Selection forces underlying aneuploidy patterns in cancer

References

• Hardy P, Zacharias H. Reappraisal of the Hansemann–Boveri hypothesis on the origin of tumors. Cell Biol Int. 2005;29(12):983–15. doi:10.1016/j.cellbi.2005.10.001.
   PubMed Web of Science ®Google Scholar
• Baudis M. Genomic imbalances in 5918 malignant epithelial tumors: An explorative meta-analysis of chromosomal CGH data. BMC Cancer. 2007;7(1):226. doi:10.1186/1471-2407-7-226.
   PubMedGoogle Scholar
• Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M. et al. The landscape of somatic copy-number alteration across human cancers. Nature. 2010;463(7283):899–905. doi:10.1038/nature08822.
   PubMed Web of Science ®Google Scholar
• Mitelman F, Johansson B, Mertens F. Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. 2023 [Accessed 2023 Aug 23]. https://mitelmandatabase.isb-cgc.org.
   Google Scholar
• Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn S-M, Aikata H, Akbani R. et al. Pan-cancer analysis of whole genomes. Nature. 2020;578(7793):82–93. doi:10.1038/s41586-020-1969-6.
   PubMed Web of Science ®Google Scholar
• Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J. et al. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018;33(4):676–689.e3. doi:10.1016/j.ccell.2018.03.007.
   PubMed Web of Science ®Google Scholar
• Weaver BA, Cleveland DW. Does aneuploidy cause cancer? Curr Opin Cell Biol. 2006;18(6):658–667. doi:10.1016/j.ceb.2006.10.002.
   PubMed Web of Science ®Google Scholar
• Adell MAY, Klockner TC, Höfler R, Wallner L, Schmid J, Markovic A, Martyniak A, Campbell CS. Adaptation to spindle assembly checkpoint inhibition through the selection of specific aneuploidies. Genes Dev. 2023;37(5–6):171–190. doi:10.1101/gad.350182.122.
   PubMed Web of Science ®Google Scholar
• Bosco N, Goldberg A, Zhao X, Mays JC, Cheng P, Johnson AF, Bianchi JJ, Toscani C, Di Tommaso E, Katsnelson L. et al. KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres. Cell. 2023;186(9):S1985–2001.e19. doi:10.1016/j.cell.2023.03.029.
   PubMed Web of Science ®Google Scholar
• Chunduri NK, Menges P, Zhang X, Wieland A, Gotsmann VL, Mardin BR, Buccitelli C, Korbel JO, Willmund F, Kschischo M. et al. Systems approaches identify the consequences of monosomy in somatic human cells. Nat Commun. 2021;12(1):5576. doi:10.1038/s41467-021-25288-x.
   PubMed Web of Science ®Google Scholar
• Girish V, Lakhani AA, Thompson SL, Scaduto CM, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Kandikuppa PK, Lukow DA. et al. Oncogene-like addiction to aneuploidy in human cancers. Science. 2023;381(6660):eadg4521. doi:10.1126/science.adg4521.
   PubMed Web of Science ®Google Scholar
• Huth T, Dreher EC, Lemke S, Fritzsche S, Sugiyanto RN, Castven D, Ibberson D, Sticht C, Eiteneuer E, Jauch A. et al. Chromosome 8p engineering reveals increased metastatic potential targetable by patient-specific synthetic lethality in liver cancer. Sci Adv. 2023;9(51):eadh1442. doi:10.1126/sciadv.adh1442.
   PubMed Web of Science ®Google Scholar
• Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC. et al. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature. 2023;619(7971):793–800. doi:10.1038/s41586-023-06266-3.
   PubMed Web of Science ®Google Scholar
• Chunduri NK, Storchová Z. The diverse consequences of aneuploidy. Nat Cell Biol. 2019;21(1):54–62. doi:10.1038/s41556-018-0243-8.
   PubMed Web of Science ®Google Scholar
• Lakhani AA, Thompson SL, Sheltzer JM. Aneuploidy in human cancer: New tools and perspectives. Trends Genet. 2023;39(12):S968–980. doi:10.1016/j.tig.2023.09.002.
   PubMed Web of Science ®Google Scholar
• Thompson SL, Bakhoum SF, Compton DA. Mechanisms of Chromosomal Instability. Curr Biol. 2010;20(6):R285–R295. doi:10.1016/j.cub.2010.01.034.
   PubMed Web of Science ®Google Scholar
• Zhu J, Tsai H-J, Gordon MR, Li R. Cellular Stress Associated with Aneuploidy. Dev Cell. 2018;44(4):420–431. doi:10.1016/j.devcel.2018.02.002.
   PubMed Web of Science ®Google Scholar
• Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu T-K, Lichtarge O. et al. Integrated Analysis of TP53 Gene and Pathway Alterations in the Cancer Genome Atlas. Cell Rep. 2019;28(5):1370–1384.e5. doi:10.1016/j.celrep.2019.07.001.
