April 26, 2024
A pan-cancer compendium of chromosomal instability – Nature

A pan-cancer compendium of chromosomal instability – Nature

  • Bakhoum, S. F. & Cantley, L. C. The multifaceted role of chromosomal instability in cancer and its microenvironment. Cell 174, 1347–1360 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Tijhuis, A. E., Johnson, S. C. & McClelland, S. E. The emerging links between chromosomal instability (CIN), metastasis, inflammation and tumour immunity. Mol. Cytogenet. 12, 17 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chakravarti, D., LaBella, K. A. & DePinho, R. A. Telomeres: history, health, and hallmarks of aging. Cell 184, 306–322 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bakhoum, S. F. et al. Chromosomal instability drives metastasis through a cytosolic DNA response. Nature 553, 467–472 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Davies, H. et al. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Nat. Med. 23, 517–525 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cohen-Sharir, Y. et al. Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 590, 486–491 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Macintyre, G. et al. Copy number signatures and mutational processes in ovarian carcinoma. Nat. Genet. 50, 1262–1270 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Steele, C. D. et al. Undifferentiated sarcomas develop through distinct evolutionary pathways. Cancer Cell 35, 441–456.e8 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ben-David, U. & Amon, A. Context is everything: aneuploidy in cancer. Nat. Rev. Genet. 21, 44–62 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Stok, C., Kok, Y. P., van den Tempel, N. & van Vugt, M. A. T. M. Shaping the BRCAness mutational landscape by alternative double-strand break repair, replication stress and mitotic aberrancies. Nucleic Acids Res. 49, 4239–4257 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Takemon, Y. et al. Multi-omic analyses reveal a role for mammalian CIC in cell cycle regulation and mitotic fidelity Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/533323v2 (2019).

  • Hell, M. P., Duda, M., Weber, T. C., Moch, H. & Krek, W. Tumor suppressor VHL functions in the control of mitotic fidelity. Cancer Res. 74, 2422–2431 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Brownlee, P. M., Chambers, A. L., Cloney, R., Bianchi, A. & Downs, J. A. BAF180 promotes cohesion and prevents genome instability and aneuploidy. Cell Rep. 6, 973–981 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Silverman, J. S., Skaar, J. R. & Pagano, M. SCF ubiquitin ligases in the maintenance of genome stability. Trends Biochem. Sci. 37, 66–73 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Godinho, S. A. & Pellman, D. Causes and consequences of centrosome abnormalities in cancer. Phil. Trans. R. Soc. B 369, 20130467 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Menghi, F. et al. The tandem duplicator phenotype is a prevalent genome-wide cancer configuration driven by distinct gene mutations. Cancer Cell 34, 197–210.e5 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Abkevich, V. et al. Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. Br. J. Cancer 107, 1776–1782 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Popova, T. et al. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res. 72, 5454–5462 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

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

    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47–54 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Ogden, A., Rida, P. C. G. & Aneja, R. Prognostic value of CA20, a score based on centrosome amplification-associated genes, in breast tumors. Sci Rep. 7, 262 (2017).

    PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Piazza, A. & Heyer, W.-D. Homologous recombination and the formation of complex genomic rearrangements. Trends Cell Biol. 29, 135–149 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Guirouilh-Barbat, J., Lambert, S., Bertrand, P. & Lopez, B. S. Is homologous recombination really an error-free process? Front. Genet. 5, 175 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Knijnenburg, T. A. et al. Genomic and molecular landscape of dna damage repair deficiency across The Cancer Genome Atlas. Cell Rep. 23, 239–254.e6 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Saavedra, H. I., Fukasawa, K., Conn, C. W. & Stambrook, P. J. MAPK mediates RAS-induced chromosome instability. J. Biol. Chem. 274, 38083–38090 (1999).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Perl, A. L. et al. Protein phosphatase 2A controls ongoing DNA replication by binding to and regulating cell division cycle 45 (CDC45). J. Biol. Chem. 294, 17043–17059 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chen, L. et al. The augmented R-loop is a unifying mechanism for myelodysplastic syndromes induced by high-risk splicing factor mutations. Mol. Cell 69, 412–425.e6 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Li, Q. et al. ERCC2 helicase domain mutations confer nucleotide excision repair deficiency and drive cisplatin sensitivity in muscle-invasive bladder cancer. Clin. Cancer Res. 25, 977–988 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Menon, V. & Povirk, L. Involvement of p53 in the repair of DNA double strand breaks: multifaceted roles of p53 in homologous recombination repair (HRR) and non-homologous end joining (NHEJ). Subcell. Biochem. 85, 321–336 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254.e39 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 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).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Berenjeno, I. M. et al. Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling. Nat. Commun. 8, 1773 (2017).

    PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Darp, R., Vittoria, M. A., Ganem, N. J. & Ceol, C. J. Oncogenic BRAF induces whole-genome doubling through suppression of cytokinesis. Preprint at bioRxiv https://doi.org/10.1101/2021.04.08.439023 (2021).

  • Zhang, Q. et al. FBXW7 facilitates nonhomologous end-joining via K63-linked polyubiquitylation of XRCC4. Mol. Cell 61, 419–433 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Citri, A., Skaria, K. B. & Yarden, Y. The deaf and the dumb: the biology of ErbB-2 and ErbB-3. Exp. Cell Res. 284, 54–65 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Venkatesan, S. et al. Induction of APOBEC3 exacerbates DNA replication stress and chromosomal instability in early breast and lung cancer evolution. Cancer Discov. 11, 2456–2473 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Crockford, A. et al. Cyclin D mediates tolerance of genome-doubling in cancers with functional p53. Ann. Oncol. 28, 149–156 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Ray Chaudhuri, A. & Nussenzweig, A. The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat. Rev. Mol. Cell Biol. 18, 610–621 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Goel, S. et al. CDK4/6 inhibition triggers anti-tumour immunity. Nature 548, 471–475 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Brownlee, P. M., Meisenberg, C. & Downs, J. A. The SWI/SNF chromatin remodelling complex: Its role in maintaining genome stability and preventing tumourigenesis. DNA Repair 32, 127–133 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Kops, G. J. P., Foltz, D. R. & Cleveland, D. W. Lethality to human cancer cells through massive chromosome loss by inhibition of the mitotic checkpoint. Proc. Natl Acad. Sci. USA 101, 8699–8704 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Quinton, R. J. et al. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature 590, 492–497 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Janssen, A., Kops, G. J. P. L. & Medema, R. H. Elevating the frequency of chromosome mis-segregation as a strategy to kill tumor cells. Proc. Natl Acad. Sci. USA 106, 19108–19113 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Datta, D. et al. Nucleolar GTP-binding protein-1 (NGP-1) promotes G1 to S phase transition by activating cyclin-dependent kinase inhibitor p21 Cip1/Waf1. J. Biol. Chem. 290, 21536–21552 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Martin, L. P., Hamilton, T. C. & Schilder, R. J. Platinum resistance: the role of DNA repair pathways. Clin. Cancer Res. 14, 1291–1295 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

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

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Scheinin, I. et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 24, 2022–2032 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

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