Methods of identifying responders to treatment for inflammatory bowel disease

Abstract

The present disclosure relates to the use of biomarkers, e.g., TNF-α, IL-17F, GM-CSF, and combinations thereof, to identify the responsiveness of IBD patients to treatment with an anti-IL23 antagonist (e.g., anti-IL23 antibodies). The levels of biomarkers are compared to the levels of the same biomarkers in an individual having a known responsiveness status. Information provided by the disclosed method may be used to determine whether an IBD patient should be treated with an IL-23 antagonist or a treatment that does not target IL-23. Such information may also be used to determine if treatment with a certain agent should be commenced, suspended, or modified. Also disclosed herein are methods of determining the level of a biomarker associated with responsiveness of an individual to treatment with an IL-23 antagonist.

Description

METHODS OF IDENTIFYING RESPONDERS TO TREATMENT FOR INFLAMMATORY BOWEL DISEASECROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit under 35 U. S. C. § 119(e) of U. S. Provisional Patent Application No. 63 / 749,278, filed January 24, 2025, the entire disclosure of which is incorporated herein by reference.FIELD

[0002] The present disclosure generally relates to the use of biomarkers, e.g., TNF-a, IL-17F, GM-CSF, and combinations thereof, to identify the responsiveness of IBD patients to treatment with an anti-IL23 antagonist (e.g., anti-IL23 antibodies).BACKGROUND

[0003] Inflammatory bowel disease (IBD), which is a term encompassing ulcerative colitis (UC) and Crohn’s disease (CD, is a chronic and debilitating inflammatory illness of the gastrointestinal tract. The exact cause of IBD remains unclear, but it is generally accepted that its pathology is multifactorial, involving a genetic predisposition, mucosal barrier dysfunction, disturbances in the gastrointestinal microbiota, dysregulated immune responses, environmental, and lifestyle factors. Over the last few decades, the epidemiology of BD has changed dramatically. In the last twenty years, the incidence of IBD has risen dramatically in industrialized countries, with more than 0.7% of the US population and 0.3% of the population of Europe suffering from this disease. Thus, IBD not only seriously endangers human health worldwide, but also brings heavy financial burdens to individuals, families, and society.

[0004] Conventional treatments for IBD have been focused on control symptoms through pharmacotherapy, including aminosalicylates, corticosteroids (CSs), immunomodulators, and biologies, with other general measures and / or surgical resection if necessary. However, over the last decade there has been an expansion in IBD therapeutic options. The introduction of specific inhibitors of tumor necrosis factor (TNF) was a groundbreaking achievement in the treatment of IBD, enabling long-standing remission, and modification of the IBD course in a significant fraction of patients. However, primary nonresponse to TNF inhibitors was observed in up to 40% of patients in clinical trials. Most recently, targeted biologic medicines that directly block important mediators ofinflammation, such as interleukin (IL)- 12, and IL-23, have become front-line treatment for IBD. While these treatments have significantly improved IBD treatment options, IBD in many patients do not respond to such treatments. For example, about 40% of patients with IBD do not respond to treatment with IL- 12 or IL-23 antagonists. Since it may take as long as 8-12 weeks to determine patient response to a drug, non-responding patients may suffer unnecessarily. Moreover, Crohn’s disease, has a window of opportunity for treatment, during which providing the appropriate treatment can avoid long-term complications of the disease. Waiting to see if the patient responds to an IL-23 antagonist may result in failing to provide appropriate treatment during a critical stage of the disease. Thus, a goal in the field of IBD treatment is to develop assays for predicting the responsiveness of patients to biologic treatments. One example, a method for determining responsiveness to anti-TNF-a therapy, is disclosed in US 12,084,722, which is incorporated herein in its entirety by reference. However, similar attempts at developing assays for IL-23 antagonists have been unsuccessful. For example, a prior study of biomarkers predictive for response to the IL-23 antagonist risankizumab, showed that serum IL-22 concentration was not predictive of clinical or endoscopic response / remission (D’Haens, et al., The Lancet, Vol. 299, Issue 10340, 2022). Thus, there is currently no way to determine which patients will respond to an IL-23 antagonist and which patients should receive a treatment that does not target IL-23.

[0005] Accordingly, there remains a need for a way to predict whether an IBD patient will respond to an IL-23 antagonist. Having such information early in the disease process would allow appropriate treatment decisions to be made, thereby reducing unnecessary suffering by patients, and avoiding, irreversible, long-term complications of IBD. The present disclosure provides such methods and provides improved methods for treating IBD.SUMMARY OF THE DISCLOSURE

[0006] One embodiment is a method of predicting the responsiveness of a subject to treatment of inflammatory bowel disease (IBD) using an interleukin-23 (IL-23) antagonist, the method comprising comparing a level of one or more biomarkers in a sample from the subject to a reference level of one or more corresponding biomarkers, and predicting the responsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers.

[0007] One embodiment is a method of predicting the responsiveness of a subject to treatment of inflammatory bowel disease (IBD) using an interleukin-23 (IL-23) antagonist, the method comprising obtaining a peripheral blood mononuclear cells (PBMC)-containing a sample from the subject, isolating the PBMC from the sample, contacting the PBMC with a Golgi-inhibitor and stimulating the PBMC with IL-23, fixing and permeabilizing the PBMC, determining the fraction of IL23 -responsive cell types selected from a Th 17 cell, a Tcl7 cell, a y8T cell, an iNKT cell, or a MAIT cell having detectable intracellular level of one or more biomarkers selected from TNF-a, IL-17F, and GM-CSF, comparing the intracellular level of the one or more biomarker in the sample from the individual to a reference level of one or more corresponding biomarker and, predicting the responsiveness of the subject based on the similitude of the level of the one or more biomarker in the subject and the reference level of the one or more corresponding biomarker. In certain aspects, the IBD may comprise Crohn’s Disease (CD). In certain aspects, the IBD may comprise Ulcerative colitis (UC). In certain aspects, the one or more biomarkers may comprise tumor necrosis factor alpha (TNF-a), interleukin- 17F (IL-17F), and / or or granulocyte-macrophage colony-stimulating factor (GM-CSF). In certain aspects, the method may comprise obtaining the sample from the subject and determining the level of the one or more biomarkers in the sample. The sample may comprise whole blood. The sample may comprise PBMC, which may be isolated from whole blood. In certain aspects, the level of the one or more biomarkers may comprise the intracellular level of at least one of the one or more biomarkers. In certain aspects, the level of the one or more biomarkers may be the intracellular level of the one or more biomarkers. The intracellular level may be determined from a cell in the PBMC. In certain aspects, the cell may be a Thl7 cell, a Tcl7 cell, a y8T cell, an iNKT cell, or a MAIT cell. In certain aspects, the cells may be subjected to stimulation with IL-23 prior to determining the level of the one or more biomarkers in the sample. In certain aspects, the cell may be contacted with a Golgi inhibitor prior to determining the level of the one or more biomarkers in the sample. The cell may be fixed and permeabilized before staining with antibodies to label the cell surface antigens or intracellular cytokines. In certain aspects, the cells may be from a subject that may or may not have been diagnosed with IBD. In certain aspects, the step of predicting the responsiveness of the subject may comprise: wherein if the reference level corresponds to the level found in an individual responsive to treatment of IBD using an IL-23 antagonist (i.e., a responder), and the level of the one or more biomarker in the sample does not differsignificantly from the reference level, predicting that the subject will be responsive to treatment of IBD using an IL-23 antagonist; wherein if the reference level corresponds to the level found in an individual responsive to treatment of IBD using an IL-23 antagonist (i.e., a responder), and the level of the one or more biomarkers in the sample is significantly different from the level of the corresponding one or more biomarkers in the refence individual, predicting that the subject will not be responsive to treatment of IBD using an IL-23 antagonist; and, wherein if the reference level corresponds to the level found in an individual non-responsive to treatment of IBD using an IL-23 antagonist, and the level of the one or more biomarkers in the subject does not differ significantly from the reference level, predicting that the subject will be non-responsive to treatment of IBD using an IL-23 antagonist.

[0008] One embodiment is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising: comparing a level of TNF-a in a sample from the individual to a reference level of TNF-a, and predicting responsiveness of the IBD based on the similitude of the level of TNF-a in the sample and the reference level of TNF-a. In certain aspects, the step of predicting may comprise: wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a responder and the level TNF-a in the sample does not differ significantly from the reference level of TNF-a, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a responder and the level TNF-a in the sample is significantly greater than the reference level of TNF-a, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist; wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a non-responder and the level TNF-a in the sample is significantly less than the reference level of TNF-a, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; and, wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a non-responder and the level TNF-a in the sample is not significantly different, or is greater, than the reference level of TNF-a, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

[0009] One embodiment is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising: comparing a level of IL-17F in a sample from the individual to a reference level of IL-17F, and predicting responsiveness of the IBD based on the similitude of the level of IL-17F in the sample andthe reference level of IL-17F. In certain aspects, the step of predicting may comprise: wherein if the reference level of IL-17F corresponds to the level of IL-17F found in a responder and the level IL-17F in the sample does not differ significantly from the reference level of IL-17F, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; wherein if the reference level of IL-17F corresponds to the level of IL-17F found in a responder and the level IL-17F in the sample is significantly greater than the reference level of IL-17F, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist; wherein if the reference level of IL-17F corresponds to the level of IL-17F found in a non-responder and the level IL-17F in the sample is significantly less than the reference level of IL-17F, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; and, wherein if the reference level of IL-17F corresponds to the level of IL-17F found in a non-responder and the level IL-17F in the sample is not significantly different, or is greater, than the reference level of IL-17F, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

[0010] One embodiment is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising: comparing a level of GM-CSF in a sample from the individual to a reference level of GM-CSF, and predicting responsiveness of the IBD based on the similitude of the level of GM-CSF in the sample and the reference level of GM-CSF. The step of predicting may comprise: wherein if the reference level of GM-CSF corresponds to, or is greater than, the level of GM-CSF found in a responder and the level GM-CSF in the sample does not differ significantly from the reference level of GM-CSF, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a responder and the level GM-CSF in the sample is significantly less than the reference level of GM-CSF, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist; wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a non-responder and the level GM-CSF in the sample is significantly greater than the reference level of GM-CSF, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; and, wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a non-responder and the level GM-CSF in the sample is not significantlydifferent than the reference level of GM-CSF, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

[0011] One embodiment is a method of identifying an IBD patient as being responsive to treatment with IL-23 antagonist, comprising using the method of any one of claim 1-23 to predict whether the patient’s IBD will positively respond to treatment with an IL-23 antagonist, wherein if the IBD is predicted to positively respond to treatment with an IL-23 antagonist, identifying the patient as being responsive to treatment with an IL-23 antagonist.

