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Roux H, Chomont N. Measuring Human Immunodeficiency Virus Reservoirs: Do We Need to Choose Between Quantity and Quality? J Infect Dis 2024; 229:635-643. [PMID: 37665978 PMCID: PMC10938203 DOI: 10.1093/infdis/jiad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
The persistence of latent viral genomes in people receiving antiretroviral therapy (ART) is the main obstacle to a cure for human immunodeficiency virus (HIV) infection. Viral reservoirs can be defined as cells harboring HIV genomes that have the ability to produce infectious virions. Precise quantification of the cellular reservoirs of HIV is challenging because these cells are rare, heterogeneous, and outnumbered by a larger number of cells carrying defective genomes. In addition, measuring the inducibility of these proviruses requires functional assays and remains technically difficult. The recent development of single-cell and single-viral genome approaches revealed additional layers of complexity: the cell subsets that harbor proviruses are heterogeneous and their ability to be induced is variable. A substantial fraction of intact HIV genomes may be permanently silenced after years of ART, revealing the underappreciated importance of induction assays. As such, a simple approach that would assess simultaneously the genetic intactness and the inducibility of the reservoir is still lacking. In this study, we review recent advances in the development of methods to quantify and characterize persistently infected cells, and we discuss how these findings can inform the design of future assays aimed at measuring the size of the intact and inducible HIV reservoir.
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Affiliation(s)
- Hélène Roux
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
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2
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Thenin-Houssier S, Machida S, Jahan C, Bonnet-Madin L, Abbou S, Chen HC, Tesfaye R, Cuvier O, Benkirane M. POLE3 is a repressor of unintegrated HIV-1 DNA required for efficient virus integration and escape from innate immune sensing. SCIENCE ADVANCES 2023; 9:eadh3642. [PMID: 37922361 PMCID: PMC10624344 DOI: 10.1126/sciadv.adh3642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Unintegrated retroviral DNA is transcriptionally silenced by host chromatin silencing factors. Here, we used the proteomics of isolated chromatin segments method to reveal viral and host factors associated with unintegrated HIV-1DNA involved in its silencing. By gene silencing using siRNAs, 46 factors were identified as potential repressors of unintegrated HIV-1DNA. Knockdown and knockout experiments revealed POLE3 as a transcriptional repressor of unintegrated HIV-1DNA. POLE3 maintains unintegrated HIV-1DNA in a repressive chromatin state, preventing RNAPII recruitment to the viral promoter. POLE3 and the recently identified host factors mediating unintegrated HIV-1 DNA silencing, CAF1 and SMC5/SMC6/SLF2, show specificity toward different forms of unintegrated HIV-1DNA. Loss of POLE3 impaired HIV-1 replication, suggesting that repression of unintegrated HIV-1DNA is important for optimal viral replication. POLE3 depletion reduces the integration efficiency of HIV-1. POLE3, by maintaining a repressive chromatin structure of unintegrated HIV-1DNA, ensures HIV-1 escape from innate immune sensing in primary CD4+ T cells.
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Affiliation(s)
- Suzie Thenin-Houssier
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Shinichi Machida
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Cyprien Jahan
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Lucie Bonnet-Madin
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Scarlette Abbou
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Heng-Chang Chen
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Robel Tesfaye
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Cuvier
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Monsef Benkirane
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
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3
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Aoki M, Aoki-Ogata H, Bulut H, Hayashi H, Takamune N, Kishimoto N, Tanaka H, Higashi-Kuwata N, Hattori SI, Das D, Venkateswara Rao K, Iwama K, Davis DA, Hasegawa K, Murayama K, Yarchoan R, Ghosh AK, Pau AK, Machida S, Misumi S, Mitsuya H. GRL-142 binds to and impairs HIV-1 integrase nuclear localization signal and potently suppresses highly INSTI-resistant HIV-1 variants. SCIENCE ADVANCES 2023; 9:eadg2955. [PMID: 37436982 PMCID: PMC10337902 DOI: 10.1126/sciadv.adg2955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Nuclear localization signal (NLS) of HIV-1 integrase (IN) is implicated in nuclear import of HIV-1 preintegration complex (PIC). Here, we established a multiclass drug-resistant HIV-1 variant (HIVKGD) by consecutively exposing an HIV-1 variant to various antiretroviral agents including IN strand transfer inhibitors (INSTIs). HIVKGD was extremely susceptible to a previously reported HIV-1 protease inhibitor, GRL-142, with IC50 of 130 femtomolar. When cells were exposed to HIVKGD IN-containing recombinant HIV in the presence of GRL-142, significant decrease of unintegrated 2-LTR circular cDNA was observed, suggesting that nuclear import of PIC was severely compromised by GRL-142. X-ray crystallographic analyses revealed that GRL-142 interacts with NLS's putative sequence (DQAEHLK) and sterically blocks the nuclear transport of GRL-142-bound HIVKGD's PIC. Highly INSTI-resistant HIV-1 variants isolated from heavily INSTI-experienced patients proved to be susceptible to GRL-142, suggesting that NLS-targeting agents would serve as salvage therapy agents for highly INSTI-resistant variant-harboring individuals. The data should offer a new modality to block HIV-1 infectivity and replication and shed light on developing NLS inhibitors for AIDS therapy.
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Affiliation(s)
- Manabu Aoki
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Medical Technology, Kumamoto Health Science University, Kumamoto, Japan
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hiromi Aoki-Ogata
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hironori Hayashi
- Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan
| | - Nobutoki Takamune
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroki Tanaka
- Department of Structural Virology, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Shin-ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Kazuya Iwama
- Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan
| | - David A. Davis
- Viral Oncology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kazuya Hasegawa
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Miyagi, Japan
| | - Robert Yarchoan
- Viral Oncology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | - Alice K. Pau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shinichi Machida
- Department of Structural Virology, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroaki Mitsuya
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Division of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan
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Corona A, Meleddu R, Delelis O, Subra F, Cottiglia F, Esposito F, Distinto S, Maccioni E, Tramontano E. 5-Nitro-3-(2-(4-phenylthiazol-2-yl)hydrazineylidene)indolin-2-one derivatives inhibit HIV-1 replication by a multitarget mechanism of action. Front Cell Infect Microbiol 2023; 13:1193280. [PMID: 37424782 PMCID: PMC10328743 DOI: 10.3389/fcimb.2023.1193280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
In the effort to identify and develop new HIV-1 inhibitors endowed with innovative mechanisms, we focused our attention on the possibility to target more than one viral encoded enzymatic function with a single molecule. In this respect, we have previously identified by virtual screening a new indolinone-based scaffold for dual allosteric inhibitors targeting both reverse transcriptase-associated functions: polymerase and RNase H. Pursuing with the structural optimization of these dual inhibitors, we synthesized a series of 35 new 3-[2-(4-aryl-1,3-thiazol-2-ylidene)hydrazin-1-ylidene]1-indol-2-one and 3-[3-methyl-4-arylthiazol-2-ylidene)hydrazine-1-ylidene)indolin-2-one derivatives, which maintain their dual inhibitory activity in the low micromolar range. Interestingly, compounds 1a, 3a, 10a, and 9b are able to block HIV-1 replication with EC50 < 20 µM. Mechanism of action studies showed that such compounds could block HIV-1 integrase. In particular, compound 10a is the most promising for further multitarget compound development.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Olivier Delelis
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Frederic Subra
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
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5
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Dekker JG, Klaver B, Berkhout B, Das AT. HIV-1 3'-Polypurine Tract Mutations Confer Dolutegravir Resistance by Switching to an Integration-Independent Replication Mechanism via 1-LTR Circles. J Virol 2023; 97:e0036123. [PMID: 37125907 PMCID: PMC10231180 DOI: 10.1128/jvi.00361-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/07/2023] [Indexed: 05/02/2023] Open
Abstract
Several recent studies indicate that mutations in the human immunodeficiency virus type 1 (HIV-1) 3'polypurine tract (3'PPT) motif can reduce sensitivity to the integrase inhibitor dolutegravir (DTG). Using an in vivo systematic evolution of ligands by exponential enrichment (SELEX) approach, we discovered that multiple different mutations in this viral RNA element can confer DTG resistance, suggesting that the inactivation of this critical reverse transcription element causes resistance. An analysis of the viral DNA products formed upon infection by these 3'PPT mutants revealed that they replicate without integration into the host cell genome, concomitant with an increased production of 1-LTR circles. As the replication of these virus variants is activated by the human T-lymphotropic virus 1 (HTLV-1) Tax protein, a factor that reverses epigenetic silencing of episomal HIV DNA, these data indicate that the 3'PPT-mutated viruses escape from the integrase inhibitor DTG by switching to an integration-independent replication mechanism. IMPORTANCE The integrase inhibitor DTG is a potent inhibitor of HIV replication and is currently recommended in drug regimens for people living with HIV. Whereas HIV normally escapes from antiviral drugs by the acquisition of specific mutations in the gene that encodes the targeted enzyme, mutational inactivation of the viral 3'PPT sequence, an RNA element that has a crucial role in the viral reverse transcription process, was found to allow HIV replication in the presence of DTG in cell culture experiments. While the integration of the viral DNA into the cellular genome is considered one of the hallmarks of retroviruses, including HIV, 3'PPT inactivation caused integration-independent replication, which can explain the reduced DTG sensitivity. Whether this exotic escape route can also contribute to viral escape in HIV-infected persons remains to be determined, but our results indicate that screening for 3'PPT mutations in patients that fail on DTG therapy should be considered.
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Affiliation(s)
- José G. Dekker
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Bep Klaver
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Atze T. Das
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
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6
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Roux HM, Figueiredo S, Sareoua L, Salmona M, Hamroune J, Adoux L, Migraine J, Hance A, Clavel F, Cheynier R, Dutrieux J. DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA. CELL REPORTS METHODS 2023; 3:100443. [PMID: 37159665 PMCID: PMC10162948 DOI: 10.1016/j.crmeth.2023.100443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 01/28/2023] [Accepted: 03/10/2023] [Indexed: 05/11/2023]
Abstract
Unintegrated HIV DNA represents between 20% and 35% of the total viral DNA in infected patients. Only the linear forms (unintegrated linear DNAs [ULDs]) can be substrates for integration and for the completion of a full viral cycle. In quiescent cells, these ULDs may be responsible for pre-integrative latency. However, their detection remains difficult due to the lack of specificity and sensitivity of existing techniques. We developed an ultra-sensitive, specific, and high-throughput technology for ULD quantification called DUSQ (DNA ultra-sensitive quantification) combining linker-mediated PCR and next-generation sequencing (NGS) using molecular barcodes. Studying cells with different activity levels, we determined that the ULD half-life goes up to 11 days in resting CD4+ T cells. Finally, we were able to quantify ULDs in samples from patients infected with HIV-1, providing a proof of concept for the use of DUSQ in vivo to track pre-integrative latency. DUSQ can be adapted to the detection of other rare DNA molecules.
