Abstract
Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways, forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also affected tumor microenvironment composition and cell states. Our melanoma models shared genotype-associated expression programs with patient melanomas, and a deep learning model showed that these models partially recapitulated genotype-associated histopathological features as well. Thus, a progressive series of genome-edited human cancer models can causally connect genotypes carrying multiple mutations to phenotype.
| Original language | English |
|---|---|
| Article number | eabi8175 |
| Journal | Science |
| Volume | 376 |
| Issue number | 6592 |
| DOIs | |
| State | Published - 29 Apr 2022 |
Bibliographical note
Publisher Copyright:Copyright © 2022 The Authors
Funding
We thank D. Kotliar, I. R. Watson, O. Ursu, C-Z. Zhang, D. E. Fisher, M. L. Meyerson, D. M. Sabatini, and W. R. Sellers for helpful discussions; L. Gaffney and A. Hupalowska for assistance with figure design and graphics; I. Avraham-Davidi for assistance with tumor dissociation protocols; G. Getz, C. Stewart, and L. Lichtenstein for assistance with whole genome sequence analysis; and J. Pfiffer, D. Kelly, J. Barnett, M. Veneskey, and B. Buckley for laboratory operations. We thank B. E. Bernstein for support during the review process of this manuscript. We thank R. Platt and the F. Zhang laboratory for the kind gift of an AAV transfer plasmid backbone. We thank the MIT KI Swanson Biotechnology Center Histology Core and the Broad Genomics Platform for their services and expertise. The results published here are in part based upon data generated by the TCGA Research Network: https://www. cancer.gov/tcga. We acknowledge the American Association for Cancer Research (AACR) and its financial and material support in the development of the AACR Project GENIE registry, as well as members of the GENIE consortium for their commitment to data sharing. Funding: This work was supported by the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (L.A.G.), the Starr Cancer Consortium (L.A.G.), the Klarman Cell Observatory at the Broad Institute (A.R.), the Howard Hughes Medical Institute (A.R.), and Ludwig Cancer Research (A.R.). E.H. is grateful for support from the Harvard Herchel Smith Fellowship, the Harvard Landry Cancer Research Fellowship, the Paul and Daisy Soros Fellowship for New Americans, and an NIH Medical Scientist Training Program grant from NIGMS (PI: L. Walensky; T32GM007753). D.S. was funded by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation (P2ZHP3_181475) and a Damon Runyon Fellowship (DRQ-03-20). Z.M. was supported by the NCI (R50-CA252138). L.A.G. and A.R. were investigators of the Howard Hughes Medical Institute while this work was conducted. Author contributions: Conceptualization: E.H., E.T.T., J.Y.H.K., T.B., L.A.G., A.R.; Investigation: E.H., E.T.T., J.Y.H.K., T.B., L.R.Z., S.P., J-C.H., L.B., T.M.D., D.P., D.D., L.T.N., D.S., Z.M., C.A.J., and A.H.; Supervision: O.R-R., M.C.M., L.A.G., and A.R.; Writing - original draft: E.H., E.T.T., J.Y.H.K., T.B., L.A.G., and A.R.; Writing - review and editing: all authors. Competing interests: E.H. is a consultant for and holds equity in Dyno Therapeutics and was a consultant for GV. T.B., J-C.H., D.P., O.R.R., L.A.G., and A.R. are employees of Genentech since 1 February 2021, 20 September 2021, 3 May 2021, 19 October 2020, 1 January 2019, and 1 August 2020, respectively. J.C.H. owns stock of F. Hoffmann-La Roche AG. D.S. is a consultant for Roche Glycart AG, since August 2021. A.R. and O.R.R. are coinventors on patent applications filed by the Broad Institute for inventions related to single-cell genomics. L.A.G. is an equity holder of Roche/Genentech and was a cofounder and equity holder at Foundation Medicine, Inc. and Tango Therapeutics. A.R. is an equity holder of Roche/Genentech and is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and until 31 July 2020, was an SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov, and ThermoFisher Scientific. E.H., L.A.G., and A.R. are named inventors on a patent application filed by the Broad Institute covering the work described in this manuscript (US Patent Application 16/631,916, National Phase of PCT/US2018/042737). Data and materials availability: Plasmids will be made available on AddGene (addgene.org/browse/article/28224839), subject to the Uniform Biological MTA. Immortalized cell lines will be made available upon request, to noncommercial entities, subject to the Uniform Biological MTA. Raw single-cell sequencing files are available in DUOS (DUOS-000136). Processed files are available and browsable on the Single Cell Portal (SCP1334). Code to reproduce the hierarchical Bayesian logistic mixed-effects model is available on Zenodo (84). All histopathological images and the associated machine-learning code are available on Image Data Resource (https://idr.openmicroscopy.org, accession number idr0135) and Code Ocean (https://codeocean.com/capsule/ 9921736/tree), respectively.
| Funders | Funder number |
|---|---|
| Harvard Herchel Smith Fellowship | |
| Harvard Landry Cancer Research Fellowship | |
| Starr Cancer Consortium | |
| National Institutes of Health | |
| Howard Hughes Medical Institute | |
| National Cancer Institute | R50CA252138 |
| National Institute of General Medical Sciences | T32GM007753 |
| Dr. Miriam and Sheldon G. Adelson Medical Research Foundation | |
| Ludwig Institute for Cancer Research | |
| Broad Institute | |
| Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung | DRQ-03-20, P2ZHP3_181475 |
