Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.
Humans
Adenocarcinoma
/ genetics
Barrett Esophagus
/ genetics
Case-Control Studies
DNA
/ genetics
Esophageal Neoplasms
/ genetics
Carcinogenesis
/ genetics
Whole Genome Sequencing
Cohort Studies
Biopsy
Disease Progression
Oncogenes
Immunomodulation
DNA Copy Number Variations
Gene Amplification
Early Detection of Cancer
/ methods
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
04 2023
04 2023
Historique:
received:
09
09
2022
accepted:
09
03
2023
medline:
28
4
2023
pubmed:
13
4
2023
entrez:
12
4
2023
Statut:
ppublish
Résumé
Oncogene amplification on extrachromosomal DNA (ecDNA) drives the evolution of tumours and their resistance to treatment, and is associated with poor outcomes for patients with cancer
Identifiants
pubmed: 37046089
doi: 10.1038/s41586-023-05937-5
pii: 10.1038/s41586-023-05937-5
pmc: PMC10132967
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
798-805Subventions
Organisme : NCI NIH HHS
ID : U54 CA217376
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA238249
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA264379
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES032547
Pays : United States
Organisme : NCI NIH HHS
ID : OT2 CA278635
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM114362
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA140657
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2023. The Author(s).
Références
Turner, K. M. et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543, 122–125 (2017).
pubmed: 28178237
pmcid: 5334176
doi: 10.1038/nature21356
Nathanson, D. A. et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science 343, 72–76 (2014).
pubmed: 24310612
doi: 10.1126/science.1241328
Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020).
pubmed: 32807987
pmcid: 7484012
doi: 10.1038/s41588-020-0678-2
Verhaak, R. G. W., Bafna, V. & Mischel, P. S. Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nat. Rev. Cancer 19, 283–288 (2019).
pubmed: 30872802
pmcid: 7168519
doi: 10.1038/s41568-019-0128-6
Wu, S., Bafna, V., Chang, H. Y. & Mischel, P. S. Extrachromosomal DNA: an emerging hallmark in human cancer. Annu. Rev. Pathol. 17, 367–386 (2022).
pubmed: 34752712
doi: 10.1146/annurev-pathmechdis-051821-114223
Lange, J. T. et al. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat. Genet. 54, 1527–1533 (2022).
pubmed: 36123406
pmcid: 9534767
doi: 10.1038/s41588-022-01177-x
Peters, Y. et al. Barrett oesophagus. Nat. Rev. Dis. Primers 5, 35 (2019).
pubmed: 31123267
doi: 10.1038/s41572-019-0086-z
Prasad, G. A., Bansal, A., Sharma, P. & Wang, K. K. Predictors of progression in Barrett’s esophagus: current knowledge and future directions. Am. J. Gastroenterol. 105, 1490 (2010).
pubmed: 20104216
pmcid: 3408387
doi: 10.1038/ajg.2010.2
Alnasser, S. et al. Predictors of dysplastic and neoplastic progression of Barrett’s esophagus. Can. J. Surg. 62, 93 (2019).
pubmed: 30907564
pmcid: 6440887
doi: 10.1503/cjs.008716
Li, X. et al. Temporal and spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett’s esophagus. Cancer Prev. Res. 7, 114–127 (2014).
doi: 10.1158/1940-6207.CAPR-13-0289
Nones, K. et al. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat. Commun. 5, 5224 (2014).
pubmed: 25351503
doi: 10.1038/ncomms6224
Killcoyne, S. et al. Genomic copy number predicts esophageal cancer years before transformation. Nat. Med. 26, 1726–1732 (2020).
pubmed: 32895572
pmcid: 7116403
doi: 10.1038/s41591-020-1033-y
Katz-Summercorn, A. C. et al. Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals early structural variation and retrotransposon activity. Nat. Commun. 13, 1407 (2022).
pubmed: 35301290
pmcid: 8931005
doi: 10.1038/s41467-022-28237-4
Paulson, T. G. et al. Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression. Nat. Commun. 13, 2300 (2022).
pubmed: 35484108
pmcid: 9050715
doi: 10.1038/s41467-022-29767-7
Campbell, P. J. et al. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).
doi: 10.1038/s41586-020-1969-6
Hung, K. L. et al. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 600, 731–736 (2021).
