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Sonela N, Mann J, Godwe C, Goni OH, Tchakoute M, Nkoue N, de Oliveira T, Brockman MA, Brumme ZL, Ndung'u T, Tongo M. No detectable differences in Nef-mediated downregulation of HLA-I and CD4 molecules among HIV-1 group M lineages circulating in Cameroon, where the pandemic originated. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2024; 4:fviro.2024.1379217. [PMID: 38883214 PMCID: PMC7616105 DOI: 10.3389/fviro.2024.1379217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
HIV-1 group M (HIV-1M) lineages downregulate HLA-I and CD4 expression via their Nef proteins. We hypothesized that these Nef functions may be partially responsible for the differences in prevalence of viruses from different lineages that co-circulate within an epidemic. Here, we characterized these two Nef activities in HIV-1M isolates from Cameroon, where multiple variants have been circulating since the pandemic's origin. Single HIV-1 Nef clones from 234 HIV-1-ART naïve individuals living in remote villages and two cosmopolitan cities of Cameroon, sampled between 2000 and 2013, were isolated from plasma HIV RNA and analyzed for their capacity to downregulate HLA-I and CD4 molecules. We found that, despite a large degree of within- and inter- lineage variation, the ability of Nef to downregulate HLA-I was similar across these different viruses. Moreover, Nef-mediated CD4 downregulation activity was also well conserved across the different lineages found in Cameroon. In addition, we observed a trend towards higher HLA-I downregulation activity of viruses circulating in the cosmopolitan cities versus the remote villages, whereas the CD4 downregulation activities were similar across the two settings. Furthermore, we noted a significant decline of HLA-I downregulation activity from 2000 to 2013, providing additional evidence supporting the attenuation of the global HIV-1M population over time. Finally, we identified 18 amino acids associated with differential HLA-I downregulation and 13 amino acids associated with differential CD4 downregulation within the dominant CRF02_AG lineage. Our lack of observation of HIV lineage-related differences in Nef-mediated HLA-I and CD4 downregulation function suggests that these activities do not substantively influence the prevalence of different HIV-1M lineages in Cameroon.
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Affiliation(s)
- Nelson Sonela
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Jaclyn Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Celestin Godwe
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Biochemistry, University of Douala, Douala, Cameroon
| | - Oumarou H Goni
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Microbiology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Mérime Tchakoute
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Nathalie Nkoue
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mark A Brockman
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
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Acharya A, Tagny CT, Mbanya D, Fonsah JY, Nchindap E, Kenmogne L, Jihyun M, Njamnshi AK, Kanmogne GD. Variability in HIV-1 Integrase Gene and 3'-Polypurine Tract Sequences in Cameroon Clinical Isolates, and Implications for Integrase Inhibitors Efficacy. Int J Mol Sci 2020; 21:ijms21051553. [PMID: 32106437 PMCID: PMC7084836 DOI: 10.3390/ijms21051553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs) are now included in preferred first-line antiretroviral therapy (ART) for HIV-infected adults. Studies of Western clade-B HIV-1 show increased resistance to INSTIs following mutations in integrase and nef 3′polypurine tract (3′-PPT). With anticipated shifts in Africa (where 25.6-million HIV-infected people resides) to INSTIs-based ART, it is critical to monitor patients in African countries for resistance-associated mutations (RAMs) affecting INSTIs efficacy. We analyzed HIV-1 integrase and 3′-PPT sequences in 345 clinical samples from INSTIs-naïve HIV-infected Cameroonians for polymorphisms and RAMs that affect INSTIs. Phylogeny showed high genetic diversity, with the predominance of HIV-1 CRF02_AG. Major INSTIs RAMs T66A and N155K were found in two (0.6%) samples. Integrase polymorphic and accessory RAMs found included T97A, E157Q, A128T, M50I, S119R, L74M, L74I, S230N, and E138D (0.3′23.5% of samples). Ten (3.2%) samples had both I72V+L74M, L74M+T97A, or I72V+T97A mutations; thirty-one (9.8%) had 3′-PPT mutations. The low frequency of major INSTIs RAMs shows that INSTIs-based ART can be successfully used in Cameroon. Several samples had ≥1 INSTIs accessory RAMs known to reduce INSTIs efficacy; thus, INSTIs-based ART would require genetic surveillance. The 3′-PPT mutations could also affect INSTIs. For patients failing INSTIs-based ART with no INSTIs RAMs, monitoring 3′-PPT sequences could reveal treatment failure etiology.
