基于TCGA数据库结肠癌RBL1基因甲基化水平的诊断与预后分析
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摘要
视网膜母细胞瘤样蛋白1(RBL1/p105)是视网膜母细胞瘤蛋白质家族的成员之一,RBL1通常被认为是抑癌基因,在细胞增殖、凋亡、分化中发挥重要作用。该文探讨RBL1基因在结肠癌诊断和预后中的作用和可能的机制。利用癌症基因组图谱(TCGA)数据库中的结肠癌病例资料和芯片数据,筛选RBL1基因差异甲基化位点,并通过Cox回归模型研究甲基化位点与结肠癌患者预后之间的关系。该研究发现,待研究的癌组织RBL1基因启动子甲基化水平高于癌旁组织(0.120±0.012 vs 0.113±0.008, P=0.000 04)。随后,研究者采用受试者工作特征(ROC)曲线来评价RBL1基因启动子甲基化水平的诊断价值,用曲线下面积(AUC)作为诊断价值的评判标准。研究发现,启动子区甲基化的AUC达到0.732,对应的灵敏度为80.5%、特异度为55.3%。Cox多因素分析结果发现, cg04086771高甲基化是结肠癌患者预后的独立危险因素(P=0.002)。该研究通过对TCGA数据库的挖掘,发现RBL1基因启动子区甲基化均值可能与结肠癌发病风险有关,同时RBL1基因的甲基化位点的甲基化水平对结肠癌的预后有影响。
Retinoblastoma-like protein 1(RBL1/p105) is a member of the retinoblastoma protein family.RBL1 is generally considered to be a tumor suppressor gene and plays an important role in cell proliferation,apoptosis and differentiation. This article explores the role of RBL1 promoter methylation in diagnosis and prognosis of colon cancer and its potential molecular mechanism. Using the methylation and expression microarray data from The Cancer Genome Atlas(TCGA), we screened for differential methylation sites of the RBL1 in colon cancer, and researched the role of RBL1 methylation sites in the prognosis of colon cancer patients using Cox regression model. This study found that the promoter methylation level of RBL1 in tumor tissues was higher than that in adjacent no-tumor tissues(0.120±0.012 vs 0.113±0.008, P=0.000 04). Subsequently, we used the receiver operating characteristic(ROC) curve to evaluate the diagnostic value of the RBL1 promoter methylation, using the area under the curve(AUC) as the criterion for the diagnostic value. We found that the promoter methylation of RBL1 could reach an AUC of 0.732 with a sensitivity of 80.5% and a specificity of 55.3%. Cox multiple regression found that cg04086771 hypermethylation was an independent risk factor for prognosis in colon cancer patients(P=0.002). This study found that the average methylation status of RBL1 promoter region may associate with the risk of colon cancer. Meanwhile, we found that the methylation level of RBL1 had an important impact in the prognosis of colon cancer.
Retinoblastoma-like protein 1(RBL1/p105) is a member of the retinoblastoma protein family.RBL1 is generally considered to be a tumor suppressor gene and plays an important role in cell proliferation,apoptosis and differentiation. This article explores the role of RBL1 promoter methylation in diagnosis and prognosis of colon cancer and its potential molecular mechanism. Using the methylation and expression microarray data from The Cancer Genome Atlas(TCGA), we screened for differential methylation sites of the RBL1 in colon cancer, and researched the role of RBL1 methylation sites in the prognosis of colon cancer patients using Cox regression model. This study found that the promoter methylation level of RBL1 in tumor tissues was higher than that in adjacent no-tumor tissues(0.120±0.012 vs 0.113±0.008, P=0.000 04). Subsequently, we used the receiver operating characteristic(ROC) curve to evaluate the diagnostic value of the RBL1 promoter methylation, using the area under the curve(AUC) as the criterion for the diagnostic value. We found that the promoter methylation of RBL1 could reach an AUC of 0.732 with a sensitivity of 80.5% and a specificity of 55.3%. Cox multiple regression found that cg04086771 hypermethylation was an independent risk factor for prognosis in colon cancer patients(P=0.002). This study found that the average methylation status of RBL1 promoter region may associate with the risk of colon cancer. Meanwhile, we found that the methylation level of RBL1 had an important impact in the prognosis of colon cancer.
