Method for detecting DDR1 phosphorylation

Abstract

The present disclosure provides a method for detecting discoidin domain receptor tyrosine kinase 1 (DDR1) phosphorylation to determine the efficacy or potential efficacy of a DDR1 antagonist therapy. The present disclosure provides antibodies for use in the treatment of DDR1-related disorders that specifically bind to DDR1. Also provided herein are compositions comprising these antibodies for detecting phosphorylated DDR1, nucleic acids encoding these antibodies, expression vectors and host cells for producing these antibodies.

Description

Technical Field

[0001] 1. Cross - Reference to Related Applications This application claims the benefit of priority to U.S. Provisional Application No. 63 / 366,567, filed on June 17, 2022, the entire content of which is hereby incorporated by reference into this specification.

[0002] 2. Reference to Sequence Listing This application includes a sequence listing that was electronically submitted in ST.26 format, the entire content of which is hereby incorporated by reference into this specification (a copy of the ST.26 created on June 16, 2023, is named "201000_seqlist.xml" and is 151,659 bytes in size).

[0003] 3. Field The present disclosure relates to a method for detecting discoidin domain receptor tyrosine kinase 1 (DDR1) phosphorylation to determine the efficacy or potential efficacy of a DDR1 inhibitor, such as an anti - DDR1 antibody, or a method for screening for such a DDR1 inhibitor.

Background Art

[0004] 4. Background Receptor tyrosine kinases (RTKs) play important roles in the communication of cells with their microenvironment. These molecules are involved in the regulation of cell growth, differentiation, and metabolism. The DDR1 protein encoded by the DDR1 gene is an RTK that is widely expressed in normal and transformed epithelial cells and is activated by various types of collagen. The DDR1 protein belongs to a subfamily of tyrosine kinase receptors that have a homologous region with discoidin I, a Dictyostelium discoideum protein, in their extracellular domains. Its autophosphorylation is achieved by all collagens (type I-VI) tested so far. In situ studies and Northern blot analysis have shown that the expression of the DDR1-encoded protein is restricted to epithelial cells, particularly in the kidney, lung, gastrointestinal tract, and brain. In addition, the DDR1 protein is significantly overexpressed in some human tumors from the breast, ovary, esophagus, and pediatric brain. In addition to its expression in cancer, the DDR1 protein is also expressed in other organs, including the kidney, lung, gastrointestinal tract, skin, and brain, and is associated with fibrosis of the skin, lung, and liver.

[0005] Therefore, a method for determining the efficacy or potential efficacy of a DDR1 inhibitor in the treatment or prevention of DDR1-related disorders is highly desirable.

Summary of the Invention

Means for Solving the Problems

[0006] 5. Summary The present disclosure demonstrates herein that an anti-DDR1 antibody can inhibit DDR1 phosphorylation. DDR1-related disorders are associated with increased collagen-mediated DDR1 phosphorylation and subsequent downstream signal transduction. Therefore, a method for detecting DDR1 phosphorylation can be used to determine the efficacy or potential efficacy of an anti-DDR1 antibody in the treatment of DDR1-related disorders.

[0007] An anti-DDR1 antibody can be considered effective for treating DDR1-related disorders if it can inhibit DDR1 phosphorylation and / or the ability of DDR1 to interact with collagen. Also, an anti-DDR1 antibody is likely to be effective for treating DDR1-related disorders if it can inhibit DDR1 phosphorylation and / or the ability of DDR1 to interact with collagen.

[0008] In one aspect, the present disclosure provides a method of monitoring the effectiveness of an anti-discoidin domain receptor tyrosine kinase 1 (DDR1) antibody or an antigen-binding fragment thereof in a subject in need thereof, comprising: a) administering to the subject an effective amount of the anti-DDR1 antibody; and b) detecting the level of DDR1 phosphorylation in a sample derived from the subject, wherein a decrease in DDR1 phosphorylation in the sample derived from the subject as compared to a positive reference sample indicates that the administration of the anti-DDR1 antibody is effective.

[0009] In some embodiments, the subject has cancer. In some embodiments, the cancer is selected from the group consisting of pancreatic cancer; lung cancer including small cell lung cancer and non-small cell lung cancer; colorectal and colorectal cancer; head and neck cancer; gastric cancer; ovarian cancer; breast cancer; kidney cancer; liver cancer; prostate cancer; cervical cancer; brain cancer; skin cancer including melanoma; sarcoma; cholangiocarcinoma; and bone cancer.

[0010] In some embodiments, the subject has a fibrotic condition. In some embodiments, the fibrotic condition is selected from the group consisting of hypertrophic scar of the skin, scleroderma, lung scar, idiopathic pulmonary fibrosis, sclerosing hepatic fibrosis, renal fibrosis, and interstitial lung disease.

[0011] In one aspect, the present disclosure provides a method of treating a DDR1-related disorder in a subject in need thereof, comprising: a) administering to the subject an effective amount of an anti-DDR1 antibody or an antigen-binding fragment thereof; and b) detecting the level of DDR1 phosphorylation in a sample derived from the subject, wherein a decrease in DDR1 phosphorylation in the sample derived from the subject as compared to a positive reference sample indicates that the treatment is effective.

[0012] In one aspect, the present disclosure provides a method of screening for a subject having a DDR1-related disorder that is likely to be effectively treated with an anti-DDR1 antibody, the method comprising detecting the level of DDR1 phosphorylation in a sample from the subject, wherein if the DDR1 phosphorylation in the sample from the subject is high compared to a negative reference sample, the DDR1-related disorder is likely to be effectively treated with an anti-DDR1 antibody.

[0013] In one aspect, the present disclosure provides a method of treating a DDR1-related disorder in a subject in need thereof, the method comprising: a) detecting the level of DDR1 phosphorylation in a sample from the subject; and b) administering to the subject an effective amount of an anti-DDR1 antibody or an antigen-binding fragment thereof if the DDR1 phosphorylation in the sample from the subject is high compared to a negative reference sample.

[0014] In some embodiments, the DDR1-related disorder is cancer. In some embodiments, the cancer is pancreatic cancer; lung cancer including small cell lung cancer and non-small cell lung cancer; colorectal and colorectal cancer; head and neck cancer; gastric cancer; ovarian cancer; breast cancer; kidney cancer; liver cancer; prostate cancer; cervical cancer; brain cancer; skin cancer including melanoma; sarcoma; cholangiocarcinoma; and bone cancer.

[0015] In some embodiments, the DDR1-related disorder is a fibrotic condition. In some embodiments, the fibrotic condition is selected from the group consisting of hypertrophic scar of the skin, scleroderma, lung scar, idiopathic pulmonary fibrosis, sclerosing hepatic fibrosis, renal fibrosis, and interstitial lung disease.

[0016] In some embodiments, the sample from the subject described herein comprises tumor tissue. In some embodiments, the sample from the subject described herein comprises one or more selected from the group consisting of blood cells, skin tissue, lung tissue, kidney tissue, and liver tissue. In some embodiments, the sample from the subject described herein comprises a skin punch biopsy sample.

[0017] In one aspect, the present disclosure provides a method of screening for an anti-DDR1 antibody or an antigen-binding fragment thereof that is effective in treating a DDR1-related disorder, the method comprising: a) administering an effective amount of the anti-DDR1 antibody or an antigen-binding fragment thereof to a cell; and b) detecting the level of DDR1 phosphorylation in the cell, wherein a decrease in DDR1 phosphorylation in the cell compared to a positive reference cell indicates that the anti-DDR1 antibody or an antigen-binding fragment thereof is effective in treating a DDR1-related disorder.

[0018] In one aspect, the present disclosure provides a method of screening for an anti-DDR1 antibody or an antigen-binding fragment thereof that is effective in reducing collagen interaction with a cell, the method comprising: a) administering an effective amount of the anti-DDR1 antibody or an antigen-binding fragment thereof to a cell; and b) detecting the level of DDR1 phosphorylation in the cell, wherein a decrease in DDR1 phosphorylation in the cell compared to a positive reference cell indicates that the anti-DDR1 antibody or an antigen-binding fragment thereof is effective in reducing collagen interaction with the cell.

[0019] In some embodiments, the cells described herein are cancer cells. In some embodiments, the cancer cells are derived from a cancer selected from the group consisting of pancreatic cancer; lung cancer, including small cell lung cancer and non-small cell lung cancer; colorectal cancer; head and neck cancer; gastric cancer; ovarian cancer; breast cancer; kidney cancer; liver cancer; prostate cancer; cervical cancer; brain cancer; skin cancer, including melanoma; sarcoma; cholangiocarcinoma; and bone cancer.

[0020] In some embodiments, the cells described herein are one or more selected from the group consisting of skin cells, lung cells, kidney cells, and liver cells.

[0021] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof described herein comprises a VH comprising the CDRH1, CDRH2, and CDRH3 amino acid sequences of the heavy chain variable domain (VH) amino acid sequence of SEQ ID NO: 4 or 13, and a VL comprising the CDRL1, CDRL2, and CDRL3 amino acid sequences of the light chain variable domain (VL) amino acid sequence of SEQ ID NO: 3, 11, or 12.

[0022] In some embodiments, a) CDRL1 comprises the amino acid sequence of SEQ ID NO: 5; b) CDRL2 comprises the amino acid sequence QAS; c) CDRL3 comprises the amino acid sequence of SEQ ID NO: 7; d) CDRH1 comprises the amino acid sequence of SEQ ID NO: 8; e) CDRH2 comprises the amino acid sequence of SEQ ID NO: 9; f) CDRH3 comprises the amino acid sequence of SEQ ID NO: 10.

[0023] In some embodiments, a) CDRL1 comprises the amino acid sequence of SEQ ID NO: 17; b) CDRL2 comprises the amino acid sequence GVF; c) CDRL3 comprises the amino acid sequence of SEQ ID NO: 19; d) CDRH1 comprises the amino acid sequence of SEQ ID NO: 20; e) CDRH2 comprises the amino acid sequence of SEQ ID NO: 21; f) CDRH3 comprises the amino acid sequence of SEQ ID NO: 22.

[0024] In some embodiments, the anti-DDR1 antibody comprises a) a VL domain comprising an amino acid sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 3, 11, and 12; and b) a VH domain comprising an amino acid sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 4 and 13.

[0025] In some embodiments, the anti-DDR1 antibody comprises a) a VL domain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 3, 11, and 12; and b) a VH domain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 4 and 13.

[0026] In some embodiments, the anti-DDR1 antibody comprises a VL domain and a VH domain selected from the group consisting of: a) SEQ ID NO: 3 and 4, respectively; b) SEQ ID NO: 11 and 13, respectively; and c) SEQ ID NO: 12 and 13, respectively.

[0027] In some embodiments, the anti-DDR1 antibody comprises a VL domain and a VH domain comprising the amino acid sequences of SEQ ID NO: 3 and 4, respectively. In some embodiments, the anti-DDR1 antibody comprises a VL domain and a VH domain comprising the amino acid sequences of SEQ ID NO: 11 and 13, respectively. In some embodiments, the anti-DDR1 antibody comprises a VL domain and a VH domain comprising the amino acid sequences of SEQ ID NO: 12 and 13, respectively.

[0028] In some embodiments, the step of detecting the level of DDR1 phosphorylation comprises detecting the level of phosphorylation of the cleaved form of DDR1. In some embodiments, the cleaved form of DDR1 has a molecular weight of approximately 65 kDa. 6. BRIEF DESCRIPTION OF THE DRAWINGS

BRIEF DESCRIPTION OF THE DRAWINGS

[0029]

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Mode for Carrying Out the Invention

[0040] 7. Detailed Description The present disclosure provides a method for detecting DDR1 phosphorylation for use in monitoring the effectiveness or potential effectiveness of a DDR1 inhibitor (e.g., an anti-DDR1 antibody) for inhibiting DDR1-mediated collagen interactions and / or treating DDR1-related disorders. 7.1 Definitions

[0041] As used herein, the term "DDR1" refers to discoidin domain receptor tyrosine kinase 1 encoded by the DDR1 gene. Unless otherwise stated, the term "DDR1" refers to the DDR1 protein encoded by the wild-type DDR1 gene (e.g., GenBank™ accession number NM_013993.3). Exemplary DNA and amino acid sequences for human DDR1 are provided in Table 1 below. "DDR1 phosphorylation" as used herein refers to the attachment of a phosphoryl group to any residue of DDR1. For example, phosphorylation can occur at serine, threonine, or tyrosine residues of the DDR1 protein and can occur by intermolecular interactions (e.g., by separate kinases) or intramolecular interactions (e.g., autophosphorylation). Exemplary DDR1 phosphorylation sites include, but are not limited to, Y484, Y513, Y520, S631, Y740, Y792, Y796, and Y797 relative to the amino acid sequence of SEQ ID NO: 2 shown in Table 1 below.

Table 1-1

Table 1-2

Table 1-3

[0042] As used herein, the term "antibody(ies)" includes full-length antibodies, antigen-binding fragments of full-length antibodies, and molecules comprising CDRs, VH regions, and / or VL regions of antibodies. Examples of antibodies include, but are not limited to, monoclonal antibodies, recombinantly produced antibodies, monospecific antibodies, multispecific antibodies (including bispecific antibodies), human antibodies, humanized antibodies, chimeric antibodies, immunoglobulins, synthetic antibodies, tetrameric antibodies comprising two heavy chains and two light chain molecules, antibody light chain monomers, antibody heavy chain monomers, antibody light chain dimers, antibody heavy chain dimers, antibody light chain-heavy chain pairs, intrabodies, heteroconjugate antibodies, antibody-drug conjugates, single domain antibodies, monovalent antibodies, single-chain antibodies or single-chain Fv (scFv), camelized antibodies, affibodies, Fab fragments, F(ab’)2 fragments, disulfide-linked Fv (sdFv), anti-idiotypic (anti-Id) antibodies (e.g., including anti-Id antibodies), and antigen-binding fragments of any of the foregoing. In certain embodiments, the antibodies described herein refer to a polyclonal antibody population. Antibodies can be of any type of immunoglobulin molecule (e.g., IgG, IgE, IgM, IgD, IgA, or IgY), any class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, or IgA2), or any subclass (e.g., IgG2a or IgG2b). In certain embodiments, the antibodies described herein are IgG antibodies, or a class (e.g., human IgG1 or IgG4) or subclass thereof. In some embodiments, the antibody is a humanized monoclonal antibody. In some embodiments, the antibody is a human monoclonal antibody.

[0043] As used herein, the term "CDR" or "complementary determining region" means the non - contiguous antigen - combining sites found within the variable regions of heavy and light chain polypeptides. These specific regions are described, for example, by Kabat et al., J. Biol. Chem. 252, 6609 - 6616 (1977) and Kabat et al., Sequences of protein of immunological interest. (1991), Chothia et al., J. Mol. Biol. 196:901 - 917 (1987), and MacCallum et al., J. Mol. Biol. 262:732 - 745 (1996), all of which are hereby incorporated by reference in their entirety, where the definitions, when compared to each other, include overlapping or subsets of amino acid residues. In certain embodiments, the term "CDR" is the CDR as defined by MacCallum et al., J. Mol. Biol. 262:732 - 745 (1996) and Martin A. "Protein Sequence and Structure Analysis of Antibody Variable Domains," in Antibody Engineering, Kontermann and Duebel, eds., Chapter 31, pp. 422 - 439, Springer - Verlag, Berlin (2001). In certain embodiments, the term "CDR" is the CDR as defined by Kabat et al., J. Biol. Chem. 252, 6609 - 6616 (1977) and Kabat et al., Sequences of protein of immunological interest. (1991). In certain embodiments, the heavy - chain CDRs and light - chain CDRs of an antibody are defined using different conventions.In certain embodiments, the heavy chain CDR and / or the light chain CDR are defined by performing a structural analysis of the antibody and identifying residues in the variable region predicted to contact the epitope region of a target molecule (e.g., human and / or mouse DDR1). CDRH1, CDRH2, and CDRH3 represent the heavy chain CDRs, and CDRL1, CDRL2, and CDRL3 represent the light chain CDRs.

[0044] As used herein, the terms "variable region" and "variable domain" are used interchangeably and are common in the art. The variable region typically refers to a portion of an antibody, generally a portion of the light or heavy chain, typically about 110-120 or 110-125 amino acids at the amino terminus in the mature heavy chain, and about 90-115 amino acids in the mature light chain, which vary extremely in sequence between antibodies and are used in the binding and specificity of a particular antibody to its specific antigen. The variability of the sequence is concentrated in regions called complementarity determining regions (CDRs), while the more highly conserved regions in the variable region are called framework regions (FRs). Without wishing to be bound by any particular mechanism or theory, the CDRs of the light and heavy chains are thought to be the main cause of antibody-antigen interaction and specificity. In certain embodiments, the variable region is a human variable region. In certain embodiments, the variable region comprises a rodent, e.g., mouse or rabbit, e.g., rabbit CDRs, and a human framework region (FR). In certain embodiments, the variable region is a primate (e.g., non-human primate) variable region. In certain embodiments, the variable region comprises a rodent, e.g., mouse or rabbit, e.g., rabbit CDRs, and a primate (e.g., non-human primate) framework region (FR).

[0045] As used herein, the terms "VH" and "VL" refer to the variable regions of the heavy and light chains of an antibody, respectively, as described in Kabat et al., (1991) Sequences of Proteins of Immunological Interest (NIH Publication No. 91 - 3242, Bethesda), which is hereby incorporated by reference in its entirety.

[0046] As used herein, the term "constant region" is common in the art. The constant region is the carboxyl-terminal portion of an antibody moiety, e.g., of a light and / or heavy chain, which is not directly involved in binding of the antibody to an antigen, but may exhibit various effector functions such as interaction with Fc receptors (e.g., Fc gamma receptors).

[0047] As used herein, the term "heavy chain" when used in reference to an antibody can refer to any distinct type, e.g., alpha (α), delta (δ), epsilon (ε), gamma (γ), and mu (μ), based on the amino acid sequence of the constant region, which give rise to antibodies of the IgA, IgD, IgE, IgG, and IgM classes, including subclasses of IgG, e.g., IgG1, IgG2, IgG3, and IgG4, respectively.

[0048] As used herein, the term "light chain" when used in reference to an antibody can refer to any distinct type, e.g., kappa (κ) or lambda (λ), based on the amino acid sequence of the constant region. Light chain amino acid sequences are well known in the art. In certain embodiments, the light chain is a human light chain.

[0049] As used herein, the term "cancer" refers to any condition characterized by the uncontrolled division of abnormal cells in the body. For example, mutations that prevent the regulation of cell division can occur in cells, leading to the formation of one or more tumors. Cancer can be benign, pre-cancerous, or malignant. Cancer occurs in various cells and tissues, including but not limited to the oral cavity (e.g., mouth, tongue, pharynx, etc.), digestive system (e.g., esophagus, stomach, small intestine, colon, rectum, liver, bile duct, gallbladder, pancreas, etc.), respiratory system (e.g., larynx, lung, bronchus, etc.), bones, joints, skin (e.g., basal cells, squamous cells, meningioma, etc.), breast, reproductive system (e.g., uterus, ovaries, prostate, testis, etc.), urinary system (e.g., bladder, kidney, ureter, etc.), eyes, nervous system (e.g., brain, etc.), endocrine system (e.g., thyroid, etc.), soft tissues (e.g., muscle, fat, etc.), and hematopoietic system (e.g., lymphoma, myeloma, leukemia, acute lymphoblastic leukemia, chronic lymphoblastic leukemia, acute myeloid leukemia, chronic myeloid leukemia, etc.).

[0050] "Cell(s)" as used herein refers to the basic structural and functional unit of a living organism. A cell contains membrane-bound cytoplasm that includes biological macromolecules (e.g., nucleic acids, carbohydrates, lipids, and proteins) and organelles necessary to sustain life. "Cancer cell" as used herein refers to an abnormal cell that undergoes uncontrolled cell division (e.g., one that has accumulated one or more harmful mutations). Healthy cells can be derived from healthy tissues such as skin tissue, while cancer cells can be derived from pathological tissues such as tumors.

[0051] As used herein, the term "interaction" refers to a non-covalent chemical bond formed between biological macromolecules during a functionally relevant period. "Collagen interaction" as used herein, with respect to DDR1, refers to a non-covalent chemical bond that occurs between the extracellular domain of the DDR1 protein and collagen with an intensity and duration sufficient to promote autophosphorylation of the intracellular domain of DDR1.

[0052] As used interchangeably herein, the terms "DDR1-related disease", "DDR1-related disorder", or "DDR1-related condition" refer to any pathological condition associated with or directly caused by abnormal expression and / or function of DDR1. For example, a DDR1-related disorder can include cancer, where overexpression of DDR1 suppresses antitumor immunity, thereby preventing tumor recognition and clearance. As a further example, a DDR1-related disorder can include a fibrotic condition, where overexpression of DDR1 is associated with excessive accumulation of extracellular matrix components (e.g., collagen) and impaired tissue functionality.

[0053] The terms "effective", "effective amount", "therapeutically effective amount", and "pharmaceutically effective amount", when used interchangeably herein with respect to a treatment, refer to the amount of an agent sufficient to achieve a desired biological result. This result can be a reduction and / or alleviation in the severity, duration, and / or frequency of one or more symptoms, signs, side effects, and / or causes of the disease or disorder being treated.

[0054] As used herein, the terms "fibrosis" and "fibrotic condition" refer to any condition characterized by replacement of normal parenchymal tissue by connective tissue. For example, tissue injury or inflammation can result in excessive accumulation of extracellular matrix components (e.g., collagen). If severe enough, this accumulation can interfere with the normal structure and / or function of the tissue.

[0055] As used herein, "reference sample" refers to one or more biological samples containing DDR1 or derivatives thereof that can be compared to a target sample. "Positive reference sample", as used herein, refers to a sample in which the entity of interest is known to be present and / or the condition is known to meet the purpose of comparison. For example, a positive reference sample may include a sample derived from a cancerous tissue known to overexpress phosphorylated DDR1. In contrast, "negative reference sample", as used herein, refers to a sample in which the entity of interest is known not to be present and / or the condition is known not to meet the purpose of comparison. For example, a negative reference sample may include a sample derived from a healthy tissue such as skin tissue known to express normal levels of phosphorylated DDR1. "Reference cell" refers to one or more cells containing phosphorylated DDR1 that can be compared to a target cell as used herein. "Positive reference cell", as used herein, refers to a cell in which the entity of interest is known to be present and / or the condition is known to meet the purpose of comparison. For example, a positive reference cell may include cells derived from a cancerous tissue known to overexpress phosphorylated DDR1. In contrast, "negative reference cell", as used herein, refers to a cell in which the entity of interest is known not to be present and / or the condition is known not to meet the purpose of comparison. For example, a negative reference sample may include cells derived from a healthy tissue such as skin tissue known to express normal levels of phosphorylated DDR1.