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Affiliation(s)
- Hélène Marie Roux
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
| | - Suzanne Figueiredo
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
| | - Lucas Sareoua
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
| | - Maud Salmona
- Université Paris Cité, Paris, France
- INSERM U976, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Saint Louis, Laboratoire de Virologie, Paris, France
| | - Juliette Hamroune
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
| | - Lucie Adoux
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
| | | | | | - François Clavel
- Université Paris Cité, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Saint Louis, Laboratoire de Virologie, Paris, France
| | - Rémi Cheynier
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
| | - Jacques Dutrieux
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, 75014 Paris, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
- Corresponding author
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7
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Zhang X, Chen J. HIV Reservoir: How to Measure It? Curr HIV/AIDS Rep 2023; 20:29-41. [PMID: 37004676 DOI: 10.1007/s11904-023-00653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 04/04/2023]
Abstract
PURPOSEOF REVIEW In the current quest for a complete cure for HIV/AIDS, the persistence of a long-lived reservoir of cells carrying replication-competent proviruses is the major challenge. Here, we describe the main elements and characteristics of several widely used assays of HIV latent reservoir detection. RECENT FINDINGS To date, researchers have developed several different HIV latent reservoir detection assays. Among them, the in vitro quantitative viral outgrowth assay (QVOA) has been the gold standard for assessing latent HIV-1 viral load. The intact proviral DNA assay (IPDA) based on PCR also demonstrated the predominance of defective viruses. However, these assays all have some drawbacks and may still be inadequate in detecting the presence of ultralow levels of latent virus in many patients who were initially thought to have been cured, but eventually showed viral rebound. An accurate and precise measurement of the HIV reservoir is therefore needed to evaluate curative strategies, aimed to functional cure or sterilizing cure.
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Affiliation(s)
- Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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Ohkura S, Horie M, Shimizu M, Nakagawa S, Osanai H, Miyagawa Y, Morita R. Characterization of Megabat-Favored, CA-Dependent Susceptibility to Retrovirus Infection. J Virol 2023; 97:e0180322. [PMID: 36779757 PMCID: PMC10062173 DOI: 10.1128/jvi.01803-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/21/2022] [Indexed: 02/14/2023] Open
Abstract
The isolation of the Koala retrovirus-like virus from Australian megabats and the identification of endogenous retroviruses in the bat genome have raised questions on bat susceptibility to retroviruses in general. To answer this, we studied the susceptibility of 12 cell lines from 11 bat species to four well-studied retroviruses (human and simian immunodeficiency viruses [HIV and SIV] and murine leukemia viruses [B- and N-MLV]). Systematic comparison of retroviral susceptibility among bats revealed that megabat cell lines were overall less susceptible to the four retroviruses than microbat cell lines, particularly to HIV-1 infection, whereas lineage-specific differences were observed for MLV susceptibility. Quantitative PCR of reverse transcription (RT) products, infection in heterokaryon cells, and point mutation analysis of the capsid (CA) revealed that (i) HIV-1 and MLV replication were blocked at the nuclear transport of the pre-integration complexes and before and/or during RT, respectively, and (ii) the observed lineage-specific restriction can be attributed to a dominant cellular factor constrained by specific positions in CA. Investigation of bat homologs of the three previously reported post-entry restriction factors constrained by the same residues in CA, tripartite motif-protein 5α (TRIM5α), myxovirus resistance 2/B (Mx2/MxB), and carboxy terminus-truncated cleavage and polyadenylation factor 6 (CPSF6-358), demonstrated poor anti-HIV-1 activity in megabat cells, whereas megabat TRIM5α restricted MLV infection, suggesting that the major known CA-dependent restriction factors were not dominant in the observed lineage-specific susceptibility to HIV-1 in bat cells. Therefore, HIV-1 susceptibility of megabat cells may be determined in a manner distinct from that of primate cells. IMPORTANCE Recent studies have demonstrated the circulation of gammaretroviruses among megabats in Australia and the bats' resistance to HIV-1 infection; however, the origins of these viruses in megabats and the contribution of bats to retrovirus spread to other mammalian species remains unclear. To determine the intrinsic susceptibility of bat cells to HIV-1 infection, we investigated 12 cell lines isolated from 11 bat species. We report that lineage-specific retrovirus restriction in the bat cell lines can be attributed to CA-dependent factors. However, in the megabat cell lines examined, factors known to bind capsid and block infection in primate cell culture, including homologs of TRIM5α, Mx2/MxB, and CPSF6, failed to exhibit significant anti-HIV-1 activities. These results suggested that the HIV-1 susceptibility of megabat cells occurs in a manner distinct from that of primate cells, where cellular factors, other than major known CA-dependent restriction factors, with lineage-specific functions could recognize retroviral proteins in megabats.
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Affiliation(s)
- Sadayuki Ohkura
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Masumi Shimizu
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Haruka Osanai
- Department of Medicine, Nippon Medical School, Tokyo, Japan
| | - Yoshitaka Miyagawa
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Rimpei Morita
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan
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9
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Richetta C, Tu NQ, Delelis O. Different Pathways Conferring Integrase Strand-Transfer Inhibitors Resistance. Viruses 2022; 14:v14122591. [PMID: 36560595 PMCID: PMC9785060 DOI: 10.3390/v14122591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Integrase Strand Transfer Inhibitors (INSTIs) are currently used as the most effective therapy in the treatment of human immunodeficiency virus (HIV) infections. Raltegravir (RAL) and Elvitegravir (EVG), the first generation of INSTIs used successfully in clinical treatment, are susceptible to the emergence of viral resistance and have a high rate of cross-resistance. To counteract these resistant mutants, second-generation INSTI drugs have been developed: Dolutegravir (DTG), Cabotegravir (CAB), and Bictegravir (BIC). However, HIV is also able to develop resistance mechanisms against the second-generation of INSTIs. This review describes the mode of action of INSTIs and then summarizes and evaluates some typical resistance mutations, such as substitution and insertion mutations. The role of unintegrated viral DNA is also discussed as a new pathway involved in conferring resistance to INSTIs. This allows us to have a more detailed understanding of HIV resistance to these inhibitors, which may contribute to the development of new INSTIs in the future.
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Abstract
Integration of the reverse-transcribed genome is a critical step of the retroviral life cycle. Strand-transfer inhibitors (INSTIs) used for antiretroviral therapy inhibit integration but can lead to resistance mutations in the integrase gene, the enzyme involved in this reaction. A significant proportion of INSTI treatment failures, particularly those with second-generation INSTIs, show no mutation in the integrase gene. Here, we show that replication of a selected dolutegravir-resistant virus with mutations in the 3'-PPT (polypurine tract) was effective, although no integrated viral DNA was detected, due to the accumulation of unintegrated viral DNA present as 1-LTR circles. Our results show that mutation in the 3'-PPT leads to 1-LTR circles and not linear DNA as classically reported. In conclusion, our data provide a molecular basis to explain a new mechanism of resistance to INSTIs, without mutation of the integrase gene and highlights the importance of unintegrated viral DNA in HIV-1 replication. IMPORTANCE Our work highlights the role of HIV-1 unintegrated viral DNA in viral replication. A virus, resistant to strand-transfer inhibitors, has been selected in vitro. This virus highlights a mutation in the 3'PPT region and not in the integrase gene. This mutation modifies the reverse transcription step leading to the accumulation of 1-LTR circles and not the linear DNA. This accumulation of 1-LTR circles leads to viral replication without integration of the viral genome.
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Quantification of Total HIV DNA as a Marker to Measure Viral Reservoir: Methods and Potential Implications for Clinical Practice. Diagnostics (Basel) 2021; 12:diagnostics12010039. [PMID: 35054206 PMCID: PMC8774405 DOI: 10.3390/diagnostics12010039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
The focus of this review is to examine the importance of quantifying total HIV DNA to target the HIV reservoir and the clinical implications and challenges involved in its future application in clinical practice. Despite intrinsic limitations, the quantification of total HIV DNA is currently the most widely used marker for exploring the HIV reservoir. As it allows estimating all forms of HIV DNA in the infected cells, total HIV DNA load is the biomarker of the HIV reservoir that provides most of the insights into HIV pathogenesis. The clinical role of total HIV-DNA in both untreated and treated patients is extensively supported by important lines of evidence. Thus, predictive models that include total HIV DNA load together with other variables could constitute a prognostic tool for use in clinical practice. To date, however, this marker has been primarily used in experimental evaluations. The main challenge is technical. Although the implementation of droplet digital PCR could improve analytical performance over real-time PCR, the lack of standardization has made cross-comparisons of the data difficult. An effort by investigators to compare protocols is needed. Furthermore, the main effort now should be to involve the biomedical industry in the development of certified assays for in vitro diagnostics use.
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12
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Davids BO, Balasubramaniam M, Sapp N, Prakash P, Ingram S, Li M, Craigie R, Hollis T, Pandhare J, Dash C. Human Three Prime Repair Exonuclease 1 Promotes HIV-1 Integration by Preferentially Degrading Unprocessed Viral DNA. J Virol 2021; 95:e0055521. [PMID: 34105995 PMCID: PMC8354242 DOI: 10.1128/jvi.00555-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/20/2022] Open
Abstract
Three prime repair exonuclease 1 (TREX1) is the most abundant 3'→5' exonuclease in mammalian cells. It has been suggested that TREX1 degrades HIV-1 DNA to enable the virus to evade the innate immune system. However, the exact role of TREX1 during early steps of HIV-1 infection is not clearly understood. In this study, we report that HIV-1 infection is associated with upregulation, perinuclear accumulation, and nuclear localization of TREX1. However, TREX1 overexpression did not affect reverse transcription or nuclear entry of the virus. Surprisingly, HIV-1 DNA integration was increased in TREX1-overexpressing cells, suggesting a role of the exonuclease in the post-nuclear entry step of infection. Accordingly, preintegration complexes (PICs) extracted from TREX1-overexpressing cells retained higher levels of DNA integration activity. TREX1 depletion resulted in reduced levels of proviral integration, and PICs formed in TREX1-depleted cells retained lower DNA integration activity. Addition of purified TREX1 to PICs also enhanced DNA integration activity, suggesting that TREX1 promotes HIV-1 integration by stimulating PIC activity. To understand the mechanism, we measured TREX1 exonuclease activity on substrates containing viral DNA ends. These studies revealed that TREX1 preferentially degrades the unprocessed viral DNA, but the integration-competent 3'-processed viral DNA remains resistant to degradation. Finally, we observed that TREX1 addition stimulates the activity of HIV-1 intasomes assembled with the unprocessed viral DNA but not that of intasomes containing the 3'-processed viral DNA. These biochemical analyses provide a mechanism by which TREX1 directly promotes HIV-1 integration. Collectively, our study demonstrates that HIV-1 infection upregulates TREX1 to facilitate viral DNA integration. IMPORTANCE Productive HIV-1 infection is dependent on a number of cellular factors. Therefore, a clear understanding of how the virus exploits the cellular machinery will identify new targets for inhibiting HIV-1 infection. The three prime repair exonuclease 1 (TREX1) is the most active cellular exonuclease in mammalian cells. It has been reported that TREX1 prevents accumulation of HIV-1 DNA and enables the virus to evade the host innate immune response. Here, we show that HIV-1 infection results in the upregulation, perinuclear accumulation, and nuclear localization of TREX1. We also provide evidence that TREX1 promotes HIV-1 integration by preferentially degrading viral DNAs that are incompatible with chromosomal insertion. These observations identify a novel role of TREX1 in a post-nuclear entry step of HIV-1 infection.
