris-HCl pH 8.0 to dilute the plasmid DNA) was between 1.85 and 1.95.
  • the cells were used in exponential growth phase, 2-2.2xl0 6 cells/ml in CHO FreeStyle medium.
  • DNA preparations (0.75mg/L) encoding for Heavy or Light chains of immunoglobulin were mixed with PEI in CHO FreeStyle medium at 1 :5 (w:w) ratio, the mixture was then incubated 8-10 min, add then added to culture. Volume of the transfection mixture was 1/10 of the final volume of the production culture.
  • immunoglobulins were from 20 to 100 mg/L.
  • the immunoglobulin production was monitored by commercially available ELISA kit (Bethyl Laboratories).
  • the Protein A Plus Agarose resin was harvested and placed into 15 -ml columns (Pierce) and then washed with 10 volumes of lx PBS, then with 10 volumes of 25mM Tris-HCl, 0.12M Glycine, 1.5M NaCl (pH 8.5), then with 10 volumes of TBS-Tween-20, then with 10 volumes of 20mM Sodium Citrate Buffer, 1M NaCl (pH 5.5) and the final wash with 10 volumes of 150mM Sodium Chloride without any buffer.
  • the elution of bound immunoglobulins was carried out with Elution Buffer (0.1 M Glycine pH 3.0, 10% Sucrose, 150mM NaCl) that was added at ratio of 1 : 1 to the volume of Protein A Plus Agarose resin.
  • Elution Buffer 0.1 M Glycine pH 3.0, 10% Sucrose, 150mM NaCl
  • the elution buffer was incubated with the Protein A Plus Agarose resin for 3 min, removed and then another portion of fresh Elution Buffer was added to the Protein A Plus Agarose resin.
  • the eluted material was immediately neutralized by 0.5 M Sodium Citrate Buffer, pH 6.0, at the 1/10 volume ratio to the eluted volume.
  • the concentration of the resulting immunoglobulin preparations was determined by measure optical density of the solution at 280nm in UV-transparent cuvettes where a mixture of 0.1 ml of 0.5 M Sodium Citrate, pH 6, with 1ml of the Elution Buffer was used as a Reference Buffer.
  • concentration of IgG the following formula that provides IgG concentration in mg/ml, was used:
  • [IgG] OD 280 * DilutionFactor ⁇ w ⁇ Q .
  • This example describes the method for determination of the affinities of the antibodies against human integrin alpha-4 receptor and provides means of comparison of properties of different antibody clones.
  • VCAM-1 was coated onto an ELISA plate by overnight incubation (lOug/ml).
  • KA4 cells K562 overexpressing Integrin alpha-4) (5xl0 3 per well) were plated on a 96-well plate.
  • Antibodies were added at various concentrations (from 0.02 nM to 500 nM) and incubated for 30 minutes. Cells were transferred onto the VCAM-1 coated plate and incubated overnight at 37°C. Unbound cells were removed by washing three times with PBS. Washing efficiency was monitored using a microscope. The cells that remained attached to the VCAM-1 coated plate were analyzed using the MTT assay for colorimetric analysis and quantitation. Background binding was assessed using BSA-coated wells and subtracted from the experimental values. As a positive control commercially available comparator anti- integrin alpha-4 antibody - Tysabri was used. The obtained data were analyzed utilizing GraphPad Prism 5.0 software and EC50 values were calculated using antagonistic 4-parameter curve fit algorithm. The results of the analysis are presented graphically in Figures 6 A and 6B.
  • Dynamic light scattering also called photon correlation spectroscopy or quasi-elastic light scattering
  • Large protein (di-, tri-, and other multimer) particles exhibit long decay times and contribute more significantly to the overall light scattering intensity compared to small particles, e.g. a monomeric form of a MAB.
  • DLS allows picking up signals arising from small populations of protein oligomers among a highly concentrated monomeric form.
  • the light scattering arising from a monomeric protein is often lost in the strong contribution of aggregates. To prevent this effect, all protein solutions to be studied by DLS are thoroughly filtrated prior to analysis.
  • natalizumab (Tysabri); and the other - on the same antibodies after eight days of incubation at 37° C.
  • the antibodies Prior to conducting measurements, the antibodies were centrifuged at 12,000 rpm for 10 min. Measuremets with IN8 were conducted without antibody stock dilution, while IN9A and IN 10 stocks were diluted twofold with the antibody storage buffer solution. DLS measurements were carried out using a Zetasizer Nano ZS (Malvern Instruments Ltd, UK) system. The backscattered light from a 4 mW He-Ne 632.8 nM laser was collected at an angle of 173°. Protein concentration was between 0.3 andl mg/ml. Buffer conditions were as follows: PBS, PMSF and NaN3 (0.02%), pH 7.4. Prior to experiments solutions were passed through 0.1 ⁇ Whatman® Anotop® 10 syringe filter. Sample temperature was kept at 25.0°C. The acquisition time for a single
  • Circular dichroism refers to the difference in absorption of left and right circularly polarized light.
  • Each of the protein secondary structure types possesses its own characteristic CD spectrum.
  • the CD spectrum of protein under study is deconvoluted into components corresponding to the contributions from different secondary structure types. Since antibodies are characterized by very high content of ⁇ -pleated sheets, their CD spectra closely resemble those for pure ⁇ -strand structure.
  • Figure 9 shows far-UV CD data for antibodies IN8, IN9A and IN10, alongside with Tysabri, all formulated in PBS, pH 7.4. Protein concentration used was between 0.11 and 0.18 ⁇ . CD studies were carried out utilizing a J-810
  • spectropolarimeter (JASCO, Inc.), equipped with a Peltier-controlled cell holder.
  • the instrument was calibrated with an aqueous solution of d-10-camphorsulfonic acid.
  • the cell compartment was purged with nitrogen.
  • a quartz cell with a path length of 1 mm was used. Buffer contribution was subtracted from experimental spectra. Bandwidth was 2 nm, averaging time - 2 s, and
  • Trosabri is a registered trademark of Biogen Po Inc., a Delaware Corporation.

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Abstract

Therapeutic antibodies are described that can be used for treating or prevention of diseases associated with modulation of activity of human integrin alpha-4. In certain aspects, the disclosed invention is based upon discovering antibodies that are capable of binding to human integrin alpha-4. The disclosed antibodies are capable of blocking the interactions between integrin alpha-4 and its VCAM-1. The disclosed antibodies could be administered to humans without additional modifications such as a "humanization" process. The antibodies could also be used as diagnostics and for research purposes. The described monoclonal antibodies are applicable for integrin alpha-4 /VCAM-1 signaling cascade targeting in drug development for cancer and immunological disorders.

Description

Fully Human Antibodies Against Human Receptor Integrin Alpha-4
FIELD
The invention generally relates to the field of molecular biology, immunology, autoimmune and inflammatory diseases and oncology. More specifically, the invention relates to antibodies that bind to human receptor integrin alpha-4.
BACKGROUND Alpha4 integrin is among 24 integrin families of cell-adhesion molecules containing noncovalently-associated alpha and beta subunits. Eighteen different integrin alpha subunits and eight different beta subunits have been reported to date in vertebrates, forming at least 24 alpha/beta heterodimers. These varied formations suggest that integrins constitute the most structurally and functionally diverse family of cell-adhesion molecules yet known. Integrins mediate cell-cell and cell extracellular matrix interactions over a wide range of biological contexts. Integrins support force-resistant stable firm adhesion as well as the dynamic adhesive interactions observed in cellular polarization and cell migration. Integrins play a crucial role in many physiological processes, including tissue morphogenesis, inflammation, wound healing, and regulation of cell growth and differentiation.
The adhesive and signaling activities carried out by integrins are vital to many of the cell-cell and cell-extracellular matrix interactions involved in immune responses. Alpha4 integrin plays a critical role in their adhesive interactions with endothelial cells during migration to lymphoid organs and extravasation to sites of inflammation. Alpha-4 integrin subunit pairs with the betal and beta7, thereby constituting integrin alpha-4-betal (also termed very late antigen-4 or VLA-4) and alpha4-beta7 (also termed lymphocyte Peyer's patch adhesion molecules or LPAM-1) receptors. Alpha4-betal binds to a major endothelial ligand vascular cell adhesion molecule (VCAM-1), and an extracellular matrix ligand fibronectin (FN) deposited in inflamed tissues, while alpha4-beta7 binds to MAdCAM-1 preferentially expressed in the gut. Alpha4 integrins are known to play crucial roles in tissue-specific leukocyte trafficking to the inflamed brain (alpha4- betal) and to the inflamed gut (alpha4-beta7). Alpha4 integrins are also known to regulate hematopoietic stem cell trafficking and retention in the bone marrow. Persistent accumulation of leukocytes is a hallmark of the chronic inflammation observed in the affected tissues of autoimmune diseases such as Multiple sclerosis (MS) and Crohn's disease. For leukocytes to accumulate within inflamed tissues, they must interact with and subsequently pass an endothelial lining on the inner surface of the vasculature. The leukocyte-endothelial interactions leading to extravasation are regulated by a sequence of multiple steps involving adhesion molecules and chemokine signaling. At inflammatory sites, circulating leukocytes that flow in blood vessels start to tether and roll along endothelial cells via selectins and their ligands. This rolling interaction serves to slow down leukocytes and place them in proximity to the inflamed endothelial cells, thereby enabling these cells to efficiently scan the endothelial surface for available chemokines. While rolling, leukocytes encounter chemokines and become activated via chemokine receptors present on the leukocytes. Chemokine signaling elicits an intracellular signaling cascade that eventually impinges on integrin cytoplasmic domains, thereby triggering integrin activation. Upon activation, global conformational changes occur that rapidly convert a low-affinity latent integrin into a high-affinity ligand-competent state. In this way, the high-affinity integrin mediates the rapid arrest of rolling leukocytes and shear-resistant firm adhesion at inflamed endothelial cells.
The cascade of leukocyte-endothelial cell interactions was originally thought to contain three steps (i.e., rolling by selectins, activation by chemokines, and upregulation of integrin affinity) before transmigration of leukocytes across the endothelial barrier could occur. A crawling step has recently been added to this cascade. Specifically, leukocytes crawl along the endothelial surface from the point of arrest to that of transmigration. The dynamic regulation of integrin affinity plays a critical role in supporting such leukocyte crawling.
During transendothelial migration (TEM), leukocytes proceed through endothelial cells via two distinct routes, either paracellular or transcellular. In the former, leukocytes transmigrate in between adjacent endothelial cells, which usually form tightly sealed junctions, thereby leaving no space between them. During paracellular TEM, the junctions between endothelial cells are dynamically disassembled, thereby creating a gap for a leukocyte to pass through. This gap is closed as soon as the trailing edge of the leukocyte passes beyond it. In contrast, during transcellular TEM, a leukocyte transmigrates through a single endothelial cell. A pore is formed for a leukocyte to move through. The pore formation that develops during transcellular TEM is thought to be mediated by a dynamic remodeling of the endothelial cell-rich plasma membrane that involves vimentin as well as caveolae or vesiculovacuolar organelles.
