A pan-cancer compendium of chromosomal instability.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
06 2022
06 2022
Historique:
received:
31
07
2020
accepted:
21
04
2022
pubmed:
16
6
2022
medline:
2
7
2022
entrez:
15
6
2022
Statut:
ppublish
Résumé
Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains and rearrangements of DNA
Identifiants
pubmed: 35705807
doi: 10.1038/s41586-022-04789-9
pii: 10.1038/s41586-022-04789-9
pmc: PMC7613102
mid: EMS150036
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
976-983Subventions
Organisme : Cancer Research UK
ID : A11592
Pays : United Kingdom
Organisme : Wellcome Trust
ID : FC001202
Pays : United Kingdom
Organisme : Cancer Research UK
ID : A19274
Pays : United Kingdom
Organisme : Arthritis Research UK
ID : FC001202
Pays : United Kingdom
Organisme : Cancer Research UK
ID : A22905
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Cancer Research UK
ID : FC001202
Pays : United Kingdom
Organisme : Medical Research Council
ID : FC001202
Pays : United Kingdom
Organisme : Wellcome Trust
ID : RG92770
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Bakhoum, S. F. & Cantley, L. C. The multifaceted role of chromosomal instability in cancer and its microenvironment. Cell 174, 1347–1360 (2018).
pubmed: 30193109
pmcid: 6136429
doi: 10.1016/j.cell.2018.08.027
Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011).
pubmed: 21376230
doi: 10.1016/j.cell.2011.02.013
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: 31114634
pmcid: 6518824
doi: 10.1186/s13039-019-0429-1
Chakravarti, D., LaBella, K. A. & DePinho, R. A. Telomeres: history, health, and hallmarks of aging. Cell 184, 306–322 (2021).
pubmed: 33450206
pmcid: 8081271
doi: 10.1016/j.cell.2020.12.028
Bakhoum, S. F. et al. Chromosomal instability drives metastasis through a cytosolic DNA response. Nature 553, 467–472 (2018).
pubmed: 29342134
pmcid: 5785464
doi: 10.1038/nature25432
Davies, H. et al. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Nat. Med. 23, 517–525 (2017).
pubmed: 28288110
pmcid: 5833945
doi: 10.1038/nm.4292
Cohen-Sharir, Y. et al. Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 590, 486–491 (2021).
pubmed: 33505028
pmcid: 8262644
doi: 10.1038/s41586-020-03114-6
Macintyre, G. et al. Copy number signatures and mutational processes in ovarian carcinoma. Nat. Genet. 50, 1262–1270 (2018).
pubmed: 30104763
pmcid: 6130818
doi: 10.1038/s41588-018-0179-8
Steele, C. D. et al. Undifferentiated sarcomas develop through distinct evolutionary pathways. Cancer Cell 35, 441–456.e8 (2019).
pubmed: 30889380
pmcid: 6428691
doi: 10.1016/j.ccell.2019.02.002
Ben-David, U. & Amon, A. Context is everything: aneuploidy in cancer. Nat. Rev. Genet. 21, 44–62 (2020).
pubmed: 31548659
doi: 10.1038/s41576-019-0171-x
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).
pubmed: 33744950
pmcid: 8096281
doi: 10.1093/nar/gkab151
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).
pubmed: 24362914
doi: 10.1158/0008-5472.CAN-13-2040
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).
pubmed: 24613357
pmcid: 3988838
doi: 10.1016/j.celrep.2014.02.012
Silverman, J. S., Skaar, J. R. & Pagano, M. SCF ubiquitin ligases in the maintenance of genome stability. Trends Biochem. Sci. 37, 66–73 (2012).
pubmed: 22099186
doi: 10.1016/j.tibs.2011.10.004
Godinho, S. A. & Pellman, D. Causes and consequences of centrosome abnormalities in cancer. Phil. Trans. R. Soc. B 369, 20130467 (2014).
pubmed: 25047621
pmcid: 4113111
doi: 10.1098/rstb.2013.0467
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).
pubmed: 30017478
pmcid: 6481635
doi: 10.1016/j.ccell.2018.06.008
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).
pubmed: 23047548
pmcid: 3493866
doi: 10.1038/bjc.2012.451
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).
