Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns
Bollen, Yannik; Stelloo, Ellen; van Leenen, Petra; van den Bos, Myrna; Ponsioen, Bas; Lu, Bingxin; van Roosmalen, Markus J.; Bolhaqueiro, Ana C.F.; Kimberley, Christopher; Mossner, Maximilian; Cross, William C.H.; Besselink, Nicolle J.M.; van der Roest, Bastiaan; Boymans, Sander; Oost, Koen C.; de Vries, Sippe G.; Rehmann, Holger; Cuppen, Edwin; Lens, Susanne M.A.; Kops, Geert J.P.L.; Kloosterman, Wigard P.; Terstappen, Leon W.M.M.; Barnes, Chris P.; Sottoriva, Andrea; Graham, Trevor A.; Snippert, Hugo J.G.
(2021) Nature Genetics, volume 53, issue 8, pp. 1187 - 1195
(Article)
Abstract
Central to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq—a protocol that integrates live-cell imaging of tumor organoid outgrowth and
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whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness.
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Keywords: Genetics
ISSN: 1061-4036
Publisher: Nature Publishing Group
Note: Funding Information: We thank members of the Snippert, Terstappen, Kloosterman, Cuppen, Sottoriva and Graham laboratories for reagents, suggestions and discussions, and A. van Oudenaarden and J. Korving for providing custom glass capillaries. We thank the Utrecht Sequencing Facility and Hartwig Medical Foundation for providing sequencing services and data. The Utrecht Sequencing Facility is subsidized by the University Medical Center Utrecht, Hubrecht Institute, Utrecht University and The Netherlands X-omics Initiative (NWO). We thank the University College London Hospital (UCLH) Biobank, led by M. Rodriguez-Justo, for providing patient materials. This work was supported by the Wellcome Trust (202778/B/16/Z to A.S.; 202778/Z/16/Z to T.A.G., supporting C.K. and W.C.H.C.; 105104/Z/14/Z to the Centre for Evolution and Cancer, The Institute of Cancer Research; and 097319/Z/11/Z to C.P.B., supporting B.L.) and Cancer Research UK (A22909 to A.S.; and A19771 to T.A.G.). A.S. and T.A.G. received support from the US National Institutes of Health National Cancer Institute (U54 CA217376), supporting M.M. This work was facilitated by the Oncode Institute, which is partly financed by the Dutch Cancer Society and was funded by the Gieskes Strijbis Foundation (1816199), a grant from the Dutch Cancer Society (UU 20130-6070), an ERC starting grant (IntratumoralNiche) and Health Holland to H.J.G.S. Y.B. was supported by a strategic alliance between the University of Twente and UMC Utrecht on Advanced Biomanufacturing (to L.W.M.M.T. and H.J.G.S.). Publisher Copyright: © 2021, The Author(s).
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