Efficient prioritization of CRISPR screen hits by accounting for targeting efficiency of guide RNA

Byung Sun Park, Heeju Jeon, Sung Gil Chi, Tackhoon Kim

Research output: Contribution to journalArticlepeer-review

Abstract

Background: CRISPR-based screens are revolutionizing drug discovery as tools to identify genes whose ablation induces a phenotype of interest. For instance, CRISPR-Cas9 screening has been successfully used to identify novel therapeutic targets in cancer where disruption of genes leads to decreased viability of malignant cells. However, low-activity guide RNAs may give rise to variable changes in phenotype, preventing easy identification of hits and leading to false negative results. Therefore, correcting the effects of bias due to differences in guide RNA efficiency in CRISPR screening data can improve the efficiency of prioritizing hits for further validation. Here, we developed an approach to identify hits from negative CRISPR screens by correcting the fold changes (FC) in gRNA frequency by the actual, observed frequency of indel mutations generated by gRNA. Results: Each gRNA was coupled with the “reporter sequence” that can be targeted by the same gRNA so that the frequency of mutations in the reporter sequence can be used as a proxy for the endogenous target gene. The measured gRNA activity was used to correct the FC. We identified indel generation efficiency as the dominant factor contributing significant bias to screening results, and our method significantly removed such bias and was better at identifying essential genes when compared to conventional fold change analysis. We successfully applied our gRNA activity data to previously published gRNA screening data, and identified novel genes whose ablation could synergize with vemurafenib in the A375 melanoma cell line. Our method identified nicotinamide N-methyltransferase, lactate dehydrogenase B, and polypyrimidine tract-binding protein 1 as synergistic targets whose ablation sensitized A375 cells to vemurafenib. Conclusions: We identified the variations in target cleavage efficiency, even in optimized sgRNA libraries, that pose a strong bias in phenotype and developed an analysis method that corrects phenotype score by the measured differences in the targeting efficiency among sgRNAs. Collectively, we expect that our new analysis method will more accurately identify genes that confer the phenotype of interest.

Original languageEnglish
Article number45
JournalBMC biology
Volume21
Issue number1
DOIs
Publication statusPublished - 2023 Dec

Bibliographical note

Funding Information:
This work was supported by the National Research Foundation of Korea (2021R1A2C1093499 to T.K.) and the Korea Institute of Science and Technology Institutional Programs (2E31624 to T.K.).

Publisher Copyright:
© 2023, The Author(s).

Keywords

  • CRISPR screens
  • CRISPR-Cas
  • Drug resistance
  • Functional genomics
  • Melanoma

ASJC Scopus subject areas

  • Biotechnology
  • Structural Biology
  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • General Biochemistry,Genetics and Molecular Biology
  • General Agricultural and Biological Sciences
  • Plant Science
  • Developmental Biology
  • Cell Biology

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