基于GEO和TCGA数据筛选和鉴定食管鳞状细胞癌关键枢纽基因

doi:10.3969/j.issn.1671-7171.2021.05.006

Abstract
Figure/Table
References (0)
Related Citation (15)

Download: PDF (1981 KB) HTML (1 KB)
Export: BibTeX | EndNote (RIS)

Abstract 【Objective】 To screen and identify the key pivotal genes of ESCC by bioinformatics methods based on transcriptome data of ESCC from geo and TCGA databases.【Methods】 GSE17351 dataset and RNA-seq data of ESCC were downloaded from GEO and TCGA databases. Then Limma package of R software was applied to screen differentially expressed genes; ClusterProfiler package was used to perform GO analysis and KEGG Pathway enrichment; STRING tool was used to analyze the interaction network among proteins encoded by differential genes and the interactome was visualized by Cytoscape software; Cytoscape's Cytohubba plug-in was subjected to analyze key hub genes among interactome; The prognostic values of hub genes were analyzed by K-M plotter. 【Results】 A total of 167 differentially expressed genes were screened by GEO and TCGA; The differentially expressed genes were mainly related to GO processes such as mitosis, ATPase activity and DNA helicase activity, and were significantly enriched in DNA cell cycle, DNA replication, mismatch repair, oocyte meiosis, ECM receptor interaction, p53 and Wnt signaling pathways; A total of 10 key genes were screened, including BUB1,MAD2L1,NUF2,KIF18A,CENPK,CENPN,CENPQ and SPC25,which were negatively correlated with the prognosis of patients with ESCC.【Conclusion】 Ten key pivotal genes of ESCC were screened, and eight of them were related to prognosis, which provided potential targets for molecular mechanism research and prognosis judgment of ESCC.

Key words： Carcinoma, Squamous Cell Esophageal Neoplasms Gene Expression Regulation, Neoplastic Genetic Techniques

Received: 28 April 2021

PACS:

R735.1

	Service

	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	LIU Rong
	HUANG Wei
	WANG Lei

Cite this article:

LIU Rong,HUANG Wei,WANG Lei. Screening and Identifying the Hub Genes in Esophageal Squamous Cell Carcinoma Based on GEO and TCGA Data[J]. JOURNAL OF CLINICAL RESEARCH, 2021, 38(5): 659-663.

URL:

http://journal07.magtech.org.cn/yxlcyj/EN/10.3969/j.issn.1671-7171.2021.05.006 OR http://journal07.magtech.org.cn/yxlcyj/EN/Y2021/V38/I5/659

