Somatic mutations, genome mosaicism, cancer and aging

Current Opinion in Genetics and Development

Volumn 26, Issue , 2014, Pages 141-149

  Vijg, Jan ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGING; ANEUPLOIDY; CARCINOGENESIS; CLONE; DETERIORATION; FUNCTIONAL DISEASE; GENE AMPLIFICATION; GENETIC VARIABILITY; GENOME MOSAICISM; GENOMICS; HUMAN; MOSAICISM; MUTAGENESIS; MUTATIONAL ANALYSIS; NEOPLASM; NONHUMAN; POINT MUTATION; REVIEW; SINGLE CELL ANALYSIS; SOMATIC CELL; SOMATIC MUTATION; TISSUE SPECIFICITY; ANIMAL; BIOLOGICAL MODEL; GENETIC ASSOCIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; PROCEDURES; TRENDS;

AGING; ANIMALS; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, GENETIC; MOSAICISM; MUTATION; NEOPLASMS; SINGLE-CELL ANALYSIS;

EID: 84904542026     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2014.04.002     Document Type: Review

References (72)

1. Baer C.F., Miyamoto M.M., Denver D.R. Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat Rev Genet 2007, 8:619-631.
2. Failla G. The aging process and carcinogenesis. Ann N Y Acad Sci 1958, 71:1124-1135.
3. Szilard L. On the nature of the aging process. Proc Natl Acad Sci U S A 1959, 45:30-45.
4. Curtis H. Biological mechanisms underlying the aging process. Science 1963, 141:686-694.
5. Vijg J. Aging of the Genome 2007, Oxford, New York.
6. Dollé M.E., Giese H., Hopkins C.L., Martus H.J., Hausdorff J.M., Vijg J. Rapid accumulation of genome rearrangements in liver but not in brain of old mice. Nat Genet 1997, 17:431-434.
7. Dollé M.E., Snyder W.K., Dunson D.B., Vijg J. Mutational fingerprints of aging. Nucleic Acids Res 2002, 30:545-549.
8. Dollé M.E., Snyder W.K., Gossen J.A., Lohman P.H., Vijg J. Distinct spectra of somatic mutations accumulated with age in mouse heart and small intestine. Proc Natl Acad Sci U S A 2000, 97:8403-8408.
9. Piotrowski A., Bruder C.E., Andersson R., Diaz de Stahl T., Menzel U., Sandgren J., Poplawski A., von Tell D., Crasto C., Bogdan A., et al. Somatic mosaicism for copy number variation in differentiated human tissues. Hum Mutat 2008, 29:1118-1124.
10. McConnell M.J., Lindberg M.R., Brennand K.J., Piper J.C., Voet T., Cowing-Zitron C., Shumilina S., Lasken R.S., Vermeesch J.R., Hall I.M., et al. Mosaic copy number variation in human neurons. Science 2013, 342:632-637.
11. Jacobs K.B., Yeager M., Zhou W., Wacholder S., Wang Z., Rodriguez-Santiago B., Hutchinson A., Deng X., Liu C., Horner M.J., et al. Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet 2012, 44:651-658.
12. Laurie C.C., Laurie C.A., Rice K., Doheny K.F., Zelnick L.R., McHugh C.P., Ling H., Hetrick K.N., Pugh E.W., Amos C., et al. Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nat Genet 2012, 44:642-650.
13. Forsberg L.A., Rasi C., Razzaghian H.R., Pakalapati G., Waite L., Thilbeault K.S., Ronowicz A., Wineinger N.E., Tiwari H.K., Boomsma D., et al. Age-related somatic structural changes in the nuclear genome of human blood cells. Am J Hum Genet 2012, 90:217-228.
14. Bruder C.E., Piotrowski A., Gijsbers A.A., Andersson R., Erickson S., de Stahl T.D., Menzel U., Sandgren J., von Tell D., Poplawski A., et al. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet 2008, 82:763-771.
15. Przybytkowski E., Ferrario C., Basik M. The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genom 2011, 4:16.
16. Ramsey M.J., Moore D.H., Briner J.F., Lee D.A., Olsen L., Senft J.R., Tucker J.D. The effects of age and lifestyle factors on the accumulation of cytogenetic damage as measured by chromosome painting. Mutat Res 1995, 338:95-106.
17. Tucker J.D., Spruill M.D., Ramsey M.J., Director A.D., Nath J. Frequency of spontaneous chromosome aberrations in mice: effects of age. Mutat Res 1999, 425:135-141.
18. Iourov I.Y., Vorsanova S.G., Yurov Y.B. Chromosomal mosaicism goes global. Mol Cytogenet 2008, 1:26.
19. Faggioli F., Wang T., Vijg J., Montagna C. Chromosome-specific accumulation of aneuploidy in the aging mouse brain. Hum Mol Genet 2012, 21:5246-5253.
