DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy

Aging

Volumn 8, Issue 2, 2016, Pages 394-401

  Lin, Qiong ^a   Weidner, Carola I ^a   Costa, Ivan G ^a   Marioni, Riccardo E ^b,c   Ferreira, Marcelo R ^a,d   Deary, Ian J ^b   Wagner, Wolfgang ^a  

^a RWTH AACHEN UNIVERSITY   (Germany)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d FEDERAL UNIVERSITY OF PARAÍBA   (Brazil)

Author keywords

Age; Aging; CLCN6; DNA methylation; Epigenetic; Mortality; PDE4C; Prediction; Predictor; Survival

Indexed keywords

AGED; AGING; CPG ISLAND; DNA METHYLATION; FEMALE; GENETIC EPIGENESIS; GENETICS; HUMAN; LIFE EXPECTANCY; MALE; PHYSIOLOGY; PROPORTIONAL HAZARDS MODEL;

AGED; AGING; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; HUMANS; LIFE EXPECTANCY; MALE; PROPORTIONAL HAZARDS MODELS;

EID: 84961207286     PISSN: 19454589     EISSN: None     Source Type: Journal    
DOI: 10.18632/aging.100908     Document Type: Article

References (32)

1. Koch CM, Wagner W. Epigenetic-aging-signature to determine age in different tissues. Aging (Albany NY) 2011; 3: 1018-1027.
2. Bork S, Pfister S, Witt H, Horn P, Korn B, Ho AD, Wagner W. DNA Methylation Pattern Changes upon Long-Term Culture and Aging of Human Mesenchymal Stromal Cells. Aging Cell 2010; 9: 54-63.
3. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, Campan M, Noushmehr H, Bell CG, Maxwell AP, Savage DA, Mueller-Holzner E, Marth C, et al. Agedependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010; 20: 440-446.
4. Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, Leslie RD, Deloukas P, Spector TD. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010; 20: 434-439.
5. Bocklandt S, Lin W, Sehl ME, Sanchez FJ, Sinsheimer JS, Horvath S, Vilain E. Epigenetic predictor of age. PLoS ONE 2011; 6: e14821.
6. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, et al. Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell 2013; 49: 459-467.
7. Horvath S. DNA methylation age of human tissues and cell types. Genome Biol 2013; 14: R115.
8. Weidner CI, Lin Q, Koch CM, Eisele L, Beier F, Ziegler P, Bauerschlag DO, Jockel KH, Erbel R, Muhleisen TW, Zenke M, Brummendorf TH, Wagner W. Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol 2014; 15: R24.
9. Marioni RE, Shah S, McRae AF, Chen BH, Colicino E, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, et al. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol 2015; 16: 25.
10. Weidner CI, Ziegler P, Hahn M, Brummendorf TH, Ho AD, Dreger P, Wagner W. Epigenetic aging upon allogeneic transplantation: the hematopoietic niche does not affect ageassociated DNA methylation. Leukemia 2015; 29: 985-988.
11. Lin Q, Wagner W. Epigenetic Aging Signatures Are Coherently Modified in Cancer. PLoS Genet 2015; 11: e1005334.
12. Alisch RS, Barwick BG, Chopra P, Myrick LK, Satten GA, Conneely KN, Warren ST. Age-associated DNA methylation in pediatric populations. Genome Res 2012; 22: 623-632.
13. Deary IJ, Gow AJ, Pattie A, Starr JM. Cohort profile: the Lothian Birth Cohorts of 1921 and 1936. Int J Epidemiol 2012; 41: 1576-1584.
14. Tomaszewski M, Debiec R, Braund PS, Nelson CP, Hardwick R, Christofidou P, Denniff M, Codd V, Rafelt S, van der Harst P, Waterworth D, Song K, Vollenweider P, et al. Genetic architecture of ambulatory blood pressure in the general population: insights from cardiovascular gene-centric array. Hypertension 2010; 56: 1069-1076.
15. Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, Dehghan A, Glazer NL, Morrison AC, Johnson AD, Aspelund T, Aulchenko Y, Lumley T, Kottgen A, et al. Genome-wide association study of blood pressure and hypertension. Nat Genet 2009; 41: 677-687.
16. Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath S. C, Eyheramendy S, Papadakis K, Voight BF, Scott LJ, et al. Genome-wide association study identifies eight loci associated with blood pressure. Nat Genet 2009; 41: 666-676.
17. Flister MJ, Tsaih SW, O'Meara CC, Endres B, Hoffman MJ, Geurts AM, Dwinell MR, Lazar J, Jacob HJ, Moreno C. Identifying multiple causative genes at a single GWAS locus. Genome Res 2013; 23: 1996-2002.
18. Marioni RE, Shah S, McRae AF, Ritchie SJ, Muniz-Terrera G, Harris SE, Gibson J, Redmond P, Cox SR, Pattie A, Corley J, Taylor A, Murphy L, et al. The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. Int J Epidemiol 2015; 44: 1388-1396.
19. Christiansen L, Lenart A, Tan Q, Vaupel JW, Aviv A, McGue M, Christensen K. DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell 2015 (Epub ahead of print).
20. R-Core-Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing 2014; Vienna, Austria.: URL http://www.R-project.org/.
21. Kuhn M. caret: Classification and Regression Training. R package version 6 0-41 2015; URL: http://CRAN.R-project.org/package=caret.
22. Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, Diez J, Sanchez-Mut JV, Setien F, Carmona FJ, Puca AA, Sayols S, Pujana MA, et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A 2012; 109: 10522-10527.
23. Harris R A, Nagy-Szakal D, Pedersen N, Opekun A, Bronsky J, Munkholm P, Jespersgaard C, Andersen P, Melegh B, Ferry G, Jess T, Kellermayer R. Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases. Inflamm Bowel Dis 2012; 18: 2334-2341.
24. Horvath S, Zhang Y, Langfelder P, Kahn RS, Boks MP, van EK, van den Berg LH, Ophoff RA. Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol 2012; 13: R97.
25. Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, Reinius L, Acevedo N, Taub M, Ronninger M, Shchetynsky K, Scheynius A, Kere J, et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 2013; 31: 142-147.
26. Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Vinuela A, Grundberg E, Nelson CP, Meduri E, Buil A, Cambien F, Hengstenberg C, et al. Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2014; 9: 1382-1396.
27. Shah S, McRae AF, Marioni RE, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, et al. Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Res 2014; 24: 1725-1733.
28. Reynolds LM, Taylor JR, Ding J, Lohman K, Johnson C, Siscovick D, Burke G, Post W, Shea S, Jacobs DR Jr, Stunnenberg H, Kritchevsky SB, Hoeschele I, et al. Age-related variations in the methylome associated with gene expression in human monocytes and T cells. Nat Commun 2014; 5: 5366.
29. Dhas DB, Ashmi AH, Bhat BV, Kalaivani S, Parija SC. Comparison of genomic DNA methylation pattern among septic and non-septic newborns-An epigenome wide association study. Genom Data 2015; 3: 36-40.
30. Tan Q, Frost M, Heijmans BT, von Bornemann HJ, Tobi EW, Christensen K, Christiansen L. Epigenetic signature of birth weight discordance in adult twins. BMC Genomics 2014; 15: 1062.
31. Rojas D, Rager JE, Smeester L, Bailey KA, Drobna Z, Rubio-Andrade M, Styblo M, Garcia-Vargas G, Fry RC. Prenatal arsenic exposure and the epigenome: identifying sites of 5-methylcytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes. Toxicol Sci 2015; 143: 97-106.
32. Therneau T. A Package for Survival Analysis in S. R package version 2 37-7 2015; URL: http://CRAN.R-project.org/package=survival.