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Paired exome analysis of Barrett's esophagus and adenocarcinoma

Nature Genetics volume 47, pages 1047–1055 (2015)Cite this article

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Abstract

Barrett's esophagus is thought to progress to esophageal adenocarcinoma (EAC) through a stepwise progression with loss of CDKN2A followed by TP53 inactivation and aneuploidy. Here we present whole-exome sequencing from 25 pairs of EAC and Barrett's esophagus and from 5 patients whose Barrett's esophagus and tumor were extensively sampled. Our analysis showed that oncogene amplification typically occurred as a late event and that TP53 mutations often occurred early in Barrett's esophagus progression, including in non-dysplastic epithelium. Reanalysis of additional EAC exome data showed that the majority (62.5%) of EACs emerged following genome doubling and that tumors with genomic doubling had different patterns of genomic alterations, with more frequent oncogenic amplification and less frequent inactivation of tumor suppressors, including CDKN2A. These data suggest that many EACs emerge not through the gradual accumulation of tumor-suppressor alterations but rather through a more direct path whereby a TP53-mutant cell undergoes genome doubling, followed by the acquisition of oncogenic amplifications.

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Figure 1: Barrett's esophagus has a mutation frequency comparable to those of many invasive cancers but shows few genomic amplifications.
Figure 2: Paired analysis identifies early shared TP53 alterations.
Figure 3: Paired analysis shows a lack of oncogene amplification in Barrett's esophagus samples.
Figure 4: Spatial and phylogenetic relationships of multiple sampled areas, where all samples within a patient share a common set of genomic alterations.
Figure 5: Spatial and phylogenetic relationships of multiple sampled areas in patients showing at least two clonally unrelated populations.
Figure 6: TSG alterations are more common in EAC without WGD.
Figure 7: Genome-doubled EAC contains more frequent amplifications in cell cycle regulators and transcription factors.
Figure 8: Genome-doubled EAC shows a distinct pathway of development.

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References

  1. Nehra, D., Howell, P., Williams, C.P., Pye, J.K. & Beynon, J. Toxic bile acids in gastro-oesophageal reflux disease: influence of gastric acidity. Gut 44, 598–602 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Wild, C.P. & Hardie, L.J. Reflux, Barrett's oesophagus and adenocarcinoma: burning questions. Nat. Rev. Cancer 3, 676–684 (2003).

    Article  CAS  PubMed  Google Scholar 

  3. Lagergren, J., Bergstromeinhold, R., Lingren, A. & Nyren, O. Symptomatic gastoroesophageal reflux as a risk factor for esophageal adenocarcinoma. N. Engl. J. Med. 340, 825–831 (1999).

    Article  CAS  PubMed  Google Scholar 

  4. Ormsby, A.H. et al. The location and frequency of intestinal metaplasia at the esophagogastric junction in 223 consecutive autopsies: implications for patient treatment and preventive strategies in Barrett's esophagus. Mod. Pathol. 13, 614–620 (2000).

    Article  CAS  PubMed  Google Scholar 

  5. Galipeau, P.C., Prevo, L.J., Sanchez, C.a., Longton, G.M. & Reid, B.J. Clonal expansion and loss of heterozygosity at chromosomes 9p and 17p in premalignant esophageal (Barrett's) tissue. J. Natl. Cancer Inst. 91, 2087–2095 (1999).

    Article  CAS  PubMed  Google Scholar 

  6. Gu, J. et al. Genome-wide catalogue of chromosomal aberrations in Barrett's esophagus and esophageal adenocarcinoma: a high-density single nucleotide polymorphism array analysis. Cancer Prev. Res. (Phila.) 3, 1176–1186 (2010).

    Article  CAS  Google Scholar 

  7. 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).

    Article  Google Scholar 

  8. Li, X. et al. Single nucleotide polymorphism–based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression. Cancer Prev. Res. (Phila.) 1, 413–423 (2008).

    Article  CAS  Google Scholar 

  9. Reid, B.J. et al. Barrett's esophagus: ordering the events that lead to cancer. Eur. J. Cancer Prev. 5, 57–65 (1996).

    Article  PubMed  Google Scholar 

  10. Wong, D.J. et al. p16INK4a lesions are common, early abnormalities that undergo clonal expansion in Barrett's metaplastic epithelium. Cancer Res. 61, 8284–8289 (2001).

    CAS  PubMed  Google Scholar 

  11. Zhang, S. & Wang, X.I. SIRT1 is a useful biomarker for high-grade dysplasia and carcinoma in Barrett's. Esophagus 43, 373–377 (2013).

    Google Scholar 

  12. Paulson, T.G. et al. p16 mutation spectrum in the premalignant condition Barrett's esophagus. PLoS ONE 3, e3809 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Carter, S.L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Dulak, A.M. et al. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis. Cancer Res. 72, 4383–4393 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Fujiwara, T. et al. Cytokinesis failure generating tetraploids promotes tumorigenesis in p53-null cells. Nature 437, 1043–1047 (2005).

