Postoperative Ileum Transcriptomics Implicate Sex-Biased Mechanisms in Crohn's Disease Recurrence

Despite widespread biologic use, more than 70% of patients with Crohn's disease require resectional surgery, most commonly of the terminal ileum. Gene expression and genetics of the neoterminal ileum at postoperative, surveillance colonoscopies highlight pathways of disease recurrence. Postoperative colonoscopy transcriptomes were interrogated to evaluate the hypothesis that specific molecular mechanisms contribute to recurrent Crohn's pathophysiology.

Ribo-depleted, paired-end sequencing was run on 339 neoterminal ileal pinch biopsies from 267 patients with (Rutgeerts i2b+) and without (Rutgeerts i2a or lower) recurrent disease. Differential gene and transcript usage were assessed. Expression quantitative trait loci link genetic variation with gene expression. Serial sampling was performed on 70 patients.

At colonoscopy, 4171 genes increased and 3579 genes decreased in recurring vs nonrecurring patients. Although gene expression was highly correlated (r = 0.71), we observed and replicated higher dynamic ranges of gene expression in male compared with female patients. Activation of both pro- (tumor necrosis factor, interferon gamma) and anti-inflammatory (transforming growth factor beta) pathways was observed; importantly, multiple nuclear hormone receptor pathways demonstrated activation, including both estrogen and dihydrotestosterone pathways, whereas progesterone was inhibited. We observed sex-specific expression quantitative trait loci driven by recurrent samples and differential transcript usage related to lipid metabolism, membrane trafficking, and the extracellular matrix.

In recurrent disease of the postoperative neoterminal ileum, markedly greater dynamic ranges of gene expression occur in male compared with female patients. Pathway analyses implicate numerous nuclear hormone pathways, highlighting new mechanisms for therapeutic targeting beyond pro-inflammatory cytokine blockade. This study identifies key covariates and pathways of disease recurrence, many of which are distinct from drivers of initial disease susceptibility.