Large-scale proteomics identifies a pretreatment Crohn’s disease core proteome and a dynamic signature for anti-TNF response

Background With modest rates of endoscopic remission to anti-TNF biologics in children with moderate-to-severe Crohn’s disease (CD), there is a critical need to develop noninvasive biomarkers associated with anti-TNF response. We performed a comprehensive proteomic evaluation to identify peripheral-blood candidate biomarkers for anti-TNF response. Methods The ENvISION study enrolled patients (2-19 years old) with CD prior to starting infliximab or adalimumab with outcomes prospectively monitored at Month 3 (M3) and Month 12 (M12). The SomaScan® (Somalogic, Boulder, CO, 7322 analytes) was performed prior to anti-TNF treatment (baseline) at M3 and M12. Endoscopic remission was assessed at M12 (simple endoscopic score-CD < 3). Results Eighty patients with CD were enrolled with the CD Core Proteome developed from 61 prednisone-naive CD and 30 healthy controls. We identified 2999 differentially abundant proteins, 1403 with lower abundance and 1596 with higher abundance (FDR < 0.05). The CD Core Proteome was then compared across the three timepoints (baseline, M3 and M12) and we found that at both M3 and M12, the Core Proteome dysregulation retains strong identity with the baseline protein signal (β = .7, P < .001; β = .63, P < .001, respectively). Although the proteome exhibits change over time, it does not revert to a control-like state; rather, it transitions to a distinct “treated CD” proteome. In an exploratory investigation of the change in (delta) protein abundance from baseline to M3, we identified 132 proteins nominally associated with M12 endoscopic remission (P < .01). Using elastic net regression, we identified a three-protein panel (IRF1, NEUROG1, and APOA5) associated with M12 endoscopic remission (AUROC 0.94, 95% CI 0.88-1.0). Conclusions In an exploratory investigation, we identified a CD Core Proteome and three-protein panel whose early changes were associated with M12 endoscopic remission, supporting their use as early pharmacodynamic response markers following external validation.