胃癌基因表达谱芯片差异基因的生物信息学分析

doi:10.3969/j.issn.1004-616x.2019.04.007

摘要/Abstract

摘要： 目的：筛选胃癌发生发展过程中的关键基因和信号通路，为寻找有价值的胃癌分子标志物提供依据。方法：从GEO数据库下载5个胃癌基因芯片数据集：GSE35809、GSE54129、GSE79973、GSE66229和GSE51105。合并5个数据集中的样本，去除数据集间的批次效应，对合并后的基因表达数据进行标准化，并通过主成分分析监测数据标准化情况。利用R语言中的limma包筛选胃癌组织和正常组织中表达差异的基因。利用DAVID数据库对胃癌发生发展过程中的差异基因进行功能富集分析，并通过STRING数据库和Cytoscape分析差异基因编码蛋白之间的相互作用网络并进行可视化。结果：总共筛选出1 205个差异基因，包括480个上调基因，725个下调基因。差异基因的生物学功能主要富集于细胞-细胞信号传导、炎症反应的调节、细胞粘附、细胞凋亡和离子的跨膜转运。KEGG信号通路分析显示差异基因主要富集于p53信号通路、PI3K-Akt信号通路、NF-κB信号通路。通过构建蛋白质相互作用网络筛选出了CENPE、KIF15、MELK、KIF2C、CENPF、KIF11、NUSAP1、UBE2C、TTK、AURKB、DLGAP5、TOP2A等29个Hub基因。结论：通过合并不同数据集，利用生物信息学方法筛选出胃癌发生发展过程中的关键基因和信号通路，为胃癌的诊疗提供新的候选标志物。

关键词: 胃癌, 生物信息学分析, 差异表达基因, 基因芯片

Abstract: OBJECTIVE:To screen the key genes and signal pathways in the development of gastric cancer and to provide the basis for finding valuable molecular markers of gastric cancer. METHODS:Five gastric cancer gene chip datasets were downloaded from the GEO database:GSE35809,GSE54129,GSE79973,GSE66229,and GSE51105. The samples in the five data sets were combined,the batch effect between the data sets was removed,the combined gene expression data was normalized,and the data standardization was monitored by principal component analysis. The limma package in the R language was used to screen for differentially expressed genes in gastric cancer tissues and normal tissues. The DAVID database was used to analyze the differential genes in the development of gastric cancer,and the interaction network between the differentially encoded proteins was analyzed and visualized by STRING database and Cytoscape. RESULTS:A total of 1205 differential genes were screened,including 480 up-regulated genes and 725 down-regulated genes. The biological functions of differential genes are mainly enriched in cell-cell signaling,regulation of inflammatory responses,cell adhesion,apoptosis,and transmembrane transport of ions. Analysis of KEGG signaling pathway revealed that differential genes are mainly enriched in the p53,PI3K-Akt and NF-κB signaling pathways. The 29 Hub genes such as CENPE,KIF15,MELK,KIF2C,CENPF,KIF11,NUSAP1,UBE2C,TTK,AURKB,DLGAP5,TOP2A were screened by constructing a protein interaction network. CONCLUSION:By combining different data sets,key genes and signal pathways for the development of gastric cancer were screened by bioinformatics method,providing new research targets for the diagnosis and treatment of gastric cancer.

Key words: gastric cancer, bioinformatics analysis, differentially expressed genes, gene chip

中图分类号:

R730.2

曾蕾, 徐雪莲, 罗曼曼, 张凡, 韩志坚, 李玉民. 胃癌基因表达谱芯片差异基因的生物信息学分析[J]. 癌变·畸变·突变, 2019, 31(4): 300-307.

ZENG Lei, XU Xuelian, LUO Manman, ZHANG Fan, HAN Zhijian, LI Yumin. Bioinformatics analyses of differential genes in gastric cancer gene expression profiles[J]. Carcinogenesis, Teratogenesis & Mutagenesis, 2019, 31(4): 300-307.