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Affiliation(s)
- Benem-Orom Davids
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Nicklas Sapp
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Shalonda Ingram
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
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13
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Dupont L, Bloor S, Williamson JC, Cuesta SM, Shah R, Teixeira-Silva A, Naamati A, Greenwood EJD, Sarafianos SG, Matheson NJ, Lehner PJ. The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr. Cell Host Microbe 2021; 29:792-805.e6. [PMID: 33811831 PMCID: PMC8118623 DOI: 10.1016/j.chom.2021.03.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/31/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022]
Abstract
Silencing of nuclear DNA is an essential feature of innate immune responses to invading pathogens. Early in infection, unintegrated lentiviral cDNA accumulates in the nucleus yet remains poorly expressed. In HIV-1-like lentiviruses, the Vpr accessory protein enhances unintegrated viral DNA expression, suggesting Vpr antagonizes cellular restriction. We previously showed how Vpr remodels the host proteome, identifying multiple cellular targets. We now screen these using a targeted CRISPR-Cas9 library and identify SMC5-SMC6 complex localization factor 2 (SLF2) as the Vpr target responsible for silencing unintegrated HIV-1. SLF2 recruits the SMC5/6 complex to unintegrated lentiviruses, and depletion of SLF2, or the SMC5/6 complex, increases viral expression. ATAC-seq demonstrates that Vpr-mediated SLF2 depletion increases chromatin accessibility of unintegrated virus, suggesting that the SMC5/6 complex compacts viral chromatin to silence gene expression. This work implicates the SMC5/6 complex in nuclear immunosurveillance of extrachromosomal DNA and defines its targeting by Vpr as an evolutionarily conserved antagonism.
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Affiliation(s)
- Liane Dupont
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stuart Bloor
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Ana Teixeira-Silva
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adi Naamati
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Edward J D Greenwood
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Nicholas J Matheson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
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14
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Vpu modulates DNA repair to suppress innate sensing and hyper-integration of HIV-1. Nat Microbiol 2020; 5:1247-1261. [PMID: 32690953 DOI: 10.1038/s41564-020-0753-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
Abstract
To avoid innate sensing and immune control, human immunodeficiency virus type 1 (HIV-1) has to prevent the accumulation of viral complementary DNA species. Here, we show that the late HIV-1 accessory protein Vpu hijacks DNA repair mechanisms to promote degradation of nuclear viral cDNA in cells that are already productively infected. Vpu achieves this by interacting with RanBP2-RanGAP1*SUMO1-Ubc9 SUMO E3-ligase complexes at the nuclear pore to reprogramme promyelocytic leukaemia protein nuclear bodies and reduce SUMOylation of Bloom syndrome protein, unleashing end degradation of viral cDNA. Concomitantly, Vpu inhibits RAD52-mediated homologous repair of viral cDNA, preventing the generation of dead-end circular forms of single copies of the long terminal repeat and permitting sustained nucleolytic attack. Our results identify Vpu as a key modulator of the DNA repair machinery. We show that Bloom syndrome protein eliminates nuclear HIV-1 cDNA and thereby suppresses immune sensing and proviral hyper-integration. Therapeutic targeting of DNA repair may facilitate the induction of antiviral immunity and suppress proviral integration replenishing latent HIV reservoirs.
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15
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Orlandi C, Canovari B, Bozzano F, Marras F, Pasquini Z, Barchiesi F, De Maria A, Magnani M, Casabianca A. A comparative analysis of unintegrated HIV-1 DNA measurement as a potential biomarker of the cellular reservoir in the blood of patients controlling and non-controlling viral replication. J Transl Med 2020; 18:204. [PMID: 32429953 PMCID: PMC7236182 DOI: 10.1186/s12967-020-02368-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023] Open
Abstract
Background The persistence of HIV-1 in reservoir cells is one of the major obstacles to eradicating the virus in infected individuals receiving combination antiretroviral therapy (ART). HIV-1 persists in infected cells as a stable integrated genome and more labile unintegrated DNA (uDNA), which includes linear, 1-LTR and 2-LTR circular DNA. 2-LTR circle DNA, although less abundant, is considered a surrogate marker of recent infection events and is currently used instead of the other unintegrated species as a diagnostic tool. This pilot study aimed to investigate how to best achieve the measurement of uDNA. Methods A comparative analysis of two qPCR-based methods (U-assay and 2-LTR assay) was performed on the blood of 12 ART-naïve, 14 viremic and 29 aviremic On-ART patients and 20 untreated spontaneous controllers (HIC), sampled at a single time point. Results The U-assay, which quantified all unintegrated DNA species, showed greater sensitivity than the 2-LTR assay (up to 75%, p < 0.0001), especially in viremic subjects, in whom other forms, in addition to 2-LTR circles, may also accumulate due to active viral replication. Indeed, in aviremic On-ART samples, the U-assay unexpectedly measured uDNA in a higher proportion of samples (76%, 22/29) than the 2-LTR assay (41%, 12/29), (p = 0.0164). A trend towards lower uDNA levels was observed in aviremic vs viremic On-ART patients, reaching significance when we combined aviremic On-ART and HIC (controllers) vs Off-ART and viremic On-ART subjects (non-controllers) (p = 0.0003), whereas 2-LTR circle levels remained constant (p ≥ 0.2174). These data were supported by the high correlation found between uDNA and total DNA (r = 0.69, p < 0.001). Conclusions The great advantage of the U-assay is that, unlike the 2-LTR assay, it allows the accurate evaluation of the totality of uDNA that can still be measured even during successful ART when plasma viremia is below the cut-off of common clinical tests (< 50 copies/mL) and 2-LTR circles are more likely to be under the quantification limit. UDNA measurement in blood cells may be used as a biomarker to reveal a so far hidden or underestimated viral reservoir. The potential clinical relevance of uDNA quantification may lead to improvements in diagnostic methods to support clinical strategies.
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Affiliation(s)
- Chiara Orlandi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Benedetta Canovari
- Malattie Infettive, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Pesaro, Italy
| | | | - Francesco Marras
- Division of Infectious Diseases, Ospedale Policlinico S. Martino IRCCS, Genoa, Italy
| | - Zeno Pasquini
- Malattie Infettive, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Pesaro, Italy.,Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Barchiesi
- Malattie Infettive, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Pesaro, Italy.,Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea De Maria
- Division of Infectious Diseases, Ospedale Policlinico S. Martino IRCCS, Genoa, Italy.,Department of Health Sciences, DISSAL, University of Genova, Genoa, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Anna Casabianca
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy.
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16
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Lee SC, Ernst E, Berube B, Borges F, Parent JS, Ledon P, Schorn A, Martienssen RA. Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA. Genome Res 2020; 30:576-588. [PMID: 32303559 PMCID: PMC7197481 DOI: 10.1101/gr.259044.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
In Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated siRNA (easiRNA) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR retrotransposons without the need for mapping transposition, as well as independent of genomic copy number. Linear replication intermediates of the functionally intact COPIA element EVADE revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which cPPTs promote nuclear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon “suicide” by auto-integration within the VLP. easiRNA targeted EVADE genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethylation. VLP DNA-seq provides a comprehensive landscape of LTR retrotransposons and their control at transcriptional, post-transcriptional, and reverse transcriptional levels.
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Benjamin Berube
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jean-Sebastien Parent
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Paul Ledon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrea Schorn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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17
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Thomas J, Ruggiero A, Paxton WA, Pollakis G. Measuring the Success of HIV-1 Cure Strategies. Front Cell Infect Microbiol 2020; 10:134. [PMID: 32318356 PMCID: PMC7154081 DOI: 10.3389/fcimb.2020.00134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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18
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Engelman AN. Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition. J Biol Chem 2019; 294:15137-15157. [PMID: 31467082 DOI: 10.1074/jbc.rev119.006901] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral inhibitors that are used to manage HIV infection/AIDS predominantly target three enzymes required for virus replication: reverse transcriptase, protease, and integrase. Although integrase inhibitors were the last among this group to be approved for treating people living with HIV, they have since risen to the forefront of treatment options. Integrase strand transfer inhibitors (INSTIs) are now recommended components of frontline and drug-switch antiretroviral therapy formulations. Integrase catalyzes two successive magnesium-dependent polynucleotidyl transferase reactions, 3' processing and strand transfer, and INSTIs tightly bind the divalent metal ions and viral DNA end after 3' processing, displacing from the integrase active site the DNA 3'-hydroxyl group that is required for strand transfer activity. Although second-generation INSTIs present higher barriers to the development of viral drug resistance than first-generation compounds, the mechanisms underlying these superior barrier profiles are incompletely understood. A separate class of HIV-1 integrase inhibitors, the allosteric integrase inhibitors (ALLINIs), engage integrase distal from the enzyme active site, namely at the binding site for the cellular cofactor lens epithelium-derived growth factor (LEDGF)/p75 that helps to guide integration into host genes. ALLINIs inhibit HIV-1 replication by inducing integrase hypermultimerization, which precludes integrase binding to genomic RNA and perturbs the morphogenesis of new viral particles. Although not yet approved for human use, ALLINIs provide important probes that can be used to investigate the link between HIV-1 integrase and viral particle morphogenesis. Herein, I review the mechanisms of retroviral integration as well as the promises and challenges of using integrase inhibitors for HIV/AIDS management.
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Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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19
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Malet I, Ambrosio FA, Subra F, Herrmann B, Leh H, Bouger MC, Artese A, Katlama C, Talarico C, Romeo I, Alcaro S, Costa G, Deprez E, Calvez V, Marcelin AG, Delelis O. Pathway involving the N155H mutation in HIV-1 integrase leads to dolutegravir resistance. J Antimicrob Chemother 2019; 73:1158-1166. [PMID: 29373677 DOI: 10.1093/jac/dkx529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Background Dolutegravir, an integrase strand-transfer inhibitor (STI), shows a high genetic barrier to resistance. Dolutegravir is reported to be effective against viruses resistant to raltegravir and elvitegravir. In this study, we report the case of a patient treated with dolutegravir monotherapy. Failure of dolutegravir treatment was observed concomitant with the appearance of N155H-K211R-E212T mutations in the integrase (IN) gene in addition to the polymorphic K156N mutation that was present at baseline in this patient. Methods The impact of N155H-K156N-K211R-E212T mutations was studied in cell-free, culture-based assays and by molecular modelling. Results Cell-free and culture-based assays confirm that selected mutations in the patient, in the context of the polymorphic mutation K156N present at the baseline, lead to high resistance to dolutegravir requiring that the analysis be done at timepoints longer than usual to properly reveal the results. Interestingly, the association of only N155H and K156N is sufficient for significant resistance to dolutegravir. Modelling studies showed that dolutegravir is less stable in IN/DNA complexes with respect to the WT sequence. Conclusions Our results indicate that the stability of STI IN/DNA complexes is an important parameter that must be taken into account when evaluating dolutegravir resistance. This study confirms that a pathway including N155H can be selected in patients treated with dolutegravir with the help of the polymorphic K156N that acts as a secondary mutation that enhances the resistance to dolutegravir.