[0056] As used herein, the terms "specifically binds," "specifically recognizes," "immunologically specifically binds," and "immunologically specifically recognizes" are similar terms in the context of antibodies and refer to a molecule that binds to an antigen (e.g., an epitope or an immune complex) such that such binding is understood by one of ordinary skill in the art. For example, a molecule that specifically binds to an antigen generally binds to other peptides or polypeptides with a lower affinity, as determined, for example, by an immunoassay, BIAcore®, KinExA 3000 instrument (Sapidyne Instruments, Boise, ID), or other assays known in the art. In certain embodiments, a molecule that specifically binds to an antigen has a K A that is at least 2 log (e.g., a factor of 10), 2.5 log, 3 log, 4 log, or higher than the K A when the molecule binds non-specifically to another antigen.

[0057] As used herein, the term "tissue" refers to a grouping of interconnected cells that share a common biological origin within an organism. By way of example, a tissue can be one that performs a physiological function in vivo (e.g., lung tissue to allow for the movement of gases) or as a result of a pathological condition (e.g., tumor tissue as a product of cancer, fibrotic tissue as a product of excessive inflammation, etc.).

[0058] As used herein, the term "EU numbering system" refers to the EU numbering conversion for the constant regions of antibodies as described in Edelman GM et al., Proc. Natl. Acad. USA, 63, 78-85 (1969) and Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Dept. Health and Human Services, 5th edition, 1991, each of which is hereby incorporated by reference in its entirety.

[0059] As used herein, the terms "treat", "treating", and "treatment" refer to the therapeutic or prophylactic measures described herein. The methods of "treatment" are for preventing, curing, delaying, reducing the severity of, or alleviating one or more symptoms of a disease or disorder or a recurrent disease or disorder, or for extending the survival of a subject longer than would be expected in the absence of such treatment, by administering an antibody to a subject having a disease or disorder or a subject susceptible to such a disease or disorder.

[0060] As used herein, the term "effective amount" in the context of administering a therapy to a subject refers to the amount of the therapy that achieves the desired prophylactic or therapeutic effect.

[0061] As used herein, the term "subject" includes any human or non-human animal. In certain embodiments, the subject is a human or non-human mammal. In certain embodiments, the subject is a human.

[0062] As used herein with respect to an antibody or polynucleotide, the term "isolated" refers to an antibody or polynucleotide that has been separated from one or more contaminants (such as polypeptides, polynucleotides, lipids, or carbohydrates, etc.) that are present in its natural source. All examples of "isolated antibodies" described herein are additionally, although not necessarily, contemplated as antibodies that may be isolated. All examples of "isolated polynucleotides" described herein are additionally, although not necessarily, contemplated as polynucleotides that may be isolated. All examples of "antibodies" described herein are additionally, although not necessarily, contemplated as antibodies that may be isolated. All examples of "polynucleotides" described herein are additionally, although not necessarily, contemplated as polynucleotides that may be isolated.

[0063] The determination of the "percent identity" between two sequences (e.g., amino acid or nucleic acid sequences) can be accomplished using mathematical algorithms. Non-limiting examples of mathematical algorithms utilized for comparison of two sequences are the algorithms of Karlin S & Altschul SF (1990) PNAS 87: 2264-2268 as modified as in Karlin S & Altschul SF (1993) PNAS 90: 5873-5877, each of which is incorporated herein by reference in its entirety. Such algorithms are incorporated into the NBLAST and XBLAST programs of Altschul SF et al., (1990) J Mol Biol 215: 403, which is incorporated herein by reference in its entirety. The BLAST nucleotide search can be performed using the NBLAST nucleotide program parameter set, e.g., score = 100, wordlength = 12, to obtain nucleotide sequences homologous to the nucleic acid molecules described herein. The BLAST protein search can be performed using the XBLAST program parameter set, e.g., score 50, wordlength = 3, to obtain amino acid sequences homologous to the protein molecules described herein. Gapped BLAST can be utilized as described in Altschul SF et al., (1997) Nuc Acids Res 25: 3389-3402 to obtain gapped alignments for comparison purposes, which is incorporated herein by reference in its entirety. Alternatively, PSI BLAST can be used to perform iterative searches to detect distant relationships between molecules (ibid.). When utilizing the BLAST, Gapped BLAST, and PSI Blast programs, the default parameters of each program (e.g., of XBLAST and NBLAST) can be used (see, e.g., National Center for Biotechnology Information (NCBI) on the world wide web ncbi.nlm.nih.gov).Another non-limiting example of a mathematical algorithm utilized for array comparison is the algorithm of Myers and Miller, 1988, CABIOS 4: 11-17, which is hereby incorporated by reference in its entirety. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG sequence alignment software package. When using the ALIGN program to compare amino acid sequences, the PAM120 weight residue table, a 12 gap length penalty, and a 4 gap penalty can be used.

[0064] The percent identity between two arrays can be determined using techniques similar to those described above, with or without allowing gaps. In calculating the percent identity, typically only exact matches are counted. 7.2 Anti-DDR1 Antibodies

[0065] In one aspect, the present disclosure provides a method of screening to determine the effectiveness of, or potential effectiveness of, one or more inhibitors of DDR1. In some embodiments, the inhibitor of DDR1 comprises an antibody specific for DDR1 (i.e., an anti-DDR1 antibody).

[0066] In one embodiment, the present disclosure provides an isolated antibody (anti-DDR1) that specifically binds to DDR1. The CDR and VH / VL amino acid sequences of exemplary antibodies that specifically bind to DDR1 are shown in Tables 2 and 3, respectively.

Table 2

Table 3

[0067] In various embodiments, the present disclosure provides anti-DDR1 antibodies comprising CDRL1, CDRL2, and CDRL3 shown in Table 2, which are isolated antibodies (anti-DDR1) that specifically bind to DDR1. In one embodiment, the anti-DDR1 antibody comprises CDRL1 shown in Table 2. In one embodiment, the anti-DDR1 antibody comprises CDRL2 shown in Table 2. In one embodiment, the anti-DDR1 antibody comprises CDRL3 shown in Table 2.

[0068] In one embodiment, the anti-DDR1 antibody comprises a VL domain comprising one, two, or all three of the CDRs of the VL domain disclosed in Table 3. In one embodiment, the anti-DDR1 antibody comprises CDRL1 of the VL domain shown in Table 3. In one embodiment, the anti-DDR1 antibody comprises CDRL2 of the VL domain shown in Table 3. In one embodiment, the anti-DDR1 antibody comprises CDRL3 of the VL domain shown in Table 3. In one embodiment, the anti-DDR1 antibody comprises the VL domain shown in Table 3.

[0069] In various embodiments, the present disclosure provides anti-DDR1 antibodies comprising CDRH1, CDRH2, and CDRH3 shown in Table 2, which are isolated antibodies (anti-DDR1) that specifically bind to DDR1. In one embodiment, the anti-DDR1 antibody comprises CDRH1 shown in Table 2. In one embodiment, the anti-DDR1 antibody comprises CDRH2 shown in Table 2. In one embodiment, the anti-DDR1 antibody comprises CDRH3 shown in Table 2.

[0070] In one embodiment, the anti-DDR1 antibody comprises a VH domain comprising one, two, or all three of the CDRs of the VH domain disclosed in Table 3. In one embodiment, the anti-DDR1 antibody comprises CDRH1 of the VH domain shown in Table 3. In one embodiment, the anti-DDR1 antibody comprises CDRH2 of the VH domain shown in Table 3. In one embodiment, the anti-DDR1 antibody comprises CDRH3 of the VH domain shown in Table 3. In one embodiment, the anti-DDR1 antibody comprises the VH domain shown in Table 3.

[0071] In one embodiment, the anti-DDR1 antibody comprises CDRL1 of SEQ ID NO: 5 or 17. In one embodiment, the anti-DDR1 antibody comprises CDRL2 of QAS or GVF. In one embodiment, the anti-DDR1 antibody comprises CDRL3 of SEQ ID NO: 7 or 19. In one embodiment, the anti-DDR1 antibody comprises at least two of CDRL1, CDRL2 or CDRL3 shown in SEQ ID NOs: 5-7 or 17-19. In one embodiment, the anti-DDR1 antibody comprises CDRL1, CDRL2 and CDRL3 of SEQ ID NOs: 5-7 or SEQ ID NOs: 17-19.

[0072] In one embodiment, the anti-DDR1 antibody comprises CDRL1 of SEQ ID NO: 5. In one embodiment, the anti-DDR1 antibody comprises CDRL2 of QAS. In one embodiment, the anti-DDR1 antibody comprises CDRL3 of SEQ ID NO: 7. In one embodiment, the anti-DDR1 antibody comprises at least two of CDRL1, CDRL2 or CDRL3 shown in SEQ ID NOs: 5-7. In one embodiment, the anti-DDR1 antibody comprises CDRL1, CDRL2 and CDRL3 of SEQ ID NOs: 5-7.

[0073] In one embodiment, the anti-DDR1 antibody comprises CDRL1 of SEQ ID NO: 17. In one embodiment, the anti-DDR1 antibody comprises CDRL2 of GVF. In one embodiment, the anti-DDR1 antibody comprises CDRL3 of SEQ ID NO: 19. In one embodiment, the anti-DDR1 antibody comprises at least two of CDRL1, CDRL2 or CDRL3 shown in SEQ ID NOs: 17-19. In one embodiment, the anti-DDR1 antibody comprises CDRL1, CDRL2 and CDRL3 of SEQ ID NOs: 17-19.

[0074] In one embodiment, the anti-DDR1 antibody comprises a VL domain that comprises one, two, or all three of the CDRs of the VL domain of SEQ ID NO: 3. In one embodiment, the anti-DDR1 antibody comprises the VL domain of SEQ ID NO: 3. In one embodiment, the anti-DDR1 antibody comprises a VL domain that comprises one, two, or all three of the CDRs of the VL domain of SEQ ID NO: 11. In one embodiment, the anti-DDR1 antibody comprises the VL domain of SEQ ID NO: 11. In one embodiment, the anti-DDR1 antibody comprises a VL domain that comprises one, two, or all three of the CDRs of the VL domain of SEQ ID NO: 12. In one embodiment, the anti-DDR1 antibody comprises the VL domain of SEQ ID NO: 12.

[0075] In one embodiment, the anti-DDR1 antibody comprises an LC that comprises the VL of the light chain (LC) sequence shown in Table 4 below. In one embodiment, the anti-DDR1 antibody comprises the LC shown in Table 4.

Table 4-1

Table 4-2

[0076] In one embodiment, the anti-DDR1 antibody comprises a light chain that comprises the VL of the light chain of SEQ ID NO: 23. In one embodiment, the anti-DDR1 antibody comprises the light chain of SEQ ID NO: 23.

[0077] In one embodiment, the anti-DDR1 antibody comprises a light chain that comprises the VL of the light chain of SEQ ID NO: 161. In one embodiment, the anti-DDR1 antibody comprises the light chain of SEQ ID NO: 161.

[0078] In one embodiment, the anti-DDR1 antibody comprises a light chain that comprises the VL of the light chain of SEQ ID NO: 164. In one embodiment, the anti-DDR1 antibody comprises the light chain of SEQ ID NO: 164.

[0079] In one embodiment, the anti-DDR1 antibody comprises CDRH1 of SEQ ID NO: 8 or 20. In one embodiment, the anti-DDR1 antibody comprises CDRH2 of SEQ ID NO: 9 or 21. In one embodiment, the anti-DDR1 antibody comprises CDRH3 of SEQ ID NO: 10 or 22. In one embodiment, the anti-DDR1 antibody comprises at least two of CDRH1, CDRH2 or CDRH3 shown in SEQ ID NOs: 8-10 or 20-22. In one embodiment, the anti-DDR1 antibody comprises CDRH1, CDRH2 and CDRH3 of SEQ ID NOs: 8-10 or SEQ ID NOs: 20-22.

[0080] In one embodiment, the anti-DDR1 antibody comprises CDRH1 of SEQ ID NO: 8. In one embodiment, the anti-DDR1 antibody comprises CDRH2 of SEQ ID NO: 9. In one embodiment, the anti-DDR1 antibody comprises CDRH3 of SEQ ID NO: 10. In one embodiment, the anti-DDR1 antibody comprises at least two of CDRH1, CDRH2 or CDRH3 shown in SEQ ID NOs: 8-10. In one embodiment, the anti-DDR1 antibody comprises CDRH1, CDRH2 and CDRH3 of SEQ ID NOs: 8-10.

[0081] In one embodiment, the anti-DDR1 antibody comprises CDRH1 of SEQ ID NO: 20. In one embodiment, the anti-DDR1 antibody comprises CDRH2 of SEQ ID NO: 21. In one embodiment, the anti-DDR1 antibody comprises CDRH3 of SEQ ID NO: 22. In one embodiment, the anti-DDR1 antibody comprises at least two of CDRH1, CDRH2 or CDRH3 shown in SEQ ID NOs: 20-22. In one embodiment, the anti-DDR1 antibody comprises CDRH1, CDRH2 and CDRH3 of SEQ ID NOs: 20-22.

[0082] In one embodiment, the anti-DDR1 antibody comprises a VH domain comprising one, two or all three of the CDRs of the VH domain of SEQ ID NO: 4. In one embodiment, the anti-DDR1 antibody comprises the VH domain of SEQ ID NO: 4. In one embodiment, the anti-DDR1 antibody comprises a VH domain comprising one, two or all three of the CDRs of the VH domain of SEQ ID NO: 13. In one embodiment, the anti-DDR1 antibody comprises the VH domain of SEQ ID NO: 13.

[0083] In one embodiment, the anti-DDR1 antibody comprises a heavy chain comprising VH of the heavy chain of SEQ ID NO: 24. In one embodiment, the anti-DDR1 antibody comprises the heavy chain of SEQ ID NO: 24.

[0084] In one embodiment, the anti-DDR1 antibody comprises a heavy chain comprising VH of the heavy chain of SEQ ID NO: 162. In one embodiment, the anti-DDR1 antibody comprises the heavy chain of SEQ ID NO: 162.

[0085] In one embodiment, the anti-DDR1 antibody comprises a heavy chain comprising VH of the heavy chain of SEQ ID NO: 163. In one embodiment, the anti-DDR1 antibody comprises the heavy chain of SEQ ID NO: 163.

[0086] In one embodiment, the anti-DDR1 antibody comprises a heavy chain comprising VH of the heavy chain of SEQ ID NO: 165. In one embodiment, the anti-DDR1 antibody comprises the heavy chain of SEQ ID NO: 165.

[0087] In one embodiment, the anti-DDR1 antibody comprises CDRL1, CDRL2, and CDRL3 of SEQ ID NO: 5, QAS, and SEQ ID NO: 7, respectively; and CDRH1, CDRH2, and CDRH3 of SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, respectively. In one embodiment, the anti-DDR1 antibody comprises the VL domain of SEQ ID NO: 3; and the VH domain of SEQ ID NO: 4.

[0088] In one embodiment, the anti-DDR1 antibody comprises CDRL1, CDRL2, and CDRL3 of SEQ ID NO: 17, GVF, and SEQ ID NO: 19, respectively; and CDRH1, CDRH2, and CDRH3 of SEQ ID NO: 20, SEQ ID NO: 21, and SEQ ID NO: 22, respectively. In one embodiment, the anti-DDR1 antibody comprises the VL domain of SEQ ID NO: 11; and the VH domain of SEQ ID NO: 13. In one embodiment, the anti-DDR1 antibody comprises the VL domain of SEQ ID NO: 12; and the VH domain of SEQ ID NO: 13.

[0089] In one embodiment, the anti-DDR1 antibody comprises a light chain of SEQ ID NO: 23; and a heavy chain of SEQ ID NO: 24. In one embodiment, the anti-DDR1 antibody comprises a light chain of SEQ ID NO: 161; and a heavy chain of SEQ ID NO: 162. In one embodiment, the anti-DDR1 antibody comprises a light chain of SEQ ID NO: 161; and a heavy chain of SEQ ID NO: 163. In one embodiment, the anti-DDR1 antibody comprises a light chain of SEQ ID NO: 164; and a heavy chain of SEQ ID NO: 165.

[0090] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 selected from the CDRL1, CDRL2, and CDRL3 sequences for each mAb shown in Table 5 below; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 selected from the CDRH1, CDRH2, and CDRH3 sequences for each mAb shown in Table 6 below, or a variant thereof in which one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

Table 5-1

Table 5-2

Table 6

[0091] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QNIYSN (SEQ ID NO: 25), GAS, and QSGYYSSSTDIA (SEQ ID NO: 44), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFSLSRYA (SEQ ID NO: 63), IGSSGLT (SEQ ID NO: 82), and ARGMWYDDSDDYEDYFNL (SEQ ID NO: 101), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0092] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QTISSW (SEQ ID NO: 26), YAF, and QQGISSSNVDNV (SEQ ID NO: 45), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GIDLSSYA (SEQ ID NO: 64), INIGGGT (SEQ ID NO: 83), and ARDVDAHTLTYFTL (SEQ ID NO: 102), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0093] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QTISSW (SEQ ID NO: 27), YAF, and QCTYGSGSSSSYGCA (SEQ ID NO: 46), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFTLSNNA (SEQ ID NO: 65), IYASGRT (SEQ ID NO: 84), and ARGDTETDYGIPYFDL (SEQ ID NO: 103), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0094] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 comprising the amino acid sequences of QSVYSNY (SEQ ID NO: 28), ETS, and QGGYSEIIENT (SEQ ID NO: 47), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 comprising the amino acid sequences of GFSFSSSYY (SEQ ID NO: 66), IYASSGST (SEQ ID NO: 85), and AILGADYRLTRLDL (SEQ ID NO: 104), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0095] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 comprising the amino acid sequences of QSIGSTY (SEQ ID NO: 29), KAS, and LYGGFGSSTGDA (SEQ ID NO: 48), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 comprising the amino acid sequences of GFSFSSGYY (SEQ ID NO: 67), IYTGRTDFT (SEQ ID NO: 86), and ARGDYSGGVGGNYWLDL (SEQ ID NO: 105), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0096] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QTIYSN (SEQ ID NO: 30), QAS, and QSYYGADDYT (SEQ ID NO: 49), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GIDLSNTW (SEQ ID NO: 68), ITDSGTT (SEQ ID NO: 87), and GRDPGDITSGTNDL (SEQ ID NO: 106), respectively, or variants thereof in which one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0097] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of KSVYNNNA (SEQ ID NO: 31), GVS, and AGDYSDISDNN (SEQ ID NO: 50), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of SGFSLNNY (SEQ ID NO: 69), IFNNGDI (SEQ ID NO: 88), and ARTGYRTGGWL (SEQ ID NO: 107), respectively, or variants thereof in which one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0098] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QSISSY (SEQ ID NO: 32), EAS, and QNNNGFSGSNFNN (SEQ ID NO: 51), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GIDLSYYA (SEQ ID NO: 70), INGRGDT (SEQ ID NO: 89), and AREDSAIPFIVGNYYGMDL (SEQ ID NO: 108), respectively, or variants thereof in which one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0099] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 comprising the amino acid sequences of QTIYSS (SEQ ID NO: 33), KAS, and QQGSSISNVDKNA (SEQ ID NO: 52), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 comprising the amino acid sequences of TFSFNSRYW (SEQ ID NO: 71), INNGDIS (SEQ ID NO: 90), and AKGGNLAGDCYGL (SEQ ID NO: 109), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0100] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 comprising the amino acid sequences of QSIGSY (SEQ ID NO: 34), EAS, and QNNNGMTVSDFNA (SEQ ID NO: 53), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 comprising the amino acid sequences of GFSLNRYA (SEQ ID NO: 72), IGSSGST (SEQ ID NO: 91), and ARDLDDSYGYTYATGMDIRLDL (SEQ ID NO: 110), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0101] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QIIDHDH (SEQ ID NO: 35), RAS, and QNNNGMTVSDFNA (SEQ ID NO: 54), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFSLSDYA (SEQ ID NO: 73), INSRDDT (SEQ ID NO: 92), and AREDSSIPFIVGNYYGMDL (SEQ ID NO: 111), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0102] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QSVVDKNW (SEQ ID NO: 36), EAS, and AGDFESGVSG (SEQ ID NO: 55), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFSLSSYG (SEQ ID NO: 74), IYPSGSI (SEQ ID NO: 93), and VRYLTGSSDLHL (SEQ ID NO: 112), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0103] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of KNIYNNNA (SEQ ID NO: 37), GAS, and AADYSDISDNN (SEQ ID NO: 56), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFSLSDYA (SEQ ID NO: 75), INNGDIY (SEQ ID NO: 94), and ARPGYRTGIWL (SEQ ID NO: 113), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0104] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QSVYSNNY (SEQ ID NO: 38), AAS, and LGGYNDDAN (SEQ ID NO: 57), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFDLRSYYY (SEQ ID NO: 76), IHGGEGNT (SEQ ID NO: 95), and RGGWTNYF (SEQ ID NO: 114), respectively, or a variant thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0105] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of ESVYSNNH (SEQ ID NO: 39), AAS, and LGGYNDDAN (SEQ ID NO: 58), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFDLSSNYY (SEQ ID NO: 77), IYSSNTRT (SEQ ID NO: 96), and RGGWTNYL (SEQ ID NO: 115), respectively, or a variant thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0106] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that comprise the amino acid sequences of QSIDNND (SEQ ID NO: 40), RTS, and QSYCVNTYGYT (SEQ ID NO: 59), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that comprise the amino acid sequences of GFSLSSHD (SEQ ID NO: 78), IISSGNT (SEQ ID NO: 97), and ARDVYSGASP (SEQ ID NO: 116), respectively, or a variant thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0107] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 comprising the amino acid sequences of QSISNH (SEQ ID NO: 41), RAS, and QSYYIINRSNYANS (SEQ ID NO: 60), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 comprising the amino acid sequences of TFSFNSRYW (SEQ ID NO: 79), INNGDIT (SEQ ID NO: 98), and AKGGNLAGDCYGL (SEQ ID NO: 117), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0108] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 comprising the amino acid sequences of ESINSW (SEQ ID NO: 42), DAS, and QSYYIINRSNYGNS (SEQ ID NO: 61), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 comprising the amino acid sequences of GFSLSSYY (SEQ ID NO: 80), ITTAGPL (SEQ ID NO: 99), and ARGHAGSIYYSYFDL (SEQ ID NO: 118), respectively, or variants thereof wherein one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0109] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having CDRL1, CDRL2, and CDRL3 that include the amino acid sequences of ENLYKDNY (SEQ ID NO: 43), GAS, and AGGYDSVVD (SEQ ID NO: 62), respectively; and a heavy chain variable region having CDRH1, CDRH2, and CDRH3 that include the amino acid sequences of GFDLSSYYY (SEQ ID NO: 81), IYTSSGAT (SEQ ID NO: 100), and RGGWCDFNL (SEQ ID NO: 119), respectively, or variants thereof in which one or more CDRLs and / or CDRHs have one, two, or three amino acid substitutions, additions, deletions, or combinations thereof.