pubmed: 34819668
pmcid: 9126690
doi: 10.1038/s41586-021-04116-8
Yi, E. et al. Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA hubs in cancer. Cancer Discov. 12, 468–483 (2022).
pubmed: 34819316
doi: 10.1158/2159-8290.CD-21-1376
Wu, S. et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699–703 (2019).
pubmed: 31748743
pmcid: 7094777
doi: 10.1038/s41586-019-1763-5
Morton, A. R. et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell 179, 1330–1341 (2019).
pubmed: 31761532
pmcid: 7241652
doi: 10.1016/j.cell.2019.10.039
Hung, K. L., Mischel, P. S. & Chang, H. Y. Gene regulation on extrachromosomal DNA. Nat. Struct. Mol. Biol. 29, 736–744 (2022).
pubmed: 35948767
doi: 10.1038/s41594-022-00806-7
Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).
pubmed: 30674876
pmcid: 6344493
doi: 10.1038/s41467-018-08200-y
Hadi, K. et al. Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs. Cell 183, 197–210 (2020).
pubmed: 33007263
pmcid: 7912537
doi: 10.1016/j.cell.2020.08.006
Shale, C. et al. Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics 2, 100112 (2022).
pubmed: 36776527
pmcid: 9903802
doi: 10.1016/j.xgen.2022.100112
Ng, A. W. T. et al. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Commun. Biol. 5, 335 (2022).
pubmed: 35396535
pmcid: 8993906
doi: 10.1038/s42003-022-03238-7
Stachler, M. D. et al. Genomic signatures of past and present chromosomal instability in the evolution of Barrett’s esophagus to esophageal adenocarcinoma. Preprint at bioRxiv https://doi.org/10.1101/2021.03.26.437288 (2023).
Rice, T. W., Patil, D. T. & Blackstone, E. H. 8th edition AJCC/UICC staging of cancers of the esophagus and esophagogastric junction: application to clinical practice. Ann. Cardiothorac. Surg. 6, 119 (2017).
pubmed: 28447000
pmcid: 5387145
doi: 10.21037/acs.2017.03.14
The Cancer Genome Atlas Research Network.Integrated genomic characterization of oesophageal carcinoma. Nature 541, 169–175 (2017).
pmcid: 5651175
doi: 10.1038/nature20805
Eischen, C. M. Genome stability requires p53. Cold Spring Harb. Perspect. Med. 6, a026096 (2016).
pubmed: 27252396
pmcid: 4888814
doi: 10.1101/cshperspect.a026096
Hanel, W. & Moll, U. Links between mutant p53 and genomic instability. J. Cell. Biochem. 113, 433–439 (2012).
pubmed: 22006292
pmcid: 4407809
doi: 10.1002/jcb.23400
Shoshani, O. et al. Chromothripsis drives the evolution of gene amplification in cancer. Nature 591, 137–141 (2020).
pubmed: 33361815
pmcid: 7933129
doi: 10.1038/s41586-020-03064-z
Rosswog, C. et al. Chromothripsis followed by circular recombination drives oncogene amplification in human cancer. Nat. Genet. 53, 1673–1685 (2021).
pubmed: 34782764
doi: 10.1038/s41588-021-00951-7
Ly, P. et al. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat. Genet. 51, 705 (2019).
pubmed: 30833795
pmcid: 6441390
doi: 10.1038/s41588-019-0360-8
Dewhurst, S. M. et al. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov. 4, 175–185 (2014).
pubmed: 24436049
pmcid: 4293454
doi: 10.1158/2159-8290.CD-13-0285
Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011).
pubmed: 21215367
pmcid: 3065307
doi: 10.1016/j.cell.2010.11.055
Umbreit, N. T. et al. Mechanisms generating cancer genome complexity from a single cell division error. Science 368, eaba0712 (2020).
pubmed: 32299917
pmcid: 7347108
doi: 10.1126/science.aba0712
Seymour, G. J. et al. Immunohistologic analysis of the inflammatory infiltrates associated with osseointegrated implants. Int. J. Oral Maxillofac. Implants 4, 191–198 (1989).
pubmed: 2639119
Lawson, K. A. et al. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature 586, 120–126 (2020).
pubmed: 32968282
pmcid: 9014559
doi: 10.1038/s41586-020-2746-2
Kobayashi, K. S. & Van Den Elsen, P. J. NLRC5: a key regulator of MHC class I-dependent immune responses. Nat. Rev. Immunol. 12, 813–820 (2012).
