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Prelli Bozzo C, Laliberté A, De Luna A, Pastorio C, Regensburger K, Krebs S, Graf A, Blum H, Volcic M, Sparrer KMJ, Kirchhoff F. Replication competent HIV-guided CRISPR screen identifies antiviral factors including targets of the accessory protein Nef. Nat Commun 2024; 15:3813. [PMID: 38714682 PMCID: PMC11076291 DOI: 10.1038/s41467-024-48228-x] [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: 12/06/2023] [Accepted: 04/24/2024] [Indexed: 05/10/2024] Open
Abstract
Innate antiviral factors are essential for effective defense against viral pathogens. However, the identity of major restriction mechanisms remains elusive. Current approaches to discover antiviral factors usually focus on the initial steps of viral replication and are limited to a single round of infection. Here, we engineered libraries of >1500 replication-competent HIV-1 constructs each expressing a single gRNAs to target >500 cellular genes for virus-driven discovery of antiviral factors. Passaging in CD4+ T cells robustly enriched HIV-1 encoding sgRNAs against GRN, CIITA, EHMT2, CEACAM3, CC2D1B and RHOA by >50-fold. Using an HIV-1 library lacking the accessory nef gene, we identified IFI16 as a Nef target. Functional analyses in cell lines and primary CD4+ T cells support that the HIV-driven CRISPR screen identified restriction factors targeting virus entry, transcription, release and infectivity. Our HIV-guided CRISPR technique enables sensitive discovery of physiologically relevant cellular defense factors throughout the entire viral replication cycle.
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Affiliation(s)
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Aurora De Luna
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Kerstin Regensburger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center, LMU Munich, 81377, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis Gene Center, LMU Munich, 81377, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis Gene Center, LMU Munich, 81377, Munich, Germany
| | - Meta Volcic
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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2
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Faivre N, Verollet C, Dumas F. The chemokine receptor CCR5: multi-faceted hook for HIV-1. Retrovirology 2024; 21:2. [PMID: 38263120 PMCID: PMC10807162 DOI: 10.1186/s12977-024-00634-1] [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: 09/27/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
Chemokines are cytokines whose primary role is cellular activation and stimulation of leukocyte migration. They perform their various functions by interacting with G protein-coupled cell surface receptors (GPCRs) and are involved in the regulation of many biological processes such as apoptosis, proliferation, angiogenesis, hematopoiesis or organogenesis. They contribute to the maintenance of the homeostasis of lymphocytes and coordinate the function of the immune system. However, chemokines and their receptors are sometimes hijacked by some pathogens to infect the host organism. For a given chemokine receptor, there is a wide structural, organizational and conformational diversity. In this review, we describe the evidence for structural variety reported for the chemokine receptor CCR5, how this variability can be exploited by HIV-1 to infect its target cells and what therapeutic solutions are currently being developed to overcome this problem.
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Affiliation(s)
- Natacha Faivre
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Christel Verollet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Fabrice Dumas
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France.
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3
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Innocenti M. Investigating Mammalian Formins with SMIFH2 Fifteen Years in: Novel Targets and Unexpected Biology. Int J Mol Sci 2023; 24:ijms24109058. [PMID: 37240404 DOI: 10.3390/ijms24109058] [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: 04/06/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The mammalian formin family comprises fifteen multi-domain proteins that regulate actin dynamics and microtubules in vitro and in cells. Evolutionarily conserved formin homology (FH) 1 and 2 domains allow formins to locally modulate the cell cytoskeleton. Formins are involved in several developmental and homeostatic processes, as well as human diseases. However, functional redundancy has long hampered studies of individual formins with genetic loss-of-function approaches and prevents the rapid inhibition of formin activities in cells. The discovery of small molecule inhibitor of formin homology 2 domains (SMIFH2) in 2009 was a disruptive change that provided a powerful chemical tool to explore formins' functions across biological scales. Here, I critically discuss the characterization of SMIFH2 as a pan-formin inhibitor, as well as growing evidence of unexpected off-target effects. By collating the literature and information hidden in public repositories, outstanding controversies and fundamental open questions about the substrates and mechanism of action of SMIFH2 emerge. Whenever possible, I propose explanations for these discrepancies and roadmaps to address the paramount open questions. Furthermore, I suggest that SMIFH2 be reclassified as a multi-target inhibitor for its appealing activities on proteins involved in pathological formin-dependent processes. Notwithstanding all drawbacks and limitations, SMIFH2 will continue to prove useful in studying formins in health and disease in the years to come.