引文
1 Chen W,Zheng R,Baade PD,Zhang S,Zeng H,Bray F,et al.Cancer statistics in China,2015.CA Cancer J Clin 2016;66(2):115-32.
2 Carethers JM,Jung BH.Genetics and genetic biomarkers in sporadic colorectal cancer.Gastroenterology 2015;149(5):1177-90 e3.
3 Okugawa Y,Grady WM,Goel A.Epigenetic alterations in colorectal cancer:emerging biomarkers.Gastroenterology 2015;149(5):1204-25 e12.
4 Brenner H,Kloor M,Pox CP.Colorectal cancer.Lancet 2014;383(9927):1490-502.
5 Zhou D,Tang W,Su G,Cai M,An HX,Zhang Y.PCDH18 is frequently inactivated by promoter methylation in colorectal cancer.Sci Rep 2017;7(1):2819.
6 Rezvani N,Alibakhshi R,Vaisi-Raygani A,Bashiri H,Saidijam M.Detection of SPG20 gene promoter-methylated DNA,as a novel epigenetic biomarker,in plasma for colorectal cancer diagnosis using the MethyLight method.Oncol Lett 2017;13(5):3277-84.
7 Li M,Gao F,Xia Y,Tang Y,Zhao W,Jin C,et al.Filtrating colorectal cancer associated genes by integrated analyses of global DNA methylation and hydroxymethylation in cancer and normal tissue.Sci Rep 2016;6:31826.
8 Li L,Li C,Mao H,Du Z,Chan WY,Murray P,et al.Epigenetic inactivation of the CpG demethylase TET1 as a DNA methylation feedback loop in human cancers.Sci Rep 2016;6:26591.
9 Baldi A,Boccia V,Claudio PP,De Luca A,Giordano A.Genomic structure of the human retinoblastoma-related Rb2/p130 gene.Proc Natl Acad Sci USA 1996;93(10):4629-32.
10 Classon M,Harlow E.The retinoblastoma tumour suppressor in development and cancer.Nat Rev Cancer 2002;2(12):910-7.
11 Mishra DK,Chen Z,Wu Y,Sarkissyan M,Koeffler HP,Vadgama JV.Global methylation pattern of genes in androgen-sensitive and androgen-independent prostate cancer cells.Mol Cancer Ther2010;9(1):33-45.
12 Buchkovich K,Duffy LA,Harlow E.The retinoblastoma protein is phosphorylated during specific phases of the cell cycle.Cell 1989;58(6):1097-105.
13 Sun A,Bagella L,Tutton S,Romano G,Giordano A.From G0 to Sphase:a view of the roles played by the retinoblastoma(Rb)family members in the Rb-E2F pathway.J Cell Biochem 2007;102(6):1400-4.
14 Barh D,Jain N,Tiwari S,Field JK,Padin-Iruegas E,Ruibal A,et al.A novel in silico reverse-transcriptomics-based identification and blood-based validation of a panel of sub-type specific biomarkers in lung cancer.BMC Genomics 2013;14 Suppl 6:S5.
15 Modi S,Kubo A,Oie H,Coxon AB,Rehmatulla A,Kaye FJ.Protein expression of the RB-related gene family and SV40 large Tantigen in mesothelioma and lung cancer.Oncogene 2000;19(40):4632-9.
16 Eyvani H,Moghaddaskho F,Kabuli M,Zekri A,Momeny M,Tavakkoly-Bazzaz J,et al.Arsenic trioxide induces cell cycle arrest and alters DNA methylation patterns of cell cycle regulatory genes in colorectal cancer cells.Life Sci 2016;167:67-77.