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Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Claude T. Tagny
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Julius Y. Fonsah
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Emilienne Nchindap
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Léopoldine Kenmogne
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Ma Jihyun
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Alfred K. Njamnshi
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Georgette D. Kanmogne
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Correspondence: ; Tel.: +402-559-4084
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Ali A, Furler RL, Pedroza-Martins L, Colantonio AD, Anisman-Posner D, Bryson Y, Yang OO, Uittenbogaart CH. A Novel HIV-1 Nef Mutation in a Primary Pediatric Isolate Impairs MHC-Class I Downregulation and Cytopathicity. AIDS Res Hum Retroviruses 2020; 36:122-130. [PMID: 31571497 DOI: 10.1089/aid.2019.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1-induced cytopathicity of thymocytes is a major cause of reduced peripheral T cells and rapid disease progression observed in HIV-1-infected infants. Understanding the virulence factors responsible for thymocyte depletion has paramount importance in addressing the pathogenesis of disease progression in children. In this study, thymocyte depletion was analyzed following infection with two primary CXCR4-tropic HIV-1 pediatric isolates (PI), PI-2 and PI-2.1, which were serially derived from an in utero-infected infant. Although highly similar to each other, PI-2 showed markedly decreased thymocyte depletion in vitro compared with PI-2.1. Further analysis showed a novel deletion in the Nef protein (NefΔK7S) of PI-2, which was absent in PI-2.1. This deletion inhibited Nef-mediated major histocompatibility complex class I (MHC-I) downregulation in infected thymocytes in vitro and in vivo; in contrast, the mutated Nef continued to downregulate CD4 surface expression in vitro. These results suggest that HIV-1 Nef contributes to thymic damage in infants through selective functions.
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Affiliation(s)
- Ayub Ali
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Robert L. Furler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Livia Pedroza-Martins
- ANRS, French National Agency for Research on AIDS and Viral Hepatitis, Paris, France
| | - Arnaud D. Colantonio
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, California
| | - Deborah Anisman-Posner
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, California
| | - Yvonne Bryson
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, California
| | - Otto O. Yang
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Christel H. Uittenbogaart
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
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HIV-1 Latency and Latency Reversal: Does Subtype Matter? Viruses 2019; 11:v11121104. [PMID: 31795223 PMCID: PMC6950696 DOI: 10.3390/v11121104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Cells that are latently infected with HIV-1 preclude an HIV-1 cure, as antiretroviral therapy does not target this latent population. HIV-1 is highly genetically diverse, with over 10 subtypes and numerous recombinant forms circulating worldwide. In spite of this vast diversity, much of our understanding of latency and latency reversal is largely based on subtype B viruses. As such, most of the development of cure strategies targeting HIV-1 are solely based on subtype B. It is currently assumed that subtype does not influence the establishment or reactivation of latent viruses. However, this has not been conclusively proven one way or the other. A better understanding of the factors that influence HIV-1 latency in all viral subtypes will help develop therapeutic strategies that can be applied worldwide. Here, we review the latest literature on subtype-specific factors that affect viral replication, pathogenesis, and, most importantly, latency and its reversal.
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Nicoli F, Chachage M, Clowes P, Bauer A, Kowour D, Ensoli B, Cafaro A, Maboko L, Hoelscher M, Gavioli R, Saathoff E, Geldmacher C. Association between different anti-Tat antibody isotypes and HIV disease progression: data from an African cohort. BMC Infect Dis 2016; 16:344. [PMID: 27450538 PMCID: PMC4957276 DOI: 10.1186/s12879-016-1647-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 06/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The presence of IgG and IgM against Tat, an HIV protein important for viral replication and immune dysfunction, is associated with slow disease progression in clade B HIV-infected individuals. However, although Tat activities strictly depend on the viral clade, our knowledge about the importance of anti-Tat antibodies in non-clade B HIV infection is poor. The objective of this study was to investigate the association of different anti-Tat antibody isotypes with disease progression in non-clade B HIV-infected subjects and to study the relationship between anti-Tat humoral responses and immunological abnormalities. METHODS Anti-clade B and -clade C Tat IgG, IgM and IgA titers were assessed in serum samples from 96 cART-naïve subjects with chronic HIV infection from Mbeya, Tanzania, and associated with CD4(+) T cell count, plasma viremia and CD4(+) and CD8(+) T cell phenotypes. RESULTS Anti-Tat IgM were preferentially detected in chronic HIV-infected subjects with low T cell activation (p-value = 0.03) and correlated with higher CD4(+) T cell counts and lower viral loads irrespective of the duration of infection (p-value = 0.019 and p-value = 0.037 respectively). Conversely, anti-Tat IgA were preferentially detected in individuals with low CD4(+) T cell counts and high viral load (p-value = 0.02 and p-value < 0.001 respectively). The simultaneous presence of anti-Tat IgG and IgM protected from fast CD4(+) T cell decline (p-value < 0.01) and accumulation of CD38(+)HLADR(+)CD8(+) T cells (p- value = 0.029). CONCLUSIONS Anti-Tat IgG alone are not protective in non-clade B infected subjects, unless concomitant with IgM, suggesting a protective role of persistent anti-Tat IgM irrespective of the infecting clade.
