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Pardons M, Cole B, Lambrechts L, van Snippenberg W, Rutsaert S, Noppe Y, De Langhe N, Dhondt A, Vega J, Eyassu F, Nijs E, Van Gulck E, Boden D, Vandekerckhove L. Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir. Nat Commun 2023; 14:8397. [PMID: 38110433 PMCID: PMC10728105 DOI: 10.1038/s41467-023-44020-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/28/2023] [Indexed: 12/20/2023] Open
Abstract
The development of latency reversing agents that potently reactivate HIV without inducing global T cell activation would benefit the field of HIV reservoir research and could pave the way to a functional cure. Here, we explore the reactivation capacity of a lipid nanoparticle containing Tat mRNA (Tat-LNP) in CD4 T cells from people living with HIV undergoing antiretroviral therapy (ART). When combined with panobinostat, Tat-LNP induces latency reversal in a significantly higher proportion of latently infected cells compared to PMA/ionomycin (≈ 4-fold higher). We demonstrate that Tat-LNP does not alter the transcriptome of CD4 T cells, enabling the characterization of latently infected cells in their near-native state. Upon latency reversal, we identify transcriptomic differences between infected cells carrying an inducible provirus and non-infected cells (e.g. LINC02964, GZMA, CCL5). We confirm the transcriptomic differences at the protein level and provide evidence that the long non-coding RNA LINC02964 plays a role in active HIV infection. Furthermore, p24+ cells exhibit heightened PI3K/Akt signaling, along with downregulation of protein translation, suggesting that HIV-infected cells display distinct signatures facilitating their long-term persistence. Tat-LNP represents a valuable research tool for in vitro reservoir studies as it greatly facilitates the in-depth characterization of HIV reservoir cells' transcriptome and proteome profiles.
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Affiliation(s)
- Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Willem van Snippenberg
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Nele De Langhe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Annemieke Dhondt
- Department of Nephrology, Ghent University Hospital, 9000, Ghent, Belgium
| | - Jerel Vega
- Arcturus Therapeutics, 10628 Science Center Drive, Suite 250, San Diego, 92121, CA, USA
| | - Filmon Eyassu
- Computational biology, Johnson and Johnson, 2340, Beerse, Belgium
| | - Erik Nijs
- Janssen infectious diseases and diagnostics, Johnson and Johnson, 2340, Beerse, Belgium
| | - Ellen Van Gulck
- Janssen infectious diseases and diagnostics, Johnson and Johnson, 2340, Beerse, Belgium
| | - Daniel Boden
- Janssen Biopharma, Johnson and Johnson, South San Francisco, 94080, CA, USA
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium.
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Lambrechts L, Bonine N, Verstraeten R, Pardons M, Noppe Y, Rutsaert S, Van Nieuwerburgh F, Van Criekinge W, Cole B, Vandekerckhove L. HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization. Nucleic Acids Res 2023; 51:e102. [PMID: 37819007 PMCID: PMC10639044 DOI: 10.1093/nar/gkad790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11 vs 18%) and overall good concordance, although at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
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Affiliation(s)
- Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Noah Bonine
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Rita Verstraeten
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Wim Van Criekinge
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
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Lambrechts L, Bonine N, Verstraeten R, Pardons M, Noppe Y, Rutsaert S, Van Nieuwerburgh F, Van Criekinge W, Cole B, Vandekerckhove L. HIV-PULSE: A long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization. bioRxiv 2023:2023.01.18.524396. [PMID: 36711686 PMCID: PMC9882219 DOI: 10.1101/2023.01.18.524396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV P roviral U MI-mediated L ong-read Se quencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
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Struyve T, Pardons M, Termote L, De Clercq J, Lambrechts L, Vega J, Boden D, Lichterfeld M, Rutsaert S, Vandekerckhove L. OP 3.8 – 00066 Characterization of the HIV-1 viral reservoir in subtype B early treated individuals. J Virus Erad 2022. [DOI: 10.1016/j.jve.2022.100180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Pardons M, Cole B, Lambrechts L, Rutsaert S, Noppe Y, Vega J, Nijs E, Van Gulck E, Boden D, Vandekerckhove L. OP 1.7 – 00194 Potent latency reversal enables in-depth transcriptomic analysis of the translation-competent HIV-1 reservoir. J Virus Erad 2022. [DOI: 10.1016/j.jve.2022.100102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Lambrechts L, Verstraeten R, Bonine N, Noppe Y, Rutsaert S, Pardons M, Cole B, Vandekerckhove L. PP 1.23 – 00130 Long-read sequencing assay allows accurate characterization of the HIV-1 reservoir. J Virus Erad 2022. [DOI: 10.1016/j.jve.2022.100127] [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: 12/24/2022] Open
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De Clercq J, Rutsaert S, De Scheerder MA, Verhofstede C, Callens S, Vandekerckhove L. Benefits of antiretroviral therapy initiation during acute HIV infection. Acta Clin Belg 2022; 77:168-176. [PMID: 32468932 DOI: 10.1080/17843286.2020.1770413] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Objectives: In the last decade, there has been increasing scientific and legislative focus on antiretroviral treatment (ART) for all people living with HIV. Especially early ART initiation, preferably during acute HIV infection, has been named as a promising strategy, both for the individual and for the society. This article will review the benefits and possible future applications of immediate ART initiation during acute HIV infection and explore the remaining hurdles towards this strategy.Results: On an individual level, initiation of ART during acute HIV infection limits the viral reservoir, preserves immune function, and decreases systemic inflammation. In addition, obtaining viral suppression soon after infection can be beneficial for the society by decreasing the chance of onward HIV transmission. Reducing the transmission will reduce HIV incidence and can curtail HIV-related health expenditure. Furthermore, the favorable immunological and virological profile obtained by treating during acute HIV infection will form an ideal starting point for several HIV cure strategies.Conclusions: Initiation of ART during acute HIV infection has shown distinct benefits for the individual, for the society, and for future research on HIV cure. In order to implement this strategy, equal focus should be placed on early diagnosis.