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Affiliation(s)
- Metello Innocenti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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4
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Alvarez-Rivera E, Rodríguez-Valentín M, Boukli NM. The Antiviral Compound PSP Inhibits HIV-1 Entry via PKR-Dependent Activation in Monocytic Cells. Viruses 2023; 15:804. [PMID: 36992512 PMCID: PMC10051440 DOI: 10.3390/v15030804] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Actin depolymerization factor (ADF) cofilin-1 is a key cytoskeleton component that serves to lessen cortical actin. HIV-1 manipulates cofilin-1 regulation as a pre- and post-entry requisite. Disruption of ADF signaling is associated with denial of entry. The unfolded protein response (UPR) marker Inositol-Requiring Enzyme-1α (IRE1α) and interferon-induced protein (IFN-IP) double-stranded RNA- activated protein kinase (PKR) are reported to overlap with actin components. In our published findings, Coriolus versicolor bioactive extract polysaccharide peptide (PSP) has demonstrated anti-HIV replicative properties in THP1 monocytic cells. However, its involvement towards viral infectivity has not been elucidated before. In the present study, we examined the roles of PKR and IRE1α in cofilin-1 phosphorylation and its HIV-1 restrictive roles in THP1. HIV-1 p24 antigen was measured through infected supernatant to determine PSP's restrictive potential. Quantitative proteomics was performed to analyze cytoskeletal and UPR regulators. PKR, IRE1α, and cofilin-1 biomarkers were measured through immunoblots. Validation of key proteome markers was done through RT-qPCR. PKR/IRE1α inhibitors were used to validate viral entry and cofilin-1 phosphorylation through Western blots. Our findings show that PSP treatment before infection leads to an overall lower infectivity. Additionally, PKR and IRE1α show to be key regulators in cofilin-1 phosphorylation and viral restriction.
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Affiliation(s)
- Eduardo Alvarez-Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe School of Medicine, Bayamόn, PR 00960, USA
| | | | - Nawal M. Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe School of Medicine, Bayamόn, PR 00960, USA
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5
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Mukim A, Smith DM, Deshmukh S, Qazi AA, Beliakova-Bethell N. A Camptothetin Analog, Topotecan, Promotes HIV Latency via Interference with HIV Transcription and RNA Splicing. J Virol 2023; 97:e0163022. [PMID: 36719238 PMCID: PMC9973035 DOI: 10.1128/jvi.01630-22] [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] [Received: 10/18/2022] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
Low level HIV transcription during modern antiretroviral therapy (ART) in persons with HIV is linked to residual inflammation and associated diseases, like cardiovascular disease and cancer. The "block and lock" approach to hold HIV in a state of deep latency may help decrease residual inflammation in a person with HIV on ART and thus improve health. A camptothecin analog topotecan (TPT) was previously implicated as an inhibitor of active HIV replication. Using an in vitro primary T cell model of HIV latency, we demonstrated that (i) TPT reduces HIV transcriptional activity in latently infected cells; (ii) downregulation of HIV RNA by TPT cannot be reversed by latency reversing agents; (iii) several primary and secondary mechanism of action of TPT may be involved in control of HIV replication; (iv) regulation of HIV RNA by TPT is dependent on splicing complexity; (v) increase in proportion of unspliced HIV transcripts was facilitated by intron retention and upregulation of splicing factors, specifically SRSF6, by TPT. Although high TPT dosing (10 μM) was needed to achieve the observed effects, viability of primary CD4+ T cells was not greatly affected. Because toxicity can be observed with TPT in persons with cancer, TPT is unlikely to be used as an anti-HIV agent in clinic, but our study provides proof that camptothetin has "block and lock" activity. Other camptothetin analogs, which are less toxic than TPT, should be designed and tested as HIV "block and lock" agents. IMPORTANCE HIV survives in a state of very low activity, called latency, for long periods in persons with HIV on antiretroviral therapy. This low activity of HIV is linked to residual inflammation and associated diseases, such as heart disease and cancer. New strategies are being explored to further silence the HIV provirus and suppress residual inflammation. This study provides strong evidence that the camptothetin analog, Topotecan, can reduce residual activity of HIV in an experimental model of HIV latency. While Topotecan itself is likely not suitable for use in the clinic due to its toxicity, other camptothetin analogs should be designed and investigated as "block and lock" agents.
