P1292 Identifying genetic markers of fibrostenosis in patients with Crohn’s disease
Authors: Celis J , Fouquaert S , Holvoet T , Jans D , Bossuyt P , De Kock I , Hindryckx P , Louis E , Vermeire S , De Vos M , Cleynen I , Laukens D ,   IBD Research Unit
Published: January 2025

Abstract

Background
While genetics has been shown to direct wound healing responses toward healing or progressive fibrosis in liver and lung disease, attempts to identify genes involved in fibrostenotic Crohn’s disease (CD) have not been successful. This knowledge gap stems partly from the challenge to uniformly define fibrostenosis, for which the golden standard currently is surgery. We aimed to investigate the genetic basis of fibrostenotic CD by conducting a case-control genetic association study in a well-defined CD cohort, and assessing the presence of protein-coding (missense) mutations in patients carrying associated single nucleotide polymorphisms (SNPs) in interesting candidate genes through whole exome sequencing.

Methods
A retrospective case-control association study was performed by applying strict inclusion criteria to CD patients from three Belgian centres; early ileal fibrostenotic CD was primarily defined based on computed tomography or magnetic resonance enterography and occurring within five years following diagnosis (N = 56). The control cohort consisted of ileal CD patients without fibrostenotic or penetrating complications for a minimum of ten years (N = 252). Previously collected Immunochip data were subjected to logistic regression analysis correcting for disease location and the first five principal components. Exome sequencing of patients homozygous for at least one of the three top associated SNPs was performed. Genes in the proximity of the top SNPs, along with other candidate genes based on literature, were screened for the presence of missense mutations via Integrative Genomics Viewer. Mutations were evaluated for functional impact (PolyPhen-2) and evolutionary conservation (PhyloP), and frequencies were compared with European population data (ALFA dataset).

Results
Eight SNPs were associated with fibrostenosis (P&lt;5e-05, Table 1), and three SNPs (rs6061883, rs9372122, and rs13176097) reached suggestive significance (P&lt;10-6). The two top SNPs were located in cadherin 4 and autophagy related 5, two genes known to contribute to fibrosis.1, 2 We observed a significant shorter time to fibrosis between patients with a high amount (&gt;3) of risk alleles (of the top eight associated SNPs), compared to patients with a low amount (&lt;3). (P&lt;0.001, Figure 1). Exome sequencing data of patients carrying associated SNPs revealed high risk variants (Table 2) in several candidate genes, including autophagy related 9B, epidermal growth factor receptor, and mitogen-activated protein kinase kinase kinase 1.

Conclusion
This carefully phenotyped association study reveals interesting SNPs and candidate genes to further study the genetic basis of early development of fibrostenosis in ileal CD.

References
1.Li H, Peng X, Wang Y, et al. Atg5-mediated autophagy deficiency in proximal tubules promotes cell cycle G2/M arrest and renal fibrosis. Autophagy. Sep 2016;12(9):1472-86. doi:10.1080/15548627.2016.1190071
2.Ding JH, Xiao Y, Zhao S, et al. Integrated analysis reveals the molecular features of fibrosis in triple-negative breast cancer. Mol Ther Oncolytics. Mar 17 2022;24:624-635. doi:10.1016/j.omto.2022.02.003