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High-throughput functional evaluation of human cancer-associated mutations using base editors

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Title
High-throughput functional evaluation of human cancer-associated mutations using base editors
Author(s)
Younggwang Kim; Seungho Lee; Soohyuk Cho; Jinman Park; Dongwoo Chae; Taeyoung Park; John D. Minna; Hyongbum Henry Kim
Publication Date
2022-06
Journal
Nature Biotechnology, v.40, no.6, pp.874 - 884
Publisher
Nature Research
Abstract
© 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.Comprehensive phenotypic characterization of the many mutations found in cancer tissues is one of the biggest challenges in cancer genomics. In this study, we evaluated the functional effects of 29,060 cancer-related transition mutations that result in protein variants on the survival and proliferation of non-tumorigenic lung cells using cytosine and adenine base editors and single guide RNA (sgRNA) libraries. By monitoring base editing efficiencies and outcomes using surrogate target sequences paired with sgRNA-encoding sequences on the lentiviral delivery construct, we identified sgRNAs that induced a single primary protein variant per sgRNA, enabling linking those mutations to the cellular phenotypes caused by base editing. The functions of the vast majority of the protein variants (28,458 variants, 98%) were classified as neutral or likely neutral; only 18 (0.06%) and 157 (0.5%) variants caused outgrowing and likely outgrowing phenotypes, respectively. We expect that our approach can be extended to more variants of unknown significance and other tumor types.
URI
https://pr.ibs.re.kr/handle/8788114/11927
DOI
10.1038/s41587-022-01276-4
ISSN
1087-0156
Appears in Collections:
Center for Nanomedicine (나노의학 연구단) > 1. Journal Papers (저널논문)
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