Introduction
Fistulizing Crohn's disease (CD) is a severe phenotype characterized by transmural inflammation, impaired epithelial repair, and chronic tissue remodeling. Despite its substantial clinical burden, the molecular determinants that distinguish fistulizing from non-fistulizing CD remain poorly defined.
Aims & Methods
We aimed to define proteomic and metabolomic signatures associated with fistula formation in CD. We analyzed 2,889 individuals with Crohn's disease, including 217 with fistulizing disease, from the UK Biobank. Baseline demographic, plasma proteomic, and metabolomic data were assessed. Differential expression analysis was performed using the limma package in R with adjustment for age and sex. Pathway enrichment and network-based integration analyses were conducted to support biological interpretation across omic layers.
Results
Fistulizing CD exhibited a distinct proteomic profile enriched for inflammatory, innate immune, and tissue-remodeling pathways. Neutrophil-associated and inflammasome-related mediators (MPO, MMP9, LCN2, CASP8, ZBP1) were significantly elevated, consistent with enhanced neutrophil activation, epithelial injury, and pro-inflammatory cell death signaling. Proteins involved in cytoskeletal organization and extracellular matrix remodeling (ARHGAP5, EFNB2, STX3, STX7) were increased, indicating active transmural tissue reorganization. In contrast, proteins associated with epithelial integrity and repair (KRT18, ROBO1, GALNT10, MAN1A2) were reduced, suggesting impaired mucosal regeneration.
Metabolomic profiling further distinguished fistulizing CD, with decreased HDL-related lipid fractions and selected amino acid metabolites, alongside increased VLDL lipids, branched-chain amino acids, acetate, and citrate, indicative of a pro-inflammatory, energy-demanding metabolic state. Integrated multi-omic analysis demonstrated strong concordance, with neutrophil-derived proteins clustering with markers of oxidative stress and NAD⁺ metabolic activation (NAMPT, NMNAT1), while lipid and amino acid alterations aligned with pathways regulating immune activation and extracellular matrix turnover. Dysregulated molecules mapped to pathways implicated in fistula pathogenesis, including MMP9-mediated matrix degradation, NAMPT-driven NAD⁺ metabolism, and branched-chain amino acid–dependent mTOR signaling.
Conclusion
Multi-omic profiling identifies a robust molecular signature distinguishing fistulizing from non-fistulizing Crohn's disease. Coordinated neutrophil activation, defective epithelial repair, extracellular matrix remodeling, and metabolic reprogramming emerge as central features of fistula biology, providing mechanistic insight and highlighting candidate biomarkers and therapeutic targets for this aggressive phenotype.