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Wilson KM, He JJ. HIV Nef Expression Down-modulated GFAP Expression and Altered Glutamate Uptake and Release and Proliferation in Astrocytes. Aging Dis 2023; 14:152-169. [PMID: 36818564 PMCID: PMC9937695 DOI: 10.14336/ad.2022.0712] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
HIV infection of astrocytes leads to restricted gene expression and replication but abundant expression of HIV early genes Tat, Nef and Rev. A great deal of neuroHIV research has so far been focused on Tat protein, its effects on astrocytes, and its roles in neuroHIV. In the current study, we aimed to determine effects of Nef expression on astrocytes and their function. Using transfection or infection of VSVG-pseudotyped HIV viruses, we showed that Nef expression down-modulated glial fibrillary acidic protein (GFAP) expression. We then showed that Nef expression also led to decreased GFAP mRNA expression. The transcriptional regulation was further confirmed using a GFAP promoter-driven reporter gene assay. We performed transcription factor profiling array to compare the expression of transcription factors between Nef-intact and Nef-deficient HIV-infected cells and identified eight transcription factors with expression changes of 1.5-fold or higher: three up-regulated by Nef (Stat1, Stat5, and TFIID), and five down-regulated by Nef (AR, GAS/ISRE, HIF, Sp1, and p53). We then demonstrated that removal of the Sp1 binding sites from the GFAP promoter resulted in a much lower level of the promoter activity and reversal of Nef effects on the GFAP promoter, confirming important roles of Sp1 in the GFAP promoter activity and for Nef-induced GFAP expression. Lastly, we showed that Nef expression led to increased glutamate uptake and decreased glutamate release by astrocytes and increased astrocyte proliferation. Taken together, these results indicate that Nef leads to down-modulation of GFAP expression and alteration of glutamate metabolism in astrocytes, and astrocyte proliferation and could be an important contributor to neuroHIV.
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Affiliation(s)
- Kelly M Wilson
- Department of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, School of Graduate and Postdoctoral Studies, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
| | - Johnny J He
- Department of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, School of Graduate and Postdoctoral Studies, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
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2
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Martínez L, Milanič M, Malaina I, Álvarez C, Pérez MB, M. de la Fuente I. Weighted lambda superstrings applied to vaccine design. PLoS One 2019; 14:e0211714. [PMID: 30735507 PMCID: PMC6368308 DOI: 10.1371/journal.pone.0211714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/19/2019] [Indexed: 11/23/2022] Open
Abstract
We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins.
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Affiliation(s)
- Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Basque Center for Applied Mathematics BCAM, Bilbao, Spain
- * E-mail:
| | - Martin Milanič
- University of Primorska, UP IAM and UP FAMNIT, Koper, Slovenia
| | - Iker Malaina
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Carmen Álvarez
- IDIVAL Valdecilla Biomedical Research Institute, Santander, Spain
| | - Martín-Blas Pérez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Ildefonso M. de la Fuente
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
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Ding J, Ma L, Zhao J, Xie Y, Zhou J, Li X, Cen S. An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers. J Transl Med 2019; 17:35. [PMID: 30665429 PMCID: PMC6341564 DOI: 10.1186/s12967-019-1777-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/09/2019] [Indexed: 01/17/2023] Open
Abstract
Background Despite that most HIV-infected individuals experience progressive CD4+ T cell loss and develop AIDS, a minority of HIV-infected individuals remain asymptomatic and maintain high level CD4+ T cell counts several years after seroconversion. Efforts have been made to understand the determinants of the nonprogressive status, exemplified by the clinical course of elite controllers (ECs) who maintain an undetectable viremia and viremic nonprogressors (VNPs) who have a normal CD4+ count in spite of circulating viral load. However, the intrinsic mechanism underlying nonprogression remained elusive. In this study, we performed an integrative analysis of transcriptional profiles to pinpoint the underlying mechanism for a naturally occurring viral control. Methods Three microarray datasets, reporting mRNA expression of the LTNPs or ECs in HIV-infected patients, were retrieved from Gene Expression Ominbus (GEO) or Arrayexpress databases. These datasets, profiled on the same type of microarray chip, were selected and merged by a bioinformatic approach to build a meta-analysis derived transcriptome (MADNT). In addition, we investigated the different transcriptional pathways and potential biomarkers in CD4+ and CD8+ cells in ECs and whole blood in VNPs compared to HIV progressors. The combined transcriptome and each subgroup was subject to gene set enrichment analysis and weighted co-expression network analysis to search potential transcription patterns related to the non-progressive status. Results 30 up-regulated genes and 83 down-regulated genes were identified in lymphocytes from integrative meta-analysis of expression data. The interferon response and innate immune activation was reduced in both CD4+ and CD8+ T cells from ECs. Several characteristic genes including CMPK1, CBX7, EIF3L, EIF4A and ZNF395 were indicated to be highly correlated with viremic control. Besides that, we indicated that the reduction of ribosome components and blockade of translation facilitated AIDS disease progression. Most interestingly, among VNPs who have a relatively high viral load, we detected a two gene-interaction networks which showed a strong correlation to immune control even with a rigorous statistical threshold (p value = 2−e4 and p value = 0.004, respectively) by WGCNA. Conclusions We have identified differentially expressed genes and transcriptional patterns in ECs and VNPs compared to normal chronic HIV-infected individuals. Our study provides new insights into the pathogenesis of HIV and AIDS and clues for the therapeutic strategies for anti-retroviral administration. Electronic supplementary material The online version of this article (10.1186/s12967-019-1777-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Yongli Xie
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, 100050, China.
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, 100050, China.
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Watkins RL, Zou W, Denton PW, Krisko JF, Foster JL, Garcia JV. In vivo analysis of highly conserved Nef activities in HIV-1 replication and pathogenesis. Retrovirology 2013; 10:125. [PMID: 24172637 PMCID: PMC3907037 DOI: 10.1186/1742-4690-10-125] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/23/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The HIV-1 accessory protein, Nef, is decisive for progression to AIDS. In vitro characterization of the protein has described many Nef activities of unknown in vivo significance including CD4 downregulation and a number of activities that depend on Nef interacting with host SH3 domain proteins. Here, we use the BLT humanized mouse model of HIV-1 infection to assess their impact on viral replication and pathogenesis and the selection pressure to restore these activities using enforced in vivo evolution. RESULTS We followed the evolution of HIV-1LAI (LAI) with a frame-shifted nef (LAINeffs) during infection of BLT mice. LAINeffs was rapidly replaced in blood by virus with short deletions in nef that restored the open reading frame (LAINeffs∆-1 and LAINeffs∆-13). Subsequently, LAINeffs∆-1 was often replaced by wild type LAI. Unexpectedly, LAINeffs∆-1 and LAINeffs∆-13 Nefs were specifically defective for CD4 downregulation activity. Viruses with these mutant nefs were used to infect BLT mice. LAINeffs∆-1 and LAINeffs∆-13 exhibited three-fold reduced viral replication (compared to LAI) and a 50% reduction of systemic CD4+ T cells (>90% for LAI) demonstrating the importance of CD4 downregulation. These results also demonstrate that functions other than CD4 downregulation enhanced viral replication and pathogenesis of LAINeffs∆-1 and LAINeffs∆-13 compared to LAINeffs. To gain insight into the nature of these activities, we constructed the double mutant P72A/P75A. Multiple Nef activities can be negated by mutating the SH3 domain binding site (P72Q73V74P75L76R77) to P72A/P75A and this mutation does not affect CD4 downregulation. Virus with nef mutated to P72A/P75A closely resembled the wild-type virus in vivo as viral replication and pathogenesis was not significantly altered. Unlike LAINeffs described above, the P72A/P75A mutation had a very weak tendency to revert to wild type sequence. CONCLUSIONS The in vivo phenotype of Nef is significantly dependent on CD4 downregulation but minimally on the numerous Nef activities that require an intact SH3 domain binding motif. These results suggest that CD4 downregulation plus one or more unknown Nef activities contribute to enhanced viral replication and pathogenesis and are suitable targets for anti-HIV therapy. Enforced evolution studies in BLT mice will greatly facilitate identification of these critical activities.
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Affiliation(s)
- Richard L Watkins
- Division of Infectious Diseases, Center for AIDS Research, 2042 Genetic Medicine, University of North Carolina, Campus Box 7042, Chapel Hill, NC 27599-7042, USA.
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5
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Watkins RL, Zou W, Denton PW, Krisko JF, Foster JL, Garcia JV. In vivo analysis of highly conserved Nef activities in HIV-1 replication and pathogenesis. Retrovirology 2013. [PMID: 24172637 DOI: 10.1186/742-4690-10-125] [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 HIV-1 accessory protein, Nef, is decisive for progression to AIDS. In vitro characterization of the protein has described many Nef activities of unknown in vivo significance including CD4 downregulation and a number of activities that depend on Nef interacting with host SH3 domain proteins. Here, we use the BLT humanized mouse model of HIV-1 infection to assess their impact on viral replication and pathogenesis and the selection pressure to restore these activities using enforced in vivo evolution. RESULTS We followed the evolution of HIV-1LAI (LAI) with a frame-shifted nef (LAINeffs) during infection of BLT mice. LAINeffs was rapidly replaced in blood by virus with short deletions in nef that restored the open reading frame (LAINeffs∆-1 and LAINeffs∆-13). Subsequently, LAINeffs∆-1 was often replaced by wild type LAI. Unexpectedly, LAINeffs∆-1 and LAINeffs∆-13 Nefs were specifically defective for CD4 downregulation activity. Viruses with these mutant nefs were used to infect BLT mice. LAINeffs∆-1 and LAINeffs∆-13 exhibited three-fold reduced viral replication (compared to LAI) and a 50% reduction of systemic CD4+ T cells (>90% for LAI) demonstrating the importance of CD4 downregulation. These results also demonstrate that functions other than CD4 downregulation enhanced viral replication and pathogenesis of LAINeffs∆-1 and LAINeffs∆-13 compared to LAINeffs. To gain insight into the nature of these activities, we constructed the double mutant P72A/P75A. Multiple Nef activities can be negated by mutating the SH3 domain binding site (P72Q73V74P75L76R77) to P72A/P75A and this mutation does not affect CD4 downregulation. Virus with nef mutated to P72A/P75A closely resembled the wild-type virus in vivo as viral replication and pathogenesis was not significantly altered. Unlike LAINeffs described above, the P72A/P75A mutation had a very weak tendency to revert to wild type sequence. CONCLUSIONS The in vivo phenotype of Nef is significantly dependent on CD4 downregulation but minimally on the numerous Nef activities that require an intact SH3 domain binding motif. These results suggest that CD4 downregulation plus one or more unknown Nef activities contribute to enhanced viral replication and pathogenesis and are suitable targets for anti-HIV therapy. Enforced evolution studies in BLT mice will greatly facilitate identification of these critical activities.