    Article  CAS  PubMed  Google Scholar 

  17. Davoli, T. & de Lange, T. Telomere-driven tetraploidization occurs in human cells undergoing crisis and promotes transformation of mouse cells. Cancer Cell 21, 765–776 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Zack, T.I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Etemadmoghadam, D. et al. Resistance to CDK2 inhibitors is associated with selection of polyploid cells in CCNE1-amplified ovarian cancer. Clin. Cancer Res. 19, 5960–5971 (2013).

    Article  CAS  PubMed  Google Scholar 

  20. Maley, C.C. et al. Selectively advantageous mutations and hitchhikers in neoplasms: p16 lesions are selected in Barrett's esophagus. Cancer Res. 64, 3414–3427 (2004).

    Article  CAS  PubMed  Google Scholar 

  21. Weaver, J.M.J. et al. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nat. Genet. 46, 837–843 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Maley, C.C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 38, 468–473 (2006).

    Article  CAS  PubMed  Google Scholar 

  23. Reid, B.J. et al. Predictors of progression in Barrett's esophagus II: baseline 17p (p53) loss of heterozygosity identifies a patient subset at increased risk for neoplastic progression. Am. J. Gastroenterol. 96, 2839–2848 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. van Wyk, R. et al. Somatic mutations of the APC, KRAS, and TP53 genes in nonpolypoid colorectal adenomas. Genes Chromosom. Cancer 27, 202–208 (2000).

    Article  CAS  PubMed  Google Scholar 

  25. Prestlow, T.P. & Prestlow, T.G. No mutant KRAS in aberrant crypt foci (ACF): initiation of colorectal cancer? Biochim. Biophys. Acta 1756, 83–96 (2005).

    Google Scholar 

  26. Lüttges, J. et al. The K-ras mutation pattern in pancreatic ductal adenocarcinoma usually is identical to that in associated normal, hyperplastic, and metaplastic ductal epithelium. Cancer 85, 1703–1710 (1999).

    Article  PubMed  Google Scholar 

  27. Deramaudt, T. & Rustgi, A. Mutant KRAS in the initiation of pancreatic cancer. Biochim. Biophys. Acta 1756, 97–101 (2005).

    CAS  PubMed  Google Scholar 

  28. Gordon, D.J., Resio, B. & Pellman, D. Causes and consequences of aneuploidy in cancer. Nat. Rev. Genet. 13, 189–203 (2012).

    Article  CAS  PubMed  Google Scholar 

  29. Dewhurst, S.M. et al. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov. 4, 175–185 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Davoli, T. & de Lange, T. The causes and consequences of polyploidy in normal development and cancer. Annu. Rev. Cell Dev. Biol. 27, 585–610 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Ganem, N.J. et al. Cytokinesis failure triggers Hippo tumor suppressor pathway activation. Cell 158, 833–848 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Nones, K. et al. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat. Commun. 5, 5224 (2014).

    Article  CAS  PubMed  Google Scholar 

  33. Rabinovitch, P.S., Reid, B.J., Haggit, R.C., Norwood, T.H. & Rubin, C.E. Progression to cancer in Barrett's esophagus is associated with genomic instability. Lab. Invest. 60, 65–71 (1989).

    CAS  PubMed  Google Scholar 

  34. Davelaar, A.L. et al. Aberrant TP53 detected by combining immunohistochemistry and DNA-FISH improves Barrett's esophagus progression prediction: a prospective follow-up study. Genes Chromosom. Cancer 54, 82–90 (2015).

    Article  CAS  PubMed  Google Scholar 

  35. Bytzer, P., Christensen, P.B., Damkier, P., Vinding, K. & Seersholm, N. Adenocarcinoma of the esophagus and Barrett's esophagus: a population-based study. Am. J. Gastroenterol. 94, 86–91 (1999).

    Article  CAS  PubMed  Google Scholar 

  36. Weston, A.P. et al. Long-term follow-up of Barrett's high-grade dysplasia. Am. J. Gastroenterol. 95, 1888–1893 (2000).

    Article  CAS  PubMed  Google Scholar 

  37. Corley, D.A., Levin, T.R., Habel, L.A., Weiss, N.S. & Buffler, P.A. Surveillance and survival in Barrett's adenocarcinomas: a population-based study. Gastroenterology 122, 633–640 (2002).

    Article  PubMed  Google Scholar 

  38. Hvid-Jensen, F., Pedersen, L., Drewes, A., Sorensen, H. & Funch-Jensen, P. Incidence of adenocarcinoma among patients with Barrett's esophagus. N. Engl. J. Med. 365, 1375–1383 (2011).

    Article  CAS  PubMed  Google Scholar 

  39. Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Berger, M.F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214–220 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Chapman, M.A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471, 467–472 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Barbieri, C.E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685–689 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157–1160 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).

  45. Cibulskis, K. et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 27, 2601–2602 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876–D882 (2011).

    Article  CAS  PubMed  Google Scholar 

  47. Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Griffith, O.L. et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36, D107–D113 (2008).

