基于GWAS的乙肝相关肝癌关联lncRNA SNPs生物信息学分析
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摘要
目的利用生物信息学方法挖掘乙肝相关肝癌相关的lncRNA SNPs,为肝癌生物标志物筛选及致病机制研究提供线索和方向。方法通过SNAP工具获取GWAS识别的乙肝相关肝癌关联SNPs的易感区域。结合dbSNP和lncRNASNP等数据库匹配易感区域上的lncRNA SNPs,并采用rVarBase、HaploReg等数据库对SNPs进行功能注释。利用TCGA数据库的乙肝相关肝癌基因表达数据进行lncRNA的差异表达分析。结果基于GWAS和生物信息学工具共挖掘9个具有潜在功能的lncRNA SNPs(lnc-RP11-150O12.3 rs1008547、rs11776545、rs2275959、rs2298320 rs2298321和lnc-ACACA-1 rs7221955、rs9891142、rs9896574、rs9908998)。功能注释结果表明所有SNPs均位于染色质交互区域或转录因子结合位点;肝组织的组蛋白修饰标识显示多数SNPs位于启动子区或增强子区,且为DNase超敏感位点,可破坏转录因子的结合基序;其中3个SNPs在HepG2细胞系中被发现影响蛋白质结合。此外,两个lncRNAs在乙肝相关肝癌患者癌组织中的表达均高于癌旁组织。结论 lnc-RP11-150O12.3和lnc-ACACA-1上的9个SNPs具有潜在生物学功能,在乙肝相关肝癌的发生和发展中可能发挥重要作用。
Objective To explore lncRNA SNPs associated with hepatitis B virus related hepatocellular carcinoma with bioinformatics methods,and to provide clues and directions for biomarkers screening and pathogenesis studies of hepatocellular carcinoma.Methods The susceptibility region of SNPs associated with hepatitis B-related liver cancer identified by GWAS was obtained by the SNAP tool.The lncRNA SNPs on the susceptible region were matched with databases such as dbSNP and lncRNASNP,and the SNPs were functionally annotated with rVarBase,HaploReg and other databases.Differential expression analysis of lncRNA was performed with the hepatitis B-related liver cancer gene expression data from the TCGA database.Results Based on GWAS and bioinformatics tools,9 potentially useful lncRNA SNPs were acquired(lnc-RP11-150O12.3 rs1008547,rs11776545,rs2275959,rs2298320,rs2298321 and lnc-ACACA-1 rs7221955,rs9891142,rs9896574,rs9908998).Functional annotation results indicated that all of SNPs were located in the chromatin interaction region or transcription factor binding site.And the histone marks of liver tissue showed that the majority of SNPs were positioned on the promoter or enhancer region,DNase hypersensitive site,and destroyed the motifs binding with a transcription factor.Three SNPs were found to affect the binding of proteins in the HepG2 cell line.In addition,the expression of two lncRNAs in tissues of hepatitis B virus-related hepatocellular carcinoma patients was higher than that in adjacent tissues.Conclusion The nine SNPs on lnc-RP11-150O12.3 and lnc-ACACA-1 have potential biological functions and may play an important role in the occurrence and development of hepatitis B virus-related hepatocellular carcinoma.
Objective To explore lncRNA SNPs associated with hepatitis B virus related hepatocellular carcinoma with bioinformatics methods,and to provide clues and directions for biomarkers screening and pathogenesis studies of hepatocellular carcinoma.Methods The susceptibility region of SNPs associated with hepatitis B-related liver cancer identified by GWAS was obtained by the SNAP tool.The lncRNA SNPs on the susceptible region were matched with databases such as dbSNP and lncRNASNP,and the SNPs were functionally annotated with rVarBase,HaploReg and other databases.Differential expression analysis of lncRNA was performed with the hepatitis B-related liver cancer gene expression data from the TCGA database.Results Based on GWAS and bioinformatics tools,9 potentially useful lncRNA SNPs were acquired(lnc-RP11-150O12.3 rs1008547,rs11776545,rs2275959,rs2298320,rs2298321 and lnc-ACACA-1 rs7221955,rs9891142,rs9896574,rs9908998).Functional annotation results indicated that all of SNPs were located in the chromatin interaction region or transcription factor binding site.And the histone marks of liver tissue showed that the majority of SNPs were positioned on the promoter or enhancer region,DNase hypersensitive site,and destroyed the motifs binding with a transcription factor.Three SNPs were found to affect the binding of proteins in the HepG2 cell line.In addition,the expression of two lncRNAs in tissues of hepatitis B virus-related hepatocellular carcinoma patients was higher than that in adjacent tissues.Conclusion The nine SNPs on lnc-RP11-150O12.3 and lnc-ACACA-1 have potential biological functions and may play an important role in the occurrence and development of hepatitis B virus-related hepatocellular carcinoma.
引文
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[25] Du R,Wu SS,Lv XN,et al.Overexpression of brachyury contributes to tumor metastasis by inducing epithelial-mesenchymal transition in hepatocellular carcinoma[J].Journal of Experimental&Clinical Cancer Research,2014,33:105.
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[27] Matsushima-Nishiwaki R,Okuno M,Adachi S,et al.Phosphorylation of retinoid X receptor alpha at serine 260 impairs its metabolism and function in human hepatocellular carcinoma[J].Cancer Research,2001,61(20):7675-7682.
