1
|
Malatinkova E, Thomas J, De Spiegelaere W, Rutsaert S, Geretti AM, Pollakis G, Paxton WA, Vandekerckhove L, Ruggiero A. Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human Alu Repeat Sequences. Life (Basel) 2021; 11:life11121410. [PMID: 34947941 PMCID: PMC8706387 DOI: 10.3390/life11121410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/28/2022] Open
Abstract
Integrated HIV-1 DNA persists despite antiretroviral therapy and can fuel viral rebound following treatment interruption. Hence, methods to specifically measure the integrated HIV-1 DNA portion only are important to monitor the reservoir in eradication trials. Here, we provide an up-to-date overview of the literature on the different approaches used to measure integrated HIV-1 DNA. Further, we propose an implemented standard-curve free assay to quantify integrated HIV-1 DNA, so-called Alu-5LTR PCR, which utilises novel primer combinations. We tested the Alu-5LTR PCR in 20 individuals on suppressive ART for a median of nine years; the results were compared to those produced with the standard-free Alu-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1–12) and 14 (5–26) with the Alu-gag and Alu-5LTR, respectively. The ratios between Alu-gag vs Alu-5LTR results were distributed within the cohort as follows: most patients (12/20, 60%) provided ratios between 2–5, with 3/20 (15%) and 5/20 (25%) being below or above this range, respectively. Alu-5LTR assay sensitivity was also determined using an “integrated standard”; the data confirmed the increased sensitivity of the assay, i.e., equal to 0.25 proviruses in 10,000 genomes. This work represents an improvement in the field of measuring proviral HIV-1 DNA that could be employed in future HIV-1 persistence and eradication studies.
Collapse
Affiliation(s)
- Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Faculty of Veterinary Sciences, Ghent University, B-9820 Ghent, Belgium;
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Anna Maria Geretti
- Fondazione PTV and Faculty of Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
- Department Neurosciences, Biomedicine and Movement Sciences, School of Medicine-University of Verona, 37129 Verona, Italy
- Correspondence: ; Tel.: +39-045-802-7190
| |
Collapse
|
2
|
Kint S, Trypsteen W, De Spiegelaere W, Malatinkova E, Kinloch-de Loes S, De Meyer T, Van Criekinge W, Vandekerckhove L. Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals. Clin Epigenetics 2020; 12:36. [PMID: 32111236 PMCID: PMC7049218 DOI: 10.1186/s13148-020-00829-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background The HIV-1 proviral genome harbors multiple CpG islands (CpGIs), both in the promoter and intragenic regions. DNA methylation in the promoter region has been shown to be heavily involved in HIV-1 latency regulation in cultured cells. However, its exact role in proviral transcriptional regulation in infected individuals is poorly understood or characterized. Moreover, methylation at intragenic CpGIs has never been studied in depth. Results A large, well-characterized HIV-1 patient cohort (n = 72), consisting of 17 long-term non-progressors and 8 recent seroconverters (SRCV) without combination antiretroviral therapy (cART), 15 early cART-treated, and 32 late cART-treated patients, was analyzed using a next-generation bisulfite sequencing DNA methylation method. In general, we observed low level of promoter methylation and higher levels of intragenic methylation. Additionally, SRCV showed increased promoter methylation and decreased intragenic methylation compared with the other patient groups. This data indicates that increased intragenic methylation could be involved in proviral transcriptional regulation. Conclusions Contrasting in vitro studies, our results indicate that intragenic hypermethylation of HIV-1 proviral DNA is an underestimated factor in viral control in HIV-1-infected individuals, showing the importance of analyzing the complete proviral genome in future DNA methylation studies.
Collapse
Affiliation(s)
- Sam Kint
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium.,Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bio-science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium
| | - Sabine Kinloch-de Loes
- Division of Infection and Immunity, Royal Free Hospital, Royal Free Campus, University College London, Pont St, Hampstead, London, NW3 2QG, UK
| | - Tim De Meyer
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bio-science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bio-science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium.