    Article  CAS  PubMed  Google Scholar 

  49. UniProt Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39, D214–D219 (2011).

  50. Forbes, S.A. et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39, D945–D950 (2011).

    Article  CAS  PubMed  Google Scholar 

  51. Venkatraman, E.S. & Olshen, A.B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657–663 (2007).

    Article  CAS  PubMed  Google Scholar 

  52. Olshen, A.B. et al. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27, 2038–2046 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Landau, D.A. et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714–726 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Lohr, J.G., Stojanov, P., Carter, S.L., Cruz-gordillo, P. & Lawrence, M.S. Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy. Cancer Cell 25, 91–101 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Campbell, P.J. et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109–1113 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Liu, W. et al. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat. Med. 15, 559–565 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90–94 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Shah, S.P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809–813 (2009).

    Article  CAS  PubMed  Google Scholar 

  60. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. McFadden, D.G. et al. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell 156, 1298–1311 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Nixon, K.C. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407–414 (1999).

    Article  PubMed  Google Scholar 

  63. Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank the members of the Broad Institute Genome Sequencing Platform and the molecular laboratories at Brigham and Women's Hospital and Massachusetts General Hospital for their assistance. We are grateful to the patients and families who agreed to contribute their samples to enable this research and to the physicians and hospital staff whose efforts in collecting these samples are essential to this work. This work was supported by US National Institutes of Health grant T32 HL007627 and the Dana-Farber/Harvard Gastrointestinal Cancer Specialized Programs of Research Excellence P50CA127003 (M.D.S.), the National Human Genome Research Institute (NHGRI) Large-Scale Sequencing Program (U54 HG0003067; E.S.L.), National Cancer Institute grant U54 CA163059 (D.G.B.), Broad Institute SPARC funding (A.J.B., S.L.C. and G.G.), a Research Scholar Grant from the American Cancer Society (A.J.B.) and the National Cancer Institute (P01 CA098101 and U54 CA163004; A.J.B.).

Author information

Author notes

  1. Matthew D Stachler and Amaro Taylor-Weiner: These authors contributed equally to this work.

  2. Gad Getz, Scott L Carter and Adam J Bass: These authors jointly supervised this work.

Authors and Affiliations

  1. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Matthew D Stachler, Agoston T Agoston, Robert D Odze & Massimo Loda

  2. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Matthew D Stachler, Shouyong Peng, Massimo Loda & Adam J Bass

  3. Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA

    Amaro Taylor-Weiner, Ignaty Leshchiner, Chip Stewart, Petar Stojanov, Sara Seepo, Michael S Lawrence, Stacey B Gabriel, Eric S Lander, Gad Getz, Scott L Carter & Adam J Bass

  4. University of Washington, Seattle, Washington, USA

    Aaron McKenna

  5. University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

    Jon M Davison & Katie S Nason

  6. Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA

    Daysha Ferrer-Torres, Jules Lin, Andrew C Chang & David G Beer

  7. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Eric S Lander

  8. Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA

    Gad Getz

  9. Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Broad Institute of Harvard and MIT, Harvard Medical School, Boston, Massachusetts, USA

    Scott L Carter

  10. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Scott L Carter

  11. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA

    Scott L Carter

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  1. Matthew D Stachler
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Contributions

M.D.S. performed experiments and interpreted results. A.T.-W., S.P., A.M., P.S., I.L., M.S.L. and S.L.C. performed computational analysis. A.T.A. and R.D.O. performed pathological slide review. J.M.D., K.S.N., D.F.-T., J.L., A.C.C. and D.G.B. contributed samples and clinical annotation. M.L. contributed laser-capture microdissection guidance and manuscript review. C.S., S.S., S.B.G. and E.S.L. organized and supervised sequencing. G.G., S.L.C. and A.J.B. supervised all studies. M.D.S., A.T.-W., S.L.C., G.G. and A.J.B. prepared the manuscript, and all authors read and approved the final manuscript.

Corresponding authors

Correspondence to Gad Getz, Scott L Carter or Adam J Bass.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–21 and Supplementary Tables 3–5. (PDF 46784 kb)

Supplementary Table 1

Patient, Barrett's and tumor characteristics in the 25 paired samples. (XLSX 12 kb)

Supplementary Table 2

List of tumor suppressors and their given coverage. (XLSX 233 kb)

Supplementary Table 6

EAC gene alterations. (XLSX 61 kb)

Supplementary Data Set 1

Frozen sample MAF files. (ZIP 358 kb)

Supplementary Data Set 2

Frozen sample ABSOLUTE plots. (ZIP 11192 kb)

Supplementary Data Set 3

FFPE sample MAF files. (ZIP 823 kb)

Supplementary Data Set 4

FFPE sample ABSOLUTE plots. (ZIP 24867 kb)

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Stachler, M., Taylor-Weiner, A., Peng, S. et al. Paired exome analysis of Barrett's esophagus and adenocarcinoma. Nat Genet 47, 1047–1055 (2015). https://doi.org/10.1038/ng.3343

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