Combination therapy with α4β7 inhibitor and IL-23 inhibitor

Abstract

Provided herein are combination therapies comprising an α4β7 inhibitor, eg, an anti-α4β7 antibody, eg, vedolizumab, and an IL-23 inhibitor, eg, an anti-IL-23 antibody.

Description

[Technical Field]

[0001] Related Applications This application claims priority to U.S. Provisional Patent Application No. 62 / 835,349, filed April 17, 2019, the contents of which are incorporated herein by reference.

[0002] Sequence Listing This application includes herewith a sequence listing, which is submitted in electronically readable format. The sequence listing file was created on April 14, 2020, is named "T103022_1100WO_0415_4_SL.txt", and is 24kb in size. The entire contents of the sequence listing in sequencelisting.txt are incorporated herein by reference.

[0003] Technical Field The present invention relates to methods and compositions related to combination therapies comprising an α4β7 inhibitor, eg, an anti-α4β7 antibody (eg, vedolizumab), and an IL-23 inhibitor, eg, an anti-IL-23 antibody. [Background technology]

[0004] Interleukin-23 (IL-23) is a heterodimeric cytokine composed of p40 and p19 subunits. IL-23 is generally produced by antigen-presenting cells (e.g., dendritic cells and macrophages) and monocytes in response to infection with various bacterial and fungal pathogens. The IL-23 receptor, IL-23R, is expressed on various adaptive and innate immune cells, including Th17 cells, gamma-delta T cells, natural killer (NK) cells, dendritic cells, macrophages, and innate lymphocytes. IL-23R and downstream effector cytokines play important roles in the pathogenesis of inflammatory bowel disease (IBD) in acute and chronic mouse models. IL-23R gene expression and protein levels are elevated at the intestinal mucosal surface in IBD patients.

[0005] IL-23 inhibitors are an exciting new class of targeted molecules for treating IBD. For example, monoclonal antibodies against IL-23 inhibit the T cell proliferation and proliferation of naive T cells. H It has been shown to limit differentiation into 17 cells, thereby ameliorating the pathogenesis of IBD (see, e.g., WO2018 / 112232).

[0006] Despite the development of targeted IL-23 therapy (see Kashani and Schwartz (2019) Gastroenterol Hepatol NY 15(5):255), there remains an unmet medical need for alternative therapies that may reduce the disease burden, improve remission rates, and mitigate progression of immune disorders such as IBD. Summary of the Invention

[0007] In various aspects, the present disclosure provides methods of treating autoimmune disorders and / or inflammatory bowel disease by administering a combination of an α4β7 inhibitor, such as an anti-α4β7 antibody, or an antigen-binding fragment thereof, and an IL-23 inhibitor, such as an anti-IL-23 antibody, or an antigen-binding fragment thereof.

[0008] In one aspect of the invention, provided herein is a method of treating a human patient in need thereof, the method comprising administering to the human patient an α4β7 inhibitor and an IL-23 inhibitor.

[0009] In one embodiment, the α4β7 inhibitor is an anti-α4β7 antibody. In one embodiment, the anti-α4β7 antibody is humanized. In one embodiment, the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6.

[0010] In one aspect of the present invention, provided herein is a method of treating a human patient in need thereof, the method comprising administering to the human patient an anti-α4β7 antibody and an IL-23 inhibitor, wherein the anti-α4β7 antibody is an IgG1 antibody; comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and comprises a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6.

[0011] In one embodiment, the human patient has an autoimmune disease. In one embodiment, the autoimmune disease is psoriasis or arthritis. In a specific embodiment, the autoimmune disease is rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, or axial spondyloarthritis.

[0012] In one embodiment, the human patient has inflammatory bowel disease (IBD). In one embodiment, the IBD is ulcerative colitis (e.g., moderately to severely active ulcerative colitis) or Crohn's disease (e.g., moderately to severely active Crohn's disease).

[0013] In one embodiment, the anti-α4β7 antibody is administered before the IL-23 inhibitor.

[0014] In another embodiment, the anti-α4β7 antibody is administered after the IL-23 inhibitor.

[0015] In one embodiment, the anti-α4β7 antibody is administered simultaneously with the IL-23 inhibitor.

[0016] In another embodiment, the anti-α4β7 antibody comprises a heavy chain variable domain comprising the amino acid sequence set forth in SEQ ID NO:1 and a light chain variable domain comprising the amino acid sequence set forth in SEQ ID NO:5.

[0017] In one embodiment, the anti-α4β7 antibody is a humanized antibody.

[0018] In one embodiment, the anti-α4β7 antibody is vedolizumab.

[0019] In one embodiment, a human patient receives an initial dose of 300 mg of anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of anti-α4β7 antibody at week 2, followed by a third dose of 300 mg of anti-α4β7 antibody at week 6. In one embodiment, a human patient receives 300 mg of anti-α4β7 antibody every 8 weeks starting 8 weeks after the third dose. In a further embodiment, a human patient receives 300 mg of anti-α4β7 antibody every 4 weeks if they do not show clinical improvement.

[0020] In another embodiment, administered to a human patient, the human patient has ulcerative colitis or Crohn's disease, and the clinical improvement is clinical remission.

[0021] In one embodiment, a human patient receives 300 mg of anti-α4β7 antibody every four weeks starting eight weeks after the third dose.

[0022] In an alternative embodiment, the human patient receives 108 mg of anti-α4β7 antibody every two weeks starting eight weeks after the third dose.

[0023] In one embodiment, a human patient receives an initial dose of 300 mg of anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of anti-α4β7 antibody at week 2, followed by a third dose of 108 mg of anti-α4β7 antibody at week 6, followed by doses of 108 mg every two weeks thereafter.

[0024] In yet another embodiment, the anti-α4β7 antibody is administered intravenously to a human patient. In a specific embodiment, a 300 mg dose is administered intravenously.

[0025] In one embodiment, the anti-α4β7 antibody is administered subcutaneously to a human patient. In a specific embodiment, a dose of 108 mg is administered subcutaneously.

[0026] In one embodiment, the IL-23 inhibitor is an antibody that binds to the p19 subunit of IL-23.

[0027] In one embodiment, the IL-23 inhibitor is an antibody that binds to the p40 subunit of IL-23.

[0028] In one embodiment, the IL-23 inhibitor is an antibody that binds to the p19 and p40 subunits of IL-23.

[0029] In certain embodiments, the IL-23 inhibitor is an anti-IL-23 antibody, such as, but not limited to, risankizumab, ustekinumab, guselkumab, or tildrakizumab.

[0030] In one embodiment, the IL-23 inhibitor is an antibody that binds to IL-23R.

[0031] In one embodiment, the human patient is characterized as a non-responder or non-remitter at 6 and / or 10 weeks after initiation of treatment with an α4β7 inhibitor (e.g., an anti-α4β7 antibody, e.g., vedolizumab).

[0032] In one embodiment, the human patient is characterized as having elevated levels of IL-22 in serum at the initiation of treatment with an α4β7 inhibitor (e.g., an anti-α4β7 antibody, e.g., vedolizumab) or 6 or 10 weeks after initiation.

[0033] In one embodiment, the level of IL-22 in the serum of a human patient does not decrease, decreases by more than two-fold, or decreases by more than three-fold from the start of treatment with an anti-α4β7 antibody (e.g., vedolizumab) to 10 weeks after the start of treatment, from the start of treatment with an anti-α4β7 antibody to 6 weeks after the start of treatment, or from 6 weeks to 10 weeks after the start of treatment with an anti-α4β7 antibody.

[0034] In further embodiments, the human patient is characterized as having elevated serum levels of IL-22 at the initiation of or 6 weeks after initiation of treatment with an anti-α4β7 antibody (e.g., vedolizumab), and the serum IL-22 levels do not decrease, decrease by more than two-fold, or decrease by more than three-fold from initiation to 10 weeks, from initiation to 6 weeks, or from 6 weeks to 10 weeks.

[0035] In one embodiment, the human patient is characterized as having elevated levels of IL-1β in serum at the start of treatment with an α4β7 inhibitor (e.g., an anti-α4β7 antibody, e.g., vedolizumab) or 6 or 10 weeks after the start of treatment.

[0036] In further embodiments, the human patient is characterized as having elevated fecal calprotectin levels at or 6 weeks after initiation of treatment with an anti-α4β7 antibody (e.g., vedolizumab), and the fecal calprotectin levels do not decrease, decrease by more than two-fold, or decrease by more than three-fold between initiation and 10 weeks, between initiation and 6 weeks, or between 6 weeks and 10 weeks.

[0037] In certain embodiments, the human patient is characterized as having elevated levels of IL-22, STAT5A, and / or IL-1β compared to control levels. In certain embodiments, the human patient is characterized as having elevated levels of IL-22, STAT5A, and / or IL-1β compared to reference levels.

[0038] In one embodiment, the control levels of IL-22, STAT5A, and / or IL-1β are levels in any one or more of a subject not afflicted with IBD, a healthy subject, non-inflamed colon tissue from a patient, or non-colon tissue. In one embodiment, the reference levels of IL-22 and / or STAT5A are levels determined from baseline levels in patients who respond to treatment with vedolizumab.

[0039] In one embodiment, a patient's IL-22, STAT5A, and / or IL-1β levels are measured initially, for example, before treatment with vedolizumab or on the first day of treatment.

[0040] In another embodiment, the patient's IL-22, STAT5A, and / or IL-1β levels, e.g., starting levels, are measured 1, 2, 3, 4, 5, 6, 7, 8, 9, and / or 10 days prior to treatment with vedolizumab.

[0041] In one embodiment, the patient's IL-22, STAT5A, and / or IL-1β nucleic acid and / or protein levels are measured. In certain embodiments, the IL-22, STAT5A, and / or IL-1β levels are elevated by 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or more compared to the control or reference level. In certain embodiments, IL-22, STAT5A, and / or IL-1β levels are increased by 5% to 35%, 5% to 25%, 5% to 20%, 5% to 15%, 5% to 10%, 10% to 20%, 10% to 15%, 10% to 30%, 15% to 40%, 20% to 50%, 25% to 60%, 30% to 70%, or 40% to 100%, or more, compared to a control or reference level.

[0042] In some aspects, the invention provides methods of treating inflammatory bowel disease in a patient in need thereof, the method comprising administering to the patient an anti-α4β7 antibody (e.g., vedolizumab) and an antibody that binds to the p19 subunit of IL-23, wherein the anti-α4β7 antibody is administered to the human patient by administering an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, a third dose of 300 mg of the anti-α4β7 antibody at week 6, and then administering the anti-α4β7 antibody every 8 weeks starting 8 weeks after the third dose. and a 300 mg dose of the anti-α4β7 antibody, wherein the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, and the patient is characterized as having elevated levels of IL-22, STAT5A, and / or IL-1β compared to control levels.

[0043] In some aspects, the invention provides methods of treating inflammatory bowel disease in a patient in need thereof, the method comprising administering to the patient an anti-α4β7 antibody (e.g., vedolizumab) and an antibody that binds to the p40 subunit of IL-23, wherein the anti-α4β7 antibody is administered to the human patient by administering an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, a third dose of 300 mg of the anti-α4β7 antibody at week 6, and then administering the anti-α4β7 antibody every 8 weeks starting 8 weeks after the third dose. and a 300 mg dose of the anti-α4β7 antibody, wherein the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, and the patient is characterized as having elevated levels of IL-22, STAT5A, and / or IL-1β compared to control levels.

[0044] In some aspects, the invention provides a method of treating inflammatory bowel disease in a patient in need thereof, the method comprising administering to the patient an anti-α4β7 antibody (e.g., vedolizumab) and an antibody that binds to the p19 subunit of IL-23, wherein the anti-α4β7 antibody is administered as follows: an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, followed by a third dose of 108 mg of the anti-α4β7 antibody at week 6, followed by doses of 108 mg every two weeks thereafter, wherein the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, wherein the patient is characterized as having elevated levels of IL-22, STAT5A, and / or IL-1β compared to control levels.

[0045] In some aspects, the invention provides methods of treating inflammatory bowel disease in a patient in need thereof, the method comprising administering to the patient an anti-α4β7 antibody (e.g., vedolizumab) and an antibody that binds to the p40 subunit of IL-23, wherein the anti-α4β7 antibody is administered as follows: an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, followed by a third dose of 108 mg of the anti-α4β7 antibody at week 6, followed by doses of 108 mg every two weeks thereafter, wherein the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, wherein the patient is characterized as having elevated levels of IL-22, STAT5A, and / or IL-1β compared to control levels.

[0046] In certain embodiments, the control level is a level in one or more of a subject not afflicted with IBD, a healthy subject, non-inflamed colon tissue from the patient, or non-colon tissue. [Brief explanation of the drawings]

[0047] [Figure 1] Baseline IL22 (A) and STAT5A (B) mRNA levels were higher in colonic tissues from VDZ non-responder (VDZ-NR) UC patients compared with responder (VDZ-R) UC patients. mRNA expression was derived from microarray data generated in moderate / severe UC patients (Gene Expression Omnibus: GSE73661). Horizontal rectangle: healthy controls (mean ± 1 SD). [Figure 2]Serum IL-22 levels at baseline were similar in VDZ-remitters and non-remitters, but remained proportionally higher in non-remitters. Serum IL-22 was assessed in patients with moderate-to-severe CD. (A) IL-22 levels at baseline and week 10 in VDZ-remitters and non-remitters. IL-22 levels were censored at the lower limit of quantification (2.7 pg / ml). (B) Fold change in IL-22 from baseline to week 10. [Figure 3] 1 provides a schematic diagram of the study described in Example 1. [Figure 4A] The results of the mouse colitis study described in Example 1 are presented graphically, in which colon weight, diarrhea score, and histopathology score were quantified for healthy mice (normal), mice injected with a negative IgG control, anti-MAdCAM antibody, anti-p40 antibody, and both anti-MAdCAM antibody and anti-p40 antibody. [Figure 4B] The results of the mouse colitis study described in Example 1 are presented graphically, in which colon weight, diarrhea score, and histopathology score were quantified for healthy mice (normal), mice injected with a negative IgG control, anti-MAdCAM antibody, anti-p40 antibody, and both anti-MAdCAM antibody and anti-p40 antibody. [Figure 4C] The results of the mouse colitis study described in Example 1 are presented graphically, in which colon weight, diarrhea score, and histopathology score were quantified for healthy mice (normal), mice injected with a negative IgG control, anti-MAdCAM antibody, anti-p40 antibody, and both anti-MAdCAM antibody and anti-p40 antibody. [Figure 5] (A) Graphical representation of the results of the study in Example 1 showing CD3% in the lamina propria (LP) and epithelium (EL) for the IgG-injected group (negative control), the anti-MAdCAM antibody-injected group, the anti-p40 antibody-injected group, and the anti-MAdCAM antibody and anti-p40 antibody-injected group. (B) Correlation between the percentage of CD3 and total inflammatory cell infiltration. [Figure 6] Panels A and B graphically depict the results showing the levels of neutrophils (Figure 6A) and macrophages (Figure 6B) in the lamina propria 28 days after administration of IgG, anti-MAdCAM-1 antibody, anti-p40 antibody, or a combination of anti-MAdCAM-1 and anti-p40 antibodies. [Figure 7] 1 is a graphical representation of a diagram showing the synergistic effect of gene expression using a combination of anti-MAdCAM-1 and anti-p40 therapy. [Figure 8] Figures A-C show graphs of the results of administering a vehicle control (negative control), anti-MAdCAM-1 antibody (MAdCAM-1), anti-p40 antibody (p40), or a combination of anti-MAdCAM-1 and anti-p40 antibodies (combo) in a mouse model of colitis. Normal mice were used for comparison. Figure A shows the body weight (g) of mice on day 21, Figure B shows the body weight of mice on day 28, and Figure C shows the diarrhea score of mice on day 21. [Figure 9A] Figures 9A, 9B, and 9C show the results of administering a vehicle control (negative control), anti-MAdCAM-1 antibody (MAdCAM-1), anti-p40 antibody (p40), or a combination of anti-MAdCAM-1 and anti-p40 antibodies (combo) in a mouse model of colitis. Figures 9A, 9B, and 9C show the levels of CD3+ T cells, MPO+ neutrophils, and CD68+ macrophages, respectively, in the colonic mucosa of each tested group and a normal control. [Figure 9B] Figures 9A, 9B, and 9C show the results of administering a vehicle control (negative control), anti-MAdCAM-1 antibody (MAdCAM-1), anti-p40 antibody (p40), or a combination of anti-MAdCAM-1 and anti-p40 antibodies (combo) in a mouse model of colitis. Figures 9A, 9B, and 9C show the levels of CD3+ T cells, MPO+ neutrophils, and CD68+ macrophages, respectively, in the colonic mucosa of each tested group and a normal control. [Figure 9C] Figures 9A, 9B, and 9C show the results of administering a vehicle control (negative control), anti-MAdCAM-1 antibody (MAdCAM-1), anti-p40 antibody (p40), or a combination of anti-MAdCAM-1 and anti-p40 antibodies (combo) in a mouse model of colitis. Figures 9A, 9B, and 9C show the levels of CD3+ T cells, MPO+ neutrophils, and CD68+ macrophages, respectively, in the colonic mucosa of each tested group and a normal control. DETAILED DESCRIPTION OF THE INVENTION

[0048] definition In order that the present invention may be more readily understood, certain terms are first defined. Additionally, it should be noted that whenever a value or range of values ​​for a parameter is listed, it is intended that values ​​and ranges intermediate to the listed values ​​are also part of the invention.

