Optimized anti-TL1A antibodies

Abstract

Described herein are humanized anti-TL1A antibodies and pharmaceutical compositions for the treatment of inflammatory bowel diseases (IBD), such as Crohn's disease (CD) and ulcerative colitis (UC).

Description

[0001] This application is a divisional application of the Chinese patent application with an application date of April 24, 2019, application number 201980043250.4, and invention name “Optimized anti-TL1A antibody” (the application date of the corresponding PCT application is April 24, 2019, and the application number is PCT / US2019 / 028987).

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This application claims the benefit of U.S. Provisional Application No. 62 / 662,605, filed April 25, 2018, and U.S. Provisional Application No. 62 / 756,494, filed November 6, 2018, which are incorporated herein by reference. Background Art

[0004] Inflammatory bowel disease (IBD) is a general term for intestinal disorders that cause inflammatory conditions in the gastrointestinal tract. The main types of IBD are ulcerative colitis (UC) and Crohn's disease (CD). These diseases are very common, with approximately 1.86 million people diagnosed with UC and approximately 1.3 million people diagnosed with CD worldwide.

[0005] Each of these forms has various subclinical phenotypes that are unique to severe forms of IBD present in subsets of CD and UC patients. One such condition is obstructive Crohn's disease, which may be caused by long-term inflammation that can lead to scar tissue formation (fibrostenosis) or swelling of the intestinal wall. Both of these outcomes can lead to narrowing or obstruction and are referred to as fibrotic strictures or inflammatory strictures. Severe strictures can lead to intestinal obstruction, resulting in abdominal pain, bloating, nausea, and inability to pass stool. As another example, a penetrating disease phenotype characterized by intestinal obstruction or internal penetrating fistulas or both often leads to complications associated with IBD, including, for example, intra-abdominal sepsis.

[0006] Unfortunately, there are a limited number of therapies for IBD patients, and suboptimal results in clinical trials have hindered the development of new therapeutic agents. Existing anti-inflammatory therapies, such as steroids and tumor necrosis factor (TNF) inhibitors, are commonly used as first-line treatments for the treatment of IBD. Unfortunately, a considerable number of patients lack or lose response to existing anti-inflammatory therapies, particularly TNF-α inhibitors. When patients are treated with ineffective anti-inflammatory therapies, the condition worsens. For patients who are unresponsive to first-line therapy, surgery in the form of stricture plasty (structureplasty) (plastic shaping of the intestine) or resection (resection of the intestine) is the only treatment option. The surgical treatment of IBD is invasive, and it is estimated that about one-third of patients undergoing surgery will have postoperative risks such as anastomotic leakage, infection and bleeding.

[0007] The pathogenesis of IBD is thought to involve an uncontrolled immune response that may be triggered by certain environmental factors in a genetically susceptible host. The heterogeneity of disease pathogenesis and clinical course, coupled with variable responses to treatment and its associated side effects, suggests that targeted therapeutic approaches for these diseases are the best treatment strategy. However, few targeted therapies are available for patients with IBD, especially for those who may not respond to existing IBD therapies (e.g., anti-TNFα inhibitors). Therefore, new therapeutic agents for the treatment of IBD that specifically target enzymes involved in the pathogenesis of IBD are needed. Summary of the invention

[0008] The present disclosure provides antibodies useful for treating IBD, including moderate to severe forms of IBD characterized by the subclinical phenotypes disclosed herein (e.g., refractory disease, stenotic disease, penetrating disease). The antibodies described herein have superior therapeutic aspects compared to other tumor necrosis factor ligand 1A (TL1A) binding antibodies. First, the antibodies described herein have high sequence homology to human germline frameworks while still exhibiting high binding affinity, are expressed at high levels in bacterial and mammalian cultures, and have fewer sequence liabilities, such as deamidation sites, which lead to increased degradation and reduced therapeutic efficacy.

[0009] TL1A and nucleic acids encoding TL1A (tumor necrosis factor ligand superfamily member 15 (TNFSF15) are provided at Entrez Gene:9966; UniProtKB:O95150. TL1A is a proinflammatory molecule that stimulates proliferation and effector function of CD8(+) cytotoxic T cells as well as Th1, Th2, and Th17 cells in the presence of TCR stimulation. TL1A is thought to be involved in the pathogenesis of IBD by bridging innate and adaptive immune responses, regulating adaptive immunity by enhancing Th1, Th2, and Th17 effector cell function as well as T cell accumulation and immunopathology of inflamed tissues.

[0010] Certain genotypes comprising polymorphisms identified at the TNFSF15 gene are associated with, and thus predict the risk of developing, IBD (e.g., UC or CD), or a subclinical phenotype of IBD. Expression of TL1A mRNA is enriched in patients diagnosed with IBD who have these risk genotypes. Therefore, in a variety of T cell-dependent autoimmune diseases including IBD (e.g., UC and CD), inhibiting the expression and / or activity of TL1A is a promising therapeutic strategy.

[0011] In one aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by any one of SEQ ID NOs: 554 to 564 or 574 to 577; and (c) HCDR3 comprising the amino acid sequence shown by any one of SEQ ID NOs: 565 to 568 or 578 to 581; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by any one of SEQ ID NOs: 569 or 570; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by any one of SEQ ID NOs: 571 to 573 or 582 to 585. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 545. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 546. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 547 or 586 to 588. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 548. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 549. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 550. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 551. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 552.In certain embodiments, the antibody or antigen-binding fragment comprises: (a) a human heavy chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 545; (b) a human heavy chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 546; (c) a human heavy chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 547 or 586 to 588; (d) a human heavy chain framework region 4 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 548; (e) a human light chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 549; (f) a human light chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 550; (g) a human light chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 551; NO:551 is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 3; and (h) is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 4 shown in SEQ ID NO:552. In certain embodiments, as determined by ELISA, the antibody binds to human TL1A with a stronger affinity or 2 times stronger affinity than the L8 clone, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO:491 and the light chain variable region amino acid sequence shown in SEQ ID NO:490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody. In certain embodiments, the antibody or antigen-binding fragment comprises Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO:542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544. In certain embodiments, the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to treat inflammatory bowel disease, Crohn's disease or colitis.In certain embodiments, the antibody or antigen binding fragment is encoded by a nucleic acid. In certain embodiments, the cell comprises a nucleic acid. In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cell is a Chinese hamster ovary (CHO) cell. In certain embodiments, a method for treating an individual suffering from inflammatory bowel disease, Crohn's disease or colitis is described herein, comprising administering an effective amount of the antibody or antigen binding fragment or a pharmaceutical composition to the individual, wherein the individual is diagnosed with or suspected of suffering from inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen binding fragment or a pharmaceutical composition is used to prevent or reduce interferon gamma secretion by T lymphocytes. In certain embodiments, a method for preventing or reducing interferon gamma secretion by T lymphocytes in an individual is described herein, comprising administering an effective amount of the antibody or antigen binding fragment or a pharmaceutical composition to the individual. In certain embodiments, a method for preparing inflammatory bowel disease, Crohn's disease or colitis treatment is described herein, comprising incubating a cell containing a nucleic acid encoding the antibody or antigen binding fragment in the culture medium under conditions sufficient to secrete the antibody or antigen binding fragment into the culture medium. In certain embodiments, the method further comprises subjecting the culture medium to at least one purification step. In certain embodiments, described herein is a method of preparing an inflammatory bowel disease, Crohn's disease, or colitis treatment comprising mixing the antibody or antigen-binding fragment with a pharmaceutically acceptable excipient, carrier, or diluent.

[0012] In another aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown in SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown in SEQ ID NO: 559; and (c) HCDR3 comprising the amino acid sequence shown in SEQ ID NO: 567; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown in SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown in SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown in SEQ ID NO: 573. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to that shown in SEQ ID NO: 545. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 546. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 547 or 586 to 588. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 548. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 549. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 550. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 551. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 552.In certain embodiments, the antibody or antigen-binding fragment comprises: (a) a human heavy chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 545; (b) a human heavy chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 546; (c) a human heavy chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 547 or 586 to 588; (d) a human heavy chain framework region 4 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 548; (e) a human light chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 549; (f) a human light chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 550; (g) a human light chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 551; NO:551 is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 3; and (h) is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 4 shown in SEQ ID NO:552. In certain embodiments, the antibody or antigen-binding fragment that specifically binds to TL1A comprises: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:503; and (b) a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:502. In certain embodiments, the antibody binds to human TL1A with a stronger affinity or 2-fold stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody. In certain embodiments, the antibody or antigen-binding fragment comprises a Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544.In certain embodiments, the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to treat inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen-binding fragment is encoded by a nucleic acid. In certain embodiments, the cell comprises a nucleic acid. In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cell is a Chinese hamster ovary (CHO) cell. In certain embodiments, a method for treating an individual suffering from inflammatory bowel disease, Crohn's disease or colitis is described herein, comprising administering an effective amount of the antibody or antigen-binding fragment or pharmaceutical composition to the individual, wherein the individual is diagnosed as suffering from or suspected of suffering from inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen binding fragment or pharmaceutical composition is used to prevent or reduce interferon gamma secretion by T lymphocytes. In certain embodiments, described herein is a method for preventing or reducing the secretion of interferon gamma by T lymphocytes in an individual, comprising administering an effective amount of the antibody or antigen binding fragment or pharmaceutical composition to the individual. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising incubating cells containing nucleic acids encoding the antibody or antigen binding fragment in the culture medium under conditions sufficient to secrete the antibody or antigen binding fragment into the culture medium. In certain embodiments, the method further comprises subjecting the culture medium to at least one purification step. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising mixing the antibody or antigen binding fragment with a pharmaceutically acceptable excipient, carrier or diluent.

[0013] In another aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown in SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown in SEQ ID NO: 563; and (c) HCDR3 comprising the amino acid sequence shown in SEQ ID NO: 568; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown in SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown in SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown in SEQ ID NO: 572. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to that shown in SEQ ID NO: 545. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 546. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 547 or 586 to 588. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 548. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 549. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 550. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 551. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 552.In certain embodiments, the antibody or antigen-binding fragment comprises: (a) a human heavy chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 545; (b) a human heavy chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 546; (c) a human heavy chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 547 or 586 to 588; (d) a human heavy chain framework region 4 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 548; (e) a human light chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 549; (f) a human light chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 550; (g) a human light chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 551; NO:551 is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 3; and (h) is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 4 shown in SEQ ID NO:552. In certain embodiments, the antibody or antigen-binding fragment that specifically binds to TL1A comprises: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:511; and (b) a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:510. In certain embodiments, the antibody binds to human TL1A with a stronger affinity or 2-fold stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody. In certain embodiments, the antibody or antigen-binding fragment comprises a Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544.In certain embodiments, the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to treat inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen-binding fragment is encoded by a nucleic acid. In certain embodiments, the cell comprises a nucleic acid. In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cell is a Chinese hamster ovary (CHO) cell. In certain embodiments, a method for treating an individual suffering from inflammatory bowel disease, Crohn's disease or colitis is described herein, comprising administering an effective amount of the antibody or antigen-binding fragment or pharmaceutical composition to the individual, wherein the individual is diagnosed as suffering from or suspected of suffering from inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen binding fragment or pharmaceutical composition is used to prevent or reduce interferon gamma secretion by T lymphocytes. In certain embodiments, described herein is a method for preventing or reducing the secretion of interferon gamma by T lymphocytes in an individual, comprising administering an effective amount of the antibody or antigen binding fragment or pharmaceutical composition to the individual. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising incubating cells containing nucleic acids encoding the antibody or antigen binding fragment in the culture medium under conditions sufficient to secrete the antibody or antigen binding fragment into the culture medium. In certain embodiments, the method further comprises subjecting the culture medium to at least one purification step. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising mixing the antibody or antigen binding fragment with a pharmaceutically acceptable excipient, carrier or diluent.

[0014] In another aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 555; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 566; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 572. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to that shown in SEQ ID NO: 545. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 546. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 547 or 586 to 588. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 548. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 549. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 550. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 551. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 552.In certain embodiments, the antibody or antigen-binding fragment comprises: (a) a human heavy chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 545; (b) a human heavy chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 546; (c) a human heavy chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 547 or 586 to 588; (d) a human heavy chain framework region 4 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 548; (e) a human light chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 549; (f) a human light chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 550; (g) a human light chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 551; NO:551 is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 3; and (h) is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 4 shown in SEQ ID NO:552. In certain embodiments, the antibody or antigen-binding fragment that specifically binds to TL1A comprises: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:493; and (b) a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:492. In certain embodiments, the antibody binds to human TL1A with a stronger affinity or 2-fold stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody. In certain embodiments, the antibody or antigen-binding fragment comprises a Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544.In certain embodiments, the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to treat inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen-binding fragment is encoded by a nucleic acid. In certain embodiments, the cell comprises a nucleic acid. In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cell is a Chinese hamster ovary (CHO) cell. In certain embodiments, a method for treating an individual suffering from inflammatory bowel disease, Crohn's disease or colitis is described herein, comprising administering an effective amount of the antibody or antigen-binding fragment or pharmaceutical composition to the individual, wherein the individual is diagnosed as suffering from or suspected of suffering from inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen binding fragment or pharmaceutical composition is used to prevent or reduce interferon gamma secretion by T lymphocytes. In certain embodiments, described herein is a method for preventing or reducing the secretion of interferon gamma by T lymphocytes in an individual, comprising administering an effective amount of the antibody or antigen binding fragment or pharmaceutical composition to the individual. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising incubating cells containing nucleic acids encoding the antibody or antigen binding fragment in the culture medium under conditions sufficient to secrete the antibody or antigen binding fragment into the culture medium. In certain embodiments, the method further comprises subjecting the culture medium to at least one purification step. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising mixing the antibody or antigen binding fragment with a pharmaceutically acceptable excipient, carrier or diluent.

[0015] In another aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 558; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 566; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 572. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to that shown in SEQ ID NO: 545. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 546. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 547 or 586 to 588. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 548. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 549. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 550. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 551. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 552.In certain embodiments, the antibody or antigen-binding fragment comprises: (a) a human heavy chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 545; (b) a human heavy chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 546; (c) a human heavy chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 547 or 586 to 588; (d) a human heavy chain framework region 4 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 548; (e) a human light chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 549; (f) a human light chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 550; (g) a human light chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 551; NO:551 is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 3; and (h) is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 4 shown in SEQ ID NO:552. In certain embodiments, the antibody or antigen-binding fragment that specifically binds to TL1A comprises: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:501; and (b) a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:500. In certain embodiments, the antibody binds to human TL1A with a stronger affinity or 2-fold stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody. In certain embodiments, the antibody or antigen-binding fragment comprises a Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544.In certain embodiments, the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to treat inflammatory bowel disease. In certain embodiments, the antibody or antigen-binding fragment is encoded by a nucleic acid. In certain embodiments, the cell comprises a nucleic acid. In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cell is a Chinese hamster ovary (CHO) cell. In certain embodiments, a method for treating an individual with inflammatory bowel disease, Crohn's disease or colitis is described herein, comprising administering an effective amount of the antibody or antigen-binding fragment or pharmaceutical composition to the individual, wherein the individual is diagnosed with or suspected of having inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to prevent or reduce interferon gamma secretion by T lymphocytes. In certain embodiments, described herein is a method for preventing or reducing the secretion of interferon gamma by T lymphocytes in an individual, comprising administering an effective amount of the antibody or antigen binding fragment or pharmaceutical composition to the individual. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising incubating cells containing nucleic acids encoding the antibody or antigen binding fragment in the culture medium under conditions sufficient to secrete the antibody or antigen binding fragment into the culture medium. In certain embodiments, the method further comprises subjecting the culture medium to at least one purification step. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising mixing the antibody or antigen binding fragment with a pharmaceutically acceptable excipient, carrier or diluent.

[0016] In another aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown in SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown in SEQ ID NO: 564; and (c) HCDR3 comprising the amino acid sequence shown in SEQ ID NO: 568; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown in SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown in SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown in SEQ ID NO: 572. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to that shown in SEQ ID NO: 545. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 546. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 547 or 586 to 588. In certain embodiments, the antibody or antigen-binding fragment comprises a human heavy chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 548. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 549. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 550. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 551. In certain embodiments, the antibody or antigen-binding fragment comprises a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98%, 99% identical to SEQ ID NO: 552.In certain embodiments, the antibody or antigen-binding fragment comprises: (a) a human heavy chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 545; (b) a human heavy chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 546; (c) a human heavy chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 547 or 586 to 588; (d) a human heavy chain framework region 4 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 548; (e) a human light chain framework region 1 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 549; (f) a human light chain framework region 2 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 550; (g) a human light chain framework region 3 at least 90%, 95%, 97% or 98% identical to SEQ ID NO: 551; NO:551 is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 3; and (h) is at least 90%, 95%, 97% or 98% identical to the human light chain framework region 4 shown in SEQ ID NO:552. In certain embodiments, the antibody or antigen-binding fragment that specifically binds to TL1A comprises: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:515; and (b) a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO:514. In certain embodiments, the antibody binds to human TL1A with a stronger affinity or 2-fold stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody. In certain embodiments, the antibody or antigen-binding fragment comprises a Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544.In certain embodiments, the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration. In certain embodiments, the antibody or antigen-binding fragment or pharmaceutical composition is used to treat inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen-binding fragment is encoded by a nucleic acid. In certain embodiments, the cell comprises a nucleic acid. In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cell is a Chinese hamster ovary (CHO) cell. In certain embodiments, a method for treating an individual suffering from inflammatory bowel disease, Crohn's disease or colitis is described herein, comprising administering an effective amount of the antibody or antigen-binding fragment or pharmaceutical composition to the individual, wherein the individual is diagnosed as suffering from or suspected of suffering from inflammatory bowel disease, Crohn's disease or colitis. In certain embodiments, the antibody or antigen binding fragment or pharmaceutical composition is used to prevent or reduce interferon gamma secretion by T lymphocytes. In certain embodiments, described herein is a method for preventing or reducing the secretion of interferon gamma by T lymphocytes in an individual, comprising administering an effective amount of the antibody or antigen binding fragment or pharmaceutical composition to the individual. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising incubating cells containing nucleic acids encoding the antibody or antigen binding fragment in the culture medium under conditions sufficient to secrete the antibody or antigen binding fragment into the culture medium. In certain embodiments, the method further comprises subjecting the culture medium to at least one purification step. In certain embodiments, described herein is a method for preparing for the treatment of inflammatory bowel disease, Crohn's disease or colitis, comprising mixing the antibody or antigen binding fragment with a pharmaceutically acceptable excipient, carrier or diluent.

[0017] In another aspect, provided herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: (a) a heavy chain variable region comprising HCDR1, HCDR2 and HCDR3 from any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; and (b) a light chain variable region comprising HCDR1, HCDR2 and HCDR3 from any one of SEQ ID NO: NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540; wherein the CDRs are defined by the Kabat, Chothia or IMGT methods or a combination thereof. In certain embodiments, the antibody or antigen-binding fragment that specifically binds to TL1A comprises: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; and (b) a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to any one of SEQ ID NO: NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540. In certain embodiments, the antibody binds to human TL1A with a stronger affinity or 2-fold stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises a heavy chain variable region amino acid sequence set forth in SEQ ID NO:491 and a light chain variable region amino acid sequence set forth in SEQ ID NO:490. In certain embodiments, the antibody or antigen-binding fragment is chimeric or humanized. In certain embodiments, the antibody or antigen-binding fragment is an IgG antibody.In certain embodiments, the antibody or antigen-binding fragment comprises Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody.In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising an amino acid sequence as shown in SEQ ID NO: 542 or 543. In certain embodiments, the antibody or antigen-binding fragment comprises a heavy chain constant region comprising an amino acid sequence as shown in SEQ ID NO: 542. In certain embodiments, the antibody or antigen-binding fragment comprises a light chain constant region comprising an amino acid sequence as shown in SEQ ID NO: 544. In certain embodiments, the antibody or antigen-binding fragment is a component of a pharmaceutical composition comprising the antibody or antigen-binding fragment and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the pharmaceutical composition is formulated for intravenous administration.

[0018] On the other hand, described herein is a method for treating a disease or condition in an individual with a risk variant associated with the disease or condition, the method comprising administering an effective amount of an antibody or antigen-binding fragment of the present disclosure to an individual with a risk variant, wherein the disease or condition includes at least one of inflammatory bowel disease (IBD), Crohn's disease (CD), or colitis. In certain embodiments, the individual has multiple risk variants. In certain embodiments, the multiple risk variants are at least 3, 4, 5, or 10 risk variants. In certain embodiments, the risk variants of the multiple risk variants are associated with a subclinical phenotype of the disease or condition. In certain embodiments, the disease or condition is a severe form of at least one of IBD, CD, or colitis. BRIEF DESCRIPTION OF THE DRAWINGS

[0019] Exemplary embodiments are described in reference to the accompanying drawings. The embodiments and drawings disclosed herein are intended to be considered illustrative rather than restrictive.

[0020] Figure 1 Depicted are the results of a filter lift-off assay performed as a qualitative assessment of chimeric 5C3D11 Fab expression and antigen binding. Part A of the filter shows expression of the heavy chain 5C3D11, part B of the filter shows expression of the light chain 5C3D11, and part C of the filter shows binding of 5C3D11 Fab to human TL1A antigen.

[0021] Figure 2 Depicted are the binding of chimeric 5C3D11 and humanized clone 12835 antibodies to human TL1A by enzyme-linked immunosorbent assay (ELISA).

[0022] Figure 3 Depicted are the results of a capture filter lift assay demonstrating high sensitivity and high binding strength of chimeric 5C3D11 to human TL1A.

[0023] Figure 4ADepicted are the results of an ELISA showing binding of CDR-grafted antibody clones 18-7, 21-3 and humanized clone 12835 to human TL1A.

[0024] Figure 4B Depicted are the results of an ELISA showing binding of the CDR-grafted antibody clone L8 to human TL1A compared to binding of the humanized clone 12835 to human TL1A.

[0025] Figure 5 Depicted are the results of an ELISA demonstrating strong binding of immobilized Fabs (chimeric 5C3D11, humanized clone 12835, clone 18-7, clone 21-3, and CDR-grafted clone L8) to soluble human TL1A antigen.

