Introduction

Ulcerative colitis (UC) is a chronic inflammatory bowel disease where accurate assessment of disease activity is essential for effective patient management. Endoscopy is the gold standard for evaluating mucosal inflammation, but non-invasive alternatives, such as transabdominal ultrasound (TAUS), are garnering interest.

Aims & Methods

This study aimed to evaluate the sensitivity of rectal wall thickness measurements using TAUS in assessing disease activity in ulcerative colitis, and to identify an ideal cut-off threshold by comparing results with endoscopic and histological findings.
In a prospective, observational study, we enrolled consecutive patients with UC who were referred to our tertiary center from May 2024 to April 2025. Eligibility required a scheduled TAUS within 30 days of a staging colonoscopy, without intervening therapy adjustments. Exclusion criteria included technically inadequate TAUS readings (e.g., due to anatomical variations or excessive gas interposition) and minor-aged patients. Each patient underwent TAUS performed by a single, experienced operator. A second experienced operator blind assessments were recorded to evaluate inter-observer variability. Rectal wall thickness was measured and compared with clinical, laboratory (CRP, fecal calprotectin), and endoscopic (MAYO score) indicators of disease activity. Histological status (active/inactive) and additional clinical data, including disease duration, extent, and therapy, were recorded.

Results

A total of 74 patients were analyzed, of whom 51.4% were female, with a median age of 55 years (IQR: 42–68). The majority presented with left-sided colitis (Montreal E2, 62.2%), followed by extensive colitis (E3, 25.7%) and proctitis (E1, 12.1%). The median disease duration was 12 years (IQR 5–23). Patients with an endoscopic MAYO score of 0 or 1 had a median rectal wall thickness of 4.95 mm (IQR 4.5–5.88), while those with a score of 2 or 3 had a median of 6.15 mm (IQR 5.3–6.7; p=0.003). Receiver Operating Characteristic (ROC) analysis for TAUS rectal wall thickness showed good discriminatory ability for endoscopic activity (cut-off: 5.55 mm, AUC 0.725, 95CI 0.597-0.853, Se 0.80, Sp 0.71), comparable to fecal calprotectin (cut-off: 277 µg/g, AUC 0.717, 95CI 0.589-0.845, Se 0.70, Sp 0.66; p=0.256) and superior to CRP (cut-off: 1 mg/L, AUC 0.511, 95CI 0.357-0.664, Se 0.50, Sp 0.50; p<0.0001). For histological activity, TAUS again performed well (cut-off: 5.55 mm, AUC 0.794, 95CI 0.682-0.906, Se 0.76, Sp 0.80), closely matching fecal calprotectin (cut-off 302, AUC 0.744, 95CI 0.627-0.861, Se 0.69, Sp 0.73; p=0.425) and outperforming CRP (cut-off 1.5, AUC: 0.631, 95CI 0.497-0.765, Se 0.62, Sp 0.63; p<0.0001). Inter-observer agreement for TAUS rectal wall thickness was excellent, with an intraclass correlation coefficient of 0.923 (p<0.0001), underscoring the reproducibility of this non-invasive method.

Conclusion

TAUS measurement of rectal wall thickness demonstrates promising sensitivity and reproducibility in detecting mucosal and histological activity in UC, aligning closely with established markers such as fecal calprotectin. A cut-off value of 5.55 mm showed good discriminatory performance in this cohort, suggesting potential utility as a non-invasive marker of disease activity..Given its non-invasive nature, low cost, and strong inter-observer agreement, TAUS is a valuable adjunct for routine UC monitoring. Combined with clinical and biochemical data, it may reduce the need for repeated endoscopy, minimizing patient burden, healthcare costs, and environmental impact.

Introduction

Inflammatory bowel disease (IBD) - characterized by chronic inflammation of the gastrointestinal tract – is believed to be caused by an interplay of host genetics, environment and gut microbiome. Recent studies have started investigating the role of somatic DNA mutations in immune-mediated disorders (1, 2). Somatic mutations are mutations that are not present in the germline, but are acquired later in life. We hypothesize that somatic mutations in gut tissue in inflammation-related genes could contribute to the pathogenesis of IBD.