[0049] The cell surface molecule "α4β7 integrin" or "α4β7" (used interchangeably throughout) is a heterodimer of the α4 chain (CD49D, ITGA4, OMIM 192975, human GeneID 3676) and the β7 chain (ITGB7, OMIM 147559, human GeneID 3695). The human α4-integrin and β7-integrin genes (GenBank (National Center for Biotechnology Information, Bethesda, MD) RefSeq accession numbers NM_000885 and NM_000889, respectively) are expressed by B and T lymphocytes, particularly memory CD4+ lymphocytes. Unique to many integrins, α4β7 can exist in either a resting or active state. Ligands for α4β7 include vascular cell adhesion molecule (VCAM), fibronectin, and mucosal addressin (MAdCAM (e.g., MAdCAM-1)).

[0050] As used herein, an "inhibitor of α4β7 integrin" or "α4β7 inhibitor" inhibits the binding of α4β7 integrin to a ligand, e.g., MAdCAM, VCAM, or fibronectin. α4β7 inhibitors that inhibit the binding of α4β7 integrin to MAdCAM include antibodies that bind to α4 integrin, β7 integrin, or an integrin protein complex comprising α4 integrin and β7 integrin. Administering a polypeptide that inhibits MAdCAM-α4β7 integrin binding to inhibit α4β7 integrin activity is "anti-α4β7 integrin therapy." In certain embodiments, the polypeptide that inhibits MAdCAM-α4β7 integrin binding is an anti-α4β7 integrin antibody, e.g., an antibody that binds to α4 or β7 only in the presence of the other, e.g., vedolizumab, or a related antibody, or an antigen-binding fragment thereof. In some embodiments, the α4β7 inhibitor binds to α4β7 integrin, blocks the interaction of α4β7 integrin with MAdCAM-1, and inhibits the migration of memory T lymphocytes across the endothelium into inflamed gastrointestinal parenchyma.

[0051] As used herein, an antibody or antigen-binding fragment thereof that has "binding specificity for the α4β7 complex" binds to α4β7 but does not bind to α4β1 or αEB7. Vedolizumab is an example of an antibody that has binding specificity for the α4β7 complex.

[0052] As used herein, "anti-α4β7 antibody" or "anti-α4β7 integrin antibody" refers to an antibody that specifically binds to α4β7 integrin. In one embodiment, the anti-α4β7 antibody blocks or inhibits the binding of α4β7 integrin to one or more of its ligands. In one embodiment, the anti-α4β7 antibody binds to α4β7 but does not bind to α4β1 or αEB7. In one embodiment, the anti-α4β7 antibody is vedolizumab.

[0053] The term "antibody" broadly refers to an immunoglobulin molecule composed of four polypeptide chains, two heavy (H) chains and two light (L) chains, interconnected by disulfide bonds. Each heavy chain consists of a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region (CH). The heavy chain constant region consists of three domains: CH1, CH2, and CH3. Each light chain consists of a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region. The light chain constant region consists of one domain, CL. The VH and VL regions can be further subdivided into regions of hypervariability, called complementarity-determining regions (CDRs), interspersed with more conserved regions, called framework regions (FRs). Each VH and VL consists of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.

[0054] As used herein, the term "antibody fragment" or "antigen-binding fragment" of an antibody refers to Fab, Fab', F(ab)2, and Fv fragments, single-chain antibodies, functional heavy-chain antibodies (nanobodies), and any portion of an antibody that has specificity for at least one desired epitope (e.g., an isolated portion of the complementarity-determining regions with sufficient framework sequences such that it specifically binds to the epitope) that competes with the intact antibody for specific binding. Antigen-binding fragments can be produced by recombinant techniques or by enzymatic or chemical cleavage of antibodies.

[0055] As used herein, the term "humanized antibody" refers to an antibody derived from a non-human antibody (e.g., a mouse) that retains or substantially retains the antigen-binding properties of the parent antibody, but is less immunogenic in humans and contains minimal sequence derived from the non-human immunoglobulin. Generally, humanized antibodies are human immunoglobulins (recipient antibodies) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit, or a non-human primate having the desired specificity, affinity, and capacity. In some cases, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or the donor antibody. These modifications are made to further improve antibody performance. Generally, a humanized antibody will comprise substantially all of at least one, and usually two, variable domains, in which all or substantially all of the hypervariable loops (complementarity-determining regions) correspond to those of a non-human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992).

[0056] As used herein, the term "IL-23 inhibitor" refers to an agent that inhibits or reduces IL-23 activity. The agent may, for example, bind to IL-23 and / or IL-23R, thereby inhibiting IL-23 activity. Alternatively, the agent may act to reduce the levels of IL-23 mRNA or IL-23 protein. Examples of IL-23 inhibitors include, but are not limited to, antibodies or antigen-binding fragments thereof, small molecules, and nucleic acids (e.g., mRNA, DNA, siRNA, shRNA, antisense RNA, miRNA). IL-23 inhibitors may act on either subunit of IL-23 (i.e., p19 or p40), or alternatively, on both subunits, e.g., overlapping or combinatorial epitopes. Thus, in some embodiments, an IL-23 inhibitor binds to p19 (e.g., an anti-p19 antibody) and inhibits or reduces IL-23 activity. In other embodiments, the IL-23 inhibitor binds to p40 (e.g., an anti-p40 antibody). As used herein, the terms "p19" and "p40" refer to the respective subunits that make up human IL-23. In some embodiments, the IL-23 inhibitor binds to IL-23R (its subunits IL-23R and / or IL-12RB1). Thus, in some embodiments, the term "IL-23 inhibitor" encompasses agents that bind to or inhibit any one or more of p19 (e.g., an anti-p19 antibody), p40 (e.g., an anti-p40 antibody), or IL-23R (an anti-IL-23R antibody), and such terms are used interchangeably.

[0057] As used herein, the term "monoclonal antibody" refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and / or bind the same epitope, except for possible variations that may arise during the generation of the monoclonal antibody, and such variations are generally present in minor amounts. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies and is not to be construed as requiring production of the antibody by any particular method. For example, monoclonal antibodies to be used in accordance with the present invention may be produced using the hybridoma method first described by Kohler et al., Nature, 256:495 (1975), or may be produced by recombinant DNA methods (e.g., U.S. Pat. No. 4,816,567). The "monoclonal antibodies" may also be isolated from phage antibody libraries using, for example, the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991).

[0058] As used herein, the term "recombinant antibody" refers to an antibody produced as a result of transcription and translation of a gene carried on a recombinant expression vector. In one embodiment, the vector has been introduced into a host cell. Alternatively, the vector can be used in a cell-free system.

[0059] The term "initial time" refers to the starting point used for comparison. In one embodiment, initial time refers to a time point prior to treatment with an anti-α4β7 antibody or antigen-binding fragment thereof, e.g., day 0.

[0060] Terms like "treatment" or "treating" refer to any treatment of a disease or disorder in a human subject, including preventing or preventing the disease or disorder, i.e., preventing or inhibiting the development of clinical symptoms; inhibiting the disease or disorder, i.e., preventing or inhibiting the development of clinical symptoms; and / or ameliorating the disease or disorder, i.e., causing regression of clinical symptoms. In one embodiment, treatment of IBD is achieved, and the subject with IBD experiences improvement in symptoms as measured by a dosing regimen using an anti-α4β7 antibody and an IL-23 inhibitor in a recognized IBD index (e.g., a clinical measure of Crohn's disease or ulcerative colitis).

[0061] The term "therapeutically effective dose" is defined as an amount sufficient to cure or at least partially prevent the disease and its complications in a patient already suffering from the disease. In one embodiment, a therapeutically effective dose is a dose of an anti-α4β7 antibody and a dose of an IL-23 inhibitor that is capable of improving symptoms and / or eliminating or reducing complications associated with IBD (e.g., those due to long-term steroid use) in a human subject with the disease. In one embodiment, a therapeutically effective dose is a dose of an anti-α4β7 antibody and a dose of an IL-23 inhibitor that is capable of reducing the Crohn's Disease Activity Index (CDAI) score or reducing the modified CDAI to a score lower than that defined for Crohn's disease in a human subject diagnosed with Crohn's disease. In one embodiment, a therapeutically effective dose is a dose of an anti-α4β7 antibody and a dose of an IL-23 inhibitor that is capable of reducing the Mayo score or reducing the ulcerative colitis to a score lower than that defined for ulcerative colitis in a human subject diagnosed with ulcerative colitis.

[0062] As used herein, the term "clinical remission" as used herein with respect to an ulcerative colitis subject refers to a complete Mayo score of 2 points or less and no individual subscores greater than 1 point. Crohn's disease "clinical remission" refers to a CDAI score of 150 points or less.

[0063] The term "clinical response" as used herein with respect to ulcerative colitis subjects refers to a reduction in the complete Mayo score of 3 or more points and 30% from baseline (or a partial Mayo score of 2 or more points and 25% or more from baseline if a complete Mayo score was not performed at the visit), with a reduction in the rectal bleeding subscore of 1 or more points or an absolute rectal bleeding score of 1 point or less. As used herein with respect to Crohn's disease subjects, "clinical response" refers to a reduction in the CDAI score of 70 or more points from baseline (week 0).

[0064] As used herein, the terms "non-remitters," "remitters," or "vedolizumab non-remitters" are used interchangeably to refer to a subset of patients with an autoimmune disease and / or IBD (e.g., Crohn's disease or ulcerative colitis), who have received a first and second induction dose, or a third induction dose, of an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), and who show signs of non-remission early in the therapy, e.g., vedolizumab therapy (e.g., about 3 or 4 weeks after the second or third induction dose). For example, the patient may receive an anti-α4β7 antibody (e.g., vedolizumab) at 0 and 2 weeks, or at 0, 2, and 6 weeks. A patient may exhibit a clinical response to treatment, but not clinical remission, for example, about 3-4 weeks after the second dose, e.g., 5 or 6 weeks after initiation of treatment with an anti-α4β7 antibody (e.g., vedolizumab), or about 3-8 weeks after the third dose, e.g., 10 or 14 weeks after initiation. Indications of non-remission may include, for example, a failure to achieve clinical remission measures and / or measures described herein.

[0065] As used herein, the term "about" is used synonymously with the term "approximately." Descriptively, use of the term "about" indicates a value slightly outside of the cited value, i.e., ±5%.

[0066] Therapeutic Uses and Methods Provided herein are methods for treating a human patient in need thereof using a combination therapy comprising an α4β7 inhibitor, e.g., an anti-α4β7 antibody, and an IL-23 inhibitor. The combination therapy is based, at least in part, on the discoveries described in the Examples below. For example, an anti-α4β7 antibody, or an antigen-binding portion thereof, such as vedolizumab, reduces inflammation associated with IBD, e.g., Crohn's disease, by blocking the trafficking of α4β7 T cells to the lamina propria of the colon, while an IL-23 inhibitor, such as an anti-IL23 antibody, or an antigen-binding portion thereof, reduces inflammation in a human subject with Crohn's disease through blocking IL-23 derived from innate immune cells in the lamina propria.

[0067] By suppressing or downregulating the gut adaptive and innate immune systems with vedolizumab and IL-23 inhibitors, the two agents complement each other to provide therapeutic improvement against intestinal inflammation in subjects with IBD.

[0068] "Combination therapy," in the context of administration, is intended to mean the use of two or more therapies, e.g., two or more agents, e.g., an α4β7 inhibitor, e.g., an anti-α4β7 antibody, or antigen-binding portion thereof, and an IL-23 inhibitor, e.g., an anti-p40, anti-p19 antibody, or anti-IL-23R antibody, or antigen-binding fragments thereof. The use of the terms "in combination" or "combination therapy" does not restrict the order in which therapies are administered to a subject with a disease. The first treatment can be administered before (e.g., 1 minute, 45 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 ​​hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks), simultaneously with, or after (e.g., 1 minute, 45 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 ​​hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks) the administration of the second treatment to a subject with a disease such as inflammatory bowel disease (IBD). Any additional therapy can be administered in any order with the other additional treatments.

[0069] In one embodiment, the present invention provides a method of treating a human patient in need thereof, the method comprising administering to the human patient an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody (e.g., vedolizumab), or an antigen-binding portion thereof, and an IL-23 inhibitor (e.g., an anti-p40, anti-p19 antibody, anti-IL-23R antibody, or an antigen-binding portion thereof). In certain embodiments, the human patient has an autoimmune disease, including, but not limited to, psoriasis or arthritis (e.g., rheumatoid arthritis, psoriatic arthritis, axial spondyloarthritis, juvenile arthritis), and / or an inflammatory bowel disease (IBD), such as, but not limited to, ulcerative colitis or Crohn's disease. In certain embodiments, the human patient has moderately to severely active ulcerative colitis. In other embodiments, the human patient has moderately to severely active Crohn's disease.

[0070] In one embodiment, the α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), or antigen-binding portion thereof, is administered before the IL-23 inhibitor (e.g., an anti-p40, anti-p19, anti-IL-23R antibody, or antigen-binding portion thereof) for treatment. In other embodiments, the anti-α4β7 antibody (e.g., vedolizumab), or antigen-binding portion thereof, is administered after the IL-23 inhibitor (e.g., an anti-p40, anti-p19, or anti-IL-23R antibody, or antigen-binding portion thereof). In yet other embodiments, the anti-α4β7 antibody (e.g., vedolizumab), or antigen-binding portion thereof, is administered in combination with the IL-23 inhibitor (e.g., an anti-p40, anti-p19, or anti-IL-23R antibody, or antigen-binding portion thereof). at the same time It is administered.

[0071] The methods disclosed herein include combination therapy comprising administering both an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab) or an antigen-binding portion thereof, and an IL-23 inhibitor (e.g., an anti-p40, anti-p19 antibody, anti-IL-23R antibody, or antigen-binding portion thereof). In some embodiments, the α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab) or antigen-binding portion thereof, may be administered according to an approved protocol, and the IL23 inhibitor (e.g., an anti-p40, anti-p19 antibody, anti-IL-23R antibody, or antigen-binding portion thereof) may be administered according to an approved protocol.

[0072] In the combination therapies disclosed herein, the α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), or antigen-binding portion thereof, and the IL-23 inhibitor (e.g., an anti-p40 or anti-p19 antibody, or antigen-binding portion thereof) may be administered by a variety of routes known in the art, e.g., orally, transdermally, subcutaneously, intranasally, intravenously, intramuscularly, intraocularly, or parenterally. The most suitable route for administration in any given case will depend, for example, on the particular α4β7 inhibitor, e.g., anti-α4β7 antibody and IL-23 inhibitor, being administered, as well as the patient, the formulation, the method of administration (e.g., time of administration), the patient's age, weight, body surface area, sex, severity of the disease being treated, the patient's diet, and the patient's excretion rate.

