Exploratory multiomics analysis of biologic switching in perianal fistulizing Crohn’s disease highlights oxidative phosphorylation-related pathways

Perianal fistulizing Crohn’s disease (pfCD) is a severe form of Crohn’s disease (CD) associated with a poor prognosis and frequent treatment failure. Although biologic switching is often regarded as a marker of therapeutic refractoriness, its clinical significance and molecular basis in pfCD remain poorly understood. In this retrospective study, 169 patients with pfCD were enrolled, including 124 in the discovery cohort and 45 in the validation cohort. Clinical and laboratory variables were analyzed to identify factors associated with disease status, and discriminative performance was evaluated using logistic regression, receiver operating characteristic (ROC) analysis, and nomogram modeling. Serum proteomic and metabolomic profiling was subsequently performed to characterize molecular changes associated with biologic switching, followed by integrated pathway enrichment analysis. Functional validation was conducted in LPS-stimulated intestinal epithelial cells overexpressing NDUFS3. Biologic switching was associated with disease status after adjustment for the clinical variables included in the multivariable logistic regression model. The model demonstrated good discriminative performance in the discovery cohort and excellent performance in the validation cohort. Exploratory multiomics analysis suggested potential differences in serum molecular profiles between patients with switched and fixed biologic regimens, involving pathways related to inflammatory responses, extracellular matrix regulation, lipid remodeling, and energy metabolism. Exploratory pathway analysis highlighted oxidative phosphorylation as a potential pathway of interest; however, the evidence remained limited because proteomic enrichment did not reach statistical significance after multiple-testing correction and metabolomic support was based on only one mapped metabolite. In vitro, NDUFS3 modulated mitochondrial respiration and inflammatory responses in LPS-stimulated intestinal epithelial cells. Together, these findings suggest that biologic switching is associated with observed disease status and potentially distinct serum molecular profiles in patients with pfCD. The exploratory molecular findings and in vitro functional results warrant further investigation but do not establish a direct mechanistic relationship between biologic switching, NDUFS3, and pfCD in patients.