Introduction

Very early onset inflammatory bowel disease (VEO-IBD) is often associated with a severe disease course and unique characteristics including an underlying monogenic defect. In this study, we identified new pathogenic mutations in CGNL1 associated with VEO-IBD and other inflammatory GI disease. CGNL1 (Cingulin Like 1) encodes an epithelial junctional protein whose function was previously unknown in the gastrointestinal tract.

Aims & Methods

Whole exome sequencing (WES) was performed on the affected patient with VEO-IBD and all first-degree relatives with IBD and other inflammatory disease. Intestinal epithelial organoids (IEOs) were generated from the affected patient and were characterized by transepithelial electrical resistance (TEER), FITC-dextran permeability assay on epithelial cell monolayer, immunostaining, RNA sequencing, and transmission electron microscopy (TEM). In addition, we generated a new Cgnl1^-/- mouse model, which was characterized using FITC-dextran permeability assay, TEM, dextran-sodium sulfate (DSS)-induced colitis, and infections by Citrobacter rodentium and Clostridioides difficile. Single-cell datasets were analyzed to determine CGNL1 expression in IBD, primary sclerosing cholangitis (PSC), and autoimmune hepatitis (AIH).

Results

In the affected patient with VEO-IBD who required early total colectomy and pouch formation with coexistent PSC and celiac disease, WES identified two rare, new, pathogenic variants in the CGNL1 gene. Both pathogenic variants were also present in the patient’s younger sister, who has a similar history including early-onset, fulminant ulcerative colitis requiring total colectomy with ileostomy and PSC-AIH overlap syndrome. Furthermore, multiple relatives of the patient suffer from IBD and other inflammatory conditions including celiac disease, eosinophilic esophagitis, and type-1 diabetes. The RNA and protein levels of CGNL1 were significantly diminished in the patient’s intestinal epithelial cells compared to that of healthy individuals and other IBD patients by RNA-seq, immunoblotting, and immunostaining. The patient’s IEOs from pouch body and pre-pouch ileum formed smaller 3D spheroids with altered cell composition and significantly impaired barrier function compared to those from healthy controls and other IBD patients. Immunofluorescence and TEM demonstrated that CGNL1 is required for the assembly of junctional complexes in human IEOs and an epithelial cell line. Similarly to findings from the patient, impaired junctional complexes in intestinal epithelial cells and elevated intestinal permeability were present in Cgnl1^-/- mice at steady state. Cgnl1^-/- mice showed substantial vulnerability to DSS-induced colitis and bacterial infections that directly compromise the epithelial barrier. In addition, 6-month-old Cgnl1^-/- mice exhibited spontaneous inflammation in the colon and terminal ileum due to disrupted intestinal barrier, which was microbiome-dependent. Furthermore, single-cell analysis revealed diminished expression of CGNL1 in the intestinal and hepatic epithelial cells from patients with IBD or PSC/AIH, respectively.

Conclusion

The pathogenic CGNL1 variants contribute to VEO-IBD by disrupting gut barrier integrity, as demonstrated by patient’s cells and novel murine models. This study expands our understanding of epithelial barrier impairment in the pathogenesis of VEO-IBD, and highlights intestinal epithelium as a therapeutic target in some IBD patients.

Introduction

Inflammatory bowel disease (IBD) is a growing global health problem with increasing prevalence. Current therapeutic strategies for IBD are mainly aimed at modulating the dysregulated immune activity in the intestinal mucosa. Targeting the JAK/STAT signalling pathway has been shown to be highly effective in ulcerative colitis, but not in Crohn's disease (CD), where efficacy was found to be insufficient in the initiation phase of a clinical trial [1]. Failure of the therapeutic response in Crohn’s disease may be influenced by the unique immune microenvironments in the small and large intestine and their characteristic cytokine profiles and immune cell compositions.

Aims & Methods

To gain deeper insight into region-specific efficacy in the inflamed ileum versus colon, this study investigates the immunomodulatory effects of filgotinib, a Jak1 inhibitor, using precision-cut intestinal slices (PCIS) from patients with Crohn's diseases. PCIS are viable, ultra-thin human tissue slices that retain the original intestinal architecture ex vivo and contain important cell types, including resident immune cells.
PCIS were prepared from resected ileal and colonic tissue of CD patients. The slices were cultured ex vivo and stimulated with concanavalin A or anti-CD3/CD28 antibodies to induce T cell-driven inflammatory responses. Filgotinib (1-100 µM) was applied to assess the immunomodulatory effects of JAK1 inhibition following Concanavalin A preactivation. To exclude treatment-related toxicity, cellular integrity was evaluated using an LDH release assay. Tissue morphology was examined by H&E staining and immunofluorescence. The immune response was assessed by multiplex ELISA of 20 cytokines.

