1
|
Thapa G, Bhattacharya A, Bhattacharya S. Molecular dynamics investigation of DNA fragments bound to the anti-HIV protein SAMHD1 reveals alterations in allosteric communications. J Mol Graph Model 2024; 129:108748. [PMID: 38452417 DOI: 10.1016/j.jmgm.2024.108748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
The sterile alpha motif and histidine-aspartate domain-containing protein 1 (or SAMHD1), a human dNTP-triphosphohydrolase, contributes to HIV-1 restriction in select terminally differentiated cells of the immune system. While the prevailing hypothesis is that the catalytically active form of the protein is an allosterically triggered tetramer, whose HIV-1 restriction properties are attributed to its dNTP - triphosphohydrolase activity, it is also known to bind to ssRNA and ssDNA oligomers. A complete picture of the structure-function relationship of the enzyme is still elusive and the function corresponding to its nucleic acid binding ability is debated. In this in silico study, we investigate the stability, preference and allosteric effects of DNA oligomers bound to SAMHD1. In particular, we compare the binding of DNA and RNA oligomers of the same sequence and also consider the binding of DNA fragments with phosphorothioate bonds in the backbone. The results are compared with the canonical form with the monomers connected by GTP/dATP crossbridges. The simulations indicate that SAMHD1 dimers preferably bind to DNA and RNA oligomers compared to GTP/dATP. However, allosteric communication channels are altered in the nucleic acid acid bound complexes compared to the canonical form. All results are consistent with the hypothesis that the DNA bound form of the protein correspond to an unproductive off-pathway state where the protein is sequestered and not available for dNTP hydrolysis.
Collapse
Affiliation(s)
- Gauri Thapa
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | | | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| |
Collapse
|
2
|
Abdelrazak Morsy MH, Lilienthal I, Lord M, Merrien M, Wasik AM, Sureda-Gómez M, Amador V, Johansson HJ, Lehtiö J, Garcia-Torre B, Martin-Subero JI, Tsesmetzis N, Tao S, Schinazi RF, Kim B, Sorteberg AL, Wickström M, Sheppard D, Rassidakis GZ, Taylor IA, Christensson B, Campo E, Herold N, Sander B. SOX11 is a novel binding partner and endogenous inhibitor of SAMHD1 ara-CTPase activity in mantle cell lymphoma. Blood 2024; 143:1953-1964. [PMID: 38237141 PMCID: PMC11103171 DOI: 10.1182/blood.2023022241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
ABSTRACT Sterile alpha motif and histidine-aspartate (HD) domain-containing protein 1 (SAMHD1) is a deoxynucleoside triphosphate triphosphohydrolase with ara-CTPase activity that confers cytarabine (ara-C) resistance in several hematological malignancies. Targeting SAMHD1's ara-CTPase activity has recently been demonstrated to enhance ara-C efficacy in acute myeloid leukemia. Here, we identify the transcription factor SRY-related HMG-box containing protein 11 (SOX11) as a novel direct binding partner and first known endogenous inhibitor of SAMHD1. SOX11 is aberrantly expressed not only in mantle cell lymphoma (MCL), but also in some Burkitt lymphomas. Coimmunoprecipitation of SOX11 followed by mass spectrometry in MCL cell lines identified SAMHD1 as the top SOX11 interaction partner, which was validated by proximity ligation assay. In vitro, SAMHD1 bound to the HMG box of SOX11 with low-micromolar affinity. In situ crosslinking studies further indicated that SOX11-SAMHD1 binding resulted in a reduced tetramerization of SAMHD1. Functionally, expression of SOX11 inhibited SAMHD1 ara-CTPase activity in a dose-dependent manner resulting in ara-C sensitization in cell lines and in a SOX11-inducible mouse model of MCL. In SOX11-negative MCL, SOX11-mediated ara-CTPase inhibition could be mimicked by adding the recently identified SAMHD1 inhibitor hydroxyurea. Taken together, our results identify SOX11 as a novel SAMHD1 interaction partner and its first known endogenous inhibitor with potentially important implications for clinical therapy stratification.
Collapse
Affiliation(s)
- Mohammad Hamdy Abdelrazak Morsy
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Applied Medical Chemistry, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ingrid Lilienthal
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Martin Lord
- Department of Pharmaceutical Biosciences, Immuno-oncology, Uppsala University Biomedical Centre, Uppsala, Sweden
| | - Magali Merrien
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Agata Magdalena Wasik
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Marta Sureda-Gómez
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
| | - Virginia Amador
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | | | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Raymond F. Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Agnes L. Sorteberg
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Georgios Z. Rassidakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Birger Christensson
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clinic Barcelona, University of Barcelona, Barcelona, Spain
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
- Paediatric Oncology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
3
|
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA. Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun 2024; 15:3775. [PMID: 38710701 PMCID: PMC11074143 DOI: 10.1038/s41467-024-48237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
Collapse
Affiliation(s)
- Oliver J Acton
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ailidh J O Burgess
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| |
Collapse
|
4
|
Ananth S, Ambiel I, Schifferdecker S, Müller TG, Wratil PR, Mejias-Perez E, Kräusslich HG, Müller B, Keppler OT, Fackler OT. Spatial resolution of HIV-1 post-entry steps in resting CD4 T cells. Cell Rep 2024; 43:113941. [PMID: 38478523 DOI: 10.1016/j.celrep.2024.113941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Resting CD4 T cells resist productive HIV-1 infection. The HIV-2/simian immunodeficiency virus protein viral accessory protein X (Vpx) renders these cells permissive to infection, presumably by alleviating blocks at cytoplasmic reverse transcription and subsequent nuclear import of reverse-transcription/pre-integration complexes (RTC/PICs). Here, spatial analyses using quantitative virus imaging techniques reveal that HIV-1 capsids containing RTC/PICs are readily imported into the nucleus, recruit the host dependency factor CPSF6, and translocate to nuclear speckles in resting CD4 T cells. Reverse transcription, however, remains incomplete, impeding proviral integration and viral gene expression. Vpx or pharmacological inhibition of the deoxynucleotide triphosphohydrolase (dNTPase) activity of the restriction factor SAM domain and HD domain-containing protein 1 (SAMHD1) increases levels of nuclear reverse-transcribed cDNA and facilitates HIV-1 integration. Nuclear import and intranuclear transport of viral complexes therefore do not pose important blocks to HIV-1 in resting CD4 T cells, and the limitation to reverse transcription by SAMHD1's dNTPase activity constitutes the main pre-integration block to infection.
Collapse
Affiliation(s)
- Swetha Ananth
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Integrative Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Ina Ambiel
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Integrative Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Sandra Schifferdecker
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Thorsten G Müller
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site München, Munich, Germany
| | - Ernesto Mejias-Perez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site München, Munich, Germany
| | - Hans-Georg Kräusslich
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site München, Munich, Germany
| | - Oliver T Fackler
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Integrative Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.
| |
Collapse
|
5
|
Zhao Z, Han S, Zhang Q, Wang Y, Yue K, Abbas S, He H. Impaired influenza A virus replication by the host restriction factor SAMHD1 which inhibited by PA-mediated dephosphorylation of the host transcription factor IRF3. Virol J 2024; 21:33. [PMID: 38287375 PMCID: PMC10826253 DOI: 10.1186/s12985-024-02295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Influenza A virus (IAV) can cause severe and life-threatening illness in humans and animals. Therefore, it is important to search for host antiviral proteins and elucidate their antiviral mechanisms for the development of potential treatments. As a part of human innate immunity, host restriction factors can inhibit the replication of viruses, among which SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) can restrict the replication of viruses, such as HIV and enterovirus EV71. Viruses also developed countermeasures in the arms race with their hosts. There are few reports about whether SAMHD1 has a restriction effect on IAV. METHODS To investigate the impact of IAV infection on SAMHD1 expression in A549 cells, we infected A549 cells with a varying multiplicity of infection (MOI) of IAV and collected cell samples at different time points for WB and RT-qPCR analysis to detect viral protein and SAMHD1 levels. The virus replication level in the cell culture supernatant was determined using TCID50 assay. Luciferase assay was used to reveal that H5N1 virus polymerase acidic protein (PA) affected the activity of the SAMHD1 promoter. To assess the antiviral capacity of SAMHD1, we generated a knockdown and overexpressed cell line for detecting H5N1 replication. RESULTS In this study, we observed that SAMHD1 can restrict the intracellular replication of H5N1 and that the H5N1 viral protein PA can downregulate the expression of SAMHD1 by affecting SAMHD1 transcriptional promoter activity. We also found that SAMHD1's ability to restrict H5N1 is related to phosphorylation at 592-tyrosine. CONCLUSIONS In conclusion, we found that SAMHD1 may affect the replication of IAVs as a host restriction factor and be countered by PA. Furthermore, SAMHD1 may be a potential target for developing antiviral drugs.
Collapse
Affiliation(s)
- Zhilei Zhao
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingxun Zhang
- Beijing Milu Ecological Research Center, Beijing, 100076, China
| | - Ye Wang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Kening Yue
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Salbia Abbas
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
6
|
Morsy MHA, Lilienthal I, Lord M, Merrien M, Wasik AM, Sureda-Gómez M, Amador V, Johansson HJ, Lehtiö J, Garcia-Torre B, Martin-Subero JI, Tsesmetzis N, Tao S, Schinazi RF, Kim B, Sorteberg AL, Wickström M, Sheppard D, Rassidakis GZ, Taylor IA, Christensson B, Campo E, Herold N, Sander B. SOX11 is a novel binding partner and endogenous inhibitor of SAMHD1 ara-CTPase activity in mantle cell lymphoma. Blood 2024; 143:1953-1964. [PMID: 38774451 PMCID: PMC7615944 DOI: 10.1182/blood.2023022241/2210808/blood.2023022241.pdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024] Open
Abstract
The sterile alpha motif and histidine-aspartate (HD) domain containing protein 1 (SAMHD1) is a deoxynucleoside triphosphate triphosphohydrolase with ara-CTPase activity that confers cytarabine (ara-C) resistance in several haematological malignancies. Targeting SAMHD1's ara-CTPase activity has recently been demonstrated to enhance ara-C efficacy in acute myeloid leukemia. Here, we identify the transcription factor SRY-related HMG-box containing protein 11 (SOX11) as a novel direct binding partner and first known endogenous inhibitor of SAMHD1. SOX11 is aberrantly expressed not only in mantle cell lymphoma (MCL), but also in some Burkitt lymphomas. Co-immunoprecipitation of SOX11 followed by mass spectrometry in MCL cell lines identified SAMHD1 as the top SOX11 interaction partner which was validated by proximity ligation assay. In vitro, SAMHD1 bound to the HMG box of SOX11 with low-micromolar affinity. In situ crosslinking studies further indicated that SOX11-SAMHD1 binding resulted in a reduced tetramerization of SAMHD1. Functionally, expression of SOX11 inhibited SAMHD1 ara-CTPase activity in a dose-dependent manner resulting in ara-C sensitization in cell lines and in a SOX11-inducible mouse model of MCL. In SOX11-negative MCL, SOX11-mediated ara-CTPase inhibition could be mimicked by adding the recently identified SAMHD1 inhibitor hydroxyurea. Taken together, our results identify SOX11 as a novel SAMHD1 interaction partner and its first known endogenous inhibitor with potentially important implications for clinical therapy stratification.
