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Pascucci GR, Morrocchi E, Pighi C, Rotili A, Neri A, Medri C, Olivieri G, Sanna M, Rasi G, Persaud D, Chahroudi A, Lichterfeld M, Nastouli E, Cancrini C, Amodio D, Rossi P, Cotugno N, Palma P. How CD4 + T Cells Transcriptional Profile Is Affected by Culture Conditions: Towards the Design of Optimal In Vitro HIV Reactivation Assays. Biomedicines 2023; 11:888. [PMID: 36979867 PMCID: PMC10045592 DOI: 10.3390/biomedicines11030888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/15/2023] [Accepted: 02/25/2023] [Indexed: 03/16/2023] Open
Abstract
Most of the current assays directed at the investigation of HIV reactivation are based on cultures of infected cells such as Peripheral Blood Mononuclear Cells (PBMCs) or isolated CD4+ T cells, stimulated in vitro with different activator molecules. The culture media in these in vitro tests lack many age- and donor-specific immunomodulatory components normally found within the autologous plasma. This triggered our interest in understanding the impact that different matrices and cell types have on T cell transcriptional profiles following in vitro culture and stimulation. METHODS Unstimulated or stimulated CD4+ T cells of three young adults with perinatal HIV-infection were isolated from PBMCs before or after culture in RPMI medium or autologous plasma. Transcriptomes were sequenced using Oxford Nanopore technologies. RESULTS Transcriptional profiles revealed the activation of similar pathways upon stimulation in both media with a higher magnitude of TCR cascade activation in CD4+ lymphocytes cultured in RPMI. CONCLUSIONS These results suggest that for studies aiming at quantifying the magnitude of biological mechanisms under T cell activation, the autologous plasma could better approximate the in vivo environment. Conversely, if the study aims at defining qualitative aspects, then RPMI culture could provide more evident results.
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Affiliation(s)
- Giuseppe Rubens Pascucci
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Elena Morrocchi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Chiara Pighi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Arianna Rotili
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Alessia Neri
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Chiara Medri
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Giulio Olivieri
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Marco Sanna
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Gianmarco Rasi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Deborah Persaud
- Department of Pediatric Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ann Chahroudi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eleni Nastouli
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Caterina Cancrini
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Donato Amodio
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Paolo Rossi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Nicola Cotugno
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Paolo Palma
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
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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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3
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Myerski A, Siegel A, Engstrom J, McGowan I, Brand RM. The Use of Droplet Digital PCR to Quantify HIV-1 Replication in the Colorectal Explant Model. AIDS Res Hum Retroviruses 2019; 35:326-334. [PMID: 30618283 DOI: 10.1089/aid.2018.0227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ex vivo explant models are used to characterize in vitro efficacy of preexposure prophylaxis (PrEP) agents. Tissue is challenged with virus in culture and HIV-1 p24 levels are quantified with enzyme-linked immunosorbent assay (ELISA) on supernatants collected throughout a 14-21-day incubation. Due to the narrow dynamic range of HIV-1 p24 kits, we evaluated whether droplet digital PCR (ddPCR) provides an alternative method to quantify HIV-1 replication in supernatant samples. We used samples from the MWRI-01 study, which evaluated the pharmacokinetic/pharmacodynamic profile of long-acting rilpivirine using the explant model (McGowan et al. Lancet HIV 2016). HIV-1 pol RNA was measured with ddPCR, either directly with a one-step method or reverse transcribed to cDNA before ddPCR (two-step method) on supernatants from the MWRI-01 study. Previously analyzed HIV-1 p24 antigen levels (Alliance; Perkin-Elmer) were available for comparison purposes. Both ddPCR methods strongly correlated with HIV-1 p24 and displayed similar patterns of HIV-1 suppression before and after rilpivirine. Compared to the p24 ELISA, two-step and one-step ddPCR reduced the amount of hands-on time by approximately one-half and two-thirds, respectively. ddPCR also required less sample and based on p24 versus ddPCR correlation, could potentially reduce the explant culture time from 14 to 10 days (r2 = 0.78, p < .001) due to the increased sensitivity of ddPCR. We demonstrate that ddPCR is a suitable alternative to HIV-1 p24 ELISA to quantify HIV-1 infection in the explant model and has the potential to decrease explant culture time.
