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

Younggwang Kim, Seungho Lee, Soohyuk Cho, Jinman Park, Dongwoo Chae, Taeyoung Park, John D. Minna, Hyongbum Henry Kim

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)874-884
Number of pages11
JournalNature Biotechnology
Issue number6
Publication statusPublished - 2022 Jun

Bibliographical note

Funding Information:
We thank J. W. Choi for assisting with computational analysis. This work was supported, in part, by the National Research Foundation of Korea (grants 2017R1A2B3004198 (H.H.K.), 2017M3A9B4062403 (H.H.K.) and 2018R1A5A2025079 (H.H.K)); the Brain Korea 21 Plus Project (Yonsei University College of Medicine); the Yonsei Signature Research Cluster Program of 2021-22-0014 (H.H.K.); a grant of the MD-PhD/Medical Scientist Training Program (S.L.) through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea; Lung Cancer SPORE P50 (CA070907; J.D.M.); and the Korean Health Technology R&D Project, Ministry of Health and Welfare, Republic of Korea (grant HI21C1314 (H.H.K.)).

Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Biomedical Engineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine


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