[0026] Fig. 6A Depicted are the results of an ELISA demonstrating that anti-TL1A antibodies H3-7(V102M)-SEQ ID NOs:44, 38, H3-7(V102K)-SEQ ID NOs:43, 38, and H3-7(V102Q)-SEQ ID NOs:45, 38 and humanized clone 12835 with heavy chain CDR3 mutations have increased affinity to human TL1A compared to the CDR graft (clone L8).

[0027] Figure 6B Depicted are the results of an ELISA demonstrating increased affinity of anti-TL1A antibodies H3-7(V102W)-SEQ ID NO: 46, 38 and humanized clone 12835 with heavy chain CDR3 mutations to human TL1A compared to CDR-grafted clone L8.

[0028] Fig. 7A Depicted are the results of an ELISA demonstrating that anti-TL1A antibodies L3-4(S92D)—SEQ ID NOs: 47, 40, L3-4(S92E)—SEQ ID NOs: 48, 40, L3-4(S92H)—SEQ ID NOs: 49, 40, L3-4(S92N)—SEQ ID NOs: 50, 40, and humanized clone 12835 with light chain CDR3 mutations have increased affinity to human TL1A compared to CDR-grafted clone L8.

[0029] Figure 7B Depicted are the results of an ELISA demonstrating increased affinity of anti-TL1A antibodies L3-4(S92Q)-SEQ ID NO:51, 40 and humanized clone 12835 with light chain CDR3 mutations to human TL1A compared to CDR-grafted clone L8.

[0030] Fig. 8A , 8B and 8C depict an ELISA demonstrating binding of Fabs comprising 5C3D11 CDR variants grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01 to immobilized human TL1A.

[0031] Fig. 9A and 9B Depicted is an ELISA demonstrating binding of Fabs comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-3*01 and human light chain germline IGKV3-20*01 to immobilized human TL1A.

[0032] Fig. 10A and 10B Depicted is an ELISA demonstrating binding of immobilized Fabs comprising 5C3D11 CDR variants grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01 to soluble biotinylated human TL1A.

[0033] Fig.11A and 11B Depicted is an ELISA demonstrating binding of immobilized Fabs comprising 5C3D11 CDR variants grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01 to soluble biotinylated human TL1A.

[0034] Fig. 12A and 12B Depicted is an ELISA demonstrating binding of immobilized Fabs comprising 5C3D11 CDR variants grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01 to soluble biotinylated human TL1A.

[0035] Fig.13A and 13B Depicted is an ELISA demonstrating binding of immobilized Fabs comprising 5C3D11 CDR variants grafted onto human heavy chain germline IGH1-3*01 and human light chain germline IGKV3-20*01 to soluble biotinylated human TL1A.

[0036] Fig.14A and 14B Binding of Fabs comprising the 5C3D11 CDR variants to membrane-associated human TL1A was demonstrated.

[0037] Fig.15A and 15BDepicted is the lack of binding to TRAIL of a Fab comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01.

[0038] Fig.16A and 16B Depicted is the lack of binding to LIGHT of a Fab comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01.

[0039] Fig.17A and 17B Depicted is the lack of binding to Fas of a Fab comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01.

[0040] Fig.18 Depicted is the lack of binding to TRAIL of a Fab comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-3*01 and human light chain germline IGKV3-20*01.

[0041] Fig.19 Depicted is the lack of binding to LIGHT of a Fab comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-3*01 and human light chain germline IGKV3-20*01.

[0042] Fig. 20 Depicted is the lack of binding to Fas of a Fab comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-3*01 and human light chain germline IGKV3-20*01.

[0043] Fig.21A and 21B Depicted are ELISAs demonstrating binding of heavy and light chain variable regions comprising 5C3D11 CDR variants with IgG1 heavy chain (modified) and kappa light chain constant regions (21A) or with IgG2 heavy chain and kappa light chain constant regions (21B) to immobilized human TL1A.

[0044] Fig.22A and 22B Depicted are ELISAs demonstrating binding of soluble biotinylated human TL1A to immobilized heavy and light chain variable regions comprising 5C3D11 CDR variants with IgG1 heavy chain (modified) and kappa light chain constant regions (22A) or with IgG2 heavy chain and kappa light chain constant regions (22B).

[0045] Fig.23Maintenance of binding of heavy and light chain variable regions comprising 5C3D11 CDR variants with either IgG1 heavy chain (modified) and kappa light chain constant regions or with IgG2 heavy chain and kappa light chain constant regions to a membrane associated form of human TL1A was demonstrated.

[0046] Fig.24A , 24B and 24C depict ELISAs demonstrating lack of binding of heavy and light chain variable regions comprising 5C3D11 CDR variants with IgG1 heavy chain (modified) and kappa light chain constant regions or with IgG2 heavy chain and kappa light chain constant regions to TNFSF family members Fas (24A), TRAIL (24B), or LIGHT (24C).

[0047] Fig.25 Inhibition of TL1A-induced IFN-γ production in whole blood of cynomolgus monkeys was demonstrated by a humanized Ig construct comprising the 5C3D11 CDR variant grafted onto human heavy chain germline IGH1-46*02 and human light chain germline IGKV3-20*01, with IgG1 heavy chain (modified) and kappa light chain constant regions.

[0048] Fig.26A , 26B and 26C show that the antibodies described herein inhibit TL1A-induced IFN-γ production from human whole blood. Results from 3 different donors (26A), (26B) and (26C) are shown, with antibody concentration (nanomolar) indicated on the x-axis.

[0049] Fig.27A , 27B and 27C show that the antibodies described herein inhibit TL1A-induced IFN-γ production from cynomolgus monkey whole blood. Results from 3 different donors (27A), (27B) and (27C) are shown, with antibody concentration (nanomolar) indicated on the x-axis. DETAILED DESCRIPTION

[0050] Tumor necrosis factor-like protein 1A (TL1A) is associated with the development and severity of severe inflammatory bowel disease (IBD), including severe forms of colitis and Crohn's disease (CD). In addition, preclinical and human genetic association data suggest that TL1A is a potential therapeutic target for Crohn's disease. The present disclosure describes optimized antibodies against TL1A and provides novel therapeutic agents for the treatment of IBD.

[0051] In one aspect, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by any one of SEQ ID NOs: 554 to 564 or 574 to 577; and (c) HCDR3 comprising the amino acid sequence shown by any one of SEQ ID NOs: 565 to 568 or 578 to 581; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by any one of SEQ ID NOs: 569 or 570; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by any one of SEQ ID NOs: 571 to 573 or 582 to 585.

[0052] In another aspect, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, or 541; and (b) a light chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, or 541; any one of NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540 has at least about 90% identical amino acid sequence.

[0053] In some embodiments, an antibody refers to an immunoglobulin molecule that recognizes and specifically binds to a target such as a protein, polypeptide, peptide, carbohydrate, polynucleotide, lipid, or a combination of the foregoing through at least one antigen recognition site in the variable region of the immunoglobulin molecule. In some embodiments, antibodies include complete polyclonal antibodies, complete monoclonal antibodies, antibody fragments (such as Fab, Fab', F(ab')2, and Fv fragments), single-chain Fv (scFv) mutants, CDR-grafted antibodies, multispecific antibodies, chimeric antibodies, humanized antibodies, human antibodies, fusion proteins comprising antigenic determinants of antibodies, and any other modified immunoglobulin molecules comprising antigen recognition sites, as long as the antibody exhibits the desired biological activity. Antibodies can be any of the five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, or their subclasses (isotypes) (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2), which are referred to as α, δ, ε, γ, and μ, respectively, based on the identity of their heavy chain constant domains. Different classes of immunoglobulins have different and well-known subunit structures and three-dimensional configurations. Antibodies can be naked or conjugated to other molecules such as toxins, radioisotopes, etc.

[0054] In some embodiments, one or more amino acid modifications can be introduced into the Fc region of the antibody provided herein, thereby producing Fc region variants. The Fc region herein is the C-terminal region of the immunoglobulin heavy chain comprising at least a portion of the constant region. The Fc region includes a native sequence Fc region and a variant Fc region. The Fc region variant may be included in a human Fc region sequence (e.g., human IgG1, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g., replacement) at one or more amino acid positions.

[0055] In some embodiments, the antibodies of the present disclosure have reduced antibody-dependent cell-mediated cytotoxicity (ADCC) or reduced ability to fix complement. This is ideal in the case of needing to inhibit the target function, but the activation of the downstream immune response may produce undesirable side effects. Some Fc regions naturally lack effector functions (e.g., IgG2, SEQ ID NO: 543), and some Fc regions may include mutations that reduce effector functions (e.g., modified IgG1, SEQ ID NO: 542). In certain embodiments, the antibodies of the present disclosure have reduced effector functions. In certain embodiments, the antibodies of the present disclosure include IgG2 constant regions as shown in SEQ ID NO: 543. In certain embodiments, the antibodies of the present disclosure include modified IgG1 constant regions as shown in SEQ ID NO: 542.

[0056] In some embodiments, the antibodies of the present disclosure are variants with some but not all effector functions, making them ideal candidates for applications where the in vivo half-life of the antibody is critical but certain effector functions (such as complement and ADCC) are non-essential or detrimental. In vitro and / or in vivo cytotoxicity assays can be performed to confirm reduction / depletion of CDC and / or ADCC activity. For example, Fc receptor (FcR) binding assays can be performed to ensure that the antibody lacks FcγR binding (and therefore may lack ADCC activity), but retains FcRn binding ability. Non-limiting examples of in vitro assays used to assess ADCC activity of a molecule of interest are described in U.S. Patents 5,500,362 and 5,821,337. Alternatively, non-radioactive assays (e.g., ACTI TM and CytoTox Non-radioactive cytotoxicity assays). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMCs), monocytes, macrophages, and natural killer (NK) cells.

[0057] The antibody may have increased half-life and / or improved binding to the neonatal Fc receptor (FcRn) (see, e.g., US 2005 / 0014934). Such antibodies may comprise an Fc region having one or more substitutions therein that improve binding of the Fc region to FcRn, and include antibodies having substitutions at one or more of the following Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, ​​413, 424 or 434, according to the EU numbering system (see, e.g., U.S. Pat. No. 7,371,826). Other examples of Fc region variants are also contemplated (see, e.g., Duncan & Winter, Nature 322: 738-40 (1988); U.S. Patents 5,648,260 and 5,624,821; and WO94 / 29351). In certain embodiments, the antibodies of the present disclosure have increased serum half-life due to changes in the Fc region. In certain embodiments, the changes include M252Y / S254T / T256E mutations for IgG1, or M428L / N434S mutations for IgG1.

[0058] In some embodiments, the antibody comprises an antigen binding fragment, which refers to an antibody portion having an antigen-determining variable region of the antibody. Examples of antibody fragments include, but are not limited to, Fab, Fab', F(ab')2 and Fv fragments, linear antibodies, single-chain antibodies, and multispecific antibodies formed from antibody fragments.

[0059] In some embodiments, humanized antibody refers to a form of non-human (e.g., mouse) antibody with a specific immunoglobulin chain, chimeric immunoglobulin or its fragment, which contains minimal non-human (e.g., mouse) sequences. In non-limiting examples, humanized antibodies contain less than about 40% non-human sequences in the variable region. In some cases, humanized antibodies contain less than about 20% non-human sequences in the full-length antibody sequence. In some cases, humanized antibodies are such human immunoglobulins, wherein the residues from the complementary determining region (CDR) are replaced by the residues of the CDR from non-human species (e.g., mouse, rat, rabbit, hamster) with the desired specificity, affinity and ability.

[0060] In some embodiments, a chimeric antibody refers to an antibody in which the sequence of the immunoglobulin molecule is derived from two or more species. As a non-limiting example, the variable regions of the light and heavy chains correspond to the variable regions of antibodies derived from one mammalian species (e.g., mouse, rat, rabbit, etc.) with the desired specificity, affinity, and capacity, while the constant regions are homologous to sequences in antibodies derived from another species (usually humans) to avoid eliciting an immune response in that species.

[0061] As used herein, the term "about" means within 10% of the stated amount.

[0062] As used herein, "risk variant" refers to any genetic sequence of an individual, typically a DNA sequence, that increases the risk of an individual developing a phenotype (e.g., inflammatory bowel disease, Crohn's disease, colitis, or a subclinical phenotype thereof). Risk variants include, but are not limited to, single nucleotide polymorphisms (SNPs), insertions and deletions of any length, short tandem repeats (STRs), and chromosomal translocations, duplications, or deletions. The risk variants include those associated with severe forms of inflammatory bowel disease, Crohn's disease, or colitis. The risk variants include those that may indicate that an individual may be refractory to any current therapy for inflammatory bowel disease, Crohn's disease, or colitis. As contemplated herein, risk variants can be used to inform treatment decisions using any of the antibodies described herein.

[0063] The terms "complementarity determining region" and "CDR", which are synonymous with "hypervariable region" or "HVR", are known in the art and refer to non-contiguous amino acid sequences within the variable region of an antibody that confer antigen specificity and / or binding affinity. Typically, there are three CDRs (CDR-H1, CDR-H2, CDR-H3) in each heavy chain variable region, and three CDRs (CDR-L1, CDR-L2, CDR-L3) in each light chain variable region. "Framework region" and "FR" are known in the art and refer to the non-CDR portions of the variable regions of the heavy and light chains. Typically, there are four FRs (FR-H1, FR-H2, FR-H3, and FR-H4) in each full-length heavy chain variable region, and four FRs (FR-L1, FR-L2, FR-L3, and FR-L4) in each full-length light chain variable region.The precise amino acid sequence boundaries of a given CDR or FR can be readily determined using any of a number of well-known schemes, including those described in Kabat et al. (1991), "Sequences of Proteins of Immunological Interest," 5th ed. Public Health Service, National Institutes of Health, Bethesda, MD ("Kabat" numbering scheme), Al-Lazikani et al., (1997) JMB 273, 927-948 ("Chothia" numbering scheme); MacCallum et al., J. Mol. Biol. 262:732-745 (1996), "Antibody-antigen interactions: Contact analysis and binding site topography," J. Mol. Biol. 262, 732-745. ("Contact" numbering scheme); Lefranc MP et al., "IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains," Dev Comp Immunol, 2003 Jan;27(1):55-77 ("IMGT" numbering scheme); Honegger A and Plückthun A, "Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool," J Mol Biol, 2001 Jun 8;309(3):657-70 ("Aho" numbering scheme); and Whitelegg NR and Rees AR, "WAM: an improved algorithm for modelling antibodies on the WEB," Protein Eng. 2000 Dec;13(12):819-24 ("AbM" numbering scheme). In certain embodiments, the CDRs of the antibodies described herein can be defined by a method selected from Kabat, Chothia, IMGT, Aho, AbM, or a combination thereof.

[0064] In some embodiments, an antibody that specifically binds to a protein means that the antibody reacts or associates with the protein more frequently, more rapidly, for a longer period of time, with a higher affinity, or some combination of the foregoing, than with alternative substances, including unrelated proteins.

[0065] In some embodiments, the terms "polypeptide", "peptide" and "protein" are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may contain modified amino acids, and it may be interrupted by non-amino acids. These terms also include amino acid polymers modified naturally or by intervention; for example, by disulfide bond formation, glycosylation, esterification, acetylation, phosphorylation, or any other manipulation or modification, such as fusion and / or conjugation with another polypeptide, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more amino acid analogs (e.g., non-natural amino acids, etc.), as well as other modifications known in the art.

[0066] In some embodiments, "polynucleotide" or "nucleic acid" used interchangeably herein refers to nucleotide polymers of any length, and includes DNA and RNA. Nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases and / or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase. Polynucleotides can include modified nucleotides, such as but not limited to methylated nucleotides and their analogs or non-nucleotide components. Modifications to the nucleotide structure can be imparted before or after polymer assembly. Polynucleotides can be further modified after polymerization, for example by conjugation with a labeling component.

[0067] The percentage of sequence identity (%) relative to a reference polypeptide sequence is the percentage of the amino acid residues in the candidate sequence that are identical to the amino acid residues in the reference polypeptide sequence after the sequences are aligned and, if necessary, spaces are introduced to achieve the maximum percentage of sequence identity, and any conservative substitution is not considered to be part of the sequence identity. The comparison intended to determine the percentage of amino acid sequence identity can be achieved in various known ways, such as using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Appropriate parameters for aligning sequences can be determined, including algorithms required for achieving maximum alignment over the full length of the compared sequences. However, for this article, the amino acid sequence identity percentage is generated using the sequence comparison computer program ALIGN-2. The ALIGN-2 sequence comparison computer program is developed by Genentech, Inc., and the source code has been submitted to the U.S. Copyright Office (Washington D.C., 20559) as a user document and registered with U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, Calif. and can also be compiled from source code. The ALIGN-2 program should be compiled for use on a UNIX operating system (including digital UNIX V4.0D). All sequence comparison parameters are set by the ALIGN-2 program and remain unchanged.

[0068] In the case of amino acid sequence comparison using ALIGN-2, the percentage of amino acid sequence identity of a given amino acid sequence A with or relative to a given amino acid sequence B (or may be represented by the following phrase: a given amino acid A has or comprises a certain percentage of amino acid sequence identity with or relative to a given amino acid sequence B) is calculated as follows: the fraction X / Y multiplied by 100, where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in the program's alignment of A and B, and where Y is the total number of amino acid residues in B. It should be understood that when the length of amino acid sequence A is not equal to the length of amino acid sequence B, the percentage of amino acid sequence identity of A to B will not be equal to the percentage of amino acid sequence identity of B to A. Unless specifically stated otherwise, all amino acid sequence identity percentage values ​​used herein are obtained as described in the preceding paragraph using the ALIGN-2 computer program.

[0069] In some embodiments, the terms "individual" or "subject" are used interchangeably and refer to any animal, including but not limited to humans, non-human primates, rodents, and domestic and game animals, which will be recipients of a specific treatment. Primates include chimpanzees, crab-eating monkeys, spider monkeys, and macaques, such as rhesus monkeys. Rodents include mice, rats, marmots, ferrets, rabbits, and hamsters. Domestic and game animals include cattle, horses, pigs, deer, bison, buffalo, feline species, such as house cats, canine species, such as dogs, foxes, wolves, avian species, such as chickens, emus, ostriches, and fish, such as trout, catfish, and salmon. In various embodiments, the subject may be a subject who has previously been diagnosed with or determined to have or have a condition that requires treatment. In certain embodiments, the subject is a human. In various other embodiments, a subject who has previously been diagnosed with or determined to have or have a condition may or may not have experienced treatment for the condition. In yet other embodiments, the subject may also be a subject who has not been previously diagnosed with a condition (i.e., a subject who exhibits one or more risk factors for a condition). A "subject in need of treatment for a particular condition" may be a subject who has the condition, has been diagnosed with the condition, or is at risk of developing the condition. In some embodiments, a subject is a "patient" who has been diagnosed with a disease or condition described herein.

[0070] In some embodiments, the term "therapeutically effective amount" refers to the amount of an antibody, polypeptide, polynucleotide, organic small molecule or other drug that effectively "treats" a disease or condition of a subject or mammal. In some cases, a therapeutically effective amount of a drug reduces the severity of the symptoms of a disease or condition. In some cases, the disease or condition includes inflammatory bowel disease (IBD), Crohn's disease (CD) or ulcerative colitis (UC). In some cases, the IBD, CD and / or UC are severe or medically refractory forms of IBD, CD and / or UC. Non-limiting examples of IBD, CD and / or UC symptoms include, but are not limited to, diarrhea, fever, fatigue, abdominal pain, abdominal cramps, inflammation, ulcers, nausea, vomiting, bleeding, blood in the stool, decreased appetite and weight loss.

[0071] In some embodiments, the terms "treat" or "treatment" as used herein refer to both therapeutic treatment and prophylactic or preventative measures, wherein the purpose is to prevent or slow down (mitigate) the target pathological condition, prevent the pathological condition, pursue or obtain a good overall survival rate, or reduce the chance of an individual developing the condition, even if the treatment is ultimately unsuccessful. In some aspects provided herein, subjects in need of treatment include subjects who already have a disease or condition, as well as subjects who are susceptible to the disease or condition or subjects in whom the disease or condition is to be prevented. The disease or condition may include an inflammatory disease or condition, a fibrostenotic disease or a fibrotic disease, thiopurine toxicity or a disease associated with thiopurine toxicity, unresponsiveness to anti-TNF therapy, steroids, or immunomodulators.

[0072] Anti-TL1A antibody

[0073] Various embodiments provide antibodies that bind to TL1A. In some embodiments, the antibodies specifically bind to soluble TL1A. In some embodiments, the antibodies specifically bind to membrane-bound TL1A. In some embodiments, an anti-TL1A antibody is provided, which has a heavy chain comprising four heavy chain framework regions (HCFRs) and three heavy chain complementary determining regions (HCDRs): HCFR1, HCDR1, HCFR2, HCDR2, HCFR3, HCDR3, and HCFR4; and a light chain comprising four light chain framework regions (LCFRs) and three light chain complementary determining regions (LCDRs): LCFR1, LCDR1, LCFR2, LCDR2, LCFR3, LCDR3, and LCFR4. The anti-TL1A antibody may comprise any region provided herein, for example, as provided in Tables 1, 2, 3, Examples, and SEQ ID NOs: 1 to 54, 490 to 588. In some embodiments, the anti-TL1A antibody comprises a variable domain, for example, as provided herein, having one or more CDR mutations as shown in Tables 2 or 19 to 22. In some embodiments, an anti-TL1A antibody comprises one or more CDRs comprising the sequences shown in Tables 19-22.

[0074] In certain embodiments, the anti-TL1A antibody comprises CDRs corresponding to those shown in Tables 19 to 22. In certain embodiments, the anti-TL1A antibody or antigen-binding fragment comprises: a heavy chain variable region comprising: (a) a HCDR1 comprising the amino acid sequence (DTYMH) set forth by SEQ ID NO: 484; (b) a HCDR2 comprising the amino acid sequence (PASGH) set forth by SEQ ID NO: 485; and (c) a HCDR3 comprising the amino acid sequence (SGGLPD) set forth by SEQ ID NO: 486; and a light chain variable region comprising: (d) a LCDR1 comprising the amino acid sequence (ASSSVSYMY) set forth by SEQ ID NO: 487; (e) a LCDR2 comprising the amino acid sequence (ATSNLAS) set forth by SEQ ID NO: 488; and (f) a LCDR3 comprising the amino acid sequence (GNPRT) set forth by SEQ ID NO: 489.