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Affiliation(s)
- Richard L Watkins
- Division of Infectious Diseases, Center for AIDS Research, 2042 Genetic Medicine, University of North Carolina, Campus Box 7042, Chapel Hill, NC 27599-7042, USA.
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Cruz NVG, Amorim R, Oliveira FE, Speranza FAC, Costa LJ. Mutations in the nef and vif genes associated with progression to AIDS in elite controller and slow-progressor patients. J Med Virol 2013; 85:563-74. [PMID: 23417613 DOI: 10.1002/jmv.23512] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2012] [Indexed: 11/07/2022]
Abstract
Progression towards AIDS can vary from 5 to 10 years from the establishment of the primary infection by HIV-1 to more than 10 years in the complete absence of antiretroviral therapy. Several factors can contribute to the outcome of HIV infection, including host genetic and viral replicating characteristics. Historically, nef-deleted viral genomes have been associated with disease progression. Therefore, the lentiviral Nef protein is regarded as a progression factor. The objective of this work was to characterize the nef gene from a group of treatment naive patients infected with HIV-1 for more than 10 years. These patients were classified as long-term non-progressors, elite controller, and slow-progressors according to clinical and laboratorial data. A premature stop codon within the nef gene leading to the expression of a truncated peptide was observed on samples from the elite controller patient. For the slow-progressor patients, several degrees of deletions at the C-terminal of Nef were observed predicting a loss of function of this protein. The vif gene was characterized for these patients and a rare mutation that predicts a miss localization of the Vif protein to the nucleus of infected cells that could prevent its function as an APOBEC neutralization factor was also observed. These data indicate the importance of the HIV accessory proteins as factors that contribute to the outcome of AIDS.
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Affiliation(s)
- Nadia V G Cruz
- Department of Virology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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7
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Corró G, Rocco CA, De Candia C, Catano G, Turk G, Mangano A, Aulicino PC, Bologna R, Sen L. Genetic and functional analysis of HIV type 1 nef gene derived from long-term nonprogressor children: association of attenuated variants with slow progression to pediatric AIDS. AIDS Res Hum Retroviruses 2012; 28:1617-26. [PMID: 22583022 DOI: 10.1089/aid.2012.0020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Among persons infected by HIV-1, the rate of progression to AIDS is multifactorial being affected by host and viral factors, including the HIV-encoded negative factor (Nef). Our aim was to define whether variations in the nef gene as well as its functions may be associated with slower HIV disease course in infected children. The proviral HIV-1 nef gene was cloned, sequenced, and compared in children with contrasting disease course: 10 long-term nonprogressors (LTNP) and six rapid progressor (RP). The CD4 and MHC-I down-modulation ability of nef alleles derived from LTNP and RP children was analyzed. We observed that only one of our 10 LTNP had a protective genetic background, and out of them, 40% had defective nef genes, carrying substitutions at the (AWLEAQ(56-61)) and the (Rxx(22-24)) domains, and that those alleles were unable of down-regulate CD4 and MHC-I. The emergence or presence of Nef L58V substitution was associated with viral attenuation, indicated by a reduction in HIV viral loads, a persistent preservation of CD4(+) T cell counts, and lack of AIDS-related symptoms. Our results demonstrate that HIV-1 perinatally infected children carrying functionally defective nef HIV-1 strains have prolonged asymptomatic phases without therapy, suggesting a relevant role of CD4 and MHC-I down-modulation Nef domains on in vivo HIV-1 pathogenesis and pediatric immunodeficiency outcome.
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Affiliation(s)
- Guillermo Corró
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Carlos A Rocco
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
| | - Cristian De Candia
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | - Gabriel Catano
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System and Department of Medicine, University of Texas Health Science Care at San Antonio, San Antonio, Texas
| | - Gabriela Turk
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Paula C. Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Infectología, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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Riva A, Vicenzi E, Galli M, Poli G. Strenuous resistance to natural HIV-1 disease progression: viral controllers and long-term nonprogressors. Future Virol 2011. [DOI: 10.2217/fvl.11.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 infection leads to AIDS and death within 8–10 years for most individuals in the absence of antiretroviral therapy (ART). However, a minority of infected individuals show the unusual capacity to spontaneously control disease progression after infection in the absence of any ART. So-called ‘long-term nonprogressors’ are defined by maintenance of peripheral CD4+ T-cell counts >500 cells/µl and good health without ART for >7 years since infection. More recently, ART-naive individuals who spontaneously control their viremia levels at either <50 or <2000 copies of RNA/ml for at least 12 months in the absence of ART have been named ‘elite controllers’ and ‘HIV controllers’, respectively. The overlap between long-term nonprogressors and elite controllers/HIV controllers is partial, and both groups collectively account for <5% of all infected individuals. Unraveling the nature of their relative resistance to HIV-1 disease progression would be of great value for HIV-prevention strategies.
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Affiliation(s)
- Agostino Riva
- Infectious Diseases & Immunopathology Section, Department of Clinical Sciences, L Sacco Hospital, Università di Milano, Italy
| | - Elisa Vicenzi
- Viral Pathogens & Biosafety & AIDS Immunopathogenesis Units, Division of Immunology, Transplantation & Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy; P2/P3 Laboratories, Via Olgettina n 58, 20132, Milano, Italy
| | - Massimo Galli
- Infectious Diseases & Immunopathology Section, Department of Clinical Sciences, L Sacco Hospital, Università di Milano, Italy
| | - Guido Poli
- Vita-Salute San Raffaele University, School of Medicine, Milano, Italy
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Pushker R, Jacqué JM, Shields DC. Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression. J Virol 2010; 84:3644-53. [PMID: 20071583 PMCID: PMC2838144 DOI: 10.1128/jvi.01959-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 12/30/2009] [Indexed: 11/20/2022] Open
Abstract
Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1 nef gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular nef amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients. LTNPs had more defective nefs (interrupted by frameshifts or stop codons), but on a per-patient basis there was no excess of LTNP patients with one or more defective nef sequences compared to the Ps (P = 0.47). The high frequency of amino acid replacement at residues S(8), V(10), I(11), A(15), V(85), V(133), N(157), S(163), V(168), D(174), R(178), E(182), and R(188) in LTNPs was also seen in permuted datasets, implying that these are simply rapidly evolving residues. Permutation testing revealed that residues showing the greatest excess over expectation (A(15), V(85), N(157), S(163), V(168), D(174), R(178), and R(188)) were not significant (P = 0.77). Exploratory analysis suggested a hypothetical excess of frameshifting in the regions (9)SVIG and (118)QGYF among LTNPs. The regions V(10) and (152)KVEEA of nef were commonly deleted in LTNPs. However, permutation testing indicated that none of the regions displayed significantly excessive deletion in LTNPs. In conclusion, meta-analysis of HIV-1 nef sequences provides no clear evidence of whether defective nef sequences or particular regions of the protein play a significant role in disease progression.
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Affiliation(s)
- Ravindra Pushker
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jean-Marc Jacqué
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin 4, Ireland
| | - Denis C. Shields
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin 4, Ireland
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10
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Priceputu E, Hanna Z, Hu C, Simard MC, Vincent P, Wildum S, Schindler M, Kirchhoff F, Jolicoeur P. Primary human immunodeficiency virus type 1 nef alleles show major differences in pathogenicity in transgenic mice. J Virol 2007; 81:4677-93. [PMID: 17314161 PMCID: PMC1900134 DOI: 10.1128/jvi.02691-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously reported that the human immunodeficiency virus type 1 NL4-3 Nef is necessary and sufficient to induce a severe AIDS-like disease in transgenic (Tg) mice when the protein is expressed under the regulatory sequences of the human CD4 gene. We have now assayed additional Nef alleles (SF2, JR-CSF, YU10x, and NL4-3 [T71R] Nef alleles), including some from long-term nonprogressors (AD-93, 032an, and 039nm alleles) in the same Tg system and compared their pathogenicities. All these Nef alleles downregulated cell surface CD4 in human cells in vitro and also, with the exception of Nef(YU10x), in Tg CD4(+) T cells. Depletion of double-positive and single-positive thymocytes occurred with all alleles but was less pronounced in Nef(YU10x) Tg mice. A loss of peripheral CD4(+) T cells was observed with all alleles but was minimal in Nef(YU10x) Tg mice. In Nef(032an) and Nef(SF2) Tg mice, T-cell loss was severe despite lower levels of Tg expression, suggesting a higher virulence of these alleles. All Nef alleles except the Nef(YU10x) and Nef(NL4-3(T71R)) alleles induced an enhanced activated memory (CD25(+) CD69(+) CD44(high) CD45RB(low) CD62L(low)) and apoptotic phenotype. Also, all could interact with and/or activate PAK2 except the Nef(JR-CSF) allele. Organ (lung and kidney) diseases were present in Nef(NL4-3(T71R)), Nef(032an), Nef(039nm), and Nef(SF2) Tg mice, despite very low levels of Tg expression for the last strain. However, no organ disease or minimal organ disease developed in Nef(YU10x) and Nef(AD-93) Tg mice and Nef(JR-CSF) Tg mice, respectively, despite high levels of Tg expression. Our data show that important differences in the pathogenicities of various Nef alleles can be scored in Tg mice. Interestingly, our results also revealed that some phenotypes can segregate independently, such as CD4(+) T-cell depletion and activation, as well as severe depletion of thymic CD4(+) T cells and peripheral CD4(+) T cells. Therefore, expression of Nef alleles in Tg mice under the CD4C regulatory elements represents a novel assay for measuring their pathogenicity. Because of the very high similarity of this murine AIDS-like disease to human AIDS, this assay may have a predictive value regarding the behavior of Nef in infected humans.
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Affiliation(s)
- Elena Priceputu
- Laboratory of Molecular Biology, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, Quebec H2W 1R7, Canada
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11
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Walker PR, Ketunuti M, Choge IA, Meyers T, Gray G, Holmes EC, Morris L. Polymorphisms in Nef associated with different clinical outcomes in HIV type 1 subtype C-infected children. AIDS Res Hum Retroviruses 2007; 23:204-15. [PMID: 17331028 DOI: 10.1089/aid.2006.0080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) negative factor, or Nef, has a variety of functions that are important in viral pathogenesis. Sequence analysis has identified nef mutations that are linked to the rate of disease progression in adults and children infected with HIV-1 subtype B. Here we have sequenced and analyzed HIV-1 subtype C nef sequences from 34 children with rapid (RP) or slow progressing (SP) disease and identified polymorphisms associated with disease stage including motifs involved in specific pathogenic functions. Unlike subtype B, insertions and deletions in the N-terminal variable region were observed exclusively in SP children (8 out of 25). Strong positive selection pressures were found in sites of known functional importance among SP sequences, whereas RP had strong negative selection across the gene. A lineage analysis of selection pressures indicated weaker pressure across the nef gene in SP sequences bearing a deletion in region 8-12, suggesting this deletion has functional importance in vivo. Together these results suggest a differential adaptation of certain Nef functions related to disease progression, some of which may be attributable to immune-imposed pressures. These data broadly reflect previous studies on subtype B, corroborate the decreased cytopathicity of SP viruses, but also highlight potential subtype differences that require further investigation.