[0012] One embodiment is a method of identifying an IBD patient as being responsive to treatment with an IL-23 antagonist, the method comprising identifying the patient as being responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient responsive to treatment with an IL-23 antagonist.

[0013] One embodiment is a method of identifying an IBD patient as being non-responsive to treatment with IL-23 antagonist, comprising using the method of any one of claim 1-23 to predict whether the patient’s IBD will positively respond to treatment with an IL-23 antagonist, wherein if the IBD is predicted to be non-responsive to treatment with an IL-23 antagonist, identifying the patient as being non- responsive to treatment with an IL-23 antagonist.

[0014] One embodiment is a method of identifying an IBD patient as being non-responsive to treatment with an IL-23 antagonist, the method comprising: i) identifying the patient as being non-responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient non-responsive to treatment with an IL-23 antagonist; or ii) identifying the patient as being non-responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to theTNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient responsive to treatment with an IL-23 antagonist.

[0015] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of the disclosure to identify the patient as responsive or non-responsive to treatment with an IL-23 antagonist, wherein if the patient is identified as being responsive to treatment with an IL-23 antagonist, administering an IL-23 antagonist to the patient, and wherein if the patient is identified as being non-responsive to treatment with an IL-23 antagonist, not initiating, suspending, or having suspended, administration of an IL-23 antagonist. In certain aspects, the method may comprise, wherein if the patient is identified as being non-responsive to treatment with an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0016] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of any one of claim 1-25 to identify the patient as being responsive to treatment with an IL-23 antagonist, and prescribing, administering, or having administered, to the patient an IL-23 antagonist.

[0017] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of any one of claims 1-23, claims 26 or claim 27 to identify the patient as non-responsive to treatment with an IL-23 antagonist, and not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, the method may comprise, following not initiating, suspending, or having suspended, administration of an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0018] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by: a) comparing a level of TNF-a and / or IL-17F in a sample from the patient to a reference level of TNF-a and / or IL-17F; b) identifying the responsiveness of the IBD based on the similitude of the level of the one or more biomarkers in the subject and the reference level of TNF-a and / or IL-17F; wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a found in a responder and the level TNF-a and / or IL-17F in the sample does not differ significantly from the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being responsiveto treatment with an IL-23 antagonist; wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-α and / or IL-17F found in a responder and the level TNF-a and / or IL-17F in the sample is significantly greater than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level TNF-a and / or IL-17F in the sample is significantly lower than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; and, wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-α and / or IL-17F found in a non-responder and the level TNF-α and / or IL-17F in the sample is not significantly different, or is greater, than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; and, c) using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, and, wherein if the patient’s IBD is identified as being non-responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, the method may comprise, wherein following identification of the patient as non-responsive to treatment with an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0019] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by: a) comparing a level of GM-CSF in a sample from the patient to a reference level of GM-CSF; b) identifying the responsiveness of the IBD based on the similitude of the level of the one or more biomarkers in the subject and the reference level of GM-CSF; wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a responder and the level GM-CSF in the sample does not differ significantly from the reference level of GM-CSF, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a responder and the level GM-CSF in the sample is significantly less than the reference level of GM-CSF, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; wherein if the referencelevel of GM-CSF corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level GM-CSF in the sample is significantly higher than the reference level of GM-CSF, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; and, wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a non-responder and the level GM-CSF in the sample is not significantly different, or is less, than the reference level of GM-CSF, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; and c) using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, and, wherein if the patient’s IBD is identified as being non-responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, the method may comprise, wherein following identification of the patient as non-responsive to treatment with an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0020] One embodiment is a method of treating a subject having inflammatory bowel disease (IBD), comprising predicting the responsiveness of a subject to treatment of IBD using an interleukin-23 (IL-23) antagonist, by comparing a level of one or more biomarkers in a sample from the individual to a reference level of one or more corresponding biomarkers; and, predicting the responsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers; wherein if the subject is predicted to be responsive to treatment of IBD using an IL-23 antagonist, prescribing, administering, or having administered, to the subject an IL-23 antagonist; and, wherein if the subject is predicted to be non-responsive to treatment of IBD using an IL-23 antagonist, prescribing, administering, or having administered, to the subject an IBD treatment that does not target IL-23.

[0021] One embodiment is a method of treating a subject having inflammatory bowel disease (IBD) and that is receiving an IL-23 targeted treatment, comprising predicting the responsiveness of a subject to treatment of IBD using an IL-23 antagonist, by comparing a level of one or more biomarkers in a sample from the individual to a reference level of one or more corresponding biomarkers, and predicting theresponsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers; wherein if the subject is predicted to be responsive to treatment of IBD using an IL-23 antagonist, prescribing continuation of, continuing, or having continued, the IL-23-targted treatment; and, wherein if the subject is predicted to be non-responsive to treatment of IBD using an IL-23 antagonist, stopping, or having stopped, the IL-23-targted treatment. In certain aspects, the method may comprise prescribing, administering, or having administered, to the subject an IBD treatment that does not target IL-23.

[0022] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising administering an IL-23 antagonist to the patient if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient that is responsive to treatment with an IL-23 antagonist.

[0023] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient if the patient is determined to have a level of TNF-a that is significantly higher than a reference level of TNF-a that corresponds to the TNF-a level observed in an individual identified as a responder.

[0024] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient if the patient is determined to have a level of IL-17F that is significantly higher than a reference level of IL-17F that corresponds to the IL-17F level observed in an individual identified as a responder.

[0025] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient if the patient is determined to have a level of GM-CSF that is significantly less than a reference level of GM-CSF that corresponds to the GM-CSF level observed in an individual identified as a responder.

[0026] One embodiment is a method of determining the level of a biomarker associated with responsiveness of an IBD patient to treatment with an IL-23 antagonist, the method comprising: obtaining a peripheral blood mononuclear cells (PBMC)-containingsample from the patient, subjecting the PMBC to IL-23 stimulation, and determining the level of the biomarker produced by the PBMC. The biomarker may comprise TNF-a, IL-17F, and / or GM-CSF. In certain aspects, the PBMC may be isolated from the sample prior to IL-23 stimulation. Isolation of the PBMC may comprise centrifugation, filtration, or chromatography. In certain aspects, the PBMC may be contacted with a Golgi inhibitor, which may be prior to, in conjunction with, or following stimulation with IL-23. In certain aspects, the step of determining the level of the biomarker may comprise determining the intracellular level of the biomarker. Determining the intracellular level of the biomarker may comprise determining the level of the biomarker in Th17 cells, Tc17 cells, γδT cells, iNKT cells, and / or MAIT cells, which may be present in the PBMC. The biomarker may be a protein. Determining the level of the biomarker protein may comprise detecting the presence, absence, level, or level of activity, of the biomarker protein, which may comprise cell sorting, PAGE analysis, chromatography, mass cytometry, immunoprecipitation, an immunoassay, fluorescence, or luminescence. Determining the level of the biomarker produced by the PBMC may comprise contacting the cells with a detection molecule that binds the biomarker protein, the detection molecule comprising a detectable label, and determining the level of detectable label. The detection molecule may be a receptor or an antibody that binds the biomarker protein. The detectable label may comprise a fluorescent protein, a luminescent protein, an enzyme, a metal isotope, or a radiolabel. In certain aspects, the step of determining the level of detectable label may comprise separating individual cells in the sample and detecting the level of the detectable label in each individual cell. The method may comprise counting the individual cells and determining the percentage of cells comprising the detectable label.BRIEF DESCRIPTION OF THE DRAWINGS

[0027] FIG. 1 illustrates a general methodology of a method of the disclosure.

[0028] FIG. 2 illustrates the lineage makeup (by percent) of T-cells and innate lymphoid cells ILCs (by percent) obtained from responding patients and nonresponding patients, following stimulation by IL-23.

[0029] FIGS. 3A-3E show the percentage of Th17 cells (FIG. 3A), Tc17 cells (FIG. 3B), γδT cells (FIG. 3C), iNKT cells (FIG. 3D), and MAIT cells (FIG. 3E)obtained from responding patients and non-responding patients that express various cytokines intracellularly.

[0030] FIG. 4 shows logistic regression, using the receiver operator characteristic (ROC) curve, of TNF-a+ cells at baseline (BL) before risankizumab.

[0031] FIG. 5 shows logistic regression, using the receiver operator characteristic (ROC) curve, of TNF-a+ cells 4 weeks after starting risankizumab.

[0032] FIG. 6 shows the combined ROC for TNF-a+ cells in predicting risankizumab response.

[0033] FIGS. 7A-7D show expanded IL-23 -activated cells at baseline associated with RZB non-response. FIGS.7A & 7B show UMAP showing immune cell populations in the PBMCs from responders and non-responders. FIG. 7C shows percentage of immune cell populations in the PBMCs from responders and non-responders (based on FIG. 7A & 7B). FIG. 7D shows percentage of TNF-α+ ILC (innate lymphoid cells) and Th17 cells.

[0034] FIG. 8 shows exhaustion scores of immune cell populations based on gene expression. T-cell exhaustion is implicated in IBD although its clinical significance remains elusive. Here, it is reported that patients with higher exhaustion scores in multiple T-cell populations at baseline were more likely to fail RZB.

