Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy
Clustered regularly interspaced short palindromic repeats (CRISPR)-based HIV-1 genome editing has shown promising outcomes in in vitro and in vivo viral infection models. However, existing HIV-1 sequence variants have been shown to reduce CRISPR-mediated efficiency and induce viral escape. Two metri...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2021.593077/full |
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| author | Cheng-Han Chung Cheng-Han Chung Alexander G. Allen Alexander G. Allen Andrew Atkins Andrew Atkins Robert W. Link Robert W. Link Michael R. Nonnemacher Michael R. Nonnemacher Michael R. Nonnemacher Will Dampier Will Dampier Brian Wigdahl Brian Wigdahl Brian Wigdahl |
| author_facet | Cheng-Han Chung Cheng-Han Chung Alexander G. Allen Alexander G. Allen Andrew Atkins Andrew Atkins Robert W. Link Robert W. Link Michael R. Nonnemacher Michael R. Nonnemacher Michael R. Nonnemacher Will Dampier Will Dampier Brian Wigdahl Brian Wigdahl Brian Wigdahl |
| author_sort | Cheng-Han Chung |
| collection | DOAJ |
| description | Clustered regularly interspaced short palindromic repeats (CRISPR)-based HIV-1 genome editing has shown promising outcomes in in vitro and in vivo viral infection models. However, existing HIV-1 sequence variants have been shown to reduce CRISPR-mediated efficiency and induce viral escape. Two metrics, global patient coverage and global subtype coverage, were used to identify guide RNA (gRNA) sequences that account for this viral diversity from the perspectives of cross-patient and cross-subtype gRNA design, respectively. Computational evaluation using these parameters and over 3.6 million possible 20-bp sequences resulted in nine lead gRNAs, two of which were previously published. This analysis revealed the benefit and necessity of considering all sequence variants for gRNA design. Of the other seven identified novel gRNAs, two were of note as they targeted interesting functional regions. One was a gRNA predicted to induce structural disruption in the nucleocapsid binding site (Ψ), which holds the potential to stop HIV-1 replication during the viral genome packaging process. The other was a reverse transcriptase (RT)-targeting gRNA that was predicted to cleave the subdomain responsible for dNTP incorporation. CRISPR-mediated sequence edits were predicted to occur on critical residues where HIV-1 has been shown to develop resistance against antiretroviral therapy (ART), which may provide additional evolutionary pressure at the DNA level. Given these observations, consideration of broad-spectrum gRNAs and cross-subtype diversity for gRNA design is not only required for the development of generalizable CRISPR-based HIV-1 therapy, but also helps identify optimal target sites. |
| first_indexed | 2024-12-14T18:05:21Z |
| format | Article |
| id | doaj.art-ea35d33ad04a48eaa63b98608e3704b4 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-12-14T18:05:21Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-ea35d33ad04a48eaa63b98608e3704b42022-12-21T22:52:22ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882021-03-011110.3389/fcimb.2021.593077593077Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral TherapyCheng-Han Chung0Cheng-Han Chung1Alexander G. Allen2Alexander G. Allen3Andrew Atkins4Andrew Atkins5Robert W. Link6Robert W. Link7Michael R. Nonnemacher8Michael R. Nonnemacher9Michael R. Nonnemacher10Will Dampier11Will Dampier12Brian Wigdahl13Brian Wigdahl14Brian Wigdahl15Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesDepartment of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesDepartment of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesDepartment of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesDepartment of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesSidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United StatesDepartment of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesDepartment of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United StatesCenter for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United StatesSidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United StatesClustered regularly interspaced short palindromic repeats (CRISPR)-based HIV-1 genome editing has shown promising outcomes in in vitro and in vivo viral infection models. However, existing HIV-1 sequence variants have been shown to reduce CRISPR-mediated efficiency and induce viral escape. Two metrics, global patient coverage and global subtype coverage, were used to identify guide RNA (gRNA) sequences that account for this viral diversity from the perspectives of cross-patient and cross-subtype gRNA design, respectively. Computational evaluation using these parameters and over 3.6 million possible 20-bp sequences resulted in nine lead gRNAs, two of which were previously published. This analysis revealed the benefit and necessity of considering all sequence variants for gRNA design. Of the other seven identified novel gRNAs, two were of note as they targeted interesting functional regions. One was a gRNA predicted to induce structural disruption in the nucleocapsid binding site (Ψ), which holds the potential to stop HIV-1 replication during the viral genome packaging process. The other was a reverse transcriptase (RT)-targeting gRNA that was predicted to cleave the subdomain responsible for dNTP incorporation. CRISPR-mediated sequence edits were predicted to occur on critical residues where HIV-1 has been shown to develop resistance against antiretroviral therapy (ART), which may provide additional evolutionary pressure at the DNA level. Given these observations, consideration of broad-spectrum gRNAs and cross-subtype diversity for gRNA design is not only required for the development of generalizable CRISPR-based HIV-1 therapy, but also helps identify optimal target sites.https://www.frontiersin.org/articles/10.3389/fcimb.2021.593077/fullhuman immunodeficiency virus type 1 (HIV-1)CRISPR/Cas9gene therapygenetic variationHIV-1 subtypesbioinformatics |
| spellingShingle | Cheng-Han Chung Cheng-Han Chung Alexander G. Allen Alexander G. Allen Andrew Atkins Andrew Atkins Robert W. Link Robert W. Link Michael R. Nonnemacher Michael R. Nonnemacher Michael R. Nonnemacher Will Dampier Will Dampier Brian Wigdahl Brian Wigdahl Brian Wigdahl Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy Frontiers in Cellular and Infection Microbiology human immunodeficiency virus type 1 (HIV-1) CRISPR/Cas9 gene therapy genetic variation HIV-1 subtypes bioinformatics |
| title | Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy |
| title_full | Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy |
| title_fullStr | Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy |
| title_full_unstemmed | Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy |
| title_short | Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy |
| title_sort | computational design of grnas targeting genetic variants across hiv 1 subtypes for crispr mediated antiviral therapy |
| topic | human immunodeficiency virus type 1 (HIV-1) CRISPR/Cas9 gene therapy genetic variation HIV-1 subtypes bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2021.593077/full |
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