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Affiliation(s)
- Jozefien De Clercq
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Chris Verhofstede
- AIDS Reference Laboratory, Ghent University Hospital, Ghent, Belgium
| | - Steven Callens
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
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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.
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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
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Zhang Z, Trypsteen W, Blaauw M, Chu X, Rutsaert S, Vandekerckhove L, van der Heijden W, Dos Santos JC, Xu CJ, Swertz MA, van der Ven A, Li Y. IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis. BMC Med 2021; 19:282. [PMID: 34781942 PMCID: PMC8594146 DOI: 10.1186/s12916-021-02156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/07/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Combination antiretroviral treatment (cART) cannot eradicate HIV-1 from the body due to the establishment of persisting viral reservoirs which are not affected by therapy and reinitiate new rounds of HIV-1 replication after treatment interruption. These HIV-1 reservoirs mainly comprise long-lived resting memory CD4+ T cells and are established early after infection. There is a high variation in the size of these viral reservoirs among virally suppressed individuals. Identification of host factors that contribute to or can explain this observed variation could open avenues for new HIV-1 treatment strategies. METHODS In this study, we conducted a genome-wide quantitative trait locus (QTL) analysis to probe functionally relevant genetic variants linked to levels of cell-associated (CA) HIV-1 DNA, CA HIV-1 RNA, and RNA:DNA ratio in CD4+ T cells isolated from blood from a cohort of 207 (Caucasian) people living with HIV-1 (PLHIV) on long-term suppressive antiretroviral treatment (median = 6.6 years). CA HIV-1 DNA and CA HIV-1 RNA levels were measured with corresponding droplet digital PCR (ddPCR) assays, and genotype information of 522,455 single-nucleotide variants was retrieved via the Infinium Global Screening array platform. RESULTS The analysis resulted in one significant association with CA HIV-1 DNA (rs2613996, P < 5 × 10-8) and two suggestive associations with RNA:DNA ratio (rs7113204 and rs7817589, P < 5 × 10-7). Then, we prioritized PTDSS2, IRF7, RNH1, and DEAF1 as potential HIV-1 reservoir modifiers and validated that higher expressions of IRF7 and RNH1 were accompanied by rs7113204-G. Moreover, RNA:DNA ratio, indicating relative HIV-1 transcription activity, was lower in PLHIV carrying this variant. CONCLUSIONS The presented data suggests that the amount of CA HIV-1 DNA and RNA:DNA ratio can be influenced through PTDSS2, RNH1, and IRF7 that were anchored by our genome-wide association analysis. Further, these observations reveal potential host genetic factors affecting the size and transcriptional activity of HIV-1 reservoirs and could indicate new targets for HIV-1 therapeutic strategies.
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Affiliation(s)
- Zhenhua Zhang
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands.,Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Genomics Coordination Center, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Marc Blaauw
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Xiaojing Chu
- Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Genomics Coordination Center, University Medical Center Groningen, 9700RB, Groningen, the Netherlands
| | - Andre van der Ven
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands.