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Affiliation(s)
- Francesco Nicoli
- Center for International Health, Ludwig-Maximilians-Universität München, Leopoldstraße 7, 80802, Munich, Germany. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy. .,Current address: CIMI INSERM U1135, 91 bd del'Hopital, 75013, Paris, France.
| | - Mkunde Chachage
- Center for International Health, Ludwig-Maximilians-Universität München, Leopoldstraße 7, 80802, Munich, Germany.,National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Petra Clowes
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Asli Bauer
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Dickens Kowour
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Barbara Ensoli
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Aurelio Cafaro
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Leonard Maboko
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Riccardo Gavioli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Elmar Saathoff
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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Comparison of HIV-1 nef and gag Variations and Host HLA Characteristics as Determinants of Disease Progression among HIV-1 Vertically Infected Kenyan Children. PLoS One 2015; 10:e0137140. [PMID: 26317223 PMCID: PMC4552823 DOI: 10.1371/journal.pone.0137140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/12/2015] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Disease progression varies among HIV-1-infected individuals. The present study aimed to explore possible viral and host factors affecting disease progression in HIV-1-infected children. METHODS Since 2000, 102 HIV-1 vertically-infected children have been followed-up in Kenya. Here we studied 29 children (15 male/14 female) who started antiretroviral treatment at <5 years of age (rapid progressors; RP), and 32 (17 male/15 female) who started at >10 years of age (slow progressors; SP). Sequence variations in the HIV-1 gag and nef genes and the HLA class I-related epitopes were compared between the two groups. RESULTS Based on nef sequences, HIV-1 subtypes A1/D were detected in 62.5%/12.5% of RP and 66.7%/20% of SP, with no significant difference in subtype distribution between groups (p = 0.8). In the ten Nef functional domains, only the PxxP3 region showed significantly greater variation in RP (33.3%) than SP (7.7%, p = 0.048). Gag sequences did not significantly differ between groups. The reportedly protective HLA-A alleles, A*74:01, A*32:01 and A*26, were more commonly observed in SP (50.0%) than RP (11.1%, p = 0.010), whereas the reportedly disease-susceptible HLA-B*45:01 was more common in RP (33.3%) than SP (7.4%, p = 0.045). Compared to RP, SP showed a significantly higher median number of predicted HLA-B-related 12-mer epitopes in Nef (3 vs. 2, p = 0.037), HLA-B-related 11-mer epitopes in Gag (2 vs. 1, p = 0.029), and HLA-A-related 9-mer epitopes in Gag (4 vs. 1, p = 0.051). SP also had fewer HLA-C-related epitopes in Nef (median 4 vs. 5, p = 0.046) and HLA-C-related 11-mer epitopes in Gag (median 1 vs. 1.5, p = 0.044) than RP. CONCLUSIONS Compared to rapid progressors, slow progressors had more protective HLA-A alleles and more HLA-B-related epitopes in both the Nef and Gag proteins. These results suggest that the host factor HLA plays a stronger role in disease progression than the Nef and Gag sequence variations in HIV-1-infected Kenyan children.
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Association between a naturally arising polymorphism within a functional region of HIV-1 Nef and disease progression in chronic HIV-1 infection. Arch Virol 2015; 160:2033-41. [PMID: 26060058 DOI: 10.1007/s00705-015-2480-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/31/2015] [Indexed: 01/24/2023]
Abstract
HIV-1 Nef mediates downregulation of HLA class I (HLA-I) through a number of highly conserved sequence motifs. We investigated the in vivo implication(s) of naturally arising polymorphisms in functional motifs in HIV-1 Nef that are associated with HLA-I downregulation, including the acidic cluster, polyproline, di-arginine and Met-20 regions. Plasma samples from treatment-naive, chronically HIV-1 infected subjects were collected after obtaining informed consent, and viral RNA was extracted and amplified by nested RT-PCR. The resultant nef amplicons were sequenced directly, and subtype-B sequences with an intact open reading frame (n = 406) were included in our analyses. There was over-representation of isoleucine at position 20 (Ile-20) in our dataset when compared to sequences in the Los Alamos sequence database (17.7 vs. 6.9 %, p = 0.0309). The presence of having Ile-20 in Nef was found to be associated with higher median plasma viral load (p = 0.013), independent of associated codons or viral lineage effects, whereas no clinical association was found with polymorphisms in the other functional motifs. Moreover, introduction of a Met-20-to-Ile mutation in a laboratory strain SF2 Nef resulted in a modest, albeit not statistically significant, increase in HLA class I downregulation activity (p = 0.06). Taken together, we have identified a naturally arising polymorphism, Ile-20, within HIV-1 subtype B Nef that is associated with poorer disease outcome.
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Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJR, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology 2013; 10:100. [PMID: 24041011 PMCID: PMC3849644 DOI: 10.1186/1742-4690-10-100] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022] Open
Abstract
Background The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef’s most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D. Results Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function. Conclusions Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.
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Affiliation(s)
- Jaclyn K Mann
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJR, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology 2013. [PMID: 24041011 DOI: 10.1186/742-4690-10-100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D. RESULTS Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function. CONCLUSIONS Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.