17 Tokarz P,Blasiak J.Role of DNA methylation in colorectal cancer.Postepy Biochem 2013;59(3):267-79.
18 Pfeifer GP,Rauch TA.DNA methylation patterns in lung carcinomas.Semin Cancer Biol 2009;19(3):181-7.
19 Naumov VA,Generozov EV,Zaharjevskaya NB,Matushkina DS,Larin AK,Chernyshov SV,et al.Genome-scale analysis of DNA methylation in colorectal cancer using Infinium Human Methylation450 BeadChips.Epigenetics 2013;8(9):921-34.
20 Sabir M,Baig RM,Ali K,Mahjabeen I,Saeed M,Kayani MA.Retinoblastoma(RB1)pocket domain mutations and promoter hyper-methylation in head and neck cancer.Cell Oncol(Dordr)2014;37(3):203-13.
21 Jovanovic J,Ronneberg JA,Tost J,Kristensen V.The epigenetics of breast cancer.Mol Oncol 2010;4(3):242-54.
22 Li Y,Song L,Gong Y,He B.Detection of colorectal cancer by DNA methylation biomarker SEPT9:past,present and future.Biomark Med 2014;8(5):755-69.
23 Committee ASoP,Fisher DA,Maple JT,Ben-Menachem T,Cash BD,Decker GA,et al.Complications of colonoscopy.Gastrointest Endosc 2011;74(4):745-52.
24 Hrasovec S,Hauptman N,Glavac D,Jelenc F,Ravnik-Glavac M.TMEM25 is a candidate biomarker methylated and downregulated in colorectal cancer.Dis Markers 2013;34(2):93-104.
25 Warren JD,Xiong W,Bunker AM,Vaughn CP,Furtado LV,Roberts WL,et al.Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer.BMC Med 2011;9:133.
26 Takane K,Midorikawa Y,Yagi K,Sakai A,Aburatani H,Takayama T,et al.Aberrant promoter methylation of PPP1R3C and EFHD1in plasma of colorectal cancer patients.Cancer Med 2014;3(5):1235-45.
27 Kadonaga JT.Perspectives on the RNA polymerase II core promoter.Wiley Interdiscip Rev Dev Biol 2012;1(1):40-51.
28 Juven-Gershon T,Kadonaga JT.Regulation of gene expression via the core promoter and the basal transcriptional machinery.Dev Biol 2010;339(2):225-9.
29 Danino YM,Even D,Ideses D,Juven-Gershon T.The core promoter:At the heart of gene expression.Biochim Biophys Acta2015;1849(8):1116-31.
30 Croes L,Beyens M,Fransen E,Ibrahim J,Vanden Berghe W,Suls A,et al.Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer.Clin Epigenetics 2018;10:51.
31 Brenner H,Stock C,Hoffmeister M.Effect of screening sigmoidoscopy and screening colonoscopy on colorectal cancer incidence and mortality:systematic review and meta-analysis of randomised controlled trials and observational studies.BMJ 2014;348:g2467.
32 Kulis M,Esteller M.DNA methylation and cancer.Adv Genet2010;70:27-56.
33 Lee YC,Lee YL,Chuang JP,Lee JC.Differences in survival between colon and rectal cancer from SEER data.PLoS One 2013;8(11):e78709.
34 Mileo AM,Mattarocci S,Matarrese P,Anticoli S,Abbruzzese C,Catone S,et al.Hepatitis C virus core protein modulates pRb2/p130 expression in human hepatocellular carcinoma cell lines through promoter methylation.J Exp Clin Cancer Res 2015;34:140.
35 Couraud S,Vaca-Paniagua F,Villar S,Oliver J,Schuster T,Blanche H,et al.Noninvasive diagnosis of actionable mutations by deep sequencing of circulating free DNA in lung cancer from never-smokers:a proof-of-concept study from BioCAST/IFCT-1002.Clin Cancer Res 2014;20(17):4613-24.
36 Jung K,Fleischhacker M,Rabien A.Cell-free DNA in the blood as a solid tumor biomarker-a critical appraisal of the literature.Clin Chim Acta 2010;411(21/22):1611-24.