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Affiliation(s)
- Polly R Walker
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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12
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Agopian K, Wei BL, Garcia JV, Gabuzda D. CD4 and MHC-I downregulation are conserved in primary HIV-1 Nef alleles from brain and lymphoid tissues, but Pak2 activation is highly variable. Virology 2006; 358:119-35. [PMID: 16979207 PMCID: PMC1995023 DOI: 10.1016/j.virol.2006.07.053] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 07/06/2006] [Accepted: 07/27/2006] [Indexed: 01/06/2023]
Abstract
HIV-1 compartmentalization in the CNS has been demonstrated for gag, pol, and env genes. However, little is known about tissue compartmentalization of nef genes and their functional characteristics in brain. We have cloned 97 nef genes and characterized 10 Nef proteins from autopsy brain and lymphoid tissues from 2 patients with AIDS and HIV-1-associated dementia. Distinct compartmentalization of brain versus lymphoid nef genes was demonstrated within each patient. CD4 and MHC-I downregulation were conserved in all tissue-derived Nefs. However, MHC-I downregulation by brain-derived Nefs was weaker than downregulation by lymphoid-derived Nefs. The motifs KEEE- or EKEE- at the PACS-1 binding site represented brain-specific signature patterns in these 2 patients and contributed to the reduced MHC-I downregulation activity of brain-derived Nefs from these patients. Pak2 association was highly variable in Nefs from both patients. Three of 10 tissue-derived Nefs coimmunoprecipitated activated Pak2, with strong association demonstrated for only 2 Nefs. The ability of Nef to associate with activated Pak2 did not correlate with brain or lymphoid tissue origin. Nef genes from viruses isolated from brain by coculture with PBMC were not closely related to sequences amplified directly from brain tissue, suggesting that viral selection or adaptation occurred during coculture. This study of tissue-derived HIV-1 Nefs demonstrates that CD4 and MHC-I downregulation are highly conserved Nef functions, while Pak2 association is variable in late stage AIDS patients.
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Affiliation(s)
- Kristin Agopian
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Bangdong L. Wei
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - J. Victor Garcia
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- *Corresponding Author. Mailing Address: Dana-Farber Cancer Institute, JFB 816 44 Binney St. Boston, MA 02115 Phone: (617) 632-2154 Fax: (617) 632 3113 E-mail:
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13
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Crotti A, Neri F, Corti D, Ghezzi S, Heltai S, Baur A, Poli G, Santagostino E, Vicenzi E. Nef alleles from human immunodeficiency virus type 1-infected long-term-nonprogressor hemophiliacs with or without late disease progression are defective in enhancing virus replication and CD4 down-regulation. J Virol 2006; 80:10663-74. [PMID: 16943296 PMCID: PMC1641799 DOI: 10.1128/jvi.02621-05] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infection with human immunodeficiency virus (HIV)-encoding defective nef variants may contribute to a relatively benign course of disease in a minority of long-term nonprogressors (LTNP). We have examined the functions of nef alleles from six individuals belonging to the same cohort of hemophiliacs infected with HIV-1 prior to 1985 and classified as LTNP in 1995. Three out of six individuals have progressed to HIV disease (late progressors [LP]), whereas the three remainders have maintained their LTNP status at least up to 2003. The nef alleles were obtained from both plasma virus and peripheral blood mononuclear cells of all six individuals in 1995 and 1998. The proportion of sequences containing mutations not yielding Nef expression significantly diminished in 1998 versus that in 1995. Several previously defined functional regions of intact nef alleles were highly conserved. However, the major variant obtained in 1998 from plasma RNA of five out of six individuals significantly reduced HIV infectivity/replication and impaired Nef-mediated CD4 but not major histocompatibility complex class I antigen down-modulation from the cell surface. Thus, functional alterations of the nef gene are present in both LP and LTNP, suggesting that Nef defectiveness in vitro is not necessarily associated with the long-term maintenance of LTNP status. Of interest is the fact that isolates from three out of three LP showed a dual CCR5/CXCR4 coreceptor use (R5X4), in contrast to those from LTNP, which were exclusively R5. Thus, in vivo evolution of gp120 Env to CXCR4 use appears to be associated with HIV disease progression in individuals infected with nef-defective viruses.
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Affiliation(s)
- Andrea Crotti
- AIDS Immunopathogenesis Unit, San Raffaele Scientific Institute, Milan, Italy
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14
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Hanna Z, Priceputu E, Hu C, Vincent P, Jolicoeur P. HIV-1 Nef mutations abrogating downregulation of CD4 affect other Nef functions and show reduced pathogenicity in transgenic mice. Virology 2006; 346:40-52. [PMID: 16310238 DOI: 10.1016/j.virol.2005.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 08/01/2005] [Accepted: 10/04/2005] [Indexed: 11/15/2022]
Abstract
HIV-1 Nef has the ability to downmodulate CD4 cell surface expression. Several studies have shown that CD4 downregulation is required for efficient virus replication and high infectivity. However, the pathophysiological relevance of this phenomenon in vivo, independently of its role in sustaining high virus loads, remains unclear. We studied the impact of the CD4 downregulation function of Nef on its pathogenesis in vivo, in the absence of viral replication, in the CD4C/HIV transgenic (Tg) mouse model. Two independent Nef mutants (RD35/36AA and D174K), known to abrogate CD4 downregulation, were tested in Tg mice. Flow cytometry analysis showed that downregulation of murine CD4 was severely decreased or abrogated on Tg T cells expressing respectively Nef(RD35/36AA) and Nef(D174K). Similarly, the severe depletion of double-positive CD4+CD8+ and of single-positive CD4+CD8- thymocytes, usually observed with Nef(Wt), was not detected in Nef(RD35/36AA) and Nef(D174K) Tg mice. However, both mutant Tg mice showed a partial depletion of peripheral CD4+ T cells. This was accompanied, as previously reported for Net(Wt) Tg mice, by the presence of an activated/memory-like phenotype (CD69+, CD25+, CD44+, CD45RB(Low), CD62(Low)) of CD4+ T cells expressing Nef(RD35/36AA) and to a lesser extent Nef(D174K). In addition, both mutants retained the ability to block CD4+ T cell proliferation in vitro after anti-CD3 stimulation, but not to enhance apoptosis/death of CD4+ T cells. Therefore, it appears that Nef-mediated CD4 downregulation is associated with thymic defects, but segregates independently of the activated/memory-like phenotype, of the partial depletion and of the impaired in vitro proliferation of peripheral CD4+ T cells. Histopathological assessment revealed the total absence of or decrease severity and frequency of organ AIDS-like diseases (lung, heart and kidney pathologies) in respectively Nef(RD35/36AA) and Nef(D174K) Tg mice, relative to those developing in Nef(Wt) Tg mice. Our data suggest that the RD35/36AA and D174K mutations affect other Nef functions, namely those involved in the development of lung and kidney diseases, in addition to their known role in CD4 downregulation. Similarly, in HIV-1-infected individuals, loss of CD4 downregulation by Nef alleles may reflect their lower intrinsic pathogenicity, independently of their effects on virus replication.
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Affiliation(s)
- Zaher Hanna
- Laboratory of Molecular Biology, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7.
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15
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O'Neill E, Kuo LS, Krisko JF, Tomchick DR, Garcia JV, Foster JL. Dynamic evolution of the human immunodeficiency virus type 1 pathogenic factor, Nef. J Virol 2006; 80:1311-20. [PMID: 16415008 PMCID: PMC1346962 DOI: 10.1128/jvi.80.3.1311-1320.2006] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Accepted: 10/27/2005] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) early gene product Nef is a multifunctional protein that alters numerous pathways of T-cell function, including endocytosis, signal transduction, vesicular trafficking, and immune modulation, and is a major determinant of pathogenesis. Individual Nef functions include PAK-2 activation, CD4 downregulation, major histocompatibility complex (MHC) class I downregulation, and enhancement of viral particle infectivity. How Nef accomplishes its multiple tasks presents a difficult problem of mechanistic analysis because of the complications associated with multiple, overlapping functional domains in the context of significant sequence variability. To address these issues we determined the conservation of each Nef residue based on 1,643 subtype B Nef sequences. Mutational analysis based on conservative substitutions and Nef sequence data allowed us to search for amino acids on the surface of Nef that are specifically required for PAK-2 activation. We found residues 85, 89, and 191 to be highly significant determinants for Nef's PAK-2 activation function but functionally unlinked to CD4 and MHC class I downregulation or enhancement of infectivity. These residues are not conserved across HIV-1 subtypes but are confined to separate sets of surface elements within a subtype. Thus, L85/H89/F191 and F85/F89/R191 are dominant in subtype B and subtype E or C, respectively. Our results provide support for developing subtype-specific interventions in HIV-1 disease.
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Affiliation(s)
- Eduardo O'Neill
- Department of Internal Medicine, Division of Infectious Diseases Y9.206, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9113, USA
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16
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Mikhail M, Wang B, Lemey P, Beckthold B, Vandamme AM, Gill MJ, Saksena NK. Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort. Retrovirology 2005; 2:41. [PMID: 15985187 PMCID: PMC1190217 DOI: 10.1186/1742-4690-2-41] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Accepted: 06/29/2005] [Indexed: 12/13/2022] Open
Abstract
Background The actual relationship between viral variability and HIV disease progression and/or non-progression can only be extrapolated through epidemiologically-linked HIV-infected cohorts. The rarity of such cohorts accents their existence as invaluable human models for a clear understanding of molecular factors that may contribute to the various rates of HIV disease. We present here a cohort of three patients with the source termed donor A – a non-progressor and two recipients called B and C. Both recipients gradually progressed to HIV disease and patient C has died of AIDS recently. By conducting 15 near full-length genome (8.7 kb) analysis from longitudinally derived patient PBMC samples enabled us to investigate the extent of molecular factors, which govern HIV disease progression. Results Four time points were successfully amplified for patient A, 4 for patient B and 7 from patient C. Using phylogenetic analysis our data confirms the epidemiological-linkage and transmission of HIV-1 from a non-progressor to two recipients. Following transmission the two recipients gradually progressed to AIDS and one died of AIDS. Viral divergence, selective pressures, recombination, and evolutionary rates of HIV-1 in each member of the cohort were investigated over time. Genetic recombination and selective pressure was evident in the entire cohort. However, there was a striking correlation between evolutionary rate and disease progression. Conclusion Non-progressing individuals have the potential to transmit pathogenic variants, which in other host can lead to faster HIV disease progression. This was evident from our study and the accelerated disease progression in the recipient members of he cohort correlated with faster evolutionary rate of HIV-1, which is a unique aspect of this study.