[0075] In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by any one of SEQ ID NO: 554 to 564 or 574 to 577; and (c) HCDR3 comprising the amino acid sequence shown by any one of SEQ ID NO: 565 to 568 or 578 to 581; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by any one of SEQ ID NO: 569 or 570; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by any one of SEQ ID NO: 571 to 573 or 582 to 585.

[0076] In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 559; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 567; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 573. In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 503; and a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 502. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG1 heavy chain constant region. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG2 heavy chain constant region.

[0077] In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 563; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 568; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 572. In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 511; and a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 510. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG1 heavy chain constant region. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG2 heavy chain constant region.

[0078] In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 555; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 566; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 572. In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 493; and a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 492. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG1 heavy chain constant region. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG2 heavy chain constant region.

[0079] In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 558; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 566; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 572. In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 501; and a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 500. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG1 heavy chain constant region. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG2 heavy chain constant region.

[0080] In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown by SEQ ID NO: 553; (b) HCDR2 comprising the amino acid sequence shown by SEQ ID NO: 564; and (c) HCDR3 comprising the amino acid sequence shown by SEQ ID NO: 568; and a light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown by SEQ ID NO: 569; (e) LCDR2 comprising the amino acid sequence shown by SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown by SEQ ID NO: 572. In certain embodiments, described herein is an antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 515; and a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 514. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG1 heavy chain constant region. In certain embodiments, the antibody or antigen-binding fragment comprises a kappa light chain constant region and an IgG2 heavy chain constant region.

[0081] In certain embodiments, the anti-TL1A antibody or antigen-binding fragment comprises: a heavy chain variable region comprising HCDR1, HCDR2 and HCDR3 from any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; and a light chain variable region comprising HCDR1, HCDR2 and HCDR3 from any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540, wherein the CDRs are defined by the Kabat method, the IMGT method, the Chothia method or a combination thereof. In certain embodiments, the anti-TL1A antibody or antigen-binding fragment comprises: a heavy chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; and a light chain variable region comprising an amino acid sequence that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to any one of SEQ ID NO: any of NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540 that is at least about 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to an amino acid sequence.

[0082] In certain embodiments, the anti-TL1A antibody or antigen-binding fragment comprises: a heavy chain variable region comprising: (a) a human heavy chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 545; (b) a HCDR1 comprising the amino acid sequence (DTYMH) set forth in SEQ ID NO: 484; (c) a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 546; (d) a HCDR2 comprising the amino acid sequence (PASGH) set forth in SEQ ID NO: 485; (e) a human heavy chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 547 or 586 to 588; (f) a HCDR3 comprising the amino acid sequence (SGGLPD) set forth in SEQ ID NO: 486; and (g) a human heavy chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 547 or 586 to 588. NO:548 is at least 90%, 95%, 96%, 97%, 98% or 99% identical to the human heavy chain framework region 4; and a light chain variable region, which comprises: (h) a human light chain framework region 1 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO:549; (i) a LCDR1 comprising the amino acid sequence (ASSSVSYMY) shown by SEQ ID NO:487; (j) a human light chain framework region 2 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO:550; (k) a LCDR2 comprising the amino acid sequence (ATSNLAS) shown by SEQ ID NO:488; (l) a human light chain framework region 3 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO:551; (m) a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO:552; LCDR3 of the amino acid sequence (GNPRT) shown in NO:489; and (n) a human light chain framework region 4 that is at least 90%, 95%, 96%, 97%, 98% or 99% identical to that shown in SEQ ID NO:552.

[0083] Table 1. Exemplary anti-TL1A antibodies

[0084]

[0085]

[0086] Table 2. Exemplary anti-TL1A CDR sequences

[0087]

[0088]

[0089] In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 3, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 6. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 26, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 28. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 36, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 38. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 40, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 42. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with the region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO:40 and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO:38.In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 503, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 502. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 511, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 510. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 493, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 492. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with a region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 501, and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO: 500. In various embodiments, the anti-TL1A antibody specifically binds to the same region of TL1A, or specifically binds to a region of TL1A that overlaps with the region of TL1A specifically bound by an antibody comprising a heavy chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO:515 and a light chain comprising a sequence at least about 90%, 92%, 95%, 98%, or 100% identical to SEQ ID NO:514.

[0090] In various embodiments, the anti-TL1A antibody or fragment has a binding affinity for TL1A of at least about 1E -7 , 1E -8 , 1E -9 , 1E -10 or 1E -11In some cases, the binding affinity is about 1E -9 to about 1E -11 .

[0091] Various embodiments provide anti-TL1A antibodies that bind to the same region of a TL1A protein or portion thereof as a reference antibody, such as any anti-TL1A antibody described herein. In some embodiments, the reference antibody comprises the heavy chain CDRs of SEQ ID NOs: 150, 12, and 152 and the light chain CDRs of SEQ ID NOs: 18, 21, and 155.

[0092] Non-limiting methods for determining whether an anti-TL1A antibody (i.e., a test antibody) binds to the same region of a TL1A protein or a portion thereof as an antibody described herein are provided. Exemplary embodiments include competition assays. For example, the methods include determining whether a test antibody can compete for binding between a reference antibody and a TL1A protein or a portion thereof, or determining whether a reference antibody can compete for binding between a test antibody and a TL1A protein or a portion thereof. Exemplary methods include using surface plasmon resonance to evaluate whether an anti-TL1A antibody can compete for binding between TL1A and another anti-TL1A antibody. In some cases, surface plasmon resonance is utilized in the competition assay. Non-limiting methods are described in the Examples.

[0093] The TL1A antibodies described herein bind to specific regions or epitopes of human TL1A. It is demonstrated herein that these regions can be used to inhibit the secretion of interferon gamma from T lymphocytes. In certain embodiments, antibodies that compete with the antibodies described herein for binding to TL1A are disclosed herein. In certain embodiments, antibodies that bind to the same epitope of TL1A as the antibodies described herein are disclosed herein. In certain embodiments, antibodies that bind to a discrete epitope of TL1A that overlaps with the epitope of TL1A bound by the antibodies described herein are disclosed herein. In certain embodiments, antibodies that bind to the same epitope of TL1A, overlap with an epitope of TL1A by one or more amino acid residues, or compete for binding to an epitope of TL1A with the following antibodies or fragments thereof: the antibodies or fragments thereof comprise a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 503; and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 502. In certain embodiments, disclosed herein are antibodies that bind to the same epitope of TL1A, overlap one or more amino acid residues with an epitope of TL1A, or compete for binding to an epitope of TL1A with the following antibodies or fragments thereof: the antibodies or fragments thereof comprise a heavy chain variable region comprising an amino acid sequence of SEQ ID NO: 511; and a light chain variable region comprising an amino acid sequence of SEQ ID NO: 510. In certain embodiments, disclosed herein are antibodies that bind to the same epitope of TL1A, overlap one or more amino acid residues with an epitope of TL1A, or compete for binding to an epitope of TL1A with the following antibodies or fragments thereof: the antibodies or fragments thereof comprise a heavy chain variable region comprising an amino acid sequence of SEQ ID NO: 493; and a light chain variable region comprising an amino acid sequence of SEQ ID NO: 492. In certain embodiments, disclosed herein are antibodies that bind to the same epitope of TL1A, overlap one or more amino acid residues with an epitope of TL1A, or compete for binding to an epitope of TL1A with the following antibodies or fragments thereof: the antibodies or fragments thereof comprise a heavy chain variable region comprising an amino acid sequence of SEQ ID NO: 501; and a light chain variable region comprising an amino acid sequence of SEQ ID NO: 500. In certain embodiments, disclosed herein are antibodies that bind to the same epitope of TL1A, overlap one or more amino acid residues with an epitope of TL1A, or compete for binding to an epitope of TL1A with the following antibodies or fragments thereof: the antibodies or fragments thereof comprise an amino acid sequence of SEQ ID NO: 515; and a light chain variable region comprising an amino acid sequence of SEQ ID NO: 514.

[0094] Methods of producing antibodies

[0095] Various embodiments provide antibodies generated using polypeptide or nucleotide sequences. In some embodiments, the antibody is a monoclonal antibody. In some embodiments, the antibody is a human antibody or a humanized antibody. In some embodiments, the antibody is an antibody fragment. For example, the antibody is a Fab, scFv or (Fab)2. In some embodiments, the antibody is a chimeric antibody.

[0096] The specific binding of antibodies described herein can be determined by any method known in the art. The immunoassays that can be used include, but are not limited to, competitive and non-competitive assay systems using technologies such as BIAcore analysis, FACS analysis, immunofluorescence, immunocytochemistry, Western blotting, radioimmunoassay, ELISA, "sandwich" immunoassay, immunoprecipitation assay, precipitation reaction, gel diffusion precipitation reaction, immunodiffusion assay, agglutination assay, complement fixation assay, immunoradiometric assay, fluorescent immunoassay, and protein A immunoassay. Such assays are provided, for example, in Ausubel et al., 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York.

[0097] In various embodiments, the anti-TL1A antibody is an antagonist of a TL1A receptor, such as, but not limited to, DR3 and TR6 / DcR3. In certain embodiments, the antibody inhibits at least about 10%, at least about 20%, at least about 30%, at least about 50%, at least about 75%, at least about 90%, or about 100% of one or more activities of the bound TL1A receptor. In certain embodiments, the antibody inhibits TL1A activation as measured by interferon gamma release in human blood. In certain embodiments, the antibody has an IC of about 1 nanomolar to about 100 picomolar. 50 Inhibits the release of interferon gamma in human blood. In certain embodiments, the antibody has an IC of about 500 picomolar to about 100 picomolar 50 Inhibits the release of interferon gamma in human blood. In certain embodiments, the antibody has an IC of about 500 picomolar 50 Inhibits the release of interferon gamma in human blood. In certain embodiments, the antibody has an IC of about 250 picomolar 50 Inhibits the release of interferon-γ in human blood.

[0098] In various embodiments, monoclonal antibodies are prepared using methods known in the art, such as, but not limited to, the hybridoma method, in which a host animal is immunized as described above to elicit lymphocytes to produce antibodies that specifically bind to the immunizing antigen (Kohler and Milstein (1975) Nature 256:495). The hybridoma produces monoclonal antibodies specific for the selected antigen. When propagated in vitro or in vivo, the monoclonal antibodies are purified from the culture medium or ascites by techniques known in the art.

[0099] In some embodiments, monoclonal antibodies are prepared using a recombinant DNA method as described in U.S. Patent No. 4,816,567. Polynucleotides encoding monoclonal antibodies are isolated from mature B cells or hybridoma cells. The polynucleotides encoding the heavy and light chains of the separation are then cloned into a suitable expression vector, which generates monoclonal antibodies when being transfected into a host cell (e.g., Escherichia coli cells, simian COS cells, Chinese hamster ovary (CHO) cells or myeloma cells). Recombinant DNA techniques can be used to further modify the polynucleotides encoding monoclonal antibodies in a variety of different ways to generate alternative antibodies.

[0100] In various embodiments, chimeric antibodies, i.e., molecules in which different portions are derived from different animal species, such as those having variable regions derived from mouse monoclonal antibodies and human immunoglobulin constant regions (e.g., humanized antibodies), can be generated. Chimeric antibodies can be produced using a variety of techniques, such as Morrison et al., Proc. Natl. Acad. Sci. 81: 851-855 (1984); Neuberger et al., Nature 312: 604-608 (1984); Takeda et al., Nature 314: 452-454 (1985).

[0101] In some embodiments, the anti-TL1A monoclonal antibody is a humanized antibody to reduce antigenicity and HAMA (human anti-mouse antibody) response when administered to a human subject. Humanized antibodies can be produced using a variety of techniques known in the art. For example, antibodies are humanized by the following steps: (1) determining the nucleotide and predicted amino acid sequences of the starting antibody light chain and heavy chain variable domains; (2) designing the humanized antibody, for example, determining which antibody framework region to use in the humanization process; (3) actual humanization methods / techniques; and (4) transfection and expression of the humanized antibody (see, e.g., U.S. Patents 5,585,089; 6,835,823; 6,824,989). In various embodiments, the humanized antibody can be further optimized to reduce potential immunogenicity while maintaining functional activity for use in human therapy.

[0102] Humanized antibodies can also be prepared in transgenic mice containing human immunoglobulin loci that are capable of producing a full repertoire of human antibodies after immunization without producing endogenous immunoglobulins. This approach is described in U.S. Patents 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; and 5,661,016. Humanized antibodies can also be obtained by novel genetic engineering methods that can produce affinity-matured human-like polyclonal antibodies in large animals, such as rabbits and mice. (See, e.g., U.S. Patent 6,632,976).

[0103] A fully humanized antibody can be created by first designing a variable region amino acid sequence containing a non-human source, such as a rodent-derived CDR, embedded in a human framework sequence. Non-human CDRs provide the required specificity. Therefore, in some cases, these residues are substantially unchanged and included in the design of the reshaped variable region. Therefore, in some cases, modifications should be limited to a minimum, and close attention should be paid to changes in antibody specificity and affinity. On the other hand, in theory, framework residues can be derived from any human variable region. Human framework sequences should be selected, which are also suitable for creating reshaped variable regions and maintaining antibody affinity, so as to create reshaped antibodies that show acceptable or even improved affinity. The human framework can be of germline origin, or can be derived from a non-germline (e.g., mutated or affinity matured) sequence. Genetic engineering techniques well known to those skilled in the art, such as, but not limited to, phage display of human antibody libraries, transgenic mice, human-human hybridomas, hybrid hybridomas, B cell immortalization and cloning, single cell RT-PCR or HuRAb technology, can be used to generate humanized antibodies with hybrid DNA sequences comprising human frameworks and non-human CDRs. Methods for obtaining "humanized antibodies" are well known to those skilled in the art (e.g., U.S. Pat. No. 5,861,155, U.S. Pat. No. 6,479,284, U.S. Pat. No. 6,407,213, U.S. Pat. No. 5,624,821, US2003166871, US20020078757, Queen et al., Proc. Natl. Acad Sci USA, 86: 10029-10032 (1989) and Hodgson et al., Bio / Technology, 9: 421 (1991)).

[0104] In certain embodiments, the anti-TL1A antibody is a human antibody. Human antibodies can be directly prepared using a variety of techniques known in the art. Immortalized human B lymphocytes that produce antibodies against a target antigen can be generated by in vitro immunization or isolation from an immunized individual (see, e.g., Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985); Boerner et al., 1991, J. Immunol., 147 (1): 86-95; and U.S. Pat. No. 5,750,373). Human antibodies can be selected from phage libraries. Techniques for generating and using antibody phage libraries are described in U.S. Patents 5,969,108, 6,172,197, 5,885,793, 6,521,404; 6,544,731; 6,555,313; 6,582,915; 6,593,081; 6,300,064; 6,653,068; 6,706,484; and 7,264,963; and in Rothe et al., 2007, J. Mol. Bio., doi: 10.1016 / j.jmb.2007.12.018.

[0105] Chimeric, humanized and human antibodies can be produced by recombinant expression. Recombinant polynucleotide constructs generally include expression control sequences operably connected to the coding sequence of the antibody chain, including naturally associated or heterologous promoter regions. In certain embodiments, it may be desirable to generate amino acid sequence variants of these humanized antibodies, particularly in the case of these improved antibody binding affinity or other biological properties.

[0106] In certain embodiments, antibody fragments are used to treat and / or improve IBD. Various techniques for producing antibody fragments are known. Typically, these fragments are derived by proteolytic digestion of intact antibodies (e.g., Morimoto et al., 1993, Journal of Biochemical and Biophysical Methods 24: 107-117; Brennan et al., 1985, Science, 229: 81). Fab, Fv and scFv antibody fragments can all be expressed in Escherichia coli or other host cells and secreted therefrom, thereby allowing the production of a large number of these fragments. Other techniques for producing antibody fragments will be apparent to the skilled artisan.

[0107] In light of the present disclosure, techniques can be adapted to produce single chain antibodies specific for TL1A (see, e.g., U.S. Pat. No. 4,946,778). In addition, methods can be adapted to the construction of Fab expression libraries (see, e.g., Huse et al., Science 246: 1275-1281 (1989)) to allow for rapid and efficient identification of monoclonal Fab fragments or derivatives, fragments, analogs or homologs thereof having the desired specificity for TL1A. Antibody fragments can be produced by techniques in the art, including but not limited to: (a) F(ab')2 fragments produced by pepsin digestion of antibody molecules; (b) Fab fragments produced by reducing disulfide bonds of F(ab')2 fragments, (c) Fab fragments produced by treating antibody molecules with papain and a reducing agent, and (d) Fv fragments.

[0108] Also provided herein are modified antibodies comprising any type of variable region that provides for the association of the antibody with TL1A. One skilled in the art will appreciate that a modified antibody may comprise an antibody (e.g., a full-length antibody or an immunoreactive fragment thereof) in which at least a portion of one or more constant region domains has been deleted or otherwise altered to provide the desired biochemical properties, such as reduction of TL1A. In certain embodiments, the variable regions in both the heavy and light chains are altered by at least partially replacing one or more CDRs, and if necessary, by partial framework region replacement and sequence changes. In some embodiments, the replaced CDRs may be derived from antibodies of the same class, subclass, from antibodies of different classes, such as from antibodies from different species, and / or combinations thereof. In some embodiments, the constant region of the modified antibody will comprise a human constant region. Modifications of the constant region compatible with the present disclosure include additions, deletions, or substitutions of one or more amino acids in one or more domains.

[0109] In various embodiments, the expression of antibodies or antigen-binding fragments thereof as described herein can occur in prokaryotic or eukaryotic cells. Suitable hosts include bacterial or eukaryotic hosts, including yeast, insects, fungi, birds and mammalian cells in vivo or in situ, or host cells of mammalian, insect, bird or yeast origin. Mammalian cells or tissues can be human, primate, hamster, rabbit, rodent, cattle, pig, sheep, horse, goat, dog or cat origin, but any other mammalian cells can be used. In other embodiments, antibodies or antigenic fragments thereof as described herein can be transfected into a host.

[0110] In some embodiments, the expression vector is transfected into a recipient cell line to produce the chimeric, humanized or composite human antibodies described herein. In various embodiments, mammalian cells can be used as hosts for producing antibody proteins, which may include, but are not limited to, fibroblast-derived cells such as Vero (ATCC CRL 81) or CHO-K1 (ATCC CRL 61) cells, HeLa cells, and L cells. Exemplary eukaryotic cells that can be used to express polypeptides include, but are not limited to, COS cells, including COS7 cells; 293 cells, including 293-6E cells; CHO cells, including CHO-S and DG44 cells; PER.C6 TM In some embodiments, a particular eukaryotic host cell is selected based on its ability to perform the desired post-translational modification of the heavy chain and / or light chain.

[0111] Many suitable host cell lines capable of secreting intact heterologous proteins have been developed in the art, including but not limited to CHO cell lines, various COS cell lines, HeLa cells, L cells, and multiple myeloma cell lines.

[0112] Depending on the type of cell host, expression vectors carrying chimeric, humanized or composite human antibody constructs, antibodies or antigen-binding fragments thereof described herein can be introduced into suitable host cells by any of a variety of suitable means, including but not limited to transformation, transfection, lipofection, conjugation, electroporation, direct microinjection and microprojectile bombardment known to those of ordinary skill in the art. Expression vectors for these cells may contain expression control sequences, such as origins of replication, promoters, enhancers and necessary processing information sites, such as ribosome binding sites, RNA splicing sites, polyadenylation sites and transcription terminator sequences.

[0113] In various embodiments, yeast can also be used as a host for producing antibody molecules or peptides described herein. In various other embodiments, bacterial strains can also be used as hosts for producing antibody molecules or peptides described herein. Examples of bacterial strains include, but are not limited to, species of Escherichia coli, Bacillus, enterobacteria, and various Pseudomonas.

[0114] In some embodiments, one or more antibodies or their antigen-binding fragments as described herein can be produced in an animal body that has been engineered (transgenic) or transfected with one or more nucleic acid molecules encoding the polypeptide according to any suitable method. In order to produce transgenic animals, the transgene can be microinjected into a fertilized oocyte, or it can be introduced into the genome of an embryonic stem cell, and the nucleus of such cells can be transferred into an enucleated oocyte. Once expressed, the antibody can be purified according to standard procedures in the art, including HPLC purification, column chromatography, gel electrophoresis, etc. (generally referring to Scopes, Protein Purification (Springer-Verlag, NY, 1982)).

[0115] Once expressed in a host, the complete antibodies, antibody fragments (e.g., single light and heavy chains) or other immunoglobulin forms of the present disclosure can be recovered and purified by known techniques, such as immunoadsorption or immunoaffinity chromatography, chromatographic methods such as HPLC (high performance liquid chromatography), ammonium sulfate precipitation, gel electrophoresis, or any combination of these methods. See generally Scopes, PROTEIN PURIF. (Springer-Verlag, NY, 1982). Substantially pure immunoglobulins with at least about 90% to 95% homogeneity are advantageous, and those with 98% to 99% or higher homogeneity are also advantageous, especially for pharmaceutical use. Once partially purified or purified to the desired homogeneity, humanized antibodies or composite human antibodies can then be used therapeutically, or for developing and conducting assay procedures, immunofluorescence staining, etc. See generally Volumes I and II of Immunol. Meth. (Lefkovits & Pernis, Acad. Press, NY, 1979 and 1981).

[0116] Various embodiments provide genetic constructs comprising nucleic acids encoding the anti-TL1A antibodies or fragments provided herein. The genetic construct of the antibody can be in the form of an expression cassette, which can be suitable for expressing the encoded anti-TL1A antibody or fragment. The genetic construct can be introduced into a host cell with or without incorporation into a vector. For example, the genetic construct can be incorporated into a liposome or a viral particle. Alternatively, the purified nucleic acid molecule can be directly inserted into a host cell by methods known in the art. The genetic construct can be introduced directly into the cells of a host subject by transfection, infection, electroporation, cell fusion, protoplast fusion, microinjection, or ballistic bombardment.