Organ-specific homing of leukocytes is made possible primarily by unique combinations of cell-adhesionmolecules and chemokine receptors. Naive lymphocytes recirculate between the blood stream and peripheral lymphoid tissues, thereby patrolling the body for microorganisms and transformed cells. Gut-tropic effector T cells, which play a pathogenic role in inflammatory bowel diseases, upregulate in integrin alpha-4-beta7 and the chemokine receptor CCR9. Brain-tropic effector T cells, which are responsible for the pathogenesis of multiple sclerosis, upregulate in integrin alpha-4-betal .
Migration of leukocytes from the blood into the central nervous system (CNS) involves multiple events that occur in a defined chronological and spatial order, including rolling, chemoattraction, cell adhesion, and proteolytic degradation of biological membranes. It is thought that slow rolling on endothelial walls allows leukocytes to identify proper arrays of
chemoattractants and integrin ligands. Prolonged selectin-mediated rolling of neutrophils and lymphocytes may also lead to integrin activation. Once firmly arrested, integrins serve for leukocytes to bind to other blood-borne leukocytes and platelets. VLA-4 have been shown to facilitate leukocyte migration across the basement membrane of blood vessels, as well as across extracellular matrix (ECM). The interaction of these integrins with ECM may propagate leukocyte immobilization, or bridging between cells. Eventually, VLA-4 integration leads to extravasation of neutrophils and lymphocytes into peripheral tissues and CNS. Thus antibodies that inhibit the interaction between integrin alpha-4 and it's ligand VCAM1 may serve as a therapy for MS and Crohn's disease.
MS is an inflammatory demyelinating disorder of CNS. Histopatho logically, most acute active MS lesions are characterized by monocytes and lymphocytes infiltration in to the brain. This is considered a critical event in the pathogenesis of MS. Cell adhesion of leukocytes to the endothelial wall has been a major target of drug development against MS. Antibodies against integrin alpha-4 (VLA-4) were the first pharmacological agents that were successfully brought to clinical trials and approved for the treatment of relapsing-remitting MS (RR-MS). Natalizumab is a humanized anti-integrin alpha-4 monoclonal antibody which under the trade name TYSABRI was approved by the U.S. Food and Drug Administration (FDA) for the treatment of RR-MS and of Crohn's disease. Currently natalizumab is regarded as the most potent treatment for RR-MS. The scientific rationale for the therapy with antibodies that block integrin alpha-4 is the reduction of leukocyte extravasations into the peripheral tissues, including the brain and the spinal cord by interfering with the physical interaction of VLA-4 with its natural ligands, VCAM-1 and FN.
Further discussion of integrin molecules and their therapeutic utility can be found in the references provided below:
Olaf Stuve and Jeffrey L. Bennett (2007) Pharmacological properties, Toxicology and Scientific rationale for the use of Natalizumab (Tysabri) in Inflammatory Diseases. CNS Drug Review Vol.13, No. l, pp.79-95;
Lucchinetti C, Bruck W, Parisi J, Scheithauer B, Rodriguez M, Lassmann H (2000)
Heterogeneity of multiple sclerosis lesions: Implications for the pathogenesis of demyelination. Ann Neurol 47:101 -111;
Yednock TA, Cannon C, Fritz LC, Sanchez-Madrid F, Steinman L, Karin N (1992)
Prevention of experimental autoimmune encephalomyelitis by antibodies against alpha 4 beta 1 integrin. Nature 356:63-66;
Theien BE, Vanderlugt CL, Eagar TN, Nickerson-Nutter C, Nazareno R, Kuchroo VK,
Miller SD (2001) Discordant effects of anti-VLA-4 treatment before and after onset of relapsing experimental autoimmune encephalomyelitis. J Clin Invest 707:995-1006;
Piraino PS, Yednock TA, Freedman SB, Messersmith EK, Pleiss MA, Vandevert C, Thorsett ED, Karlik SJ (2002) Prolonged reversal of chronic experimental allergic encephalomyelitis using a small molecule inhibitor of alpha4 integrin. J Neuroimmunol 131: 141-159;
Piraino PS, Yednock TA, Messersmith EK, Pleiss MA, Freedman SB, Hammond RR, Karlik SJ (2005b) Spontaneous remyelination following prolonged inhibition of alpha4 integrin in chronic EAE. J Neuroimmunol 167:53-63;
Miller DH, Khan OA, Sheremata WA, Blumhardt LD, Rice GP, Libonati MA, Willmer- Hulme AJ, Dalton CM, Miszkiel KA, O'Connor PW (2003) A controlled trial of natalizumab for relapsing multiple sclerosis. N. Engl J Med 348: 15-23;
Rudick RA, Stuart WH, Calabresi PA, Confavreux C, Galetta SL, Radue EW, Lublin FD, Weinstock-Guttman B, Wynn DR, Lynn F, et al. (2006) Natalizumab plus interferon beta- la for relapsing multiple sclerosis. N. Engl J Med 354:911-923;
Luster AD, Alon R, von AndrianUH (2005) Immune cell migration in inflammation: Present and future therapeutic targets. Nat Immunol 6:1182-1190; Smith ML, Olson TS, Ley K (2004) CXCR2- and E-selectin-induced neutrophil arrest during inflammation in vivo. J Exp Med 200:935-939;
Shimizu Y, van Seventer GA, Horgan KJ, Shaw S (1990b) Roles of adhesion molecules in T- cell recognition: Fundamental similarities between four integrins on resting human T cells (LFA-1, VLA-4, VLA-5, VLA-6) in expression, binding, and costimulation. Immunol Rev 114: 109-143;
Kawamoto E, Nakahashi S, Okamoto T, Imai H, Shimaoka M. Anti-integrin therapy for multiple sclerosis. Autoimmune Dis. 2012;2012:357101. doi: 10.1155/2012/357101. Epub 2012 Dec 17;
D. M. Rose, J. Han, and M. H. Ginsberg, " 4 integrins and the immune response,"
Immunological Reviews, vol. 186, pp. 118-124, 2002;
C. Kim, F. Ye, and M. H. Ginsberg, "Regulation of integrin activation," Annual Review of Cell and Developmental Biology, vol. 27, pp. 321-345, 2011;
Y. Imai, M. Shimaoka, and M. Kurokawa, "Essential roles of VLA-4 in the hematopoietic system," InternationalJournal of Hematology, vol. 91, no. 4, pp. 569-575, 2010;
M. Phillipson, B. Heit, P. Colarusso, L. Liu, C. M. Ballantyne, and P. Kubes, "Intraluminal crawling of neutrophils to emigration sites: a molecularly distinct process from adhesion in the recruitment cascade," Journal of Experimental;
J. R. Mora and U. H. von Andrian, "T-cell homing specificity and plasticity: new concepts and future challenges," Trends in Immunology, vol. 27, no. 5, pp. 235-243, 2006.
SUMMARY OF THE INVENTION
The invention is based, in part, upon the discovery of antibodies that specifically bind to human integrin alpha-4 blocking the VCAM-1 /integrin alpha-4 interactions. Series of antibodies were isolated from antibody libraries that contained fully human antibody frames. The CDRs (Complementarity Determining Regions) of integrin alpha-4 -specific antibodies differ from each other, consistent with the design of the antibody libraries used. In these libraries, CDRl and CDR2 of the antibody heavy chain were randomized to provide limited number of variation and CDR3 of the heavy chain was randomized to include all possible amino acid combinations. For the light chain, CDRl and CDR2 were invariant and CDR3 was randomized completely. Since the frameworks for both heavy and light chain of antibodies were corresponding to human sequences, the antibodies described herein could be administered to humans without additional modifications such as a "humanization" process. The antibodies could also be used as diagnostics and for research purposes.
The monoclonal antibodies disclosed herein are applicable for integrin alpha-4 /VCAM-1 signaling cascade targeting in drug development for cancer and immunological disorders, such as Crohn's and MS, and others.
In one aspect the invention provides for an isolated antibody (IN8), or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor. The antibody comprises an immunoglobulin light chain of SEQ. ID NO. 90, and an immunoglobulin heavy chain of SEQ. ID NO. 82. The antibody can be a monoclonal antibody.
The invention further provides for an isolated antibody (integrin IN9A), or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor. The antibody comprises an immunoglobulin light chain of SEQ. ID NO. 92, and an immunoglobulin heavy chain of SEQ. ID NO. 84. The antibody can be a monoclonal antibody.
The invention even further provides for an isolated antibody (IN 10), or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor. The antibody comprises an immunoglobulin light chain of SEQ. ID NO. 94, and an immunoglobulin heavy chain of SEQ. ID NO. 86. The antibody can be a monoclonal antibody.
In another aspect the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4. The antibody comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 57, a CDRL2 comprising the sequence of SEQ. ID NO. 58, and a CDRL3 comprising the sequence of SEQ. ID NO. 59. The antibody further comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the sequence of SEQ. ID NO. 17, a CDRH2 comprising the sequence of SEQ. ID NO. 18, and a CDRH3 comprising the sequence of SEQ. ID NO. 19. The CDR sequences of the antibody can be interposed between human or humanized framework sequences.
In another aspect the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4. The antibody comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 58, a CDRL2 comprising the sequence of SEQ. ID NO. 59, and a CDRL3 comprising the sequence of SEQ. ID NO. 61. The antibody further comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the sequence of SEQ. ID NO. 23, a CDRH2 comprising the sequence of SEQ. ID NO. 24, and a CDRH3 comprising the sequence of SEQ. ID NO. 25. The CDR sequences of the antibody can be interposed between human or humanized framework sequences.
In another aspect the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4. The antibody comprises an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 58, a CDRL2 comprising the sequence of SEQ. ID NO. 59, and a CDRL3 comprising the sequence of SEQ. ID NO. 63. The antibody further comprises an immunoglobulin heavy chain variable region comprising a CDRH1 comprising the sequence of SEQ. ID NO. 29, a CDRH2 comprising the sequence of SEQ. ID NO. 30, and a CDRH3 comprising the sequence of SEQ. ID NO. 31. The CDR sequences of the antibody can be interposed between human or humanized framework sequences.
In yet another aspect the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4. The antibody comprises an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ. ID NO. 41, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ. ID NO. 01. The antibody can be a monoclonal antibody.
In yet another aspect the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4. The antibody comprises an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ. ID NO. 45, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ. ID NO. 05. The antibody can be a monoclonal antibody.
In yet another aspect the invention provides for an isolated antibody, or an antigen binding fragment of the antibody, that binds human integrin alpha-4 receptor. The antibody comprises an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ. ID NO. 49, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ. ID NO. 09. The antibody can be a monoclonal antibody. These and other aspects and advantages of the invention described herein will become apparent upon consideration of the Figures and detailed description of antibody properties below.
BRIEF DESCRIPTION OF THE DRAWINGS
The following drawings and descriptions provide complete understanding of the invention: Figure 1 schematically shows representation of a typical antibody. Gray areas on the scheme depict Constant Regions of both antibody light and heavy chains, black areas depict Variable
Regions of the antibody light chain, white areas depict Variable Regions of the antibody heavy chain. CHI , CH2 and CH3 - constant regions 1 , 2 and 3of the antibody heavy chain respectively.
