Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency
<jats:title>Abstract</jats:title><jats:p>Mutational outcomes following CRISPR-Cas9-nuclease cutting in mammalian cells have recently been shown to be predictable and, in certain cases, skewed toward single genotypes. However, the ability to control these outcomes remains limited, e...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2022
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| Online Access: | https://hdl.handle.net/1721.1/143566 |
| _version_ | 1826208209001512960 |
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| author | Bermudez-Cabrera, Heysol C Culbertson, Sannie Barkal, Sammy Holmes, Benjamin Shen, Max W Zhang, Sophia Gifford, David K Sherwood, Richard I |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Bermudez-Cabrera, Heysol C Culbertson, Sannie Barkal, Sammy Holmes, Benjamin Shen, Max W Zhang, Sophia Gifford, David K Sherwood, Richard I |
| author_sort | Bermudez-Cabrera, Heysol C |
| collection | MIT |
| description | <jats:title>Abstract</jats:title><jats:p>Mutational outcomes following CRISPR-Cas9-nuclease cutting in mammalian cells have recently been shown to be predictable and, in certain cases, skewed toward single genotypes. However, the ability to control these outcomes remains limited, especially for 1-bp insertions, a common and therapeutically relevant class of repair outcomes. Here, through a small molecule screen, we identify the ATM kinase inhibitor KU-60019 as a compound capable of reproducibly increasing the fraction of 1-bp insertions relative to other Cas9 repair outcomes. Small molecule or genetic ATM inhibition increases 1-bp insertion outcome fraction across three human and mouse cell lines, two Cas9 species, and dozens of target sites, although concomitantly reducing the fraction of edited alleles. Notably, KU-60019 increases the relative frequency of 1-bp insertions to over 80% of edited alleles at several native human genomic loci and improves the efficiency of correction for pathogenic 1-bp deletion variants. The ability to increase 1-bp insertion frequency adds another dimension to precise template-free Cas9-nuclease genome editing.</jats:p> |
| first_indexed | 2024-09-23T14:02:15Z |
| format | Article |
| id | mit-1721.1/143566 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:02:15Z |
| publishDate | 2022 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1435662023-04-10T14:49:00Z Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency Bermudez-Cabrera, Heysol C Culbertson, Sannie Barkal, Sammy Holmes, Benjamin Shen, Max W Zhang, Sophia Gifford, David K Sherwood, Richard I Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Computational and Systems Biology Program <jats:title>Abstract</jats:title><jats:p>Mutational outcomes following CRISPR-Cas9-nuclease cutting in mammalian cells have recently been shown to be predictable and, in certain cases, skewed toward single genotypes. However, the ability to control these outcomes remains limited, especially for 1-bp insertions, a common and therapeutically relevant class of repair outcomes. Here, through a small molecule screen, we identify the ATM kinase inhibitor KU-60019 as a compound capable of reproducibly increasing the fraction of 1-bp insertions relative to other Cas9 repair outcomes. Small molecule or genetic ATM inhibition increases 1-bp insertion outcome fraction across three human and mouse cell lines, two Cas9 species, and dozens of target sites, although concomitantly reducing the fraction of edited alleles. Notably, KU-60019 increases the relative frequency of 1-bp insertions to over 80% of edited alleles at several native human genomic loci and improves the efficiency of correction for pathogenic 1-bp deletion variants. The ability to increase 1-bp insertion frequency adds another dimension to precise template-free Cas9-nuclease genome editing.</jats:p> 2022-06-27T18:54:55Z 2022-06-27T18:54:55Z 2021 2022-06-27T18:51:18Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/143566 Bermudez-Cabrera, Heysol C, Culbertson, Sannie, Barkal, Sammy, Holmes, Benjamin, Shen, Max W et al. 2021. "Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency." Nature Communications, 12 (1). en 10.1038/S41467-021-25415-8 Nature Communications Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Bermudez-Cabrera, Heysol C Culbertson, Sannie Barkal, Sammy Holmes, Benjamin Shen, Max W Zhang, Sophia Gifford, David K Sherwood, Richard I Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency |
| title | Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency |
| title_full | Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency |
| title_fullStr | Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency |
| title_full_unstemmed | Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency |
| title_short | Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency |
| title_sort | small molecule inhibition of atm kinase increases crispr cas9 1 bp insertion frequency |
| url | https://hdl.handle.net/1721.1/143566 |
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