[0073] In the combination therapies disclosed herein, an IL-23 inhibitor (e.g., an anti-IL23 antibody or an anti-IL23R antibody) can be administered to a patient in need thereof (e.g., a patient with an autoimmune disease such as arthritis or psoriasis, and / or an inflammatory disease such as IBD) prior to administration of an anti-α4β7 antibody (e.g., vedolizumab). In some embodiments, in the combination therapies disclosed herein, the IL-23 inhibitor can be administered to the patient 1 minute to 1 week (e.g., 1 minute, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, or 7 days) or more prior to the administration of the α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab).

[0074] Alternatively, in the combination therapies disclosed herein, an IL-23 inhibitor (e.g., an anti-IL-23 antibody or an anti-IL23 antibody) can be administered to a patient in need thereof (e.g., a patient with an autoimmune disease, such as arthritis or psoriasis, and / or an inflammatory disease, such as IBD) after administration of an α4β7 inhibitor, e.g., an anti-α4β7 antibody. In some embodiments, in the combination therapies disclosed herein, the IL-23 inhibitor can be administered to the patient 1 minute to 1 week (e.g., 1 minute, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, or 7 days) or more after administration of the α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab).

[0075] The combination therapies disclosed herein may be continued for any given amount of time necessary to treat a disease, e.g., IBD, including from 1 week to 10 years (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 2 years, 3 years, 4 years, 5 years, 6 years, 7 years, 8 years, 9 years, 10 years) or more. For example, in the combination therapies disclosed herein, an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab) and an IL-23 inhibitor (e.g., an anti-IL-23 antibody), can be administered at the doses and frequencies described herein to a patient in need thereof (e.g., a patient with an autoimmune disease, such as arthritis or psoriasis, and / or an inflammatory disease, such as IBD) for between 1 week and 10 years (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 1 year, 2 years, 3 years, 4 years, 5 years, 6 years, 7 years, 8 years, 9 years, 10 years).

[0076] In some embodiments, a patient with an autoimmune disease (e.g., arthritis or psoriasis—e.g., rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, axial spondyloarthritis) or a chronic inflammatory disease (e.g., IBD) may continue to be administered a combination therapy disclosed herein until one or more symptoms of the patient's disease are reduced (e.g., by 5% or more, e.g., 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or more). For example, an IBD patient may continue to receive a combination of an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab) and an IL-23 inhibitor (e.g., an anti-IL-23 antibody or an anti-IL-23R antibody), in accordance with the methods described herein until one or more symptoms of the patient's IBD are reduced (e.g., by 5% or more, e.g., 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or more) compared to when the patient initially began. For example, the IBD patient will exhibit clinical remission or mucosal healing.

[0077] In one aspect, the present invention provides a method of treating a disease or disorder in a subject, comprising administering to the subject an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), and an IL-23 inhibitor (e.g., an anti-IL-23 antibody or an anti-IL-23R antibody), each in an amount effective to treat the disease or disorder, e.g., in a human. The human subject may be an adult (e.g., 18 years of age or older), an adolescent, or a child (juvenile or toddler). The human subject may be 65 years of age or older. In a specific embodiment, the human subject is a child under 18 years of age.

[0078] In certain embodiments, the subject is a responder to treatment with a method according to an embodiment disclosed herein and is confirmed as having at least one of the following: (1) endoscopic cure; (2) clinical response; (3) change from baseline (e.g., improvement) in Inflammatory Bowel Disease Questionnaire (IBDQ) score; (4) mucosal healing; (5) decrease in Mayo score from baseline; (6) normalization of one or more biomarkers selected from the group consisting of C-reactive protein, fecal lactoferrin, albumin, and fecal calprotectin; (7) improvement in Psoriasis Area and Severity Index 75 (PASI) from baseline; and (8) improvement according to the American College of Rheumatology 20% response criteria (ACR20) or 28-joint Disease Activity Score (DAS28).

[0079] In certain embodiments, the present invention provides a clinically proven, safe, and clinically proven, effective method of treating moderately to severely active ulcerative colitis in a subject, wherein the subject is identified as a responder to treatment with the antibody combination and has a statistically significant improvement in disease activity as determined by endoscopic cure, with a Mayo endoscopy subscore of 0 or 1, at a given time point, e.g., by week 8, week 12, week 16 of treatment with the combination therapy.

[0080] In another embodiment, the present invention provides a clinically proven, safe, and clinically proven, effective method of treating moderately to severely active ulcerative colitis in a subject, wherein the subject is a confirmed responder to treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), and an IL-23 inhibitor (e.g., an anti-IL-23 antibody), and has a statistically significant improvement in disease activity (as determined by an Ulcerative Colitis Endoscopic Index of Severity (UCEIS) score of 4 or less) at a given time point, e.g., by week 8, week 12, or week 16 of treatment with the combination therapy.

[0081] In some embodiments, the invention provides methods of treating an inflammatory disorder (e.g., moderately to severely active ulcerative colitis) in a subject, wherein the subject is a non-responder to treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), either by treatment with an IL-23 inhibitor, as described herein. In certain embodiments, a non-responder or non-remitter is refractory to α4β7 inhibitor, e.g., anti-α4β7 antibody, treatment, as described herein, and / or has elevated IL22 or STAT5. Other indicia of non-response may include measures of clinical response and / or the measures described herein. By way of example, a patient may be characterized as a non-responder after the patient receives at least two challenge doses of an α4β7 inhibitor, e.g., at weeks 0 and 2, but after about 3-4 weeks, the patient shows no significant improvement in symptoms and / or a clinical response without clinical remission. Non-responder patients continue to receive α4β7 inhibitor treatment (e.g., vedolizumab 300 mg every 4 or 8 weeks, or 108 mg every 2, 3, or 4 weeks) in combination with an IL-23 inhibitor. Combination therapy can last, for example, 4 to 20 weeks, 4 to 14 weeks, or 6 to 12 weeks. In some embodiments, the IL-23 inhibitor is selected from the group consisting of Itgal (αL chain / CD11a / LFA-1A), Itgb2 (β2 integrin chain / CD18), Itgax (αX chain / CD11c), Itga3, Itga9, Itgb1bk, Il21r, Il12rb1, Il12a, IL2ra, IL10ra, Il17re, Il34, Il18rap, Il1rl1, Il1b, Il1r2, Il3ra, Il1f9, Il23a, Iltifb, Il6, Il18bp, Il1a, The administration is continued until at least one gene selected from the group consisting of Il15, Il1r1, Stat4, Stat2, and Cd3g is altered (e.g., upregulated or downregulated) and / or maintained for at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 8 weeks, at least 9 weeks, at least 10 weeks, at least 11 weeks, at least 12 weeks, or longer until at least one of the genes is altered.In some embodiments, the IL-23 inhibitor is administered until downregulation of integrin-beta-2 (Itgb2 (beta2 integrin chain / CD18)) is achieved. In some embodiments, the IL-23 inhibitor is administered until downregulation of IL1B (interleukin 1 beta) is achieved. In some embodiments, the IL-23 inhibitor is administered until downregulation of IL23a is achieved. Downregulation can be, for example, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or more compared to before combination therapy of an IL-23 inhibitor with an alpha4beta7 inhibitor, e.g., an anti-alpha4beta7 antibody (e.g., vedolizumab). Downregulation can be 5% to 35%, 5% to 25%, 5% to 20%, 5% to 15%, 5% to 10%, 10% to 20%, 10% to 15%, 10% to 30%, 15% to 40%, 20% to 50%, 25% to 60%, 30% to 70%, or 40% to 100% or more compared to before combination therapy of an IL-23 inhibitor with an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab). In some embodiments, patients receiving combination therapy may return to α4β7 inhibitor (e.g., an anti-α4β7 antibody, e.g., vedolizumab) monotherapy when the patient achieves remission.

[0082] In certain embodiments, the combination therapies described herein result in a human subject with IBD achieving a clinical response as defined herein for Crohn's disease or ulcerative colitis, e.g., as determined by a 30% or greater reduction in Mayo score from baseline and a 3 or greater reduction in rectal bleeding subscore of 1 or greater reduction in rectal bleeding subscore from baseline, or a reduction of 0 or 1, by week 8 of treatment with the combination therapy.

[0083] In certain embodiments, the present invention provides a clinically proven, safe, and clinically proven, effective method of treating IBD, e.g., moderately to severely active ulcerative colitis or moderately to severely active Crohn's disease, in a human subject, wherein a subject identified as a non-responder to initial treatment is administered a combination therapy described herein.

[0084] In certain embodiments, the combination therapy described herein results in a human subject with IBD achieving clinical remission as defined herein for Crohn's disease or ulcerative colitis, and subjects identified as non-remitters to initial treatment are administered the combination therapy described herein.

[0085] In certain embodiments, the subject receiving the combination therapy of the present invention may have had an inadequate response to, lost response to, or intolerance to treatment, e.g., initial treatment, with an immunomodulator, a TNF-α antagonist, or a combination thereof. In some embodiments, the subject receiving the combination therapy of the present invention may have had an inadequate response or no remission after initial treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab). In certain embodiments, the subject receiving the combination therapy of the present invention may have had an inadequate response to, lost response to, or become dependent on corticosteroid therapy. The patient may have previously received treatment with at least one corticosteroid (e.g., prednisone) for inflammatory bowel disease. Inadequate response to corticosteroids refers to persistent signs and symptoms of active disease despite a history of at least one 4-week induction regimen, including oral administration for 2 weeks or the equivalent of 30 mg of prednisone once daily intravenously for 1 week. Loss of response to corticosteroids refers to two unsuccessful attempts to taper corticosteroids to a dose below the equivalent of 10 mg of oral prednisone daily. Corticosteroid intolerance includes Cushing's syndrome, osteopenia / osteoporosis, hyperglycemia, insomnia, and / or a history of infection. Complications from long-term steroid use may include venous thromboembolism, fragility fractures, or infection.

[0086] The immunomodulator may be, for example, oral azathioprine, 6-mercaptopurine, or methotrexate. Inadequate response to an immunomodulator refers to persistent signs and symptoms of active disease despite at least one 8-week regimen or a history of oral azathioprine, 6-mercaptopurine, or methotrexate. Intolerance to immunomodulators includes, but is not limited to, nausea / vomiting, abdominal pain, pancreatitis, LFT abnormalities, and lymphopenia. TPMT gene mutations and / or infections.

[0087] In one embodiment, the subject has had an inadequate response to, lost response to, or intolerance to treatment with a TNFα antagonist. A TNFα antagonist is, for example, an agent that inhibits the biological activity of TNFα, preferably binding to TNFα, for example, a monoclonal antibody such as REMICADE (infliximab), HUMIRA (adalimumab), CIMZIA (certolizumab pegol), SIMPONI (golimumab), or an Fc fusion protein such as ENBREL (etanercept). Inadequate response to a TNF-α antagonist refers to persistent signs and symptoms of active disease despite a history of at least one 4-week induction regimen of infliximab 5 mg / kg IV, administered at least twice every two weeks; one subcutaneous dose of adalimumab 80 mg, followed by one subcutaneous dose of 40 mg every two weeks; or two subcutaneous doses of certolizumab pegol 400 mg every two weeks. Loss of response to a TNF-α antagonist refers to a recurrence of symptoms during maintenance dosing after previous clinical benefit. Intolerance to a TNF-α antagonist includes, but is not limited to, infusion-related reactions, demyelination, congestive heart failure, and / or infection.

[0088] In one embodiment, diseases that can be appropriately treated with the combination therapy described herein include inflammatory bowel diseases (IBD) resulting from proctocolectomy and ileoanal anastomosis, such as ulcerative colitis, Crohn's disease, ileitis, celiac disease, nontropical sprue, enteropathy associated with seronegative arthropathy, microscopic or collagenous colitis, eosinophilic gastroenteritis, or pouchitis. In one embodiment, the inflammatory bowel disease is Crohn's disease or ulcerative colitis. The ulcerative colitis can be moderately to severely active ulcerative colitis. Treatment can result in mucosal healing in patients with moderately to severely active ulcerative colitis. Treatment can also result in the reduction, elimination, or reduction and elimination of corticosteroid use by the patient.

[0089] In other embodiments, the present invention also provides uses of a combination of an α4β7 inhibitor and an IL-23 inhibitor to treat an autoimmune disease (e.g., arthritis or psoriasis, e.g., rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, or axial spondyloarthritis), or inflammatory bowel disease (e.g., ulcerative colitis or Crohn's disease, e.g., moderately to severely active ulcerative colitis; or moderately to severely active Crohn's disease), wherein the use comprises administering the α4β7 inhibitor and the IL-23 inhibitor to a patient characterized as a non-responder or non-remitter to the α4β7 inhibitor, as described herein. In some embodiments, the α4β7 inhibitor is, for example, an anti-α4β7 antibody, e.g., vedolizumab. In some embodiments, vedolizumab is administered according to a dosing regimen described herein.

[0090] In some embodiments, the patient is characterized as a non-responder or non-remitter at 6 and / or 10 weeks after initiation of treatment with an α4β7 inhibitor (e.g., an anti-α4β7 antibody, e.g., vedolizumab). In some embodiments, the patient is characterized as having elevated serum IL-22 levels at the initiation of or 6 weeks after initiation of treatment with an α4β7 inhibitor (e.g., an anti-α4β7 antibody, e.g., vedolizumab). In some embodiments, the patient is characterized as having elevated serum IL-22 levels at the initiation of or 6 weeks after initiation of treatment with vedolizumab, where the serum IL-22 levels do not decrease, decrease by more than two-fold, or decrease by more than three-fold from initiation to 10 weeks, from initiation to 6 weeks, or from 6 weeks to 10 weeks. In some embodiments, the patient is characterized as having elevated levels of IL-22 and / or STAT5A compared to control levels.

[0091] In some embodiments, the characterization is performed prior to treatment with the α4β7 inhibitor. In some embodiments, the characterization is performed after initial treatment with the α4β7 inhibitor. In one embodiment, the IL-23 inhibitor is administered simultaneously with the α4β7 inhibitor. In one embodiment, the IL-23 inhibitor is administered after initial treatment with the α4β7 inhibitor. In some embodiments, the IL-23 inhibitor is administered for 2 weeks to 6 months, e.g., 2 to 4 weeks, 2 to 6 weeks, 2 to 8 weeks, 4 to 6 weeks, 4 to 8 weeks, 4 to 10 weeks, 1 to 2 months, 1 to 3 months, 2 to 3 months, 2 to 4 months, 3 to 4 months, 3 to 5 months, 4 to 5 months, 4 to 6 months, or 5 to 6 months. In some embodiments, the IL-23 inhibitor is administered until clinical remission is achieved. In certain embodiments, the IL-23 inhibitor is administered up to 1 to 3 months (e.g., 4 to 6 weeks, 4 to 8 weeks, 4 to 10 weeks, 6 to 8 weeks, 6 to 10 weeks, 6 to 12 weeks, or 2 to 3 months) after clinical remission is achieved. In some embodiments, the IL-23 inhibitor is administered up to at least one gene selected from a specific integrin chain gene or a specific cytokine gene. In some embodiments, the IL-23 inhibitor is administered until at least one gene selected from the group consisting of Itgal (alpha L chain / CD11a / LFA-1A), Itgb2 (beta 2 integrin chain / CD18), Itgax (alpha X chain / CD11c), Itga3, Itga9, Itgb1bk, Il21r, Il12rb1, Il12a, IL2ra, IL10ra, Il17re, Il34, Il18rap, Il1rl1, Il1b, Il1r2, Il3ra, Il1f9, Il23a, Iltifb, Il6, Il18bp, Il1a, Il15, Il1r1, Stat4, Stat2, and Cd3g is altered (e.g., upregulated or downregulated) as exemplified herein. In certain embodiments, administration of the α4β7 inhibitor (eg, an anti-α4β7 antibody, eg, vedolizumab) continues after the IL-23 inhibitor is no longer administered.

