{"doi":"10.1101/2025.11.17.688458","title":"RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells","abstract":"Abstract Ulcerative colitis (UC) is characterized by chronic mucosal inflammation, recurrent epithelial injury, and impaired colonic mucosal wound healing. While WNT/β-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 β-catenin levels in 3D colonoids and restored VIL1 expression and junctional β-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. Graphical Abstract summary Single-nucleus RNA and ATAC sequencing of UC patient-derived colonoids reveals a RUNX2-associated WNT signature in active inflammation. Elevated β-catenin and reduced OLFM4 and VIL1 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":581618,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9499,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":392730,"name":"Zachary Wilson","orcid":"0000-0003-1482-7757","position":1,"is_corresponding":false},{"id":1058796,"name":"Jael Miranda","orcid":"0000-0003-0122-5132","position":2,"is_corresponding":false},{"id":931731,"name":"Shuling Fan","orcid":"0000-0001-8315-0124","position":3,"is_corresponding":false},{"id":473265,"name":"Michael K. Dame","orcid":"0000-0003-3760-1654","position":4,"is_corresponding":false},{"id":109668,"name":"Shrinivas Bishu","orcid":"0000-0003-4823-5805","position":5,"is_corresponding":false},{"id":28520,"name":"Jason R. Spence","orcid":"0000-0001-7869-3992","position":6,"is_corresponding":false},{"id":109663,"name":"Jennifer Brazil","orcid":"0000-0002-5013-5291","position":7,"is_corresponding":false},{"id":324124,"name":"Justin A. Colacino","orcid":"0000-0002-5882-4569","position":8,"is_corresponding":false},{"id":109671,"name":"Asma Nusrat","orcid":"0000-0002-8954-3188","position":9,"is_corresponding":false},{"id":297250,"name":"Charles A. Parkos","orcid":"0000-0002-2490-7657","position":10,"is_corresponding":false},{"id":1227846,"name":"Rodolfo Ismael Cabrera-Silva","orcid":null,"position":0,"is_corresponding":true}],"reference_count":58,"raw_metadata":null,"created_at":"2026-07-19T02:58:51.328454Z","pmid":"41332536","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}