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Faua C, Ursenbach A, Fuchs A, Caspar S, Jegou F, Ruch Y, Hoellinger B, Laugel E, Velay A, Rey D, Fafi-Kremer S, Gantner P. HIV Productively Infects Highly Differentiated and Exhausted CD4+ T Cells During AIDS. Pathog Immun 2024; 8:92-114. [PMID: 38420260 PMCID: PMC10901154 DOI: 10.20411/pai.v8i2.638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Background Throughout HIV infection, productively infected cells generate billions of viral particles and are thus responsible for body-wide HIV dissemination, but their phenotype during AIDS is unknown. As AIDS is associated with immunological changes, analyzing the phenotype of productively infected cells can help understand HIV production during this terminal stage. Methods Blood samples from 15 untreated viremic participants (recent infection, n=5; long-term infection, n=5; active opportunistic AIDS-defining disease, n=5) and 5 participants virologically controlled on antiretroviral therapy (ART) enrolled in the Analysis of the Persistence, Reservoir and HIV Latency (APRIL) study (NCT05752318) were analyzed. Cells expressing the capsid protein p24 (p24+ cells) after 18 hours of resting or 24 hours of stimulation (HIV-Flow) revealed productively infected cells from viremic participants or translation-competent reservoir cells from treated participants, respectively. Results The frequency of productively infected cells tended to be higher during AIDS in comparison with recent and long-term infections (median, 340, 72, and 32/million CD4+ T cells, respectively) and correlated with the plasma viral load at all stages of infection. Altogether, these cells were more frequently CD4low, HLA-ABClow, CD45RA-, Ki67+, PD-1+, with a non-negligible contribution from pTfh (CXCR5+PD-1+) cells, and were not significantly enriched in HIV coreceptors CCR5 nor CXCR4 expression. The comparison markers expression between stages showed that productively infected cells during AIDS were enriched in memory and exhausted cells. In contrast, the frequencies of infected pTfh were lower during AIDS compared to non-AIDS stages. A UMAP analysis revealed that total CD4+ T cells were grouped in 7 clusters and that productive p24+ cells were skewed to given clusters throughout the course of infection. Overall, the preferential targets of HIV during the latest stages seemed to be more frequently highly differentiated (memory, TTD-like) and exhausted cells and less frequently pTfh-like cells. In contrast, translation-competent reservoir cells were less frequent (5/million CD4+ T cells) and expressed more frequently HLA-ABC and less frequently PD-1. Conclusions In long-term infection and AIDS, productively infected cells were differentiated and exhausted. This could indicate that cells with these given features are responsible for HIV production and dissemination in an immune dysfunction environment occurring during the last stages of infection.
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Affiliation(s)
- Clayton Faua
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
| | - Axel Ursenbach
- Le Trait d'Union, HIV-Infection Care Center, Strasbourg University Hospital, Strasbourg, France
| | - Anne Fuchs
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Stéphanie Caspar
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Frédérick Jegou
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Yvon Ruch
- Infectious Diseases Department, Strasbourg University Hospital, Strasbourg, France
| | - Baptiste Hoellinger
- Infectious Diseases Department, Strasbourg University Hospital, Strasbourg, France
| | - Elodie Laugel
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Aurélie Velay
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - David Rey
- Le Trait d'Union, HIV-Infection Care Center, Strasbourg University Hospital, Strasbourg, France
| | - Samira Fafi-Kremer
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Pierre Gantner
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
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Dean LS, SahBandar IN, Shikuma CM. Identification and Implications of HIV-1 CRF01_AE Subtype in Hawai'i. HAWAI'I JOURNAL OF HEALTH & SOCIAL WELFARE 2022; 81:215-217. [PMID: 35923383 PMCID: PMC9344534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Human Immunodeficiency Virus has a high propensity for genetic variation, demonstrated by its complex phylogeny and multiplicity of subtypes. Subtype B is predominant in North America as well as in Hawai'i while CRF01_AE is found in over 50% of cases in the Philippines and Southeast Asia. In a small collaborative study between the Hawai'i Center for AIDS and Philippines General Hospital, molecular phylogenetic subtyping was conducted on HIV+ participants. Two of 15 (13%) participants from the Hawai'i cohort and 12 of 21 (57%) participants from the Philippines cohort were identified as having CRF01_AE subtype of HIV-1, with remaining participants identified as subtype B. While one individual in Hawai'i with CRF01_AE had emigrated from the Philippines, the other participant from Hawai'i with CRF01_AE subtype was a local individual, born and raised in Hawai'i. The authors report that HIV subtype diversity may be increased in Hawai'i and discuss its potential clinical and public health implications.
