EGFR Variant Heterogeneity in Glioblastoma Resolved through Single-Nucleus Sequencing
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Love_EGFR variant.pdf
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Author(s)
Francis, Joshua M.
Zhang, Cheng-Zhong
Maire, Cecile L.
Jung, Joonil
Manzo, Veronica E.
Homer, Heather
Haidar, Sam
Blumenstiel, Brendan
Pedamallu, Chandra Sekhar
Ligon, Azra H.
Date Issued
June 2014
Journal
Cancer Discovery
Publisher
American Association for Cancer Research
Citation
Francis, J. M., C.-Z. Zhang, C. L. Maire, J. Jung, V. E. Manzo, V. A. Adalsteinsson, H. Homer, et al. “EGFR Variant Heterogeneity in Glioblastoma Resolved through Single-Nucleus Sequencing.” Cancer Discovery 4, no. 8 (June 3, 2014): 956–971.
Version
Author's final manuscript
Abstract
Glioblastomas (GBM) with EGFR amplification represent approximately 50% of newly diagnosed cases, and recent studies have revealed frequent coexistence of multiple EGFR aberrations within the same tumor, which has implications for mutation cooperation and treatment resistance. However, bulk tumor sequencing studies cannot resolve the patterns of how the multiple EGFR aberrations coexist with other mutations within single tumor cells. Here, we applied a population-based single-cell whole-genome sequencing methodology to characterize genomic heterogeneity in EGFR-amplified glioblastomas. Our analysis effectively identified clonal events, including a novel translocation of a super enhancer to the TERT promoter, as well as subclonal LOH and multiple EGFR mutational variants within tumors. Correlating the EGFR mutations onto the cellular hierarchy revealed that EGFR truncation variants (EGFRvII and EGFR carboxyl-terminal deletions) identified in the bulk tumor segregate into nonoverlapping subclonal populations. In vitro and in vivo functional studies show that EGFRvII is oncogenic and sensitive to EGFR inhibitors currently in clinical trials. Thus, the association between diverse activating mutations in EGFR and other subclonal mutations within a single tumor supports an intrinsic mechanism for proliferative and clonal diversification with broad implications in resistance to treatment.
Significance: We developed a novel single-cell sequencing methodology capable of identifying unique, nonoverlapping subclonal alterations from archived frozen clinical specimens. Using GBM as an example, we validated our method to successfully define tumor cell subpopulations containing distinct genetic and treatment resistance profiles and potentially mutually cooperative combinations of alterations in EGFR and other genes.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Koch Institute for Integrative Cancer Research at MIT
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DOI of Published Version
https://doi.org/10.1158/2159-8290.cd-13-0879