[2] Allemani C,Matsuda T,Di Carlo V,et al.Global surveillance of trends in cancer survival 2000-14(CONCORD-3):analysis of individual records for 37 513 025 patients diagnosed with one of 18 cancers from 322 population-based registries in 71 countries[J].Lancet,2018,391(1125):1023-1075.
[3] Wang FS.Current status and prospects of studies on human genetic alleles associated with hepatitis B virus infection[J].World Journal of Gastroenterology,2003,9(4):641-644.
[4] World Health Organization.Hepatitis B[EB/OL].[2019-03-06].http://www.who.int/mediacentre/factsheets/fs204/en/.
[5] Zhang HX,Zhai Y,Hu ZB,et al.Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers[J].Nature Genetics,2010,42(9):U39-755.
[6] Chan KY,Wong CM,Kwan JS,et al.Genome-Wide association study of hepatocellular carcinoma in southern Chinese patients with chronic hepatitis B virus infection[J].PLOS One,2011,6(12):e28798.
[7] Li SP,Qian J,Yang Y,et al.GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers[J].PLOS Genetics,2012,8(7):e1002791.
[8] Jiang DK,Sun J,Cao G,et al.Genetic variants in STAT4 and HLA-DQ genes confer risk of hepatitis B virus-related hepatocellular carcinoma[J].Nature Genetics,2013,45(1):72-75.
[9] Qu LS,Jin F,Guo YM,et al.Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage,genome-wide association study[J].Oncology Letters,2016,11(1,B):624-632.
[10] Li YF,Zhai Y,Song QF,et al.Genome-Wide association study identifies a new locus at 7q21.13 associated with hepatitis B Virus-Related hepatocellular carcinoma[J].Clinical Cancer Research,2018,24(4):906-915.
[11] Brosnan CA,Voinnet O.The long and the short of noncoding RNAs[J].Current Opinion in Cell Biology,2009,21(3):416-425.
[12] Mercer TR,Dinger ME,Mattick JS.Long non-coding RNAs:insights into functions[J].Nature Reviews Genetics,2009,10(3):155-159.
[13] Li C,Chen J,Zhang K,et al.Progress and prospects of long noncoding RNAs(lncRNAs)in hepatocellular carcinoma[J].Cellular Physiology and Biochemistry,2015,36(2):423-434.
[14] Macarthur J,Bowler E,Cerezo M,et al.The new NHGRI-EBI Catalog of published genome-wide association studies(GWAS Catalog)[J].Nucleic Acids Research,2017,45(D1):D896-D901.
[15] Johnson AD,Handsaker RE,Pulit SL,et al.SNAP:a web-based tool for identification and annotation of proxy SNPs using HapMap[J].Bioinformatics,2008,24(24):2938-2939.
[16] Gong J,Liu W,Zhang JY,et al.IncRNASNP:a database of SNPs in lncRNAs and their potential functions in human and mouse[J].Nucleic Acids Research,2015,43(D1):D181-D186.
[17] Ward LD,Kellis M.HaploReg:a resource for exploring chromatin states,conservation,and regulatory motif alterations within sets of genetically linked variants[J].Nucleic Acids Research,2012,40(D1):D930-D934.
[18] Guo LY,Du Y,Qu SS,et al.rVarBase:an updated database for regulatory features of human variants[J].Nucleic Acids Research,2016,44(D1):D888-D893.
[19] Boyle AP,Hong EL,Hariharan M,et al.Annotation of functional variation in personal genomes using RegulomeDB[J].Genome Research,2012,22(9,SI):1790-1797.
[20] Xu ZL,Taylor JA.SNPinfo:integrating GWAS and candidate gene information into functional SNP selection for genetic association studies[J].Nucleic Acids Research,2009,37(S):W600-W605.
[21] Tomczak K,Czerwińska P,Wiznerowicz M.The cancer genome Atlas(TCGA):an immeasurable source of knowledge[J].Contemporary Oncology(Poznan,Poland),2015,19(1A):A68-A77.
[22] Robinson MD,Mccarthy DJ,Smyth GK.EdgeR:a bioconductor package for differential expression analysis of digital gene expression data[J].Bioinformatics,2010,26(1):139-140.
[23] Ren W,Zhang J,Li W,et al.A Tumor-Specific prognostic long Non-Coding RNA signature in gastric cancer[J].Medical Science Monitor,2016,22:3647-3657.
[24] Wang ZH,Wu Q,Feng S,et al.Identification of four prognostic LncRNAs for survival prediction of patients with hepatocellular carcinoma[J].PeerJ,2017,5:e3575.
[25] Du R,Wu SS,Lv XN,et al.Overexpression of brachyury contributes to tumor metastasis by inducing epithelial-mesenchymal transition in hepatocellular carcinoma[J].Journal of Experimental&Clinical Cancer Research,2014,33:105.
[26] Zhu PP,Wang YY,Du Y,et al.C8orf4 negatively regulates self-renewal of liver cancer stem cells via suppression of NOTCH2 signalling[J].Nature Communications,2015,6:7122.
[27] Matsushima-Nishiwaki R,Okuno M,Adachi S,et al.Phosphorylation of retinoid X receptor alpha at serine 260 impairs its metabolism and function in human hepatocellular carcinoma[J].Cancer Research,2001,61(20):7675-7682.