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands. .,Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands. .,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany. .,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
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10
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De Scheerder MA, Van Hecke C, Zetterberg H, Fuchs D, De Langhe N, Rutsaert S, Vrancken B, Trypsteen W, Noppe Y, Van Der Gucht B, Pelgrom J, Van Wanzeele F, Palmer S, Lemey P, Gisslén M, Vandekerckhove L. Evaluating predictive markers for viral rebound and safety assessment in blood and lumbar fluid during HIV-1 treatment interruption. J Antimicrob Chemother 2021; 75:1311-1320. [PMID: 32053203 DOI: 10.1093/jac/dkaa003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Validated biomarkers to evaluate HIV-1 cure strategies are currently lacking, therefore requiring analytical treatment interruption (ATI) in study participants. Little is known about the safety of ATI and its long-term impact on patient health. OBJECTIVES ATI safety was assessed and potential biomarkers predicting viral rebound were evaluated. METHODS PBMCs, plasma and CSF were collected from 11 HIV-1-positive individuals at four different timepoints during ATI (NCT02641756). Total and integrated HIV-1 DNA, cell-associated (CA) HIV-1 RNA transcripts and restriction factor (RF) expression were measured by PCR-based assays. Markers of neuroinflammation and neuronal injury [neurofilament light chain (NFL) and YKL-40 protein] were measured in CSF. Additionally, neopterin, tryptophan and kynurenine were measured, both in plasma and CSF, as markers of immune activation. RESULTS Total HIV-1 DNA, integrated HIV-1 DNA and CA viral RNA transcripts did not differ pre- and post-ATI. Similarly, no significant NFL or YKL-40 increases in CSF were observed between baseline and viral rebound. Furthermore, markers of immune activation did not increase during ATI. Interestingly, the RFs SLFN11 and APOBEC3G increased after ATI before viral rebound. Similarly, Tat-Rev transcripts were increased preceding viral rebound after interruption. CONCLUSIONS ATI did not increase viral reservoir size and it did not reveal signs of increased neuronal injury or inflammation, suggesting that these well-monitored ATIs are safe. Elevation of Tat-Rev transcription and induced expression of the RFs SLFN11 and APOBEC3G after ATI, prior to viral rebound, indicates that these factors could be used as potential biomarkers predicting viral rebound.
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Affiliation(s)
- Marie-Angélique De Scheerder
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.,Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Clarissa Van Hecke
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 52, Christoph-Probst-Platz, 6020 Innsbruck, Austria
| | - Nele De Langhe
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, 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 Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Bram Vrancken
- KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Bea Van Der Gucht
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Jolanda Pelgrom
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Filip Van Wanzeele
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, New South Wales 2145, Australia
| | - Philippe Lemey
- KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Wallinsgatan 6, Mölndal, Sweden.,Department of Infectious Diseases, Sahlgrenska University Hospital, 11 Region Västra Götaland, Gothenburg, Sweden
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.,Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
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11
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Van de Wijer L, van der Heijden WA, Ter Horst R, Jaeger M, Trypsteen W, Rutsaert S, van Cranenbroek B, van Rijssen E, Joosten I, Joosten L, Vandekerckhove L, Schoofs T, van Lunzen J, Netea MG, Koenen HJPM, van der Ven AJAM, de Mast Q. The Architecture of Circulating Immune Cells Is Dysregulated in People Living With HIV on Long Term Antiretroviral Treatment and Relates With Markers of the HIV-1 Reservoir, Cytomegalovirus, and Microbial Translocation. Front Immunol 2021; 12:661990. [PMID: 33953724 PMCID: PMC8091964 DOI: 10.3389/fimmu.2021.661990] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 01/31/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Long-term changes in the immune system of successfully treated people living with HIV (PLHIV) remain incompletely understood. In this study, we assessed 108 white blood cell (WBC) populations in a cohort of 211 PLHIV on stable antiretroviral therapy and in 56 HIV-uninfected controls using flow cytometry. We show that marked differences exist in T cell maturation and differentiation between PLHIV and HIV-uninfected controls: PLHIV had reduced percentages of CD4+ T cells and naïve T cells and increased percentages of CD8+ T cells, effector T cells, and T helper 17 (Th17) cells, together with increased Th17/regulatory T cell (Treg) ratios. PLHIV also exhibited altered B cell maturation with reduced percentages of memory B cells and increased numbers of plasmablasts. Determinants of the T and B cell composition in PLHIV included host factors (age, sex, and smoking), markers of the HIV reservoir, and CMV serostatus. Moreover, higher circulating Th17 percentages were associated with higher plasma concentrations of interleukin (IL) 6, soluble CD14, the gut homing chemokine CCL20, and intestinal fatty acid binding protein (IFABP). The changes in circulating lymphocytes translated into functional changes with reduced interferon (IFN)- γ responses of peripheral blood mononuclear cells to stimulation with Candida albicans and Mycobacterium tuberculosis. In conclusion, this comprehensive analysis confirms the importance of persistent abnormalities in the number and function of circulating immune cells in PLHIV on stable treatment.
