Correlation of an epigenetic mitotic clock with cancer risk.
Correlation of an epigenetic mitotic clock with cancer risk.
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表观遗传有丝分裂时钟与癌症风险的相关性
DOI：
10.1186/s13059-016-1064-3
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发表时间：
2016-10-03
期刊：
影响因子：
12.3
通讯作者：
Teschendorff AE
中科院分区：
文献类型：
--
作者：
Yang Z;Wong A;Kuh D;Paul DS;Rakyan VK;Leslie RD;Zheng SC;Widschwendter M;Beck S;Teschendorff AE
体细胞组织中癌症风险的变化归因于干细胞分裂的潜在速率的变化。对于给定的组织类型，个体之间可变的癌症风险被认为受到调节干细胞分裂速率的外部因素的影响。到目前为止，还没有开发出分子有丝分裂钟来估计个体组织中干细胞分裂的数量，以及它与癌症风险的关系。在这里，我们将数学建模与先前的生物学知识相结合，构建了一个基于DNA甲基化的年龄相关模型，该模型近似于正常和癌症组织中的有丝分裂时钟。通过关注11种不同胎儿组织类型中未甲基化的Polycomb组靶基因上的启动子CpG位点，我们发现这些位点DNA甲基化的增加决定了正常组织中干细胞分裂的估计率。使用匹配的DNA甲基化和RNA-seq数据，我们进一步表明它与癌组织中基于表达的有丝分裂指数相关。我们证明这种有丝分裂样时钟在癌症中普遍加速，包括癌前病变，并且在暴露于主要致癌物质的正常上皮细胞中也加速。结论与其他表观遗传和突变时钟或端粒时钟不同，本文提出的表观遗传时钟提供了一个在癌症和癌前病变中普遍加速的有丝分裂样时钟的具体例子。
BackgroundVariation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk.ResultsHere, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue. By focusing on promoter CpG sites that localize to Polycomb group target genes that are unmethylated in 11 different fetal tissue types, we show that increases in DNA methylation at these sites defines a tick rate which correlates with the estimated rate of stem cell division in normal tissues. Using matched DNA methylation and RNA-seq data, we further show that it correlates with an expression-based mitotic index in cancer tissue. We demonstrate that this mitotic-like clock is universally accelerated in cancer, including pre-cancerous lesions, and that it is also accelerated in normal epithelial cells exposed to a major carcinogen.ConclusionsUnlike other epigenetic and mutational clocks or the telomere clock, the epigenetic clock proposed here provides a concrete example of a mitotic-like clock which is universally accelerated in cancer and precancerous lesions.
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DOI：
10.1056/nejmoa1409405
发表时间：
2014-12-25
期刊：
The New England journal of medicine
影响因子：
--
作者：
Genovese G;Kähler AK;Handsaker RE;Lindberg J;Rose SA;Bakhoum SF;Chambert K;Mick E;Neale BM;Fromer M;Purcell SM;Svantesson O;Landén M;Höglund M;Lehmann S;Gabriel SB;Moran JL;Lander ES;Sullivan PF;Sklar P;Grönberg H;Hultman CM;McCarroll SA
通讯作者：
McCarroll SA
影响因子：
12.3
作者：
Jaffe AE;Irizarry RA
通讯作者：
Irizarry RA
影响因子：
16.6
作者：
Domcke, Silvia;Sinha, Rileen;Levine, Douglas A.;Sander, Chris;Schultz, Nikolaus
通讯作者：
Schultz, Nikolaus
全基因组甲基化谱揭示了人类衰老速度的定量观点。
影响因子：
16
作者：
Hannum, Gregory;Guinney, Justin;Zhao, Ling;Zhang, Li;Hughes, Guy;Sadda, SriniVas;Klotzle, Brandy;Bibikova, Marina;Fan, Jian-Bing;Gao, Yuan;Deconde, Rob;Chen, Menzies;Rajapakse, Indika;Friend, Stephen;Ideker, Trey;Zhang, Kang
通讯作者：
Zhang, Kang
影响因子：
30.8
作者：
