{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T17:54:14Z","timestamp":1789062854149,"version":"build-2803163510"},"reference-count":66,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2024,11,29]],"date-time":"2024-11-29T00:00:00Z","timestamp":1732838400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Demonstration Pilot Project of Traditional Chinese Medicine Inheritance and Innovation in Pudong New District shanghai-Flagship Community Health Service Centre for Integrative Chinese and Western Medicine","award":["YC-2023-0408"],"award-info":[{"award-number":["YC-2023-0408"]}]},{"name":"Demonstration Pilot Project of Traditional Chinese Medicine Inheritance and Innovation in Pudong New District shanghai-Flagship Community Health Service Centre for Integrative Chinese and Western Medicine","award":["CSC202308310088"],"award-info":[{"award-number":["CSC202308310088"]}]},{"name":"Demonstration Pilot Project of Traditional Chinese Medicine Inheritance and Innovation in Pudong New District shanghai-Flagship Community Health Service Centre for Integrative Chinese and Western Medicine","award":["CSC202108440109"],"award-info":[{"award-number":["CSC202108440109"]}]},{"name":"Demonstration Pilot Project of Traditional Chinese Medicine Inheritance and Innovation in Pudong New District shanghai-Flagship Community Health Service Centre for Integrative Chinese and Western Medicine","award":["Pudong New District Health Committee"],"award-info":[{"award-number":["Pudong New District Health Committee"]}]},{"DOI":"10.13039\/501100004543","name":"Chinese Scholarship Council","doi-asserted-by":"publisher","award":["YC-2023-0408"],"award-info":[{"award-number":["YC-2023-0408"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004543","name":"Chinese Scholarship Council","doi-asserted-by":"publisher","award":["CSC202308310088"],"award-info":[{"award-number":["CSC202308310088"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004543","name":"Chinese Scholarship Council","doi-asserted-by":"publisher","award":["CSC202108440109"],"award-info":[{"award-number":["CSC202108440109"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004543","name":"Chinese Scholarship Council","doi-asserted-by":"publisher","award":["Pudong New District Health Committee"],"award-info":[{"award-number":["Pudong New District Health Committee"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai, Pudong New District Health Committee","award":["YC-2023-0408"],"award-info":[{"award-number":["YC-2023-0408"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai, Pudong New District Health Committee","award":["CSC202308310088"],"award-info":[{"award-number":["CSC202308310088"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai, Pudong New District Health Committee","award":["CSC202108440109"],"award-info":[{"award-number":["CSC202108440109"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai, Pudong New District Health Committee","award":["Pudong New District Health Committee"],"award-info":[{"award-number":["Pudong New District Health Committee"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai","award":["YC-2023-0408"],"award-info":[{"award-number":["YC-2023-0408"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai","award":["CSC202308310088"],"award-info":[{"award-number":["CSC202308310088"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai","award":["CSC202108440109"],"award-info":[{"award-number":["CSC202108440109"]}]},{"name":"2024 High-level Talent Mentor Teaching Young Talents Project of Shanghai","award":["Pudong New District Health Committee"],"award-info":[{"award-number":["Pudong New District Health Committee"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) with a relapsing nature and complex etiology. Bioinformatics analysis has been widely applied to investigate various diseases. This study aimed to identify crucial differentially expressed genes (DEGs) and explore potential therapeutic agents for UC. Methods: The GSE47908 and GSE55306 colon tissue transcriptome gene datasets were downloaded from the Gene Expression Omnibus-NCBI (GEO) database. GEO2R and Gene Set Enrichment Analysis (GSEA) were used to screen for DEGs in patients with UC compared to the normal population based on weighted gene co-expression network analysis (WGCNA). GO-BP analysis and KEGG enrichment analysis were performed on the intersecting differential genes via the Metascape website, while hub genes were analyzed by STRING11.0 and Cytoscape3.7.1. The expression of hub genes was verified in the dataset GSE38713 colon tissue specimens. Finally, the gene expression profiles of the validation set were analyzed by immuno-infiltration through the ImmuCellAI online tool, and the CMap database was used to screen for negatively correlated small molecule compounds. Results: A total of 595 and 926 genes were screened by analysis of GSE47908 and GSE55306 datasets, respectively. Combined WGCNA hub module intersection yielded 12 hub genes (CXCL8, IL1\u03b2, CXCL1, CCL20, CXCL2, CXCR2, LCN2, SELL, AGT, LILRB3, MMP3, IDO1) associated with the pathogenesis of UC. GSEA analysis yielded intersecting pathways for both datasets (colorectal cancer pathway, base excision repair, cell cycle, apoptosis). GO-BP and KEGG enrichment analyses were performed to obtain key biological processes (inflammatory response, response to bacteria, leukocyte activation involved in the immune response, leukocyte\u2013cell adhesion, apoptosis, positive regulation of immune effector processes) and key signaling pathways (cytokine\u2013cytokine receptor interactions, IBD, NOD-like receptor signaling pathways). The immune cell infiltration analysis suggested that the incidence of UC was mainly related to the increase in CD4+T cells, depletion of T cells, T follicular helper cells, natural killer cells, \u03b3\u03b4 T cells and the decrease in CD8 naive T cells, helper T cells 17 and effector T cells. The CMap database results showed that small molecule compounds such as vorinostat, roxarsone, and wortmannin may be therapeutic candidates for UC. Conclusions: This study not only aids in early prediction and prevention but also provides novel insights into the pathogenesis and treatment of UC.<\/jats:p>","DOI":"10.3390\/genes15121548","type":"journal-article","created":{"date-parts":[[2024,11,29]],"date-time":"2024-11-29T05:02:22Z","timestamp":1732856542000},"page":"1548","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Exploring Immune Cell Infiltration and Small Molecule Compounds for Ulcerative Colitis Treatment"],"prefix":"10.3390","volume":"15","author":[{"given":"Yi","family":"Lu","sequence":"first","affiliation":[{"name":"Shanghai Tufeng Pharmaceutical Technology Co., Ltd., Shanghai 201203, China"},{"name":"Jiangsu Kanion Pharmaceutical Co., Ltd., Lianyungang 222001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongqing","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Traditional Chinese Medicine, Beicai Community Health Service Center of Pudong New District, 271 Lianyuan Road, Pudong New District, Shanghai 201024, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3362-072X","authenticated-orcid":false,"given":"Chujie","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Personalized Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands"},{"name":"The M-Lab., Department of Precision Medicine, GROW\u2014Research Institute for Oncology and Repro-Duction, Maastricht University, 6200 MD Maastricht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2114-8672","authenticated-orcid":false,"given":"Luping","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2686","DOI":"10.1038\/s41467-019-10387-7","article-title":"Mass cytometry reveals systemic and local immune signatures that distinguish inflammatory bowel diseases","volume":"10","author":"Rubin","year":"2019","journal-title":"Nat. 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