[0035] FIG. 9 shows TCR-seq identified altered baseline clonal expansion in specific T-cells associated with RZB response.DETAILED DESCRIPTION

[0036] The present disclosure relates to the use of biomarkers for determining whether an individual will respond to a treatment for inflammatory bowel disease (IBD). More specifically, the present disclosure relates to using the levels of one or more specific biomarkers present in a sample from an individual suffering IBD to determine whether the individual will benefit from treatment with an interleukin-23 (IL-23) antagonist. In certain aspects, the biomarker may include one or more of tumor necrosis factor-alpha (TNF-a), interleukin- 17F (IL-17F), and granulocyte-macrophage colony-stimulating factor (GM-CSF). Thus, a method of the disclosure may be practiced by obtaining the level of one or more biomarkers in a sample from an individual having IBD, comparing the level of the one or more biomarker with one or more corresponding reference level(s), and based on the comparison, determining whether the individual’s IBD would positively respond totreatment with an IL-23 antagonist. In certain aspects, the one or more biomarkers may comprise TNF-a, IL-17F, or GM-CSF. In certain aspects, a significant difference in the level of TNF-a, IL-17F, or GM-CSF, in a sample from the individual, and the corresponding reference level, is indicative of whether the individual’s IBD will be responsive or non-responsive to treatment with an IL-23 antagonist. Such information may be used to determine a course of treatment for the individual, which may include altering the dosage of a drug, altering the frequency of administration of a drug, stopping, or having stopped, administration of a drug, or selecting or prescribing for administration, administering, or having administered, a different drug, including selecting or prescribing for administration, administering, or having administered, a drug that does not target IL-23.

[0037] It is to be understood that this disclosure is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present disclosure will be limited only by the claims.

[0038] It must be noted that as used herein and in the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. For example, a protein may refer to one or more of a protein (e.g., TNF-a) may refer to one or more molecules of that protein. As such, the terms "a", "an", "one or more" and "at least one" can be used interchangeably.

[0039] Similarly, the terms "comprising", "including" and "having" can be used interchangeably. As used herein, the term “comprising” may be replaced with “consisting” or with “consisting essentially of’ in particular aspect, as desired.

[0040] It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as "solely," "only" and the like in connection with the recitation of claim elements, or use of a "negative" limitation.

[0041] Various terms relating to aspects of the present disclosure are used throughout the specification and claims. Such terms are to be given their ordinary meaning in the art, unless otherwise indicated. Other specifically defined terms are to be construed in a manner consistent with the definitions provided herein.

[0042] As used herein, the term “about”, when used in comparison of protein biomarker levels, means that the recited numerical value is approximate and smallvariations would not significantly affect the practice of the disclosed embodiments. Where a percent value is used, unless indicated otherwise by the context, the term “about” means the numerical value can vary by ±10% and remain within the scope of the disclosed embodiments.

[0043] Unless otherwise expressly stated, it is in no way intended that any method or aspect set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not specifically state in the claims or descriptions that the steps are to be limited to a specific order, it is in no way intended that an order be inferred, in any respect. This holds for any possible non-expressed basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, or the number or type of aspects described in the specification.

[0044] It is appreciated that certain features of the disclosure, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the disclosure, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments are specifically embraced by the present disclosure and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub¬ combinations are also specifically embraced by the present disclosure and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.

[0045] One embodiment of the disclosure is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising comparing a level of one or more biomarkers in a sample from the individual to a reference level of one or more corresponding biomarkers, and predicting responsiveness of the IBD based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers. In certain aspects, the IBD may comprise CD. In certain aspects, the IBD may comprise UC.

[0046] As used herein, the phrase “responsiveness of IBD”, “responsiveness of an individual having IBD”, ‘responsiveness of an individual”, and the like, means a change in the signs and / or symptoms related to IBD. Such signs and symptoms may include, but are not limited to, abdominal pain and / or cramping, diarrhea, blood in stool,rectal bleeding weight loss, fever, weight loss, nausea, joint pain, skin rash, urgent bowel movements, and mucus in stool. Unless otherwise specified (e.g., negative change), a change in signs and symptoms means a positive change (which may be referred to as a “positive response”), which indicates a reduction in signs and symptoms of IBD. Several tools for quantifying signs and symptoms of IBD are known in the art. Examples of such tools include, but are not limited to, the Crohn’s Disease Activity Index (CD Al), the Mayo Score / Disease Activity Index (DAI), the Geboes Score (GS), and the Ulcerative Colitis Endoscopic Index of Severity Score (UCEIS). Such tools may be used to grade the severity of IBD and determine positive or negative responses thereto. For example, a positive response to treatment would be reflected as a decrease in the Mayo Score. As use herein, an individual is “responsive” when administration of an IL-23 antagonist results in a positive response in their IBD. The “responsiveness status” of such an individual may be referred to as “responsive” and such individual may be referred to as a “responder”. Likewise, an individual is “non-responsive” when administration of an IL-23 antagonist does not result in a positive response of their IBD to treatment. The “responsiveness status” of such an individual may be referred to as “non-responsive” and such individual may be referred to as a “non-responder”.

[0047] For ease of discussion throughout this disclosure, an individual for which a method of the disclosure is being used to predict, determine, assign, and the like, a responsiveness status may be referred to as a test individual. The level of a biomarker obtained from such an individual may be referred to as a test level. An individual whose responsiveness status is known may be referred to as a reference individual. The level of a biomarker obtained from such an individual may be referred to as a reference level.

[0048] The terms individual, subject, and patient are well-recognized in the art, and are herein used interchangeably to refer to any human or other animal. Examples include, but are not limited to, humans and other primates, including non-human primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, seals, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs; birds, including domestic, wild and game birds such as chickens, turkeys and other gallinaceous birds, ducks, geese, and the like. The terms individual, subject, and patient by themselves, do not denote a particular age, sex, race, and the like. Thus, individuals of any age, whether male or female, are intended to be covered by the present disclosure and include, but are not limited to the elderly, adults,children, babies, infants, and toddlers. Likewise, the methods of the present disclosure can be applied to any race, including, for example, Caucasian (white), African-American (black), Native American, Native Hawaiian, Hispanic, Latino, Asian, and European.

[0049] An “IL-23 antagonist” is any molecule that binds to IL-23 thereby preventing it from interacting with a receptor, such as an IL-23 receptor. Thus, an IL-23 antagonist inhibits activation of a receptor-mediated pathway. Accordingly, the terms “IL- 23 antagonist” and “IL-23 inhibitor” may be used interchangeably herein. In certain aspects, the IL-23 antagonist may bind to the pl9 and / or the p40 subunit of IL-23. In certain aspects, the IL-23 antagonist binds to the pl9 subunit. In certain aspects, the IL-23 antagonist binds to the p40 subunit. In certain aspects, an IL-23 antagonist may comprise a small molecule, a nucleic acid molecule, or a protein. In certain aspects, the IL-23 antagonist may be an antibody, such as a monoclonal antibody. IL-23 antagonists for the treatment of IBD are known in the art. Examples of IL-23 antagonists include, but are not limited to, risankizumab (Skyrizi®), mirikizumab (Omvoh®), and guselkumab (TREMFYA®).

[0050] As used herein, “biomarker” refers to any biological molecule in an individual, the presence, absence or level, of which is indicative of the individual’s responsiveness to treatment of IBD with an IL-23 antagonist. Biomarkers may be an organic molecule and include, but are not limited to, proteins, DNA, RNA, lipids, and sugars. In certain aspect, a biomarker may be a protein, or a nucleic acid molecule encoding such protein. In certain aspects, a biomarker may be a protein of the immune system, such as a cytokine. In certain aspects, a biomarker may be selected from the group consisting of TNF-a, IL-17F, and GM-CSF.

[0051] As used herein, a “level” of a biomarker may refer to the concentration of the biomarker or an absolute amount of the biomarker in a sample, such as a biological sample. For example, in certain aspects, the biomarker may be a cytokine. In such aspects, the level of the biomarker may be reported as a concentration, for example pg / m or molar amount (e.g., pM), or as an absolute level (e.g., pg, ng, etc.). Alternatively, the level of the cytokine may be measured based on its biological activity. For example, the level of the cytokine may be reported in International Units (IU). In certain aspects, the level of a biomarker may comprise the intracellular presence, absence, or amount, of a biomarker of the disclosure in the biological sample. In such instances, the level of the biomarker may comprise the percent of cells in the sample that express the biomarker. For example, cells in the sample may be contacted with a detection molecule that binds to an intracellularbiomarker, the detection molecule comprising a detectable label. The labeled cells may then be subjected to methodology that counts a number of cells and detects the presence or amount of the detectable label, if present, in each cell, thereby detecting the number of cells containing the biomarker identified. The level of the biomarker may then be reported as the percentage of cells containing the biomarker.

[0052] In certain aspects, determining the level of a biomarker comprises detecting the biomarkers and such detection may comprise using any assay known to those skilled in the art. Assays suitable for measuring the level of a biomarker of the disclosure may comprise, without limitation, PAGE analysis, chromatography, mass cytometry, an immunoassay, immunoprecipitation, fluorescence, or luminescence. In certain aspects, detecting the presence or absence of, or measuring the level of a biomarker of the disclosure may comprise using a detection molecule that binds to the biomarker. For example, in an aspect in which the biomarker comprises TNF-a, the detection molecule may comprise a TNF-a receptor or an anti-TNF-a antibody. In certain aspects, the detection molecule may comprise a detectable label, such as a fluorescent protein, a luminescent protein, an enzyme, a metal isotope, or a radiolabel.

[0053] As used herein, “reference level” refers to the level of a corresponding biomarker in an individual having a known responsiveness status (in a reference individual). Corresponding biomarkers refers to the fact that the levels of biomarker being compared are from the same biomarker. For example, if the biomarker being measured in the test individual is the level of TNF-a, then the measured level would be compared to the level of TNF-a obtained from an individual of known responsiveness status (a refence individual). In certain aspects, the reference level may be from a responsive individual. In certain aspects, the reference level may be from a non-responsive individual. In certain aspects, the reference level may comprise a mean or average from two or more reference levels obtained from two or more individuals having the same responsiveness status. In certain aspects, a reference level may be a historical reference level. That is, the reference level may have been obtained prior to the time when a method of the disclosure is to be performed on a test individual. In such aspects, the reference level may be obtained from a written record, or from a computer memory.

[0054] The term “biological sample” refers to a sample obtained from a biological subject, including a sample of biological tissue or fluid origin obtained in vivo or in vitro. Such samples may be, but are not limited to, tissues, cell-containing fluids, and cellsisolated from mammals, including humans. In certain aspects, the biological sample may comprise blood, which may be whole blood. In certain aspects the biological sample may comprise peripheral blood mononuclear cells (PBMC). In certain aspects, the biological sample may be derived from blood. In certain aspects, the sample may comprise one or more type of cell selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells.

