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
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...
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| Veröffentlicht in: | PloS one 2022-01, Vol.17 (1), p.e0262299-e0262299 |
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| creator | Carneiro, Paola de Freitas, Martiela Vaz Matte, Ursula |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0262299 |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0262299</identifier><identifier>PMID: 35073349</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bioinformatics ; Biology and Life Sciences ; Care and treatment ; Computer Simulation ; CRISPR ; CRISPR-Associated Protein 9 ; CRISPR-Cas Systems ; Engineering and Technology ; Gene Editing - methods ; Gene Targeting - methods ; Gene therapy ; Genes ; Genetic disorders ; Genetic modification ; Genetics ; Genome editing ; Genomes ; Humans ; IDUA gene ; L-Iduronidase ; Laboratories ; Metabolic disorders ; Methods ; Molecular biology ; Mucopolysaccharidosis ; Mucopolysaccharidosis I - genetics ; Mucopolysaccharidosis I - therapy ; People and Places ; Polymorphism, Genetic ; Probability ; Research and Analysis Methods</subject><ispartof>PloS one, 2022-01, Vol.17 (1), p.e0262299-e0262299</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Carneiro et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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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.</description><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Care and treatment</subject><subject>Computer Simulation</subject><subject>CRISPR</subject><subject>CRISPR-Associated Protein 9</subject><subject>CRISPR-Cas Systems</subject><subject>Engineering and Technology</subject><subject>Gene Editing - methods</subject><subject>Gene Targeting - methods</subject><subject>Gene therapy</subject><subject>Genes</subject><subject>Genetic disorders</subject><subject>Genetic modification</subject><subject>Genetics</subject><subject>Genome editing</subject><subject>Genomes</subject><subject>Humans</subject><subject>IDUA gene</subject><subject>L-Iduronidase</subject><subject>Laboratories</subject><subject>Metabolic disorders</subject><subject>Methods</subject><subject>Molecular biology</subject><subject>Mucopolysaccharidosis</subject><subject>Mucopolysaccharidosis I - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Carneiro, Paola</au><au>de Freitas, Martiela Vaz</au><au>Matte, Ursula</au><au>Xu, Shuang-yong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2022-01-24</date><risdate>2022</risdate><volume>17</volume><issue>1</issue><spage>e0262299</spage><epage>e0262299</epage><pages>e0262299-e0262299</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35073349</pmid><doi>10.1371/journal.pone.0262299</doi><tpages>e0262299</tpages><orcidid>https://orcid.org/0000-0001-8401-3332</orcidid><orcidid>https://orcid.org/0000-0003-4178-6604</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Bioinformatics Biology and Life Sciences Care and treatment Computer Simulation CRISPR CRISPR-Associated Protein 9 CRISPR-Cas Systems Engineering and Technology Gene Editing - methods Gene Targeting - methods Gene therapy Genes Genetic disorders Genetic modification Genetics Genome editing Genomes Humans IDUA gene L-Iduronidase Laboratories Metabolic disorders Methods Molecular biology Mucopolysaccharidosis Mucopolysaccharidosis I - genetics Mucopolysaccharidosis I - therapy People and Places Polymorphism, Genetic Probability Research and Analysis Methods |
| title | 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 |
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