Collapse
Affiliation(s)
- Mohammad Hamdy Abdelrazak Morsy
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
- Department of Applied Medical Chemistry, Medical Research Institute, Alexandria University, 21561, Alexandria, Egypt
| | - Ingrid Lilienthal
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Martin Lord
- Department of Pharmaceutical Biosciences, Immuno-oncology, Uppsala University Biomedical Centre (BMC), SE-751 24, Uppsala, Sweden
| | - Magali Merrien
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| | - Agata Magdalena Wasik
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| | - Marta Sureda-Gómez
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Virginia Amador
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, USA
| | - Agnes L Sorteberg
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Georgios Z Rassidakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Birger Christensson
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clinic Barcelona, University of Barcelona, Barcelona, Spain
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
- Paediatric Oncology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| |
Collapse
|
7
|
Orris B, Sung MW, Bhat S, Xu Y, Huynh KW, Han S, Johnson DC, Bosbach B, Shields DJ, Stivers JT. Guanine-containing ssDNA and RNA induce dimeric and tetrameric structural forms of SAMHD1. Nucleic Acids Res 2023; 51:12443-12458. [PMID: 37930833 PMCID: PMC10711556 DOI: 10.1093/nar/gkad971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/19/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023] Open
Abstract
The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish in cryo-EM and biochemical studies that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ∼20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
Collapse
Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | | | - Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | - Yingrong Xu
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Seungil Han
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Darren C Johnson
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016, USA
| | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016, USA
| | - David J Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| |
Collapse
|
8
|
Schüssler M, Schott K, Fuchs NV, Oo A, Zahadi M, Rauch P, Kim B, König R. Gene editing of SAMHD1 in macrophage-like cells reveals complex relationships between SAMHD1 phospho-regulation, HIV-1 restriction, and cellular dNTP levels. mBio 2023; 14:e0225223. [PMID: 37800914 PMCID: PMC10653793 DOI: 10.1128/mbio.02252-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE We introduce BLaER1 cells as an alternative myeloid cell model in combination with CRISPR/Cas9-mediated gene editing to study the influence of sterile α motif and HD domain-containing protein 1 (SAMHD1) T592 phosphorylation on anti-viral restriction and the control of cellular dNTP levels in an endogenous, physiologically relevant context. A proper understanding of the mechanism of the anti-viral function of SAMHD1 will provide attractive strategies aiming at selectively manipulating SAMHD1 without affecting other cellular functions. Even more, our toolkit may inspire further genetic analysis and investigation of restriction factors inhibiting retroviruses and their cellular function and regulation, leading to a deeper understanding of intrinsic anti-viral immunity.
Collapse
Affiliation(s)
- Moritz Schüssler
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | | | - Adrian Oo
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Morssal Zahadi
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Paula Rauch
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Baek Kim
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| |
Collapse
|
9
|
Egleston M, Dong L, Howlader AH, Bhat S, Orris B, Bianchet MA, Greenberg MM, Stivers JT. Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding. ACS Chem Biol 2023; 18:2200-2210. [PMID: 37233733 PMCID: PMC10596003 DOI: 10.1021/acschembio.3c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase that exists in monomeric, dimeric, and tetrameric forms. It is activated by GTP binding to an A1 allosteric site on each monomer subunit, which induces dimerization, a prerequisite for dNTP-induced tetramerization. SAMHD1 is a validated drug target stemming from its inactivation of many anticancer nucleoside drugs leading to drug resistance. The enzyme also possesses a single-strand nucleic acid binding function that promotes RNA and DNA homeostasis by several mechanisms. To discover small molecule inhibitors of SAMHD1, we screened a custom ∼69 000-compound library for dNTPase inhibitors. Surprisingly, this effort yielded no viable hits and indicated that exceptional barriers for discovery of small molecule inhibitors existed. We then took a rational fragment-based inhibitor design approach using a deoxyguanosine (dG) A1 site targeting fragment. A targeted chemical library was synthesized by coupling a 5'-phosphoryl propylamine dG fragment (dGpC3NH2) to 376 carboxylic acids (RCOOH). Direct screening of the products (dGpC3NHCO-R) yielded nine initial hits, one of which (R = 3-(3'-bromo-[1,1'-biphenyl]), 5a) was investigated extensively. Amide 5a is a competitive inhibitor against GTP binding to the A1 site and induces inactive dimers that are deficient in tetramerization. Surprisingly, 5a also prevented ssDNA and ssRNA binding, demonstrating that the dNTPase and nucleic acid binding functions of SAMHD1 can be disrupted by a single small molecule. A structure of the SAMHD1-5a complex indicates that the biphenyl fragment impedes a conformational change in the C-terminal lobe that is required for tetramerization.
Collapse
Affiliation(s)
- Matthew Egleston
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Linghao Dong
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - A. Hasan Howlader
- Department
of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Shridhar Bhat
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Benjamin Orris
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Mario A. Bianchet
- Department
of Neurology and Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Marc M. Greenberg
- Department
of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - James T. Stivers
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| |
Collapse
|
10
|
Cai Y, Chen X, Lu T, Fang X, Ding M, Yu Z, Hu S, Liu J, Zhou X, Wang X. Activation of STING by SAMHD1 Deficiency Promotes PANoptosis and Enhances Efficacy of PD-L1 Blockade in Diffuse Large B-cell Lymphoma. Int J Biol Sci 2023; 19:4627-4643. [PMID: 37781035 PMCID: PMC10535696 DOI: 10.7150/ijbs.85236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023] Open
Abstract
Genomic instability is a significant driver of cancer. As the sensor of cytosolic DNA, the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway plays a critical role in regulating anti-tumor immunity and cell death. However, the role and regulatory mechanisms of STING in diffuse large B-cell lymphoma (DLBCL) are still undefined. In this study, we reported that sterile alpha motif and HD domain-containing protein 1 (SAMHD1) deficiency induced STING expression and inhibited tumor growth in DLBCL. High level of SAMHD1 was associated with poor prognosis in DLBCL patients. Down-regulation of SAMHD1 inhibited DLBCL cell proliferation both in vitro and in vivo. Moreover, we found that SAMHD1 deficiency induced DNA damage and promoted the expression of DNA damage adaptor STING. STING overexpression promoted the formation of Caspase 8/RIPK3/ASC, further leading to MLKL phosphorylation, Caspase 3 cleavage, and GSDME cleavage. Up-regulation of necroptotic, apoptotic, and pyroptotic effectors indicated STING-mediated PANoptosis. Finally, we demonstrated that the STING agonist, DMXAA, enhanced the efficacy of a PD-L1 inhibitor in DLBCL. Our findings highlight the important role of STING-mediated PANoptosis in restricting DLBCL progression and provide a potential strategy for enhancing the efficacy of immune checkpoint inhibitor agents in DLBCL.
Collapse
Affiliation(s)
- Yiqing Cai
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiaomin Chen
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Tiange Lu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiaosheng Fang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Mengfei Ding
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Zhuoya Yu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Shunfeng Hu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Jiarui Liu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| |
Collapse
|
11
|
Antequera-Parrilla P, Castillo-Acosta VM, Bosch-Navarrete C, Ruiz-Pérez LM, González-Pacanowska D. A nuclear orthologue of the dNTP triphosphohydrolase SAMHD1 controls dNTP homeostasis and genomic stability in Trypanosoma brucei. Front Cell Infect Microbiol 2023; 13:1241305. [PMID: 37674581 PMCID: PMC10478004 DOI: 10.3389/fcimb.2023.1241305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
Maintenance of dNTPs pools in Trypanosoma brucei is dependent on both biosynthetic and degradation pathways that together ensure correct cellular homeostasis throughout the cell cycle which is essential for the preservation of genomic stability. Both the salvage and de novo pathways participate in the provision of pyrimidine dNTPs while purine dNTPs are made available solely through salvage. In order to identify enzymes involved in degradation here we have characterized the role of a trypanosomal SAMHD1 orthologue denominated TbHD82. Our results show that TbHD82 is a nuclear enzyme in both procyclic and bloodstream forms of T. brucei. Knockout forms exhibit a hypermutator phenotype, cell cycle perturbations and an activation of the DNA repair response. Furthermore, dNTP quantification of TbHD82 null mutant cells revealed perturbations in nucleotide metabolism with a substantial accumulation of dATP, dCTP and dTTP. We propose that this HD domain-containing protein present in kinetoplastids plays an essential role acting as a sentinel of genomic fidelity by modulating the unnecessary and detrimental accumulation of dNTPs.
Collapse
Affiliation(s)
| | - Víctor M. Castillo-Acosta
- Instituto de Parasitología y Biomedicina “López-Neyra, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | | | | | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina “López-Neyra, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| |
Collapse
|
12
|
Bowen NE, Tao S, Cho YJ, Schinazi RF, Kim B. Vpx requires active cellular dNTP biosynthesis to effectively counteract the anti-lentivirus activity of SAMHD1 in macrophages. J Biol Chem 2023; 299:104984. [PMID: 37390988 PMCID: PMC10374972 DOI: 10.1016/j.jbc.2023.104984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
HIV-1 replication in primary monocyte-derived macrophages (MDMs) is kinetically restricted at the reverse transcription step due to the low deoxynucleoside triphosphates (dNTP) pools established by host dNTPase, SAM and HD domain containing protein 1 (SAMHD1). Lentiviruses such as HIV-2 and some Simian immunodeficiency virus counteract this restriction using viral protein X (Vpx), which proteosomally degrades SAMHD1 and elevates intracellular dNTP pools. However, how dNTP pools increase after Vpx degrades SAMHD1 in nondividing MDMs where no active dNTP biosynthesis is expected to exists remains unclear. In this study, we monitored known dNTP biosynthesis machinery during primary human monocyte differentiation to MDMs and unexpectedly found MDMs actively express dNTP biosynthesis enzymes such as ribonucleotide reductase, thymidine kinase 1, and nucleoside-diphosphate kinase. During differentiation from monocytes the expression levels of several biosynthesis enzymes are upregulated, while there is an increase in inactivating SAMHD1 phosphorylation. Correspondingly, we observed significantly lower levels of dNTPs in monocytes compared to MDMs. Without dNTP biosynthesis availability, Vpx failed to elevate dNTPs in monocytes, despite SAMHD1 degradation. These extremely low monocyte dNTP concentrations, which cannot be elevated by Vpx, impaired HIV-1 reverse transcription in a biochemical simulation. Furthermore, Vpx failed to rescue the transduction efficiency of a HIV-1 GFP vector in monocytes. Collectively, these data suggest that MDMs harbor active dNTP biosynthesis and Vpx requires this dNTP biosynthesis to elevate dNTP levels to effectively counteract SAMHD1 and relieve the kinetic block to HIV-1 reverse transcription in MDMs.
Collapse
Affiliation(s)
- Nicole E Bowen
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Sijia Tao
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Young-Jae Cho
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Baek Kim
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
| |
Collapse
|
13
|
Espada CE, Sari L, Cahill MP, Yang H, Phillips S, Martinez N, Kenney AD, Yount JS, Xiong Y, Lin MM, Wu L. SAMHD1 impairs type I interferon induction through the MAVS, IKKε, and IRF7 signaling axis during viral infection. J Biol Chem 2023; 299:104925. [PMID: 37328105 PMCID: PMC10404699 DOI: 10.1016/j.jbc.2023.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) restricts human immunodeficiency virus type 1 (HIV-1) infection by reducing the intracellular dNTP pool. We have shown that SAMHD1 suppresses nuclear factor kappa-B activation and type I interferon (IFN-I) induction by viral infection and inflammatory stimuli. However, the mechanism by which SAMHD1 inhibits IFN-I remains unclear. Here, we show that SAMHD1 inhibits IFN-I activation induced by the mitochondrial antiviral-signaling protein (MAVS). SAMHD1 interacted with MAVS and suppressed MAVS aggregation in response to Sendai virus infection in human monocytic THP-1 cells. This resulted in increased phosphorylation of TANK binding kinase 1 (TBK1), inhibitor of nuclear factor kappa-B kinase epsilon (IKKε), and IFN regulatory factor 3 (IRF3). SAMHD1 suppressed IFN-I activation induced by IKKε and prevented IRF7 binding to the kinase domain of IKKε. We found that SAMHD1 interaction with the inhibitory domain (ID) of IRF7 (IRF7-ID) was necessary and sufficient for SAMHD1 suppression of IRF7-mediated IFN-I activation in HEK293T cells. Computational docking and molecular dynamics simulations revealed possible binding sites between IRF7-ID and full-length SAMHD1. Individual substitution of F411, E416, or V460 in IRF7-ID significantly reduced IRF7 transactivation activity and SAMHD1 binding. Furthermore, we investigated the role of SAMHD1 inhibition of IRF7-mediated IFN-I induction during HIV-1 infection. We found that THP-1 cells lacking IRF7 expression had reduced HIV-1 infection and viral transcription compared to control cells, indicating a positive role of IRF7 in HIV-1 infection. Our findings suggest that SAMHD1 suppresses IFN-I induction through the MAVS, IKKε, and IRF7 signaling axis.