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Affiliation(s)
- Amey Mukim
- Veterans Medical Research Foundation, San Diego, California, USA
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, California, USA
| | - Savitha Deshmukh
- Veterans Medical Research Foundation, San Diego, California, USA
| | - Andrew A. Qazi
- Veterans Medical Research Foundation, San Diego, California, USA
| | - Nadejda Beliakova-Bethell
- Veterans Medical Research Foundation, San Diego, California, USA
- Department of Medicine, University of California, San Diego, California, USA
- VA San Diego Healthcare System, San Diego, California, USA
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6
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Kumar R, Chander Y, Khandelwal N, Verma A, Rawat KD, Shringi BN, Pal Y, Tripathi BN, Barua S, Kumar N. ROCK1/MLC2 inhibition induces decay of viral mRNA in BPXV infected cells. Sci Rep 2022; 12:17811. [PMID: 36280692 PMCID: PMC9592580 DOI: 10.1038/s41598-022-21610-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/29/2022] [Indexed: 01/19/2023] Open
Abstract
Rho-associated coiled-coil containing protein kinase 1 (ROCK1) intracellular cell signaling pathway regulates cell morphology, polarity, and cytoskeletal remodeling. We observed the activation of ROCK1/myosin light chain (MLC2) signaling pathway in buffalopox virus (BPXV) infected Vero cells. ROCK1 depletion by siRNA and specific small molecule chemical inhibitors (Thiazovivin and Y27632) resulted in a reduced BPXV replication, as evidenced by reductions in viral mRNA/protein synthesis, genome copy numbers and progeny virus particles. Further, we demonstrated that ROCK1 inhibition promotes deadenylation of viral mRNA (mRNA decay), mediated via inhibiting interaction with PABP [(poly(A)-binding protein] and enhancing the expression of CCR4-NOT (a multi-protein complex that plays an important role in deadenylation of mRNA). In addition, ROCK1/MLC2 mediated cell contraction, and perinuclear accumulation of p-MLC2 was shown to positively correlate with viral mRNA/protein synthesis. Finally, it was demonstrated that the long-term sequential passage (P = 50) of BPXV in the presence of Thiazovivin does not select for any drug-resistant virus variants. In conclusion, ROCK1/MLC2 cell signaling pathway facilitates BPXV replication by preventing viral mRNA decay and that the inhibitors targeting this pathway may have novel therapeutic effects against buffalopox.
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Affiliation(s)
- Ram Kumar
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India ,grid.464655.00000 0004 1768 5915Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India ,grid.418105.90000 0001 0643 7375Present Address: Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India
| | - Yogesh Chander
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India ,grid.418105.90000 0001 0643 7375Present Address: Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India ,grid.411892.70000 0004 0500 4297Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana India
| | - Nitin Khandelwal
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Assim Verma
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Krishan Dutt Rawat
- grid.411892.70000 0004 0500 4297Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana India
| | - Brij N. Shringi
- grid.464655.00000 0004 1768 5915Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
| | - Yash Pal
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Bhupendra N. Tripathi
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India ,grid.418105.90000 0001 0643 7375Present Address: Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India
| | - Sanjay Barua
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Naveen Kumar
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
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7
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Nickoloff-Bybel EA, Festa L, Meucci O, Gaskill PJ. Co-receptor signaling in the pathogenesis of neuroHIV. Retrovirology 2021; 18:24. [PMID: 34429135 PMCID: PMC8385912 DOI: 10.1186/s12977-021-00569-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
The HIV co-receptors, CCR5 and CXCR4, are necessary for HIV entry into target cells, interacting with the HIV envelope protein, gp120, to initiate several signaling cascades thought to be important to the entry process. Co-receptor signaling may also promote the development of neuroHIV by contributing to both persistent neuroinflammation and indirect neurotoxicity. But despite the critical importance of CXCR4 and CCR5 signaling to HIV pathogenesis, there is only one therapeutic (the CCR5 inhibitor Maraviroc) that targets these receptors. Moreover, our understanding of co-receptor signaling in the specific context of neuroHIV is relatively poor. Research into co-receptor signaling has largely stalled in the past decade, possibly owing to the complexity of the signaling cascades and functions mediated by these receptors. Examining the many signaling pathways triggered by co-receptor activation has been challenging due to the