Principles of CRISPR-Cas13 Mismatch Intolerance Enable Selective Silencing of Point-mutated Oncogenic RNA with Single-base Precision

Overview

Journal Sci Adv

Specialties Biology
Science

Date 2024 Dec 18

PMID 39693429

Authors

Carolyn Shembrey

Ray Yang

Joshua Casan

Wenxin Hu

Honglin Chen

Gurjeet J Singh

Teresa Sadras

Krishneel Prasad

Jake Shortt

Ricky W Johnstone

Joseph A Trapani

Paul G Ekert

Mohamed Fareh

Affiliations

Soon will be listed here.

Abstract

Single-nucleotide variants (SNVs) are extremely prevalent in human cancers, although most of these remain clinically unactionable. The programmable RNA nuclease CRISPR-Cas13 has been deployed to specifically target oncogenic RNAs. However, silencing oncogenic SNVs with single-base precision remains extremely challenging due to the intrinsic mismatch tolerance of Cas13. Here, we show that introducing synthetic mismatches at precise positions of the spacer sequence enables de novo design of guide RNAs [CRISPR RNAs (crRNAs)] with strong preferential silencing of point-mutated transcripts. We applied these design principles to effectively silence the oncogenic G12 hotspot, and transcripts with minimal off-target silencing of the wild-type transcripts, underscoring the adaptability of this platform to silence various SNVs. Unexpectedly, the SNV-selective crRNAs harboring mismatched nucleotides reduce the promiscuous collateral activity of the Cas13d ortholog. These findings demonstrate that the CRISPR-Cas13 system can be reprogrammed to target mutant transcripts with single-base precision, showcasing the tremendous potential of this tool in personalized transcriptome editing.

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