[0055] In certain aspects, determining the level of a biomarker may comprise determining an intracellular level of the biomarker. In certain aspects, the intracellular level may be the level of biomarker present in a cell in a sample from the individual. In certain aspects, the cell may be a Th17 cell, Tc17 cell, γδT cell, iNKT cell, or a MAIT cell. In certain aspects, determining the intracellular level of a biomarker may comprise determining the level of the biomarker in one or more type of cell selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells. In certain aspects, a cell in which the intracellular level of a biomarker is being measured may be isolated from the biological sample. As used herein, the term “isolated” means separating the cells in the biological sample away from other components of the biological sample. “Isolated” does not denote a particular degree of purity. The cells only need be separated from other components in the biological sample to the degree that they are sufficient for determining the level of a biomarker therewithin. For example, PBMC obtained from whole blood by centrifugation would be considered isolated cells. Any suitable method of isolating the cells may be used. Methods of isolating cells from a biological sample, such as blood, are known to those skilled in the art.

[0056] In certain aspects, the level of a biomarker may comprise the intracellular presence, absence, or amount, of a biomarker of the disclosure in the biological sample. In such instances, the level of the biomarker may comprise the percent of cells in the sample that express the biomarker. For example, cells in the sample may be contacted with a detection molecule that binds to intracellular biomarker, the detection molecule comprising a detectable label. The labeled cells may then be subjected to methodology that counts a number of cells and detects the presence or amount of the detectable label, if present, in each cell, thereby detecting the number of cells containing the biomarker identified. The level of the biomarker may then be reported as the percentage of cells containing the biomarker.

[0057] In certain aspects, the isolated cells may be treated prior to determining the level of a biomarker therewithin. Examples of suitable treatments include,but are not limited to, treatment that increase the number and / or metabolic activity of the cells, and / or that affect transport of an intracellular biomarker within the cell, such as transport through the Golgi apparatus. For example, treating the isolated cells may comprise contacting the cells with a Golgi inhibitor. A “Golgi inhibitor” is any compound that disrupts the Golgi apparatus. Examples of Golgi inhibitors include, but are not limited to, brefeldin A (BFA), deoxymannojirimycin (DM J), Kifunensein (KIF), IQ, Exol, BML-265, and tyrphostin AG 1478. In certain aspects, treating the cell may also comprise contacting the cells with a cytokine, such as IL-23. In certain aspects, the cells are contacted with a Golgi inhibitor and with IL-23.

[0058] As noted above, the responsiveness of IBD in a patient is based on the similitude of the level of the one or more biomarkers in the individual being tested and a reference level of the corresponding one or more biomarkers. That is, if the level of a biomarker in the test individual does not significantly differ from a reference level of the corresponding biomarker in a reference individual, then the test individual is assigned the same responsiveness status as the reference individual. For example, if the level of a biomarker in the test individual does not significantly differ from a reference level of the same biomarker in a responder, then the IBD in the test individual would be considered responsive and the test individual would be identified as a responder. Likewise, if the level of a biomarker in test individual is significantly different from a reference level of the same biomarker in a responder, then the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be assigned a responsiveness status of “non-responsive”.

[0059] As used herein, the phrases “significantly different”, “differs significantly”, “significantly greater”, “significantly lower”, and the like, mean that the levels of biomarkers being compared differ by greater than at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50%. Likewise, in aspects in which a level of biomarker is reported as the percent of cells containing intracellular biomarker, “significantly different” and the like, mean the percentage of cells having intracellular biomarker differ by greater than at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50%. Correspondingly, levels that “do not differ significantly” or “essentially the same”, and the like, would differ by less than less than 10%, or less than about 5%.

[0060] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of TNF-a and comparing the determined level of TNF-a to a reference level of TNF-a from a responder. In such aspects, if the level of TNF-a is not significantly different from the reference level of TNF-a, then the IBD in the test individual would be considered responsive and the test individual would be identified as being responsive (a responder). If the determined level of TNF-a is significantly greater than the reference level of TNF-a, then the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be identified as being non-responsive (a non-responder).

[0061] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of TNF-a and comparing the determined level of TNF-a to a reference level of TNF-a from a non-responder. In such aspects, if the level of TNF-a is not significantly different from, or is significantly greater than, the reference level of TNF-a, then the IBD in the test individual would be considered non-responsive and the test individual would be identified as being non-responsive (a non-responder). If the determined level of TNF-a is significantly less than the reference level of TNF-a, then the IBD in the test individual would be considered responsive. Accordingly, the test individual would be identified as being responsive (a responder).

[0062] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of IL-17F and comparing the determined level of IL-17F to a reference level of IL-17F from a responder. In such aspects, if the level of IL-17F is not significantly different from the reference level of IL-17F, then the IBD in the test individual would be considered responsive and the test individual would be identified as being responsive (a responder). If the determined level of IL-17F is significantly greater than the reference level of IL-17F, then the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be identified as being non-responsive (a non-responder).

[0063] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of IL-17F and comparing the determined level of IL-17F to a reference level of IL-17F from a non-responder. In such aspects, if the level of IL-17F is not significantly different from, or is significantly greater than, the reference level of IL-17F, then the IBD in the test individual would be considered non-responsive and the test individual would be identified as being non-responsive (a non-responder). If the determined level of IL-17F is significantly less than the reference level of IL-17F, then the IBD in the test individual would be considered responsive. Accordingly, the test individual would be identified as being responsive (a responder).

[0064] In certain aspects, determining the level(s) of one or more biomarker in a test individual may comprise determining the level of TNF-a and / or IL-17F and comparing the determined level to a reference level(s) of TNF-a and / or IL-17F from a responder. In such aspects, if the level(s) of TNF-a and / or IL-17F from the test individual is / are not significantly different from the reference level(s), then the IBD in the test individual would be considered responsive and the test individual would be identified as being responsive (a responder). If the level of TNF-a and / or IL-17F from the test individual is / are significantly greater than the reference level, then the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be identified as being non-responsive (a non-responder). If the level of TNF-a or IL-17F from the test individual is significantly greater than the reference level, then the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be identified as being non-responsive (a non-responder).

[0065] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of TNF-a and / or IL-17F and comparing the determined level to a reference level of TNF-a and / or IL-17F from a non-responder. In such aspects, if the level(s) of TNF-a and / or IL-17F from the test individual is / are not significantly different from, or is / are significantly greater than, the reference level(s) of TNF-a and / or IL-17F, the IBD in the test individual would be considered non-responsive and the test individual would be identified as being non-responsive (a non-responder).

[0066] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of GM-CSF and comparing the level to a reference level of GM-CSF from a responder. In such aspects, if the level of GM-CSF is not significantly different from the reference level, then the IBD in the test individual would be considered responsive. Accordingly, the test individual would be identified as being responsive (a responder). If the level of GM-CSF is significantly less than the reference level, then the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be identified as being non-responsive (a non-responder).

[0067] In certain aspects, determining the level of one or more biomarker in a test individual may comprise determining the level of GM-CSF and comparing the level to a reference level of GM-CSF from a non-responder. In such aspects, if the level of GM-CSF is not significantly different from the reference level, the IBD in the test individual would be considered non-responsive. Accordingly, the test individual would be identified as being non-responsive (a non-responder). If the level of GM-CSF is significantly greater than the reference level, then the IBD in the test individual would be considered responsive. Accordingly, the test individual would be identified as being responsive (a responder).

[0068] One embodiment of the disclosure is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising comparing a level of TNF-a in a sample from the individual to a reference level of TNF-a, and predicting responsiveness of the IBD based on the similitude of the level of TNF-α in the sample and the reference level of TNF-a. In certain aspects the step of predicting comprises, wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a responder and the level of TNF-a in the sample does not differ significantly from the reference level of TNF-a, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a responder and the level TNF-a in the sample is significantly greater than the reference level of TNF-a, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a non- responder and the level TNF-a in the sample is significantly less than the reference level of TNF-a, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a non-responder and the level TNF-a in the sample is not significantly different, or is greater, than the reference level of TNF-a, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

[0069] One embodiment of the disclosure is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising comparing a level of IL-17F in a sample from the individual to a reference level of IL-17F and predicting responsiveness of the IBD based on the similitude of the level ofIL-17F in the sample and the reference level of IL-17F. In certain aspects the step of predicting comprises, wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a responder and the level IL-17F in the sample does not differ significantly from the reference level of IL-17F, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a responder and the level IL-17F in the sample is significantly greater than the reference level of IL-17F, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a non-responder and the level of IL-17F in the sample is significantly less than the reference level of IL-17F, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a non-responder and the level of IL-17F in the sample is not significantly different, or is greater, than the reference level of IL-17F, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

[0070] One embodiment of the disclosure is a method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising comparing a level of GM-CSF in a sample from the individual to a reference level of GM-CSF and predicting responsiveness of the IBD based on the similitude of the level of GM-CSF in the sample and the reference level of GM-CSF. In certain aspects the step of predicting comprises, wherein if the reference level of GM-CSF corresponds to, or is greater than, the level of GM-CSF observed in a responder and the level of GM-CSF in the sample does not differ significantly from the reference level of GM-CSF, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of GM-CSF corresponds to the level of GM-CSF observed in a responder and the level of GM-CSF in the sample is significantly less than the reference level of GM-CSF, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of GM-CSF corresponds to the level of GM-CSF observed in a non-responder and the level of GM-CSF in the sample is significantly greater than the reference level of GM-CSF, predicting that theIBD in the individual will be responsive to treatment with an IL-23 antagonist. In certain aspects the step of predicting comprises, wherein if the reference level of GM-CSF corresponds to the level of GM-CSF observed in a non-responder and the level of GM-CSF in the sample is not significantly different than the reference level of GM-CSF, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

[0071] One embodiment of the disclosure is a method of identifying an IBD patient as being responsive to treatment with an IL-23 antagonist, the method comprising identifying the patient as being responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient responsive to treatment with an IL-23 antagonist. Methods of determining if the patient’s level of TNF-a, IL-17F and / or GM-CSF is, or is not, significantly different from a corresponding refence level are disclosed herein. In certain aspects, the method may comprise using a method of the disclosure to predict whether the patient’s IBD will positively respond to treatment with an IL-23 antagonist, wherein if the IBD is predicted to positively respond to treatment with an IL-23 antagonist, identifying the patient as being responsive to treatment with an IL-23 antagonist. In certain aspects, the method of determining that a patient is responsive to treatment with an IL-23 antagonist may be used to select an IBD patient for treatment with an IL-23 antagonist. In certain aspects, once the patient has been identified as being responsive to treatment with an IL-23 antagonist, an IL-23 antagonist is prescribed or administered to the patient.