lack of specific molecular tools targeting many of the proteins involved in these pathways and the wide array of model systems used across these experiments. Studies examining the impact of co-receptor signaling on HIV neuropathogenesis often show activation of multiple overlapping pathways by similar stimuli, leading to contradictory data on the effects of co-receptor activation. To address this, we will broadly review HIV infection and neuropathogenesis, examine different co-receptor mediated signaling pathways and functions, then discuss the HIV mediated signaling and the differences between activation induced by HIV and cognate ligands. We will assess the specific effects of co-receptor activation on neuropathogenesis, focusing on neuroinflammation. We will also explore how the use of substances of abuse, which are highly prevalent in people living with HIV, can exacerbate the neuropathogenic effects of co-receptor signaling. Finally, we will discuss the current state of therapeutics targeting co-receptors, highlighting challenges the field has faced and areas in which research into co-receptor signaling would yield the most therapeutic benefit in the context of HIV infection. This discussion will provide a comprehensive overview of what is known and what remains to be explored in regard to co-receptor signaling and HIV infection, and will emphasize the potential value of HIV co-receptors as a target for future therapeutic development. ![]()
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Affiliation(s)
- E A Nickoloff-Bybel
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - L Festa
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 S. 40th Street, Philadelphia, PA, 19104, USA
| | - O Meucci
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - P J Gaskill
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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8
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Tavares LA, Januário YC, daSilva LLP. HIV-1 Hijacking of Host ATPases and GTPases That Control Protein Trafficking. Front Cell Dev Biol 2021; 9:622610. [PMID: 34307340 PMCID: PMC8295591 DOI: 10.3389/fcell.2021.622610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) modifies the host cell environment to ensure efficient and sustained viral replication. Key to these processes is the capacity of the virus to hijack ATPases, GTPases and the associated proteins that control intracellular protein trafficking. The functions of these energy-harnessing enzymes can be seized by HIV-1 to allow the intracellular transport of viral components within the host cell or to change the subcellular distribution of antiviral factors, leading to immune evasion. Here, we summarize how energy-related proteins deviate from their normal functions in host protein trafficking to aid the virus in different phases of its replicative cycle. Recent discoveries regarding the interplay among HIV-1 and host ATPases and GTPases may shed light on potential targets for pharmacological intervention.
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Affiliation(s)
- Lucas A Tavares
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Yunan C Januário
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luis L P daSilva
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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9
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Yuan Y, Jacobs CA, Llorente Garcia I, Pereira PM, Lawrence SP, Laine RF, Marsh M, Henriques R. Single-Molecule Super-Resolution Imaging of T-Cell Plasma Membrane CD4 Redistribution upon HIV-1 Binding. Viruses 2021; 13:142. [PMID: 33478139 PMCID: PMC7835772 DOI: 10.3390/v13010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
The first step of cellular entry for the human immunodeficiency virus type-1 (HIV-1) occurs through the binding of its envelope protein (Env) with the plasma membrane receptor CD4 and co-receptor CCR5 or CXCR4 on susceptible cells, primarily CD4+ T cells and macrophages. Although there is considerable knowledge of the molecular interactions between Env and host cell receptors that lead to successful fusion, the precise way in which HIV-1 receptors redistribute to sites of virus binding at the nanoscale remains unknown. Here, we quantitatively examine changes in the nanoscale organisation of CD4 on the surface of CD4+ T cells following HIV-1 binding. Using single-molecule super-resolution imaging, we show that CD4 molecules are distributed mostly as either individual molecules or small clusters of up to 4 molecules. Following virus binding, we observe a local 3-to-10-fold increase in cluster diameter and molecule number for virus-associated CD4 clusters. Moreover, a similar but smaller magnitude reorganisation of CD4 was also observed with recombinant gp120. For one of the first times, our results quantify the nanoscale CD4 reorganisation triggered by HIV-1 on host CD4+ T cells. Our quantitative approach provides a robust methodology for characterising the nanoscale organisation of plasma membrane receptors in general with the potential to link spatial organisation to function.
