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No. 1"],"award-info":[{"award-number":["2021. No. 1"]}]},{"name":"Xingdian Talent Support Program-Youth Talent Special Project","award":["2023. No. 166"],"award-info":[{"award-number":["2023. No. 166"]}]},{"name":"Yunnan Provincial Science and Technology Department - Yunnan University of Traditional Chinese Medicine Joint special Project","award":["202201AG070192"],"award-info":[{"award-number":["202201AG070192"]}]},{"DOI":"10.13039\/501100005147","name":"Applied Basic Research Key Project of Yunnan","doi-asserted-by":"publisher","award":["202501AS070155"],"award-info":[{"award-number":["202501AS070155"]}],"id":[{"id":"10.13039\/501100005147","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Yunnan University of Chinese Medicine Joint Fund Project","award":["XYLH2025001"],"award-info":[{"award-number":["XYLH2025001"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Mitophagy\u2019s role in ulcerative colitis (UC) is not fully understood. This study explores mitophagy\u2019s impact on UC and aims to create a diagnostic model. The transcriptomic datasets of patients with UC and healthy controls were obtained from the Gene Expression Omnibus database. The mitophagy-related differentially expressed genes (MRDEGs) and hub genes were identified by weighted gene co-expression network and protein-protein interaction (PPI) network analysis. Networks of mRNA-miRNA and mRNA-TF were established to detect pertinent mechanisms. CIBERSORT was used to evaluate association between immune cells with hub genes. A diagnostic model was developed utilizing logistic regression. Single-cell RNA sequencing was used to characterize the expression of hub genes in specific cell clusters and the results of the differential analysis were annotated with the hub genes identified in the logistic model. Finally, a mice model of colitis was established, and the results were verified using qRT-PCR and western blot. The study identified 28 MRDEGs and 20 hub genes. A significant link was found between immune cell infiltration and hub genes, highlighting mitophagy\u2019s interaction with the immune response. A diagnostic model with 13 potential markers was developed, achieving high accuracy. Single-cell RNA sequencing delineated key cell types and confirmed varied hub gene expression, with validation through RT-qPCR and western blot. These findings not only deepens our understanding of mitochondrial autophagy in UC but also establishe a robust diagnostic model through interdisciplinary approaches, laying the groundwork for the development of targeted diagnostic and therapeutic strategies that warrant further research for clinical application.<\/jats:p>","DOI":"10.1371\/journal.pone.0346974","type":"journal-article","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T17:33:25Z","timestamp":1776706405000},"page":"e0346974","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated RNA-seq and scRNA-seq to explore the biological mechanisms of mitophagy-related genes in ulcerative colitis"],"prefix":"10.1371","volume":"21","author":[{"given":"Jianguo","family":"Ma","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rongyi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunfei","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junli","family":"Shao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7880-7790","authenticated-orcid":true,"given":"Yan","family":"Qi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,4,20]]},"reference":[{"key":"pone.0346974.ref001","article-title":"British Society of Gastroenterology consensus guidelines on the management of inflammatory bowel disease in adults","volume":"68","author":"CA Lamb","year":"2019","journal-title":"Gut"},{"issue":"4","key":"pone.0346974.ref002","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.gtc.2020.07.005","article-title":"Epidemiology and Pathogenesis of Ulcerative Colitis","volume":"49","author":"L Du","year":"2020","journal-title":"Gastroenterol Clin North Am"},{"issue":"5","key":"pone.0346974.ref003","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1016\/j.dld.2020.02.006","article-title":"Does mucosal inflammation drive recurrence of primary sclerosing cholangitis in liver transplantion recipients with ulcerative colitis?","volume":"52","author":"N Dekkers","year":"2020","journal-title":"Dig Liver Dis"},{"issue":"13","key":"pone.0346974.ref004","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.3390\/cells12131779","article-title":"Autophagy in Crohn\u2019s Disease: Converging on Dysfunctional Innate Immunity","volume":"12","author":"KM Alula","year":"2023","journal-title":"Cells"},{"issue":"7","key":"pone.0346974.ref005","doi-asserted-by":"crossref","first-page":"954","DOI":"10.3390\/biom15070954","article-title":"Postbiotics as Mitochondrial Modulators in Inflammatory Bowel Disease: Mechanistic Insights and Therapeutic Potential","volume":"15","author":"SK Prajapati","year":"2025","journal-title":"Biomolecules"},{"issue":"11","key":"pone.0346974.ref006","doi-asserted-by":"crossref","first-page":"4258","DOI":"10.7150\/ijbs.97263","article-title":"The PI3K\/Akt-Nrf2 Signaling Pathway and Mitophagy Synergistically Mediate Hydroxytyrosol to Alleviate Intestinal Oxidative Damage","volume":"20","author":"X Wen","year":"2024","journal-title":"Int J Biol Sci"},{"key":"pone.0346974.ref007","doi-asserted-by":"crossref","unstructured":"Ramos GP, Papadakis KA. 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