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Roesmann F, Sertznig H, Klaassen K, Wilhelm A, Heininger D, Heß S, Elsner C, Marschalek R, Santiago ML, Esser S, Sutter K, Dittmer U, Widera M. The interferon-regulated host factor hnRNPA0 modulates HIV-1 production by interference with LTR activity, mRNA trafficking, and programmed ribosomal frameshifting. J Virol 2024:e0053424. [PMID: 38899932 DOI: 10.1128/jvi.00534-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The interplay between host factors and viral components impacts viral replication efficiency profoundly. Members of the cellular heterogeneous nuclear ribonucleoprotein family (hnRNPs) have been extensively studied as HIV-1 host dependency factors, but whether they play a role in innate immunity is currently unknown. This study aimed to identify hnRNPA0 as a type I interferon (IFN)-repressed host factor in HIV-1-infected cells. Knockdown of hnRNPA0, a situation that mirrors conditions under IFN stimulation, increased LTR activity, export of unspliced HIV-1 mRNA, viral particle production, and thus, increased infectivity. Conversely, hnRNPA0 overexpression primarily reduced plasmid-driven and integrated HIV-1 long terminal repeat (LTR) activity, significantly decreasing total viral mRNA and protein levels. In addition, high levels of hnRNPA0 significantly reduced the HIV-1 programmed ribosomal frameshifting efficiency, resulting in a shift in the HIV-1 p55/p15 ratio. The HIV-1 alternative splice site usage remained largely unaffected by altered hnRNPA0 levels suggesting that the synergistic inhibition of the LTR activity and viral mRNA transcription, as well as impaired ribosomal frameshifting efficiency, are critical factors for efficient HIV-1 replication regulated by hnRNPA0. The pleiotropic dose-dependent effects under high or low hnRNPA0 levels were further confirmed in HIV-1-infected Jurkat cells. Finally, our study revealed that hnRNPA0 levels in PBMCs were lower in therapy-naive HIV-1-infected individuals compared to healthy controls. Our findings highlight a significant role for hnRNPA0 in HIV-1 replication and suggest that its IFN-I-regulated expression levels are critical for viral fitness allowing replication in an antiviral environment.IMPORTANCERNA-binding proteins, in particular, heterogeneous nuclear ribonucleoproteins (hnRNPs), have been extensively studied. Some act as host dependency factors for HIV-1 since they are involved in multiple cellular gene expression processes. Our study revealed hnRNPA0 as an IFN-regulated host factor, that is differently expressed after IFN-I treatment in HIV-1 target cells and lower expressed in therapy-naïve HIV-1-infected individuals. Our findings demonstrate the significant pleiotropic role of hnRNPA0 in viral replication: In high concentrations, hnRNPA0 limits viral replication by negatively regulating Tat-LTR transcription, retaining unspliced mRNA in the nucleus, and significantly impairing programmed ribosomal frameshifting. Low hnRNPA0 levels as observed in IFN-treated THP-1 cells, particularly facilitate HIV LTR activity and unspliced mRNA export, suggesting a role in innate immunity in favor of HIV replication. Understanding the mode of action between hnRNPA0 and HIV-1 gene expression might help to identify novel therapeutically strategies against HIV-1 and other viruses.
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Affiliation(s)
- Fabian Roesmann
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Katleen Klaassen
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Delia Heininger
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Stefanie Heß
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Mario L Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Stefan Esser
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Dermatology, HPSTD Outpatient Clinic, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
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2
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Mier NC, Roper DK. Effects of an indole derivative on cell proliferation, transfection, and alternative splicing in production of lentiviral vectors by transient co-transfection. PLoS One 2024; 19:e0297817. [PMID: 38833479 PMCID: PMC11149887 DOI: 10.1371/journal.pone.0297817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/12/2024] [Indexed: 06/06/2024] Open
Abstract
Lentiviral vectors derived from human immunodeficiency virus type I are widely used to deliver functional gene copies to mammalian cells for research and gene therapies. Post-transcriptional splicing of lentiviral vector transgene in transduced host and transfected producer cells presents barriers to widespread application of lentiviral vector-based therapies. The present study examined effects of indole derivative compound IDC16 on splicing of lentiviral vector transcripts in producer cells and corresponding yield of infectious lentiviral vectors. Indole IDC16 was shown previously to modify alternative splicing in human immunodeficiency virus type I. Human embryonic kidney 293T cells were transiently transfected by 3rd generation backbone and packaging plasmids using polyethyleneimine. Reverse transcription-quantitative polymerase chain reaction of the fraction of unspliced genomes in human embryonic kidney 293T cells increased up to 31% upon the indole's treatment at 2.5 uM. Corresponding yield of infectious lentiviral vectors decreased up to 4.5-fold in a cell transduction assay. Adjusting timing and duration of IDC16 treatment indicated that the indole's disruption of early stages of transfection and cell cycle had a greater effect on exponential time course of lentiviral vector production than its reduction of post-transcriptional splicing. Decrease in transfected human embryonic kidney 293T proliferation by IDC16 became significant at 10 uM. These findings indicated contributions by early-stage transfection, cell proliferation, and post-transcriptional splicing in transient transfection of human embryonic kidney 293T cells for lentiviral vector production.