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Affiliation(s)
- Lisa Van de Wijer
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wouter A van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bram van Cranenbroek
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Esther van Rijssen
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Irma Joosten
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | | | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences 12 Institute (LIMES), University of Bonn, Bonn, Germany
| | - Hans J P M Koenen
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - André J A M van der Ven
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
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12
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van der Heijden WA, Van de Wijer L, Keramati F, Trypsteen W, Rutsaert S, Horst RT, Jaeger M, Koenen HJ, Stunnenberg HG, Joosten I, Verweij PE, van Lunzen J, Dinarello CA, Joosten LA, Vandekerckhove L, Netea MG, van der Ven AJ, de Mast Q. Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells. JCI Insight 2021; 6:145928. [PMID: 33630761 PMCID: PMC8119206 DOI: 10.1172/jci.insight.145928] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 11/16/2020] [Accepted: 02/18/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic inflammation and immune dysfunction play a key role in the development of non-AIDS–related comorbidities. The aim of our study was to characterize the functional phenotype of immune cells in people living with HIV (PLHIV). We enrolled a cross-sectional cohort study of PLHIV on stable antiretroviral therapy and healthy controls. We assessed ex vivo cytokine production capacity and transcriptomics of monocytes and T cells upon bacterial, fungal, and viral stimulation. PLHIV exhibited an exacerbated proinflammatory profile in monocyte-derived cytokines, but not in lymphocyte-derived cytokines. Particularly, the production of the IL-1β to imiquimod, E. coli LPS, and Mycobacterium tuberculosis was increased, and this production correlated with plasma concentrations of high-sensitivity C-reactive protein and soluble CD14. This increase in monocyte responsiveness remained stable over time in subsequent blood sampling after more than 1 year. Transcriptome analyses confirmed priming of the monocyte IL-1β pathway, consistent with a monocyte-trained immunity phenotype. Increased plasma concentrations of β-glucan, a well-known inducer of trained immunity, were associated with increased innate cytokine responses. Monocytes of PLHIV exhibited a sustained proinflammatory immune phenotype with priming of the IL-1β pathway. Training of the innate immune system in PLHIV likely plays a role in long-term HIV complications and provides a promising therapeutic target for inflammation-related comorbidities.
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Affiliation(s)
- Wouter A van der Heijden
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisa Van de Wijer
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Farid Keramati
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, 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, Ghent, Belgium
| | - Rob Ter Horst
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Martin Jaeger
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hans Jpm Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands
| | | | - Charles A Dinarello
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Medicine and Immunology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Leo Ab Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - André Jam van der Ven
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
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13
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Adams P, Fievez V, Schober R, Amand M, Iserentant G, Rutsaert S, Dessilly G, Vanham G, Hedin F, Cosma A, Moutschen M, Vandekerckhove L, Seguin-Devaux C. CD32 +CD4 + memory T cells are enriched for total HIV-1 DNA in tissues from humanized mice. iScience 2020; 24:101881. [PMID: 33364576 PMCID: PMC7753142 DOI: 10.1016/j.isci.2020.101881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 03/26/2020] [Revised: 09/04/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022] Open
Abstract
CD32 has raised conflicting results as a putative marker of the HIV-1 reservoir. We measured CD32 expression in tissues from viremic and virally suppressed humanized mice treated relatively early or late after HIV-1 infection with combined antiretroviral therapy. CD32 was expressed in a small fraction of the memory CD4+ T-cell subsets from different tissues in viremic and aviremic mice, regardless of treatment initiation time. CD32+ memory CD4+ T cells were enriched in cell-associated (CA) HIV-1 DNA but not in CA HIV-1 RNA as compared to the CD32−CD4+ fraction. Using multidimensional reduction analysis, several memory CD4+CD32+ T-cell clusters were identified expressing HLA-DR, TIGIT, or PD-1. Importantly, although tissue-resident CD32+CD4+ memory cells were enriched with translation-competent reservoirs, most of it was detected in memory CD32-CD4+ T cells. Our findings support that CD32 labels highly activated/exhausted memory CD4+ T-cell subsets that contain only a small proportion of the translation-competent reservoir. CD32 is rarely expressed in memory CD4+T cells in humanized mice infected with HIV-1 Tissue-resident CD32+CD4+ memory T cells are enriched for HIV-1 DNA but not for RNA CD32+CD4+ memory cells are enriched for translation-competent reservoirs CD32 labels highly activated/exhausted memory T-cell subsets in tissues
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Affiliation(s)
- Philipp Adams
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg.,Department of Biomedical and Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp 2000, Belgium
| | - Virginie Fievez
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Rafaëla Schober
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Mathieu Amand
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Gilles Iserentant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent 9000, Belgium
| | - Géraldine Dessilly
- AIDS Reference Laboratory, Catholic University of Louvain, Brussels 1348, Belgium
| | - Guido Vanham
- Department of Biomedical and Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp 2000, Belgium