VH - Variable Regions of the antibody heavy chain; VL - Variable Regions of the antibody light chain; CL - Constant Region of the antibody light chain. Links between heavy and light chains and between two heavy chains depict intermolecular disulfide bridges;
Figure 2 schematically shows the amino acid sequences defining a complete immunoglobulin Heavy Chain Variable Region of the antibodies assigned as IN8, IN9, IN9A, IN9B, INIO, IN20,
IN22, and IR24; the amino acid sequences are aligned relative to each other where the regions defining CDR1, CDR2 and CDR3 respectively are identified in boxes; the unboxed sequences represent immunoglobulin framework; the length of shorter CDRs is adjusted for the alignment purpose by introducing dashes (-);
Figure 3 schematically shows amino acid sequences of CDR1, CDR2 and CDR3 for each immunoglobulin Heavy Chain Variable Region shown in Figure 2;
Figure 4 schematically shows the amino acid sequences defining a complete immunoglobulin
Light Chain (Kappa) Variable Region of the antibodies assigned as IN8, IN9, IN9A, IN9B, INIO,
IN20, IN22, and IR24; the amino acid sequences are aligned relative to each other where the regions defining CDR1, CDR2 and CDR3 respectively are identified in boxes; the unboxed sequences represent immunoglobulin framework; the length of shorter CDRs is adjusted for the alignment purpose by introducing dashes (-);
Figure 5 schematically shows amino acid sequences of CDR1, CDR2 and CDR3 for each immunoglobulin Light Chain (Kappa) Variable Region shown in Figure 4;
Figure 6 A show a graphic representation of VCAM-1 adhesion assay results performed with
Tysabri (positive control) and antibodies IN8, IN9, and IN9A; Figure 6B show a graphic representation of VCAM-1 adhesion assay results performed with antibodies IN9B, IN 10, IN20, and IN24;
Figure 7 shows the distribution of hydrodymanic sizes of antibodies IN8 (top peak), IN9A (middle peak), and IN 10 (lower peak) on freshly isolated (top panel a) and stored at 37°C for 8 days (bottom panel b) preparations, the table insert in top panel a) shows the average diameters of antibody molecules in solution after incubation, the graph for Tysabri is not shown but in also appears with a hydrodinamyc diameter of around 12.55 nM, all measurements have been carried out at a final protein concentartions of 2 mg/ml;
Figure 8 shows a graphic representation of specific heat capacity (Cp) measurements of antibodies IN8 (dot line), IN9A (dashed line), and IN 10 (solid line), derived from DSC data; and
Figure 9 shows a graphic representation of far-UV circular dichroism (CD) data for antibodies IN8, IN9A and IN10, alongside with Tysabri, while the curves are virtually
indistinguishable.
DETAILED DESCRIPTION OF THE INVENTION
The invention is based, in part, upon the discovery of antibodies that specifically bind to human integrin alpha-4 (UniProtKB/Swiss-Prot: P13612) and block interactions with its cognate ligand VCAM-1 (UniProtKB/Swiss-Prot: PI 9320). The antibodies could be used for a variety of diagnostic and therapeutic applications and as research tools. The antibodies were selected for their ability to bind to human integrin alpha-4 with high affinity, specificity and selectivity.
Additionally, the functional properties of the abtibodies were tested in a quantitative VCAM-1 adhesion assay.
Since the antibodies described herein are engineered on the basis of human sequences, all of them could be administered to humans directly. Depending on a particular application, the described antibodies could be used as targeting moieties for various payloads such as
radionuclides, drugs, toxins and other effector molecules. Certain features and aspect of the application of the invention are described in more details below. I - ANTIBODIES AGAINST HUMAN INTEGRIN ALPHA-4
In one aspect, the invention provides for an isolated antibody that specifically binds to human integrin alpha-4. The antibody is comprised of (1) an immunoglobulin light chain variable region comprised of three CDRs and (2) an immunoglobulin heavy chain variable region comprised of three other CDRs. The CDRs are embedded into the immunoglobulin framework generated by less variable FR domains. The CDRs of the immunoglobulin light and heavy chain brought together in immunoglobulin molecule define a unique binding site that specifically binds to a native conformation of integrin alpha-4. The terms "binds specifically" or "specifically binds" are interchangeable and mean that binding affinities (EC50 values) of the antibodies described herein are below 50 nM (5* 10~8 M).
It is understood that the antibodies can comprise both immunoglobulin heavy and light chain sequences of fragments thereof, such as Fab or Fab2 fragments. It is understood that specific binding and functional properties can be displayed by a full-length intact immunoglobulin or antigen binding fragment thereof or biosynthetic antibody site.
It is understood that each of the antibody molecules can be an intact antibody, for example, a monoclonal antibody. Alternatively, the antigen binding could be displayed by an antigen binding fragment of an antibody or can be a biosynthetic antibody binding site. Antibody fragments include Fab, Fab2 or Fv fragments. Techniques for making such antibody fragments are known to those skilled in the art. A number of biosynthetic antibody binding sites are known in the art and include single Fv or sFv molecules, for example as described in US Patent # 5,476,786. Other biosynthetic antibody binding sites include bi-specific or bi-functional antibodies that bind to at least two different target molecules. For example, a bi-specific antibody can bind to human integrin alpha-4 and to another antigen of interest. Methods for making bi-specific antibodies are known in art and include fusing hybridomas or linking Fab fragment together.
II - PRODUCTION OF INTEGRIN ALPHA-4 ANTIBODIES
Antibodies described in this invention can be produced in different ways utilizing previously developed approaches. For example, DNA encoding variable regions of light and heavy chains can be synthesized chemically using commercially available services and sequence information provided in this invention. Alternatively, the DNA encoding variable regions of heavy and light chains can be amplified by Polymerase Chain Reaction (PCR) using the original clones of Fab fragments of the antibodies described herein, as templates. Synthetic or PCR-amplified DNA fragments can be genetically fused with appropriate nucleotide sequences to generate full-size antibodies or fragments thereof. Antibody expression constructs can be generated by including immunoglobulin constant region coding sequences, sequences providing expression control and other standard elements of expression systems. Generation of specific gene expression constructs is within ordinary skill in the art.
The DNA sequences encoding antibodies of interest can be genetically inserted into expression vectors that can be introduced into host cells using standard transfection of
transformation procedures known in the art. Examples of expression approaches include bacterial expression (E. coli) or mammalian expression (Chinese Hamster Ovary (CHO) cells, HeLa cells, Baby Hamster Kidney (BHK) cells, monkey kidney (COS) cells, Human Embryo Kidney (HEK- 293) cells and myeloma cells that do not produce endogenous immunoglobulins. Transfected or transformed host cells can be propagated under conditions providing expression of genes of interest, such as immunoglobulin light and heavy chains and fragments thereof. The expressed proteins can be harvested using common techniques known in the art.
The particular conditions for production of antibodies or fragments thereof vary depending on the expression system utilized. For example, E. co/z'-based expression system is particularly suitable for production of Fab, Fab2 or sFv antibody fragments. The engineered antibody gene is cloned into a vector suitable for bacterial expression downstream from a commonly used bacterial promoters, e.g. T5 of Lac. Genetic fusion of a signal sequence providing targeting on the expressed protein into the periplasm may enable production and accumulation of soluble forms of antibody fragments into the periplasm of bacterial cells. Extraction of proteins of interest and, specifically, of antibody fragments from the periplasm of bacteria is a well-established array of standard methods known in the art.
If the antibodies are produced in mammalian expression systems, DNA coding sequences must be inserted into appropriate expression vectors containing adequate eukaryotic promoter, signal peptide for secretion from the cells and other genetic elements known in the arts.
Mammalian expression systems are particularly suitable for production of full-size
immunoglobulins. One of the approaches for antibody production is transient co-expression of heavy (variable + constant) and light (variable + constant) chains of immunoglobulin genetically introduced into two separate expression vectors. Another approach for antibody production is expression on both heavy and light chains from a single bi-cistronic vector. Alternatively, stable cell lines constitutively expressing both heavy and light chains can be generated using single vector approach or utilizing two-vector systems.
Alternative approaches for antibody production include expression in yeast (P. Pastoris or similar strains) or plant cells. Each expression system requires generation of host-specific genetic constructs and generation of expression constructs is very similar to described above bacterial and mammalian expression systems.
It is understood that regardless of the expression system utilized for production of antibodies of fragments thereof, the protein sequence of each antibody remains the same and directly corresponds to the sequence of this invention. It is also understood that DNA sequence may be altered, for example, by the process known as codon optimization that provides higher protein production, depending on host-specific codon usage.
It is understood that during the process of generation of expression constructs for antibodies and fragments thereof, various genetic modifications can be introduced. For example, epitope or purification tags or peptide and protein toxins can be genetically fused to the expression constructs encoding heavy chain, light chain or combination of both immunoglobulin chains.
Ill - MODIFICATIONS OF INTEGRIN ALPHA-4 ANTIBODIES
It is understood that the antibodies disclosed herein can be modified to improve performance which largely depends on the intended use. For example, if used as therapeutic agent, the antibody can be genetically modified to reduce its immunogenicity in the intended recipient. Additionally, or as an alternative, the antibody can be genetically fused or coupled to another peptide or protein, such as epitope tag, purification tag, a growth factor, cytokine or natural or modified toxin. These modifications can be readily achieved by utilizing genetic manipulations known in the art. IV - USE OF INTEGRIN ALPHA-4 ANTIBODIES
The integrin alpha-4 -specific antibodies described herein can be used as therapeutic and diagnostic agents or as reagents for basic and applied research and development.
(1) Therapeutic Applications
Because the antibodies in the invention specifically bind to human integrin alpha-4 and block interactions with its cognate ligand VCAM-1, they can be utilized in a variety of therapeutic applications. It is contemplated that the antibodies of the invention can be used for the treatment of a variety of disorders in which integrin alpha-4 mediated signaling is involved. This includes Multiple Sclerosis, Crohn's desease and alike, as well as various types of cancers.
(2) Diagnostic Applications
Whenever the antibodies are used for diagnostic purposes, either in vivo or in vitro, the antibodies are typically modified directly or indirectly with a detection moiety. The detection moiety is a functional addition to the antibody that can be detected either directly or indirectly or is capable of generating a detectable signal. For example, the detectable moiety can be a
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radionuclide ( Iodine, Phosphorus, Carbon or others), fluorescent or chemiluminescent compound, such as fluorescein, rhodamine or luciferine. Enzyme moieties include alkaline phosphatase, horse radish peroxidase, beta-galactozidase and others. Methods for conjugation of the detection moieties largely depend on the nature of the moiety and routinely can be reproduced by those experienced in the art.
The antibodies of the invention can be used in a broad range of immunological techniques know in the art. Examples of such techniques include sandwich immunoassays (ELISA), competitive immunoassays, cell surface staining procedures combined with FACS analysis, immunocyto- and immunohistochemical procedures. Protocols and method all of these procedures and assays are well-established and can be routinely carried out by those skilled in the art. EXAMPLES
The following examples illustrate selection, identification and characterization of a number of fully human recombinant antibodies against human integrin alpha-4 receptor.