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Affiliation(s)
- Isabelle Malet
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), 75013 Paris, France.,Department of Virology, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Francesca A Ambrosio
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Frédéric Subra
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Béatrice Herrmann
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Hervé Leh
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Marie-Christine Bouger
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Anna Artese
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Christine Katlama
- Department of Infectious Diseases, Hôpital Pitié Salpetriere, Paris, France
| | - Carmine Talarico
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Isabella Romeo
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Eric Deprez
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), 75013 Paris, France.,Department of Virology, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), 75013 Paris, France.,Department of Virology, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
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20
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Richetta C, Thierry S, Thierry E, Lesbats P, Lapaillerie D, Munir S, Subra F, Leh H, Deprez E, Parissi V, Delelis O. Two-long terminal repeat (LTR) DNA circles are a substrate for HIV-1 integrase. J Biol Chem 2019; 294:8286-8295. [PMID: 30971426 DOI: 10.1074/jbc.ra118.006755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/08/2019] [Indexed: 02/01/2023] Open
Abstract
Integration of the HIV-1 DNA into the host genome is essential for viral replication and is catalyzed by the retroviral integrase. To date, the only substrate described to be involved in this critical reaction is the linear viral DNA produced in reverse transcription. However, during HIV-1 infection, two-long terminal repeat DNA circles (2-LTRcs) are also generated through the ligation of the viral DNA ends by the host cell's nonhomologous DNA end-joining pathway. These DNAs contain all the genetic information required for viral replication, but their role in HIV-1's life cycle remains unknown. We previously showed that both linear and circular DNA fragments containing the 2-LTR palindrome junction can be efficiently cleaved in vitro by recombinant integrases, leading to the formation of linear 3'-processed-like DNA. In this report, using in vitro experiments with purified proteins and DNAs along with DNA endonuclease and in vivo integration assays, we show that this circularized genome can also be efficiently used as a substrate in HIV-1 integrase-mediated integration both in vitro and in eukaryotic cells. Notably, we demonstrate that the palindrome cleavage occurs via a two-step mechanism leading to a blunt-ended DNA product, followed by a classical 3'-processing reaction; this cleavage leads to integrase-dependent integration, highlighted by a 5-bp duplication of the host genome. Our results suggest that 2-LTRc may constitute a reserve supply of HIV-1 genomes for proviral integration.
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Affiliation(s)
- Clémence Richetta
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Sylvain Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Eloise Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Paul Lesbats
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Centre National de la Recherche Scientifique UMR5234, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France
| | - Delphine Lapaillerie
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Centre National de la Recherche Scientifique UMR5234, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France
| | - Soundasse Munir
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Frédéric Subra
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Hervé Leh
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Centre National de la Recherche Scientifique UMR5234, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan.
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21
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Balasubramaniam M, Zhou J, Addai A, Martinez P, Pandhare J, Aiken C, Dash C. PF74 Inhibits HIV-1 Integration by Altering the Composition of the Preintegration Complex. J Virol 2019; 93:e01741-18. [PMID: 30567984 PMCID: PMC6401427 DOI: 10.1128/jvi.01741-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 capsid protein (CA) facilitates reverse transcription and nuclear entry of the virus. However, CA's role in post-nuclear entry steps remains speculative. We describe a direct link between CA and integration by employing the capsid inhibitor PF74 as a probe coupled with the biochemical analysis of HIV-1 preintegration complexes (PICs) isolated from acutely infected cells. At a low micromolar concentration, PF74 potently inhibited HIV-1 infection without affecting reverse transcription. Surprisingly, PF74 markedly reduced proviral integration owing to inhibition of nuclear entry and/or integration. However, a 2-fold reduction in nuclear entry by PF74 did not quantitatively correlate with the level of antiviral activity. Titration of PF74 against the integrase inhibitor raltegravir showed an additive antiviral effect that is dependent on a block at the post-nuclear entry step. PF74's inhibitory effect was not due to the formation of defective viral DNA ends or a delay in integration, suggesting that the compound inhibits PIC-associated integration activity. Unexpectedly, PICs recovered from cells infected in the presence of PF74 exhibited elevated integration activity. PF74's effect on PIC activity is CA specific since the compound did not increase the integration activity of PICs of a PF74-resistant HIV-1 CA mutant. Sucrose gradient-based fractionation studies revealed that PICs assembled in the presence of PF74 contained lower levels of CA, suggesting a negative association between CA and PIC-associated integration activity. Finally, the addition of a CA-specific antibody or PF74 inhibited PIC-associated integration activity. Collectively, our results demonstrate that PF74's targeting of PIC-associated CA results in impaired HIV-1 integration.IMPORTANCE Antiretroviral therapy (ART) that uses various combinations of small molecule inhibitors has been highly effective in controlling HIV. However, the drugs used in the ART regimen are expensive, cause side effects, and face viral resistance. The HIV-1 CA plays critical roles in the virus life cycle and is an attractive therapeutic target. While currently there is no CA-based therapy, highly potent CA-specific inhibitors are being developed as a new class of antivirals. Efforts to develop a CA-targeted therapy can be aided through a clear understanding of the role of CA in HIV-1 infection. CA is well established to coordinate reverse transcription and nuclear entry of the virus. However, the role of CA in post-nuclear entry steps of HIV-1 infection is poorly understood. We show that a CA-specific drug PF74 inhibits HIV-1 integration revealing a novel role of this multifunctional viral protein in a post-nuclear entry step of HIV-1 infection.
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Affiliation(s)
- Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Jing Zhou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amma Addai
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Phillip Martinez
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
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22
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Surdo M, Cortese MF, Orlandi C, Di Santo F, Aquaro S, Magnani M, Perno CF, Casabianca A, Ceccherini-Silberstein F. Different kinetics of viral replication and DNA integration in the main HIV-1 cellular reservoirs in the presence and absence of integrase inhibitors. Antiviral Res 2018; 160:165-174. [PMID: 30420339 DOI: 10.1016/j.antiviral.2018.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/21/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022]
Abstract
To compare the kinetics of integration, p24 production and equilibrium of the different HIV-DNA forms in human primary cells in the presence/absence of integrase-inhibitors (INIs) in vitro. Monocyte-derived-macrophages (MDMs), CD4+ T-cells and peripheral blood mononuclear cells (PBMCs) were infected with HIV-1 in the presence/absence of raltegravir and dolutegravir. HIV-DNA levels and p24 production were measured by qPCR and ELISA assays, respectively. In the absence of INIs, levels of HIV-DNA forms were initially very low, with an increase in the integration process starting at 3 dpi. HIV-DNA increased more slowly in MDMs than it did in CD4+ T-cells and PMBCs peaking at 21 dpi with a mean of 1580 (±890) and 615 (±37) copies/103 cells for proviral and unintegrated HIV-DNA, and 455,972 (±213,255) pg/mL of p24 at the same time point. In CD4+ T-cells the proviral HIV-DNA increased together with unintegrated HIV-DNA peaking at 7 dpi (583 ± 261 and 338 ± 254 copies/103 cells) when the p24 was 218,000 (±75,600) pg/mL. A similar trend was observed in PBMCs (494 ± 361 and 350 ± 123 copies/103 cells for proviral and unintegrated HIV-DNA, and p24 production of 149,400 ± 131,800 pg/mL). Both INIs inhibited viral replication and integration in all the cell types that were tested, especially starting at 3 dpi. However, a small but measurable amount of HIV-DNA (<5 copies/103 cells) was still observed in treated-MDMs up to 30 dpi. In conclusion, our study showed differences in HIV-DNA kinetic integration between CD4+ T-cells and MDMs, which could explain the divergent kinetics of viral-replication. Both INIs inhibited HIV-1 integration and replication with no difference found between CD4+ T-cells and MDMs. However, residual HIV-DNA remained detectable up to 30 dpi in INI-treated MDMs although complete inhibition of HIV replication was achieved. The clinical significance of this minor DNA persistence deserves further investigation considering the role of macrophages as reservoirs.
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Affiliation(s)
- Matteo Surdo
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Maria Francesca Cortese
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Chiara Orlandi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy.
| | - Fabiola Di Santo
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy.
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy.
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Anna Casabianca
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy.
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23
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Martinez-Picado J, Zurakowski R, Buzón MJ, Stevenson M. Episomal HIV-1 DNA and its relationship to other markers of HIV-1 persistence. Retrovirology 2018; 15:15. [PMID: 29378611 PMCID: PMC5789633 DOI: 10.1186/s12977-018-0398-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/19/2018] [Indexed: 11/30/2022] Open
Abstract
Reverse transcription of HIV-1 results in the generation of a linear cDNA that serves as the precursor to the integrated provirus. Other classes of extrachromosomal viral cDNA molecules can be found in acutely infected cells including the 1-LTR and 2-LTR circles of viral DNA, also referred as episomal HIV-1 DNA. Circulating CD4+ T-cells of treatment-naïve individuals contain significant levels of unintegrated forms of HIV-1 DNA. However, the importance of episomal HIV-1 DNA in the study of viral persistence during antiviral therapy (ART) is debatable. 2-LTR circles are preferentially observed in the effector memory CD4+ T cell subset of long-term treated subjects. Treatment intensification of standard regimens has been used to determine if more potent ART can impact viral reservoir activity. Adding a potent antiretroviral drug to a stable triple-drug regimen has no measurable impact on plasma HIV-1 RNA levels, suggesting that ongoing cycles of HIV-1 replication are not a major mechanism driving persistent plasma viremia during triple-drug ART. However, in randomized clinical trials of HIV-1-infected adults on apparently effective ART, the addition of an integrase inhibitor (raltegravir) to stable regimens resulted in a transient increase in 2-LTR circles in some patients, suggesting a pre-intensification steady-state in which the processes of virion generation and de novo infection were occurring. Mathematical modeling of 2-LTR production during integrase inhibitor intensification suggests the coexistence, at different levels, of ongoing de novo infection and de novo replication mechanisms, specifically in inflamed lymphoid drug sanctuaries. Most reports looking into potential changes in 2-LTR circles in interventional clinical studies have simultaneously assessed other potential surrogate markers of viral persistence. Transient increases in 2-LTR circles have been correlated to decreases in CD8+ T-cell activation, transient CD45RA−CD4+ T-cell redistribution, and decreases in the hypercoagulation biomarker D-dimer in ART-intensified individuals. It is difficult, however, to establish a systematic association because the level of correlation with different types of markers differs significantly among studies. In conclusion, despite suppressive ART, a steady-state of de novo infection may persist in some infected individuals and that this may drive immune activation and inflammation changes reflecting residual viral reservoir activity during otherwise apparently suppressive ART.
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Affiliation(s)
- Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, University Hospital Germans Trias i Pujol, Ctra. de Canyet s/n, Badalona, 08916, Barcelona, Spain. .,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - María José Buzón
- Infectious Diseases Department, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Mario Stevenson
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
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24
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Benleulmi MS, Matysiak J, Robert X, Miskey C, Mauro E, Lapaillerie D, Lesbats P, Chaignepain S, Henriquez DR, Calmels C, Oladosu O, Thierry E, Leon O, Lavigne M, Andreola ML, Delelis O, Ivics Z, Ruff M, Gouet P, Parissi V. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails. Retrovirology 2017; 14:54. [PMID: 29179726 PMCID: PMC5704366 DOI: 10.1186/s12977-017-0378-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/20/2017] [Indexed: 01/28/2023] Open
Abstract
Background Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein–protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. Results We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Conclusions Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin. Electronic supplementary material The online version of this article (10.1186/s12977-017-0378-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed S Benleulmi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Julien Matysiak
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Xavier Robert
- MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Stéphane Chaignepain
- UMR CNRS 5248 CBMN (Chimie Biologie des Membranes et Nanoobjets), Université de Bordeaux, 33076, Bordeaux, France
| | - Daniel R Henriquez
- Virology Program, ICBM, Faculty of Medicine, University of Chile, Santiago of Chile, Chile
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Oyindamola Oladosu
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
| | | | - Oscar Leon
- Virology Program, ICBM, Faculty of Medicine, University of Chile, Santiago of Chile, Chile
| | - Marc Lavigne
- Dpt de Virologie, UMR 3569, CNRS, Institut Pasteur, Paris, France.,Institut Cochin-Inserm U1016-CNRS UMR8104-Université Paris Descartes, Paris, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Marie-Line Andreola
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Olivier Delelis
- LBPA, UMR8113, CNRS, ENS-Cachan, 94235, Cachan, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Marc Ruff
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Patrice Gouet
- MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France. .,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France. .,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France.