| |
Collapse
|
3
|
Van Hecke C, Trypsteen W, Malatinkova E, De Spiegelaere W, Vervisch K, Rutsaert S, Kinloch-de Loes S, Sips M, Vandekerckhove L. Early treated HIV-1 positive individuals demonstrate similar restriction factor expression profile as long-term non-progressors. EBioMedicine 2019; 41:443-454. [PMID: 30770230 PMCID: PMC6442000 DOI: 10.1016/j.ebiom.2019.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
- Clarissa Van Hecke
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Karen Vervisch
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Sabine Kinloch-de Loes
- Division of Infection and Immunitys, Royal Free Hospital and Royal Free Campus, University College London, Pont St, Hampstead, London NW3 2QG, United Kingdom
| | - Magdalena Sips
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| |
Collapse
|
4
|
Höhne K, Businger R, van Nuffel A, Bolduan S, Koppensteiner H, Baeyens A, Vermeire J, Malatinkova E, Verhasselt B, Schindler M. Virion encapsidated HIV-1 Vpr induces NFAT to prime non-activated T cells for productive infection. Open Biol 2017; 6:rsob.160046. [PMID: 27383627 PMCID: PMC4967821 DOI: 10.1098/rsob.160046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/13/2016] [Indexed: 01/01/2023] Open
Abstract
The majority of T cells encountered by HIV-1 are non-activated and do not readily allow productive infection. HIV-1 Vpr is highly abundant in progeny virions, and induces signalling and HIV-1 LTR transcription. We hence hypothesized that Vpr might be a determinant of non-activated T-cell infection. Virion-delivered Vpr activated nuclear factor of activated T cells (NFAT) through Ca2+ influx and interference with the NFAT export kinase GSK3β. This leads to NFAT translocation and accumulation within the nucleus and was required for productive infection of unstimulated primary CD4+ T cells. A mutagenesis approach revealed correlation of Vpr-mediated NFAT activation with its ability to enhance LTR transcription and mediate cell cycle arrest. Upon NFAT inhibition, Vpr did not augment resting T-cell infection, and showed reduced G2/M arrest and LTR transactivation. Altogether, Vpr renders unstimulated T cells more permissive for productive HIV-1 infection and stimulates activation of productively infected as well as virus-exposed T cells. Therefore, it could be involved in the establishment and reactivation of HIV-1 from viral reservoirs and might have an impact on the levels of immune activation, which are determinants of HIV-1 pathogenesis.
Collapse
Affiliation(s)
- Kristin Höhne
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ramona Businger
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Anouk van Nuffel
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Bolduan
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Herwig Koppensteiner
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ann Baeyens
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Jolien Vermeire
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Michael Schindler
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| |
Collapse
|
5
|
Van Hecke C, Malatinkova E, De Spiegelaere W, Sips M, Vervisch K, Verhofstede C, Johnson M, Kinloch-de Loës S, Trypsteen W, Vandekerckhove L. O5 The expression profile of host restriction factors in different cohorts of HIV-1-infected patients. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
6
|
Ruggiero A, Malatinkova E, Rutsaert S, Paxton WA, Vandekerckhove L, De Spiegelaere W. Utility of integrated HIV-1 DNA quantification in cure studies. Future Virol 2017. [DOI: 10.2217/fvl-2016-0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerous HIV-1 curative strategies have been proposed to eradicate the virus reservoir pool that remains integrated within target cells, despite successful antiretroviral therapy. To test the impact of such interventions on this reservoir, a universal marker of persistence is needed. Quantifying integrated HIV-1 DNA load has been proposed as a strong virological marker. In this paper, we provide a detailed description of the most commonly used assays to quantify integrated HIV-1 DNA and applications in relevant clinical studies produced over the last 20 years with a major focus on the recent literature. We discuss the potential for using this marker of virological persistence and the technical limitations that need to be addressed.
Collapse
Affiliation(s)
- Alessandra Ruggiero
- Department of Clinical Infection, Microbiology & Immunology (CIMI), Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - William A Paxton
- Department of Clinical Infection, Microbiology & Immunology (CIMI), Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Sciences, Ghent University, Belgium
| |
Collapse
|
7
|
Crowell TA, Lyall H, Malatinkova E, Bhagani S, Hsu D, Colby DJ, Polyak C, Psomas C, Hill A, Gathogo EN, Trypsteen W, Vandekerckhove L, Kinloch S. Highlights from the 24th Conference on Retroviruses and Opportunistic Infections. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30291-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
8
|
Crowell TA, Lyall H, Malatinkova E, Bhagani S, Hsu D, Colby DJ, Polyak C, Psomas C, Hill A, Gathogo EN, Trypsteen W, Vandekerckhove L, Kinloch S. Highlights from the 24 th Conference on Retroviruses and Opportunistic Infections: 13-16 February 2017, Seattle, Washington, USA. J Virus Erad 2017; 3:101-108. [PMID: 28435696 PMCID: PMC5384268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
From the 13th to 16th February 2017, researchers from around the world convened for the 24th annual Conference on Retroviruses and Opportunistic Infections (CROI) at the Washington State Convention Center in Seattle, Washington. The conference was organised by the International Antiviral Society-USA (IAS-USA) in partnership with the CROI Foundation. The conference included over 1000 oral and poster presentations of peer-reviewed original research as well as lectures and symposia featuring insights from leading basic, translational and clinical researchers. Highlighted here are key data presented at the conference.