[0110] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region having a light chain variable region amino acid sequence selected from the sequences presented in Table 7 below (e.g., SEQ ID NOs: 120-139). In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a heavy chain variable region having a heavy chain variable region amino acid sequence selected from the sequences presented in Table 8 below (e.g., SEQ ID NOs: 140-159).

Table 7-1

Table 7-2

Table 8-1

Table 8-2

Table 8-3

[0111] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region having a light chain variable region amino acid sequence selected from SEQ ID NOs: 120-139, and a heavy chain variable region amino acid sequence selected from SEQ ID NOs: 140-159. In various embodiments, any one of the variable light chain amino acid sequences corresponding to SEQ ID NOs: 120-139 can be used in combination with any one of the variable heavy chain amino acid sequences corresponding to SEQ ID NOs: 140-159.

[0112] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-1K) having the amino acid sequence of SEQ ID NO: 120 and a heavy chain variable region (DDR1-1H) having the amino acid sequence of SEQ ID NO: 140.

[0113] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-3K) having the amino acid sequence of SEQ ID NO: 121 and a heavy chain variable region (DDR1-3H) having the amino acid sequence of SEQ ID NO: 141.

[0114] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-5K) having the amino acid sequence of SEQ ID NO: 122 and a heavy chain variable region (DDR1-5H) having the amino acid sequence of SEQ ID NO: 142.

[0115] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-6K) having the amino acid sequence of SEQ ID NO: 123 and a heavy chain variable region (DDR1-6H) having the amino acid sequence of SEQ ID NO: 143.

[0116] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-9K) having the amino acid sequence of SEQ ID NO: 124 and a heavy chain variable region (DDR1-9H) having the amino acid sequence of SEQ ID NO: 144.

[0117] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-11K) having the amino acid sequence of SEQ ID NO: 125 and a heavy chain variable region (DDR1-11H) having the amino acid sequence of SEQ ID NO: 145.

[0118] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-12K) having the amino acid sequence of SEQ ID NO: 126 and a heavy chain variable region (DDR1-12H) having the amino acid sequence of SEQ ID NO: 146.

[0119] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-13K) having the amino acid sequence of SEQ ID NO: 127 and a heavy chain variable region (DDR1-13H) having the amino acid sequence of SEQ ID NO: 147.

[0120] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-14K) having the amino acid sequence of SEQ ID NO: 128 and a heavy chain variable region (DDR1-14H) having the amino acid sequence of SEQ ID NO: 148.

[0121] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-15K) having the amino acid sequence of SEQ ID NO: 129 and a heavy chain variable region (DDR1-15H) having the amino acid sequence of SEQ ID NO: 149.

[0122] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-17K) having the amino acid sequence of SEQ ID NO: 130 and a heavy chain variable region (DDR1-17H) having the amino acid sequence of SEQ ID NO: 150.

[0123] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-20K) having the amino acid sequence of SEQ ID NO: 131 and a heavy chain variable region (DDR1-20H) having the amino acid sequence of SEQ ID NO: 151.

[0124] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-21K) having the amino acid sequence of SEQ ID NO: 132 and a heavy chain variable region (DDR1-21H) having the amino acid sequence of SEQ ID NO: 152.

[0125] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-22K) having the amino acid sequence of SEQ ID NO: 133 and a heavy chain variable region (DDR1-22H) having the amino acid sequence of SEQ ID NO: 153.

[0126] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-23K) having the amino acid sequence of SEQ ID NO: 134 and a heavy chain variable region (DDR1-23H) having the amino acid sequence of SEQ ID NO: 154.

[0127] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-26K) having the amino acid sequence of SEQ ID NO: 135 and a heavy chain variable region (DDR1-26H) having the amino acid sequence of SEQ ID NO: 155.

[0128] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-28K) having the amino acid sequence of SEQ ID NO: 136 and a heavy chain variable region (DDR1-28H) having the amino acid sequence of SEQ ID NO: 156.

[0129] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-29K) having the amino acid sequence of SEQ ID NO: 137 and a heavy chain variable region (DDR1-29H) having the amino acid sequence of SEQ ID NO: 157.

[0130] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a light chain variable region (DDR1-32K) having the amino acid sequence of SEQ ID NO: 138 and a heavy chain variable region (DDR1-32H) having the amino acid sequence of SEQ ID NO: 158.

[0131] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a light chain variable region (DDR1-34K) having the amino acid sequence of SEQ ID NO: 139 and a heavy chain variable region (DDR1-34H) having the amino acid sequence of SEQ ID NO: 159.

[0132] The individual CDRs of the antibodies disclosed herein can be determined according to any CDR numbering scheme known in the art.

[0133] In some embodiments, one or more of the CDRs of the antibodies disclosed herein can be determined according to the Kabat et al., J. Biol. Chem. 252, 6609-6616 (1977) and Kabat et al., Sequences of protein of immunological interest (1991), each of which is incorporated herein by reference in its entirety.

[0134] In some embodiments, one or more of the CDRs of the antibodies disclosed herein can be determined according to the Chothia numbering scheme that refers to the location of immunoglobulin structural loops (see, for example, Chothia C & Lesk AM, (1987), J Mol Biol 196: 901-917; Al-Lazikani B et al., (1997) J Mol Biol 273: 927-948; Chothia C et al., (1992) J Mol Biol 227: 799-817; Tramontano A et al., (1990) J Mol Biol 215(1): 175-82; and U.S. Patent No. 7,709,226, all of which are incorporated herein by reference in their entirety).

[0135] In some embodiments, one or more of the CDRs of the antibodies disclosed herein can be determined according to MacCallum RM et al., (1996) J Mol Biol 262: 732-745, which is hereby incorporated by reference in its entirety. Also, for example, see Martin A. "Protein Sequence and Structure Analysis of Antibody Variable Domains," in Antibody Engineering, Kontermann and Duebel, eds., Chapter 31, pp. 422-439, Springer-Verlag, Berlin (2001), which is hereby incorporated by reference in its entirety.

[0136] In some embodiments, the CDRs of the antibodies disclosed herein can each be determined according to the IMGT numbering system described in Lefranc M-P, (1999) The Immunologist 7: 132-136; Lefranc M-P et al., (1999) Nucleic Acids Res 27: 209-212; and Lefranc M-P et al., (2009) Nucleic Acids Res 37: D1006-D1012, which are hereby incorporated by reference in their entirety.

[0137] In some embodiments, the CDRs of the antibodies disclosed herein can be determined according to the AbM numbering scheme, which refers to the AbM hypervariable regions and represents a compromise between Kabat CDRs and Chothia structural loops and is used by Oxford Molecular’s AbM antibody modeling software (Oxford Molecular Group, Inc.), which is hereby incorporated by reference in its entirety.

[0138] In some embodiments, the CDRs of the antibodies disclosed herein can be determined according to the AHo numbering system described in Honegger and Plueckthun A. J. Mol. Biol. 309:657-670 (2001), which is hereby incorporated by reference in its entirety.

[0139] In some embodiments, the individual CDRs of the antibodies disclosed herein are each independently determined according to one of the Kabat, Chothia, MacCallum, IMGT, AHo, or AbM numbering schemes, or by structural analysis of the multispecific molecule, where the structural analysis identifies residues in the variable region predicted to contact the epitope region of DDR1.

[0140] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof is a variant, wherein the light chain variable region sequence and / or heavy chain variable region sequence of the variant has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid substitutions, additions, deletions, or combinations thereof as compared to the parental light chain variable region sequence or heavy chain variable region sequence, and the variant retains binding specificity and / or other functional properties for the DDR1 protein. In some embodiments, the light chain variable region sequence and / or heavy chain variable region sequence of the variant has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more conservative or non-conservative amino acid substitutions. In some embodiments, the variant has 1, 2 or 3 amino acid substitutions, additions, deletions, or combinations thereof in one or more of the CDRLs and / or CDRHs of the variant light chain variable region or variant heavy chain variable region as compared to the parental CDRL or CDRH. In some embodiments, the variant antibody or antigen-binding fragment thereof has 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions, additions, deletions, or combinations thereof in the framework region sequence of the light chain variable region and / or heavy chain variable region as compared to the parental light chain variable region sequence or heavy chain variable region sequence. In some embodiments, the antibody or antigen-binding fragment thereof has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more conservative or non-conservative amino acid substitutions in the framework region sequence of the light chain variable region and / or heavy chain variable region. The foregoing variants apply to each of the light chain variable regions and heavy chain variable regions shown in Tables 3, 7, and 8.

[0141] In some embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 3, 11, or 12. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising the amino acid sequence set forth in SEQ ID NO: 3, 11, or 12. In certain embodiments, the amino acid sequence of the VL consists of the amino acid sequence set forth in SEQ ID NO: 3, 11, or 12.

[0142] In some embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 3. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising the amino acid sequence set forth in SEQ ID NO: 3. In certain embodiments, the amino acid sequence of the VL consists of the amino acid sequence set forth in SEQ ID NO: 3.

[0143] In some embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 11. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising the amino acid sequence set forth in SEQ ID NO: 11. In certain embodiments, the amino acid sequence of the VL consists of the amino acid sequence set forth in SEQ ID NO: 11.

[0144] In some embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 12. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VL comprising the amino acid sequence shown in SEQ ID NO: 12. In certain embodiments, the amino acid sequence of the VL consists of the amino acid sequence shown in SEQ ID NO: 12.

[0145] In some embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 4. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising the amino acid sequence shown in SEQ ID NO: 4. In certain embodiments, the amino acid sequence of the VH consists of the amino acid sequence shown in SEQ ID NO: 4.

[0146] In some embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 13. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising the amino acid sequence shown in SEQ ID NO: 13. In certain embodiments, the amino acid sequence of the VH consists of the amino acid sequence shown in SEQ ID NO: 13.

[0147] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 4 or 13, and a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 3, 11, or 12. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising the amino acid sequence of SEQ ID NO: 4 or 13, and a VL comprising the amino acid sequence of SEQ ID NO: 3, 11, or 12. In certain embodiments, the amino acid sequence of the VH consists of the amino acid sequence set forth in SEQ ID NO: 4 or 13; and the amino acid sequence of the VL consists of the amino acid sequence set forth in SEQ ID NO: 3, 11, or 12.

[0148] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 4, and a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence set forth in SEQ ID NO: 3. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising the amino acid sequence of SEQ ID NO: 4, and a VL comprising the amino acid sequence of SEQ ID NO: 3. In certain embodiments, the amino acid sequence of the VH consists of the amino acid sequence set forth in SEQ ID NO: 4; and the amino acid sequence of the VL consists of the amino acid sequence set forth in SEQ ID NO: 3.

[0149] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 13, and a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 11. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising the amino acid sequence of SEQ ID NO: 13 and a VL comprising the amino acid sequence of SEQ ID NO: 11. In certain embodiments, the amino acid sequence of the VH consists of the amino acid sequence shown in SEQ ID NO: 13; and the amino acid sequence of the VL consists of the amino acid sequence shown in SEQ ID NO: 11.

[0150] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 13, and a VL comprising an amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, or 100% (e.g., at least 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%) identical to the amino acid sequence shown in SEQ ID NO: 12. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises a VH comprising the amino acid sequence of SEQ ID NO: 13 and a VL comprising the amino acid sequence of SEQ ID NO: 12. In certain embodiments, the amino acid sequence of the VH consists of the amino acid sequence shown in SEQ ID NO: 13; and the amino acid sequence of the VL consists of the amino acid sequence shown in SEQ ID NO: 12.

[0151] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and comprises VH and VL amino acid sequences set forth in SEQ ID NOs: 3 and 4; 11 and 13; or 12 and 13, respectively. In certain embodiments, the amino acid sequences of VH and VL consist of the amino acid sequences set forth in SEQ ID NOs: 3 and 4; 11 and 13; or 12 and 13, respectively.

[0152] In certain embodiments, the present disclosure provides an isolated antibody that cross-competes for binding to DDR1 with an antibody comprising VH and VL amino acid sequences set forth in SEQ ID NOs: 3 and 4; 11 and 13; or 12 and 13, respectively.

[0153] In certain embodiments, the present disclosure provides an isolated antibody that binds to the same or overlapping epitopes of DDR1 as an antibody described herein, e.g., an antibody comprising VH and VL amino acid sequences set forth in SEQ ID NOs: 3 and 4; 11 and 13; or 12 and 13, respectively.

[0154] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 120. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 140. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 120, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 140.

[0155] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 121. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 141. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 121 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 141.

[0156] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 122. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 142. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 122 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 142.

[0157] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 123. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 143. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 123, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 143.

[0158] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 124. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 144. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 124, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 144.

[0159] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 125. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 145. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 125, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 145.

[0160] In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 126. In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 146. In some embodiments, the anti-DDR1 antibody or an antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 126, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 146.

[0161] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 127. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 147. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 127, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 147.

[0162] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 128. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 148. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 128, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 148.

[0163] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 129. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 149. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 129 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 149.

[0164] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 130. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 150. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 130, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 150.

[0165] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 131. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 151. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 131 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 151.

[0166] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 132. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 152. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 132 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 152.

[0167] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 133. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 153. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 133, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 153.

[0168] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 134. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 154. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 134, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 154.

[0169] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 135. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 155. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 135, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 155.

[0170] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 136. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 156. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 136 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 156.

[0171] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 137. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 157. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 137 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 157.

[0172] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 138. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 158. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 138, and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 158.

[0173] In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 139. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 159. In some embodiments, the anti-DDR1 antibody or antigen-binding fragment thereof comprises a VL amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VL amino acid sequence of SEQ ID NO: 139 and a VH amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the VH amino acid sequence of SEQ ID NO: 159.

[0174] In certain embodiments, the epitope of an antibody can be determined, for example, by NMR spectroscopy, surface plasmon resonance (BIAcore®), X-ray crystallographic studies, ELISA assays, hydrogen / deuterium exchange combined with mass spectrometry (e.g., liquid chromatography electrospray mass spectrometry), array-based oligopeptide scanning assays, and / or mutagenesis mapping (e.g., site-directed mutagenesis mapping). For X-ray crystallography, crystallization can be achieved using any of the methods known in the art (e.g., Giege R et al., (1994) Acta Crystallogr D Biol Crystallogr 50(Pt 4): 339-350; McPherson A (1990) Eur J Biochem 189: 1-23; Chayen NE (1997) Structure 5: 1269-1274; McPherson A (1976) J Biol Chem 251: 6300-6303, all of which are incorporated herein by reference in their entirety). Antibody:antigen crystals can be studied using well-known X-ray diffraction techniques and refined using computer software such as X-PLOR (Yale University, 1992, distributed by Molecular Simulations, Inc.; e.g., Meth Enzymol (1985) volumes 114 & 115, eds Wyckoff HW et al., U.S. Patent Application No. 2004 / 0014194), and BUSTER (Bricogne G (1993) Acta Crystallogr D Biol Crystallogr 49(Pt 1): 37-60; Bricogne G (1997) Meth Enzymol 276A: 361-423, ed. Carter CW; Roversi P et al., (2000) Acta Crystallogr D Biol Crystallogr 56(Pt 10): 1316-1323, all of which are incorporated herein by reference in their entirety). Mutagenesis mapping studies can be achieved using any method known to those of skill in the art.For a description of mutagenesis techniques, including alanine scanning mutagenesis techniques, see, for example, Champe M et al., (1995) supra and Cunningham BC & Wells JA (1989) supra. In certain embodiments, the epitope of an antibody is determined using alanine scanning mutagenesis studies. Additionally, or alternatively, an antibody that recognizes and binds to the same or overlapping epitope of DDR1 (e.g., human DDR1 or mouse DDR1) can be identified by demonstrating the ability of one antibody to block the binding of another antibody to the target antigen, e.g., using routine techniques such as immunoassays, i.e., by competitive binding assays. Competitive binding assays can also be used to determine whether two antibodies have similar binding specificities for an epitope. Competitive binding can be determined in an assay where the immunoglobulin under test inhibits the specific binding of a reference antibody to a common antigen such as DDR1 (e.g., human DDR1 or mouse DDR1). Many types of competitive binding assays are known.For example, solid-phase direct or indirect radioimmunoassay (RIA), solid-phase direct or indirect enzyme immunoassay (EIA), sandwich competitive assay (see Stahli C et al., (1983) Methods Enzymol 9: 242-253); solid-phase direct biotin-avidin EIA (see Kirkland TN et al., (1986) J Immunol 137: 3614-9); solid-phase direct labeled assay, solid-phase direct labeled sandwich assay (see Harlow E & Lane D, (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Press); solid-phase direct labeled RIA using I-125 label (see Morel GA et al., (1988) Mol Immunol 25(1): 7-15); solid-phase direct biotin-avidin EIA (see Cheung RC et al., (1990) Virology 176: 546-52); and direct labeled RIA (see Moldenhauer G et al., (1990) Scand J Immunol 32: 77-82), all of which are hereby incorporated by reference in their entirety. Typically, such assays involve the use of a purified antigen (such as DDR1, e.g., human DDR1 or mouse DDR1) bound to a solid surface or cells that hold any of these, an unlabeled test immunoglobulin, and a labeled reference immunoglobulin. Competitive inhibition can be measured by determining the amount of label bound to the solid surface or cells in the presence of the test immunoglobulin. Usually, the test immunoglobulin is present in excess. Usually, when competing antibodies are present in excess, this inhibits the reference or specific binding of the antibody to the common antigen by at least 50-55%, 55-60%, 60-65%, 65-70%, 70-75% or higher. Competitive binding assays can be configured in a number of different formats using either a labeled antigen or a labeled antibody. In a common version of this assay, the antigen is immobilized on a 96-well plate.Next, the ability of the unlabeled antibody to block the binding of the labeled antibody to the antigen is measured using a radioactive label or an enzyme label. For further details, see, for example, Wagener C et al., (1983) J Immunol 130: 2308-2315; Wagener C et al., (1984) J Immunol Methods 68: 269-274; Kuroki M et al., (1990) Cancer Res 50: 4872-4879; Kuroki M et al., (1992) Immunol Invest 21: 523-538; Kuroki M et al., (1992) Hybridoma 11: 391-407 and Antibodies: A Laboratory Manual, ed. Harlow E & Lane D editors supra, pp. 386-389, all of which are hereby incorporated by reference in their entirety.

[0175] In certain embodiments, the antibody inhibits the binding of human DDR1 to human collagen. In certain embodiments, the binding of human DDR1 to human collagen is reduced by 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% in the presence of the antibody compared to the binding of human DDR1 to human collagen in the absence of the antibody.

[0176] In certain embodiments, the antibodies disclosed herein are conjugated to a cytotoxic agent, a cell division inhibitor, a toxin, a radionuclide, or a detectable label. In certain embodiments, the cytotoxic agent can induce death or destruction of cells contacted therewith. In certain embodiments, the cell division inhibitor can prevent or substantially reduce the proliferation of cells contacted therewith and / or inhibit its activity or function. In certain embodiments, the cytotoxic agent or cell division inhibitor is a chemotherapeutic agent. In certain embodiments, the radionuclide is an isotope 3 H, 14 C, 32 P, 35 S,36 Cl, 51 Cr, 57 Co, 58 Co, 59 Fe, 67 Cu, 90 Y, 99 Tc, 111 In, 117 Lu, 121 I, 124 I, 125 I, 131 I, 198 Au, 211 At, 213 Bi, 225 Ac, and 186 is selected from the group consisting of Re. In certain embodiments, the detectable label comprises a fluorescent moiety or a click chemistry handle.

[0177] Any immunoglobulin (Ig) constant region can be used in the antibodies disclosed herein. In certain embodiments, the Ig region is a human IgG, IgE, IgM, IgD, IgA, or IgY immunoglobulin molecule, any class of immunoglobulin molecule (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2) or any subclass (e.g., IgG2a and IgG2b).

[0178] In certain embodiments, one, two or more mutations (e.g., amino acid substitutions) are introduced into the Fc region (e.g., CH2 domain (residues 231 - 340 of human IgG1)) and / or CH3 domain (residues 341 - 447 of human IgG1 numbered according to the EU numbering system) and / or hinge region (residues 216 - 230 numbered according to the EU numbering system) of the antibodies described herein, such that one or more functional properties of the antibody, such as serum half-life, complement fixation, Fc receptor binding, and / or antibody-dependent cell cytotoxicity, are altered.

[0179] In one embodiment, one, two, or more mutations (e.g., amino acid substitutions) are introduced into the hinge region of the antibodies described herein, resulting in, for example, a change (e.g., an increase or decrease) in the number of cysteine residues in the hinge region as described in U.S. Patent No. 5,677,425, which is hereby incorporated by reference in its entirety. Changing the number of cysteine residues in the hinge region can, for example, facilitate the assembly of the light and heavy chains or alter (e.g., increase or decrease) the stability of the antibody.

[0180] In certain embodiments, one, two, or more amino acid mutations (e.g., substitutions, insertions, or deletions) are introduced into the IgG constant region, or an FcRn-binding fragment thereof (preferably, the Fc or hinge-Fc fragment), to alter (e.g., decrease or increase) the in vivo half-life of the antibody. Examples of mutations that alter (e.g., decrease or increase) the in vivo half-life of an antibody can be found, for example, in International Publication Nos. WO02 / 060919; WO98 / 23289; and WO97 / 34631; as well as U.S. Patent Nos. 5,869,046; 6,121,022; 6,277,375; and 6,165,745, all of which are incorporated herein by reference in their entirety. In certain embodiments, one, two, or more amino acid mutations (e.g., substitutions, insertions, or deletions) are introduced into the IgG constant region, or an FcRn-binding fragment thereof (preferably, the Fc or hinge-Fc fragment), to decrease the in vivo half-life of the antibody. In other embodiments, one, two, or more amino acid mutations (e.g., substitutions, insertions, or deletions) are introduced into the IgG constant region, or an FcRn-binding fragment thereof (preferably, the Fc or hinge-Fc fragment), to increase the in vivo half-life of the antibody. In certain embodiments, the antibody can have one or more amino acid mutations (e.g., substitutions) in the second constant (CH2) domain (residues 231-340 of human IgG1) and / or the third constant (CH3) domain (residues 341-447 of human IgG1) numbered according to the EU numbering system. In certain embodiments, the constant region of IgG1 of the antibodies described herein contains a substitution of methionine (M) to tyrosine (Y) at position 252, a substitution of serine (S) to threonine (T) at position 254, and a substitution of threonine (T) to glutamic acid (E) at position 256, numbered according to the EU numbering system. See U.S. Patent No. 7,658,921, which is incorporated herein by reference in its entirety.This type of mutant IgG, termed a "YTE mutant", has been shown to exhibit a four-fold increased half-life compared to the wild-type version of the same antibody (see Dall'Acqua WF et al., (2006) J Biol Chem 281: 23514-24, which is hereby incorporated by reference in its entirety). In certain embodiments, the antibody comprises an IgG constant region having one, two, three or more amino acid substitutions at amino acid residues 251-257, 285-290, 308-314, 385-389, and 428-436 numbered according to the EU numbering system.