[1] REICHENBACH Z W, MURRAY M G, SAXENA R, et al. Clinical and translational advances in esophageal squamous cell carcinoma[J].Adv Cancer Res,2019, 144:95-135.
[2] ABNET C C, ARNOLD M, WEI W Q. Epidemiology of esophageal squamous cell carcinoma [J].Gastroenterology,2018, 154(2):360-373.
[3] CODIPILLY D C, QIN Y, DAWSEY S M, et al. Screening for esophageal squamous cell carcinoma: Recent advances [J].Gastrointest Endosc,2018, 88(3):413-426.
[4] DAS T.Integration of online omics-data resources for cancer research [J].Front Genet,2020, 11:578345.
[5] 张卓.面向肿瘤精准医学的综合数据资源tcga及其相关在线分析工具推荐[J].中华医学图书情报杂志, 2018,27(3):5-9.
[6] BLUM A, WANG P, ZENKLUSEN J C. Snapshot: Tcga-analyzed tumors[J].Cell,2018, 173 (2): 530.
[7] EDGAR R, DOMRACHEV M, LASH A E. Gene expression omnibus: Ncbi gene expression and hybridization array data repository[J].Nucleic Acids Res,2002, 30 (1): 207-210.
[8] RITCHIE M E, PHIPSON B, WU D, et al. Limma powers differential expression analyses for rna-sequencing and microarray studies[J].Nucleic Acids Res,2015, 43 (7): e47.
[9] YU G, WANG L G, HAN Y, et al. Clusterprofiler: An r package for comparing biological themes among gene clusters [J].OMICS,2012, 16 (5): 284-287.
[10] SZKLARCZYK D, MORRIS J H, COOK H, et al. The string database in 2017: Quality-controlled protein-protein association networks, made broadly accessible [J].Nucleic Acids Res,2017, 45 (D1): D362-D368.
[11] SHANNON P, MARKIEL A, OZIER O, et al.Cytoscape: A software environment for integrated models of biomolecular interaction networks [J].Genome Res,2003, 13 (11): 2498-2504.
[12] CHIN C H, CHEN S H, WU H H, et al.Cytohubba: Identifying hub objects and sub-networks from complex interactome [J].BMC Syst Biol,2014, 8 Suppl 4 S11.
[13] 李小燕, 何杰, 余觅, 等.Bub1基因在胃癌组织中高表达:基于oncomine数据库及生物信息学方法[J].南方医科大学学报, 2020, 40(5):81-90.
[14] YANG W X, PAN Y Y, YOU C G, Cdk1,ccnb1,cdc20,bub1,mad2l1,mcm3,bub1b,mcm2,and rfc4 may be potential therapeutic targets for hepatocellular carcinoma using integrated bioinformatic analysis [J].Biomed Res Int,2019, 2019:1245072.
[15] ZHU L J, PAN Y, CHEN X Y, et al.Bub1 promotes proliferation of liver cancer cells by activating smad2 phosphorylation [J].Oncol Lett,2020, 19(5):3506-3512.
[16] PIAO J, ZHU L, SUN J, et al.High expression of cdk1 and bub1 predicts poor prognosis of pancreatic ductal adenocarcinoma [J].Gene,2019, 701:15-22.
[17] ZHU X F, YI M, HE J, et al. Pathological significance of mad2l1 in breast cancer: An immunohistochemical study and meta analysis [J].Int J Clin Exp Pathol,2017, 10 (9): 9190-9201.
[18] WANG Y, WANG F, HE J, et al. Mir-30a-3p targets mad2l1 and regulates proliferation of gastric cancer cells [J].Onco Targets Ther,2019, 12:11313-11324.
[19] LV S, XU W, ZHANG Y, et al. Nuf2 as an anticancer therapeutic target and prognostic factor in breast cancer[J].Int J Oncol,2020, 57 (6): 1358-1367.
[20] XU W, WANG Y, WANG Y, et al.Screening of differentially expressed genes and identification of nuf2 as a prognostic marker in breast cancer [J].Int J Mol Med,2019, 44 (2): 390-404.
[21] ZHAI X, YANG Z, LIU X, et al.Identification of nuf2 and fam83d as potential biomarkers in triple-negative breast cancer [J].PeerJ,2020, 8:e9975.
[22] 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].Cell Mol Biol (Noisy-le-grand),2014, 60 (4): 30-36.
[23] HU P, CHEN X, SUN J, et al. Sirna-mediated knockdown against nuf2 suppresses pancreatic cancer proliferation in vitro and in vivo [J].Biosci Rep,2015, 35(1):e00170.
[24] LIU Q, DAI S J, LI H, et al.Silencing of nuf2 inhibits tumor growth and induces apoptosis in human hepatocellular carcinomas [J].Asian Pac J Cancer Prev,2014, 15 (20): 8623-8629.
[25] XIE X, LIN J, FAN X, et al.Lncrna cdkn2b-as1 stabilized by igf2bp3 drives the malignancy of renal clear cell carcinoma through epigenetically activating nuf2 transcription [J].Cell Death Dis,2021, 12 (2): 201.
[26] ZHANG H, SHEN T, ZHANG Z, et al. Expression of kif18a is associated with increased tumor stage and cell proliferation in prostate cancer [J].Med Sci Monit,2019, 25:6418-6428.
[27] 王立, 杨松, 孙若川, 等. 驱动蛋白超家族18a在胃癌组织中的表达及其与患者预后的关系 [J].中华胃肠外科杂志, 2016, (19): 585-589.
[28] ZHONG Y, JIANG L, LIN H, et al. Overexpression of kif18a promotes cell proliferation, inhibits apoptosis, and independently predicts unfavorable prognosis in lung adenocarcinoma [J].IUBMB Life,2019, 71 (7): 942-955.
[29] ALFARSI L H, ELANSARI R, TOSS M S, et al. Kinesin family member-18a (kif18a) is a predictive biomarker of poor benefit from endocrine therapy in early er+ breast cancer, [J].Breast Cancer Res Treat,2019, 173 (1): 93-102.
[30] ZHANG C, ZHU C, CHEN H, et al. Kif18a is involved in human breast carcinogenesis[J].Carcinogenesis,2010, 31 (9): 1676-1684.
[31] NAGAHARA M, NISHIDA N, IWATSUKI M, et al.Kinesin 18a expression: Clinical relevance to colorectal cancer progression [J].Int J Cancer,2011, 129 (11): 2543-2552.