Collapse
Affiliation(s)
- Trevor A. Crowell
- US Military HIV Research Program,
Walter Reed Army Institute of Research,
Silver Spring,
MD,
USA
- Henry M Jackson Foundation for the Advancement of Military Medicine,
Bethesda,
MD,
USA
| | - Hermione Lyall
- Department of Paediatrics,
Imperial College Healthcare NHS,
London,
UK
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine,
Ghent University,
Belgium
| | - Sanjay Bhagani
- Royal Free London NHS Trust and University College London,
UK
| | - Denise Hsu
- Henry M Jackson Foundation for the Advancement of Military Medicine,
Bethesda,
MD,
USA
- Armed Forces Research Institute of Medical Sciences,
Bangkok,
Thailand
| | - Donn J Colby
- SEARCH-Thailand, Bangkok, Thailand and Thai Red Cross AIDS Research Centre,
Bangkok,
Thailand
| | - Christina Polyak
- US Military HIV Research Program,
Walter Reed Army Institute of Research,
Silver Spring,
MD,
USA
- Henry M Jackson Foundation for the Advancement of Military Medicine,
Bethesda,
MD,
USA
| | - Christina Psomas
- Department of Infectious Diseases,
University Hospital of Montpellier,
France
- Institute of Human Genetics,
Université de Montpellier,
France
| | - Andrew Hill
- Department of Translational Medicine,
University of Liverpool,
UK
| | | | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine,
Ghent University,
Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine,
Ghent University,
Belgium
| | - Sabine Kinloch
- Royal Free London NHS Trust and University College London,
UK
| |
Collapse
|
9
|
Symons J, Chopra A, Malatinkova E, De Spiegelaere W, Leary S, Cooper D, Abana CO, Rhodes A, Rezaei SD, Vandekerckhove L, Mallal S, Lewin SR, Cameron PU. Erratum to: HIV integration sites in latently infected cell lines: evidence of ongoing replication. Retrovirology 2017; 14:23. [PMID: 28347330 PMCID: PMC5366998 DOI: 10.1186/s12977-017-0340-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Shay Leary
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Don Cooper
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Chike O Abana
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Simin D Rezaei
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia.,Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia. .,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia.
| |
Collapse
|
10
|
Symons J, Chopra A, Malatinkova E, De Spiegelaere W, Leary S, Cooper D, Abana CO, Rhodes A, Rezaei SD, Vandekerckhove L, Mallal S, Lewin SR, Cameron PU. HIV integration sites in latently infected cell lines: evidence of ongoing replication. Retrovirology 2017; 14:2. [PMID: 28086908 PMCID: PMC5237276 DOI: 10.1186/s12977-016-0325-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Assessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding of how HIV persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate HIV integration sites in latently infected cell lines to determine whether there was virus replication or clonal expansion in these cell lines observed as multiple integration events at the same position. RESULTS We modified a previously reported method using random DNA shearing and PCR to allow for high throughput robotic processing to identify the site and frequency of HIV integration in latently infected cell lines. Latently infected cell lines infected with intact virus demonstrated multiple distinct HIV integration sites (28 different sites in U1, 110 in ACH-2 and 117 in J1.1 per 150,000 cells). In contrast, cell lines infected with replication-incompetent viruses (J-Lat cells) demonstrated single integration sites. Following in vitro passaging of the ACH-2 cell line, we observed a significant increase in the frequency of unique HIV integration sites and there were multiple mutations and large deletions in the proviral DNA. When the ACH-2 cell line was cultured with the integrase inhibitor raltegravir, there was a significant decrease in the number of unique HIV integration sites and a transient increase in the frequency of 2-LTR circles consistent with virus replication in these cells. CONCLUSION Cell lines latently infected with intact HIV demonstrated multiple unique HIV integration sites indicating that these cell lines are not clonal and in the ACH-2 cell line there was evidence of low level virus replication. These findings have implications for the use of latently infected cell lines as models of HIV latency and for the use of these cells as standards.