[0117] Various embodiments provide a recombinant vector comprising a genetic construct of an antibody provided herein. The recombinant vector may be a plasmid, a cosmid or a phage. The recombinant vector may include other functional elements; for example, a suitable promoter to initiate gene expression.

[0118] Various embodiments provide host cells comprising the genetic constructs and / or recombinant vectors described herein.

[0119] Various host systems are also advantageously used to express recombinant proteins. Examples of suitable mammalian host cell lines include the COS-7 line of monkey kidney cells, and other cell lines capable of expressing appropriate vectors, including, for example, L cells, C127, 3T3, Chinese hamster ovary (CHO), HeLa, and BHK cell lines. Mammalian expression vectors may include non-transcribed elements, such as an origin of replication, a suitable promoter and enhancer connected to the gene to be expressed, and other 5' or 3' flanking non-transcribed sequences, and 5' or 3' non-translated sequences, such as necessary ribosome binding sites, polyadenylation sites, splice donor and acceptor sites, and transcription termination sequences.

[0120] The protein produced by the transformed host can be purified according to any suitable method. Such standard methods include chromatography (e.g., ion exchange chromatography, affinity chromatography and size column chromatography), centrifugation, differential solubility or by any other standard techniques for protein purification. Affinity tags such as hexa-histidine, maltose binding domain, influenza capsid sequence and glutathione-S-transferase can be attached to the protein to make it easy to purify by suitable affinity columns. The separated protein can also be physically characterized using techniques such as proteolysis, nuclear magnetic resonance and X-ray crystallography. The recombinant protein produced in bacterial culture can be separated. Methods known in the art for purifying antibodies and other proteins also include, for example, those described in U.S. Patent Publications 2008 / 0177048 and 2009 / 0187005.

[0121] The skilled person will recognize that individual substitutions, deletions or additions to nucleic acid, peptide, polypeptide or protein sequences to change one amino acid or a small portion of amino acids in the coding sequence are "conservatively modified variants" where the changes result in the replacement of an amino acid with a chemically similar amino acid and retain the ability to specifically bind to the target antigen. Such conservatively modified variants are in addition to polymorphic variants, interspecies homologs and alleles consistent with the present disclosure, and do not exclude them.

[0122] A given amino acid can be replaced with a residue having similar physicochemical properties, for example, replacing one aliphatic residue with another (e.g., He, Val, Leu, or Ala with each other), or replacing one polar residue with another (e.g., between Lys and Arg; between Glu and Asp; or between Gln and Asn). Other such conservative substitutions, such as substitutions of entire regions with similar hydrophobic properties, are well known. Polypeptides containing conservative amino acid substitutions can be tested in any of the assays described herein to confirm that the desired activity of the native or reference polypeptide, such as antigen binding activity and specificity, is retained.

[0123] Specific conservative substitutions include, for example: Ala is replaced by Gly or Ser; Arg is replaced by Lys; Asn is replaced by Gin or His; Asp is replaced by Glu; Cys is replaced by Ser; Gin is replaced by Asn; Glu is replaced by Asp; Gly is replaced by Ala or Pro; His is replaced by Asn or Gin; lie is replaced by Leu or Val; Leu is replaced by lie or Val; Lys is replaced by Arg, Gin or Glu; Met is replaced by Leu, Tyr or lie; Phe is replaced by Met, Leu or Tyr; Ser is replaced by Thr; Thr is replaced by Ser; Trp is replaced by Tyr; Tyr is replaced by Trp; and / or Phe is replaced by Val, lie or Leu.

[0124] In some embodiments, the antibodies and / or antigen-binding fragments thereof described herein may be variants of the sequences described herein, such as conservative substitution variants of antibody polypeptides. In some embodiments, the variant is a conservatively modified variant. A variant may refer to a polypeptide substantially homologous to a natural or reference polypeptide, but having an amino acid sequence different from the amino acid sequence of a natural or reference polypeptide due to one or more deletions, insertions or substitutions. The DNA sequence encoding a variant polypeptide includes a sequence that includes one or more additions, deletions or substitutions of nucleotides compared to a natural or reference DNA sequence, but encodes a variant protein or fragment thereof that retains an activity such as an antigen-specific binding activity for a related target polypeptide.

[0125] The change of the native amino acid sequence can be accomplished by any of a variety of techniques known to those skilled in the art. Mutations can be introduced at specific loci or by oligonucleotide-directed site-specific mutagenesis procedures. The techniques for making such changes are well established and include, for example, Walder et al. (Gene 42: 133, 1986); Bauer et al. (Gene 37: 73, 1985); Craik (BioTechniques, January 1985, 12-19); Smith et al. (Genetic Engineering: Principles and Methods, Plenum Press, 1981); and those disclosed in U.S. Pat. Nos. 4,518,584 and 4,737,462.

[0126] Nucleic acid molecules encoding amino acid sequence variants of antibodies are prepared by a variety of methods known in the art. These methods include, but are not limited to, preparing by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of previously prepared antibody variants or non-variant forms. The nucleic acid sequence encoding at least one antibody, part, or polypeptide described herein can be recombined with a vector DNA according to conventional techniques, including but not limited to blunt ends or staggered ends for connection and restriction enzyme digestion. The technology of such operations is disclosed in, for example, Maniatis et al., Molecular Cloning, Lab. Manual (Cold Spring Harbor Lab. Press, NY, 1982 and 1989), and can be used to construct nucleic acid sequences encoding monoclonal antibody molecules or antigen binding regions.

[0127] In some embodiments, the nucleic acid encoding the antibody or its antigen-binding fragment described herein is comprised by a vector. In some aspects described herein, the nucleic acid sequence encoding the antibody or its antigen-binding fragment described herein or any module thereof is operably connected to a vector. The term "vector" as used herein refers to a nucleic acid construct designed for delivery to a host cell or for transfer between different host cells. As used herein, a vector can be a viral vector or a non-viral vector. The term "vector" encompasses any genetic element that can replicate and can transfer a gene sequence to a cell when associated with an appropriate control element. A vector may include, but is not limited to, a cloning vector, an expression vector, a plasmid, a phage, a transposon, a cosmid, a chromosome, a virus, a virion, etc.

[0128] As used herein, the term "expression vector" refers to a vector that directs the expression of RNA or polypeptides from a sequence connected to a transcriptional regulatory sequence on a vector. The term "expression" refers to a cellular process involving the production of RNA and protein and secretion of proteins when appropriate, including but not limited to, for example, transcription, transcript processing, translation, and protein folding, modification, and processing when applicable. "Expression products" include RNA transcribed from a gene and polypeptides obtained by translation of mRNA transcribed from a gene. The term "gene" refers to a nucleic acid sequence that is transcribed (DNA) into RNA in vitro or in vivo when operably linked to a suitable regulatory sequence. The gene may or may not include regions before and after the coding region, for example, 5' non-translated (5'UTR) or "leader" sequence and 3'UTR or "trailing" sequence, as well as intervening sequences (introns) between each coding segment (exon).

[0129] As used herein, the term "viral vector" refers to a nucleic acid vector construct that contains at least one element of viral origin and has the ability to be packaged into viral vector particles. The viral vector may contain nucleic acids encoding antibodies or antigen-binding portions thereof as described herein in place of non-essential viral genes. The vector and / or particle may be used for the purpose of transferring any nucleic acid into a cell in vitro or in vivo. Various forms of viral vectors are known in the art.

[0130] By "recombinant vector" is meant that the vector comprises a heterologous nucleic acid sequence or "transgene" capable of being expressed in vivo.

[0131] Pharmaceutical compositions, administration and dosage

[0132] The provided anti-TL1A antibodies can be used for a variety of applications, including but not limited to therapeutic treatment methods, such as the treatment of IBD. The methods of use can be in vitro, ex vivo or in vivo methods. In certain embodiments, the anti-TL1A antibody is an antagonist of the TL1A receptor.

[0133] In certain embodiments, the disease treated with the anti-TL1A antibody or TL1A receptor antagonist is IBD, CD, UC and / or MR-UC.

[0134] In various embodiments, the pharmaceutical composition is formulated for delivery by any route of administration."Route of administration" may refer to any route of administration known in the art, including but not limited to aerosol, nasal, oral, transmucosal, transdermal, or parenteral.

[0135] "Transdermal" administration can be accomplished using topical creams or ointments or with the aid of a transdermal patch.

[0136] "Parenteral" refers to routes of administration usually associated with injection, including intraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrasternal, intrathecal, intrauterine, intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal or transtracheal. By parenteral routes, the composition can be in the form of a solution or suspension for infusion or injection, or a lyophilized powder.

[0137] By enteral route, the pharmaceutical composition may be in the form of tablets, gel capsules, sugar-coated tablets, syrups, suspensions, solutions, powders, granules, emulsions, microspheres or nanospheres or lipid vesicles or polymer vesicles allowing controlled release.

[0138] By topical route, pharmaceutical compositions are formulated for the treatment of skin and mucous membranes and are in the form of ointments, creams, emulsions, salves, powders, impregnated pads, solutions, gels, sprays, lotions or suspensions. They can also be in the form of microspheres or nanospheres or lipid vesicles or polymer vesicles or polymer patches and hydrogels, thereby allowing controlled release. Depending on the clinical indication, these topical route compositions can be in anhydrous or aqueous form.

[0139] By the ocular route, they may be in the form of eye drops.

[0140] In various embodiments, the agent can be administered intravenously by injection or by gradual infusion over time. Given an appropriate formulation for a given route, for example, the agents useful in the methods and compositions described herein can be administered intravenously, intranasally, by inhalation, intraperitoneally, intramuscularly, subcutaneously, intracavitary, and if desired, delivered by peristaltic means or by other means known to those skilled in the art. In specific embodiments, the compounds used herein are administered orally, intravenously or intramuscularly to patients with IBD, CD, UC and / or MR-UC.

[0141] The pharmaceutical composition may also contain any pharmaceutically acceptable carrier. "Pharmaceutically acceptable carrier" refers to a pharmaceutically acceptable material, composition or vehicle involved in carrying or transporting the compound of interest from one tissue, organ or body part to another tissue, organ or body part. For example, the carrier can be a liquid or solid filler, diluent, excipient, solvent or encapsulating material or a combination thereof. Each component of the carrier must be "pharmaceutically acceptable" in that it must be compatible with the other ingredients of the formulation. It must also be suitable for contact with any tissue or organ with which it may come into contact, which means that it must not carry the risk of toxicity, irritation, allergic reaction, immunogenicity or any other complications that far outweigh its therapeutic benefits.

[0142] In various embodiments, a pharmaceutical composition comprising a pharmaceutically acceptable excipient and a therapeutically effective amount of an anti-TL1A antibody is provided. "Pharmaceutically acceptable excipient" means an excipient that is generally safe, non-toxic and desirable for use in the preparation of a pharmaceutical composition, and includes excipients that are acceptable for veterinary use as well as for human pharmaceutical use. The active ingredient may be mixed with an excipient that is pharmaceutically acceptable and compatible with the active ingredient, and in an amount suitable for use in the methods of treatment described herein. Such excipients may be solid, liquid, semisolid, or, in the case of an aerosol composition, gaseous. Suitable excipients are, for example, starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glyceryl monostearate, talc, sodium chloride, skimmed milk powder, water, saline, dextrose, propylene glycol, glycerol, ethanol, mannitol, polysorbate, and the like, and combinations thereof. In addition, if desired, the composition may contain a small amount of auxiliary substances, such as wetting agents or emulsifiers, pH buffers, and the like, which enhance or maintain the effectiveness of the active ingredient. The therapeutic composition described herein may include a pharmaceutically acceptable salt.Pharmaceutically acceptable salts include acid addition salts formed with inorganic acids such as hydrochloric acid or phosphoric acid, acid addition salts formed with organic acids such as acetic acid, tartaric acid or mandelic acid, salts formed by inorganic bases such as sodium hydroxide, potassium hydroxide, ammonium hydroxide, calcium hydroxide or ferric hydroxide, and salts formed by organic bases such as isopropylamine, trimethylamine, 2-ethylaminoethanol, histidine, procaine, etc. The liquid composition may also include a liquid phase other than water, such as glycerol, vegetable oils such as cottonseed oil and water-in-oil emulsions, and the composition includes water and does not include water. Physiologically tolerable carriers are well known in the art. The amount of active agent (i.e., antibody or its fragment) used in the treatment of a particular disorder or condition will depend on the nature of the disorder or condition, and can be determined by standard clinical techniques by those skilled in the art.

[0143] The pharmaceutical composition can also be encapsulated, tableted or prepared as an emulsion or syrup for oral administration. Pharmaceutically acceptable solid or liquid carriers can be added to enhance or stabilize the composition, or to promote the preparation of the composition. Liquid carriers include syrups, peanut oil, olive oil, glycerine, saline, alcohol and water. Solid carriers include starch, lactose, calcium sulfate, dihydrate, carclazyte, magnesium stearate or stearic acid, talc, pectin, gum arabic, agar or gelatin. The carrier can also include a sustained release material alone or with wax, such as glyceryl monostearate or glyceryl distearate.

[0144] The pharmaceutical preparations are prepared according to conventional pharmaceutical techniques, which include grinding, mixing, granulating and, if necessary, compressing for tablet form, or grinding, mixing and filling for hard gelatin capsule form. When a liquid carrier is used, the preparation will be in the form of a syrup, elixir, emulsion or aqueous or non-aqueous suspension. Such liquid preparations can be administered orally directly or filled into soft gelatin capsules.

[0145] The pharmaceutical composition can be delivered in a therapeutically effective amount. An accurate therapeutically effective amount is the amount of the composition that will produce the most effective results in terms of the therapeutic effect in a given subject. This amount will vary according to a variety of factors, including but not limited to the characteristics of the therapeutic compound (including activity, pharmacokinetics, pharmacodynamics and bioavailability), the subject's physiological condition (including age, sex, disease type and stage, general physical condition, responsiveness to a given dose and drug type), the properties of one or more pharmaceutically acceptable carriers in the preparation, and the route of administration. The technicians in the clinical and pharmacological fields will be able to determine the therapeutically effective amount by routine experiments, such as by monitoring the subject's response to the administration of the compound and adjusting the dosage accordingly. For other guidance, see Remington: The Science and Practice of Pharmacy (Gennaro, 20th edition, Williams & Wilkins PA, USA) (2000).

[0146] Typical dosages of effective anti-TL1A antibodies can be provided to the skilled artisan by in vitro reactions or reactions in animal models. Such dosages can generally be reduced by up to about one order of magnitude in concentration or amount without loss of relevant biological activity. Therefore, the actual dosage will depend on the physician's judgment, the patient's condition, and the effectiveness of the treatment method, for example, based on the in vitro reactivity of relevant primary cultured cells or tissue culture tissue samples such as obtained biological samples, or based on the reactions observed in appropriate animal models.

[0147] For the treatment of disease, the appropriate dose of the antibody depends on the type of disease to be treated, the severity and course of the disease, the responsiveness of the disease, whether the antibody is administered for therapeutic or preventive purposes, previous treatments, and the patient's clinical history. In the event of any complications, the dose may also be adjusted by a separate physician at the discretion of the attending physician. The medication physician can determine the optimal dose, dosing method, and repetition frequency. The TL1A antibody may be administered once or during a series of treatments lasting from several days to several months, or until a cure is achieved or a reduction in the disease state is achieved (e.g., treatment or improvement of IBD). The duration of treatment depends on the subject's clinical progression and responsiveness to treatment. In certain embodiments, the dose is 0.01 μg to 100 mg per kg of body weight and may be administered once or more per day, weekly, monthly, or yearly. For systemic administration, a therapeutic amount can be administered to a subject, for example, about 0.1 mg / kg, 0.5 mg / kg, 1.0 mg / kg, 2.0 mg / kg, 2.5 mg / kg, 5 mg / kg, 10 mg / kg, 15 mg / kg, 20 mg / kg, 25 mg / kg, 30 mg / kg, 40 mg / kg, 50 mg / kg or more. In certain embodiments, the therapeutic amount is selected from about 1, 3, 10, 30, 100, 300, 600 and 800 milligrams administered as a steady dose. In certain embodiments, the therapeutic amount is about 1, 2, 3, 4, 5, 6, 7, 8 or 9 milligrams administered as a steady dose. In certain embodiments, the therapeutic amount is about 10, 20, 30, 40, 50, 60, 70, 80 or 90 milligrams administered as a steady dose. In certain embodiments, the therapeutic amount is about 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850 or 900 mg administered as a steady dose. In certain embodiments, the therapeutic amount is about 5 to about 30 mg / kg. In certain embodiments, the therapeutic amount is about 5 to about 30 mg / kg, administered weekly or every other week. In certain embodiments, the therapeutic amount is about 5, 10, 15, 20, 25 or 30 mg / kg. In certain embodiments, the therapeutic amount is about 5, 10, 15, 20, 25 or 30 mg / kg, administered weekly or every other week.

[0148] Treatment

[0149] Various embodiments provide methods of treating inflammatory bowel disease (IBD) comprising administering an anti-TL1A antibody described herein to a subject in need thereof. In some embodiments, the subject comprises one or more risk genotypes. In some embodiments, the IBD is a severe form of IBD. Severe forms of IBD may be characterized by a subclinical phenotype described herein.

[0150] In various embodiments, provided herein is a method of treating inflammatory bowel disease (IBD) in a subject in need thereof, comprising: administering to the subject a therapeutically effective amount of an antibody or antigen-binding fragment that specifically binds to TL1A. In some embodiments, the anti-TL1A antibody comprises HCFR1, the HCFR1 comprising SEQ ID NO: 545, or a sequence that differs from SEQ ID NO: 545 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises HCDR1, the HCDR1 selected from SEQ ID NO: 9, 150, 484, and 553, or a sequence that differs from a sequence selected from SEQ ID NO: 9, 150, 484, and 553 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises HCFR2, the HCFR2 comprising SEQ ID NO: 546, or a sequence that differs from SEQ ID NO: 546 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises a HCDR2 selected from the group consisting of SEQ ID NOs: 12, 554 to 564, and 574 to 577, or a sequence that differs by at most about 5, 4, 3, or 2 amino acids from a sequence selected from the group consisting of SEQ ID NOs: 12, 554 to 564, and 574 to 577. In some embodiments, the anti-TL1A antibody comprises a HCFR3 comprising a sequence selected from the group consisting of SEQ ID NOs: 547 and 586 to 588, or a sequence that differs by at most about 5, 4, 3, or 2 amino acids from a sequence selected from the group consisting of SEQ ID NOs: 547 and 586 to 588. In some embodiments, the anti-TL1A antibody comprises a HCDR3 selected from the group consisting of SEQ ID NOs: 15, 152, 565 to 568, and 578 to 581, or a sequence that differs by at most about 5, 4, 3, or 2 amino acids from a sequence selected from the group consisting of SEQ ID NOs: 15, 152, 565 to 568, and 578 to 581. In some embodiments, the anti-TL1A antibody comprises a HCFR4 comprising SEQ ID NO: 548, or a sequence that differs by at most about 5, 4, 3, or 2 amino acids from SEQ ID NO: 548. In some embodiments, the anti-TL1A antibody comprises a LCFR1 comprising SEQ ID NO: 549, or a sequence that differs by at most about 5, 4, 3, or 2 amino acids from SEQ ID NO: 549. In some embodiments, the anti-TL1A antibody comprises a LCDR1 selected from SEQ ID NOs: 487, 569, and 570, or a sequence that differs from SEQ ID NOs: 487, 569, and 570 by at most about 5, 4, 3, or 2 amino acids.In some embodiments, the anti-TL1A antibody comprises a LCFR2 comprising SEQ ID NO: 550, or a sequence that differs from SEQ ID NO: 550 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises a LCDR2 comprising SEQ ID NO: 488, or a sequence that differs from SEQ ID NO: 488 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises a LCFR3 comprising SEQ ID NO: 551, or a sequence that differs from SEQ ID NO: 551 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises a LCDR3 selected from the group consisting of SEQ ID NOs: 571 to 573 and 582 to 585, or a sequence that differs from a sequence selected from the group consisting of SEQ ID NOs: 571 to 573 and 582 to 585 by at most about 5, 4, 3, or 2 amino acids. In some embodiments, the anti-TL1A antibody comprises a LCFR4 comprising SEQ ID NO:552, or a sequence that differs from SEQ ID NO:552 by at most about 5, 4, 3, or 2 amino acids.

[0151] The subject disclosed herein can be a mammal, such as a mouse, a rat, a guinea pig, a rabbit, a non-human primate or a farm animal. In some cases, the subject is a human. In some cases, the subject is a patient diagnosed with IBD. In some cases, the subject is not diagnosed with IBD. In some cases, the subject suffers from symptoms (e.g., abdominal pain, colic, diarrhea, rectal bleeding, fever, weight loss, fatigue, loss of appetite, dehydration and malnutrition, anemia or ulcer) related to a disease or condition disclosed herein.

[0152] In various embodiments, the subject is unresponsive to the induction of anti-TNF therapy (e.g., adalimumab, certolizumab, etanercept, golimumab, infliximab) (anti-TNF unresponsiveness), or loses response to the anti-TNF therapy after a period of time during treatment (loss of anti-TNF response). In various embodiments, the subject is at risk of developing anti-TNF unresponsiveness or loss of anti-TNF response. In some embodiments, the subject is treated by administering an anti-TL1A antibody disclosed herein to the subject, provided that the subject is at risk of developing anti-TNF unresponsiveness or loss of anti-TNF response or is already anti-TNF unresponsiveness or loss of anti-TNF response.

[0153] In various other embodiments, the subject is determined to have increased expression of TL1A.In some embodiments, administration of a therapeutically effective amount of an anti-TL1A antibody results in a decrease in TL1A in the treated subject.

[0154] The methods disclosed herein provide methods of treating inflammatory bowel disease (IBD) in a subject by administering to the subject an anti-TL1A antibody described herein. In various embodiments, the IBD is Crohn's disease (CD) or ulcerative colitis (UC). In some embodiments, the IBD is a severe form of IBD. In some embodiments, the severe form of the IBD is characterized by a subclinical phenotype. In some embodiments, the IBD is a moderate to severe form of IBD. In some embodiments, the IBD is a moderate form of IBD.

