A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas

Cancer Research

Volumn 72, Issue 23, 2012, Pages 6279-6289

  Nikolaev, Sergey I ^a   Sotiriou, Sotirios K ^b   Pateras, Ioannis S ^d   Santoni, Federico ^a   Sougioultzis, Stavros ^e   Edgren, Henrik ^f   Almusa, Henrikki ^f   Robyr, Daniel ^a   Guipponi, Michel ^a   Saarela, Janna ^f   Gorgoulis, Vassilis G ^d   Antonarakis, Stylianos E ^a,c   Halazonetis, Thanos D ^b,c  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c Institute of Genetics and Genomics of Geneva (iGE3)   (Switzerland)

^d UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

^e UNIVERSITY OF ATHENS   (Greece)

^f UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

APC PROTEIN; B RAF KINASE;

APC GENE; ARTICLE; BRAF GENE; COLON ADENOMA; COLON POLYP; CONTROLLED STUDY; CTNNB1 GENE; DNA REPLICATION; EXOME; GENE; GENE DELETION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENOMIC INSTABILITY; HUMAN; HUMAN TISSUE; MUTATION RATE; MUTATOR PHENOTYPE; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE SUBSTITUTION;

ADENOMA; COLORECTAL NEOPLASMS; DNA REPAIR; EXOME; GENOME, HUMAN; GENOMIC INSTABILITY; HUMANS; MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84870377034     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-12-3869     Document Type: Article

References (56)

1. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011;144:646-74.
2. Luo J, Solimini NL, Elledge SJ. Principles of cancer therapy: oncogene and non-oncogene addiction. Cell 2009;136:823-37.
3. Grady WM, Carethers JM. Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology 2008;135:1079-99.
4. Negrini S, Gorgoulis VG, Halazonetis TD. Genomic instability - an evolving hallmark of cancer. Nat Rev Mol Cell Biol 2010;11:220-8.
5. Halazonetis TD, Gorgoulis VG, Bartek J. An oncogene-induced DNA damage model for cancer development. Science 2008;319: 1352-5. (Pubitemid 351354863)
6. Dereli-Oz A, Versini G, Halazonetis TD. Studies of genomic copy number changes in human cancers reveal signatures of DNA replication stress. Mol Oncol 2011;5:308-14.
7. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010;463:899-905.
8. Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, et al. Signatures of mutation and selection in the cancer genome. Nature 2010;463:893-8.
9. Arlt MF, Casper AM, Glover TW. Common fragile sites. Cytogenet Genome Res 2003;100:92-100. (Pubitemid 37467795)
10. Arlt MF, Mulle JG, Schaibley VM, Ragland RL, Durkin SG, Warren ST, et al. Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants.Am J Hum Genet 2009;84:339-50.
11. Pasi CE, Dereli-Oz A, Negrini S, Friedli M, Fragola G, Lombardo A, et al. Genomic instability in induced stem cells. Cell Death Differ 2011;18:745-53.
12. Arlt MF, Ozdemir AC, Birkeland SR, Wilson TE, Glover TW. Hydroxyurea induces de novo copy number variants in human cells. Proc Natl Acad Sci U S A 2011;108:17360-5.
13. Bartkova J, Rezaei N, Liontos M, Karakaidos P, Kletsas D, Issaeva N, et al. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature 2006;444:633-7. (Pubitemid 44864442)
14. Di Micco R, Fumagalli M, Cicalese A, Piccinin S, Gasparini P, Luise C, et al. Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 2006;444:638-42. (Pubitemid 44864443)
15. Tsantoulis PK, Kotsinas A, Sfikakis PP, Evangelou K, Sideridou M, Levy B, et al. Oncogene-induced replication stress preferentially targets common fragile sites in preneoplastic lesions. A genome-wide study. Oncogene 2008;27:3256-64. (Pubitemid 351733389)
16. Gorgoulis VG, Vassiliou LV, Karakaidos P, Zacharatos P, Kotsinas A, Liloglou T, et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 2005;434:907-13. (Pubitemid 40559004)
17. Bartkova J, Horejsi Z, Koed K, Kramer A, Tort F, Zieger K, et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature 2005;434:864-70. (Pubitemid 40558993)
18. Schepeler T, Lamy P, Laurberg JR, Fristrup N, Reinert T, Bartkova J, et al. A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response. Oncogene. Epub 2012 Aug 27.
19. Loeb LA, Springgate CF, Battula N. Errors in DNA replication as a basis of malignant changes. Cancer Res 1974;34:2311-21.
20. Loeb LA, Bielas JH, Beckman RA. Cancers exhibit a mutator phenotype: clinical implications. Cancer Res 2008;68:3551-7.
21. Loeb LA. Human cancers express mutator phenotypes: origin, consequences and targeting. Nat Rev Cancer 2011;11:450-7.
22. Sieber OM, Heinimann K, Tomlinson IP. Genomic instability - the engine of tumorigenesis? Nat Rev Cancer 2003;3:701-8. (Pubitemid 37328825)
23. Bodmer W. Genetic instability is not a requirement for tumor development. Cancer Res 2008;68:3558-60.
24. Shibata D, Lieber MR. Is there any genetic instability in human cancer? DNA Repair 2010;9:858.
25. Fox EJ, Beckman RA, Loeb LA. Reply: is there any genetic instability in human cancer? DNA Repair 2010;9:859-60.
26. Wu J, Jiao Y, Dal Molin M, Maitra A, de Wilde RF, Wood LD, et al. Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proc Natl Acad Sci U S A 2011;108:21188-93.
27. Furukawa T, Kuboki Y, Tanji E, Yoshida S, Hatori T, Yamamoto M, et al. Whole-exome sequencing uncovers frequent GNAS mutations in intraductal papillary mucinous neoplasms of the pancreas. Sci Rep 2011;1:161.
28. Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, Gehrig C, et al. Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Gen 2012;44:133-9.
29. Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, et al. MuSiC: identifying mutational significance in cancer genomes. Genome Res 2012;22:1589-98.
30. Sulonen AM, Ellonen P, Almusa H, Lepisto M, Eldfors S, Hannula S, et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol 2011;12:r94.
31. Fearon ER. Molecular genetics of colorectal cancer. Annu Rev Pathol Mech Dis 2011;6:479-507.
32. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006;314:268-74. (Pubitemid 44571966)
33. Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet 2011;43:964-8.
34. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330-7.
35. Clevers H, Nusse R. Wnt/beta-catenin signaling and disease. Cell 2012;149:1192-205.
36. Chan TL, Zhao W, Leung SY, Yuen ST, Cancer Genome Project. BRAF and KRAS mutations in colorectal hyperplastic polyps and serrated adenomas. Cancer Res 2003;63:4878-81. (Pubitemid 37022620)
37. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, et al. COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res 2011;39:d945-50.
38. Jones S, Li M, Parsons DW, Zhang X, Wesseling J, Kristel P, et al. Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types. Hum Mutat 2012;33:100-3.
39. Blache P, van de Wetering M, Duluc I, Domon C, Berta P, Freund JN, et al. SOX9 is an intestine crypt transcription factor, is regulated by the Wnt pathway, and represses the CDX2 and MUC2 genes. J Cell Biol 2004;166:37-47. (Pubitemid 38931915)
40. Yu J, Cheng YY, Tao Q, Cheung KF, Lam CN, Geng H, et al. Methylation of protocadherin 10, a novel tumor suppressor, is associated with poor prognosis in patients with gastric cancer. Gastroenterology 2009;136:640-51.
41. Greaves M, Maley CC. Clonal evolution in cancer. Nature 2012;481:306-13.
42. Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 2010;465:473-7.
43. Lipkin M, Bell B, Sherlock P. Cell proliferation kinetics in the gastrointestinal tract of man. I. Cell renewal in colon and rectum. J Clin Invest 1963;42:767-76.
44. Wang TL, Rago C, Silliman N, Ptak J, Markowitz S, Willson JK, et al. Prevalence of somatic alterations in the colorectal cancer cell genome. Proc Natl Acad Sci U S A 2002;99:3076-80. (Pubitemid 34240588)
45. Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, et al. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol 2009;19:1453-7.
46. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 2010;328:636-9.
47. Lipkin M. Proliferation and differentiation of normal and neoplastic cells in the colon of man. Cancer 1971;28:38-40.
48. Smith DI, Zhu Y, McAvoy S, Kuhn R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett 2006;232:48-57. (Pubitemid 43053933)
49. Helmrich A, Stout-Weider K, Hermann K, Schrock E, Heiden T. Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes. Genome Res 2006;16:1222-30. (Pubitemid 44506955)
50. McAvoy S, Ganapathiraju SC, Ducharme-Smith AL, Pritchett JR, Kosari F, Perez DS, et al. Non-random inactivation of large common fragile site genes in different cancers. Cytogenet Genome Res 2007;118:260-9. (Pubitemid 350125265)
51. Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, et al. The mutational landscape of head and neck squamous cell carcinoma. Science 2011;333:1157-60.
52. Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, et al. A landscape of driver mutations in melanoma. Cell 2012;150:251-63.
53. Leung CT, Brugge JS. Outgrowth of single oncogene-expressing cells from suppressive epithelial environments. Nature 2012;482:410-3.
54. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 2012;150:264-78.
55. Cooper DN, Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet 1988;78:151-5. (Pubitemid 18069872)
56. Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 1999;401:301-4.