This project will evaluate predictive biomarkers of response to anti-tumor necrosis factor alpha (anti-TNF) therapy in early Crohn's disease (CD) patients. Candidate: The primary objective of this application is to support Dr. Ryan Ungaro's career development into an independent patient-oriented investigator in the field of personalized medicine for inflammatory bowel disease (IBD) patients. Dr. Ungaro's career goal is to become an independent researcher and leader in the application of predictive biomarkers and models to select the best treatment and optimize care for recently diagnosed IBD patients. Dr. Ungaro's proposed training activities are in four areas: 1) advanced biostatistical analysis, 2) predictive biomarker analysis, 3) computational genomics, and 4) principles of immune monitoring. To achieve this, he has assembled a mentoring and advisory team led by Dr. Judy Cho, Director of the Charles Bronfman Institute of Personalized Medicine and an expert in translational genomics, and Dr. Bruce Sands, Chief of the Division of Gastroenterology, who has expertise in clinical and translational investigation of IBD therapeutics, having driven much of the pioneering research in anti-TNFs. Environment: The Icahn School of Medicine at Mount Sinai has a strong tradition of outstanding research and is one of the top 20 medical schools in NIH funding. The Mount Sinai Division of Gastroenterology is consistently considered one of the top 10 divisions in the country by US News and World Report and is an international leader in IBD research and clinical care. Research: CD is a chronic, progressive, inflammatory condition affecting the gastrointestinal tract. Anti-TNF medications have vastly improved the treatment of CD patients, however a significant number of individuals do not respond to these agents which are very costly and have potentially fatal side effects. New classes of medications for CD are being released bringing the opportunity for personalized medicine. Clinicians will need the tools to help decide which medication will work best for each individual CD patient. This will be particularly important in recently diagnosed patients since effective early treatment can decrease long-term complications. Therefore our specific aims are to (1) determine the association of peripheral blood proteomic markers with response to anti- TNF (2) assess the association of intestinal tissue gene expression markers with anti-TNF response and (3) explore the mucosal immune architecture and predictive capacity for anti-TNF response of single cell RNA sequencing (scRNASeq) of intestinal biopsies. We will study recently diagnosed CD patients (within 2 years of diagnosis) from 3 prospective cohorts with biosamples: a population-based IBD inception cohort, a multi-center cohort of recently diagnosed pediatric CD patients, and a single-center biorepository of IBD patients linked to health records data. In addition, a cohort of recently diagnosed CD patients will be recruited for scRNASeq analysis. The general approaches and skills developed during this award can also be applied to new targeted medications and form the basis for future research on biomarkers of treatment response in early IBD.

Anti-tumor necrosis factor alpha inhibitors (anti-TNF) are the most effective medications for Crohn's disease (CD). However, a significant number of patients do not respond to these agents, which are costly and have serious potential side effects. We aim to evaluate peripheral blood and intestinal tissue predictive biomarkers of anti-TNF response in order to develop more personalized medicine approaches for recently diagnosed CD patients.