20. Yurov Y.B., Iourov I.Y., Vorsanova S.G., Liehr T., Kolotii A.D., Kutsev S.I., Pellestor F., Beresheva A.K., Demidova I.A., Kravets V.S., et al. Aneuploidy and confined chromosomal mosaicism in the developing human brain. PLoS ONE 2007, 2:e558.
21. Rehen S.K., McConnell M.J., Kaushal D., Kingsbury M.A., Yang A.H., Chun J. Chromosomal variation in neurons of the developing and adult mammalian nervous system. Proc Natl Acad Sci U S A 2001, 98:13361-13366.
22. Vanneste E., Voet T., Le Caignec C., Ampe M., Konings P., Melotte C., Debrock S., Amyere M., Vikkula M., Schuit F., et al. Chromosome instability is common in human cleavage-stage embryos. Nat Med 2009, 15:577-583.
23. Coolbaugh-Murphy M.I., Xu J., Ramagli L.S., Brown B.W., Siciliano M.J. Microsatellite instability (MSI) increases with age in normal somatic cells. Mech Ageing Dev 2005, 126:1051-1059.
24. Muotri A.R., Chu V.T., Marchetto M.C., Deng W., Moran J.V., Gage F.H. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 2005, 435:903-910.
25. Perrat P.N., DasGupta S., Wang J., Theurkauf W., Weng Z., Rosbash M., Waddell S. Transposition-driven genomic heterogeneity in the Drosophila brain. Science 2013, 340:91-95.
26. Evrony G.D., Cai X., Lee E., Hills L.B., Elhosary P.C., Lehmann H.S., Parker J.J., Atabay K.D., Gilmore E.C., Poduri A., et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 2012, 151:483-496.
27. Hu Z., Chen K., Xia Z., Chavez M., Pal S., Seol J.H., Chen C.C., Li W., Tyler J.K. Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes Dev 2014, 28:396-408.
28. Aubert G., Lansdorp P.M. Telomeres and aging. Physiol Rev 2008, 88:557-579.
29. Olovnikov A.M. A theory of marginotomy. The incomplete copying of template margin in enzymic synthesis of polynucleotides and biological significance of the phenomenon. J Theor Biol 1973, 41:181-190.
30. Gundry M., Vijg J. Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat Res 2012, 729:1-15.
31. Mardis E.R. A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203.
32. Weber-Lehmann J., Schilling E., Gradl G., Richter D.C., Wiehler J., Rolf B. Finding the needle in the haystack: Differentiating "identical" twins in paternity testing and forensics by ultra-deep next generation sequencing. Forensic Sci Int Genet 2014, 9:42-46.
33. Quail M.A., Swerdlow H., Turner D.J. Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet 2009, Chapter 18: Unit 18.2.
34. Kinde I., Wu J., Papadopoulos N., Kinzler K.W., Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A 2011, 108:9530-9535.
35. Salk J.J., Fox E.J., Loeb L.A. Mutational heterogeneity in human cancers: origin and consequences. Ann Rev Pathol 2010, 5:51-75.
36. Gundry M., Li W., Maqbool S.B., Vijg J. Direct, genome-wide assessment of DNA mutations in single cells. Nucleic Acids Res 2012, 40:2032-2040.
37. Campbell P.J., Stephens P.J., Pleasance E.D., O'Meara S., Li H., Santarius T., Stebbings L.A., Leroy C., Edkins S., Hardy C., et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40:722-729.
38. Lasken R.S. Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans 2009, 37:450-453.
39. Dear P.H. One by one: single molecule tools for genomics. Brief Funct Genomic Proteomic 2003, 1:397-416.
40. Zong C., Lu S., Chapman A.R., Xie X.S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 2012, 338:1622-1626.
41. Michaelson J.J., Shi Y., Gujral M., Zheng H., Malhotra D., Jin X., Jian M., Liu G., Greer D., Bhandari A., et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 2012, 151:1431-1442.
42. Yancik R., Ries L.A. Cancer in older persons: an international issue in an aging world. Semin Oncol 2004, 31:128-136.
43. Ershler W.B., Longo D.L. Aging and cancer: issues of basic and clinical science. J Natl Cancer Inst 1997, 89:1489-1497.
44. Levine B., Kroemer G. Autophagy in the pathogenesis of disease. Cell 2008, 132:27-42.
45. DePinho R.A. The age of cancer. Nature 2000, 408:248-254.
46. Ames B.N., Gold L.S. Endogenous mutagens and the causes of aging and cancer. Mutat Res 1991, 250:3-16.
47. Doll R., Peto R. Cigarette smoking and bronchial carcinoma: dose and time relationships among regular smokers and lifelong non-smokers. J Epidemiol Commun Health 1978, 32:303-313.
