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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
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).
Wild, C.P. & Hardie, L.J. Reflux, Barrett's oesophagus and adenocarcinoma: burning questions. Nat. Rev. Cancer 3, 676–684 (2003).
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).
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).
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).
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).
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).
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).
Reid, B.J. et al. Barrett's esophagus: ordering the events that lead to cancer. Eur. J. Cancer Prev. 5, 57–65 (1996).
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).
Zhang, S. & Wang, X.I. SIRT1 is a useful biomarker for high-grade dysplasia and carcinoma in Barrett's. Esophagus 43, 373–377 (2013).
Paulson, T.G. et al. p16 mutation spectrum in the premalignant condition Barrett's esophagus. PLoS ONE 3, e3809 (2008).
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).
Carter, S.L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).
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).
Fujiwara, T. et al. Cytokinesis failure generating tetraploids promotes tumorigenesis in p53-null cells. Nature 437, 1043–1047 (2005).
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).
Zack, T.I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).
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).
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).
Weaver, J.M.J. et al. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nat. Genet. 46, 837–843 (2014).
Maley, C.C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 38, 468–473 (2006).
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).
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).
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).
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).
Deramaudt, T. & Rustgi, A. Mutant KRAS in the initiation of pancreatic cancer. Biochim. Biophys. Acta 1756, 97–101 (2005).
Gordon, D.J., Resio, B. & Pellman, D. Causes and consequences of aneuploidy in cancer. Nat. Rev. Genet. 13, 189–203 (2012).
Dewhurst, S.M. et al. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov. 4, 175–185 (2014).
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).
Ganem, N.J. et al. Cytokinesis failure triggers Hippo tumor suppressor pathway activation. Cell 158, 833–848 (2014).
Nones, K. et al. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat. Commun. 5, 5224 (2014).
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).
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).
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).
Weston, A.P. et al. Long-term follow-up of Barrett's high-grade dysplasia. Am. J. Gastroenterol. 95, 1888–1893 (2000).
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).
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).
Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).
Berger, M.F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214–220 (2011).
Chapman, M.A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471, 467–472 (2011).
Barbieri, C.E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685–689 (2012).
Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157–1160 (2011).
Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
Cibulskis, K. et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 27, 2601–2602 (2011).
Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876–D882 (2011).
Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
Griffith, O.L. et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36, D107–D113 (2008).
UniProt Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39, D214–D219 (2011).
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).
Venkatraman, E.S. & Olshen, A.B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657–663 (2007).
Olshen, A.B. et al. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27, 2038–2046 (2011).
Landau, D.A. et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714–726 (2013).
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).
Campbell, P.J. et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109–1113 (2010).
Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012).
Liu, W. et al. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat. Med. 15, 559–565 (2009).
Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90–94 (2011).
Shah, S.P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809–813 (2009).
Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).
McFadden, D.G. et al. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell 156, 1298–1311 (2014).
Nixon, K.C. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407–414 (1999).
Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).
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
Authors and Affiliations
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
Ethics declarations
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)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng.3343
This article is cited by
-
The prognostic value of 11th Japanese classification and 8th AJCC staging systems in Chinese patients with esophageal squamous cell carcinoma
Journal of Cardiothoracic Surgery (2023)
-
Extrachromosomal DNA appears before cancer forms
Nature (2023)
-
Improving outcomes in patients with oesophageal cancer
Nature Reviews Clinical Oncology (2023)
-
Whole-genome doubling drives oncogenic loss of chromatin segregation
Nature (2023)
-
Single-cell and spatial dissection of precancerous lesions underlying the initiation process of oral squamous cell carcinoma
Cell Discovery (2023)