Abstract Background Very early onset inflammatory bowel disease (VEO-IBD) is often associated with a severe disease course and unique characteristics including underlying monogenic etiologies in some cases. In this study, we mechanistically defined the function of CGNL1, an epithelial junctional protein gene whose pathogenic variants may contribute to VEO-IBD. Methods Whole exome sequencing (WES) was performed on the affected patient and all first-degree relatives. Intestinal epithelial organoids (IEOs) were generated from the patient’s mucosal biopsies and were characterized by microscopy, whole-mount immunostaining, transcriptomics and transmission electron microscopy (TEM). In addition, we generated a new Cgnl1-/- mice for dextran-sodium sulfate (DSS)-induced colitis and infection by Citrobacter rodentium which directly compromises intestinal epithelium. Integrated analysis was performed to determine CGNL1 expression in single-cell datasets. Results In this patient with VEO-IBD who required early total colectomy with pouch formation, coexistent primary sclerosing cholangitis (PSC) and celiac disease, WES identified two rare, novel, pathogenic variants in the CGNL1 gene. Both pathogenic variants were also present in the patient’s younger sister, who has a similar history including fulminant UC and PSC-autoimmune hepatitis 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 diminished in the patient’s intestinal epithelium compared to that of healthy individuals and other IBD patients. 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 normal controls (Figure 1). TEM demonstrated disrupted tight junctions and adherens junctions in the patient’s IEOs. Similarly, impaired junctional complexes in intestinal epithelial cells and elevated intestinal permeability were present in Cgnl1-/- mice, which also showed increased susceptibility to DSS-induced colitis (Figure 2) and C. rodentium infection. Single-cell analysis revealed diminished expression of CGNL1 in intestinal and hepatic epithelial cells from patients with IBD or PSC, respectively. Conclusion The pathogenic CGNL1 variants may contribute to VEO-IBD and other inflammatory GI disease by disrupting gut barrier integrity. This study expands our understanding of epithelial barrier impairment in the pathogenesis of VEO-IBD and suggests the intestinal epithelium as a therapeutic target for some IBD patients.
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