   PubMed Web of Science ®Google Scholar
• Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER, Barretina J, Gelfand ET, Bielski CM, Li H. et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019;569(7757):503–508. doi:10.1038/s41586-019-1186-3.
   PubMed Web of Science ®Google Scholar
• Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017;23(6):703–713. doi:10.1038/nm.4333.
   PubMed Web of Science ®Google Scholar
• Nicholson JM, Cimini D. Cancer Karyotypes: Survival of the Fittest. Front Oncol. 2013;3:3. doi:10.3389/fonc.2013.00148.
   PubMedGoogle Scholar
• Ried T, Hu Y, Difilippantonio MJ, Ghadimi BM, Grade M, Camps J. The consequences of chromosomal aneuploidy on the transcriptome of cancer cells. Biochim Biophys Acta (BBA) - Gene Regulatory Mechanisms. 2012;1819(7):784–793. doi:10.1016/j.bbagrm.2012.02.020.
   PubMed Web of Science ®Google Scholar
• The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330–337. doi:10.1038/nature11252.
   PubMed Web of Science ®Google Scholar
• Crespo I, Vital AL, Nieto AB, Rebelo O, Tão H, Lopes MC, Oliveira CR, French PJ, Orfao A, Tabernero MD. Detailed Characterization of Alterations of Chromosomes 7, 9, and 10 in Glioblastomas as Assessed by Single-Nucleotide Polymorphism Arrays. J Mol Diagn. 2011;13(6):634–647. doi:10.1016/j.jmoldx.2011.06.003.
   PubMed Web of Science ®Google Scholar
• Buerger H, Otterbach F, Simon R, Poremba C, Diallo R, Decker T, Riethdorf L, Brinkschmidt C, Dockhorn-Dworniczak B, Boecker W. Comparative genomic hybridization of ductal carcinoma in situ of the breast-evidence of multiple genetic pathways. J Pathol. 1999;187(4):396–402. doi:10.1002/(SICI)1096-9896(199903)187:4<396:AID-PATH286>3.0.CO;2-L.
   PubMed Web of Science ®Google Scholar
• Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013;45(10):1127–1133. doi:10.1038/ng.2762.
   PubMed Web of Science ®Google Scholar
• Watkins TB. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature. 2020;587(7832):126–132. doi:10.1038/s41586-020-2698-6.
   PubMed Web of Science ®Google Scholar
• Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K. et al. The evolutionary history of 2,658 cancers. Nature. 2020;578(7793):122–128. doi:10.1038/s41586-019-1907-7.
   PubMed Web of Science ®Google Scholar
• Douville C, Moinova HR, Thota PN, Shaheen NJ, Iyer PG, Canto MI, Wang JS, Dumot JA, Faulx A, Kinzler KW. et al. Massively Parallel Sequencing of Esophageal Brushings Enables an Aneuploidy-Based Classification of Patients with Barrett’s Esophagus. Gastroenterology. 2021;160(6):2043–2054.e2. doi:10.1053/j.gastro.2021.01.209.
   PubMedGoogle Scholar
• Abe I, Suzuki K, Kimura Y, Tamaki S, Endo Y, Ichida K, Muto Y, Watanabe F, Saito M, Konishi F. et al. Enhancement of DNA hypomethylation alterations by gastric and bile acids promotes chromosomal instability in Barrett’s epithelial cell line. Sci Rep. 2022;12(1):20710. doi:10.1038/s41598-022-25279-y.
   PubMed Web of Science ®Google Scholar
• Mitchell TJ, Turajlic S, Rowan A, Nicol D, Farmery JHR, O’Brien T, Martincorena I, Tarpey P, Angelopoulos N, Yates LR. et al. Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal. Cell. 2018;173(3):611–623.e17. doi:10.1016/j.cell.2018.02.020.
   PubMed Web of Science ®Google Scholar
• Körber V, Yang J, Barah P, Wu Y, Stichel D, Gu Z, Fletcher MNC, Jones D, Hentschel B, Lamszus K. et al. Evolutionary Trajectories of IDHWT Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis. Cancer Cell. 2019;35(4):692–704.e12. doi:10.1016/j.ccell.2019.02.007.
   PubMed Web of Science ®Google Scholar
• Hasle H, Clemmensen IH, Mikkelsen M. Risks of leukaemia and solid tumours in individuals with Down’s syndrome. Lancet (Engl). 2000;355(9199):165–169. doi:10.1016/S0140-6736(99)05264-2.
   PubMed Web of Science ®Google Scholar
• Hasle H, Friedman JM, Olsen JH, Rasmussen SA. Low risk of solid tumors in persons with Down syndrome. Genet Med. 2016;18(11):1151–1157. doi:10.1038/gim.2016.23.
