骨肉瘤基因表达谱芯片的生物信息学分析
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摘要
目的应用生物信息学的方法对骨肉瘤(osteosarcoma,OS)基因表达谱芯片进行分析,从分子水平探讨OS的发病机制。方法从GEO数据库下载OS基因芯片数据集的原始数据,应用生物信息学方法筛选差异表达基因(differentially expressed genes,DEGs),并利用R语言enrichplot软件包对差异基因进行基因本体论(Gene ontology,GO)及通路富集(KEGG)分析,通过STRING在线软件、Cytoscape及其插件cytoHubba、Network Analyzer对OS的显著差异基因进行蛋白质-蛋白质相互作用网络分析(PPI分析),寻找关键(Hub)基因。结果共筛选出408个DEGs,其中包括274个上调基因和134个下调基因。对其进行生物信息学分析发现,SPP1、HLA-DPA1、MAFB、PRAME、RPS11、FOSL1、S100A2、PPID、DHRS2等基因及PI3K-Akt信号通路、趋化因子信号通路、Toll样受体信号通路、p53信号通路在OS的发生发展中起着重要作用。通过STRING分析发现,包括GINS2、RFC3、TRIP13等在内的10个基因处于核心节点位置。结论 CDC6、FEN1、OIP5、GINS2和RFC3可能在OS的发生发展中起重要作用,为研究OS的发病机制提供了新线索。
Objective To analyze the gene expression profile of osteosarcoma(OS) using bioinformatics methods and to explore the pathogenesis of OS from the molecular level.Methods The raw data of the OS microarray dataset was downloaded from the GEO database.Deferentially expressed genes(DEGs) were screened using bioinformatics methods.Gene Ontology(GO)analysis and pathway enrichment analysis(KEGG)was performed using the R language enrichplot package for differential genes.Through the STRING online software,Cytoscape and its plug-in cytoHubba,Network Analyzer,protein-protein interaction network analysis(PPI analysis)was performed for significant differential genes of OS,in order to seek the key(Hub) gene.Results A total of 408 DEGs were screened,including 274 up-regulated genes and 134 down-regulated genes.Bioinformatics analysis found that SPP1,HLA-DPA1,MAFB,PRAME,RPS11,FOSL1,S100 A2,PPID,DHRS2 and PI3 K-Akt signaling pathways,chemotactic factor signaling pathways,Toll-like receptor signaling pathways,p53 signaling played important roles in the development of OS.Through the STRING analysis,it was found that 10 genes including GINS2,RFC3,and TRIP13 were located at the core node position.Conclusion CDC6,FEN1,OIP5,GINS2 and RFC3 may play an important role in the development of OS and provide new clues for the study of the pathogenesis of OS.
Objective To analyze the gene expression profile of osteosarcoma(OS) using bioinformatics methods and to explore the pathogenesis of OS from the molecular level.Methods The raw data of the OS microarray dataset was downloaded from the GEO database.Deferentially expressed genes(DEGs) were screened using bioinformatics methods.Gene Ontology(GO)analysis and pathway enrichment analysis(KEGG)was performed using the R language enrichplot package for differential genes.Through the STRING online software,Cytoscape and its plug-in cytoHubba,Network Analyzer,protein-protein interaction network analysis(PPI analysis)was performed for significant differential genes of OS,in order to seek the key(Hub) gene.Results A total of 408 DEGs were screened,including 274 up-regulated genes and 134 down-regulated genes.Bioinformatics analysis found that SPP1,HLA-DPA1,MAFB,PRAME,RPS11,FOSL1,S100 A2,PPID,DHRS2 and PI3 K-Akt signaling pathways,chemotactic factor signaling pathways,Toll-like receptor signaling pathways,p53 signaling played important roles in the development of OS.Through the STRING analysis,it was found that 10 genes including GINS2,RFC3,and TRIP13 were located at the core node position.Conclusion CDC6,FEN1,OIP5,GINS2 and RFC3 may play an important role in the development of OS and provide new clues for the study of the pathogenesis of OS.
引文
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[35]Sato M,Girard L,Sekine I,et al.Increased expression and no mutation of the Flap endonuclease(FEN1)gene in human lung cancer[J].Oncogene,2003,22(46):7243-7246.
[36]Zhang K,Keymeulen S,Nelson R,et al.Overexpression of Flap endonuclease 1correlates with enhanced proliferation and poor prognosis of non-small-cell lung cancer[J].Am JPathol,2018,188(1):242-251.