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Affiliation(s)
- Nataly Carolina Mier
- Department of Biological Engineering, Utah State University, Logan, Utah, United States of America
| | - Donald Keith Roper
- Department of Biological Engineering, Utah State University, Logan, Utah, United States of America
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Thanaskody K, Natashah FN, Nordin F, Kamarul Zaman WSW, Tye GJ. Designing molecules: directing stem cell differentiation. Front Bioeng Biotechnol 2024; 12:1396405. [PMID: 38803845 PMCID: PMC11129639 DOI: 10.3389/fbioe.2024.1396405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Stem cells have been widely applied in regenerative and therapeutic medicine for their unique regenerative properties. Although much research has shown their potential, it remains tricky in directing stem cell differentiation. The advancement of genetic and therapeutic technologies, however, has facilitated this issue through development of design molecules. These molecules are designed to overcome the drawbacks previously faced, such as unexpected differentiation outcomes and insufficient migration of endogenous or exogenous MSCs. Here, we introduced aptamer, bacteriophage, and biological vectors as design molecules and described their characteristics. The methods of designing/developing discussed include various Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedures, in silico approaches, and non-SELEX methods for aptamers, and genetic engineering methods such as homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), Bacteriophage Recombineering with Infectious Particles (BRIP), and genome rebooting for bacteriophage. For biological vectors, methods such as alternate splicing, multiple promoters, internal ribosomal entry site, CRISPR-Cas9 system and Cre recombinase mediated recombination were used to design viral vectors, while non-viral vectors like exosomes are generated through parental cell-based direct engineering. Besides that, we also discussed the pros and cons, and applications of each design molecule in directing stem cell differentiation to illustrate their great potential in stem cells research. Finally, we highlighted some safety and efficacy concerns to be considered for future studies.
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Affiliation(s)
- Kalaiselvaan Thanaskody
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Fajriyah Nur Natashah
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Fazlina Nordin
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Wan Safwani Wan Kamarul Zaman
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
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Fombellida-Lopez C, Berkhout B, Darcis G, Pasternak AO. Persistent HIV-1 transcription during ART: time to reassess its significance? Curr Opin HIV AIDS 2024; 19:124-132. [PMID: 38502547 PMCID: PMC10990031 DOI: 10.1097/coh.0000000000000849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), HIV-1 reservoirs persist and reignite viral replication if therapy is interrupted. Persistence of the viral reservoir in people with HIV-1 (PWH) is the main obstacle to an HIV-1 cure. The reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. Here, we review the recent progress in the characterization of persistent HIV-1 transcription during ART. RECENT FINDINGS Evidence from several studies indicates that, although cell-associated unspliced (US) HIV-1 RNA is abundantly expressed in ART-treated PWH, intact full-length US transcripts are rare and most US RNA is derived from defective proviruses. The transcription- and translation-competent defective proviruses, previously considered irrelevant, are increasingly being linked to residual HIV-1 pathogenesis under suppressive ART. Recent data suggest a continuous crosstalk between the residual HIV-1 activity under ART and the immune system. Persistent HIV-1 transcription on ART, despite being mostly derived from defective proviruses, predicts viral rebound upon therapy interruption, suggesting its role as an indicator of the strength of the host antiviral immune response that is shaping the viral rebound. SUMMARY In light of the recent findings, the significance of persistent HIV-1 transcription during ART for the long-term health of PWH and the cure research should be reassessed.
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Affiliation(s)
- Céline Fombellida-Lopez
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gilles Darcis
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
- Department of General Internal Medicine and Infectious Diseases, University Hospital of Liège, Liège, Belgium
| | - Alexander O. Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m 6As. Nat Microbiol 2024; 9:1340-1355. [PMID: 38605174 PMCID: PMC11087264 DOI: 10.1038/s41564-024-01638-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 02/15/2024] [Indexed: 04/13/2024]
Abstract
Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N6-methyladenosine (m6A) modifications near the 3' end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m6As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple of these m6As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Ga-Eun Lee
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Sarah Golconda
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Anastasios A Manganaris
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
- Department of Computer Science and Engineering, Ohio State University, Columbus, OH, USA
| | - Shuliang Chen
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Nagaraja Tirumuru
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Hannah Yu
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Christopher Kimmel
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sanggu Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA.
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA.
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA.
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, Ohio State University, Columbus, OH, USA.
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6
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Duchon A, Hu WS. HIV-1 RNA genome packaging: it's G-rated. mBio 2024; 15:e0086123. [PMID: 38411060 PMCID: PMC11005445 DOI: 10.1128/mbio.00861-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its progeny. The genome packaging step is a highly regulated and extremely efficient process as a vast majority of virus particles contain two copies of full-length unspliced HIV-1 RNA that form a dimer. Thus, during virus assembly HIV-1 can identify and selectively encapsidate HIV-1 unspliced RNA from an abundant pool of cellular RNAs and various spliced HIV-1 RNAs. Several "G" features facilitate the packaging of a dimeric RNA genome. The viral polyprotein Gag orchestrates virus assembly and mediates RNA genome packaging. During this process, Gag preferentially binds unpaired guanosines within the highly structured 5' untranslated region (UTR) of HIV-1 RNA. In addition, the HIV-1 unspliced RNA provides a scaffold that promotes Gag:Gag interactions and virus assembly, thereby ensuring its packaging. Intriguingly, recent studies have shown that the use of different guanosines at the junction of U3 and R as transcription start sites results in HIV-1 unspliced RNA species with 99.9% identical sequences but dramatically distinct 5' UTR conformations. Consequently, one species of unspliced RNA is preferentially packaged over other nearly identical RNAs. These studies reveal how conformations affect the functions of HIV-1 RNA elements and the complex regulation of HIV-1 replication. In this review, we summarize cis- and trans-acting elements critical for HIV-1 RNA packaging, locations of Gag:RNA interactions that mediate genome encapsidation, and the effects of transcription start sites on the structure and packaging of HIV-1 RNA.
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Affiliation(s)
- Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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Crespo R, Ne E, Reinders J, Meier JI, Li C, Jansen S, Górska A, Koçer S, Kan TW, Doff W, Dekkers D, Demmers J, Palstra RJ, Rao S, Mahmoudi T. PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency. iScience 2024; 27:109152. [PMID: 38384833 PMCID: PMC10879814 DOI: 10.1016/j.isci.2024.109152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/06/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
HIV-1 latency results from tightly regulated molecular processes that act at distinct steps of HIV-1 gene expression. Here, we characterize PCI domain-containing 2 (PCID2) protein, a subunit of the transcription and export complex 2 (TREX2) complex, to enforce transcriptional repression and post-transcriptional blocks to HIV-1 gene expression during latency. PCID2 bound the latent HIV-1 LTR (long terminal repeat) and repressed transcription initiation during latency. Depletion of PCID2 remodeled the chromatin landscape at the HIV-1 promoter and resulted in transcriptional activation and latency reversal. Immunoprecipitation coupled to mass spectrometry identified PCID2-interacting proteins to include negative viral RNA (vRNA) splicing regulators, and PCID2 depletion resulted in over-splicing of intron-containing vRNA in cell lines and primary cells obtained from PWH. MCM3AP and DSS1, two other RNA-binding TREX2 complex subunits, also inhibit transcription initiation and vRNA alternative splicing during latency. Thus, PCID2 is a novel HIV-1 latency-promoting factor, which in context of the TREX2 sub-complex PCID2-DSS1-MCM3AP blocks transcription and dysregulates vRNA processing.
