KRAS突变对人肺腺癌转录组影响的生物信息学分析
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摘要
目的鼠肉瘤病毒致癌基因(Kirsten rat sarcoma viral oncogene,KRAS)突变型肺腺癌是临床常见肺癌亚型,发病机制不清,预后不良。推测可能与KRAS突变对整个基因组的影响有关。本研究通过对KRAS突变型肺腺癌的转录组分析,探讨其预后不良和耐药的组学机制。为研究KRAS突变型肺腺癌的发病机制和临床治疗提供指导。方法从公共基因表达数据库(gene expression omnibus,GEO)中下载KRAS突变型肺腺癌的转录组数据库,首先利用R语言Impute程序包进行数据标准化,然后利用Limma程序包筛选差异基因,最后利用Robust rank aggregation算法筛选显著性基因。为进一步研究其表观调控机制,我们利用R语言Clusterprofile程序包和STRING数据库分别进行了KEGG pathway分析和蛋白质互作网络分析。结果KRAS突变对全转录组影响复杂,包括改变细胞周期促进肿瘤细胞异常增殖;影响白细胞介素-17信号通路促炎反应导致免疫耐受,促进肿瘤生长;影响细胞色素P450信号通路导致耐药。结论 KRAS突变能够引起整个基因组发生异常变化,并与促进肿瘤生长、抑制抗肿瘤免疫以及耐药相关基因的表达密切相关。
Objective Kirsten rat sarcoma viral oncogene( KRAS) mutant lung adenocarcinoma is a common clinical lung cancer subtype with unclear pathogenesis and poor prognosis. It is speculated that it may be related to the impact of KRAS mutations on the entire genome. In this study,the transcriptome analysis of KRAS mutant lung adenocarcinoma was performed to investigate the histological mechanism of poor prognosis and drug resistance. To provide guidance for studying the pathogenesis and clinical treatment of KRAS mutant lung adenocarcinoma. Methods The transcriptome database of KRAS mutant lung adenocarcinoma was downloaded from the public gene expression database( GEO). The data was normalized using the R language Impute package,then the differential expressiongenes were screened using Limma package,and finally Robust rank aggregation was used to screened significant genes. To further study its apparent regulatory mechanism,we performed KEGG pathway analysis and protein interaction network analysis using the DAVID database and the STRING database. Results KRAS mutations had a complex effect on the whole transcriptome,and including altered cell cycle to promote abnormal proliferation of tumor cells; leading to immune tolerance and promotes tumor growth by influence interleukin-17 signaling pathway on proinflammatory response,and influences cytochrome P450 signaling pathway leading to drug resistance. Conclusion KRAS mutations can cause abnormal changes in the entire genome,and are closely related to the promotion of tumor growth,inhibition of anti-tumor immunity,and expression of resistance-related genes.
Objective Kirsten rat sarcoma viral oncogene( KRAS) mutant lung adenocarcinoma is a common clinical lung cancer subtype with unclear pathogenesis and poor prognosis. It is speculated that it may be related to the impact of KRAS mutations on the entire genome. In this study,the transcriptome analysis of KRAS mutant lung adenocarcinoma was performed to investigate the histological mechanism of poor prognosis and drug resistance. To provide guidance for studying the pathogenesis and clinical treatment of KRAS mutant lung adenocarcinoma. Methods The transcriptome database of KRAS mutant lung adenocarcinoma was downloaded from the public gene expression database( GEO). The data was normalized using the R language Impute package,then the differential expressiongenes were screened using Limma package,and finally Robust rank aggregation was used to screened significant genes. To further study its apparent regulatory mechanism,we performed KEGG pathway analysis and protein interaction network analysis using the DAVID database and the STRING database. Results KRAS mutations had a complex effect on the whole transcriptome,and including altered cell cycle to promote abnormal proliferation of tumor cells; leading to immune tolerance and promotes tumor growth by influence interleukin-17 signaling pathway on proinflammatory response,and influences cytochrome P450 signaling pathway leading to drug resistance. Conclusion KRAS mutations can cause abnormal changes in the entire genome,and are closely related to the promotion of tumor growth,inhibition of anti-tumor immunity,and expression of resistance-related genes.
引文
[1]中国癌症研究基金会.中国肿瘤临床年鉴:2016[M].北京:中国协和医科大学出版社,2017.
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[17] Ashburner M,Ball CA,Blake JA,et al.Gene ontology:tool for the unification of biology.The Gene Ontology Consortium[J].Nat Genet,2000,25(1):25-29.
[18] Kanehisa M,Goto S. KEGG:kyoto encyclopedia of genes and genomes[J].Nucleic Acids Res,2000,28(1):27-30.
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[20] Du L,Xiao X,Wang C,et al.Human leukocyte antigen-G is closely associated with tumor immune escape in gastric cancer by increasing local regulatory T cells[J]. Cancer Sci,2011,102(7):1272-1280.