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Affiliation(s)
- Jaclyn K Mann
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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Khan SZ, Mitra D. Cyclin K inhibits HIV-1 gene expression and replication by interfering with cyclin-dependent kinase 9 (CDK9)-cyclin T1 interaction in Nef-dependent manner. J Biol Chem 2011; 286:22943-54. [PMID: 21555514 DOI: 10.1074/jbc.m110.201194] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) exploits a number of host cellular factors for successful survival and propagation. The viral protein Nef plays an important role in HIV-1 pathogenesis by interacting with various cellular proteins. In the present work, we identified Cyclin K (CycK) as a novel Nef-interacting protein, and for the first time, we showed that CycK inhibits HIV-1 gene expression and replication in a Nef-dependent manner. The positive elongation factor b complex comprising cyclin-dependent kinase 9 (CDK9) and Cyclin T1 is a critical cellular complex required for viral gene expression and replication. Enhanced expression of CycK in the presence of Nef induced CycK-CDK9 binding, which prevented CDK9-Cyclin T1 complex formation and nuclear translocation of CDK9, resulting in inhibition of HIV-1 long terminal repeat-driven gene expression. Furthermore, this effect of CycK was not observed with Nef-deleted virus, indicating the importance of Nef in this phenomenon. Finally, silencing of CycK in HIV-1-infected cells resulted in increased translocation of CDK9 into the nucleus, leading to increased viral gene expression and replication. These data also suggest that endogenous CycK might act as an inhibitory factor for HIV-1 gene expression and replication in T-cells. Thus, our results clearly demonstrate that CycK utilizes HIV-1 Nef protein to displace CycT1 from the positive elongation factor b complex, resulting in inhibition of HIV-1 gene expression and replication.
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11
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Turk G, Gundlach S, Carobene M, Schindler M, Salomon H, Benaroch P. Single Nef proteins from HIV type 1 subtypes C and F fail to upregulate invariant chain cell surface expression but are active for other functions. AIDS Res Hum Retroviruses 2009; 25:285-96. [PMID: 19327048 DOI: 10.1089/aid.2008.0132] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 Nef protein plays a major role in viral immunopathogenesis, modulating surface expression of several immune receptors, altering signal transduction pathways, and enhancing viral infectivity, among other activities. Nef also exhibits great intersubtype diversity, but most studies have been focused only on Nef proteins from subtype B. Thus, little is known about the functional capacities of nonsubtype B Nef proteins in host cells. Here, we investigated cell surface regulation of MHC-I, MHC-II, the MHC-II-associated chaperone invariant chain (Ii), CD4, CD3, and CD28 in cells transfected or infected with five different Nef alleles including one HIV-1 subtype C and F allele. No significant difference among the Nef proteins regarding CD3, CD28, and MHC-II downregulation was observed. The NefC showed a slightly, yet significant, diminished capacity to downregulate MHC-I in all cells, as well as to downregulate CD4 in Jurkat cells and PBMCs. Strikingly, the two alleles from NefC and NefF were unable to upregulate the Ii chain both in transfected and infected cells. Moreover, the internalization rate of the surface Ii chain was only slightly affected by NefC and NefF, whereas it was drastically reduced by NefB. Nef domains known to be involved in Ii chain upregulation were conserved among the five alleles analyzed here. In summary, we identified two primary HIV-1 NefC and NefF alleles that are selectively impaired for Ii upregulation and that may help to elucidate the mechanism of this Nef function in the future. It will be important to determine whether the observed differences are HIV-1 subtype dependent and influence viral immunopathogenesis.
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Affiliation(s)
- Gabriela Turk
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Mauricio Carobene
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Horacio Salomon
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | - Philippe Benaroch
- Institut Curie, Centre de Recherche, Paris F-75248, France
- INSERM U653, F-75248 Paris Cedex 05, France
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12
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Kumar M, Jain SK, Pasha ST, Chattopadhaya D, Lal S, Rai A. Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV type 1: emergence of a distinct subclade and predicted implications. AIDS Res Hum Retroviruses 2006; 22:1206-19. [PMID: 17209762 DOI: 10.1089/aid.2006.22.1206] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The regulatory functional nef gene is known to mediate a cascade of events during pathogenesis in HIV infection. Variability in the nef gene sequences of HIV-1 A and B subtypes has been well documented. Reasonable data are also available on the pattern of genomic changes in the nef gene of African strains of HIV-1 subtype C, but very little is known about heterogeneity in the nef gene of Indian strains of HIV-1 subtype C, which accounts for 90% of the estimated 5.2 million cases of HIV infection in India. This is a huge number and, therefore, it is important to reveal the extent of sequence variability in the nef gene of HIV-1 subtypes circulating in different parts of India. We carried out full-length nef gene (approximately 620 bp) sequencing on a large number of clinical isolates of HIV-1 circulating in different geographic regions of India. Comparative and phylogenetic analysis revealed 88% (38/43) of cases was HIV-1 subtype C; four cases were diagnosed as subtype A and only one as subtype B. Although most of the crucial functional motifs of the nef gene were conserved, we did observe a few important variations in juxtapositions to functional domains. Interestingly, analyzed nef sequences showed an evolving pattern of segregation away from those reported from other parts of the world, to form a distinct Indian subclade. Deduced amino acid (aa) sequences used to predict HLA binding epitopes for consensus nef gene sequences of Indian strains of HIV-1 revealed two HLA subtype binding domains, GAFDLSFFL (at aa 83) and LTFGWCFKL (at aa 136), in high frequency. The findings from the present study may encourage use of nef gene in molecular diagnostics/genotyping, keeping track of the evolutionary trend and pinpointing the emergence of recombinant strains, and in the future, designing a multiepitope HIV vaccine suitable for the Indian population.
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Affiliation(s)
- Manoj Kumar
- National Institute of Communicable Diseases, Delhi-110054, India.