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Affiliation(s)
- Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Enrico Ne
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Julian Reinders
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Jenny I.J. Meier
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Chengcheng Li
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Sanne Jansen
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Alicja Górska
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Selin Koçer
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wouter Doff
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Dick Dekkers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000 CA Rotterdam, the Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, the Netherlands
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Vanegas-Torres CA, Schindler M. HIV-1 Vpr Functions in Primary CD4 + T Cells. Viruses 2024; 16:420. [PMID: 38543785 PMCID: PMC10975730 DOI: 10.3390/v16030420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
HIV-1 encodes four accesory proteins in addition to its structural and regulatory genes. Uniquely amongst them, Vpr is abundantly present within virions, meaning it is poised to exert various biological effects on the host cell upon delivery. In this way, Vpr contributes towards the establishment of a successful infection, as evidenced by the extent to which HIV-1 depends on this factor to achieve full pathogenicity in vivo. Although HIV infects various cell types in the host organism, CD4+ T cells are preferentially targeted since they are highly permissive towards productive infection, concomitantly bringing about the hallmark immune dysfunction that accompanies HIV-1 spread. The last several decades have seen unprecedented progress in unraveling the activities Vpr possesses in the host cell at the molecular scale, increasingly underscoring the importance of this viral component. Nevertheless, it remains controversial whether some of these advances bear in vivo relevance, since commonly employed cellular models significantly differ from primary T lymphocytes. One prominent example is the "established" ability of Vpr to induce G2 cell cycle arrest, with enigmatic physiological relevance in infected primary T lymphocytes. The objective of this review is to present these discoveries in their biological context to illustrate the mechanisms whereby Vpr supports HIV-1 infection in CD4+ T cells, whilst identifying findings that require validation in physiologically relevant models.
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Affiliation(s)
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany;
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Dwivedi R, Prakash P, Kumbhar BV, Balasubramaniam M, Dash C. HIV-1 capsid and viral DNA integration. mBio 2024; 15:e0021222. [PMID: 38085100 PMCID: PMC10790781 DOI: 10.1128/mbio.00212-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE HIV-1 capsid protein (CA)-independently or by recruiting host factors-mediates several key steps of virus replication in the cytoplasm and nucleus of the target cell. Research in the recent years have established that CA is multifunctional and genetically fragile of all the HIV-1 proteins. Accordingly, CA has emerged as a validated and high priority therapeutic target, and the first CA-targeting antiviral drug was recently approved for treating multi-drug resistant HIV-1 infection. However, development of next generation CA inhibitors depends on a better understanding of CA's known roles, as well as probing of CA's novel roles, in HIV-1 replication. In this timely review, we present an updated overview of the current state of our understanding of CA's multifunctional role in HIV-1 replication-with a special emphasis on CA's newfound post-nuclear roles, highlight the pressing knowledge gaps, and discuss directions for future research.
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Affiliation(s)
- Richa Dwivedi
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Mumbai, Maharashtra, India
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
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10
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Barton K, Ferguson JM, Deveson IW, Falcinelli SD, James KS, Kirchherr J, Ramirez C, Gay CL, Hammond JM, Bevear B, Carswell SL, Margolis DM, Smith MA, Adimora AA, Archin NM. HIVepsilon-seq-scalable characterization of intact persistent proviral HIV reservoirs in women. J Virol 2023; 97:e0070523. [PMID: 37843370 PMCID: PMC10688329 DOI: 10.1128/jvi.00705-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The lack of a reliable method to accurately detect when replication-competent HIV has been cleared is a major challenge in developing a cure. This study introduces a new approach called the HIVepsilon-seq (HIVε-seq) assay, which uses long-read sequencing technology and bioinformatics to scrutinize the HIV genome at the nucleotide level, distinguishing between defective and intact HIV. This study included 30 participants on antiretroviral therapy, including 17 women, and was able to discriminate between defective and genetically intact viruses at the single DNA strand level. The HIVε-seq assay is an improvement over previous methods, as it requires minimal sample, less specialized lab equipment, and offers a shorter turnaround time. The HIVε-seq assay offers a promising new tool for researchers to measure the intact HIV reservoir, advancing efforts towards finding a cure for this devastating disease.
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Affiliation(s)
- Kirston Barton
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- The Kirby Institute, University of New South Wales, Randwick, New South Wales, Australia
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, New South Wales, Australia
| | - James M. Ferguson
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ira W. Deveson
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Shane D. Falcinelli
- Department of Microbiology, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katherine S. James
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Catalina Ramirez
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Cynthia L. Gay
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jillian M. Hammond
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Brent Bevear
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Shaun L. Carswell
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- National Institute of Water and Atmospheric Research, Auckland, New Zealand
| | - David M. Margolis
- Department of Microbiology, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Martin A. Smith
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
- CHU Sainte-Justine Research Centre, Montreal, Canada
| | - Adaora A. Adimora
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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11
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Behrens RT, Sherer NM. Retroviral hijacking of host transport pathways for genome nuclear export. mBio 2023; 14:e0007023. [PMID: 37909783 PMCID: PMC10746203 DOI: 10.1128/mbio.00070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways to export these genomes to the cytoplasm where they access virion egress pathways. These findings shed light on novel aspects of viral life cycles relevant to the development of new antiviral strategies and can yield new tractable, virus-based tools for exposing additional secrets of the cell. The goal of this review is to summarize defined and emerging modes of virus-host interactions that drive the transit of viral genomes out of the nucleus across the nuclear envelope barrier, with an emphasis on retroviruses that are most extensively studied. In this context, we prioritize discussion of recent progress in understanding the trafficking and function of the human immunodeficiency virus type 1 Rev protein, exemplifying a relatively refined example of stepwise, cooperativity-driven viral subversion of multi-subunit host transport receptor complexes.