[0092] Antibodies useful as anti-α4β7 or anti-IL-23 antibodies suitable for the methods and uses described herein can be identified using techniques known in the art, such as hybridoma production. Hybridomas can be prepared, for example, using a mouse system. Protocols for immunization and subsequent isolation of splenocytes for fusion are known in the art. Fusion partners and procedures for hybridoma production are also known. In generating the desired antibody, the target protein (antigen) of choice (whole protein or a fragment thereof) is isolated and / or purified. Animal immunization can be carried out by any method known in the art. See, for example, Harlow and Lane, *Antibodies: A Laboratory Manual*, *New York: Cold Spring Harbor Press*, 1990. Methods for immunizing animals such as mice, rats, sheep, goats, pigs, cattle, and horses are well known in the art. See, for example, Harlow and Lane, supra, and U.S. Pat. No. 5,994,619. The desired antigen may be administered with an adjuvant to stimulate the immune response. Adjuvants known in the art include complete or incomplete Freund's adjuvant, RIBI (muramyl dipeptide), or ISCOM (immunostimulating complexes). After immunization of an animal with the desired antigen, antibody-producing immortalized cell lines are prepared from cells isolated from the immunized animal. After immunization, the animal is killed, and lymph node and / or splenic B cells are immortalized by methods known in the art (e.g., oncogene transduction, oncogenic viral transduction, exposure to oncogenic or mutating compounds, fusion with immortalized cells, e.g., myeloma cells, and inactivation of tumor suppressor genes). See, e.g., Harlow and Lane, supra. Hybridomas can be selected, cloned, and further screened for desirable properties, including robust growth, high antibody production, and desirable antibody characteristics. Human anti-PCDH17 antibodies can also be generated in mice, such as HuMAb-Mouse® or XenoMouse™.

[0093] Methods for high-throughput screening of antibody or antibody fragment libraries for molecules capable of binding to a target protein (antigen) can be used to identify affinity-matured antibodies useful in the methods of the present disclosure. Such methods include, inter alia, in vitro display techniques known in the art, such as phage display, bacterial display, yeast display, mammalian cell display, ribosome display, mRNA display, and cDNA display. The use of phage display to isolate ligands that bind to biologically relevant molecules is reviewed, for example, in Felici et al., Biotechnol. Annual Rev. 1:149-183, 1995; Katz, Annual Rev. Biophys. Biomol. Struct. 26:27-45, 1997; and Hoogenboom et al., Immunotechnology 4:1-20, 1998 (the disclosures of each of which are incorporated herein by reference with respect to in vitro display techniques). Randomized combinatorial peptide libraries have been created to select for polypeptides that bind to cell surface antigens as described in Kay, Perspective. Drug Discovery Des. 2:251-268, 1995 and Kay et al., Mol. Divers. 1:139-140, 1996 (the disclosures of each of which, insofar as they relate to the discovery of antigen-binding molecules, are incorporated herein by reference). Proteins, such as multimeric proteins, have been efficiently phage-displayed as functional molecules (see, e.g., EP 0349578; EP 4527839; and EP 0589877, and Chiswell and McCafferty, Trends Biotechnol. 10:80-84, 1992 (the disclosures of each of which are incorporated herein by reference regarding the use of in vitro display techniques for the discovery of antigen-binding molecules)).In addition, functional antibody fragments, such as Fab and scFv fragments, have been expressed in in vitro display formats (see, e.g., McCafferty et al., Nature 348:552-554, 1990; Barbas et al., Proc. Natl. Acad. Sci. USA 88:7978-7982, 1991; and Clackson et al., Nature 352:624-628, 1991, the disclosures of each of which are incorporated herein by reference regarding in vitro display platforms for the discovery of antigen-binding molecules). These techniques can be used, inter alia, to identify and improve the affinity of antibodies for binding to target antigens.

[0094] In addition to in vitro display techniques, computational modeling techniques can be used to design and identify antibodies or antibody fragments in silico that bind to a target antigen. For example, using computational modeling techniques, one skilled in the art can screen libraries of antibodies, or antibody fragments in silico, for molecules capable of binding a particular epitope, such as an extracellular epitope, of a target antigen.

[0095] Examples of α4β7 inhibitors, eg, anti-α4β7 antibodies, or fragments thereof, and IL-23 inhibitors that can be used in the methods disclosed herein are provided below.

[0096] α4β7 antagonists The methods disclosed herein include administering both an α4β7 inhibitor, e.g., an anti-α4β7 antibody, or antigen-binding portion thereof, and an IL-23 inhibitor, e.g., an anti-IL-23 antibody, to a subject having an autoimmune disease, e.g., arthritis or psoriasis (e.g., rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, axial spondyloarthritis), and / or an inflammatory disease, e.g., IBD (e.g., Crohn's disease or ulcerative colitis), for treatment.

[0097] Various polypeptides can inhibit α4β7 integrin from binding to MAdCAM, including the anti-α4β7 antibodies, anti-MAdCAM antibodies, soluble integrin subunits (including fusion proteins such as Fc fusions), and soluble MAdCAM (including fusion proteins such as Fc fusions) described herein. Primate MAdCAM is described, for example, in PCT Publication No. WO 96 / 24673, the entire teachings of which are incorporated herein by reference. Polypeptides that inhibit MAdCAM-α4β7 integrin binding and can be used in accordance with the present invention include anti-MAdCAM antibodies (e.g., antibodies described in U.S. Patent No. 8,277,808, PF-00547659, SHP647, ontamalimab, or WO 2005 / 067620), e.g., as described in U.S. Patent No. 7,803,904; soluble integrin subunits (e.g., complexes comprising α4 and / or β7, which lack the transmembrane domain or lack the transmembrane and intracellular domains), including fusion proteins such as Fc fusions comprising soluble integrin subunits, e.g., soluble α4 integrin, soluble β7 integrin, or soluble α4β7 integrin complexes; and soluble MAdCAM (e.g., lacking the transmembrane domain or lacking the transmembrane and intracellular domains), including fusion proteins comprising MAdCAM, such as MAdCAM-Fc chimeras.

[0098] The present invention relies, at least in part, on an anti-α4β7 antibody or antigen-binding portion thereof, which (1) can bind to α4β7 integrin in vitro and / or in vivo; and (2) can modulate the ability or function of α4β7 integrin, for example, (a) binding function (e.g., the ability of α4β7 integrin to bind to MAdCAM (e.g., MAdCAM-1), fibronectin, and / or VCAM-1) and / or (b) leukocyte infiltration function, including leukocyte recruitment and / or accumulation within tissue (e.g., the ability to inhibit lymphocyte migration into intestinal mucosal tissue). In one embodiment, the antibody used herein can bind to α4β7 integrin and inhibit α4β7 integrin from binding to one or more of its ligands (e.g., MAdCAM-1, VCAM-1, fibronectin), thereby inhibiting leukocyte infiltration of tissue (including leukocyte recruitment and / or accumulation within tissue). In another embodiment, the anti-α4β7 antibody used herein can bind to α4β7 integrin and selectively inhibit the binding of α4β7 integrin to one or more of its ligands (e.g., MAdCAM (e.g., MAdCAM-1), VCAM-1, fibronectin), thereby inhibiting leukocyte infiltration of tissues (including the recruitment and / or accumulation of leukocytes within tissues). Such anti-α4β7 antibodies can inhibit the adhesion of cells bearing α4β7 integrin to vascular endothelial cells in gut-related tissues, lymphoid organs, or mucosal tissues containing leukocytes (particularly lymphocytes such as T cells or B cells) in vitro and / or in vivo. In yet another embodiment, the anti-α4β7 antibody used herein can inhibit the interaction of α4β7 with MAdCAM (e.g., MAdCAM-1) and / or fibronectin. In yet another embodiment, the anti-α4β7 antibodies used herein may inhibit the interaction of α4β7 with MAdCAM (e.g., MAdCAM-1) and / or fibronectin selection, for example, without inhibiting the interaction of α4β7 with VCAM.

[0099] Thus, the anti-α4β7 antibodies used in the methods disclosed herein can be used to modulate (e.g., inhibit (reduce or prevent)) the binding and / or leukocyte (e.g., lymphocyte, monocyte) infiltration functions of α4β7 integrin. For example, a humanized immunoglobulin that inhibits the binding of α4β7 integrin to a ligand (i.e., one or more ligands) can be administered according to the methods in the treatment of diseases associated with leukocyte (e.g., lymphocyte, monocyte) infiltration of tissues (including leukocyte recruitment and / or accumulation in tissues), particularly tissues that express the molecule MAdCAM (e.g., MAdCAM-1).

[0100] The anti-α4β7 antibody used in the methods provided herein may, in certain embodiments, bind to an epitope on the α4 chain, the β7 chain, or a combined epitope formed by the association of the α4 chain with the β7 chain. In one aspect, the antibody is specific for the α4β7 integrin complex, e.g., the antibody binds to a combined epitope on the α4β7 complex, but does not bind to an epitope on the α4 chain or the β7 chain unless the chains are associated with each other. In another aspect, the anti-α4β7 antibody binds to both the α4 integrin chain and the β7 integrin chain, and is therefore specific for the α4β7 integrin complex. Such an antibody specific for the α4β7 integrin complex may, for example, bind to α4β7 but not to α4β1, and / or may not bind to α4β1. EIn another embodiment, the anti-α4β7 antibody binds to the same or substantially the same epitope as the Act-1 antibody (Lazarovits, AI et al., J. Immunol., 133(4):1857-1862 (1984), Schweighoffer et al., J. Immunol., 151(2):717-729, 1993; Bednarczyk et al., J. Biol. Chem., 269(11):8348-8354, 1994). A mouse ACT-1 hybridoma cell line producing the mouse Act-1 monoclonal antibody was deposited under the provisions of the Budapest Treaty on August 22, 2001, for Millennium Pharmaceuticals, Inc., 40 Lansdowne Street, Cambridge, Massachusetts 02139, USA, at the American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA, under accession number PTA-3663. In another embodiment, the anti-α4β7 antibody is a human antibody or α4β7 binding protein using the CDRs provided in U.S. Patent Application Publication No. 2010 / 0254975. In other embodiments, the anti-α4β7 integrin antibody is AMG181 (avrilumab, specific for α4β7, see e.g., U.S. Pat. No. 8,444,981), etrolizumab (β7 specific, FIB504 or a humanized derivative (e.g., Fong et al., U.S. Pat. No. 7,528,236), CAS1044758-60-2, KEGG D09901, PubChem 124490613; see e.g., U.S. Pat. No. 7,528,236), natalizumab (α4 specific, humanized MAb 21.6, TYSABRI®, CAS 189261-10-7, KEGG D06886, PubChem 49661786; see e.g., U.S. Pat. No. 5,840,299), any of the above-mentioned related antibodies, any of the above-mentioned antigen-binding fragments, or a combination thereof. Methods of treatment using anti-α4β7 integrin antibodies are described in publications US2005 / 0095238, WO2012151248, and WO2012 / 151247.

[0101] An effective amount of an α4β7 inhibitor, e.g., an anti-α4β7 antibody, is administered to a human subject to treat such diseases. For example, inflammatory diseases, including diseases associated with leukocyte infiltration of the gastrointestinal tract (including gut-associated endothelium), other mucosal tissues, or tissues expressing the molecule MAdCAM (e.g., MAdCAM-1) (e.g., gut-associated tissues, e.g., venules in the lamina propria of the small intestine and large intestine; and mammary glands (e.g., lactating mammary glands)), can be treated according to this method. Similarly, individuals with diseases associated with leukocyte infiltration of tissues as a result of leukocyte binding to cells (e.g., endothelial cells) expressing MAdCAM (e.g., MAdCAM-1) can be treated according to the present invention.

[0102] In certain embodiments, the α4β7 inhibitor, e.g., an anti-α4β7 antibody, or antigen-binding fragment thereof, is a humanized anti-α4β7 antibody, or antigen-binding fragment thereof, i.e., an IgG1 antibody; comprising a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and comprising a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6.

[0103] In certain embodiments, the anti-α4β7 antibody, or antigen-binding fragment thereof, is a humanized anti-α4β7 antibody comprising a heavy chain variable domain comprising the amino acid sequence set forth in SEQ ID NO: 1 and a light chain variable domain comprising the amino acid sequence set forth in SEQ ID NO: 5.

[0104] In a specific embodiment, the anti-α4β7 antibody is vedolizumab.

[0105] In some embodiments where the anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, is vedolizumab or an antibody having a vedolizumab binding region, the human patient is administered a first dose of 300 mg of the anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, at week 2, followed by a third dose of 300 mg of the anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, at week 6. The method may further comprise administering to the human patient 300 mg of the anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, every eight weeks beginning eight weeks after the third dose. In alternative embodiments, the methods described herein may comprise administering 300 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, to a human patient every four weeks if the human patient with Crohn's disease or ulcerative colitis does not show clinical improvement, e.g., clinical remission. In other embodiments, the methods comprise intravenously administering, e.g., 300 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, to a human patient every four weeks, beginning eight weeks after the third administration. In further embodiments, in certain instances, the methods comprise administering 108 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, to a human patient every two weeks, beginning eight weeks after the third administration. In certain embodiments, the method comprises administering an initial dose of 300 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, at week 0, followed by a second dose of 300 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, at week 2, followed by a third dose of 108 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, at week 6, followed by 108 mg doses every two weeks thereafter. In certain embodiments, the 108 mg dose is administered subcutaneously. In certain embodiments, the 108 mg dose is self-administered.

[0106] In some embodiments, in which the anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, is vedolizumab or an antibody having a vedolizumab binding region, a young (pediatric) human patient can be treated according to the methods provided herein. For example, a young human patient is administered an initial dose of 200 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, followed by a second dose of 200 mg of the antibody two weeks after the initial dose, and a third dose of 200 mg of the antibody six weeks after the initial dose. The method may further include administering a fourth dose of 200 mg 14 weeks after the initial dose. The method may also further include administering subsequent doses of 200 mg every eight weeks thereafter. In an alternative embodiment, a young human patient is administered an initial dose of 100 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, followed by a second dose of 100 mg of the antibody two weeks after the initial dose, and a third dose of 100 mg of the antibody six weeks after the initial dose. The method may further include administering a fourth dose of 200 mg 14 weeks after the first dose. The method may further include a fifth and subsequent doses of 200 mg every eight weeks after the fourth dose. In another embodiment, a young human patient is administered an initial dose of 150 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, followed by a second dose of 150 mg of the antibody two weeks after the first dose, and a third dose of 150 mg of the antibody six weeks after the first dose. The method may further include a fourth dose of 150 mg 14 weeks after the first dose. The method may further include a fourth dose of 300 mg 14 weeks after the first dose. The method may further include a fifth and subsequent doses of 150 mg or 300 mg every eight weeks after the fourth dose. In certain embodiments, a young human patient is administered an initial dose of 300 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, followed by a second dose of 300 mg of the antibody two weeks after the initial dose, and a third dose of 300 mg of the antibody six weeks after the initial dose. The method may further include a fourth dose of 300 mg 14 weeks after the initial dose. The method may also include a fifth and subsequent doses of 300 mg every eight weeks after the fourth dose.In certain embodiments, a young human patient receives an initial dose of 200 mg of an anti-α4β7 antibody, e.g., a humanized anti-α4β7 antibody, followed by a second dose of 200 mg of the antibody two weeks after the initial dose, a third dose of 108 mg of the antibody six weeks after the initial dose, and subsequent doses of 108 mg of the antibody every two, three, or four weeks thereafter. In some embodiments, pediatric patients weighing less than 30 kg are administered a higher dose than pediatric patients weighing more than 30 kg. Other specific embodiments are described, for example, in PCT Publication No. WO2018 / 200818, which is incorporated by reference in its entirety.

[0107] In particular, the methods disclosed herein involve administration of the anti-α4β7 antibody vedolizumab, or an antibody having the antigen-binding region of vedolizumab. Vedolizumab is also known by the trade name ENTYVIO® (Pharmaceuticals, Inc.). Vedolizumab is a humanized antibody containing mutated human IgG1 framework regions and the antigen-binding CDRs from the murine antibody Act-1 (described in U.S. Pat. No. 7,147,851, incorporated herein by reference).

[0108] Vedolizumab specifically binds to α4β7 integrin, blocks its interaction with mucosal addressin cell adhesion molecule-1 (MAdCAM-1) and fibronectin, and inhibits the migration of memory T lymphocytes across the endothelium into inflamed gastrointestinal parenchyma. Vedolizumab does not bind to or inhibit the function of α4β1 and αEβ7 integrins, and does not neutralize the interaction of α4 integrin with vascular cell adhesion molecule-1 (VCAM-1).