Collapse
Affiliation(s)
- Constanza E Espada
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Levent Sari
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael P Cahill
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Hua Yang
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Nicholas Martinez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Milo M Lin
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
| |
Collapse
|
14
|
Abstract
Telomere length in humans is associated with lifespan and severe diseases, yet the genetic determinants of telomere length remain incompletely defined. Here we performed genome-wide CRISPR-Cas9 functional telomere length screening and identified thymidine (dT) nucleotide metabolism as a limiting factor in human telomere maintenance. Targeted genetic disruption using CRISPR-Cas9 revealed multiple telomere length control points across the thymidine nucleotide metabolism pathway: decreasing dT nucleotide salvage via deletion of the gene encoding nuclear thymidine kinase (TK1) or de novo production by knockout of the thymidylate synthase gene (TYMS) decreased telomere length, whereas inactivation of the deoxynucleoside triphosphohydrolase-encoding gene SAMHD1 lengthened telomeres. Remarkably, supplementation with dT alone drove robust telomere elongation by telomerase in cells, and thymidine triphosphate stimulated telomerase activity in a substrate-independent manner in vitro. In induced pluripotent stem cells derived from patients with genetic telomere biology disorders, dT supplementation or inhibition of SAMHD1 promoted telomere restoration. Our results demonstrate a critical role of thymidine metabolism in controlling human telomerase and telomere length, which may be therapeutically actionable in patients with fatal degenerative diseases.
Collapse
Affiliation(s)
- William Mannherz
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard/MIT MD-PhD Program, Harvard Stem Cell Institute, Harvard Initiative for RNA Medicine, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Suneet Agarwal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Biological and Biomedical Sciences Program, Harvard/MIT MD-PhD Program, Harvard Stem Cell Institute, Harvard Initiative for RNA Medicine, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
15
|
Sharifi HJ, Paine DN, Fazzari VA, Tipple AF, Patterson E, de Noronha CMC. Sulforaphane Reduces SAMHD1 Phosphorylation To Protect Macrophages from HIV-1 Infection. J Virol 2022; 96:e0118722. [PMID: 36377871 PMCID: PMC9749475 DOI: 10.1128/jvi.01187-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
The cellular protein SAMHD1 is important for DNA repair, suppressing LINE elements, controlling deoxynucleoside triphosphate (dNTP) concentrations, maintaining HIV-1 latency, and preventing excessive type I interferon responses. SAMHD1 is also a potent inhibitor of HIV-1 and other significant viral pathogens. Infection restriction is due in part to the deoxynucleoside triphosphatase (dNTPase) activity of SAMHD1 but is also mediated through a dNTPase-independent mechanism that has been described but not explored. The phosphorylation of SAMHD1 at threonine 592 (T592) controls many of its functions. Retroviral restriction, irrespective of dNTPase activity, is linked to unphosphorylated T592. Sulforaphane (SFN), an isothiocyanate, protects macrophages from HIV infection by mobilizing the transcription factor and antioxidant response regulator Nrf2. Here, we show that SFN and other clinically relevant Nrf2 mobilizers reduce SAMHD1 T592 phosphorylation to protect macrophages from HIV-1. We further show that SFN, through Nrf2, triggers the upregulation of the cell cycle control protein p21 in human monocyte-derived macrophages to contribute to SAMHD1 activation. We additionally present data that support another, potentially redox-dependent mechanism employed by SFN to contribute to SAMHD1 activation through reduced phosphorylation. This work establishes the use of exogenous Nrf2 mobilizers as a novel way to study virus restriction by SAMHD1 and highlights the Nrf2 pathway as a potential target for the therapeutic control of SAMHD1 cellular and antiviral functions. IMPORTANCE Here, we show, for the first time, that the treatment of macrophages with Nrf2 mobilizers, known activators of antioxidant responses, increases the fraction of SAMHD1 without a regulatory phosphate at position 592. We demonstrate that this decreases infection of macrophages by HIV-1. Phosphorylated SAMHD1 is important for DNA repair, the suppression of LINE elements, the maintenance of HIV-1 in a latent state, and the prevention of excessive type I interferon responses, while unphosphorylated SAMHD1 blocks HIV infection. SAMHD1 impacts many viruses and is involved in various cancers, so knowledge of how it works and how it is regulated has broad implications for the development of therapeutics. Redox-modulating therapeutics are already in clinical use or under investigation for the treatment of many conditions. Thus, understanding the impact of redox modifiers on controlling SAMHD1 phosphorylation is important for many areas of research in microbiology and beyond.
Collapse
Affiliation(s)
- H. John Sharifi
- Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Dakota N. Paine
- Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | | | | | - Emilee Patterson
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Carlos M. C. de Noronha
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| |
Collapse
|
16
|
Wang H, Tu R, Ruan Z, Wu D, Peng Z, Zhou X, Liu Q, Wu W, Cao L, Cheng S, Sun L, Zhan X, Shen X. STRIPE3, encoding a human dNTPase SAMHD1 homolog, regulates chloroplast development in rice. Plant Sci 2022; 323:111395. [PMID: 35878695 DOI: 10.1016/j.plantsci.2022.111395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast is an important organelle for photosynthesis and numerous essential metabolic processes, thus ensuring plant fitness or survival. Although many genes involved in chloroplast development have been identified, mechanisms underlying such development are not fully understood. Here, we isolated and characterized the stripe3 (st3) mutant which exhibited white-striped leaves with reduced chlorophyll content and abnormal chloroplast development during the seedling stage, but gradually produced nearly normal green leaves as it developed. Map-based cloning and transgenic tests demonstrated that a splicing mutation in ST3, encoding a human deoxynucleoside triphosphate triphosphohydrolase (dNTPase) SAMHD1 homolog, was responsible for st3 phenotypes. ST3 is highly expressed in the third leaf at three-leaf stage and expressed constitutively in root, stem, leaf, sheath, and panicle, and the encoded protein, OsSAMHD1, is localized to the cytoplasm. The st3 mutant showed more severe albino leaf phenotype under exogenous 1-mM dATP/dA, dCTP/dC, and dGTP/dG treatments compared with the control conditions, indicating that ST3 is involved in dNTP metabolism. This study reveals a gene associated with dNTP catabolism, and propose a model in which chloroplast development in rice is regulated by the dNTP pool, providing a potential application of these results to hybrid rice breeding.
Collapse
Affiliation(s)
- Hong Wang
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Ranran Tu
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Zheyan Ruan
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Duo Wu
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zequn Peng
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Xingpeng Zhou
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Qunen Liu
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Weixun Wu
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Liyong Cao
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Lianping Sun
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China.
| | - Xiaodeng Zhan
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China.
| | - Xihong Shen
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China.
| |
Collapse
|
17
|
Bowen NE, Oo A, Kim B. Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis. Viruses 2022; 14:v14081622. [PMID: 35893688 PMCID: PMC9331428 DOI: 10.3390/v14081622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) has been the primary interest among studies on antiviral discovery, viral replication kinetics, drug resistance, and viral evolution. Following infection and entry into target cells, the HIV-1 core disassembles, and the viral RT concomitantly converts the viral RNA into double-stranded proviral DNA, which is integrated into the host genome. The successful completion of the viral life cycle highly depends on the enzymatic DNA polymerase activity of RT. Furthermore, HIV-1 RT has long been known as an error-prone DNA polymerase due to its lack of proofreading exonuclease properties. Indeed, the low fidelity of HIV-1 RT has been considered as one of the key factors in the uniquely high rate of mutagenesis of HIV-1, which leads to efficient viral escape from immune and therapeutic antiviral selective pressures. Interestingly, a series of studies on the replication kinetics of HIV-1 in non-dividing myeloid cells and myeloid specific host restriction factor, SAM domain, and HD domain-containing protein, SAMHD1, suggest that the myeloid cell tropism and high rate of mutagenesis of HIV-1 are mechanistically connected. Here, we review not only HIV-1 RT as a key antiviral target, but also potential evolutionary and mechanistic crosstalk among the unique enzymatic features of HIV-1 RT, the replication kinetics of HIV-1, cell tropism, viral genetic mutation, and host SAMHD1 protein.
Collapse
Affiliation(s)
- Nicole E. Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
- Correspondence:
| |
Collapse
|
18
|
Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM. High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J Biol Chem 2022; 298:102073. [PMID: 35643313 PMCID: PMC9257424 DOI: 10.1016/j.jbc.2022.102073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 10/27/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a tetrameric dNTPase, and the hexameric Escherichia coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 Å) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 Å) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.
Collapse
Affiliation(s)
- Bradley P Klemm
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Andrew P Sikkema
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - James C Horng
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA.
| |
Collapse
|
19
|
LIU Z, ZHANG Q, DENG B, SANG F, WANG D, KANG N, LI J, ZHANG M, LIANG S, DUAN C, LIU Z, XU Q, LI Q. Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 expression and its relationship with T cell activation in human immunodeficiency virus/acquired immune deficiency syndrome patients with lung-spleen deficiency syndrome pattern. J TRADIT CHIN MED 2022; 42:451-457. [PMID: 35610016 PMCID: PMC9924747 DOI: 10.19852/j.cnki.jtcm.20220408.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
OBJECTIVE To investigate the relationship between antiviral restriction factor Sterile Alpha Motif and Histidine-Aspartic acid domain-containing protein 1 (SAMHD1) expression and T cell activation, furthermore, identifying objective indexes of lung-spleen deficiency symptom pattern. METHODS We assessed the profile of T lymphocyte subsets, characteristics of SAMHD1 and human leukocyte antigen DR (HLA-DR) expression in lung-spleen deficiency patients. At the same time, people living with human immunodeficiency virus / acquired immune deficiency syndrome (HIV/AIDS) (PLWHA) without obvious clinical symptoms and healthy donors in this area were used as controls. RESULTS Immunohematologic indexes lower CD4 count, lower CD4/CD8 ratio and higher SAMHD1 level were found in lung-spleen deficiency patients. Furthermore, we demonstrated a positive relationship between SAMHD1 and HLA-DR level as well as with interferon factor in lung-spleen deficiency syndrome and patients without obvious clinical signs and symptoms groups. CONCLUSIONS These data indicated the positive relationship between SAMHD1 and T cell activation which further elucidated the role of SAMHD1 in cellular immune response. Furthermore, combination of T lymphocyte subsets counts and SAMHD1 level may be used as clinical and biological reference basis for the differentiation and diagnosis of HIV / AIDS traditional Chinese medicine syndromes.