[0072] One embodiment of the disclosure is a method of identifying an IBD patient as being non-responsive to treatment with an IL-23 antagonist, the method comprising: i) identifying the patient as being non-responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient non-responsive to treatment with an IL-23 antagonist; or ii) identifying the patient as being non-responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL- 17F, and / or a level of GMCSF, that is significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17Fand / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient responsive to treatment with an IL-23 antagonist. Methods of determining if the patient’s level of TNF-a, IL-17F and / or GM-CSF is, or is not, significantly different from a corresponding refence level are disclosed herein. In certain aspects, the method may comprise using a method of the disclosure to predict whether the patient’s IBD will positively respond to treatment with an IL-23 antagonist, wherein if the IBD is predicted to be non-responsive to treatment with an IL-23 antagonist, identifying the patient as being non-responsive to treatment with an IL-23 antagonist. In certain aspects, following identification of the patient as being non-responsive to treatment with an IL-23 antagonist, treatment with an IL-23 antagonist may be not initiated or suspended. In certain aspects, following identification of the patient as being non-responsive to treatment with an IL-23 antagonist, the method may comprise prescribing, administering, or having administered to the patient and IBD treatment that does not target IL-23. IBD treatments that do not target IL-23 are well known in the art. Examples of IBD treatments that do not target IL-23 include, but are not limited to, aminosalicylates, immunosuppressive drugs (e.g., azathioprine, mercaptopurine, methotrexate), JAK inhibitors (e.g., tofacitinib, upadacitinib), sphingosine-1 -phosphate receptor modulators (e.g., ozanimod), antibiotics, corticosteroids, anti-TNF-a antibodies, anti-integrin antibodies, and anti-il-12 antibodies.

[0073] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of the disclosure to identify the patient as responsive or non-responsive to treatment with an IL-23 antagonist, wherein if the patient is identified as being responsive to treatment with an IL-23 antagonist, administering an IL-23 antagonist to the patient, and wherein if the patient is identified as being non-responsive to treatment with an IL-23 antagonist, not initiating, suspending, or having suspended, administration of an IL-23 antagonist. In certain aspects, the method may comprise wherein if the patient is identified as being non-responsive to treatment with an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0074] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of the disclosure to identify the patient as being responsive to treatment with an IL-23 antagonist, and prescribing, administering, or having administered, to the patient an IL-23 antagonist.

[0075] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of the disclosure to identify the patient as non-responsive to treatment with an IL-23 antagonist, and not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, following identification of the patient as non-responsive to treatment with an IL-23 antagonist, the method may comprise prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0076] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising: a) identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by comparing a level of TNF-a and / or IL-17F in a sample from the patient to a reference level of TNF-a and / or IL-17F, and b) identifying the responsiveness of the IBD based on the similitude of the level of TNF-a and / or IL-17F in the sample from the patient and the reference level of TNF-a and / or IL-17F;wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-α observed in a responder and the level of TNF-a and / or IL-17F in the sample does not differ significantly from the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a and / or IL- 17F corresponds to the level of TNF-a and / or IL-17F observed in a responder and the level of TNF-a and / or IL- 17F in the sample is significantly greater than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a and IL-17F correspond to the level of TNF-a and / or IL-17F observed in a non-responder and the levels of TNF-α and IL- 17F in the sample are significantly lower than the reference level of TNF-a and IL- 17F, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; and,wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level of TNF-a and / or IL- 17F in the sample is not significantly different, or is greater, than the reference levelof TNF-a and / or IL-17F, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; and,c) using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, and, wherein if the patient’s IBD is identified as being non-responsive, prescribing, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, following identification of the patient as non-responsive to treatment with an IL-23 antagonist, the method may comprise prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0077] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising: a) identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by comparing a level of TNF-a in a sample from the patient to a reference level of TNF-a, and b) identifying the responsiveness of the IBD based on the similitude of the level of TNF-a in the sample from the patient and the reference level of TNF-a;wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a responder and the level of TNF-a in the sample does not differ significantly from the reference level of TNF-a, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a responder and the level of TNF-a in the sample is significantly greater than the reference level of TNF-a, identifying the patient’s IBD as being non- responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a non-responder and the level of TNF-a in the sample is significantly lower than the reference level of TNF-a, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; and,wherein if the reference level of TNF-a corresponds to the level of TNF-a observed in a non-responder and the level of TNF-a in the sample is not significantly different, or is greater, than the reference level of TNF-a, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; and,c) using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, and,

[0078] wherein if the patient’s IBD is identified as being non-responsive, prescribing, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, following identification of the patient as non-responsive to treatment with an IL-23 antagonist, the method may comprise prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0079] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising: a) identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by comparing a level of IL-17F in a sample from the patient to a reference level of IL-17F, and b) identifying the responsiveness of the IBD based on the similitude of the level of IL-17F in the sample from the patient and the reference level of IL-17F;wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a responder and the level of IL-17F in the sample does not differ significantly from the reference level of IL-17F, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a responder and the level of IL-17F in the sample is significantly greater than the reference level of IL-17F, identifying the patient’s IBD as being non- responsive to treatment with an IL-23 antagonist;wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a non-responder and the level of IL-17F in the sample is significantly lower than the reference level of IL-17F, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; and,wherein if the reference level of IL-17F corresponds to the level of IL-17F observed in a non-responder and the level of IL-17F in the sample is not significantly different, or is greater, than the reference level of IL-17F, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; and,c) using the identified responsiveness of the patient’s IBD to treat the patient,wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, and,

[0080] wherein if the patient’s IBD is identified as being non-responsive, prescribing, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, following identification of the patient as non-responsive to treatment with an IL-23 antagonist, the method may comprise prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0081] One embodiment of the disclosure is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising: a) identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by comparing a level of GM-CSF in a sample from the patient to a reference level of GM-CSF, and b) identifying the responsiveness of the IBD based on the similitude of the level of the one or more biomarkers in the subject and the reference level of GM-CSF;wherein if the reference level of GM-CSF corresponds to the level of GM- CSF found in a responder and the level of GM-CSF in the sample does not differ significantly from the reference level of GM-CSF, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of GM-CSF corresponds to the level of GM- CSF found in a responder and the level of GM-CSF in the sample is significantly less than the reference level of GM-CSF, identifying the patient’s IBD as being non- responsive to treatment with an IL-23 antagonist;wherein if the reference level of GM-CSF corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level of GM-CSF in the sample is significantly higher than the reference level of GM-CSF, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist; and,wherein if the reference level of GM-CSF corresponds to the level of GM- CSF found in a non-responder and the level of GM-CSF in the sample is not significantly different, or is less, than the reference level of GM-CSF, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; and, c) using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, and,wherein if the patient’s IBD is identified as being non-responsive, prescribing, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient. In certain aspects, following identification of the patient as non-responsive to treatment with an IL-23 antagonist, the method may comprise prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

[0082] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising administering an IL-23 antagonist to the patient if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or GM-CSF, corresponds to the level of TNF-a, IL-17F, and / or GM-CSF observed in an IBD patient that is responsive to treatment with an IL-23 antagonist.

[0083] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising prescribing, administering, or having administered, an IL-23 antagonist to the patient if the patient is determined to have a level of TNF-a that is not significantly different from a reference level of TNF-a that corresponds to the TNF-a level observed in an individual identified as a responder.

[0084] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising prescribing, administering, or having administered, an IL-23 antagonist to the patient if the patient is determined to have a level of IL-17F that is not significantly different from a reference level of IL-17F that corresponds to the IL-17F level observed in an individual identified as a responder.

[0085] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising prescribing, administering, or having administered, an IL-23 antagonist to the patient if the patient is determined to have a level of GM-CSF that is not significantly different from a reference level of GM-CSF that corresponds to the GM-CSF level observed in an individual identified as a responder.

[0086] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending, or having suspended, administration of, an IL-23 antagonist to the patient, if the patient is determined to have a level of TNF-a that is significantly different from a reference level of TNF-a corresponding to the level of TNF-a observed in an individual identified as a responder. Incertain aspects, the patient is determined to have a level of TNF-a significantly higher than the reference level of TNF-a corresponding to the level of TNF-a observed in an individual identified as a responder.

[0087] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient, if the patient is determined to have a level of IL-17F that is significantly different from a reference level of IL-17F corresponding to the IL-17F level observed in an individual identified as a responder. In certain aspects, the patient is determined to have a level of IL- 17F that is significantly higher than the reference level of IL-17F corresponding to the level of IL-17F observed in an individual identified as a responder.

[0088] One embodiment is a method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient if the patient is determined to have a level of GM-CSF that is significantly different from a reference level of GM-CSF corresponding to the GM-CSF level observed in an individual identified as a responder. In certain aspects, the patient is determined to have a level of GM-CSF that is significantly lower than the reference level of GM-CSF corresponding to the level of IL-17F observed in an individual identified as a responder.

[0089] In certain aspects of treatment methods of the disclosure, the level of a biomarker (e.g., TNF-a, IL- 17, or GM-CSF) may be determined or measured using any method or assay disclosed herein or known to those skilled in the art. Assays suitable for measuring the level of a biomarker of the disclosure may comprise, without limitation, PAGE analysis, chromatography, mass cytometry, an immunoassay, immunoprecipitation, fluorescence, or luminescence. In certain aspects, detecting the presence or absence of, or measuring the level of a biomarker of the disclosure may comprise using a detection molecule that binds to the biomarker. For example, in aspects in which the biomarker comprises TNF-a, the detection molecule may comprise a TNF-a receptor or an anti-TNF-a antibody. In certain aspects, the detection molecule may comprise a detectable label, such as a fluorescent protein, a luminescent protein, an enzyme, a metal isotope, or a radiolabel.