参考文献

[1] KARIMI P, ISLAMI F, ANANDASABAPATHY S, et al. Gastric cancer:descriptive epidemiology, risk factors, screening, and prevention[J]. Cancer Epidemiol Biomarkers Prev, 2014, 23(5):700-713.
[2] WAGNER A D, UNVERZAGT S, GROTHE W, et al. Chemotherapy for advanced gastric cancer[J]. Cochrane Database Syst Rev, 2010(3):CD004064.
[3] VAN CUTSEM E, SAGAERT X, TOPAL B, et al. Gastric cancer[J]. Lancet, 2016, 388(10060):2654-2664.
[4] JIANG L, YANG K H, GUAN Q L, et al. Survival benefit of neoadjuvant chemotherapy for resectable cancer of the gastric and gastroesophageal junction:a meta-analysis[J]. J Clin Gastroenterol, 2015, 49(5):387-394.
[5] GASTRIC (Global Advanced/Adjuvant Stomach Tumor Research International Collaboration) Group, PAOLETTI X, OBA K, et al. Benefit of adjuvant chemotherapy for resectable gastric cancer:a meta-analysis[J]. JAMA, 2010, 303(17):1729-1737.
[6] PFEIFER S P. From next-generation resequencing reads to a high-quality variant data set[J]. Heredity (Edinb), 2017, 118(2):111-124.
[7] HUANG D W, SHERMAN B T, LEMPICKI R A. Bioinformat-ics enrichment tools:paths toward the comprehensive functional analysis of large gene lists[J]. Nucleic Acids Res, 2009, 37(1):1-13.
[8] KIM Y H, KIM N G, LIM J G, et al. Chromosomal alterations in paired gastric adenomas and carcinomas[J]. Am J Pathol, 2001, 158(2):655-662.
[9] MELATO M, SIDARI L, RIZZARDI C, et al. Gastric epithelium proliferation in early Hp⁺ and Hp^- gastritis:a flow cytometry study[J]. Anticancer Res, 2001, 21(2B):1347-1353.
[10] OKI E, HISAMATSU Y, ANDO K, et al. Clinical aspect and molecular mechanism of DNA aneuploidy in gastric cancers[J]. J Gastroenterol, 2012, 47(4):351-358.
[11] THOMA C R, TOSO A, MERALDI P, et al. Mechanisms of aneuploidy and its suppression by tumour suppressor proteins[J]. Swiss Med Wkly, 2011, 141:w13170.
[12] SAEKI H, KITAO H, YOSHINAGA K, et al. Copy-neutral loss of heterozygosity at the p53 locus in carcinogenesis of esophageal squamous cell carcinomas associated with p53 mutations[J]. Clin Cancer Res, 2011, 17(7):1731-1740.
[13] KIM H S, PARK K H, KIM S A, et al. Frequent mutations of human Mad2, but not Bub1, in gastric cancers cause defective mitotic spindle checkpoint[J]. Mutat Res, 2005, 578(1/2):187-201.
[14] GRABSCH H, TAKENO S, PARSONS W J, et al. Overexpression of the mitotic checkpoint genes BUB1, BUBR1, and BUB3 in gastric cancer:association with tumour cell proliferation[J]. J Pathol, 2003, 200(1):16-22.
[15] PACHATHUNDIKANDI S K, MüLLER A, BACKERT S. Inflammasome activation by Helicobacter pylori and its implications for persistence and immunity[J]. Curr Top Microbiol Immunol, 2016, 397:117-131.
[16] YUASA Y. Control of gut differentiation and intestinal-type gastric carcinogenesis[J]. Nat Rev Cancer, 2003, 3(8):592-600.
[17] YU F, TIAN T, DENG B, et al. Multi-marker analysis of genomic annotation on gastric cancer GWAS data from Chinese populations[J]. Gastric Cancer, 2019, 22(1):60-68.
[18] BRUNER H C, DERKSEN P W B. Loss of E-cadherin-dependent cell-cell adhesion and the development and progression of cancer[J]. Cold Spring Harb Perspect Biol, 2018, 10(3):a029330.
[19] OUYANG J, PAN X H, LIN H, et al. GKN2 increases apoptosis, reduces the proliferation and invasion ability of gastric cancer cells through down-regulating the JAK/STAT signaling pathway[J]. Am J Transl Res, 2017, 9(2):803-811.