| | - Fanny Hedin
- Quantitative Biology Unit, National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Antonio Cosma
- Quantitative Biology Unit, National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Michel Moutschen
- Department of Infectious Diseases, University of Liège, CHU de Liège, Liège 4000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent 9000, Belgium
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
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14
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Morón-López S, Navarro J, Jimenez M, Rutsaert S, Urrea V, Puertas MC, Torrella A, De Clercq L, Ribas BP, Gálvez C, Salgado M, Vandekerckhove L, Blanco J, Crespo M, Martinez-Picado J. Switching From a Protease Inhibitor-based Regimen to a Dolutegravir-based Regimen: A Randomized Clinical Trial to Determine the Effect on Peripheral Blood and Ileum Biopsies From Antiretroviral Therapy-suppressed Human Immunodeficiency Virus-infected Individuals. Clin Infect Dis 2020; 69:1320-1328. [PMID: 30590412 PMCID: PMC6763634 DOI: 10.1093/cid/ciy1095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 12/23/2022] Open
Abstract
Background Optimization of combination antiretroviral therapy (cART) can impact the human immunodeficiency virus (HIV) reservoir. We evaluated the effect on the HIV reservoir in peripheral blood and ileum biopsies in patients switching from boosted protease inhibitor (PI/r)–based therapy to dolutegravir (DTG)–based therapy. Methods Impact of Integrase-inhibitor DOlutegravir On the viral Reservoir (INDOOR) is a phase 4 open-label clinical trial that randomly included 42 HIV type 1–infected individuals on effective cART: 20 who switched from PI/r-based to DTG-based cART (switch group), and 22 who remained in PI/r-based regimens (control group). We analyzed blood and ileum biopsies to quantify episomal, total, and integrated HIV DNA, cell-associated HIV RNA, residual plasma viremia, T-cell subsets, cell activation, and inflammation markers. Results There were no related adverse events or treatment discontinuations due to drug intolerance. The HIV reservoir was consistently larger in ileal than in peripheral CD4+ T cells in both groups (P < .01). Residual viremia in plasma decreased in the switch group (P = .03). However, we did not observe significant longitudinal changes in low-level viral replication, total and integrated HIV reservoir, HIV transcription, T-cell maturation subsets, immunoactivation markers, inflammatory soluble proteins, or cellular markers of latently infected cells. Conclusions The INDOOR study is the first evaluation of changes in HIV reservoir size in ileum biopsies and in peripheral blood in individuals switched from PI/r- to DTG-based cART. Although this switch was safe and well tolerated, it had no impact on a large array of immunological and inflammatory markers or on HIV reservoir markers in peripheral or in ileal CD4+ T cells. Clinical Trials Registration EudraCT 2014-004331-39.
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Affiliation(s)
| | - Jordi Navarro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron.,Departament de Medicina, Universitat Autònoma de Barcelona.,Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Sofie Rutsaert
- Human Immunodeficiency Virus Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Belgium
| | | | | | - Ariadna Torrella
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron
| | - Laura De Clercq
- Human Immunodeficiency Virus Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Belgium
| | | | | | | | - Linos Vandekerckhove
- Human Immunodeficiency Virus Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Belgium
| | - Julià Blanco
- AIDS Research Institute IrsiCaixa, Badalona.,University of Vic-Central University of Catalonia
| | - Manel Crespo
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron.,Infectious Diseases Unit, Internal Medicine Department, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Sanitaria Galicia Sur
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Badalona.,University of Vic-Central University of Catalonia.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
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15
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Rutsaert S, De Spiegelaere W, De Clercq L, Vandekerckhove L. Evaluation of HIV-1 reservoir levels as possible markers for virological failure during boosted darunavir monotherapy. J Antimicrob Chemother 2020; 74:3030-3034. [PMID: 31314108 DOI: 10.1093/jac/dkz269] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The gold standard for HIV-1 treatment is to administer triple antiretroviral therapy, but a shift to simplified regimens is being explored. Boosted darunavir monotherapy can be considered for patients who are for specific reasons not good candidates for dual or triple therapy. Still, a number of patients fail virologically or need to switch treatment. OBJECTIVES To identify predictive markers for those patients that are more likely to sustain virological control under monotherapy, virological and immunological markers were explored in HIV-1-positive patients that experienced virological failure on ritonavir-boosted darunavir monotherapy in the PROTEA trial. METHODS As a retrospective nested study of the PROTEA study (NCT01448707), we analysed 77 HIV-1-infected patients who were on darunavir/ritonavir 800/100 mg monotherapy up to 96 weeks. Patients were appointed to three distinct cohorts based on viral loads (VLs): (i) undetectable VL after 96 weeks; (ii) very-low-level viraemia (5-39 copies/mL); and (iii) failing treatment. Total HIV-1 DNA, integrated HIV-1 DNA and 2-long terminal repeat circular HIV-1 DNA (2LTR circles) were measured in PBMCs at baseline, week 48 and week 96. RESULTS Total HIV-1 DNA and integrated HIV-1 DNA at baseline differed significantly between patients who experienced virological failure on monotherapy (P < 0.01 and P < 0.001). Although a higher level of HIV-1 DNA was measured in failures, this marker by itself does not provide enough predictive value to prospectively predict virological failure in patients on monotherapy. CONCLUSIONS HIV-1 reservoir markers correlate with therapy failure in ritonavir-boosted darunavir monotherapy. However, their role as a predictive marker combined with other markers in a routine clinical setting should be further explored.