48. Pfeifer G.P., Denissenko M.F., Olivier M., Tretyakova N., Hecht S.S., Hainaut P. Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers. Oncogene 2002, 21:7435-7451.
49. Govindan R., Ding L., Griffith M., Subramanian J., Dees N.D., Kanchi K.L., Maher C.A., Fulton R., Fulton L., Wallis J., et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012, 150:1121-1134.
50. Fearon E.R., Vogelstein B. A genetic model for colorectal tumorigenesis. Cell 1990, 61:759-767.
51. Tomasetti C., Vogelstein B., Parmigiani G. Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proc Natl Acad Sci U S A 2013, 110:1999-2004.
52. Lawrence M.S., Stojanov P., Polak P., Kryukov G.V., Cibulskis K., Sivachenko A., Carter S.L., Stewart C., Mermel C.H., Roberts S.A., et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013, 499:214-218.
53. Welch J.S., Ley T.J., Link D.C., Miller C.A., Larson D.E., Koboldt D.C., Wartman L.D., Lamprecht T.L., Liu F., Xia J., et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 2012, 150:264-278.
54. Martin G.M. Somatic mutagenesis and antimutagenesis in aging research. Mutat Res 1996, 350:35-41.
55. Vijg J., Calder R.B. Transcripts of aging. Trends Genet 2004, 20:221-224.
56. Hasty P., Campisi J., Hoeijmakers J., van Steeg H., Vijg J. Aging and genome maintenance: lessons from the mouse?. Science 2003, 299:1355-1359.
57. Ness K.K., Krull K.R., Jones K.E., Mulrooney D.A., Armstrong G.T., Green D.M., Chemaitilly W., Smith W.A., Wilson C.L., Sklar C.A., et al. Physiologic frailty as a sign of accelerated aging among adult survivors of childhood cancer: a report from the st jude lifetime cohort study. J Clin Oncol 2013, 31:4496-4503.
58. Henderson T.O., Whitton J., Stovall M., Mertens A.C., Mitby P., Friedman D., Strong L.C., Hammond S., Neglia J.P., Meadows A.T., et al. Secondary sarcomas in childhood cancer survivors: a report from the Childhood Cancer Survivor Study. J Natl Cancer Inst 2007, 99:300-308.
59. O'Roak B.J., Deriziotis P., Lee C., Vives L., Schwartz J.J., Girirajan S., Karakoc E., Mackenzie A.P., Ng S.B., Baker C., et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet 2011, 43:585-589.
60. Sanders S.J., Ercan-Sencicek A.G., Hus V., Luo R., Murtha M.T., Moreno-De-Luca D., Chu S.H., Moreau M.P., Gupta A.R., Thomson S.A., et al. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron 2011, 70:863-885.
61. Erickson R. Somatic gene mutation and human disease other than cancer. Mut Res/Rev Mutat Res 2003, 543:125-136.
62. Garcia-Linares C., Fernandez-Rodriguez J., Terribas E., Mercade J., Pros E., Benito L., Benavente Y., Capella G., Ravella A., Blanco I., et al. Dissecting loss of heterozygosity (LOH) in neurofibromatosis type 1-associated neurofibromas: Importance of copy neutral LOH. Hum Mutat 2011, 32:78-90.
63. Beck J.A., Poulter M., Campbell T.A., Uphill J.B., Adamson G., Geddes J.F., Revesz T., Davis M.B., Wood N.W., Collinge J., et al. Somatic and germline mosaicism in sporadic early-onset Alzheimer's disease. Hum Mol Genet 2004, 13:1219-1224.
64. Andreassi M.G. Coronary atherosclerosis and somatic mutations: an overview of the contributive factors for oxidative DNA damage. Mutat Res 2003, 543:67-86.
65. Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
66. Kong A., Frigge M.L., Masson G., Besenbacher S., Sulem P., Magnusson G., Gudjonsson S.A., Sigurdsson A., Jonasdottir A., Wong W.S., et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 2012, 488:471-475.
67. Lynch M. Evolution of the mutation rate. Trends Genet: TIG 2010, 26:345-352.
68. Vogelstein B., Papadopoulos N., Velculescu V.E., Zhou S., Diaz L.A., Kinzler K.W. Cancer genome landscapes. Science 2013, 339:1546-1558.
69. Orgel L.E. The maintenance of the accuracy of protein synthesis and its relevance to ageing. Proc Natl Acad Sci U S A 1963, 49:517-521.
70. Sacher G.A. Evolutionary theory in gerontology. Perspect Biol Med 1982, 25:339-353.
71. Kirkwood T.B. Understanding the odd science of aging. Cell 2005, 120:437-447.
72. Singer T., McConnell M.J., Marchetto M.C., Coufal N.G., Gage F.H. LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes?. Trends Neurosci 2010, 33:345-354.