Example 1 - Generation of Magnetic Proteo liposomes as antigen presenting platforms.
Isolation of antibodies that recognize native conformations of integrin alpha-4 is absolutely critical for the development of such antibodies as therapeutics. In the human body and tissues integrin alpha-4 is present in its native form, therefore only the antibodies that bind to the native receptor have practical utility. Preparation of antigen-presenting platforms that provide oriented and functional receptor in its native conformation is far from being trivial. Many methods of antibody generation, for example generation of antibodies against peptide epitopes or receptor fragments, usually are not successful for complex targets such as integrin alpha-4. Previously patented technology that relies on the generation of magnetic proteoliposomes (MPLs) (Sodroski, J.G. and T. Mirzabekov, Proteoliposomes containing an integral membrane protein having one or more transmembrane domains; US Patent 6,761,902;) has been used for isolation of antibodies against integrin alpha-4.
The main advantage of the core technology that relies on usage of MPLs is the ability to present highly purified and concentrated antigen (human integrin alpha-4 in this invention) properly oriented and, most importantly, in its native conformation and functional state. Although the technology disclosed in US Patent 6,761,902 can be applied to a variety of complex membrane proteins, each target requires extensive optimization of protein extraction and MPL formation conditions.
Prior to preparing MPL particles, a stable cell line was prepared, utilizing established protocols, overexpressing human recombinant integrin alpha-4. The condition for extraction of human integrin alpha-4 were tested and optimized prior to the initiation of the antibody selection procedure. An extensive matrix of combinations of various detergents, salts and buffer components was analyzed to identify conditions providing a balance between effective extraction of the integrin alpha-4 and retaining of its function and native conformation. The integrin alpha-4 functionality was tested by assaying binding of its ligand, VCAM-1, to the integrin alpha-4 immobilized on the surface of the MPLs. Stability of the MPL particles (as judged by VCAM-1 and Tysabri (natalizumab)) binding was also tested to ensure that the native conformation of the integrin alpha-4 is retained for the duration of the antibody selection protocol. Example 2 - Antibody libraries and selection of anti-integrin alpha-4 antibodies.
Selection of human integrin alpha-4-specific antibodies was carried out from antibody libraries encoding a series of fully human Fab antibody fragments consisting of 1010 - 1011 independent antibody clones. Randomization of all three CDRs (CDRl, CDR2 and CDR3) was carried out for the heavy chain of Fab fragments. Randomization of CDR3 was carried out for the light chain of Fab fragments whereas CDRl, CDR2 were kept invariant. A phage display library represents a collection of individual phage particles that express only a certain type of a genetic fusion of an individual Fab antibody fragment with a surface protein intrinsic for this particular type of phage. A fraction of the phage display library usually containing 1012-1013 phage particles is used as a primary source of the antibody variety.
A fraction of the phage display library (1012-1013 phage particles) was incubated with MPL preparations containing functional integrin alpha-4 in its native conformation. The phage particles that did not bind to the integrin alpha-4-MPLs were removed by a series of subsequent washes under conditions providing retention of the native conformation of integrin alpha-4. The pool of phage particles that was bound to integrin alpha-4-MPLs was removed by acidic elution. The deconvo luted phage output (usually 106-108 phage particles) was harvested and further amplified by propagation in E. coli. The pool of the amplified phage is then used further for the second selection round as described for the first round above. A minimum of 2 and maximum of 4 selection rounds are carried out for a standard selection procedure.
Example 3 - Screening of anti-integrin alpha-4 antibodies.
This example describes a procedure for screening antibodies specific against native conformations of integrin alpha-4 receptor. The screening procedure is based on the usage of live cells expressing human integrin alpha- 4 receptor on their surface. Generation of stable cell lines expressing integrin alpha-4 is described in Example 6 below. R1610 cells expressing integrin alpha-4 were used for screening.
Phage outputs from 3rd or 4th selection rounds represented pools of page particles that were used to infect E. coli to produce phagemid DNA. The phagemid DNA was digested with Nhel and BstEII to excise the entire Fab fragment and further introduced (ligated) into pQE3-Kan expression vector (Quiagen) digested with the same restriction enzymes, Nhel-BstEII. The resulting genetic construct was suitable for expression of Fab antibody fragment in bacteria under control of T5 promoter.
Pool of pQE3-Kan vector with inserted Fab fragments was used for transformation of E. coli.
The individual colonies resulting from the transformation were picked up and propagated in 96- well plates. Expression of Fab fragments was induced by IPTG and the expressed protein was harvested using standard biochemical approaches know to those in the art. Each well of 96-well plate containing single Fab clone was harvested separately and used further for binding property testing. A minimum of 500 and maximum of 50,000 individual clones were usually analyzed in the screening procedure.
The cells expressing human integrin alpha-4 were mixed with individual Fab preparations and allowed to interact for 30 min at 4°C. Unbound material was removed by pelleting the cells and by aspirating the supernatant. Binding the Fab antibody fragments to the cells was analyzed by secondary antibodies conjugated to phycoerythrin. The antibody binding was quantified by FACS analysis using 96-well plate compatible Guava flow cytometer. Clones that gave increase of the signal >5 fold over the background were scored as positive and kept for further analysis.
The antibody clones that bound to integrin alpha-4 were re-tested for their ability to interact with parental cells that did not express integrin alpha-4 in order to identify specific integrin alpha- 4 binders. The test was performed as described above and the final candidates from the screening had the following properties: they bind to the integrin alpha-4-expressing cells but not the integrin alpha-4-negative parental cells. Example 4 - Sequencing of anti-integrin alpha-4 antibodies.
The candidate Fab antibody clones identified in Example 3 were subjected to a sequencing analysis to identify independent clones. Bacterial cultures were submitted to Beckman Genomics automated sequencing facility.
The experimental sequencing data were analyzed by appropriate software, specifically the nucleic acid sequences were aligned to identify identical clones and to determine the differences in the deduced protein sequences. For example, variable regions can be identified using IMGT ACQUEST webserver-based software at http://^vw.imgi org/IMGT_ yq¾est/share/textes/. The sequencing analysis enabled detection of clones with identical sequences and only clones with unique and distinct DNA and protein sequences were kept for further evaluation.
In order to create a complete heavy chain and light chain immunoglobulin sequences, the variable region of the sequences shown below are combined with the corresponding constant region sequences. Signal peptides are not presented in the sequence; each sequence starts from the actual beginning of the antibody molecule according to Kabat numbering system.
IN8 Variable Region, Heavy Chain (Seq. ID NO. 02)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCAGT GCCTATACGA TGCATTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCGAG ATTGATTCGT ATT AT AG CG C TACCGACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGAATGTCT 3 01 AACTGGGAAT CTATGTCTGA CGGTCCGGCC TTGGACTACT GGGGCCAGGG AACCTTGGTC 361 ACCGTCTCGA GT
IN9 Variable Region, Heavy Chain (Seq. ID NO. 04) 1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCAGT GGCTATACTA TGCATTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCCTT ATTGAGTCGT ATACTGGCGA TACCTACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGATACTCT 301 TCTTACGACT ACGCCTTGGA CTATTGGGGC CAGGGAACCT TGGTCACCGT CTCGAGT
IN9A Variable Region, Heavy Chain (Seq. ID NO. 06)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCAGT GGCTATACTA TGCATTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCCTT ATTGAGTCGT ATACTGGCGA TACCTACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGATACTCT 301 TCTTACGACT ACGCCTTGGA CTATTGGGGC CAGGGAACCT TGGTCACCGT CTCGAGT
IN9B Variable Region, Heavy Chain (Seq. ID NO. 08)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCAGT GGCTATACTA TGCATTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCCTT ATTGAGTCGT ATACTGGCGA TACCTACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGGAGATAC 301 TCTTCTTACG ACTACGCCTT GGACTATTGG GGCCAGGGAA CCTTGGTCAC CGTCTCGAGT
IN10 Variable Region, Heavy Chain (Seq. ID NO. 10)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCAAT GCCTATTATA TGAGCTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCACT ATTTATCCGT ATTATAGCAA TACCGACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGAGGTATG 301 CATTACATGT CTGGTGCCTT GGACTACTGG GGCCAGGGAA CCTTGGTCAC CGTCTCGAGT IN20 Variable Region, Heavy Chain (Seq. ID NO. 12)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCACT GCCTATACTA TCCATTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCAAT ATTGATCCGT ATTATGGCTA TACCAACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGAACCTCC 301 TTCGGCCTGA GCAACGGGTT CGACTACTGG GGCCAGGGAA CCTTGGTCAC CGTCTCGAGT
IN22 Variable Region, Heavy Chain (Seq. ID NO. 14)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCAGT GACTATTATA TCTCATGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCAAT ATTGGGCCGT GGAATGGCTC TACCTACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGAGAGACG 301 AGGACTTATT GGGCTTATTC CTCTTCCGGC TTTGACTACT GGGGCCAGGG AACCTTGGTC 361 ACCGTCTCGA GT
IN24 Variable Region, Heavy Chain (Seq. ID NO. 16)
1 GAGGTGCAGC TGCTGGAGTC CGGTGGTGGT CTGGTACAGC CGGGTGGTTC TCTGCGTCTG 61 AGTTGCGCGG CCAGTGGCTT TACCTTCACT GACTATGCTA TGCATTGGGT GCGTCAGGCT 121 CCGGGCAAAG GTCTGGAATG GGTTAGCAGT ATTTATCCGT CTAATAGCTA TACCGACTAT 181 GCGGATAGCG TGAAAGGCCG TTTTACCATT TCTCGCGACA ACAGCAAGAA CACGCTGTAC 241 CTGCAGATGA ACTCACTGCG TGCCGAAGAT ACGGCCGTGT ATTACTGTGC GAGAGACAGG 301 AGCGTGATCG GGTTCGACTA CTGGGGCCAG GGAACCTTGG TCACCGTCTC GAGT
IN8 Variable Region, Light Chain, Kappa (Seq. ID NO. 42)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATCTTATT CTGCTGATCC TTTCACGTTC 301 GGCCAAGGGA CCAAGGTGGA AATCAAACGT A
IN9 Variable Region, Light Chain, Kappa (Seq. ID NO. 44)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATCTTATG CTTCTCCTTT CACGTTCGGC 301 CAAGGGACCA AGGTGGAAAT CAAACGTA IN9A Variable Region, Light Chain, Kappa (Seq. ID NO. 46)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATATTATG ATTATCCTGT CACGTTCGGC 301 CAAGGGACCA AGGTGGAAAT CAAACGTA
IN9B Variable Region, Light Chain, Kappa (Seq. ID NO. 48)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATATTATG ATTATCCTGT CACGTTCGGC 301 CAAGGGACCA AGGTGGAAAT CAAACGTA