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Affiliation(s)
- Ashley Myerski
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - Aaron Siegel
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - Jarret Engstrom
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - Ian McGowan
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
- Department of Medicine University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Rhonda M. Brand
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
- Department of Medicine University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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4
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A Pilot Study of the Immunologic, Virologic, and Pathologic Consequences of Intra-anal 5% Imiquimod in HIV-1-Infected Men With High-Grade Squamous Intraepithelial Lesions. Dis Colon Rectum 2018; 61:298-305. [PMID: 29360679 DOI: 10.1097/dcr.0000000000000991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Imiquimod can be used to treat internal anal high-grade squamous intraepithelial lesions. In HIV-1-infected individuals there is a theoretical concern for increased HIV replication in anorectal tissue secondary to imiquimod-induced mucosal inflammation. OBJECTIVE The purpose of this study was to assess local virologic, immunologic, and pathologic effects of imiquimod treatment in HIV-infected individuals. DESIGN This was a pilot study at a single academic center. SETTINGS The study was conducted at the University of Pittsburgh Anal Dysplasia Clinic. PATIENTS HIV-1-infected individuals with biopsy-confirmed internal anal high-grade squamous intraepithelial lesions were included. INTERVENTION Imiquimod cream was prescribed for intra-anal use 3 times per week for 9 weeks. MAIN OUTCOME MEASURES Anal human papillomavirus typing, anal and rectal tissue HIV-1 RNA and DNA quantification, cytokine gene expression, and anal histology were measured. RESULTS Nine evaluable participants (1 participant was lost to follow-up) were all white men with a median age of 46 years (interquartile range = 12 y) and a median CD4 T-cell count of 480 cells per cubic millimeter (interquartile range = 835). All were taking antiretroviral therapy, and 7 of 9 had HIV-1 RNA <50 copies per milliliter. The median dose of imiquimod used was 27.0 (interquartile range = 3.5), and there was a median of 11 days (interquartile range = 10 d) from last dose to assessment. There was no progression to cancer, no significant change in the number of human papillomavirus types detected, and no significant change in quantifiable cytokines/HIV-1 RNA or DNA levels in anal or rectal tissue. Seven (35%) of 20 high-grade lesions resolved to low-grade squamous intraepithelial lesions. LIMITATIONS The study was limited by the small number of participants and variable time to final assessment. CONCLUSIONS Intra-anal imiquimod showed no evidence of immune activation or increase in HIV-1 viral replication in anal and rectal tissue and confirmed efficacy for intra-anal high-grade squamous intraepithelial lesion treatment morbidity. See Video Abstract at http://links.lww.com/DCR/A498.
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Agyei D, Pan S, Acquah C, Bekhit AEDA, Danquah MK. Structure-informed detection and quantification of peptides in food and biological fluids. J Food Biochem 2017; 43:e12482. [PMID: 31353495 DOI: 10.1111/jfbc.12482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 02/06/2023]
Abstract
Peptides with biological properties, that is, bioactive peptides, are a class of biomolecules whose health-promoting properties are increasingly being exploited in food and health products. However, research on targeted techniques for the detection and quantification of these peptides is still in its infancy. Such information is needed in order to enhance the biological and chemometric characterization of peptides and their subsequent application in the functional food and pharmaceutical industries. In this review, the role of classic techniques such as electrophoretic, chromatographic, and peptide mass spectrometry in the structure-informed detection and quantitation of bioactive peptides are discussed. Prospects for the use of aptamers in the characterization of bioactive peptides are also discussed. PRACTICAL APPLICATIONS: Although bioactive peptides have huge potential applications in the functional foods and health area, there are limited techniques in enhancing throughput detection, quantification, and characterization of these peptides. This review discusses state-of-the-art techniques relevant in complementing bioactive detection and profiling irrespective of the small number of amino acid units. Insights into challenges, possible remedies and prevailing areas requiring thorough research in the extant literature for food chemists and biotechnologists are also presented.