Collapse
Affiliation(s)
- Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Shay Leary
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Don Cooper
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Chike O Abana
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Simin D Rezaei
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia.,Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia. .,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia.
| |
Collapse
|
11
|
Malatinkova E, De Spiegelaere W, Vandekerckhove L, Sips M. HIV Reservoir Characterization Symposium: 19 September 2016, Ghent, Belgium. J Virus Erad 2017; 3:66-68. [PMID: 28275461 PMCID: PMC5337424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The HIV Cure Research Center (HCRC) in Ghent organised the first HIV Reservoir Characterization Symposium, and brought together virologists, molecular biologists, immunologists and clinicians to discuss the most recent developments in HIV reservoir characterisation with a view to achieving an HIV cure. The one-day symposium covered new developments in the field of HIV reservoir and HIV cure research, with the latest news on the European HIV cure trials. This report summarises the major themes discussed during the symposium.
Collapse
Affiliation(s)
- Eva Malatinkova
- HIV Cure Research Center,
Department of Internal Medicine,
Faculty of Medicine and Health Sciences,
Ghent University,
Belgium
| | - Ward De Spiegelaere
- Department of Morphology,
Faculty of Veterinary Sciences,
Ghent University,
Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center,
Department of Internal Medicine,
Faculty of Medicine and Health Sciences,
Ghent University,
Belgium
| | - Magdalena Sips
- HIV Cure Research Center,
Department of Internal Medicine,
Faculty of Medicine and Health Sciences,
Ghent University,
Belgium
| |
Collapse
|
12
|
|
13
|
Bonczkowski P, De Scheerder MA, Malatinkova E, Borch A, Melkova Z, Koenig R, De Spiegelaere W, Vandekerckhove L. P1 Protein expression from unintegrated HIV-1 DNA introduces bias in primary in vitro latency models. J Virus Erad 2016. [DOI: 10.1016/s2055-6640(20)31088-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
14
|
Kiselinova M, De Spiegelaere W, Buzon MJ, Malatinkova E, Lichterfeld M, Vandekerckhove L. Correction: Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth. PLoS Pathog 2016; 12:e1005532. [PMID: 27003005 PMCID: PMC4803328 DOI: 10.1371/journal.ppat.1005532] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
15
|
Martins LJ, Bonczkowski P, Spivak AM, De Spiegelaere W, Novis CL, DePaula-Silva AB, Malatinkova E, Trypsteen W, Bosque A, Vanderkerckhove L, Planelles V. Modeling HIV-1 Latency in Primary T Cells Using a Replication-Competent Virus. AIDS Res Hum Retroviruses 2016; 32:187-93. [PMID: 26171776 DOI: 10.1089/aid.2015.0106] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
HIV-1 latently infected cells in vivo can be found in extremely low frequencies. Therefore, in vitro cell culture models have been used extensively for the study of HIV-1 latency. Often, these in vitro systems utilize defective viruses. Defective viruses allow for synchronized infections and circumvent the use of antiretrovirals. In addition, replication-defective viruses cause minimal cytopathicity because they fail to spread and usually do not encode env or accessory genes. On the other hand, replication-competent viruses encode all or most viral genes and better recapitulate the nuances of the viral replication cycle. The study of latency with replication-competent viruses requires the use of antiretroviral drugs in culture, and this mirrors the use of antiretroviral treatment (ART) in vivo. We describe a model that utilizes cultured central memory CD4(+) T cells and replication-competent HIV-1. This method generates latently infected cells that can be reactivated using latency reversing agents in the presence of antiretroviral drugs. We also describe a method for the removal of productively infected cells prior to viral reactivation, which takes advantage of the downregulation of CD4 by HIV-1, and the use of a GFP-encoding virus for increased throughput.
