Epigenetic Aging Signatures Are Coherently Modified in Cancer
Our genome harbors epigenetic marks, such as DNA methylation (DNAm) at cytosine residues, which govern cellular differentiation. Some epigenetic modifications accumulate throughout life in a highly reproducible manner–they may contribute to the aging process and facilitate reliable age-predictions. So far, little is known how these “epigenetic aging signatures” are modified in cancer tissue and whether or not they are accelerated as compared to normal tissue. In this study, we systematically analyzed age-associated DNAm patterns in many types of cancer. In contrast to non-malignant tissue the epigenetic aging signatures hardly reflect chronological age of cancer patients. This may at least partially be attributed to the fact that cancer is a clonal disease capturing only the epigenetic make-up of the tumor-initiating cell. Notably, the aberrant DNAm patterns are not randomly distributed but reveal co-regulation at regions that become methylated upon aging in non-malignant tissue. Furthermore, we demonstrate that deviations of epigenetic age-predictions correlate with clinical parameters. In fact, they are clearly associated with overall survival in many types of cancer. These findings are particularly important, as they indicate relevance of age-associated DNA methylation patterns for malignant transformation, cancer development and prognosis.
Vyšlo v časopise:
Epigenetic Aging Signatures Are Coherently Modified in Cancer. PLoS Genet 11(6): e32767. doi:10.1371/journal.pgen.1005334
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005334
Souhrn
Our genome harbors epigenetic marks, such as DNA methylation (DNAm) at cytosine residues, which govern cellular differentiation. Some epigenetic modifications accumulate throughout life in a highly reproducible manner–they may contribute to the aging process and facilitate reliable age-predictions. So far, little is known how these “epigenetic aging signatures” are modified in cancer tissue and whether or not they are accelerated as compared to normal tissue. In this study, we systematically analyzed age-associated DNAm patterns in many types of cancer. In contrast to non-malignant tissue the epigenetic aging signatures hardly reflect chronological age of cancer patients. This may at least partially be attributed to the fact that cancer is a clonal disease capturing only the epigenetic make-up of the tumor-initiating cell. Notably, the aberrant DNAm patterns are not randomly distributed but reveal co-regulation at regions that become methylated upon aging in non-malignant tissue. Furthermore, we demonstrate that deviations of epigenetic age-predictions correlate with clinical parameters. In fact, they are clearly associated with overall survival in many types of cancer. These findings are particularly important, as they indicate relevance of age-associated DNA methylation patterns for malignant transformation, cancer development and prognosis.
Zdroje
1. Genovese G, Kahler AK, Handsaker RE, Lindberg J, Rose SA, et al. (2014) Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence. N Engl J Med 25: 2477–2487.
2. Gonzalo S, Jaco I, Fraga MF, Chen T, Li E, et al. (2006) DNA methyltransferases control telomere length and telomere recombination in mammalian cells. Nat Cell Biol 8: 416–424. 16565708
3. Wagner W, Weidner CI, Lin Q (2015) Do age-associated DNA methylation changes increase the risk of malignant transformation? Bioessays 37: 20–24. doi: 10.1002/bies.201400063 25303747
4. Teschendorff AE, West J, Beck S (2013) Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum Mol Genet 22: 7–15.
5. Bocklandt S, Lin W, Sehl ME, Sanchez FJ, Sinsheimer JS, et al. (2011) Epigenetic predictor of age. PLoS ONE 6: e14821. doi: 10.1371/journal.pone.0014821 21731603
6. Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biol 14: R115. 24138928
7. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, et al. (2013) Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell 49: 459–367.
8. Weidner CI, Lin Q, Koch CM, Eisele L, Beier F, et al. (2014) Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol 15: R24. doi: 10.1186/gb-2014-15-2-r24 24490752
9. Horvath S, Erhart W, Brosch M, Ammerpohl O, von SW, et al. (2014) Obesity accelerates epigenetic aging of human liver. Proc Natl Acad Sci U S A 111: 15538–15543. doi: 10.1073/pnas.1412759111 25313081
10. Koch CM, Reck K, Shao K, Lin Q, Joussen S, et al. (2013) Pluripotent stem cells escape from senescence-associated DNA methylation changes. Genome Res 23: 248–259. doi: 10.1101/gr.141945.112 23080539
11. Rando TA, Chang HY (2012) Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock. Cell 148: 46–57. doi: 10.1016/j.cell.2012.01.003 22265401
12. Jones PA, Baylin SB (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3: 415–428. 12042769
13. Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome—biological and translational implications. Nat Rev Cancer 11: 726–734. doi: 10.1038/nrc3130 21941284
14. Esteller M (2008) Epigenetics in cancer. N Engl J Med 358: 1148–1159. doi: 10.1056/NEJMra072067 18337604
15. Jost E, Lin Q, Ingrid WC, Wilop S, Hoffmann M, et al. (2014) Epimutations mimic genomic mutations of DNMT3A in acute myeloid leukemia. Leukemia 28: 1227–1234. doi: 10.1038/leu.2013.362 24280869
16. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, et al. (2010) Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 20: 440–446. doi: 10.1101/gr.103606.109 20219944
17. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics 98: 288–295. doi: 10.1016/j.ygeno.2011.07.007 21839163