[37]Jiang Z,Jiang J,Yang H,et al.Silencing of Aurora kinase Aby RNA interference inhibits tumor growth in human osteosarcoma cells by inducing apoptosis and G2/M cell cycle arrest[J].Onco Rep,2014,31(3):1249-1254.
[38]Wang M,Sun X,Yang Y,et al.Long non-coding RNA OIP5-AS1promotes proliferation of lung cancer cells and leads to poor prognosis by targeting miR-378a-3p[J].Thorac Cancer,2018,9(8):939-949.
[39]He J,Zhao Y,Zhao E,et al.Cancer-testis specific gene OIP5:a downstream gene of E2F1that promotes tumorigenesis and metastasis in glioblastoma by stabilizing E2F1signaling[J].Neuro Oncol,2018,20(9):1173-1184.
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[2]Gümbel D,Bekeschus S,Gelbrich N,et al.Cold atmospheric plasma in the treatment of osteosarcoma[J].Int J Mol Sci,2017,18(9).pii:E2004.doi:10.3390/ijms18092004.
[3]Xi L,Zhang Y,Kong S,et al.miR-34inhibits growth and promotes apoptosis of osteosarcoma in nude mice through targetly regulating TGIF2expression[J].Biosci Rep,2018,38(3).pii:BSR20180078.doi:10.1042/BSR20180078.
[4]Gosling L C C,Rushton A B.Identification of adult knee primary bone tumour symptom presentation:A qualitative study[J].Man Ther,2016,26:54-61.
[5]Gdowski A S,Ranjan A,Vishwanatha J K.Current concepts in bone metastasis,contemporary therapeutic strategies and ongoing clinical trials[J].J Exp Clin Cancer Res,2017,36(1):108.
[6]Fu Y,Yu W,Cai H,et al.Forecast of actin-binding proteins as the oncotarget in osteosarcoma-a review of mechanism,diagnosis and therapy[J].Onco Targets Ther,2018,11:1553-1561.
[7]Lin Y H,Jewell B E,Gingold J,et al.Osteosarcoma:molecular pathogenesis and iPSC modeling[J].Trends Mol Med,2017,23(8):737-755.
[8]Yang X,Zhu S,Li L,et al.Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis[J].Onco Targets Ther,2018,11:1457-1474.
[9]Chen F,Shen C,Wang X,et al.Identification of genes and pathways in nasopharyngeal carcinoma by bioinformatics analysis[J].Oncotarget,2017,8(38):63738-63749.
[10]Liu M,Xu Z,Du Z,et al.The identification of key genes and pathways in glioma by bioinformatics analysis[J].J Immunol Res,2017,2017:1278081.
[11]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.
[12]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.
[13]Du J,Yuan Z,Ma Z,et al.KEGG-PATH:Kyoto encyclopedia of genes and genomes-based pathway analysis using apath analysis model[J].Mol Biosyst,2014,10(9):2441-2447.
[14]Harris M A,Clark J,Ireland A,et al.The Gene Ontology(GO)database and informatics resource[J].Nucleic Acids Res,2004,32(Database issue):D258-D261.
[15]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.
[16]Szklarczyk D,Franceschini A,Kuhn M,et al.The STRINGdatabase in 2011:functional interaction networks of proteins,globally integrated and scored[J].Nucleic Acids Res,2011,39(Database issue):D561-D568.
[17]von Mering C,Huynen M,Jaeggi D,et al.STRING:a database of predicted functional associations between proteins[J].Nucleic Acids Res,2003,31(1):258-261.
[18]Kohl M,Wiese S,Warscheid B.Cytoscape:software for visualization and analysis of biological networks[J].Methods Mol Biol,2011,696:291-303.
[19]Mirabello L,Yeager M,Mai P L,et al.Germline TP53variants and susceptibility to osteosarcoma[J].J Natl Cancer Inst,2015,107(7).pii:djv101.doi:10.1093/jnci/djv101.
[20]Lussier D M,Johnson J L,Hingorani P,et al.Combination immunotherapy with alpha-CTLA-4and alpha-PD-L1antibody blockade prevents immune escape and leads to complete control of metastatic osteosarcoma[J].J Immunother Cancer,2015,3:21.
[21]任娟,徐叶峰,匡唐洪,等.104例骨肉瘤肺转移患者的预后及其影响因素[J].中华肿瘤杂志,2017,39(4):263-268.
