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Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens

BACKGROUND: Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting mu...

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Autores principales: Fortin, Jean-Philippe, Tan, Jenille, Gascoigne, Karen E., Haverty, Peter M., Forrest, William F., Costa, Michael R., Martin, Scott E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346559/
https://www.ncbi.nlm.nih.gov/pubmed/30683138
http://dx.doi.org/10.1186/s13059-019-1621-7
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author Fortin, Jean-Philippe
Tan, Jenille
Gascoigne, Karen E.
Haverty, Peter M.
Forrest, William F.
Costa, Michael R.
Martin, Scott E.
author_facet Fortin, Jean-Philippe
Tan, Jenille
Gascoigne, Karen E.
Haverty, Peter M.
Forrest, William F.
Costa, Michael R.
Martin, Scott E.
author_sort Fortin, Jean-Philippe
collection PubMed
description BACKGROUND: Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting multiple genomic loci in CRISPR screens have not been discussed. RESULTS: In this work, we analyze CRISPR essentiality screen data from 391 cancer cell lines to characterize biases induced by multi-target sgRNAs. We investigate two types of multi-targets: on-targets predicted through perfect sequence complementarity and off-targets predicted through sequence complementarity with up to two nucleotide mismatches. We find that the number of on-targets and off-targets both increase sgRNA activity in a cell line-specific manner and that existing additive models of gene knockout effects fail at capturing genetic interactions that may occur between co-targeted genes. We use synthetic lethality between paralog genes to show that genetic interactions can introduce biases in essentiality scores estimated from multi-target sgRNAs. We further show that single-mismatch tolerant sgRNAs can confound the analysis of gene essentiality and lead to incorrect co-essentiality functional networks. Lastly, we also find that single nucleotide polymorphisms located in protospacer regions can impair on-target activity as a result of mismatch tolerance. CONCLUSION: We show the impact of multi-target effects on estimating cancer cell dependencies and the impact of off-target effects caused by mismatch tolerance in sgRNA-DNA binding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1621-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-63465592019-01-29 Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens Fortin, Jean-Philippe Tan, Jenille Gascoigne, Karen E. Haverty, Peter M. Forrest, William F. Costa, Michael R. Martin, Scott E. Genome Biol Research BACKGROUND: Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting multiple genomic loci in CRISPR screens have not been discussed. RESULTS: In this work, we analyze CRISPR essentiality screen data from 391 cancer cell lines to characterize biases induced by multi-target sgRNAs. We investigate two types of multi-targets: on-targets predicted through perfect sequence complementarity and off-targets predicted through sequence complementarity with up to two nucleotide mismatches. We find that the number of on-targets and off-targets both increase sgRNA activity in a cell line-specific manner and that existing additive models of gene knockout effects fail at capturing genetic interactions that may occur between co-targeted genes. We use synthetic lethality between paralog genes to show that genetic interactions can introduce biases in essentiality scores estimated from multi-target sgRNAs. We further show that single-mismatch tolerant sgRNAs can confound the analysis of gene essentiality and lead to incorrect co-essentiality functional networks. Lastly, we also find that single nucleotide polymorphisms located in protospacer regions can impair on-target activity as a result of mismatch tolerance. CONCLUSION: We show the impact of multi-target effects on estimating cancer cell dependencies and the impact of off-target effects caused by mismatch tolerance in sgRNA-DNA binding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1621-7) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-25 /pmc/articles/PMC6346559/ /pubmed/30683138 http://dx.doi.org/10.1186/s13059-019-1621-7 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Fortin, Jean-Philippe
Tan, Jenille
Gascoigne, Karen E.
Haverty, Peter M.
Forrest, William F.
Costa, Michael R.
Martin, Scott E.
Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
title Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
title_full Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
title_fullStr Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
title_full_unstemmed Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
title_short Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
title_sort multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled crispr screens
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346559/
https://www.ncbi.nlm.nih.gov/pubmed/30683138
http://dx.doi.org/10.1186/s13059-019-1621-7
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