Human genetic diversity alters off-target outcomes of therapeutic gene editing.

Autor: Cancellieri S; Department of Computer Science, University of Verona, Verona, Italy., Zeng J; Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA., Lin LY; Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA., Tognon M; Department of Computer Science, University of Verona, Verona, Italy.; Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA., Nguyen MA; Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA., Lin J; Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA., Bombieri N; Department of Computer Science, University of Verona, Verona, Italy., Maitland SA; Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA., Ciuculescu MF; TransLab, Boston Children's Hospital, Boston, MA, USA., Katta V; Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA., Tsai SQ; Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA., Armant M; TransLab, Boston Children's Hospital, Boston, MA, USA., Wolfe SA; Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA., Giugno R; Department of Computer Science, University of Verona, Verona, Italy. rosalba.giugno@univr.it., Bauer DE; Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA. bauer@bloodgroup.tch.harvard.edu.; Broad Institute of MIT and Harvard, Cambridge, MA, USA. bauer@bloodgroup.tch.harvard.edu., Pinello L; Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA. lpinello@mgh.harvard.edu.; Broad Institute of MIT and Harvard, Cambridge, MA, USA. lpinello@mgh.harvard.edu.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2023 Jan; Vol. 55 (1), pp. 34-43. Date of Electronic Publication: 2022 Dec 15.
DOI: 10.1038/s41588-022-01257-y
Abstrakt: CRISPR gene editing holds great promise to modify DNA sequences in somatic cells to treat disease. However, standard computational and biochemical methods to predict off-target potential focus on reference genomes. We developed an efficient tool called CRISPRme that considers single-nucleotide polymorphism (SNP) and indel genetic variants to nominate and prioritize off-target sites. We tested the software with a BCL11A enhancer targeting guide RNA (gRNA) showing promise in clinical trials for sickle cell disease and β-thalassemia and found that the top candidate off-target is produced by an allele common in African-ancestry populations (MAF 4.5%) that introduces a protospacer adjacent motif (PAM) sequence. We validated that SpCas9 generates strictly allele-specific indels and pericentric inversions in CD34 + hematopoietic stem and progenitor cells (HSPCs), although high-fidelity Cas9 mitigates this off-target. This report illustrates how genetic variants should be considered as modifiers of gene editing outcomes. We expect that variant-aware off-target assessment will become integral to therapeutic genome editing evaluation and provide a powerful approach for comprehensive off-target nomination.
(© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
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