Results

After filgotinib treatment, primary tissue slices from the ileum and colon of CD patients remained viable. Regional morphological characteristics of ileum and colon tissue were preserved after ex vivo cultivation, with prominent villi and smaller crypts in the ileum, and larger, more frequent crypts and flattened villi in the colon. Compared to non-CD tissue slices, Crohn’s disease-related changes, such as immune cell accumulation, were also observed in CD tissue slices ex vivo. Upon T cell-specific stimulation with anti-CD3/CD28 antibodies, region-specific immune reactivity was observed. Colonic PCIS showed an increased release of IL-2 (~3-fold), IL-10 (~2‑fold) and TRAIL (~4-fold) compared to ileal PCIS, indicating a stronger involvement of Th and regulatory T cells in the colon. In contrast, ileal PCIS showed higher levels of MIP-3α (2-fold) and granzyme A (~8-fold) after stimulation, suggesting increased cytotoxic T cell activity in this region. Filgotinib treatment showed region-specific differences in its ability to modulate cytokine release in PCIS of CD patients. In colonic PCIS, filgotinib reduced the induced secretion of Th17-associated cytokines such as IL-17F and IL-22 by up to 95%, whereas in ileal PCIS it showed no effect on the same cytokines.

Conclusion

In conclusion, filgotinib exhibited more potent anti‑inflammatory effect on Th17 cells in the colon, and a markedly reduced efficacy in the ileum. This study demonstrates for the first time that precision-cut intestinal slices can be used to predict region-specific drug response in inflamed intestinal tissue ex vivo, underscoring the critical importance of region-specific immune profiling in IBD and highlight the limited efficacy of JAK1 inhibition in ileum. This ex vivo, patient-derived model represents a valuable platform for evaluating localised treatment efficacy and advancing personalised therapeutic strategies in IBD.

References

[1] Rogler G. Efficacy of JAK inhibitors in Crohn's Disease. J Crohns Colitis. 2020 Aug 1;14(Supplement_2):S746-S754. doi: 10.1093/ecco-jcc/jjz186

Introduction

Post-operative recurrence (POR) affects a substantial proportion of Crohn's disease (CD) patients following intestinal resection. While ileocolonoscopy remains the gold standard for detecting recurrence, its invasive nature and patient burden have spurred interest in non-invasive monitoring approaches. This study evaluates the performance of faecal calprotectin (FC) and cross-sectional imaging at different timepoints in predicting endoscopic recurrence in postoperative CD patients.

Aims & Methods

In this multicenter retrospective cohort of 895 CD patients who underwent ileocecal resection, we analyzed the diagnostic accuracy of FC measurements at 3, 6-12, and 18-24 months postoperatively for predicting endoscopic recurrence (Rutgeerts score ≥i2 or SES-CD ≥3). Additionally, we assessed the concordance between intestinal ultrasound (IUS) and magnetic resonance imagings (MRI) and endoscopic findings at both 6-12- and 18-24-months using kappa statistics.

Results

FC demonstrated modest discriminatory ability at 3 months (AUC 0.642, 95% CI: 0.530-0.753) and 6-12 months (AUC 0.653, 95% CI: 0.593-0.713), with improved performance at 18-24 months (AUC 0.676, 95% CI: 0.608-0.744). The optimal cutoff values for FC (47.5 μg/g at 3 and 6-12 months; 80.0 μg/g at 18-24 months) were substantially lower than standard thresholds (150-250 μg/g) used in non-operated patients.
At 6-12 months, radiological and endoscopic assessments showed moderate agreement (κ=0.426, p<0.001) with 63.2% concordance. At 18-24 months, IUS demonstrated superior agreement with endoscopic findings (κ=0.531, p<0.001; sensitivity 83.8%, specificity 72.7%) compared to MRI (κ=0.324, p<0.001). Notably, radiological remission at 18-24 months was identified as a significant protective factor against surgical recurrence (OR 0.356, 95% CI: 0.179-0.705, p=0.003).

Table I: Concordance between endoscopic and radiologic findings (IUS and MRI) for inflammation and remission at 18–24 months post-ileocecal resection. Abbreviations: IUS: Intestinal ultrasound, MRI: Magnetic resonance imaging.

Conclusion

Non-invasive monitoring with FC shows promise in postoperative CD surveillance, though diagnostic thresholds differ substantially from those established for non-operated patients. IUS demonstrates superior concordance with endoscopic findings compared to MRI, particularly at later timepoints. The protective role of radiological remission against surgical recurrence highlights the importance of transmural healing. Combining FC with radiological assessment, especially IUS, may provide a comprehensive, patient-friendly approach to monitoring postoperative CD, potentially reducing the need for invasive procedures in selected patients but further studies are needed in this direction.