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While WNT\/\u03b2-catenin dysregulation has been reported in UC, the mechanisms of such abnormalities remain unclear. To investigate epithelial intrinsic alterations associated with UC, we performed single-nucleus RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) multiomics on human primary colonic epithelial cells (colonoids) from healthy donors and patients with inactive or active UC. Colonoids were cultured in a 3D matrix recapitulating crypt base cells or grown as 2D monolayers in differentiation medium to recapitulate luminal epithelial cells. Colonoids from active UC had a unique cell population with elevated CTNNB1 and reduced APC expression. Chromatin profiling identified enrichment of RUNX2 motifs in this UC-associated cell population. Active UC colonoids exhibited reduced OLFM4 expression in 3D and the differentiation marker VIL1 in 2D, suggesting impaired self-renewal and maturation. RUNX2 inhibition using CADD522 reduced \u03b2-catenin levels in 3D colonoids and restored VIL1 expression and junctional \u03b2-catenin localization in 2D cultures. These findings reveal an intrinsic defect in epithelial renewal in UC, driven in part by RUNX2-dependent WNT dysregulation. Our study identifies RUNX2 as a transcriptional regulator of epithelial stem cell function and WNT signaling in the inflamed human colon.<\/jats:p>\n                <jats:sec>\n                  <jats:title>Graphical Abstract summary<\/jats:title>\n                  <jats:p>\n                    Single-nucleus RNA and ATAC sequencing of UC patient-derived colonoids reveals a RUNX2-associated WNT signature in active inflammation. Elevated \u03b2-catenin and reduced\n                    <jats:italic>OLFM4<\/jats:italic>\n                    and\n                    <jats:italic>VIL1<\/jats:italic>\n                    expression indicate impaired self-renewal and differentiation. Pharmacologic inhibition of RUNX2 restores epithelial maturation, identifying RUNX2 as a key regulator of epithelial dysfunction in UC.\n                  <\/jats:p>\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"688458v1_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>","DOI":"10.1101\/2025.11.17.688458","type":"posted-content","created":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T03:20:14Z","timestamp":1763436014000},"source":"Crossref","is-referenced-by-count":1,"title":["RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells"],"prefix":"10.64898","author":[{"given":"Rodolfo I","family":"Cabrera-Silva","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary S.","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jael","family":"Miranda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuling","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Dame","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shrinivas","family":"Bishu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason R","family":"Spence","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer C","family":"Brazil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin","family":"Colacino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asma","family":"Nusrat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles A","family":"Parkos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025112004251000000_2025.11.17.688458v1.1","doi-asserted-by":"publisher","DOI":"10.1111\/febs.13771"},{"issue":"2","key":"2025112004251000000_2025.11.17.688458v1.2","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1007\/s10620-024-08803-0","article-title":"Trends in Mortality Due to Inflammatory Bowel Disease in the United States: A CDC WONDER Database Analysis (1999-2020)","volume":"70","year":"2025","journal-title":"Dig Dis Sci"},{"key":"2025112004251000000_2025.11.17.688458v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nrgastro.2015.150"},{"issue":"1","key":"2025112004251000000_2025.11.17.688458v1.4","doi-asserted-by":"crossref","first-page":"26142","DOI":"10.1038\/s41598-024-75947-4","article-title":"Single-cell transcriptomics of rectal organoids from individuals with perianal fistulizing Crohn\u2019s disease reveals patient-specific signatures","volume":"14","year":"2024","journal-title":"Sci Rep"},{"key":"2025112004251000000_2025.11.17.688458v1.5","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.physiol.010908.163145"},{"key":"2025112004251000000_2025.11.17.688458v1.6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0078128"},{"key":"2025112004251000000_2025.11.17.688458v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/mi.2015.123"},{"key":"2025112004251000000_2025.11.17.688458v1.8","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.02297"},{"key":"2025112004251000000_2025.11.17.688458v1.9","doi-asserted-by":"crossref","unstructured":"Macias-Ceja DC , Coll S , Bauset C , Seco-Cervera M , Gisbert-Ferrandiz L , Navarro F , et al. 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