[0181] In certain embodiments, one, two or more mutations (e.g., amino acid substitutions) are introduced into the Fc region of the antibodies described herein (e.g., the CH2 domain (residues 231-340 of human IgG1) and / or the CH3 domain (residues 341-447 of human IgG1 numbered according to the EU numbering system) and / or the hinge region (residues 216-230 numbered according to the EU numbering system)) such that the affinity of the antibody for Fc receptors (e.g., activating Fc receptors) on the surface of effector cells is increased or decreased. Mutations in the Fc region of antibodies that decrease or increase the affinity of the antibody for Fc receptors and techniques for introducing such mutations into Fc receptors or fragments thereof are known to those of skill in the art. Examples of mutations in the Fc region of antibodies that can alter the affinity of the antibody for Fc receptors are described, for example, in Smith P et al., (2012) PNAS 109: 6181-6186, U.S. Patent No. 6,737,056, and International Publications WO02 / 060919; WO98 / 23289; and WO97 / 34631, all of which are hereby incorporated by reference in their entirety.

[0182] In certain embodiments, the antibody comprises a heavy chain constant region that is a variant of a wild-type heavy chain constant region, wherein the variant heavy chain constant region binds to FcγRIIB with a higher affinity than the wild-type heavy chain constant region binds to FcγRIIB. In certain embodiments, the variant heavy chain constant region is a variant human heavy chain constant region, such as a variant human IgG1, variant human IgG2, or variant human IgG4 heavy chain constant region. In certain embodiments, the variant human IgG heavy chain constant region comprises one or more of the following amino acid mutations according to the EU numbering system: G236D, P238D, S239D, S267E, L328F, and L328E. In certain embodiments, the variant human IgG heavy chain constant region comprises one or more substitutions selected from the group consisting of: S267E and L328F; P238D and L328E; P238D, and E233D, G237D, H268D, P271G, and A330R according to the EU numbering system; P238D, E233D, G237D, H268D, P271G, and A330R; G236D and S267E; S239D and S267E; V262E, S267E and L328F; and V264E, S267E and L328F; or a set of amino acid mutations. In certain embodiments, FcγRIIB is expressed on a cell selected from the group consisting of macrophages, monocytes, B cells, dendritic cells, endothelial cells, and activated T cells.

[0183] In certain embodiments, one, two, or more amino acid substitutions are introduced into the Fc region of the IgG constant region, altering the effector function of the antibody. For example, one or more amino acids selected from amino acid residues 234, 235, 236, 237, 239, 243, 267, 292, 297, 300, 318, 320, 322, 328, 330, 332, and 396, numbered according to the EU numbering system, can be replaced with different amino acid residues, such that the antibody has an altered affinity for effector ligands but maintains the antigen-binding ability of the parental antibody. Effector ligands with altered affinity can be, for example, Fc receptors or the C1 component of complement. This approach is described in more detail in U.S. Pat. Nos. 5,624,821 and 5,648,260, each of which is incorporated herein by reference in its entirety. In certain embodiments, deletion or inactivation (by point mutation or other means) of the constant region domain can reduce Fc receptor binding of the circulating antibody, thereby increasing tumor localization. For a description of mutations that delete or inactivate the constant region and thereby increase tumor localization, see, for example, U.S. Pat. Nos. 5,585,097 and 8,591,886, each of which is incorporated herein by reference in its entirety. In certain embodiments, one or more amino acid substitutions can be introduced into the Fc region of the antibodies described herein to remove potential glycosylation sites on the Fc region, which can reduce Fc receptor binding (see, for example, Shields RL et al., (2001) J Biol Chem 276: 6591-604, which is incorporated herein by reference in its entirety).In various embodiments, one or more of the following mutations in the constant region of the antibodies described herein may be made: N297A substitution numbered according to the EU numbering system; N297Q substitution; L234A substitution; L234F substitution; L235A substitution; L235F substitution; L235V substitution; L237A substitution; S239D substitution; E233P substitution; L234V substitution; L235A substitution; C236 deletion; P238A substitution; S239D substitution; F243L substitution; D265A substitution; S267E substitution; L328F substitution; R292P substitution; Y300L substitution; A327Q substitution; P329A substitution; A330L substitution; I332E substitution; or P396L substitution. In some embodiments, the following mutations are made in the constant region of the antibody: L234A, L235E, G237A, A330S, and P331S. In some embodiments, the following mutations are made in the constant region of the antibody: P329G, L234A and L235A.

[0184] In certain embodiments, mutations selected from the group consisting of D265A, P329A, and combinations thereof, numbered according to the EU numbering system, can be made in the constant region of the antibodies described herein. In certain embodiments, mutations selected from the group consisting of L235A, L237A, and combinations thereof, numbered according to the EU numbering system, can be made in the constant region of the antibodies described herein. In certain embodiments, mutations selected from the group consisting of S267E, L328F, and combinations thereof, numbered according to the EU numbering system, can be made in the constant region of the antibodies described herein. In certain embodiments, mutations selected from the group consisting of S239D, I332E, optionally A330L, and combinations thereof, numbered according to the EU numbering system, can be made in the constant region of the antibodies described herein. In certain embodiments, mutations selected from the group consisting of L235V, F243L, R292P, Y300L, P396L, and combinations thereof, numbered according to the EU numbering system, can be made in the constant region of the antibodies described herein. In certain embodiments, mutations selected from the group consisting of S267E, L328F, and combinations thereof, numbered according to the EU numbering system, can be made in the constant region of the antibodies described herein.

[0185] In certain embodiments, the antibodies described herein include a constant region of IgG1 having an N297Q or N297A amino acid substitution numbered according to the EU numbering system. In certain specific embodiments, the antibodies described herein include a constant region of IgG1 having a mutation selected from the group consisting of D265A, P329A, and combinations thereof numbered according to the EU numbering system. In another embodiment, the antibodies described herein include a constant region of IgG1 having a mutation selected from the group consisting of L234A, L235A, and combinations thereof numbered according to the EU numbering system. In another embodiment, the antibodies described herein include a constant region of IgG1 having a mutation selected from the group consisting of L234F, L235F, N297A, and combinations thereof numbered according to the EU numbering system. In certain specific embodiments, the amino acid residues in the constant region of the antibodies described herein at positions corresponding to positions L234, L235 and D265 in the human IgG1 heavy chain numbered according to the EU numbering system are not L, L and D, respectively. This approach is described in detail in International Publication No. WO14 / 108483, which is hereby incorporated by reference in its entirety. In certain embodiments, the amino acids at positions corresponding to positions L234, L235 and D265 in the human IgG1 heavy chain numbered according to the EU numbering system are F, E and A; or A, A and A, respectively.

[0186] In certain embodiments, the amino acids at positions 433, 434 and 436 of the heavy chain constant region according to the EU numbering system are K, F and Y, respectively. In certain embodiments, the amino acids at positions 252, 254 and 256 of the heavy chain constant region according to the EU numbering system are Y, T and E, respectively. In certain embodiments, the amino acids at positions 428 and 434 of the heavy chain constant region according to the EU numbering system are L and S, respectively. In certain embodiments, the amino acids at positions 309, 311 and 434 of the heavy chain constant region according to the EU numbering system are D, H and S, respectively.

[0187] In certain embodiments, one or more amino acids selected from amino acid residues 329, 331, and 322 in the constant region of the antibodies described herein that are numbered according to the EU numbering system can be replaced with different amino acid residues, such that the antibody modifies C1q binding and / or reduces or abrogates complement-dependent cytotoxicity (CDC). This approach is described in further detail in U.S. Patent No. 6,194,551 (Idusogie et al.), which is hereby incorporated by reference in its entirety. In certain embodiments, one or more amino acid residues within positions 231 to 238 in the N-terminal region of the CH2 domain of the antibodies described herein that are numbered according to the EU numbering system are altered, whereby the ability of the antibody to fix complement is modified. This approach is further described in International Publication No. WO94 / 29351, which is hereby incorporated by reference in its entirety. In certain embodiments, the Fc region of the antibodies described herein is mutated (e.g., by introducing amino acid substitutions) at one or more of the following positions that are numbered according to the EU numbering system: 238, 239, 248, 249, 252, 254, 255, 256, 258, 265, 267, 268, 269, 270, 272, 276, 278, 280, 283, 285, 286, 289, 290, 292, 293, 294, 295, 296, 298, 301, 303, 305, 307, 309, 312, 315, 320, 322, 324, 326, 327, 328, 329, 330, 331, 333, 334, 335, 337, 338, 340, 360, 373, 376, 378, 382, 388, 389, 398, 414, 416, 419, 430, 434, 435, 437, 438, or 439 so as to increase the ability of the antibody to mediate antibody-dependent cell cytotoxicity (ADCC) and / or increase the affinity of the antibody for Fcγ receptors. This approach is further described in International Publication No. WO00 / 42072, which is hereby incorporated by reference in its entirety.

[0188] In certain embodiments, any of the mutations or modifications of the constant regions described herein can be introduced into one or both of the heavy chain constant regions of an antibody described herein that has two heavy chain constant regions.

[0189] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and functions as an antagonist (e.g., reduces or inhibits DDR1 activity).

[0190] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and, as compared to DDR1 activity in the absence of any antibody or in the presence of an irrelevant antibody (e.g., an antibody that does not specifically bind to DDR1), reduces or inhibits DDR1 activity by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%, as evaluated by methods described herein and / or known to those of skill in the art. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and, as compared to DDR1 activity in the absence of any antibody or in the presence of an irrelevant antibody (e.g., an antibody that does not specifically bind to DDR1), reduces or inhibits DDR1 activity to at most about 1 / 1.2, 1 / 1.3, 1 / 1.4, 1 / 1.5, 1 / 2, 1 / 2.5, 1 / 3, 1 / 3.5, 1 / 4, 1 / 4.5, 1 / 5, 1 / 6, 1 / 7, 1 / 8, 1 / 9, 1 / 10, 1 / 15, 1 / 20, 1 / 30, 1 / 40, 1 / 50, 1 / 60, 1 / 70, 1 / 80, 1 / 90, 1 / 100, or less, as evaluated by methods described herein and / or known to those of skill in the art. Non-limiting examples of DDR1 activity can include DDR1 signaling; binding of DDR1 to collagen (e.g., collagen I, II, III, IV, or V); or DDR1 phosphorylation. In certain embodiments, the reduction of DDR1 activity is evaluated as described in the Examples.

[0191] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and reduces or inhibits DDR1 phosphorylation by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as evaluated by methods described herein and / or known to those of skill in the art, compared to DDR1 phosphorylation in the absence of any antibody or in the presence of an irrelevant antibody (e.g., an antibody that does not specifically bind to DDR1). In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and reduces or inhibits DDR1 phosphorylation to at most about one-half, one-third, one-fourth, one-fifth, one-sixth, one-seventh, one-eighth, one-ninth, one-tenth, one-fifteenth, one-twentieth, one-thirtieth, one-fortieth, one-fiftieth, one-sixtieth, one-seventieth, one-eightieth, one-ninetieth, one-hundredth, or less thereof, as evaluated by methods described herein and / or known to those of skill in the art, compared to DDR1 phosphorylation in the absence of any antibody or in the presence of an irrelevant antibody (e.g., an antibody that does not specifically bind to DDR1).

[0192] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and reduces or inhibits DDR1 binding to collagen by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as compared to DDR1 binding to collagen without any antibody or with an irrelevant antibody (e.g., an antibody that does not specifically bind to DDR1), as evaluated by methods described herein and / or known to those of skill in the art. In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 and reduces or inhibits DDR1 binding to collagen to at most about one-half, one-third, one-fourth, one-fifth, one-sixth, one-seventh, one-eighth, one-ninth, one-tenth, one-fifteenth, one-twentieth, one-thirtieth, one-fortieth, one-fiftieth, one-sixtieth, one-seventieth, one-eightieth, one-ninetieth, one-hundredth, or less thereof as compared to DDR1 binding to collagen without any antibody or with an irrelevant antibody (e.g., an antibody that does not specifically bind to DDR1), as evaluated by methods described herein and / or known to those of skill in the art.

[0193] In certain embodiments, the present disclosure provides an isolated antibody that specifically binds to DDR1 with a dissociation constant (K D ) value of less than 10 nM, less than 5 nM, less than 2 nM, less than 1 nM, less than 0.5 nM, or less than 0.1 nM. 7.3 Pharmaceutical Compositions

[0194] Compositions are provided herein that include an isolated anti-DDR1 antibody disclosed herein, having a physiologically acceptable carrier, excipient, or stabilizer of the desired purity (see, e.g., Remington's Pharmaceutical Sciences (1990) Mack Publishing Co., Easton, PA). Acceptable carriers, excipients, or stabilizers are non-toxic to the recipient at the dosages and concentrations employed, and include buffers, such as phosphates, citrates, and other organic acids; antioxidants, including ascorbic acid and methionine; preservatives (e.g., octadecyl dimethyl benzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens, such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers, such as polyvinylpyrrolidone; amino acids, such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates, including glucose, mannose, or dextrin; chelating agents, such as EDTA; sugars, such as sucrose, mannitol, trehalose, or sorbitol; salt-forming counterions, such as sodium; metal complexes (e.g., Zn-protein complexes); and / or nonionic surfactants, such as TWEEN®, PLURONICS® or polyethylene glycol (PEG).

[0195] In certain embodiments, the pharmaceutical composition comprises, in a pharmaceutically acceptable carrier, the isolated anti-DDR1 antibody disclosed herein, and optionally one or more additional prophylactic or therapeutic agents. In certain embodiments, the antibody is the sole active ingredient contained in the pharmaceutical composition. In certain embodiments, the present disclosure provides a pharmaceutical composition comprising the isolated anti-DDR1 antibody disclosed herein for use as a medicament. In another embodiment, the present disclosure provides a pharmaceutical composition for use in a method for the treatment of a DDR1-related disease. In some embodiments, the DDR1-related disease is cancer or a fibrotic condition.

[0196] Pharmaceutically acceptable carriers for parenteral preparations include aqueous media, non-aqueous media, antibacterial agents, isotonic agents, buffering agents, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents, and other pharmaceutically acceptable substances. Examples of aqueous media include sodium chloride injection, Ringer's injection, isotonic dextrose injection, sterile water injection, and dextrose and lactated Ringer's injection. Examples of non-aqueous parenteral media include fixed oils of vegetable origin, cottonseed oil, corn oil, sesame oil, and peanut oil. Antibacterial agents at bactericidal or fungicidal concentrations can be added to parenteral preparations packaged in multi-dose containers containing phenol or cresol, mercury, benzyl alcohol, chlorobutanol, methyl and propyl p-hydroxybenzoate esters, thimerosal, benzalkonium chloride, and benzethonium chloride. Isotonic agents include sodium chloride and dextrose. Buffering agents include phosphates and citrates. Antioxidants include sodium bisulfite. Local anesthetics include procaine hydrochloride. Suspending and dispersing agents include sodium carboxymethylcellulose, hydroxypropylmethylcellulose, and polyvinylpyrrolidone. Emulsifying agents include polysorbate 80 (TWEEN® 80). Sequestering or chelating agents for metal ions include EDTA. Pharmaceutical carriers also include ethyl alcohol, polyethylene glycol, and propylene glycol for water-miscible media, and sodium hydroxide, hydrochloric acid, citric acid, or lactic acid for pH adjustment.

[0197] The pharmaceutical composition can be formulated for any route of administration to a subject. Specific examples of routes of administration include intranasal, oral, pulmonary, transdermal, intradermal, and parenteral. Parenteral administration characterized by any of subcutaneous, intramuscular, or intravenous injection is also contemplated herein. Injectables can be prepared in any conventional form of a liquid solution or suspension, a solid form suitable for a liquid solution or suspension prior to injection, or an emulsion. Injectables, solutions, and emulsions also contain one or more excipients. Suitable excipients are, for example, water, saline, dextrose, glycerol, or ethanol. Additionally, optionally, the pharmaceutical composition to be administered can also contain small amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, stabilizers, solubilizing enhancers, and other such agents such as sodium acetate, sorbitan monolaurate, triethanolamine oleate, and cyclodextrin.

[0198] Preparations for parenteral administration of an antibody include sterile solutions ready for injection, sterile dry soluble products, such as prepared lyophilized powders that are combined with a solvent immediately prior to use, including subcutaneous tablets, sterile suspensions ready for injection, prepared sterile dry insoluble products that are combined with a vehicle immediately prior to use, and sterile emulsions. Solutions can be either aqueous or non-aqueous.

[0199] When administered intravenously, suitable carriers include physiological saline or phosphate-buffered saline (PBS), and solutions containing thickening and solubilizing agents such as dextrose, polyethylene glycol, and polypropylene glycol, and mixtures thereof.

[0200] The topical mixture containing the antibody is prepared as described for topical and systemic administration. The resulting mixture can be a solution, suspension, emulsion, etc., and can be formulated as a cream, gel, ointment, emulsion, solution, elixir, lotion, suspension, tincture, paste, foam, aerosol, irrigation, spray, suppository, bandage, skin patch, or any other formulation suitable for topical administration.

[0201] The isolated anti-DDR1 antibody disclosed herein can be formulated for topical or local application in the form of a gel, cream, and lotion, for topical application to the skin and mucous membranes in, for example, the eye, etc., and for application to the eye, or for intracapsular or intraspinal application. Topical administration is contemplated for transdermal delivery and for administration to the eye or mucous membranes, or for inhalation therapy. Nasal drops, either alone or in combination with other pharmaceutically acceptable excipients, can also be administered.

[0202] Transdermal patches containing iontophoresis and electrophoresis devices are well known to those skilled in the art and can be used to administer the antibody. For example, such patches are disclosed in U.S. Patent Nos. 6,267,983; 6,261,595; 6,256,533; 6,167,301; 6,024,975; 6,010715; 5,985,317; 5,983,134; 5,948,433; and 5,860,957, all of which are incorporated herein by reference in their entirety.

[0203] In certain embodiments, the pharmaceutical composition comprising the antibodies described herein is a lyophilized powder, which can be reconstituted as a solution, emulsion, and other mixtures for administration. It may also be reconstituted and formulated as a solid or a gel. The lyophilized powder is prepared by dissolving the antibodies described herein or pharmaceutically acceptable derivatives thereof in a suitable solvent. In certain embodiments, the lyophilized powder is sterile. The solvent may contain excipients that improve the stability of the powder, or the reconstituted solution prepared from the powder, or other pharmacological components. Excipients that may be used include, but are not limited to, dextrose, sorbitol, fructose, corn syrup, xylitol, glycerin, glucose, sucrose, or another suitable agent. The solvent may also contain a buffer, such as citrate, sodium or potassium phosphate, or other such buffers known to those of skill in the art, at a substantially neutral pH in certain specific embodiments. Subsequent sterile filtration of the solution and subsequent lyophilization under standard conditions known to those of skill in the art provide the desired formulation. In certain embodiments, the resulting solution is dispensed into vials for lyophilization. Each vial contains a single or multiple dosages of the compound. The lyophilized powder can be stored at room temperature under suitable conditions, such as about 4°C. Reconstitution of this lyophilized powder with water for injection provides a formulation for use in parenteral administration. For reconstitution, the lyophilized powder is added to sterile water or other suitable carriers. The exact amount depends on the compound selected. Such amounts can be determined empirically.

[0204] The isolated anti-DDR1 antibodies disclosed herein, and the other compositions provided herein, can also be formulated for targeting a specific tissue, receptor or other area of the body of a subject to be treated. Many such targeting methods are well known to those of skill in the art. All such targeting methods are contemplated herein for use with the compositions. For non-limiting examples of targeting methods, see, e.g., U.S. Patent Nos. 6,316,652; 6,274,552; 6,271,359; 6,253,872; 6,139,865; 6,131,570; 6,120,751; 6,071,495; 6,060,082; 6,048,736; 6,039,975; 6,004,534; 5,985,307; 5,972,366; 5,900,252; 5,840,674; 5,759,542; and 5,709,874, all of which are incorporated herein by reference in their entirety. In certain embodiments, the antibodies described herein are targeted to tumors.

[0205] Compositions used for in vivo administration can be sterile. This can be readily accomplished, for example, by filtration through sterile filtration membranes. 7.4 Methods of Producing Polynucleotides, Vectors and Antibodies

[0206] In certain aspects, provided herein are polynucleotides comprising nucleotide sequences encoding an antibody or a portion thereof, or a fragment thereof (e.g., VL and / or VH; and light and / or heavy chains) that specifically binds to a DDR1 antigen, and vectors, e.g., vectors comprising such polynucleotides for recombinant expression in host cells (e.g., E. coli and mammalian cells). Also provided herein are polynucleotides comprising nucleotide sequences encoding the heavy and / or light chains of the antibodies provided herein, and vectors, e.g., expression vectors for their efficient expression in host cells, e.g., mammalian cells, comprising such polynucleotide sequences.

[0207] As used herein, an "isolated" polynucleotide or nucleic acid molecule is one that is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid molecule (e.g., in a mouse or human). Also, an "isolated" nucleic acid molecule, e.g., a cDNA molecule, may be substantially free of other cellular material or culture medium if produced by recombinant techniques, or substantially free of chemical precursors or other chemicals if chemically synthesized. For example, the phrase "substantially free of" includes preparations of polynucleotides or nucleic acid molecules having less than about 15%, 10%, 5%, 2%, 1%, 0.5%, or 0.1% (in particular, less than about 10%) of other materials, such as cellular material, culture medium, other nucleic acid molecules, chemical precursors, and / or other chemicals. In certain embodiments, the nucleic acid molecules encoding the antibodies described herein are isolated or purified.

[0208] In one aspect, provided herein are polynucleotides comprising nucleotide sequences encoding antibodies that specifically bind to a DDR1 polypeptide, comprise the amino acid sequences described herein, and compete with such antibodies for binding to the DDR1 polypeptide (e.g., in a dose-dependent manner), or bind to the same epitope as such antibodies.