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Affiliation(s)
- Meriet Mikhail
- Retroviral Genetics Laboratory, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW 2145. Sydney, Australia
| | - Bin Wang
- Retroviral Genetics Laboratory, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW 2145. Sydney, Australia
| | - Philippe Lemey
- Department of Clinical and Epidemiological Virology, Rega Institute, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Brenda Beckthold
- Department of Medicine, University of Calgary, 3330 Hospital Drive NW Calgary, Albert, T2N 4N1, Canada
| | - Anne-Mieke Vandamme
- Department of Clinical and Epidemiological Virology, Rega Institute, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - M John Gill
- Department of Medicine, University of Calgary, 3330 Hospital Drive NW Calgary, Albert, T2N 4N1, Canada
| | - Nitin K Saksena
- Retroviral Genetics Laboratory, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW 2145. Sydney, Australia
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17
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Majumder B, Gray B, McBurney S, Schaefer TM, Dentchev T, Mahalingam S, Reinhart TA, Ayyavoo V. Attenuated nef DNA vaccine construct induces cellular immune response: role in HIV-1 multiprotein vaccine. Immunol Lett 2004; 89:207-14. [PMID: 14556980 DOI: 10.1016/s0165-2478(03)00141-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 positive patients generate Nef-specific CTL response, indicating that Nef is a potent immunogen. However, Nef is also known to down regulate the expression of CD4 and MHC-I molecules, thereby protecting virally infected target cells. We compared the immunogenicity of non-functional nef vaccine constructs to wild type functional nef as potential immunogen. Mice were immunized with different nef constructs and assessed for their ability to induce cellular immune responses. Evaluation of T cell immune responses in mice showed that non-functional nef vaccine constructs are capable of inducing a significant T cell immune response measured by IFN-gamma ELISPOT. Further epitope mapping studies indicate that one of our attenuated constructs, Nef R-38, has multiple CTL epitopes spanning throughout the gene. Our results indicate that functionally attenuated Nef antigen might be a better candidate for future multiprotein HIV-1 vaccine.
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Affiliation(s)
- Biswanath Majumder
- Department of Infectious Diseases and Microbiology, University of Pittsburgh/GSPH, 130 DeSoto Street, Pittsburgh, PA 15261, USA
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18
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Tsui R, Herring BL, Barbour JD, Grant RM, Bacchetti P, Kral A, Edlin BR, Delwart EL. Human immunodeficiency virus type 1 superinfection was not detected following 215 years of injection drug user exposure. J Virol 2004; 78:94-103. [PMID: 14671091 PMCID: PMC303392 DOI: 10.1128/jvi.78.1.94-103.2004] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evidence for human immunodeficiency virus type 1 (HIV-1) superinfection was sought among 37 HIV-1-positive street-recruited active injection drug users (IDUs) from the San Francisco Bay area. HIV-1 sequences from pairs of samples collected 1 to 12 years apart, spanning a total of 215 years of exposure, were generated at p17 gag, the V3-V5 region of env, and/or the first exon of tat and phylogenetically analyzed. No evidence of HIV-1 superinfection was detected in which a highly divergent HIV-1 variant emerged at a frequency >20% of the serum viral quasispecies. Based on the reported risk behavior of the IDUs and the HIV-1 incidence in uninfected subjects in the same cohort, a total of 3.4 new infections would have been expected if existing infection conferred no protection from superinfection. Adjusted for risk behaviors, the estimated relative risk of superinfection compared with initial infection was therefore 0.0 (95% confidence interval, 0.00, 0.79; P = 0.02), indicating that existing infection conferred a statistically significant level of protection against superinfection with an HIV-1 strain of the same subtype, which was between 21 and 100%.
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Affiliation(s)
- Rose Tsui
- Blood Systems Research Institute, University of California, San Francisco, San Francisco, California, USA
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19
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Casartelli N, Di Matteo G, Potestà M, Rossi P, Doria M. CD4 and major histocompatibility complex class I downregulation by the human immunodeficiency virus type 1 nef protein in pediatric AIDS progression. J Virol 2003; 77:11536-45. [PMID: 14557639 PMCID: PMC229262 DOI: 10.1128/jvi.77.21.11536-11545.2003] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2003] [Accepted: 07/29/2003] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) nef gene is a crucial determinant in AIDS disease progression. Although several in vitro activities have been attributed to the Nef protein, identifying the one critical for in vivo pathogenicity remains elusive. In this study, we examined a large number of nef alleles derived at various time points from 13 perinatally infected children showing different progression rates: six nonprogressors (NPs), three slow progressors (SPs), and four rapid progressors (RPs). The patient-derived nef alleles were analyzed for their steady-state expression of a Nef protein, for their relative ability to downregulate cell surface expression of CD4 and major histocompatibility complex class I (MHC-I) and for their capacity to bind the clathrin adaptor AP-1 complex. We found that NP-derived nef alleles, compared to nef alleles isolated from SPs and RPs, had reduced CD4 and MHC-I downregulation activities. In contrast, SP- and RP-derived nef alleles did not differ and efficiently downregulated both CD4 and MHC-I. AP-1 binding was a conserved function of primary nef alleles not correlated with clinical progression. Defective Nef proteins from NPs, rather than sharing common specific changes in their sequences, accumulated various amino acid substitutions, mainly located outside the conserved domains previously associated with Nef biological properties. Our data indicate that Nef-mediated downregulation of cell surface CD4 and MHC-I significantly contributes to the expression of the pathogenic potential of HIV-1.
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Affiliation(s)
- Nicoletta Casartelli
- Division of Immunology and Infectious Disease, Children's Hospital Bambino Gesù, Rome, Italy
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20
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Tobiume M, Takahoko M, Yamada T, Tatsumi M, Iwamoto A, Matsuda M. Inefficient enhancement of viral infectivity and CD4 downregulation by human immunodeficiency virus type 1 Nef from Japanese long-term nonprogressors. J Virol 2002; 76:5959-65. [PMID: 12021328 PMCID: PMC136235 DOI: 10.1128/jvi.76.12.5959-5965.2002] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has been reported that patients infected with nef-defective human immunodeficiency virus type 1 (HIV-1) do not progress to AIDS; however, mutations that abrogate Nef expression are not common in long-term nonprogressors (LTNPs). We postulated that Nef function might be impaired in LTNPs, irrespective of the presence or absence of detectable amino acid sequence anomalies. To challenge this hypothesis we compared in vitro function of nef alleles that were derived from three groups of Japanese patients: LTNPs, progressors, and asymptomatic carriers (ACs). The patient-derived nef alleles were subcloned into a nef-defective infectious HIV-1 molecular clone and an expression vector. We first examined Nef-dependent enhancement of infection in a single-round infectivity assay by the use of MAGNEF cells, in which Nef is required more strictly for the infection than in the parent MAGI cells. All nef alleles from LTNPs showed reduced enhancement in the infectivity of nef-defective HIV-1 mutants compared to the nef alleles of progressors or ACs. Second, we found that nef alleles from LTNPs were less efficient in CD4 downregulation than those of progressors or ACs. Third, all nef alleles from LTNPs, progressors, and ACs reduced the cell surface expression of major histocompatibility complex class I to a similar level. Last, there was no correlation between Hck-binding activity of Nef and clinical grouping. In conclusion, we detected inefficient enhancement of HIV-1 infectivity and CD4 downregulation by HIV-1 nef alleles of LTNPs. It awaits further study to conclude that these characteristics of nef alleles are the cause or the consequence of the long-term nonprogression after HIV-1 infection.
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Affiliation(s)
- Minoru Tobiume
- Department of Tumor Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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21
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Federico M, Percario Z, Olivetta E, Fiorucci G, Muratori C, Micheli A, Romeo G, Affabris E. HIV-1 Nef activates STAT1 in human monocytes/macrophages through the release of soluble factors. Blood 2001; 98:2752-61. [PMID: 11675348 DOI: 10.1182/blood.v98.9.2752] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Monocytes/macrophages play a predominant role in the immunologic network by secreting and reacting to a wide range of soluble factors. Human immunodeficiency virus (HIV) infection leads to deep immunologic dysfunctions, also as a consequence of alterations in the pattern of cytokine release. Recent studies on in vivo models demonstrated that the expression of HIV Nef alone mimics many pathogenetic effects of HIV infection. In particular, Nef expression in monocytes/macrophages has been correlated with remarkable modifications in the pattern of secreted soluble factors, suggesting that the interaction of Nef with monocytes/macrophages plays a role in the pathogenesis of acquired immunodeficiency syndrome (AIDS). This study sought to define possible alterations in intracellular signaling induced by Nef in monocytes/macrophages. Results demonstrate that HIV-1 Nef specifically activates both alpha and beta isoforms of the signal transducer and activator of transcription 1 (STAT1). This was observed both by infecting human monocyte-derived macrophages (MDMs) with HIV-1 deletion mutants, and by exploiting the ability of MDMs to internalize soluble, recombinant Nef protein (rNef). STAT1-alpha activation occurs on phosphorylation of both C-terminal Tyr701 and Ser727 and leads to a strong binding activity. Nef-dependent STAT1 activation is followed by increased expression of both STAT1 and interferon regulatory factor-1, a transcription factor transcriptionally regulated by STAT1 activation. It was also established that Nef-induced STAT1- alpha/beta activation occurs through the secretion of soluble factors. Taken together, the results indicate that HIV-1 Nef could interfere with STAT1-governed intracellular signaling in human monocytes/macrophages.
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Affiliation(s)
- M Federico
- Laboratory of Virology, Istituto Superiore di Sanità, Rome, Italy.