[21] Shao L,Zhang B,Wang L,et al. MMP-9-cleaved osteopontin isoform mediates tumor immune escape by inducing expansion of myeloid-derived suppressor cells[J].Biochem Biophys Res Commun,2017,493(4):1478-1484.
[22] Hung MS,Chen IC,Lung JH,et al.Epidermal growth factor receptor mutation enhances expression of cadherin-5in lung cancer cells[J]. PLoS One,2016,11(6):e0158395.
[23] Fong KM,Kida Y,Zimmerman PV,et al.TIMP1 and adverse prognosis innon-small cell lung cancer[J]. Clin Cancer Res,1996,2(8):1369-1372.
[24] Huang H,Liu J,Meng Q,et al.Multidrug resistance protein and topoisomerase 2 alpha expression in non-small cell lung cancer are related with brain metastasis postoperatively[J].Int J Clin Exp Pathol,2015,8(9):11537-11542.
[25] Bai L,Zhao J,Yu H,et al.The CD36 dynamic change after radiation therapy in lung cancer patients and its correlation with symptomatic radiation pneumonitis[J].Radiother Oncol,2013,107(3):389-391.
[26] Tian W,Li YS,Zhang JH,et al.Comprehensive analysis of DNA methylation and gene expressiondatasets identified MMP9 and TWIST1 as important pathogenic genes of lung adenocarcinoma[J]. DNA Cell Biol,2018,37(4):336-346.
[27] Ma SC,Li Q,Peng JY,et al.Claudin-5 regulates bloodbrain barrier permeability by modifying brainmicrovascular endothelial cell proliferation,migration,and adhesion to prevent lung cancer metastasis[J]. CNS Neurosci Ther,2017,23(12):947-960.
[28] Wang Y,Qian W,Yuan B.A graphical model of smokinginduced globalinstability in lung cancer[J]. IEEE/ACM Trans Comput Biol Bioinform,2018,15(1):1-14.
[29] Zhang Y,Du W,Chen Z,et al.Upregulation of PD-L1 by SPP1 mediates macrophage polarization and facilitates immune escape in lung adenocarcinoma[J]. Exp Cell Res,2017,359(2):449-457.
[30] Caetano MS,Zhang H,Cumpian AM,et al. IL6 blockade reprograms the lung tumor microenvironment to limit the development and progression of K-ras-mutant lung cancer[J].Cancer Res,2016,76(11):3189-3199.
[31] Xu X,Cao L,Zhang Y,et al. Network analysis of DEGs and verification experiments reveal the notable roles of PTTG1 and MMP9 in lung cancer[J]. Oncol Lett,2018,15(1):257-263.
[32] Lin WW,Karin M.A cytokine-mediated link between innate immunity,inflammation,and cancer[J]. J Clin Invest,2007,117(5):1175-1183.
[33] Qiao Y,Zhang C,Li A,et al.IL6 derived from cancer-associated fibroblasts promoteschemoresistance via CXCR7in esophageal squamous cell carcinoma[J]. Oncogene,2018,37(7):873-883.
[34] Bai Y,Li LD,Li J,et al. Targeting of topoisomerases for prognosis and drug resistance in ovarian cancer[J].J Ovarian Res,2016,9(1):35.
[35] Akbay EA,Koyama S,Liu Y,et al.Interleukin-17A promotes lung tumor progression through neutrophil attraction to tumor sites and mediating resistance to PD-1 blockade[J].J Thorac Oncol,2017,12(8):1268-1279.
[2]董忠谊.KRAS突变非小细胞肺癌精准靶向治疗迎来新曙光[J].循证医学,2016,16(6):328.
[3] Poulos RC,Wong JWH.Finding cancer driver mutations in the era of big data research[J]. Biophys Rev,2019,11(1):21-29.
[4] Edgar R,Domrachev M,Lash AE.Gene Expression Omnibus:NCBI gene expressionand hybridization array data repository[J].Nucleic Acids Res,2002,30(1):207-210.
[5] Wilhite SE,Barrett T. Strategies to explore functional genomics data sets in NCBI’s GEO database[J]. Methods Mol Biol,2012,802:41-53.
[6] Okayama H,Kohno T,Ishii Y,et al.Identification of genes upregulated in ALK positive and EGFR/KRAS/ALK-negative lung adenocarcinomas[J]. Cancer Res,2012,72(1):100-111.
[7] Yamauchi M,Yamaguchi R,Nakata A,et al. Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma[J]. PLoS One,2012,7(9):e43923.
[8] Selamat SA,Chung BS,Girard L,et al.Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression[J].Genome Res,2012,22(7):1197-1211.
[9] Girard L,Rodriguez-Canales J,Behrens C,et al. An expression signature as an aid to the histologic classification of non-small cell lung cancer[J].Clin Cancer Res,2016,22(19):4880-4889.
[10] Gentleman RC,Carey VJ,Bates DM,et al. Bioconductor:open software development for computational biology and bioinformatics[J].Genome Biol,2004,5(10):R80.
[11] Hastie T,Tibshirani R,Narasimhan B,et al.Impute:imputation for microarray data[EB/OL].[2019-03-01]. http://master. bioconductor. org/packages/release/bioc/manuals/impute/man/impute.pdf.