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Affiliation(s)
- Logan S. Dean
- John A. Burns School of Medicine, University of Hawai‘i, Honolulu, HI (LSD, INS, CMS)
| | | | - Cecilia M. Shikuma
- John A. Burns School of Medicine, University of Hawai‘i, Honolulu, HI (LSD, INS, CMS)
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Bouba Y, Armenia D, Forbici F, Bertoli A, Borghi V, Gagliardini R, Vergori A, Cicalini S, Mazzotta V, Malagnino V, Lichtner M, Latini A, Mussini C, Andreoni M, Antinori A, Perno CF, Ceccherini-Silberstein F, Santoro MM. Genotypic HIV-1 tropism determination might help to identify people with exhausted treatment options and advanced disease. J Antimicrob Chemother 2021; 76:3272-3279. [PMID: 34529797 DOI: 10.1093/jac/dkab322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To evaluate HIV-1 tropism in 1382 combined antiretroviral therapy (cART)-experienced patients failing therapy to characterize those with exhausted therapeutic options. METHODS HIV-1 genotypic tropism was inferred through Geno2Pheno by estimating the false-positive-rate (FPR) values. Cumulative resistance and drug activity were evaluated by Stanford algorithm. RESULTS Overall, median (IQR) CD4 count (cells/mm3) nadir and at last genotypic resistance test (GRT) available were 98 (33-211) and 312 (155-517), respectively. Considering HIV-1 tropism, 30.5% had X4/dual-mixed strains (FPR ≤5%: 22.2%; FPR 5%-10%: 8.3%). By stratifying according to tropism, by decreasing FPR, a significant decrease of CD4 nadir and at last GRT was observed. The proportion of individuals with CD4 count <200 cells/mm3, who were perinatally infected and with a long treatment history significantly increased as FPR levels decreased. Regarding resistance, 933 (67.5%) individuals accumulated at least one class resistance, with 52.7%, 48.2%, 23.5% and 13.2% of individuals showing resistance to NRTIs, NNRTIs, PIs and INIs; while 23.2%, 27.2%, 14.3% and 2.8% harboured resistance to 1, 2, 3 and 4 classes, respectively. Individuals with FPR ≤5% showed a significantly higher level of resistance to PIs, NRTIs and INIs compared with others. The proportion of individuals harbouring strains susceptible to ≤2 active drugs was only about 2%; nonetheless, this proportion doubled (4.6%) in patients infected with FPR ≤5%. CONCLUSIONS Our findings showed that a small proportion of cART failing individuals have limited therapeutic options. However, tropism determination might help to identify people who have accumulated a high level of resistance and have a greater risk of advanced disease.
