肾透明细胞癌进展枢纽基因的WGCNA筛选
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摘要
目的通过加权基因共表达网络分析(WGCNA)识别肾透明细胞癌发生及进展过程中的枢纽基因。方法从基因表达综合数据库下载GSE73731数据,通过WGCNA筛选枢纽基因,分析枢纽基因的表达水平及其与肿瘤分级、分期、预后的关系,使用GEPIA数据库和UALCAN数据库进行验证,并对枢纽模块基因进行GO和KEGG富集分析。结果通过构建共表达网络,确定green模块(包括355个基因)为枢纽模块,进一步筛选得到CEP55、CCNB1、NUF2、BUB1B、KIF14共5个枢纽基因。各枢纽基因与肾透明细胞癌组织学分级密切相关(t=17.53～25.18,P<0.01),且BUB1B基因对低级别与高级别肾透明细胞癌具有较高的诊断价值(AUC=0.706,P<0.01)。GEPIA和UALCAN数据库验证结果显示,各枢纽基因与肿瘤的分级及分期相关,且CEP55、BUB1B高表达与肿瘤的总生存期及无病生存期较差明显相关。基因功能富集分析结果显示,枢纽模块基因主要富集在细胞周期生物学过程及通路上。结论本研究通过构建基因共表达网络筛选出5个枢纽基因,这5个基因与肿瘤的分期分级及预后密切相关;枢纽基因可能通过细胞周期相关通路来影响肾透明细胞癌的发生、进展及预后。
Objective To identify the hub genes associated with the development and progression of clear cell renal cell carcinoma(ccRCC) using weighted gene co-expression network analysis(WGCNA). Methods The dataset GSE73731 was downloaded from Gene Expression Omnibus database. Besides, the hub genes were identified using WGCNA. The correlations between the expression levels of the hub genes and tumor grade, stage, and prognosis were analyzed, and then were validated using GEPIA and UALCAN databases. Moreover, gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analyses were performed for the genes in hub module. Results Through constructing the co-expression network, green module(involving 355 genes) was identified as the hub module. Afterwards, five hub genes(CEP55, CCNB1, NUF2, BUB1B, and KIF14) were further screened out. All the hub genes showed close correlations with the histological grade of ccRCC(t=17.53-25.18,P<0.01), and BUB1B exhibited high diagnostic values for low-grade and high-grade ccRCCs(AUC=0.706,P<0.01). The validation results of GEPIA and UALCAN databases showed that all the hub genes were associated with tumor grade and stage, and increased CEP55 and BUB1B were significantly related to poor overall survival and disease-free survival. Enrichment analysis showed that the genes in green module were mainly involved in the biological processes and pathways related to cell cycle. Conclusion Five hub genes were identified by WGCNA, which were associated with tumor grade, stage, and prognosis. These hub genes might affect the development, progression, and prognosis of ccRCC through cell cycle-associated pathways.
Objective To identify the hub genes associated with the development and progression of clear cell renal cell carcinoma(ccRCC) using weighted gene co-expression network analysis(WGCNA). Methods The dataset GSE73731 was downloaded from Gene Expression Omnibus database. Besides, the hub genes were identified using WGCNA. The correlations between the expression levels of the hub genes and tumor grade, stage, and prognosis were analyzed, and then were validated using GEPIA and UALCAN databases. Moreover, gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analyses were performed for the genes in hub module. Results Through constructing the co-expression network, green module(involving 355 genes) was identified as the hub module. Afterwards, five hub genes(CEP55, CCNB1, NUF2, BUB1B, and KIF14) were further screened out. All the hub genes showed close correlations with the histological grade of ccRCC(t=17.53-25.18,P<0.01), and BUB1B exhibited high diagnostic values for low-grade and high-grade ccRCCs(AUC=0.706,P<0.01). The validation results of GEPIA and UALCAN databases showed that all the hub genes were associated with tumor grade and stage, and increased CEP55 and BUB1B were significantly related to poor overall survival and disease-free survival. Enrichment analysis showed that the genes in green module were mainly involved in the biological processes and pathways related to cell cycle. Conclusion Five hub genes were identified by WGCNA, which were associated with tumor grade, stage, and prognosis. These hub genes might affect the development, progression, and prognosis of ccRCC through cell cycle-associated pathways.