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Affiliation(s)
- Dominic Agyei
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Sharadwata Pan
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising 85354, Germany
| | - Caleb Acquah
- Curtin Malaysia Research Institute, Curtin University, Sarawak 98009, Malaysia.,Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia
| | | | - Michael K Danquah
- Curtin Malaysia Research Institute, Curtin University, Sarawak 98009, Malaysia.,Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia
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6
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Guichet E, Aghokeng A, Eymard-Duvernay S, Vidal N, Ayouba A, Mpoudi Ngole E, Delaporte E, Ciaffi L, Peeters M. Field evaluation of an open and polyvalent universal HIV-1/SIVcpz/SIVgor quantitative RT-PCR assay for HIV-1 viral load monitoring in comparison to Abbott RealTime HIV-1 in Cameroon. J Virol Methods 2016; 237:121-126. [PMID: 27609535 DOI: 10.1016/j.jviromet.2016.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/03/2016] [Accepted: 09/04/2016] [Indexed: 11/19/2022]
Abstract
With the increasing demand of HIV viral load (VL) tests in resource-limited countries (RLCs) there is a need for assays at affordable cost and able to quantify all known HIV-1 variants. VLs obtained with a recently developed open and polyvalent universal HIV-1/SIVcpz/SIVgor RT-qPCR were compared to Abbott RealTime HIV-1 assay in Cameroon. On 474 plasma samples, characterized by a wide range of VLs and a broad HIV-1 group M genetic diversity, 97.5% concordance was observed when using the lower detection limit of each assay. When using the threshold of 3.00 log10 copies/mL, according to WHO guidelines to define virological failure (VF) in RLCs, the concordance was 94.7%, 360/474 versus 339/474 patients were identified with VF with the new assay and Abbott RealTime HIV-1, respectively. Higher VLs were measured with the new assay, +0.47 log10 copies/mL (95% CI; 0.42-0.52) as shown with Bland-Altman analysis. Eleven samples from patients on VF with drug resistance were not detected by Abbott RealTime HIV-1 versus two only with the new assay. Overall, our study showed that the new assay can be easily implemented in a laboratory in RLCs with VL experience and showed good performance on a wide diversity of HIV-1 group M variants.
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Affiliation(s)
- Emilande Guichet
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Avelin Aghokeng
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France; Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Virology laboratory IMPM-IRD, Yaoundé, Cameroon
| | - Sabrina Eymard-Duvernay
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Nicole Vidal
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Ahidjo Ayouba
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Eitel Mpoudi Ngole
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Virology laboratory IMPM-IRD, Yaoundé, Cameroon
| | - Eric Delaporte
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Laura Ciaffi
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Martine Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France.
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Janocko L, Althouse AD, Brand RM, Cranston RD, McGowan I. The Molecular Characterization of Intestinal Explant HIV Infection Using Polymerase Chain Reaction-Based Techniques. AIDS Res Hum Retroviruses 2015; 31:981-91. [PMID: 26214703 PMCID: PMC4576939 DOI: 10.1089/aid.2015.0165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The ex vivo mucosal explant model is frequently used to test the efficacy of microbicides that have the potential for preventing HIV-1 transmission. The conventional assessment of product efficacy has been the extent of HIV-1 p24 suppression in supernatant fluids sampled up to day 14 after HIV-1 challenge ex vivo. The purpose of this study was to determine if measurement of HIV-1 nucleic acids by real-time PCR and HIV-1 integration by Alu-gag PCR provides advantages with regard to monitoring HIV-1 infection in explants. Rectal biopsies from HIV-1-negative individuals were challenged with 1 × 10(5) virions/ml of HIV-1BaL or HIV-1CH077 ex vivo. HIV-1 RNA and HIV-1 p24 in supernatant fluids and HIV-1 nucleic acids and integrated provirus in individual biopsies were measured at days 1-14 after infection. HIV-1 RNA and proviral DNA were measured by quantitative real-time PCR (qRT-PCR) while integrated virus was detected by Alu-gag PCR. Real-time PCR assays detecting HIV-1 DNA and RNA performed similarly provided that the infecting virus sequences were a good match with the sequences of the assay primers and probes. Increased HIV-1 nucleic acid levels and DNA integration were measurable on days 11 and 14 after infection. The magnitude of explant infection was similar after challenge with HIV-1BaL and HIV-1CH077, although the trajectory of infection was delayed in the HIV-1CH077-infected biopsies. In the majority of experiments, qRT-PCR did not appreciably shorten the time necessary to detect evidence of HIV-1 infection.