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Affiliation(s)
- Ryan T. Behrens
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, USA
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12
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Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. J Gen Virol 2023; 104:001898. [PMID: 37801004 PMCID: PMC10721937 DOI: 10.1099/jgv.0.001898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5'-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5'-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher's exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.
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Affiliation(s)
- Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Philip Lei Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Miri Krupkin
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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13
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Horvath RM, Brumme ZL, Sadowski I. CDK8 inhibitors antagonize HIV-1 reactivation and promote provirus latency in T cells. J Virol 2023; 97:e0092323. [PMID: 37671866 PMCID: PMC10537590 DOI: 10.1128/jvi.00923-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/15/2023] [Indexed: 09/07/2023] Open
Abstract
Latent HIV-1 provirus represents the barrier toward a cure for infection and is dependent upon the host RNA Polymerase (Pol) II machinery for reemergence. Here, we find that inhibitors of the RNA Pol II mediator kinases CDK8/19, Senexin A and BRD6989, inhibit induction of HIV-1 expression in response to latency-reversing agents and T cell signaling agonists. These inhibitors were found to impair recruitment of RNA Pol II to the HIV-1 LTR. Furthermore, HIV-1 expression in response to several latency reversal agents was impaired upon disruption of CDK8 by shRNA or gene knockout. However, the effects of CDK8 depletion did not entirely mimic CDK8/19 kinase inhibition suggesting that the mediator kinases are not functionally redundant. Additionally, treatment of CD4+ peripheral blood mononuclear cells isolated from people living with HIV-1 and who are receiving antiretroviral therapy with Senexin A inhibited induction of viral replication in response to T cell stimulation by PMA and ionomycin. These observations indicate that the mediator kinases, CDK8 and CDK19, play a significant role for regulation of HIV-1 transcription and that small molecule inhibitors of these enzymes may contribute to therapies designed to promote deep latency involving the durable suppression of provirus expression. IMPORTANCE A cure for HIV-1 infection will require novel therapies that can force elimination of cells that contain copies of the virus genome inserted into the cell chromosome, but which is shut off, or silenced. These are known as latently-infected cells, which represent the main reason why current treatment for HIV/AIDS cannot cure the infection because the virus in these cells is unaffected by current drugs. Our results indicate that chemical inhibitors of Cdk8 also inhibit the expression of latent HIV provirus. Cdk8 is an important enzyme that regulates the expression of genes in response to signals to which cells need to respond and which is produced by a gene that is frequently mutated in cancers. Our observations indicate that Cdk8 inhibitors may be employed in novel therapies to prevent expression from latent provirus, which might eventually enable infected individuals to cease treatment with antiretroviral drugs.
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Affiliation(s)
- Riley M. Horvath
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Lo R, Gonçalves-Carneiro D. Sensing nucleotide composition in virus RNA. Biosci Rep 2023; 43:BSR20230372. [PMID: 37606964 PMCID: PMC10500230 DOI: 10.1042/bsr20230372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/23/2023] Open
Abstract
Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host-virus interactions and uncover potential targets for antiviral strategies.
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Affiliation(s)
- Raymon Lo
- Imperial College London, Department of Infectious Disease, Imperial College London, London, U.K
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15
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Nikolaitchik OA, Islam S, Kitzrow JP, Duchon A, Cheng Z, Liu Y, Rawson JMO, Shao W, Nikolaitchik M, Kearney MF, Maldarelli F, Musier-Forsyth K, Pathak VK, Hu WS. HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness. Proc Natl Acad Sci U S A 2023; 120:e2305103120. [PMID: 37252967 PMCID: PMC10266039 DOI: 10.1073/pnas.2305103120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
HIV-1 relies on host RNA polymeraseII (Pol II) to transcribe its genome and uses multiple transcription start sites (TSS), including three consecutive guanosines located near the U3-R junction, to generate transcripts containing three, two, and one guanosine at the 5' end, referred to as 3G, 2G, and 1G RNA, respectively. The 1G RNA is preferentially selected for packaging, indicating that these 99.9% identical RNAs exhibit functional differences and highlighting the importance of TSS selection. Here, we demonstrate that TSS selection is regulated by sequences between the CATA/TATA box and the beginning of R. Furthermore, we have generated two HIV-1 mutants with distinct 2-nucleotide modifications that predominantly express 3G RNA or 1G RNA. Both mutants can generate infectious viruses and undergo multiple rounds of replication in T cells. However, both mutants exhibit replication defects compared to the wild-type virus. The 3G-RNA-expressing mutant displays an RNA genome-packaging defect and delayed replication kinetics, whereas the 1G-RNA-expressing mutant exhibits reduced Gag expression and a replication fitness defect. Additionally, reversion of the latter mutant is frequently observed, consistent with sequence correction by plus-strand DNA transfer during reverse transcription. These findings demonstrate that HIV-1 maximizes its replication fitness by usurping the TSS heterogeneity of host RNA Pol II to generate unspliced RNAs with different specialized roles in viral replication. The three consecutive guanosines at the junction of U3 and R may also maintain HIV-1 genome integrity during reverse transcription. These studies reveal the intricate regulation of HIV-1 RNA and complex replication strategy.