Collapse
Affiliation(s)
- Laura J. Martins
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Pawel Bonczkowski
- Department of Internal Medicine, HIV Translational Research Unit, Ghent University, Ghent, Belgium
| | - Adam M. Spivak
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ward De Spiegelaere
- Department of Internal Medicine, HIV Translational Research Unit, Ghent University, Ghent, Belgium
| | - Camille L. Novis
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ana Beatriz DePaula-Silva
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Eva Malatinkova
- Department of Internal Medicine, HIV Translational Research Unit, Ghent University, Ghent, Belgium
| | - Wim Trypsteen
- Department of Internal Medicine, HIV Translational Research Unit, Ghent University, Ghent, Belgium
| | - Alberto Bosque
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Linos Vanderkerckhove
- Department of Internal Medicine, HIV Translational Research Unit, Ghent University, Ghent, Belgium
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| |
Collapse
|
16
|
De Spiegelaere W, Kiselinova M, Buzon M, Malatinkova E, Lichterfeld M, Vandekerckhove L. Integrated and total HIV-1 DNA can predict quantitative viral outgrowth in patients on long-term ART. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)31368-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
17
|
Kinloch S, Malatinkova E, De Spiegelaere W, Bonczkowsk P, Kiselinova M, Vervisch K, Trypsteen W, Johnson M, de Looze D, Vandekerckhove L. Impact of a decade of sustained antiretroviral therapy started during HIV-1 seroconversion on blood and gut reservoirs. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)31382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
18
|
Kinloch-de Loes S, Dorrell L, Yang H, Hardy GAD, Yerly S, Cellerai C, Vandekerckhove L, De Spielgelaere W, Malatinkova E, Wee Lee Koh W, Johnson MA. Aviremia 10 Years Postdiscontinuation of Antiretroviral Therapy Initiated During Primary Human Immunodeficiency Virus-1 Infection and Association With Gag-Specific T-Cell Responses. Open Forum Infect Dis 2015; 2:ofv144. [PMID: 26613092 PMCID: PMC4659693 DOI: 10.1093/ofid/ofv144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/24/2015] [Indexed: 11/13/2022] Open
Abstract
Combination antiretroviral therapy during primary human immunodeficiency virus-1 infection may enable long-term drug-free virological control in rare individuals. We describe a female who maintained aviremia and a normal CD4(+)/CD8(+) T cell ratio for 10 years after stopping therapy, despite a persistent viral reservoir. Cellular immune responses may have contributed to this outcome.
Collapse
Affiliation(s)
- Sabine Kinloch-de Loes
- Division of Infection and Immunity , Royal Free Campus, University College London ; Royal Free Hospital , London ; Department of Immunology , University College London Medical School , Royal Free Campus
| | - Lucy Dorrell
- Nuffield Department of Medicine ; Oxford National Institute of Health Research Biomedical Research Centre , University of Oxford
| | - Hongbing Yang
- Nuffield Department of Medicine ; Oxford National Institute of Health Research Biomedical Research Centre , University of Oxford
| | - Gareth A D Hardy
- Centre for Immunology and Virology , Imperial College London ; Chelsea and Westminster Hospital , London , United Kingdom
| | - Sabine Yerly
- Laboratory of Virology , Geneva University Hospital
| | - Cristina Cellerai
- Division of Infection and Immunity , Royal Free Campus, University College London ; Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Linos Vandekerckhove
- HIV Translational Research Unit , Ghent University ; University Hospital Ghent , Belgium
| | - Ward De Spielgelaere
- HIV Translational Research Unit , Ghent University ; University Hospital Ghent , Belgium
| | - Eva Malatinkova
- HIV Translational Research Unit , Ghent University ; University Hospital Ghent , Belgium
| | - Willie Wee Lee Koh
- Department of Immunology and Molecular Pathology , University College London Medical School , University College London Campus , United Kingdom
| | - Margaret A Johnson
- Division of Infection and Immunity , Royal Free Campus, University College London ; Royal Free Hospital , London
| |
Collapse
|
19
|
Malatinkova E, De Spiegelaere W, Bonczkowski P, Kiselinova M, Vervisch K, Trypsteen W, Johnson M, Verhofstede C, de Looze D, Murray C, Kinloch-de Loes S, Vandekerckhove L. Impact of a decade of successful antiretroviral therapy initiated at HIV-1 seroconversion on blood and rectal reservoirs. eLife 2015; 4:e09115. [PMID: 26439007 PMCID: PMC4657623 DOI: 10.7554/elife.09115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/01/2015] [Indexed: 12/14/2022] Open
Abstract