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25
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Probing Resistance Mutations in Retroviral Integrases by Direct Measurement of Dolutegravir Fluorescence. Sci Rep 2017; 7:14067. [PMID: 29070877 PMCID: PMC5656594 DOI: 10.1038/s41598-017-14564-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022] Open
Abstract
FDA-approved integrase strand transfer inhibitors (raltegravir, elvitegravir and dolutegravir) efficiently inhibit HIV-1 replication. Here, we present fluorescence properties of these inhibitors. Dolutegravir displays an excitation mode particularly dependent on Mg2+ chelation, allowing to directly probe its Mg2+-dependent binding to the prototype foamy virus (PFV) integrase. Dolutegravir-binding studied by both its fluorescence anisotropy and subsequent emission enhancement, strictly requires a preformed integrase/DNA complex, the ten terminal base pairs from the 3′-end of the DNA reactive strand being crucial to optimize dolutegravir-binding in the context of the ternary complex. From the protein side, mutation of any catalytic residue fully abolishes dolutegravir-binding. We also compared dolutegravir-binding to PFV F190Y, G187R and S217K mutants, corresponding to HIV-1 F121Y, G118R and G140S/Q148K mutations that confer low-to-high resistance levels against raltegravir/dolutegravir. The dolutegravir-binding properties derived from fluorescence-based binding assays and drug susceptibilities in terms of catalytic activity, are well correlated. Indeed, dolutegravir-binding to wild-type and F190Y integrases are comparable while strongly compromised with G187R and S217K. Accordingly, the two latter mutants are highly resistant to dolutegravir while F190Y shows only moderate or no resistance. Intrinsic fluorescence properties of dolutegravir are thus particularly suitable for a thorough characterization of both DNA-binding properties of integrase and resistance mutations.
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26
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Bueno MTD, Reyes D, Llano M. LEDGF/p75 Deficiency Increases Deletions at the HIV-1 cDNA Ends. Viruses 2017; 9:v9090259. [PMID: 28914817 PMCID: PMC5618025 DOI: 10.3390/v9090259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Processing of unintegrated linear HIV-1 cDNA by the host DNA repair system results in its degradation and/or circularization. As a consequence, deficient viral cDNA integration generally leads to an increase in the levels of HIV-1 cDNA circles containing one or two long terminal repeats (LTRs). Intriguingly, impaired HIV-1 integration in LEDGF/p75-deficient cells does not result in a correspondent increase in viral cDNA circles. We postulate that increased degradation of unintegrated linear viral cDNA in cells lacking the lens epithelium-derived growth factor (LEDGF/p75) account for this inconsistency. To evaluate this hypothesis, we characterized the nucleotide sequence spanning 2-LTR junctions isolated from LEDGF/p75-deficient and control cells. LEDGF/p75 deficiency resulted in a significant increase in the frequency of 2-LTRs harboring large deletions. Of note, these deletions were dependent on the 3′ processing activity of integrase and were not originated by aberrant reverse transcription. Our findings suggest a novel role of LEDGF/p75 in protecting the unintegrated 3′ processed linear HIV-1 cDNA from exonucleolytic degradation.
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Affiliation(s)
- Murilo T D Bueno
- Department of Biological Sciences, University of Texas at El Paso. El Paso, TX 79968, USA.
| | - Daniel Reyes
- Department of Biological Sciences, University of Texas at El Paso. El Paso, TX 79968, USA.
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso. El Paso, TX 79968, USA.
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27
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Matysiak J, Lesbats P, Mauro E, Lapaillerie D, Dupuy JW, Lopez AP, Benleulmi MS, Calmels C, Andreola ML, Ruff M, Llano M, Delelis O, Lavigne M, Parissi V. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration. Retrovirology 2017; 14:39. [PMID: 28754126 PMCID: PMC5534098 DOI: 10.1186/s12977-017-0363-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/24/2017] [Indexed: 01/23/2023] Open
Abstract
Background Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Results Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Conclusions Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0363-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Matysiak
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Jean-William Dupuy
- Centre Génomique fonctionnelle Bordeaux, Plateforme Proteome, Université de Bordeaux, Bordeaux, France
| | - Angelica P Lopez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Mohamed Salah Benleulmi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marie-Line Andreola
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marc Ruff
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch-Graffenstaden, France
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Olivier Delelis
- LBPA, UMR8113, CNRS, ENS-Cachan, Cachan, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marc Lavigne
- Department of Virology, UMR 3569, CNRS, Institut Pasteur, Paris, France.,Institut Cochin-INSERM U1016-CNRS UMR8104, Université Paris Descartes, Paris, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France. .,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France. .,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France.
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Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications. Clin Microbiol Rev 2017; 29:859-80. [PMID: 27559075 DOI: 10.1128/cmr.00015-16] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.
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29
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Hamid FB, Kim J, Shin CG. Distribution and fate of HIV-1 unintegrated DNA species: a comprehensive update. AIDS Res Ther 2017; 14:9. [PMID: 28209198 PMCID: PMC5314604 DOI: 10.1186/s12981-016-0127-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 12/07/2016] [Indexed: 12/30/2022] Open
Abstract
Reverse transcription of viral RNA and the subsequent integration of reverse transcripts are the classical early events of the HIV-1 life-cycle. Simultaneously, abundant unintegrated DNAs (uDNAs), are formed in cells ubiquitously. The uDNAs either undergo recombination or degradation or persist inactively for long periods in the nucleus as future resources. Among them, 2-LTR circles are considered a dead-end for viral spread. Their contribution to the HIV-1 infection is still poorly understood. Nevertheless, the preintegration transcription of the aberrant DNAs and the consequent alterations of cellular factors have already been reported. Since the major fate of the viral genome is to persist as episomal DNA, precise characterization is required for studying the biology of HIV-1. This review compiles the biochemical and genetic updates on uDNA in the HIV-1 life cycle and could provide direction to further study of their roles in HIV-1 replication and application in HIV-1 pathogenesis.
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30
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2017; 7:2165. [PMID: 28123383 PMCID: PMC5225119 DOI: 10.3389/fmicb.2016.02165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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31
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Esposito F, Carli I, Del Vecchio C, Xu L, Corona A, Grandi N, Piano D, Maccioni E, Distinto S, Parolin C, Tramontano E. Sennoside A, derived from the traditional chinese medicine plant Rheum L., is a new dual HIV-1 inhibitor effective on HIV-1 replication. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2016; 23:1383-1391. [PMID: 27765358 DOI: 10.1016/j.phymed.2016.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/19/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Despite the availability of effective antiretroviral therapies, drugs for HIV-1 treatment with new mode of action are still needed. An innovative approach is aimed to identify dual HIV-1 inhibitors, small molecules that can inhibit two viral functions at the same time. Rhubarb, originated from Rheum palmatum L. and Rheum officinale Baill., is one of the earliest and most commonly used medicinal plants in Traditional Chinese Medicine (TCM) practice. We wanted to explore TCM for the identification of new chemical scaffolds with dual action abilities against HIV-1. METHODS R. palmatum L. and R. officinale Baill. extracts along with their main single isolated constituents anthraquinone derivatives were tested on both HIV-1 Reverse Transcriptase (RT)-associated DNA Polymerase (RDDP) and Ribonuclease H (RNase H) activities in biochemical assays. Active compounds were then assayed for their effects on HIV-1 mutated RTs, integrase (IN) and viral replication. RESULTS Both R. palmatum L. and R. officinale Baill. extracts inhibited the HIV-1 RT-associated RNase H activity. Among the isolated constituents, Sennoside A and B were effective on both RDDP and RNase H RT-associated functions in biochemical assays. Sennoside A was less potent when tested on K103N, Y181C, Y188L, N474A and Q475A mutated RTs, suggesting the involvement of two RT binding sites for its antiviral activity. Sennoside A affected also HIV-1 IN activity in vitro and HIV-1 replication in cell-based assays. Viral DNA production and time of addition studies showed that Sennoside A targets the HIV-1 reverse transcription process. CONCLUSION Sennoside A is a new scaffold for the development of HIV-1 dual RT inhibitors.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Ilaria Carli
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121 Padova, Italy
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121 Padova, Italy
| | - Lijia Xu
- Institute of Medicinal Plant Development (IMPLAD), 151 Malianwa North Road Haidian District, 100193 Beijing, China
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Dario Piano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121 Padova, Italy.
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy; Genetics and Biomedical Research institute, National Research Council (CNR), Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy.
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32
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Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res 2016; 27:38-52. [PMID: 27831498 PMCID: PMC5204343 DOI: 10.1101/gr.212092.116] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/08/2016] [Indexed: 11/24/2022]
Abstract
Candidate enhancers can be identified on the basis of chromatin modifications, the binding of chromatin modifiers and transcription factors and cofactors, or chromatin accessibility. However, validating such candidates as bona fide enhancers requires functional characterization, typically achieved through reporter assays that test whether a sequence can increase expression of a transcriptional reporter via a minimal promoter. A longstanding concern is that reporter assays are mainly implemented on episomes, which are thought to lack physiological chromatin. However, the magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this systematically, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated with different subsets of ENCODE annotations. The results of chromosomally based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson's R2 of 0.362 for predicting the results of chromosomally integrated reporter assays. This level of prediction is better than with either chromatin annotations or sequence information alone and also outperforms predictive models of episomal assays. Our results have broad implications for how cis-regulatory elements are identified, prioritized and functionally validated.
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Affiliation(s)
- Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Daniela M Witten
- Departments of Statistics and Biostatistics, University of Washington, Seattle, Washington 98195, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, California 94143, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, Seattle, Washington 98195, USA
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33
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Corona A, di Leva FS, Rigogliuso G, Pescatori L, Madia VN, Subra F, Delelis O, Esposito F, Cadeddu M, Costi R, Cosconati S, Novellino E, di Santo R, Tramontano E. New insights into the interaction between pyrrolyl diketoacids and HIV-1 integrase active site and comparison with RNase H. Antiviral Res 2016; 134:236-243. [PMID: 27659398 DOI: 10.1016/j.antiviral.2016.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
HIV-1 integrase (IN) inhibitors are one of the most recent innovations in the treatment of HIV infection. The selection of drug resistance viral strains is however a still open issue requiring constant efforts to identify new anti-HIV-1 drugs. Pyrrolyl diketo acid (DKA) derivatives inhibit HIV-1 replication by interacting with the Mg2+ cofactors within the HIV-1 IN active site or within the HIV-1 reverse-transcriptase associated ribonuclease H (RNase H) active site. While the interaction mode of pyrrolyl DKAs with the RNase H active site has been recently reported and substantiated by mutagenesis experiments, their interaction within the IN active site still lacks a detailed understanding. In this study, we investigated the binding mode of four pyrrolyl DKAs to the HIV-1 IN active site by molecular modeling coupled with site-directed mutagenesis studies showing that the DKA pyrrolyl scaffold primarily interacts with the IN amino residues P145, Q146 and Q148. Importantly, the tested DKAs demonstrated good effectiveness against HIV-1 Raltegravir resistant Y143A and N155H INs, thus showing an interaction pattern with relevant differences if compared with the first generation IN inhibitors. These data provide precious insights for the design of new HIV inhibitors active on clinically selected Raltegravir resistant variants. Furthermore, this study provides new structural information to modulate IN and RNase H inhibitory activities for development of dual-acting anti-HIV agents.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Francesco Saverio di Leva
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Giuseppe Rigogliuso
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy; LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Luca Pescatori
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Frederic Subra
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Roberto di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy.