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Affiliation(s)
- Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Saiful Islam
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Jonathan P. Kitzrow
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Zetao Cheng
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Yang Liu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Jonathan M. O. Rawson
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Maria Nikolaitchik
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Mary F. Kearney
- Translation Research Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Frank Maldarelli
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Ohio State University, Columbus, OH43210
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
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16
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Allan MF, Brivanlou A, Rouskin S. RNA levers and switches controlling viral gene expression. Trends Biochem Sci 2023; 48:391-406. [PMID: 36710231 DOI: 10.1016/j.tibs.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 01/29/2023]
Abstract
RNA viruses are diverse and abundant pathogens that are responsible for numerous human diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often by encoding overlapping reading frames. These reading frames are then decoded by mechanisms such as alternative splicing and ribosomal frameshifting to produce multiple distinct proteins. These solutions are enabled by the ability of the RNA genome to fold into 3D structures that can mimic cellular RNAs, hijack host proteins, and expose or occlude regulatory protein-binding motifs to ultimately control key process in the viral life cycle. We highlight recent findings focusing on less conventional mechanisms of gene expression and new discoveries on the role of RNA structures.
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Affiliation(s)
- Matthew F Allan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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17
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Marasco LE, Kornblihtt AR. The physiology of alternative splicing. Nat Rev Mol Cell Biol 2023; 24:242-254. [PMID: 36229538 DOI: 10.1038/s41580-022-00545-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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18
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White JA, Wu F, Yasin S, Moskovljevic M, Varriale J, Dragoni F, Camilo-Contreras A, Duan J, Zheng MY, Tadzong NF, Patel HB, Quiambao JMC, Rhodehouse K, Zhang H, Lai J, Beg SA, Delannoy M, Kilcrease C, Hoffmann CJ, Poulin S, Chano F, Tremblay C, Cherian J, Barditch-Crovo P, Chida N, Moore RD, Summers MF, Siliciano RF, Siliciano JD, Simonetti FR. Clonally expanded HIV-1 proviruses with 5'-leader defects can give rise to nonsuppressible residual viremia. J Clin Invest 2023; 133:165245. [PMID: 36602866 PMCID: PMC10014112 DOI: 10.1172/jci165245] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
BackgroundAntiretroviral therapy (ART) halts HIV-1 replication, decreasing viremia to below the detection limit of clinical assays. However, some individuals experience persistent nonsuppressible viremia (NSV) originating from CD4+ T cell clones carrying infectious proviruses. Defective proviruses represent over 90% of all proviruses persisting during ART and can express viral genes, but whether they can cause NSV and complicate ART management is unknown.MethodsWe undertook an in-depth characterization of proviruses causing NSV in 4 study participants with optimal adherence and no drug resistance. We investigated the impact of the observed defects on 5'-leader RNA properties, virus infectivity, and gene expression. Integration-site specific assays were used to track these proviruses over time and among cell subsets.ResultsClones carrying proviruses with 5'-leader defects can cause persistent NSV up to approximately 103 copies/mL. These proviruses had small, often identical deletions or point mutations involving the major splicing donor (MSD) site and showed partially reduced RNA dimerization and nucleocapsid binding. Nevertheless, they were inducible and produced noninfectious virions containing viral RNA, but lacking envelope.ConclusionThese findings show that proviruses with 5'-leader defects in CD4+ T cell clones can give rise to NSV, affecting clinical care. Sequencing of the 5'-leader can help in understanding failure to completely suppress viremia.FundingOffice of the NIH Director and National Institute of Dental and Craniofacial Research, NIH; Howard Hughes Medical Institute; Johns Hopkins University Center for AIDS Research; National Institute for Allergy and Infectious Diseases (NIAID), NIH, to the PAVE, BEAT-HIV, and DARE Martin Delaney collaboratories.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saif Yasin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Filippo Dragoni
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mei Y Zheng
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Ndeh F Tadzong
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Heer B Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeanelle Mae C Quiambao
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Delannoy
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christin Kilcrease
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher J Hoffmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Canada
| | - Jerald Cherian
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia Barditch-Crovo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natasha Chida
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Ode H, Saito A, Washizaki A, Seki Y, Yoshida T, Harada S, Ishii H, Shioda T, Yasutomi Y, Matano T, Miura T, Akari H, Iwatani Y. Development of a novel Macaque-Tropic HIV-1 adapted to cynomolgus macaques. J Gen Virol 2022; 103. [PMID: 36205476 DOI: 10.1099/jgv.0.001790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Macaque-tropic HIV-1 (HIV-1mt) variants have been developed to establish preferable primate models that are advantageous in understanding HIV-1 infection pathogenesis and in assessing the preclinical efficacy of novel prevention/treatment strategies. We previously reported that a CXCR4-tropic HIV-1mt, MN4Rh-3, efficiently replicates in peripheral blood mononuclear cells (PBMCs) of cynomolgus macaques homozygous for TRIMCyp (CMsTC). However, the CMsTC challenged with MN4Rh-3 displayed low viral loads during the acute infection phase and subsequently exhibited short-term viremia. These virological phenotypes in vivo differed from those observed in most HIV-1-infected people. Therefore, further development of the HIV-1mt variant was needed. In this study, we first reconstructed the MN4Rh-3 clone to produce a CCR5-tropic HIV-1mt, AS38. In addition, serial in vivo passages allowed us to produce a highly adapted AS38-derived virus that exhibits high viral loads (up to approximately 106 copies ml-1) during the acute infection phase and prolonged periods of persistent viremia (lasting approximately 16 weeks postinfection) upon infection of CMsTC. Whole-genome sequencing of the viral genomes demonstrated that the emergence of a unique 15-nt deletion within the vif gene was associated with in vivo adaptation. The deletion resulted in a significant increase in Vpr protein expression but did not affect Vif-mediated antagonism of antiretroviral APOBEC3s, suggesting that Vpr is important for HIV-1mt adaptation to CMsTC. In summary, we developed a novel CCR5-tropic HIV-1mt that can induce high peak viral loads and long-term viremia and exhibits increased Vpr expression in CMsTC.
