Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Nature Communications

Volumn 5, Issue , 2014, Pages

  Nones, Katia ^a,b   Waddell, Nicola ^a,b   Wayte, Nicci ^a   Patch, Ann Marie ^a   Bailey, Peter ^a   Newell, Felicity ^a   Holmes, Oliver ^a,b   Fink, J Lynn ^a   Quinn, Michael C J ^a   Tang, Yue Hang ^a   Lampe, Guy ^c   Quek, Kelly ^a   Loffler, Kelly A ^a   Manning, Suzanne ^a   Idrisoglu, Senel ^a   Miller, David ^a   Xu, Qinying ^a,b   Waddell, Nick ^a   Wilson, Peter J ^a   Bruxner, Timothy J C ^a   Christ, Angelika N ^a   Harliwong, Ivon ^a   Nourse, Craig ^a   Nourbakhsh, Ehsan ^a   Anderson, Matthew ^a   Kazakoff, Stephen ^a   Leonard, Conrad ^a,b   Wood, Scott ^a,b   Simpson, Peter T ^a,b,d   Reid, Lynne E ^b,d   Krause, Lutz ^b   Hussey, Damian J ^e   Watson, David I ^e   Lord, Reginald V ^f   Nancarrow, Derek ^b   Phillips, Wayne A ^g   Gotley, David ^a   Smithers, B Mark ^a   Whiteman, David C ^b   Hayward, Nicholas K ^b   Campbell, Peter J ^h   Pearson, John V ^a,b   Grimmond, Sean M ^a,i   Barbour, Andrew P ^a   more..

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^c PRINCESS ALEXANDRA HOSPITAL   (Australia)

^d UNIVERSITY OF QUEENSLAND   (Australia)

^e FLINDERS UNIVERSITY   (Australia)

^f UNIVERSITY OF NOTRE DAME   (Australia)

^g PETER MACCALLUM CANCER CENTRE   (Australia)

^h WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

ⁱ UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER; CHROMOSOME; DIGESTIVE SYSTEM DISORDER; DISEASE INCIDENCE; GENOMICS; MUTATION; TUMOR;

ARTICLE; CARCINOGENESIS; CHROMOSOME; CHROMOSOME 8; DISASTER; DOUBLE MINUTE CHROMOSOME; ESOPHAGEAL ADENOCARCINOMA; FUSION GENE; GENOMIC INSTABILITY; GENOMICS; HUMAN; MALIGNANT TRANSFORMATION; NONHUMAN; PATHOGENICITY; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; TELOMERE SHORTENING; ADENOCARCINOMA; CHROMOSOME BREAKAGE; ESOPHAGUS TUMOR; GENE REARRANGEMENT; GENETICS; HUMAN CHROMOSOME; HUMAN GENOME; MUTATION; PATHOLOGY;

ADENOCARCINOMA; CARCINOGENESIS; CHROMOSOME BREAKAGE; CHROMOSOMES, HUMAN; ESOPHAGEAL NEOPLASMS; GENE REARRANGEMENT; GENOME, HUMAN; HUMANS; MUTATION;

EID: 84923538176     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6224     Document Type: Article

References (37)

1. Eloubeidi, M. A., Mason, A. C., Desmond, R. A. & El-Serag, H. B. Temporal trends (1973-1997) in survival of patients with esophageal adenocarcinoma in the United States: a glimmer of hope? Am. J. Gastroenterol. 98, 1627-1633 (2003).
2. Li, X. et al. Temporal and Spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett's esophagus. Cancer Prev. Res. (Phila) 7, 114-127 (2014).
3. Dulak, A. M. et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat. Genet. 45, 478-486 (2013).
4. Weaver, J. M. et al. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nat. Genet. 46, 837-843 (2014).
5. Goh, X. Y. et al. Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma. Gut 60, 1317-1326 (2011).
6. Frankel, A. et al. Genome-wide analysis of esophageal adenocarcinoma yields specific copy number aberrations that correlate with prognosis. Genes Chromosomes Cancer 53, 324-338 (2014).
7. Shiraishi, H. et al. Telomere shortening in Barrett's mucosa and esophageal adenocarcinoma and its association with loss of heterozygosity. Scand. J. Gastroenterol. 44, 538-544 (2009).
8. Shammas, M. A. et al. Telomere maintenance in laser capture microdissection-purified Barrett's adenocarcinoma cells and effect of telomerase inhibition in vivo. Clin. Cancer Res. 14, 4971-4980 (2008).
9. Finley, J. C. et al. Chromosomal instability in Barrett's esophagus is related to telomere shortening. Cancer Epidemiol. Biomarkers Prev. 15, 1451-1457 (2006).
10. Xing, J. et al. Constitutive short telomere length of chromosome 17p and 12q but not 11q and 2p is associated with an increased risk for esophageal cancer. Cancer Prev. Res. (Phila) 2, 459-465 (2009).
11. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
12. Song, S. et al. qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS ONE 7, e45835 (2012).
13. McKenna, A. et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
14. Kassahn, K. S. et al. Somatic point mutation calling in low cellularity tumors. PLoS ONE 8, e74380 (2013).
15. Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871 (2009).
16. Popova, T. et al. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol. 10, R128 (2009).
17. Agrawal, N. et al. Comparative genomic analysis of esophageal adenocarcinoma and squamous cell carcinoma. Cancer Discov. 2, 899-905 (2012).
18. Dvorak, K. et al. Bile acids in combination with low pH induce oxidative stress and oxidative DNA damage: relevance to the pathogenesis of Barrett's oesophagus. Gut. 56, 763-771 (2007).
19. Inoue, M. et al. Induction of chromosomal gene mutations in Escherichia coli by direct incorporation of oxidatively damaged nucleotides. New evaluation method for mutagenesis by damaged DNA precursors in vivo. J. Biol. Chem. 273, 11069-11074 (1998).
20. Satou, K. et al. Involvement of specialized DNA polymerases in mutagenesis by 8-hydroxy-dGTP in human cells. DNA Repair (Amst) 8, 637-642 (2009).
21. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-993 (2012).
22. Taylor, B. J. et al. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. Elife 2, e00534 (2013).
23. Campbell, P. J. et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109-1113 (2010).
24. Popova, T. et al. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res. 72, 5454-5462 (2012).
25. Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27-40 (2011).
26. Molenaar, J. J. et al. Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483, 589-593 (2012).
27. Rausch, T. et al. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148, 59-71 (2012).
28. Li, Y. et al. Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 508, 98-102 (2014).
29. Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134-1140 (2013).
30. Kloosterman, W. P., Koster, J. & Molenaar, J. J. Prevalence and clinical implications of chromothripsis in cancer genomes. Curr. Opin. Oncol. 26, 64-72 (2014).
31. Crasta, K. et al. DNA breaks and chromosome pulverization from errors in mitosis. Nature 482, 53-58 (2012).
32. Thanasoula, M. et al. p53 prevents entry into mitosis with uncapped telomeres. Curr. Biol. 20, 521-526 (2010).
33. Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
34. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
35. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
36. Korbel, J. O. & Campbell, P. J. Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226-1236 (2013).
37. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).