Evolution of the cancer genome

Trends in Genetics

Volumn 28, Issue 4, 2012, Pages 155-163

  Podlaha, Ondrej ^a   Riester, Markus ^a   De, Subhajyoti ^a   Michor, Franziska ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BREAST CANCER; CANCER CELL; CANCER RESEARCH; CANCER RESISTANCE; CANCER SUSCEPTIBILITY; CHROMOSOME REARRANGEMENT; DNA METHYLATION; EPIGENETICS; GENE AMPLIFICATION; GENE DELETION; GENE FUSION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENOMIC INSTABILITY; GERM LINE; GLIOBLASTOMA; HISTONE MODIFICATION; HUMAN; HUMAN GENOME; LYMPHATIC LEUKEMIA; NEOPLASM; NONHUMAN; OVARY CANCER; POINT MUTATION; PRIORITY JOURNAL; REVIEW; SOMATIC MUTATION;

ANIMALS; DISEASE PROGRESSION; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENOME; HUMANS; NEOPLASMS;

EID: 84859000573     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2012.01.003     Document Type: Review

References (100)

1. Futuyma D.J. Evolutionary Biology 1997, Sinauer Associates.
2. Hanahan D., Weinberg R.A. The hallmarks of cancer. Cell 2000, 100:57-70.
3. Campbell P.J., et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 2010, 467:1109-1113.
4. Nowell P.C. The clonal evolution of tumor cell populations. Science 1976, 194:23-28.
5. Cairns J. Mutation selection and the natural history of cancer. Nature 1975, 255:197-200.
6. Fisher J.C. Multiple-mutation theory of carcinogenesis. Nature 1958, 181:651-652.
7. De S. Somatic mosaicism in healthy human tissues. Trends Genet. 2011, 27:217-223.
8. Boveri T. Zur Frage der Entstehung Maligner Tumoren 1914, Gustav Fisher.
9. Rowley J.D. Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 1973, 243:290-293.
10. Deininger M.W., et al. The molecular biology of chronic myeloid leukemia. Blood 2000, 96:3343-3356.
11. Forbes S.A., et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet. 2008, Chapter 10, Unit 10.11.
12. Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068.
13. Cancer Genome Atlas Research Network Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615.
14. Parsons D.W., et al. The genetic landscape of the childhood cancer medulloblastoma. Science 2011, 331:435-439.
15. Lee W., et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 2010, 465:473-477.
16. Lengauer C., et al. Genetic instabilities in human cancers. Nature 1998, 396:643-649.
17. De S., Babu M.M A time-invariant principle of genome evolution. Natl Acad Sci U. S. A. 2010, 107:13004-13009.
18. Sahin E., Depinho R.A. Linking functional decline of telomeres, mitochondria and stem cells during ageing. Nature 2010, 464:520-528.
19. Olivier M., et al. TP53 mutation spectra and load: a tool for generating hypotheses on the etiology of cancer. IARC Sci. Publ. 2004, 247-270.
20. Heng H.H., et al. Evolutionary mechanisms and diversity in cancer. Adv. Cancer Res. 2011, 112:217-253.
21. Heng H.H., et al. Stochastic cancer progression driven by non-clonal chromosome aberrations. J. Cell. Physiol. 2006, 208:461-472.
22. Stephens P.J., et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011, 144:27-40.
23. Navin N., et al. Tumour evolution inferred by single-cell sequencing. Nature 2011, 472:90-94.
24. Eldredge N., Gould S.J. Punctuated equilibria: an alternative to phyletic gradualism. Models in Paleobiology 1972, 82-115. Freeman Cooper. T.J.M. Schopf (Ed.).
25. Gould S.J., Eldredge N. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 1977, 115-151.
26. Gould S.J., Eldredge N. Punctuated equilibrium comes of age. Nature 1993, 223-227.
27. Scheble V.J., et al. ERG rearrangement is specific to prostate cancer and does not occur in any other common tumor. Mod. Pathol. 2010, 23:1061-1067.
28. Shtivelman E., et al. Fused transcript of abl and bcr genes in chronic myelogenous leukaemia. Nature 1985, 315:550-554.
29. Forbes S.A., et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011, 39:D945-D950.
30. Charlesworth B., Charlesworth D. Elements of Evolutionary Genetics 2010, Roberts and Company Publishers.
31. Akavia U.D., et al. An integrated approach to uncover drivers of cancer. Cell 2010, 143:1005-1017.