Jacobs, Kevin B.;Yeager, Meredith;Zhou, Weiyin;Wacholder, Sholom;Wang, Zhaoming;Rodriguez-Santiago, Benjamin;Hutchinson, Amy;Deng, Xiang;Liu, Chenwei;Horner, Marie-Josephe;Cullen, Michael;Epstein, Caroline G.;Burdett, Laurie;Dean, Michael C.;Chatterjee, Nilanjan;Sampson, Joshua;Chung, Charles C.;Kovaks, Joseph;Gapstur, Susan M.;Stevens, Victoria L.;Teras, Lauren T.;Gaudet, Mia M.;Albanes, Demetrius;Weinstein, Stephanie J.;Virtamo, Jarmo;Taylor, Philip R.;Freedman, Neal D.;Abnet, Christian C.;Goldstein, Alisa M.;Hu, Nan;Yu, Kai;Yuan, Jian-Min;Liao, Linda;Ding, Ti;Qiao, You-Lin;Gao, Yu-Tang;Koh, Woon-Puay;Xiang, Yong-Bing;Tang, Ze-Zhong;Fan, Jin-Hu;Aldrich, Melinda C.;Amos, Christopher;Blot, William J.;Bock, Cathryn H.;Gillanders, Elizabeth M.;Harris, Curtis C.;Haiman, Christopher A.;Henderson, Brian E.;Kolonel, Laurence N.;Le Marchand, Loic;McNeill, Lorna H.;Rybicki, Benjamin A.;Schwartz, Ann G.;Signorello, Lisa B.;Spitz, Margaret R.;Wiencke, John K.;Wrensch, Margaret;Wu, Xifeng;Zanetti, Krista A.;Ziegler, Regina G.;Figueroa, Jonine D.;Garcia-Closas, Montserrat;Malats, Nuria;Marenne, Gaelle;Prokunina-Olsson, Ludmila;Baris, Dalsu;Schwenn, Molly;Johnson, Alison;Landi, Maria Teresa;Goldin, Lynn;Consonni, Dario;Bertazzi, Pier Alberto;Rotunno, Melissa;Rajaraman, Preetha;Andersson, Ulrika;Freeman, Laura E. Beane;Berg, Christine D.;Buring, Julie E.;Butler, Mary A.;Carreon, Tania;Feychting, Maria;Ahlbom, Anders;Gaziano, J. Michael;Giles, Graham G.;Hallmans, Goran;Hankinson, Susan E.;Hartge, Patricia;Henriksson, Roger;Inskip, Peter D.;Johansen, Christoffer;Landgren, Annelie;McKean-Cowdin, Roberta;Michaud, Dominique S.;Melin, Beatrice S.;Peters, Ulrike;Ruder, Avima M.;Sesso, Howard D.;Severi, Gianluca;Shu, Xiao-Ou;Visvanathan, Kala;White, Emily;Wolk, Alicja;Zeleniuch-Jacquotte, Anne;Zheng, Wei;Silverman, Debra T.;Kogevinas, Manolis;Gonzalez, Juan R.;Villa, Olaya;Li, Donghui;Duell, Eric J.;Risch, Harvey A.;Olson, Sara H.;Kooperberg, Charles;Wolpin, Brian M.;Jiao, Li;Hassan, Manal;Wheeler, William;Arslan, Alan A.;Bueno-de-Mesquita, H. Bas;Fuchs, Charles S.;Gallinger, Steven;Gross, Myron D.;Holly, Elizabeth A.;Klein, Alison P.;LaCroix, Andrea;Mandelson, Margaret T.;Petersen, Gloria;Boutron-Ruault, Marie-Christine;Bracci, Paige M.;Canzian, Federico;Chang, Kenneth;Cotterchio, Michelle;Giovannucci, Edward L.;Goggins, Michael;Bolton, Judith A. Hoffman;Jenab, Mazda;Khaw, Kay-Tee;Krogh, Vittorio;Kurtz, Robert C.;McWilliams, Robert R.;Mendelsohn, Julie B.;Rabe, Kari G.;Riboli, Elio;Tjonneland, Anne;Tobias, Geoffrey S.;Trichopoulos, Dimitrios;Elena, Joanne W.;Yu, Herbert;Amundadottir, Laufey;Stolzenberg-Solomon, Rachael Z.;Kraft, Peter;Schumacher, Fredrick;Stram, Daniel;Savage, Sharon A.;Mirabello, Lisa;Andrulis, Irene L.;Wunder, Jay S.;Patino Garcia, Ana;Sierrasesumaga, Luis;Barkauskas, Donald A.;Gorlick, Richard G.;Purdue, Mark;Chow, Wong-Ho;Moore, Lee E.;Schwartz, Kendra L.;Davis, Faith G.;Hsing, Ann W.;Berndt, Sonja I.;Black, Amanda;Wentzensen, Nicolas;Brinton, Louise A.;Lissowska, Jolanta;Peplonska, Beata;McGlynn, Katherine A.;Cook, Michael B.;Graubard, Barry I.;Kratz, Christian P.;Greene, Mark H.;Erickson, Ralph L.;Hunter, David J.;Thomas, Gilles;Hoover, Robert N.;Real, Francisco X.;Fraumeni, Joseph F., Jr.;Caporaso, Neil E.;Tucker, Margaret;Rothman, Nathaniel;Perez-Jurado, Luis A.;Chanock, Stephen J.
通讯作者：
Chanock, Stephen J.