[0090] In certain aspects of treatment methods of the disclosure, the biological sample may comprise, but is not limited to, tissues, cell-containing fluids, and cells isolated from mammals including, humans. In certain aspects, the biological samplemay comprise blood, such as whole blood. In certain aspects the biological sample may comprise peripheral blood mononuclear cells (PBMC), which may be isolated from whole blood. In certain aspects, the biological sample may comprise one of more of Thl7 cells, Tcl7 cells, y8T cells, iNKT cells, or MAIT cells.

[0091] In certain aspects of treatment methods of the disclosure, determining the level of a biomarker, such as TNF-a, IL-23, or GM-CSF, may comprise determining an intracellular level of the biomarker. In certain aspects, the intracellular level may be the level in a cell present in a sample of blood from the individual. In such aspects, the cell may be a Thl7 cell, a Tcl7 cell, a y8T cell, an iNKT cell, or a MAIT cell. In certain aspects, determining the intracellular level of a biomarker, such as TNF-a, IL-23, or GM-CSF, may comprise determining the level of the biomarker in one or more type of cells selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells. In certain aspects, cells in which the intracellular level of a biomarker is being measured may be isolated from the biological sample.

[0092] In certain aspects of treatment methods of the disclosure, the level of a biomarker may be reported as a concentration of a total amount. In certain aspects, the level of a biomarker may be reported as the percent of cells containing the biomarker. For example, once the cells have been isolated, the cells may be contacted with a detection molecule that bind to an intracellular biomarker. Such cells may then be subjected to mass cytometry so that cells are counted and the number of cells containing the biomarker identified, allowing for the determination of the percentage of cells containing the biomarker.

[0093] In certain aspects of treatment methods of the disclosure, the isolated cells may be treated prior to determining the level of a biomarker therewithin. Examples of suitable treatments include, but are not limited to, treatment that increase the number or metabolic activity of the cells, and / or that affect transport of an intracellular biomarker out of a cell. For example, treating the isolated cells may comprise contacting the cells with a Golgi inhibitor. A “Golgi inhibitor” is any compound that disrupts the Golgi apparatus. Examples of Golgi inhibitors include, but are not limited to, brefeldin A (BFA), deoxymannojirimycin (DMJ), Kifunensein (KIF), IQ, Exo, BML-265, and tyrphostin AG 1478. In certain aspects, treating the cell may also comprise contacting the cells with a cytokine, such as IL-23. In certain aspects, the cells may be contacted with a Golgi inhibitor and with IL-23.

[0094] One embodiment of the disclosure is a method of determining the level of a biomarker associated with responsiveness of IBD in an individual to treatment with an IL-23 antagonist. In certain aspects, the method may comprise obtaining a biological sample from the individual and determining the level of the biomarker in the biological sample. In certain aspects, the biological sample may comprise a blood sample, such as whole blood. In certain aspects the biological sample may comprise peripheral blood mononuclear cells (PBMC), which may be isolated from a whole blood sample. In certain aspects, the biological sample may comprise one of more cells selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells. In certain aspects, the method may comprise determining the presence, absence, or level, of the biomarker in one or more of the cells present in the sample. In certain aspects, the method may comprise determining the level of the biomarker in one or more of the cells selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells. In certain aspects, cells in the biological sample may be treated prior to determining the level of biomarkers contained therein. For example, in certain aspects, the cells may be stimulated by contacting the cells with a cytokine such as IL-23. In certain aspects, the cells are contacted with IL-23 prior to determining the level of biomarker contained therein. Inhibition of the Golgi apparatus may also be beneficial. Thus, in certain aspects, the cells may be contacted with a Golgi inhibitor, non-limiting examples of which have been disclosed herein. Contact of the cells with a Golgi inhibitor may occur in the absence of, prior to, during, or after contact of the cells with IL-23. In certain aspects, the cells are contacted with IL-23 and a Golgi inhibitor prior to determining the intracellular level of a biomarker contained therein.

[0095] Any method of detecting and measuring biomolecules known in the art may be used to determine the level of biomarker in the cells. Suitable methods include, but are not limited to, PAGE analysis, chromatography, mass cytometry, an immunoassay, immunoprecipitation, fluorescence, or luminescence. In certain aspects, the level of a biomarker in a cell may be determined using a detection molecule, such as an antibody or a receptor, that binds to the biomarker. For example, in aspects in which the biomarker comprises TNF-a, the detection molecule may comprise a TNF-a receptor or an anti-TNF-a antibody. In certain aspects, the detection molecule may comprise a detectable label, such as a fluorescent protein, a luminescent protein, an enzyme, a metal isotope, or a radiolabel.

[0096] In certain aspects, following contact of the cells with a labeled detection molecule, the cells may be subjected to methodology that counts the number ofindividual cells and determines the presence, absence, and / or level, of biomarker in each cell. In certain aspects, prior to determining the presence, absence, and / or level, of biomarker in each cell, the lineage of each cell may be identified, which may comprise contacting the cells with individual lineage markers, such as labeled, lineage-specific antibodies. In certain aspects, the percentage of cells comprising a biomarker may be determined. In certain aspects, the method may comprise subjecting the cells to mass cytometry.

[0097] One embodiment of the disclosure is a method of determining the level of a biomarker associated with responsiveness of an individual having IBD to treatment with an IL-23 antagonist, comprising:

[0098] obtaining a peripheral blood mononuclear cell (PBMC)-containing sample and isolating the PBMC;

[0099] contacting the isolated PBMC with IL-23 and a Golgi inhibitor;

[0100] contacting the cells with a detection molecule that binds to the biomarker, the detection molecule having a detectable label, thereby producing labeled cells; and,

[0101] detecting and quantifying the detectable label using a detection method suitable for the detectable label, thereby determining the level of the biomarker.

[0102] In certain aspects, the biomarker may comprise TNFa, IL-17F, or GM-CSF. In certain aspects, the PBMC may comprise one of more type of cell selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells. In certain aspects, the method may comprise determining the level of the biomarker in one or more of the cells selected from the group consisting of Th17 cells, Tc17 cells, γδT cells, iNKT cells, and MAIT cells. In certain aspects, the detection molecule may be an antibody. In certain aspects, the detection molecule may be an anti-TNFa antibody, an IL-17F antibody, or an anti-GM-CSF antibody. In certain aspects, the detection molecule may comprise a detectable label, such a fluorescent protein, a luminescent protein, an enzyme, a metal isotope, or a radiolabel. In certain aspects, the step of detecting and quantifying may comprise CyTOF.

[0103] Once the biomarker in the cell has been labeled, the amount of biomarker in one or more of the cells may be quantified. Detection and / or quantification of the labeled detection molecule may be made using any suitable method known in the art. In certain aspects, following contact of the cells with a labeled detection molecule, the cells may be subjected to methodology that counts the number of individual cells and determinesthe presence, absence, level, and / or level, of biomarker in each cell. In certain aspects, the level of biomarkers in each cell may be determined by detecting the detectable label. In certain aspects, prior to determining the presence, absence, and / or level, of biomarker in each cell, the lineage of each cell is identified, which may comprise contacting the cells with individual lineage markers, such as labeled, lineage-specific antibodies. In certain aspects, the percentage of cells comprising the biomarkers may be determined. In certain aspects, the level of biomarker may be reported as the average amount of intracellular biomarker from a given number of cells. In certain aspects, the level may be reported as the percentage of cells containing the biomarker.

[0104] Publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosure. Further, the dates of publication provided may be different from the actual publication dates, which may need to be independently confirmed.

[0105] This written description uses examples to disclose the methods of the disclosure, including the best mode, and also to enable any person skilled in the art to practice the methods of the disclosure, including making and using any devices or systems and performing any incorporated methods. The patentable scope of the disclosure is defined by the claims, and may include other examples that occur to those skilled in the art. Such other examples are intended to be within the scope of the claims if they have structural elements that do not differ from the literal language of the claims, or if they include equivalent structural elements with insubstantial differences from the literal language of the claims.EXAMPLES

[0106] Example 1. High dimensional profiling of IL-23 -responsive cells revealed molecular signatures that predict response to anti-IL-23 therapy in patients with Crohn’s Disease

[0107] This study was conducted to identify biomarkers that predict response to IL-23 therapy in Crohn’s patients. Adult patients with a history of ileal, colonic, or ileocolonic CD were included. Active CD in terminal ileum and / or colon were confirmed by colonoscopy and / or MRI. Blood samples were collected within 3 months before and 4, 8, 12, and 52 weeks after the initiation of the IL-23 antagonist Risankizumab (SKYRIZI®).Peripheral blood mononuclear cells (PBMC) were isolated and cryopreserved for batch analysis using mass cytometry (CyTOF). Pre-treatment PBMCs were stimulated ex vivo with IL-23, and stained for lineage markers to identify Thl7, Tcl7, y8T, NKT cells, and ILC3, as well as intracellular cytokines including IL- 17, IFN-g, TNF-a, IL-22, IL-6, and GM-CSF, using a pre-optimized and validated antibody panel. The CyTOF data were analyzed using the viSNE tool in Cytobank and Flow Jo™. Patients’ responses were evaluated 12-40 weeks after the initiation of risankizumab based on clinical symptoms and endoscopic / radiographic assessment.

[0108] The results show that among IL-23 -responsive cells, increased frequency of NKT cells was identified in the peripheral blood of non-responders before initiation of risankizumab (FIG. 2A). In non-responders, Tcl7 cells, y8T cells, and ILC3 demonstrated significant elevations in TNF-a, a key pathogenic mediator in CD. y8T cells from non-responders also showed increased IL-17F before treatment. In contrast, NKT cells from non-responders expressed significantly lower GM-CSF, which was previously shown to alleviate intestinal inflammation in patients and mouse models (FIGS. 2B-2F). Ongoing study is investigating the cytokine production in IL-23 -responsive cells after the initiation of risankizumab, as well as before and after starting ustekinumab, an anti-IL-12 / IL-23 antibody.

[0109] The results demonstrate that high dimensional profiling of pretreatment PBMCs revealed molecular signatures, e.g., elevated TNF-a in multiple IL-23-responsive cells, which are associated with resistance to risankizumab in CD patients. Those findings may help identify response biomarkers for IL-23 antagonists and provide a rationale for using anti-IL-23 / anti-TNF combination therapy in some patients with refractory CD.

