Methods and compositions for prediction of response to a therapy of an inflammatory bowel disease

A method of treating a subject diagnosed with an inflammatory bowel disease (IBD), comprising:

• (i) identifying a subject diagnosed with an IBD to be a responder to an IBD treatment comprising an anti-interleukin 23 (anti-IL23) antibody, the method comprising:
• a). contacting a sample from a subject with a set of probes capable of detecting a panel of biomarkers comprising 13 biomarkers selected from the group consisting of CKLF-like MARVEL transmembrane domain containing 2 (CMTM2), complement C5a receptor 1 (C5AR1), fibroblast growth factor 2 (FGF2), glycerol kinase (GK), hepatocyte growth factor (HGF), interleukin 1 receptor antagonist (IL1RN), leukocyte immunoglobulin like receptor A2 (LILRA2), nicotinamide phosphoribosyltransferase (NAMPT), pappalysin 1 (PAPPA), synuclein alpha (SNCA), superoxide dismutase 2, mitochondrial (SOD2), STEAP4 metalloreductase (STEAP4), and zinc finger BED-type containing 3 (ZBED3);
• b). determining a signature score of the panel of biomarkers, wherein the determining comprises determining the baseline gene expression levels of the panel of biomarkers;
• and
• c). identifying a subject to be a responder to the IBD treatment if the signature score of the panel of biomarkers is above a pre-specified threshold indicative of response;
• and
• (ii) administering to the subject who has been identified as a responder in c) a therapeutically effective amount of the IBD treatment.