Collapse
Affiliation(s)
- Zhen LIU
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Qingyan ZHANG
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Bowen DENG
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Feng SANG
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Danni WANG
- 2 Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Ning KANG
- 3 Department of Obstetrics and Gynecology, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Jie LI
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Min ZHANG
- 2 Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Shoupei LIANG
- 4 Medical Department, Medical Department of Zhengzhou People’s Hospital, Zhengzhou 450000, China
| | - Chenchen DUAN
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Zhibin LIU
- 2 Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
| | - Qianlei XU
- 2 Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
- XU Qianlei, Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China.
| | - Qiang LI
- 1 Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
- XU Qianlei, Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China.
| |
Collapse
|
20
|
Fink DL, Cai J, Whelan MVX, Monit C, Maluquer de Motes C, Towers GJ, Sumner RP. HIV-2/SIV Vpx antagonises NF-κB activation by targeting p65. Retrovirology 2022; 19:2. [PMID: 35073912 PMCID: PMC8785589 DOI: 10.1186/s12977-021-00586-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/24/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The NF-κB family of transcription factors and associated signalling pathways are abundant and ubiquitous in human immune responses. Activation of NF-κB transcription factors by viral pathogen-associated molecular patterns, such as viral RNA and DNA, is fundamental to anti-viral innate immune defences and pro-inflammatory cytokine production that steers adaptive immune responses. Diverse non-viral stimuli, such as lipopolysaccharide and cytokines, also activate NF-κB and the same anti-pathogen gene networks. Viruses adapted to human cells often encode multiple proteins targeting the NF-κB pathway to mitigate the anti-viral effects of NF-κB-dependent host immunity. RESULTS In this study we have demonstrated using a variety of assays, in a number of different cell types including primary cells, that plasmid-encoded or virus-delivered simian immunodeficiency virus (SIV) accessory protein Vpx is a broad antagonist of NF-κB signalling active against diverse innate NF-κB agonists. Using targeted Vpx mutagenesis, we showed that this novel Vpx phenotype is independent of known Vpx cofactor DCAF1 and other cellular binding partners, including SAMHD1, STING and the HUSH complex. We found that Vpx co-immunoprecipitated with canonical NF-κB transcription factor p65, but not NF-κB family members p50 or p100, preventing nuclear translocation of p65. We found that broad antagonism of NF-κB activation by Vpx was conserved across distantly related lentiviruses as well as for Vpr from SIV Mona monkey (SIVmon), which has Vpx-like SAMHD1-degradation activity. CONCLUSIONS We have discovered a novel mechanism by which lentiviruses antagonise NF-κB activation by targeting p65. These findings extend our knowledge of how lentiviruses manipulate universal regulators of immunity to avoid the anti-viral sequelae of pro-inflammatory gene expression stimulated by both viral and extra-viral agonists. Importantly our findings are also relevant to the gene therapy field where virus-like particle associated Vpx is routinely used to enhance vector transduction through antagonism of SAMHD1, and perhaps also through manipulation of NF-κB.
Collapse
Affiliation(s)
- Douglas L Fink
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - James Cai
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Christopher Monit
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Carlos Maluquer de Motes
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Rebecca P Sumner
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK.
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
| |
Collapse
|
21
|
Martin MM, Matkovic R, Larrous P, Morel M, Lasserre A, Vauthier V, Margottin-Goguet F. Binding to DCAF1 distinguishes TASOR and SAMHD1 degradation by HIV-2 Vpx. PLoS Pathog 2021; 17:e1009609. [PMID: 34699574 PMCID: PMC8570500 DOI: 10.1371/journal.ppat.1009609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/05/2021] [Accepted: 10/15/2021] [Indexed: 01/18/2023] Open
Abstract
Human Immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) succeed to evade host immune defenses by using their viral auxiliary proteins to antagonize host restriction factors. HIV-2/SIVsmm Vpx is known for degrading SAMHD1, a factor impeding the reverse transcription. More recently, Vpx was also shown to counteract HUSH, a complex constituted of TASOR, MPP8 and periphilin, which blocks viral expression from the integrated viral DNA. In a classical ubiquitin ligase hijacking model, Vpx bridges the DCAF1 ubiquitin ligase substrate adaptor to SAMHD1, for subsequent ubiquitination and degradation. Here, we investigated whether the same mechanism is at stake for Vpx-mediated HUSH degradation. While we confirm that Vpx bridges SAMHD1 to DCAF1, we show that TASOR can interact with DCAF1 in the absence of Vpx. Nonetheless, this association was stabilized in the presence of Vpx, suggesting the existence of a ternary complex. The N-terminal PARP-like domain of TASOR is involved in DCAF1 binding, but not in Vpx binding. We also characterized a series of HIV-2 Vpx point mutants impaired in TASOR degradation, while still degrading SAMHD1. Vpx mutants ability to degrade TASOR correlated with their capacity to enhance HIV-1 minigenome expression as expected. Strikingly, several Vpx mutants impaired for TASOR degradation, but not for SAMHD1 degradation, had a reduced binding affinity for DCAF1, but not for TASOR. In macrophages, Vpx R34A-R42A and Vpx R42A-Q47A-V48A, strongly impaired in DCAF1, but not in TASOR binding, could not degrade TASOR, while being efficient in degrading SAMHD1. Altogether, our results highlight the central role of a robust Vpx-DCAF1 association to trigger TASOR degradation. We then propose a model in which Vpx interacts with both TASOR and DCAF1 to stabilize a TASOR-DCAF1 complex. Furthermore, our work identifies Vpx mutants enabling the study of HUSH restriction independently from SAMHD1 restriction in primary myeloid cells. Human Immunodeficiency Virus (HIV) is still a major public health issue. The understanding of the molecular battle occurring during viral infection, between HIV components and cellular antiviral factors, the so-called restriction factors, is a key determinant for new treatment development. Namely, HIV auxiliary proteins are powerful to induce the downregulation of cellular restriction factors by hijacking the Ubiquitin/proteasome pathway, in order to facilitate the completion of a well-processed HIV replication cycle. For instance, HIV-2 Vpx eases reverse transcription in myeloid cells by counteracting the SAMDH1 restriction factor. More recently, we discovered the ability of Vpx to induce the degradation of the HUSH epigenetic repressor complex to favor in turn, the expression of the provirus. In this study, we uncovered the mechanisms by which Vpx antagonizes TASOR, the core subunit of the HUSH complex. We highlighted key differences between Vpx-induced TASOR and SAMHD1 degradation. These findings will help to propose strategies to study or to target either HUSH or SAMHD1, especially in myeloid cells where SAMHD1 restriction operates.
Collapse
Affiliation(s)
| | - Roy Matkovic
- Institut Cochin, Université de Paris, INSERM U1016, Paris, France
| | - Pauline Larrous
- Institut Cochin, Université de Paris, INSERM U1016, Paris, France
| | - Marina Morel
- Institut Cochin, Université de Paris, INSERM U1016, Paris, France
| | | | | | | |
Collapse
|
22
|
Mohamed A, Bakir T, Al-Hawel H, Al-Sharif I, Bakheet R, Kouser L, Murugaiah V, Al-Mozaini M. HIV-2 Vpx neutralizes host restriction factor SAMHD1 to promote viral pathogenesis. Sci Rep 2021; 11:20984. [PMID: 34697376 PMCID: PMC8545964 DOI: 10.1038/s41598-021-00415-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 10/12/2021] [Indexed: 11/21/2022] Open
Abstract
SAMHD1, a human host factor found in myeloid cells which restricts HIV-1 replication. It depletes the dNTPs pool for viral cDNA syntheses, thus preventing the viral replication in the cells. The viral accessory protein, Vpx, exists only in SIVmac/HIV-2 particles. Vpx in SIVmac can induce proteosomal degradation of SAMHD1, which then leads to a decrease in the cytoplasmic dNTP pool. The protein-protein interaction between Vpx and SAMHD1 and its consequences are still unclear. Methods: In this study, we cloned, for the first time, Vpx gene from a HIV-2 infected patient and found up to 30% sequence variation compared to known HIV-2 strains. We then analyzed the role of SAMHD1 protein expression in transfected THP-1 and U937 cells by transfecting with the Vpx gene derived from SIVmac, HIV-2 from the NIH sample as well as HIV-2 from a Saudi patient. We found that Vpx gene expression led to reduced levels of intracellular SAMHD1. When the supernatants of the transfected cell lines were examined for secreted cytokines, chemokines and growth factors, Vpx expression seemed to be suppressive of pro-inflammatory response, and skewed the immune response towards an anti-inflammatory response. These results suggest that Vpx can act at two levels: clearance of intracellular restriction factor and suppression of cytokine storm: both aimed at long-term latency and host-pathogen stand-off, suggesting that Vpx is likely to be a potential therapeutic target.
Collapse
Affiliation(s)
- Ahlam Mohamed
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, PO Box 3354 (MBC-03), Riyadh, 11211, Kingdom of Saudi Arabia
| | - Talal Bakir
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Huda Al-Hawel
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, PO Box 3354 (MBC-03), Riyadh, 11211, Kingdom of Saudi Arabia
| | - Ibtihaj Al-Sharif
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, PO Box 3354 (MBC-03), Riyadh, 11211, Kingdom of Saudi Arabia
| | - Razan Bakheet
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, PO Box 3354 (MBC-03), Riyadh, 11211, Kingdom of Saudi Arabia
| | | | - Valarmathy Murugaiah
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
| | - Maha Al-Mozaini
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, PO Box 3354 (MBC-03), Riyadh, 11211, Kingdom of Saudi Arabia.
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
| |
Collapse
|
23
|
Bowen NE, Temple J, Shepard C, Oo A, Arizaga F, Kapoor-Vazirani P, Persaud M, Yu CH, Kim DH, Schinazi RF, Ivanov DN, Diaz-Griffero F, Yu DS, Xiong Y, Kim B. Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins. J Biol Chem 2021; 297:101170. [PMID: 34492268 PMCID: PMC8497992 DOI: 10.1016/j.jbc.2021.101170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Elevated intracellular levels of dNTPs have been shown to be a biochemical marker of cancer cells. Recently, a series of mutations in the multifunctional dNTP triphosphohydrolase (dNTPase), sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), have been reported in various cancers. Here, we investigated the structure and functions of SAMHD1 R366C/H mutants, found in colon cancer and leukemia. Unlike many other cancer-specific mutations, the SAMHD1 R366 mutations do not alter cellular protein levels of the enzyme. However, R366C/H mutant proteins exhibit a loss of dNTPase activity, and their X-ray structures demonstrate the absence of dGTP substrate in their active site, likely because of a loss of interaction with the γ-phosphate of the substrate. The R366C/H mutants failed to reduce intracellular dNTP levels and restrict HIV-1 replication, functions of SAMHD1 that are dependent on the ability of the enzyme to hydrolyze dNTPs. However, these mutants retain dNTPase-independent functions, including mediating dsDNA break repair, interacting with CtIP and cyclin A2, and suppressing innate immune responses. Finally, SAMHD1 degradation in human primary-activated/dividing CD4+ T cells further elevates cellular dNTP levels. This study suggests that the loss of SAMHD1 dNTPase activity induced by R366 mutations can mechanistically contribute to the elevated dNTP levels commonly found in cancer cells.
Collapse
Affiliation(s)
- Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Caitlin Shepard
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Fidel Arizaga
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Priya Kapoor-Vazirani
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Dong-Hyun Kim
- School of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David S Yu
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
| |
Collapse
|
24
|
Schott K, Majer C, Bulashevska A, Childs L, Schmidt MHH, Rajalingam K, Munder M, König R. SAMHD1 in cancer: curse or cure? J Mol Med (Berl) 2021; 100:351-372. [PMID: 34480199 PMCID: PMC8843919 DOI: 10.1007/s00109-021-02131-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/15/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Human sterile α motif and HD domain-containing protein 1 (SAMHD1), originally described as the major cellular deoxyribonucleoside triphosphate triphosphohydrolase (dNTPase) balancing the intracellular deoxynucleotide (dNTP) pool, has come recently into focus of cancer research. As outlined in this review, SAMHD1 has been reported to be mutated in a variety of cancer types and the expression of SAMHD1 is dysregulated in many cancers. Therefore, SAMHD1 is regarded as a tumor suppressor in certain tumors. Moreover, it has been proposed that SAMHD1 might fulfill the requirements of a driver gene in tumor development or might promote a so-called mutator phenotype. Besides its role as a dNTPase, several novel cellular functions of SAMHD1 have come to light only recently, including a role as negative regulator of innate immune responses and as facilitator of DNA end resection during DNA replication and repair. Therefore, SAMHD1 can be placed at the crossroads of various cellular processes. The present review summarizes the negative role of SAMHD1 in chemotherapy sensitivity, highlights reported SAMHD1 mutations found in various cancer types, and aims to discuss functional consequences as well as underlying mechanisms of SAMHD1 dysregulation potentially involved in cancer development.