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13
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O'Neill E, Baugh LL, Novitsky VA, Essex ME, Garcia JV. Intra- and intersubtype alternative Pak2-activating structural motifs of human immunodeficiency virus type 1 Nef. J Virol 2006; 80:8824-9. [PMID: 16912329 PMCID: PMC1563850 DOI: 10.1128/jvi.00910-06] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The design of antiviral strategies against human immunodeficiency virus type 1 (HIV-1) has been largely derived from studies of subtype B viruses, although they constitute only 12% of infections worldwide. At 50% of all HIV-1 infections worldwide, subtype C viruses are the most predominant. Here, we present evidence that subtype C Nefs display functional Pak2-activating motifs that differ from those found in subtype B and E Nefs. The identification of multiple Pak2-activating structural motifs that singly affect one Nef activity revealed a functional plasticity that has implications for future drug and vaccine design aimed at HIV-1 Nef and its effects on the deregulation of the immune system.
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Affiliation(s)
- Eduardo O'Neill
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, 75390, USA.
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14
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Moncany MLJ, Dalet K, Courtois PRR. Identification of conserved lentiviral sequences as landmarks of genomic flexibility. C R Biol 2006; 329:751-64. [PMID: 17027636 PMCID: PMC7172886 DOI: 10.1016/j.crvi.2006.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 06/29/2006] [Accepted: 07/05/2006] [Indexed: 11/25/2022]
Abstract
Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of ‘species self’ besides that of ‘lentiviral self’. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported. To cite this article: M.L.J. Moncany et al., C. R. Biologies 329 (2006).
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Affiliation(s)
- Maurice L J Moncany
- Laboratoire de biologie cellulaire et moléculaire, UFR de sciences, Université de La Rochelle, av. Michel-Crépeau, 17042 La Rochelle cedex 1, France.
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15
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Kumar M, Mitra D. Heat Shock Protein 40 Is Necessary for Human Immunodeficiency Virus-1 Nef-mediated Enhancement of Viral Gene Expression and Replication. J Biol Chem 2005; 280:40041-50. [PMID: 16179353 DOI: 10.1074/jbc.m508904200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The human immunodeficiency virus-1 (HIV-1) Nef protein, originally identified as a negative factor, has now emerged as one of the most important viral proteins necessary for viral pathogenesis and disease progression. Nef has been also implicated in viral infectivity and replication, however, the molecular mechanism of Nef-induced viral gene expression and replication is not clearly understood. Although involvement of heat shock proteins in viral pathogenesis has been reported earlier, a clear understanding of their role remains to be elucidated. Here we report for the first time that Nef not only interacts with heat shock protein 40 (Hsp40) but it also induces the expression of Hsp40 in HIV-1-infected cells. The interaction between Nef and Hsp40 is important for increased Hsp40 translocation into the nucleus of infected cells, which seems to facilitate viral gene expression by becoming part of the cyclin-dependent kinase 9-associated transcription complex regulating long terminal repeat-mediated gene expression. The finding is consistent with the failure of the nef-deleted virus to induce Hsp40, resulting in reduced virus production. Our data further shows that, whereas, Hsp40 overexpression induces viral gene expression, silencing of Hsp40 reduces the gene expression in a Nef-dependent manner. Thus our results clearly indicate that Hsp40 is crucial for Nef-mediated enhancement of viral gene expression and replication.
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Affiliation(s)
- Manish Kumar
- National Centre for Cell Science, Ganeshkhind, Pune-411007, India
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16
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Barugahare B, Baker C, K'Aluoch O, Donovan R, Elrefaei M, Eggena M, Jones N, Mutalya S, Kityo C, Mugyenyi P, Cao H. Human immunodeficiency virus-specific responses in adult Ugandans: patterns of cross-clade recognition. J Virol 2005; 79:4132-9. [PMID: 15767414 PMCID: PMC1061582 DOI: 10.1128/jvi.79.7.4132-4139.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) or AIDS is currently the leading cause of death in Uganda, with at least three HIV clades (subtypes) accounting for most new infections. Whether an effective vaccine formulated on viruses from a single clade will be able to protect against infection from other local clades remains unresolved. We examined the T-cell immune responses from a cohort of HIV-seropositive individuals in Uganda with predominantly clade A and D infections. Surprisingly, we observed similar frequencies of cross-clade T-cell responses to the gag, env, and nef regions. Our data suggest that the level of viral sequence variability between distinct HIV strains does not predict the degree of cross-clade responses. High sequence homologies were also observed between consensus peptides and sequences from viral isolates, supporting the use of consensus amino acid sequences to identify immunogenic regions in studies of large populations.