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Affiliation(s)
- Yagai Bouba
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy.,Saint Camillus International, University of Health Sciences, Rome, Italy
| | - Federica Forbici
- Laboratory of Virology, INMI 'Lazzaro Spallanzani'-IRCCS, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy.,Laboratory of Virology, University Hospital 'Tor Vergata', Rome, Italy
| | - Vanni Borghi
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | | | | | | | | | - Vincenzo Malagnino
- Clinical Infectious Diseases, University Hospital, 'Tor Vergata', Rome, Italy
| | - Miriam Lichtner
- Infectious Diseases Unit, 'Sapienza' University, Polo Pontino, Latina, Italy
| | - Alessandra Latini
- Unit of Dermatology and Sexually Transmitted Diseases, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Massimo Andreoni
- Clinical Infectious Diseases, University Hospital, 'Tor Vergata', Rome, Italy
| | - Andrea Antinori
- Clinical Department, INMI 'Lazzaro Spallanzani'-IRCCS, Rome, Italy
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4
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Basso M, Zago D, Scaggiante R, Cavinato S, Pozzetto I, Stagni C, Parisatto B, Cattelan AM, Battagin G, Sarmati L, Parisi SG. HIV tropism switch in archived DNA of HIV-HCV subjects successfully treated with direct-acting antivirals for HCV infection. Sci Rep 2021; 11:9274. [PMID: 33927306 PMCID: PMC8085114 DOI: 10.1038/s41598-021-88811-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/16/2021] [Indexed: 02/02/2023] Open
Abstract
We described short-term HIV tropism changes occurring in peripheral blood mononuclear cells and the correlations with HIV DNA value in HIV-HCV co-infected patients cured for HCV disease and with undetectable HIV viremia or residual viremia (RV). Plasma HIV RNA, cellular HIV DNA and tropism were evaluated pre-HCV treatment (baseline, BL) and at 12(T1) and 24(T2) weeks after HCV treatment start. V3 sequences were interpreted using Geno2pheno and classified as R5 only if all three sequences had an FPR ≥ 10% and as X4 when at least one replicate sequence had an FPR < 10%. Forty-nine patients (21 with X4 and 28 with R5 virus) were enrolled. Five X4 patients and 9 R5 subjects experienced at least one tropism change,11 with RV:1/5 patients with X4 infection at BL switched at T1 versus 8/9 in the R5 group (p = 0.022977) and the difference was confirmed in subjects with RV (p = 0.02);6/9 R5 patients switching at T1 confirmed the tropism change at T2. No significant differences in HIV DNA values between patients with RV starting with a R5 or X4 tropism and experienced tropism switch or not were found. Short-term tropism switch involved almost a third of patients, in all but three cases with HIV RV. Being R5 at BL is associated to a higher instability, expressed as number of tropism changes and confirmed switch at T2.
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Affiliation(s)
- Monica Basso
- grid.5608.b0000 0004 1757 3470Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padua, Italy
| | - Daniela Zago
- grid.5608.b0000 0004 1757 3470Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padua, Italy
| | | | - Silvia Cavinato
- grid.411474.30000 0004 1760 2630Infectious Diseases Unit, Azienda Ospedaliera-Universitaria di Padova, Padua, Italy
| | - Irene Pozzetto
- grid.5608.b0000 0004 1757 3470Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padua, Italy
| | - Camilla Stagni
- grid.5608.b0000 0004 1757 3470Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padua, Italy
| | - Beatrice Parisatto
- grid.5608.b0000 0004 1757 3470Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padua, Italy
| | - Anna Maria Cattelan
- grid.411474.30000 0004 1760 2630Infectious Diseases Unit, Azienda Ospedaliera-Universitaria di Padova, Padua, Italy
| | | | - Loredana Sarmati
- grid.6530.00000 0001 2300 0941Infectious Diseases Clinic, Università Tor Vergata, Rome, Italy
| | - Saverio Giuseppe Parisi
- grid.5608.b0000 0004 1757 3470Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padua, Italy
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Karuppusamy KV, Babu P, Thangavel S. The Strategies and Challenges of CCR5 Gene Editing in Hematopoietic Stem and Progenitor Cells for the Treatment of HIV. Stem Cell Rev Rep 2021; 17:1607-1618. [PMID: 33788143 DOI: 10.1007/s12015-021-10145-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/29/2022]
Abstract
HIV infection continues to be a serious health issue with an alarming global spread, owing to the fact that attempts at developing an effective vaccine or a permanent cure remains futile. So far, the only available treatment for the clinical management of HIV is the combined Anti-Retroviral Therapy (cART), but the long-term cART is associated with metabolic changes, organ damages, and development and transmission of drug resistant HIV strains. Thus, there is a need for the development of one-time curative treatment for HIV infection. The allogeneic transplantation with the Hematopoietic Stem and Progenitor cells (HSPCs) having 32 bp deletion in Chemokine receptor 5 gene (CCR5 Δ32) demonstrated successful HIV remission in the Berlin and London patients, and highlighted that transplantation of CCR5 null HSPCs is a promising approach for a long- term HIV remission. The advent of gene editing technologies offers a new choice of generating ex vivo CCR5 ablated allogeneic or autologous HSPCs for stem cell transplantation into HIV patients. Many groups are attempting CCR5 disruption in HSPCs using various gene-editing strategies. At least two such studies, involving CCR5 gene editing in HSPCs have entered the clinical trials. This review aims to outline the strategies taken for CCR5 gene editing and discuss the challenges associated with the development of CCR5 manipulated HSPCs for the gene therapy of HIV infection.
