Prioritisation of oncology therapeutic targets using CRISPR-Cas9 screening

Prioritisation of oncology therapeutic targets using CRISPR-Cas9 screening

December 20, 2018 | Fiona M Behan, Francesco Iorio, Emanuel Gonçalves, Gabriele Picco, Charlotte M Beaver, Rita Santos, Yanhua Rao, Rizwan Ansari, Sarah Harper, David Adam Jackson, Rebecca McRae, Rachel Pooley, Piers Wilkinson, David Dow, Carolyn Buser-Doepner, Euan A. Stronach, Julio Saez-Rodriguez, Kosuke Yusa, Mathew J Garnett
This study presents a genome-scale CRISPR-Cas9 screening approach to prioritize oncology therapeutic targets in 204 human cancer cell lines across 12 cancer types. The researchers developed a data-driven framework that integrates gene fitness effects, genomic biomarkers, and target tractability to systematically prioritize new oncology targets in defined tissues and genotypes. They validated Werner syndrome RecQ helicase (WRN) as a candidate target for tumors with microsatellite instability (MSI-H), demonstrating its essentiality in MSI-H cell lines and its association with MLH1 promoter hypermethylation. The study identified a median of 1,413 fitness genes across all cell lines, with 38% of targeted genes showing loss of fitness effect in one or more cell lines. The researchers developed a novel statistical method, ADaM, to identify core fitness (CF) genes, distinguishing context-specific fitness genes from CF genes. They identified 764 cancer-type CF genes and 582 pan-cancer CF genes, highlighting the importance of distinguishing these for target prioritization. A quantitative framework was developed to prioritize therapeutic targets, integrating CRISPR-Cas9 experimental evidence with genomic features. This framework identified 497 priority targets, including 83 pan-cancer and 470 cancer-type specific targets. The majority of these targets were associated with cancer driver events, making them promising candidates for drug development. The study also assessed the tractability of these targets, categorizing them into three groups based on their suitability for pharmaceutical intervention. Tractability Group 1 included 32 priority targets with approved or pre-clinical drugs, while Group 2 and 3 included targets with potential for drug repurposing or novel therapeutic modalities. WRN was identified as a promising target in MSI-H cancers, with its essentiality validated through CRISPR-based co-competition assays and functional redundancy studies. The study highlights the potential of CRISPR-Cas9 screening in identifying and prioritizing oncology targets, providing a comprehensive resource for cancer research and drug development. The findings suggest that targeting WRN could be a viable strategy for MSI-H cancers, with potential applications in combination therapies and resistance management. The study underscores the importance of integrating genomic and functional data to improve the efficiency and success rate of oncology drug development.This study presents a genome-scale CRISPR-Cas9 screening approach to prioritize oncology therapeutic targets in 204 human cancer cell lines across 12 cancer types. The researchers developed a data-driven framework that integrates gene fitness effects, genomic biomarkers, and target tractability to systematically prioritize new oncology targets in defined tissues and genotypes. They validated Werner syndrome RecQ helicase (WRN) as a candidate target for tumors with microsatellite instability (MSI-H), demonstrating its essentiality in MSI-H cell lines and its association with MLH1 promoter hypermethylation. The study identified a median of 1,413 fitness genes across all cell lines, with 38% of targeted genes showing loss of fitness effect in one or more cell lines. The researchers developed a novel statistical method, ADaM, to identify core fitness (CF) genes, distinguishing context-specific fitness genes from CF genes. They identified 764 cancer-type CF genes and 582 pan-cancer CF genes, highlighting the importance of distinguishing these for target prioritization. A quantitative framework was developed to prioritize therapeutic targets, integrating CRISPR-Cas9 experimental evidence with genomic features. This framework identified 497 priority targets, including 83 pan-cancer and 470 cancer-type specific targets. The majority of these targets were associated with cancer driver events, making them promising candidates for drug development. The study also assessed the tractability of these targets, categorizing them into three groups based on their suitability for pharmaceutical intervention. Tractability Group 1 included 32 priority targets with approved or pre-clinical drugs, while Group 2 and 3 included targets with potential for drug repurposing or novel therapeutic modalities. WRN was identified as a promising target in MSI-H cancers, with its essentiality validated through CRISPR-based co-competition assays and functional redundancy studies. The study highlights the potential of CRISPR-Cas9 screening in identifying and prioritizing oncology targets, providing a comprehensive resource for cancer research and drug development. The findings suggest that targeting WRN could be a viable strategy for MSI-H cancers, with potential applications in combination therapies and resistance management. The study underscores the importance of integrating genomic and functional data to improve the efficiency and success rate of oncology drug development.
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