pubmed: 22933060
doi: 10.1158/0008-5472.CAN-12-1470
The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
pmcid: 3163504
doi: 10.1038/nature10166
Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47–54 (2016).
pubmed: 27135926
pmcid: 4910866
doi: 10.1038/nature17676
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: 28325915
pmcid: 5428291
doi: 10.1038/s41598-017-00363-w
Piazza, A. & Heyer, W.-D. Homologous recombination and the formation of complex genomic rearrangements. Trends Cell Biol. 29, 135–149 (2019).
pubmed: 30497856
doi: 10.1016/j.tcb.2018.10.006
Guirouilh-Barbat, J., Lambert, S., Bertrand, P. & Lopez, B. S. Is homologous recombination really an error-free process? Front. Genet. 5, 175 (2014).
pubmed: 24966870
pmcid: 4052342
doi: 10.3389/fgene.2014.00175
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).
pubmed: 29617664
pmcid: 5961503
doi: 10.1016/j.celrep.2018.03.076
Saavedra, H. I., Fukasawa, K., Conn, C. W. & Stambrook, P. J. MAPK mediates RAS-induced chromosome instability. J. Biol. Chem. 274, 38083–38090 (1999).
pubmed: 10608877
doi: 10.1074/jbc.274.53.38083
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).
pubmed: 31562245
pmcid: 6851307
doi: 10.1074/jbc.RA119.010432
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).
pubmed: 29395063
pmcid: 5957072
doi: 10.1016/j.molcel.2017.12.029
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).
pubmed: 29980530
doi: 10.1158/1078-0432.CCR-18-1001
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: 25201202
pmcid: 4235614
doi: 10.1007/978-94-017-9211-0_17
Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254.e39 (2021).
pubmed: 33831375
pmcid: 8054914
doi: 10.1016/j.cell.2021.03.009
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
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).
pubmed: 21801013
doi: 10.1146/annurev-cellbio-092910-154234
Berenjeno, I. M. et al. Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling. Nat. Commun. 8, 1773 (2017).
pubmed: 29170395
pmcid: 5701070
doi: 10.1038/s41467-017-02002-4
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).
pubmed: 26774286
pmcid: 4744117
doi: 10.1016/j.molcel.2015.12.010
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).
pubmed: 12648465
doi: 10.1016/S0014-4827(02)00101-5
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
pubmed: 32025018
pmcid: 7054213
doi: 10.1038/s41586-020-1943-3
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: 33947663
pmcid: 8487921
doi: 10.1158/2159-8290.CD-20-0725
Crockford, A. et al. Cyclin D mediates tolerance of genome-doubling in cancers with functional p53. Ann. Oncol. 28, 149–156 (2017).
pubmed: 28177473
doi: 10.1093/annonc/mdw612
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).
pubmed: 28676700
pmcid: 6591728
doi: 10.1038/nrm.2017.53
Goel, S. et al. CDK4/6 inhibition triggers anti-tumour immunity. Nature 548, 471–475 (2017).
pubmed: 28813415
pmcid: 5570667
doi: 10.1038/nature23465
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).
pubmed: 25981841
doi: 10.1016/j.dnarep.2015.04.023
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).
pubmed: 15159543
pmcid: 423258
doi: 10.1073/pnas.0401142101
Quinton, R. J. et al. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature 590, 492–497 (2021).
pubmed: 33505027
pmcid: 7889737
doi: 10.1038/s41586-020-03133-3
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).
pubmed: 19855003
pmcid: 2776415
doi: 10.1073/pnas.0904343106
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).
pubmed: 26203195
pmcid: 4571879
doi: 10.1074/jbc.M115.637280
Martin, L. P., Hamilton, T. C. & Schilder, R. J. Platinum resistance: the role of DNA repair pathways. Clin. Cancer Res. 14, 1291–1295 (2008).
pubmed: 18316546
doi: 10.1158/1078-0432.CCR-07-2238
Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).
pubmed: 24071852
pmcid: 3966983
doi: 10.1038/ng.2760
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).
pubmed: 25236618
pmcid: 4248318
doi: 10.1101/gr.175141.114