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17
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Parreira R, Pádua E, Piedade J, Venenno T, Paixão MT, Esteves A. Genetic analysis of human immunodeficiency virus type 1nef in portugal: Subtyping, identification of mosaic genes, and amino acid sequence variability. J Med Virol 2005; 77:8-16. [PMID: 16032733 DOI: 10.1002/jmv.20408] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Extending our previous genetic characterization of human immunodeficiency virus type 1 (HIV-1) strains circulating in Portugal, we here report the first phylogenetic and putative amino acid sequence variability analyses of nef accessory gene. Viral sequences (n = 53) were amplified by nested PCR from proviral DNA purified from peripheral blood mononuclear cells of HIV-1 infected individuals (n = 49). Phylogenetic inference analysis demonstrated a distribution of the viral sequences between subtypes A (sub-subtype A1), B, D, F (sub-subtype F1), G, H, and J, with subtypes G and B accounting altogether for more than half of the genotypes found. A significant number of the proviral DNA sequences analyzed (18.4%) were shown to correspond to intragenic nef recombinants, with the majority having the typical CRF02_AG nef structure. In addition, three novel intragenic recombinant structures were found (B/G/B, CRF02_AG/H, and D/G). From phylogenetic analysis, it was concluded that part of the non-recombinant nef genes might have actually been amplified from mosaic viruses: CRF06_cpx, CRF14_BG, and a new envA/nefJ recombinant. While comparing all the putative Nef sequences, significant amino acid sequence variability was observed. However, most of the described nef functional motifs were relatively well conserved in the majority of the sequences analyzed and numerous amino acid changes fell outside these regions. The results presented unambiguously endorse the high level of complexity of HIV-1 epidemics in Portugal.
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Affiliation(s)
- Ricardo Parreira
- Unidade de Virologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
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18
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Shinoda K, Xin KQ, Jounai N, Kojima Y, Tamura Y, Okada E, Kawamoto S, Okuda K, Klinman D, Okuda K. Polygene DNA vaccine induces a high level of protective effect against HIV-vaccinia virus challenge in mice. Vaccine 2004; 22:3676-90. [PMID: 15315847 DOI: 10.1016/j.vaccine.2004.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2003] [Accepted: 03/14/2004] [Indexed: 11/21/2022]
Abstract
Single HIV-1 subtype DNA vaccine is unlikely to provide reactive protection across a wide range of HIV strains since the HIV virus changes the antigenic sites, particularly, in env gene. To overcome these issues, we constructed a multivalent poly-epitope DNA vaccine. A polygenic DNA vaccine encoding 20 antigenic epitopes from the HIV-1 Env, Gag, and Pol proteins of several clades was constructed using humanized and optimized codons and it was named here hDNA vaccine. In mice, this hDNA vaccine stimulated the following strong (1) antigen-specific serum antibody (Ab) responses, (2) delayed-type hypersensitivity, (3) the activation of IFN-gamma secretion cells targeting gp120 and synthetic antigenic peptides, in addition (4) a significant level of several peptide specific cytotoxic T lymphocytes (CTL) responses. Challenged with modified vaccinia viruses vPE16 and vP1206 expressing HIV-1 env and gag.pol genes, respectively, demonstrated the viral titers in the ovary of the mice vaccinated with hDNA significantly less compared to the unvaccinated mice. Thus, the use of polygene DNA vaccine appears to induce a high level of HIV-specific immune responses and is very effective against challenge with recombinant HIV-vaccinia viruses.
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MESH Headings
- AIDS Vaccines/immunology
- AIDS Vaccines/therapeutic use
- Amino Acid Sequence
- Animals
- Antibody Formation/immunology
- Cytokines/metabolism
- Enzyme-Linked Immunosorbent Assay
- Gene Products, gag/immunology
- HIV Antibodies/analysis
- HIV Antibodies/biosynthesis
- HIV Envelope Protein gp120/immunology
- HIV Infections/prevention & control
- HIV-1/genetics
- HIV-1/immunology
- Hypersensitivity, Delayed/immunology
- Image Processing, Computer-Assisted
- Immunity, Cellular/immunology
- Immunization
- Interferon-gamma/immunology
- Mice
- Mice, Inbred BALB C
- Molecular Sequence Data
- Plasmids/genetics
- Plasmids/immunology
- Promoter Regions, Genetic/genetics
- T-Lymphocytes, Cytotoxic/immunology
- Vaccines, DNA/immunology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Vaccinia virus/immunology
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Affiliation(s)
- Kaori Shinoda
- Department of Bacteriology, Yokohama City University School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
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19
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Machuca A, Ding L, Taffs R, Lee S, Wood O, Hu J, Hewlett I. HIV type 2 primary isolates induce a lower degree of apoptosis "in vitro" compared with HIV type 1 primary isolates. AIDS Res Hum Retroviruses 2004; 20:507-12. [PMID: 15186525 DOI: 10.1089/088922204323087750] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To determine whether subtypes of HIV-1 and HIV-2 vary in their ability to induce T cell apoptosis in vitro, human peripheral blood mononuclear cells (PBMC) from healthy donors and CEM.NKR-CCR5 cells were infected with a variety of HIV-1 and HIV-2 isolates in vitro. Apoptotic cell levels and chemokine and cytokine production were analyzed. Significant variations in cytopathic effects following in vitro infection with primary isolates of HIV-1 or HIV-2 subtypes were observed in PBMCs. The percent of apoptotic cells from each individual ranged from 2 to 78% after HIV-1 infection and from 0 to 28% after HIV-2 infection (p < 0.01). We did not observe significant differences in the degree of apoptosis induced among cells infected with different HIV-1 group M subtypes or group O virus, nor among cells infected with different HIV-2 isolates. However, HIV-2 induced significantly lower degree of apoptosis overall in PBMC and CEM.NKR-CC5 cells when compared with HIV-1 subtypes (p < 0.0001). No significant differences were observed in the production of chemokines, such as RANTES, MIP-1alpha, and MIP-1beta, and cytokines, such as TNF-alpha and TNF-beta when PBMC cultures were infected with different HIV-1 subtype viruses, or HIV-2 isolates. In conclusion, HIV-2 isolates induced significantly lower levels of T cell apoptosis in both PBMC and CEM.NKR-CCR5 cells than HIV-1 isolates. No differences in T cell apoptosis levels were seen between different subtypes of HIV-1 group M or group O isolates. This is consistent with the mild clinical course of infection with HIV-2 that has been reported relative to that observed with HIV-1.
