通过WGCNA和DEG确定并验证GPC4和VCAN作为原发性双侧大结节肾上腺增生的枢纽基因

Identifying and Validating GPC4 and VCAN as Hub Genes in Primary Bilateral Macronodular Adrenal Hyperplasia by WGCNA and DEG

摘要: 目的：通过生信分析筛选原发性双侧大结节肾上腺增生的核心基因，探索疾病治疗的新靶点。方法：本研究从基因表达数据库(Gene Expression Omnibus, GEO) (http://www.ncbi.nlm.nih.gov/geo)检索并下载了与原发性双侧大结节肾上腺增生相关的转录组测序数据和表达谱数据集GSE171558。我们筛选了差异表达基因(Differentially Expressed Genes, DEGs)，并对该数据集进行了加权基因共表达网络分析(Weighted Gene Co-Expression Network Analysis, WGCNA)。对蓝色模块基因进行了基因本体论(Gene Ontology, GO)、京都基因和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)通路富集分析和基因集富集分析(Gene Set Enrichment Analysis, GSEA)。根据差异表达基因进行了蛋白质–蛋白质相互作用网络(Protein-Protein Interaction Network, PPI)。我们选择了蓝色模块中的中枢基因和PPI中的枢纽基因的重叠基因作为PBMAH的最终中枢基因。并且我们在GSE25031数据集中验证了最终枢纽基因。结果：蓝色基因模块(677个基因)主要富集在脂质代谢领域，与PBMAH具有最高的相关系数。通过差异分析，我们筛选出487个DEGs，其中包括231个上调基因和256个下调基因。蛋白质–蛋白质相互作用网络分析鉴定出30个中枢基因。GPC4和VCAN被确定为PBMAH的最终中枢基因。与正常对照组相比，GPC4在PBMAH组中的表达显著下调，而VCAN与正常组相比显著上调。GSEA数据分析显示，VCAN与PI3K-Akt信号通路、磷脂酶D信号通路、Rap1信号通路、Ras信号通路、MAPK信号通路等相关联。GPC4与癌症相关通路、Rap1信号通路、PI3K-Akt信号通路、Wnt信号通路等相关。GSE25031的原始数据验证了分析结果。结论：基于生物信息学分析初步筛选出GPC4和VCAN可能参与PBMAH的致病和发展。为进一步研究原发性双侧大结节肾上腺增生的诊断及治疗提供了新的方向。

Abstract: Objective: To identify hub genes in primary bilateral macronodular adrenal hyperplasia (PBMAH) through bioinformatics analysis and explore novel targets for disease treatment. Methods: This study searched and downloaded the transcriptome sequencing data and expression profile dataset GSE171558 related to primary bilateral adrenal macronodular hyperplasia from the gene expres-sion omnibus, GEO, http://www.ncbi.nlm.nih.gov/geo). We filtered the differentially expressed genes (DEGs) and performed weighted gene coexpression network analysis (WGCNA) on this da-taset. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment Analysis and Gene Set Enrichment Analysis (GSEA) were performed for the blue module genes. Protein-protein interaction network (PPI) analysis was performed based on the differentially ex-pressed gene. We selected the overlapping genes of the hub gene in the blue gene module and the hub gene in PPI as the final hub gene of PBMAH. And we verified the final hub gene in the GSE25031 dataset. Results: The blue gene model (677 genes) is mainly enriched in lipid metabolism, with the highest correlation coefficient with PBMAH. Through differential analysis, we screened out 487 DEGs, including 231 up-regulated genes and 256 down-regulated genes. PPI analysis identified 30 hub genes. GPC4 and VCAN were identified as the final hub genes of PBMAH. The raw data of GSE25031 verified the analysis results. The expression of GPC4 was significantly down-regulated in the PBMAH group compared with the normal control group, and VCAN was up-regulated considera-bly compared with the normal group. Analysis of GSEA data showed that VCAN was connected to PI3K-Akt signalling pathway, Phospholipase D signalling pathway, Rap1 signalling route, Ras sig-nalling pathway, MAPK signalling pathway, etc. GPC4 was associated to cancer-related Pathways, Rap1 signalling pathway, PI3K-Akt signalling pathway, Wnt signalling pathway, etc. Conclusions: Based on bioinformatics analysis, GPC4 and VCAN have been initially identified as potential players in the pathogenesis and development of PBMAH. This provides a new direction for further research on the diagnosis and treatment of primary bilateral macronodular adrenal hyperplasia.