   PubMed Web of Science ®Google Scholar
• Duijf PHG, Schultz N, Benezra R. Cancer cells preferentially lose small chromosomes. Int J Cancer. 2013;132(10):2316–2326. doi:10.1002/ijc.27924.
   PubMed Web of Science ®Google Scholar
• Mitelman F, Heim S, Mandahl N. Trisomy 21 in neoplastic cells. Am J Med Genet. 2005;37(S7):262–266. doi:10.1002/ajmg.1320370752.
   Google Scholar
• Williams BR, Prabhu VR, Hunter KE, Glazier CM, Whittaker CA, Housman DE, Amon A. Aneuploidy Affects Proliferation and Spontaneous Immortalization in Mammalian Cells. Science. 2008;322(5902):703–709. doi:10.1126/science.1160058.
   PubMed Web of Science ®Google Scholar
• Foijer F, Xie SZ, Simon JE, Bakker PL, Conte N, Davis SH, Kregel E, Jonkers J, Bradley A, Sorger PK. Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress. Proc Natl Acad Sci USA. 2014;111(37):13427–13432. doi:10.1073/pnas.1400892111.
   PubMed Web of Science ®Google Scholar
• Hoevenaar WHM, Janssen A, Quirindongo AI, Ma H, Klaasen SJ, Teixeira A, Van Gerwen B, Lansu N, Morsink FHM, Offerhaus GJA. et al. Degree and site of chromosomal instability define its oncogenic potential. Nat Commun. 2020;11(1):1501. doi:10.1038/s41467-020-15279-9.
   PubMed Web of Science ®Google Scholar
• Jeganathan K, Malureanu L, Baker DJ, Abraham SC, Van Deursen JM. Bub1 mediates cell death in response to chromosome missegregation and acts to suppress spontaneous tumorigenesis. J Cell Biol. 2007;179(2):255–267. doi:10.1083/jcb.200706015.
   PubMed Web of Science ®Google Scholar
• Levine MS, Bakker B, Boeckx B, Moyett J, Lu J, Vitre B, Spierings DC, Lansdorp PM, Cleveland DW, Lambrechts D. et al. Centrosome Amplification is Sufficient to Promote Spontaneous Tumorigenesis in Mammals. Dev Cell. 2017;40(3):313–322.e5. doi:10.1016/j.devcel.2016.12.022.
   PubMed Web of Science ®Google Scholar
• Li M, Fang X, Wei Z, York JP, Zhang P. Loss of spindle assembly checkpoint–mediated inhibition of Cdc20 promotes tumorigenesis in mice. J Cell Biol. 2009;185(6):983–994. doi:10.1083/jcb.200904020.
   PubMed Web of Science ®Google Scholar
• Weaver BAA, Silk AD, Montagna C, Verdier-Pinard P, Cleveland DW. Aneuploidy Acts Both Oncogenically and as a Tumor Suppressor. Cancer Cell. 2007;11(1):25–36. doi:10.1016/j.ccr.2006.12.003.
   PubMed Web of Science ®Google Scholar
• Trakala M, Aggarwal M, Sniffen C, Zasadil L, Carroll A, Ma D, Su XA, Wangsa D, Meyer A, Sieben CJ. et al. Clonal selection of stable aneuploidies in progenitor cells drives high-prevalence tumorigenesis. Genes Dev. 2021;35(15–16):1079–1092. doi:10.1101/gad.348341.121.
   PubMed Web of Science ®Google Scholar
• Santaguida S, Richardson A, Iyer DR, M’Saad O, Zasadil L, Knouse KA, Wong YL, Rhind N, Desai A, Amon A. Chromosome mis-segregation generates cell-cycle-arrested cells with complex karyotypes that are eliminated by the Immune System. Dev Cell. 2017;41(6):638–651.e5. doi:10.1016/j.devcel.2017.05.022.
   PubMed Web of Science ®Google Scholar
• Sheltzer JM, Ko JH, Replogle JM, Habibe Burgos NC, Chung ES, Meehl CM, Sayles NM, Passerini V, Storchova Z, Amon A. Single-chromosome gains commonly function as tumor suppressors. Cancer Cell. 2017;31(2):240–255. doi:10.1016/j.ccell.2016.12.004.
   PubMed Web of Science ®Google Scholar
• Stopsack KH, Whittaker CA, Gerke TA, Loda M, Kantoff PW, Mucci LA, Amon A. Aneuploidy drives lethal progression in prostate cancer. Proc Natl Acad Sci USA. 2019;116(23):11390–11395. doi:10.1073/pnas.1902645116.
   PubMed Web of Science ®Google Scholar
• Vasudevan A, Baruah PS, Smith JC, Wang Z, Sayles NM, Andrews P, Kendall J, Leu J, Chunduri NK, Levy D. et al. Single-chromosomal gains can function as metastasis suppressors and promoters in colon cancer. Dev Cell. 2020;52(4):413–428.e6. doi:10.1016/j.devcel.2020.01.034.
