Efficient Correction of Oncogenic KRAS and TP53 Mutations through CRISPR Base Editing

Cancer Res. 2022 Sep 2;82(17):3002-3015. doi: 10.1158/0008-5472.CAN-21-2519.

Abstract

KRAS is the most frequently mutated oncogene in human cancer, and its activating mutations represent long-sought therapeutic targets. Programmable nucleases, particularly the CRISPR-Cas9 system, provide an attractive tool for genetically targeting KRAS mutations in cancer cells. Here, we show that cleavage of a panel of KRAS driver mutations suppresses growth in various human cancer cell lines, revealing their dependence on mutant KRAS. However, analysis of the remaining cell population after long-term Cas9 expression unmasked the occurence of oncogenic KRAS escape variants that were resistant to Cas9-cleavage. In contrast, the use of an adenine base editor to correct oncogenic KRAS mutations progressively depleted the targeted cells without the appearance of escape variants and allowed efficient and simultaneous correction of a cancer-associated TP53 mutation. Oncogenic KRAS and TP53 base editing was possible in patient-derived cancer organoids, suggesting that base editor approaches to correct oncogenic mutations could be developed for functional interrogation of vulnerabilities in a personalized manner for future precision oncology applications.

Significance: Repairing KRAS mutations with base editors can be used for providing a better understanding of RAS biology and may lay the foundation for improved treatments for KRAS-mutant cancers.

MeSH terms

  • CRISPR-Cas Systems
  • Carcinogenesis / genetics
  • Gene Editing
  • Humans
  • Mutation
  • Neoplasms* / genetics
  • Oncogenes
  • Precision Medicine
  • Proto-Oncogene Proteins p21(ras)* / genetics
  • Tumor Suppressor Protein p53 / genetics

Substances

  • KRAS protein, human
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • Proto-Oncogene Proteins p21(ras)