[0109] The α4β7 integrin is expressed on the surface of a distinct subset of memory T lymphocytes that preferentially migrate to the gastrointestinal tract. MAdCAM-1 is expressed on intestinal endothelial cells and plays an important role in the homing of T lymphocytes to the intestine through lymphoid tissues. The interaction of α4β7 integrin with MAdCAM-1 has been implicated as an important cause of mucosal inflammation, such as the chronic inflammation characteristic of ulcerative colitis and Crohn's disease. Vedolizumab may be used to treat inflammatory bowel diseases, including Crohn's disease and ulcerative colitis, HIV, pouchitis, including chronic pouchitis, fistulizing Crohn's disease, graft-versus-host disease, and celiac disease. These diseases are contemplated for the combination therapy described herein.

[0110] The heavy chain variable region of vedolizumab is provided herein as SEQ ID NO: 1, and the light chain variable region of vedolizumab is provided herein as SEQ ID NO: 5. Vedolizumab comprises a heavy chain variable region comprising CDR1 of SEQ ID NO: 2, CDR2 of SEQ ID NO: 3, and CDR3 of SEQ ID NO: 4. Vedolizumab comprises a light chain variable region comprising CDR1 of SEQ ID NO: 6, CDR2 of SEQ ID NO: 7, and CDR3 of SEQ ID NO: 8. Vedolizumab and vedolizumab sequences are also described in U.S. Patent Publication Nos. 2014 / 0341885 and 2014 / 0377251, the entire contents of each of which are expressly incorporated herein by reference in their entireties. α4β7 antibodies and their corresponding amino acid sequences are described in U.S. Patent Publication No. 10,143,752, incorporated herein by reference.

[0111] The use of the methods disclosed herein with other antibodies is also encompassed by the present invention. Specifically, the methods described herein may be practiced using an antibody or antigen-binding fragment thereof that binds to α4 integrin, including but not limited to natalizumab. In another alternative, the methods described herein may be practiced using an antibody or antigen-binding fragment thereof that binds to β7 integrin, including but not limited to etrolizumab, which binds to both integrins α4β7 and αEβ7 (the sequence of etrolizumab is described in US20180086833, which is incorporated herein by reference).

[0112] IL-23 inhibitors As described above, the methods disclosed herein include administering both an α4β7 inhibitor, e.g., an anti-α4β7 antibody, or antigen-binding portion thereof, and an IL-23 inhibitor, e.g., an anti-IL-23 antibody or an anti-IL-23R antibody, to a subject having an autoimmune disease, e.g., arthritis or psoriasis, and / or an inflammatory disease, e.g., IBD (e.g., Crohn's disease or ulcerative colitis), for treatment.

[0113] As used herein, the term "human interleukin-23" or "hIL-23" refers to the heterodimeric proinflammatory cytokine formed by the IL12B subunit (RefSeq Accession Nos. NM_002187.3; NP_002178.2) and the IL23A subunit (RefSeq Accession Nos. NM_016584.3; NP_057668.1). "IL12B" is also known as p40, IL-12p40, CLFM2, and NKSF2; the p40 subunit is also the subunit that forms IL-12. The amino acid sequence of p40 is set forth in SEQ ID NO: 13. "IL23A" is also known as p19, IL-23p19, IL-23 subunit alpha, and SGRF. The amino acid sequence of p19 is set forth in SEQ ID NO: 14. IL-23 binds to its receptor, IL-23R, which contains two subunits: IL23R (RefSeq Accession Nos. NM_144701.3; NP_653302.2) and IL-12RB1 (RefSeq Accession Nos. NM_005535.3; NP_005526.1). Both subunits are required for IL-23 signaling.

[0114] In certain embodiments, an IL-23 inhibitor that can be used in the combination therapies disclosed herein is an anti-IL-23 antibody or antigen-binding fragment thereof that specifically binds to either the p19 subunit, the p40 subunit, or a shared epitope thereof of human IL-23. In certain embodiments, an IL-23 inhibitor that can be used in the combination therapies disclosed herein is an anti-IL-23R antibody or antigen-binding fragment thereof that specifically binds to human IL-23R.

[0115] In one embodiment, the anti-IL-23 antibody that can be used in the combination therapy disclosed herein is brazikumab. Brazikumab is also known as AMG 139, MEDI2070, or MEDI-2070. Brazikumab is known in the art, including, for example, as described in U.S. Pat. Nos. US8722033 and US9487580 (which are incorporated by reference in their entireties with respect to brazikumab, including its sequence).

[0116] In some embodiments, an anti-IL-23 antibody (e.g., an anti-p19 antibody) suitable for use in the combination therapy disclosed herein is guselkumab. Guselkumab is also known as TREMFYA™ or CNTO1959. Guselkumab is known in the art, including, for example, as described in U.S. Pat. Nos. US7491391 and US10030070 (which are incorporated by reference in their entireties with respect to guselkumab, including its sequence).

[0117] In some embodiments, an anti-IL-23 antibody (e.g., an anti-p19 antibody) suitable for use in the combination therapy disclosed herein is risankizumab. Risankizumab is also known as SKYRIZI™, BI655066, or ABBV-066. Risankizumab is known in the art, including, for example, as described in U.S. Pat. Nos. US8778346 and US9441036 (incorporated by reference in their entireties with respect to risankizumab, including its sequence).

[0118] In some embodiments, an anti-IL-23 antibody (e.g., an anti-p40 antibody) suitable for use in the combination therapies disclosed herein is briakinumab. Briakinumab is also known as ABT-874, J695, BSF 415977, LU 415977, A-796874.0, and WAY-165772. Briakinumab is described, for example, in US6914128, US7504485, US9072725, and US20150037348 (incorporated by reference in their entireties with respect to briakinumab, including its sequence).

[0119] In some embodiments, an anti-IL-23 antibody (e.g., an anti-p19 antibody) suitable for use in the combination therapy disclosed herein is tildrakizumab. Tildrakizumab is also known as ILUMYA™, tildrakizumab-asmn, MK-3222, SCH 900222, or hum13B8-b. Tildrakizumab is known in the art, including, for example, those described in U.S. Pat. Nos. US8362212, US8404813, and US9803010 (which are incorporated by reference in their entireties with respect to tildrakizumab, including its sequence).

[0120] In some embodiments, the anti-IL-23 antibody (e.g., anti-p40 antibody) that can be used in the combination therapy disclosed herein is ustekinumab. Ustekinumab is also known as CNTO1275, TT-20, C01275, or STELARA™. Ustekinumab is known in the art, for example, US6902734, WO2002012500, US7279157, US20200095315 (the entirety of which is incorporated by reference for ustekinumab, including its sequence).

[0121] Another example of an anti-IL-23 antibody that can be used in the combination therapy disclosed herein is LY2525623. LY2525623 is known in the art, including, for example, those described in U.S. Pat. Nos. US7872102 and US9023358 (incorporated by reference in their entireties with respect to LY2525623, including its sequence).

[0122] In one embodiment, an anti-IL-23 antibody that can be used in the combination therapy disclosed herein is CNTO4088. CNTO4088 is known in the art, including, for example, as described in U.S. Patent Nos. US7807414 and US7935344 (incorporated by reference in their entireties with respect to CNTO4088).

[0123] In some embodiments, the anti-IL-23 antibody that can be used in the combination therapy disclosed herein is mirikizumab. Mirikizumab is also known as LY3074828. Mirikizumab is described, for example, in Ma et al. (Expert Opin Investig Drugs, 27:649-660 (2018)) and Reich et al. (Br J Dermatol, 181:88-95 (2019)), which are incorporated herein by reference in their entireties with respect to mirikizumab.

[0124] Other anti-IL-23 antibodies suitable for use in the combination therapies disclosed herein are known in the art, including, for example, those described in U.S. Publication Nos. US20110206686 and US20120264917, U.S. Patent Nos. US9127057 and US7510709, and Li et al. (Anal Chem 89:2250-2258(2017)) (incorporated by reference in its entirety with respect to IL-23 antibodies). Other anti-IL-23 antibodies (e.g., anti-p19 antibodies) suitable for use in the combination therapies disclosed herein are described, for example, in WO2007147019, WO2008134659, WO2009082624, US8333968, US20110159589, US20120294862, US20130309235, US9464134, and US20150197566 (incorporated by reference in their entirety with respect to IL-23 antibodies).

[0125] Other anti-IL-23 antibodies (e.g., anti-p40 antibodies) suitable for use in the combination therapies disclosed herein are described, for example, in US20150010544, US9708395, and US20160333085 (incorporated by reference in their entirety with respect to IL-23 antibodies).

[0126] In certain embodiments, IL-23 inhibitors suitable for use in the methods described herein are small molecule inhibitors of IL-23. In some embodiments, small molecule inhibitors of IL-23 may reduce or inhibit IL-23 production, e.g., by reducing or inhibiting IL-23 production at the transcriptional or translational level. In some embodiments, small molecule inhibitors of IL-23 may reduce or inhibit IL-23 function, e.g., by reducing or inhibiting the interaction of IL-23 with its receptor (IL-23R) and / or by reducing or inhibiting the ability of the subunits p19 and p40 to form a complex.

[0127] In some embodiments, a small molecule inhibitor of IL-23 suitable for use in the combination therapies disclosed herein is STA-5326. STA-5326 suppresses IL-23 production by preventing the nuclear translocation of c-Rel. STA-5326 is also known as Apilimod mesylate, Apilimod, and LAM-002. The chemical name for STA-5326 is (E)-4-(6-(2-(3-methylbenzylidene)hydrazinyl)-2-(2-(pyridin-2-yl)ethoxy)pyrimidin-4-yl)morpholine dimethanesulfonate. STA-5326 is described, for example, in Burakoff et al. (Inflamm Bowel Dis, 12:558-565 (2006)) and Wada et al. (Blood, 109:1156-1164 (2007)), which are incorporated by reference in their entireties.

[0128] In some embodiments, an anti-IL-23R antibody suitable for use in the combination therapy disclosed herein is AS2762900-00, which is described, e.g., in US9556276, US20140275490, WO2012137676, US9371391, US20150126713, WO2013129454, Imamura et al. (Eur J Pharmacol, 824:163-169(2018)), Sasaki-Iwaoka et al. (Eur J Pharmacol, 828:89-96(2018)), and Sasaki-Iwaoka et al. (Eur J Pharmacol, 843:190-198(2019)) (incorporated by reference in their entirety with respect to IL-23R antibodies).

[0129] Other examples of anti-IL-23R antibodies suitable for use in the combination therapies disclosed herein are described, for example, in US20100166767, WO2008106134, US20110158992, WO2010027767, US20120148582, US8691532, and US20140170154 (incorporated by reference in their entirety with respect to IL-23R antibodies).

[0130] Patient selection In some embodiments, patients are selected for treatment with the combination therapy disclosed herein based on certain characteristics. In some embodiments, the patient is a non-responder to α4β7 inhibitor therapy. As used herein, a "non-responder," "non-responder," or "vedolizumab non-responder" refers to a subset of patients with an autoimmune disease and / or IBD (e.g., Crohn's disease or ulcerative colitis) who have received a first and second induction dose of an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), and who show signs of non-response early in the therapy, e.g., vedolizumab treatment (e.g., about 3 or 4 weeks after the second induction dose). Signs of non-response may include, for example, failure to achieve clinical response measures and / or measures described herein. In some embodiments, the patient is a non-remitter to α4β7 inhibitor therapy. As used herein, a "non-remitter," "remitter," or "vedolizumab non-remitter" is a subset of patients with an autoimmune disease and / or IBD (e.g., Crohn's disease or ulcerative colitis), who have received a first and second induction dose, or a third induction dose, of an α4β7 inhibitor, e.g., an anti-α4β7 antibody (e.g., vedolizumab), and who show signs of non-remission early in the therapy, e.g., vedolizumab therapy (e.g., about 3 or 4 weeks after the second or third induction dose). For example, the patient may receive an anti-α4β7 antibody (e.g., vedolizumab) at 0 and 2 weeks, or at 0, 2, and 6 weeks. A patient may demonstrate a clinical response to treatment but not demonstrate clinical remission, for example, about 3-4 weeks after the second dose, e.g., 5 or 6 weeks after initiation of treatment with an anti-α4β7 antibody (e.g., vedolizumab), or about 3-8 weeks after the third dose, e.g., 10 or 14 weeks after initiation. Indications of non-remission may include, for example, failure to achieve clinical remission measures and / or measures described herein.

[0131] In some embodiments, non-responders may be identified using an algorithm that includes components including, but not limited to, α4β7 inhibitor, e.g., anti-α4β7 antibody concentration and / or antibody clearance. Antibody concentration may be measured in serum obtained from the patient. In further embodiments, components of the algorithm for identifying non-responders may include body weight and / or albumin levels. Non-responders to α4β7 inhibitor therapy may have, for example, high inhibitor clearance, low albumin levels, high fecal calprotectin levels, no decrease in fecal calprotectin levels after initial treatment, and / or high body weight.

[0132] In some embodiments, the patient is characterized as having elevated levels of a marker gene, e.g., IL-22, STAT5A, and / or IL-1β. In some embodiments, the IL-22, STAT5A, and / or IL-1β levels are elevated by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or more, or in certain ... e.g., from a non-IBD subject. The level of α4β7 is elevated by 5% to 35%, 5% to 25%, 5% to 20%, 5% to 15%, 5% to 10%, 10% to 20%, 10% to 15%, 10% to 30%, 15% to 40%, 20% to 50%, 25% to 60%, 30% to 70%, or 40% to 100%, or more, compared to a control level in a normal human control sample or control non-inflamed colon or non-colon tissue obtained from the patient, or compared to a reference level in a responder to an α4β7 inhibitor. Elevated levels may be measured in a colon tissue biopsy obtained from the patient. The biopsy sample may be obtained before treatment (e.g., 2 to 10 days before), or on the day before or the first day of treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab. Measurements may examine the levels of nucleic acids, for example on a microarray, or the levels of proteins, for example by immunohistochemistry using methods well known in the art.

[0133] In some embodiments, IL-22 (Interleukin-22) has gene ID 50616 (GenBank Accession No. NM_020525.5) that is at least 95%, 97%, 99%, or 100% identical to SEQ ID NO: 9 in the database maintained by the National Center for Biotechnology Information (Bethesda, MD), or the protein of SEQ ID NO: 10 (represented as GenPept Accession No. NP_065386.1). In some embodiments, STAT5A (Signal Transducer and Activator of Transcription 5A) has gene ID 6776 (GenBank Accession No. NM_003152.3) that is at least 95%, 97%, 99%, or 100% identical to SEQ ID NO: 11 in the database maintained by the National Center for Biotechnology Information (Bethesda, MD), or the protein of SEQ ID NO: 12 (represented as GenPept Accession No. NP_003143.2). In some embodiments, IL-1β (Interleukin-1β) is at least 95%, 97%, 99%, or 100% identical to SEQ ID NO: 11 in the database maintained by the National Center for Biotechnology Information (Bethesda, MD). Gene ID 3553, which is at least 95%, 97%, 99%, or 100% identical to GenBank accession number NM_000576 in the database maintained by the Center for Biotechnology Information (Bethesda, MD), or a protein designated as GenPept accession number NP_000567.

[0134] In some embodiments, patients to receive combination therapy are characterized by elevated serum levels of IL-22 at the initiation of, 6 weeks after initiation of, or 10 weeks after initiation of treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab. In some embodiments, patients to receive combination therapy are characterized by elevated serum levels of IL-22 at the initiation of, or 6 weeks after initiation of, treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab, which do not decrease, decrease by more than two-fold, or decrease by more than three-fold between initiation and 10 weeks, between initiation and 6 weeks, or between 6 and 10 weeks. In some embodiments, the elevated serum levels of IL-22 are greater than 3 pg / ml, 5-100 pg / ml, greater than 5 pg / ml, greater than 10 pg / ml, 10-120 pg / ml, greater than 10 pg / ml, or greater than 10 pg / ml. In some embodiments, in remitters, serum IL-22 levels decrease to less than 10 pg / ml, less than 5 pg / ml, less than 3 pg / ml, less than 2.7 pg / ml, less than 2 pg / ml, or are undetectable after initial treatment, e.g., by week 6 or 10 of treatment. In some embodiments, in non-remitters, serum IL-22 levels do not decrease to less than 10 pg / ml, less than 5 pg / ml, less than 3 pg / ml, less than 2.7 pg / ml, less than 2 pg / ml, or are not undetectable after initial treatment, e.g., by week 6 and / or 10 of treatment.