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Affiliation(s)
- Laura Janocko
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Andrew D. Althouse
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rhonda M. Brand
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Ian McGowan
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- University of Pittsburgh, Pittsburgh, Pennsylvania
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8
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Procopio FA, Fromentin R, Kulpa DA, Brehm JH, Bebin AG, Strain MC, Richman DD, O'Doherty U, Palmer S, Hecht FM, Hoh R, Barnard RJO, Miller MD, Hazuda DJ, Deeks SG, Sékaly RP, Chomont N. A Novel Assay to Measure the Magnitude of the Inducible Viral Reservoir in HIV-infected Individuals. EBioMedicine 2015; 2:874-83. [PMID: 26425694 PMCID: PMC4563128 DOI: 10.1016/j.ebiom.2015.06.019] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Quantifying latently infected cells is critical to evaluate the efficacy of therapeutic strategies aimed at reducing the size of the long-lived viral reservoir, but the low frequency of these cells makes this very challenging. Methods We developed TILDA (Tat/rev Induced Limiting Dilution Assay) to measure the frequency of cells with inducible multiply-spliced HIV RNA, as these transcripts are usually absent in latently infected cells but induced upon viral reactivation. TILDA requires less than a million cells, does not require RNA extraction and can be completed in two days. Findings In suppressed individuals on ART, we found the median frequency of latently infected CD4 + T cells as estimated by TILDA to be 24 cells/million, which was 48 times more than the frequency measured by the quantitative viral outgrowth assay, and 6–27 times less than the frequencies of cells harbouring viral DNA measured by PCR-based assays. TILDA measurements strongly correlated with most HIV DNA assays. The size of the latent reservoir measured by TILDA was lower in subjects who initiated ART during the early compared to late stage of infection (p = 0.011). In untreated HIV disease, the frequency of CD4 + cells carrying latent but inducible HIV largely exceeded the frequency of actively producing cells, demonstrating that the majority of infected cells are transcriptionally silent even in the absence of ART. Interpretations Our results suggest that TILDA is a reproducible and sensitive approach to measure the frequency of productively and latently infected cells in clinical settings. We demonstrate that the latent reservoir represents a substantial fraction of all infected cells prior to ART initiation. Research in context In this manuscript, we describe the development of a novel assay that measures the magnitude of the latent HIV reservoir, the main barrier to HIV eradication. This novel assay, termed TILDA for Tat/rev Induced Limiting Dilution Assay, requires only 10 ml of blood, does not necessitate extraction of viral nucleic acids, is highly reproducible, covers a wide dynamic range of reservoir sizes and can be completed in two days. As such, TILDA may represent an alternative to existing assays used to evaluate the efficacy of therapeutic strategies aimed at reducing the size of the latent HIV reservoir. We developed TILDA (Tat/rev Induced Limiting Dilution Assay) to measure the frequency of cells with inducible multiply-spliced HIV RNA in HIV-infected individuals on suppressive ART. Our results suggest that TILDA is a reproducible and sensitive approach to measure the frequency of productively and latently infected cells in clinical settings. Using TILDA, We demonstrate that the latent reservoir represents a substantial fraction of all infected cells prior to ART initiation.
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Affiliation(s)
| | - Rémi Fromentin
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | - Deanna A Kulpa
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | - Jessica H Brehm
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | | | - Matthew C Strain
- University of California San Diego, La Jolla, California and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Douglas D Richman
- University of California San Diego, La Jolla, California and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Palmer
- Centre for Virus Research, Westmead Millennium Institute, Westmead, Australia ; Sydney Medical School, University of Sydney, Sydney, Australia
| | - Frederick M Hecht
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Michael D Miller
- Infectious Disease, Merck Research Laboratories, West Point, PA, USA
| | - Daria J Hazuda
- Infectious Disease, Merck Research Laboratories, West Point, PA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Nicolas Chomont
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
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Abstract
INTRODUCTION Individuals practicing unprotected receptive anal intercourse are at particularly high risk of HIV infection. Men who have sex with men in the developed and developing world continue to have disproportionate and increasing levels of HIV infection. The last few years have seen important progress in demonstrating the efficacy of oral antiretroviral pre-exposure prophylaxis, vaginal microbicides, and treatment as prevention, but there has also been significant progress in the development of rectal microbicides for HIV prevention. AREAS COVERED The purpose of this review is to summarize the status of rectal microbicide research and to identify opportunities, challenges, and future directions in this important field of HIV prevention research. The design of completed and ongoing Phase I rectal microbicide studies that include the generation of comprehensive pharmacokinetic/pharmacodynamic data may allow for more rational decisions about which rectal microbicides should be advanced to later stage development. EXPERT OPINION There is a strong rationale for the development of rectal microbicides for HIV prevention. Preclinical data provide supportive evidence for the feasibility of this approach, and there is significant interest in rectal microbicide development from communities at risk of HIV acquisition through unprotected receptive anal intercourse in both the developed and developing world. Demonstration of sustained safety, acceptability, and product adherence in the MTN-017 Phase II study of tenofovir 1% gel will be an important step in rectal microbicide development and will hopefully lead to Phase III effectiveness testing of this novel HIV prevention strategy.
