Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

Creators: Yang, Dian; Jones, Matthew G.; Naranjo, Santiago; Rideout, William M., III; Min, Kyung Hoi (Joseph); Ho, Raymond; Wu, Wei; Replogle, Joseph M.; Page, Jennifer L.; Quinn, Jeffrey J.; Horns, Felix; Qiu, Xiaojie; Chen, Michael Z.; Freed-Pastor, William A.; McGinnis, Christopher S.; Patterson, David M.; Gartner, Zev J.; Chow, Eric D.; Bivona, Trever G.; Chan, Michelle M.; Yosef, Nir; Jacks, Tyler; Weissman, Jonathan S.

Abstract

Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.

Additional Information

© 2022 The Authors. Published by Elsevier Under a Creative Commons license. Attribution 4.0 International (CC BY 4.0). Received 21 September 2021, Revised 9 February 2022, Accepted 8 April 2022, Available online 5 May 2022. We thank Marco Jost, Jeffrey Hussmann, Luke Koblan, Yocef Ouadah, Lindsay LaFave, Luke Gilbert, Julien Sage, Xin Ye, Brittany Adamson, Sebastian Prillo, and all members of the Weissman, Jacks, and Yosef labs for helpful discussions. We thank Liming Tao, Demi Sandel, Caterina Colon, Laura Liao, Kieren Marini, Alejandro Sweet-Cordero, Danielle Dionne, Toni Delorey, Jenna Pfiffner-Borges, Orit Rozenblatt-Rosen, and Aviv Regev for technical help. We thank Joan Kanter, Cristen Muresan, Karen Yee, and Judy Teixeira for administrative support. We thank the UCSF Center for Advanced Technology and the Chan Zuckerberg Biohub for assistance with high-throughput sequencing. We thank UCSF Flow Cytometry Facility, UCSF Cell and Genome Engineering Core, MIT Koch Institute Animal Facility, and MIT Swanson Biotechnology Center Flow Cytometry Facility. Research reported in this publication was supported in part by the NCI Cancer Target Discovery And Development (CTD∧2) and the NIH Centers of Excellence in Genomic Science (CEGS), the NCI Cancer Center Support (core) grant P30-CA14051, the Howard Hughes Medical Institute, and the Ludwig Center at MIT. D.Y. is supported by a Damon Runyon Cancer Research Foundation Postdoctoral Fellowship (DRG-2238-18). M.G.J. is supported by a UCSF Discovery Fellowship. S.N. is supported by a predoctoral training grant T32GM007287 and a Howard Hughes Medical Institute Gilliam Award. J.M.R. is supported by the NIH F31NS115380. J.J.Q. is supported by a NIH NIGMS F32GM125247. F.H. is supported by a Helen Hay Whitney Foundation Fellowship. C.S.M. is supported by the NIH-NCI F31CA257349. D.M.P. is supported by the NIH-NIGMS F32GM128366. M.M.C. is a Gordon and Betty Moore fellow of the Life Sciences Research Foundation. J.S.W. and T.J. were supported by the Howard Hughes Medical Institute and the Ludwig Center at MIT. T.J. is supported by the Break Through Cancer Foundation, Johnson & Johnson Lung Cancer Initiative, and The Lustgarten Foundation. T.G.B. received funding support from the National Institutes of Health (R01CA231300, U54CA224081, R01CA204302, R01CA211052, and R01CA169338). Author contributions. D.Y., M.G.J., T.J., N.Y., and J.S.W. conceived of, designed, and led the analysis of the KP-Tracer project. D.Y. constructed lineage-tracing targeting vectors and engineered the mouse ES cells with the help from J.L.P. and W.F-P. W.M.R. III generated the KP-Tracer chimeric mice, and S.N. transduced the mice. D.Y. and S.N. harvested tumors. D.Y. generated the single-cell RNA-seq data with help from C.S.M., D.M.P., Z.J.G., and E.D.C.; W.W. and T.G.B analyzed the TCGA data. M.G.J. and N.Y. conceived of computational approaches, and M.G.J. implemented these approaches. M.G.J., K.H.(J.)M., and D.Y. analyzed the data with help from F.H., X.Q., J.J.Q., R.H., M.Z.C., and M.M.C.; D.Y., M.G.J., N.Y., T.J., and J.S.W. interpreted results. D.Y., M.G.J., T.J., N.Y., and J.S.W. wrote the manuscript with input from all authors. J.S.W., T.J., and N.Y. supervised the project. Declaration of interests. J.S.W. declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, and Tessera Therapeutics. T.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific, is a co-founder of Dragonfly Therapeutics and T2 Biosystems, and is the president of Break Through Cancer. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. None of these affiliations represent a conflict of interest with respect to this study. T.G.B. is an advisor to Array BioPharma, Revolution Medicines, Novartis, AstraZeneca, Takeda, Springworks, Jazz Pharmaceuticals, Relay Therapeutics, Rain Therapeutics, and Engine Biosciences and receives research funding from Novartis, Strategia, Kinnate, and Revolution Medicines. J.M.R. consults for Maze Therapeutics and Waypoint Bio. Z.J.G. is an equity holder in Scribe Biosciences and Provenance bio and a member of the SAB of Serotiny Bio. Inclusion and diversity One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in science. One or more of the authors of this paper self-identifies as a member of the LGBTQ+ community. One or more of the authors of this paper received support from a program designed to increase minority representation in science. Data and code availability. Raw single-cell RNA-sequencing data has been deposited at the NCBI Sequence Read Archive database and are publicly available as of the date of the publication. Accession numbers are listed in the key resources table. Processed single-cell data, reconstructed phylogenies, derived statistics, interactive VISION (DeTomaso et al., 2019) and PhyloVision (Jones et al., 2022) reports have been deposited at Zenodo and are publicly available as of the date of the publication. DOIs are listed in the key resources table. All original code is available on Github (https://github.com/mattjones315/KPTracer-release) and has been deposited at Zenodo and is publicly available as of the date of the publication. DOIs are listed in the key resources table. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

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Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

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