[0135] In some embodiments, patients to receive combination therapy are characterized as having elevated fecal calprotectin levels at the initiation of, 6 weeks after initiation of, or 10 weeks after initiation of treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab. In some embodiments, patients to receive combination therapy are characterized as having elevated fecal calprotectin levels at the initiation of, or 6 weeks after initiation of, treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab, which do not decrease, decrease by more than two-fold, or decrease by more than three-fold between initiation and 10 weeks, between initiation and 6 weeks, or between 6 weeks and 10 weeks. See, e.g., US2017360926, incorporated by reference in its entirety. In some embodiments, patients to be administered the combination therapy are characterized as having an elevation in fecal calprotectin levels relative to normal levels of fecal calprotectin of 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or more, or between 5% and 35%, 5% and 25%, 5% and 20%, 5% and 15%, 5% and 10%, 10% and 20%, 10% and 15%, 10% and 30%, 15% and 40%, 20% and 50%, 25% and 60%, 30% and 70%, 40% and 100% or more.

[0136] Relative to normal levels, or in certain embodiments, elevated levels of IL-22, STAT5A, and / or IL-1β. In some embodiments, patients to receive combination therapy are characterized as having elevated levels of both IL-22 and fecal calprotectin at the initiation of, 6 weeks after initiation of, or 10 weeks after initiation of, treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab. In some embodiments, patients to receive combination therapy are characterized as having elevated levels of both IL-22 and fecal calprotectin at the initiation of, or 6 weeks after initiation of, treatment with an α4β7 inhibitor, e.g., an anti-α4β7 antibody, e.g., vedolizumab, which do not decrease, decrease by more than a two-fold, or decrease by more than a three-fold from initiation to 10 weeks, from initiation to 6 weeks, or from 6 weeks to 10 weeks.

[0137] In some embodiments, the patient to be administered the combination therapy is a non-responder, e.g., does not show a clinical response to vedolizumab at 6 and / or 10 weeks after initiation of vedolizumab treatment. In some embodiments, the patient to be administered the combination therapy is a non-remitter, e.g., does not show a clinical remission to vedolizumab at 6 and / or 10 weeks after initiation of vedolizumab treatment.

[0138] The term "sample" as used herein is intended to include samples isolated from a subject, such as tissues, cells, biological fluids, and isolates thereof, as well as tissues, cells, and fluids present within a subject and obtainable from a patient or normal subject. For example, a non-invasive sample for in vitro measurement of a marker that identifies responders or non-responders may include a blood or serum sample. Thus, a blood sample can be tested for marker characteristics, such as size, sequence, composition, activity, or amount (i.e., level). In the case of a patient with an autoimmune disease or IBD, a control, reference sample of normal marker characteristics, such as size, sequence, composition, activity, or amount (i.e., level), can be obtained from a healthy subject without IBD.

[0139] The blood collection container may contain an anticoagulant, such as an additive that preserves the integrity of the blood, such as dextrose or albumin, or a buffer, such as phosphate, including heparin or ethylenediaminetetraacetic acid (EDTA), sodium citrate, or a citrate solution. If the amount of a marker is being measured by measuring the level of DNA in a sample, a DNA stabilizer, such as a drug that inhibits DNAse, can be added to the sample. If the amount of a marker is being measured by measuring the level of RNA in a sample, an RNA stabilizer, such as a drug that inhibits RNAse, can be added to the sample. If the amount of a marker is being measured by measuring the level of protein in a sample, a protein stabilizer, such as a drug that inhibits proteases, can be added to the sample. An example of a blood collection container is the PAXGENE™ tube (PREANALYTIX, Valencia, California), which is useful for RNA stabilization during blood collection. Peripheral blood samples can be modified, such as fractionated, sorted, or concentrated (e.g., in the case of a reference sample).

[0140] The sample, e.g., blood or modified blood, and / or reference, e.g., matched control (e.g., germline), sample can be subjected to a variety of well-known post-collection preparation and storage techniques (e.g., nucleic acid and / or protein extraction, fixation, storage, freezing, ultrafiltration, concentration, evaporation, centrifugation, etc.) before assessing the characteristics, e.g., size, sequence, composition, activity, or amount (i.e., level), of the marker genes (e.g., IL-22, STAT5A, and / or IL-1β) in the sample.

[0141] In some embodiments, markers can be identified by sequencing nucleic acid markers, e.g., DNA, RNA, cDNA, or protein markers correlated with marker genes, e.g., IL-22, STAT5A, and / or IL-1β. Several sequencing methods for nucleic acid sequencing are known in the art. A primer or primer pair can be used to sequence one or both strands of DNA corresponding to the marker gene. Primers can be used in combination with a probe, e.g., a nucleic acid probe, e.g., a hybridization probe, to amplify the region of interest before sequencing to increase the amount of sequence for marker gene detection. Examples of regions that can be sequenced include entire genes, gene transcripts, and gene fragments or transcripts, e.g., one or more exons or untranslated regions, or portions of markers containing mutation sites. Examples of target sequences for primer selection and sequence or composition analysis can be found in public databases that collect sequence or mutation information, e.g., RefSeq, COSMIC, and dbGaP.

[0142] Sequencing methods are known to those skilled in the art.Examples of methods include the Sanger method, SEQUENOM™ method, and next-generation sequencing (NGS).The Sanger method, which involves using electrophoresis, for example, capillary electrophoresis, to separate primer-extended labeled DNA fragments, can be automated for high-throughput applications.Primer extension sequencing can be carried out after PCR amplification of the region of interest.

[0143] In some embodiments, DNA markers, e.g., genomic DNA of marker genes (e.g., IL-22, STAT5A, and / or IL-1β), can be analyzed in biological samples using methods known in the art, both in situ and in vitro. DNA can be isolated directly from the sample or after isolating other cellular components, e.g., RNA or protein. Kits, e.g., the QIAAMP™ DNA Micro Kit (Qiagen, Valencia, CA), are available for DNA isolation. DNA can also be amplified using such kits.

[0144] In another embodiment, mRNA markers of marker genes (e.g., IL-22, STAT5A, and / or IL-1β) can be analyzed in both in situ and in vitro formats in biological samples using methods known in the art. Many expression detection methods use isolated RNA. For in vitro methods, any RNA isolation technique that does not select for mRNA isolation can be utilized for purifying RNA from cells (e.g., Ausubel et al., ed., Current Protocols in Molecular Biology, John Wiley & Sons, New York 1987-1999). Furthermore, large numbers of tissue samples can be easily processed using techniques well known to those skilled in the art, such as the single-step RNA isolation process of Chomczynski (1989, U.S. Patent No. 4,843,155). RNA can be isolated using standard procedures (e.g., Chomczynski and Sacchi (1987) Anal. Biochem. 162:156-159), solutions (e.g., trizol, TRI REAGENT™ (Molecular Research Center, Inc., Cincinnati, Ohio; see U.S. Pat. No. 5,346,994) or kits (e.g., QIAGEN™ Group RNEASY.RTM. Isolation Kit (Valencia, Calif.) or LEUKOLOCK™ Total RNA Isolation System, Ambion division of Applied Biosystems, Austin, Texas).

[0145] An additional step of removing DNA from RNA samples may be employed. Cell lysis can be achieved using a non-ionic detergent followed by microcentrifugation, which removes the nuclei and thus the majority of the cellular DNA. DNA can then be isolated from the nuclei for DNA analysis. In one embodiment, RNA is extracted from various cell types of interest using guanidine thiocyanate lysis followed by CsCl centrifugation, which separates RNA from DNA (Chirgwin et al. (1979) Biochemistry 18:5294-99). Poly(A)+ RNA is selected by selection using oligo-dT cellulose (see Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual (2nd ed.), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY). Alternatively, separation of RNA from DNA can be achieved by organic extraction, for example, using hot phenol or phenol / chloroform / isoamyl alcohol. If necessary, an RNAse inhibitor may be added to the lysis buffer. Similarly, for certain cell types, it may be desirable to add a protein denaturation / digestion step to the protocol. In many applications, it is desirable to enrich mRNA with respect to other cellular RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA). Most mRNAs contain poly(A) tails at their 3' ends. This allows for their enrichment using affinity chromatography, e.g., oligo(dT) or poly(U) bound to a solid support such as cellulose or SEPHADEX™ media (see Ausubel et al. (1994) Current Protocols in Molecular Biology, vol. 2, Current Protocols Publishing, New York). Once bound, poly(A)+ mRNA is eluted from the affinity column using 2 mM EDTA / 0.1% SDS.

[0146] Analyzing the characteristics of the marker genes described herein in a biological sample involves obtaining a biological sample (e.g., a blood sample or a reference sample) from a test subject. The characteristics can be assessed by any of a wide variety of well-known methods for detecting or measuring characteristics, e.g., of a marker or multiple markers, of nucleic acids (e.g., RNA, mRNA, genomic DNA, or cDNA) and / or translated proteins. Non-limiting examples of such methods include immunological methods for detecting secreted, cell surface, cytoplasmic, or nuclear proteins; protein purification methods; protein function or activity assays; nucleic acid hybridization methods, optionally including a "mismatch cleavage" step in which mismatched, i.e., regions of variability or diversity, are digested and mutants or variants are separated and identified from the resulting digestion fragments (Myers, et al. (1985) Science 230:1242); nucleic acid reverse transcription methods; and nucleic acid amplification methods and analysis of the amplification products. These methods include gene array / chip technologies, such as RT-PCR, TAQMAN™ Gene Expression Assays (Applied Biosystems, Foster City, CA), in situ hybridization, immunohistochemistry, immunoblotting, FISH (fluorescence in situ hybridization), FACS analysis, Northern blot, Southern blot, INFINIUM™ DNA analysis bead chip (Illumina, Inc., San Diego, CA), quantitative PCR, bacterial artificial chromosome arrays, single nucleotide polymorphism (SNP) arrays (Affymetrix, Santa Clara, CA) or cytogenetic analysis under GLP-approved laboratory conditions.

[0147] Detection methods can be used, for example, to detect RNA, mRNA, protein, cDNA, or genomic DNA in biological samples in vitro and in vivo. Furthermore, in vivo techniques for detecting polypeptide or nucleic acid markers described herein include introducing into a subject a labeled probe that detects the marker, e.g., a marker or labeled antibody, Fc receptor, or antigen for the polypeptide, e.g., a wild-type or mutant marker. For example, the antibody can be labeled with a radioisotope, and its presence and location within the subject can be detected by standard imaging techniques. These assays can be performed in a variety of ways. Those skilled in the art can select from these or other appropriate available methods based on the marker(s) in question, the tissue sample, and the nature of the mutation. Some methods are described in detail in later sections. Different methods or combinations of methods may be appropriate in different cases or, for example, in different patient populations.

[0148] In vitro techniques for detecting polypeptides corresponding to markers of the invention include enzyme-linked immunosorbent assays (ELISAs), Western blots, protein arrays, immunoprecipitation, immunochemistry, and immunofluorescence. In such examples, marker expression is assessed using antibodies (e.g., unlabeled, radiolabeled, chromophore-labeled, fluorophore-labeled, or enzyme-labeled antibodies), antibody derivatives (e.g., antibodies conjugated to substrates or proteins or ligands of protein-ligand pairs (e.g., biotin-streptavidin)), or antibody fragments (e.g., single-chain antibodies, isolated antibody hypervariable domains, etc.) that specifically bind to marker proteins or fragments thereof, including marker proteins that undergo all or some of their normal post-translational modifications, such as proteins or fragments containing regions that can be mutated or portions containing mutated residues in a mutant sequence or structural context. Antibodies may detect proteins having an amino acid sequence selected from the group consisting of SEQ ID NOs: 10 and 12. Assays such as sandwich ELISA assays may detect, for example, gain or loss of the amount of marker in a sample compared to a reference sample, or standard ELISAs would compare the level of antibody binding between patient and reference samples.

[0149] In some embodiments, the method includes measuring the amount (i.e., level) of a marker protein. In some embodiments, the amount of marker protein is quantified by immunohistochemistry of a sample, for example, using quantification products and methods from Ventana Medical Systems (Arizona) or Illumina (San Diego). In some embodiments, the amount of marker protein is quantified by immunohistochemistry of the marker from blood. In some embodiments, the amount of marker protein is determined by scoring antibody binding or staining intensity. In some embodiments, the amount of marker protein is determined by comparing antibody binding or staining in healthy cells or tissue versus cells or tissue from a subject with an autoimmune disease or IBD.

[0150] In one embodiment, marker expression is assessed by preparing mRNA / cDNA (i.e., transcribed polynucleotides) from cells in a patient sample and hybridizing the mRNA / cDNA with a reference polynucleotide that is the complement of the marker nucleic acid or a fragment thereof. The cDNA can optionally be amplified using any of a variety of polymerase chain reaction methods prior to hybridization with the reference polynucleotide. Similarly, expression of one or more markers can be detected using quantitative PCR to assess the expression level of the marker(s). An example use of measuring mRNA levels is that an inactivating mutation in a marker gene can result in changes in mRNA levels in cells. Levels can be upregulated due to feedback signaling protein production, allowing for a non-functional or absent protein, or downregulated due to instability of the altered mRNA sequence. Alternatively, any of the many known methods for detecting mutations or variants of the markers of the present invention (e.g., the single nucleotide polymorphisms, deletions, etc. described above) can be used to detect the occurrence of mutations in the marker genes of patients.

[0151] An example of direct measurement is the quantification of transcripts. As used herein, the expression level or amount refers to the absolute amount of expression of the mRNA encoded by the marker or the absolute amount of expression of the protein encoded by the marker. Instead of making a determination based on the absolute expression amount of a selected marker, the determination may be based on a normalized expression amount. Expression amount can be normalized by correcting the absolute expression level of a marker, for example, when comparing its expression with that of a control marker that is not a marker, in the role of a constitutively expressed housekeeping marker. Markers suitable for normalization also include housekeeping genes such as the actin gene or β2 microglobulin. Reference markers for data normalization purposes include markers that are ubiquitously expressed and / or whose expression is not regulated by oncogenes or cytokines. Constitutively expressed genes are known in the art and can be identified and selected according to the relevant tissue and / or patient conditions and analytical methods. Such normalization allows, for example, comparing the expression level of one sample with another sample at different times or between samples from different subjects. Furthermore, expression levels can be provided as relative expression levels. The initial value of genomic DNA sample, for example, the diploid copy number, can be determined by measuring the amount in cells from subjects who do not have autoimmune disorders or IBD.To determine the relative amount of marker or marker set, the amount of marker or marker set is determined for at least 1, or 2, 3, 4, 5 or more samples, for example, 7, 10, 15, 20, or 50 or more samples, to determine the starting time before determining the expression level for the sample in question.To determine the initial measurement, the average amount or level of each marker or marker set assayed in many samples is determined, and this is used as the starting expression level for the biomarker or biomarker set in question.Then, the amount (for example, absolute expression level) of marker or marker set determined for test sample is divided by the initial value obtained for that marker or marker set.This provides relative amounts and helps identify abnormal levels of marker protein activity.

[0152] Probes based on the sequences of the nucleic acid molecules of the present invention can be used to detect transcripts or genome sequences corresponding to one or more markers of the present invention.Probes can contain a labeling group attached thereto, for example, a radioisotope, a fluorescent compound, an enzyme, or an enzyme cofactor.Such probes can be used as part of a diagnostic test kit to identify cells or tissues that express proteins, for example, by measuring the level of nucleic acid molecules that code for proteins in a sample of cells from a subject, for example, by detecting mRNA levels, or by determining whether the gene that codes for proteins is mutated or deleted.

