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Paired exome analysis of Barrett's esophagus and adenocarcinoma

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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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

Authors

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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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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