37 Ling ZQ,LüP,Lu XX,Yu JL,Han J,Ying LS,et al.Circulating methylated XAF1 DNA indicates poor prognosis for gastric cancer.PLo S One 2013;8(6):e67195.
2 Carethers JM,Jung BH.Genetics and genetic biomarkers in sporadic colorectal cancer.Gastroenterology 2015;149(5):1177-90 e3.
3 Okugawa Y,Grady WM,Goel A.Epigenetic alterations in colorectal cancer:emerging biomarkers.Gastroenterology 2015;149(5):1204-25 e12.
4 Brenner H,Kloor M,Pox CP.Colorectal cancer.Lancet 2014;383(9927):1490-502.
5 Zhou D,Tang W,Su G,Cai M,An HX,Zhang Y.PCDH18 is frequently inactivated by promoter methylation in colorectal cancer.Sci Rep 2017;7(1):2819.
6 Rezvani N,Alibakhshi R,Vaisi-Raygani A,Bashiri H,Saidijam M.Detection of SPG20 gene promoter-methylated DNA,as a novel epigenetic biomarker,in plasma for colorectal cancer diagnosis using the MethyLight method.Oncol Lett 2017;13(5):3277-84.
7 Li M,Gao F,Xia Y,Tang Y,Zhao W,Jin C,et al.Filtrating colorectal cancer associated genes by integrated analyses of global DNA methylation and hydroxymethylation in cancer and normal tissue.Sci Rep 2016;6:31826.
8 Li L,Li C,Mao H,Du Z,Chan WY,Murray P,et al.Epigenetic inactivation of the CpG demethylase TET1 as a DNA methylation feedback loop in human cancers.Sci Rep 2016;6:26591.
9 Baldi A,Boccia V,Claudio PP,De Luca A,Giordano A.Genomic structure of the human retinoblastoma-related Rb2/p130 gene.Proc Natl Acad Sci USA 1996;93(10):4629-32.
10 Classon M,Harlow E.The retinoblastoma tumour suppressor in development and cancer.Nat Rev Cancer 2002;2(12):910-7.
11 Mishra DK,Chen Z,Wu Y,Sarkissyan M,Koeffler HP,Vadgama JV.Global methylation pattern of genes in androgen-sensitive and androgen-independent prostate cancer cells.Mol Cancer Ther2010;9(1):33-45.
12 Buchkovich K,Duffy LA,Harlow E.The retinoblastoma protein is phosphorylated during specific phases of the cell cycle.Cell 1989;58(6):1097-105.
13 Sun A,Bagella L,Tutton S,Romano G,Giordano A.From G0 to Sphase:a view of the roles played by the retinoblastoma(Rb)family members in the Rb-E2F pathway.J Cell Biochem 2007;102(6):1400-4.
14 Barh D,Jain N,Tiwari S,Field JK,Padin-Iruegas E,Ruibal A,et al.A novel in silico reverse-transcriptomics-based identification and blood-based validation of a panel of sub-type specific biomarkers in lung cancer.BMC Genomics 2013;14 Suppl 6:S5.
15 Modi S,Kubo A,Oie H,Coxon AB,Rehmatulla A,Kaye FJ.Protein expression of the RB-related gene family and SV40 large Tantigen in mesothelioma and lung cancer.Oncogene 2000;19(40):4632-9.
16 Eyvani H,Moghaddaskho F,Kabuli M,Zekri A,Momeny M,Tavakkoly-Bazzaz J,et al.Arsenic trioxide induces cell cycle arrest and alters DNA methylation patterns of cell cycle regulatory genes in colorectal cancer cells.Life Sci 2016;167:67-77.
17 Tokarz P,Blasiak J.Role of DNA methylation in colorectal cancer.Postepy Biochem 2013;59(3):267-79.
18 Pfeifer GP,Rauch TA.DNA methylation patterns in lung carcinomas.Semin Cancer Biol 2009;19(3):181-7.
19 Naumov VA,Generozov EV,Zaharjevskaya NB,Matushkina DS,Larin AK,Chernyshov SV,et al.Genome-scale analysis of DNA methylation in colorectal cancer using Infinium Human Methylation450 BeadChips.Epigenetics 2013;8(9):921-34.
