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Ambrosini C, Destefanis E, Kheir E, Broso F, Alessandrini F, Longhi S, Battisti N, Pesce I, Dassi E, Petris G, Cereseto A, Quattrone A. Translational enhancement by base editing of the Kozak sequence rescues haploinsufficiency. Nucleic Acids Res 2022; 50:10756-10771. [PMID: 36165847 PMCID: PMC9561285 DOI: 10.1093/nar/gkac799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
A variety of single-gene human diseases are caused by haploinsufficiency, a genetic condition by which mutational inactivation of one allele leads to reduced protein levels and functional impairment. Translational enhancement of the spare allele could exert a therapeutic effect. Here we developed BOOST, a novel gene-editing approach to rescue haploinsufficiency loci by the change of specific single nucleotides in the Kozak sequence, which controls translation by regulating start codon recognition. We evaluated for translational strength 230 Kozak sequences of annotated human haploinsufficient genes and 4621 derived variants, which can be installed by base editing, by a high-throughput reporter assay. Of these variants, 149 increased the translation of 47 Kozak sequences, demonstrating that a substantial proportion of haploinsufficient genes are controlled by suboptimal Kozak sequences. Validation of 18 variants for 8 genes produced an average enhancement in an expression window compatible with the rescue of the genetic imbalance. Base editing of the NCF1 gene, whose monoallelic loss causes chronic granulomatous disease, resulted in the desired increase of NCF1 (p47phox) protein levels in a relevant cell model. We propose BOOST as a fine-tuned approach to modulate translation, applicable to the correction of dozens of haploinsufficient monogenic disorders independently of the causing mutation.
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Affiliation(s)
- Chiara Ambrosini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Eliana Destefanis
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Eyemen Kheir
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Francesca Broso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Federica Alessandrini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Nicolò Battisti
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Isabella Pesce
- Cell Analysis and Separation Core Facility, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge CB2 0QH, UK
| | - Anna Cereseto
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
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