Intrinsic deletion at 10q23.31, including thePTENgene locus, is aggravated upon CRISPR-Cas9–mediated genome engineering in HAP1 cells mimicking cancer profiles
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Published:2023-11-20
Issue:2
Volume:7
Page:e202302128
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ISSN:2575-1077
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Container-title:Life Science Alliance
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language:en
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Short-container-title:Life Sci. Alliance
Author:
Geng Keyi1ORCID,
Merino Lara G1ORCID,
Veiga Raül G1ORCID,
Sommerauer Christian1ORCID,
Epperlein Janine1ORCID,
Brinkman Eva K1ORCID,
Kutter Claudia1ORCID
Affiliation:
1. Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute
Abstract
The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, includingPAPSS2,ATAD1,KLLN, andPTEN. We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9–modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9–modified cells, which could impact cancer research.
Funder
Chinese Scholarship Council
EMBO Postdoctoral Fellowship
Knut och Alice Wallenbergs Stiftelse
Ruth och Richard Julins Stiftelse
SFO SciLifeLab fellowship
Karolinska Institutet - KID
Vetenskapsrådet
Lillian Sagen & Curt Ericsson Research Foundation
Gösta Milton’s Research Foundation
Cancerfonden
Uppsala University | Uppsala Multidisciplinary Center for Advanced Computational Science
Publisher
Life Science Alliance, LLC
Subject
Health, Toxicology and Mutagenesis,Plant Science,Biochemistry, Genetics and Molecular Biology (miscellaneous),Ecology