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Affiliation(s)
- Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Laura De Clercq
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
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16
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Pannus P, Rutsaert S, De Wit S, Allard SD, Vanham G, Cole B, Nescoi C, Aerts J, De Spiegelaere W, Tsoumanis A, Couttenye M, Herssens N, De Scheerder M, Vandekerckhove L, Florence E. Rapid viral rebound after analytical treatment interruption in patients with very small HIV reservoir and minimal on-going viral transcription. J Int AIDS Soc 2020; 23:e25453. [PMID: 32107887 PMCID: PMC7046528 DOI: 10.1002/jia2.25453] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/20/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Viral remission after analytical treatment interruption (ATI), termed post-treatment control, has been described in a small proportion of HIV-positive patients. This phenomenon has been separately associated to both low levels of HIV-1 proviral DNA as well as cell-associated RNA. We investigated whether the combination of both parameters could help predict delayed viral rebound after treatment interruption (TI). METHODS We conducted an open single-arm ATI study in four Belgian HIV reference centres from January 2016 to July 2018. Eligible participants were adults who had fewer than 50 HIV-1 RNA copies/mL for more than two years, more than 500 CD4 cells/µL for more than three months, and were in general good health. Consenting participants who had fewer than 66 copies total HIV-1 DNA (t-DNA) and fewer than 10 copies cell-associated HIV-1 unspliced RNA (US-RNA) per million peripheral blood mononuclear cells (PBMCs), interrupted therapy and were monitored closely. Antiretroviral therapy (ART) was resumed after two consecutive viral loads exceeding 1000 copies or one exceeding 10,000 copies/mL. The primary outcome was the proportion of participants with fewer than 50 HIV-1 RNA copies/mL 48 weeks after TI. Secondary outcomes were time to viral rebound, the frequency of serious adverse events (AEs) and evolution of t-DNA and US-RNA after TI. RESULTS All 16 consenting participants who interrupted therapy experienced rapid viral rebound two to eight weeks after TI. No serious AEs were observed. Levels of t-DNA and US-RNA increased after TI but returned to pre-ATI levels after treatment restart. None of the studied demographic, clinical and biological parameters were predictive of time of viral rebound. CONCLUSIONS The combination of low levels of t-DNA and US-RNA in PBMCs, corresponding respectively to a small and transcriptionally silent viral reservoir, is not predictive of viral remission after TI in patients on ART.
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Affiliation(s)
- Pieter Pannus
- Departments of Clinical and Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Sofie Rutsaert
- Department of General Internal MedicineHIV Cure Research CentreGhent University Hospital and Ghent UniversityGhentBelgium
| | - Stéphane De Wit
- Saint Pierre University HospitalUniversité Libre de BruxellesBrusselsBelgium
| | - Sabine D Allard
- HIV Reference CentreUniversitair Ziekenhuis BrusselBrusselsBelgium
| | - Guido Vanham
- Departments of Clinical and Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Basiel Cole
- Department of General Internal MedicineHIV Cure Research CentreGhent University Hospital and Ghent UniversityGhentBelgium
| | - Coca Nescoi
- Saint Pierre University HospitalUniversité Libre de BruxellesBrusselsBelgium
| | | | - Ward De Spiegelaere
- Department of MorphologyFaculty of Veterinary MedicineGhent UniversityGhentBelgium
| | - Achilleas Tsoumanis
- Departments of Clinical and Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | | | - Natacha Herssens
- Departments of Clinical and Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | - Marie‐Angélique De Scheerder
- Department of General Internal MedicineHIV Cure Research CentreGhent University Hospital and Ghent UniversityGhentBelgium
| | - Linos Vandekerckhove
- Department of General Internal MedicineHIV Cure Research CentreGhent University Hospital and Ghent UniversityGhentBelgium
| | - Eric Florence
- Departments of Clinical and Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
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17
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Lambrechts L, Cole B, Rutsaert S, Trypsteen W, Vandekerckhove L. Emerging PCR-Based Techniques to Study HIV-1 Reservoir Persistence. Viruses 2020; 12:E149. [PMID: 32012811 PMCID: PMC7077278 DOI: 10.3390/v12020149] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 02/04/2023] Open
Abstract
While current antiretroviral therapies are able to halt HIV-1 progression, they are not curative, as an interruption of treatment usually leads to viral rebound. The persistence of this stable HIV-1 latent reservoir forms the major barrier in HIV-1 cure research. The need for a better understanding of the mechanisms behind reservoir persistence resulted in the development of several novel assays allowing to perform an extensive in-depth characterization. The objective of this review is to present an overview of the current state-of-the-art PCR-based technologies to study the replication-competent HIV-1 reservoir. Here, we outline the advantages, limitations, and clinical relevance of different approaches. Future HIV-1 eradication studies would benefit from information-rich, high-throughput assays as they provide a more efficient and standardized way of characterizing the persisting HIV-1 reservoir.
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Affiliation(s)
- Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (L.L.); (B.C.); (S.R.); (W.T.)
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (L.L.); (B.C.); (S.R.); (W.T.)
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (L.L.); (B.C.); (S.R.); (W.T.)
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (L.L.); (B.C.); (S.R.); (W.T.)
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; (L.L.); (B.C.); (S.R.); (W.T.)
