通过生物信息学分析鉴定克罗恩病中的免疫细胞浸润和有效诊断生物标志物。
Identifying immune cell infiltration and effective diagnostic biomarkers in Crohn's disease by bioinformatics analysis.
机构信息
Key Laboratory of Acupuncture and Immunological Effects, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
出版信息
Front Immunol. 2023 Aug 9;14:1162473. doi: 10.3389/fimmu.2023.1162473. eCollection 2023.
BACKGROUND
Crohn's disease (CD) has an increasing incidence and prevalence worldwide. It is currently believed that both the onset and progression of the disease are closely related to immune system imbalance and the infiltration of immune cells. The aim of this study was to investigate the molecular immune mechanisms associated with CD and its fibrosis through bioinformatics analysis.
METHODS
Three datasets from the Gene Expression Omnibus data base (GEO) were downloaded for data analysis and validation. Single sample gene enrichment analysis (ssGSEA) was used to evaluate the infiltration of immune cells in CD samples. Immune cell types with significant differences were identified by Wilcoxon test and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. Differentially expressed genes (DEGs) were screened and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional correlation analysis, as well as protein-protein interaction (PPI) network analysis. The cytoHubba program and the GSE75214 dataset were used to screen for hub genes and plot Receiver operating characteristic (ROC)curves to screen for possible biomarkers of CD based on diagnostic efficacy. The hub genes of CD were correlated with five significantly different immune cells. In addition, validation was performed by real time quantitative PCR (RT-qPCR) experiments in colonic tissue of CD intestinal fibrosis rats to further identify hub genes that are more related to CD intestinal fibrosis.
RESULTS
The DEGs were analyzed separately by 10 algorithms and narrowed down to 9 DEGs after taking the intersection. 4 hub genes were further screened by the GSE75214 validation set, namely COL1A1, CXCL10, MMP2 and FGF2. COL1A1 has the highest specificity and sensitivity for the diagnosis of CD and is considered to have the potential to diagnose CD. Five immune cells with significant differences were screened between CD and health controls (HC). Through the correlation analysis between five kinds of immune cells and four biomarkers, it was found that CXCL10 was positively correlated with activated dendritic cells, effector memory CD8 T cells. MMP2 was positively correlated with activated dendritic cells, gamma delta T cells (γδ T) and mast cells. MMP2 and COL1A1 were significantly increased in colon tissue of CD fibrosis rats.
CONCLUSION
MMP2, COL1A1, CXCL10 and FGF2 can be used as hub genes for CD. Among them, COL1A1 can be used as a biomarker for the diagnosis of CD. MMP2 and CXCL10 may be involved in the development and progression of CD by regulating activated dendritic cell, effector memory CD8 T cell, γδ T cell and mast cell. In addition, MMP2 and COL1A1 may be more closely related to CD intestinal fibrosis.
背景
克罗恩病（CD）的发病率和患病率在全球范围内呈上升趋势。目前认为，疾病的发病和进展都与免疫系统失衡和免疫细胞浸润密切相关。本研究旨在通过生物信息学分析探讨与 CD 及其纤维化相关的分子免疫机制。
方法
从基因表达综合数据库（GEO）下载了 3 个数据集进行数据分析和验证。使用单样本基因富集分析（ssGSEA）评估 CD 样本中免疫细胞的浸润情况。通过 Wilcoxon 检验和最小绝对收缩和选择算子（LASSO）回归分析鉴定差异浸润的免疫细胞类型。筛选差异表达基因（DEGs），并进行基因本体（GO）和京都基因与基因组百科全书（KEGG）功能关联分析以及蛋白质-蛋白质相互作用（PPI）网络分析。利用 cytoHubba 程序和 GSE75214 数据集筛选枢纽基因，并绘制受试者工作特征（ROC）曲线，根据诊断效果筛选 CD 的可能生物标志物。分析 CD 的枢纽基因与 5 种差异显著的免疫细胞的相关性。此外，通过 CD 肠纤维化大鼠结肠组织的实时定量 PCR（RT-qPCR）实验进行验证，进一步鉴定与 CD 肠纤维化更相关的枢纽基因。
结果
通过 10 种算法分别对 DEGs 进行分析，取交集后缩小到 9 个 DEGs。通过 GSE75214 验证集进一步筛选出 4 个枢纽基因，即 COL1A1、CXCL10、MMP2 和 FGF2。COL1A1 对 CD 的诊断具有最高的特异性和灵敏度，被认为具有诊断 CD 的潜力。在 CD 与健康对照（HC）之间筛选出 5 种差异显著的免疫细胞。通过五种免疫细胞与四个生物标志物之间的相关性分析，发现 CXCL10 与活化树突状细胞、效应记忆 CD8 T 细胞呈正相关。MMP2 与活化树突状细胞、γδ T 细胞和肥大细胞呈正相关。MMP2 和 COL1A1 在 CD 纤维化大鼠结肠组织中明显增加。
结论
MMP2、COL1A1、CXCL10 和 FGF2 可用作 CD 的枢纽基因。其中，COL1A1 可作为 CD 诊断的生物标志物。MMP2 和 CXCL10 可能通过调节活化树突状细胞、效应记忆 CD8 T 细胞、γδ T 细胞和肥大细胞参与 CD 的发生和发展。此外，MMP2 和 COL1A1 可能与 CD 肠纤维化更为密切相关。
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