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Affiliation(s)
- Ana Machuca
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
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20
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De Baar MP, Abebe A, Kliphuis A, Tesfaye G, Goudsmit J, Pollakis G. HIV type 1 C and C' subclusters based on long terminal repeat sequences in the Ethiopian type 1 subtype C epidemic. AIDS Res Hum Retroviruses 2003; 19:917-22. [PMID: 14601586 DOI: 10.1089/088922203322493094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
While the Ethiopian HIV-1 epidemic is dominated by subtype C, two distinguishable cocirculating C genotypes have been identified based on sequences of the C2V3 envelope region. In this study we sequenced and analyzed the long terminal repeat (LTR) sequence from 22 Ethiopian HIV-1-positive individuals. The two phylogenetically distinguishable genotypes C (n = 13) and C' (n = 4) are separated by significant bootstrap values. Nucleotide differences between the two groups were identified in the NF-AT, TCF-1alpha, and SP1 transcription factor binding sites, whereas the NF-kappaB and NRE-core sequences were identical between the two groups. Five isolates that could not be classified C or C' were found to be recombinants within the LTR sequence upon boots can analysis. Comparison of all the LTR sequences with their corresponding C2V3 envelope sequence revealed four intersubtype C/C' recombinant isolates. Thus, the prevalence of C/C' recombinant viruses is well over 40%. Interestingly, the C2V3 envelope sequences of all recombinant viruses belonged to the genotype C', whereas every LTR sequence belonged to the genotype C. This result indicates that recombination between the two genotypes is unidirectional, possibly as the result of evolutionary pressure on the respective biological functions of the LTR promoter and the envelope protein.
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Affiliation(s)
- Michel P De Baar
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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21
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Padua E, Jenkins A, Brown S, Bootman J, Paixao MT, Almond N, Berry N. Natural variation of the nef gene in human immunodeficiency virus type 2 infections in Portugal. J Gen Virol 2003; 84:1287-1299. [PMID: 12692296 DOI: 10.1099/vir.0.18908-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) infections cause severe immunodeficiency in humans, although HIV-2 is associated frequently with reduced virulence and pathogenicity compared to HIV-1. Genetic determinants that play a role in HIV pathogenesis are relatively poorly understood but nef has been implicated in inducing a more pathogenic phenotype in vivo. However, relatively little is known about the role of nef in HIV-2 pathogenesis. To address this, the genetic composition of 44 nef alleles from 37 HIV-2-infected individuals in Portugal, encompassing a wide spectrum of disease associations, CD4 counts and virus load, has been assessed. All nef alleles were subtype A, with no evidence of gross deletions, truncations or disruptions in the nef-encoding sequence; all were full-length and intact. HIV-2 long terminal repeat sequences were conserved and also indicated subtype A infections. Detailed analysis of motifs that mediate nef function in HIV-1 and simian immunodeficiency virus, such as CD4 downregulation and putative SH2/SH3 interactions, revealed significant natural variation. In particular, the central P(104)xxPLR motif exhibited wide interpatient variation, ranging from an HIV-1-like tetra-proline structure (PxxP)(3) to a disrupted minimal core motif (P(104)xxQLR). The P(107)-->Q substitution was associated with an asymptomatic phenotype (Fisher's exact test, P=0.026) and low virus loads. These data indicate that discrete differences in the nef gene sequence rather than gross structural changes are more likely to play a role in HIV-2 pathogenesis mediated via specific functional interactions.
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Affiliation(s)
- Elizabeth Padua
- AIDS Reference Laboratory, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Adrian Jenkins
- Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Stuart Brown
- Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Janet Bootman
- Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Maria Teresa Paixao
- AIDS Reference Laboratory, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Neil Almond
- Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Neil Berry
- Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
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22
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Koulinska IN, Msamanga G, Mwakagile D, Essex M, Renjifo B. Common genetic arrangements among human immunodeficiency virus type 1 subtype A and D recombinant genomes vertically transmitted in Tanzania. AIDS Res Hum Retroviruses 2002; 18:947-56. [PMID: 12230937 DOI: 10.1089/088922202760265614] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtypes A, C, and D are cocirculating in Tanzania, and large numbers of recombinant genomes have been reported from this region. Here we describe full-length sequences of six unlinked HIV-1 subtype A and D recombinants. The samples came from newborns, indicating that the recombination patterns were vertically transmitted and were functionally competent. All six genomes had different recombination patterns with one to eight cross-over points frequently located at the beginning or end of functionally defined regions. In five of the six viruses most of gag, pol, tat, and rev and the intracytoplasmic domain of gp41 were classified as subtype D. In all but one genome, the external domain of gp41 and the majority of gp120 belonged to subtype A. A recombination site common to four of the six genomes was located at the transmembrane domain of gp41, at the end of the rev response element. The identification of subtype patterns among intersubtype recombinant genomes from recently infected individuals may reveal genetic determinants of improved viral fitness or advantage for transmission.