[0155] Subclinical phenotypes of IBD may include, but are not limited to, non-stenotic, stenotic, stenotic and penetrating, as well as isolated internal penetrating disease and perianal CD (pCD). Stenosis is a progressive narrowing of the intestine. Internal penetrating disease creates abnormal passages (fistulas) between the intestine and other structures. pCD is a form of Crohn's disease that causes inflammation around the anus.

[0156] The IBD can be refractory. As used herein, the term "medically refractory" or "refractory" refers to the remission of a disease that cannot be induced by standard treatment. In some embodiments, the disease includes an inflammatory disease disclosed herein. Non-limiting examples of refractory inflammatory diseases include refractory Crohn's disease and refractory ulcerative colitis (e.g., mrUC). Non-limiting examples of standard treatments include glucocorticoids, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), thalidomide and cytotoxins. In some embodiments, the UC is medically refractory UC (mrUC). In some embodiments, the CD is refractory.

[0157] Disclosed herein are methods of administering an anti-TL1A antibody to a subject in need thereof. In various embodiments, the antibody is a monoclonal antibody. In some embodiments, the antibody is a human antibody. In various embodiments, the antibody is a humanized antibody. In various embodiments, the antibody is a neutralizing antibody.

[0158] In various aspects, an anti-TL1A antibody is administered to a subject for treatment of an IBD described herein. In various other embodiments, the anti-TL1A antibody is administered in a series of treatments. In some embodiments, the anti-TL1A antibody and the second IBD treatment may be administered in any order or simultaneously. In selected embodiments, the anti-TL1A antibody is administered to a patient who has previously received a second IBD treatment. In certain other embodiments, the anti-TL1A antibody and the second IBD treatment will be administered substantially simultaneously or in parallel. For example, the subject may be given an anti-TL1A antibody during treatment of the subject for the second IBD treatment. In certain embodiments, the anti-TL1A antibody will be administered within 1 year of the second IBD treatment. In certain alternative embodiments, the anti-TL1A antibody will be administered within 10, 8, 6, 4, or 2 months of any treatment for the second IBD treatment. In certain other embodiments, the anti-TL1A antibody will be administered within 4, 3, 2, or 1 week of any treatment for the second IBD treatment. In some embodiments, the anti-TL1A antibody will be administered within 5, 4, 3, 2, or 1 day of any treatment for the second IBD treatment. It will be further appreciated that both treatments may be administered to the subject within a matter of hours or minutes (ie, simultaneously).

[0159] Other IBD treatments include, but are not limited to, 1) anti-inflammatory drugs (e.g., aminosalicylates, such as, but not limited to, Azulfidine, 5-aminosalicylate, mesalamine, Asacol, Lialda, Rowasa, Canasa, Colazal, and Olsalazine Dipentum); 2) corticosteroids (e.g., prednisone and hydrocortisone); 3) immune system suppressants (e.g., azathioprine, Azasan, Imuran, thiopurine Purinethol, Purixan, cyclosporine, Gengraf, Neural, and Sandimmune, infliximab, Remicade, adalimumab, Humi ra, golimumab and Simponi, tumor necrosis factor (TNF)-α inhibitors (e.g., infliximab), methotrexate, Rheumatrex, natalizumab, Tysabri, vedolizumab, Entyvio, ustekinumab and Stelara; 4) antibiotics (e.g., metronidazole, Flagyl, ciprofloxacin, Cipro); 5) antidiarrheal drugs (e.g., fiber supplements-Metamucil or Citrucel) or loperamide; 6) analgesics (e.g., Tylenol, ibuprofen, naproxen sodium and diclofenac sodium); and 7) surgery (e.g., colon resection, partial digestive tract resection, colectomy, proctocolectomy and / or strictureplasty). In some embodiments, these IBD treatments can be administered in combination with anti-TL1A antibodies. Treatment with antibodies can be performed before, at the same time, or after the administration of IBD treatments. Administration in combination may include co-administration in a single pharmaceutical formulation or using separate formulations, or sequential administration in either order, but generally over a period of time so that all active agents can simultaneously exert their biological activities. Any dosing schedule for such IBD treatment may also be used as determined by a skilled artisan.

[0160] In some embodiments, the second IBD treatment comprises an antibody. Thus, treatment may involve administering the antibodies provided herein in combination with other antibodies directed against additional IBD-associated antigens, such as, but not limited to, tumor necrosis factor (TNF)-α. Co-administration may include co-administration in a single pharmaceutical formulation or using separate formulations, or continuous administration in either order, but typically over a period of time so that all active agents can simultaneously exert their biological activity.

[0161] Reagent test kit

[0162] A kit for treating IBD (e.g., CD, UC and / or mrUC) is further provided. The kit comprises an antibody as described herein that can be used to perform the methods described herein. The kit can be used to implement the methods of the present invention for providing treatment for IBD, CD, UC and / or mrUC patients by administering an anti-TL1A antibody. The kit is a collection of materials or components, including at least one composition of the present invention. Thus, in some embodiments, the kit comprises a composition comprising an anti-TL1A antibody for treating IBD, CD, UC and / or MR-UC as described above. In other embodiments, the kit comprises all components necessary and / or sufficient to perform a detection assay for TL1A, including all controls, instructions for performing the assay, and any necessary software for analyzing and presenting the results.

[0163] The exact nature of the components configured in the kit of the present invention depends on its intended purpose. For example, some embodiments are configured for the purpose of treating IBD, CD, UC and / or MR-UC. In one embodiment, the kit is particularly configured for the purpose of treating mammalian subjects. In another embodiment, the kit is particularly configured for the purpose of treating human subjects. In a further embodiment, the kit is configured for veterinary applications, thereby treating subjects, such as but not limited to farm animals, domestic animals and laboratory animals.

[0164] Instructions for use may be included in the kit. "Instructions for use" generally include a tangible representation describing the techniques employed in using the components of the kit to achieve the desired results (e.g., treating or alleviating IBD, CD, UC and / or MR-UC). Optionally, the kit also includes other useful components, such as diluents, buffers, pharmaceutically acceptable carriers, syringes, catheters, applicators, pipetting or measuring tools, dressing materials, or other useful utensils readily recognized by those skilled in the art.

[0165] The materials or components assembled in the kit can be provided to the practitioner in any convenient and suitable manner that maintains its operability and practicality. For example, the components can be dissolved, dehydrated or lyophilized; they can be provided at room temperature, refrigerated or frozen temperature. These components are usually contained in suitable packaging materials. As used herein, the phrase "packaging material" refers to one or more physical structures used to contain the contents of the kit, such as the composition of the present invention, etc. The packaging material is constructed by well-known methods to preferably provide a sterile, contamination-free environment. The packaging materials used in the kit are those conventionally used in gene expression experiments and in therapeutic administration. As used herein, the term "packaging" refers to a suitable solid matrix or material capable of containing the various kit components, such as glass, plastic, paper, foil, etc. Thus, for example, the package can be a glass vial or a prefilled syringe, which is used to contain an appropriate amount of the composition of the present invention comprising an anti-TL1A antibody and / or primers and probes for TL1A. The packaging material usually has an external label indicating the contents and / or purpose of the kit and / or its components.

[0166] The present invention provides embodiments including but not limited to the following:

[0167] 1. An antibody or antigen-binding fragment that specifically binds to TL1A, comprising:

[0168] A heavy chain variable region comprising:

[0169] (g) HCDR1 comprising the amino acid sequence shown in SEQ ID NO: 553;

[0170] (h) a HCDR2 comprising the amino acid sequence shown in any one of SEQ ID NOs: 554 to 564 or 574 to 577; and

[0171] (i) a HCDR3 comprising the amino acid sequence shown in any one of SEQ ID NOs: 565 to 568 or 578 to 581; and

[0172] A light chain variable region comprising:

[0173] (j) LCDR1 comprising the amino acid sequence shown in any one of SEQ ID NO: 569 or 570;

[0174] (k) LCDR2 comprising the amino acid sequence shown in SEQ ID NO: 488; and

[0175] (l) LCDR3 comprising the amino acid sequence shown in any one of SEQ ID NOs: 571 to 573 or 582 to 585.

[0176] 2. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 1, wherein:

[0177] (a) the HCDR1 comprises the amino acid sequence shown in SEQ ID NO: 553;

[0178] (b) the HCDR2 comprises the amino acid sequence shown in SEQ ID NO: 559;

[0179] (c) the HCDR3 comprises the amino acid sequence shown in SEQ ID NO: 567;

[0180] (d) the LCDR1 comprises the amino acid sequence shown in SEQ ID NO: 569;

[0181] (e) the LCDR2 comprises the amino acid sequence shown in SEQ ID NO: 488; and

[0182] (f) The LCDR3 comprises the amino acid sequence shown in SEQ ID NO:573.

[0183] 3. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 1, wherein:

[0184] (a) the HCDR1 comprises the amino acid sequence shown in SEQ ID NO: 553;

[0185] (b) the HCDR2 comprises the amino acid sequence shown in SEQ ID NO: 563;

[0186] (c) the HCDR3 comprises the amino acid sequence shown in SEQ ID NO: 568;

[0187] (d) the LCDR1 comprises the amino acid sequence shown in SEQ ID NO: 569;

[0188] (e) the LCDR2 comprises the amino acid sequence shown in SEQ ID NO: 488; and

[0189] (f) The LCDR3 comprises the amino acid sequence shown in SEQ ID NO:572.

[0190] 4. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 1, wherein:

[0191] (a) the HCDR1 comprises the amino acid sequence shown in SEQ ID NO: 553;

[0192] (b) the HCDR2 comprises the amino acid sequence shown in SEQ ID NO: 555;

[0193] (c) the HCDR3 comprises the amino acid sequence shown in SEQ ID NO: 566;

[0194] (d) the LCDR1 comprises the amino acid sequence shown in SEQ ID NO: 569;

[0195] (e) the LCDR2 comprises the amino acid sequence shown in SEQ ID NO: 488; and

[0196] (f) The LCDR3 comprises the amino acid sequence shown in SEQ ID NO:572.

[0197] 5. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 1, wherein:

[0198] (a) the HCDR1 comprises the amino acid sequence shown in SEQ ID NO: 553;

[0199] (b) the HCDR2 comprises the amino acid sequence shown in SEQ ID NO: 558;

[0200] (c) the HCDR3 comprises the amino acid sequence shown in SEQ ID NO: 566;

[0201] (d) the LCDR1 comprises the amino acid sequence shown in SEQ ID NO: 569;

[0202] (e) the LCDR2 comprises the amino acid sequence shown in SEQ ID NO: 488; and

[0203] (f) The LCDR3 comprises the amino acid sequence shown in SEQ ID NO:572.

[0204] 6. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 1, wherein:

[0205] (a) the HCDR1 comprises the amino acid sequence shown in SEQ ID NO: 553;

[0206] (b) the HCDR2 comprises the amino acid sequence shown in SEQ ID NO: 564;

[0207] (c) the HCDR3 comprises the amino acid sequence shown in SEQ ID NO: 568;

[0208] (d) the LCDR1 comprises the amino acid sequence shown in SEQ ID NO: 569;

[0209] (e) the LCDR2 comprises the amino acid sequence shown in SEQ ID NO: 488; and

[0210] (f) The LCDR3 comprises the amino acid sequence shown in SEQ ID NO:572.

[0211] 7. An antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising:

[0212] (c) a HCDR1, HCDR2, and HCDR3 selected from any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, or 541; and

[0213] The light chain variable region comprises

[0214] (d) a LCDR1, LCDR2, and LCDR3 selected from any one of SEQ ID NO: 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, or 540;

[0215] Wherein the CDRs are defined by the Kabat, Chothia or IMGT methods or a combination thereof.

[0216] 8. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 7, comprising:

[0217] (a) a human heavy chain framework region 1 that is at least 95% identical to that shown in SEQ ID NO:545;

[0218] (b) a human heavy chain framework region 2 that is at least 95% identical to that shown in SEQ ID NO:546;

[0219] (c) a human heavy chain framework region 3 that is at least 95% identical to that shown in SEQ ID NO: 547 or 586 to 588;

[0220] (d) a human heavy chain framework region 4 that is at least 95% identical to that shown in SEQ ID NO:548;

[0221] (e) a human light chain framework region 1 that is at least 95% identical to that shown in SEQ ID NO:549;

[0222] (f) a human light chain framework region 2 that is at least 95% identical to that shown in SEQ ID NO:550;

[0223] (g) a human light chain framework region 3 that is at least 95% identical to that shown in SEQ ID NO:551; and

[0224] (h) a human light chain framework region 4 that is at least 95% identical to that shown in SEQ ID NO:552.

[0225] 9. An antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 8, which comprises a heavy chain variable region and a light chain variable region, the heavy chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO: 503, 511, 493, 501 or 515; the light chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO: 502, 510, 492, 500 or 514.

[0226] 10. An antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 8, which comprises a heavy chain variable region and a light chain variable region, the heavy chain variable region comprising the amino acid sequence shown in any one of SEQ ID NO: 503, 511, 493, 501 or 515; the light chain variable region comprising the amino acid sequence shown in any one of SEQ ID NO: 502, 510, 492, 500 or 514.

[0227] 11. An antibody or antigen-binding fragment that specifically binds to TL1A, comprising:

[0228] (c) a heavy chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; and

[0229] (d) a light chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540.

[0230] 12. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 11, wherein the heavy chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:503; and wherein the light chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:502.

[0231] 13. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 12, wherein the heavy chain variable region comprises the amino acid sequence of SEQ ID NO: 503; and wherein the light chain variable region comprises the amino acid sequence of SEQ ID NO: 502.

[0232] 14. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 11, wherein the heavy chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:511; and wherein the light chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:510.

[0233] 15. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 14, wherein the heavy chain variable region comprises the amino acid sequence of SEQ ID NO: 511; and wherein the light chain variable region comprises the amino acid sequence of SEQ ID NO: 510.

[0234] 16. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 11, wherein the heavy chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO: 493; and wherein the light chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO: 492.

[0235] 17. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 16, wherein the heavy chain variable region comprises the amino acid sequence of SEQ ID NO: 493; and wherein the light chain variable region comprises the amino acid sequence of SEQ ID NO: 492.

[0236] 18. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 11, wherein the heavy chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:501; and wherein the light chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:500.

[0237] 19. The antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 18, wherein the heavy chain variable region comprises the amino acid sequence of SEQ ID NO: 501; and wherein the light chain variable region comprises the amino acid sequence of SEQ ID NO: 500.

[0238] 20. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 11, wherein the heavy chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:515; and wherein the light chain variable region comprises an amino acid sequence that is at least about 90% identical to SEQ ID NO:514.

[0239] 21. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 20, wherein the heavy chain variable region comprises the amino acid sequence of SEQ ID NO: 515; and wherein the light chain variable region comprises the amino acid sequence of SEQ ID NO: 514.

[0240] 22. An antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 21, wherein the antibody binds to human TL1A with a stronger affinity than the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490.

[0241] 23. An antibody or antigen-binding fragment that specifically binds to TL1A according to embodiment 22, wherein the antibody binds to human TL1A with an affinity at least 2 times stronger than that of the L8 clone as determined by ELISA, wherein the L8 clone comprises the heavy chain variable region amino acid sequence shown in SEQ ID NO: 491 and the light chain variable region amino acid sequence shown in SEQ ID NO: 490.

[0242] 24. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 23, wherein the antibody or antigen-binding fragment is chimeric or humanized.

[0243] 25. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 23, wherein the antibody or antigen-binding fragment is an IgG antibody.

[0244] 26. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 25, wherein the antibody or antigen-binding fragment comprises Fab, F(ab)2, a single domain antibody, a single chain variable fragment (scFv) or a nanobody.

[0245] 27. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 26, which comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO: 542 or 543.

[0246] 28. An antibody or antigen-binding fragment according to any one of embodiments 1 to 26, which comprises a heavy chain constant region comprising the amino acid sequence shown in SEQ ID NO:542.

[0247] 29. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 26, which comprises a light chain constant region comprising the amino acid sequence shown in SEQ ID NO: 544.

[0248] 30. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 29, wherein the antibody or antigen-binding fragment thereof inhibits TL1A-induced secretion of interferon gamma by T lymphocytes.

[0249] 31. A pharmaceutical composition comprising the antibody or antigen-binding fragment specifically binding to TL1A according to any one of embodiments 1 to 30 and a pharmaceutically acceptable excipient, carrier or diluent.

[0250] 32. The pharmaceutical composition of embodiment 31, which is formulated for intravenous administration.

[0251] 33. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 30 or the pharmaceutical composition according to embodiment 31 or 32, for use in treating inflammatory bowel disease, Crohn's disease or colitis.

[0252] 34. A method of treating inflammatory bowel disease, Crohn's disease or colitis in an individual, comprising administering to the individual an effective amount of the antibody or antigen-binding fragment that specifically binds to TL1A of any one of embodiments 1 to 30, or the pharmaceutical composition of embodiment 31 or 32, wherein the individual is diagnosed with or suspected of having inflammatory bowel disease, Crohn's disease or colitis.

[0253] 35. The antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 30 or the pharmaceutical composition according to embodiment 31 or 32, for use in preventing or reducing interferon gamma secretion by T lymphocytes.

[0254] 36. A method for preventing or reducing interferon-γ secretion by T lymphocytes in an individual, comprising administering to the individual an effective amount of the antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 30 or the pharmaceutical composition of embodiment 31 or 32.

[0255] 37. A nucleic acid encoding the antibody or antigen-binding fragment of any one of embodiments 1 to 30 that specifically binds to TL1A.

[0256] 38. A cell comprising the nucleic acid of embodiment 37.

[0257] 39. A cell according to embodiment 38, wherein the cell is a eukaryotic cell.

[0258] 40. The cell of embodiment 38, wherein the cell is a Chinese Hamster Ovary (CHO) cell.

[0259] 41. A method of preparing a treatment for inflammatory bowel disease, Crohn's disease or colitis, comprising incubating the cell of any one of embodiments 38 to 40 in a culture medium under conditions sufficient to secrete the antibody or antigen-binding fragment of any one of embodiments 1 to 30 that specifically binds to TL1A into the culture medium.

[0260] 42. The method of embodiment 41, further comprising subjecting the culture medium to at least one purification step.

[0261] 43. A method for preparing a treatment for inflammatory bowel disease, Crohn's disease or colitis comprising mixing an antibody or antigen-binding fragment that specifically binds to TL1A according to any one of embodiments 1 to 30 with a pharmaceutically acceptable excipient, carrier or diluent.

[0262] 44. A method for treating a disease or condition in an individual having a risk variant associated with the disease or condition, the method comprising administering to the individual having the risk variant for the disease or condition an effective amount of an antibody or antigen-binding fragment that specifically binds to TL1A of any one of embodiments 1 to 30, or a pharmaceutical composition of embodiment 31 or 32, wherein the disease or condition comprises at least one of inflammatory bowel disease (IBD), Crohn's disease (CD), or colitis.

[0263] 45. A method according to embodiment 44, wherein the individual has multiple risk variants.

[0264] 46. ​​A method according to embodiment 45, wherein the multiple risk variants are at least 3, 4, 5 or 10 risk variants.

[0265] 47. A method according to any one of embodiments 44 to 46, wherein a risk variant of the multiple risk variants is associated with a subclinical phenotype of the disease or condition.

[0266] 48. The method of embodiment 44, wherein the disease or condition is a severe form of at least one of IBD, CD, or colitis.

[0267] Example

[0268] The following examples illustrate embodiments described herein and should not be construed as limiting the scope of the present disclosure. When specific materials are mentioned, this is merely for illustrative purposes and is not intended to be limiting. Those skilled in the art may develop equivalent means or reactants without having creative ability and without departing from the scope of the present disclosure.

[0269] Example 1: Generation and characterization of humanized anti-TL1A antibodies

[0270] The murine anti-TL1A antibody was humanized to reduce potential immunogenicity. The first variant, 12835, was generated, consisting of the murine 5C3D11 CDRs (SEQ ID NOs: 9, 12, 15, 18, 21, 24) grafted into the human variable region framework to generate a heavy chain variable region comprising SEQ ID NO: 26 and a light chain variable region comprising SEQ ID NO: 28. Unfortunately, clone 12835 contained nine (9) framework back mutations (murine framework residues), resulting in an incompletely humanized variant. Complete humanization is essential to reduce the chance that a subject will develop an immune response to the administered antibody. Therefore, the goal was to generate a humanized antibody that contained fewer murine framework residues while retaining the functional activity of the parent 12835 antibody. Unfortunately, by visual inspection of the sequence, it is not directly possible to distinguish the murine framework residues that are critical to antibody function from those that are not critical, and therefore it is not easy to determine which amino acid residues can be replaced by the corresponding human framework residues. Therefore, as a first step, 12835 was re-humanized by transplanting the CDRs into the closest fully human germline frameworks (IGV1-46*02 and IGKV3-20*01 determined by NCBI's igblast tool). This clone was L8 and contained 5C3D11 and 12835 CDRs defined by a combination of Kabat, Chothia, and IMGT methods (HCDR1, GFDIQDTYMH; HCDR2, RIDPASGHTKYDPKFQV; HCDR3, SRSGGLPDV; LCDR1, RASSSVSYMY; LCDR2, ATSNLAS; LCDR3, QQWSGNPRT).

[0271] In this study, many variants of 12835 were prepared and tested to identify more human-like antibodies that retain the functional activity of the parental 12835 antibody. In the first stage, variants containing significantly fewer mouse framework residues were identified. Subsequently, the CDR library of 12835 was combined with a fully human germline framework to identify multiple variants that did not contain any mouse framework residues but still retained the functional activity and / or affinity of the parental 12835 antibody.

[0272] Cloning of murine 5C3D11 and humanized construct 12835 into phage expression system

[0273] DNA encoding the heavy and light chain variable regions of murine 5C3D11 and humanized 12835 were cloned into a phage expression vector containing the human kappa light chain constant region and the human G1 heavy chain constant region 1. In addition, the vector contained a his tag and a hemagglutinin A tag at the carboxyl terminus of the heavy chain to facilitate purification and detection. Cloning of the murine variable regions into a phage expression vector containing human constant domains resulted in expression of the chimeric 5C3D11.

