Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

Area of Science:

• Genomics
• Cancer Biology
• Drug Discovery

Background:

• Functional genomic screens, including the Cancer Dependency Map, identify gene dependencies crucial for cancer cell survival.
• The shift from RNA interference (RNAi) to CRISPR-Cas9 in large-scale screening offers higher efficacy and specificity.
• The partial inhibition of targets by many cancer drugs prompts an investigation into RNAi's potential for uncovering vulnerabilities missed by complete gene knockout.

Purpose of the Study:

• To compare CRISPR-Cas9 and RNAi gene dependency profiles across approximately 400 cancer cell lines.
• To determine if partial gene suppression using RNAi can identify cancer vulnerabilities overlooked by CRISPR-Cas9 knockout screens.
• To assess the utility of integrating RNAi data with CRISPR data for a more comprehensive cancer dependency map.

Main Methods:

• Comparative analysis of CRISPR-Cas9 and RNAi dependency profiles.
• Screening approximately 400 matched cancer cell lines.
• Analysis of gene dependency patterns, including shared (pan-lethal) and selective dependencies.

Main Results:

• CRISPR screens identify more gene dependencies per cell line, with most falling into a set of 1867 shared pan-lethal genes.
• RNAi knockdown of ~30% of these pan-lethal genes is also pan-lethal.
• ~50% of genes show selective dependency patterns with RNAi, indicating potential cancer vulnerabilities.
• RNAi selectivity is validated by associations with multi-omics data, drug sensitivity, and co-dependencies.

Conclusions:

• Integrating RNAi data with CRISPR screens broadens the discovery of gene targets compared to using CRISPR data alone.
• RNAi's ability to reveal selective gene dependencies is crucial for a comprehensive cancer dependency map.
• Partial gene suppression methods like RNAi are vital for uncovering a wider spectrum of cancer vulnerabilities.