[0209] In one aspect, provided herein is a polynucleotide comprising a nucleotide sequence encoding a light or heavy chain of an antibody described herein. The polynucleotide can comprise a nucleotide sequence encoding a light chain comprising the VL FR and CDRs of an antibody described herein (see, e.g., Tables 2-8) or a nucleotide sequence encoding a heavy chain comprising the VH FR and CDRs of an antibody described herein (see, e.g., Tables 2-8). In certain embodiments, the polynucleotide encodes a VH, VL, heavy chain, and / or light chain of an antibody described herein. In certain embodiments, the polynucleotide encodes a first VH and a first VL of an antibody described herein. In certain embodiments, the polynucleotide encodes a second VH and a second VL of an antibody described herein. In certain embodiments, the polynucleotide encodes a first heavy chain and a first light chain of an antibody described herein. In certain embodiments, the polynucleotide encodes a second heavy chain and a second light chain of an antibody described herein. In certain embodiments, the polynucleotide encodes a VH and / or VL, or a heavy chain and / or light chain of an isolated antibody described herein.

[0210] In some embodiments, the polynucleotide encoding the heavy and / or light chain of the isolated antibody described herein further encodes one or more signal peptides. In some embodiments, the signal peptide includes a secretion signal peptide. In some embodiments, the secretion signal peptide includes an immunoglobulin secretion signal peptide. Exemplary signal peptides include, but are not limited to, heavy chain IgM, IgG, IgD, IgA, and IgE signal peptides, and light chain kappa and lambda signal peptides. In certain embodiments, the signal peptide is a mammalian signal peptide. In certain embodiments, the signal peptide is a human signal peptide. In certain embodiments, the signal peptide includes a rodent, e.g., mouse or rabbit, e.g., rabbit signal peptide. In some embodiments, the signal peptide is a primate (e.g., non-human primate) signal peptide.

[0211] Also provided herein are polynucleotides encoding isolated anti-DDR1 antibodies that are optimized, for example, by codon / RNA optimization, replacement with heterologous signal sequences, and elimination of mRNA destabilizing elements. Methods for generating optimized nucleic acids encoding an isolated anti-DDR1 antibody or fragment thereof (e.g., light chain, heavy chain, VH domain, or VL domain) isolated for recombinant expression by introducing codon changes and / or eliminating inhibitory regions in the mRNA can be performed, for example, by adapting the optimization methods described in U.S. Patent Nos. 5,965,726; 6,174,666; 6,291,664; 6,414,132; and 6,794,498, and accordingly, all of these are hereby incorporated by reference in their entirety. For example, potential splice sites and destabilizing elements (e.g., A / T or A / U rich elements) within the RNA can be mutated without changing the amino acids encoded by the nucleic acid sequence to increase the stability of the RNA for recombinant expression. The changes can utilize the degeneracy of the genetic code, for example, by using alternative codons for the same amino acid. In certain embodiments, it may be desirable to change one or more codons to encode conservative mutations, e.g., similar amino acids having a similar chemical structure and properties and / or function as the original amino acid. Such methods can increase the expression of the isolated anti-DDR1 antibody or fragment thereof by at least 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, or 100-fold, or more, compared to the expression of the isolated anti-DDR1 antibody encoded by an unoptimized polynucleotide.

[0212] In certain embodiments, the optimized polynucleotide sequences encoding the isolated anti-DDR1 antibodies or fragments thereof (e.g., VL domain and / or VH domain) described herein can hybridize to the antisense (e.g., complementary) polynucleotides of the non-optimized polynucleotide sequences encoding the isolated anti-DDR1 antibodies or fragments thereof (e.g., VL domain and / or VH domain) described herein. In certain embodiments, the optimized nucleotide sequences encoding the isolated anti-DDR1 antibodies or fragments thereof described herein hybridize to the antisense polynucleotides of the non-optimized polynucleotide sequences encoding the isolated anti-DDR1 antibodies or fragments thereof described herein under high stringency conditions. In certain embodiments, the optimized nucleotide sequences encoding the isolated anti-DDR1 antibodies or fragments thereof described herein hybridize to the antisense polynucleotides of the non-optimized nucleotide sequences encoding the isolated anti-DDR1 antibodies or fragments thereof described herein under high, medium or low stringency hybridization conditions. Information regarding hybridization conditions is described, for example, see U.S. Patent Application Publication No. US2005 / 0048549 (e.g., paragraphs 72-73), which is incorporated herein by reference in its entirety.

[0213] Polynucleotides can be obtained by any method known in the art, and the nucleotide sequences of the polynucleotides can be determined. The nucleotide sequences encoding the antibodies described herein, such as the antibodies described in Tables 2-8, and modified versions of these antibodies, can be determined using methods well known in the art, i.e., nucleotide codons known to encode specific amino acids are assembled in such a way to produce a nucleic acid encoding the antibody. Such polynucleotides encoding antibodies can be assembled from chemically synthesized oligonucleotides (e.g., as described in Kutmeier G et al., (1994), BioTechniques 17: 242-6, which is hereby incorporated by reference in its entirety), which briefly involves the synthesis of overlapping oligonucleotides containing portions of the sequence encoding the antibody, the annealing and ligation of these oligonucleotides, and then the amplification of the ligated oligonucleotides by PCR.

[0214] Alternatively, polynucleotides encoding the antigen-binding regions of the antibodies described herein can be prepared from nucleic acids from suitable sources (e.g., hybridomas) using methods well known in the art (e.g., PCR and other molecular cloning methods). For example, PCR amplification using synthetic primers that hybridize to the 3' and 5' ends of a known sequence can be performed using genomic DNA obtained from hybridoma cells that produce the antibody of interest. Using such PCR amplification methods, nucleic acids containing sequences encoding the light and / or heavy chains of the antibody can be obtained. Using such PCR amplification methods, nucleic acids containing sequences encoding the variable light chain region and / or variable heavy chain region of the antibody can be obtained. The amplified nucleic acids can be cloned into vectors for expression in host cells and for further cloning.

[0215] Clones containing nucleic acids encoding specific antigen-binding regions or antibodies may not be available, but if the sequences of the antigen-binding regions or antibody molecules are known, the nucleic acids encoding immunoglobulins can be chemically synthesized or by PCR amplification using synthetic primers capable of hybridizing to the 3' and 5' ends of the sequence, or from a cDNA library encoding an antibody, for example, a cDNA clone, by cloning using an oligonucleotide probe specific for a particular gene sequence for identification, from a suitable source (e.g., an antibody cDNA library, or any tissue or cell expressing the antibody, e.g., a cDNA library prepared from hybridoma cells selected to express the antibodies described herein, or nucleic acids isolated therefrom, preferably polyA+ RNA). The amplified nucleic acids produced by PCR can then be cloned into a replicable cloning vector using any method well known in the art.

[0216] The DNA encoding the isolated anti-DDR1 antibodies described herein can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes capable of specifically binding to the genes encoding the heavy and light chains of anti-DDR1). Hybridoma cells can serve as a source of such DNA. Once isolated, the DNA can be placed into an expression vector, which can then be transfected into a host cell, e.g., E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells (e.g., CHO cells from the CHO GS System™ (Lonza)), or otherwise myeloma cells that do not produce immunoglobulin proteins, to obtain the synthesis of anti-DDR1 antibodies in the recombinant host cell.

[0217] To generate a full antibody or antigen-binding region, the VH or VL sequences in an scFv clone can be amplified using PCR primers that contain the VH or VL nucleotide sequence, a restriction site, and flanking sequences to protect the restriction site. Using cloning techniques known to those of skill in the art, the PCR-amplified VH domain can be cloned into a vector that expresses a heavy chain constant region, such as a human gamma 1 or human gamma 4 constant region, and the PCR-amplified VL domain can be cloned into a vector that expresses a light chain constant region, such as a human kappa or lambda constant region. In certain embodiments, the vector for expressing the VH or VL domain contains an EF-1α promoter, a secretion signal, a cloning site for the variable region, a constant region, and a selectable marker such as neomycin. The VH and VL domains can also be cloned into one vector that expresses the required constant regions. The heavy chain conversion vector and the light chain conversion vector are then co-transfected into a cell line using techniques known to those of skill in the art to generate a stable or transient cell line that expresses a full-length antibody, such as IgG.

[0218] DNA can also be modified, for example, by substituting the coding sequences for human heavy and light chain constant regions for mouse sequences, or by covalently conjugating all or part of the coding sequence for a non-immunoglobulin polypeptide to an immunoglobulin coding sequence.

[0219] Also provided are polynucleotides that hybridize to the polynucleotides encoding the antibodies described herein under high stringency, medium or low stringency hybridization conditions. In certain embodiments, the polynucleotides described herein hybridize to the polynucleotides encoding the VH domain and / or VL domain provided herein under high stringency, medium or low stringency hybridization conditions.

[0220] Hybridization conditions are described in the art and are known to those of skill in the art. For example, hybridization under stringent conditions can include hybridization to filter-bound DNA in 6× sodium chloride / sodium citrate (SSC) at about 45° C. followed by one or more washes in 0.2× SSC / 0.1% SDS at about 50-65° C., and hybridization under highly stringent conditions can include hybridization to filter-bound nucleic acid in 6× SSC at about 45° C. followed by one or more washes in 0.1× SSC / 0.2% SDS at about 68° C. Hybridization under other stringent conditions is known to and described for those of skill in the art, see, for example, Ausubel FM et al., eds., (1989) Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc. and John Wiley & Sons, Inc,, New York at pages 6.3.1-6.3.6 and 2.10.3, which is hereby incorporated by reference in its entirety.

[0221] In certain embodiments, cells (e.g., host cells) that express (e.g., recombinantly) an antibody described herein that specifically binds to DDR1, as well as related polynucleotides and expression vectors are provided herein. Vectors (e.g., expression vectors) are provided herein that include a polynucleotide that includes a nucleotide sequence encoding an anti-DDR1 antibody or fragment thereof for recombinant expression in a host cell, preferably a mammalian cell (e.g., a CHO cell). Host cells that include such vectors for recombinantly expressing an anti-DDR1 antibody (e.g., a human or humanized antibody) described herein are also provided herein. In certain embodiments, methods are provided herein for producing an antibody described herein, the method including the step of expressing the antibody from a host cell.

[0222] The recombinant expression of an antibody described herein that specifically binds to DDR1 (e.g., a full-length antigen-binding region, or an antibody, or the heavy and / or light chains of an antibody as described herein) generally involves the construction of an expression vector containing a polynucleotide encoding the antibody. Once a polynucleotide encoding an antibody molecule, the heavy and / or light chains of an antibody, or a fragment thereof (e.g., the heavy and / or light chain variable regions) as described herein is obtained, the vector for the production of the antibody molecule can be produced by recombinant DNA techniques using techniques well known in the art. Thus, methods for preparing a protein by expressing a polynucleotide containing an antibody or antibody fragment (e.g., a light or heavy chain) encoding a nucleotide sequence are described herein. An expression vector containing an antibody or antibody fragment (e.g., a light or heavy chain) coding sequence and appropriate transcriptional and translational control signals can be constructed using methods well known to those skilled in the art. Such methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo gene recombination. Also provided are replicable vectors containing a nucleotide sequence encoding an antibody molecule, the heavy or light chain of an antibody, the heavy or light chain variable region of an antibody or a fragment thereof, or a heavy or light chain CDR as described herein operably linked to a promoter. Such vectors can include, for example, a nucleotide sequence encoding a constant region of an antibody molecule (see, e.g., International Publication Nos. WO86 / 05807 and WO89 / 01036; and U.S. Patent No. 5,122,464, which are incorporated herein by reference in their entirety), and the variable regions of the antibody can be cloned into such vectors for expression of the entire heavy chain, entire light chain, or both the entire heavy and light chains.

[0223] In certain embodiments, the vector comprises a polynucleotide encoding the VH, VL, heavy chain, and / or light chain of an antibody described herein. In another embodiment, the vector comprises a polynucleotide encoding the VH and VL of an antibody described herein. In another embodiment, the vector comprises a polynucleotide encoding the heavy and light chains of an antibody described herein.

[0224] Expression vectors can be introduced into cells (e.g., host cells) by conventional techniques, and the resulting cells can then be cultured by conventional techniques to produce an antibody or fragment thereof described herein. Accordingly, provided herein are host cells containing a polynucleotide encoding an antibody or fragment thereof described herein, or a heavy or light chain thereof, or a fragment thereof, or a single-chain antibody described herein, operably linked to a promoter for expression of such a sequence in a host cell.

[0225] In certain embodiments, the host cell comprises a polynucleotide encoding the VH and VL of an isolated antibody described herein. In another embodiment, the host cell comprises a vector comprising a polynucleotide encoding the VH and VL of an isolated antibody described herein. In another embodiment, the host cell comprises a first polynucleotide encoding the VH of an isolated antibody described herein and a second polynucleotide encoding the VL of an isolated antibody described herein. In another embodiment, the host cell comprises a first vector comprising a first polynucleotide encoding the VH of an isolated antibody described herein and a second vector comprising a second polynucleotide encoding the VL of an isolated antibody described herein.

[0226] In certain embodiments, the heavy chain / heavy chain variable region expressed by the first host cell associates with the light chain / light chain variable region of the second host cell to form the anti-DDR1 antibodies described herein. In certain embodiments, a population of host cells comprising such a first host cell and such a second host cell is provided herein.

[0227] In certain embodiments, a population of vectors is provided herein that includes a first vector comprising a polynucleotide encoding the light chain / light chain variable region of the anti-DDR1 antibodies described herein and a second vector comprising a polynucleotide encoding the heavy chain / heavy chain variable region of the anti-DDR1 antibodies described herein.

[0228] Using various host-expression vector systems, the antibody molecules described herein can be expressed (see, e.g., U.S. Patent No. 5,807,715, which is hereby incorporated by reference in its entirety). Such host-expression systems not only represent a medium in which the desired coding sequence can be produced and then purified, but also cells that can express the antibody molecules described herein in situ when transformed or transfected with an appropriate nucleotide coding sequence. These include, but are not limited to, microorganisms such as bacteria (e.g., E. coli and B. subtilis) transformed with an antibody coding sequence-containing, e.g., recombinant bacteriophage DNA, plasmid DNA, or cosmid DNA expression vector; yeast (e.g., Saccharomyces and Pichia) transformed with an antibody coding sequence-containing, e.g., recombinant yeast expression vector; insect cell systems infected with, e.g., a recombinant virus expression vector containing an antibody coding sequence (e.g., baculovirus); plant cell systems (e.g., green algae such as Chlamydomonas reinhardlii) infected with, e.g., a recombinant virus expression vector containing an antibody coding sequence (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV), or transformed with, e.g., a recombinant plasmid expression vector (e.g., Ti plasmid); or mammalian cell systems (e.g., COS (e.g., COS1 or COS), CHO, BHK, MDCK, HEK 293, NS0, PER.C6, VERO, CRL7O3O, HsS78Bst, HeLa, and NIH 3T3, HEK-293T, HepG2, SP210, R1.1, B-W, L-M, BSC1, BSC40, YB / 20, and BMT10 cells) carrying a recombinant expression construct containing a promoter derived from, e.g., the genome of a mammalian cell (e.g., the metallothionein promoter) or a promoter derived from a mammalian virus (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter).In certain embodiments, the cells for expressing the antibodies described herein are Chinese hamster ovary (CHO) cells, e.g., CHO cells from the CHO GS System™ (Lonza). In certain embodiments, the heavy and / or light chains of the antibodies produced by CHO cells may have N-terminal glutamine or glutamate residues replaced by pyroglutamic acid. In certain embodiments, the cells for expressing the antibodies described herein are human cells, e.g., a human cell line. In certain embodiments, the mammalian expression vector is pOptiVEC™ or pcDNA3.3. In certain embodiments, bacterial cells such as E. coli, or eukaryotic cells (e.g., mammalian cells), especially for the expression of full recombinant antibody molecules, are used for the expression of recombinant antibody molecules. For example, mammalian cells such as CHO cells, in combination with vectors such as the major intermediate early gene promoter element from human cytomegalovirus, are an effective expression system for antibodies (Foecking MK & Hofstetter H (1986) Gene 45: 101 -5; and Cockett MI et al., (1990) Biotechnology 8(7): 662-7, each of which is incorporated herein by reference in its entirety). In certain embodiments, the antibodies described herein are produced by CHO cells or NS0 cells. In certain embodiments, the expression of the nucleotide sequence encoding the antibodies described herein that specifically bind to DDR1 is regulated by a constitutive promoter, an inducible promoter or a tissue-specific promoter.

[0229] In a bacterial system, several expression vectors can be advantageously selected according to the intended use for the antibody molecules to be expressed. For example, when large amounts of such antibodies are to be produced for the preparation of a pharmaceutical composition of the antibody molecule, a vector targeting the expression of a high level of fusion protein product that can be easily purified may be desirable. Such vectors include, but are not limited to, E. coli expression vector pUR278 (Ruether U & Mueller-Hill B (1983) EMBO J 2: 1791-1794); pIN vector (Inouye S & Inouye M(1985)Nuc Acids Res 13: 3101-3109; Van Heeke G & Schuster SM(1989)J Biol Chem 24: 5503-5509), etc., all of which are incorporated herein by reference in their entirety. For example, the pGEX vector can also be used to express a foreign polypeptide as a fusion protein with glutathione S-transferase (GST). Generally, such fusion proteins are soluble and can be easily purified from lysed cells by adsorption and binding to matrix glutathione agarose beads followed by elution in the presence of free glutathione. The pGEX vector is designed to contain a thrombin or factor Xa protease cleavage site, so that the cloned target gene product can be released from the GST moiety.

[0230] In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) can be used, for example, as a vector to express a foreign gene. The virus grows in Spodoptera frugiperda cells. The coding sequences can be individually cloned into non-essential regions of the virus (e.g., the polyhedrin gene) and placed under the control of an AcNPV promoter (e.g., the polyhedrin promoter).

[0231] In mammalian host cells, several viral expression systems can be utilized. In the case where adenovirus is used as an expression vector, the coding sequence of interest can be ligated to an adenovirus transcription / translation control complex, such as a late promoter and a tripartite leader sequence. This chimeric gene can then be inserted into the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E1 or E3) results in a recombinant virus that is viable in the infected host and can express the molecule (see, for example, Logan J & Shenk T (1984) PNAS 81(12): 3655-9, which is incorporated herein by reference in its entirety). Specific initiation signals may also be required for efficient translation of the inserted coding sequence. These signals include the ATG initiation codon and adjacent sequences. Furthermore, the initiation codon must be in frame with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translation control signals and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of appropriate transcriptional enhancer elements, transcriptional terminators, etc. (see, for example, Bitter G et al., (1987) Methods Enzymol. 153: 516-544, which is incorporated herein by reference in its entirety).

[0232] In addition, host cell lines can be selected that modulate the expression of the inserted array or modify and process the gene product in a desired specific manner. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of the protein product can be important for the function of the protein. Different host cells have characteristic and specific mechanisms for post-translational processing as well as modification of proteins and gene products. An appropriate cell line or host system can be selected to ensure the correct modification and processing of the foreign protein being expressed. For this purpose, eukaryotic host cells having cellular machinery for proper processing of primary transcripts, glycosylation, and phosphorylation of gene products can be used. Such mammalian host cells include, but are not limited to, CHO, VERO, BHK, Hela, MDCK, HEK 293, NIH 3T3, W138, BT483, Hs578T, HTB2, BT2O, and T47D, NS0 (a mouse myeloma cell line that does not endogenously produce any immunoglobulin chains), CRL7O3O, COS (e.g., COS1 or COS), PER.C6, VERO, HEK-293T, HepG2, SP210, R1.1, B-W, L-M, BSC1, BSC40, YB / 20, BMT10, and HsS78Bst cells. In certain embodiments, the anti-DDR1 antibodies described herein are produced in mammalian cells, such as CHO cells.

[0233] In certain embodiments, the antibodies described herein have a reduced fucose content or no fucose content. Such antibodies can be produced using techniques known to those of skill in the art. For example, the antibodies can be expressed in cells that are deficient or lacking in the ability to fucosylate. In one example, a cell line having a knockout of both alleles of α1,6-fucosyltransferase can be used to produce antibodies having a reduced fucose content. The Potelligent® system (Lonza) is an example of such a system that can be used to produce antibodies having a reduced fucose content.

[0234] For the production of recombinant proteins with high yields over a long period, stable expression cells can be generated. For example, cell lines that stably express the anti-DDR1 antibodies described herein can be engineered. In certain embodiments, the cells provided herein stably express a light chain / light chain variable region and a heavy chain / heavy chain variable region that associate to form an antigen-binding region, or an antibody, as described herein.

[0235] In certain embodiments, instead of using an expression vector containing a viral origin of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoters, enhancers, sequences, transcription terminators, polyadenylation sites, etc.) and a selectable marker. After introduction of the foreign DNA / polynucleotide, the engineered cells can be grown in rich medium for 1-2 days and then switched to selective medium. The selectable marker in the recombinant plasmid confers resistance to the selection and allows the cells to stably integrate the plasmid into their chromosomes and form foci that can then be cloned and expanded into cell lines. This method can be advantageously used to engineer cell lines that express the anti-DDR1 or fragments thereof described herein. Such engineered cell lines can be particularly useful in screening and evaluating compositions that interact directly or indirectly with the antibody molecule.

[0236] Several selection systems can be used, including, but not limited to, the herpes simplex virus thymidine kinase in tk, hgprt or aprt cells (Wigler M et al., (1977) Cell 11(1): 223-32), hypoxanthine guanine phosphoribosyl transferase (Szybalska EH & Szybalski W (1962) PNAS 48(12): 2026-2034) and adenine phosphoribosyl transferase (Lowy I et al., (1980) Cell 22(3): 817-23) genes, all of which are hereby incorporated by reference in their entirety. Also, metabolic antagonist resistance can be used as the basis for selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler M et al., (1980) PNAS 77(6): 3567-70; O'Hare K et al., (1981) PNAS 78: 1527-31); gpt, which confers resistance to mycophenolic acid (Mulligan RC & Berg P (1981) PNAS 78(4): 2072-6); neo, which confers resistance to aminoglycoside G-418 (Wu GY & Wu CH (1991) Biotherapy 3: 87-95; Tolstoshev P (1993) Ann Rev Pharmacol Toxicol 32: 573-596; Mulligan RC (1993) Science 260: 926-932; and Morgan RA & Anderson WF (1993) Ann Rev Biochem 62: 191-217; Nabel GJ & Felgner PL (1993) Trends Biotechnol 11(5): 211-5); and hygro, which confers resistance to hygromycin (Santerre RF et al., (1984) Gene 30(1-3): 147-56), all of which are hereby incorporated by reference in their entirety.Methods generally known in the art of recombinant DNA technology can be routinely applied to select the desired recombinant clones, and such methods are described, for example, in Ausubel FM et al., (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY (1993); Kriegler M, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY (1990); and Chapters 12 and 13, Dracopoli NC et al., (eds.), Current Protocols in Human Genetics, John Wiley & Sons, NY (1994); Colbere-Garapin F et al., (1981) J Mol Biol 150: 1-14, all of which are hereby incorporated by reference in their entirety.