   PubMed Web of Science ®Google Scholar
• Shukla A, Nguyen THM, Moka SB, Ellis JJ, Grady JP, Oey H, Cristino AS, Khanna KK, Kroese DP, Krause L. et al. Chromosome arm aneuploidies shape tumour evolution and drug response. Nat Commun. 2020;11(1):449. doi:10.1038/s41467-020-14286-0.
   PubMed Web of Science ®Google Scholar
• Su XA, Ma D, Parsons JV, Replogle JM, Amatruda JF, Whittaker CA, Stegmaier K, Amon A. RAD21 is a driver of chromosome 8 gain in Ewing sarcoma to mitigate replication stress. Genes Dev. 2021;35(7–8):556–572. doi:10.1101/gad.345454.120.
   PubMed Web of Science ®Google Scholar
• Davoli T, Uno H, Wooten EC, Elledge SJ. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science. 2017;355(6322):eaaf8399. doi:10.1126/science.aaf8399.
   PubMed Web of Science ®Google Scholar
• Chang T-G, Cao Y, Shulman ED, Ben-David U, Schäffer AA, Ruppin E. Optimizing cancer immunotherapy response prediction by tumor aneuploidy score and fraction of copy number alterations. NPJ Precis Oncol. 2023;7(1):54. doi:10.1038/s41698-023-00408-6.
   PubMed Web of Science ®Google Scholar
• Spurr LF, Weichselbaum RR, Pitroda SP. Tumor aneuploidy predicts survival following immunotherapy across multiple cancers. Nat Genet. 2022;54(12):1782–1785. doi:10.1038/s41588-022-01235-4.
   PubMed Web of Science ®Google Scholar
• William WN, Zhao X, Bianchi JJ, Lin HY, Cheng P, Lee JJ, Carter H, Alexandrov LB, Abraham JP, Spetzler DB. et al. Immune evasion in HPV − head and neck precancer–cancer transition is driven by an aneuploid switch involving chromosome 9p loss. Proc Natl Acad Sci USA. 2021;118(19):e2022655118. doi:10.1073/pnas.2022655118.
   PubMed Web of Science ®Google Scholar
• Bakhoum SF, Ngo B, Laughney AM, Cavallo J-A, Murphy CJ, Ly P, Shah P, Sriram RK, Watkins TBK, Taunk NK. et al. Chromosomal instability drives metastasis through a cytosolic DNA response. Nature. 2018;553(7689):467–472. doi:10.1038/nature25432.
   PubMed Web of Science ®Google Scholar
• Hong C, Schubert M, Tijhuis AE, Requesens M, Roorda M, van den Brink A, Ruiz LA, Bakker PL, van der Sluis T, Pieters W. et al. cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers. Nature. 2022;607(7918):366–373. doi:10.1038/s41586-022-04847-2.
   PubMed Web of Science ®Google Scholar
• Li J, Hubisz MJ, Earlie EM, Duran MA, Hong C, Varela AA, Lettera E, Deyell M, Tavora B, Havel JJ. et al. Non-cell-autonomous cancer progression from chromosomal instability. Nature. 2023;620(7976):1080–1088. doi:10.1038/s41586-023-06464-z.
   PubMed Web of Science ®Google Scholar
• Gadd S, Huff V, Skol AD, Renfro LA, Fernandez CV, Mullen EA, Jones CD, Hoadley KA, Yap KL, Ramirez NC. et al. Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology group AREN03B2 study. Cell Rep Med. 2022;3(6):100644. doi:10.1016/j.xcrm.2022.100644.
   PubMedGoogle Scholar
• Ippolito MR, Martis V, Martin S, Tijhuis AE, Hong C, Wardenaar R, Dumont M, Zerbib J, Spierings DCJ, Fachinetti D. et al. Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy. Dev Cell. 2021;56(17):2440–2454.e6. doi:10.1016/j.devcel.2021.07.006.
   PubMed Web of Science ®Google Scholar
• Lukow DA, Sausville EL, Suri P, Chunduri NK, Wieland A, Leu J, Smith JC, Girish V, Kumar AA, Kendall J. et al. Chromosomal instability accelerates the evolution of resistance to anti-cancer therapies. Dev Cell. 2021;56(17):2427–2439.e4. doi:10.1016/j.devcel.2021.07.009.
   PubMed Web of Science ®Google Scholar
• Martínez-Jiménez F, Movasati A, Brunner SR, Nguyen L, Priestley P, Cuppen E, Van Hoeck A. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature. 2023;618(7964):333–341. doi:10.1038/s41586-023-06054-z.
   PubMed Web of Science ®Google Scholar
• Nguyen B, Fong C, Luthra A, Smith SA, DiNatale RG, Nandakumar S, Walch H, Chatila WK, Madupuri R, Kundra R. et al. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell. 2022;185(3):563–575.e11. doi:10.1016/j.cell.2022.01.003.
