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Mask E, Hodara VL, Callery JE, Parodi LM, Obregon-Perko V, Yagi S, Glenn J, Frost P, Clemmons E, Patterson JL, Cox LA, Giavedoni LD. Molecular Approaches for the Validation of the Baboon as a Nonhuman Primate Model for the Study of Zika Virus Infection. Front Cell Infect Microbiol 2022; 12:880860. [PMID: 35493734 PMCID: PMC9046911 DOI: 10.3389/fcimb.2022.880860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Nonhuman primates (NHP) are particularly important for modeling infections with viruses that do not naturally replicate in rodent cells. Zika virus (ZIKV) has been responsible for sporadic epidemics, but in 2015 a disseminated outbreak of ZIKV resulted in the World Health Organization declaring it a global health emergency. Since the advent of this last epidemic, several NHP species, including the baboon, have been utilized for modeling and understanding the complications of ZIKV infection in humans; several health issues related to the outcome of infection have not been resolved yet and require further investigation. This study was designed to validate, in baboons, the molecular signatures that have previously been identified in ZIKV-infected humans and macaque models. We performed a comprehensive molecular analysis of baboons during acute ZIKV infection, including flow cytometry, cytokine, immunological, and transcriptomic analyses. We show here that, similar to most human cases, ZIKV infection of male baboons tends to be subclinical, but is associated with a rapid and transient antiviral interferon-based response signature that induces a detectable humoral and cell-mediated immune response. This immunity against the virus protects animals from challenge with a divergent ZIKV strain, as evidenced by undetectable viremia but clear anamnestic responses. These results provide additional support for the use of baboons as an alternative animal model to macaques and validate omic techniques that could help identify the molecular basis of complications associated with ZIKV infections in humans.
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Affiliation(s)
- Emma Mask
- Department of Biology, Trinity University, San Antonio, TX, United States
| | - Vida L. Hodara
- Southwest National Primate Research Center, San Antonio, TX, United States,Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Jessica E. Callery
- Department of Biology, Trinity University, San Antonio, TX, United States
| | - Laura M. Parodi
- Southwest National Primate Research Center, San Antonio, TX, United States,Texas Biomedical Research Institute, San Antonio, TX, United States
| | | | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, United States
| | - Jeremy Glenn
- Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Patrice Frost
- Southwest National Primate Research Center, San Antonio, TX, United States
| | - Elizabeth Clemmons
- Southwest National Primate Research Center, San Antonio, TX, United States
| | | | - Laura A. Cox
- Southwest National Primate Research Center, San Antonio, TX, United States,Center for Precision Medicine, Wake Forest Health Sciences University, Winston Salem, NC, United States
| | - Luis D. Giavedoni
- Department of Biology, Trinity University, San Antonio, TX, United States,Southwest National Primate Research Center, San Antonio, TX, United States,*Correspondence: Luis D. Giavedoni,
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Smith LM, Ladner JT, Hodara VL, Parodi LM, Harris RA, Callery JE, Lai Z, Zou Y, Raveedran M, Rogers J, Giavedoni LD. Multiplexed Simian Immunodeficiency Virus-Specific Paired RNA-Guided Cas9 Nickases Inactivate Proviral DNA. J Virol 2021; 95:e0088221. [PMID: 34549979 PMCID: PMC8577357 DOI: 10.1128/jvi.00882-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
Human and simian immunodeficiency virus (HIV and SIV) infections establish lifelong reservoirs of cells harboring an integrated proviral genome. Genome editing CRISPR-associated Cas9 nucleases, combined with SIV-specific guiding RNA (gRNA) molecules, inactivate integrated provirus DNA in vitro and in animal models. We generated RNA-guided Cas9 nucleases (RGNu) and nickases (RGNi) targeting conserved SIV regions with no homology in the human or rhesus macaque genome. Assays in cells cotransfected with SIV provirus and plasmids coding for RGNus identified SIV long terminal repeat (LTR), trans-activation response (TAR) element, and ribosome slip site (RSS) regions as the most effective at virus suppression; RGNi targeting these regions inhibited virus production significantly. Multiplex plasmids that coexpressed these three RGNu (Nu3), or six (three pairs) RGNi (Ni6), were more efficient at virus suppression than any combination of individual RGNu and RGNi plasmids. Both Nu3 and Ni6 plasmids were tested in lymphoid cells chronically infected with SIVmac239, and whole-genome sequencing was used to determine on- and off-target mutations. Treatment with these all-in-one plasmids resulted in similar levels of mutations of viral sequences from the cellular genome; Nu3 induced indels at the 3 SIV-specific sites, whereas for Ni6 indels were present at the LTR and TAR sites. Levels of off-target effects detected by two different algorithms were indistinguishable from background mutations. In summary, we demonstrate that Cas9 nickase in association with gRNA pairs can specifically eliminate parts of the integrated provirus DNA; also, we show that careful design of an all-in-one plasmid coding for 3 gRNAs and Cas9 nuclease inhibits SIV production with undetectable off-target mutations, making these tools a desirable prospect for moving into animal studies. IMPORTANCE Our approach to HIV cure, utilizing the translatable SIV/rhesus macaque model system, aims at provirus inactivation and its removal with the least possible off-target side effects. We developed single molecules that delivered either three truncated SIV-specific gRNAs along with Cas9 nuclease or three pairs of SIV-specific gRNAs (six individual gRNAs) along with Cas9 nickase to enhance efficacy of on-target mutagenesis. Whole-genome sequencing demonstrated effective SIV sequence mutation and inactivation and the absence of demonstrable off-target mutations. These results open the possibility to employ Cas9 variants that introduce single-strand DNA breaks to eliminate integrated proviral DNA.
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Affiliation(s)
- Lisa M. Smith
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UT Health San Antonio, San Antonio, Texas, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Vida L. Hodara
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura M. Parodi
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jessica E. Callery
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Zhao Lai
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, Texas, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas, USA
| | - Yi Zou
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas, USA
| | - Muthuswamy Raveedran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Luis D. Giavedoni
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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Smith LM, Hodara VL, Parodi LM, Callery JE, Giavedoni LD. Silencing integrated SIV proviral DNA with TAR-specific CRISPR tools. J Med Primatol 2020; 49:269-279. [PMID: 32905624 DOI: 10.1111/jmp.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND One approach for a functional HIV cure is to prevent transcription from integrated proviral DNA. A critical step in HIV transcription is the Tat protein interaction with the TAR element viral RNA. We tested the strategy of blocking this Tat-TAR interaction in the SIVmac model. METHODS We designed five CRISPR short guiding RNAs (sgRNAs) targeting the SIVmac TAR element, along with inactive versions of Cas9 (dCas9). These sgRNA constructs were delivered as ribonucleoproteins or plasmid DNA, along with SIV DNA. The constructs were also tested in integrated viral DNA in a cell line chronically infected by SIV. RESULTS The sgRNAs targeting the coding strand of the TAR element inhibited SIV RNA transcription in association with dCas9-KRAB, but not with dCas9. CONCLUSIONS Induction of epigenetic modifications may be more effective in inactivating provirus than transcriptional interference and thus may be a better strategy to achieve a functional cure in vivo.
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Affiliation(s)
- Lisa M Smith
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA.,Department of Microbiology, Immunology, and Molecular Genetics, UT Health San Antonio, San Antonio, Texas, USA
| | - Vida L Hodara
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura M Parodi
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Jessica E Callery
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Luis D Giavedoni
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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