利用生物信息学分析鉴定原位骨肉瘤以及肺转移的信号通路和核心基因
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摘要
目的应用综合生物信息学来识别骨肉瘤中涉及的肺转移的关键致病基因并揭示潜在的分子机制。方法 GSE85537的表达谱从Gene Expression Omnibus(GEO)数据库下载,该数据库包含6个样品,包括3个原位骨肉瘤样品和3个骨肉瘤肺转移样品。整理微阵列数据集以获得差异表达的基因(DEG),并通过生物信息学方法进行深入分析。利用基因本体论(GO)和京都百科全书基因和基因组(KEGG)途径对DEGs富集并通过DAVID在线进行分析。DEG的蛋白质-蛋白质相互作用(PPI)网络由STRING数据库构建。MCODE分析通过Cytoscape软件中的MCODE插件制作。关键基因的生存分析通过在线(http://www.ualcan.path.edu/index.html)分析获得。结果从GEO数据集中共鉴定出差异基因662个,其中234个基因被上调,428个基因被下调,通过基因拓扑学分析从PPI网络中鉴定出DEG中最密切相关的137个基因。其中38个基因被上调,99个基因被下调。GO分析表明DEGs的生物学功能主要集中在血管生成,转录中RNA聚合酶II启动子的正向调节。主要的细胞成分包括外泌体和细胞外基质。分子功能包括ATP结合。KEGG通路分析显示这些DEG主要参与PI3K-Akt信号通路和肿瘤信号通路。MCODE插件分析从PPI网络中检测到3个重要模块,此外选择了15个具有高度关联性的差异基因,并经过总体存活率和相关性分析,发现基因ACTA2可能在防治骨肉瘤肺转移中发生作用。结论利用生物信息学分析筛查骨肿瘤转移前后的DEGs和通路可以帮助了解骨肉瘤转移发生的分子机制,对早期诊断和预防骨肉瘤转移具有临床意义,并提供有效的指导治疗骨肉瘤转移的联合用药。
Objective We apply comprehensive bioinformatics to identify key pathogenic genes involved in lung metastasis in osteosarcoma and to reveal potential molecular mechanisms. Methods The expression profile of GSE85537 was downloaded from the Gene Expression Omnibus(GEO) database, which contained 6 samples including 3 orthotopic osteosarcoma samples and 3 osteosarcoma lung metastasis samples. Microarray datasets were sequenced to obtain differentially expressed genes(DEGs) and analyzed in depth by bioinformatics methods. Gene ontology(GO) and DEGs enrichment of the Kyoto Encyclopedia Gene and Genome(KEGG) pathway were performed by DAVID online analysis. DEG's protein-protein interaction(PPI) network was constructed from the STRING database. MCODE analysis was made using the MCODE plugin in Cytoscape software. Survival analysis of key genes was obtained via online(http://www. ualcan.path.edu/index.html). Results A total of 662 differential genes were identified in the GEO dataset, of which 234 genes were up-regulated and 428 genes were down-regulated. The most closely related 137 genes in DEG were identified from the PPI network by gene topology analysis. Of these, 38 genes were up-regulated and 99 genes were down-regulated. GO analysis indicated that the biological functions of DEGs were mainly concentrated in angiogenesis, and the forward regulation of RNA polymerase II promoter in transcription. The main cellular components included exosomes and extracellular matrices. Molecular functions included ATP binding. KEGG pathway analysis revealed that these DEGs are mainly involved in the PI3 K-Akt signaling pathway and tumor signaling pathway. The MCODE analysis detected three important modules from the PPI network. In addition, 15 hub genes were selected. After overall survival analysis, it was found that the gene ACTA2 might play a role in the prevention and treatment of osteosarcoma lung metastasis. Conclusion This study demonstrates that the use of bioinformatics analysis to screen DEGs and pathways before and after bone tumor metastasis can help us understand the molecular mechanisms of bone tumor metastasis, has clinical implications for early diagnosis and prevention of osteosarcoma metastasis, and provides effective guidance for the treatment of osteosarcoma metastasis with drug combination.