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Affiliation(s)
- Irene N Koulinska
- Harvard AIDS Institute and Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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23
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Guimaraes ML, Moreira AS, Morgado MG. Polymorphism of the Human Immunodeficiency Virus Type 1 in Brazil: genetic characterization of the nef gene and implications for vaccine design. Mem Inst Oswaldo Cruz 2002; 97:523-6. [PMID: 12118284 DOI: 10.1590/s0074-02762002000400013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Most of the Brazilian HIV-1 samples have been characterized based on the structural genes (env, gag and pol) and no data concerning the variability of the accessory genes such as nef have been available so far. Considering the role of the nef on virus biology and the inclusion of this region in some HIV/AIDS vaccine products under testing, the purpose of this study was to document the genetic diversity of the nef gene in third-four HIV-1 Brazilian samples previously subtyped based on the env C2-V3 region. Although only few non-subtype B samples have already been analyzed so far, the cytotoxic Tlymphocyte epitopes encoded in this region were relatively conserved among the subtypes, with some amino acid signatures mainly in the subtype C samples. Considering the increasing of the non-B HIV-1 subtypes worldwide, in special the subtype C, more data should be generated concerning the genetic and antigenic variability of these subtypes, as well as the study of the impact of such polymorphism in HIV/AIDS vaccine design and testing.
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Affiliation(s)
- M L Guimaraes
- Departamento de Imunologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, 21045-900, Brasil
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24
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Koulinska IN, Ndung'u T, Mwakagile D, Msamanga G, Kagoma C, Fawzi W, Essex M, Renjifo B. A new human immunodeficiency virus type 1 circulating recombinant form from Tanzania. AIDS Res Hum Retroviruses 2001; 17:423-31. [PMID: 11282011 DOI: 10.1089/088922201750102508] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is becoming increasingly important to identify and to study human immunodeficiency virus type 1 (HIV-1) circulating recombinant forms (CRFs) with evidence of epidemic spread, since mosaic strains arise frequently, especially in populations where multiple subtypes cocirculate. We describe the almost complete nucleotide sequence of 3 subtype C and D recombinant viruses, selected from a pool of 13 D(gag)-D/C/D(env) perinatally infected infants from Dar es Salaam, Tanzania. All three genomes had cross-over points with approximately the same genomic localization. The subtype C-like sequences were located within pol, vif, vpr, vpu, the first exons of rev and tat, V3, and the U3-R regions of the LTR. Phylogenetic analyses of the full-length genomic sequences from these viruses showed the formation of a distinct subcluster on the HIV-1 subtype D branch. The pattern of recombination of genomes belonging to this new CRF, named CRF10_CD, might have resulted from independent recombination events occurring at high frequency or from a single source that originated earlier in this population. Future surveys will be needed to determine the potential of this CRF for epidemic spread.
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Affiliation(s)
- I N Koulinska
- Harvard AIDS Institute and Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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Athanassakis I, Papadimitriou L, Koumantakis E, Vassiliadis S. Th1- and Th2-type lymphokine-assisted induction and release of chemokine receptors from primary human trophoblast cells. Hum Immunol 2000; 61:651-7. [PMID: 10880735 DOI: 10.1016/s0198-8859(00)00128-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Chemokine receptors (CCRs) have been demonstrated to facilitate the entry of HIV in different cell types of infected individuals, including CD4(+) T cells and dendritic cells. The natural or inducible expression of CCRs on trophoblast cells could provide a valid mechanism for the in utero transmission of HIV from mother to fetus. Because of the rapid turnover of these receptors, we attempted to define the natural and inducible expression of surface CCR3 and CXCR4 on primary human trophoblasts during short periods of cell culture. In the absence of any external stimulus the expression of CCR3 and CXCR4 varied from 1% to 24%. Kinetic experiments show that the levels of both CCR3 and CXCR4 reach a peak of expression after 6 h of culture, whereas by 24 h they have almost disappeared. In the presence of IFN-gamma, CCR3 is showing an increasing pattern of expression after 4 h of incubation, reaching highest levels after 24 h of culture, whereas CXCR4 is kept at lower levels as compared with nontreated cells. Furthermore, in the presence of IL-4, CCR3 expression declines from 2 to 8 h of culture to increase again at 24 h, where 50% of the cell population is expressing the receptors. Under the IL-4 stimulus, CXCR4 shows a peak of expression at 8 h of culture. An interesting feature of this study is that we were able to detect soluble CCR activity in the culture supernatants of trophoblast cells, which followed an inverse pattern of this of surface expression. Thus, the inability of many laboratories to detect high levels of CCRs in placentae of HIV infected mothers may be due on these fast turnover of these receptors, which by the assaying time have either been released in the culture medium or been internalized to the cell.
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