IN10 Variable Region, Light Chain, Kappa (Seq. ID NO. 50)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATCTGCTT CTGATGATCC TTTCACGTTC 301 GGCCAAGGGA CCAAGGTGGA AATCAAACGT A
IN20 Variable Region, Light Chain, Kappa (Seq. ID NO. 52)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATCTTATG ATGATCCTAT CACGTTCGGC 301 CAAGGGACCA AGGTGGAAAT CAAACGTA IN22 Variable Region, Light Chain, Kappa (Seq. ID NO. 54)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATATTCTT ATTCTCCTAT CACGTTCGGC 301 CAAGGGACCA AGGTGGAAAT CAAACGTA
IN24 Variable Region, Light Chain, Kappa (Seq. ID NO. 56)
1 GAAATTGTGC TGACCCAGTC TCCGGGCACG TTATCTCTGA GCCCTGGTGA GCGCGCCACT 61 CTGTCATGCC GGGCTTCTCA AAGTGTTAGC AGTAGCTACC TGGCGTGGTA TCAGCAAAAA 121 CCGGGCCAGG CCCCGCGTCT GCTGATTTAC GGTGCATCCA GCCGTGCCAC CGGCATTCCA 181 GATCGTTTTT CCGGTAGTGG TTCTGGGACG GACTTCACTC TGACAATCTC ACGCCTGGAA 241 CCGGAGGATT TTGCGGTGTA TTACTGCCAG CAATATGCTT CTTATTCTCC TCTCACGTTC 301 GGCCAAGGGA CCAAGGTGGA AATCAAACGT A
Reference Human IgGl Heavy Chain Constant Region, nucleotide sequence (Seq. ID NO. 78) 1 GCTAGCACCA AGGGCCCATC GGTCTTCCCC CTGGCACCCT CCTCCAAGAG CACCTCTGGG
61 GGCACAGCGG CCCTGGGCTG CCTGGTCAAG GACTACTTCC CCGAACCGGT GACGGTGTCG
121 TGGAACTCAG GCGCCCTGAC CAGCGGCGTG CACACCTTCC CGGCTGTCCT ACAGTCCTCA
181 GGACTCTACT CCCTCAGCAG CGTGGTGACC GTGCCCTCCA GCAGCTTGGG CACCCAGACC
241 TACATCTGCA ACGTGAATCA CAAGCCCAGC AACACCAAGG TGGACAAGAA AGTTGAGCCC
301 AAATCTTGTG ACAAAACTCA CACATGCCCA CCGTGCCCAG CACCTGAACT CCTGGGGGGA
361 CCGTCAGTCT TCCTCTTCCC CCCAAAACCC AAGGACACCC TCATGATCTC CCGGACCCCT
421 GAGGTCACAT GCGTGGTGGT GGACGTGAGC CACGAAGACC CTGAGGTCAA GTTCAACTGG
481 TACGTGGACG GCGTGGAGGT GCATAATGCC AAGACAAAGC CGCGGGAGGA GCAGTACAAC
541 AGCACGTACC GTGTGGTCAG CGTCCTCACC GTCCTGCACC AGGACTGGCT GAATGGCAAG
601 GAGTACAAGT GCAAGGTCTC CAACAAAGCC CTCCCAGCCC CCATCGAGAA AACCATCTCC
661 AAAGCCAAAG GGCAGCCCCG AGAACCACAG GTGTACACCC TGCCCCCATC CCGGGAGGAG
721 ATGACCAAGA ACCAGGTCAG CCTGACCTGC CTGGTCAAAG GCTTCTATCC CAGCGACATC
781 GCCGTGGAGT GGGAGAGCAA TGGGCAGCCG GAGAACAACT ACAAGACCAC GCCTCCCGTG
841 CTGGACTCCG ACGGCTCCTT CTTCCTCTAC AGCAAGCTCA CCGTGGACAA GAGCAGGTGG
901 CAGCAGGGGA ACGTCTTCTC ATGCTCCGTG ATGCATGAGG CTCTGCACAA CCACTACACG
961 CAGAAGAGCC TCTCCCTGTC TCCGGGTAAA TGA
Reference Human IgGl Heavy Chain Constant Region, amino acid sequence (Seq. ID NO. 79)
1 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS
61 GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG
121 PSVFLFPPKP KDTLMISRTP EVTCWVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYN
181 STYRWSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE
241 MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW
301 QQGNVFSCSV MHEALHNHYT QKSLSLSPGK
Reference Human Light Chain Kappa Constant Region, nucleotide sequence (Seq. ID NO. 80)
1 CCGGTCACCA TGGAAATCAA ACGTACGGTG GCTGCACCAT CTGTCTTCAT CTTCCCGCCA
61 TCTGATGAGC AGTTGAAATC TGGAACTGCC TCTGTTGTGT GCCTGCTGAA TAACTTCTAT
121 CCCAGAGAGG CCAAAGTACA GTGGAAGGTG GATAACGCCC TCCAATCGGG TAACTCCCAG
181 GAGAGTGTCA CAGAGCAGGA CAGCAAGGAC AGCACCTACA GCCTCAGCAG CACCCTGACG 241 CTGAGCAAAG CAGACTACGA GAAACACAAA GTCTACGCCT GCGAAGTCAC CCATCAGGGC
301 CTGAGCTCGC CCGTCACAAA GAGCTTCAAC AGGGGAGAGT GTTAG
Reference Human Light Chain Kappa Constant Region, amino acid sequence (Seq. ID NO. 81)
1 PVTMEIKRTV AAPSVFIFPP SDEQLKSGTA SWCLLNNFY PREAKVQWKV DNALQSGNSQ
61 ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC
Heavy Chain of the antibody IN8, full amino acid sequence (Seq. ID NO. 82)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFS AYTMHWVRQA PGKGLEWVSE I DSYYSATDY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARMS NWESMSDGPA LDYWGQGTLV
121 TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV
181 LQSSGLYSLS SWTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTCPPCPAPE
241 LLGGPSVFLF PPKPKDTLMI SRTPEVTCW VDVSHEDPEV KFNWYVDGVE VHNAKTKPRE
301 EQYNSTYRW SVLTVLHQDW LNGKEYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP
361 SREEMTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT TPPVLDSDGS FFLYSKLTVD
421 KSRWQQGNVF SCSVMHEALH NHYTQKSLSL SPGK
Heavy Chain of the antibody IN9, full amino acid sequence (Seq. ID NO. 83)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFS GYTMHWVRQA PGKGLEWVSL IESYTGDTYY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARRY SSYDYALDYW GQGTLVTVSS
121 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS
181 GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG
241 PSVFLFPPKP KDTLMISRTP EVTCWVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYN
301 STYRWSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE
361 MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW
421 QQGNVFSCSV MHEALHNHYT QKSLSLSPGK
Heavy Chain of the antibody IN9A, full amino acid sequence (Seq. ID NO. 84)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFS GYTMHWVRQA PGKGLEWVSL IESYTGDTYY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARRY SSYDYALDYW GQGTLVTVSS 121 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS
181 GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG
241 PSVFLFPPKP KDTLMISRTP EVTCWVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYN
301 STYRWSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE
361 MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW
421 QQGNVFSCSV MHEALHNHYT QKSLSLSPGK
Heavy Chain of the antibody IN9B, full amino acid sequence (Seq. ID NO. 85)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFS GYTMHWVRQA PGKGLEWVSL IESYTGDTYY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARYS SYDYALDYWG QGTLVTVSSA
121 STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG
181 LYSLSSWTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTHTCPP CPAPELLGGP
241 SVFLFPPKPK DTLMI SRTPE VTCVWDVSH EDPEVKFNWY VDGVEVHNAK TKPREEQYNS
301 TYRVVSVLTV LHQDWLNGKE YKCKVSNKAL PAPIEKTISK AKGQPREPQV YTLPPSREEM
361 TKNQVSLTCL VKGFYPSDIA VEWESNGQPE NNYKTTPPVL DSDGSFFLYS KLTVDKSRWQ
421 QGNVFSCSVM HEALHNHYTQ KSLSLSPGK
Heavy Chain of the antibody IN10, full amino acid sequence (Seq. ID NO. 86)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFN AYYMSWVRQA PGKGLEWVST IYPYYSNTDY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGM HYMSGALDYW GQGTLVTVSS
121 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS
181 GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG
241 PSVFLFPPKP KDTLMISRTP EVTCWVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYN
301 STYRWSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE
361 MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW
421 QQGNVFSCSV MHEALHNHYT QKSLSLSPGK
Heavy Chain of the antibody IN20, full amino acid sequence (Seq. ID NO. 87)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFT AYTIHWVRQA PGKGLEWVSN I DPYYGYTNY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARTS FGLSNGFDYW GQGTLVTVSS
121 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS 181 GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG
241 PSVFLFPPKP KDTLMISRTP EVTCWVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYN
301 STYRWSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE
361 MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW
421 QQGNVFSCSV MHEALHNHYT QKSLSLSPGK
Heavy Chain of the antibody IN22, full amino acid sequence (Seq. ID NO. 88)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFS DYYISWVRQA PGKGLEWVSN IGPWNGSTYY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARET RTYWAYSSSG FDYWGQGTLV
121 TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV
181 LQSSGLYSLS SWTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTCPPCPAPE
241 LLGGPSVFLF PPKPKDTLMI SRTPEVTCW VDVSHEDPEV KFNWYVDGVE VHNAKTKPRE
301 EQYNSTYRW SVLTVLHQDW LNGKEYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP
361 SREEMTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT TPPVLDSDGS FFLYSKLTVD
421 KSRWQQGNVF SCSVMHEALH NHYTQKSLSL SPGK
Heavy Chain of the antibody IN22, full amino acid sequence (Seq. ID NO. 89)
1 EVQLLESGGG LVQPGGSLRL SCAASGFTFT DYAMHWVRQA PGKGLEWVSS IYPSNSYTDY
61 ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARDR SVIGFDYWGQ GTLVTVSSAS
121 TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL
181 YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHTCPPC PAPELLGGPS
241 VFLFPPKPKD TLMISRTPEV TCWVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNST
301 YRWSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTI SKA KGQPREPQVY TLPPSREEMT
361 KNQVSLTCLV KGFYPSDIAV EWESNGQPEN NYKTTPPVLD SDGSFFLYSK LTVDKSRWQQ
421 GNVFSCSVMH EALHNHYTQK SLSLSPGK
Light Chain Kappa of the antibody IN8, full amino acid sequence (Seq. ID NO. 90)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QSYSADPFTF GQGTKVEIKR TVAAPSVFIF
121 PPSDEQLKSG TASWCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST
181 LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC Light Chain Kappa of the antibody IN9, full amino acid sequence (Seq. ID NO. 91)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP 61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QSYASPFTFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL 181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
Light Chain Kappa of the antibody IN9A, full amino acid sequence (Seq. ID NO. 92)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP 61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYYDYPVTFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL 181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
Light Chain Kappa of the antibody IN9B, full amino acid sequence (Seq. ID NO. 93)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYYDYPVTFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL
181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
Light Chain Kappa of the antibody IN10, full amino acid sequence (Seq. ID NO. 94) 1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QSASDDPFTF GQGTKVEIKR TVAAPSVFIF 121 PPSDEQLKSG TASWCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST 181 LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC Light Chain Kappa of the antibody IR20, full amino acid sequence (Seq. ID NO. 95)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP 61 DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QSYDDPITFG QGTKVEIKRT VAAPSVFIFP 121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL 181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
Light Chain Kappa of the antibody IN22, full amino acid sequence (Seq. ID NO.96)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
61 DRFSGSGSGT DFTLTI SRLE PEDFAVYYCQ QYSYSPITFG QGTKVEIKRT VAAPSVFIFP
121 PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL
181 TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC
Light Chain Kappa of the antibody IR24, full amino acid sequence (Seq. ID NO.97)
1 EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
61 DRFSGSGSGT DFTLTI SRLE PEDFAVYYCQ QYASYSPLTF GQGTKVEIKR TVAAPSVFIF 121 PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST
181 LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC
The sequences of Fab antibody fragments defining Variable Regions of immunoglobulin heavy chain selected from the phage display libraries as described in Example 2, screened as set forth in Example 3 and sequences of which identified in the Example 4 are shown in Figure 2. The sequences are aligned to each other due to homology of the antibody framework where CDRl, CDR2 and CDR3 are identified by boxes. Figure 3 shown an alignment of each CDR separately where dashes (-) are inserted to shorter CDRs for the alignment purpose.
