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Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov JP, Loeffler JS, Schreiber SL, Hammerman PS, Meyerson M. Integrative radiogenomic profiling of squamous cell lung cancer. Cancer Res 2013; 73:6289-98. [PMID: 23980093 PMCID: PMC3856255 DOI: 10.1158/0008-5472.can-13-1616] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Radiotherapy is one of the mainstays of anticancer treatment, but the relationship between the radiosensitivity of cancer cells and their genomic characteristics is still not well defined. Here, we report the development of a high-throughput platform for measuring radiation survival in vitro and its validation in comparison with conventional clonogenic radiation survival analysis. We combined results from this high-throughput assay with genomic parameters in cell lines from squamous cell lung carcinoma, which is standardly treated by radiotherapy, to identify parameters that predict radiation sensitivity. We showed that activation of NFE2L2, a frequent event in lung squamous cancers, confers radiation resistance. An expression-based, in silico screen nominated inhibitors of phosphoinositide 3-kinase (PI3K) as NFE2L2 antagonists. We showed that the selective PI3K inhibitor, NVP-BKM120, both decreased NRF2 protein levels and sensitized NFE2L2 or KEAP1-mutant cells to radiation. We then combined results from this high-throughput assay with single-sample gene set enrichment analysis of gene expression data. The resulting analysis identified pathways implicated in cell survival, genotoxic stress, detoxification, and innate and adaptive immunity as key correlates of radiation sensitivity. The integrative and high-throughput methods shown here for large-scale profiling of radiation survival and genomic features of solid-tumor-derived cell lines should facilitate tumor radiogenomics and the discovery of genotype-selective radiation sensitizers and protective agents.
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Affiliation(s)
| | - Drew J. Adams
- Chemical Biology Program, Broad Institute, Cambridge, MA 02142
| | | | - Pablo Tamayo
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chad J. Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030
| | - Dmitriy Sonkin
- Novartis Institute for Biomedical Research, Cambridge, MA 02139
| | | | | | - Daniel F. Fries
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02214
| | | | - Jay S. Loeffler
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Stuart L. Schreiber
- Chemical Biology Program, Broad Institute, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Broad Institute, Cambridge, MA 02142
| | - Peter S. Hammerman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts 02215
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