   PubMed Web of Science ®Google Scholar
• Turajlic S, Xu H, Litchfield K, Rowan A, Horswell S, Chambers T, O’Brien T, Lopez JI, Watkins TBK, Nicol D. et al. Deterministic evolutionary trajectories influence primary tumor growth: TRACERx Renal. Cell. 2018;173(3):595–610.e11. doi:10.1016/j.cell.2018.03.043.
   PubMed Web of Science ®Google Scholar
• Perelli L, Carbone F, Zhang L, Huang JK, Le C, Khan H, Citron F, Del Poggetto E, Gutschner T, Tomihara H. et al. Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer. Nat Cancer. 2023;4(7):984–1000. doi:10.1038/s43018-023-00584-1.
   PubMedGoogle Scholar
• Holland AJ, Cleveland DW. Losing balance: The origin and impact of aneuploidy in cancer: ‘Exploring aneuploidy: the significance of chromosomal imbalance’ review series. EMBO Rep. 2012;13(6):501–514. doi:10.1038/embor.2012.55.
   PubMed Web of Science ®Google Scholar
• Klaasen SJ, Truong MA, Van Jaarsveld RH, Koprivec I, Štimac V, De Vries SG, Risteski P, Kodba S, Vukušić K, De Luca KL. et al. Nuclear chromosome locations dictate segregation error frequencies. Nature. 2022;607(7919):604–609. doi:10.1038/s41586-022-04938-0.
   PubMed Web of Science ®Google Scholar
• Worrall JT, Tamura N, Mazzagatti A, Shaikh N, van Lingen T, Bakker B, Spierings DCJ, Vladimirou E, Foijer F, McClelland SE. Non-random Mis-segregation of Human Chromosomes. Cell Rep. 2018;23(11):3366–3380. doi:10.1016/j.celrep.2018.05.047.
   PubMed Web of Science ®Google Scholar
• Dephoure N, Hwang S, O’Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM. Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast. eLife. 2014;3:e03023. doi:10.7554/eLife.03023.
   PubMed Web of Science ®Google Scholar
• Stingele S, Stoehr G, Peplowska K, Cox J, Mann M, Storchova Z. Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Mol Syst Biol. 2012;8(1):608. doi:10.1038/msb.2012.40.
   PubMedGoogle Scholar
• Torres EM, Springer M, Amon A. No current evidence for widespread dosage compensation in S. cerevisiae. eLife. 2016;5:e10996. doi:10.7554/eLife.10996.
   PubMed Web of Science ®Google Scholar
• Upender MB, Habermann JK, McShane LM, Korn EL, Barrett JC, Difilippantonio MJ, Ried T. Chromosome Transfer Induced Aneuploidy Results in Complex Dysregulation of the Cellular Transcriptome in Immortalized and Cancer Cells. Cancer Res. 2004;64(19):6941–6949. doi:10.1158/0008-5472.CAN-04-0474.
   PubMed Web of Science ®Google Scholar
• Brennan CM, Vaites LP, Wells JN, Santaguida S, Paulo JA, Storchova Z, Harper JW, Marsh JA, Amon A. Protein aggregation mediates stoichiometry of protein complexes in aneuploid cells. Genes Dev. 2019;33(15–16):1031–1047. doi:10.1101/gad.327494.119.
   PubMed Web of Science ®Google Scholar
• Schukken KM, Sheltzer JM. Extensive protein dosage compensation in aneuploid human cancers. Genome Res. 2022;32(7):1254–1270. doi:10.1101/gr.276378.121.
   PubMed Web of Science ®Google Scholar
• Muenzner J. Natural proteome diversity links aneuploidy tolerance to protein turnover. Nature. 2024;630(8015):149–157. doi:10.1038/s41586-024-07442-9.
   PubMedGoogle Scholar
• Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell. 2013;155(4):948–962. doi:10.1016/j.cell.2013.10.011.
   PubMed Web of Science ®Google Scholar
• Sack LM, Davoli T, Li MZ, Li Y, Xu Q, Naxerova K, Wooten EC, Bernardi RJ, Martin TD, Chen T. et al. Profound tissue specificity in proliferation control underlies cancer drivers and aneuploidy patterns. Cell. 2018;173(2):499–514.e23. doi:10.1016/j.cell.2018.02.037.
   PubMed Web of Science ®Google Scholar
• Selmecki A, Forche A, Berman J. Aneuploidy and isochromosome formation in drug-resistant Candida albicans. Sci (New Y). 2006;313(5785):367–370. doi:10.1126/science.1128242.
   PubMed Web of Science ®Google Scholar
• Selmecki A, Gerami‐Nejad M, Paulson C, Forche A, Berman J. An isochromosome confers drug resistance in vivo by amplification of two genes, ERG11 and TAC1. Mol Microbiol. 2008;68(3):624–641. doi:10.1111/j.1365-2958.2008.06176.x.