[20] 张扬, 熊建波, 陈和平, 等. PTEN/PI3K/AKT信号通路在胃癌中的研究进展[J]. 重庆医学, 2018, 47(19):2601-2603, 2607.
[21] 李燕雪, 夏蕾, 刘清华, 等. NF-κB p50和NF-κB p65在胃癌组织中的表达及临床意义[J]. 徐州医科大学学报, 2018, 38(4):211-216.
[22] HUANG Y X, ZHANG J, WANG G, et al. Oxymatrine exhibits anti-tumor activity in gastric cancer through inhibition of IL-21R-mediated JAK2/STAT3 pathway[J]. Int J Immunopathol Pharmacol, 2018, 32:2058738418781634.
[23] VOS S M, TRETTER E M, SCHMIDT B H, et al. All tangled up:how cells direct, manage and exploit topoisomerase function[J]. Nat Rev Mol Cell Biol, 2011, 12(12):827-841.
[24] TERASHIMA M, ICHIKAWA W, OCHIAI A, et al. TOP2A, GGH, and PECAM1 are associated with hematogenous, lymph node, and peritoneal recurrence in stage Ⅱ/Ⅲ gastric cancer patients enrolled in the ACTS-GC study[J]. Oncotarget, 2017, 8(34):57574-57582.
[25] LAZARIS A C, KAVANTZAS N G, ZORZOS H S, et al. Markers of drug resistance in relapsing colon cancer[J]. J Cancer Res Clin Oncol, 2002, 128(2):114-118.
[26] LAN J, HUANG H Y, LEE S W, et al. TOP2A overexpression as a poor prognostic factor in patients with nasopharyngeal carcinoma[J]. Tumour Biol, 2014, 35(1):179-187.
[27] COSTA M J, HANSEN C L, HOLDEN J A, et al. Topoisomerase Ⅱ alpha:prognostic predictor and cell cycle marker in surface epithelial neoplasms of the ovary and peritoneum[J]. Int J Gynecol Pathol, 2000, 19(3):248-257.
[28] NICOLAU-NETO P, PALUMBO A, DE MARTINO M, et al. UBE2C is a transcriptional target of the cell cycle regulator FOXM1[J]. Genes (Basel), 2018, 9(4):E188.
[29] ZHANG J, LIU X Y, YU G Z, et al. UBE2C is a potential biomarker of intestinal-type gastric cancer with chromosomal instability[J]. Front Pharmacol, 2018, 9:847.
[30] LI S, LI Z Y, GUO T, et al. Maternal embryonic leucine zipper kinase serves as a poor prognosis marker and therapeutic target in gastric cancer[J]. Oncotarget, 2016, 7(5):6266-6280.
[31] DU T, QU Y, LI J F, et al. Maternal embryonic leucine zipper kinase enhances gastric cancer progression via the FAK/Paxillin pathway[J]. Mol Cancer, 2014, 13:100.
[32] WIMAN K G, ZHIVOTOVSKY B. Understanding cell cycle and cell death regulation provides novel weapons against human diseases[J]. J Intern Med, 2017, 281(5):483-495.
[33] ZHANG H P, LI S Y, WANG J P, et al. Clinical significance and biological roles of cyclins in gastric cancer[J]. Onco Targets Ther, 2018, 11:6673-6685.
[34] ZHONG Z H, CAO Y D, YANG S, et al. Overexpression of RRM2 in gastric cancer cell promotes their invasiveness via AKT/NF-κB signaling pathway[J]. Pharmazie, 2016, 71(5):280-284.
[35] TOMⅡ C, INOKUCHI M, TAKAGI Y, et al. TPX2 expression is associated with poor survival in gastric cancer[J]. World J Surg Onc, 2017, 15:14.
[36] TAO J Q, ZHI X F, TIAN Y, et al. CEP55 contributes to human gastric carcinoma by regulating cell proliferation[J]. Tumour Biol, 2014, 35(5):4389-4399.
[37] OHASHI T, KOMATSU S, ICHIKAWA D, et al. Overexpression of PBK/TOPK relates to tumour malignant potential and poor outcome of gastric carcinoma[J]. Br J Cancer, 2017, 116(2):218-226.
[38] BARGIELA-IPARRAGUIRRE J, PRADO-MARCHAL L, PAJUELO-LOZANO N, et al. Mad2 and BubR1 modulates tumourigenesis and paclitaxel response in MKN45 gastric cancer cells[J]. Cell Cycle, 2014, 13(22):3590-3601.