[0237] The expression level of the antibody molecule can be increased by vector amplification (for a review, see Bebbington CR & Hentschel CCG, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol. 3 (Academic Press, New York, 1987), which is hereby incorporated by reference in its entirety). When the marker in the vector system is amplifiable, an increase in the level of the inhibitor present in the culture of the host cell increases the number of copies of the marker gene. Since the amplified region associates with the gene of interest, protein production also increases (Crouse GF et al., (1983) Mol Cell Biol 3: 257-66, which is hereby incorporated by reference in its entirety).

[0238] A host cell can be co-transfected with two or more expression vectors described herein, a first vector encoding a heavy chain-derived polypeptide and a second vector encoding a light chain-derived polypeptide. The two vectors can contain the same selectable marker, which allows for equal expression of the heavy and light chain polypeptides. A host cell can be co-transfected with different amounts of two or more expression vectors. For example, a host cell can be transfected with any one of the following ratios of a first expression vector and a second expression vector: about 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:15, 1:20, 1:25, 1:30, 1:35, 1:40, 1:45, or 1:50.

[0239] Alternatively, a single vector that encodes both the heavy and light chain polypeptides and is capable of expressing them can be used. In such situations, the light chain must be placed upstream of the heavy chain in order to avoid free heavy chains of excessive toxicity (Proudfoot NJ (1986) Nature 322: 562-565; and Koehler G (1980) PNAS 77: 2197-2199, each of which is incorporated herein by reference in its entirety). The coding sequences for the heavy and light chains can include cDNA or genomic DNA. The expression vector can be monocistronic or polycistronic. A polycistronic nucleic acid construct can encode 2, 3, 4, 5, 6, 7, 8, 9, 10 or more genes / nucleotide sequences, or gene / nucleotide sequences in the range of 2-5, 5-10, or 10-20. For example, a dicistronic nucleic acid construct can include a promoter, a first gene (e.g., the heavy chain of an antibody described herein), and a second gene (e.g., the light chain of an antibody described herein) in the following order. In such an expression vector, transcription of both genes can be driven by the promoter, but translation of the mRNA from the first gene can be by cap-dependent scanning mechanism, and translation of the mRNA from the second gene can be by a cap-independent mechanism, e.g., by IRES.

[0240] Once the antibody molecules described herein are produced by recombinant expression, they can be purified by any method known in the art for the purification of immunoglobulin molecules, e.g., by chromatography (e.g., ion exchange, affinity, specifically affinity for a specific antigen after protein A, and sizing column chromatography), centrifugation, differences in solubility, or any other standard technique for protein purification. Furthermore, the antibodies described herein can be fused to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification.

[0241] In certain embodiments, the antibodies described herein are isolated or purified. In certain embodiments, an isolated antibody substantially lacks other antibodies having different antigen specificities from the isolated antibody. For example, in certain specific embodiments, preparations of the antibodies described herein substantially lack cellular material and / or chemical precursors. The phrase "substantially lacks cellular material" includes preparations of antibodies where the antibody is separated from the cellular components of the cells from which it is isolated or recombinantly produced. Thus, an antibody substantially lacking cellular material has less than about 30%, 20%, 10%, 5%, 2%, 1%, 0.5%, or 0.1% (by dry weight) of heterologous proteins (also referred to herein as "contaminating proteins") and / or variants of the antibody, e.g., antibodies having different post-translational modification forms of the antibody or other different versions of the antibody (e.g., antibody fragments). When the antibody is recombinantly produced, this generally also substantially lacks the culture medium, i.e., the culture medium is less than about 20%, 10%, 2%, 1%, 0.5%, or 0.1% of the volume of the protein preparation. When the antibody is produced by chemical synthesis, this generally also substantially lacks chemical precursors or other chemicals, i.e., it is separated from the chemical precursors or other chemicals involved in the synthesis of the protein. Thus, such preparations of the antibody have less than about 30%, 20%, 10%, or 5% (by dry weight) of chemical precursors or compounds other than the antibody of interest. In certain embodiments, the antibodies described herein are isolated or purified.

[0242] The anti-DDR1 antibody or fragment thereof can be produced by any method known in the art for the synthesis of proteins or antibodies, for example, by chemical synthesis or by recombinant expression techniques. The methods described herein use conventional techniques in molecular biology, microbiology, genetic analysis, recombinant DNA, organic chemistry, biochemistry, PCR, oligonucleotide synthesis and modification, nucleic acid hybridization, and related fields within the skill of the art, unless otherwise indicated. These techniques are described, for example, in the references cited herein and are fully explained in the literature.For example, reference is made to Maniatis T et al., (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; Sambrook J et al., (1989), Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press; Sambrook J et al., (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Ausubel FM et al., Current Protocols in Molecular Biology, John Wiley & Sons (1987 and annual revisions); Current Protocols in Immunology, John Wiley & Sons (1987 and annual revisions); Gait (ed.) (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press; Eckstein (ed.) (1991) Oligonucleotides and Analogues: A Practical Approach, IRL Press; Birren B et al., (eds.) (1999) Genome Analysis: A Laboratory Manual, Cold Spring Harbor Laboratory Press, all of which are hereby incorporated by reference in their entirety.

[0243] In certain embodiments, the antibodies described herein are prepared, expressed, produced, or isolated by any means including, for example, synthesis of DNA sequences, production by genetic engineering. In certain specific embodiments, such antibodies include sequences (e.g., DNA sequences or amino acid sequences) that do not naturally occur within the antibody germline repertoire of an animal or mammal (e.g., human) in vivo.

[0244] In one aspect, provided herein is a method of making an anti-DDR1 antibody, the method comprising culturing a cell or host cell described herein. In certain embodiments, the method is performed in vitro. In one aspect, provided herein is a method of making an anti-DDR1 antibody, the method comprising expressing (e.g., recombinantly expressing) an antibody using a cell or host cell described herein (e.g., a cell or host cell comprising a polynucleotide encoding an antibody described herein). In certain embodiments, the cell is an isolated cell. In certain embodiments, an exogenous polynucleotide has been introduced into the cell. In certain embodiments, the method further comprises purifying the antibody obtained from the cell or host cell.

[0245] In certain embodiments, an isolated antibody is produced by expressing in a cell, under suitable conditions in which the polynucleotide is expressed and the antibody is produced, a polynucleotide encoding the VH and VL of the antibody described herein. In another embodiment, an isolated antibody is produced by expressing in a cell, under suitable conditions in which the polynucleotide is expressed and the antibody is produced, a polynucleotide encoding the heavy and light chains of the antibody described herein. In certain embodiments, an isolated antibody is produced by expressing in a cell, under suitable conditions in which the polynucleotide is expressed and the antibody is produced, a first polynucleotide encoding the VH of the antibody described herein and a second polynucleotide encoding the VL of the antibody described herein. In certain embodiments, an isolated antibody is produced by expressing in a cell, under suitable conditions in which the polynucleotide is expressed and the antibody is produced, a first polynucleotide encoding the heavy chain of the antibody described herein and a second polynucleotide encoding the light chain of the antibody described herein.

[0246] Methods for producing polyclonal antibodies are known in the art (see, e.g., Chapter 11 in: Short Protocols in Molecular Biology, (2002) 5th Ed., Ausubel FM et al., eds., John Wiley and Sons, New York, which is hereby incorporated by reference in its entirety).

[0247] Monoclonal antibodies can be prepared using a variety of techniques known in the art, including the use of hybridoma, recombinant, and phage display technologies, or combinations thereof. For example, monoclonal antibodies can be produced using hybridoma techniques known in the art and those taught, for example, in Harlow E & Lane D, Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling GJ et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563 681 (Elsevier, N.Y., 1981), each of which is incorporated herein by reference in its entirety. The term "monoclonal antibody" as used herein is not limited to antibodies produced by hybridoma technology. For example, monoclonal antibodies can be produced recombinantly from host cells that ectopically express an antibody or fragment thereof described herein, such as the light chain and / or heavy chain of such an antibody.

[0248] In certain embodiments, a "monoclonal antibody" as used herein is an antibody produced by a single cell (e.g., a hybridoma or a host cell producing a recombinant antibody), where the antibody specifically binds to anti-DDR1 as determined, for example, by ELISA or other antigen-binding or competitive-binding assays known in the art or provided in the examples herein. In certain embodiments, the monoclonal antibody can be a chimeric antibody or a humanized antibody. In certain embodiments, the monoclonal antibody is a monovalent antibody or a multivalent (e.g., bivalent) antibody. In certain embodiments, the monoclonal antibody is a monospecific or multispecific antibody (e.g., a bispecific antibody). The monoclonal antibodies described herein can be made, for example, by the hybridoma method described in Kohler G & Milstein C (1975) Nature 256: 495, which is hereby incorporated by reference in its entirety, or can be isolated, for example, from a phage library using techniques described herein. Other methods for the preparation of clonal cell lines and the monoclonal antibodies expressed thereby are well known in the art (see, e.g., Chapter 11 in: Short Protocols in Molecular Biology, (2002) 5th Ed., Ausubel FM et al., see above).

[0249] As used herein, an antibody binds to an antigen in a multivalent (e.g., bivalent) manner if the antibody comprises at least two (e.g., two or more) monovalent binding regions, each monovalent binding region being capable of binding to an epitope on the antigen. Each monovalent binding region can bind to the same or a different epitope on the antigen.

[0250] Methods for producing and screening for specific antibodies using hybridoma technology are routine and well known in the art. For example, in the hybridoma method, a mouse, or other suitable host animal, such as a sheep, goat, rabbit, rat, hamster or macaque, is immunized to elicit lymphocytes that produce or can produce antibodies that specifically bind to the protein (e.g., DDR1) used for immunization. Alternatively, the lymphocytes may be immunized in vitro. The lymphocytes are then fused with myeloma cells using a suitable fusogen, such as polyethylene glycol, to form hybridoma cells (Goding JW (ed.), Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986), which is hereby incorporated by reference in its entirety). In addition, the RIMMS (Repeated Multiple Site Immunization) technique can be used to immunize animals (Kilpatrick KE et al., (1997) Hybridoma 16:381-9, which is hereby incorporated by reference in its entirety).

[0251] In certain embodiments, a mouse (or other animal, such as a rat, monkey, donkey, pig, sheep, hamster, or dog) can be immunized with an antigen (e.g., DDR1), and if an immune response is detected, e.g., if antibodies specific for the antigen are detected in the mouse serum, the mouse spleen is harvested and splenocytes are isolated. The splenocytes are then fused, by well-known techniques, to cells from any suitable myeloma cell line, such as the cell line SP20 available from the American Type Culture Collection (ATCC®) (Manassas, VA), to form hybridomas. The hybridomas are selected and cloned by limiting dilution. In certain embodiments, the lymph nodes of an immunized mouse are harvested and fused with NS0 myeloma cells.

[0252] The hybridoma cells thus prepared are preferably seeded and grown in a suitable culture medium containing one or more substances that inhibit the growth or survival of unfused parental myeloma cells. For example, when the parental myeloma cells lack the enzyme hypoxanthine-guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridoma typically contains hypoxanthine, aminopterin, and thymidine (HAT medium), and these substances prevent the growth of HGPRT-deficient cells.

[0253] In certain embodiments, myeloma cells that fuse efficiently, support stable high-level production of antibodies by the selected antibody-producing cells, and are sensitive to media such as HAT medium are used. These myeloma cell lines include mouse myeloma lines, such as those derived from the NS0 cell line or MOPC-21 and MPC-11 mouse tumors available from the Salk Institute Cell Distribution Center, San Diego, CA, USA, as well as SP-2 or X63-Ag8.653 cells available from the American Type Culture Collection, Rockville, MD, USA. Human myeloma and mouse-human heteromyeloma cell lines have also been described for the production of human monoclonal antibodies (Kozbor D (1984) J Immunol 133: 3001-5; Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987), each of which is incorporated herein by reference in its entirety).

[0254] The culture medium in which hybridoma cells are growing is assayed for the production of monoclonal antibodies against DDR1. The binding specificity of the monoclonal antibodies produced by the hybridoma cells is determined by methods known in the art, such as by immunoprecipitation, or by in vitro binding assays, such as radioimmunoassay (RIA) or enzyme-linked immunosorbent assay (ELISA).

[0255] After hybridoma cells producing antibodies with the desired specificity, affinity and / or activity are identified, the clones are subcloned by limiting dilution procedures and can be grown by standard methods (Goding JW (ed.), Monoclonal Antibodies: Principles and Practice, supra). Suitable culture media for this purpose include, for example, D-MEM or RPMI 1640 medium. In addition, the hybridoma cells may be grown in vivo as ascites tumors in animals.

[0256] Monoclonal antibodies secreted by the subclones are preferably separated from the culture medium, ascites, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.

[0257] The antibodies described herein include, for example, antibody fragments that recognize DDR1 and can be made by any technique known to those of skill in the art. For example, the Fab and F(ab’)2 fragments described herein can be produced by proteolytic cleavage of the immunoglobulin molecule using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab’)2 fragments). Fab fragments correspond to one of the two identical arms of the antibody molecule and contain a complete light chain paired with the VH and CH1 domains of the heavy chain. F(ab’)2 fragments contain the two antigen-binding arms of the antibody molecule linked by disulfide bonds in the hinge region.

[0258] Furthermore, the antibodies described herein can also be produced using various phage display methods known in the art. In phage display methods, functional antibody domains are displayed on the surface of phage particles that carry the polynucleotide sequences encoding them. In particular, the DNA sequences encoding the VH and VL domains are amplified from an animal cDNA library (e.g., a human or mouse cDNA library of diseased tissue). The DNA encoding the VH and VL domains is recombinantly joined with an scFv linker by PCR and cloned into a phagemid vector. The vector is electroporated into E. coli, and E. coli is infected with helper phage. The phage used in these methods are typically filamentous phage, including fd and M13, and the VH and VL domains are usually recombinantly fused to either gene III or gene VIII of the phage. Phage expressing antigen-binding regions that bind to a particular antigen can be selected or identified using the antigen, for example, a labeled antigen or an antigen bound to or captured on a solid surface or beads.Examples of phage display methods that can be used to produce the antibodies described in this specification include Brinkman U et al., (1995) J Immunol Methods 182: 41-50; Ames RS et al., (1995) J Immunol Methods 184: 177-186; Kettleborough CA et al., (1994) Eur J Immunol 24: 952-958; Persic L et al., (1997) Gene 187: 9-18; Burton DR & Barbas CF (1994) Advan Immunol 57: 191-280; International Publication Nos. WO90 / 02809, WO91 / 10737, WO92 / 01047, WO92 / 18619, WO93 / 11236, WO95 / 15982, WO95 / 20401, and WO97 / 13844; and U.S. Patent Nos. 5,698,426, 5,223,409, 5,403,484, 5,427,908, 5,516,637, 5,571,698, 5,580,717, 5,658,727, 5,733,743, 5,780,225, 5,821,047, and 5,969,108, all of which are hereby incorporated by reference in their entirety.

[0259] As described in the above references, after phage selection, the antibody coding regions derived from the phage are isolated and used to generate whole antibodies, including human antibodies or any other desired antigen-binding fragments, and can be expressed, for example, in any desired host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, as described below. Techniques for recombinantly producing antibody fragments such as Fab, Fab', and F(ab')2 fragments are also known in the art, such as those disclosed in PCT Publication No. WO92 / 22324; Mullinax RL et al., (1992) BioTechniques 12(6): 864-9; Sawai H et al., (1995) Am J Reprod Immunol 34: 26-34; and Better M et al., (1988) Science 240: 1041-1043, all of which are hereby incorporated by reference in their entirety.

[0260] In certain embodiments, to generate whole antibodies, VH or VL nucleotide sequences, restriction sites, and PCR primers containing flanking sequences to protect the restriction sites can be used to amplify VH or VL sequences from a template, such as an scFv clone. Using cloning techniques known to those of skill in the art, the PCR-amplified VH domain can be cloned into a vector expressing the VH constant region, and the PCR-amplified VL domain can be cloned into a vector expressing a VL constant region, such as a human kappa or lambda constant region. The VH and VL domains can also be cloned into one vector expressing the necessary constant regions. The heavy chain conversion vector and the light chain conversion vector are then co-transfected into a cell line using techniques known to those of skill in the art to generate a stable or transient cell line expressing a full-length antibody, such as IgG.

[0261] A chimeric antibody is one in which different parts of the antibody are molecules derived from different immunoglobulin molecules. For example, a chimeric antibody can contain the variable region of a monoclonal antibody from a non-human mammal (e.g., mouse, rat, rabbit, etc.) fused to the constant region of a human antibody. Methods for producing chimeric antibodies are known in the art. See, for example, Morrison SL (1985) Science 229: 1202-7; Oi VT & Morrison SL (1986) BioTechniques 4: 214-221; Gillies SD et al., (1989) J Immunol Methods 125: 191-202; and U.S. Patent Nos. 4,816,397, 4,816,567, 5,807,715, and 6,331,415, all of which are hereby incorporated by reference in their entirety.

[0262] A humanized antibody is capable of binding to a predetermined antigen and comprises a framework region substantially having the amino acid sequence of a human immunoglobulin and CDRs substantially having the amino acid sequence of a non-human immunoglobulin (e.g., a mouse immunoglobulin). In certain embodiments, a humanized antibody typically also comprises at least a portion (Fc) of the immunoglobulin constant region of that of a human immunoglobulin. The antibody can also comprise the CH1, hinge, CH2, CH3, and CH4 regions of the heavy chain. A humanized antibody can be selected from any class of immunoglobulins including IgM, IgG, IgD, IgA, and IgE, as well as any isotype including IgG1, IgG2, IgG3 and IgG4.Humanized antibodies can be produced using a variety of techniques known in the art, including, but not limited to, CDR grafting (European Patent No. EP239400; International Publication No. WO91 / 09967; and U.S. Patent Nos. 5,225,539, 5,530,101, and 5,585,089), veneering or resurfacing (European Patent Nos. EP592106 and EP519596; Padlan EA (1991) Mol Immunol 28(4 / 5): 489-498; Studnicka GM et al., (1994) Prot Engineering 7(6): 805-814; and Roguska MA et al., (1994) PNAS 91: 969-973), chain shuffling (U.S. Patent No. 5,565,332), and, for example, U.S. Patent Nos. 5,766,886 and 6,407,213, International Publication No. WO93 / 17105; Tan P et al., (2002) J Immunol 169: 1119-25; Caldas C et al., (2000) Protein Eng. 13(5): 353-60; Morea V et al., (2000) Methods 20(3): 267-79; Baca M et al., (1997) J Biol Chem 272(16): 10678-84; Roguska MA et al., (1996) Protein Eng 9(10): 895 904; Couto JR et al., (1995) Cancer Res. 55 (23 Supp): 5973s-5977s; Couto JR et al., (1995) Cancer Res 55(8): 1717-22; Sandhu JS (1994) Gene 150(2): 409-10; and Pedersen JT et al., (1994) J Mol Biol 235(3): 959-73, all of which are hereby incorporated by reference in their entirety. Reference is also made to U.S. Patent Application Publication No. US2005 / 0042664A1, which is hereby incorporated by reference in its entirety.

[0263] Methods for making multispecific antibodies (e.g., bispecific antibodies) have been described, see, e.g., U.S. Patent Nos. 5,837,242; 5,869,620; 5,989,830; 6,132,992; 7,183,076; 7,951,917; 8,227,577; and 8,586,713, all of which are hereby incorporated by reference in their entirety.

[0264] Bispecific bivalent antibodies, and methods for making them, are described, e.g., in U.S. Patent Nos. 5,731,168; 5,807,706; and 5,821,333, and U.S. Patent Application Publication No. 2002 / 0155537, each of which is hereby incorporated by reference in its entirety. Bispecific tetravalent antibodies, and methods for making them, are described, e.g., in International Publication Nos. WO02 / 096948 and WO00 / 44788, the disclosures of both of which are hereby incorporated by reference in their entirety. Generally, see International Publication Nos. WO91 / 00360; WO92 / 08802; WO92 / 05793; and WO93 / 17715; Tutt et al., J. Immunol. 147:60-69 (1991); U.S. Patent Nos. 4,474,893; 4,714,681; 4,925,648; 5,573,920; and 5,601,819; and Kostelny et al., J. Immunol. 148:1547-1553 (1992), each of which is hereby incorporated by reference in its entirety.

[0265] The bispecific antibodies described herein can be prepared, for example, according to the DuoBody technology platform (Genmab A / S) described in International Publication Nos. WO2008 / 119353; WO2011 / 131746; WO2011 / 147986; and WO2013 / 060867, as well as Labrijn AF et al., (2013) PNAS 110(13): 5145-5150. Using the DuoBody technology, a first monospecific antibody or half of a first antigen-binding domain containing two heavy chains and two light chains can be combined with a second monospecific antibody or half of a second antigen-binding domain containing two heavy chains and two light chains. The resulting heterodimer contains one heavy chain and one light chain from the first antibody or first antigen-binding domain paired with one heavy chain and one light chain from the second antibody or second antigen-binding domain. When both the monospecific antibody or antigen-binding domain recognize different epitopes on different antigens, the resulting heterodimer is a bispecific antibody.

[0266] The DuoBody technology requires that each of the monospecific antibodies or antigen-binding regions comprises a heavy chain constant region having a single point mutation in the CH3 domain. The point mutation enables a stronger interaction between the CH3 domains in the resulting bispecific antibody than between the CH3 domains in either of the monospecific antibodies or antigen-binding regions. The single point mutation in each monospecific antibody or antigen-binding region is, for example, at residue 366, 368, 370, 399, 405, 407, or 409 numbered according to the EU numbering system in the CH3 domain of the heavy chain constant region, as described in International Publication No. WO2011 / 131746. Also, the single point mutation is located at a different residue in one monospecific antibody or antigen-binding region compared to the other monospecific antibodies or antigen-binding regions. For example, one monospecific antibody or antigen-binding region can comprise the mutation F405L (i.e., a mutation from phenylalanine to leucine at residue 405) numbered according to the EU numbering system, while another monospecific antibody or antigen-binding region can comprise the mutation K409R (i.e., a mutation from lysine to arginine at residue 409). The heavy chain constant region of the monospecific antibody or antigen-binding region can be of the IgG1, IgG2, IgG3, or IgG4 isotype (e.g., the human IgG1 isotype), and the bispecific antibody produced by the DuoBody technology can retain Fc-mediated effector functions.