[0153] The primer or nucleic acid probe contains a nucleotide sequence complementary to a specific marker and is of sufficient length to selectively hybridize to a marker gene or a nucleic acid associated with the marker gene. Primers and probes can be used to aid in the isolation and sequencing of marker nucleic acids. In one embodiment, the primer or nucleic acid probe, e.g., a substantially purified oligonucleotide, contains a region having a nucleotide sequence that hybridizes under stringent conditions to approximately 6, 8, 10, 12, 15, 20, 25, 30, 40, 50, 60, 75, 100, or more consecutive nucleotides (within ±5% of the value) of the marker gene. In another embodiment, the primer or nucleic acid probe is capable of hybridizing to a marker nucleic acid containing any of the nucleotide sequences set forth in SEQ ID NO: 9 or 11. For example, the primer or nucleic acid probe contains a nucleotide sequence of at least about 15 consecutive nucleotides, at least about 25 nucleotides, or about 15 to about 20 nucleotides set forth in SEQ ID NO: 9 or 11. Nucleic acid analogs can be used as binding sites for hybridization. An example of a suitable nucleic acid analog is peptide nucleic acid (see, e.g., Egholm et al., Nature 363:566 568 (1993); U.S. Patent No. 5,539,083).

[0154] Primers or nucleic acid probes can be selected using algorithms that take into account binding energy, base composition, sequence complexity, cross-hybridization binding energy, and secondary structure (see Friend et al., International Patent Publication WO01 / 05935, published January 25, 2001; Hughes et al., Nat. Biotech. 19:342-7 (2001)). Those skilled in the art can use techniques in the art, such as manipulating the degeneracy or GC content in the primer or nucleic acid probe to adjust the likelihood of the primer or nucleic acid probe binding to a standard sequence, a mutant, or an allelic variant, to design primers and nucleic acid probes for the markers disclosed herein or related markers with similar characteristics, e.g., markers on chromosomal loci, or mutations in different regions of the same marker gene described herein. Computer programs well known in the art are useful for designing primers with the required specificity and optimal amplification properties, such as Oligo version 5.0 (National Biosciences, Plymouth, Minnesota). Perfectly complementary nucleic acid probes and primers can be used to detect the markers described herein and their variants, polymorphisms, or alleles, and deviations from perfect complementarity are contemplated as long as such deviations do not prevent the molecule from specifically hybridizing to the target region. For example, an oligonucleotide primer can have a non-complementary fragment at its 5' end, with the remainder of the primer being complementary to the target region. Alternatively, non-complementary nucleotides can be interspersed in a nucleic acid probe or primer, as long as the resulting probe or primer is still capable of specifically hybridizing to the target region.

[0155] The following examples illustrate improvements to the methods and compositions described herein. The following examples are provided for illustrative purposes only and are not intended to limit the scope of the invention in any way. Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. [Example]

[0156] Example 1. Efficacy of a combination of anti-MAdCAM-1 antibody and anti-p40 antibody in a mouse colitis model The following study evaluated the combined therapeutic effect of a combination therapy containing an anti-MAdCAM-1 antibody and an IL-23 inhibitor, specifically an antibody that binds to and blocks the p40 subunit of IL-23 (and IL-12), using a mouse colitis model. As shown below, the combination of the two therapeutic agents (anti-MAdCAM-1 (MECA-367, catalog no. BE0035, from BioXCell) and anti-p40 IL-23 / IL-12 (clone C17.8, catalog no. BE0051, from BioXCell)) resulted in improvements in colon weight, diarrhea, and histopathology in the tested mice versus controls.

[0157] The model used was the naive T cell transfer (TCT) model. CD4+ adoptive transfer colitis is primarily driven by a Th1 / Th17-mediated immune response. Disease in mice is characterized by infiltration of the lamina propria with CD4+ T cells, neutrophils, and macrophages, which leads to progressive weight loss, colonic inflammation, and diarrhea.

[0158] A schematic diagram of the study is shown in Figure 3. In summary, naive T cells (CD4+CD62L+) from BALB / c mice were transfected into SCID mice (approximately 2x10 5 Mice were treated with an isotype control antibody ("vehicle"), 10 mg / kg anti-MAdCAM antibody, 1 mg / kg anti-p40 IL12 / IL23 antibody (anti-p40 antibody), or a combination of 10 mg / kg anti-MAdCAM antibody and 1 mg / kg anti-p40 IL12 / IL23 antibody.

[0159] As shown in Figure 3, vehicle or 10 mg / kg anti-MAdCAM antibody was administered on days 0, 7, 14, 21, and 28 (Q1W). Vehicle or 1 mg / kg anti-p40 IL12 / IL23 antibody was administered once every four days (Q4d) from days 14 to 26. Samples were collected for analysis, e.g., diarrhea score, colon weight, colon histology, colon mRNA.

[0160] The results of the study are provided in Figures 4A, 4B, 4C, Figures 5A and 5B, and Figures 6A and 6B.

[0161] The combination of anti-MAdCAM antibody and anti-p40 IL12 / IL23 antibody demonstrated superior effects on colon weights as shown in the results provided in Figure 4A at day 28. The benefit of the combination therapy was also observed in diarrhea scores as shown in Figure 4B at day 21, although diarrhea scores showed a positive trend in the data at day 28 (data not shown) versus day 21 as shown in Figure 4B. Figure 4C provides a graph of histopathology scores at day 28 from H&E staining, demonstrating the superior therapeutic effect of the combination therapy over antibody treatment alone or the control.

[0162] Furthermore, CD3 (T cell) staining of the lamina propria / epithelium on day 28 suggested that the primary effect of the anti-MAdCAM1 antibody was on T cell infiltration. As shown in Figure 5A, T cells in the lamina propria / epithelium were quantified for each treatment group. As shown in Figure 5B, T cell infiltration correlated with the total inflammatory cell score.

[0163] Myeloperoxidase (MPO) staining of neutrophils in the lamina propria on day 28 showed that anti-p40 antibody reduced the proportion of MPO(+) neutrophils in the colonic mucosa, and the combination of anti-MAdCAM1 inhibitor and anti-p40 IL-23 / IL-12 inhibitor tended to reduce macrophages (CD68). These results are presented in Figures 6A and 6B.

[0164] The results of this study suggest that MAdCAM-1 pathway inhibition and IL-23 pathway inhibition have complementary effects on adaptive and innate immune cells in the colonic mucosa. More specifically, anti-MAdCAM-1 and anti-p40 antibodies reduced the proportion of CD3+ T cells in the colonic mucosa, with a superior effect observed in combination. Anti-p40 antibody activity reduced the proportion of MPO+ neutrophils in the colonic mucosa, whereas CD68+ macrophages were not significantly affected by anti-MAdCAM-1, anti-p40, or their combination (although a trend was observed with the latter).

[0165] Example 2. Combination effects of anti-MAdCAM-1 and anti-p40 on mRNA expression in a TCT-induced mouse chronic colitis model Gene expression in the colon was studied to determine the effects of administering anti-MAdCAM-1, anti-p40 IL-23, and a combination of MAdCAM-1 and p40 IL-23. A false discovery rate (FDR) of 0.05 was used to define differentially expressed genes (DEGs). Figure 7 provides a Venn diagram showing gene expression counts. Results revealed that 4,422 genes had altered expression when the two treatments were combined, and approximately 3,489 genes were synergistically expressed. Differential gene expression between treatments and controls is depicted in the graph in Figure 7.

[0166] The combination of anti-MAdCAM1 and anti-p40 antibodies resulted in a number of genes showing synergistic expression (up- or down-regulated), which are genes that are affected only by the combination of anti-MAdCAM-1 and anti-p40, but not by the individual treatments. These synergistically expressed genes included the mRNA expression of specific integrin chains, such as Itgal (αL chain / CD11a / LFA-1A), Itgb2 (β2 integrin chain / CD18), Itgax (αX chain / CD11c), Itga3, Itga9, and Itgb1bk. In particular, Itgal (αL chain / CD11a / LFA-1A), Itgb2 (β2 integrin chain / CD18), Itgax (αX chain / CD11c), Itga3, and Itgb1bk were synergistically down-regulated. In contrast, Itga9 was shown to be synergistically up-regulated.

[0167] Additionally, certain cytokine genes were identified as having synergistic mRNA expression with combination therapy, including Il21r, Il12rb1, Il12a, IL2ra, IL10ra, Il17re, Il34, Il18rap, Il1rl1, Il1b, Il1r2, Il3ra, Il1f9, Il23a, Iltifb, Il6, Il18bp, Il1a, Il15, and Il1r1. In particular, Il21r, Il12rb1, Il12a, IL2ra, IL10ra, Il34, Il18rap, Il1rl1, Il1b, Il1r2, Il3ra, Il1f9, Il23a, Iltifb, Il6, Il18bp, Il1a, and Il1r1 were synergistically downregulated. In contrast, Il17re and Il15 were synergistically upregulated. Other genes identified as having synergistic mRNA expression in the presence of combination therapy (vs. therapy alone) included Stat4, Stat2, and Cd3g (synergistically downregulated).

[0168] Overall, anti-MAdCAM-1 antibody treatment induced broad gene expression changes, including ITGB7, ITGAE, and interleukin receptors, when compared with controls. Anti-p40 antibody treatment also induced broad gene expression changes distinct from those induced by anti-MAdCAM-1 when compared with controls. Combining anti-MAdCAM-1 and anti-p40 antibody treatment induced broad gene expression changes of approximately 4,422 genes, including increased interleukins, integrins, stats, and downregulation of Cd3. The synergistic inhibition of IL12 / IL23A and complementary inhibition of ITGB7 and ITGA4 demonstrate that the combination therapy exerts its effect in the "right" direction against both drug targets; that is, inhibiting one target does not increase the expression of the other target.

[0169] Example 3. Activity of a combination of anti-MAdCAM-1 and anti-p40 antibodies in T cell transfer (TCT) induced mouse chronic colitis model. The experiment described in Example 1 was repeated using the treatment groups summarized in Table 1. [Table 1] Samples were collected and analyzed for α4β7+CD4+ T cells, diarrhea score, colon weight, colon histology, and colon mRNA.

[0170] The combination showed improvements in body weight on days 21 and 28, as shown in Figures 8A and 8B, respectively, and a significantly positive effect on diarrhea scores on day 21 (Figure 8C), but not on day 28. Unlike the results described in Example 1, no positive effect on mouse colon weight or histopathology was observed with the combination therapy.

[0171] The effects of the combination therapy on T cell, neutrophil, and macrophage infiltration were observed and were similar to those provided in Example 1. The results of this replicate study are provided in Figures 9A-9C. Anti-MAdCAM-1 antibody treatment and anti-p40 antibody treatment reduced the proportion of CD3(+) T cells in the colonic mucosa, with a superior effect observed in combination (shown in Figure 9A). Furthermore, anti-p40 antibody treatment reduced MPO(+) neutrophils in the colonic mucosa (shown in Figure 9B), and CD68(+) macrophages were significantly affected by anti-p40 antibody treatment and the combination therapy (shown in Figure 9C). Overall, the results were very similar to those described from the study in Example 1.

[0172] Additionally, RNA sequencing was used to determine gene expression in the colon, and DEGs were identified with an FDR of 0.05. Approximately 343 genes were identified as having novel synergistic gene expression in the combination therapy.

[0173] To summarize the studies described in Example 1 and above, a significantly superior effect on diarrhea scores on day 21 was observed in both studies. Although a trend toward improved body weight from days 21 to 28 with the combo was noted in the replicate study (but not in Study 1), the superior combo effect on colon weight and histopathology in the first study was not replicated in the second study. Immunohistology results were highly similar between studies, indicating complementary effects on T cells, neutrophils, and macrophages in the colon. Overall, the two studies provide observations suggesting that inhibiting both the MAdCAM-1 pathway and the p40 subunit of IL-23 provides significant activity. Furthermore, RNA sequencing results demonstrated synergistic gene expression changes with the combination therapy.

[0174] Example 4. Differential regulation of the IL-22 pathway in vedolizumab responder vs. non-responder IBD patients Vedolizumab (VDZ) is a monoclonal antibody (mAb) targeting the α4β7 integrin approved for the treatment of moderate to severe Crohn's disease (CD) and ulcerative colitis (UC). Due to its inherent safety profile, VDZ may be an excellent choice as the backbone of biologic combination therapy to increase efficacy. Vedolizumab blocks the interaction between MAdCAM-1 and α4β7.

[0175] Anti-p19 (interleukin-23 (IL-23)) mAbs with acceptable safety profiles are effective in CD and UC, but it has not yet been shown whether the combination of anti-p19 and VDZ has additive efficacy.

[0176] Serum IL-22 levels have been shown to be higher in CD patients who respond to anti-p19 therapy, suggesting that increased activity of the IL-22 pathway is associated with the success of this treatment. Therefore, it is hypothesized that IL-22, when increased in VDZ non-responders, would support a combination with anti-p19 therapy that provides superior efficacy.

[0177] Publicly available microarray data were originally generated in 41 moderate / severe bio-naive UC patients. Analysis was performed using a robust multichip averaging method to calculate log2 expression values ​​of IL22 and STAT5A probes within the array data and compare VDZ responders, non-responders, and healthy controls. Serum IL-22 levels were assessed using Quantikine® ELISA (R&D Systems) in CD patients with moderate / severe disease in the Gemini-III trial: 59 remitters (VDZ-R) at weeks 6 and 10, and 59 non-remitters (VDZ-NR) at both time points (mean CDAI at baseline: 297 ± 49; median CRP: 9.7 mg / L [range: 3.7-24.5]; median FCP: 583 mg / kg [range: 229-1380]; 74.5% anti-TNF failure). Remitters and non-remitters were matched for disease severity at baseline using the CDAI and FCP.

[0178] Although colonic IL-22 mRNA at baseline was significantly higher in VDZ non-responder UC patients than in healthy controls (endoscopic subscore >1), STAT5A mRNA (IL-22 signaling) was higher in VDZ non-responders compared with responders (Figure 1). In addition, serum IL-22 at baseline did not differ between VDZ remitters (CDAI < 150) and non-remitters, but the decrease in IL-22 levels at week 10 was smaller in VDZ non-remitters (Figure 2).

[0179] Responses to VDZ were predominantly seen in IBD patients in the absence of increased IL-22 pathway activity. This suggests that the addition of anti-p19 / IL-23 therapy is complementary to VDZ and could potentially increase efficacy when administered as a combination regimen. The results suggest a pilot clinical trial to test this hypothesis. *(Arijs et al. Gut, 67:43-52, 2018; Gene Expression Omnibus database accession number GSE73661)

[0180] equivalent Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the scope of the following claims. The contents of all references, patents, and published patent applications cited throughout this application are hereby incorporated by reference.

[0181] [Table 2]

[0182] [Table 3]

[0183] [Table 4]

[0184] Table 5

[0185] Table 6

[0186] Table 7

[0187] Table 8 The present invention includes the following embodiments. [1] 1. A method of treating a human patient in need thereof, said method comprising administering to said human patient an α4β7 inhibitor and an IL-23 inhibitor. [2] The method according to [1] above, wherein the α4β7 inhibitor is an anti-α4β7 antibody. [3] The method according to [2] above, wherein the anti-α4β7 antibody is humanized. [4] The method according to [2] or [3] above, wherein the anti-α4β7 antibody comprises a heavy chain variable region comprising the CDR3 domain set forth in SEQ ID NO: 4, the CDR2 domain set forth in SEQ ID NO: 3, and the CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising the CDR3 domain set forth in SEQ ID NO: 8, the CDR2 domain set forth in SEQ ID NO: 7, and the CDR1 domain set forth in SEQ ID NO: 6. [5] 1. A method of treating a human patient in need thereof, said method comprising administering to said human patient an anti-α4β7 antibody and an IL-23 inhibitor; The method, wherein the anti-α4β7 antibody is an IgG1 antibody; comprises a heavy chain variable region comprising the CDR3 domain set forth in SEQ ID NO: 4, the CDR2 domain set forth in SEQ ID NO: 3, and the CDR1 domain set forth in SEQ ID NO: 2; and comprises a light chain variable region comprising the CDR3 domain set forth in SEQ ID NO: 8, the CDR2 domain set forth in SEQ ID NO: 7, and the CDR1 domain set forth in SEQ ID NO: 6. [6] The method according to [1] or [5] above, wherein the human patient has an autoimmune disease. [7] The method according to [6] above, wherein the autoimmune disease is arthritis or psoriasis. [8] The method according to [6] above, wherein the autoimmune disease is rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, or axial spondyloarthritis. [9] The method according to [1] or [5] above, wherein the human patient has inflammatory bowel disease (IBD).