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22
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Katzman M, Harper AL, Sudol M, Skinner LM, Eyster ME. Activity of HIV-1 integrases recovered from subjects with varied rates of disease progression. J Acquir Immune Defic Syndr 2001; 28:203-10. [PMID: 11694825 DOI: 10.1097/00042560-200111010-00001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We recently described 102 HIV-1 integrase sequences that were amplified from blood cells or plasma obtained up to 18 years ago from 5 hemophiliacs who later died of AIDS and 5 hemophiliacs subsequently classified as slow or nonprogressors ( J Acquir Immune Defic Syndr Hum Retrovirol 1998;19:99-110). Although the region of the HIV-1 genome that encodes integrase was highly conserved, none of the deduced protein sequences of the patient-derived enzymes matched that of the clade B consensus or standard laboratory integrases. To test the hypothesis that the activity of HIV-1 integrases prevalent within an infected person contributes to the rate of disease progression, we have now expressed and purified these proteins and compared them in various assays. Most of the 75 unique full-length integrase proteins from the 102 clones were enzymatically active. Comparison of proteins derived from samples obtained soon after infection showed that the specificity and extent of viral DNA processing and the amount of DNA joining (the two biologically relevant activities of integrase) did not differ between the two groups of patients. In addition, the relative usage of alternative nucleophiles for processing and the amount of nonspecific nicking catalyzed by the proteins were indistinguishable between the patient groups. Although the patient-derived enzymes often exhibited different patterns of target site preferences compared with the laboratory integrase, there was no correlation with clinical course. Thus, the activities of HIV-1 integrases prevalent within these infected individuals, at least as reflected by standard assays, did not influence or predict the rate of disease progression.
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Affiliation(s)
- M Katzman
- Department of Medicine, Pennsylvania State University College of Medicine, The Milton S. Hershey Medical Center, Hershey 17033-0850, USA.
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23
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Bell I, Schaefer TM, Trible RP, Amedee A, Reinhart TA. Down-modulation of the costimulatory molecule, CD28, is a conserved activity of multiple SIV Nefs and is dependent on histidine 196 of Nef. Virology 2001; 283:148-58. [PMID: 11312671 DOI: 10.1006/viro.2001.0872] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study Nef proteins derived from simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) were compared to assess their abilities to down-modulate the cell surface levels of the T-cell costimulatory molecule CD28. We demonstrate that in addition to Nef derived from the prototypic SIVmac239, Nef proteins encoded by the pathogenic SIVsmmPBj molecular clone and the SIVsmmB670 isolate also down-modulate cell surface CD28. In contrast, Nef proteins derived from HIV failed to down-modulate CD28. We have also identified H196 as a critical residue which influences the capacity of SIVmac Nef to down-modulate CD28. Nef derived from SIVmacJ5 failed to down-modulate cell surface CD28, whereas a Q196H substitution mutant of SIVmacJ5 Nef was able to down-modulate cell surface CD28. Conversely, substitution of H196 to Q196 in SIVmac239 Nef resulted in a mutant that had minimal effect on cell surface CD28 expression, despite retaining the capacity to down-modulate cell surface CD3epsilon. H196 lies immediately adjacent to a documented di-leucine endocytic motif and mutation of this motif also abrogated the ability of SIVmac239 Nef to down-modulate CD28. These findings demonstrate that down-modulation of the costimulatory molecule, CD28, and clonotypic TCR/CD3 complex are conserved attributes of SIV Nef.
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Affiliation(s)
- I Bell
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA 15261, USA
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24
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Komoto S, Kinomoto M, Ibrahim MS, Zhong Q, Auwanit W, Ayuthaya PI, Otake T, Mori H, Oishi I, Kurosu T, Takahashi H, Mukai T, Ikuta K. Low or no antibody responses to human immunodeficiency virus type 1 Nef in infected carriers with subtype E, in contrast to subtype B that showed antibodies preferentially recognizing subtype-specific Nef epitopes. Vaccine 2001; 19:3019-32. [PMID: 11282214 DOI: 10.1016/s0264-410x(00)00444-8] [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: 11/21/2022]
Abstract
The viral accessory gene product Nef has been shown to play an important role in human immunodeficiency virus type 1 (HIV-1)-induced pathogenesis. Only little information is available regarding the differences in the host immune responses against Nef protein and its function in vivo among different subtypes of HIV-1. In the present study, we showed marked differences in the immune responses to Nef protein between subtypes B and E. The amino acid sequence in subtype E Nef showed 72% homology with that in subtype B. Most murine monoclonal antibodies obtained by immunization with subtype B or E Nef protein showed cross-reactivity with both Nef proteins (80 and 67%, respectively). Next, we focused on the immune responses among infected Japanese and Thai individuals. Subtyping of the individuals into B and E was carried out by enzyme-linked immunosorbent assay (ELISA) using synthetic peptides corresponding to the V3 loop representing the principal neutralizing domain. Most of the sera from these individuals reacted strongly with Gag p24 proteins derived from subtypes B and E at similar levels. However, the immune responses among these individuals to Nef protein were markedly different. Some subtype B-infected Japanese and Thai individuals (40 and 35%, respectively) showed higher levels of anti-Nef antibodies, although these antibodies preferentially recognized epitopes specific to subtype B. On the other hand, most of the subtype E-infected Japanese and Thai individuals showed low or no antibody responses to Nef proteins. Thus, immune responses to Nef were markedly different between subtypes B- and E-infected carriers, suggesting different function(s) for Nef in AIDS pathogenesis. Further, vaccine design must take into account the different subtypes of HIV-1.
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Affiliation(s)
- S Komoto
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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Janvier K, Craig H, Le Gall S, Benarous R, Guatelli J, Schwartz O, Benichou S. Nef-induced CD4 downregulation: a diacidic sequence in human immunodeficiency virus type 1 Nef does not function as a protein sorting motif through direct binding to beta-COP. J Virol 2001; 75:3971-6. [PMID: 11264386 PMCID: PMC114888 DOI: 10.1128/jvi.75.8.3971-3976.2001] [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] [Received: 11/20/2000] [Accepted: 01/26/2001] [Indexed: 11/20/2022] Open
Abstract
The Nef protein from the human immunodeficiency virus (HIV) induces CD4 cell surface downregulation by interfering with the endocytic machinery. It has been recently proposed that binding of HIV type 1 Nef to the beta subunit of COPI coatomers participated in the Nef-induced CD4 downregulation through recognition of a novel diacidic motif found in the C-terminal disordered loop of Nef (V. Piguet, F. Gu, M. Foti, N. Demaurex, J. Gruenberg, J. L. Carpentier, and D. Trono, Cell 97:63-73, 1999). We have mutated the glutamate residues which formed this motif in order to document this observation. Surprisingly, mutation of the diacidic sequence of Nef did not significantly affect its ability (i) to interact with beta-COP, (ii) to downregulate CD4 cell surface expression, and (iii) to address an integral resident membrane protein containing Nef as the cytoplasmic domain to the endocytic pathway. Our results indicate that these acidic residues are not involved in the connection of Nef with the endocytic machinery through binding to beta-COP. Additional studies are thus required to characterize the residues of Nef involved in the binding to beta-COP and to evaluate the contribution of this interaction to the Nef-induced perturbations of membrane trafficking.
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Affiliation(s)
- K Janvier
- Institut Cochin de Génétique Moléculaire, INSERM U529, Université Paris V, Paris, France
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26
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Greenway AL, Holloway G, McPhee DA. HIV-1 Nef: a critical factor in viral-induced pathogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 48:299-343. [PMID: 10987095 DOI: 10.1016/s1054-3589(00)48010-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- A L Greenway
- AIDS Cellular Biology Unit, Macfarlane Burnet Centre for Medical Research, Fairfield, Victoria, Australia
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27
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Khatissian E, Monceaux V, Cumont MC, Kieny MP, Aubertin AM, Hurtrel B. Persistence of pathogenic challenge virus in macaques protected by simian immunodeficiency virus SIVmacDeltanef. J Virol 2001; 75:1507-15. [PMID: 11152522 PMCID: PMC114055 DOI: 10.1128/jvi.75.3.1507-1515.2001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Live attenuated simian immunodeficiency virus (SIV) is the most efficient vaccine yet developed in monkey models of human immunodeficiency virus infection. In all successful vaccine trials, attenuation was achieved by inactivating at least the nef gene. We investigated some virological and immunological characteristics of five rhesus macaques immunized with a nef-inactivated SIVmac251 molecular clone (SIVmac251Deltanef) and challenged 15 months later with the pathogenic SIVmac251 isolate. Three animals were killed 2 weeks postchallenge (p.c.) to search for the challenge virus and to assess immunological changes in various organs. The other two animals have been monitored up for 7 years p.c., with clinical and nef gene changes being noted. The animals killed showed no increase in viral load and no sign of a secondary immune response, although the challenged virus was occasionally detected by PCR. In one of the monkeys being monitored, the vaccine virus persisted and an additional deletion occurred in nef. In the other monkey that was monitored, the challenge and the vaccine (Deltanef) viruses were both detected by PCR until a virus with a hybrid nef allele was isolated 48 months p.c. This nef hybrid encodes a 245-amino-acid protein. Thus, our results show (i) that monkeys were not totally protected against homologous virus challenge but controlled the challenge very efficiently in the absence of a secondary immune response, and (ii) that the challenge and vaccine viruses may persist in a replication-competent form for long periods after the challenge, possibly resulting in recombination between the two viruses.
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Affiliation(s)
- E Khatissian
- Unité d'Oncologie Virale, Institut Pasteur, 75015 Paris, France.
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28
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Foster JL, Molina RP, Luo T, Arora VK, Huang Y, Ho DD, Garcia JV. Genetic and functional diversity of human immunodeficiency virus type 1 subtype B Nef primary isolates. J Virol 2001; 75:1672-80. [PMID: 11160665 PMCID: PMC114076 DOI: 10.1128/jvi.75.4.1672-1680.2001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have characterized the functional integrity of seven primary Nef isolates: five from a long-term nonprogressing human immunodeficiency virus (HIV)-infected individual and one each from two patients with AIDS. One of the seven Nefs was defective for CD4 downregulation, two others were defective for PAK-2 activation, and one Nef was defective for PAK-2 activation and major histocompatibility complex (MHC) class I downregulation. Five of the Nefs were tested and found to be functional for the enhancement of virus particle infectivity. The structural basis for each of the functional defects has been analyzed by constructing a consensus nef, followed by mutational analysis of the variant amino acid residues. Mutations A29V and F193I were deleterious to CD4 downregulation and PAK-2 activation, respectively, while S189R rendered Nef defective for both MHC class I downregulation and PAK-2 activation. A search of the literature identified HIVs from five patients with Nefs predominantly mutated at F193 and from one patient with Nefs predominantly mutated at A29. A29 is highly conserved in all HIV subtypes except for subtype E. F193 is conserved in subtype B (and possibly in the closely related subtype D), but none of the other HIV group M subtypes. Our results suggest that functional distinctions may exist between HIV subtypes.