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Affiliation(s)
- Karthik V Karuppusamy
- Centre for Stem Cell Research (A unit of inStem, Bengaluru), Christian Medical College, Vellore, Tamil Nadu, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prathibha Babu
- Centre for Stem Cell Research (A unit of inStem, Bengaluru), Christian Medical College, Vellore, Tamil Nadu, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (A unit of inStem, Bengaluru), Christian Medical College, Vellore, Tamil Nadu, India. .,Manipal Academy of Higher Education, Manipal, Karnataka, India.
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6
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Alteri C, Scutari R, Bertoli A, Armenia D, Gori C, Fabbri G, Mastroianni CM, Cerva C, Cristaudo A, Vicenti I, Bruzzone B, Zazzi M, Andreoni M, Antinori A, Svicher V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Integrase strand transfer inhibitor-based regimen is related with a limited HIV-1 V3 loop evolution in clinical practice. Virus Genes 2019; 55:290-297. [PMID: 30796743 DOI: 10.1007/s11262-019-01649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Integrase-strand-transfer inhibitors (INSTIs) are known to rapidly reduce HIV-1 plasma viral load, replication cycles, and new viral integrations, thus potentially limiting viral evolution. Here, we assessed the role of INSTIs on HIV-1 V3 evolution in a cohort of 89 HIV-1-infected individuals starting an INSTI- (N = 41, [dolutegravir: N = 1; elvitegravir: N = 3; raltegravir: N = 37]) or a non-INSTI-based (N = 48) combined antiretroviral therapy (cART), with two plasma RNA V3 genotypic tests available (one before [baseline] and one during cART). V3 sequences were analysed for genetic distance (Tajima-Nei model) and positive selection (dN/dS ratio). Individuals were mainly infected by B subtype (71.9%). Median (interquartile-range, IQR) plasma viral load and CD4 + T cell count at baseline were 4.8 (3.5-5.5) log10 copies/mL and 207 (67-441) cells/mm3, respectively. Genetic distance (median, IQR) between the V3 sequences obtained during cART and those obtained at baseline was 0.04 (0.01-0.07). By considering treatment, genetic distance was significantly lower in INSTI-treated than in non-INSTI-treated individuals (median [IQR]: 0.03[0.01-0.04] vs. 0.05[0.02-0.08], p = 0.026). In line with this, a positive selection (defined as dN/dS ≥ 1) was observed in 36.6% of V3 sequences belonging to the INSTI-treated group and in 56.3% of non-INSTI group (p = 0.05). Multivariable logistic regression confirmed the independent correlation of INSTI-based regimens with a lower probability of both V3 evolution (adjusted odds-ratio: 0.35 [confidence interval (CI) 0.13-0.88], p = 0.027) and positive selection (even if with a trend) (adjusted odds-ratio: 0.46 [CI 0.19-1.11], p = 0.083). Overall, this study suggests a role of INSTI-based regimen in limiting HIV-1 V3 evolution over time. Further studies are required to confirm these findings.
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Affiliation(s)
- Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy. .,Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italia.
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,UniCamillus, Saint Camillus International University of Health Sciences, Via di Sant'Alessandro, 8, 00131, Rome, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Gabriele Fabbri
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | | | - Carlotta Cerva
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", Viale Oxford 81, 00133, Rome, Italy
| | - Antonio Cristaudo
- Infectious Dermatology and Allergology Unit, San Gallicano Dermatological Institute, IFO-IRCCS, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnology, University of Siena, Viale Bracci 2, 53100, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, IRCCS AOU San Martino - IST, Largo R. Benzi 10, 16132, Genoa, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Viale Bracci 2, 53100, Siena, Italy
| | - Massimo Andreoni
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", Viale Oxford 81, 00133, Rome, Italy
| | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | | | - Carlo Federico Perno
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italia.,National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
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