DataSheet1_Identification of Hub Genes and Pathways Associated With Idiopathic Pulmonary Fibrosis via Bioinformatics Analysis.docx

Idiopathic pulmonary fibrosis (IPF) is a progressive disease whose etiology remains unknown. The purpose of this study was to explore hub genes and pathways related to IPF development and prognosis. Multiple gene expression datasets were downloaded from the Gene Expression Omnibus database. Weighted correlation network analysis (WGCNA) was performed and differentially expressed genes (DEGs) identified to investigate Hub modules and genes correlated with IPF. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein-protein interaction (PPI) network analysis were performed on selected key genes. In the PPI network and cytoHubba plugin, 11 hub genes were identified, including ASPN, CDH2, COL1A1, COL1A2, COL3A1, COL14A1, CTSK, MMP1, MMP7, POSTN, and SPP1. Correlation between hub genes was displayed and validated. Expression levels of hub genes were verified using quantitative real-time PCR (qRT-PCR). Dysregulated expression of these genes and their crosstalk might impact the development of IPF through modulating IPF-related biological processes and signaling pathways. Among these genes, expression levels of COL1A1, COL3A1, CTSK, MMP1, MMP7, POSTN, and SPP1 were positively correlated with IPF prognosis. The present study provides further insights into individualized treatment and prognosis for IPF.

特发性肺纤维化（Idiopathic Pulmonary Fibrosis, IPF）是一种病因尚未明确的进行性肺部疾病。本研究旨在探索与IPF发生发展及预后相关的核心基因与信号通路。研究团队从基因表达汇编（Gene Expression Omnibus, GEO）数据库下载了多组基因表达数据集，通过加权基因共表达网络分析（Weighted Correlation Network Analysis, WGCNA）筛选差异表达基因（Differentially Expressed Genes, DEGs），以挖掘与IPF相关的核心模块及核心基因。随后对筛选得到的关键基因开展基因本体（Gene Ontology, GO）富集分析、京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析，以及蛋白质相互作用（Protein-Protein Interaction, PPI）网络分析。借助PPI网络与cytoHubba插件，共鉴定出11个核心基因，分别为ASPN、CDH2、COL1A1、COL1A2、COL3A1、COL14A1、CTSK、MMP1、MMP7、POSTN及SPP1。研究对这些核心基因的表达相关性进行了展示与验证，并通过实时定量聚合酶链反应（quantitative Real-Time PCR, qRT-PCR）验证了核心基因的表达水平。结果显示，这些基因的表达失调及其相互作用可能通过调控IPF相关生物学过程与信号通路影响IPF的发生发展。其中，COL1A1、COL3A1、CTSK、MMP1、MMP7、POSTN及SPP1的表达水平与IPF预后呈正相关。本研究为IPF的个体化治疗与预后评估提供了进一步的理论见解。