32. Beroukhim R., et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463:899-905.
33. Bignell G.R., et al. Signatures of mutation and selection in the cancer genome. Nature 2010, 463:893-898.
34. Sjoblom T., et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274.
35. Forrest W.F., Cavet G. Comment on 'The consensus coding sequences of human breast and colorectal cancers'. Science 2007, 317:1500.
36. Getz G., et al. Comment on 'The consensus coding sequences of human breast and colorectal cancers'. Science 2007, 317:1500.
37. Rubin A.F., Green P. Comment on 'The consensus coding sequences of human breast and colorectal cancers'. Science 2007, 317:1500.
38. Goldman N., Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 1994, 11:725-736.
39. Greenman C., et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446:153-158.
40. Beroukhim R., et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:20007-20012.
41. Reva B., et al. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011, 39:e118.
42. Zhang Y., et al. Molecular evolutionary analysis of cancer cell lines. Mol. Cancer Ther. 2010, 9:279-291.
43. Jones A.V., et al. JAK2 haplotype is a major risk factor for the development of myeloproliferative neoplasms. Nat. Genet. 2009, 41:446-449.
44. Kilpivaara O., et al. A germline JAK2 SNP is associated with predisposition to the development of JAK2(V617F)-positive myeloproliferative neoplasms. Nat. Genet. 2009, 41:455-459.
45. Olcaydu D., et al. A common JAK2 haplotype confers susceptibility to myeloproliferative neoplasms. Nat. Genet. 2009, 41:450-454.
46. Stratton M.R., Rahman N. The emerging landscape of breast cancer susceptibility. Nat. Genet. 2008, 40:17-22.
47. Macgregor S., et al. Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3. Nat. Genet. 2011, 43:1114-1118.
48. Shi Y., et al. A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1. Nat. Genet. 2011, 43:1215-1218.
49. Haiman C.A., et al. A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer. Nat. Genet. 2011, 43:1210-1214.
50. Rafnar T., et al. Mutations in BRIP1 confer high risk of ovarian cancer. Nat. Genet. 2011, 43:1104-1107.
51. Jones P.A., Baylin S.B. The epigenomics of cancer. Cell 2007, 128:683-692.
52. Feinberg A.P., Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983, 301:89-92.
53. Jones P.A., Baylin S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 2002, 3:415-428.
54. Johnson D.S., et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502.
55. Meissner A., et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454:766-770.
56. Chen R.Z., et al. DNA hypomethylation leads to elevated mutation rates. Nature 1998, 395:89-93.
57. Gaudet F., et al. Induction of tumors in mice by genomic hypomethylation. Science 2003, 300:489-492.
58. Bennett-Baker P.E., et al. Age-associated activation of epigenetically repressed genes in the mouse. Genetics 2003, 165:2055-2062.
59. Bocker M.T., et al. Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging. Blood 2011, 117:e182-e189.
60. Esteller M., et al. Promoter hypermethylation of the DNA repair gene O(6)-methylguanine-DNA methyltransferase is associated with the presence of G:C to A:T transition mutations in p53 in human colorectal tumorigenesis. Cancer Res. 2001, 61:4689-4692.
61. Chiang J.W., et al. BRCA1 promoter methylation predicts adverse ovarian cancer prognosis. Gynecol. Oncol. 2006, 101:403-410.
62. Goel A., et al. De novo constitutional MLH1 epimutations confer early-onset colorectal cancer in two new sporadic Lynch syndrome cases, with derivation of the epimutation on the paternal allele in one. Int. J. Cancer 2011, 128:869-878.
63. Issa J.P., et al. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nat. Genet. 1994, 7:536-540.
64. Suzuki H., et al. Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer. Nat. Genet. 2004, 36:417-422.
65. Baylin S.B., Ohm J.E. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?. Nat. Rev. Cancer 2006, 6:107-116.
66. De S., Michor F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat. Struct. Mol. Biol. 2011, 18:950-955.