[0110] Example 2. PBMC Stimulation and Processing

[0111] PBMC Isolation / Preparation.

[0112] METHODS: PBMCs were isolated from whole blood using density gradient centrifugation (FicolLPaque) to obtain high-purity mononuclear cell layer. The isolated PBMCs were washed multiple times to remove platelets and debris, then resuspended in complete culture medium (RPMI 1640 with FBS). Viable cells were counted and the concentration was adjusted (1 million cells / mL in a 6-well plate).

[0113] Stimulation

[0114] Stimulation was preformed with recombinant IL-23 (R& D, 11392-IL-100) at 50 ng / mL for 12 hours. Incubation then followed with protein transport inhibitors3115060-2081 (020960 / WO)PCTsuch as GolgiPlug (lug / mL) and Brefeldin A for 4 hours to trap cytokines inside the cell for intracellular staining.

[0115] Downstream Analysis

[0116] CyTOF and flow cytometry were performed after staining for cell surface and intracellular markers including transcription factors and cytokines after fixation and permeabilization following standard protocol (www.thermofisher.com). The marker panel used for CyTOF included: Thl7: CD45+, CD3+, CD4+, CD161, RORyt+; y5 T: CD45+, CD3+, y5 TCR+, NKp30; Tcl7: CD45+, CD3+, CD8+, CD161, RORyt+; NKT cells: CD45+, CD3+, CD94+, CD161+, ocp TCR+, TCR Va24; MAIT cells: CD45+, CD3+, Va7.2_TCR+, CD161+; Lineage markers: CD3, CD5, CDllb, CDllc, CD14, CD19, CD66a / b, CD130, FcsRl; and Cytokines: IL-22, IL-17A, IL-17F, IL-10, GM-CSF, TNF-oc, IL-6, IFN-y. The simplified marker panel proposed for flow cytometry included: Thl7: CD45+, CD3+, CD4+, CD161, RORyt+; y5 T: CD45+, CD3+, y5 TCR+, NKp30; Tcl7: CD45+, CD3+, CD8+, CD161, RORyt+; NKT cells: CD45+, CD3+, CD94+, CD161+, ocp TCR+, TCR Va24; MAIT cells: CD45+, CD3+, CD161+, Va7.2_TCR+; Lineage markers: CD3, CD5, CDllb, CDllc, CD14, CD19; and Cytokines: TNF-oc, IFN-y.

[0117] Example 3. scRNA-seq

[0118] scRNA-seq studies revealed expanded IL-23 -activated cells at baseline associated with RZB non-response (FIGS. 7A-7D). In addition, scRNA-seq showed increased T cell exhaustion at baseline associated with RZB non-response (FIG. 8). Finally, TCR-seq identified altered clonal expansion at baseline associated with RZB non-response (FIG. 9).

[0119] Example 4. Potential treatments

[0120] Effective anti-TNF therapy results in a decrease in TNF-a and interferon (IFN)-y levels, signifying reduced inflammation at the mucosal level (Kumar et al. J Transl Med, 2024, 22(1), 284). Accordingly, it is expected the patients identified as nonresponders to an anti-IL23 due to higher pre-treatment TNF-a and interferon (IFN)-y levels, may respond to treatment with an anti-TNF therapy such as infliximab, adalimumab, golimumab or certolizumab (Kumar et al. J Transl Med, 2024, 22(1), 284). Additional approaches in the patients with elevated TNF-a could also include upfront treatment with a combination of an anti-TNF and an anti-IL23 as shown in data from proof-of-concept VEGAtrial which suggests that combination therapy with guselkumab (an anti-IL23) and golimumab (an anti-TNF) might be more effective for ulcerative colitis than therapy with either drug alone (Feagan et al. Lancet Gastoenterol Hepatol, 2023, 8(4), 307-320). These findings require confirmation in larger trials such as the ongoing 'A Study of Combination Therapy With Guselkumab and Golimumab in Participants With Moderately to Severely Active Crohn's Disease (DUET-CD)' and similarly DUET-UC (https: / / clinicaltrials.gov / study / NCT05242471).

Claims

CTWHAT IS CLAIMED IS:

1. A method of predicting the responsiveness of a subject to treatment of inflammatory bowel disease (IBD) using an interleukin-23 (IL-23) antagonist, the method comprising:comparing a level of one or more biomarkers in a sample from the subject to a reference level of one or more corresponding biomarkers; andpredicting the responsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers.

2. A method of predicting the responsiveness of a subject to treatment of inflammatory bowel disease (IBD) using an interleukin-23 (IL-23) antagonist, the method comprising:obtaining a sample containing PBMC from the subject;isolating the PBMC from the sample;contacting the PBMC with a Golgi-inhibitor and stimulating the PBMC with IL-23; determining the intracellular level of one or more biomarkers selected from TNF-a, IL-17F, and GM-CSF;comparing the intracellular level of the one or more biomarkers in the sample from the subject to a reference level of one or more corresponding biomarkers; and predicting the responsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the one or more corresponding biomarkers.

3. The method of claim 1, wherein the IBD comprises Crohn’s Disease (CD).

4. The method of claim 1, wherein the IBD comprises Ulcerative colitis (UC).

5. The method of claim 1, wherein the one or more biomarkers comprises tumor necrosis factor alpha (TNF-a), interleukin- 17F (IL-17F), or granulocytemacrophage colony-stimulating factor (GM-CSF).

6. The method of claim 1, wherein the level of the one or more biomarkers comprises the intracellular level of at least one of the one or more biomarkers.

7. The method of claim 1, wherein the level of the one or more biomarkers is the intracellular level of the at least one of the one or more biomarkers.CT8. The method of claim 1, wherein the method comprises obtaining the sample from the subject and determining the level of the one or more biomarkers in the sample.

9. The method of claim 8, wherein the sample comprises peripheral blood mononuclear cells (PBMC).

10. The method of claim 9, wherein the sample comprises whole blood.

11. The method of claim 8, wherein the sample comprises PBMC isolated from whole blood.

12. The method of claim 9, comprising subjecting the PBMC to stimulation with IL-23 prior to determining the level of the one or more biomarkers in the sample.

13. The method of claim 9, comprising isolating the PBMC prior to stimulation with IL-23 and determining the level of the one or more biomarkers in the stimulated PBMC.

14. The method of claim 9, comprising contacting the PBMCs with a Golgi inhibitor.

15. The method of claim 1, wherein the subject has been diagnosed with IBD.

16. The method of claim 1, wherein the subject has not been diagnosed with IBD.

17. The method of claim 1, wherein the step of predicting comprises:wherein if the reference level corresponds to the level found in an individual responsive to treatment of IBD using an IL-23 antagonist, and the level of the one or more biomarkers in the sample does not differ significantly from the reference level, predicting that the subject will be responsive to treatment of IBD using an IL- 23 antagonist;wherein if the reference level corresponds to the level found in an individual responsive to treatment of IBD using an IL-23 antagonist, and the level of the one or more biomarkers in the sample is significantly different from the reference level of the corresponding one or more biomarkers in the subject, predicting that the subject will not be responsive to treatment of IBD using an IL-23 antagonist; and wherein if the reference level corresponds to the level found in an individual non- responsive to treatment of IBD using an IL-23 antagonist, and the level of the one or more biomarkers in the subject does not differ significantly from the reference level, predicting that the subject will be non-responsive to treatment of IBD using an IL-23 antagonist.

18. A method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising:CTcomparing a level of TNF-a in a sample from the individual to a reference level of TNF-a; andpredicting responsiveness of the IBD based on the similitude of the level of TNF-a in the sample and the reference level of TNF-a.

19. The method of claim 18, wherein the step of predicting comprises:wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a responder and the level TNF-a in the sample does not differ significantly from the reference level of TNF-a, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a responder and the level TNF-a in the sample is significantly greater than the reference level of TNF-a, predicting that the IBD in the individual will be non- responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a corresponds to the level of TNF-a found in a non-responder and the level TNF-a in the sample is significantly less than the reference level of TNF-a, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; andwherein if the reference level of TNF-a corresponds to the level of TNF-a found in a non-responder and the level TNF-a in the sample is not significantly different, or is greater, than the reference level of TNF-a, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

20. A method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising:comparing a level of IL-17F in a sample from the individual to a reference level of IL-17F; andpredicting responsiveness of the IBD based on the similitude of the level of IL-17F in the sample and the reference level of IL-17F.

21. The method of claim 21, wherein the step of predicting comprises:wherein if the reference level of IL-17F corresponds to the level of IL-17F found in a responder and the level IL-17F in the sample does not differ significantly from the reference level of IL-17F, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist;CTwherein if the reference level of IL-17F corresponds to the level of IL-17F found in a responder and the level IL-17F in the sample is significantly greater than the reference level of IL-17F, predicting that the IBD in the individual will be non- responsive to treatment with an IL-23 antagonist;wherein if the reference level of IL-17F corresponds to the level of IL-17F found in a non-responder and the level IL-17F in the sample is significantly less than the reference level of IL-17F, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; andwherein if the reference level of IL-17F corresponds to the level of IL-17F found in a non-responder and the level IL-17F in the sample is not significantly different, or is greater, than the reference level of IL-17F, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

22. A method of predicting responsiveness of IBD in an individual to treatment with an IL-23 antagonist, the method comprising:comparing a level of GM-CSF in a sample from the individual to a reference level of GM-CSF; andpredicting responsiveness of the IBD based on the similitude of the level of GM- CSF in the sample and the reference level of GM-CSF.

23. The method of claim 22, wherein the step of predicting comprises:wherein if the reference level of GM-CSF corresponds to, or is greater than, the level of GM-CSF found in a responder and the level GM-CSF in the sample does not differ significantly from the reference level of GM-CSF, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a responder and the level GM-CSF in the sample is significantly less than the reference level of GM-CSF, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist;wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a non-responder and the level GM-CSF in the sample is significantly greater than the reference level of GM-CSF, predicting that the IBD in the individual will be responsive to treatment with an IL-23 antagonist; and wherein if the reference level of GM-CSF corresponds to the level of GM-CSF found in a non-responder and the level GM-CSF in the sample is not significantlyCTdifferent than the reference level of GM-CSF, predicting that the IBD in the individual will be non-responsive to treatment with an IL-23 antagonist.