引文
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[22] PAN Xiuwu,CHEN Lu,HONG Yi,et al.EIF3D silencing suppresses renal cell carcinoma tumorigenesis via inducing G2/M arrest through downregulation of Cyclin B1/CDK1 signaling[J].International Journal of Oncology,2016,48(6):2580-2590.
[23] XU Leilei,XIA Chao,SHENG Fei,et al.CEP55 promotes the proliferation and invasion of tumour cells via the AKT signalling pathway in osteosarcoma[J].Carcinogenesis,2018,39(4):623-631.
[24] ZHAO W M,SEKI A,FANG G W.Cep55,a microtubule-bundling protein,associates with centralspindlin to control the midbody integrity and cell abscission during cytokinesis[J].Molecular Biology of the Cell,2006,17(9):3881-3896.
[25] LIU Qiang,DAI Shejiao,LI Hong,et al.Silencing of NUF2 inhibits tumor growth and induces apoptosis in human hepatocellular carcinomas[J].Asian Pacific Journal of Cancer Prevention,2014,15(20):8623-8629.
[26] YANG Ye,GU Chunyan,LUO Chen,et al.BUB1B promotes multiple myeloma cell proliferation through CDC20/CCNB axis[J].Medical Oncology,2015,32(3):81.
[27] XU H,CHOE C,SHIN S H,et al.Silencing of KIF14 interferes with cell cycle progression and cytokinesis by blocking the p27Kip1 ubiquitination pathway in hepatocellular carcinoma[J].Experimental & Molecular Medicinee,2014,46(5):e97.
[28] HUANG S K,QIAN J X,YUAN B Q,et al.SiRNA-mediated knockdown against NUF2 suppresses tumor growth and induces cell apoptosis in human glioma cells[J].Cellular and Molecular Biology,2014,60(4):30-36.
[2] ZNAOR A,LORTET-TIEULENT J,LAVERSANNE M A,et al.International variations and trends in renal cell carcinoma incidence and mortality[J].European Urology,2015,67(3):519-530.
[3] SCELO G,LAROSE T L.Epidemiology and risk factors for kidney cancer[J].Journal of Clinical Oncology,2018,36:3574-3581.
[4] LJUNGBERG B,BENSALAH K,CANFIELD S,et al.EAU guidelines on renal cell carcinoma:2014 update[J].European Urology,2015,67(5):913-924.
[5] GAUTIER L,COPE L,BOLSTAD B M,et al.Affy—analysis of affymetrix GeneChip data at the probe level[J].Bioinformatics,2004,20(3):307-315.
[6] RITCHIE M E,PHIPSON B,WU D,et al.Limma powers differential expression analyses for RNA-sequencing and microarray studies[J].Nucleic Acids Research,2015,43(7):e47.
[7] LANGFELDER P,HORVATH S.WGCNA:an R package for weighted correlation network analysis[J].BMC Bioinforma-tics,2008,9:559.
[8] JEFFERY J,SINHA D,SRIHARI S,et al.Beyond cytokinesis:the emerging roles of CEP55 in tumorigenesis[J].Oncogene,2016,35(6):683-690.
[9] ZHANG Weijing,NIU Chunhao,HE Weiling,et al.Upregulation of centrosomal protein 55 is associated with unfavorable prognosis and tumor invasion in epithelial ovarian carcinoma[J].Tumor Biology,2016,37(5):6239-6254.
[10] CHENG W Y,YANG T H,ANASTASSIOU D.Biomolecular events in cancer revealed by attractor metagenes[J].PLoS Computational Biology,2013,9(2):e1002920.
[11] FANG Yifeng,YU Hong,LIANG Xiao,et al.Chk1-induced CCNB1 overexpression promotes cell proliferation and tumor growth in human colorectal cancer[J].Cancer Biology & Therapy,2014,15(9):1268-1279.
[12] PFAFF K L,KING R W.Determinants of human cyclin B1 association with mitotic chromosomes[J].PLoS One,2013,8(3):e59169.
