南方医科大学学报

南方医科大学学报 ›› 2021, Vol. 41 ›› Issue (11): 1631-1640.doi: 10.12122/j.issn.1673-4254.2021.11.06

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加权基因共表达网络挖掘并验证调控前列腺癌转移的枢纽基因

张河元，陈南辉，王晓红，高白云，凌木安，陈 果，吴志明，李宇同，钟伟枫，潘 斌   

  1. 广东省梅州市人民医院泌尿外科，广东 梅州 514021；南方医科大学南方医院泌尿外科，广东 广州 510515； 南方医科大学第三附属医院肾内科，广东 广州 510630；暨南大学附属第一医院泌尿外科，广东 广州 510630；广州市第十二人民医院泌尿外科，广东 广州 510630；中山大学肿瘤防治中心泌尿外科，广东 广州 510060
  • 出版日期:2021-11-20 发布日期:2021-12-10

Identification and validation of hub genes in prostate cancer progression based on weighted gene co-expression network analysis

ZHANG Heyuan, CHEN Nanhui, WANG Xiaohong, GAO Baiyun, LING Muan, CHEN Guo, WU Zhiming, LI Yutong, ZHONG Weifeng, PAN Bin   

  • Online:2021-11-20 Published:2021-12-10

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摘要： 目的 通过加权基因共表达网络分析（WGCNA）挖掘并验证前列腺癌转移的关键枢纽基因。方法 对前列腺癌全基因组芯片GSE6919进行主成分分析（PCA），通过R语言分析差异表达基因（DEGs）；利用WGCNA构建基因共表达网络并筛选关键基因；在 TCGA 公共数据中分析基因表达量及其与患者预后的关系；设计和验证针对转移相关的关键基因HNRNPA2B1的小分子干扰片段，通过MTT、流式细胞术、克隆形成、Transwell等实验验证其对前列腺癌细胞系生长、凋亡、克隆形成、迁移和侵袭的影响。结果 PCA分析显示癌转移组和原位及癌旁组明显分开聚类，基因表达差异显著。WGCNA分析得到与癌转移组密切相关的模块，与干细胞分化、氨基酸代谢及免疫反应密切相关。进一步筛选得到与前列腺癌发生相关的（BDH1、PAK4、EXTL3）和转移相关的（NKTR、CTBP2、HNRNPA2B1）6个枢纽基因，在TCGA数据库中有表达差异，且与患者的总生存期相关。Western blotting结果显示HNRNPA2B1小分子干扰成功；干扰片段转染PC3及LNCap细胞，MTT实验结果显示沉默HNRNPA2B1可抑制前列腺癌细胞的生长，流式细胞术结果显示沉默HNRNPA2B1可诱导细胞凋亡，克隆形成实验显示沉默HNRNPA2B1可抑制其克隆形成，Transwell实验显示沉默HNRNPA2B1显著抑制前列腺癌细胞的迁移和侵袭（P<0.05）。结论 发现前列腺癌发生相关的BDH1、PAK4、EXTL3和转移相关的NKTR、CTBP2、HNRNPA2B1 6个枢纽基因，为前列腺癌调控机制的研究提供了新思路。

关键词: 前列腺癌；转移；加权基因共表达网络分析；枢纽基因；TCGA

Abstract: Objective To identify the key hub genes in prostate cancer metastasis based on weighted gene co-expression network analysis (WGCNA) and verify the identified genes. Methods Whole-genome chip data GSE6919 of prostate cancer study were analyzed using principal component analysis (PCA), and the differentially expressed genes (DEGs) were analyzed using R software. WGCNA was performed to construct a gene co-expression network for screening the key genes. TCGA database was used to explore the expressions of the DEGs and their association with the prognosis. To validate the results, we designed siRNA fragments targeting the metastasis-related gene HNRNPA2B1, and observed its effect on growth, apoptosis, clone formation, migration and invasion of prostate cancer cell lines using MTT assay, flow cytometry, clone formation assay, and Transwell assay. Results PCA analysis showed obvious clustering of significant DEGs in metastatic cancer group. The modules obtained by WGCNA analysis in metastasis group involved stem cell differentiation, amino acid metabolism and immune response. Further screening of the genes identified 3 genes related with prostate cancer occurrence (BDH1, PAK4 and EXTL3) and another 3 with prostate cancer metastasis (NKTR, CTBP2 and HNRNPA2B1), which were shown to have differential expressions in TCGA database and were correlated with the patient's overall survival. In the cell experiment, PC3 and LNCap cells transfected with the siRNA fragment targeting HNRNPA2B1 showed obvious growth inhibition with increased cell apoptosis, lowered clone formation ability, and suppressed capacities for migration and invasion. Conclusion We identified 3 hub genes related with the occurrence (BDH1, PAK4 and EXTL3) and another 3 with metastasis of prostate cancer (NKTR, CTBP2 and HNRNPA2B1) using WGCNA, which provides a new approach for studying the regulatory mechanisms of prostate cancer.

Key words: prostate cancer; metastasis; weighted gene co-expression network analysis; hub gene; TCGA