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18
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De Scheerder MA, Vrancken B, Dellicour S, Schlub T, Lee E, Shao W, Rutsaert S, Verhofstede C, Kerre T, Malfait T, Hemelsoet D, Coppens M, Dhondt A, De Looze D, Vermassen F, Lemey P, Palmer S, Vandekerckhove L. HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs. Cell Host Microbe 2019; 26:347-358.e7. [PMID: 31471273 PMCID: PMC11021134 DOI: 10.1016/j.chom.2019.08.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/16/2019] [Accepted: 07/31/2019] [Indexed: 02/01/2023]
Abstract
Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for reinitiating viral replication remain a subject of ardent debate, despite extensive research efforts. To unravel the source of rebounding viruses, we conducted a large-scale HIV-STAR (HIV-1 sequencing before analytical treatment interruption to identify the anatomically relevant HIV reservoir) clinical trial. We collected samples from 11 participants and compared the genetic composition of (pro)viruses collected under treatment from different cellular and anatomical compartments with that of plasma viruses sampled during analytical treatment interruption. We found a remarkably heterogeneous source of viral rebound. In addition, irrespective of the compartment or cell subset, genetically identical viral expansions played a significant role in viral rebound. Our study suggests that although there does not seem to be a primary source for rebound HIV, cellular proliferation is an important driver of HIV persistence and should therefore be considered in future curative strategies.
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Affiliation(s)
- Marie-Angélique De Scheerder
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium
| | - Simon Dellicour
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium; Spatial Epidemiology Laboratory (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Timothy Schlub
- University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney 2000, NSW, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney 2145, NSW, Australia
| | - Wei Shao
- Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Ghent University Hospital, Ghent 9000, Belgium
| | - Tessa Kerre
- Department of Hematology, Ghent University Hospital, Ghent 9000, Belgium
| | - Thomas Malfait
- Department of Pulmonology, Ghent University Hospital, Ghent 9000, Belgium
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, Ghent 9000, Belgium
| | - Marc Coppens
- Department of Anesthesiology, Ghent University Hospital, Ghent 9000, Belgium
| | - Annemieke Dhondt
- Department of Nephrology, Ghent University Hospital, Ghent 9000, Belgium
| | - Danny De Looze
- Department of Gastro-Enterology, Ghent University Hospital, Ghent 9000, Belgium
| | - Frank Vermassen
- Department of Vascular Surgery, Ghent University Hospital, Ghent 9000, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney 2145, NSW, Australia
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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19
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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.
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20
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Rutsaert S, Steens JM, Gineste P, Cole B, Kint S, Barrett PN, Tazi J, Scherrer D, Ehrlich HJ, Vandekerckhove L. Safety, tolerability and impact on viral reservoirs of the addition to antiretroviral therapy of ABX464, an investigational antiviral drug, in individuals living with HIV-1: a Phase IIa randomised controlled study. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30273-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Rutsaert S. Total HIV DNA as guidance for simplification strategies. J Virus Erad 2018. [DOI: 10.1016/s2055-6640(20)30444-1] [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
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22
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Vibholm L, Schleimann MH, Højen JF, Benfield T, Offersen R, Rasmussen K, Olesen R, Dige A, Agnholt J, Grau J, Buzon M, Wittig B, Lichterfeld M, Petersen AM, Deng X, Abdel-Mohsen M, Pillai SK, Rutsaert S, Trypsteen W, De Spiegelaere W, Vandekerchove L, Østergaard L, Rasmussen TA, Denton PW, Tolstrup M, Søgaard OS. Short-Course Toll-Like Receptor 9 Agonist Treatment Impacts Innate Immunity and Plasma Viremia in Individuals With Human Immunodeficiency Virus Infection. Clin Infect Dis 2018; 64:1686-1695. [PMID: 28329286 DOI: 10.1093/cid/cix201] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
Background. Treatment with latency reversing agents (LRAs) enhances human immunodeficiency virus type 1 (HIV-1) transcription in vivo but leads to only modest reductions in the size of the reservoir, possibly due to insufficient immune-mediated elimination of infected cells. We hypothesized that a single drug molecule-a novel Toll-like receptor 9 (TLR9) agonist, MGN1703-could function as an enhancer of innate immunity and an LRA in vivo. Methods. We conducted a single-arm, open-label study in which 15 virologically suppressed HIV-1-infected individuals on antiretroviral therapy received 60 mg MGN1703 subcutaneously twice weekly for 4 weeks. We characterized plasmacytoid dendritic cell, natural killer (NK), and T-cell activation using flow cytometry on baseline and after 4 weeks of treatment. HIV-1 transcription was quantified by measuring plasma HIV-1 RNA during MGN1703 administration. Results. In accordance with the cell type-specific expression of TLR9, MGN1703 treatment led to pronounced activation of plasmacytoid dendritic cells and substantial increases in plasma interferon-α2 levels (P < .0001). Consistently, transcription of interferon-stimulated genes (eg, OAS1, ISG15, Mx1; each P < .0001) were upregulated in CD4+ T cells as demonstrated by RNA sequencing. Further, proportions of activated cytotoxic NK cells and CD8+ T cells increased significantly during MGN1703 dosing, suggesting an enhancement of cellular immune responses. In 6 of 15 participants, plasma HIV-1 RNA increased from <20 copies/mL to >1500 copies/mL (range, 21-1571 copies/mL) during treatment. Conclusions. TLR9 agonist treatment in HIV infection has a dual potential by increasing HIV-1 transcription and enhancing cytotoxic NK cell activation, both of which are key outcomes in HIV-1 eradication therapy. Clinical Trials Registration. NCT02443935.