Collapse
Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Catharina Majer
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Alla Bulashevska
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Liam Childs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mirko H H Schmidt
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, Dresden, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, Mainz, Germany
| | - Markus Munder
- Third Department of Medicine, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany.
| |
Collapse
|
25
|
Banchenko S, Krupp F, Gotthold C, Bürger J, Graziadei A, O’Reilly FJ, Sinn L, Ruda O, Rappsilber J, Spahn CMT, Mielke T, Taylor IA, Schwefel D. Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses. PLoS Pathog 2021; 17:e1009775. [PMID: 34339457 PMCID: PMC8360603 DOI: 10.1371/journal.ppat.1009775] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/12/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
Viruses have evolved means to manipulate the host's ubiquitin-proteasome system, in order to down-regulate antiviral host factors. The Vpx/Vpr family of lentiviral accessory proteins usurp the substrate receptor DCAF1 of host Cullin4-RING ligases (CRL4), a family of modular ubiquitin ligases involved in DNA replication, DNA repair and cell cycle regulation. CRL4DCAF1 specificity modulation by Vpx and Vpr from certain simian immunodeficiency viruses (SIV) leads to recruitment, poly-ubiquitylation and subsequent proteasomal degradation of the host restriction factor SAMHD1, resulting in enhanced virus replication in differentiated cells. To unravel the mechanism of SIV Vpr-induced SAMHD1 ubiquitylation, we conducted integrative biochemical and structural analyses of the Vpr protein from SIVs infecting Cercopithecus cephus (SIVmus). X-ray crystallography reveals commonalities between SIVmus Vpr and other members of the Vpx/Vpr family with regard to DCAF1 interaction, while cryo-electron microscopy and cross-linking mass spectrometry highlight a divergent molecular mechanism of SAMHD1 recruitment. In addition, these studies demonstrate how SIVmus Vpr exploits the dynamic architecture of the multi-subunit CRL4DCAF1 assembly to optimise SAMHD1 ubiquitylation. Together, the present work provides detailed molecular insight into variability and species-specificity of the evolutionary arms race between host SAMHD1 restriction and lentiviral counteraction through Vpx/Vpr proteins.
Collapse
Affiliation(s)
- Sofia Banchenko
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Ferdinand Krupp
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Christine Gotthold
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Francis J. O’Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ludwig Sinn
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Olga Ruda
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Christian M. T. Spahn
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David Schwefel
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| |
Collapse
|
26
|
Desrosiers V, Barat C, Breton Y, Ouellet M, Tremblay MJ. Thymidylate synthase is essential for efficient HIV-1 replication in macrophages. Virology 2021; 561:47-57. [PMID: 34146963 DOI: 10.1016/j.virol.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/09/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022]
Abstract
Thymidylate synthase (TS) is a key enzyme in nucleotide biosynthesis. A study performed by our group on human monocyte-derived macrophages (MDMs) infected with HIV-1 showed that many enzymes related to the folate cycle pathway, such as TS, are upregulated in productively infected cells. Here, we suggest that TS is essential for an effective HIV-1 infection in MDMs. Indeed, a TS specific small interfering RNA (siRNA) as well as the TS specific inhibitor Raltitrexed (RTX) caused a reduction in productively infected cells. Quantitative PCR analysis showed that this treatment decreased the efficacy of the early steps of the viral cycle. The RTX inhibitory effect was counteracted by dNTP addition. These results suggest that TS is essential for the early stages of HIV-1 infection by providing optimal dNTP concentrations in MDMs. TS and its related pathway may thus be considered as a potential therapeutic target for HIV-1 treatment.
Collapse
Affiliation(s)
- Vincent Desrosiers
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Corinne Barat
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Yann Breton
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Michel Ouellet
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Michel J Tremblay
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada; Département de Microbiologie-infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, G1V 0A6, Canada.
| |
Collapse
|
27
|
Coggins SA, Kim DH, Schinazi RF, Desrosier RC, Kim B. Enhanced enzyme kinetics of reverse transcriptase variants cloned from animals infected with SIVmac239 lacking viral protein X. J Biol Chem 2020; 295:16975-16986. [PMID: 33008888 PMCID: PMC7863885 DOI: 10.1074/jbc.ra120.015273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Type 1 (HIV-1) and simian immunodeficiency virus (SIV) display differential replication kinetics in macrophages. This is because high expression levels of the active host deoxynucleotide triphosphohydrolase sterile α motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) deplete intracellular dNTPs, which restrict HIV-1 reverse transcription, and result in a restrictive infection in this myeloid cell type. Some SIVs overcome SAMHD1 restriction using viral protein X (Vpx), a viral accessory protein that induces proteasomal degradation of SAMHD1, increasing cellular dNTP concentrations and enabling efficient proviral DNA synthesis. We previously reported that SAMHD1-noncounteracting lentiviruses may have evolved to harbor RT proteins that efficiently polymerize DNA, even at low dNTP concentrations, to circumvent SAMHD1 restriction. Here we investigated whether RTs from SIVmac239 virus lacking a Vpx protein evolve during in vivo infection to more efficiently synthesize DNA at the low dNTP concentrations found in macrophages. Sequence analysis of RTs cloned from Vpx (+) and Vpx (-) SIVmac239-infected animals revealed that Vpx (-) RTs contained more extensive mutations than Vpx (+) RTs. Although the amino acid substitutions were dispersed indiscriminately across the protein, steady-state and pre-steady-state analysis demonstrated that selected SIVmac239 Vpx (-) RTs are characterized by higher catalytic efficiency and incorporation efficiency values than RTs cloned from SIVmac239 Vpx (+) infections. Overall, this study supports the possibility that the loss of Vpx may generate in vivo SIVmac239 RT variants that can counteract the limited availability of dNTP substrate in macrophages.
Collapse
Affiliation(s)
- Si'Ana A Coggins
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Dong-Hyun Kim
- Department of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ronald C Desrosier
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
| |
Collapse
|
28
|
Resop RS, Fromentin R, Newman D, Rigsby H, Dubrovsky L, Bukrinsky M, Chomont N, Bosque A. Fingolimod inhibits multiple stages of the HIV-1 life cycle. PLoS Pathog 2020; 16:e1008679. [PMID: 32790802 PMCID: PMC7425850 DOI: 10.1371/journal.ppat.1008679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Antiretroviral drugs that target various stages of the Human Immunodeficiency Virus (HIV) life cycle have been effective in curbing the AIDS epidemic. However, drug resistance, off-target effects of antiretroviral therapy (ART), and varying efficacy in prevention underscore the need to develop novel and alternative therapeutics. In this study, we investigated whether targeting the signaling molecule Sphingosine-1-phosphate (S1P) would inhibit HIV-1 infection and generation of the latent reservoir in primary CD4 T cells. We show that FTY720 (Fingolimod), an FDA-approved functional antagonist of S1P receptors, blocks cell-free and cell-to-cell transmission of HIV and consequently reduces detectable latent virus. Mechanistically, FTY720 impacts the HIV-1 life cycle at two levels. Firstly, FTY720 reduces the surface density of CD4, thereby inhibiting viral binding and fusion. Secondly, FTY720 decreases the phosphorylation of the innate HIV restriction factor SAMHD1 which is associated with reduced levels of total and integrated HIV, while reducing the expression of Cyclin D3. In conclusion, targeting the S1P pathway with FTY720 could be a novel strategy to inhibit HIV replication and reduce the seeding of the latent reservoir.
Collapse
Affiliation(s)
- Rachel S. Resop
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Rémi Fromentin
- Centre de recherche du CHUM and Department of microbiology, infectiology and immunology, Université de Montréal, Montreal, Canada
| | - Daniel Newman
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Hawley Rigsby
- Centre de recherche du CHUM and Department of microbiology, infectiology and immunology, Université de Montréal, Montreal, Canada
| | - Larisa Dubrovsky
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Michael Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Nicolas Chomont
- Centre de recherche du CHUM and Department of microbiology, infectiology and immunology, Université de Montréal, Montreal, Canada
| | - Alberto Bosque
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
- * E-mail:
| |
Collapse
|
29
|
Benayas B, Sastre I, López-Martín S, Oo A, Kim B, Bullido MJ, Aldudo J, Yáñez-Mó M. Tetraspanin CD81 regulates HSV-1 infection. Med Microbiol Immunol 2020; 209:489-498. [PMID: 32500359 PMCID: PMC7271138 DOI: 10.1007/s00430-020-00684-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/27/2020] [Indexed: 02/08/2023]
Abstract
Different members of the tetraspanin superfamily have been described to regulate different virus infectious cycles at several stages: viral entry, viral replication or virion exit or infectivity. In addition, tetraspanin CD81 regulates HIV reverse transcription through its association with the dNTP hydrolase SAMHD1. Here we aimed at analysing the role of CD81 in Herpes simplex virus 1 infectivity using a neuroblastoma cell model. For this purpose, we generated a CD81 KO cell line using the CRISPR/Cas9 technology. Despite being CD81 a plasma membrane protein, CD81 KO cells showed no defects in viral entry nor in the expression of early protein markers. In contrast, glycoprotein B and C, which require viral DNA replication for their expression, were significantly reduced in CD81 KO infected cells. Indeed, HSV-1 DNA replication and the formation of new infectious particles were severely compromised in CD81 KO cells. We could not detect significant changes in SAMHD1 total expression levels, but a relocalization into endosomal structures was observed in CD81 KO cells. In summary, CD81 KO cells showed impaired viral DNA replication and produced greatly diminished viral titers.
Collapse
Affiliation(s)
- Beatriz Benayas
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), 28006, Madrid, Spain
| | - Isabel Sastre
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Investigacion Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Soraya López-Martín
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), 28006, Madrid, Spain
| | - Adrian Oo
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Maria J Bullido
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Investigacion Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto de Investigación Sanitaria "Hospital la Paz" (IdIPaz), Madrid, Spain
| | - Jesús Aldudo
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain.
- Centro de Investigacion Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Instituto de Investigación Sanitaria "Hospital la Paz" (IdIPaz), Madrid, Spain.
| | - María Yáñez-Mó
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain.
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), 28006, Madrid, Spain.
- Departamento de Bioquímica y Biología Molecular, UAM, Centro de Biología Molecular Severo Ochoa, Lab 412, C/Nicolás Cabrera, 1, 28049, Madrid, Spain.
| |
Collapse
|
30
|
Ferreira IATM, Porterfield JZ, Gupta RK, Mlcochova P. Cell Cycle Regulation in Macrophages and Susceptibility to HIV-1. Viruses 2020; 12:v12080839. [PMID: 32751972 PMCID: PMC7472357 DOI: 10.3390/v12080839] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Macrophages are the first line of defence against invading pathogens. They play a crucial role in immunity but also in regeneration and homeostasis. Their remarkable plasticity in their phenotypes and function provides them with the ability to quickly respond to environmental changes and infection. Recent work shows that macrophages undergo cell cycle transition from a G0/terminally differentiated state to a G1 state. This G0-to-G1 transition presents a window of opportunity for HIV-1 infection. Macrophages are an important target for HIV-1 but express high levels of the deoxynucleotide-triphosphate hydrolase SAMHD1, which restricts viral DNA synthesis by decreasing levels of dNTPs. While the G0 state is non-permissive to HIV-1 infection, a G1 state is very permissive to HIV-1 infection. This is because macrophages in a G1 state switch off the antiviral restriction factor SAMHD1 by phosphorylation, thereby allowing productive HIV-1 infection. Here, we explore the macrophage cell cycle and the interplay between its regulation and permissivity to HIV-1 infection.
Collapse
Affiliation(s)
- Isabella A. T. M. Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB20AW, UK; (I.A.T.M.F.); (R.K.G.)
- Department of Medicine, University of Cambridge, Cambridge CB20QQ, UK
| | - J. Zachary Porterfield
- Department of Microbiology, University of Kentucky, Lexington, KY 40536, USA;
- Africa Health Research Institute, Durban 4001, South Africa
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB20AW, UK; (I.A.T.M.F.); (R.K.G.)
- Department of Medicine, University of Cambridge, Cambridge CB20QQ, UK
- Africa Health Research Institute, Durban 4001, South Africa
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB20AW, UK; (I.A.T.M.F.); (R.K.G.)