pubmed: 23175229
doi: 10.1038/nri3339
Steidl, C. et al. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature 471, 377–383 (2011).
pubmed: 21368758
pmcid: 3902849
doi: 10.1038/nature09754
Zhan, W. et al. RMI2 plays crucial roles in growth and metastasis of lung cancer. Signal Transduct. Target. Ther. 5, 188 (2020).
pubmed: 32883952
pmcid: 7471275
doi: 10.1038/s41392-020-00295-4
Schmidt, M. et al. Evolutionary dynamics in Barrett oesophagus: implications for surveillance, risk stratification and therapy. Nat. Rev. Gastroenterol. Hepatol. 19, 95–111 (2022).
pubmed: 34728819
doi: 10.1038/s41575-021-00531-4
Zahir, N., Sun, R., Gallahan, D., Gatenby, R. A. & Curtis, C. Characterizing the ecological and evolutionary dynamics of cancer. Nat. Genet. 52, 759–767 (2020).
pubmed: 32719518
doi: 10.1038/s41588-020-0668-4
Sarmashghi, S. & Bafna, V. Computing the statistical significance of overlap between genome annotations with iStat. Cell Syst. 8, 523 (2019).
pubmed: 31202632
pmcid: 7200088
doi: 10.1016/j.cels.2019.05.006
McGranahan, N. & Swanton, C. Clonal heterogeneity and tumor evolution: past, present, and the future. Cell 168, 613–628 (2017).
pubmed: 28187284
doi: 10.1016/j.cell.2017.01.018
Redston, M. et al. Abnormal TP53 predicts risk of progression in patients with Barrett’s esophagus regardless of a diagnosis of dysplasia. Gastroenterology 162, 468–481 (2022).
pubmed: 34757142
doi: 10.1053/j.gastro.2021.10.038
Baslan, T. et al. Ordered and deterministic cancer genome evolution after p53 loss. Nature 608, 795–802 (2022).
pubmed: 35978189
pmcid: 9402436
doi: 10.1038/s41586-022-05082-5
Talevich, E., Shain, A. H., Botton, T. & Bastian, B. C. CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput. Biol. 12, e1004873 (2016).
pubmed: 27100738
pmcid: 4839673
doi: 10.1371/journal.pcbi.1004873
Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910–16915 (2010).
pubmed: 20837533
pmcid: 2947907
doi: 10.1073/pnas.1009843107
Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).
pubmed: 32015543
pmcid: 7056644
doi: 10.1038/s41592-019-0686-2
Haldane, J. B. S. The mean and variance of the moments of chi-squared when used as a test of homogeneity, when expectations are small. Biometrika 29, 133–134 (1940).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv https://doi.org/10.48550/arXiv.1303.3997 (2013).
Depristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–501 (2011).
pubmed: 21478889
pmcid: 3083463
doi: 10.1038/ng.806
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).
pubmed: 22728672
pmcid: 3679285
doi: 10.4161/fly.19695
Thorvaldsdóttir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).
pubmed: 22517427
doi: 10.1093/bib/bbs017
Kim, S. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods 15, 591–594 (2018).
pubmed: 30013048
doi: 10.1038/s41592-018-0051-x
McLaren, W. et al. The Ensembl Variant Effect Predictor. Genome Biol. 17, 2891 (2016).
doi: 10.1186/s13059-016-0974-4
Liu, Y., Sun, J. & Zhao, M. ONGene: a literature-based database for human oncogenes. J. Genet. Genomics 44, 119–121 (2017).
pubmed: 28162959
doi: 10.1016/j.jgg.2016.12.004
Frankell, A. M. et al. The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic. Nat. Genet. 51, 506–516 (2019).
pubmed: 30718927
pmcid: 6420087
doi: 10.1038/s41588-018-0331-5
Stachler, M. D. et al. Paired exome analysis of Barrett’s esophagus and adenocarcinoma. Nat. Genet. 47, 1047–1055 (2015).
pubmed: 26192918
pmcid: 4552571
doi: 10.1038/ng.3343
Liu, Y. et al. HisgAtlas 1.0: a human immunosuppression gene database. Database 2017, bax094 (2017).
pubmed: 31725860
pmcid: 7243927
doi: 10.1093/database/bax094