Persistent reservoirs remain the major obstacles to achieve an HIV-1 cure. Prolonged early antiretroviral therapy (ART) may reduce the extent of reservoirs and allow for virological control after ART discontinuation. We compared HIV-1 reservoirs in a cross-sectional study using polymerase chain reaction-based techniques in blood and tissue of early-treated seroconverters, late-treated patients, ART-naïve seroconverters, and long-term non-progressors (LTNPs) who have spontaneous virological control without treatment. A decade of early ART reduced the total and integrated HIV-1 DNA levels compared with later treatment initiation, but not reaching the low levels found in LTNPs. Total HIV-1 DNA in rectal biopsies did not differ between cohorts. Importantly, lower viral transcription (HIV-1 unspliced RNA) and enhanced immune preservation (CD4/CD8), reminiscent of LTNPs, were found in early compared to late-treated patients. This suggests that early treatment is associated with some immunovirological features of LTNPs that may improve the outcome of future interventions aimed at a functional cure. DOI:http://dx.doi.org/10.7554/eLife.09115.001 Many people with HIV infections are able to live relatively normal lives thanks to major advances in drug therapies. A cure, however, remains elusive. One reason for this is that the virus can hide in certain types of human cells, where it is protected from the immune system and the effects of “antiretroviral” drugs. This creates reservoirs of virus particles in the body that can quickly multiply and spread if treatment stops. Some people who become infected with HIV are able to contain the virus without the help of drug treatments. These individuals – known as long-term non-progressors – do not become ill and only have low numbers of HIV particles in reservoirs. People who receive treatment early in the course of an HIV infection also have fewer viruses in reservoirs and are less likely to develop severe illness. Therefore, it might be possible to develop a “functional” cure that may not completely eliminate the virus from the body, but would prevent illness and allow the individuals to eventually stop taking antiretroviral drugs. Now, Malatinkova, De Spiegelaere et al. studied samples from 84 patients with HIV-1 to find how much effect an early start to treatment has on the amount of the virus in reservoirs. People who started treatment soon after infection had lower levels of HIV-1 in their blood than people who started treatment later (even after 10 years of treatment). However, patients that started treatment early had higher levels of HIV-1 in the blood than the patients who were long-term non-progressors. All the patients had similar levels of HIV-1 in tissue samples taken from the rectum, regardless of when they started treatment. The experiments suggest that HIV-1 reservoirs form very soon after infection. Malatinkova, De Spiegelaere et al. found that in addition to reducing reservoirs of HIV-1, an early start to drug treatment reduced the ability of the virus to make copies of its genetic code. People who started treatment earlier also had healthier immune cells. Together, the experiments support the benefits of starting drug treatments as soon as possible after a person is infected with HIV-1. It is important to further characterize thoroughly the viral reservoir in patients with limited HIV-1 reservoirs and to look for other immune factors involved in virus control, in the search for a functional cure of HIV. DOI:http://dx.doi.org/10.7554/eLife.09115.002
Collapse
Affiliation(s)
- Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Pawel Bonczkowski
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Maja Kiselinova
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Karen Vervisch
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wim Trypsteen
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Margaret Johnson
- Division of Infection and Immunity, Royal Free Hospital, London, United Kingdom
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Danny de Looze
- Department of Gastroenterology, Ghent University Hospital, Ghent, Belgium
| | - Charles Murray
- Department of Gastroenterology, Royal Free Hospital, London, United Kingdom
| | | | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
20
|
Fidler S, Thornhill J, Malatinkova E, Reinhard R, Lamplough R, Ananworanich J, Chahroudi A. IAS Towards an HIV Cure Symposium: people focused, science driven 18–19 July 2015, Vancouver, Canada. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)30923-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
21
|
Fidler S, Thornhill J, Malatinkova E, Reinhard R, Lamplough R, Ananworanich J, Chahroudi A. IAS Towards an HIV Cure Symposium: people focused, science driven: 18-19 July 2015, Vancouver, Canada. J Virus Erad 2015; 1:276-81. [PMID: 27482425 PMCID: PMC4946661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The International AIDS Society (IAS) convened the Towards an HIV Cure Symposium on 18-19 July 2015 in Vancouver, Canada, bringing together researchers and community to discuss the most recent advances in our understanding of HIV latency, reservoirs and a summary of the current clinical approaches towards an HIV cure. The symposium objectives were to: (1) gather researchers and stakeholders to present, review, and discuss the latest research towards an HIV cure; (2) promote cross-disciplinary global interactions between basic, clinical and social scientists; and (3) provide a platform for sharing information among scientists, clinicians, funders, media and civil society. The symposium examined basic molecular science and animal model data, and emerging and ongoing clinical trial results to prioritise strategies and determine the viral and immune responses that could lead to HIV remission without antiretroviral therapy. This report summarises some of the major findings discussed during the symposium.