- Department of Medicine, University of Cambridge, Cambridge CB20QQ, UK
- Correspondence:
| |
Collapse
|
31
|
Rothenburger T, McLaughlin KM, Herold T, Schneider C, Oellerich T, Rothweiler F, Feber A, Fenton TR, Wass MN, Keppler OT, Michaelis M, Cinatl J. SAMHD1 is a key regulator of the lineage-specific response of acute lymphoblastic leukaemias to nelarabine. Commun Biol 2020; 3:324. [PMID: 32581304 PMCID: PMC7314829 DOI: 10.1038/s42003-020-1052-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
The nucleoside analogue nelarabine, the prodrug of arabinosylguanine (AraG), is effective against T-cell acute lymphoblastic leukaemia (T-ALL) but not against B-cell ALL (B-ALL). The underlying mechanisms have remained elusive. Here, data from pharmacogenomics studies and a panel of ALL cell lines reveal an inverse correlation between nelarabine sensitivity and the expression of SAMHD1, which can hydrolyse and inactivate triphosphorylated nucleoside analogues. Lower SAMHD1 abundance is detected in T-ALL than in B-ALL in cell lines and patient-derived leukaemic blasts. Mechanistically, T-ALL cells display increased SAMHD1 promoter methylation without increased global DNA methylation. SAMHD1 depletion sensitises B-ALL cells to AraG, while ectopic SAMHD1 expression in SAMHD1-null T-ALL cells induces AraG resistance. SAMHD1 has a larger impact on nelarabine/AraG than on cytarabine in ALL cells. Opposite effects are observed in acute myeloid leukaemia cells, indicating entity-specific differences. In conclusion, SAMHD1 promoter methylation and, in turn, SAMHD1 expression levels determine ALL cell response to nelarabine.
Collapse
Affiliation(s)
- Tamara Rothenburger
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
| | | | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistraße 15, 81377, Munich, Germany
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Feodor-Lynenstraße 21, 81377, Munich, Germany
| | - Constanze Schneider
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
- Department of Medicine II, Hematology/Oncology, Goethe-Universität, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Cancer Consortium/German Cancer Research Center, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Florian Rothweiler
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Oliver T Keppler
- Faculty of Medicine, Max von Pettenkofer Institute, Virology, LMU München, Pettenkoferstraße 9a, 80336, Munich, Germany
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Jindrich Cinatl
- Institut für Medizinische Virologie, Klinikum der Goethe-Universität, Paul Ehrlich-Straße 40, 60596, Frankfurt am Main, Germany.
| |
Collapse
|
32
|
Davenne T, Klintman J, Sharma S, Rigby RE, Blest HTW, Cursi C, Bridgeman A, Dadonaite B, De Keersmaecker K, Hillmen P, Chabes A, Schuh A, Rehwinkel J. SAMHD1 Limits the Efficacy of Forodesine in Leukemia by Protecting Cells against the Cytotoxicity of dGTP. Cell Rep 2020; 31:107640. [PMID: 32402273 PMCID: PMC7225753 DOI: 10.1016/j.celrep.2020.107640] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
The anti-leukemia agent forodesine causes cytotoxic overload of intracellular deoxyguanosine triphosphate (dGTP) but is efficacious only in a subset of patients. We report that SAMHD1, a phosphohydrolase degrading deoxyribonucleoside triphosphate (dNTP), protects cells against the effects of dNTP imbalances. SAMHD1-deficient cells induce intrinsic apoptosis upon provision of deoxyribonucleosides, particularly deoxyguanosine (dG). Moreover, dG and forodesine act synergistically to kill cells lacking SAMHD1. Using mass cytometry, we find that these compounds kill SAMHD1-deficient malignant cells in patients with chronic lymphocytic leukemia (CLL). Normal cells and CLL cells from patients without SAMHD1 mutation are unaffected. We therefore propose to use forodesine as a precision medicine for leukemia, stratifying patients by SAMHD1 genotype or expression.
Collapse
Affiliation(s)
- Tamara Davenne
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Jenny Klintman
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Rachel E Rigby
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Henry T W Blest
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chiara Cursi
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Bernadeta Dadonaite
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Peter Hillmen
- St James' Institute of Oncology, St James' University Hospital, Leeds LS9 7TF, UK
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Anna Schuh
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Department of Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK; Department of Haematology, Oxford University Hospitals NHS Trust, Oxford OX3 7JL, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
33
|
Mlcochova P, Winstone H, Zuliani-Alvarez L, Gupta RK. TLR4-Mediated Pathway Triggers Interferon-Independent G0 Arrest and Antiviral SAMHD1 Activity in Macrophages. Cell Rep 2020; 30:3972-3980.e5. [PMID: 32209460 PMCID: PMC7109521 DOI: 10.1016/j.celrep.2020.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/09/2020] [Accepted: 02/28/2020] [Indexed: 12/20/2022] Open
Abstract
Macrophages exist predominantly in two distinct states, G0 and a G1-like state that is accompanied by phosphorylation of SAMHD1 at T592. Here, we demonstrate that Toll-like receptor 4 (TLR4) activation can potently induce G0 arrest and SAMHD1 antiretroviral activity by an interferon (IFN)-independent pathway. This pathway requires TLR4 engagement with TRIF, but not involvement of TBK1 or IRF3. Exclusive Myd88 activators are unable to trigger G0 arrest or SAMHD1 dephosphorylation, demonstrating this arrest is also Myd88/nuclear factor κB (NF-κB) independent. The G0 arrest is accompanied by p21 upregulation and CDK1 depletion, consistent with the observed SAMHD1 dephosphorylation at T592. Furthermore, we show by SAMHD1 knockdown that the TLR4-activated pathway potently blocks HIV-1 infection in macrophages specifically via SAMHD1. Together, these data demonstrate that macrophages can mobilize an intrinsic cell arrest and anti-viral state by activating TLR4 prior to IFN secretion, thereby highlighting the importance of cell-cycle regulation as a response to pathogen-associated danger signals in macrophages.
Collapse
Affiliation(s)
- Petra Mlcochova
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, KwaZulu Natal, South Africa.
| |
Collapse
|
34
|
Rudd SG, Tsesmetzis N, Sanjiv K, Paulin CBJ, Sandhow L, Kutzner J, Hed Myrberg I, Bunten SS, Axelsson H, Zhang SM, Rasti A, Mäkelä P, Coggins SA, Tao S, Suman S, Branca RM, Mermelekas G, Wiita E, Lee S, Walfridsson J, Schinazi RF, Kim B, Lehtiö J, Rassidakis GZ, Pokrovskaja Tamm K, Warpman‐Berglund U, Heyman M, Grandér D, Lehmann S, Lundbäck T, Qian H, Henter J, Schaller T, Helleday T, Herold N. Ribonucleotide reductase inhibitors suppress SAMHD1 ara-CTPase activity enhancing cytarabine efficacy. EMBO Mol Med 2020; 12:e10419. [PMID: 31950591 PMCID: PMC7059017 DOI: 10.15252/emmm.201910419] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 01/23/2023] Open
Abstract
The deoxycytidine analogue cytarabine (ara-C) remains the backbone treatment of acute myeloid leukaemia (AML) as well as other haematological and lymphoid malignancies, but must be combined with other chemotherapeutics to achieve cure. Yet, the underlying mechanism dictating synergistic efficacy of combination chemotherapy remains largely unknown. The dNTPase SAMHD1, which regulates dNTP homoeostasis antagonistically to ribonucleotide reductase (RNR), limits ara-C efficacy by hydrolysing the active triphosphate metabolite ara-CTP. Here, we report that clinically used inhibitors of RNR, such as gemcitabine and hydroxyurea, overcome the SAMHD1-mediated barrier to ara-C efficacy in primary blasts and mouse models of AML, displaying SAMHD1-dependent synergy with ara-C. We present evidence that this is mediated by dNTP pool imbalances leading to allosteric reduction of SAMHD1 ara-CTPase activity. Thus, SAMHD1 constitutes a novel biomarker for combination therapies of ara-C and RNR inhibitors with immediate consequences for clinical practice to improve treatment of AML.
Collapse
|
35
|
Xu D, Leister D, Kleine T. VENOSA4, a Human dNTPase SAMHD1 Homolog, Contributes to Chloroplast Development and Abiotic Stress Tolerance. Plant Physiol 2020; 182:721-729. [PMID: 31792148 PMCID: PMC6997687 DOI: 10.1104/pp.19.01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/12/2019] [Indexed: 05/07/2023]
Abstract
Chloroplast biogenesis depends on an extensive interplay between the nucleus, cytosol, and chloroplasts, involving regulatory nucleus-encoded chloroplast proteins, as well as nucleocytosolic photoreceptors such as phytochromes (phys) and other extrachloroplastic factors. However, this whole process is only partially understood. Here, we describe the role of VENOSA4 (VEN4) in chloroplast development and acclimation to adverse growth conditions. A 35S:VEN4-eGFP fusion protein localizes to the nucleus in Arabidopsis (Arabidopsis thaliana) protoplasts, and VEN4 homologs are present in a wide range of eukaryotes including humans, where the corresponding homolog (SAMHD1) cleaves dNTPs. Defective photosynthesis in ven4 seedlings results from reduced accumulation of photosynthetic proteins and appears to be caused by a reduction in the translational capacity of chloroplasts. The negative effect of the ven4 mutation on photosynthesis can be phenotypically suppressed by germinating seeds in the presence of excess dCTP or a pool of dNTPs, implying that VEN4, like human SAMHD1, is involved in dNTP catabolism. Moreover, VEN4 activity is also required for optimal responses to cold and salt stresses. In conclusion, our work emphasizes the importance of the nucleocytosolic compartment and the fine-tuning of dNTP levels for chloroplast translation and development.
Collapse
Affiliation(s)
- Duorong Xu
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
36
|
Oo A, Kim DH, Schinazi RF, Kim B. Viral protein X reduces the incorporation of mutagenic noncanonical rNTPs during lentivirus reverse transcription in macrophages. J Biol Chem 2020; 295:657-666. [PMID: 31806704 PMCID: PMC6956541 DOI: 10.1074/jbc.ra119.011466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/02/2019] [Indexed: 11/21/2022] Open
Abstract
Unlike activated CD4+ T cells, nondividing macrophages have an extremely small dNTP pool, which restricts HIV-1 reverse transcription. However, rNTPs are equally abundant in both of these cell types and reach much higher concentrations than dNTPs. The greater difference in concentration between dNTPs and rNTPs in macrophages results in frequent misincorporation of noncanonical rNTPs during HIV-1 reverse transcription. Here, we tested whether the highly abundant SAM domain- and HD domain-containing protein 1 (SAMHD1) deoxynucleoside triphosphorylase in macrophages is responsible for frequent rNTP incorporation during HIV-1 reverse transcription. We also assessed whether Vpx (viral protein X), an accessory protein of HIV-2 and some simian immunodeficiency virus strains that targets SAMHD1 for proteolytic degradation, can counteract the rNTP incorporation. Results from biochemical simulation of HIV-1 reverse transcriptase-mediated DNA synthesis confirmed that rNTP incorporation is reduced under Vpx-mediated dNTP elevation. Using HIV-1 vector, we further demonstrated that dNTP pool elevation by Vpx or deoxynucleosides in human primary monocyte-derived macrophages reduces noncanonical rNTP incorporation during HIV-1 reverse transcription, an outcome similarly observed with the infectious HIV-1 89.6 strain. Furthermore, the simian immunodeficiency virus mac239 strain, encoding Vpx, displayed a much lower level of rNTP incorporation than its ΔVpx mutant in macrophages. Finally, the amount of rNMPs incorporated in HIV-1 proviral DNAs remained unchanged for ∼2 weeks in macrophages. These findings suggest that noncanonical rNTP incorporation is regulated by SAMHD1 in macrophages, whereas rNMPs incorporated in HIV-1 proviral DNA remain unrepaired. This suggests a potential long-term DNA damage impact of SAMHD1-mediated rNTP incorporation in macrophages.
