Sánchez-Rivera, Francisco J, Diaz, Bianca J, Kastenhuber, Edward R, Schmidt, Henri, Katti, Alyna, Kennedy, Margaret, Tem, Vincent, Ho, Yu-Jui, Leibold, Josef, Paffenholz, Stella V, Barriga, Francisco M, Chu, Kevan, Goswami, Sukanya, Wuest, Alexandra N, Simon, Janelle M, Tsanov, Kaloyan M, Chakravarty, Debyani, Zhang, Hongxin, Leslie, Christina S, Lowe, Scott W, Dow, Lukas E (February 2022) Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Nature Biotechnology. ISSN 1087-0156
Abstract
Base editing can be applied to characterize single nucleotide variants of unknown function, yet defining effective combinations of single guide RNAs (sgRNAs) and base editors remains challenging. Here, we describe modular base-editing-activity 'sensors' that link sgRNAs and cognate target sites in cis and use them to systematically measure the editing efficiency and precision of thousands of sgRNAs paired with functionally distinct base editors. By quantifying sensor editing across >200,000 editor-sgRNA combinations, we provide a comprehensive resource of sgRNAs for introducing and interrogating cancer-associated single nucleotide variants in multiple model systems. We demonstrate that sensor-validated tools streamline production of in vivo cancer models and that integrating sensor modules in pooled sgRNA libraries can aid interpretation of high-throughput base editing screens. Using this approach, we identify several previously uncharacterized mutant TP53 alleles as drivers of cancer cell proliferation and in vivo tumor development. We anticipate that the framework described here will facilitate the functional interrogation of cancer variants in cell and animal models.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics diseases & disorders > cancer bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification diseases & disorders bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment diseases & disorders > neoplasms Investigative techniques and equipment > CRISPR-Cas9 bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism |
| CSHL Authors: | |
| Communities: | CSHL labs > Lowe lab CSHL Cancer Center Program CSHL Cancer Center Program > Cancer Genetics and Genomics Program |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 14 February 2022 |
| Date Deposited: | 02 Mar 2022 22:38 |
| Last Modified: | 09 Feb 2024 20:21 |
| PMCID: | PMC9232935 |
| URI: | https://repository.cshl.edu/id/eprint/40537 |
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