   PubMed Web of Science ®Google Scholar
• Tsai H-J, Nelliat A. A double-edged sword: aneuploidy is a prevalent strategy in fungal adaptation. Genes. 2019;10(10):787. doi:10.3390/genes10100787.
   PubMed Web of Science ®Google Scholar
• Ravichandran MC, Fink S, Clarke MN, Hofer FC, Campbell CS. Genetic interactions between specific chromosome copy number alterations dictate complex aneuploidy patterns. Genes Dev. 2018;32(23–24):1485–1498. doi:10.1101/gad.319400.118.
   PubMed Web of Science ®Google Scholar
• Barriga FM, Tsanov KM, Ho Y-J, Sohail N, Zhang A, Baslan T, Wuest AN, Del Priore I, Meškauskaitė B, Livshits G. et al. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. Nat Cancer. 2022;3(11):1367–1385. doi:10.1038/s43018-022-00443-5.
   PubMedGoogle Scholar
• Watson EV, Lee J-K, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K. et al. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet. 2024;56(5):900–912. doi:10.1038/s41588-024-01665-2.
   PubMed Web of Science ®Google Scholar
• Gialesaki S, Bräuer-Hartmann D, Issa H, Bhayadia R, Alejo-Valle O, Verboon L, Schmell A-L, Laszig S, Regényi E, Schuschel K. et al. RUNX1 isoform disequilibrium promotes the development of trisomy 21–associated myeloid leukemia. Blood. 2023;141(10):1105–1118. doi:10.1182/blood.2022017619.
   PubMed Web of Science ®Google Scholar
• Laurent AP, Kotecha RS, Malinge S. Gain of chromosome 21 in hematological malignancies: Lessons from studying leukemia in children with Down syndrome. Leukemia. 2020;34(8):1984–1999. doi:10.1038/s41375-020-0854-5.
   PubMed Web of Science ®Google Scholar
• Bakhoum SF, Landau DA. Cancer Evolution: No Room for Negative Selection. Cell. 2017;171(5):987–989. doi:10.1016/j.cell.2017.10.039.
   PubMed Web of Science ®Google Scholar
• Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Universal Patterns of Selection in Cancer and Somatic Tissues. Cell. 2017;171(5):1029–1041.e21. doi:10.1016/j.cell.2017.09.042.
   PubMed Web of Science ®Google Scholar
• Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A. Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science. 2007;317(5840):916–924. doi:10.1126/science.1142210.
   PubMed Web of Science ®Google Scholar
• Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu P-H, Hua B, Silberman RE, Springer M, Amon A. Aneuploidy Causes Non-genetic Individuality. Cell. 2017;169(2):229–242.e21. doi:10.1016/j.cell.2017.03.021.
   PubMed Web of Science ®Google Scholar
• Hintzen DC, Soto M, Schubert M, Bakker B, Spierings DCJ, Szuhai K, Lansdorp PM, Kluin RJC, Foijer F, Medema RH. et al. The impact of monosomies, trisomies and segmental aneuploidies on chromosomal stability. PLOS ONE. 2022;17(7):e0268579. doi:10.1371/journal.pone.0268579.
   PubMed Web of Science ®Google Scholar
• Donnelly N, Passerini V, Dürrbaum M, Stingele S, Storchová Z. HSF1 deficiency and impaired HSP90‐dependent protein folding are hallmarks of aneuploid human cells. Embo J. 2014;33(20):2374–2387. doi:10.15252/embj.201488648.
   PubMed Web of Science ®Google Scholar
• Oromendia AB, Dodgson SE, Amon A. Aneuploidy causes proteotoxic stress in yeast. Genes Dev. 2012;26(24):2696–2708. doi:10.1101/gad.207407.112.
   PubMed Web of Science ®Google Scholar
• Passerini V, Ozeri-Galai E, de Pagter MS, Donnelly N, Schmalbrock S, Kloosterman WP, Kerem B, Storchová Z. The presence of extra chromosomes leads to genomic instability. Nat Commun. 2016;7(1):10754. doi:10.1038/ncomms10754.
   PubMedGoogle Scholar
• Santaguida S, Vasile E, White E, Amon A. Aneuploidy-induced cellular stresses limit autophagic degradation. Genes Dev. 2015;29(19):2010–2021. doi:10.1101/gad.269118.115.
   PubMed Web of Science ®Google Scholar
• Sheltzer JM, Blank HM, Pfau SJ, Tange Y, George BM, Humpton TJ, Brito IL, Hiraoka Y, Niwa O, Amon A. Aneuploidy Drives Genomic Instability in Yeast. Science. 2011;333(6045):1026–1030. doi:10.1126/science.1206412.