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Affiliation(s)
- Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Akatsuki Saito
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Ayaka Washizaki
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Yohei Seki
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Takeshi Yoshida
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Shigeyoshi Harada
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Ishii
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuhiro Yasutomi
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tomoyuki Miura
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hirofumi Akari
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki, Japan
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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20
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Chiu LY, Emery A, Jain N, Sugarman A, Kendrick N, Luo L, Ford W, Swanstrom R, Tolbert BS. Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors. J Mol Biol 2022; 434:167728. [PMID: 35870649 PMCID: PMC9945881 DOI: 10.1016/j.jmb.2022.167728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/19/2023]
Abstract
Alternative splicing of the HIV transcriptome is controlled through cis regulatory elements functioning as enhancers or silencers depending on their context and the type of host RNA binding proteins they recruit. Splice site acceptor A3 (ssA3) is one of the least used acceptor sites in the HIV transcriptome and its activity determines the levels of tat mRNA. Splice acceptor 3 is regulated by a combination of cis regulatory sequences, auxiliary splicing factors, and presumably RNA structure. The mechanisms by which these multiple regulatory components coordinate to determine the frequency in which ssA3 is utilized is poorly understood. By NMR spectroscopy and phylogenetic analysis, we show that the ssA3 regulatory locus is conformationally heterogeneous and that the sequences that encompass the locus are conserved across most HIV isolates. Despite the conformational heterogeneity, the major stem loop (A3SL1) observed in vitro folds to base pair the Polypyrimdine Tract (PPyT) to the Exon Splicing Silencer 2p (ESS2p) element and to a conserved downstream linker. The 3D structure as determined by NMR spectroscopy further reveals that the A3 consensus cleavage site is embedded within a unique stereochemical environment within the apical loop, where it is surrounded by alternating base-base interactions. Despite being described as a receptor for hnRNP H, the ESS2p element is sequestered by base pairing to the 3' end of the PPyT and within this context it cannot form a stable complex with hnRNP H. By comparison, hnRNP A1 directly binds to the A3 consensus cleavage site located within the apical loop, suggesting that it can directly modulate U2AF assembly. Sequence mutations designed to destabilize the PPyT:ESS2p helix results in an increase usage of ssA3 within HIV-infected cells, consistent with the PPyT becoming more accessible for U2AF recognition. Additional mutations introduced into the downstream ESS2 element synergize with ESS2p to cause further increases in ssA3 usage. When taken together, our work provides a unifying picture by which cis regulatory sequences, splicing auxiliary factors and RNA structure cooperate to provide stringent control over ssA3. We describe this as the pair-and-lock mechanism to restrict access of the PPyT, and posit that it operates to regulate a subset of the heterogenous structures encompassing the ssA3 regulatory locus.
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Affiliation(s)
- Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Ann Emery
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Niyati Jain
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Nashea Kendrick
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Le Luo
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - William Ford
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Ronald Swanstrom
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599,Center for AIDS Research, University of North Carolina, Chapel Hill, NC 27599
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
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21
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Linden N, Jones RB. Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses. Trends Immunol 2022; 43:617-629. [PMID: 35817699 PMCID: PMC9429957 DOI: 10.1016/j.it.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
Despite antiretroviral therapy (ART), HIV-1 persists as proviruses integrated into the genomic DNA of CD4+ T cells. The mechanisms underlying the persistence and clonal expansion of these cells remain incompletely understood. Cases have been described in which proviral integration can alter host gene expression to drive cellular proliferation. Here, we review observations from other genome-integrating human viruses to propose additional putative modalities by which HIV-1 integration may alter cellular function to favor persistence, such as by altering susceptibility to cytotoxicity in virus-expressing cells. We propose that signals implicating such mechanisms may have been masked thus far by the preponderance of defective and/or nonreactivatable HIV-1 proviruses, but could be revealed by focusing on the integration sites of intact proviruses with expression potential.
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Affiliation(s)
- Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA.
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22
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Beemon KL. Retroviral RNA Processing. Viruses 2022; 14:v14051113. [PMID: 35632854 PMCID: PMC9143442 DOI: 10.3390/v14051113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
This review is an accompaniment to a Special Issue on “Retroviral RNA Processing”. It discusses post-transcriptional regulation of retroviruses, ranging from the ancient foamy viruses to more modern viruses, such as HIV-1, HTLV-1, Rous sarcoma virus, murine leukemia virus, mouse mammary tumor virus, and Mason-Pfizer monkey virus. This review is not comprehensive. However, it tries to address some of the major questions in the field with examples of how different retroviruses express their genes. It is amazing that a single primary RNA transcript can have so many possible fates: genomic RNA, unspliced mRNA, and up to 50 different alternatively spliced mRNAs. This review will discuss the sorting of RNAs for packaging or translation, RNA nuclear export mechanisms, splicing, translation, RNA modifications, and avoidance of nonsense-mediated RNA decay.
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Affiliation(s)
- Karen L Beemon
- Biology Department, Johns Hopkins University, Baltimore, MD 21218, USA
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23
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Boris-Lawrie K, Singh G, Osmer PS, Zucko D, Staller S, Heng X. Anomalous HIV-1 RNA, How Cap-Methylation Segregates Viral Transcripts by Form and Function. Viruses 2022; 14:935. [PMID: 35632676 PMCID: PMC9145092 DOI: 10.3390/v14050935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022] Open
Abstract
The acquisition of m7G-cap-binding proteins is now recognized as a major variable driving the form and function of host RNAs. This manuscript compares the 5'-cap-RNA binding proteins that engage HIV-1 precursor RNAs, host mRNAs, small nuclear (sn)- and small nucleolar (sno) RNAs and sort into disparate RNA-fate pathways. Before completion of the transcription cycle, the transcription start site of nascent class II RNAs is appended to a non-templated guanosine that is methylated (m7G-cap) and bound by hetero-dimeric CBP80-CBP20 cap binding complex (CBC). The CBC is a nexus for the co-transcriptional processing of precursor RNAs to mRNAs and the snRNA and snoRNA of spliceosomal and ribosomal ribonucleoproteins (RNPs). Just as sn/sno-RNAs experience hyper-methylation of m7G-cap to trimethylguanosine (TMG)-cap, so do select HIV RNAs and an emerging cohort of mRNAs. TMG-cap is blocked from Watson:Crick base pairing and disqualified from participating in secondary structure. The HIV TMG-cap has been shown to license select viral transcripts for specialized cap-dependent translation initiation without eIF4E that is dependent upon CBP80/NCBP3. The exceptional activity of HIV precursor RNAs secures their access to maturation pathways of sn/snoRNAs, canonical and non-canonical host mRNAs in proper stoichiometry to execute the retroviral replication cycle.
