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Li C, Lin WY, Rizvi H, Cai H, McFarland CD, Rogers ZN, Yousefi M, Winters IP, Rudin CM, Petrov DA, Winslow MM. Quantitative In Vivo Analyses Reveal a Complex Pharmacogenomic Landscape in Lung Adenocarcinoma. Cancer Res 2021; 81:4570-4580. [PMID: 34215621 PMCID: PMC8416777 DOI: 10.1158/0008-5472.can-21-0716] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/04/2021] [Accepted: 07/01/2021] [Indexed: 01/02/2023]
Abstract
The lack of knowledge about the relationship between tumor genotypes and therapeutic responses remains one of the most critical gaps in enabling the effective use of cancer therapies. Here, we couple a multiplexed and quantitative experimental platform with robust statistical methods to enable pharmacogenomic mapping of lung cancer treatment responses in vivo. The complex map of genotype-specific treatment responses uncovered that over 20% of possible interactions show significant resistance or sensitivity. Known and novel interactions were identified, and one of these interactions, the resistance of KEAP1-mutant lung tumors to platinum therapy, was validated using a large patient response data set. These results highlight the broad impact of tumor suppressor genotype on treatment responses and define a strategy to identify the determinants of precision therapies. SIGNIFICANCE: An experimental and analytical framework to generate in vivo pharmacogenomic maps that relate tumor genotypes to therapeutic responses reveals a surprisingly complex map of genotype-specific resistance and sensitivity.
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Affiliation(s)
- Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Zoe N Rogers
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Ian P Winters
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California. .,Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California. .,Cancer Biology Program, Stanford University School of Medicine, Stanford, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
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