In silico analysis of potential off-target sites to gene editing for Mucopolysaccharidosis type I using the CRISPR/Cas9 system: Implications for population-specific treatments

Paola Carneiro; Martiela Vaz de Freitas; Ursula Matte

doi:10.1371/journal.pone.0262299

In silico analysis of potential off-target sites to gene editing for Mucopolysaccharidosis type I using the CRISPR/Cas9 system: Implications for population-specific treatments

PLoS One. 2022 Jan 24;17(1):e0262299. doi: 10.1371/journal.pone.0262299. eCollection 2022.

Authors

Paola Carneiro^{1

2

3}, Martiela Vaz de Freitas^{1

2

3}, Ursula Matte^{1

2

3

4}

Affiliations

¹ Post-Graduation Program on Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
² Bioinformatics Core, Experimental Research Center, Hospital de Clínicas, Porto Alegre, Rio Grande do Sul, Brazil.
³ Cell, Tissue and Genes Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil.
⁴ Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.

Abstract

Mucopolysaccharidosis type I (MPS I) is caused by alpha-L-iduronidase deficiency encoded by the IDUA gene. Therapy with CRISPR/Cas9 is being developed for treatment, however a detailed investigation of off-target effects must be performed. This study aims to evaluate possible off-targets for a sgRNA aiming to correct the most common variant found in MPS I patients (p.Trp402*). A total of 272 potential off-target sequences was obtained and 84 polymorphic sites were identified in these sequences with a frequency equal to or greater than 1% in at least one of the populations. In the majority of cases, polymorphic sites decrease the chance of off-target cleavage and a new PAM was created, which indicates the importance of such analysis. This study highlights the importance of screening off-targets in a population-specific context using Mucopolysaccharidosis type I as an example of a problem that concerns all therapeutic treatments. Our results can have broader applications for other targets already clinically in use, as they could affect CRISPR/Cas9 safety and efficiency.

MeSH terms

CRISPR-Associated Protein 9*
CRISPR-Cas Systems*
Computer Simulation
Gene Editing* / methods
Gene Targeting / methods
Humans
Mucopolysaccharidosis I / genetics
Mucopolysaccharidosis I / therapy*
Polymorphism, Genetic

Substances

CRISPR-Associated Protein 9

Grants and funding

The author(s) received no specific funding for this work.