[0274] Murine 5C3D11 heavy chain variable region DNA (SEQ ID NO: 1) and light chain variable region DNA (SEQ ID NO: 4) were codon optimized for bacterial expression to generate SEQ ID NOs: 2 and 5, respectively. Humanized 12835 heavy chain variable region DNA was codon optimized to generate SEQ ID NO: 25, and light chain variable region DNA was codon optimized to generate SEQ ID NO: 27.

[0275] Expression and quantification of Fab in the periplasmic space of E. coli.

[0276] The clones were verified by expression and quantification of Fab in the periplasmic space of E. coli. Briefly, XL-0 bacteria were grown in 2X YT medium at 37°C until the culture reached a density of 0.9-1.1 at OD600. Isopropyl β-D-thiogalactoside was then added to the cells to a final concentration of 1 mM, and 3.0 mL of the culture was transferred to a 14 mL snap-top tube. Each tube was transfected with 25 uL of high titer phage stock solution, and the culture was placed in a 37°C shaker (225 rpm). After one hour, the temperature was changed to 25°C and the culture was grown for another 14-16 h. Cells were collected by centrifugation at 3900 rpm for 30 min in Eppendorf 5810R centrifuge (approximately 3,200 x g), supernatant was poured out, and cells were resuspended in 0.3 mL lysis buffer (30 mM Tris, pH 8.0, 2 mM EDTA, 20% sucrose, 2 mg / ml lysozyme, 5 U / mL DNA enzyme I) and placed on ice for 15 min. Cell suspension was transferred to 1.5 mL tubes, and cell debris was precipitated by centrifugation at 15,000 rpm for 15 min in Eppendorf 5424 microcentrifuge (approximately 21,000 x g). Supernatant was carefully taken out without disturbing the precipitate, and stored at 4 ° C until use.

[0277] To quantify Fab expression, 96-well Costar-3366 plates were coated with 50 μl / well of 2 μg / ml sheep anti-human Fd (Southern Biotech, product number 2046-01, lot number A7212-VJ06) in PBS at 4°C overnight. The plates were washed 3 times with PBS containing 0.05% Tween 20 (PBS-T) and 50 μl / well of sample diluent was added. Sample dilutions were performed with PBS-T. A standard curve was generated using a human Fab (Rockland, product number 009-01015, lot number 38543) serially diluted 3-fold starting from 500 ng / ml. The plate was incubated at 25°C for 1 h, washed 3 times with PBS-T, and incubated at 25°C for 1 h with 50 μl / well of anti-κ HRP conjugate (Southern Biotech, product number 2060-05, batch number K3114-S506B) diluted 10,000 times in PBS-T. The plate was washed 3 times with PBS-T and developed with 50 μl / well of 1-Step Ultra TMB-ELISA (ThermoScientific, product number 34028, batch number SF2405221). The reaction was stopped by adding 2N H2SO4, and A650 and A450 were determined before and after adding H2SO4 using a Spectramax microplate reader.

[0278] Characterization of chimeric 5C3D11 and 12835 - filter lift assay

[0279] A filter lift assay was developed to facilitate characterization of heavy and light chain expression and to verify functional activity of Fab constructs by binding to biotinylated antigen. For the filter lift assay, a lawn is infected with phage under conditions where each phage produces distinct plaques (areas of slower bacterial growth). A nitrocellulose filter is placed on the lawn to capture the expressed Fab. The filter can then be probed with biotinylated antigen and / or reagents directed against immunoglobulin or peptide tags.

[0280] High titer phage stock solution (usually 10 6The dilution (2000x) was combined with 0.35ml of the confluent E. coli strain XL culture and 20μg / ml tetracycline. The mixture was combined with 3.5ml of top agar (0.7% Bacto-agar in Luria broth) and covered on LB agar plates (1.5% Bacto-agar in Luria broth). The plate was incubated at 37°C for 6-8h, at which time a nitrocellulose filter (Whatman 82-mm diameter, 0.45μm pore size, GE Healthcare, product number 10401116) was placed on top, and the plate was incubated at 25°C for 12-15h. The filter was removed, rinsed briefly in PBS, and transferred to 5% MP blocking solution for 2h at 25°C, constant stirring.

[0281] Subsequently, the filter was cut into three parts: one for evaluating light chain expression, one for evaluating heavy chain expression, and one for evaluating antigen binding. Each part was transferred to the primary detection reagent: goat anti-human κ, HRP conjugate (Southern Biotech, product number 2060-05, lot number K3114-S506B) diluted 1000-fold in 5% MP for detection of light chain, rat anti-HA, HRP conjugate (Roche, product number 12013819001) diluted 1000-fold in 5% MP for detection of heavy chain, or biotinylated antigen at the desired concentration in 5% MP.

[0282] To label the antigen with biotin, 500 μg of human TL1A (Fitzgerald, product number 30R-AT070, batch number A13102302) was resuspended in water to 1 mg / ml. After suspension in water, the protein was in 10 mM Tris, pH 8.5 containing 75 mM arginine. Tris and arginine were removed by buffer exchange using a 7KMW cutoff 5 ml Zeba spin desalting column (Thermo product number 89891) that had been balanced with 10 mM phosphate buffer pH 8.0 containing 65 mM NaCl. After recovering the protein, it was immediately biotinylated by mixing it with EZ-Link Sulfo-NHS-LC-Biotin (Thermo product number 21327) at a 5:1 molar ratio at 25°C for 30 min. The reaction was terminated by adding 750 mM arginine to reach a final concentration of 75 mM. The reaction was transferred to ice and stored at 4°C.

[0283] The filters were incubated at 25°C for 2 h with constant agitation and washed 5 times in PBS-0.05% Tween 20 (2 min each time with constant agitation). The filters probed with biotinylated antigen were transferred to 10 ml of High Sensitivity Neutravidin, HRP conjugate (Thermo Scientific, Product No. 31030) diluted 5000-fold in PBS containing 1% BSA and incubated at 25°C for 1 h. The filters were then washed 5 times in PBS-0.05% Tween 20 (2 min each wash with constant agitation). All filters were developed with 1-Step Ultra TMB-Blotting (Thermo Scientific, Product No. 37574).

[0284] Using this approach, it was demonstrated that the heavy chain ( Figure 1 A) and light chain ( Figure 1 In addition, when the filter was probed with 8 nM biotinylated human TL1A, staining was observed ( Figure 1 C), indicating that the bacteria express functional Fab.

[0285] Characterization of Fab binding by ELISA

[0286] The filter lift test provides a qualitative assessment of antigen binding. In order to compare the binding activity of chimeric 5C3D11 and humanized construct 12835 in a more quantitative manner, an ELISA was developed. 96-well Costar-3366 plates were coated overnight at 4°C with 50 μl / well of 2 μg / ml human TL1A (Fitzgerald, product number 30R-AT070, batch number A13102302) in PBS. The plate was rinsed once with PBS-T and blocked with 1% BSA (1% BSA) in 100 μl / well of PBS for 1h at 25°C. The Fab samples were serially diluted 3 times using 1% BSA and incubated for 1h at 25°C (50 μl / well). The plate was washed 3 times with PBS-T and 50 μl / well of anti-human κ, HRP conjugate (Southern Biotech, product number 2060-05, batch number K3114-S506B) diluted 10,000 times in 1% BSA was added and kept at 25°C for 1 h. In some experiments (extended wash format), the plate was placed in a large volume (up to 1L) of PBS-T and incubated for 2-5 hours with mixing before adding anti-human κ, HRP conjugate. The plate was washed 3 times with PBS-T and developed with 50 μl / well of 1-Step Ultra TMB-ELISA (Thermo Scientific, product number 34028, batch number SF2405221). The reaction was stopped by adding 2N H2SO4, and A650 and A450 were determined before and after adding H2SO4 using a Spectramax microplate reader. To measure binding to murine TL1A, the same protocol was used, but the plates were coated with 2 μg / ml murine TL1A (BioLegend, product number 753004, lot number B204691) and the Fab samples were serially diluted 2-fold.

[0287] The binding activity of the chimeric 5C3D11 Fab was compared with that of the humanized 12835 Fab ( Figure 2 ). Although the binding activities of 5C3D11 and humanized 12835 in IgG form (divalent) appeared similar, a slight decrease in the binding activity of 12835 in Fab form (monovalent) was observed compared to the chimeric Fab ( Figure 2 ). This difference may reflect the difference between the true affinity (monovalent format) and the similar affinity (bivalent format). Using the monovalent assay format, the affinity of the chimeric Fab appears to be 2 to 3 times that of the humanized 12835 Fab.

[0288] Capture lift test

[0289] A nitrocellulose filter (Whatman 82-mm diameter, 0.45 μm pore size, GE Healthcare, Product No. 10401116) was floated on top of 10 ml of 10 mg / ml goat anti-human kappa (Southern Biotech Product No. 2060-01) at 25°C for 2 h. The filter was briefly submerged, then removed and transferred to 10 ml of 5% MP at 25°C for 2 h. The filter was removed from the 5% MP, rinsed once briefly with PBS, and air-dried. The filter was then processed in the same manner as the filter lift assay described above, with minor modifications. Briefly, a high titer phage stock (usually 10 6 A 1000x (200x) dilution was combined with 0.35 ml of a confluent E. coli strain XL culture and 20 μg / ml tetracycline. This mixture was combined with 3.5 ml of top agar (0.7% Bacto-agar in Luria broth) and overlaid on LB agar plates (1.5% Bacto-agar in Luria broth). The plates were incubated at 37°C for 6-8 h, at which time the pretreated nitrocellulose filter (described above) was placed on top and the plates were incubated at 25°C for 12-15 h. The filter was removed, rinsed briefly in PBS, and transferred to the desired concentration of biotinylated antigen in 5% MP. The filters were incubated at 25°C for 2 h with constant agitation, washed 5 times in PBS-0.05% Tween 20 (2 min per wash with constant agitation), and transferred to 10 ml of High Sensitivity Neutravidin, HRP conjugate (Thermo Scientific, Product No. 31030) diluted 5000-fold in PBS containing 1% BSA and incubated at 25°C for 1 h. The filters were then washed 5 times in PBS-0.05% Tween 20 (2 min per wash with constant agitation). All filters were developed with 1-Step Ultra TMB-Blotting (Thermo Scientific, Product No. 37574). Figure 3 The developed filters shown demonstrate the high sensitivity and affinity of 5C3D11 for TL1A.

[0290] Murine framework residues were removed from 12835 to identify multiple active humanized clones, including 18-7 and 21-3. Kunkel mutagenesis (Kunkel TA 1985. PNAS 82: 488-492) was used to remove the murine framework residues. In brief, single-stranded M13 plasmids were isolated and DNA replication was initiated with mutagenic oligonucleotides encoding human framework residues instead of oligonucleotides encoding mouse framework residues. After extension to circularize, bacterial transformation produced a mixture of wild-type (unpaired mouse framework residues) and mutant (human framework residues) plasmids. Mutagenesis was performed simultaneously at multiple sites to generate a small combinatorial library containing a mixture of clones containing various combinations of mouse and human framework mutations. Subsequently, the mixture was inoculated on a plate and screened by capture promotion to identify the most active framework combination. The library clones were characterized by DNA sequencing.

[0291] Fab was expressed in E. coli, quantified by ELISA and its binding activity was assessed by ELISA by titration against immobilized antigen. Expression of Fab, isolation of periplasmic fraction, quantification of Fab expression and binding to antigen by ELISA were performed as described above.

[0292] Using this approach, multiple active clones containing different numbers of murine framework residues were identified. Table 3 summarizes examples of active clones with different numbers and positions of murine framework residues.

[0293] Table 3. Active humanized 5C3D11 constructs with different amounts of framework back mutations

[0294]

[0295]

[0296] Synthesis of CDR-grafted constructs

[0297] Two clones identified, 18-7 and 21-3, contained only two murine framework back mutations. The light chain of clone 18-7 did not contain any murine framework residues, while the heavy chain of clone 21-3 did not contain any murine framework residues. Screening of the framework combinatorial library did not identify CDR-grafted variants (no murine framework residues on both the heavy and light chains). For comparison, CDR-grafted variants were synthesized using Kunkel mutagenesis and compared, and their binding activity was characterized by ELISA. Although the CDR-grafted constructs bound to the antigen, the humanized 12835 variants consistently showed stronger binding to the antigen ( Figure 4B ).

[0298] After back mutation of the mouse framework residues as shown in Table 3, the heavy chain variable region frameworks 1-3 were identical to human germline IGHV1-46*01, IGHV1-46*02 and IGHV1-46*03, while the light chain variable region framework was identical to human germline IGKV3-20*01.

[0299] In addition, different back mutations were introduced into the third framework of the heavy chain variable region, making the new heavy chain variable region homologous to human germline IGHV1-3*01 (see VH SEQ ID 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 and 541). Collectively, clones containing these back mutations are referred to as alternative framework variants.

[0300] Characterization of humanized variants in alternative ELISA formats

[0301] Using an alternative format (Watkins et al. 1997, Analytical Biochemistry 253) that allows rapid and direct comparison (without the need for a single-well assay of a dilution series) of the relative affinity of different Fab clones isolated from different cultures, without regard to the relative expression level of the clone, multiple Fab variants were characterized by ELISA. This assay enables a more quantitative comparison of the relative binding strength of the variants, because the plates are saturated with different Fabs despite the different expression levels of the plates. Therefore, the subtle differences in the binding profiles caused by the changes in the quantitative assay of Fab are eliminated. In brief, 96-well Costar-3366 plates were coated with 50 μl / well of 2 μg / ml goat anti-human κ (Southern Biotech product number 2060-01) at 25°C for 2h, washed once with PBS-0.05% Tween 20, and incubated with 50 μl / well of sample Fab for 2h at 50°C. The plates were washed 4 times with PBS-0.05% Tween 20 and incubated with 50 μl / well of serial dilutions of biotinylated antigen at 25°C for 2 h. The preparation of biotinylated antigens is described above. The plates were washed 4 times with PBS-0.05% Tween 20 and incubated with 50 μl / well of high-sensitivity Neutravidin, HRP conjugate (Thermo Scientific, product number 31030) diluted 5000 times in PBS solution containing 1% BSA at 25°C for 1 h. The plates were washed 3 times with PBS-T and developed with 50 μl / well of 1-Step Ultra TMB-ELISA (Thermo Scientific, product number 34028, batch number SF2405221). The reaction was stopped by adding 2N H2SO4, and A650 and A450 were determined before and after the addition of H2SO4 using a Spectramax microplate reader.

[0302] In an alternative ELISA format, the chimeric Fab bound antigen more strongly than the CDR-grafted Fab ( Figure 5 , compare open circles with solid circles). Humanized clone 12835 had slightly reduced binding compared to the chimera (compare open triangles with open circles), followed by clones 18-7 and 21-3. Clone 21-3 had the most similar binding to the CDR-grafted variant, suggesting that one of the murine heavy chain framework backmutations may be critical for maintaining full binding activity with the parental (wild-type) CDRs.

[0303] Example 2: Generation and characterization of anti-TL1A antibodies with optimized CDRs

[0304] To identify CDR mutations that can restore and improve the binding activity of CDR-grafted constructs (complete human germline frameworks), each position of all six CDRs (LCDR1, LCDR2, LCDR3, HCDR1, HCDR2, and HCDR3) was mutagenized separately by Kunkel mutagenesis using degenerate oligonucleotides in which the codons encoding the target amino acids were replaced by NNK. Initially, a library was synthesized at each position of HCDR3 and LCDR3. These positional libraries were screened by capture promotion, with a theoretical diversity of 32 codons / 20 amino acids / 1 stop codon. In some cases, each position was screened by itself (theoretical diversity of the library was equal to 32), while in other cases, the positions of specific CDRs were merged and screened as CDR libraries (theoretical diversity of the library was equal to 32 times the number of merged positions; for example, HCDR3 consists of 7 positions, so the theoretical library size is 32 x 7, which equals 224 members). The library was screened at a concentration of 15 to 1,000 pM of biotinylated human TL1A. Positive plaques were picked and sequenced. As previously described, Fabs were expressed, isolated from the periplasmic fraction, and characterized by ELISA. Tables 4 and 5 show a summary of capture-enhanced screening, DNA sequencing, and relative binding activity by ELISA for some initial screenings of LCDR3 and HCDR3, respectively. Tables 6 to 12 summarize the more detailed capture-enhanced screening results for all 6 CDRs.

[0305] In addition, LCDR3 and HCDR3 libraries constructed using alternative heavy chain variable region frameworks were prepared and screened by capture enhancement (Tables 13 and 14). Screening of CDR libraries constructed on alternative frameworks identified some mutations identified on the VH1-46*01 framework, and also identified novel mutations that were not previously identified (e.g., heavy chain CDR3 L98S, V102H, V102F and light chain CDR3 S92A, S92F, and S92Y).

[0306] Table 4. Light chain CDR3 position scanning (screening with 200 pM antigen)

[0307]

[0308]

[0309] Table 5. Heavy chain CDR3 position scanning (screening with 500 pM antigen)

[0310]

[0311] Table 6. Summary of heavy chain CDR1 screening (L8 template; 1-46*02 framework)

[0312]

[0313]

[0314] Table 7. Summary of heavy chain CDR2a screening (L8 template; 1-46*02 framework)

[0315]

[0316] Table 8. Summary of heavy chain CDR2b screening (various templates; 1-46*02 framework)

[0317]

[0318]

[0319] Table 9. Summary of heavy chain CDR3 screening (L8 template; 1-46*02 framework)

[0320]

[0321] Table 10. Summary of light chain CDR1 screening (L8 template; paired with heavy chain 1-46*02 framework)

[0322]

[0323]

[0324] Table 11. Summary of light chain CDR2 screening (L8 template; paired with heavy chain 1-46*02 framework)

[0325]

[0326] Table 12. Summary of light chain CDR3 screening (various templates; paired with heavy chain 1-46*02 framework)

[0327]

[0328]

[0329] Table 13. Summary of heavy chain CDR3 screening (L8mod template; heavy chain 1-3*01 related framework)

[0330]

[0331] Table 14. Summary of light chain CDR3 screening (L8mod template; paired with heavy chain 1-3*01 related framework)

[0332]

[0333] Example 3. Generation and characterization of anti-TL1A antibodies with optimized CDRs using mutant (S93) heavy chains

[0334] The clones (CDR-grafted and 21-3) of the heavy chain comprising CDR grafting have lower binding activity than the clones comprising mouse back mutation (S) at heavy chain position 93. Therefore, another HCDR3 library was constructed. The library was constructed as described above, except that the degenerate oligonucleotides of all positions were mixed before mutagenesis, and the library was synthesized and expressed as a pool, which was different from each position being checked separately. Similar to the HCDR3 positional scanning performed on the L8 heavy chain backbone (S93A), the position 102 of HCDR3 produced multiple mutations, which enhanced antigen binding in the capture and promotion form. Based on the heavy chain S93 template screening HCDR3 library identified some mutations identified on the heavy chain A93 template, and also identified previously unidentified novel mutations (e.g., heavy chain CDR3 V102I and V102Y). Table 15 shows the summary of capture and promotion screening and DNA sequencing.

[0335] Table 15. Capture boost screening of HCDR3 library pool on heavy chain template with S93

[0336] mutation frequency V102K 10 V102M 7 V102Y 4 V102L 2 V102I 1 V102E 1 V102T 1

[0337] Example 4. Identification and Engineering of Potential Sequence Libraries

[0338] Using Molecular Operating Environment (MOE) 2018.01 software (Chemical Computing Group, Montreal, Canada), a structural homology model of the variable region of the CDR-grafted construct L8 was established based on the known PDB antibody structure. The model and the BioMOE prediction algorithm are used to evaluate sequence liabilities. In addition, based on known potential unstable sequence motifs, the potential sequence liabilities of variants 12835 and L8 were analyzed (Jarasch et al., J. Pharm. Sci. 104: 1885-1898 (2015); Sydow et al., PLOS ONE 9: e100736 (2014); Vlasak and Ionescu mAbs 3: 253-263 (2011)). Using these methods, multiple residues were identified as potentially destabilizing, including: light chain M33, W35, W47, W91, and N94; heavy chain D31T32, M34, D52P52a, M69, and W103 (summarized in Table 17; FR denotes framework).

[0339] Exhaustive capture and promotion screening was carried out at all potential unstable sites located in CDR to identify amino acid substitutions that can eliminate these residues while retaining antigen binding. For example, a screening focused on light chain CDR3 N94 (potential deamidation site). The initial capture and promotion screening of LCDR3 position 94 could not identify mutations that showed enhanced affinity relative to the wild-type sequence. Therefore, in order to identify acceptable mutations to eliminate these potentially unstable residues, the conditions of the initial capture and promotion screening were changed. Specifically, instead of screening with antigen at a concentration where the wild-type sequence does not provide a signal, the antigen concentration was increased so that the clones expressing the wild-type sequence were visible in the promotion. In this way, variants that bind with an affinity similar to the wild-type sequence but eliminate problematic residues can be identified.

[0340] For the LCDR3 position 94 library, approximately 3,000 clones were plated and analyzed by capture boosting. 1000pM human TL1A was used to screen capture boosting, and plaques showing eight darkest and six lighter staining intensities were picked and sequenced. The results are summarized in Table 16. As expected, the two darkest stained plaques expressed wild-type residue N94. However, the other six dark-stained plaques expressed T94, indicating that variant N94T retained the binding affinity of the wild-type sequence to a large extent while eliminating potential deamidation sites. In addition, five different sequences were identified from the lighter-stained plaques. They include D, F, K, R and S. Although the affinity of these alternative sequences may be slightly lower than that of the wild-type sequence, all of these alternative sequences can also serve as substitutes for N94 when combined with other higher affinity mutations identified elsewhere.