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Affiliation(s)
- Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
| | - Caron A. Jacobs
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town 7925, South Africa
| | | | - Pedro M. Pereira
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- Bacterial Cell Biology, MOSTMICRO, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Scott P. Lawrence
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- The Francis Crick Institute, London NW1 1AT, UK
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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10
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Wong RW, Balachandran A, Cheung PK, Cheng R, Pan Q, Stoilov P, Harrigan PR, Blencowe BJ, Branch DR, Cochrane A. An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS Pathog 2020; 16:e1008307. [PMID: 32069328 PMCID: PMC7048317 DOI: 10.1371/journal.ppat.1008307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/28/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022] Open
Abstract
The ability of HIV-1 to evolve resistance to combined antiretroviral therapies (cARTs) has stimulated research into alternative means of controlling this infection. We assayed >60 modulators of RNA alternative splicing (AS) to identify new inhibitors of HIV-1 RNA processing-a segment of the viral lifecycle not targeted by current drugs-and discovered compound N-[4-chloro-3-(trifluoromethyl)phenyl]-7-nitro-2,1,3-benzoxadiazol-4-amine (5342191) as a potent inhibitor of both wild-type (Ba-L, NL4-3, LAI, IIIB, and N54) and drug-resistant strains of HIV-1 (IC50: ~700 nM) with no significant effect on cell viability at doses tested. 5342191 blocks expression of four essential HIV-1 structural and regulatory proteins (Gag, Env, Tat, and Rev) without affecting total protein synthesis of the cell. This response is associated with altered unspliced (US) and singly-spliced (SS) HIV-1 RNA accumulation (~60% reduction) and transport to the cytoplasm (loss of Rev) whereas parallel analysis of cellular RNAs revealed less than a 0.7% of host alternative splicing (AS) events (0.25-0.67% by ≥ 10-20%), gene expression (0.01-0.46% by ≥ 2-5 fold), and protein abundance (0.02-0.34% by ≥ 1.5-2 fold) being affected. Decreased expression of Tat, but not Gag/Env, upon 5342191 treatment was reversed by a proteasome inhibitor, suggesting that this compound alters the synthesis/degradation of this key viral factor. Consistent with an affect on HIV-1 RNA processing, 5342191 treatment of cells altered the abundance and phosphorylation of serine/arginine-rich splicing factor (SRSF) 1, 3, and 4. Despite the activation of several intracellular signaling pathways by 5342191 (Ras, MEK1/2-ERK1/2, and JNK1/2/3), inhibition of HIV-1 gene expression by this compound could be reversed by pre-treatment with either a G-protein α-subunit inhibitor or two different MEK1/2 inhibitors. These observations demonstrate enhanced sensitivity of HIV-1 gene expression to small changes in host RNA processing and highlights the potential of modulating host intracellular signaling as an alternative approach for controlling HIV-1 infection.
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Affiliation(s)
- Raymond W. Wong
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter K. Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Qun Pan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin J. Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Donald R. Branch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Advanced Diagnostics, Infection and Immunity Group, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Centre for Innovation, Canadian Blood Services, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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11
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Wenzel ED, Avdoshina V, Mocchetti I. HIV-associated neurodegeneration: exploitation of the neuronal cytoskeleton. J Neurovirol 2019; 25:301-312. [PMID: 30850975 DOI: 10.1007/s13365-019-00737-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/16/2019] [Accepted: 02/18/2019] [Indexed: 01/23/2023]
Abstract
Human immunodeficiency virus-1 (HIV) infection of the central nervous system damages synapses and promotes axonal injury, ultimately resulting in HIV-associated neurocognitive disorders (HAND). The mechanisms through which HIV causes damage to neurons are still under investigation. The cytoskeleton and associated proteins are fundamental for axonal and dendritic integrity. In this article, we review evidence that HIV proteins, such as the envelope protein gp120 and transactivator of transcription (Tat), impair the structure and function of the neuronal cytoskeleton. Investigation into the effects of viral proteins on the neuronal cytoskeleton may provide a better understanding of HIV neurotoxicity and suggest new avenues for additional therapies.
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Affiliation(s)
- Erin D Wenzel
- Department of Pharmacology & Physiology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Valeria Avdoshina
- Department of Neuroscience, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Italo Mocchetti
- Department of Pharmacology & Physiology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA. .,Department of Neuroscience, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA.
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12
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Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 2019; 9:213. [PMID: 30659199 PMCID: PMC6338737 DOI: 10.1038/s41598-018-36135-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023] Open
Abstract
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in the infected cell, leading to the production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while counteracting intracellular defense mechanisms. We investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptomic, proteomic, and phosphoproteomic expression changes in infected and uninfected SupT1 CD4+ T cells at five time points of the viral replication process. By means of a Gaussian mixed-effects model implemented in the new R/Bioconductor package TMixClust, we clustered host genes based on their temporal expression patterns. We identified a proteo-transcriptomic gene expression signature of 388 host genes specific for HIV-1 replication. Comprehensive functional analyses of these genes confirmed the previously described roles of some of the genes and revealed novel key virus-host interactions affecting multiple molecular processes within the host cell, including signal transduction, metabolism, cell cycle, and immune system. The results of our analysis are accessible through a freely available, dedicated and user-friendly R/Shiny application, called PEACHi2.0. This resource constitutes a catalogue of dynamic host responses to HIV-1 infection that provides a basis for a more comprehensive understanding of virus-host interactions.
