Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Author(s)
Salehi, Sohrab; Kabeer, Farhia; Ceglia, Nicholas; Andronescu, Mirela; Williams, Marc J.; Campbell, Kieran R.; Masud, Tehmina; Wang, Beixi; Biele, Justina; Brimhall, Jazmine; Gee, David; Lee, Hakwoo; Ting, Jerome; Zhang, Allen W.; Tran, Hoa; O’Flanagan, Ciara; Dorri, Fatemeh; Rusk, Nicole; de Algara, Teresa Ruiz; Lee, So Ra; Cheng, Brian Yu Chieh; Eirew, Peter; Kono, Takako; Pham, Jenifer; Grewal, Diljot; Lai, Daniel; Moore, Richard; Mungall, Andrew J.; Marra, Marco A.; Hannon, Gregory J.; Battistoni, Giorgia; Bressan, Dario; Cannell, Ian Gordon; Casbolt, Hannah; Fatemi, Atefeh; Jauset, Cristina; Kovačević, Tatjana; Mulvey, Claire M.; Nugent, Fiona; Ribes, Marta Paez; Pearsall, Isabella; Qosaj, Fatime; Sawicka, Kirsty; Wild, Sophia A.; Williams, Elena; Laks, Emma; Li, Yangguang; O’Flanagan, Ciara H.; Smith, Austin; Ruiz, Teresa; Lai, Daniel; Roth, Andrew; Balasubramanian, Shankar; Lee, Maximillian; Bodenmiller, Bernd; Burger, Marcel; Kuett, Laura; Tietscher, Sandra; Windhager, Jonas; Boyden, Edward S.; Alon, Shahar; Cui, Yi; Emenari, Amauche; Goodwin, Dan; Karagiannis, Emmanouil D.; Sinha, Anubhav; Wassie, Asmamaw T.; Caldas, Carlos; Bruna, Alejandra; Callari, Maurizio; Greenwood, Wendy; Lerda, Giulia; Eyal-Lubling, Yaniv; Rueda, Oscar M.; Shea, Abigail; Harris, Owen; Becker, Robby; Grimaldi, Flaminia; Harris, Suvi; Vogl, Sara Lisa; Weselak, Joanna; Joyce, Johanna A.; Watson, Spencer S.; Vázquez-Garćıa, Ignacio; Tavaré, Simon; Dinh, Khanh N.; Fisher, Eyal; Kunes, Russell; Walton, Nicholas A.; Sa’d, Mohammad Al; Chornay, Nick; Dariush, Ali; González-Solares, Eduardo A.; González-Fernández, Carlos; Yoldas, Aybüke Küpcü; Millar, Neil; Whitmarsh, Tristan; Zhuang, Xiaowei; Fan, Jean; Lee, Hsuan; Sepúlveda, Leonardo A.; Xia, Chenglong; Zheng, Pu; McPherson, Andrew; Bouchard-Côté, Alexandre; Aparicio, Samuel; Shah, Sohrab P.; ... Show more Show less
DownloadAccepted version (4.689Mb)
Open Access Policy
Open Access Policy
Creative Commons Attribution-Noncommercial-Share Alike
Terms of use
Metadata
Show full item recordAbstract
Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.
Date issued
2021-06Department
Massachusetts Institute of Technology. Department of Brain and Cognitive SciencesJournal
Nature
Publisher
Springer Science and Business Media LLC
Citation
Boyden, Edward S. 2021. "Clonal fitness inferred from time-series modelling of single-cell cancer genomes." Nature, 595 (7868).
Version: Author's final manuscript
ISSN
0028-0836
1476-4687