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Affiliation(s)
- Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Seth Staller
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
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24
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Falcinelli SD, Peterson JJ, Turner AMW, Irlbeck D, Read J, Raines SL, James KS, Sutton C, Sanchez A, Emery A, Sampey G, Ferris R, Allard B, Ghofrani S, Kirchherr JL, Baker C, Kuruc JD, Gay CL, James LI, Wu G, Zuck P, Rioja I, Furze RC, Prinjha RK, Howell BJ, Swanstrom R, Browne EP, Strahl BD, Dunham RM, Archin NM, Margolis DM. Combined noncanonical NF-κB agonism and targeted BET bromodomain inhibition reverse HIV latency ex vivo. J Clin Invest 2022; 132:e157281. [PMID: 35426377 PMCID: PMC9012286 DOI: 10.1172/jci157281] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022] Open
Abstract
Latency reversal strategies for HIV cure using inhibitor of apoptosis protein (IAP) antagonists (IAPi) induce unprecedented levels of latent reservoir expression without immunotoxicity during suppressive antiretroviral therapy (ART). However, full targeting of the reservoir may require combinatorial approaches. A Jurkat latency model screen for IAPi combination partners demonstrated synergistic latency reversal with bromodomain (BD) and extraterminal domain protein inhibitors (BETi). Mechanistic investigations using CRISPR-CAS9 and single-cell RNA-Seq informed comprehensive ex vivo evaluations of IAPi plus pan-BET, bD-selective BET, or selective BET isoform targeting in CD4+ T cells from ART-suppressed donors. IAPi+BETi treatment resulted in striking induction of cell-associated HIV gag RNA, but lesser induction of fully elongated and tat-rev RNA compared with T cell activation-positive controls. IAPi+BETi resulted in HIV protein induction in bulk cultures of CD4+ T cells using an ultrasensitive p24 assay, but did not result in enhanced viral outgrowth frequency using a standard quantitative viral outgrowth assay. This study defines HIV transcriptional elongation and splicing as important barriers to latent HIV protein expression following latency reversal, delineates the roles of BET proteins and their BDs in HIV latency, and provides a rationale for exploration of IAPi+BETi in animal models of HIV latency.
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Affiliation(s)
- Shane D. Falcinelli
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Jackson J. Peterson
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Anne-Marie W. Turner
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - David Irlbeck
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, North Carolina, USA
| | - Jenna Read
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Samuel L.M. Raines
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Katherine S. James
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Cameron Sutton
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Anthony Sanchez
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Ann Emery
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Gavin Sampey
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Robert Ferris
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, North Carolina, USA
| | - Brigitte Allard
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Simon Ghofrani
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Jennifer L. Kirchherr
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Caroline Baker
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - JoAnn D. Kuruc
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - Cynthia L. Gay
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - Lindsey I. James
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Paul Zuck
- Department of Infectious Disease, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Inmaculada Rioja
- Immuno-Epigenetics, Immunology Research Unit, GSK Medicines Research Centre, Stevenage, United Kingdom
| | - Rebecca C. Furze
- Immuno-Epigenetics, Immunology Research Unit, GSK Medicines Research Centre, Stevenage, United Kingdom
| | - Rab K. Prinjha
- Immuno-Epigenetics, Immunology Research Unit, GSK Medicines Research Centre, Stevenage, United Kingdom
| | - Bonnie J. Howell
- Department of Infectious Disease, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Ronald Swanstrom
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Edward P. Browne
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - Brian D. Strahl
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Richard M. Dunham
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, North Carolina, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
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25
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Abstract
Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact genomes and for comparing these RNA genomes to proviral DNA. We have developed a method for sequencing plasma-derived RNA using long-range sequencing (PRLS assay; ∼8.3 kb from gag to the 3′ end or ∼5 kb from integrase to the 3′ end). We employed the gag-3′ PRLS assay to sequence HIV-1 RNA genomes from ART-naive participants during acute/early infection (n = 6) or chronic infection (n = 2). On average, only 65% of plasma-derived genomes were genetically-intact. Defects were found in all genomic regions but were concentrated in env and pol. We compared these genomes to near-full-length proviral sequences from paired peripheral blood mononuclear cell (PBMC) samples for the acute/early group and found that near-identical (>99.98% identical) sequences were identified only during acute infection. For three participants who initiated therapy during acute infection, we used the int-3′ PRLS assay to sequence plasma-derived genomes from an analytical treatment interruption and identified 100% identical genomes between pretherapy and rebound time points. The PRLS assay provides a new level of sensitivity for understanding the genetic composition of plasma-derived HIV-1 RNA from viremic individuals either pretherapy or after treatment interruption, which will be invaluable in assessing possible HIV-1 curative strategies. IMPORTANCE We developed novel plasma-derived RNA using long-range sequencing assays (PRLS assay; 8.3 kb, gag-3′, and 5.0 kb, int-3′). Employing the gag-3′ PRLS assay, we found that 26% to 51% of plasma-derived genomes are genetically-defective, largely as a result of frameshift mutations and deletions. These genetic defects were concentrated in the env region compared to gag and pol, likely a reflection of viral immune escape in env during untreated HIV-1 infection. Employing the int-3′ PRLS assay, we found that analytical treatment interruption (ATI) plasma-derived sequences were identical and genetically-intact. Several sequences from the ATI plasma samples were identical to viral sequences from pretherapy plasma and PBMC samples, indicating that HIV-1 reservoirs established prior to therapy contribute to viral rebound during an ATI. Therefore, near-full-length sequencing of HIV-1 particles is required to gain an accurate picture of the genetic landscape of plasma HIV-1 virions in studies of HIV-1 replication and persistence.