Aims & Methods

Therefore, we investigated somatic mutation patterns in 589 intestinal biopsies of 268 IBD patients and 17 non-IBD controls. We performed whole exome sequencing (WES) on DNA isolated from blood and bulk RNA sequencing (RNAseq) on RNA isolated from intestinal biopsies. Somatic mutations were called using the mutect2 software which compares RNAseq data to the reference genome and the WES data. Somatic mutations were subsequently filtered to reduce the chance of sequencing errors (somatic mutation presence >25% of the RNAseq reads, coverage of at least 10 RNAseq reads). We used 4 gene sets of interest, monogenic very-early-onset IBD (VEO-IBD) genes (n=103), monogenic primary immunodeficiency genes (n=475), the most recent IBD GWAS candidate genes (n=318) and all genes in the IBD GWAS loci (n=3504) and tested whether somatic mutations were more often present in these gene sets compared to the rest of the genome. Finally, we used the MOLGENIS Variant Interpretation Pipeline which uses the CAPICE pathogenicity prediction score and the Clinvar variant database to annotate the called and filtered somatic mutations as benign, likely benign, VUS, likely pathogenic, or pathogenic (3).

Results

We identified 400544 somatic mutations (average 745 per biopsy). We observed a significantly higher accumulation of somatic mutations in the gut biopsies of IBD patients compared to non-IBD controls (p=2e-04). This difference was bigger when only likely pathogenic and pathogenic (LP/P) somatic mutations were considered (p=3e-14). We observed a significant enrichment of somatic mutations in the genes of all 4 gene panels in the biopsies of IBD patients compared to controls (VEO-IBD p=0.0006, PID p=0.0001, GWAS candidate p=0.0015, GWAS loci p=0.0003). Biopsies taken from inflamed tissue contained statistically significantly more LP/P somatic mutations in PID, GWAS candidate and GWAS loci genes. 273 somatic mutations identified in IBD biopsies have been previously reported to the Clinvar database, including stop-gain point mutations in HPS1 c.517C>T and HPS4 c.1132C>T, pathogenic missense mutation IL10RA c.301C>T and pathogenic missense mutation in STAT1 c.884C>A. In-depth analysis of a subset of key genes in the IBD pathogenesis revealed multiple LP/P mutations in several patients in both JAK1 (n=35 LP/P) and JAK2 (n=31 LP/P), primarily in the FERM and protein kinase domains. Additionally, we observed 21 LP/P mutations in PLCG2, a gene in which missense mutations can cause immune dysregulation. (4)

Conclusion

Here, in the largest somatic mutation study in IBD patients to date, we show that there is an increased accumulation of likely pathogenic and pathogenic somatic mutations in gut tissue, particularly in genes in which mutations can cause monogenic very-early-onset IBD and/or primary immune deficiencies. Thus, we show that that somatic mutations in the gut could contribute to the pathogenesis of IBD.

References

1) Nanki, Kosaku, Masayuki Fujii, Mariko Shimokawa, Mami Matano, Shingo Nishikori, Shoichi Date, Ai Takano, et al. 2020. “Somatic Inflammatory Gene Mutations in Human Ulcerative Colitis Epithelium.” Nature 577 (7789): 254–59. https://doi.org/10.1038/s41586-019-1844-5.

3) Maassen, W. T. K., L. F. Johansson, B. Charbon, D. Hendriksen, S. van den Hoek, M. K. Slofstra, R. Mulder, et al. 2024. “MOLGENIS VIP: An Open-Source and Modular Pipeline for High-Throughput and Integrated DNA Variant Analysis.” medRxiv. https://doi.org/10.1101/2024.04.11.24305656.

4) Lange, Katrina M. de, Loukas Moutsianas, James C. Lee, Christopher A. Lamb, Yang Luo, Nicholas A. Kennedy, Luke Jostins, et al. 2017. “Genome-Wide Association Study Implicates Immune Activation of Multiple Integrin Genes in Inflammatory Bowel Disease.” Nature Genetics 49 (2): 256–61. https://doi.org/10.1038/ng.3760.