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Affiliation(s)
- Ian McGowan
- University of Pittsburgh, Department of Medicine , Pittsburgh , USA
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10
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Kibirige C. The Use of Ultra-Sensitive Molecular Assays in HIV Cure-Related Research. JOURNAL OF AIDS & CLINICAL RESEARCH 2013; Suppl 6. [PMID: 25328815 PMCID: PMC4198944 DOI: 10.4172/2155-6113.s6-002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ultra-sensitive laboratory assays based on the Polymerase Chain Reaction (PCR) are playing an increasingly important role in HIV cure-related research. This article reviews the different assays available and how they have evolved. There is a great need for their standardization and for the establishment of reference reagents and testing algorithms to evaluate potential HIV cure-related treatments.
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11
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Single real-time reverse transcription-PCR assay for detection and quantification of genetically diverse HIV-1, SIVcpz, and SIVgor strains. J Clin Microbiol 2012; 51:787-98. [PMID: 23254130 DOI: 10.1128/jcm.02792-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Although antiretroviral treatment availability has improved, the virological monitoring of patients remains largely uneven across regions. In addition, viral quantification tests are suffering from human immunodeficiency virus type 1 (HIV-1) genetic diversity, fueled by the emergence of new recombinants and of lentiviruses from nonhuman primates. We developed a real-time reverse transcription-PCR (RT-PCR) assay that is relatively inexpensive and able to detect and quantify all circulating forms of HIV-1 and its simian immunodeficiency virus (SIV) precursors, SIVcpz and SIVgor. Primers and a probe were designed to detect all variants of the HIV-1/SIVcpz/SIVgor lineage. HIV-1 M plasma (n = 190; 1.68 to 7.78 log(10) copies/ml) representing eight subtypes, nine circulating recombinant forms, and 21 unique recombinant forms were tested. The mean PCR efficiency was 99%, with low coefficients of intra- and interassay variation (<5%) and a limit of quantification of <2.50 log(10) copies/ml, with a 200-μl plasma volume. On the studied range, the specificity and the analytical sensitivity were 100 and 97.4%, respectively. The viral loads were highly correlated (r = 0.95, P < 0.0001) with the reference method (generic HIV assay; Biocentric) and had no systematic difference, irrespective of genotype. Furthermore, 22 HIV-1 O plasmas were screened and were better quantified compared to the gold-standard RealTime HIV-1 assay (Abbott), including four samples that were only quantified by our assay. Finally, we could quantify SIVcpzPtt and SIVcpzPts from chimpanzee plasma (n = 5) and amplify SIVcpz and SIVgor from feces. Thus, the newly developed real-time RT-PCR assay detects and quantifies strains from the HIV-1/SIVcpz/SIVgor lineage, including a wide diversity of group M strains and HIV-1 O. It can therefore be useful in geographical areas of high HIV diversity and at risk for the emergence of new HIV variants.
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Yu D, Chen Y, Wu S, Wang B, Tang YW, Li L. Simultaneous detection and differentiation of human papillomavirus genotypes 6, 11, 16 and 18 by AllGlo quadruplex quantitative PCR. PLoS One 2012; 7:e48972. [PMID: 23152833 PMCID: PMC3494670 DOI: 10.1371/journal.pone.0048972] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 10/03/2012] [Indexed: 12/12/2022] Open
Abstract
Background Human papillomaviruses (HPV) are classified into high-risk HPV and low-risk HPV. The most common high-risk HPV types in cervical cancer are HPV 16 and 18, and the most common low-risk types causing genital warts are HPV 6 and HPV 11. In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. Methods The specificity, the sensitivity, the detection limit, the reproducibility and the standard curve of this method were examined. Finally, clinical samples that had been tested previously by TaqMan PCR and HPV GenoArray (GA) test were used to verify the accuracy and sensitivity of the method. Results The assay has a sensitivity of 101 to 102 copies/test and a linear detection range from 101 to 108 copies/test. The mean amplification efficiencies for HPV 6, 11, 16, and 18 were 0.97, 1.10, 0.93 and 1.20, respectively, and the mean correlation coefficient (r2) of each standard curve was above 0.99 for plasmid templates ranging from 103 to 107 copies/test. There was 100% agreement between the AllGlo quadruplex quantitative PCR, HPV GA test and TaqMan uniplex qPCR methods. Conclusions AllGlo quadruplex quantitative PCR in a single tube has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, and a wide linear range of detection. The convenient single tube format makes this assay a powerful tool for the studies of mixed infections by multiple pathogens, viral typing and viral load quantification.