[12] Benjamini Y,Hochberg Y. Controlling the false discovery rate:a practical and powerful approach to multiple testing[J].J R Stat Soc B,1995,51(1):289-300.
[13] Kolde R,Laur S,Adler P,et al. Robust rank aggregation for gene listintegration and meta-analysis[J].Bioinformatics,2012,28(4):573-580.
[14] Franceschini A,Szklarczyk D,Frankild S,et al. STRING v9.1:protein-protein interaction networks,with increased coverage and integration[J]. Nucleic Acids Res,2013,41(Database issue):D808-D815.
[15] 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.
[16] Huang da W,Sherman BT,Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources[J].Nat Protoc,2009,4(1):44-57.
[17] Ashburner M,Ball CA,Blake JA,et al.Gene ontology:tool for the unification of biology.The Gene Ontology Consortium[J].Nat Genet,2000,25(1):25-29.
[18] Kanehisa M,Goto S. KEGG:kyoto encyclopedia of genes and genomes[J].Nucleic Acids Res,2000,28(1):27-30.
[19]张煜坤,戈伟.KRAS基因突变的非小细胞肺癌靶向治疗进展[J].中国医药导报,2017,14(16):32-35.
[20] Du L,Xiao X,Wang C,et al.Human leukocyte antigen-G is closely associated with tumor immune escape in gastric cancer by increasing local regulatory T cells[J]. Cancer Sci,2011,102(7):1272-1280.
[21] Shao L,Zhang B,Wang L,et al. MMP-9-cleaved osteopontin isoform mediates tumor immune escape by inducing expansion of myeloid-derived suppressor cells[J].Biochem Biophys Res Commun,2017,493(4):1478-1484.
[22] Hung MS,Chen IC,Lung JH,et al.Epidermal growth factor receptor mutation enhances expression of cadherin-5in lung cancer cells[J]. PLoS One,2016,11(6):e0158395.
[23] Fong KM,Kida Y,Zimmerman PV,et al.TIMP1 and adverse prognosis innon-small cell lung cancer[J]. Clin Cancer Res,1996,2(8):1369-1372.
[24] Huang H,Liu J,Meng Q,et al.Multidrug resistance protein and topoisomerase 2 alpha expression in non-small cell lung cancer are related with brain metastasis postoperatively[J].Int J Clin Exp Pathol,2015,8(9):11537-11542.
[25] Bai L,Zhao J,Yu H,et al.The CD36 dynamic change after radiation therapy in lung cancer patients and its correlation with symptomatic radiation pneumonitis[J].Radiother Oncol,2013,107(3):389-391.
[26] Tian W,Li YS,Zhang JH,et al.Comprehensive analysis of DNA methylation and gene expressiondatasets identified MMP9 and TWIST1 as important pathogenic genes of lung adenocarcinoma[J]. DNA Cell Biol,2018,37(4):336-346.
[27] Ma SC,Li Q,Peng JY,et al.Claudin-5 regulates bloodbrain barrier permeability by modifying brainmicrovascular endothelial cell proliferation,migration,and adhesion to prevent lung cancer metastasis[J]. CNS Neurosci Ther,2017,23(12):947-960.
[28] Wang Y,Qian W,Yuan B.A graphical model of smokinginduced globalinstability in lung cancer[J]. IEEE/ACM Trans Comput Biol Bioinform,2018,15(1):1-14.
[29] Zhang Y,Du W,Chen Z,et al.Upregulation of PD-L1 by SPP1 mediates macrophage polarization and facilitates immune escape in lung adenocarcinoma[J]. Exp Cell Res,2017,359(2):449-457.
[30] Caetano MS,Zhang H,Cumpian AM,et al. IL6 blockade reprograms the lung tumor microenvironment to limit the development and progression of K-ras-mutant lung cancer[J].Cancer Res,2016,76(11):3189-3199.
[31] Xu X,Cao L,Zhang Y,et al. Network analysis of DEGs and verification experiments reveal the notable roles of PTTG1 and MMP9 in lung cancer[J]. Oncol Lett,2018,15(1):257-263.
[32] Lin WW,Karin M.A cytokine-mediated link between innate immunity,inflammation,and cancer[J]. J Clin Invest,2007,117(5):1175-1183.
[33] Qiao Y,Zhang C,Li A,et al.IL6 derived from cancer-associated fibroblasts promoteschemoresistance via CXCR7in esophageal squamous cell carcinoma[J]. Oncogene,2018,37(7):873-883.
[34] Bai Y,Li LD,Li J,et al. Targeting of topoisomerases for prognosis and drug resistance in ovarian cancer[J].J Ovarian Res,2016,9(1):35.
[35] Akbay EA,Koyama S,Liu Y,et al.Interleukin-17A promotes lung tumor progression through neutrophil attraction to tumor sites and mediating resistance to PD-1 blockade[J].J Thorac Oncol,2017,12(8):1268-1279.