Objective We apply comprehensive bioinformatics to identify key pathogenic genes involved in lung metastasis in osteosarcoma and to reveal potential molecular mechanisms. Methods The expression profile of GSE85537 was downloaded from the Gene Expression Omnibus(GEO) database, which contained 6 samples including 3 orthotopic osteosarcoma samples and 3 osteosarcoma lung metastasis samples. Microarray datasets were sequenced to obtain differentially expressed genes(DEGs) and analyzed in depth by bioinformatics methods. Gene ontology(GO) and DEGs enrichment of the Kyoto Encyclopedia Gene and Genome(KEGG) pathway were performed by DAVID online analysis. DEG's protein-protein interaction(PPI) network was constructed from the STRING database. MCODE analysis was made using the MCODE plugin in Cytoscape software. Survival analysis of key genes was obtained via online(http://www. ualcan.path.edu/index.html). Results A total of 662 differential genes were identified in the GEO dataset, of which 234 genes were up-regulated and 428 genes were down-regulated. The most closely related 137 genes in DEG were identified from the PPI network by gene topology analysis. Of these, 38 genes were up-regulated and 99 genes were down-regulated. GO analysis indicated that the biological functions of DEGs were mainly concentrated in angiogenesis, and the forward regulation of RNA polymerase II promoter in transcription. The main cellular components included exosomes and extracellular matrices. Molecular functions included ATP binding. KEGG pathway analysis revealed that these DEGs are mainly involved in the PI3 K-Akt signaling pathway and tumor signaling pathway. The MCODE analysis detected three important modules from the PPI network. In addition, 15 hub genes were selected. After overall survival analysis, it was found that the gene ACTA2 might play a role in the prevention and treatment of osteosarcoma lung metastasis. Conclusion This study demonstrates that the use of bioinformatics analysis to screen DEGs and pathways before and after bone tumor metastasis can help us understand the molecular mechanisms of bone tumor metastasis, has clinical implications for early diagnosis and prevention of osteosarcoma metastasis, and provides effective guidance for the treatment of osteosarcoma metastasis with drug combination.
引文
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[15]Whelan JS,Davis LE.Osteosarcoma,chondrosarcoma,and chordoma.J Clin Oncol,2018,36(2):188-193.
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[17]Wang ZY,Mei J,Gao YS,et al.Primary tumorectomy promotes angiogenesis and pulmonary metastasis in osteosarcoma-bearing nude mice.Acta Cir Bras,2013,28(3):190-194.
[18]Song R,Tian K,Wang W,et al.P53 suppresses cell proliferation,metastasis,and angiogenesis of osteosarcoma through inhibition of the PI3K/AKT/mTOR pathway.Int J Surg,2015,20:80-87.
[19]Shimbo K,Miyaki S,Ishitobi H,et al.Exosome-formed synthetic microRNA-143 is transferred to osteosarcoma cells and inhibits their migration.Biochem Biophys Res Commun,2014,445(2):381-387.
[20]Holzer G,Hamilton G,Angelberger P,et al.Imaging of highly malignant osteosarcoma with iodine-123-vascular endothelial growth factor.Oncology,2012,83(1):45-49.
[21]Tu B,Du L,Fan QM,et al.STAT3 activation by IL-6 from mesenchymal stem cells promotes the proliferation and metastasis of osteosarcoma.Cancer Lett,2012,325(1):80-88.
[22]Lissat A,Joerschke M,Shinde DA,et al.IL6 secreted by Ewing sarcoma tumor microenvironment confers anti-apoptotic and cell-disseminating paracrine responses in Ewing sarcoma cells.BMCCancer,2015,15:552.
[2]Yu W,Tang L,Lin F,et al.Stereotactic radiosurgery,a potential alternative treatment for pulmonary metastases from osteosarcoma.Int J Oncol,2014,44(4):1091-1098.