The sequences of Fab antibody fragments defining Variable Regions of immunoglobulin light chain (kappa) selected from the phage display libraries as described in Example 2, screened as set forth in Example 3 and sequences of which identified in the Example 4 are shown in Figure 4. The sequences are aligned to each other due to homology of the antibody framework where CDRl, CDR2 and CDR3 are identified by boxes. Figure 5 shown an alignment of each CDR separately where dashes (-) are inserted to shorter CDRs for the alignment purpose.
Table 1 provides a correspondence between sequences discussed in these Examples with
Sequence Listing (Seq. ID NO). TABLE 1
Seq. ID
Protein or Nucleic acid Description
NO
01 Heavy Chain Variable region of IN8 - Protein
02 Heavy Chain Variable region of IN8 - Nucleic acid
03 Heavy Chain Variable region of IN9 - Protein
04 Heavy Chain Variable region of IN9 - Nucleic acid
05 Heavy Chain Variable region of IN9A - Protein
06 Heavy Chain Variable region of IN9A - Nucleic acid
07 Heavy Chain Variable region of IN9B - Protein
08 Heavy Chain Variable region of IN9B - Nucleic acid
09 Heavy Chain Variable region of INI 0 - - Protein
10 Heavy Chain Variable region of IN 10 - - Nucleic acid
1 1 Heavy Chain Variable region of IN20 - - Protein
12 Heavy Chain Variable region of IN20 - - Nucleic acid
13 Heavy Chain Variable region of IN22 - - Protein
14 Heavy Chain Variable region of IN22 - - Nucleic acid
15 Heavy Chain Variable region of IN24 - - Protein
16 Heavy Chain Variable region of IN24 - - Nucleic acid
17 Heavy Chain CDR1 of IN8 - Protein
18 Heavy Chain CDR2 of IN8 - Protein
19 Heavy Chain CDR3 of IN8 - Protein
20 Heavy Chain CDR1 of IN9 - Protein
21 Heavy Chain CDR2 of IN9 - Protein
22 Heavy Chain CDR3 of IN9 - Protein
23 Heavy Chain CDR1 of ΓΝ9Α - Protein
24 Heavy Chain CDR2 of ΓΝ9Α - Protein
25 Heavy Chain CDR3 of IN9A - Protein
26 Heavy Chain CDR1 of IN9B - Protein
27 Heavy Chain CDR2 of IN9B - Protein Seq. ID
Protein or Nucleic acid Description
NO
28 Heavy Chain CDR3 of IN9B - Protein
29 Heavy Chain CDR1 of INI 0 - Protein
30 Heavy Chain CDR2 of INI 0 - Protein
31 Heavy Chain CDR3 of INI 0 - Protein
32 Heavy Chain CDR1 of IR20 - Protein
33 Heavy Chain CDR2 of IR20 - Protein
34 Heavy Chain CDR3 of IR20 - Protein
35 Heavy Chain CDR1 of IN22 - Protein
36 Heavy Chain CDR2 of IN22 - Protein
37 Heavy Chain CDR3 of IN22 - Protein
38 Heavy Chain CDR1 of IR24 - Protein
39 Heavy Chain CDR2 of IR24 - Protein
40 Heavy Chain CDR3 of IR24 - Protein
41 Light Chain (Kappa) Variable region of IN8 - Protein
42 Light Chain (Kappa) Variable region of IN8 - Nucleic acid
43 Light Chain (Kappa) Variable region of IN9 - Protein
44 Light Chain (Kappa) Variable region of IN9 - Nucleic acid
45 Light Chain (Kappa) Variable region of IN9A - Protein
46 Light Chain (Kappa) Variable region of IN9A - Nucleic acid
47 Light Chain (Kappa) Variable region of IN9B - Protein
48 Light Chain (Kappa) Variable region of IN9B - Nucleic acid
49 Light Chain (Kappa) Variable region of IN 10 - Protein
50 Light Chain (Kappa) Variable region of IN 10 - Nucleic acid
51 Light Chain (Kappa) Variable region of IN20 - - Protein
52 Light Chain (Kappa) Variable region of IN20 - Nucleic acid
53 Light Chain (Kappa) Variable region of IN22 - - Protein
54 Light Chain (Kappa) Variable region of IN22 - Nucleic acid
55 Light Chain (Kappa) Variable region of IN24 - - Protein
56 Light Chain (Kappa) Variable region of IN24 - - Nucleic acid Seq. ID
Protein or Nucleic acid Description
NO
Light Chain (Kappa) CDRl of IN8; IN9; IN9A; IN9B; IRIO; IN20; IN22; IN24
57
-Protein
Light Chain (Kappa) CDR2 of IN8; IN9; IN9A; IN9B; IRIO; IN20; IN22; IN24
58
- Protein
59 Light Chain (Kappa) CDR3 of IN8 - Protein
60 Light Chain (Kappa) CDR3 of IN9 - Protein
61 Light Chain (Kappa) CDR3 of IN9A - Protein
62 Light Chain (Kappa) CDR3 of IN9B - Protein
63 Light Chain (Kappa) CDR3 of IN 10 - Protein
64 Light Chain (Kappa) CDR3 of IN20 - Protein
65 Light Chain (Kappa) CDR3 of IN22 - Protein
66 Light Chain (Kappa) CDR3 of IN24 - Protein
67 IA-003 direct primer
68 IA-004 reverse primer
69 AC-001 Direct 'structural' primer
70 AC-002 Reverse 'structural' primer
71 AC-003 direct primer
72 AC-004 reverse primer
73 Immunoglobulin 20-amino acid signal peptide sequence
74 A-370 Direct PCR primer for Variable Region of Heavy Chain IgGl
75 A-371 Reverse PCR primer for Variable Region of Heavy Chain IgGl
76 A-340 Direct PCR primer for Variable Region of Light Chain Kappa
77 A-341 Reverse PCR primer for Variable Region of Light Chain Kappa
78 Reference Human IgGl Heavy Chain Constant Region, nucleotide sequence
79 Reference Human IgGl Heavy Chain Constant Region, amino acid sequence
80 Reference Human Light Chain Kappa Constant Region, nucleotide sequence
81 Reference Human Light Chain Kappa Constant Region, amino acid sequence Seq. ID
Protein or Nucleic acid Description
NO
82 Heavy Chain of the antibody IN8, full amino acid sequence
83 Heavy Chain of the antibody IN9, full amino acid sequence
84 Heavy Chain of the antibody IN9A, full amino acid sequence
85 Heavy Chain of the antibody IN9B, full amino acid sequence
86 Heavy Chain of the antibody IN 10, full amino acid sequence
87 Heavy Chain of the antibody IN20, full amino acid sequence
88 Heavy Chain of the antibody IN22, full amino acid sequence
89 Heavy Chain of the antibody IN24, full amino acid sequence
90 Light Chain Kappa of the antibody IN8, full amino acid sequence
91 Light Chain Kappa of the antibody IN9, full amino acid sequence
92 Light Chain Kappa of the antibody IN9A, full amino acid sequence
93 Light Chain Kappa of the antibody IN9B, full amino acid sequence
94 Light Chain Kappa of the antibody IN 10, full amino acid sequence
95 Light Chain Kappa of the antibody IN20, full amino acid sequence
96 Light Chain Kappa of the antibody IN22, full amino acid sequence
97 Light Chain Kappa of the antibody IN24, full amino acid sequence
Example 5 - Production of recombinant human integrin alpha-4.
This Example describes design and generation of expression constructs for inducible expression of human integrin alpha-4 receptor. In particular, this example describes epitope and purification tags genetically fused to the nucleic acid sequences encoding integrin alpha-4 and its orthologs.
Human integrin alpha-4 receptor (NCBI Reference Sequence: NM_000885.4) was amplified by PCR using Clone ID HsCD00446160 (DNASU Plasmid Repository) as a template. To the coding sequence of integrin alpha-4, Nhel restriction site for cloning purpose and Kozak sequence was genetically fused upstream of the starting native ATG codon using IA-003 Direct primer. The endogenous native Stop codon of integrin alpha-4 was removed using IA-004 Reverse primer to provide in- frame genetic fusion with Strep-tag (h.ttp://www.iba-go.de/prottoojs/prot_stT ptag.html.. a 8-amino acid peptide tag) and FLAG epitope tag for detection purposes, and Aflll restriction site was introduced for cloning purpose. The PCR product obtained from the reaction using IA-003 and IA-004 primers and human integrin alpha-4 as the template, was Nhel-Aflll digested and cloned into pcDNA3.1-FlagStr vector (Invitrogen). Cloning of pcDNA3.1-FlagStr vector was performed by PCR assembly of the epitope tag: -Link-FLAG-SBP-* (where SBP stands for Streptavidin Binding Peptide) into the cloning site between Aflll and Apal cloning clonig sites. Combining of AC-001 , AC-002 'structural' primers and AC-003 and AC-004 direct and reverse PCR primers was required for assembly of the tag.
Following is the epitope tag that was cloned into pcDNA3.1-Zeo-(+) using 5'-end Aflll and 3 '-end Apal restriction sites: ATCCTTAAGGGCAGCGGGTCCTCTGGAGGGGGAGACTATAAGGATGACGATGACA
AGagtatggatgagaaaaccacaggttggcgcggcgggcatgtcgttgaaggac
tggccggtgagctggaacaactcagggctagattggagcaccaccctcagggcc agcgggaaccttagGGCCCATA where Aflll cloning site (CTTAAG) and Apal cloning site (GGGCCC) are shown
underlined, GS-linker in shown in italics, and SBP is shown in small cap letters.
