Cen Feng, J. Y. C. | Search bioRxiv

bioRxiv2025

Epigenetic Reprogramming Alters Intestinal Stem Cell Fate in Pouchitis

Intestinal stem cells (ISCs) mediate the continuous renewal of the epithelium during homeostasis and recovery from injury. To investigate the molecular impact of inflammation on human ISCs and the role of janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling, we established an organoid model derived from individuals with pouchitis, a form of inflammatory bowel disease that develops in an organ generated from ileal pouch-anal anastomosis (IPAA) surgery. Compared with non-inflamed specimens, pouchitis organoids exhibited increased apoptosis and secretory lineage differentiation that were stable after multiple passages, mirroring findings in primary pouch tissue. Chromatin accessibility and histone modification profiling of ISCs revealed inflammation-driven epigenetic remodeling, particularly involving activator protein 1 (AP-1) transcription factors such as c-Jun and excessive STAT1 activity. Loss of c-Jun disrupted ISC viability and enhanced secretory cell differentiation in non-inflamed organoids, whereas therapies targeting JAK/STAT reversed these ISC defects and chromatin changes in pouchitis organoids. Together, these results associated inflammation with epigenetic changes in human ISCs, suggesting that immune-mediated injury has lasting effects on the pouch epithelium that can potentially be reversed through JAK/STAT therapies.

cell biology↗

bioRxiv2024

Tofacitinib uptake by patient-derived intestinal organoids predicts individual clinical responsiveness

Background & AimsDespite increasing therapeutic options in the treatment of ulcerative colitis (UC), achieving disease remission remains a major clinical challenge. Nonresponse to therapy is common and clinicians have little guidance in selecting the optimal therapy for an individual patient. This study examined whether patient-derived materials could predict individual clinical responsiveness to the Janus kinase (JAK) inhibitor, tofacitinib, prior to treatment initiation. MethodIn 48 patients with UC initiating tofacitinib, we longitudinally collected clinical covariates, stool, and colonic biopsies to analyze the microbiota, transcriptome, and exome variations associated with clinical responsiveness at week 24. We established patient-derived organoids (n = 23) to determine how their viability upon stimulation with proinflammatory cytokines in the presence of tofacitinib related to drug responsiveness in patients. We performed additional biochemical analyses of organoids and primary tissues to identify the mechanism underlying differential tofacitinib sensitivity. ResultsThe composition of the gut microbiota, rectal transcriptome, inflammatory biomarkers, and exome variations were indistinguishable among UC patients prior to tofacitinib treatment. However, a subset of patient-derived organoids displayed reduced sensitivity to tofacitinib as determined by the ability of the drug to inhibit STAT1 phosphorylation and loss of viability upon cytokine stimulation. Remarkably, sensitivity of organoids to tofacitinib predicted individual clinical patient responsiveness. Reduced responsiveness to tofacitinib was associated with decreased levels of the cationic transporter MATE1, which mediates tofacitinib uptake. ConclusionsPatient-derived intestinal organoids predict and identify mechanisms of individual tofacitinib responsiveness in UC. Specifically, MATE1 expression predicted clinical response to tofacitinib.

cell biology↗