Collapse
Affiliation(s)
- Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Dong-Hyun Kim
- Department of Pharmacy, Kyung Hee University, Seoul 02447, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia 30322; Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, Georgia 30322.
| |
Collapse
|
37
|
Wang Z, Bhattacharya A, White T, Buffone C, McCabe A, Nguyen LA, Shepard CN, Pardo S, Kim B, Weintraub ST, Demeler B, Diaz-Griffero F, Ivanov DN. Functionality of Redox-Active Cysteines Is Required for Restriction of Retroviral Replication by SAMHD1. Cell Rep 2020; 24:815-823. [PMID: 30044979 PMCID: PMC6067006 DOI: 10.1016/j.celrep.2018.06.090] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/01/2018] [Accepted: 06/21/2018] [Indexed: 01/04/2023] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase (dNTPase) that impairs retroviral replication in a subset of noncycling immune cells. Here we show that SAMHD1 is a redox-sensitive enzyme and identify three redox-active cysteines within the protein: C341, C350, and C522. The three cysteines reside near one another and the allosteric nucleotide binding site. Mutations C341S and C522S abolish the ability of SAMHD1 to restrict HIV replication, whereas the C350S mutant remains restriction competent. The C522S mutation makes the protein resistant to inhibition by hydrogen peroxide but has no effect on the tetramerization-dependent dNTPase activity of SAMHD1 in vitro or on the ability of SAMHD1 to deplete cellular dNTPs. Our results reveal that enzymatic activation of SAMHD1 via nucleotide-dependent tetramerization is not sufficient for the establishment of the antiviral state and that retroviral restriction depends on the ability of the protein to undergo redox transformations.
Collapse
Affiliation(s)
- Zhonghua Wang
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Akash Bhattacharya
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Tommy White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aine McCabe
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura A Nguyen
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Caitlin N Shepard
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Sammy Pardo
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA; School of Pharmacy, Kyunghee University, Seoul, South Korea
| | - Susan T Weintraub
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Borries Demeler
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Dmitri N Ivanov
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA.
| |
Collapse
|
38
|
Monit C, Morris ER, Ruis C, Szafran B, Thiltgen G, Tsai MHC, Mitchison NA, Bishop KN, Stoye JP, Taylor IA, Fassati A, Goldstein RA. Positive selection in dNTPase SAMHD1 throughout mammalian evolution. Proc Natl Acad Sci U S A 2019; 116:18647-18654. [PMID: 31451672 PMCID: PMC6744909 DOI: 10.1073/pnas.1908755116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The vertebrate protein SAMHD1 is highly unusual in having roles in cellular metabolic regulation, antiviral restriction, and regulation of innate immunity. Its deoxynucleoside triphosphohydrolase activity regulates cellular dNTP concentration, reducing levels below those required by lentiviruses and other viruses to replicate. To counter this threat, some primate lentiviruses encode accessory proteins that bind SAMHD1 and induce its degradation; in turn, positive diversifying selection has been observed in regions bound by these lentiviral proteins, suggesting that primate SAMHD1 has coevolved to evade these countermeasures. Moreover, deleterious polymorphisms in human SAMHD1 are associated with autoimmune disease linked to uncontrolled DNA synthesis of endogenous retroelements. Little is known about how evolutionary pressures affect these different SAMHD1 functions. Here, we examine the deeper history of these interactions by testing whether evolutionary signatures in SAMHD1 extend to other mammalian groups and exploring the molecular basis of this coevolution. Using codon-based likelihood models, we find positive selection in SAMHD1 within each mammal lineage for which sequence data are available. We observe positive selection at sites clustered around T592, a residue that is phosphorylated to regulate SAMHD1 activity. We verify experimentally that mutations within this cluster affect catalytic rate and lentiviral restriction, suggesting that virus-host coevolution has required adaptations of enzymatic function. Thus, persistent positive selection may have involved the adaptation of SAMHD1 regulation to balance antiviral, metabolic, and innate immunity functions.
Collapse
Affiliation(s)
- Christopher Monit
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Christopher Ruis
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Bart Szafran
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Grant Thiltgen
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Ming-Han Chloe Tsai
- Retroviral Replication Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - N Avrion Mitchison
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Kate N Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Ariberto Fassati
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom;
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom;
| |
Collapse
|
39
|
Jiang H, Li C, Liu Z. Expression and Relationship of SAMHD1 with Other Apoptotic and Autophagic Genes in Acute Myeloid Leukemia Patients. Acta Haematol 2019; 143:51-59. [PMID: 31434075 DOI: 10.1159/000500822] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND SAM domain- and HD domain-containing protein 1 (SAMHD1) is a cellular enzyme which is responsible for blocking replication in viruses and participates in the progression of many cancers. OBJECTIVE The aim of this study was to correlate the expression level of SAMHD1 with other apoptotic and autophagic genes in acute myeloid leukemia (AML) patients. METHODS In the present study, mRNA levels of SAMHD1 with other apoptotic and autophagic-related genes were evaluated in patients who were newly diagnosed with AML. RESULTS SAMHD1, Bcl-xl, Bax, Bak, XIAP, and cIAP1 were downregulated in the AML group compared to the non-AML group (p < 0.05). SAMHD1 expression did not correlate with the other genes, while most apoptotic genes were positively correlated with each other. SAMHD1 expression was not associated with the blood routine or blast percentage of the AML patients, while Bax, Bak, cIAP2, and LC3 were significantly correlated with white blood cells. No statistically significant differences were found between the studied genes and prognosis stratifications, but Bcl-xl, Bak, cIAP1, and Mcl-1, LC3 were expressed at lower levels in the unfavorable AML group compared to the controls. CONCLUSION SAMHD1 and Bcl-xl, Bax, Bak, XIAP, and cIAP1 were downregulated in AML patients, while there were no significant differences in the clinical characteristics and prognosis with reference to SAMHD1 expression.
Collapse
Affiliation(s)
- Huinan Jiang
- Hematology Department, Shengjing Hospital, China Medical University, Shenyang, China
| | - Chuan Li
- Hematology Department, Shengjing Hospital, China Medical University, Shenyang, China
| | - Zhuogang Liu
- Hematology Department, Shengjing Hospital, China Medical University, Shenyang, China
| |
Collapse
|
40
|
Xu X, Li M, Li D, Jiang Z, Liu C, Shi X, Wu C, Chen X, Lin G, Hu C. Identification of the SAMHD1 gene in grass carp and its roles in inducing apoptosis and inhibiting GCRV proliferation. Fish Shellfish Immunol 2019; 88:606-618. [PMID: 30885743 DOI: 10.1016/j.fsi.2019.03.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
SAMHD1 is an innate immunity restriction factor that inhibits virus infection through IRF3-mediated antiviral and apoptotic responses. Fish SAMHD1 shares some similar properties with those in mammals. In this study, a SAMHD1 orthologue from grass carp (Ctenopharyngodon idellus) was cloned and characterized. The full-length cDNA of CiSAMHD1 is 2792 bp with an ORF of 1884 bp encoding a polypeptide of 627 amino acids. Multiple alignments showed that SAMHD1 is highly conserved among different species. Phylogenetic tree analysis revealed that CiSAMHD1 shared a high degree of homology with Sinocyclocheilus rhinocerous SAMHD1. Expression analysis indicated that CiSAMHD1 was widely expressed in all tissues tested including the brain, eyes, spleen, gill, intestine, liver, heart and kidney. It was significantly up-regulated in spleen, liver and intestines after treatment with poly I:C. Also, CiSAMHD1 can be induced following stimulation with recombinant IFN in CIK cells. The promoter sequence of CiSAMHD1 was identified to explore the mechanism underlying the transcriptional regulation of CiSAMHD1. The promoter sequence of CiSAMHD1 (1370 bp) consists of IRF1, IRF3, IRF9 and p65 binding elements. Gel mobility shift assay also showed that IRF1, IRF3, IRF9 and p65 prokaryotic proteins can separately interact with CiSAMHD1 promoter. Dual luciferase assay and q-PCR suggested that the promoter of CiSAMHD1 can be activated by the overexpression of CiIRF3 and CiIRF9, but cannot be triggered by CiIRF1 and Cip65. In contrast, knockdown of CiIRF3 or CiIRF9 inhibits the transcription of CiSAMHD1. Intriguingly, CCK assay suggested that CiSAMHD1 decreased cell viability. TUNEL apoptosis assay and Hoechst 33258 staining assay indicated that apoptosis is induced by the overexpression of CiSAMHD1. Crystal violet staining, detection of two GCRV genes (vp3 and vp5) and viral titration showed that CiSAMHD1 can suppress the proliferation of grass carp reovirus (GCRV) in CIK cells.
Collapse
Affiliation(s)
- Xiaowen Xu
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Meifeng Li
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Dongming Li
- Fuzhou Medical College, Nanchang University, Fuzhou 344000, China
| | - Zeyin Jiang
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Changxin Liu
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xiao Shi
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chuxin Wu
- Yuzhang Normal University, Nanchang 330031, China
| | - Xingxing Chen
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Gang Lin
- College of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Chengyu Hu
- College of Life Science, Nanchang University, Nanchang, 330031, China.
| |
Collapse
|
41
|
Szaniawski MA, Spivak AM, Bosque A, Planelles V. Sex Influences SAMHD1 Activity and Susceptibility to Human Immunodeficiency Virus-1 in Primary Human Macrophages. J Infect Dis 2019; 219:777-785. [PMID: 30299483 PMCID: PMC6376916 DOI: 10.1093/infdis/jiy583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/04/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Macrophages are major targets for HIV-1, contribute to viral propagation in vivo, and are instrumental in the pathogenesis of HAND. While it is known that host sex affects HIV-1 viremia and influences the severity of HIV-1-associated neurocognitive disease, a cellular or molecular basis for these findings remains elusive. METHODS We explored whether sex affects HIV-1 infectivity of primary human macrophages and CD4+ T cells in vitro. RESULTS Macrophages derived from female donors were less susceptible to HIV-1 infection than those derived from males. This sex-dependent difference in macrophage infectivity was independent of the requirement for CD4/CCR5-mediated virus entry and was not observed in CD4+ T cells. Investigations into the mechanism governing these sex-dependent differences revealed that the host restriction factor SAMHD1 exists in a hyperphosphorylated, less active state in male-derived macrophages. In addition, the major kinase responsible for SAMHD1 phosphorylation, CDK1, exhibited lower levels of expression in female-derived macrophages in all tested donor pairs. The sex-dependent differences in viral restriction imposed by SAMHD1 were abrogated upon its depletion. CONCLUSIONS We conclude that SAMHD1 is an essential modulator of infectivity in a sex-dependent manner in macrophages, constituting a novel component of sex differences in innate immune control of HIV-1.
Collapse
Affiliation(s)
- Matthew A Szaniawski
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine
| | - Adam M Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City
| | - Alberto Bosque
- Department of Microbiology Immunology and Tropical Medicine, George Washington University, Washington, District of Columbia
| | - Vicente Planelles
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine
| |
Collapse
|
42
|
Martinez-Lopez A, Martin-Fernandez M, Buta S, Kim B, Bogunovic D, Diaz-Griffero F. SAMHD1 deficient human monocytes autonomously trigger type I interferon. Mol Immunol 2018; 101:450-460. [PMID: 30099227 DOI: 10.1016/j.molimm.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023]
Abstract
Germline mutations in the human SAMHD1 gene cause the development of Aicardi-Goutières Syndrome (AGS), with a dominant feature being increased systemic type I interferon(IFN) production. Here we tested the state of type I IFN induction and response to, in SAMHD1 knockout (KO) human monocytic cells. SAMHD1 KO cells exhibited spontaneous transcription and translation of IFN-β and subsequent interferon-stimulated genes (ISGs) as compared to parental wild-type cells. This elevation of IFN-β and ISGs was abrogated via inhibition of the TBK1-IRF3 pathway in the SAMHD1 KO cells. In agreement, we found that SAMHD1 KO cells present high levels of phosphorylated TBK1 when compared to control cells. Moreover, addition of blocking antibody against type I IFN also reversed elevation of ISGs. These experiments suggested that SAMHD1 KO cells are persistently auto-stimulating the TBK1-IRF3 pathway, leading to an enhanced production of type I IFN and subsequent self-induction of ISGs.