   PubMed Web of Science ®Google Scholar
• Knouse KA, Wu J, Whittaker CA, Amon A. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proc Natl Acad Sci USA. 2014;111(37):13409–13414. doi:10.1073/pnas.1415287111.
   PubMed Web of Science ®Google Scholar
• Hassold T, Hunt P. To err (meiotically) is human: The genesis of human aneuploidy. Nat Rev Genet. 2001;2(4):280–291. doi:10.1038/35066065.
   PubMed Web of Science ®Google Scholar
• The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609–615. doi:10.1038/nature10166.
   PubMed Web of Science ®Google Scholar
• Morrill SA, Amon A. Why haploinsufficiency persists. Proceedings of the National Academy of Sciences of the United States of America; Vol. 10. 2019. p. 201900437. doi:10.1073/pnas.1900437116.
   Google Scholar
• Bonney ME, Moriya H, Amon A. Aneuploid proliferation defects in yeast are not driven by copy number changes of a few dosage-sensitive genes. Genes Dev. 2015;29(9):898–903. doi:10.1101/gad.261743.115.
   PubMed Web of Science ®Google Scholar
• Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj L-M, Ulirsch J. et al. A cross-disorder dosage sensitivity map of the human genome. Cell. 2022;185(16):3041–3055.e25. doi:10.1016/j.cell.2022.06.036.
   PubMed Web of Science ®Google Scholar
• Zhao H, Cui Y, Dupont J, Sun H, Hennighausen L, Yakar S. Overexpression of the tumor suppressor gene phosphatase and tensin homologue partially inhibits Wnt-1–Induced mammary Tumorigenesis. Cancer Res. 2005;65(15):6864–6873. doi:10.1158/0008-5472.CAN-05-0181.
   PubMed Web of Science ®Google Scholar
• Valente P, Melchiori A, Paggi MG, Masiello L, Ribatti D, Santi L, Takahashi R, Albini A, Noonan DM. RB1 oncosuppressor gene over-expression inhibits tumor progression and induces melanogenesis in metastatic melanoma cells. Oncogene. 1996;13(6):1169–1178. PMID: 8808691.
   PubMed Web of Science ®Google Scholar
• Ozery-Flato M, Linhart C, Trakhtenbrot L, Izraeli S, Shamir R. Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy. Genome Biol. 2011;12(6):R61. doi:10.1186/gb-2011-12-6-r61.
   PubMed Web of Science ®Google Scholar
• Ciani Y, Fedrizzi T, Prandi D, Lorenzin F, Locallo A, Gasperini P, Franceschini GM, Benelli M, Elemento O, Fava LL. et al. Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer. Cell Syst. 2022;13(2):183–193.e7. doi:10.1016/j.cels.2021.10.001.
   PubMed Web of Science ®Google Scholar
• Nichols CA, Gibson WJ, Brown MS, Kosmicki JA, Busanovich JP, Wei H, Urbanski LM, Curimjee N, Berger AC, Gao GF. et al. Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nat Commun. 2020;11(1):2517. doi:10.1038/s41467-020-16399-y.
   PubMed Web of Science ®Google Scholar
• Van Den Eynden J, Basu S, Larsson E, Gordenin DA. Somatic mutation patterns in hemizygous genomic regions unveil purifying selection during tumor evolution. PLOS Genet. 2016;12(12):e1006506. doi:10.1371/journal.pgen.1006506.
   PubMed Web of Science ®Google Scholar
• Qi M, Pang J, Mitsiades I, Lane AA, Rheinbay E. Loss of chromosome Y in primary tumors. Cell. 2023;186(14):3125–3136.e11. doi:10.1016/j.cell.2023.06.006.
   Web of Science ®Google Scholar
• Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D. Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature. 2023;619(7970):624–631. doi:10.1038/s41586-023-06234-x.
   PubMed Web of Science ®Google Scholar
• Hsieh JJ, Le VH, Oyama T, Ricketts CJ, Ho TH, Cheng EH. Chromosome 3p loss–orchestrated VHL, HIF, and epigenetic deregulation in clear cell renal cell carcinoma. J Clin Oncol. 2018;36(36):3533–3539. doi:10.1200/JCO.2018.79.2549.
   Web of Science ®Google Scholar
• Pavelka N, Rancati G, Zhu J, Bradford WD, Saraf A, Florens L, Sanderson BW, Hattem GL, Li R. Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature. 2010;468(7321):321–325. doi:10.1038/nature09529.
   PubMed Web of Science ®Google Scholar
• Liu Y, Chen C, Xu Z, Scuoppo C, Rillahan CD, Gao J, Spitzer B, Bosbach B, Kastenhuber ER, Baslan T. et al. Deletions linked to TP53 loss drive cancer through p53-independent mechanisms. Nature. 2016;531(7595):471–475. doi:10.1038/nature17157.
