生物信息学筛选相关肺纤维化诊断的生物标志物研究

doi:10.3877/cma.j.issn.1674-6902.2025.04.007

目的

急性呼吸窘迫综合征(acute respiratory distress syndrome, ARDS)相关肺纤维化(pulmonary fibrosis, PF)目前缺乏应用于临床的诊断生物标志物，本文应用转录组学寻找ARDS中的肺纤维化相关基因并探索ARDS-PF的诊断生物标志物。

方法

联合分析GEO数据库中ARDS-PF转录组数据集GSE190496和特发性肺纤维化转录组数据集GSE10667获得共有差异表达基因(differentially expressed genes, DEGs)，通过基因本体论(Gene Ontology, GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)数据库对DEGs进行功能富集分析、STRING数据库构建DEGs的蛋白质-蛋白质相互作用网络(protein-protein interaction, PPI)、cytoscape软件cytoHubba插件筛选核心基因，在ARDS-PF转录组数据集GSE206788中验证，绘制核心基因的受试者工作特征(receiver operating characteristic, ROC)曲线并计算曲线下面积(area under the curve, AUC)。

结果

筛选出234个共有DEGs，上调DEGs有132个，下调DEGs有102个。GO和KEGG富集显示这些基因主要参与胶原蛋白生成、细胞外基质胶原沉积、细胞外基质受体互作、局灶黏附、PI3K-Akt通路等生物过程和途径。STRING构建PPI网络并利用cytoscape筛选出的10个核心基因为COL1A1、COL1A2、COL3A1、COL5A2、CXCL12、IGF1、MMP2、SPP1、PTGS2和THBS2，其中9个核心基因在GSE206788中差异表达显著(P<0.05)，ROC曲线显示COL1A1、COL1A2、COL3A1、CXCL12、IGF1、SPP1和PTGS2的AUC值≥0.9(P<0.01)。

结论

COL1A1、COL1A2、COL3A1、CXCL12、IGF1、SPP1和PTGS2可能是潜在的ARDS-PF诊断生物标志物。

关键词: 急性呼吸窘迫综合征, 肺纤维化, 转录组学, 生物标志物

Objective

Currently, there is a lack of clinically applicable diagnostic biomarkers for pulmonary fibrosis (PF) associated with acute respiratory distress syndrome (ARDS). This study aimed to identify PF-related genes in ARDS through transcriptomic analysis and explore potential diagnostic biomarkers for ARDS-associated pulmonary fibrosis (ARDS-PF).

Methods

Transcriptomic datasets GSE190496 (ARDS-PF) and GSE10667 (idiopathic pulmonary fibrosis) were jointly analyzed from the GEO database to identify common differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the functions of DEGs. A protein-protein interaction (PPI) network was constructed using the STRING database, and key hub genes were identified with the cytoHubba plugin in Cytoscape. The identified hub genes were validated in the ARDS-PF transcriptomic dataset GSE206788. Receiver operating characteristic (ROC) curves were generated, and the area under the curve (AUC) was calculated to evaluate the diagnostic performance of the hub genes.

Results

A total of 234 common DEGs were identified, including 132 upregulated and 102 downregulated genes. GO and KEGG enrichment analyses revealed that these genes were mainly involved in biological processes and pathways such as collagen formation, extracellular matrix (ECM) collagen deposition, ECM-receptor interaction, focal adhesion, and the PI3K-Akt signaling pathway. The PPI network constructed via STRING and analyzed with Cytoscape identified 10 hub genes: COL1A1, COL1A2, COL3A1, COL5A2, CXCL12, IGF1, MMP2, SPP1, PTGS2, and THBS2. Among them, 9 hub genes were significantly differentially expressed in GSE206788 (P<0.05). ROC curve analysis showed that COL1A1, COL1A2, COL3A1, CXCL12, IGF1, SPP1, and PTGS2 had AUC≥0.9 (P<0.01).

Conclusion

COL1A1, COL1A2, COL3A1, CXCL12, IGF1, SPP1, and PTGS2 may serve as potential diagnostic biomarkers for ARDS-PF.

Key words: Acute respiratory distress syndrome, Pulmonary fibrosis, Transcriptomics, Biomarker

图1 GSE190496和GSE10667共有DEGs筛选。图A为GSE190496数据集DEGs火山图，上调DEGs1253个，下调DEGs1000个；图B为GSE10667数据集DEGs火山图，上调DEGs844个，下调DEGs405个；图C为GSE190496和GSE10667两个数据集共有DEGs的韦恩图，红色区域代表GSE190496中特有的2 019个DEGs，蓝色区域代表GSE10667中特有的1 015个DEGs，阴影部分代表共有的234个DEGs。深红色原点：上调DEGs；深蓝色原点：下调DEGs；浅红色和浅蓝色原点：差异倍数小于1的基因；灰色原点：无差异表达基因；X轴：差异倍数取log₂后数值；Y轴：P值取－log₁₀后数值

图2 共有DEGs的GO和KEGG富集分析。图A为GO功能富集的前30条结果绘制的条形图，柱子的长度代表该条目中对应DEGs的数量，Y轴代表P值取－log₁₀后数值；图B为KEGG富集分析的前20条通路绘制的气泡图，气泡的大小表示该通路中差异基因的数量，气泡颜色代表P值注：BP为生物过程；CC为细胞组分；MF为分子功能；CellP.(Cellular Processes)为细胞过程；EnvIP.(Environmental Information Processing)为环境信息处理；HumaD.(Human Diseases)为人类疾病；Metab.(Metabolism)为代谢；OrgaS.(Organismal Systems)为生物系统

图3 GSE206788的DEGs和GO和KEGG富集。图A为DEGs火山图，上调DEGs有160个，下调DEGs有121个，深红色原点代表上调DEGs，深蓝色原点代表下调DEGs，方框中的基因为GSE206788中包含的核心基因，X轴：差异倍数取log₂后数值；Y轴：P值取－log₁₀后数值；图B为DEGs的GO功能富集的前30条，柱子的长度代表该条目中对应DEGs的数量，Y轴代表P值取－log₁₀后数值；图C为DEGs的KEGG通路富集的前20条，气泡的大小表示该通路中差异基因的数量，气泡颜色代表P值注：BP为生物过程；CC为细胞组分；MF为分子功能；CellP.(Cellular Processes)为细胞过程；EnvIP.(Environmental Information Processing)为环境信息处理；HumaD.(Human Diseases)为人类疾病；Metab.(Metabolism)为代谢；OrgaS.(Organismal Systems)为生物系统

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Identification of diagnostic biomarkers for acute respiratory distress syndrome-related pulmonary fibrosis based on boinformatics

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Identification of diagnostic biomarkers for acute respiratory distress syndrome-related pulmonary fibrosis based on boinformatics