[0341] Table 16. Identification of candidate residues at potential unstable site LCDR3 N94 (screened with 1000 pM antigen)

[0342]

[0343] Table 17. Summary of potentially destabilizing residues and active variants that eliminate destabilization

[0344]

[0345]

[0346] Example 5. Identification of mutations resulting in enhanced expression in E. coli

[0347] Certain mutations identified during the CDR library screening process by capture boosting did not always show enhanced binding in the ELISA format, but continued to express soluble Fabs at higher levels in the periplasmic space of bacteria than other variants. In particular, this phenomenon was observed at heavy chain CDR2 position V65 (V65G, V65T, and V65K) and light chain CDR1 position R24 (R24G). These results were surprising because the capture boosting screening format was configured to minimize the effects of different expression levels while maximizing the effects of affinity on signal intensity. Therefore, these mutations were noted and incorporated into subsequent combinatorial libraries that included mutations that enhanced affinity to determine whether these mutations would confer expression and / or thermal stability benefits to candidates expressed as complete immunoglobulins in mammalian expression systems.

[0348] Example 6. Generation and characterization of anti-TL1A antibodies with combined HCDR3 and LCDR3 mutations.

[0349] Based on the preliminary identification of beneficial mutations in HCDR3 and LCDR3, another library was synthesized, expressed and screened to identify combinations of independent mutations that can further improve binding affinity. The library was constructed by two-site mutagenesis using oligonucleotides encoding a subset of mutations identified in the positional scan. Oligonucleotides encoding wild-type residues were also included. The combinatorial library contained 30 different variants: wild type (no mutation), 9 variants containing single mutations (with redundancy of variants identified in the positional screening, as shown in Tables 4 and 5), and 20 unique combinations. Capture enhancement screening with 200 pM antigen identified 21 active clones. DNA sequencing of the 21 clones identified certain combinations more frequently than other clones (Table 18).

[0350] Table 18. Summary of combinatorial library screening and DNA sequences

[0351]

[0352] Subsequently, multiple combinatorial libraries were synthesized, expressed, and screened (described in detail below). In general, these library combinations were identified as mutations that improved affinity (Examples 2 and 3) and mutations that altered potentially destabilizing residues (Example 4) and mutations that might confer enhanced thermal stability / expression (Example 5). The combinatorial libraries were screened in multiple ELISA formats to identify clones with the best attributes (affinity, selectivity, binding to membrane-associated TL1A, and developability) for further development. As summarized in Tables 19 to 22, multiple variants with optimized and diversified CDR sequences using different VH germline templates were identified.

[0353] Table 19. Heavy chain CDRs on 1-46*02 heavy chain template

[0354]

[0355]

[0356] Table 20.3-20*01 Light Chain CDRs on Light Chain Template

[0357]

[0358] Table 21. Heavy chain CDRs on 1-3*01 heavy chain template

[0359]

[0360]

[0361] Table 22. Light chain CDRs on 3-20*01 light chain template

[0362]

[0363] Fabs with the CDRs shown in Tables 19 to 22 were tested for binding to human TL1A in multiple formats. First, human TL1A was immobilized on the surface of an ELISA plate and soluble Fab variants were titrated as shown in Figures 8 and 9. Next, a uniform (saturating) amount of soluble Fab variants was captured on the surface of the ELISA plate and soluble biotinylated human TL1A was titrated as shown in Figures 10 to 13. In both ELISA formats, all Fab variants bound to human TL1A and showed significantly enhanced binding relative to the CDR-grafted variant L8. In addition, these variants all bound equally or better to variant 12835, while having no or significantly fewer murine back mutations in the framework. As a result, these experiments elucidated a group of anti-TL1A variable regions that showed high binding affinity and high homology to human germline Ig sequences.

[0364] All Fab variants were tested for binding to membrane-associated TL1A. For these studies, a HEK293 cell line that had been transfected with human TL1A was used. 293 cells expressing membrane-bound human TL1A were maintained in DMEM containing L-glutamine, glucose, sodium pyruvate, and phenol red (ThermoFisher catalog number 11995-065) plus 10% fetal bovine serum, 1X penicillin-streptomycin (Fisher catalog number 15140122), and 2 μg / ml puromycin (Gibco catalog number A11138-03) in a 37°C incubator containing 5% CO2. Three days prior to the assay, 3x 10 6 Plate 10 cells into a T-75 flask so that the flask is 90-95% confluent on the day of the assay. Aspirate the medium and gently wash the cell monolayer with 5 ml PBS. Remove adherent cells by repeatedly pipetting 10 ml of ice-cold 1% BSA / PBS over the monolayer. Count the cells and aliquot 5x10 cells for each sample to be analyzed. 5. Collect the cells by centrifugation at 300xg for 5 minutes at 4°C, and discard the wash. Resuspend the cells in 100μl Fab or IgG diluted in 1% BSA / PBS and place on ice for 30min. Next, wash the cells with 1ml 1% BSA / PBS and collect by centrifugation at 300xg for 5min at 4°C. Discard the wash and add 100μl of a second goat F(ab')2 anti-human kappa FITC (Southern Biotech catalog number 2062-02) or goat F(ab')2 anti-human IgG PE (Southern Biotech catalog number 2043-09) conjugate diluted 1:200 in BSA / PBS. Place the cells on ice for 30min. Finally, wash the cells with 1ml BSA / PBS and collect the cells by centrifugation at 300xg for 5min at 4°C. Remove the wash and resuspend the cells in 500μl 1% BSA / PBS. One drop of Sytox AADvanced ReadyFlow Reagent (ThermoFisher Cat. No. R37173) was added to each sample and samples were analyzed on an Attune NxT flow cytometer (ThermoFisher). All variants bound to membrane associated human TL1A as shown in FIG14 .

[0365] Next, characterize the selectivity of all Fab variants for human TL1A relative to other TNFSF members TRAIL, LIGHT and Fas. Briefly, ELISA plates were coated overnight at 4°C with 50 μl / well of antigen (Fas / TNFSF6, R&D Systems, catalog number 126-FL / CF; TRAIL / TNFSF10, R&D Systems, catalog number 375-TL / CF; LIGHT / TNFSF14, R&D Systems, catalog number 664-LI / CF) at 1 μg / ml in PBS. The plate was washed 3 times with PBS-T and blocked with 100 μl 1% BSA / PBS. Blocking solution was discarded and Fab variants or control antibodies (Fas / TNFSF6, R&D Systems, catalog number AF126; TRAIL / TNFSF10, R&D Systems, catalog number AF375; LIGHT / TNFSF14, R&D Systems, catalog number AF664) were titrated in 50 μl 1% BSA / PBS and incubated at 25°C for 1 h. The plates were washed 3 times with PBS-T and HRP-conjugated secondary antibodies (diluted 5,000-fold in 1% BSA / PBS) were added for 1 h at 25°C. The plates were washed 3 times with PBS-T and developed. As shown in Figures 15 to 15 Fig. 20As shown, none of the variants showed detectable binding to related family members, suggesting that selectivity for human TL1A over other TNFSF family members is retained when designing higher affinity using the human germline framework template.

[0366] Example 7: Characterization of selected humanized variants expressed on different IgG constant regions

[0367] The light chain and heavy chain variable regions of clones 14, 17L, 23, 34, 47 and 53 from Tables 19 and 20 above are cloned into a kappa light chain constant region and a modified IgG1 or IgG2 heavy chain backbone, respectively. Modified IgG1 backbone and IgG2 are selected to reduce the potential effector functions of the antibody. Transient expression and purification characteristics are shown in Table 23 below. For these variants, expression as modified IgG1 is better than expression as IgG2. In addition, the yields obtained are consistent with the observations about the effects of certain mutations on bacterial expression (see Example 5). Specifically, the variants 14, 34 and 47 with the highest expression all contain mutations at heavy chain CDR2 V65G, V65T or V65K, while the variants 17L, 23 and 53 with the lowest expression do not contain.

[0368] In general, binding of all variants to human TL1A was retained in both formats (modified IgG1 and IgG2) as assessed by ELISA binding to antigen-coated plates ( FIG. 21 ) and by ELISA capture of soluble biotinylated antigen ( FIG. 22 ). In addition, binding to membrane-associated human TL1A was retained for all variants except when variant 53 was expressed as IgG2 ( Fig.23 Finally, the selectivity for human TL1A over other TNFSF members was maintained as no clones showed significant binding to the TNFSF family members Fas, TRAIL or LIGHT (Figure 24).

[0369] Table 23. Selected CDR variants expressed as human IgG1 (modified) and IgG2

[0370]

[0371]

[0372] Example 8: Characterization of potency and species selectivity in a whole blood assay.

[0373] The neutralizing activity and potency of the variants described herein expressed as IgG1 (modified) and IgG2 were tested in a human whole blood assay using healthy donors. This assay is a modification of Cassatella et al., "Soluble TNF-like cytokine (TL1A) production by immune complexes stimulated monocytes in rheumatoid arthritis" J Immunol. 2007 Jun 1 1; 178(11): 7325-33; and IFN-γ production is measured under conditions of upregulation and activation of TL1A and its receptor DR3. In this assay, soluble and membrane-associated TL1A are produced. The results of this assay have been shown to correlate with in vivo results in a colitis mouse model. See Takedatsu, “TL1A (TNFSF15) regulates the development of chronic colitis by modulating both T-helper 1 and T-helper 17 activation. Gastroenterology. 2008 Aug;135(2):552–567.

[0374] In brief, 96-well plates were coated with human gamma globulin in PBS at 4°C overnight, washed with PBS, and then incubated with anti-human IgG (Fc fragment specific) at 25°C for at least 1 hour to produce immune complexes (IC). Immediately before use, the plates were washed 3 times with PBS. The collected blood samples were treated with IL-12 and IL-18, antibodies were titrated in the samples, the samples were added to the plates and placed at 37°C for 24 hours. Next, 100 μl PBS / 5% BSA was added to each well and mixed. The plate was centrifuged at 500g for 5 minutes, and then about 150 μl of diluted plasma was collected for IFN-γ measurement. PBS was added to make it easier to collect cell plasma from the plate because the blood percentage was high (95%). All samples were diluted to ensure that their values ​​were within the linear range of the standard curve. All variants, regardless of the IgG form (modified IgG1 or IgG2), showed effective inhibition of IFN-γ production (Table 24). For comparison, typical IC50 values ​​for the murine parent antibody 5C3D11 and humanized 12835 were 1.38±0.95 nM (donor n=16) and 9.28±10.71 nM (donor n=4), respectively.

[0375] Table 24. Potency in human whole blood assay

[0376]

[0377]

[0378] Next, samples were evaluated in the same assay using blood obtained from cynomolgus monkeys to evaluate the cross-reactivity of the optimized humanized variants with cynomolgus monkey TL1A. The assay was performed similarly to the assay using human whole blood, except that the variants were tested at a single concentration (10 nM) rather than being fully titrated. The variants all inhibited IFN-γ production, but variants 47 and 53 did not inhibit to the extent of variants 14, 23, or 34 and murine 5C3D11 ( Fig.25 ). These data demonstrate that the optimized humanized variants retain cross-reactivity with cynomolgus monkey TL1A.

[0379] Neutralizing TL1A antibodies were also formatted as effector-free IgG1 (shown as SEQ ID NO: 542) molecules, expressed and purified from CHO cells, and used as described above using human ( Fig.26A -C) and cynomolgus monkeys ( Fig.27A The results are summarized in Table 25 below.

[0380] Table 25. Potency of CHO-expressed variants in human and cynomolgus monkey whole blood assay (IC50, nM)

[0381]

[0382] These experiments determined that all variants were active and potent, with variants 14 and 34 generally showing the greatest potency when using human blood. All variants were potent when using cynomolgus monkey blood. Variants 14, 23, and 34 showed similar potency against human and cynomolgus monkey TL1A, while variant 53 showed approximately 2-fold potency against human TL1A.

[0383] Example 9: Competition Assay

[0384] Binding competition assays using surface plasmon resonance (SPR) were performed to evaluate whether the test anti-TL1A antibodies bind to the same region on TL1A as any of the anti-TL1A antibodies described herein.

[0385] Reference antibodies were immobilized directly on the carboxymethylated dextran sensor chip surface (CMS) by amine coupling using a Biacore 2000 or 3000 instrument. Recombinant soluble human TL1A or mouse TL1A diluted to 10 nM in 8.1 mM Na2HPO4, 1.47 mM KF2PO4, pH 7.2, 237 mM NaCI, 2.7 mM KCI, 3.4 mM EDTA and 0.01% Tween 20 (PBS-NET) was injected at a flow rate of 10R1 / min for about 1 minute to achieve binding levels of at least 100 response units (RU) on the immobilized antibody. The reference antibody was then injected at 30 nM for 5 minutes to saturate all potential binding sites on TL1A. The reference antibody was injected repeatedly to confirm this saturation. Next, the test antibody in PBS-NET or PBS-NET alone as a control was injected at 30 nM for 5 minutes. If the test antibody binds to TL1A saturated with the first antibody, it indicates that the test antibody binds to a non-competing region on TL1A compared to the reference antibody. If the test antibody does not bind to saturated TL1A, it indicates that the two antibodies bind to the same region or compete for binding to TL1A. This strategy can be repeated with an immobilized test antibody and a reference antibody injected after the test antibody binds to TL1A. Each cycle can be repeated. At the end of each cycle, the immobilized antibody surface is regenerated by a 30 s pulse of 3 M MgCl2 or by 0.1% TFA followed by two consecutive 15 s PBS-NET pulses. All injections were performed at 25 °C with a collection rate of 10 Hz. All sensorgrams were double referenced by using a control surface and buffer injections.

[0386] Another binding competition assay is performed using SPR to evaluate whether the test anti-TL1A antibody binds to the same region on TL1A as any of the anti-TL1A antibodies described herein. The reference antibody is immobilized on the SPR chip by amine coupling on the array at three or four different densities. The TL1A protein is injected in an increasing concentration series to estimate kinetic parameters and appropriate concentrations for injection during competition binning experiments. Once the optimal antigen concentration for binning experiments is determined, regeneration conditions (usually brief low pH injections) are evaluated to establish optimal conditions for regeneration between binning assay cycles.

[0387] Binning is performed using a premixing approach, where a medium concentration of TL1A, either alone or pre-complexed with the test antibody at a saturating antibody concentration (e.g., 30-50 μg / mL), is injected across the array. The assay can be run so that the test antibody is immobilized and the reference antibody is pre-complexed with TL1A. Clones that bind to unique regions of the immobilized antibody provide signal enhancement, while competing clones reduce the antigen binding signal. Competition assays are run so that all clones are tested as ligands and analytes.

[0388] Example 10: Comparison of Binding of 5C3D11 with Other Anti-TL1A Antibodies

[0389] Two epitope binning studies were performed to compare the epitopes recognized by 5C3D11 and 12835 with those recognized by other TL1A antibodies including 1D1, 1681, 1B4 and 1A9, as shown in Table 26.

[0390] Table 26. Antibody variable region sequences used for epitope binning studies

[0391]

[0392] To minimize the avidity effect, a planar carboxymethyl dextran surface sensor chip (Xantec product number SPMXCMDP) was used in the first study, while a HC30M sensor chip (Xantec product number SPMXHC30M) was used in the second study. The running buffer for continuous flow micro-spotting was HBS-EP+, and the flow rate was 65μl / min. The chip was activated with 18mM EDC and 4.5nM sulfo-NHS in 100mM MES, pH 5.5 for 7 minutes. The antibody was then fixed with two repeated prints for 15min. The antibody was diluted to 10μg / ml in 10mM acetate at pH 4.5. The antibody was titrated at three locations on the plate with a 3-fold serial dilution to establish a concentration series of different spot densities. Each antibody was spotted 8 times - twice for each of the four dilutions. This created an array of 10x 8. The remaining active groups were neutralized with 1M ethanolamine (pH 8.5) with a 7-minute quench. Since the antigen is a homotrimeric protein and IgG is bivalent, epitope binning was performed using premix conditions.

[0393] First epitope binning study – TL1A was prepared at 50 nM final concentration (3.3 μg / ml) and mixed with 333 nM (50 μg / ml) analyte (solution phase antibody) or running buffer (control). For samples in IgG format, 50 μg / ml is 333 nM, while for samples in Fab format, 50 μg / ml is 1 μM. The mixed samples were injected on the array for 5 min and regenerated for 30 seconds after each cycle using a 4:1 mixture of Pierce IgG elution buffer and 5M NaCl (1M final concentration).

[0394] Second epitope binning study – TL1A was prepared at 50 nM final concentration (3.3 μg / ml) and mixed with 1 μM (150 μg / ml) IgG or 2 μM (200 μg / ml) Fab analyte (solution phase antibody) or running buffer (control). Antibody samples were serially diluted 2-fold seven times (7.8 nM final concentration for IgG and 15 nM final concentration for Fab). The mixed samples were injected on the array for 5 min and regenerated for 30 s after each cycle using a 4:1 mixture of Pierce IgG elution buffer and 5 M NaCl (1 M final concentration).

[0395] In the epitope binning study, clear signals (sandwich) were observed with immobilized 5C3D11 and 12835, and all control antibodies were tested as analytes (Table 27, first two rows). These results demonstrate that 5C3D11 and 12835 can bind to TL1A simultaneously with other antibodies, thereby recognizing different epitopes.

[0396] Table 27. Summary of the ability of antibodies to form a sandwich structure (yes)

[0397]

[0398]

[0399] Example 11: In vivo evaluation of anti-TL1A efficacy

[0400] The efficacy of anti-TL1A antibodies in animal models of colitis was evaluated. In rodent models of acute colitis induced by intrarectal administration of dinitrobenzene sulfonic acid or trinitrobenzene sulfonic acid (D / TNBS) or oxazolone, and by administration of DSS in the drinking water or transfer of CD45RB hi Anti-TL1A antibodies were tested in rodent models of T-induced chronic colitis. DNBS and oxazolidinone induce local ulcers and inflammation. DSS administration induces strong, generalized inflammation of the intestine, characterized by erosive lesions and inflammatory infiltrates. Symptoms of all these models typically include diarrhea, occult blood, weight loss, and occasional rectal prolapse. In the preventive model, antibody treatment begins with the start of administration of the compound that induces colitis. In the therapeutic model, antibody treatment begins a few days after the start of induction. The effects of the treatment on body weight, stool consistency and occult blood, as well as the effects on epithelial integrity and the degree of inflammatory infiltrates observed under the microscope were determined. Daily clinical scoring was performed based on stool consistency and the presence of occult blood, and a disease activity index (DAI) score was given.

[0401] Example 12: Phase 1 clinical trial

[0402] A Phase 1 clinical trial was conducted to evaluate the safety, tolerability, pharmacokinetics, and pharmacodynamics of the anti-TL1A antibodies provided herein in subjects with Crohn's disease.

[0403] Single ascending dose (SAD) arm: Subjects in each group (subjects are grouped according to the presence or absence of risk variants) receive a single dose of antibody or placebo. Exemplary doses are 1, 3, 10, 30, 100, 300, 600 and 800 mg of antibody, or 5 to 30 mg / kg. Safety monitoring and PK evaluation are performed over a predetermined period of time. Based on the evaluation of PK data, if the antibody is considered well tolerated, the dose is increased in the same group of subjects or another group of healthy subjects. Continue to increase the dose until the maximum dose is reached unless the predetermined maximum exposure is reached or obvious intolerable side effects occur.

[0404] Multiple ascending dose (MAD) arm: Subjects in each group (subjects are grouped according to the presence or absence of risk variants) receive multiple doses of antibody or placebo. The dose level and dosing interval are selected as the dose level and dosing interval predicted to be safe based on the SAD data. The dose level and dosing frequency are selected to achieve therapeutic drug levels in the systemic circulation that maintain a steady state for several days to allow monitoring of appropriate safety parameters. Samples are collected and analyzed to determine the PK profile.

[0405] Inclusion criteria: Healthy subjects of infertile potential between the ages of 18 and 55 years. Health was defined as the absence of clinically relevant abnormalities as determined by a detailed medical history, a complete physical examination (including blood pressure and pulse rate measurement), a 12-lead ECG, and clinical laboratory tests. Female subjects of infertile potential must meet at least one of the following criteria: (1) achieved postmenopausal status, defined as: cessation of regular menstruation for at least 12 consecutive months without other pathological or physiological causes; serum follicle-stimulating hormone (FSH) levels within the laboratory reference range for postmenopausal women; (2) had a documented hysterectomy and / or bilateral oophorectomy; (3) had medically confirmed ovarian failure. All other female subjects (including women with tubal ligation and those without a documented hysterectomy, bilateral oophorectomy, and / or ovarian failure) will be considered to be of fertile potential. Body mass index (BMI) of 17.5 to 30.5 kg / m2; weight >50 kg (110 pounds). Evidence of a signed and dated informed consent document indicating that the subject (or legal representative) has been informed of all relevant aspects of the research.

[0406] Two groups of healthy subjects were selected: subjects with a risk variant, the presence of which is associated with increased susceptibility to Crohn's disease, and subjects lacking the risk variant.

[0407] Exclusion Criteria: Evidence or history of clinically significant hematologic, renal, endocrine, pulmonary, gastrointestinal, cardiovascular, hepatic, psychiatric, neurological, or allergic disease (including drug allergy, but excluding untreated, asymptomatic, seasonal allergy at the time of dosing). Subjects with a historical or current positive result for any of the following serological tests: hepatitis B surface antigen (HBsAg), hepatitis B core antibody (HBcAb), anti-hepatitis C antibody (HCV Ab), or human immunodeficiency virus (HIV). Subjects with a history of allergic or anaphylactic reaction to therapeutic drugs. Treatment with study drug within 30 days prior to the first dose of study drug (or as determined by local requirements, whichever is longer) or within the previous 5 half-lives or 180 days for biologics. Pregnant women; lactating women; and women of childbearing potential.

[0408] Main outcome measures: Incidence of dose-limiting or intolerance treatment-related adverse events (AEs) [time frame: 12 weeks]. Incidence, severity, and causality of treatment-emergent AEs (TEAEs), and discontinuations due to treatment-emergent AEs [time frame: 12 weeks]. Incidence and severity of abnormal laboratory test results [time frame: 12 weeks]. Abnormal and clinically relevant changes in vital signs, blood pressure (BP), and electrocardiogram (ECG) parameters [time frame: 12 weeks].