Collapse
Affiliation(s)
- Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Marta Martin-Fernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Sofija Buta
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Baek Kim
- Department of Pediatrics, Emory University, Atlanta, GA 30322, United States
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
| |
Collapse
|
43
|
Antonucci JM, Kim SH, St Gelais C, Bonifati S, Li TW, Buzovetsky O, Knecht KM, Duchon AA, Xiong Y, Musier-Forsyth K, Wu L. SAMHD1 Impairs HIV-1 Gene Expression and Negatively Modulates Reactivation of Viral Latency in CD4 + T Cells. J Virol 2018; 92:e00292-18. [PMID: 29793958 PMCID: PMC6052313 DOI: 10.1128/jvi.00292-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/15/2018] [Indexed: 11/20/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) restricts human immunodeficiency virus type 1 (HIV-1) replication in nondividing cells by degrading intracellular deoxynucleoside triphosphates (dNTPs). SAMHD1 is highly expressed in resting CD4+ T cells, which are important for the HIV-1 reservoir and viral latency; however, whether SAMHD1 affects HIV-1 latency is unknown. Recombinant SAMHD1 binds HIV-1 DNA or RNA fragments in vitro, but the function of this binding remains unclear. Here we investigate the effect of SAMHD1 on HIV-1 gene expression and reactivation of viral latency. We found that endogenous SAMHD1 impaired HIV-1 long terminal repeat (LTR) activity in monocytic THP-1 cells and HIV-1 reactivation in latently infected primary CD4+ T cells. Overexpression of wild-type (WT) SAMHD1 suppressed HIV-1 LTR-driven gene expression at a transcriptional level. Tat coexpression abrogated SAMHD1-mediated suppression of HIV-1 LTR-driven luciferase expression. SAMHD1 overexpression also suppressed the LTR activity of human T-cell leukemia virus type 1 (HTLV-1), but not that of murine leukemia virus (MLV), suggesting specific suppression of retroviral LTR-driven gene expression. WT SAMHD1 bound to proviral DNA and impaired reactivation of HIV-1 gene expression in latently infected J-Lat cells. In contrast, a nonphosphorylated mutant (T592A) and a dNTP triphosphohydrolase (dNTPase) inactive mutant (H206D R207N [HD/RN]) of SAMHD1 failed to efficiently suppress HIV-1 LTR-driven gene expression and reactivation of latent virus. Purified recombinant WT SAMHD1, but not the T592A and HD/RN mutants, bound to fragments of the HIV-1 LTR in vitro These findings suggest that SAMHD1-mediated suppression of HIV-1 LTR-driven gene expression potentially regulates viral latency in CD4+ T cells.IMPORTANCE A critical barrier to developing a cure for HIV-1 infection is the long-lived viral reservoir that exists in resting CD4+ T cells, the main targets of HIV-1. The viral reservoir is maintained through a variety of mechanisms, including regulation of the HIV-1 LTR promoter. The host protein SAMHD1 restricts HIV-1 replication in nondividing cells, but its role in HIV-1 latency remains unknown. Here we report a new function of SAMHD1 in regulating HIV-1 latency. We found that SAMHD1 suppressed HIV-1 LTR promoter-driven gene expression and reactivation of viral latency in cell lines and primary CD4+ T cells. Furthermore, SAMHD1 bound to the HIV-1 LTR in vitro and in a latently infected CD4+ T-cell line, suggesting that the binding may negatively modulate reactivation of HIV-1 latency. Our findings indicate a novel role for SAMHD1 in regulating HIV-1 latency, which enhances our understanding of the mechanisms regulating proviral gene expression in CD4+ T cells.
Collapse
Affiliation(s)
- Jenna M Antonucci
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Sun Hee Kim
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Corine St Gelais
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Serena Bonifati
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Tai-Wei Li
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Olga Buzovetsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Alice A Duchon
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Karin Musier-Forsyth
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Li Wu
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
44
|
Tramentozzi E, Ferraro P, Hossain M, Stillman B, Bianchi V, Pontarin G. The dNTP triphosphohydrolase activity of SAMHD1 persists during S-phase when the enzyme is phosphorylated at T592. Cell Cycle 2018; 17:1102-1114. [PMID: 30039733 PMCID: PMC6110608 DOI: 10.1080/15384101.2018.1480216] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 06/01/2018] [Accepted: 05/16/2018] [Indexed: 01/31/2023] Open
Abstract
SAMHD1 is the major catabolic enzyme regulating the intracellular concentrations of DNA precursors (dNTPs). The S-phase kinase CDK2-cyclinA phosphorylates SAMHD1 at Thr-592. How this modification affects SAMHD1 function is highly debated. We investigated the role of endogenous SAMHD1 phosphorylation during the cell cycle. Thr-592 phosphorylation occurs first at the G1/S border and is removed during mitotic exit parallel with Thr-phosphorylations of most CDK1 targets. Differential sensitivity to the phosphatase inhibitor okadaic acid suggested different involvement of the PP1 and PP2 families dependent upon the time of the cell cycle. SAMHD1 turn-over indicates that Thr-592 phosphorylation does not cause rapid protein degradation. Furthermore, SAMHD1 influenced the size of the four dNTP pools independently of its phosphorylation. Our findings reveal that SAMHD1 is active during the entire cell cycle and performs an important regulatory role during S-phase by contributing with ribonucleotide reductase to maintain dNTP pool balance for proper DNA replication.
Collapse
Affiliation(s)
| | - Paola Ferraro
- Department of Biology, University of Padova, Padova, Italy
| | - Manzar Hossain
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Vera Bianchi
- Department of Biology, University of Padova, Padova, Italy
| | - Giovanna Pontarin
- Department of Biology, University of Padova, Padova, Italy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| |
Collapse
|
45
|
Roesch F, OhAinle M, Emerman M. A CRISPR screen for factors regulating SAMHD1 degradation identifies IFITMs as potent inhibitors of lentiviral particle delivery. Retrovirology 2018; 15:26. [PMID: 29554922 PMCID: PMC5859395 DOI: 10.1186/s12977-018-0409-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
The InterFeron Induced TransMembrane (IFITM) proteins are interferon stimulated genes that restrict many viruses, including HIV-1. SAMHD1 is another restriction factor blocking replication of HIV-1 and other viruses. Some lentiviruses evolved Vpx/Vpr proteins to degrade SAMHD1. However, this viral antagonism can be perturbed by host mechanisms: a recent study showed that in interferon (IFN) treated THP1 cells, Vpx is unable to degrade SAMHD1. In the present work, we designed an Interferon Stimulated Genes (ISGs)-targeted CRISPR knockout screen in order to identify ISGs regulating this phenotype. We found that IFITM proteins contribute to the IFNα-mediated protection of SAMHD1 by blocking VSV-G-mediated entry of the lentiviral particles delivering Vpx. Consistent with this, IFNα treatment and IFITM expression had no effect when the A-MLV envelope was used for pseudotyping. Using an assay measuring viral entry, we show that IFNα and IFITMs directly block the delivery of Vpx into cells by inhibiting VSV-G viral fusion. Strikingly, the VSV-G envelope was significantly more sensitive to this IFNα entry block and to IFITMs than HIV-1's natural envelope. This highlights important differences between VSV-G pseudotyped and wild-type HIV-1, in particular relative to the pathways they use for viral entry, suggesting that HIV-1 may have evolved to escape restriction factors blocking entry.
Collapse
Affiliation(s)
- Ferdinand Roesch
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Mailstop C2-023, Seattle, WA 98109 USA
| | - Molly OhAinle
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Mailstop C2-023, Seattle, WA 98109 USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Mailstop C2-023, Seattle, WA 98109 USA
| |
Collapse
|
46
|
Oh C, Ryoo J, Park K, Kim B, Daly MB, Cho D, Ahn K. A central role for PI3K-AKT signaling pathway in linking SAMHD1-deficiency to the type I interferon signature. Sci Rep 2018; 8:84. [PMID: 29311560 PMCID: PMC5758801 DOI: 10.1038/s41598-017-18308-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/08/2017] [Indexed: 11/08/2022] Open
Abstract
The autoimmune disorder Aicardi-Goutières syndrome (AGS) is characterized by a constitutive type I interferon response. SAMHD1 possesses both dNTPase and RNase activities and mutations in SAMHD1 cause AGS; however, how SAMHD1-deficiency causes the type I interferon response in patients with AGS remains unknown. Here, we show that endogenous RNA substrates accumulated in the absence of SAMHD1 act as a major immunogenic source for the type I interferon response. Reconstitution of SAMHD1-negative human cells with wild-type but not RNase-defective SAMHD1 abolishes spontaneous type I interferon induction. We further identify that the PI3K/AKT/IRF3 signaling pathway is essential for the type I interferon response in SAMHD1-deficient human monocytic cells. Treatment of PI3K or AKT inhibitors dramatically reduces the type I interferon signatures in SAMHD1-deficient cells. Moreover, SAMHD1/AKT1 double knockout relieves the type I interferon signatures to the levels observed for wild-type cells. Identification of AGS-related RNA sensing pathway provides critical insights into the molecular pathogenesis of the type I interferonopathies such as AGS and overlapping autoimmune disorders.
Collapse
Affiliation(s)
- Changhoon Oh
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Department of the Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeongmin Ryoo
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Kiwon Park
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
| | - Michele B Daly
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
| | - DongYeon Cho
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Kwangseog Ahn
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea.
| |
Collapse
|
47
|
Mlcochova P, Caswell SJ, Taylor IA, Towers GJ, Gupta RK. DNA damage induced by topoisomerase inhibitors activates SAMHD1 and blocks HIV-1 infection of macrophages. EMBO J 2018; 37:50-62. [PMID: 29084722 PMCID: PMC5753034 DOI: 10.15252/embj.201796880] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
We report that DNA damage induced by topoisomerase inhibitors, including etoposide (ETO), results in a potent block to HIV-1 infection in human monocyte-derived macrophages (MDM). SAMHD1 suppresses viral reverse transcription (RT) through depletion of cellular dNTPs but is naturally switched off by phosphorylation in a subpopulation of MDM found in a G1-like state. We report that SAMHD1 was activated by dephosphorylation following ETO treatment, along with loss of expression of MCM2 and CDK1, and reduction in dNTP levels. Suppression of infection occurred after completion of viral DNA synthesis, at the step of 2LTR circle and provirus formation. The ETO-induced block was completely rescued by depletion of SAMHD1 in MDM Concordantly, infection by HIV-2 and SIVsm encoding the SAMHD1 antagonist Vpx was insensitive to ETO treatment. The mechanism of DNA damage-induced blockade of HIV-1 infection involved activation of p53, p21, decrease in CDK1 expression, and SAMHD1 dephosphorylation. Therefore, topoisomerase inhibitors regulate SAMHD1 and HIV permissivity at a post-RT step, revealing a mechanism by which the HIV-1 reservoir may be limited by chemotherapeutic drugs.
Collapse
Affiliation(s)
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | | | - Ravindra K Gupta
- Division of Infection and Immunity, UCL, London, UK
- Africa Health Research Institute, Durban, KwaZulu Natal, South Africa
| |
Collapse
|
48
|
Hou J, Du J, Zhao K, Yu X. [Research Progress in Viral Protein Vpx induction of Proteasomal Degradation of the Antiviral Factor SAMHD1]. Bing Du Xue Bao 2016; 32:355-360. [PMID: 29963825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
HIV the pathogen responsible for the transmission of AIDS, which is associated with a high mortality rate. Vpx is expressed in HIV-2/SIV and promotes retroviral infection in specific cells. This promotion is achieved by Vpx-induced formation of the CRL4E3 complex, which removes the endogenous SAMHD1 via proteasomal degradation. Multiple domains of SAMHD1(e.g., N-terminus, nuclear localization signal, linker, HD domain, and C-terminus)are essential for Vpx-induced degradation.HIV-1that does not express Vpx is also evolved with mechanisms to bypass or suppress the antiviral function of SAMHD1,such as the tolerance against a low level of dNTPs and induction of SAMHD1 degradation through cyclin L2.Based on previous reports published chronologically, as well as the latest findings in the field, this review focuses on the mechanism of Vpx-mediated degradation of SAMHD1,and its promotion of HIV-1infection.
Collapse
|