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26
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van Heuvel Y, Schatz S, Rosengarten JF, Stitz J. Infectious RNA: Human Immunodeficiency Virus (HIV) Biology, Therapeutic Intervention, and the Quest for a Vaccine. Toxins (Basel) 2022; 14:toxins14020138. [PMID: 35202165 PMCID: PMC8876946 DOI: 10.3390/toxins14020138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Different mechanisms mediate the toxicity of RNA. Genomic retroviral mRNA hijacks infected host cell factors to enable virus replication. The viral genomic RNA of the human immunodeficiency virus (HIV) encompasses nine genes encoding in less than 10 kb all proteins needed for replication in susceptible host cells. To do so, the genomic RNA undergoes complex alternative splicing to facilitate the synthesis of the structural, accessory, and regulatory proteins. However, HIV strongly relies on the host cell machinery recruiting cellular factors to complete its replication cycle. Antiretroviral therapy (ART) targets different steps in the cycle, preventing disease progression to the acquired immunodeficiency syndrome (AIDS). The comprehension of the host immune system interaction with the virus has fostered the development of a variety of vaccine platforms. Despite encouraging provisional results in vaccine trials, no effective vaccine has been developed, yet. However, novel promising vaccine platforms are currently under investigation.
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Affiliation(s)
- Yasemin van Heuvel
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Stefanie Schatz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jamila Franca Rosengarten
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jörn Stitz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Correspondence:
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27
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Koma T, Doi N, Takemoto M, Watanabe K, Yamamoto H, Nakashima S, Adachi A, Nomaguchi M. The Expression Level of HIV-1 Vif Is Optimized by Nucleotide Changes in the Genomic SA1D2prox Region during the Viral Adaptation Process. Viruses 2021; 13:2079. [PMID: 34696508 PMCID: PMC8537775 DOI: 10.3390/v13102079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
HIV-1 Vif plays an essential role in viral replication by antagonizing anti-viral cellular restriction factors, a family of APOBEC3 proteins. We have previously shown that naturally-occurring single-nucleotide mutations in the SA1D2prox region, which surrounds the splicing acceptor 1 and splicing donor 2 sites of the HIV-1 genome, dramatically alter the Vif expression level, resulting in variants with low or excessive Vif expression. In this study, we investigated how these HIV-1 variants with poor replication ability adapt and evolve under the pressure of APOBEC3 proteins. Adapted clones obtained through adaptation experiments exhibited an altered replication ability and Vif expression level compared to each parental clone. While various mutations were present throughout the viral genome, all replication-competent adapted clones with altered Vif expression levels were found to bear them within SA1D2prox, without exception. Indeed, the mutations identified within SA1D2prox were responsible for changes in the Vif expression levels and altered the splicing pattern. Moreover, for samples collected from HIV-1-infected patients, we showed that the nucleotide sequences of SA1D2prox can be chronologically changed and concomitantly affect the Vif expression levels. Taken together, these results demonstrated the importance of the SA1D2prox nucleotide sequence for modulating the Vif expression level during HIV-1 replication and adaptation.
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Affiliation(s)
- Takaaki Koma
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
| | - Naoya Doi
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
| | - Mai Takemoto
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Kyosuke Watanabe
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Hideki Yamamoto
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Satoshi Nakashima
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Akio Adachi
- Department of Microbiology, Kansai Medical University, Osaka 573-1010, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
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28
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Interplay between Host tRNAs and HIV-1: A Structural Perspective. Viruses 2021; 13:v13091819. [PMID: 34578400 PMCID: PMC8473020 DOI: 10.3390/v13091819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
The cellular metabolism of host tRNAs and life cycle of HIV-1 cross paths at several key virus-host interfaces. Emerging data suggest a multi-faceted interplay between host tRNAs and HIV-1 that plays essential roles, both structural and regulatory, in viral genome replication, genome packaging, and virion biogenesis. HIV-1 not only hijacks host tRNAs and transforms them into obligatory reverse transcription primers but further commandeers tRNAs to regulate the localization of its major structural protein, Gag, via a specific interface. This review highlights recent advances in understanding tRNA-HIV-1 interactions, primarily from a structural perspective, which start to elucidate their underlying molecular mechanisms, intrinsic specificities, and biological significances. Such understanding may provide new avenues toward developing HIV/AIDS treatments and therapeutics including small molecules and RNA biologics that target these host-virus interfaces.
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29
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Pasternak AO, Berkhout B. The Splice of Life: Does RNA Processing Have a Role in HIV-1 Persistence? Viruses 2021; 13:v13091751. [PMID: 34578332 PMCID: PMC8471011 DOI: 10.3390/v13091751] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/28/2022] Open
Abstract
Antiretroviral therapy (ART) suppresses HIV-1 replication but does not eradicate the virus. Persistence of HIV-1 latent reservoirs in ART-treated individuals is considered the main obstacle to achieving an HIV-1 cure. However, these HIV-1 reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. HIV-1 latency is regulated at the transcriptional and at multiple post-transcriptional levels. Here, we review recent insights into the possible contribution of viral RNA processing to the persistence of HIV-1 reservoirs, and discuss the clinical implications of persistence of viral RNA species in ART-treated individuals.
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Abstract
After human immunodeficiency virus type 1 (HIV-1) was identified in the early 1980s, intensive work began to understand the molecular basis of HIV-1 gene expression. Subgenomic HIV-1 RNA regions, spread throughout the viral genome, were described to have a negative impact on the nuclear export of some viral transcripts. Those studies revealed an intrinsic RNA code as a new form of nuclear export regulation. Since such regulatory regions were later also identified in other viruses, as well as in cellular genes, it can be assumed that, during evolution, viruses took advantage of them to achieve more sophisticated replication mechanisms. Here, we review HIV-1 cis-acting repressive sequences that have been identified, and we discuss their possible underlying mechanisms and importance. Additionally, we show how current bioinformatic tools might allow more predictive approaches to identify and investigate them.
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Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
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