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Affiliation(s)
- Line Vibholm
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Mariane H Schleimann
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Jesper F Højen
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, and
| | - Rasmus Offersen
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | | | - Rikke Olesen
- Department of Infectious Diseases, Aarhus University Hospital
| | - Anders Dige
- Institute of Clinical Medicine, Aarhus University.,Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
| | - Jørgen Agnholt
- Institute of Clinical Medicine, Aarhus University.,Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
| | - Judith Grau
- Hebron Institute of Research, Department of Infectious Diseases, Barcelona, Spain
| | - Maria Buzon
- Hebron Institute of Research, Department of Infectious Diseases, Barcelona, Spain
| | - Burghardt Wittig
- Foundation Institute Molecular Biology and Bioinformatics, Freie Universitaet, Berlin, Germany
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston; Departments of
| | - Andreas Munk Petersen
- Gastroenterology and.,Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, and.,University of California, San Francisco
| | - Mohamed Abdel-Mohsen
- Blood Systems Research Institute, San Francisco, California, and.,University of California, San Francisco.,The Wistar Institute, Philadelphia, Pennsylvania; and Departments of
| | - Satish K Pillai
- Blood Systems Research Institute, San Francisco, California, and.,University of California, San Francisco
| | | | | | - Ward De Spiegelaere
- Internal Medicine; and.,Morphology, Faculty of Veterinary Medicine, Ghent University, Belgium
| | | | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | | | - Paul W Denton
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Ole S Søgaard
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
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23
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Rutsaert S, Bosman K, Trypsteen W, Nijhuis M, Vandekerckhove L. Digital PCR as a tool to measure HIV persistence. Retrovirology 2018; 15:16. [PMID: 29378600 PMCID: PMC5789538 DOI: 10.1186/s12977-018-0399-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 11/12/2022] Open
Abstract
Although antiretroviral therapy is able to suppress HIV replication in infected patients, the virus persists and rebounds when treatment is stopped. In order to find a cure that can eradicate the latent reservoir, one must be able to quantify the persisting virus. Traditionally, HIV persistence studies have used real-time PCR (qPCR) to measure the viral reservoir represented by HIV DNA and RNA. Most recently, digital PCR is gaining popularity as a novel approach to nucleic acid quantification as it allows for absolute target quantification. Various commercial digital PCR platforms are nowadays available that implement the principle of digital PCR, of which Bio-Rad’s QX200 ddPCR is currently the most used platform in HIV research. Quantification of HIV by digital PCR is proving to be a valuable improvement over qPCR as it is argued to have a higher robustness to mismatches between the primers-probe set and heterogeneous HIV, and forfeits the need for a standard curve, both of which are known to complicate reliable quantification. However, currently available digital PCR platforms occasionally struggle with unexplained false-positive partitions, and reliable segregation between positive and negative droplets remains disputed. Future developments and advancements of the digital PCR technology are promising to aid in the accurate quantification and characterization of the persistent HIV reservoir.
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Affiliation(s)
- Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Kobus Bosman
- Department of Medical Microbiology, Virology, UMC Utrecht, Utrecht, The Netherlands
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, UMC Utrecht, Utrecht, The Netherlands
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Ghent University, Ghent, Belgium.
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24
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Psomas CK, Barber TJ, Rutsaert S, Kinloch-de Loës S. Highlights from the 9th IAS Conference on HIV Science, 23-26 July 2017, Paris, France. J Virus Erad 2017; 3:242-249. [PMID: 29057090 PMCID: PMC5632553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Christina K Psomas
- Corresponding author: Christina K Psomas,
Department of Infectious Diseases,
University Hospital of Montpellier,
80 A Fiche Avenue,
34295MontpellierCedex 5,
France
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25
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Psomas CK, Barber TJ, Rutsaert S, Kinloch-de Loës S. Highlights from the 9th IAS Conference on HIV Science, 23–26 July 2017, Paris, France. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30321-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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26
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Pannus P, Adams P, Willems E, Heyndrickx L, Van Frankenhuijsen M, Florence E, Kiselinova M, Rutsaert S, Vervisch K, Despiegelaere W, Devaux C, Vandekerckhove L, Vanham G. O7 Does viral suppressive capacity in cART-treated HIV-infected patients correlate with disease parameters, viral reservoir measures or cytotoxic T cell phenotype? J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30823-2] [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: 11/29/2022] Open
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27
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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.
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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
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28
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Rutsaert S, Trypsteen W, Van Hecke C, De Scheerder M, Kiselinova M, Vervisch K, De Spiegelaere W, Vandekerckhove L. O2 Cross-validation of HIV DNA assays to quantify different HIV-1 subtypes by ddPCR. J Virus Erad 2016. [DOI: 10.1016/s2055-6640(20)31081-5] [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: 11/29/2022] Open
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