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Affiliation(s)
- Daojun Yu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Clinical Laboratories, Hangzhou First People’s Hospital, Hangzhou, China
| | - Yu Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shenghai Wu
- Department of Clinical Laboratories, Hangzhou First People’s Hospital, Hangzhou, China
| | - Baohong Wang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi-Wei Tang
- Clinical Microbiology Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lanjuan Li
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- * E-mail:
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van der Sluis RM, van Montfort T, Centlivre M, Schopman NCT, Cornelissen M, Sanders RW, Berkhout B, Jeeninga RE, Paxton WA, Pollakis G. Quantitation of HIV-1 DNA with a sensitive TaqMan assay that has broad subtype specificity. J Virol Methods 2012; 187:94-102. [PMID: 23059551 DOI: 10.1016/j.jviromet.2012.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 09/04/2012] [Accepted: 09/10/2012] [Indexed: 11/30/2022]
Abstract
The increasing diversity of HIV-1 isolates makes virus quantitation challenging, especially when diverse isolates co-circulate in a geographical area. Measuring the HIV-1 DNA levels in cells has become a valuable practical tool for fundamental and clinical research. A quantitative HIV-1 DNA assay was developed based on TaqMan(®) technology. Primers that target the highly conserved LTR region were designed to detect a broad array of HIV-1 variants, including viral isolates from many subtypes, with high sensitivity. Introduction of a pre-amplification step prior to the TaqMan(®) reaction allowed the specific amplification of fully reverse transcribed viral DNA. Execution of the pre-amplification step with a second primer set enables for the exclusive quantitation of the 2-LTR circular HIV-1 DNA form.
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Affiliation(s)
- Renée M van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
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Yukl SA, Shergill AK, McQuaid K, Gianella S, Lampiris H, Hare CB, Pandori M, Sinclair E, Günthard HF, Fischer M, Wong JK, Havlir DV. Effect of raltegravir-containing intensification on HIV burden and T-cell activation in multiple gut sites of HIV-positive adults on suppressive antiretroviral therapy. AIDS 2010; 24:2451-60. [PMID: 20827162 PMCID: PMC2997807 DOI: 10.1097/qad.0b013e32833ef7bb] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To determine whether raltegravir-containing antiretroviral therapy (ART) intensification reduces HIV levels in the gut. DESIGN Open-label study in HIV-positive adults on ART with plasma HIV RNA below 40 copies/ml. METHODS Seven HIV-positive adults received 12 weeks of ART intensification with raltegravir alone or in combination with efavirenz or darunavir. Gut cells were obtained by upper and lower endoscopy with biopsies from duodenum, ileum, colon, and rectum at baseline and 12 weeks. Study outcomes included plasma HIV RNA, HIV DNA and RNA from peripheral blood mononuclear cells (PBMC) and four gut sites, T-cell subsets, and activation markers. RESULTS Intensification produced no consistent decrease in HIV RNA in the plasma, PBMC, duodenum, colon, or rectum. However, five of seven participants had a decrease in unspliced HIV RNA per 10 CD4(+) T cells in the ileum. There was a trend towards decreased T-cell activation in all sites, which was greatest for CD8(+) T cells in the ileum and PBMC, and a trend towards increased CD4(+) T cells in the ileum. CONCLUSION Most HIV RNA and DNA in the blood and gut is not the result of ongoing replication that can be impacted by short-term intensification with raltegravir. However, the ileum may support ongoing productive infection in some patients on ART, even if the contribution to plasma RNA is not discernible.
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Affiliation(s)
- Steven A Yukl
- San Francisco VA Medical Center (SFVAMC) and University of California, San Francisco (UCSF), San Francisco, California, USA.
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