[3]Bacci G,Briccoli A,Rocca M,et al.Neoadjuvant chemotherapy for osteosarcoma of the extremities with metastases at presentation:recent experience at the Rizzoli Institute in 57 patients treated with cisplatin,doxorubicin,and a high dose of methotrexate and ifosfamide.Ann Oncol,2003,14(7):1126-1134.
[4]Geller DS,Gorlick R.Osteosarcoma:a review of diagnosis,management,and treatment strategies.Clin Adv Hematol Oncol,2010,8(10):705-718.
[5]Isakoff MS,Bielack SS,Meltzer P,et al.Osteosarcoma:Current treatment and a collaborative pathway to success.J Clin Oncol,2015,33(27):3029-3035.
[6]Briccoli A,Rocca M,Salone M,et al.Resection of recurrent pulmonary metastases in patients with osteosarcoma.Cancer,2005,104(8):1721-1725.
[7]Min L,Choy E,Tu C,et al.Application of metabolomics in sarcoma:From biomarkers to therapeutic targets.Crit Rev Oncol Hematol,2017,116:1-10.
[8]Perry JA,Kiezun A,Tonzi P,et al.Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma.Proc Natl Acad Sci U S A,2014,111(51):E5564-E5573.
[9]Allegretti M,Casini B,Mandoj C,et al.Precision diagnostics of Ewing's sarcoma by liquid biopsy:circulating EWS-FLI1 fusion transcripts.Ther Adv Med Oncol,2018,10:1758835918774337.
[10]Bersani F,Lingua MF,Morena D,et al.Deep sequencing reveals a novel miR-22 regulatory network with therapeutic potential in rhabdomyosarcoma.Cancer Res,2016,76(20):6095-6106.
[11]Nannini M,Pantaleo MA,Maleddu A,et al.Gene expression profiling in colorectal cancer using microarray technologies:results and perspectives.Cancer Treat Rev,2009,35(3):201-209.
[12]Petryszak R,Burdett T,Fiorelli B,et al.Expression atlas update--a database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments.Nucleic Acids Res,2014,42(Database issue):D926-D932.
[13]von Mering C,Huynen M,Jaeggi D,et al.STRING:a database of predicted functional associations between proteins.Nucleic Acids Res,2003,31(1):258-261.
[14]Sherman BT,Huang da W,Tan Q,et al.DAVID knowledgebase:a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.BMCBioinformatics,2007,8:426.
[15]Whelan JS,Davis LE.Osteosarcoma,chondrosarcoma,and chordoma.J Clin Oncol,2018,36(2):188-193.
[16]Torre LA,Bray F,Siegel RL,et al.Global cancer statistics,2012.CACancer J Clin,2015,65(2):87-108.
[17]Wang ZY,Mei J,Gao YS,et al.Primary tumorectomy promotes angiogenesis and pulmonary metastasis in osteosarcoma-bearing nude mice.Acta Cir Bras,2013,28(3):190-194.
[18]Song R,Tian K,Wang W,et al.P53 suppresses cell proliferation,metastasis,and angiogenesis of osteosarcoma through inhibition of the PI3K/AKT/mTOR pathway.Int J Surg,2015,20:80-87.
[19]Shimbo K,Miyaki S,Ishitobi H,et al.Exosome-formed synthetic microRNA-143 is transferred to osteosarcoma cells and inhibits their migration.Biochem Biophys Res Commun,2014,445(2):381-387.
[20]Holzer G,Hamilton G,Angelberger P,et al.Imaging of highly malignant osteosarcoma with iodine-123-vascular endothelial growth factor.Oncology,2012,83(1):45-49.
[21]Tu B,Du L,Fan QM,et al.STAT3 activation by IL-6 from mesenchymal stem cells promotes the proliferation and metastasis of osteosarcoma.Cancer Lett,2012,325(1):80-88.
[22]Lissat A,Joerschke M,Shinde DA,et al.IL6 secreted by Ewing sarcoma tumor microenvironment confers anti-apoptotic and cell-disseminating paracrine responses in Ewing sarcoma cells.BMCCancer,2015,15:552.