The genetic predisposition of Inflammatory bowel disease (IBD) in the germline is well-established, while the potential role of somatic mutations in IBD remains underexplored. We aim to identify somatic mutations in intestinal mucosa and study their potential role in IBD pathogenesis. We identified somatic mutations using 538 intestinal biopsies and 268 blood samples from 268 IBD patients and 51 intestinal biopsies from 19 non-IBD controls. Mutations were called from RNA-seq data and whole exome sequencing data using Mutect2 software. Pathogenicity of mutations was predicted using the Variant Interpretation Pipeline. Mutation frequency and patterns were compared between IBD and controls, and within IBD-subgroups, considering both inflammation status and tissue of origin. IBD-affected tissue exhibited a significantly higher burden of somatic mutations compared to controls (p=0.02), with a striking enrichment for predicted likely pathogenic or pathogenic (pLP-P) mutations (p=2.07e-09). Notably, within IBD biopsies, pLP-P mutations were enriched in very early onset-IBD (VEO-IBD) genes (p≤2.2e-16) and primary immune deficiency (PID) genes (p≤2.2e-16), showing a 5.5-fold increase compared to non-IBD. Inflamed tissue showed an increase in mutations in PID and IBD-GWAS associated genes. Additionally, we identified pathogenic mutations in many IBD genes, such as the stop-gained mutation (c.517C>T) in HPS1, and many pLP-P mutations across the JAK-STAT pathway. Our analysis reveals widespread accumulation of pLP-P somatic mutations in IBD-affected tissue compared to non-IBD controls, with significant enrichment in genes that cause monogenic VEO-IBD. These findings suggest that somatic mutations can contribute to the initiation and perpetuation of inflammation in IBD.

Part of this study was funded by Takeda Development Center Americas, Inc. RKW acted as a consultant for Takeda and received unrestricted research grants from Takeda and Johnson and Johnson pharmaceuticals and speaker fees from AbbVie, MSD, Olympus and AstraZeneca. A.R.B. received a research grant from Janssen Pharmaceuticals and received speaker's fees from AbbVie and Ferring, outside the submitted work. MCV received speaker fees from Jansen-Cilag, Abbvie, Ferring and Galapagos. No disclosures: All other authors have nothing to disclose.

RKW is supported by the Seerave Foundation, the EU Horizon Health consortium grant ID-DarkMatter-NCD (101136582) and the EU Horizon Europe Program grant miGut-Health: Personalised blueprint of intestinal health (101095470). FI received a UMCG Mandema Stipend. A.R.B. is supported by a Rubicon fellowship from NWO (452022317) and the EU Horizon Health consortium grant ID-DarkMatter-NCD (101136582). VIP received funding from the EU projects Solve-RD, EJP-RD and CINECA (H2020 779257, H2020 825575, H2020 825775, respectively) and NWO grant numbers 917.164.455 and 184.034.019. AVV is supported by a Horizon-MSCA grant (Project 101149152).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The 1000IBD project was approved by the UMCG IRB (IRB number 2008.338)

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Data are uploaded to the European Genome-Phenome Archive (EGA) and are available upon request. The data for the Groningen IBD cohort can be requested with EGA the accession number EGAS00001002702 (https://ega-archive.org/).

https://ega-archive.org/studies/EGAS00001002702