20 Sabir M,Baig RM,Ali K,Mahjabeen I,Saeed M,Kayani MA.Retinoblastoma(RB1)pocket domain mutations and promoter hyper-methylation in head and neck cancer.Cell Oncol(Dordr)2014;37(3):203-13.
21 Jovanovic J,Ronneberg JA,Tost J,Kristensen V.The epigenetics of breast cancer.Mol Oncol 2010;4(3):242-54.
22 Li Y,Song L,Gong Y,He B.Detection of colorectal cancer by DNA methylation biomarker SEPT9:past,present and future.Biomark Med 2014;8(5):755-69.
23 Committee ASoP,Fisher DA,Maple JT,Ben-Menachem T,Cash BD,Decker GA,et al.Complications of colonoscopy.Gastrointest Endosc 2011;74(4):745-52.
24 Hrasovec S,Hauptman N,Glavac D,Jelenc F,Ravnik-Glavac M.TMEM25 is a candidate biomarker methylated and downregulated in colorectal cancer.Dis Markers 2013;34(2):93-104.
25 Warren JD,Xiong W,Bunker AM,Vaughn CP,Furtado LV,Roberts WL,et al.Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer.BMC Med 2011;9:133.
26 Takane K,Midorikawa Y,Yagi K,Sakai A,Aburatani H,Takayama T,et al.Aberrant promoter methylation of PPP1R3C and EFHD1in plasma of colorectal cancer patients.Cancer Med 2014;3(5):1235-45.
27 Kadonaga JT.Perspectives on the RNA polymerase II core promoter.Wiley Interdiscip Rev Dev Biol 2012;1(1):40-51.
28 Juven-Gershon T,Kadonaga JT.Regulation of gene expression via the core promoter and the basal transcriptional machinery.Dev Biol 2010;339(2):225-9.
29 Danino YM,Even D,Ideses D,Juven-Gershon T.The core promoter:At the heart of gene expression.Biochim Biophys Acta2015;1849(8):1116-31.
30 Croes L,Beyens M,Fransen E,Ibrahim J,Vanden Berghe W,Suls A,et al.Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer.Clin Epigenetics 2018;10:51.
31 Brenner H,Stock C,Hoffmeister M.Effect of screening sigmoidoscopy and screening colonoscopy on colorectal cancer incidence and mortality:systematic review and meta-analysis of randomised controlled trials and observational studies.BMJ 2014;348:g2467.
32 Kulis M,Esteller M.DNA methylation and cancer.Adv Genet2010;70:27-56.
33 Lee YC,Lee YL,Chuang JP,Lee JC.Differences in survival between colon and rectal cancer from SEER data.PLoS One 2013;8(11):e78709.
34 Mileo AM,Mattarocci S,Matarrese P,Anticoli S,Abbruzzese C,Catone S,et al.Hepatitis C virus core protein modulates pRb2/p130 expression in human hepatocellular carcinoma cell lines through promoter methylation.J Exp Clin Cancer Res 2015;34:140.
35 Couraud S,Vaca-Paniagua F,Villar S,Oliver J,Schuster T,Blanche H,et al.Noninvasive diagnosis of actionable mutations by deep sequencing of circulating free DNA in lung cancer from never-smokers:a proof-of-concept study from BioCAST/IFCT-1002.Clin Cancer Res 2014;20(17):4613-24.
36 Jung K,Fleischhacker M,Rabien A.Cell-free DNA in the blood as a solid tumor biomarker-a critical appraisal of the literature.Clin Chim Acta 2010;411(21/22):1611-24.
37 Ling ZQ,LüP,Lu XX,Yu JL,Han J,Ying LS,et al.Circulating methylated XAF1 DNA indicates poor prognosis for gastric cancer.PLo S One 2013;8(6):e67195.