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Affiliation(s)
- J L Foster
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
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29
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Alessandrini L, Santarcangelo AC, Olivetta E, Ferrantelli F, d'Aloja P, Pugliese K, Pelosi E, Chelucci C, Mattia G, Peschle C, Verani P, Federico M. T-tropic human immunodeficiency virus (HIV) type 1 Nef protein enters human monocyte-macrophages and induces resistance to HIV replication: a possible mechanism of HIV T-tropic emergence in AIDS. J Gen Virol 2000; 81:2905-2917. [PMID: 11086122 DOI: 10.1099/0022-1317-81-12-2905] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Increasing interest has been devoted to the role that monocyte-macrophages play in the pathogenesis of AIDS. The hypothesis of an involvement in AIDS pathogenesis of human/simian immunodeficiency virus (HIV/SIV) Nef also is currently under evaluation by many investigators. The original basis of this hypothesis came from evidence that monkeys infected with a nef-deleted SIV strain failed to develop simian AIDS. Here, we show that treatment of human monocyte-derived macrophages (MDM) with recombinant HIV-1 Nef protein (rNef) induces a strong inhibition of the replication of either macrophage (M-) or dual-tropic HIV-1 strains. Through cytofluorimetric analyses, we detected internalization of FITC-conjugated rNef in MDM as early as 6 h after treatment. Confocal microscope observations demonstrated that the intracellular distribution of internalized rNef was identical to that of endogenously produced Nef. Down-regulation of the CD4 HIV receptor detected upon rNef treatment of MDM suggested that the rNef-induced HIV inhibition occurred at the virus entry step. This deduction was strengthened by the observation that CD4-independent infection was totally insensitive to rNef treatment. The specificity of all observed effects was demonstrated by immunodepletion of rNef. Finally, we showed that the resistance to HIV replication induced by rNef treatment in MDM favours the spread of T-tropic over M-tropic HIV strains in doubly infected CD4(+) lymphocyte-MDM co-cultures. We propose that extracellular Nef contributes to AIDS pathogenesis by inducing resistance to M-tropic HIV replication in MDM, thereby facilitating the switching from M- to T-tropic HIV prevalence that correlates frequently with AIDS progression.
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Affiliation(s)
- Laura Alessandrini
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Anna Claudia Santarcangelo
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Eleonora Olivetta
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Flavia Ferrantelli
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Paola d'Aloja
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Katherina Pugliese
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Elvira Pelosi
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Cristiana Chelucci
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Gianfranco Mattia
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Cesare Peschle
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Paola Verani
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
| | - Maurizio Federico
- Laboratory of Virology1, Laboratory of Haematology-Oncology2 and Laboratory of Clinical Biochemistry3, Istituto Superiore di Sanità, Viale Regina Elena 299, 0061 Roma, Italy
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30
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Hassaïne G, Agostini I, Candotti D, Bessou G, Caballero M, Agut H, Autran B, Barthalay Y, Vigne R. Characterization of human immunodeficiency virus type 1 vif gene in long-term asymptomatic individuals. Virology 2000; 276:169-80. [PMID: 11022005 DOI: 10.1006/viro.2000.0543] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have determined the sequence of the human immunodeficiency virus type 1 (HIV-1) vif genes from a cohort of 42 long-term nonprogressors (LTNP) and compared these sequences to those of 8 late progressors. The coding potential of the vif open reading frame directly derived by nested PCR from uncultured peripheral blood mononuclear cell DNA was conserved in all 50 individuals. The nucleotide distances between vif sequences were not significantly different between LTNP and late progressors, indicating similar selections of viruses within both types of long-term HIV-1-infected subjects. However, a statistically significant correlation between an amino acid signature at position 132 of Vif and the viral load was found within LTNP. Namely, amino acid Ser was associated with low viral load and amino acid Arg with high viral load. This signature was also observed when LTNP with low viral load were compared to progressors. The Ser132 signature was introduced in place of Arg132 present in the HIV-1 YU-2 Vif prototype into chimeric viruses to assess the impact of Vif signature on the virus. While the replication properties in the SupT1 cell line were unmodified, the mutagenized virus revealed a fivefold decreased replication in activated PBMC, suggesting a possible role of this Vif signature for viral production in vivo.
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Affiliation(s)
- G Hassaïne
- INSERM Unit U372, Université de la Méditerranée, Marseille Cedex 9, 13276, France
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31
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Azad AA. Could Nef and Vpr proteins contribute to disease progression by promoting depletion of bystander cells and prolonged survival of HIV-infected cells? Biochem Biophys Res Commun 2000; 267:677-85. [PMID: 10673351 DOI: 10.1006/bbrc.1999.1708] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A growing body of literature suggests that the HIV accessory proteins Nef and Vpr could be involved in depletion of CD4(+) and non-CD4(+) cells and tissue atrophy, and in delaying the death of HIV-infected cells. Cell depletion is likely to be predominantly a bystander effect because the number of cells dying far outnumbers HIV-infected cells and is not confined to CD4(+) cells. The myristylated N-terminal region of Nef has severe membrane disordering properties, and when present in the extracellular medium causes rapid lysis in vitro of a wide range of CD4(+) and non-CD4(+) cells, suggesting a role for extracellular Nef in the depletion of bystander cells. A direct role for HIV-1 Nef in cytopathicity is supported by studies in HIV-infected Hu Liv/Thy SCID mice, in transgenic mice expressing nef gene alone, and in rhesus macaques infected with SIV/HIV chimeric virus containing HIV-1 nef. The N-terminal region of Nef has been directly implicated in development of simian AIDS. Extracellular Vpr and C-terminal fragments of Vpr cause membrane permeabilization and apoptosis of a wide range of CD4(+) and non-CD4(+) cells, and could also contribute to depletion of bystander cells. A direct in vivo role for Vpr in thymocyte depletion, thymic atrophy, and nephropathy is suggested in studies with vpr transgenic mice. Intracellular Nef and Vpr could help HIV-infected cells evade cell death by inhibiting apoptosis of infected cells and by avoiding virus-specific CTL response. Nef and Vpr are potential targets for therapeutic intervention and vaccine development, and strategies that prevent the death of bystander cells while promoting the early death of HIV-infected cells could arrest or retard progression to AIDS.
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Affiliation(s)
- A A Azad
- Biomolecular Research Institute, 343 Royal Parade, Parkville, Victoria, 3052, Australia.
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32
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Mourich DV, Lee S, Reyes-Teran G, Mackewicz CE, Levy JA. Lack of differences in nef alleles among HIV-infected asymptomatic long-term survivors and those who progressed to disease. AIDS Res Hum Retroviruses 1999; 15:1573-5. [PMID: 10580408 DOI: 10.1089/088922299309865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequences of the human immunodeficiency virus (HIV) nef gene in virus isolates from 12 long-term survivors (LTSs) and 7 progressors were compared to determine if any association existed between the sequences and the corresponding clinical status. The sequences of at least five clones were determined for each subject. Conceptual translations of the open reading frames (ORFs) were examined with respect to a consensus with a prototypic nef sequence (HIV-1SF2) and for conservation of functionally described motifs. Premature stops were observed at equivalent, yet low, frequencies among the different clinical groups: 2 of 60 (3.33%) and 1 of 45 (2.22%) respectively. No remarkable differences in protein motifs implicated in several activities ascribed to Nef were noted. An association between nef sequence characteristics and the clinical state was not found.
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Affiliation(s)
- D V Mourich
- Department of Medicine, University of California, San Francisco 94143, USA
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33
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Kirchhoff F, Münch J, Carl S, Stolte N, Mätz-Rensing K, Fuchs D, Haaft PT, Heeney JL, Swigut T, Skowronski J, Stahl-Hennig C. The human immunodeficiency virus type 1 nef gene can to a large extent replace simian immunodeficiency virus nef in vivo. J Virol 1999; 73:8371-83. [PMID: 10482588 PMCID: PMC112855 DOI: 10.1128/jvi.73.10.8371-8383.1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nef gene of the pathogenic simian immunodeficiency virus (SIV) 239 clone was replaced with primary human immunodeficiency virus type 1 (HIV-1) nef alleles to investigate whether HIV-1 Nef can substitute for SIV Nef in vivo. Initially, two rhesus macaques were infected with the chimeric viruses (Nef-SHIVs). Most of the nef alleles obtained from both animals predicted intact open reading frames. Furthermore, forms containing upstream nucleotide substitutions that enhanced expression of the inserted gene became predominant. One animal maintained high viral loads and slowly progressed to immunodeficiency. nef long terminal repeat sequences amplified from this animal were used to generate a second generation of Nef-SHIVs. Two macaques, which were subsequently infected with a mixture of cloned chimeric viruses, showed high viral loads and progressed to fatal immunodeficiency. Five macaques received a single molecular clone, named SHIV-40K6. The SHIV-40K6 nef allele was active in CD4 and class I major histocompatibility complex downregulation and enhanced viral infectivity and replication. Notably, all of the macaques inoculated with SHIV-40K6 showed high levels of viral replication early in infection. During later stages, however, the course of infection was variable. Three animals maintained high viral loads and developed immunodeficiency. Of the remaining two macaques, which showed decreasing viral loads after the acute phase of infection, only one efficiently controlled viral replication and remained asymptomatic during 1.5 years of follow-up. The other animal showed an increasing viral load and developed signs of progressive infection during later stages. Our data demonstrate that HIV-1 nef can, to a large extent, functionally replace SIVmac nef in vivo.
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Affiliation(s)
- F Kirchhoff
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuernberg, 91054 Erlangen, Germany.
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34
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Abstract
There is currently much interest in the numerical and functional loss of antigen-presenting cells (APC) in HIV-1 disease and the contribution that this may make to HIV-1 pathology. The HIV-1 virus can interfere with the normal function of APC in a number of ways involving inappropriate signalling. These include changes in cytokine balance, cell-surface molecule expression and intracellular signalling pathways. This review examines how HIV-1 is able to disregulate APC function and discusses possible outcomes for the function of the immune system.
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Affiliation(s)
- T Hewson
- Department of Pathology, University of Edinburgh Medical School, Edinburgh, United Kingdom.