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34
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Rawson JMO, Roth ME, Xie J, Daly MB, Clouser CL, Landman SR, Reilly CS, Bonnac L, Kim B, Patterson SE, Mansky LM. Synergistic reduction of HIV-1 infectivity by 5-azacytidine and inhibitors of ribonucleotide reductase. Bioorg Med Chem 2016; 24:2410-2422. [PMID: 27117260 DOI: 10.1016/j.bmc.2016.03.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/18/2016] [Accepted: 03/27/2016] [Indexed: 11/29/2022]
Abstract
Although many compounds have been approved for the treatment of human immunodeficiency type-1 (HIV-1) infection, additional anti-HIV-1 drugs (particularly those belonging to new drug classes) are still needed due to issues such as long-term drug-associated toxicities, transmission of drug-resistant variants, and development of multi-class resistance. Lethal mutagenesis represents an antiviral strategy that has not yet been clinically translated for HIV-1 and is based on the use of small molecules to induce excessive levels of deleterious mutations within the viral genome. Here, we show that 5-azacytidine (5-aza-C), a ribonucleoside analog that induces the lethal mutagenesis of HIV-1, and multiple inhibitors of the enzyme ribonucleotide reductase (RNR) interact in a synergistic fashion to more effectively reduce the infectivity of HIV-1. In these drug combinations, RNR inhibitors failed to significantly inhibit the conversion of 5-aza-C to 5-aza-2'-deoxycytidine, suggesting that 5-aza-C acts primarily as a deoxyribonucleoside even in the presence of RNR inhibitors. The mechanism of antiviral synergy was further investigated for the combination of 5-aza-C and one specific RNR inhibitor, resveratrol, as this combination improved the selectivity index of 5-aza-C to the greatest extent. Antiviral synergy was found to be primarily due to the reduced accumulation of reverse transcription products rather than the enhancement of viral mutagenesis. To our knowledge, these observations represent the first demonstration of antiretroviral synergy between a ribonucleoside analog and RNR inhibitors, and encourage the development of additional ribonucleoside analogs and RNR inhibitors with improved antiretroviral activity.
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Affiliation(s)
- Jonathan M O Rawson
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Megan E Roth
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Michele B Daly
- Emory Center for AIDS Research, Emory University, 1518 Clifton Road NE, Suite 8050, Atlanta, GA 30322, USA
| | - Christine L Clouser
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Sean R Landman
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union Street SE, Minneapolis, MN 55455, USA
| | - Cavan S Reilly
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Laurent Bonnac
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Baek Kim
- Emory Center for AIDS Research, Emory University, 1518 Clifton Road NE, Suite 8050, Atlanta, GA 30322, USA
| | - Steven E Patterson
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Microbiology and Immunology, Medical School, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA; Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA.
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35
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Thierry S, Thierry E, Subra F, Deprez E, Leh H, Bury-Moné S, Delelis O. Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway. Sci Rep 2016; 6:25678. [PMID: 27167871 PMCID: PMC4863372 DOI: 10.1038/srep25678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
Integration of HIV-1 linear DNA into host chromatin is required for high levels of viral expression, and constitutes a key therapeutic target. Unintegrated viral DNA (uDNA) can support only limited transcription but may contribute to viral propagation, persistence and/or treatment escape under specific situations. The molecular mechanisms involved in the differential expression of HIV uDNA vs integrated genome (iDNA) remain to be elucidated. Here, we demonstrate, for the first time, that the expression of HIV uDNA is mainly supported by 1-LTR circles, and regulated in the opposite way, relatively to iDNA, following NF-κB pathway modulation. Upon treatment activating the NF-κB pathway, NF-κB p65 and AP-1 (cFos/cJun) binding to HIV LTR iDNA correlates with increased iDNA expression, while uDNA expression decreases. On the contrary, inhibition of the NF-κB pathway promotes the expression of circular uDNA, and correlates with Bcl-3 and AP-1 binding to its LTR region. Finally, this study identifies NF-κB subunits and Bcl-3 as transcription factors binding the HIV promoter differently depending on viral genome topology, and opens new insights on the potential roles of episomal genomes during the HIV-1 latency and persistence.
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Affiliation(s)
- Sylvain Thierry
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Eloïse Thierry
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Frédéric Subra
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Eric Deprez
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Hervé Leh
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Stéphanie Bury-Moné
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
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36
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Chin CJ, Cooper AR, Lill GR, Evseenko D, Zhu Y, He CB, Casero D, Pellegrini M, Kohn DB, Crooks GM. Genetic Tagging During Human Mesoderm Differentiation Reveals Tripotent Lateral Plate Mesodermal Progenitors. Stem Cells 2016; 34:1239-50. [PMID: 26934332 DOI: 10.1002/stem.2351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/08/2016] [Indexed: 02/02/2023]
Abstract
Although clonal studies of lineage potential have been extensively applied to organ specific stem and progenitor cells, much less is known about the clonal origins of lineages formed from the germ layers in early embryogenesis. We applied lentiviral tagging followed by vector integration site analysis (VISA) with high-throughput sequencing to investigate the ontogeny of the hematopoietic, endothelial and mesenchymal lineages as they emerge from human embryonic mesoderm. In contrast to studies that have used VISA to track differentiation of self-renewing stem cell clones that amplify significantly over time, we focused on a population of progenitor clones with limited self-renewal capability. Our analyses uncovered the critical influence of sampling on the interpretation of lentiviral tag sharing, particularly among complex populations with minimal clonal duplication. By applying a quantitative framework to estimate the degree of undersampling we revealed the existence of tripotent mesodermal progenitors derived from pluripotent stem cells, and the subsequent bifurcation of their differentiation into bipotent endothelial/hematopoietic or endothelial/mesenchymal progenitors. Stem Cells 2016;34:1239-1250.
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Affiliation(s)
- Chee Jia Chin
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine (DGSOM)
| | - Aaron R Cooper
- Molecular Biology Interdepartmental PhD Program, DGSOM University of California Los Angeles.,Department of Microbiology, Immunology and Molecular Genetics, DGSOM, DGSOM University of California Los Angeles
| | - Georgia R Lill
- Department of Microbiology, Immunology and Molecular Genetics, DGSOM, DGSOM University of California Los Angeles
| | - Denis Evseenko
- Department of Orthopedic Surgery, Keck School of Medicine of University of Southern California (USC). All in, Los Angeles, CA, United States
| | - Yuhua Zhu
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine (DGSOM)
| | - Chong Bin He
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine (DGSOM)
| | - David Casero
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine (DGSOM)
| | - Matteo Pellegrini
- Department of Molecular, Cell and Development Biology, DGSOM University of California Los Angeles.,Molecular Biology Institute (MBI)
| | - Donald B Kohn
- Department of Microbiology, Immunology and Molecular Genetics, DGSOM, DGSOM University of California Los Angeles.,Molecular Biology Institute (MBI).,Department of Pediatrics, DGSOM University of California Los Angeles.,Broad Stem Cell Research Center (BSCRC), DGSOM University of California Los Angeles.,Jonsson Comprehensive Cancer Center (JCCC), DGSOM University of California Los Angeles
| | - Gay M Crooks
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine (DGSOM).,Department of Pediatrics, DGSOM University of California Los Angeles.,Broad Stem Cell Research Center (BSCRC), DGSOM University of California Los Angeles.,Department of Pathology & Laboratory Medicine, DGSOM University of California Los Angeles
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A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin. Proc Natl Acad Sci U S A 2016; 113:E1054-63. [PMID: 26858452 DOI: 10.1073/pnas.1524213113] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Integration is vital to retroviral replication and influences the establishment of the latent HIV reservoir. HIV-1 integration favors active genes, which is in part determined by the interaction between integrase and lens epithelium-derived growth factor (LEDGF)/p75. Because gene targeting remains significantly enriched, relative to random in LEDGF/p75 deficient cells, other host factors likely contribute to gene-tropic integration. Nucleoporins 153 and 358, which bind HIV-1 capsid, play comparatively minor roles in integration targeting, but the influence of another capsid binding protein, cleavage and polyadenylation specificity factor 6 (CPSF6), has not been reported. In this study we knocked down or knocked out CPSF6 in parallel or in tandem with LEDGF/p75. CPSF6 knockout changed viral infectivity kinetics, decreased proviral formation, and preferentially decreased integration into transcriptionally active genes, spliced genes, and regions of chromatin enriched in genes and activating histone modifications. LEDGF/p75 depletion by contrast preferentially altered positional integration targeting within gene bodies. Dual factor knockout reduced integration into genes to below the levels observed with either single knockout and revealed that CPSF6 played a more dominant role than LEDGF/p75 in directing integration to euchromatin. CPSF6 complementation rescued HIV-1 integration site distribution in CPSF6 knockout cells, but complementation with a capsid binding mutant of CPSF6 did not. We conclude that integration targeting proceeds via two distinct mechanisms: capsid-CPSF6 binding directs HIV-1 to actively transcribed euchromatin, where the integrase-LEDGF/p75 interaction drives integration into gene bodies.
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2016. [PMID: 28123383 DOI: 10.3389/fmicb.2016.02165/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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Malet I, Thierry E, Wirden M, Lebourgeois S, Subra F, Katlama C, Deprez E, Calvez V, Marcelin AG, Delelis O. Combination of two pathways involved in raltegravir resistance confers dolutegravir resistance. J Antimicrob Chemother 2015. [PMID: 26205139 DOI: 10.1093/jac/dkv197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES HIV-1 integration can be efficiently inhibited by strand-transfer inhibitors such as raltegravir, elvitegravir or dolutegravir. Three pathways conferring raltegravir/elvitegravir cross-resistance (involving integrase residues Q148, N155 and Y143) were identified. Dolutegravir, belonging to the second generation of strand-transfer compounds, inhibits the Y143 and N155 pathways, but is less efficient at inhibiting the Q148 pathway. The aim of this study was to characterize the combination of two pathways involved in raltegravir resistance described in one patient failing a dolutegravir regimen for their propensity to confer dolutegravir resistance. METHODS In this study, a patient first failing a regimen including raltegravir was treated with dolutegravir and showed an increase in viruses carrying a combination of two pathways (N155 and Q148). Impacts of these mutations on integrase activity and resistance to strand-transfer inhibitors were characterized using both in vitro and virological assays. RESULTS Our data showed that the combination of N155H, G140S and Q148H mutations led to strong resistance to dolutegravir. CONCLUSIONS Combination of N155H, G140S and Q148H mutations originating from two distinct resistance pathways to raltegravir or elvitegravir led to a high level of dolutegravir resistance. Due to its high genetic barrier of resistance, it would be reasonable to use dolutegravir in first-line therapy before emergence of raltegravir or elvitegravir resistance.