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Affiliation(s)
- Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Sébastien Desfarges
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- InvivoGen, Toulouse, France
| | - Céline Hernandez
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Computational Systems Biology Team, Institut de Biologie de I'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, ENS, PSL Université, Paris, France
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sylvie Rato
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA.
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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13
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Wiredja DD, Tabler CO, Schlatzer DM, Li M, Chance MR, Tilton JC. Global phosphoproteomics of CCR5-tropic HIV-1 signaling reveals reprogramming of cellular protein production pathways and identifies p70-S6K1 and MK2 as HIV-responsive kinases required for optimal infection of CD4+ T cells. Retrovirology 2018; 15:44. [PMID: 29970186 PMCID: PMC6029029 DOI: 10.1186/s12977-018-0423-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/26/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Viral reprogramming of host cells enhances replication and is initiated by viral interaction with the cell surface. Upon human immunodeficiency virus (HIV) binding to CD4+ T cells, a signal transduction cascade is initiated that reorganizes the actin cytoskeleton, activates transcription factors, and alters mRNA splicing pathways. METHODS We used a quantitative mass spectrometry-based phosphoproteomic approach to investigate signal transduction cascades initiated by CCR5-tropic HIV, which accounts for virtually all transmitted viruses and the vast majority of viruses worldwide. RESULTS CCR5-HIV signaling induced significant reprogramming of the actin cytoskeleton and mRNA splicing pathways, as previously described. In addition, CCR5-HIV signaling induced profound changes to the mRNA transcription, processing, translation, and post-translational modifications pathways, indicating that virtually every stage of protein production is affected. Furthermore, we identified two kinases regulated by CCR5-HIV signaling-p70-S6K1 (RPS6KB1) and MK2 (MAPKAPK2)-that were also required for optimal HIV infection of CD4+ T cells. These kinases regulate protein translation and cytoskeletal architecture, respectively, reinforcing the importance of these pathways in viral replication. Additionally, we found that blockade of CCR5 signaling by maraviroc had relatively modest effects on CCR5-HIV signaling, in agreement with reports that signaling by CCR5 is dispensable for HIV infection but in contrast to the critical effects of CXCR4 on cortical actin reorganization. CONCLUSIONS These results demonstrate that CCR5-tropic HIV induces significant reprogramming of host CD4+ T cell protein production pathways and identifies two novel kinases induced upon viral binding to the cell surface that are critical for HIV replication in host cells.
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Affiliation(s)
- Danica D Wiredja
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Caroline O Tabler
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniela M Schlatzer
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Ming Li
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mark R Chance
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - John C Tilton
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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14
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Ospina Stella A, Turville S. All-Round Manipulation of the Actin Cytoskeleton by HIV. Viruses 2018; 10:v10020063. [PMID: 29401736 PMCID: PMC5850370 DOI: 10.3390/v10020063] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
While significant progress has been made in terms of human immunodeficiency virus (HIV) therapy, treatment does not represent a cure and remains inaccessible to many people living with HIV. Continued mechanistic research into the viral life cycle and its intersection with many aspects of cellular biology are not only fundamental in the continued fight against HIV, but also provide many key observations of the workings of our immune system. Decades of HIV research have testified to the integral role of the actin cytoskeleton in both establishing and spreading the infection. Here, we review how the virus uses different strategies to manipulate cellular actin networks and increase the efficiency of various stages of its life cycle. While some HIV proteins seem able to bind to actin filaments directly, subversion of the cytoskeleton occurs indirectly by exploiting the power of actin regulatory proteins, which are corrupted at multiple levels. Furthermore, this manipulation is not restricted to a discrete class of proteins, but rather extends throughout all layers of the cytoskeleton. We discuss prominent examples of actin regulators that are exploited, neutralized or hijacked by the virus, and address how their coordinated deregulation can lead to changes in cellular behavior that promote viral spreading.
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Affiliation(s)
- Alberto Ospina Stella
- The Kirby Institute, University of New South Wales (UNSW), Sydney NSW 2052, Australia.
| | - Stuart Turville
- The Kirby Institute, University of New South Wales (UNSW), Sydney NSW 2052, Australia.
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