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35
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Brambilla A, Turchetto L, Gatti A, Bovolenta C, Veglia F, Santagostino E, Gringeri A, Clementi M, Poli G, Bagnarelli P, Vicenzi E. Defective nef alleles in a cohort of hemophiliacs with progressing and nonprogressing HIV-1 infection. Virology 1999; 259:349-68. [PMID: 10388660 DOI: 10.1006/viro.1999.9783] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Deletion of the nef gene results in viral attenuation and confers protection against challenge with wild-type simian immunodeficiency virus in macaques. Regarding HIV-1 infection, a few long-term nonprogressors (LTNP) with nef deletions have been described. In this study, the nef genes of a group of seven LTNP and eight progressors, all belonging to the same cohort of infected hemophiliacs, were analyzed by cloning and sequencing from both virion RNA and peripheral blood mononuclear cell-associated proviral DNA. Defective nef sequences coexisted with full-length nef open reading frames in five of seven LTNP and two of eight progressors. The proportion of disrupted nef sequences within each individual was significantly higher in LTNP (ranging from 10 to 63%) than in progressors (ranging from 9 to 21%) (P = 0.013). Moreover, in-frame small deletions predicting to encode Nef were found in all RNA- and DNA-derived clones from one LTNP and four progressors. A chimeric virus in which the nef gene of NL4.3 was substituted with the nef allele containing the deletion of two alanines at position 49-50 found in two progressors showed a defective replicative capacity compared to NL4.3 virus. In summary, hemophiliacs with either progressing or nonprogressing HIV-1 infection are characterized by the presence of defective nef variants.
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MESH Headings
- Adolescent
- Adult
- Alleles
- Amino Acid Sequence
- Cloning, Molecular
- Cohort Studies
- DNA, Viral/analysis
- DNA, Viral/genetics
- Disease Progression
- Gene Products, nef/chemistry
- Gene Products, nef/genetics
- Genes, nef
- Genetic Variation
- HIV Infections/complications
- HIV Infections/virology
- HIV Long-Term Survivors
- HIV-1/genetics
- HIV-1/immunology
- Hemophilia A/complications
- Humans
- Leukocytes, Mononuclear/virology
- Middle Aged
- Molecular Sequence Data
- Phylogeny
- RNA, Viral/analysis
- RNA, Viral/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- nef Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- A Brambilla
- AIDS Immunopathogenesis Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
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36
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Kirchhoff F, Easterbrook PJ, Douglas N, Troop M, Greenough TC, Weber J, Carl S, Sullivan JL, Daniels RS. Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease. J Virol 1999; 73:5497-508. [PMID: 10364298 PMCID: PMC112607 DOI: 10.1128/jvi.73.7.5497-5508.1999] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
nef alleles derived from a large number of individuals infected with human immunodeficiency virus type 1 (HIV-1) were analyzed to investigate the frequency of disrupted nef genes and to elucidate whether specific amino acid substitutions in Nef are associated with different stages of disease. We confirm that deletions or gross abnormalities in nef are rarely present. However, a comparison of Nef consensus sequences derived from 41 long-term nonprogressors and from 50 individuals with progressive HIV-1 infection revealed that specific variations are associated with different stages of infection. Five amino acid variations in Nef (T15, N51, H102, L170, and E182) were more frequently observed among nonprogressors, while nine features (an additional N-terminal PxxP motif, A15, R39, T51, T157, C163, N169, Q170, and M182) were more frequently found in progressors. Strong correlations between the frequency of these variations in Nef and both the CD4(+)-cell count and the viral load were observed. Moreover, analysis of sequential samples obtained from two progressors revealed that several variations in Nef, which were more commonly observed in patients with low CD4(+)-T-cell counts, were detected only during or after progression to immunodeficiency. Our results indicate that sequence variations in Nef are associated with different stages of HIV-1 infection and suggest a link between nef gene function and the immune status of the infected individual.
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Affiliation(s)
- F Kirchhoff
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University, D-91054 Erlangen, Germany.
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37
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Carl S, Iafrate AJ, Lang SM, Stahl-Hennig C, Kuhn EM, Fuchs D, Mätz-Rensing K, ten Haaft P, Heeney JL, Skowronski J, Kirchhoff F. The acidic region and conserved putative protein kinase C phosphorylation site in Nef are important for SIV replication in rhesus macaques. Virology 1999; 257:138-55. [PMID: 10208928 DOI: 10.1006/viro.1999.9645] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Variants of the pathogenic SIVmac239 clone with changes in Nef were analyzed to assess the functional relevance of two highly conserved regions in Nef in vitro and in vivo. Changes in a region with an acidic charge (Aci-Nef), or a potential protein kinase C phosphorylation site (PKC-Nef), impaired the ability of Nef to down-regulate CD4 and MHC class I surface expression and to alter CD3-initiated signal transduction in Jurkat T cells. The Aci-Nef, but not the PKC-Nef, associated with the previously described p65 phosphoprotein. SIV containing Aci-Nef, but not SIV containing PKC-Nef, showed reduced infectivity and replication in cell culture systems. One of two rhesus macaques infected with the PKC-Nef mutant virus showed rapid reversion and progressed to disease. In the second animal no reversions and nonprogressive infection was observed. In one of two macaques infected with the Aci-Nef variant, the mutations were stable during the first 40 weeks after infection. Thereafter, variants evolved in which up to six of the eight mutated positions in Nef were reverted and functional activity in vitro was partially restored. These changes occurred concomitantly with increasing viral load and disease progression. The second animal infected with the Aci-Nef variant showed no reversions and remained asymptomatic. Our study suggests that the acidic region and conserved PKC phosphorylation site in Nef are important for SIV replication in rhesus macaques and for several in vitro Nef functions. An almost wild-type activity in in vitro infectivity and replication assays seems insufficient to confer a full nef-positive phenotype in vivo.
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Affiliation(s)
- S Carl
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuernberg, Schlossgarten 4, Erlangen, 91054, Germany
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38
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Jubier-Maurin V, Saragosti S, Perret JL, Mpoudi E, Esu-Williams E, Mulanga C, Liegeois F, Ekwalanga M, Delaporte E, Peeters M. Genetic characterization of the nef gene from human immunodeficiency virus type 1 group M strains representing genetic subtypes A, B, C, E, F, G, and H. AIDS Res Hum Retroviruses 1999; 15:23-32. [PMID: 10024049 DOI: 10.1089/088922299311673] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most efforts to characterize sequence variation of HIV isolates has been directed toward the structural envelope gene. Few studies have evaluated the sequence variability of auxiliary genes such as nef. In this study 41 new HIV-1 strains, representing the majority of the described envelope subtypes of HIV-1 (A to H), were genetically characterized in the nef region. Phylogenetic analysis showed that 34 strains could be classified in the same subtype in nef and env, and 7 (19%) of the 41 new viruses were recombinants. For two of the seven strains, recombination occurred upstream of the nef gene, whereas for five of the seven strains recombination occurred within the nef gene with a crossover close to the 5' end of the LTR (long terminal repeat). The low intersubtype distance between subtype B and D in the nef gene confirms previous observations in the pol, env, and gag genes, which suggest a common ancestor for these subtypes. The majority of all the previously described functional domains in the nef gene were relatively conserved among the different subtypes, with only minor differences being observed. The myristoylation signal among the different subtypes, with only minor differences being observed. The myristoylation signal was less conserved for subtype C, with one or more amino acid changes being observed at positions 3, 4, and 5. The highly conserved acidic region (positions 62 to 65), critical for the enhancement of viral synthesis with an increased virus growth rate, was less conserved among the subtype G strains from our study. At least three epitopic regions of the nef gene have been defined and each can be recognized by CTLs under a variety of HLA restrictions; all were also relatively well conserved between the different genetic subtypes. Despite the relatively important genetic variation in nef sequences obtained among the different genetic subtypes, functional domains and CTL epitopes were relatively well conserved. In vitro and/or in vivo studies are necessary to study the relevance of the observed differences.
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39
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Grovit-Ferbas K, Ferbas J, Gudeman V, Sadeghi S, Goetz MB, Giorgi JV, Chen IS, O'Brien WA. Potential contributions of viral envelope and host genetic factors in a human immunodeficiency virus type 1-infected long-term survivor. J Virol 1998; 72:8650-8. [PMID: 9765405 PMCID: PMC110277 DOI: 10.1128/jvi.72.11.8650-8658.1998] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lack of clinical progression in some individuals despite prolonged human immunodeficiency virus type 1 (HIV-1) infection may result from infection with less-pathogenic viral strains. To address this question, we examined the HIV-1 envelope protein from a donor with a low viral burden, stable CD4(+) T-lymphocyte counts, and little evidence of CD8(+) T-cell expansion, activation, or immune activity. To avoid potential changes in envelope function resulting from selection in vitro, envelope clones were constructed by using viral RNA isolated from uncultured peripheral blood mononuclear cells (PBMC). The data showed that recombinant viruses containing envelope sequences derived from RNA isolated from patient PBMC replicated poorly in primary CD4(+) T cells but demonstrated efficient growth in macrophages. The unusual phenotype of these viruses could not be explained solely by differential utilization of coreceptors since the chimeric viruses, as well as an uncloned isolate obtained from the same visit date, can utilize CCR5. In addition, the donor's own cells appeared resistant to infection with chimeric viruses containing autologous envelope sequences. Genotype analysis revealed that the donor was heterozygous for the previously described 32-bp deletion in CCR5 which may be linked with prolonged survival in HIV-1-infected individuals. These data suggest that the changes in envelope sequences confer properties of viral attenuation, which together with the CCR5 +/Delta32 genotype could account for the long-term survival of this patient.
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Affiliation(s)
- K Grovit-Ferbas
- Division of Hematology-Oncology, Department of Medicine, UCLA School of Medicine and UCLA AIDS Institute, Los Angeles, California 90095-1678, USA
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40
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Easterbrook PJ, Schrager LK. Long-term nonprogression in HIV infection: methodological issues and scientific priorities. Report of an international European community-National Institutes of Health Workshop, The Royal Society, London, England, November 27-29, 1995. Scientific Coordinating Committee. AIDS Res Hum Retroviruses 1998; 14:1211-28. [PMID: 9764904 DOI: 10.1089/aid.1998.14.1211] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- P J Easterbrook
- HIV Epidemiology Unit, Imperial College School of Medicine, Chelsea and Westminster Hospital, London, UK
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41
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Nerurkar VR, Wu Z, Dashwood WM, Woodward CL, Zhang M, Detels R, Yanagihara R. Complete nef gene sequence of HIV type 1 subtype B' from professional plasma donors in the People's Republic of China. AIDS Res Hum Retroviruses 1998; 14:461-4. [PMID: 9546806 DOI: 10.1089/aid.1998.14.461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- V R Nerurkar
- Retrovirology Research Laboratory, Pacific Biomedical Research Center, University of Hawaii at Manoa, Honolulu 96816, USA.