[0267] Another method for generating bispecific antibodies is referred to as the "knob-into-hole" strategy (see, e.g., WO 2006 / 028936). In this technique, mispairing of Ig heavy chains is reduced by mutating selected amino acids that form the interface of the CH3 domain in IgG. At positions within the CH3 domain where the two heavy chains directly interact, amino acids with small side chains (holes) are introduced into the sequence of one heavy chain, and amino acids with large side chains (knobs) are introduced into the corresponding residues on the other heavy chain where they interact. In some embodiments, the compositions of the invention have immunoglobulin chains in which the CH3 domain is modified by mutating selected amino acids that interact at the interface between two polypeptides such that the bispecific antibody is preferentially formed. The bispecific antibodies can be composed of immunoglobulin chains of the same subclass (e.g., IgG1 or IgG3) or different subclasses (e.g., IgG1 and IgG3, or IgG3 and IgG4).

[0268] In some instances, the bispecific antibodies can contain heterodimers of IgG4 and IgG1, IgG4 and IgG2, IgG4 and IgG2, IgG4 and IgG3, or IgG1 and IgG3 chains. Such heterodimeric heavy chain antibodies can be routinely engineered, for example, by modifying selected amino acids that form the interface of the CH3 domain in human IgG4 and IgG1 or IgG3 such that heterodimeric heavy chain formation is favored.

[0269] In certain embodiments, an antibody described herein that binds to the same epitope of DDR1 as the anti-DDR1 antibodies described herein is a human antibody. In certain embodiments, an antibody described herein that competitively blocks (e.g., in a dose-dependent manner) the binding of any one of the antibodies described herein to DDR1 is a human antibody. Human antibodies can be produced using any method known in the art. For example, transgenic mice that cannot express functional endogenous immunoglobulins but can express human immunoglobulin genes can be used. In particular, the human heavy and light chain immunoglobulin gene complexes can be introduced into mouse embryonic stem cells randomly or by homologous recombination. Alternatively, the human variable, constant, and diversity regions can be introduced into mouse embryonic stem cells in addition to the human heavy and light chain genes. The mouse heavy and light chain immunoglobulin genes can be rendered non-functional by homologous recombination, separately or simultaneously, from the introduction of the human immunoglobulin gene locus. In particular, J HHomozygous deletion of the region prevents endogenous antibody production. The modified embryonic stem cells are expanded and microinjected into blastocysts to generate chimeric mice. The chimeric mice are then mated to generate homozygous offspring that express human antibodies. Transgenic mice are immunized in the normal way with a selected antigen, e.g., all or part of an antigen (e.g., DDR1). Monoclonal antibodies against the antigen can be obtained from the immunized transgenic mice using conventional hybridoma technology. The human immunoglobulin transgene carried by the transgenic mice is rearranged during B cell differentiation and then undergoes class switching and somatic hypermutation. Thus, it is possible to produce therapeutically useful IgG, IgA, IgM, and IgE antibodies using such techniques. For an overview of this technology for producing human antibodies, see Lonberg N & Huszar D (1995) Int Rev Immunol 13:65-93, which is hereby incorporated by reference in its entirety. For a detailed discussion of this technology for producing human antibodies and human monoclonal antibodies and the protocols for producing such antibodies, see, for example, International Publication Nos. WO96 / 33735; WO96 / 34096; and WO98 / 24893; and U.S. Patent Nos. 5,413,923; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016; 5,814,318; and 5,939,598, all of which are hereby incorporated by reference in their entirety.Examples of mice capable of producing human antibodies include XenoMouse™ (Abgenix, Inc.; U.S. Patent Nos. 6,075,181 and 6,150,184), HuAb-Mouse™ (Medarex, Inc. / Gen Pharm; U.S. Patent Nos. 5,545,806 and 5,569,825), TransChromo Mouse™ (Kirin) and KM Mouse™ (Medarex / Kirin), all of which are hereby incorporated by reference in their entirety.

[0270] Human antibodies that specifically bind to DDR1 can be made by a variety of methods known in the art, including the phage display methods described above using antibody libraries derived from human immunoglobulin sequences. See also U.S. Patent Nos. 4,444,887; 4,716,111; and 5,885,793; and International Publication Nos. WO91 / 10741; WO96 / 34096; WO96 / 33735; WO98 / 16654; WO98 / 24893; WO98 / 46645; and WO98 / 50433, all of which are hereby incorporated by reference in their entirety.

[0271] In certain embodiments, human antibodies can be produced using mouse-human hybridomas. For example, human peripheral blood lymphocytes transformed with Epstein-Barr virus (EBV) can be fused with mouse myeloma cells to produce mouse-human hybridomas that secrete human monoclonal antibodies, and these mouse-human hybridomas can be screened to determine those that secrete human monoclonal antibodies that specifically bind to a target antigen (e.g., DDR1). Such methods are known and described in the art, and reference is made, for example, to Shinmoto H et al., (2004) Cytotechnology 46: 19-23; Naganawa Y et al., (2005) Human Antibodies 14: 27-31, each of which is hereby incorporated by reference in its entirety. 7.5 Methods of Use

[0272] In one aspect, the present disclosure provides a method of monitoring the efficacy of an anti-DDR1 antibody in a subject in need thereof. In one embodiment, the method includes administering to the subject an effective amount of an anti-DDR1 antibody and detecting the level of DDR1 phosphorylation in a sample derived from the subject. In some embodiments, the anti-DDR1 antibody comprises an anti-DDR1 antibody disclosed herein or a nucleic acid encoding an anti-DDR1 antibody. In some embodiments, the anti-DDR1 antibody is administered via a suitable route. Non-limiting examples of suitable routes of administration include intravenous, oral, parenteral, ocular, pulmonary, and topical administration.

[0273] In some embodiments, the level of DDR1 phosphorylation includes the percentage of total DDR1 in a sample phosphorylated at one or more phosphorylation sites. In one embodiment, the one or more phosphorylation sites include tyrosine residues. In one embodiment, the tyrosine residues are residues known to autophosphorylate in response to stimulation of the extracellular portion of DDR1. In one embodiment, the tyrosine residues are residues known to autophosphorylate in response to stimulation of the extracellular portion of DDR1 via one or more types of collagen. In some embodiments, the level of DDR1 phosphorylation includes the absolute amount of phosphorylated DDR1 protein in the sample. In some embodiments, the level of DDR1 phosphorylation includes the absolute amount of phosphorylated DDR1 sites in the sample.

[0274] In some embodiments, the level of DDR1 phosphorylation includes the percentage of the cleaved form of DDR1 in the sample phosphorylated at one or more phosphorylation sites. In some embodiments, the cleaved form of DDR1 has a lower molecular weight compared to the uncleaved form. In some embodiments, the cleaved form has a molecular weight of less than 125 kDa (e.g., less than 120 kDa, less than 115 kDa, less than 110 kDa, less than 105 kDa, less than 100 kDa, less than 95 kDa, less than 90 kDa, less than 85 kDa, less than 80 kDa, less than 75 kDa, less than 70 kDa, less than 65 kDa, less than 60 kDa, less than 55 kDa, less than 50 kDa, less than 45 kDa, less than 40 kDa, less than 35 kDa, less than 30 kDa, less than 25 kDa, less than 20 kDa, less than 15 kDa, less than 10 kDa, or less than 5 kDa). In some embodiments, the cleaved form has a molecular weight of approximately 60 kDa.

[0275] Those skilled in the art will recognize that any method for detecting DDR1 phosphorylation can be used in conjunction with the methods of the present invention. Various methods for detecting phosphorylation are known in the art, including, but not limited to, radioisotope labeling, mass spectrometry, immunoassays using phospho-specific antibodies (e.g., immunoblotting, enzyme-linked immunosorbent assay, intracellular flow cytometry, etc.). A variety of antibodies specific for phosphorylated DDR1 are readily available and known in the art. Exemplary phospho-specific DDR1 antibodies include, but are not limited to, phospho-DDR1 (Tyr513) (E1N8F) rabbit mAb #14531 (Cell Signaling Technology), phospho-DDR1 (Tyr792) antibody #11994 (Cell Signaling Technology), phospho-DDR1 (Tyr796) polyclonal antibody phospho-DDR1 (Tyr796) polyclonal antibody PA5-106123 (Thermo Fisher Scientific), and anti-phospho-DDR1 (pTyr513) SAB4504671 (Millipore Sigma).

[0276] Those skilled in the art will further recognize that any method for preparing a sample for detecting DDR1 phosphorylation can be used in the methods of the present invention. By way of non-limiting example, cells or tissues can be lysed by physical (e.g., sonication) and / or chemical (e.g., surfactant) means and processed (e.g., centrifuged) to remove cell debris. In some embodiments, one or more phosphatase inhibitors are included in the sample to prevent premature dephosphorylation of DDR1. In some embodiments, one or more protease inhibitors are included in the sample to prevent premature degradation of DDR1.

[0277] In some embodiments, the subject in need thereof has an elevated level of DDR1 phosphorylation as compared to a reference sample. In some embodiments, the level of DDR1 phosphorylation is elevated by at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 75%, 100%, 150%, 200%, 300%, or 400% as compared to the reference sample. In some embodiments, the level of DDR1 phosphorylation is elevated by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, or 15-fold as compared to the reference sample. In some embodiments, the elevated level of DDR1 is associated with a disease or disorder. In some embodiments, the elevated level of DDR1 is a direct result of a disease or disorder. In some embodiments, a level of DDR1 phosphorylation that is elevated by at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 75%, 100%, 150%, 200%, 300%, or 400% as compared to the reference sample indicates a disease or disorder. In some embodiments, a level of DDR1 phosphorylation that is elevated by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, or 15-fold as compared to the reference sample indicates a disease or disorder. In some embodiments, the disease or disorder is associated with an elevated level of DDR1 expression (e.g., cancer, fibrosis, etc.). In some embodiments, the disease or disorder is associated with an increased binding of DDR1 to collagen. In some embodiments, the disease or disorder is associated with an elevated level of DDR1 phosphorylation. In some embodiments, the disease or disorder is associated with elevated levels of DDR1 expression, binding to collagen, and / or phosphorylation.

[0278] In one embodiment, a decrease in DDR1 phosphorylation in a sample derived from a subject compared to a reference sample indicates that administration of an anti-DDR1 antibody is effective. In one embodiment, a decrease in DDR1 phosphorylation in a sample derived from a subject compared to a reference sample indicates that administration of an anti-DDR1 antibody is effective for treating a disease or disorder associated with elevated DDR1 phosphorylation levels. In one embodiment, a decrease in DDR1 phosphorylation in a sample derived from a subject of at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 75%, or 100% compared to a reference sample indicates that administration of an anti-DDR1 antibody is effective for treating a disease or disorder associated with elevated DDR1 phosphorylation levels. In one embodiment, a decrease in DDR1 phosphorylation in a sample derived from a subject to 1 / 0.9, 1 / 0.8, 1 / 0.7, 1 / 0.6, 1 / 0.5, 1 / 0.4, 1 / 0.3, 1 / 0.2, or 1 / 0.1 or less compared to a reference sample indicates that administration of an anti-DDR1 antibody is effective for treating a disease or disorder associated with elevated DDR1 phosphorylation levels.

[0279] In one aspect, the present disclosure provides a method of treating a DDR1-related disorder in a subject. In one embodiment, the method includes administering to the subject an effective amount of an anti-DDR1 antibody, and detecting the levels of DDR1 phosphorylation in a sample derived from the subject and a reference sample. In some embodiments, a decrease in DDR1 phosphorylation in a sample derived from a subject compared to the reference sample indicates that the treatment is effective. In one embodiment, a decrease in DDR1 phosphorylation in a sample derived from a subject of at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 75%, or 100% compared to the reference sample indicates that administration of the anti-DDR1 antibody is effective for treating a DDR1-related disease or disorder. In one embodiment, a decrease in DDR1 phosphorylation in a sample derived from a subject to 1 / 0.9, 1 / 0.8, 1 / 0.7, 1 / 0.6, 1 / 0.5, 1 / 0.4, 1 / 0.3, 1 / 0.2, or 1 / 0.1 or less compared to the reference sample indicates that administration of the anti-DDR1 antibody is effective for treating a DDR1-related disease or disorder.

[0280] In one embodiment, the method includes detecting the level of DDR1 phosphorylation in a sample from a subject, and administering an effective amount of an anti-DDR1 antibody to the subject when DDR1 phosphorylation in the sample from the subject is high compared to a reference sample. In one embodiment, the effective amount of the anti-DDR1 antibody is administered when DDR1 phosphorylation in the subject sample is at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 75%, 100%, 150%, 200%, 300%, or 400% higher than in the reference sample. In one embodiment, the effective amount of the anti-DDR1 antibody is administered when DDR1 phosphorylation in the subject sample is at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, or 15-fold higher than in the reference sample.

[0281] In one aspect, the present disclosure provides a method of screening a subject having a DDR1-related disorder that is likely to be effectively treated with an anti-DDR1 antibody. In one embodiment, the method includes detecting the level of DDR1 phosphorylation in a sample from the subject, wherein if the DDR1 phosphorylation in the sample from the subject is high compared to a reference sample, the DDR1-related disorder is likely to be effectively treated with an anti-DDR1 antibody. In some embodiments, the DDR1-related disorder is likely to be effectively treated with anti-DDR1 if the DDR1 phosphorylation in the subject sample is at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 75%, 100%, 150%, 200%, 300%, or 400% higher than the reference sample. In some embodiments, the DDR1-related disorder is likely to be effectively treated with anti-DDR1 if the DDR1 phosphorylation in the subject sample is at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, or 15-fold higher than the reference sample. In some embodiments, a DDR1-related disorder comprising an elevated DDR1 phosphorylation level is likely to be effectively treated with an anti-DDR1 antibody 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-fold more effectively than a therapeutic agent that does not specifically target DDR1. In some embodiments, a DDR1-related disorder comprising an elevated DDR1 phosphorylation level is likely to be effectively treated with an anti-DDR1 antibody 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-fold more effectively than an antibody that does not specifically target DDR1.

[0282] In various embodiments of the methods described herein, the subject sample or reference sample comprises a subject cell, tissue, biological fluid, or a derivative thereof. In some embodiments, the cell comprises a blood cell, a skin cell, a cancer cell, or a cell derived from a fibrous tissue. In some embodiments, the blood cell comprises a red blood cell, a white blood cell, or a platelet. In some embodiments, the white blood cell comprises a monocyte, a lymphocyte, a neutrophil, an eosinophil, a basophil, or a macrophage. In some embodiments, the tissue comprises a skin tissue, a cancer tissue, or a fibrous tissue. In some embodiments, the skin tissue is collected by a skin punch biopsy. In some embodiments, the biological fluid comprises blood (e.g., whole blood, plasma, serum, etc.), saliva, or sputum. In some embodiments, the derivative of the subject or reference cell or tissue is a lysate. In some embodiments, the derivative of the subject or reference biological fluid is an isolate.

[0283] In various embodiments of the methods described herein, the level of DDR1 phosphorylation in the subject sample is compared to the level of DDR1 phosphorylation in the reference sample. Non-limiting examples of reference samples include, but are not limited to, a negative control, a positive control, a standard control, a standard value, an expected normal background value of the subject, a historical normal background value of the subject, a reference standard, a reference level, an expected normal background value of a population of which the subject is a member, or a historical normal background value of a population of which the subject is a member. In some embodiments, the reference sample comprises a sample from a healthy individual. In some embodiments, the reference sample comprises a sample from a healthy individual obtained after successful treatment for a DDR1-related disease or disorder. In some embodiments, the reference sample comprises a sample from a healthy individual with no known medical history of a DDR1-related disease or disorder. In some embodiments, the reference sample comprises a sample of the subject. In some embodiments, the reference sample comprises a sample of the subject obtained prior to the occurrence of a DDR1-related disease or disorder. In some embodiments, the reference sample comprises a sample of the subject obtained after the occurrence of a DDR1-related disease or disorder.

[0284] In one aspect, the present disclosure provides a method for screening for anti-DDR1 antibodies. In some embodiments, the method includes administering an effective amount of an anti-DDR1 antibody to a cell and detecting the level of DDR1 phosphorylation in the cell. In one embodiment, the method includes screening for an anti-DDR1 antibody that is effective in treating a DDR1-related disorder, wherein a decrease in DDR1 phosphorylation in the cell compared to a reference cell indicates that the anti-DDR1 antibody is effective in treating cancer. In another embodiment, the method includes screening for an anti-DDR1 antibody that is effective in reducing collagen interaction with a cell, wherein a decrease in DDR1 phosphorylation in the cell compared to a reference cell indicates that the anti-DDR1 antibody is effective in reducing collagen interaction with the cell. Exemplary collagen types include, but are not limited to, collagen I, collagen II, collagen III, collagen IV, collagen V, collagen VI, collagen VII, collagen VIII, collagen IX, collagen X, collagen XI, collagen XII, collagen XIII, collagen XIV, collagen XV, collagen XVI, collagen XVII, collagen XVIII, collagen XIX, collagen XX, collagen XXI, collagen XXII, collagen XXIII, collagen XXIV, collagen XXV, collagen XXVI, collagen XXVII, and collagen XXVIII. In some embodiments, the collagen type includes collagen I, collagen II, collagen III, or collagen V.

[0285] In various embodiments of the methods described herein, the disease or disorder associated with elevated DDR1 phosphorylation (i.e., DDR1-related disease or disorder) includes cancer. Exemplary cancer tissues that may be associated with elevated DDR1 phosphorylation include, but are not limited to, cancer or cancer cells of the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, intestine, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, pancreas, testis, tongue, cervix, or uterus.

[0286] Exemplary histological types of cancer that may be associated with elevated DDR1 phosphorylation include, but are not limited to, malignant neoplasms; carcinomas; undifferentiated carcinomas; giant cell carcinomas and spindle cell carcinomas; small cell carcinomas; papillary carcinomas; squamous cell carcinomas; lymphoepithelial carcinomas; basal cell carcinomas; pyromatrices carcinomas; transitional cell carcinomas; papillary transitional cell carcinomas; adenocarcinomas; malignant gastrinomas; cholangiocarcinomas; hepatocellular carcinomas; combinations of hepatocellular carcinomas and cholangiocarcinomas; fibrolamellar adenocarcinomas; adenoid cystic carcinomas; adenocarcinomas in adenomatous polyps; familial adenomatous polyposis adenocarcinomas; solid carcinomas; malignant carcinoid tumors; bronchioloalveolar adenocarcinomas; papillary adenocarcinomas; anaplastic carcinomas; eosinophilic carcinomas; eosinophilic adenocarcinomas; basophilic carcinomas; clear cell adenocarcinomas; granular cell carcinomas; follicular adenocarcinomas; papillary and follicular adenocarcinomas; unencapsulated sclerosing carcinomas; adrenocortical carcinomas; endometrial carcinomas; skin appendage carcinomas; apocrine adenocarcinomas; sebaceous gland carcinomas; adenocarcinomas of the ear canal; mucoepidermoid carcinomas; cystadenocarcinomas; papillary cystadenocarcinomas; papillary serous cystadenocarcinomas; mucinous cystadenocarcinomas; mucinous adenocarcinomas; bookmark ring cell carcinomas; invasive ductal carcinomas; medullary carcinomas; lobular carcinomas; inflammatory carcinomas; Paget's disease of the breast; acinar cell carcinomas; adenosquamous carcinomas; adenocarcinomas with squamous metaplasia; malignant thymomas; malignant ovarian stromal tumors; malignant mesotheliomas; malignant granular cell tumors; malignant sertoli stromal cell tumors; sertoli cell carcinomas; malignant leydig cell tumors; malignant lipoid cell tumors; malignant paragangliomas; malignant extra-mammary paragangliomas; pheochromocytomas; glomus angiosarcomas; malignant melanomas; amelanotic melanomas; superficially spreading melanomas; malignant melanomas in giant congenital nevi; epitheloid cell melanomas; malignant blue nevi; sarcomas; fibrosarcomas; malignant fibrous histiocytomas; myxosarcomas; liposarcomas; leiomyosarcomas; rhabdomyosarcomas; fetal rhabdomyosarcomas; alveolar rhabdomyosarcomas; stromal sarcomas; malignant mixed tumors; müllerian mixed tumors; nephroblastomas; hepatoblastomas; carcinosarcomas; malignant mesenchymal tumors; malignant Brenner tumors; malignant phyllodes tumors; synovial sarcomas; malignant mesotheliomas; undifferentiated embryonal cell tumors; embryonal carcinomas; malignant teratomas; malignant ovarian teratomas; choriocarcinomas; malignant mesonephromas; angiosarcomas; malignant angioendotheliomas; Kaposi sarcomas; malignant perivascular cell tumors; lymphangiosarcomas; osteosarcomas; juxtacortical osteosarcomas; chondrosarcomas; malignant chondroblastomas; mesenchymal chondrosarcomas; giant cell tumors of bone; Ewing sarcomas; malignant odontogenic tumors; ameloblastic sarcomas; malignant ameloblastic tumors; ameloblastic fibrosarcomas; malignant pineal tumors; chordomas; malignant gliomas; epitheliomas; astrocytomas; protoplasmic astrocytomas; fibrous astrocytomas; astroblastomas; glioblastomas;Anaplastic glioma; anaplastic glioblastoma; primitive neuroectodermal; cerebellar sarcoma; ganglioblastoma; neuroblastoma; retinoblastoma; olfactory neurogenic tumor; malignant meningioma; neurofibrosarcoma; malignant schwannoma; malignant granular cell tumor; malignant lymphoma; Hodgkin's disease; lateral granuloma; small lymphocyte malignant lymphoma; large cell diffuse malignant lymphoma; malignant follicular lymphoma; fungating polyposis; other specified non-Hodgkin lymphoma; malignant histiocytosis; multiple myeloma; mast cell sarcoma; immunoproliferative small intestinal disease; leukemia; lymphocytic leukemia; plasma cell leukemia; erythroleukemia; lymphosarcoma cell leukemia; myeloid leukemia; basophilic leukemia; eosinophilic leukemia; monocytic leukemia; mast cell leukemia; megakaryoblast leukemia; myeloid sarcoma; and hairy cell leukemia. In some embodiments, tumors can include osteosarcoma, angiosarcoma, rhabdomyosarcoma, leiomyosarcoma, Ewing's sarcoma, glioblastoma, neuroblastoma, or leukemia.;

[0287] In various embodiments of the methods described herein, a disease or disorder associated with elevated DDR1 phosphorylation (i.e., a DDR1-related disease or disorder) includes a fibrotic condition. In some embodiments, the fibrotic condition includes organ fibrosis. In some embodiments, the fibrotic condition includes fibrosis of the skin, kidney, liver, lung, or heart. In some embodiments, the fibrotic condition includes hypertrophic scar of the skin, scleroderma, pulmonary scar, interstitial lung disease, idiopathic pulmonary fibrosis, sclerosing hepatic fibrosis, or renal fibrosis.; 7.6 Kit

[0288] Also provided are kits comprising one or more of the antibodies described herein, or pharmaceutical compositions or conjugates thereof. In certain embodiments, provided herein are pharmaceutical packs or kits comprising one or more containers filled with one or more of the components of the pharmaceutical compositions described herein, such as one or more of the antibodies provided herein. In certain embodiments, the kit contains the pharmaceutical composition described herein, and any prophylactic or therapeutic agent, such as those described herein. In certain embodiments, the kit may contain, for example, T cell mitogens such as phytohemagglutinin (PHA) and / or phorbol myristate acetate (PMA), or antibodies that stimulate the TCR complex such as anti-CD3 antibody and anti-CD28 antibody. Optionally, such containers may be accompanied by a notice in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which notice reflects approval by the agency for manufacture, use, or sale for human administration.