Collapse
Affiliation(s)
- Sarah Fidler
- Department of Medicine,
Imperial College London,
UK
| | | | - Eva Malatinkova
- HIV Translational Research Unit,
Department of Internal Medicine, Faculty of Medicine and Health Sciences,
Ghent University and Ghent University Hospital,
Ghent,
Belgium
| | - Robert Reinhard
- University of Toronto,
Toronto,
Canada; and ,Institut de Recherches Cliniques de Montréal,
Montréal,
Canada
| | | | - Jintanat Ananworanich
- The Henry M. Jackson Foundation for the Advancement of Military Medicine,
Bethesda,
MD,
USA; ,United States Military HIV Research Program,
Bethesda,
MD,
USA
| | - Ann Chahroudi
- Department of Pediatrics,
Emory University School of Medicine Atlanta,
Georgia,
USA
| |
Collapse
|
22
|
Kiselinova M, Geretti AM, Malatinkova E, Vervisch K, Beloukas A, Messiaen P, Bonczkowski P, Trypsteen W, Callens S, Verhofstede C, De Spiegelaere W, Vandekerckhove L. HIV-1 RNA and HIV-1 DNA persistence during suppressive ART with PI-based or nevirapine-based regimens. J Antimicrob Chemother 2015; 70:3311-6. [PMID: 26324076 DOI: 10.1093/jac/dkv250] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/14/2015] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Whether ART regimens differ in their propensity to allow persistent HIV-1 detection remains unclear. To investigate this, we performed a cross-sectional study to characterize HIV-1 persistence in peripheral blood during suppressive therapy with NRTIs plus a PI or nevirapine. METHODS Residual plasma HIV-1 RNA was quantified by real-time PCR. Cell-associated proviral total HIV-1 DNA, unspliced and multiply spliced HIV-1 RNA and 2-long terminal repeat (2-LTR) circles were quantified by digital PCR. RESULTS Comparing PI with nevirapine recipients, residual plasma HIV-1 RNA detection rates were 47/80 (58.8%) versus 37/81 (45.7%), with median (IQR) levels of 4 (3-8) versus 4 (3-7) copies/mL (P = 0.207); detection was less likely with longer duration of suppressive ART (P = 0.020), independently of treatment. HIV-1 DNA was detected in all patients, with median levels of 2.3 (IQR 2.0-2.7) versus 2.5 (IQR 2.1-2.7) log10 copies/10(6) PBMCs, respectively; HIV-1 DNA levels were associated with pre-ART viral load (P = 0.004) and with residual HIV-1 RNA (P = 0.034), unspliced HIV-1 RNA (P = 0.001) and 2-LTR circles (P = 0.005), independently of treatment. CONCLUSIONS No significant differences were revealed in levels of residual plasma HIV-1 RNA, total HIV-1 DNA or intracellular markers of ongoing virus replication (unspliced and multiply spliced HIV-1 RNA and 2-LTR circles) between treatment groups.
Collapse
Affiliation(s)
- Maja Kiselinova
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, UK
| | - Eva Malatinkova
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Karen Vervisch
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Apostolos Beloukas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, UK
| | - Peter Messiaen
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium
| | - Pawel Bonczkowski
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wim Trypsteen
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Steven Callens
- Department of Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium Department of Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
23
|
De Spiegelaere W, Philippé J, Vervisch K, Verhofstede C, Malatinkova E, Kiselinova M, Trypsteen W, Bonczkowski P, Vogelaers D, Callens S, Ruelle J, Kabeya K, De Wit S, Van Acker P, Van Sandt V, Emonds MP, Coucke P, Sermijn E, Vandekerckhove L. Comparison of methods for in-house screening of HLA-B*57:01 to prevent abacavir hypersensitivity in HIV-1 care. PLoS One 2015; 10:e0123525. [PMID: 25874872 PMCID: PMC4398410 DOI: 10.1371/journal.pone.0123525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 03/04/2015] [Indexed: 12/27/2022] Open
Abstract
Abacavir is a nucleoside reverse transcriptase inhibitor used as part of combination antiretroviral therapy in HIV-1-infected patients. Because this drug can cause a hypersensitivity reaction that is correlated with the presence of the HLA-B*57:01 allotype, screening for the presence of HLA-B*57:01 is recommended before abacavir initiation. Different genetic assays have been developed for HLA-B*57:01 screening, each with specific sensitivity, turnaround time and assay costs. Here, a new real-time PCR (qPCR) based analysis is described and compared to sequence specific primer PCR with capillary electrophoresis (SSP PCR CE) on 149 patient-derived samples, using sequence specific oligonucleotide hybridization combined with high resolution SSP PCR as gold standard. In addition to these PCR based methods, a complementary approach was developed using flow cytometry with an HLA-B17 specific monoclonal antibody as a pre-screening assay to diminish the number of samples for genetic testing. All three assays had a maximum sensitivity of >99. However, differences in specificity were recorded, i.e. 84.3%, 97.2% and >99% for flow cytometry, qPCR and SSP PCR CE respectively. Our data indicate that the most specific and sensitive of the compared methods is the SSP PCR CE. Flow cytometry pre-screening can substantially decrease the number of genetic tests for HLA-B*57:01 typing in a clinical setting.