[10] The method according to [1] or [5] above, wherein the human patient has an autoimmune disease and an inflammatory bowel disease.

[11] The method according to [9] or

[10] above, wherein the IBD is ulcerative colitis or Crohn's disease.

[12] The method according to

[11] above, wherein the ulcerative colitis is moderate to severe active ulcerative colitis.

[13] The method according to

[11] above, wherein the Crohn's disease is moderate to severe active Crohn's disease.

[14] The method according to any one of the above-mentioned [1] to

[13] , wherein the anti-α4β7 antibody is administered before the IL-23 inhibitor.

[15] The method according to any one of the above-mentioned [1] to

[13] , wherein the anti-α4β7 antibody is administered after the IL-23 inhibitor.

[16] The method according to any one of the above-mentioned [1] to

[13] , wherein the anti-α4β7 antibody is administered simultaneously with the IL-23 inhibitor.

[17] The method described in any of [2] to

[16] above, wherein the anti-α4β7 antibody comprises a heavy chain variable domain comprising the amino acid sequence set forth in SEQ ID NO: 1 and a light chain variable domain comprising the amino acid sequence set forth in SEQ ID NO: 5.

[18] The method according to any one of [2] to

[17] above, wherein the anti-α4β7 antibody is a humanized antibody.

[19] The method according to any one of [2] to

[18] above, wherein the anti-α4β7 antibody is vedolizumab.

[20] The method according to any one of [2] to

[19] above, wherein the human patient receives a first administration of 300 mg of the anti-α4β7 antibody at week 0, followed by a second administration of 300 mg of the anti-α4β7 antibody at week 2, and then a third administration of 300 mg of the anti-α4β7 antibody at week 6.

[21] The method according to

[20] above, further comprising administering 300 mg of the anti-α4β7 antibody to the human patient every 8 weeks starting 8 weeks after the third administration.

[22] The method of

[21] above, further comprising administering 300 mg of the anti-α4β7 antibody to the human patient every four weeks if the human patient does not show clinical improvement.

[23] The method according to

[22] above, wherein the human patient has ulcerative colitis or Crohn's disease, and the clinical improvement is clinical remission.

[24] The method according to

[20] above, further comprising administering 300 mg of the anti-α4β7 antibody to the human patient every four weeks starting eight weeks after the third administration.

[25] The method according to any one of

[20] to

[24] above, wherein the anti-α4β7 antibody is administered intravenously.

[26] The method according to

[20] above, further comprising administering 108 mg of the anti-α4β7 antibody to the human patient every two weeks starting eight weeks after the third administration.

[27] The method of any of [2] to

[19] above, wherein the human patient receives an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, followed by a third dose of 108 mg of the anti-α4β7 antibody at week 6, followed by doses of 108 mg every two weeks thereafter.

[28] The method according to any one of claims 26 to 27, wherein the 108 mg dose is administered subcutaneously.

[29] The method according to

[28] above, wherein the 108 mg dose is self-administered.

[30] The method according to any one of the above-mentioned [1] to

[29] , wherein the IL-23 inhibitor is an antibody that binds to the p19 subunit of IL-23.

[31] The method according to any one of the above-mentioned [1] to

[29] , wherein the IL-23 inhibitor is an antibody that binds to the p40 subunit of IL-23.

[32] The method according to any one of the above-mentioned [1] to

[29] , wherein the IL-23 inhibitor is risankizumab, ustekinumab, guselkumab, or tildrakizumab.

[33] The method according to any one of the above-mentioned [1] to

[27] , wherein the IL-23 inhibitor is an antibody that binds to IL-23R.

[34] The method according to any one of the above [1] to

[33] , wherein the patient is characterized as a non-responder or non-remitter at 6 and / or 10 weeks after the start of treatment with an α4β7 inhibitor.

[35] The method according to any one of the above [1] to

[33] , wherein the patient is characterized as having elevated serum IL-22 levels at the start of treatment with an α4β7 inhibitor or 6 weeks after the start.

[36] The method according to

[34] or

[35] above, wherein the α4β7 inhibitor is an anti-α4β7 antibody.

[37] The method according to

[36] above, wherein the anti-α4β7 antibody is vedolizumab.

[38] The method according to [5] above, wherein the IL-22 level in the serum of the human patient does not decrease at all, decreases by less than half, or decreases by less than one-third from the start of treatment with the anti-α4β7 antibody to 10 weeks after the start, from the start of treatment with the anti-α4β7 antibody to 6 weeks after the start, or from 6 weeks to 10 weeks after the start of treatment including the anti-α4β7 antibody.

[39] The method of [5] above, wherein the patient is characterized as having elevated serum IL-22 levels at the start of treatment with the anti-α4β7 antibody or 6 weeks after the start, and the serum IL-22 levels do not decrease at all, decrease by more than half, or decrease by more than one-third between the start and 10 weeks, between the start and 6 weeks, or between 6 weeks and 10 weeks.

[40] The method according to [1] or [5] above, wherein the patient is characterized as having elevated levels of IL-22 and / or STAT5A compared to control levels.

[41] The method according to

[40] above, wherein the control level is a level in one or more of a subject not suffering from IBD, a healthy subject, non-inflamed colon tissue from the patient, or non-colon tissue.

[42] The method according to any one of the above

[40] and

[41] , wherein the patient's IL-22 and / or STAT5A levels are measured before or on the first day of treatment with the anti-α4β7 antibody.

[43] The method according to

[42] above, wherein the patient's IL-22 and / or STAT5A levels are measured 1, 2, 3, 4, 5, 6, 7, 8, 9, and / or 10 days before treatment with the anti-α4β7 antibody.

[44] The method according to any one of

[35] to

[42] above, wherein the patient's IL-22 and / or STAT5A nucleic acid and / or protein levels are measured.

[45] The method of

[40] above, wherein the IL-22 and / or STAT5A levels are increased by 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or more compared to control levels.

[46] 1. A method of treating inflammatory bowel disease in a patient in need thereof, comprising administering to the patient an anti-α4β7 antibody and an antibody that binds to the p19 subunit of IL-23, wherein the anti-α4β7 antibody is administered to the human patient by administering an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, a third dose of 300 mg of the anti-α4β7 antibody at week 6, and subsequently every eight weeks beginning eight weeks after the third dose; the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, The method, wherein the patient is characterized as having elevated levels of IL-22 and / or STAT5A compared to control levels.

[47] 1. A method of treating inflammatory bowel disease in a patient in need thereof, comprising administering to the patient an anti-α4β7 antibody and an antibody that binds to the p40 subunit of IL-23, wherein the anti-α4β7 antibody is administered to the human patient in the following manner: an initial dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, a third dose of 300 mg of the anti-α4β7 antibody at week 6, and then every eight weeks starting eight weeks after the third dose; the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, The method, wherein the patient is characterized as having elevated levels of IL-22 and / or STAT5A compared to control levels.

[48] 1. A method of treating inflammatory bowel disease in a patient in need thereof, comprising administering to the patient an anti-α4β7 antibody and an antibody that binds to the p19 subunit of IL-23, wherein the anti-α4β7 antibody is administered as follows: a first dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, followed by a third dose of 108 mg of the anti-α4β7 antibody at week 6, and then every two weeks thereafter at doses of 108 mg; the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, The method, wherein the patient is characterized as having elevated levels of IL-22 and / or STAT5A compared to control levels.

[49] 1. A method of treating inflammatory bowel disease in a patient in need thereof, comprising administering to the patient an anti-α4β7 antibody and an antibody that binds to the p40 subunit of IL-23, wherein the anti-α4β7 antibody is administered as follows: a first dose of 300 mg of the anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the anti-α4β7 antibody at week 2, followed by a third dose of 108 mg of the anti-α4β7 antibody at week 6, and then every two weeks thereafter at doses of 108 mg; the anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 4, a CDR2 domain set forth in SEQ ID NO: 3, and a CDR1 domain set forth in SEQ ID NO: 2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO: 8, a CDR2 domain set forth in SEQ ID NO: 7, and a CDR1 domain set forth in SEQ ID NO: 6, The method, wherein the patient is characterized as having elevated levels of IL-22 and / or STAT5A compared to control levels.

[50] The method according to any one of

[46] to

[49] above, wherein the control level is a level in one or more of a subject not suffering from IBD, a healthy subject, non-inflamed colon tissue derived from the patient, or non-colon tissue.

Claims

1. 1. A composition for treating an autoimmune disease or inflammatory bowel disease in a human patient, comprising a humanized anti-α4β7 antibody, the composition is administered in combination with an IL-23 inhibitor; the IL-23 inhibitor is an antibody that binds to the p40 subunit of IL-23; the patient is characterized as having elevated levels of IL-22 and STAT5A compared to control levels; the control level is a level in one or more of a subject not afflicted with IBD, a healthy subject, non-inflamed colon tissue, or non-colon tissue from the patient; The humanized anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO:4, a CDR2 domain set forth in SEQ ID NO:3, and a CDR1 domain set forth in SEQ ID NO:2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO:8, a CDR2 domain set forth in SEQ ID NO:7, and a CDR1 domain set forth in SEQ ID NO:

6.

2. The composition of claim 1 , wherein the autoimmune disease is arthritis or psoriasis.

3. 2. The composition of claim 1, wherein the autoimmune disease is rheumatoid arthritis, juvenile arthritis, psoriatic arthritis, or axial spondyloarthritis.

4. 2. The composition of claim 1, wherein the inflammatory bowel disease (IBD) is ulcerative colitis or Crohn's disease.

5. 2. The composition of claim 1, wherein the humanized anti-α4β7 antibody is administered before, after, or simultaneously with the IL-23 inhibitor.

6. 6. The composition of any one of claims 1 to 5, wherein the humanized anti-α4β7 antibody comprises a heavy chain variable domain comprising the amino acid sequence set forth in SEQ ID NO: 1 and a light chain variable domain comprising the amino acid sequence set forth in SEQ ID NO:

5.

7. The composition of any one of claims 1 to 5, wherein the humanized anti-α4β7 antibody is vedolizumab.

8. 2. The composition of claim 1, wherein the human patient receives a first dose of 300 mg of the humanized anti-α4β7 antibody at week 0, followed by a second dose of 300 mg of the humanized anti-α4β7 antibody at week 2, followed by a third dose of 300 mg of the humanized anti-α4β7 antibody at week 6.

9. 9. The composition of claim 8, wherein the human patient further receives 300 mg of the humanized anti-α4β7 antibody every 8 weeks starting 8 weeks after the third administration.

10. 10. The composition of claim 9, further comprising administering 300 mg of the humanized anti-α4β7 antibody to the human patient every four weeks if the human patient does not show clinical improvement.

11. 11. The composition of claim 10, wherein the human patient has ulcerative colitis or Crohn's disease and the clinical improvement is clinical remission.

12. 9. The composition of claim 8, wherein the human patient further receives 300 mg of the humanized anti-α4β7 antibody every four weeks starting eight weeks after the third administration.

13. The composition of any one of claims 8 to 12, wherein the humanized anti-α4β7 antibody is administered intravenously.

14. 9. The composition of claim 8, wherein the human patient further receives 108 mg of the humanized anti-α4β7 antibody every two weeks starting eight weeks after the third administration.

15. 2. The composition of claim 1, wherein the human patient receives an initial dose of 300 mg of the humanized anti-a4p7 antibody at week 0, followed by a second dose of 300 mg of the humanized anti-a4p7 antibody at week 2, followed by a third dose of 108 mg of the humanized anti-a4p7 antibody at week 6, followed by 108 mg doses every two weeks thereafter, wherein the 108 mg dose is administered subcutaneously and wherein the 108 mg dose is self-administered.

16. The composition of any one of claims 1 to 5, wherein the IL-23 inhibitor is ustekinumab.

17. 6. The composition of claim 1, wherein the patient is characterized as a non-responder or non-remitter at 6 and / or 10 weeks after initiation of treatment with the humanized anti-α4β7 antibody, or the patient is characterized as having elevated levels of IL-22 in serum at the start of or 6 weeks after initiation of treatment with the humanized anti-α4β7 antibody.

18. or the level of IL-22 in the serum of the human patient is not reduced at all, is reduced by less than two-fold, or is reduced by less than three-fold from the start of treatment with the humanized anti-α4β7 antibody to 10 weeks after the start of treatment, from the start of treatment with the humanized anti-α4β7 antibody to 6 weeks after the start of treatment, or from 6 weeks to 10 weeks after the start of treatment with the humanized anti-α4β7 antibody; or the patient is characterized as having elevated serum IL-22 levels at the start of treatment with the humanized anti-α4β7 antibody or at 6 weeks after the start of treatment, and the serum IL-22 levels do not decrease, decrease by less than a half-fold, or decrease by less than a third-fold from the start to 10 weeks, from the start to 6 weeks, or from 6 weeks to 10 weeks. The composition according to any one of claims 1 to 5.

19. 20. The composition of claim 1 or 18, wherein the patient's IL-22 and STAT5A levels are measured before or on the first day of treatment with the anti-α4β7 antibody.

20. 20. The composition of claim 19, wherein the patient's IL-22 and STAT5A levels are measured 1, 2, 3, 4, 5, 6, 7, 8, 9, and / or 10 days prior to treatment with the humanized anti-α4β7 antibody.

21. The method of claim 17, wherein the patient's IL-22 nucleic acid and / or protein levels and STAT5A nucleic acid and / or protein levels are measured.

22. 2. The composition of claim 1, wherein the IL-22 and STAT5A levels are increased by 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or more compared to the control levels.

23. 1. A composition for treating inflammatory bowel disease in a patient, comprising a humanized anti-α4β7 antibody, said composition being administered to said patient in combination with an antibody that binds to the p40 subunit of IL-23; The humanized anti-α4β7 antibody is administered in the following dosing regimen: is administered to a human patient according to a dosing regimen comprising an initial administration of 300 mg of the humanized anti-α4β7 antibody at week 0, followed by a second administration of 300 mg of the humanized anti-α4β7 antibody at week 2, a third administration of 300 mg of the humanized anti-α4β7 antibody at week 6, and then every 8 weeks beginning 8 weeks after the third administration, a 300 mg dose of the humanized anti-α4β7 antibody is administered to the human patient; the humanized anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO:4, a CDR2 domain set forth in SEQ ID NO:3, and a CDR1 domain set forth in SEQ ID NO:2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO:8, a CDR2 domain set forth in SEQ ID NO:7, and a CDR1 domain set forth in SEQ ID NO:6; the patient is characterized as having elevated levels of IL-22 and STAT5A compared to control levels; The composition, wherein the control level is a level in one or more of a subject not afflicted with IBD, a healthy subject, non-inflamed colon tissue, or non-colon tissue from the patient.

24. 1. A composition for treating inflammatory bowel disease in a patient, comprising a humanized anti-α4β7 antibody, said composition being administered to said patient in combination with an antibody that binds to the p40 subunit of IL-23, wherein said humanized anti-α4β7 antibody is administered in the following dosage regimen: administering to the patient according to a dosing regimen comprising an initial administration of 300 mg of the humanized anti-a4p7 antibody at week 0, followed by a second administration of 300 mg of the humanized anti-a4p7 antibody at week 2, followed by a third administration of 108 mg of the humanized anti-a4p7 antibody at week 6, followed by doses of 108 mg every two weeks thereafter; the humanized anti-α4β7 antibody comprises a heavy chain variable region comprising a CDR3 domain set forth in SEQ ID NO:4, a CDR2 domain set forth in SEQ ID NO:3, and a CDR1 domain set forth in SEQ ID NO:2; and a light chain variable region comprising a CDR3 domain set forth in SEQ ID NO:8, a CDR2 domain set forth in SEQ ID NO:7, and a CDR1 domain set forth in SEQ ID NO:6; the patient is characterized as having elevated levels of IL-22 and STAT5A compared to control levels; The composition, wherein the control level is a level in one or more of a subject not afflicted with IBD, a healthy subject, non-inflamed colon tissue, or non-colon tissue from the patient.

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