67. De S., Michor F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat. Biotechnol. 2011, 29:1103-1108.
68. Fudenberg G., et al. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol. 2011, 29:1109-1113.
69. Tay Y., et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 2011, 147:344-357.
70. Sumazin P., et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 2011, 147:370-381.
71. Mavrakis K.J., et al. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat. Cell Biol. 2010, 12:372-379.
72. Ting D.T., et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 2011, 331:593-596.
73. Baillie J.K., et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 2011, 479:534-537.
74. Aporntewan C., et al. Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PLoS ONE 2011, 6:e17934.
75. Gupta R.A., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
76. Bjornsson H.T., et al. An integrated epigenetic and genetic approach to common human disease. Trends Genet. 2004, 20:350-358.
77. Toyota M., et al. Cancer epigenomics: implications of DNA methylation in personalized cancer therapy. Cancer Sci. 2009, 100:787-791.
78. Feinberg A.P., et al. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet. 2006, 7:21-33.
79. Navin N., et al. Inferring tumor progression from genomic heterogeneity. Genome Res. 2010, 20:68-80.
80. Park S.Y., et al. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J. Clin. Invest. 2010, 120:636-644.
81. Teixeira M.R., et al. Clonal heterogeneity in breast cancer: karyotypic comparisons of multiple intra- and extra-tumorous samples from 3 patients. Int. J. Cancer 1995, 63:63-68.
82. Torres L., et al. Intratumor genomic heterogeneity in breast cancer with clonal divergence between primary carcinomas and lymph node metastases. Breast Cancer Res. Treat. 2007, 102:143-155.
83. Yachida S., et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010, 467:1114-1117.
84. Fitzgerald P.J. Homogeneity and heterogeneity in pancreas cancer: presence of predominant and minor morphological types and implications. Int. J. Pancreatol. 1986, 1:91-94.
85. Komaki K., et al. Problems in histological grading of malignancy and its clinical significance in patients with operable breast cancer. Breast Cancer 2006, 13:249-253.
86. Maley C.C., et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 2006, 38:468-473.
87. Khalique L., et al. Genetic intra-tumour heterogeneity in epithelial ovarian cancer and its implications for molecular diagnosis of tumours. J. Pathol. 2007, 211:286-295.
88. Bachtiary B., et al. Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity. Clin. Cancer Res. 2006, 12:5632-5640.
89. Navin N., Hicks J. Future medical applications of single-cell sequencing in cancer. Genome Med. 2011, 3:31.
90. Norton L., Massague J. Is cancer a disease of self-seeding?. Nat. Med. 2006, 12:875-878.
91. Tan R.Z., van Oudenaarden A. Transcript counting in single cells reveals dynamics of rDNA transcription. Mol. Syst. Biol. 2010, 6:358.
92. Tang F., et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 2009, 6:377-382.
93. Snuderl M., et al. Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma. Cancer Cell 2011, 20:810-817.
94. Reya T., et al. Stem cells, cancer, and cancer stem cells. Nature 2001, 414:105-111.
95. Bonnet D., Dick J.E. Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat. Med. 1997, 3:730-737.
96. Al-Hajj M., et al. Prospective identification of tumorigenic breast cancer cells. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:3983-3988.
97. Dalerba P., et al. Phenotypic characterization of human colorectal cancer stem cells. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:10158-10163.
98. Navin N.E., Hicks J. Tracing the tumor lineage. Mol. Oncol. 2010, 4:267-283.
99. Liang S., et al. Resistance to experimental tumorigenesis in cells of a long-lived mammal, the naked mole-rat (Heterocephalus glaber). Aging Cell 2010, 9:626-635.
100. Kim E.B., et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 2011, 479:223-227.