[0289] Also provided is a kit that can be used in the above method. In certain embodiments, the kit comprises an antibody described herein, preferably a purified antibody, in one or more containers. In certain embodiments, the kit described herein contains a substantially isolated DDR1 antigen as a control. In certain embodiments, the kit described herein further comprises a control antibody that does not react with the DDR1 antigen. In certain embodiments, the kit described herein contains one or more elements for detecting the binding of an antibody to the DDR1 antigen (e.g., the antibody can be conjugated to a detectable substrate such as a fluorescent compound, an enzyme substrate, a radioactive compound, or a luminescent compound, or a second antibody that recognizes the first antibody can be conjugated to a detectable substrate). In certain embodiments, the kit provided herein can contain a recombinantly produced or chemically synthesized DDR1 antigen. The DDR1 antigen provided in the kit can also be attached to a solid support. In certain embodiments, the detection means of the above kit comprises a solid support to which the DDR1 antigen is attached. Such a kit can also contain an anti-human antibody or an anti-mouse / rat antibody labeled with a non-attached reporter. In this embodiment, the binding of the antibody to the DDR1 antigen can be detected by the binding of the antibody labeled with the reporter. In certain specific embodiments, the invention relates to the use of the kit of the invention for assaying in vitro and / or for detecting the DDR1 antigen in a biological sample. In certain embodiments, the kit provided herein comprises one or more antibodies that can specifically detect one or more sites of phosphorylation of DDR1. In certain embodiments, the kit provided herein contains one or more biomolecules (e.g., collagen) that can bind and / or stimulate DDR1 phosphorylation in cells. In certain embodiments, the kit provided herein contains a reference sample and / or cells described herein.

Examples

[0290] 8. Examples The examples in this section (i.e., Section 8) are provided by way of illustration and not of limitation. 8.1 (Example 1): In Vitro Characterization of Anti-DDR1 Monoclonal Antibodies (mAbs)

[0291] Anti-DDR1 mAbs were tested for their ability to inhibit collagen-induced DDR1 phosphorylation, their effects on cell proliferation and cell death in cultured cancer cells, and their effects on collagen-dependent adhesion of DDR1-overexpressing cells. A. Inhibition of Collagen-Induced DDR1 Phosphorylation in T47D Cells

[0292] Cultured T47D breast cancer cells were serum-starved for 16 hours, pretreated for 2 hours with increasing concentrations of 9H1-WT or IgG1-WT (as a negative control) monoclonal antibodies, and then treated with 50 μg / ml of human or rat collagen I for 90 minutes. Cells treated with 200 nM of 2.45-IN [2-(4-bromo-2-oxo-1'-(1H-pyrazolo[4,3-b]pyridine-5-carbonyl)spiro[indoline-3,4'-piperidine]-1-yl)-N-(2,2,2-trifluoroethyl)acetamide] were used as a positive control for inhibition of DDR1 phosphorylation. Cell lysates were then analyzed by Jess immunoassay (ProteinSimple). As shown in Figure 1, 9H1-WT was able to inhibit the phosphorylation of DDR1 induced by human collagen I (Figures 1A and 1C) and rat collagen I (Figures 1B and 1D) at low concentrations of about 0.1 μg / ml. B. Effects of 9H1-WT and Ab#33 mAbs on Cell Proliferation and Cell Death

[0293] To evaluate the potential cell growth inhibitory or cytotoxic effects of 9H1-WT and Ab#33 mAb, serum-starved T47D cells were pre-treated with 9H1-WT or Ab#33, their corresponding IgG controls, or paclitaxel, a known chemotherapeutic drug (used as a positive control for cytotoxicity), and followed up for 96 hours. To measure proliferation, nuclei were stained using Hoechst staining and cell membranes were stained using CellMask™ (Thermo Fisher Scientific) Deep Red. To measure cell death, phosphatidylserine on the cell surface, a marker of apoptosis, was stained using annexin V, and cells with compromised membrane integrity, a marker of cell death, were stained using Incucyte® Cytotox Green (Sartorius). As shown in Figure 2, 9H1-WT had no measurable effect on either cell growth (Figure 2A and 2C - 2D) or cell death (Figure 2A and 2E - 2F) compared to DMSO or IgG1 control, while paclitaxel, as expected, decreased proliferation and increased cell death. Similarly, Ab#33 had no measurable effect on either cell growth (Figure 2B and 2G - 2H) or cell death (Figure 2B and 2I - 2J), suggesting that 9H1-WT and Ab#33 do not have significant cell growth inhibitory or cytotoxic effects. C.Specific induction of DDR1 phosphorylation by collagen type

[0294] To determine which type of collagen effectively induces DDR1 phosphorylation, serum-starved T47D cells were treated with 25 μg / ml or 50 μg / ml of human or rat collagen I, human collagen IV, or human collagen V. As shown in Figures 3A and 3B, rat or human collagen I and human collagen V induced measurable amounts of DDR1 phosphorylation, while human collagen IV did not, suggesting that DDR1 responds primarily to collagen I and collagen V stimulation. D.Inhibition of collagen I and V-induced phosphorylation of DDR1

[0295] Serum-starved T47D cells were pretreated for 2 hours with increasing concentrations of 9H1-WT, IgG1-WT as a negative control, or 2.45-IN as a positive control, followed by stimulation with 50 μg / ml of human collagen I or V for 90 minutes. As shown in Figure 5A, 9H1-WT was able to inhibit both collagen I- and collagen V-induced phosphorylation of DDR1 at a low concentration of about 0.1 μg / ml. Figure 5B confirms that the total DDR1 protein level was not significantly affected by the treatment. E. Calculated IC50 of 9H1-WT for inhibition of collagen I-induced pDDR1

[0296] To determine the IC50 of 9H1-WT for inhibiting DDR1 phosphorylation, serum-starved T47D cells were pretreated for 2 hours with increasing (log scale) concentrations of 9H1-WT, IgG1-WT as a negative control, or 2.45-IN as a positive control, followed by stimulation with 50 μg / ml of human collagen I for 90 minutes. As shown in Figures 6A - 6D, 9H1-WT (PRTH-101) had an average IC50 between 0.05 - 0.06 μg / ml for inhibiting collagen I-induced phosphorylation of DDR1. F. Inhibition of adhesion of DDR1 overexpressing (DDR1 OE) cells to collagen I

[0297] To determine whether 9H1-WT can inhibit DDR1-mediated cell adhesion, HEK293 cells overexpressing DDR1 and WT HEK293 cells were pretreated with increasing concentrations of PRTH-101 or control IgG1-WT and incubated for 30 minutes on plates coated with 0.5 μg / cm 2 of collagen I, and stained for nuclei using Hoechst. As shown in Figures 7A - 7C, overexpression of DDR1 led to an increase in adhesion to collagen I, which was inhibited by 9H1-WT (PRTH-101). G. Calculated IC50 of 9H1-WT for inhibition of DDR1 OE cell adhesion

[0298] To determine the IC50 for the inhibition of 9H1-WT on DDR1 OE cell adhesion, HEK293-DDR1 OE cells were pre-treated for 1 hour with increasing concentrations (on a logarithmic scale) of 9H1-WT or control IgG1-WT and incubated for 30 minutes on plates coated with 0.5 μg / cm 2 of type I collagen, and stained for nuclei using Hoechst. As shown in Figure 8, the calculated IC50 for approximately 0.065 μg / ml of 9H1-WT (PRTH-101) was equivalent to the IC50 calculated for the collagen I-induced phosphorylation of DDR1 shown in Figure 6. H. Inhibition of collagen II- and III-induced phosphorylation of DDR1

[0299] Serum-starved T47D cells were pre-treated for 2 hours with increasing concentrations of 9H1-WT or IgG1-WT as a negative control, followed by stimulation with 50 μg / ml of human collagen I, II, or III for 90 minutes. As shown in Figure 9A, collagen II, and to a much lesser extent collagen III, induced DDR1 phosphorylation in T47D, and both were inhibited by 9H1-WT (PRTH-101). Figure 9B confirms the results of Figure 9A and shows a similar pattern for collagen I. I. Inhibition mediated by rabbit and chimeric mAb #33 against pDDR1

[0300] Serum-starved T47D cells were pre-treated for 2 hours with increasing concentrations of monoclonal antibody or IgG control, followed by stimulation with 50 μg / ml of human collagen I for 90 minutes. As shown in Figure 10A, rabbit mAb #33 was able to inhibit collagen I-induced phosphorylation of DDR1 with a pattern similar to 9H1-WT (PRTH-101) and comparable efficacy. As shown in Figure 10B, a chimeric rabbit / human mAb #33 containing the variable domains of the rabbit mAb #33 heavy and light chains fused to the human IgG1 heavy and light chain constant domains (see Table 4) yielded results similar to 9H1-WT and rabbit mAb #33. 8.2 (Example 2): In vivo characterization of anti-DDR1 mAbs

[0301] To evaluate the pharmacokinetic profile of the anti-DDR1 mAb, the mAb was administered intraperitoneally to female C57Bl6JrJ mice at a dose of 10 mg / kg, and serial blood samples were taken over time (Figure 4A), and circulating free and partially bound antibody was measured using ELISA. As shown in Figures 4B-4D, the exposures for humanized mAb#9H1 with inactivated IgG1Fc (Figure 4B), humanized mAb#9H1 with WT IgG1Fc (Figure 4C), and chimeric rabbit / human mAb #33 with inactivated IgG1 Fc (Figure 4D) were equivalent to the expected exposure for IgG1. Furthermore, as shown in Figure 4E and Table S1 below, the maximum circulating (free and partially bound) concentration of each mAb was higher than the concentration required to bind to the target (as shown by surface plasmon resonance results of the mAb binding to the mouse DDR1 extracellular domain; see Table S2 below). Also, the maximum circulating (free and partially bound) concentration of mAb#9H1 WT IgG1 was higher than the in vitro concentration required to inhibit collagen I-induced phosphorylation of DDR1 in T47D cells (see Figure 1).

Table S1

Table S2

[0302] An assay was developed to detect pDDR1 in skin samples. First, pDDR1 was detected in reference human skin samples from healthy subjects as described below. Notably, the pDDR1 detected in these reference samples was almost exclusively the cleaved form of DDR1.

[0303] Fresh frozen skin punch biopsy samples of 4 mm from healthy human subjects were obtained from Discovery Life Sciences. Sample 1 was a normal skin sample from a 36-year-old white female collected by abdominoplasty on July 13, 2022 (patient ID: 122299014). Sample 2 was a normal skin sample from a 51-year-old white female collected by abdominoplasty on July 20, 2022 (patient ID: 122305452).

[0304] To extract proteins, the samples were removed from the -80 °C freezer and suspended in 2 ml of Pierce RIPA buffer (Thermo) + 1× Halt™ Protease / Phosphatase Inhibitor Cocktail (Thermo) + 5 mM EDTA + 5 nM batimastat (R&D Systems) in GentleMacs M tubes (Miltenyi). The samples were cycled twice on the Protein 01_01 cycle on the GentleMacs Disassociator (Miltenyi) at 4 °C, spun at 220 Rcf for 1 minute 30 seconds at 4 °C to remove bubbles, and the samples were collected. 300 uL of total skin lysate was taken out (2-cycle skin lysate sample). 200 uL of 10% SDS was added to 300 uL of total skin lysate, and the mixture was boiled at 95 °C for 5 minutes (2-cycle skin lysate 4% SDS sample). The remaining lysate was centrifuged at 220 Rcf for 4 minutes at 4 °C, and the supernatant was taken out (2-cycle skin supernatant sample). The remaining lysate was run 3 times on the Protein01_01 cycle and centrifuged at 220 Rcf for 4 minutes at 4 °C. The supernatant was taken out (3-cycle skin supernatant sample). The remaining lysate was resuspended, 200 uL of 10% SDS was added to 300 uL of the lysate, and the mixture was boiled as described above (3-cycle lysate 4% SDS sample). Finally, approximately 300 uL of the remaining lysate was collected (3-cycle skin lysate sample).

[0305] All lysates were boiled at 95 °C for 20 minutes to redissolve the proteins, and 200 ug / mL samples were prepared in 0.1× sample buffer. Phosphorylated DDR1 was detected in samples using a Jess total protein detection chemiluminescence assay incorporating a fluorescence separation module from 12 - 230 kDa, a Replex module, an anti-rabbit detection module, and a total protein detection module (all from Protein Simple), as well as a phospho-DDR1 (Tyr513) (E1N8F) antibody (Cell Signaling; mAb catalog number 5583).

[0306] As shown in Figure 11A, pDDR1 was detected in all preparations of skin lysates from both healthy subjects. Interestingly, only the cleaved intracellular pDDR1 (approximately 60 kDa) was detected in skin lysate samples (Figure 11A, indicated by white arrows). In contrast, collagen-stimulated T47D breast cancer cells (e.g., as described above) showed only full-length pDDR1 (approximately 125 kDa; Figure 11A, indicated by black arrows).

[0307] The results described above do not indicate that full-length DDR1 is absent in the assayed samples, as the antibody used was specific for pDDR1. Use of a DDR1 (D1G6) antibody (Cell Signaling) that is not specific for pDDR1 shows that both full-length and cleaved DDR1 can be detected in skin lysate samples (see lanes indicated by black arrows in Figure 11B). However, only the cleaved form is phosphorylated (see lanes indicated by white arrows in Figure 11B).

[0308] The present invention is not limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described will become apparent to those skilled in the art from the foregoing description and the accompanying drawings. Such modifications are intended to be within the scope of the appended claims.

[0309] All references cited in this specification (e.g., publications or patents or patent applications) are hereby incorporated by reference in their entirety for all purposes to the same extent as if each individual reference (e.g., publication or patent or patent application) had been specifically and individually indicated to be incorporated by reference in its entirety for all purposes.

[0310] Other embodiments are within the scope of the following claims.

Claims

1. A method for monitoring the effectiveness of an anti-discoidin domain receptor tyrosine kinase 1 (DDR1) antibody or an antigen-binding fragment thereof in a subject in need thereof, comprising: a) administering an effective amount of said anti-DDR1 antibody to said subject; and b) detecting the level of DDR1 phosphorylation in a sample derived from said subject wherein a decrease in DDR1 phosphorylation in said sample derived from said subject as compared to a positive reference sample indicates that said administration of said anti-DDR1 antibody is effective.

2. The method of claim 1, wherein said subject has cancer.

3. The method of claim 2, wherein said cancer is selected from the group consisting of pancreatic cancer; lung cancer including small cell lung cancer and non-small cell lung cancer; colorectal and colorectal cancer; head and neck cancer; gastric cancer; ovarian cancer; breast cancer; kidney cancer; liver cancer; prostate cancer; cervical cancer; brain cancer; skin cancer including melanoma; sarcoma; cholangiocarcinoma; and bone cancer.

4. The method of claim 1, wherein said subject has a fibrotic condition.

5. The method of claim 4, wherein said fibrotic condition is selected from the group consisting of hypertrophic skin scar, scleroderma, lung scar, idiopathic pulmonary fibrosis, cirrhotic liver fibrosis, renal fibrosis, and interstitial lung disease.

6. A method for treating a DDR1-related disorder in a subject in need thereof, comprising: a) administering an effective amount of an anti-DDR1 antibody or an antigen-binding fragment thereof to said subject; and b) detecting the level of DDR1 phosphorylation in a sample derived from said subject wherein a decrease in DDR1 phosphorylation in said sample derived from said subject as compared to a positive reference sample indicates that said treatment is effective.

7. A method for screening a subject having a DDR1-related disorder that is likely to be effectively treated with an anti-DDR1 antibody, comprising detecting the level of DDR1 phosphorylation in a sample derived from said subject, wherein if the DDR1 phosphorylation in said sample derived from said subject is high as compared to a negative reference sample, said DDR1-related disorder is likely to be effectively treated with an anti-DDR1 antibody.

8. A method for treating a DDR1-related disorder in a subject in need thereof, comprising: a) detecting the level of DDR1 phosphorylation in a sample derived from said subject; and ​ ​ b) administering to the subject an effective amount of an anti-DDR1 antibody or an antigen-binding fragment thereof when DDR1 phosphorylation in the sample from the subject is high as compared to a negative reference sample A method comprising the above steps. **Claim 9** The method according to any one of claims 6 to 8, wherein the DDR1-related disorder is cancer. **Claim 10** The method according to claim 9, wherein the cancer is selected from the group consisting of pancreatic cancer; lung cancer including small cell lung cancer and non-small cell lung cancer; colorectal and colorectal cancer; head and neck cancer; gastric cancer; ovarian cancer; breast cancer; kidney cancer; liver cancer; prostate cancer; cervical cancer; brain cancer; skin cancer including melanoma; sarcoma; cholangiocarcinoma; and bone cancer. **Claim 11** The method according to any one of claims 6 to 8, wherein the DDR1-related disorder is a fibrotic condition. **Claim 12** The method according to claim 11, wherein the fibrotic condition is selected from the group consisting of hypertrophic scar of the skin, scleroderma, lung scar, idiopathic pulmonary fibrosis, fibrotic liver cirrhosis, renal fibrosis, and interstitial lung disease. **Claim 13** The method according to any one of claims 1 to 3 or 6 to 10, wherein the sample comprises tumor tissue. **Claim 14** The method according to any one of claims 1 to 12, wherein the sample comprises one or more selected from the group consisting of blood cells, skin tissue, lung tissue, kidney tissue, and liver tissue. **Claim 15** The method according to any one of claims 1 to 12, wherein the sample comprises a skin punch biopsy sample. **Claim 16** A method for screening an anti-DDR1 antibody or an antigen-binding fragment thereof that is effective in treating a DDR1-related disorder, comprising: a) administering an effective amount of the anti-DDR1 antibody or an antigen-binding fragment thereof to cells; and b) detecting the level of DDR1 phosphorylation in the cells wherein a decrease in DDR1 phosphorylation in the cells as compared to positive reference cells indicates that the anti-DDR1 antibody or an antigen-binding fragment thereof is effective in treating the DDR1-related disorder. **Claim 17** **Claim 23** A method for screening an anti-DDR1 antibody or an antigen-binding fragment thereof that is effective in reducing collagen interaction with cells, comprising: a) administering an effective amount of the anti-DDR1 antibody or an antigen-binding fragment thereof to the cells; and b) detecting the level of DDR1 phosphorylation in the cells wherein the method comprises the above steps. A method showing that the decrease in DDR1 phosphorylation in said cells compared to positive reference cells is effective for said anti-DDR1 antibody or antigen-binding fragment thereof to reduce the collagen interaction with said cells.

18. The method according to claim 16 or 17, wherein said cells are cancer cells.

19. The method according to claim 18, wherein said cancer cells are selected from the group consisting of pancreatic cancer; lung cancer including small cell lung cancer and non-small cell lung cancer; colorectal and colorectal cancer; head and neck cancer; gastric cancer; ovarian cancer; breast cancer; kidney cancer; liver cancer; prostate cancer; cervical cancer; brain cancer; skin cancer including melanoma; sarcoma; cholangiocarcinoma; and bone cancer.

20. The method according to claim 16 or 17, wherein said cells are one or more selected from the group consisting of skin cells, lung cells, kidney cells, and liver cells.

21. The method according to any one of claims 1 to 20, wherein said anti-DDR1 antibody or antigen-binding fragment thereof comprises a VH comprising the CDRH1, CDRH2, and CDRH3 amino acid sequences of the heavy chain variable domain (VH) amino acid sequence of SEQ ID NO: 4 or 13, and a VL comprising the CDRL1, CDRL2, and CDRL3 amino acid sequences of the light chain variable domain (VL) amino acid sequence of SEQ ID NO: 3, 11, or 12.

22. a) said CDRL1 comprises the amino acid sequence of SEQ ID NO: 5; b) said CDRL2 comprises the amino acid sequence of QAS; c) said CDRL3 comprises the amino acid sequence of SEQ ID NO: 7; d) said CDRH1 comprises the amino acid sequence of SEQ ID NO: 8; e) said CDRH2 comprises the amino acid sequence of SEQ ID NO: 9; f) said CDRH3 comprises the amino acid sequence of SEQ ID NO: 10, The method according to claim 21.

23. a) said CDRL1 comprises the amino acid sequence of SEQ ID NO: 17; b) said CDRL2 comprises the amino acid sequence of GVF; c) said CDRL3 comprises the amino acid sequence of SEQ ID NO: 19; d) said CDRH1 comprises the amino acid sequence of SEQ ID NO: 20; e) said CDRH2 comprises the amino acid sequence of SEQ ID NO: 21; f) said CDRH3 comprises the amino acid sequence of SEQ ID NO: 22, The method according to claim 21.

24. Said anti-DDR1 antibody is a) a VL domain comprising an amino acid sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 3, 11, and 12; and b) A VH domain comprising an amino acid sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 4 and 13 The method according to claim 22 or 23, comprising the same.

25. The anti-DDR1 antibody is a) A VL domain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 3, 11, and 12; and b) A VH domain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 4 and 13 The method according to claim 22 or 23, comprising the same.

26. The anti-DDR1 antibody is a) SEQ ID NO: 3 and 4 respectively; b) SEQ ID NO: 11 and 13 respectively; and c) SEQ ID NO: 12 and 13 respectively The method according to claim 25, comprising a VL domain and a VH domain selected from the group consisting of the same.

27. The method according to claim 26, wherein the anti-DDR1 antibody comprises a VL domain and a VH domain each comprising the amino acid sequences of SEQ ID NO: 3 and 4 respectively.

28. The method according to claim 26, wherein the anti-DDR1 antibody comprises a VL domain and a VH domain each comprising the amino acid sequences of SEQ ID NO: 11 and 13 respectively.

29. The method according to claim 26, wherein the anti-DDR1 antibody comprises a VL domain and a VH domain each comprising the amino acid sequences of SEQ ID NO: 12 and 13 respectively.

30. The method according to any one of claims 1 to 29, wherein the step of detecting the level of DDR1 phosphorylation comprises the step of detecting the level of phosphorylation of a cleaved form of DDR1.

31. The method according to claim 30, wherein the cleaved form of DDR1 has a molecular weight of approximately 65 kDa.

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