IA-003 direct primer (Seq. ID NO. 67)
5' - ACAGCTAGCCATGGCTTGGGAAGCGAGGCG -3'
IA-004 reverse primer (Seq. ID NO. 68)
5' - ACTCTTAAGATCATCATTGCTTTTACTGTTGATATAACTCCAAC -3'
AC-001 direct 'structural' primer (Seq. ID NO. 69) 5' - AGCGGGTCCTCTGGAGGGGGAGACTATAAGGATGACGATGACAAGAGTA TGGATGAGAAAACGACAGGTTGGCGCGGCGGGCATGTCGTT -3' AC-002 reverse 'structural' primer (Seq. ID NO. 70)
5' - GTTCCCGCTGGCCCTGAGGGTGGTGCTCCAATCTAGCCCTGAGTTGTTCC
AGCTCACCGGCCAGTCCTTCAACGACATGCCCGCCGCGCC -3' AC-003 direct PCR primer (Seq. ID NO. 71)
5'- ATCCTTAAGGGCAGCGGGTCCTCTGGAGGGGGAG -3' AC-004 reverse PCR primer (Seq. ID NO. 72)
5'- TATGGGCCCTAAGGTTCCCGCTGGCCCTGAGGG -3'
Example 6 - Generation of stable cell lines expressing recombinant integrin alpha-4. The expression constructs encoding human integrin alpha-4 receptor described in Example 5 were used for generation of stable cell lines. Commercially available cell lines, R1610, Cf2Th and HEK-293 (ATCC) were used. The expression constructs were verified for the expression of the protein of interest in a transient transfection experiment and then the cells were propagated on a medium containing Zeocin to select for stable cell lines harboring the gene of interest. Expression of the integrin alpha-4 was verified by Western blot and by FACS analysis to ensure that the expressed protein was translocated to the plasma membrane. For both techniques, commercially available antibodies were used. All steps of the cell line generation were carried out according to the manufacturers' protocols. Example 7 - Conversion of the Fab antibody fragments into immunoglobulins and their production. This Example provides description an approach for subcloning of Fab fragments into mammalian expression vectors for production of fully functional immunoglobulins. A protein production approach is also provided herein.
The candidate Fab antibody Heavy Chain variable region fragments described in the foregoing Examples 2-4 were converted into full size immunoglobulins of IgGl framework.
Variable region of the heavy chain was fused to the constant region of human IgGl isotype using expression vector pTT-5 (NRC Biotechnology Research Institute, National Research Council of Canada) modified by introducing the constant region of human IgGl from pFUSE-CHIg-hGl expression vector (Invivogen) resulting in pTT-IgGl-HC vector. The signal peptide from immunoglobulin kappa light chain variable region (Mus musculus, gb|AAG35718.1 |AF207705_l) was introduced into the construct upstream of the antibody variable sequences disclosed herein.
Immunoglobulin 20-amino acid signal peptide sequence where starting methionine is underlined (Seq. ID NO. 73)
METDTILLWVLLLWVPGSTG
The variable regions of the heavy chain were amplified by PCR to introduce into the following cloning sites: 5 '-end cloning restriction site is Sail, 3 '-end restriction site is Nhel. A set of two primers, A-370 direct primer and A-371 reverse primer, was used for the PCR
amplification. The resulting PCR fragment was digested with Sail -Nhel restriction enzymes and then introduced into pTT-IgGl-HC vector digested with the same enzymes.
A-370 direct PCR primer for amplification of Heavy Chain Variable Region (Sail restriction site is underlined) (Seq. ID NO. 74)
5' - TGTGTCGACCGGAGAAGTTCAACTGCTGGAGTCCGGTGGTGGTCTGG
TACAGCCGGGTGGTTCTCTGCGTCTGAGTTGCG -3' A-371 Reverse PCR primer for amplification of Heavy Chain Variable Region (Nhel restriction site is underlined) (SEQ. ID NO 75) 5'- TTGTGCTAGCACTCGAGACGGTGACCAAGGTTCCCTGGCC -3'
The candidate Fab antibody Light Chain variable region fragments described in the foregoing Examples 2-4 were converted into full size immunoglobulins of IgGl framework. Variable
Region of light chain was fused to the constant region of human light chain kappa using expression vector pTT-5 (NRC Biotechnology Research Institute, National Research Council of Canada) modified by introduction of the constant region of human light chain fragmen from pFUSE2- CLIg-hk expression vector (Invivogen) resulting in pTT-LC-Kappa. The signal peptide from immunoglobulin kappa light chain variable region (Mus musculus, gb|AAG35718.1 |AF207705_l) was introduced into the construct upstream of the antibody variable sequences reported in this invention.
The variable regions of the light chain were amplified by PCR to introduce for the following cloning sites: 5 '-end cloning restriction site is Sail, 3 '-end restriction site is BsiWI. The set of two primers, A-340 direct primer and A-341 reverse primer, was used for the PCR amplification. The resulting PCR fragment was digested with Sall-BsiWI restriction enzymes and then introduced into pTT-LC-Kappa vector digested with the same enzymes.
A-340 direct PCR primer for amplification of Light Chain Kappa Variable Region (Sail restriction site is underlined) (Seq. ID NO. 76)
5'- TGTGTCGACCGGGGAAATTGTGTTGACGCAGTCTCCG -3'
A-341 reverse PCR primer for amplification of Light Chain Kappa Variable Region (BsiWI restriction site is underlined) (Seq. ID NO. 77)
5'- ATGGTGCAGCCACCGTACGTTTGATTTCCACC -3'
The antibodies in a format of human IgGl framework were produced using a protocol for transfection of CHO-3E7 cells using LPEI MAX in shake flask cultures. CHO-3E7 cells provided by NRC Biotechnology Research Institute, National Research Council of Canada, were diluted to 0.8 xlO6 cells/ml 24 h before transfection. On the day of transfection cell density was adjusted to 2.0 to 2.2xl06 cells/ml using complete FreeStyle™ CHO medium and cell viability was greater than 97%.
The working solution of Polyethylenimine (PEI) was prepared as follows. To the 450 ml Milli-Q water, 1500 mg PEI "MAX" was added and stirred until complete dissolution and a final concentration of 3 mg/ml. The initial pH of the solution was around 2.2 and then it was adjusted to pH 7.0 by NaOH. The final pH adjustments were made using HC1 and/or NaOH. The final volume of the solution was adjusted to 500 ml, filter-sterilize using a 0.22 μιη membrane and stored at -20°C.
Polyethylenimine ' 'MAX' ' linear, MW 25 kDa (40 kDa nominal), 3 mg/ml stock solution in water, pH 7.0 (Polysciences Inc. cat# 24765-2) was mixed with purified and quantified plasmid DNA of interest. A260/A280 ratio (use 50 mM Tris-HCl pH 8.0 to dilute the plasmid DNA) was between 1.85 and 1.95. The cells were used in exponential growth phase, 2-2.2xl06 cells/ml in CHO FreeStyle medium. DNA preparations (0.75mg/L) encoding for Heavy or Light chains of immunoglobulin were mixed with PEI in CHO FreeStyle medium at 1 :5 (w:w) ratio, the mixture was then incubated 8-10 min, add then added to culture. Volume of the transfection mixture was 1/10 of the final volume of the production culture.
Routinely, expression level for various immunoglobulins was from 20 to 100 mg/L. The immunoglobulin production was monitored by commercially available ELISA kit (Bethyl Laboratories).
Purification of immunoglobulin preparations was carried out as follows. Tris-Gly cine-Native Buffer, lOx, pH 8.5 (Boston Bioproducts; Cat# BP- 160) was added to the supernatant (1/10 volume/volume) containing IgG at a final concentration of 20-100 mg/L and gently mixed. The supernatant volume was evenly distributed into 50-ml centrifuge tubes, 50ml per tube. Protein A Plus Agarose (Pierce, Cat. # 22812), a wet pellet, was used at 1/100 ratio to the total volume of the supernatant material. The appropriate amount of Protein A Plus Agarose was incubated with the IgG-containing supematants at an orbital shaker for overnight. After the incubation, the Protein A Plus Agarose resin was harvested and placed into 15 -ml columns (Pierce) and then washed with 10 volumes of lx PBS, then with 10 volumes of 25mM Tris-HCl, 0.12M Glycine, 1.5M NaCl (pH 8.5), then with 10 volumes of TBS-Tween-20, then with 10 volumes of 20mM Sodium Citrate Buffer, 1M NaCl (pH 5.5) and the final wash with 10 volumes of 150mM Sodium Chloride without any buffer. The elution of bound immunoglobulins was carried out with Elution Buffer (0.1 M Glycine pH 3.0, 10% Sucrose, 150mM NaCl) that was added at ratio of 1 : 1 to the volume of Protein A Plus Agarose resin. The elution buffer was incubated with the Protein A Plus Agarose resin for 3 min, removed and then another portion of fresh Elution Buffer was added to the Protein A Plus Agarose resin. The eluted material was immediately neutralized by 0.5 M Sodium Citrate Buffer, pH 6.0, at the 1/10 volume ratio to the eluted volume. The concentration of the resulting immunoglobulin preparations was determined by measure optical density of the solution at 280nm in UV-transparent cuvettes where a mixture of 0.1 ml of 0.5 M Sodium Citrate, pH 6, with 1ml of the Elution Buffer was used as a Reference Buffer. To calculate the concentration of IgG, the following formula that provides IgG concentration in mg/ml, was used:
[IgG] = OD280 * DilutionFactor ^ w^Q .Q ^ -§ ^ standard extinction coefficient for an IgG.
Example 8 - Determination of affinities (EC50 values) of integrin alpha-4 antibodies
This example describes the method for determination of the affinities of the antibodies against human integrin alpha-4 receptor and provides means of comparison of properties of different antibody clones.
Determination of EC50 values for the antibodies against Integrin alpha-4 was performed using cells overexpressing human Integrin alpha-4. The antibody at various concentrations (from 0.02 nM to 500 nM) was allowed to interact with the indicated cell lines and then the binding of the antibody to the cells was revealed by fluorescently labeled secondary antibodies. The stained cells were analyzed by FACS where Mean Fluorescence Intensity (MFI) was measured. The results of the analysis are summarized in Table 2.
TABLE 2
Figure imgf000039_0001
IN9 6.1
IN9A 2.1
IN9B 5
IN10 0.47
IN20 7.37
IN22 >100
IN24 32.35
VCAM-1 was coated onto an ELISA plate by overnight incubation (lOug/ml). KA4 cells (K562 overexpressing Integrin alpha-4) (5xl03 per well) were plated on a 96-well plate.
Antibodies were added at various concentrations (from 0.02 nM to 500 nM) and incubated for 30 minutes. Cells were transferred onto the VCAM-1 coated plate and incubated overnight at 37°C. Unbound cells were removed by washing three times with PBS. Washing efficiency was monitored using a microscope. The cells that remained attached to the VCAM-1 coated plate were analyzed using the MTT assay for colorimetric analysis and quantitation. Background binding was assessed using BSA-coated wells and subtracted from the experimental values. As a positive control commercially available comparator anti- integrin alpha-4 antibody - Tysabri was used. The obtained data were analyzed utilizing GraphPad Prism 5.0 software and EC50 values were calculated using antagonistic 4-parameter curve fit algorithm. The results of the analysis are presented graphically in Figures 6 A and 6B.
