May 27, 2024
Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus – Nature

Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus – Nature

  • Turner, K. M. et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543, 122–125 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nathanson, D. A. et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science 343, 72–76 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Verhaak, R. G. W., Bafna, V. & Mischel, P. S. Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nat. Rev. Cancer 19, 283–288 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 

    Google Scholar
     

  • Lange, J. T. et al. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat. Genet. 54, 1527–1533 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peters, Y. et al. Barrett oesophagus. Nat. Rev. Dis. Primers 5, 35 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alnasser, S. et al. Predictors of dysplastic and neoplastic progression of Barrett’s esophagus. Can. J. Surg. 62, 93 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 

    Google Scholar
     

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

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Killcoyne, S. et al. Genomic copy number predicts esophageal cancer years before transformation. Nat. Med. 26, 1726–1732 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Campbell, P. J. et al. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).

    Article 

    Google Scholar
     

  • Hung, K. L. et al. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 600, 731–736 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, S. et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699–703 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Morton, A. R. et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell 179, 1330–1341 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hung, K. L., Mischel, P. S. & Chang, H. Y. Gene regulation on extrachromosomal DNA. Nat. Struct. Mol. Biol. 29, 736–744 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hadi, K. et al. Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs. Cell 183, 197–210 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shale, C. et al. Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics 2, 100112 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ng, A. W. T. et al. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Commun. Biol. 5, 335 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • The Cancer Genome Atlas Research Network.Integrated genomic characterization of oesophageal carcinoma. Nature 541, 169–175 (2017).

    Article 
    PubMed Central 

    Google Scholar
     

  • Eischen, C. M. Genome stability requires p53. Cold Spring Harb. Perspect. Med. 6, a026096 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hanel, W. & Moll, U. Links between mutant p53 and genomic instability. J. Cell. Biochem. 113, 433–439 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shoshani, O. et al. Chromothripsis drives the evolution of gene amplification in cancer. Nature 591, 137–141 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rosswog, C. et al. Chromothripsis followed by circular recombination drives oncogene amplification in human cancer. Nat. Genet. 53, 1673–1685 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ly, P. et al. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat. Genet. 51, 705 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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
     

  • Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Umbreit, N. T. et al. Mechanisms generating cancer genome complexity from a single cell division error. Science 368, eaba0712 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seymour, G. J. et al. Immunohistologic analysis of the inflammatory infiltrates associated with osseointegrated implants. Int. J. Oral Maxillofac. Implants 4, 191–198 (1989).

    CAS 
    PubMed 

    Google Scholar
     

  • Lawson, K. A. et al. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature 586, 120–126 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Steidl, C. et al. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature 471, 377–383 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhan, W. et al. RMI2 plays crucial roles in growth and metastasis of lung cancer. Signal Transduct. Target. Ther. 5, 188 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schmidt, M. et al. Evolutionary dynamics in Barrett oesophagus: implications for surveillance, risk stratification and therapy. Nat. Rev. Gastroenterol. Hepatol. 19, 95–111 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sarmashghi, S. & Bafna, V. Computing the statistical significance of overlap between genome annotations with iStat. Cell Syst. 8, 523 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McGranahan, N. & Swanton, C. Clonal heterogeneity and tumor evolution: past, present, and the future. Cell 168, 613–628 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Baslan, T. et al. Ordered and deterministic cancer genome evolution after p53 loss. Nature 608, 795–802 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910–16915 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).


    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 

    Google Scholar
     

  • Kim, S. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods 15, 591–594 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McLaren, W. et al. The Ensembl Variant Effect Predictor. Genome Biol. 17, 2891 (2016).

    Article 

    Google Scholar
     

  • Liu, Y., Sun, J. & Zhao, M. ONGene: a literature-based database for human oncogenes. J. Genet. Genomics 44, 119–121 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stachler, M. D. et al. Paired exome analysis of Barrett’s esophagus and adenocarcinoma. Nat. Genet. 47, 1047–1055 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, Y. et al. HisgAtlas 1.0: a human immunosuppression gene database. Database 2017, bax094 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

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