A biomarker catalog for inflammatory bowel disease medications

Inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC), is a multifaceted illness with diverse manifestations. Current treatment strategies are inadequate, with low response rates, secondary loss of response, and serious side effects. We aim at identifying transcriptomics and proteomics putative biomarkers for (i) disease severity, (ii) association with medication status, and (iii) putative response-associated signatures. We leveraged a large multiomics dataset (SPARC IBD) to compile a catalog of biomarkers for the three aforementioned comparisons. Data were stratified by IBD subtype (UC and CD) and tissue type; biomarker associations were identified using mixed-effects models to account for multiple medication groups, disease status (e.g., remission, active), and repeated sampling. Our catalog lists thousands of potential biomarkers: 9678 for disease severity, 299 associated with medication status, and 59 putative response-associated. These putative biomarkers, both known and novel, span multiple diagnoses, tissues, and medications. These therapy-associated signatures are hypothesis-generating. Longitudinal prospective validation is required before use to track treatment response or disease severity.