Example 9 - Biophysical characterization of the anti-integrin alpha4 antibodies
In vitro stability of representative antibodies of the present invention was assessed utilizing a variety of biophysical methods, including Dynamic Light Scattering (DLS), proteolitic stability, Differential Scanning Calorimetry (DSC) and Circular Dichroism.
Thermal stability of the antibodies was assessed by DLS technique. Dynamic light scattering (also called photon correlation spectroscopy or quasi-elastic light scattering) is a method that is broadly used in the development of MAB therapeutics for detecting antibody oligomerization. Large protein (di-, tri-, and other multimer) particles exhibit long decay times and contribute more significantly to the overall light scattering intensity compared to small particles, e.g. a monomeric form of a MAB. DLS allows picking up signals arising from small populations of protein oligomers among a highly concentrated monomeric form. On the other hand, in the case of presence of even a relatively low concentration of aggregated protein forms the light scattering arising from a monomeric protein is often lost in the strong contribution of aggregates. To prevent this effect, all protein solutions to be studied by DLS are thoroughly filtrated prior to analysis.
Two sets of the studies were performed on representative antibodies of the present teachings - one on freshly isolated and stored at 4o C antibodies IN8, IN9A, IN10, and
natalizumab (Tysabri); and the other - on the same antibodies after eight days of incubation at 37° C. Prior to conducting measurements, the antibodies were centrifuged at 12,000 rpm for 10 min. Measuremets with IN8 were conducted without antibody stock dilution, while IN9A and IN 10 stocks were diluted twofold with the antibody storage buffer solution. DLS measurements were carried out using a Zetasizer Nano ZS (Malvern Instruments Ltd, UK) system. The backscattered light from a 4 mW He-Ne 632.8 nM laser was collected at an angle of 173°. Protein concentration was between 0.3 andl mg/ml. Buffer conditions were as follows: PBS, PMSF and NaN3 (0.02%), pH 7.4. Prior to experiments solutions were passed through 0.1 μιη Whatman® Anotop® 10 syringe filter. Sample temperature was kept at 25.0°C. The acquisition time for a single
autocorrelation function was 70 s. The resulting autocorrelation functions were calculated using averaged values from two measurements. The results of the measurements are presented in Figure 7. As is apparent from the DLS studied, all the antibodies tested exhibit nearly identical distributions of their hydrodynamic diameters, none of the antibodies form multiple molecule aggregates in solution and thus are aggregationally stable even after incubation for 8 days at 37° C.
Proteolytic stability of antibodies IN8, IN9A and IN10, alongside with natalizumab, was examined by SDS-PAGE electrophoresis after incubating the antibody stock solutions for 8 days at 37° C. SDS-PAGE run under reducing conditions did not reveal any additional bands not corresponding to the antibodies after the 8 days of incubation.
Melting temperatures of representative antibodies of the present invention were assessed by differential scanning calorimetry. Figure 8 shows the measurements of specific heat capacities
(Cp) of antibodies IN8, IN9A, and IN10 as as function of temperature. Protein formulated in PBS pH=7.4 was used at concentrations between 0.3 to 1.1 mg/ml. The DSC studies were carried out at a 1 K min heating rate and excess pressure of 4 bars (Nano DSC microcalorimeter, TA Intruments Inc., USA). Heat sorption peaks correspond to thermal denaturation of antibody fragments. As is apparent from Figure 8, all antibodies studied did not exhibit thermal denaturation below 60°C, while the most stable antibody IN9A maintained its native state up until about 65 °C.
The secondary structure analysis of representative antibodies of the present invention was performed by circular dichroism. Circular dichroism refers to the difference in absorption of left and right circularly polarized light. Each of the protein secondary structure types possesses its own characteristic CD spectrum. The CD spectrum of protein under study is deconvoluted into components corresponding to the contributions from different secondary structure types. Since antibodies are characterized by very high content of β-pleated sheets, their CD spectra closely resemble those for pure β-strand structure. Figure 9 shows far-UV CD data for antibodies IN8, IN9A and IN10, alongside with Tysabri, all formulated in PBS, pH 7.4. Protein concentration used was between 0.11 and 0.18 μΜ. CD studies were carried out utilizing a J-810
spectropolarimeter (JASCO, Inc.), equipped with a Peltier-controlled cell holder. The instrument was calibrated with an aqueous solution of d-10-camphorsulfonic acid. The cell compartment was purged with nitrogen. A quartz cell with a path length of 1 mm was used. Buffer contribution was subtracted from experimental spectra. Bandwidth was 2 nm, averaging time - 2 s, and
accumulation - 3. Measured CD data indicates that all antibodies studied are characterized by predominance of β-sheets, while closely resembling the spectra of Tysabri.
All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.
"Tysabri" is a registered trademark of Biogen Idee Inc., a Delaware Corporation.
While specific embodiments of the subject matter have been discussed, the above specification is illustrative and not restrictive. Many variations will become apparent to those skilled in the art upon review of this specification and the claims below. The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.

Claims

What is claimed is:
An isolated antibody that binds human integrin alpha-4 comprising
an immunoglobulin light chain of SEQ. ID NO. 90;
and an immunoglobulin heavy chain of SEQ ID NO. 82;
or an antigen binding fragment of the antibody.
An isolated antibody that binds human integrin alpha-4 comprising
an immunoglobulin light chain of SEQ. ID NO. 92;
and an immunoglobulin heavy chain of SEQ. ID NO. 84;
or an antigen binding fragment of the antibody.
An isolated antibody that binds human integrin alpha-4 comprising
an immunoglobulin light chain of SEQ. ID NO. 94;
and an immunoglobulin heavy chain of SEQ. ID NO. 86;
or an antigen binding fragment of the antibody.
The antibody of claim 1 , wherein the antibody is a monoclonal antibody.
The antibody of claim 2, wherein the antibody is a monoclonal antibody.
The antibody of claim 3, wherein the antibody is a monoclonal antibody
An isolated antibody that binds human integrin alpha-4 comprising
(i) an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 57, a CDRL2 comprising the sequence of SEQ. ID NO. 58, and a CDRL3 comprising the sequence of SEQ. ID NO. 59; and
(ii) an immunoglobulin heavy chain variable region comprising a CDRHl comprising the sequence of SEQ. ID NO. 17, a CDRH2 comprising the sequence of SEQ. ID NO. 18, and a CDRH3 comprising the sequence of SEQ. ID NO. 19; or an antigen binding fragment of the antibody.
8. An isolated antibody that binds human integrin alpha-4 receptor comprising
(i) an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 57, a CDRL2 comprising the sequence of SEQ. ID NO. 58, and a CDRL3 comprising the sequence of SEQ. ID NO. 61; and
(ii) an immunoglobulin heavy chain variable region comprising a CDRHl comprising the sequence of SEQ. ID NO. 23, a CDRH2 comprising the sequence of SEQ. ID NO. 24, and a CDRH3 comprising the sequence of SEQ. ID NO. 25; or an antigen binding fragment of the antibody.
9. An isolated antibody that binds human integrin alpha-4 receptor comprising
(i) an immunoglobulin light chain variable region comprising a CDRL1 comprising the sequence of SEQ. ID NO. 57, a CDRL2 comprising the sequence of SEQ. ID NO. 58, and a CDRL3 comprising the sequence of SEQ. ID NO. 63; and
(ii) an immunoglobulin heavy chain variable region comprising a CDRHl comprising the sequence of SEQ. ID NO. 29, a CDRH2 comprising the sequence of SEQ. ID NO. 30, and a CDRH3 comprising the sequence of SEQ. ID NO. 31 ; or an antigen binding fragment of the antibody.
10. The binding-protein antibody of claim 7 wherein the CDR sequences are interposed
between human or humanized framework sequences.
11. The binding-protein antibody of claim 8 wherein the CDR sequences are interposed
between human or humanized framework sequences.
12. The binding-protein antibody of claim 9 wherein the CDR sequences are interposed
between human or humanized framework sequences.
13. An isolated antibody that binds human integrin alpha-4 comprising
an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ ID NO. 41, and an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ ID NO. 01; or
an antigen binding fragment of the antibody.
14. An isolated antibody that binds human integrin alpha-4 receptor comprising
an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ ID NO. 45, and
an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ ID NO. 05; or
an antigen binding fragment of the antibody.
15. An isolated antibody that binds human integrin alpha-4 receptor comprising
an immunoglobulin light chain variable region comprising the amino acid sequence of SEQ ID NO. 49, and
an immunoglobulin heavy chain variable region comprising the amino acid sequence of SEQ ID NO. 09; or
an antigen binding fragment of the antibody.
16. The antibody of claim 13, wherein the antibody is a monoclonal antibody.
17. The antibody of claim 14, wherein the antibody is a monoclonal antibody.
18. The antibody of claim 15, wherein the antibody is a monoclonal antibody.
PCT/US2014/037325 2013-05-30 2014-05-08 Fully human antibodies against human receptor integrin alpha-4 WO2014193625A1 (en)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12304956B1 (en) 2023-05-30 2025-05-20 Paragon Therapeutics, Inc. Dosing regimen for treating inflammatory bowel disease

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997018838A1 (en) * 1995-11-21 1997-05-29 Athena Neurosciences, Inc. Therapeutic uses of humanized antibodies against alpha-4 integrin
US5968826A (en) * 1998-10-05 1999-10-19 Isis Pharmaceuticals Inc. Antisense inhibition of integrin α4 expression

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997018838A1 (en) * 1995-11-21 1997-05-29 Athena Neurosciences, Inc. Therapeutic uses of humanized antibodies against alpha-4 integrin
US5968826A (en) * 1998-10-05 1999-10-19 Isis Pharmaceuticals Inc. Antisense inhibition of integrin α4 expression

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BONIG HALVARD ET AL.: "Increased numbers of circulating hematopoietic stem/progenitor cells are chronically maintained in patients treated with the CD 49d blocking antibody natalizumab.", BLOOD, vol. 111, no. 7, 1 April 2008 (2008-04-01), pages 3439 - 3441 *
SOILU-HANNINEN M. ET AL.: "Therapy with antibody against leukocyte integrin VLA-4 ( CD 49d) is effective and safe in virus-facilitated experimental allergic encephalomyelitis.", JOURNAL OF NEUROIMMUNOLOGY, vol. 72, 1997, pages 95 - 105, XP000993010, DOI: doi:10.1016/S0165-5728(96)00158-0 *
XIAO-DONG YANG ET AL.: "A predominant role of integrin a4 in the spontaneous development of autoimmune diabetes in nonobese diabetic mice.", IMMUNOLOGY, vol. 91, 1994, pages 12604 - 12608 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12304956B1 (en) 2023-05-30 2025-05-20 Paragon Therapeutics, Inc. Dosing regimen for treating inflammatory bowel disease

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