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Affiliation(s)
- Isabelle Malet
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM UMR-S 1136, Paris 75014, France
| | - Eloise Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, Cachan 94235, France
| | - Marc Wirden
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM UMR-S 1136, Paris 75014, France
| | - Samuel Lebourgeois
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, Cachan 94235, France
| | - Frédéric Subra
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, Cachan 94235, France
| | - Christine Katlama
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM UMR-S 1136, Paris 75014, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, Cachan 94235, France
| | - Vincent Calvez
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM UMR-S 1136, Paris 75014, France
| | - Anne-Geneviève Marcelin
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM UMR-S 1136, Paris 75014, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, Cachan 94235, France
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Thierry S, Benleulmi MS, Sinzelle L, Thierry E, Calmels C, Chaignepain S, Waffo-Teguo P, Merillon JM, Budke B, Pasquet JM, Litvak S, Ciuffi A, Sung P, Connell P, Hauber I, Hauber J, Andreola ML, Delelis O, Parissi V. Dual and Opposite Effects of hRAD51 Chemical Modulation on HIV-1 Integration. ACTA ACUST UNITED AC 2015; 22:712-23. [PMID: 26051216 DOI: 10.1016/j.chembiol.2015.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/31/2015] [Accepted: 04/22/2015] [Indexed: 12/24/2022]
Abstract
The cellular DNA repair hRAD51 protein has been shown to restrict HIV-1 integration both in vitro and in vivo. To investigate its regulatory functions, we performed a pharmacological analysis of the retroviral integration modulation by hRAD51. We found that, in vitro, chemical activation of hRAD51 stimulates its integration inhibitory properties, whereas inhibition of hRAD51 decreases the integration restriction, indicating that the modulation of HIV-1 integration depends on the hRAD51 recombinase activity. Cellular analyses demonstrated that cells exhibiting high hRAD51 levels prior to de novo infection are more resistant to integration. On the other hand, when hRAD51 was activated during integration, cells were more permissive. Altogether, these data establish the functional link between hRAD51 activity and HIV-1 integration. Our results highlight the multiple and opposite effects of the recombinase during integration and provide new insights into the cellular regulation of HIV-1 replication.
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Affiliation(s)
| | | | - Ludivine Sinzelle
- MFP, UMR5234, CNRS-Université de Bordeaux, SFR Transbiomed, 33076 Bordeaux, France
| | | | - Christina Calmels
- MFP, UMR5234, CNRS-Université de Bordeaux, SFR Transbiomed, 33076 Bordeaux, France
| | | | - Pierre Waffo-Teguo
- GESVAB, EA 3675 - UFR Pharmacie, Université de Bordeaux, ISVV, 33076 Bordeaux, France
| | - Jean-Michel Merillon
- GESVAB, EA 3675 - UFR Pharmacie, Université de Bordeaux, ISVV, 33076 Bordeaux, France
| | - Brian Budke
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Jean-Max Pasquet
- Laboratoire Biothérapies des Maladies Génétiques et Cancers, INSERM U1035, Université de Bordeaux, 33076 Bordeaux, France
| | - Simon Litvak
- MFP, UMR5234, CNRS-Université de Bordeaux, SFR Transbiomed, 33076 Bordeaux, France
| | - Angela Ciuffi
- Institute of Microbiology (IMUL), Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Patrick Sung
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06320-8024, USA
| | - Philip Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Ilona Hauber
- HPI, Leibniz Institute for Experimental Virology, German Center for Infection Research (DZIF), 20251 Hamburg, Germany
| | - Joachim Hauber
- HPI, Leibniz Institute for Experimental Virology, German Center for Infection Research (DZIF), 20251 Hamburg, Germany
| | - Marie-Line Andreola
- MFP, UMR5234, CNRS-Université de Bordeaux, SFR Transbiomed, 33076 Bordeaux, France
| | | | - Vincent Parissi
- MFP, UMR5234, CNRS-Université de Bordeaux, SFR Transbiomed, 33076 Bordeaux, France.
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Novel 3'-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors. BIOMED RESEARCH INTERNATIONAL 2015; 2015:853891. [PMID: 26064960 PMCID: PMC4439469 DOI: 10.1155/2015/853891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 11/25/2022]
Abstract
The 3′-end processing (3′P) of each viral long terminal repeat (LTR) during human immunodeficiency virus type-1 (HIV-1) integration is a vital step in the HIV life cycle. Blocking the 3′P using 3′P inhibitor has recently become an attractive strategy for HIV-1 therapeutic intervention. Recently, we have developed a novel real-time PCR based assay for the detection of 3′P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase (IN), and specific primers and probe. In this novel assay, we designed the HIV-1 LTR substrate based on a sequence with a homology to HIV-1 LTR labeled at its 3′ end with biotin on the sense strand. Two nucleotides at the 3′ end were subsequently removed by IN activity. Only two nucleotides labeled biotin were captured on an avidin-coated tube; therefore, inhibiting the binding of primers and probe results in late signals in the real-time PCR. This novel assay has successfully detected both the 3′P activity of HIV-1 IN and the anti-IN activity by Raltegravir and sodium azide agent. This real-time PCR assay has been shown to be effective and inexpensive for a high-throughput screening of novel IN inhibitors.
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Thierry S, Munir S, Thierry E, Subra F, Leh H, Zamborlini A, Saenz D, Levy DN, Lesbats P, Saïb A, Parissi V, Poeschla E, Deprez E, Delelis O. Integrase inhibitor reversal dynamics indicate unintegrated HIV-1 dna initiate de novo integration. Retrovirology 2015; 12:24. [PMID: 25808736 PMCID: PMC4372172 DOI: 10.1186/s12977-015-0153-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic integration, an obligate step in the HIV-1 replication cycle, is blocked by the integrase inhibitor raltegravir. A consequence is an excess of unintegrated viral DNA genomes, which undergo intramolecular ligation and accumulate as 2-LTR circles. These circularized genomes are also reliably observed in vivo in the absence of antiviral therapy and they persist in non-dividing cells. However, they have long been considered as dead-end products that are not precursors to integration and further viral propagation. RESULTS Here, we show that raltegravir action is reversible and that unintegrated viral DNA is integrated in the host cell genome after raltegravir removal leading to HIV-1 replication. Using quantitative PCR approach, we analyzed the consequences of reversing prolonged raltegravir-induced integration blocks. We observed, after RAL removal, a decrease of 2-LTR circles and a transient increase of linear DNA that is subsequently integrated in the host cell genome and fuel new cycles of viral replication. CONCLUSIONS Our data highly suggest that 2-LTR circles can be used as a reserve supply of genomes for proviral integration highlighting their potential role in the overall HIV-1 replication cycle.
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Engelman A, Cherepanov P. Retroviral Integrase Structure and DNA Recombination Mechanism. Microbiol Spectr 2015; 2:1-22. [PMID: 25705574 PMCID: PMC4334468 DOI: 10.1128/microbiolspec.mdna3-0024-2014] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 12/13/2022] Open
Abstract
Due to the importance of human immunodeficiency virus type 1 (HIV-1) integrase as a drug target, the biochemistry and structural aspects of retroviral DNA integration have been the focus of intensive research during the past three decades. The retroviral integrase enzyme acts on the linear double-stranded viral DNA product of reverse transcription. Integrase cleaves specific phosphodiester bonds near the viral DNA ends during the 3' processing reaction. The enzyme then uses the resulting viral DNA 3'-OH groups during strand transfer to cut chromosomal target DNA, which simultaneously joins both viral DNA ends to target DNA 5'-phosphates. Both reactions proceed via direct transesterification of scissile phosphodiester bonds by attacking nucleophiles: a water molecule for 3' processing, and the viral DNA 3'-OH for strand transfer. X-ray crystal structures of prototype foamy virus integrase-DNA complexes revealed the architectures of the key nucleoprotein complexes that form sequentially during the integration process and explained the roles of active site metal ions in catalysis. X-ray crystallography furthermore elucidated the mechanism of action of HIV-1 integrase strand transfer inhibitors, which are currently used to treat AIDS patients, and provided valuable insights into the mechanisms of viral drug resistance.
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Affiliation(s)
- Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline, Avenue, CLS-1010, Boston, MA 02215
| | - Peter Cherepanov
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, Potters Bar, EN6 3LD, United Kingdom
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Comparison Between Several Integrase-defective Lentiviral Vectors Reveals Increased Integration of an HIV Vector Bearing a D167H Mutant. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e213. [PMID: 25462529 PMCID: PMC4272407 DOI: 10.1038/mtna.2014.65] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/09/2014] [Indexed: 01/20/2023]
Abstract
HIV-1 derived vectors are among the most efficient for gene transduction in mammalian tissues. As the parent virus, they carry out vector genome insertion into the host cell chromatin. Consequently, their preferential integration in transcribed genes raises several conceptual and safety issues. To address part of these questions, HIV-derived vectors have been engineered to be nonintegrating. This was mainly achieved by mutating HIV-1 integrase at functional hotspots of the enzyme enabling the development of streamlined nuclear DNA circles functional for transgene expression. Few integrase mutant vectors have been successfully tested so far for gene transfer. They are cleared with time in mitotic cells, but stable within nondividing retina cells or neurons. Here, we compared six HIV vectors carrying different integrases, either wild type or with different mutations (D64V, D167H, Q168A, K186Q+Q214L+Q216L, and RRK262-264AAH) shown to modify integrase enzymatic activity, oligomerization, or interaction with key cellular cofactor of HIV DNA integration as LEDGF/p75 or TNPO3. We show that these mutations differently affect the transduction efficiency as well as rates and patterns of integration of HIV-derived vectors suggesting their different processing in the nucleus. Surprisingly and most interestingly, we report that an integrase carrying the D167H substitution improves vector transduction efficiency and integration in both HEK-293T and primary CD34+ cells.
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Munir S, Thierry E, Malet I, Subra F, Calvez V, Marcelin AG, Deprez E, Delelis O. G118R and F121Y mutations identified in patients failing raltegravir treatment confer dolutegravir resistance. J Antimicrob Chemother 2014; 70:739-49. [PMID: 25414202 DOI: 10.1093/jac/dku474] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES Strand transfer inhibitors (raltegravir, elvitegravir and dolutegravir) are now commonly used to inhibit HIV-1 integration. To date, three main pathways conferring raltegravir/elvitegravir resistance, involving residues Y143, Q148 and N155, have been described. However, no pathway has been clearly described for dolutegravir resistance. The aim of this study was to characterize the susceptibility of two mutations, F121Y and G118R, originally described in patients failing raltegravir-containing regimens, to dolutegravir and raltegravir, and then to compare the resistance of these mutations with that of other well-known mutations involved in raltegravir resistance. METHODS Both the F121Y and G118R mutations were introduced by site-directed mutagenesis into the pNL4.3 backbone and studied in cell-based and in vitro assays. The effects of the mutations were characterized at the different steps of infection by quantitative PCR. RESULTS Results obtained with in vitro and ex vivo assays consistently showed that both mutations impaired the catalytic properties of integrase, especially at the integration step. Moreover, both mutations conferred an intermediate level of resistance to dolutegravir. Interestingly, the F121Y mutation, but not the G118R mutation, displayed differential resistance to raltegravir and dolutegravir. Indeed, the F121Y mutation was more resistant to raltegravir than to dolutegravir. CONCLUSIONS Mutations at G118 and F121, which have been described in patients failing raltegravir-containing regimens, must be included in drug-resistance-testing algorithms.
