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Journal article
Novel gRNA design pipeline to develop broad-spectrum CRISPR/Cas9 gRNAs for safe targeting of the HIV-1 quasispecies in patients
Scientific reports, v 9(1), pp 17088-19
19 Nov 2019
PMID: 31745112
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The CRISPR/Cas9 system has been proposed as a cure strategy for HIV. However, few published guide RNAs (gRNAs) are predicted to cleave the majority of HIV-1 viral quasispecies (vQS) observed within and among patients. We report the design of a novel pipeline to identify gRNAs that target HIV across a large number of infected individuals. Next generation sequencing (NGS) of LTRs from 269 HIV-1-infected samples in the Drexel CARES Cohort was used to select gRNAs with predicted broad-spectrum activity. In silico, D-LTR-P4-227913 (package of the top 4 gRNAs) accounted for all detectable genetic variation within the vQS of the 269 samples and the Los Alamos National Laboratory HIV database. In silico secondary structure analyses from NGS indicated extensive TAR stem-loop malformations predicted to inactivate proviral transcription, which was confirmed by reduced viral gene expression in TZM-bl or P4R5 cells. Similarly, a high sensitivity in vitro CRISPR/Cas9 cleavage assay showed that the top-ranked gRNA was the most effective at cleaving patient-derived HIV-1 LTRs from five patients. Furthermore, the D-LTR-P4-227913 was predicted to cleave a median of 96.1% of patient-derived sequences from other HIV subtypes. These results demonstrate that the gRNAs possess broad-spectrum cutting activity and could contribute to an HIV cure.
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Details
- Title
- Novel gRNA design pipeline to develop broad-spectrum CRISPR/Cas9 gRNAs for safe targeting of the HIV-1 quasispecies in patients
- Creators
- Neil T Sullivan - Drexel UniversityWill Dampier - Drexel UniversityCheng-Han Chung - Drexel UniversityAlexander G Allen - Drexel UniversityAndrew Atkins - Drexel UniversityVanessa Pirrone - Drexel UniversityGreg Homan - Drexel UniversityShendra Passic - Drexel UniversityJean Williams - Drexel UniversityWen Zhong - Drexel UniversityKatherine Kercher - Drexel UniversityMathew Desimone - Drexel UniversityLuna Li - Drexel UniversityGregory C Antell - School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USAJoshua Chang Mell - Drexel UniversityGarth D Ehrlich - Drexel UniversityZsofia Szep - Drexel UniversityJeffrey M Jacobson - Temple UniversityMichael R Nonnemacher - Drexel UniversityBrian Wigdahl - Drexel University
- Publication Details
- Scientific reports, v 9(1), pp 17088-19
- Publisher
- Springer Nature
- Grant note
- R01 MH110360 / NIMH NIH HHS T32 MH079785 / NIMH NIH HHS P30 MH092177 / NIMH NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology; Infectious Diseases (and HIV Medicine)
- Web of Science ID
- WOS:000497701800045
- Scopus ID
- 2-s2.0-85075195595
- Other Identifier
- 991019168821604721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Multidisciplinary Sciences