Collapse
Affiliation(s)
| | - Jan Philippé
- Ghent University, Department of Clinical Chemistry, Microbiology and Immunology, Ghent, Belgium
| | - Karen Vervisch
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Chris Verhofstede
- Ghent University, Department of Clinical Chemistry, Microbiology and Immunology, Ghent, Belgium
| | - Eva Malatinkova
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Maja Kiselinova
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Wim Trypsteen
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | | | - Dirk Vogelaers
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Steven Callens
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Jean Ruelle
- Université Catholique de Louvain, IREC, AIDS Reference Laboratory, Brussels, Belgium
| | - Kabamba Kabeya
- Saint-Pierre University Hospital, Department of Infectious Diseases, Bruxelles, Belgium
| | - Stephane De Wit
- Saint-Pierre University Hospital, Department of Infectious Diseases, Bruxelles, Belgium
| | - Petra Van Acker
- Ghent University, Center for Medical Genetics, Ghent, Belgium
| | - Vicky Van Sandt
- HILA, Laboratory for Histocompatibility & Immunogenetics Red Cross Flanders, Mechelen, Belgium
| | - Marie-Paule Emonds
- HILA, Laboratory for Histocompatibility & Immunogenetics Red Cross Flanders, Mechelen, Belgium
| | - Paul Coucke
- Ghent University, Center for Medical Genetics, Ghent, Belgium
| | - Erica Sermijn
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | | |
Collapse
|
24
|
Bonczkowski P, De Spiegelaere W, Bosque A, White CH, Van Nuffel A, Malatinkova E, Kiselinova M, Trypsteen W, Witkowski W, Vermeire J, Verhasselt B, Martins L, Woelk CH, Planelles V, Vandekerckhove L. Replication competent virus as an important source of bias in HIV latency models utilizing single round viral constructs. Retrovirology 2014; 11:70. [PMID: 25142072 PMCID: PMC4156640 DOI: 10.1186/s12977-014-0070-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022] Open
Abstract
The central memory T cell (TCM) model forms a unique HIV-1 latency model based on primary cells that closely resemble in vivo TCM. The virus employed in this model is based on an engineered vector incapable of replication after initial infection. We show that despite this strategy, replication competent viral particles are released into the culture medium due to recombination between overlapping sequences of the env deleted HIV genome that is co-transfected with intact env. This finding emphasizes the need for careful data analysis and interpretation if similar constructs are employed and urges for additional caution during laboratory work.
Collapse
|
25
|
De Spiegelaere W, Malatinkova E, Lynch L, Van Nieuwerburgh F, Messiaen P, O'Doherty U, Vandekerckhove L. Quantification of integrated HIV DNA by repetitive-sampling Alu-HIV PCR on the basis of poisson statistics. Clin Chem 2014; 60:886-95. [PMID: 24664400 DOI: 10.1373/clinchem.2013.219378] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Quantification of integrated proviral HIV DNA by repetitive-sampling Alu-HIV PCR is a candidate virological tool to monitor the HIV reservoir in patients. However, the experimental procedures and data analysis of the assay are complex and hinder its widespread use. Here, we provide an improved and simplified data analysis method by adopting binomial and Poisson statistics. METHODS A modified analysis method on the basis of Poisson statistics was used to analyze the binomial data of positive and negative reactions from a 42-replicate Alu-HIV PCR by use of dilutions of an integration standard and on samples of 57 HIV-infected patients. Results were compared with the quantitative output of the previously described Alu-HIV PCR method. RESULTS Poisson-based quantification of the Alu-HIV PCR was linearly correlated with the standard dilution series, indicating that absolute quantification with the Poisson method is a valid alternative for data analysis of repetitive-sampling Alu-HIV PCR data. Quantitative outputs of patient samples assessed by the Poisson method correlated with the previously described Alu-HIV PCR analysis, indicating that this method is a valid alternative for quantifying integrated HIV DNA. CONCLUSIONS Poisson-based analysis of the Alu-HIV PCR data enables absolute quantification without the need of a standard dilution curve. Implementation of the CI estimation permits improved qualitative analysis of the data and provides a statistical basis for the required minimal number of technical replicates.
Collapse
Affiliation(s)
| | - Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, and
| | - Lindsay Lynch
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Peter Messiaen
- HIV Translational Research Unit, Department of Internal Medicine, and
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | | |
Collapse
|