24. A method of identifying an IBD patient as being responsive to treatment with IL-23 antagonist, comprising using the method of claim 1 to predict whether the patient’s IBD will positively respond to treatment with an IL-23 antagonist, wherein if the IBD is predicted to positively respond to treatment with an IL-23 antagonist, identifying the patient as being responsive to treatment with an IL-23 antagonist.

25. A method of identifying an IBD patient as being responsive to treatment with an IL- 23 antagonist, the method comprising identifying the patient as being responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient responsive to treatment with an IL-23 antagonist.

26. A method of identifying an IBD patient as being non-responsive to treatment with IL-23 antagonist, comprising using the method of claim 1 to predict whether the patient’s IBD will positively respond to treatment with an IL-23 antagonist, wherein if the IBD is predicted to be non-responsive to treatment with an IL-23 antagonist, identifying the patient as being non- responsive to treatment with an IL-23 antagonist.

27. A method of identifying an IBD patient as being non-responsive to treatment with an IL-23 antagonist, the method comprising: i) identifying the patient as being non- responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL- 17F, and / or GM-CSF level observed in an IBD patient non-responsive to treatment with an IL-23 antagonist; or ii) identifying the patient as being non-responsive to treatment with an IL-23 antagonist if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or GM-CSF corresponds to the TNF-a, IL-17F, and / orCTGM-CSF level observed in an IBD patient responsive to treatment with an IL-23 antagonist,28. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of the disclosure to identify the patient as responsive or non-responsive to treatment with an IL-23 antagonist, wherein if the patient is identified as being responsive to treatment with an IL-23 antagonist, administering an IL-23 antagonist to the patient, and wherein if the patient is identified as being non-responsive to treatment with an IL-23 antagonist, not initiating, suspending, or having suspended, administration of an IL-23 antagonist.

29. The method of claim 27, comprising: wherein if the patient is identified as being non-responsive to treatment with an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

30. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of claim 1 to identify the patient as being responsive to treatment with an IL-23 antagonist, and prescribing, administering, or having administered, to the patient an IL-23 antagonist.

31. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising using a method of claim 1 to identify the patient as non- responsive to treatment with an IL-23 antagonist; andnot initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient.

32. The method of claim 30, comprising following not initiating, suspending, or having suspended, administration of an IL-23 antagonist, prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

33. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by:a. comparing a level of TNF-a and / or IL-17F in a sample from the patient to a reference level of TNF-a and / or IL-17F;b. identifying the responsiveness of the IBD based on the similitude of the level of the one or more biomarkers in the subject and the reference level of TNF-a and / or IL-17F;CTwherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a found in a responder and the level TNF-a and / or IL-17F in the sample does not differ significantly from the reference level of TNF-a and / or IL- 17F, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a and / or IL-17F found in a responder and the level TNF-a and / or IL- 17F in the sample is significantly greater than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist;wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level TNF-a and / or IL-17F in the sample is significantly lower than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being responsive to treatment with an IL- 23 antagonist;wherein if the reference level of TNF-a and / or IL-17F corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level TNF-a and / or IL-17F in the sample is not significantly different, or is greater, than the reference level of TNF-a and / or IL-17F, identifying the patient’s IBD as being non- responsive to treatment with an IL-23 antagonist; andc. using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist; and wherein if the patient’s IBD is identified as being non-responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient.

34. The method of claim 33, wherein following identification of the patient as non- responsive to treatment with an IL-23 antagonist, the method comprises prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.CT35. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising identifying the responsiveness of the patient’s IBD to treatment with an IL-23 antagonist by:a. comparing a level of GM-CSF in a sample from the patient to a reference level of GM-CSF;b. identifying the responsiveness of the IBD based on the similitude of the level of the one or more biomarkers in the subject and the reference level of GM-CSF;wherein if the reference level of GM-CSF corresponds to the level of GM- CSF found in a responder and the level GM-CSF in the sample does not differ significantly from the reference level of GM-CSF, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of GM-CSF corresponds to the level of GM- CSF found in a responder and the level GM-CSF in the sample is significantly less than the reference level of GM-CSF, identifying the patient’s IBD as being non- responsive to treatment with an IL-23 antagonist;wherein if the reference level of GM-CSF corresponds to the level of TNF-a and / or IL-17F found in a non-responder and the level GM-CSF in the sample is significantly higher than the reference level of GM-CSF, identifying the patient’s IBD as being responsive to treatment with an IL-23 antagonist;wherein if the reference level of GM-CSF corresponds to the level of GM- CSF found in a non-responder and the level GM-CSF in the sample is not significantly different, or is less, than the reference level of GM-CSF, identifying the patient’s IBD as being non-responsive to treatment with an IL-23 antagonist; andc. using the identified responsiveness of the patient’s IBD to treat the patient, wherein if the patient’s IBD is identified as being responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist; and wherein if the patient’s IBD is identified as being non-responsive, prescribing, administering, or having administered, to the patient an IL-23 antagonist, not initiating, or suspending, or having suspended, administration of an IL-23 antagonist to the patient.CT36. The method of claim 35, wherein following identification of the patient as non- responsive to treatment with an IL-23 antagonist, the method comprises prescribing, administering, or having administered, to the patient an IBD treatment that does not target IL-23.

37. A method of treating a subject having inflammatory bowel disease (IBD), comprising predicting the responsiveness of the subject to treatment of IBD using an interleukin-23 (IL-23) antagonist, by:comparing a level of one or more biomarkers in a sample from the subject to a reference level of one or more corresponding biomarkers;predicting the responsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers;wherein if the subject is predicted to be responsive to treatment of IBD using an IL- 23 antagonist, prescribing, administering, or having administered, to the subject an IL-23 antagonist; andwherein if the subject is predicted to be non-responsive to treatment of IBD using an IL-23 antagonist, prescribing, administering, or having administered, to the subject an IBD treatment that does not target IL-23.

38. A method of treating a subject having inflammatory bowel disease (IBD) and that is receiving an IL-23 targeted treatment, comprising predicting the responsiveness of the subject to treatment of IBD using an IL-23 antagonist, by:comparing a level of one or more biomarkers in a sample from the subject to a reference level of one or more corresponding biomarkers;predicting the responsiveness of the subject based on the similitude of the level of the one or more biomarkers in the subject and the reference level of the corresponding one or more biomarkers;wherein if the subject is predicted to be responsive to treatment of IBD using an IL- 23 antagonist, prescribing continuation of, continuing, or having continued, the IL- 23 -targted treatment; andwherein if the subject is predicted to be non-responsive to treatment of IBD using an IL-23 antagonist, stopping, or having stopped, the IL-23 -targted treatment.

39. The method of claim 38, comprising prescribing, administering, or having administered, to the subject an IBD treatment that does not target IL-23.CT40. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising administering an IL-23 antagonist to the patient if the patient is determined to have i) a level of TNF-a, ii) a level of IL-17F, and / or a level of GMCSF, that is not significantly different from a reference level of TNF-a, IL-17F and / or GM-CSF, wherein the reference level of TNF-a, IL-17F and / or corresponds to the TNF-a, IL-17F, and / or GM-CSF level observed in an IBD patient that is responsive to treatment with an IL-23 antagonist.

41. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of an IL-23 antagonist to the patient if the patient is determined to have a level of TNF-a that is significantly higher than a reference level of TNF-a that corresponds to the TNF-a level observed in an individual identified as a responder.

42. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient if the patient is determined to have a level of IL-17F that is significantly higher than a reference level of IL-17F that corresponds to the IL-17F level observed in an individual identified as a responder.

43. A method of treating IBD in a patient in need of such treatment (e.g., an IBD patient), comprising not administering, or suspending or having suspended administration of, an IL-23 antagonist to the patient if the patient is determined to have a level of GM-CSF that is significantly less than a reference level of GM-CSF that corresponds to the GM-CSF level observed in an individual identified as a responder.

44. A method of determining the level of a biomarker associated with responsiveness of an IBD patient to treatment with an IL-23 antagonist, the method comprising: obtaining a sample containing peripheral blood mononuclear cells (PBMC) from the patient;subjecting the PMBC to IL-23 stimulation; anddetermining the level of the biomarker produced by the PBMC.

45. The method of claim 44, wherein the PBMC are isolated from the sample prior to IL-23 stimulation.CT46. The method of claim 45, wherein isolation comprises centrifugation, filtration, or chromatography.

47. The method of claim 44, comprising contacting the PBMC with a Golgi inhibitor.

48. The method of claim 47, wherein the PBMC are contacted with a Golgi inhibitor prior to stimulation with IL-23.

49. The method of claim 44, wherein the step of determining the level of the biomarker comprises determining the intracellular level of the biomarker.

50. The method of claim 44, wherein the step of determining the level of the biomarker comprises determining the intracellular level of the biomarker in Th 17 cells, Tcl7 cells, y8T cells, iNKT cells, and / or MAIT cells present in the PBMC.

51. The method of claim 44, wherein the biomarker is a protein.

52. The method of claim 51, wherein determining the level of the biomarker protein comprises measuring the presence, absence, level, or level of activity, of the biomarker protein.

53. The method of claim 51, wherein determining the level of the biomarker protein comprises cell sorting, PAGE analysis, chromatography, mass cytometry, immunoprecipitation, an immunoassay, fluorescence, or luminescence.

54. The method of claim 44, wherein the step of determining the level of the biomarker produced by the PBMC comprises:contacting the cells with a detection molecule that binds the biomarker protein, the detection molecule comprising a detectable label; anddetermining the level of the detectable label.

55. The method of claim 54, wherein the detection molecule is a receptor or an antibody that binds the biomarker protein.

56. The method of claim 54, wherein the detectable label comprises a fluorescent protein, a luminescent protein, an enzyme, a metal isotope, or a radiolabel.

57. The method of claim 54, wherein the step of determining the level of detectable label comprises separating individual cells in the sample and detecting the level of detectable label in each individual cell.

58. The method of claim 57, comprising counting the individual cells and determining the percentage of cells comprising the detectable label.

59. The method of claim 44, when the biomarker is TNF-a, IL-17F, or GM-CSF.

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