[13] WANG Z,SLIPICEVIC A,FORSUND M,et al.Expression of CDK1(Tyr15),pCDK1(Thr161),cyclin B1(total)and pCyclin B1(Ser126)in vulvar squamous cell carcinoma and their relations with clinicopatological features and prognosis[J].PLoS One,2015,10(4):e0121398.
[14] 郭云韬,喻超,陈礼闻,等.siRNA干扰沉默NUF2基因对肝癌HCCLM3细胞迁移和侵袭的影响[J].贵州医科大学学报,2017,42(2):147-150.
[15] FU H L,SHAO L.Silencing of NUF2 inhibits proliferation of human osteosarcoma Saos-2 cells[J].European Review for Medical and Pharmacological Sciences,2016,20(6):1071-1079.
[16] HU Peng,SHANGGUAN Jianying,ZHANG Leida.Downregulation of NUF2 inhibits tumor growth and induces apoptosis by regulating lncRNA AF339813[J].International Journal of Clinical and Experimental Pathology,2015,8(3):2638-2648.
[17] MA Qing,LIU Yanmei,SHANG Liang,et al.The FOXM1/BUB1B signaling pathway is essential for the tumorigenicity and radioresistance of glioblastoma[J].Oncology Reports,2017,38(6):3367-3375.
[18] FU Xin,CHEN Guo,CAI Zhiduan,et al.Overexpression of BUB1B contributes to progression of prostate cancer and predicts poor outcome in patients with prostate cancer[J].Onco Targets and Therapy,2016,9(Issue 1):2211-2220.
[19] ZHANG Yixiang,YUAN Yeqing,LIANG Pei,et al.Overexpression of a novel candidate oncogene KIF14 correlates with tumor progression and poor prognosis in prostate cancer[J].Oncotarget,2017,8(28):45459-45469.
[20] LI K K,QI Y,XIA T,et al.The kinesin KIF14 is overexpressed in medulloblastoma and downregulation of KIF14 suppressed tumor proliferation and induced apoptosis[J].Laboratory Investigation,2017,97(8):946-961.
[21] QIU H L,DENG S Z,LI C,et al.High expression of KIF14 is associated with poor prognosis in patients with epithelial ovarian cancer[J].European Review for Medical and Pharmacological Sciences,2017,21(2):239-245.
[22] PAN Xiuwu,CHEN Lu,HONG Yi,et al.EIF3D silencing suppresses renal cell carcinoma tumorigenesis via inducing G2/M arrest through downregulation of Cyclin B1/CDK1 signaling[J].International Journal of Oncology,2016,48(6):2580-2590.
[23] XU Leilei,XIA Chao,SHENG Fei,et al.CEP55 promotes the proliferation and invasion of tumour cells via the AKT signalling pathway in osteosarcoma[J].Carcinogenesis,2018,39(4):623-631.
[24] ZHAO W M,SEKI A,FANG G W.Cep55,a microtubule-bundling protein,associates with centralspindlin to control the midbody integrity and cell abscission during cytokinesis[J].Molecular Biology of the Cell,2006,17(9):3881-3896.
[25] LIU Qiang,DAI Shejiao,LI Hong,et al.Silencing of NUF2 inhibits tumor growth and induces apoptosis in human hepatocellular carcinomas[J].Asian Pacific Journal of Cancer Prevention,2014,15(20):8623-8629.
[26] YANG Ye,GU Chunyan,LUO Chen,et al.BUB1B promotes multiple myeloma cell proliferation through CDC20/CCNB axis[J].Medical Oncology,2015,32(3):81.
[27] XU H,CHOE C,SHIN S H,et al.Silencing of KIF14 interferes with cell cycle progression and cytokinesis by blocking the p27Kip1 ubiquitination pathway in hepatocellular carcinoma[J].Experimental & Molecular Medicinee,2014,46(5):e97.
[28] HUANG S K,QIAN J X,YUAN B Q,et al.SiRNA-mediated knockdown against NUF2 suppresses tumor growth and induces cell apoptosis in human glioma cells[J].Cellular and Molecular Biology,2014,60(4):30-36.