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42
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Wegner SA, Ehrenberg PK, Chang G, Dayhoff DE, Sleeker AL, Michael NL. Genomic organization and functional characterization of the chemokine receptor CXCR4, a major entry co-receptor for human immunodeficiency virus type 1. J Biol Chem 1998; 273:4754-60. [PMID: 9468539 DOI: 10.1074/jbc.273.8.4754] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CXCR4 is both a chemokine receptor and entry co-receptor for T-cell line-adapted human immunodeficiency virus type 1. The genomic organization and promoter function for the entire transcription unit of CXCR4 were determined. The gene contains 2 exons of 103 and 1563 base pairs (bp) interrupted by a 2132-bp intron precisely between codons 5 and 6 of the coding sequences. A transcription start site was identified 88 bp upstream of the initiation codon, and a polyadenylate addition site was identified 22 bp 3' to a polyadenylation signal. Transient expression assays defined a minimal promoter at positions -114 to +43 relative to the transcription start site. This region contains a TATA box, a nuclear respiratory factor-1 (NRF-1) site, and two GC boxes. Specific factor binding to the NRF-1 site and GC boxes were demonstrated by gel mobility shifts and DNase I footprinting. Site-directed mutagenesis showed that the NRF-1 site is crucial for promoter activity providing the first evidence for the regulation of a signal transduction gene by NRF-1. Sequences between -691 and -191 repress CXCR4 promoter activity. Further study of these regulatory elements will be important to understanding how CXCR4 functions as both a chemokine receptor and human immunodeficiency virus type 1 entry co-receptor.
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Affiliation(s)
- S A Wegner
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850, USA
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43
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Huang Y, Zhang L, Ho DD. Characterization of gag and pol sequences from long-term survivors of human immunodeficiency virus type 1 infection. Virology 1998; 240:36-49. [PMID: 9448687 DOI: 10.1006/viro.1997.8913] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We previously identified a group of 10 long-term survivors (LTS) of human immunodeficiency virus type 1 (HIV-1) infection. Extensive biological analysis revealed that some of these individuals do well, at least in part, because they possess weakened or attenuated viruses. Also, previously, to determine the genotype associated with the attenuated phenotype in vivo, we characterized nef, vif, vpr, vpu, env, and LTR in our cohort of LTS. In this study, we analyzed gag and pol genes derived from eight individuals in our cohort. For each subject multiple full-length gag and pol clones were obtained for analysis. In most cases, the sequences derived from the LTS had an intact open reading frame. At the protein level, there were no discernible differences between the sequences derived from LTS and those derived from patients with AIDS. Thus, no common defect in gag and pol was found in our cohort. One individual (subject SF), however, had only Gag-defective proviral sequences (10 of 10) in his peripheral blood mononuclear cells. Furthermore, longitudinal studies of the samples collected from SF over a 2-year period showed that all p17 gag clones sequenced (24 of 24) were defective due to G-to-A hypermutations. This viral defect in Gag may provide the molecular basis for this individual's extremely low viral load and long-term asymptomatic state. These results, together with previous findings in our LTS cohort, reinforce the notion that it is unlikely that a single common viral genetic determinant accounts for the lack of disease progression in all cases. Multiple host and viral factors undoubtedly contribute to the well-being of LTS of HIV-1 infection.
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MESH Headings
- Acquired Immunodeficiency Syndrome/physiopathology
- Acquired Immunodeficiency Syndrome/virology
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- DNA Primers
- Gene Products, gag/biosynthesis
- Gene Products, gag/chemistry
- Gene Products, gag/genetics
- Gene Products, pol/biosynthesis
- Gene Products, pol/chemistry
- Gene Products, pol/genetics
- Genes, gag
- Genes, pol
- Genotype
- HIV Antigens/biosynthesis
- HIV Antigens/chemistry
- HIV Antigens/genetics
- HIV-1/genetics
- HIV-1/isolation & purification
- Humans
- Leukocytes, Mononuclear/virology
- Molecular Sequence Data
- Phenotype
- Phylogeny
- Polymerase Chain Reaction
- Sequence Alignment
- Survivors
- Viral Proteins
- gag Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Y Huang
- Aaron Diamond AIDS Research Center, New York, New York, USA
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44
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Kang MR, Cho YK, Chun J, Kim YB, Lee I, Lee HJ, Kim SH, Kim YK, Yoon K, Yang JM, Kim JM, Shin YO, Kang C, Lee JS, Choi KW, Kim DG, Fitch WM, Kim S. Phylogenetic analysis of the nef gene reveals a distinctive monophyletic clade in Korean HIV-1 cases. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY : OFFICIAL PUBLICATION OF THE INTERNATIONAL RETROVIROLOGY ASSOCIATION 1998; 17:58-68. [PMID: 9436760 DOI: 10.1097/00042560-199801010-00009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. This is the first report on the molecular nature of the HIV-1 infection present in South Korea.
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Affiliation(s)
- M R Kang
- Institute for Molecular Biology and Genetics and Medical College, Seoul National University, Korea
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45
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Fuller FJ. Genes controlling retroviral virulence. ADVANCES IN VETERINARY MEDICINE 1997; 40:135-55. [PMID: 9395732 DOI: 10.1016/s0065-3519(97)80007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- F J Fuller
- Department of Microbiology, Pathology, and Parasitology, North Carolina State University, College of Veterinary Medicine, Raleigh 27606, USA
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46
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Abstract
Host factors play an important role in determining rates of disease progression in human immunodeficiency virus (HIV)-infected individuals. HIV is able to subvert the host immune system by infecting CD4+ T cells that normally orchestrate immune responses and by inducing the secretion of proinflammatory cytokines that the virus can utilize to its own replicative advantage. The recognition that certain chemokine receptors serve as necessary co-factors for HIV entry into its target cells as well as the fact that ligands for these receptors can modulate the efficiency of HIV infection has expanded the number and scope of host factors that may impact the pathogenesis of HIV disease. This area of investigation will no doubt yield novel therapeutic strategies for intervention in HIV disease; however, caution is warranted in light of the enormous complexity of the pleiotropic cytokine and chemokine networks and the uncertainty inherent in manipulating these systems. HIV-infected long-term non-progressors represent an excellent model to study potential host factors involved in HIV disease pathogenesis. Genetic factors certainly have a major impact on the immune responses mounted by the host. In this regard, a polymorphism in the gene for the HIV co-receptor CC chemokine receptor 5 (CCR5), which serves as a co-receptor for macrophage (M)-tropic strains of HIV, affords a high degree of protection against HIV infection in individuals homozygous for the genetic defect and some degree of protection against disease progression in HIV-infected heterozygotes. HIV-specific immune responses, including cytotoxic T-lymphocyte (CTL) responses and neutralizing antibody responses, also appear to play salutary roles in protecting against disease progression.
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Affiliation(s)
- O J Cohen
- National Institute of Allergy and Infectious Diseases, Laboratory of Immunoregulation, Bethesda, Maryland, USA.
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47
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Blanchard A, Montagnier L, Gougeon ML. Influence of microbial infections on the progression of HIV disease. Trends Microbiol 1997; 5:326-31. [PMID: 9263412 DOI: 10.1016/s0966-842x(97)01089-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
HIV infection is associated with immune activation, which in turn stimulates HIV replication. Certain other co-infections cause immune activation and may contribute to an increased viral load. The impact of co-infections by microorganisms such as Mycobacterium tuberculosis can be important for patient survival, particularly those at high risk of exposure to infection and with poor access to medical care.
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Affiliation(s)
- A Blanchard
- Institut Pasteur, Dépt du SIDA et des Retrovirus, Paris, France.
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48
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Lang SM, Iafrate AJ, Stahl-Hennig C, Kuhn EM, Nisslein T, Kaup FJ, Haupt M, Hunsmann G, Skowronski J, Kirchhoff F. Association of simian immunodeficiency virus Nef with cellular serine/threonine kinases is dispensable for the development of AIDS in rhesus macaques. Nat Med 1997; 3:860-5. [PMID: 9256276 DOI: 10.1038/nm0897-860] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The nef gene of simian immunodeficiency virus (SIV) is essential for high viral load and induction of AIDS in rhesus monkeys. A mutant form of the SIVmac239 Nef, which contains changes in a putative SH3-binding domain (amino acids 104 and 107 have been changed from PxxP to AxxA), does not associate with cellular serine/threonine kinases, but is fully active in CD4 downregulation and associates with the cellular tyrosine kinase Src. Infection of two rhesus macaques with SIVmac239 containing the mutant AxxA-Nef caused AIDS and rapid death in both animals. No reversions were observed in the majority of nef sequences analyzed from different time points during infection and from lymphatic tissues at the time of death. Our findings indicate that the putative SH3-ligand domain in SIVmac Nef and the association with cellular serine/threonine kinases are not important for efficient replication and pathogenicity of SIVmac in rhesus macaques.
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Affiliation(s)
- S M Lang
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuernberg, Erlangen, Germany
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49
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Operskalski EA, Busch MP, Mosley JW, Stram DO. Comparative rates of disease progression among persons infected with the same or different HIV-1 strains. The Transfusion Safety Study Group. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY : OFFICIAL PUBLICATION OF THE INTERNATIONAL RETROVIROLOGY ASSOCIATION 1997; 15:145-50. [PMID: 9241114 DOI: 10.1097/00042560-199706010-00008] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Rates of HIV-1 progression vary widely. To investigate the relative effects of viral and host characteristics on course, we compared persons infected by the same and different subtype B strains. Forty-three infection chain clusters were identified, each defined by an infected blood donor, that donor's recipients, and the recipients' sexual partners, representing second and third generations of infection. Analysis of levels and rates of change in CD4 lymphocyte counts and viral load showed that members within a cluster were no more alike in their rates of change in CD4+ lymphocyte counts or viral RNA levels than among clusters. Differences in entry viral RNA levels by cluster were marginal and markedly smaller than interindividual differences. These results argue that, in general, host factors outweigh differences in viral strain in determining HIV-1 disease progression.
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Affiliation(s)
- E A Operskalski
- Department of Medicine, University of Southern California School of Medicine, Los Angeles 90032, USA
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50
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Gulizia RJ, Collman RG, Levy JA, Trono D, Mosier DE. Deletion of nef slows but does not prevent CD4-positive T-cell depletion in human immunodeficiency virus type 1-infected human-PBL-SCID mice. J Virol 1997; 71:4161-4. [PMID: 9094701 PMCID: PMC191576 DOI: 10.1128/jvi.71.5.4161-4164.1997] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The pathogenicity of four human immunodeficiency virus type 1 (HIV-1) isolates with nef deleted for SCID mice repopulated with human peripheral blood leukocytes (hu-PBL-SCID mice) was studied. Deletion of nef led to a substantial reduction in CD4-positive T-cell depletion and delayed kinetics of plasma viremia in infected hu-PBL-SCID mice. Deletion of the nef gene impacts both the efficiency of primary infection and the cytopathicity of virus for infected CD4-positive T cells in this animal model of HIV-1 infection.
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Affiliation(s)
- R J Gulizia
- Department of Immunology-IMM7, The Scripps Research Institute, La Jolla, California 92037, USA
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