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Affiliation(s)
- Soundasse Munir
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan, France
| | - Eloise Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan, France
| | - Isabelle Malet
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM U943, Paris, France
| | - Frédéric Subra
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan, France
| | - Vincent Calvez
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM U943, Paris, France
| | - Anne-Geneviève Marcelin
- Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Université Pierre et Marie Curie, INSERM U943, Paris, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR8113, ENS-Cachan, 94235 Cachan, France
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Casabianca A, Orlandi C, Canovari B, Scotti M, Acetoso M, Valentini M, Petrelli E, Magnani M. A real time PCR platform for the simultaneous quantification of total and extrachromosomal HIV DNA forms in blood of HIV-1 infected patients. PLoS One 2014; 9:e111919. [PMID: 25364909 PMCID: PMC4218859 DOI: 10.1371/journal.pone.0111919] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/01/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The quantitative measurement of various HIV-1 DNA forms including total, unintegrated and integrated provirus play an increasingly important role in HIV-1 infection monitoring and treatment-related research. We report the development and validation of a SYBR Green real time PCR (TotUFsys platform) for the simultaneous quantification of total and extrachromosomal HIV-1 DNA forms in patients. This innovative technique makes it possible to obtain both measurements in a single PCR run starting from frozen blood employing the same primers and standard curve. Moreover, due to identical amplification efficiency, it allows indirect estimation of integrated level. To specifically detect 2-LTR a qPCR method was also developed. METHODOLOGY/FINDINGS Primers used for total HIV-1 DNA quantification spanning a highly conserved region were selected and found to detect all HIV-1 clades of group M and the unintegrated forms of the same. A total of 195 samples from HIV-1 patients in a wide range of clinical conditions were analyzed with a 100% success rate, even in patients with suppressed plasma viremia, regardless of CD4+ or therapy. No significant correlation was observed between the two current prognostic markers, CD4+ and plasma viremia, while a moderate or high inverse correlation was found between CD4+ and total HIV DNA, with strong values for unintegrated HIV DNA. CONCLUSIONS/SIGNIFICANCE Taken together, the results support the use of HIV DNA as another tool, in addition to traditional assays, which can be used to estimate the state of viral infection, the risk of disease progression and to monitor the effects of ART. The TotUFsys platform allowed us to obtain a final result, expressed as the total and unintegrated HIV DNA copy number per microgram of DNA or 10(4) CD4+, for 12 patients within two working days.
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Affiliation(s)
- Anna Casabianca
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino (PU), Italy
- * E-mail:
| | - Chiara Orlandi
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino (PU), Italy
| | - Benedetta Canovari
- Azienda Ospedaliera Ospedali Riuniti Marche Nord - Presidio Ospedaliero San Salvatore, Pesaro (PU), Italy
| | - Maddalena Scotti
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino (PU), Italy
| | - Marcello Acetoso
- Azienda Ospedaliera Ospedali Riuniti Marche Nord - Presidio Ospedaliero San Salvatore, Pesaro (PU), Italy
| | - Massimo Valentini
- Azienda Ospedaliera Ospedali Riuniti Marche Nord - Presidio Ospedaliero San Salvatore, Pesaro (PU), Italy
| | - Enzo Petrelli
- Azienda Ospedaliera Ospedali Riuniti Marche Nord - Presidio Ospedaliero San Salvatore, Pesaro (PU), Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino (PU), Italy
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Matreyek KA, Wang W, Serrao E, Singh PK, Levin HL, Engelman A. Host and viral determinants for MxB restriction of HIV-1 infection. Retrovirology 2014; 11:90. [PMID: 25348155 PMCID: PMC4213484 DOI: 10.1186/s12977-014-0090-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Interferon-induced cellular proteins play important roles in the host response against viral infection. The Mx family of dynamin-like GTPases, which include MxA and MxB, target a wide variety of viruses. Despite considerable evidence demonstrating the breadth of antiviral activity of MxA, human MxB was only recently discovered to specifically inhibit lentiviruses. Here we assess both host and viral determinants that underlie MxB restriction of HIV-1 infection. RESULTS Heterologous expression of MxB in human osteosarcoma cells potently inhibited HIV-1 infection (~12-fold), yet had little to no effect on divergent retroviruses. The anti-HIV effect manifested as a partial block in the formation of 2-long terminal repeat circle DNA and hence nuclear import, and we accordingly found evidence for an additional post-nuclear entry block. A large number of previously characterized capsid mutations, as well as mutations that abrogated integrase activity, counteracted MxB restriction. MxB expression suppressed integration into gene-enriched regions of chromosomes, similar to affects observed previously when cells were depleted for nuclear transport factors such as transportin 3. MxB activity did not require predicted GTPase active site residues or a series of unstructured loops within the stalk domain that confer functional oligomerization to related dynamin family proteins. In contrast, we observed an N-terminal stretch of residues in MxB to harbor key determinants. Protein localization conferred by a nuclear localization signal (NLS) within the N-terminal 25 residues, which was critical, was fully rescuable by a heterologous NLS. Consistent with this observation, a heterologous nuclear export sequence (NES) abolished full-length MxB activity. We additionally mapped sub-regions within amino acids 26-90 that contribute to MxB activity, finding sequences present within residues 27-50 particularly important. CONCLUSIONS MxB inhibits HIV-1 by interfering with minimally two steps of infection, nuclear entry and post-nuclear trafficking and/or integration, without destabilizing the inherent catalytic activity of viral preintegration complexes. Putative MxB GTPase active site residues and stalk domain Loop 4 -- both previously shown to be necessary for MxA function -- were dispensable for MxB antiviral activity. Instead, we highlight subcellular localization and a yet-determined function(s) present in the unique MxB N-terminal region to be required for HIV-1 restriction.
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Affiliation(s)
- Kenneth A Matreyek
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA. .,Present address: Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
| | - Weifeng Wang
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA.
| | - Erik Serrao
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA.
| | - Parmit Kumar Singh
- Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Henry L Levin
- Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Alan Engelman
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA.
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Alidjinou EK, Bocket L, Hober D. Quantification of viral DNA during HIV-1 infection: A review of relevant clinical uses and laboratory methods. ACTA ACUST UNITED AC 2014; 63:53-9. [PMID: 25201144 DOI: 10.1016/j.patbio.2014.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/15/2014] [Indexed: 01/25/2023]
Abstract
Effective antiretroviral therapy usually leads to undetectable HIV-1 RNA in the plasma. However, the virus persists in some cells of infected patients as various DNA forms, both integrated and unintegrated. This reservoir represents the greatest challenge to the complete cure of HIV-1 infection and its characteristics highly impact the course of the disease. The quantification of HIV-1 DNA in blood samples constitutes currently the most practical approach to measure this residual infection. Real-time quantitative PCR (qPCR) is the most common method used for HIV-DNA quantification and many strategies have been developed to measure the different forms of HIV-1 DNA. In the literature, several "in-house" PCR methods have been used and there is a need for standardization to have comparable results. In addition, qPCR is limited for the precise quantification of low levels by background noise. Among new assays in development, digital PCR was shown to allow an accurate quantification of HIV-1 DNA. Total HIV-1 DNA is most commonly measured in clinical routine. The absolute quantification of proviruses and unintegrated forms is more often used for research purposes.
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Affiliation(s)
- E K Alidjinou
- Laboratoire de virologie EA3610, faculté de médecine, institut Hippocrate, université Lille 2, CHRU Lille, 152, rue du Dr-Yersin, 59120 Loos-lez-Lille, France
| | - L Bocket
- Laboratoire de virologie EA3610, faculté de médecine, institut Hippocrate, université Lille 2, CHRU Lille, 152, rue du Dr-Yersin, 59120 Loos-lez-Lille, France
| | - D Hober
- Laboratoire de virologie EA3610, faculté de médecine, institut Hippocrate, université Lille 2, CHRU Lille, 152, rue du Dr-Yersin, 59120 Loos-lez-Lille, France.
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Identification of highly conserved residues involved in inhibition of HIV-1 RNase H function by Diketo acid derivatives. Antimicrob Agents Chemother 2014; 58:6101-10. [PMID: 25092689 DOI: 10.1128/aac.03605-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
HIV-1 reverse transcriptase (RT)-associated RNase H activity is an essential function in viral genome retrotranscription. RNase H is a promising drug target for which no inhibitor is available for therapy. Diketo acid (DKA) derivatives are active site Mg(2+)-binding inhibitors of both HIV-1 RNase H and integrase (IN) activities. To investigate the DKA binding site of RNase H and the mechanism of action, six couples of ester and acid DKAs, derived from 6-[1-(4-fluorophenyl)methyl-1H-pyrrol-2-yl)]-2,4-dioxo-5-hexenoic acid ethyl ester (RDS1643), were synthesized and tested on both RNase H and IN functions. Most of the ester derivatives showed selectivity for HIV-1 RNase H versus IN, while acids inhibited both functions. Molecular modeling and site-directed mutagenesis studies on the RNase H domain demonstrated different binding poses for ester and acid DKAs and proved that DKAs interact with residues (R448, N474, Q475, Y501, and R557) involved not in the catalytic motif but in highly conserved portions of the RNase H primer grip motif. The ester derivative RDS1759 selectively inhibited RNase H activity and viral replication in the low micromolar range, making contacts with residues Q475, N474, and Y501. Quantitative PCR studies and fluorescence-activated cell sorting (FACS) analyses showed that RDS1759 selectively inhibited reverse transcription in cell-based assays. Overall, we provide the first demonstration that RNase H inhibition by DKAs is due not only to their chelating properties but also to specific interactions with highly conserved amino acid residues in the RNase H domain, leading to effective targeting of HIV retrotranscription in cells and hence offering important insights for the rational design of RNase H inhibitors.
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Francis AC, Di Primio C, Quercioli V, Valentini P, Boll A, Girelli G, Demichelis F, Arosio D, Cereseto A. Second generation imaging of nuclear/cytoplasmic HIV-1 complexes. AIDS Res Hum Retroviruses 2014; 30:717-26. [PMID: 24798748 DOI: 10.1089/aid.2013.0277] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ability to visualize fluorescent HIV-1 particles within the nuclei of infected cells represents an attractive tool to study the nuclear biology of the virus. To this aim we recently developed a microscopy-based fluorescent system (HIV-IN-EGFP) that has proven valid to efficiently visualize HIV-1 complexes in the nuclear compartment and to examine the nuclear import efficiency of the virus. The power of this method to investigate viral events occurring between the cytoplasmic and the nuclear compartment is further shown in this study through the analysis of HIV-IN-EGFP in cells expressing the TRIMCyp restriction factor. In these cells the HIV-IN-EGFP complexes are not detected in the nuclear compartment, while treatment with MG132 reveals an accumulation of HIV-1 complexes in the cytoplasm. However, the Vpr-mediated transincorporation strategy used to incorporate IN fused to EGFP (IN-EGFP) impaired viral infectivity. To optimize the infectivity of the HIV-IN-EGFP, we used mutated forms of IN (E11K and K186E) known to stabilize the IN complexes and to partially restore viral infectivity in transcomplementation experiments. The fluorescent particles produced with the modified IN [HIV-IN(K)EGFP_IN(E)] show almost 30% infectivity as compared to wild-type NL4.3. Detailed confocal microscopy analysis revealed that the newly generated viral particles resulted in HIV-1 complexes significantly smaller in size, thus requiring the use of brighter fluorophores for nuclear visualization [HIV-IN(K)sfGFP_IN(E)]. The second-generation visualization system HIV-IN(K)sfGFP_IN(E), in addition to allowing direct visualization of HIV-1 nuclear entry and other viral events related to nuclear import, preserves intact viral properties in terms of nuclear entry and improved infectivity.
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Affiliation(s)
| | | | | | - Paola Valentini
- Center for Bio-Molecular Nanotechnologies, Istituto Italiano di Tecnologia (IIT), Arnesano (Lecce), Italy
| | - Annegret Boll
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Girelli
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Demichelis
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Daniele Arosio
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche & Fondazione Bruno Kessler, Trento, Italy
| | - Anna Cereseto
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
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