[22]Ma S X,Bai Z F,Wang W,et al.Effects of microrna-93on mouse cardiac microvascular endothelial cells injury and inflammatory response by mediating SPP1through the NF-kappaB pathway[J].J Cell Biochem,2019,120(3):2847-2858.
[23]Ihn H J,Kim J A,Cho H S,et al.Diphlorethohydroxycarmalol from ishige okamurae suppresses osteoclast differentiation by downregulating the NF-kappaB signaling pathway[J].Int J Mol Sci,2017,18(12).pii:E2635.doi:10.3390/ijms18122635
[24]Ao R,Guan L,Wang Y,et al.Silencing of COL1A2,COL6A3,and THBS2inhibits gastric cancer cell proliferation,migration,and invasion while promoting apoptosis through the PI3K-Akt signaling pathway[J].J Cell Biochem,2018,119(6):4420-4434.
[25]Wang F,Wang N,Gao Y,et al.beta-Carotene suppresses osteoclastogenesis and bone resorption by suppressing NF-kappaB signaling pathway[J].Life Sci,2017,174:15-20.
[26]Hateboer G,Wobst A,Petersen B O,et al.Cell cycle-regulated expression of mammalian CDC6is dependent on E2F[J].Mol Cell Biol,1998,18(11):6679-6697.
[27]Komori H,Goto Y,Kurayoshi K,et al.Differential requirement for dimerization partner DP between E2F-dependent activation of tumor suppressor and growth-related genes[J].Sci Rep,2018,8(1):8438.
[28]Borlado L R,Mendez J.CDC6:from DNA replication to cell cycle checkpoints and oncogenesis[J].Carcinogenesis,2008,29(2):237-243.
[29]Feng D,Tu Z,Wu W,et al.Inhibiting the expression of DNAreplication-initiation proteins induces apoptosis in human cancer cells[J].Cancer Res,2003,63(21):7356-7364.
[30]Lee I,Kim G S,Bae J S,et al.The DNA replication protein Cdc6inhibits the microtubule-organizing activity of the centrosome[J].J Biol Chem,2017,292(39):16267-16276.
[31]Ohta S,Koide M,Tokuyama T,et al.CDC6expression as a marker of proliferative activity in brain tumors[J].Onco Rep,2001,8(5):1063-1066.
[32]Kucherlapati M,Yang K,Kuraguchi M,et al.Haploinsufficiency of Flap endonuclease(Fen1)leads to rapid tumor progression[J].Proc Natl Acad Sci U S A,2002,99(15):9924-9929.
[33]Finger L D,Atack J M,Tsutakawa S,et al.The wonders of flap endonucleases:structure,function,mechanism and regulation[J].Subcell Biochem,2012,62:301-326.
[34]Lam J S,Seligson D B,Yu H,et al.Flap endonuclease 1is overexpressed in prostate cancer and is associated with a high Gleason score[J].BJU Int,2006,98(2):445-451.
[35]Sato M,Girard L,Sekine I,et al.Increased expression and no mutation of the Flap endonuclease(FEN1)gene in human lung cancer[J].Oncogene,2003,22(46):7243-7246.
[36]Zhang K,Keymeulen S,Nelson R,et al.Overexpression of Flap endonuclease 1correlates with enhanced proliferation and poor prognosis of non-small-cell lung cancer[J].Am JPathol,2018,188(1):242-251.
[37]Jiang Z,Jiang J,Yang H,et al.Silencing of Aurora kinase Aby RNA interference inhibits tumor growth in human osteosarcoma cells by inducing apoptosis and G2/M cell cycle arrest[J].Onco Rep,2014,31(3):1249-1254.
[38]Wang M,Sun X,Yang Y,et al.Long non-coding RNA OIP5-AS1promotes proliferation of lung cancer cells and leads to poor prognosis by targeting miR-378a-3p[J].Thorac Cancer,2018,9(8):939-949.
[39]He J,Zhao Y,Zhao E,et al.Cancer-testis specific gene OIP5:a downstream gene of E2F1that promotes tumorigenesis and metastasis in glioblastoma by stabilizing E2F1signaling[J].Neuro Oncol,2018,20(9):1173-1184.
[40]黄欣,师德尧,邵增务.自噬在骨肉瘤中作用的研究进展[J].华中科技大学学报:医学版,2018,47(3):367-371.
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