Suppr超能文献

基于生物信息学的方法鉴定溃疡性结肠炎的枢纽基因和免疫浸润

Identification of hub genes and immune infiltration in ulcerative colitis using bioinformatics.

机构信息

Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, 362000, Fujian, People's Republic of China.

Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, People's Republic of China.

出版信息

Sci Rep. 2023 Apr 13;13(1):6039. doi: 10.1038/s41598-023-33292-y.

Abstract

Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine, whose pathogenesis is not fully understood. Given that immune infiltration plays a key role in UC progression, our study aimed to assess the level of immune cells in UC intestinal mucosal tissues and identify potential immune-related genes. The GSE65114 UC dataset was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between healthy and UC tissues were identified using the "limma" package in R, while their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined with the clusterProfiler package. Protein-protein interaction network analysis and visualization were performed with STRING and Cytoscape. Immune cell infiltration was calculated with CIBERSORT. The relationship between hub genes and immune-infiltrated cells in UC was determined by Pearson correlation. A total of 206 DEGs were identified, of which 174 were upregulated and 32 downregulated. GO and KEGG functional classification indicated DEG enrichment in immune response pathways, including Toll-like receptor signaling, IL-17 signaling, and immune system process and chemokine signaling. 13 hub genes were identified. Infiltration matrix analysis of immune cells showed abundant plasma cells, memory B cells, resting CD4 memory T cells, γδ T cells, M0 and M1 macrophages, and neutrophils in UC intestinal tissues. Correlation analysis revealed 13 hub genes associated with immune-infiltrated cells in UC. 13 hub genes associated with immune-infiltrated cells in UC were identified; they included CXCL13, CXCL10, CXCL9, CXCL8, CCL19, CTLA4, CCR1, CD69, CD163, IL7R, PECAM1, TLR8 and TLR2. These genes could potentially serve as markers for the diagnosis and treatment of UC.

摘要

溃疡性结肠炎(UC)是一种慢性肠道炎症性疾病,其发病机制尚未完全阐明。鉴于免疫浸润在 UC 进展中起着关键作用,我们的研究旨在评估 UC 肠黏膜组织中的免疫细胞水平,并鉴定潜在的免疫相关基因。从基因表达综合数据库(GEO)中下载 UC 的数据集 GSE65114。使用 R 中的“limma”包鉴定健康组织和 UC 组织之间的差异表达基因(DEGs),并用 clusterProfiler 包确定其基因本体论(GO)和京都基因与基因组百科全书(KEGG)途径。使用 STRING 和 Cytoscape 进行蛋白质-蛋白质相互作用网络分析和可视化。使用 CIBERSORT 计算免疫细胞浸润。通过 Pearson 相关性确定 UC 中枢纽基因与浸润免疫细胞之间的关系。共鉴定出 206 个 DEGs,其中 174 个上调,32 个下调。GO 和 KEGG 功能分类表明 DEG 富集在免疫反应途径,包括 Toll 样受体信号、IL-17 信号、免疫系统过程和趋化因子信号。鉴定出 13 个枢纽基因。免疫细胞浸润基质分析显示 UC 肠组织中存在丰富的浆细胞、记忆 B 细胞、静止 CD4 记忆 T 细胞、γδ T 细胞、M0 和 M1 巨噬细胞和嗜中性粒细胞。相关性分析显示 UC 中 13 个与浸润免疫细胞相关的枢纽基因。鉴定出与 UC 浸润免疫细胞相关的 13 个枢纽基因;它们包括 CXCL13、CXCL10、CXCL9、CXCL8、CCL19、CTLA4、CCR1、CD69、CD163、IL7R、PECAM1、TLR8 和 TLR2。这些基因可能可作为 UC 诊断和治疗的标志物。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ed4/10101977/89cf9e01a7ff/41598_2023_33292_Fig1_HTML.jpg

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验