18. Bullinger L, Ehrich M, Dohner K, Schlenk RF, Dohner H, et al. (2010) Quantitative DNA methylation predicts survival in adult acute myeloid leukemia. Blood 115: 636–642. doi: 10.1182/blood-2009-03-211003 19903898
19. Alvarez S, Suela J, Valencia A, Fernandez A, Wunderlich M, et al. (2010) DNA methylation profiles and their relationship with cytogenetic status in adult acute myeloid leukemia. PLoS ONE 5: e12197. doi: 10.1371/journal.pone.0012197 20808941
20. Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, et al. (2010) DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 17: 13–27. doi: 10.1016/j.ccr.2009.11.020 20060365
21. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, et al. (2010) Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18: 553–567. doi: 10.1016/j.ccr.2010.11.015 21130701
22. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, et al. (2009) Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 5: e1000602. doi: 10.1371/journal.pgen.1000602 19680444
23. Horvath S, Zhang Y, Langfelder P, Kahn RS, Boks MP, et al. (2012) Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol 13: R97. doi: 10.1186/gb-2012-13-10-r97 23034122
24. Kim J, Kim K, Kim H, Yoon G, Lee K (2014) Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies. BMC Genomics 15: 997. doi: 10.1186/1471-2164-15-997 25406591
25. Cancer Genome Atlas Research Network. (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 368: 2059–2074. doi: 10.1056/NEJMoa1301689 23634996
26. Douer D, Preston-Martin S, Chang E, Nichols PW, Watkins KJ, et al. (1996) High frequency of acute promyelocytic leukemia among Latinos with acute myeloid leukemia. Blood 87: 308–313. 8547657
27. Houseman EA, Molitor J, Marsit CJ (2014) Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 30: 1431–1439. doi: 10.1093/bioinformatics/btu029 24451622
28. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, et al. (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13: 86. doi: 10.1186/1471-2105-13-86 22568884
29. Yuan T, Jiao Y, de JS, Ophoff RA, Beck S, et al. (2015) An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet 11: e1004996. doi: 10.1371/journal.pgen.1004996 25692570
30. Thompson RF, Atzmon G, Gheorghe C, Liang HQ, Lowes C, et al. (2010) Tissue-specific dysregulation of DNA methylation in aging. Aging Cell 9: 506–518. doi: 10.1111/j.1474-9726.2010.00577.x 20497131
31. Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, et al. (2010) Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 20: 434–439. doi: 10.1101/gr.103101.109 20219945
32. Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, et al. (2010) Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res 20: 332–340. doi: 10.1101/gr.096826.109 20107151
33. Johansson A, Enroth S, Gyllensten U (2013) Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan. PLoS One 8: e67378. 23826282
34. McClay JL, Aberg KA, Clark SL, Nerella S, Kumar G, et al. (2014) A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet 23: 1175–1185. doi: 10.1093/hmg/ddt511 24135035
35. Day K, Waite LL, Thalacker-Mercer A, West A, Bamman MM, et al. (2013) Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol 14: R102. 24034465
36. Alisch RS, Barwick BG, Chopra P, Myrick LK, Satten GA, et al. (2012) Age-associated DNA methylation in pediatric populations. Genome Res 22: 623–632. doi: 10.1101/gr.125187.111 22300631
37. Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, et al. (2007) Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 39: 232–236. 17200670
38. Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, et al. (2007) Epigenetic stem cell signature in cancer. Nat Genet 39: 157–158. 17200673
39. Cruickshanks HA, McBryan T, Nelson DM, Vanderkraats ND, Shah PP, et al. (2013) Senescent cells harbour features of the cancer epigenome. Nat Cell Biol 15: 1495–1506. doi: 10.1038/ncb2879 24270890
40. Weidner CI, Wagner W (2014) The epigenetic tracks of aging. Biol Chem 395: 1307–1314. doi: 10.1515/hsz-2014-0180 25205717
41. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 102: 10604–10609. 16009939
42. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, et al. (2013) Signatures of mutational processes in human cancer. Nature 500: 415–421. doi: 10.1038/nature12477 23945592
43. Rideout WM III, Coetzee GA, Olumi AF, Jones PA (1990) 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 249: 1288–1290. 1697983
44. Yu DH, Waterland RA, Zhang P, Schady D, Chen MH, et al. (2014) Targeted p16(Ink4a) epimutation causes tumorigenesis and reduces survival in mice. J Clin Invest 124: 3708–3712. doi: 10.1172/JCI76507 25061879
45. Qu Y, Lennartsson A, Gaidzik VI, Deneberg S, Karimi M, et al. (2014) Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes. Epigenetics 9: 1108–1119. doi: 10.4161/epi.29315 24866170
46. Gronniger E, Weber B, Heil O, Peters N, Stab F, et al. (2010) Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet 6: e1000971. doi: 10.1371/journal.pgen.1000971 20523906
47. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43: 768–775. doi: 10.1038/ng.865 21706001
48. Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, et al. (2013) Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 8: 203–209. doi: 10.4161/epi.23470 23314698
49. Kyle RA, Rajkumar SV (2009) Criteria for diagnosis, staging, risk stratification and response assessment of multiple myeloma. Leukemia 23: 3–9. doi: 10.1038/leu.2008.291 18971951
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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