[0409] Secondary outcome measures: Single ascending dose: Maximum observed plasma concentration (C max ) [Time frame: 12 weeks]. Single ascending dose: Time to maximum observed plasma concentration (T max ) [Time frame: 12 weeks]. Single ascending dose: Area under the plasma concentration-time curve from time zero to day 14 (AUC14day) [Time frame: 12 weeks]. Single ascending dose: Area under the plasma concentration-time curve from time zero extrapolated to infinity (AUC inf ) [Time frame: 12 weeks]. Single ascending dose: The area under the plasma concentration-time curve (AUC las t) [Time frame: 12 weeks]. Single ascending dose: Dose-normalized maximum plasma concentration (C max [dn]) [Time frame: 12 weeks]. Single ascending dose: dose-normalized area under the plasma concentration-time curve (AUC) from time zero extrapolated to infinity inf [dn]) [Time frame: 12 weeks]. Single ascending dose: The dose-normalized area under the plasma concentration-time curve (AUC) from time zero to the last quantifiable concentration last[dn]) [Time frame: 12 weeks]. Single ascending dose: Plasma decay half-life (t1 / 2) [Time frame: 12 weeks]. Plasma decay half-life is the time it takes for the plasma concentration to decrease by half. Single ascending dose: Mean residence time (MRT) [Time frame: 12 weeks]. Single ascending dose: Steady-state volume of distribution (V ss ) [Time frame: 6 weeks]. The volume of distribution is defined as the theoretical volume through which the total amount of drug needs to be uniformly distributed to produce the desired blood drug concentration. Steady-state volume of distribution (V ss ) is the apparent volume of distribution at steady state. Single ascending dose: Systemic clearance (CL) [Time frame: 6]. CL is a quantitative measure of the rate at which a drug substance is eliminated from the body.

[0410] Multiple ascending doses First dose: Maximum observed plasma concentration (C max ) [Time frame: 12 weeks]. Multiple ascending doses First dose: Time to maximum observed plasma concentration (T max ) [Time frame: 12 weeks]. Multiple ascending doses First dose: The area under the plasma concentration-time curve (AUC) from time zero to time τ (dosing interval, where τ = 2 weeks) τ ) [Time frame: 12 weeks]. Multiple ascending doses First dose: Dose-normalized maximum plasma concentration (C max [dn]) [Time frame: 12 weeks]. Multiple ascending doses First dose: Dose-normalized area under the plasma concentration-time curve (AUC) from time zero to time τ (dosing interval, where τ = 2 weeks) τ [dn]) [Time frame: 12 weeks]. Plasma decay half-life (t1 / 2) [Time frame: 12 weeks]. Plasma decay half-life is the time measured for the plasma concentration to decrease by half. Multiple ascending doses First dose: Mean residence time (MRT) [Time frame: 12 weeks]. Apparent volume of distribution (Vz / F) [Time frame: 12 weeks]. The volume of distribution is defined as the theoretical volume through which the total amount of drug needs to be uniformly distributed to produce the desired blood drug concentration. The apparent volume of distribution (Vz / F) after an oral dose is affected by the fraction absorbed. Multiple ascending doses First dose: Steady-state volume of distribution (V ss ) [Time frame: 12 weeks]. The volume of distribution is defined as the theoretical volume through which the total amount of drug needs to be uniformly distributed to produce the desired blood drug concentration. Steady-state volume of distribution (V ss) is the apparent volume of distribution at steady state. Multiple ascending doses First dose: Apparent oral clearance (CL / F) [Time frame: 12 weeks]. The clearance of a drug is a measure of the rate at which the drug is metabolized or eliminated by normal biological processes. The clearance obtained after an oral dose (apparent oral clearance) is affected by the fraction of the dose absorbed. Clearance is estimated by population pharmacokinetic (PK) modeling. Drug clearance is a quantitative measure of the rate at which the drug substance is removed from the blood. Multiple ascending doses First dose: Systemic clearance (CL) [Time frame: 12 weeks]. CL is a quantitative measure of the rate at which the drug substance is removed from the body.

[0411] Multiple ascending doses Multiple doses: Maximum observed plasma concentration (C max ) [Time frame: 12 weeks]. Multiple ascending doses Multiple doses: Time to maximum observed plasma concentration (T max ) [Time frame: 12 weeks]. Multiple ascending doses Multiple doses: The area under the plasma concentration-time curve (AUC) from time zero to time τ (dosing interval, where τ = 2 weeks) τ ) [Time frame: 12 weeks]. Multiple ascending doses Multiple doses: Dose-normalized maximum plasma concentration (C max Multiple ascending doses Multiple doses: The dose-normalized area under the plasma concentration-time curve (AUC) from time zero to time τ (dosing interval, where τ = 2 weeks) τ [dn]) [Time frame: 12 weeks]. Multiple ascending doses Multiple doses: Plasma decay half-life (t1 / 2) [Time frame: 12 weeks]. Plasma decay half-life is the time measured for the plasma concentration to decrease by half. Multiple ascending doses Multiple doses: Apparent volume of distribution (Vz / F) [Time frame: 12 weeks]. The volume of distribution is defined as the theoretical volume through which the total amount of drug needs to be uniformly distributed to produce the desired blood drug concentration. The apparent volume of distribution (Vz / F) following an oral dose is affected by the fraction absorbed. Multiple ascending doses Multiple doses: Steady-state volume of distribution (V ss ) [Time frame: 12 weeks]. The volume of distribution is defined as the theoretical volume through which the total amount of drug needs to be uniformly distributed to produce the desired blood drug concentration. Steady-state volume of distribution (V ss ) is the apparent distribution volume at steady state.

[0412] Multiple Ascending DoseMultiple Dose: Apparent Oral Clearance (CL / F) [Time Frame: 12 Weeks]. The clearance of a drug is a measure of the rate at which the drug is metabolized or eliminated by normal biological processes. The clearance achieved after an oral dose (apparent oral clearance) is affected by the fraction of the dose absorbed. Clearance is estimated by population pharmacokinetic (PK) modeling. Drug clearance is a quantitative measure of the rate at which the drug substance is eliminated from the blood. Multiple Ascending DoseMultiple Dose: Systemic Clearance (CL) [Time Frame: 12 Weeks]. CL is a quantitative measure of the rate at which the drug substance is eliminated from the body. Multiple Ascending DoseMultiple Dose: Minimum Observed Plasma Trough Concentration (C min ) [Time frame: 12 weeks]. Multiple ascending dose Multiple dose: Average concentration at steady state (Cav) [Time frame: 12 weeks]. Multiple ascending dose Multiple dose: Observed accumulation ratio (Rac) [Time frame: 12 weeks]. Multiple ascending dose Multiple dose: Peak to trough fluctuation (PTF) [Time frame: 12 weeks]. Multiple ascending dose additional parameter: Estimated bioavailability of subcutaneous administration at corresponding intravenous doses (F) [Time frame: 12 weeks]. Immunogenicity of single ascending dose and multiple ascending dose: Development of anti-drug antibodies (ADA) [Time frame: 12 weeks].

[0413] Example 13: Phase 1b clinical trial

[0414] A Phase 1b open-label clinical trial is being conducted to evaluate the efficacy of the anti-TL1A antibodies provided herein in patients with risk variants associated with Crohn's disease.

[0415] Arm: 10 patients positive for a risk variant, the presence of which is associated with increased susceptibility to Crohn's disease, are given the antibody. 5-10 risk variant-negative patients are given the antibody. Patients are monitored in real time. Endoscopy and biopsies are prepared centrally, and the readers are blinded to the timing and endpoint of treatment.

[0416] Inclusion Criteria: Two groups of subjects were selected: subjects with a risk variant, the presence of which is associated with increased susceptibility to Crohn's disease, and subjects lacking the risk variant.

[0417] Main outcome measures: Simple Endoscopic Score for Crohn's Disease (SESCD), Crohn's Disease Activity Index (CDAI), and patient-reported outcomes (PROs). If the risk variant-positive group shows a 50% reduction from baseline, a Phase 2a clinical trial will be conducted.

[0418] Entry criteria: PRO entry criteria: abdominal pain score of 2 or higher, and / or stool frequency score of 4 or higher. Primary outcome was pain score of 0 or 1, stool frequency score of 3 or lower, and no worsening from baseline. Endoscopy entry criteria: If colon was involved, SESCD ileum was entered only at scores of 4 and 6. Primary endoscopic outcome was 40-50% difference in mean SESCD.

[0419] Example 14: Phase 2a clinical trial

[0420] A Phase 2a clinical trial is being conducted to evaluate the efficacy of the anti-TL1A antibodies provided herein in subjects with Crohn's disease.

[0421] Arms: 40 patients in each arm (antibody and placebo arms) were treated with antibody or placebo for 12 weeks. An interim analysis was performed after 20 patients in each group were treated at the highest dose to find a 40-50% difference between the placebo and treatment groups in the primary outcome (50% reduction in SESCD, CDAI, and PRO relative to baseline).

[0422] Main outcome measures: Simple Endoscopic Score for Crohn's Disease (SESCD), Crohn's Disease Activity Index (CDAI), and patient-reported outcomes (PROs).

[0423] Entry criteria: PRO entry criteria: abdominal pain score of 2 or higher, and / or stool frequency score of 4 or higher. Primary outcome was pain score of 0 or 1, stool frequency score of 3 or lower, and no worsening from baseline. Endoscopy entry criteria: If colon was involved, SESCD ileum was entered only at scores of 4 and 6. Primary endoscopic outcome was 40-50% difference in mean SESCD.

[0424] Various embodiments are described above in the detailed description. Although these descriptions directly describe the above embodiments, it should be understood that modifications and / or changes to the specific embodiments shown and described herein may be conceived by those skilled in the art. Any such modifications or changes that fall within the scope of this description are also intended to be included therein. Unless otherwise specified, it is the intention of the inventor that the words and phrases in this specification and claims have the common and customary meanings for those of ordinary skill in the applicable field.

[0425] The above description of various embodiments known to the applicant at the time of filing this application has been presented, and is intended for purposes of illustration and description. The description of the present invention is not exhaustive, nor is it limited to the precise form disclosed, and many modifications and changes can be made in accordance with the above teachings. The described embodiments are used to explain principles and practical applications, and to enable others skilled in the art to utilize the various embodiments, optionally with various modifications, and suitable for the specific use intended. Therefore, it is intended that the present disclosure is not limited to the specific embodiments disclosed.

[0426] Although specific embodiments have been shown and described, it will be apparent to those skilled in the art that, based on the teachings herein, changes and modifications may be made without departing from the present disclosure and its broader aspects, and the appended claims are intended to encompass all such changes and modifications within their scope and within the true spirit and scope of the present disclosure. Those skilled in the art will appreciate that, in general, the terms used herein generally mean "open" terms (e.g., the term "including" should be interpreted as "including but not limited to", the term "having" should be interpreted as "at least having", the term "including" should be interpreted as "including but not limited to", etc.).

[0427] sequence

[0428]

[0429]

[0430]

[0431]

[0432]

[0433] SEQ ID NO:490 (L8; VL)

[0434] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0435] SEQ ID NO:491 (L8; VH)

[0436] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQVRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDVWGQGTTVTVSS

[0437] SEQ ID NO:492 (Clone 34; VL)

[0438] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0439] SEQ ID NO:493 (Clone 34; VH)

[0440] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHIKYDPKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDWWGQGTTVTVSS

[0441] SEQ ID NO:494 (Clone 2; VL)

[0442] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0443] SEQ ID NO:495 (Clone 2; VH)

[0444] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHIKYSPKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDWWGQGTTVTVSS

[0445] SEQ ID NO:496 (Clone 52; VL)

[0446] EIVLTQSPGTLSLSPGERATLSCGASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0447] SEQ ID NO:497 (Clone 52; VH)

[0448] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHIKYSPKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDWWGQGTTVTVSS

[0449] SEQ ID NO:498 (Clone 46; VL)

[0450] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0451] SEQ ID NO:499 (Clone 46; VH)

[0452] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHVKYSPKFQVRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDWWGQGTTVTVSS

[0453] SEQ ID NO:500 (Clone 47; VL)

[0454] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0455] SEQ ID NO:501 (Clone 47; VH)

[0456] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHVKYDPKFQTRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDWWGQGTTVTVSS

[0457] SEQ ID NO:502 (Clone 14; VL)

[0458] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWQGNPRTFGGGTKLEIK

[0459] SEQ ID NO:503 (Clone 14; VH)

[0460] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHiKYDPKFQkRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDMWGQGTTVTVSS

[0461] SEQ ID NO:504 (Clone 16L; VL)

[0462] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWQGNPRTFGGGTKLEIK

[0463] SEQ ID NO:505 (Clone 16L; VH)

[0464] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHvKiDPKFQVRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDMWGQGTTVTVSS

[0465] SEQ ID NO:506 (Clone 17L; VL)

[0466] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWQGNPRTFGGGTKLEIK

[0467] SEQ ID NO:507 (Clone 17L; VH)

[0468] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHLKYDPKFQVRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDMWGQGTTVTVSS

[0469] SEQ ID NO:508 (Clone 17L-1; VL)

[0470] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWQGNPRTFGGGTKLEIK

[0471] SEQ ID NO:509 (Clone 17L-1; VH)

[0472] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHLKYDPKFQRRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDMWGQGTTVTVSS

[0473] SEQ ID NO:510 (Clone 23; VL)

[0474] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0475] SEQ ID NO:511 (Clone 23; VH)

[0476] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHLKYDPKFQNRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDKWGQGTTVTVSS

[0477] SEQ ID NO:512 (Clone A1; VL)

[0478] EIVLTQSPGTLSLSPGERATLSCGASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0479] SEQ ID NO:513 (Clone A1; VH)

[0480] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHLKYDPKFQNRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDKWGQGTTVTVSS

[0481] SEQ ID NO:514 (Clone 53; VL)

[0482] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0483] SEQ ID NO:515 (Clone 53; VH)

[0484] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHLKYDPKFQERVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDKWGQGTTVTVSS

[0485] SEQ ID NO:516 (Clone E1; VL)

[0486] EIVLTQSPGTLSLSPGERATLSCGASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWEGNPRTFGGGTKLEIK

[0487] SEQ ID NO:517 (Clone E1; VH)

[0488] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIEPASGHLKYDPKFQERVTMTRDTSTSTVYMELSSLRSEDTAVYYCARSGGLPDKWGQGTTVTVSS

[0489] SEQ ID NO:518 (Clone 3-17L V-A; VL)

[0490] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWQGNPRTFGGGTKLEIK

[0491] SEQ ID NO:519 (Clone 3-17L V-A; VH)

[0492] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHLKYDPKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYCARSGGLPDMWGQGTTVTVSS

[0493] SEQ ID NO:520 (Clone 3-17L; VL)

[0494] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWQGNPRTFGGGTKLEIK

[0495] SEQ ID NO:521 (Clone 3-17L; VH)

[0496] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHLKYDPKFQGRVTITRDTSASTVYMELSSLRSEDTAVYYCARSGGLPDMWGQGTTVTVSS

[0497] SEQ ID NO:522 (Clone L8mod; VL)

[0498] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0499] SEQ ID NO:523 (Clone L8mod; VH)

[0500] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDVWGQGTTVTVSS

[0501] SEQ ID NO:524 (Clone X-V; VL)

[0502] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0503] SEQ ID NO:525 (Clone X-V; VH)

[0504] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQVRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0505] SEQ ID NO:526 (Clone X; VL)

[0506] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0507] SEQ ID NO:527 (Clone X; VH)

[0508] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0509] SEQ ID NO:528 (Clone H3-1; VL)

[0510] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0511] SEQ ID NO:529 (Clone H3-1; VH)

[0512] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDLWGQGTTVTVSS

[0513] SEQ ID NO:530 (Clone XL3-6; VL)

[0514] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCSQWSGNPRTFGGGTKLEIK

[0515] SEQ ID NO:531 (Clone XL3-6; VH)

[0516] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0517] SEQ ID NO:532 (Clone XL3 - 10; VL)

[0518] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRSFGGGTKLEIK

[0519] SEQ ID NO:533 (Clone XL3 - 10; VH)

[0520] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0521] SEQ ID NO:534 (Clone XL3 - 15; VL)

[0522] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSRNPRTFGGGTKLEIK

[0523] SEQ ID NO:535 (Clone XL3 - 15; VH)

[0524] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0525] SEQ ID NO:536 (Clone L3 - 13; VL)

[0526] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWKGNPRTFGGGTKLEIK

[0527] SEQ ID NO:537 (Clone L3-13; VH)

[0528] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHTKYDPKFQGRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0529] SEQ ID NO:538 (Clone H2-2; VL)

[0530] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0531] SEQ ID NO:539 (Clone H2-2; VH)

[0532] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHSKYDPKFQVRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0533] SEQ ID NO:540 (Clone H2-5; VL)

[0534] EIVLTQSPGTLSLSPGERATLSCRASSSVSYMYWYQQKPGQAPRLLIYATSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSGNPRTFGGGTKLEIK

[0535] SEQ ID NO:541 (Clone H2-5; VH)

[0536] QVQLVQSGAEVKKPGASVKVSCKASGFDIQDTYMHWVRQAPGQGLEWMGRIDPASGHYKYDPKFQVRATITTDTSASTAYLQLSSLRSEDTAVYYCARSGGLPDFWGQGTTVTVSS

[0537] G1 modified by SEQ ID NO:542

[0538] ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGAPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

[0539] Constant region of G2 of SEQ ID NO:543

[0540] ASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKCCVECPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAPIEKTISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

[0541] Constant region of Kappa of SEQ ID NO:544

[0542] <h2 style=";text-align:left;direction:ltr">RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0543] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:545(L8 HFR1)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0544] <h2 style=";text-align:left;direction:ltr"> QVQLVQSGAEVKKPGASVKVSCKAS<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0545] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:546(L8 HFR2)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0546] <h2 style=";text-align:left;direction:ltr"> WVRQAPGQGLEWMG<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0547] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:547(L8 HFR3)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0548] <h2 style=";text-align:left;direction:ltr"> RVTMTRDTSTSTVYMELSSLRSEDTAVYYC<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0549] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:548(L8 HFR4)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0550] <h2 style=";text-align:left;direction:ltr"> WGQGTTVTVSS<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0551] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:549(L8 LFR1)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0552] <h2 style=";text-align:left;direction:ltr"> EIVLTQSPGTLSLSPGERATLSC<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0553] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:550(L8 LFR2)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0554] <h2 style=";text-align:left;direction:ltr"> WYQQKPGQAPRLLIY<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0555] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:551(L8 LFR3)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0556] <h2 style=";text-align:left;direction:ltr"> GIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0557] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:552(L8 LFR4)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0558] <h2 style=";text-align:left;direction:ltr"> FGGGTKLEIK<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0559] <h2 style=";text-align:left;direction:ltr"> SEQ ID NO:586(VH FR3)<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0560] <h2 style=";text-align:left;direction:ltr"> RATITTDTSASTAYLQLSSLRSEDTAVYYC<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr">

[0561] SEQ ID NO:587(VH FR3)

[0562] RVTITRDTSASTVYMELSSLRSEDTAVYYC

[0563] SEQ ID NO:588(VH FR3)

[0564] RVTITRDTSASTAYMELSSLRSEDTAVYYC

Claims

1. An antibody or antigen-binding fragment that specifically binds to TL1A, comprising: A heavy chain variable region comprising: (a) HCDR1 comprising the amino acid sequence shown in SEQ ID NO: 553; (b) a HCDR2 comprising the amino acid sequence shown in any one of SEQ ID NOs: 554 to 564 or 574 to 577; and (c) a HCDR3 comprising the amino acid sequence shown in any one of SEQ ID NOs: 565 to 568 or 578 to 581; and A light chain variable region comprising: (d) LCDR1 comprising the amino acid sequence shown in any one of SEQ ID NO: 569 or 570; (e) LCDR2 comprising the amino acid sequence shown in SEQ ID NO: 488; and (f) LCDR3 comprising the amino acid sequence shown in any one of SEQ ID NOs: 571 to 573 or 582 to 585.

2. An antibody or antigen-binding fragment that specifically binds to TL1A, comprising: a heavy chain variable region comprising: (a) a HCDR1, HCDR2, and HCDR3 selected from any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, or 541; and The light chain variable region comprises (b) a LCDR1, LCDR2, and LCDR3 selected from any one of SEQ ID NO: 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, or 540; Wherein the CDRs are defined by the Kabat, Chothia or IMGT methods or a combination thereof.

3. An antibody or antigen-binding fragment that specifically binds to TL1A, comprising: (a) a heavy chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO: 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539 or 541; and (b) a light chain variable region comprising an amino acid sequence that is at least about 90% identical to any one of SEQ ID NO:490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538 or 540.

4. A pharmaceutical composition comprising the antibody or antigen-binding fragment specifically binding to TL1A according to any one of claims 1 to 3 and a pharmaceutically acceptable excipient, carrier or diluent.

5. A method for treating inflammatory bowel disease, Crohn's disease or colitis in an individual, comprising administering to the individual an effective amount of the antibody or antigen-binding fragment that specifically binds to TL1A according to any one of claims 1 to 3 or the pharmaceutical composition of claim 4, wherein the individual is diagnosed with or suspected of having inflammatory bowel disease, Crohn's disease or colitis.

6. A method for preventing or reducing interferon-γ secretion by T lymphocytes in an individual, comprising administering to the individual an effective amount of the antibody or antigen-binding fragment that specifically binds to TL1A according to any one of claims 1 to 3 or the pharmaceutical composition of claim 4.

7. A nucleic acid encoding the antibody or antigen-binding fragment that specifically binds to TL1A according to any one of claims 1 to 3.

8. A method of preparing a treatment for inflammatory bowel disease, Crohn's disease or colitis comprising incubating cells comprising the nucleic acid of claim 7 in a culture medium under conditions sufficient to secrete the antibody or antigen-binding fragment that specifically binds to TL1A of any one of claims 1 to 3 into the culture medium.

9. A method for preparing a treatment for inflammatory bowel disease, Crohn's disease or colitis, comprising mixing an antibody or antigen-binding fragment that specifically binds to TL1A according to any one of claims 1 to 3 with a pharmaceutically acceptable excipient, carrier or diluent.

10. Use of an antibody or antigen-binding fragment that specifically binds to TL1A according to any one of claims 1 to 3 or a pharmaceutical composition according to claim 4 in the preparation of a medicament for treating a disease or condition in an individual having a risk variant associated with the disease or condition, wherein the disease or condition comprises at least one of inflammatory bowel disease (IBD), Crohn's disease (CD), or colitis.

Images