   PubMed Web of Science ®Google Scholar
• Bielski CM, Zehir A, Penson AV, Donoghue MTA, Chatila W, Armenia J, Chang MT, Schram AM, Jonsson P, Bandlamudi C. et al. Genome doubling shapes the evolution and prognosis of advanced cancers. Nat Genet. 2018;50(8):1189–1195. doi:10.1038/s41588-018-0165-1.
   PubMed Web of Science ®Google Scholar
• Prasad K, Bloomfield M, Levi H, Keuper K, Bernhard SV, Baudoin NC, Leor G, Eliezer Y, Giam M, Wong CK. et al. Whole-genome duplication shapes the aneuploidy landscape of human cancers. Cancer Res. 2022;82(9):1736–1752. doi:10.1158/0008-5472.CAN-21-2065.
   PubMed Web of Science ®Google Scholar
• Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang C-Z, Wala J, Mermel CH. et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45(10):1134–1140. doi:10.1038/ng.2760.
   PubMed Web of Science ®Google Scholar
• Wangsa D, Quintanilla I, Torabi K, Vila‐Casadesús M, Ercilla A, Klus G, Yuce Z, Galofré C, Cuatrecasas M, José Lozano J. et al. Near‐tetraploid cancer cells show chromosome instability triggered by replication stress and exhibit enhanced invasiveness. The FASEB J. 2018;32(7):3502–3517. doi:10.1096/fj.201700247RR.
   PubMed Web of Science ®Google Scholar
• Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30(5):413–421. doi:10.1038/nbt.2203.
   PubMed Web of Science ®Google Scholar
• Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B. et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA. 2010;107(39):16910–16915. doi:10.1073/pnas.1009843107.
   PubMed Web of Science ®Google Scholar
• Müller M, May S, Bird TG. Ploidy dynamics increase the risk of liver cancer initiation. Nat Commun. 2021;12(1):1896. doi:10.1038/s41467-021-21897-8.
   PubMed Web of Science ®Google Scholar
• Zhou L, Jilderda LJ, Foijer F. Exploiting aneuploidy-imposed stresses and coping mechanisms to battle cancer. Open Biol. 2020;10(9):200148. doi:10.1098/rsob.200148.
   PubMed Web of Science ®Google Scholar
• Guang MHZ, Kavanagh EL, Dunne LP, Dowling P, Zhang L, Bianchi G, Anderson KC, O’Gorman P, McCann A, Bianchi G. Targeting proteotoxic stress in cancer: a review of the role that protein quality control pathways play in oncogenesis. Cancers. 2019;11(1):66. doi:10.3390/cancers11010066.
   PubMed Web of Science ®Google Scholar
• Iuliano L, Dalla E, Picco R, Mallavarapu S, Minisini M, Malavasi E, Brancolini C. Proteotoxic stress-induced apoptosis in cancer cells: Understanding the susceptibility and enhancing the potency. Cell Death Discovery. 2022;8(1):407. doi:10.1038/s41420-022-01202-2.
   PubMed Web of Science ®Google Scholar
• Hosoya N, Miyagawa K. Targeting DNA damage response in cancer therapy. Cancer Sci. 2014;105(4):370–388. doi:10.1111/cas.12366.
   PubMed Web of Science ®Google Scholar
• Hwang S, Gustafsson HT, O’Sullivan C, Bisceglia G, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N. et al. Serine-dependent sphingolipid synthesis is a metabolic liability of aneuploid cells. Cell Rep. 2017;21(13):3807–3818. doi:10.1016/j.celrep.2017.11.103.
   PubMed Web of Science ®Google Scholar
• Ben-David U, Amon A. Context is everything: Aneuploidy in cancer. Nat Rev Genet. 2020;21(1):44–62. doi:10.1038/s41576-019-0171-x.
   PubMed Web of Science ®Google Scholar
• Lengauer C, Kinzler KW, Vogelstein B. Genetic instability in colorectal cancers. Nature. 1997;386(6625):623–627. doi:10.1038/386623a0.
   PubMed Web of Science ®Google Scholar
• Alessi JV, Elkrief A, Ricciuti B, Wang X, Cortellini A, Vaz VR, Lamberti G, Frias RL, Venkatraman D, Fulgenzi CAM. et al. Clinicopathologic and genomic factors impacting efficacy of first-line chemoimmunotherapy in advanced NSCLC. J Thorac Oncol. 2023;18(6):731–743. doi:10.1016/j.jtho.2023.01.091.
   PubMed Web of Science ®Google Scholar
• Bolhaqueiro ACF, Ponsioen B, Bakker B, Klaasen SJ, Kucukkose E, van Jaarsveld RH, Vivié J, Verlaan-Klink I, Hami N, Spierings DCJ. et al. Ongoing chromosomal instability and karyotype evolution in human colorectal cancer organoids. Nat Genet. 2019;51(5):824–834. doi:10.1038/s41588-019-0399-6.
   PubMed Web of Science ®Google Scholar