Human Immunodeficiency Virus Nef Protein Research Articles

The Persistence of HIV Diversity, Transcription, and Nef Protein in Kaposi's Sarcoma Tumors during Antiretroviral Therapy.

Epidemic Kaposi's sarcoma (KS), defined by co-infection with Human Herpes Virus 8 (HHV-8) and the Human Immunodeficiency Virus (HIV), is a major cause of mortality in sub-Saharan Africa. Antiretroviral therapy (ART) significantly reduces the risk of developing KS, and for those with KS, tumors frequently resolve with ART alone. However, for unknown reasons, a significant number of KS cases do not resolve and can progress to death. To explore how HIV responds to ART in the KS tumor microenvironment, we sequenced HIV env-nef found in DNA and RNA isolated from plasma, peripheral blood mononuclear cells, and tumor biopsies, before and after ART, in four Ugandan study participants who had unresponsive or progressive KS after 180-250 days of ART. We performed immunohistochemistry experiments to detect viral proteins in matched formalin-fixed tumor biopsies. Our sequencing results showed that HIV diversity and RNA expression in KS tumors are maintained after ART, despite undetectable plasma viral loads. The presence of spliced HIV transcripts in KS tumors after ART was consistent with a transcriptionally active viral reservoir. Immunohistochemistry staining found colocalization of HIV Nef protein and tissue-resident macrophages in the KS tumors. Overall, our results demonstrated that even after ART reduced plasma HIV viral load to undetectable levels and restored immune function, HIV in KS tumors continues to be transcriptionally and translationally active, which could influence tumor maintenance and progression.

Nef-induced CCL2 Expression Contributes to HIV/SIV Brain Invasion and Neuronal Dysfunction.

C-C motif chemokine ligand 2 (CCL2) is a chemoattractant for leukocytes including monocytes, T cells, and natural killer cells and it plays an important role in maintaining the integrity and function of the brain. However, there is accumulating evidence that many neurological diseases are attributable to a dysregulation of CCL2 expression. Acquired immune deficiency syndrome (AIDS) encephalopathy is a severe and frequent complication in individuals infected with the human immunodeficiency virus (HIV) or the simian immunodeficiency virus (SIV). The HIV and SIV Nef protein, a progression factor in AIDS pathology, can be transferred by microvesicles including exosomes and tunneling nanotubes (TNT) within the host even to uninfected cells, and Nef can induce CCL2 expression. This review focuses on findings which collectively add new insights on how Nef-induced CCL2 expression contributes to neurotropism and neurovirulence of HIV and SIV and elucidates why adjuvant targeting of CCL2 could be a therapeutic option for HIV-infected persons.

The Role of the Nef Protein in MHC-I Downregulation and Viral Immune Evasion by HIV-1

The Nef protein is a major determinant of pathogenicity caused by the Human Immunodeficiency virus (HIV) and is encoded by the nef gene within the genomes of primate lentiviruses HIV-1, HIV-2 and simian immunodeficiency virus (SIV). The HIV Nef protein subverts the intracellular membrane traffic to mediate endocytosis of a number of cell surface receptors to accelerate their degradation. In this review we will examine how the multifunctional Nef protein can mediate downregulation of the Major Histocompatibility Complex (MHC) I proteins from the surface of infected cells as a means of immune evasion by HIV. By selectively downregulating MHC-I HLA-A and HLA-B haplotypes, while maintaining the expression of HLA-C, HLA-E and HLA-G the HIV virus is able to avoid recognition by both the NK and cytotoxic CD8+ T cell effector responses. This protects the virus from cell lysis and enables it to hide from the cell-mediated immune system.

Nef Performance in Macrophages: The Master Orchestrator of Viral Persistence and Spread

Following transmission of human immunodeficiency virus (HIV) into a new host, cells of the monocyte/macrophage lineage play a central role in host invasion and viral replication. In particular, macrophages survive infection and support long-standing viral replication, contributing to viral persistence within the host and representing a viral reservoir in vivo. On the other hand, HIV Nef protein is a small though versatile molecule that plays an unquestioned key role in viral pathogenesis. In macrophages, Nef is able to modulate cell surface receptor expression, to intersect intracellular signaling pathways and to augment the release of pro-inflammatory and chemotactic molecules. In addition, Nef can alter macrophage phagocytic capacity, autophagy machinery and metabolism. Altogether, these Nef activities support viral replication and persistence in this cell type while at the same time favor viral dissemination. Here, we will review the newest findings describing how monocytes/macrophages natural pathways are altered by Nef protein, highlighting how viral and host biology are perturbed in consequence.

Chapter 5 - HIV Immune Evasion: Disruption of Antigen Presentation by the HIV Nef Protein

The Human Immunodeficiency Virus (HIV) Nef protein is necessary for high viral loads and for timely progression to AIDS. Nef plays a number of roles, but its effect on antigen presentation and immune evasion are among the best characterized. Cytotoxic T lymphocytes (CTLs) recognize and lyse virally infected cells by detecting viral antigens in complex with host major histocompatibility complex class I (MHC-I) molecules on the infected cell surface. The HIV Nef protein disrupts antigen presentation at the cell surface by interfering with the normal trafficking pathway of MHC-I and thus reduces CTL recognition and lysis of infected cells. The molecular mechanism by which Nef causes MHC-I downmodulation is becoming more clear, but some questions remain. A better understanding of how Nef disrupts antigen presentation may lead to the development of drugs that enhance the ability of the anti-HIV CTLs to control HIV disease.

The kinase activity of pseudorabies virus US3 is required for modulation of the actin cytoskeleton

Different viruses exploit the host cytoskeleton to facilitate replication and spread. The conserved US3 protein of the alphaherpesvirus pseudorabies virus induces actin stress fiber disassembly and formation of actin-containing cell projections, which are associated with enhanced intercellular virus spread. Proteins of members of other virus families, notably vaccinia virus F11L protein and human immunodeficiency virus Nef protein, induce actin rearrangements that are very similar to those induced by US3. Interestingly, unlike F11L and Nef, the US3 protein displays serine/threonine kinase activity. Here, we report that the kinase activity of pseudorabies virus US3 is absolutely required for its actin modulating activity. These data show that different viruses have developed independent mechanisms to induce very similar actin rearrangements.

HIV-1 Nef Alleles Show Differential Activation of Hematopoietic Cell Kinase in a Yeast Model System.

Hematopoietic cell kinase (Hck) is a member of the Src family of non-receptor protein-tyrosine kinases that is expressed strongly in macrophages, an important target cell type for human immunodeficiency virus (HIV). The HIV Nef protein, a critical AIDS progression factor, binds Hck with unusually high affinity and induces Hck activation. Nef-mediated Hck activation has been proposed to trigger signaling pathways important for the establishment of HIV infection and subsequent progression to AIDS. Previous studies have utilized sequence alignments and binding assays to predict the functionality of Hck-Nef interactions, but these studies do not directly investigate the ability of Nef alleles to activate Hck. To better address this issue, we have created a model system in Saccharomyces cerevisiae based on previous findings that ectopic expression of c-Src arrests yeast growth in a kinase-dependent fashion. To establish the utility of this system for Hck and Nef, we first created a Hck variant containing a C-terminal sequence modified to encode the high-affinity SH2-domain binding sequence Tyr-Glu-Glu-Ile (HckYEEI). This modified sequence allows for autophosphorylation of the new tail and the subsequent intramolecular binding to the Hck SH2 domain. The resulting HckYEEI molecule models the physiologically down-regulated (inactive) form of Hck in structure and function. Unlike wild-type Hck, HckYEEI showed little kinase activity and failed to induce growth suppression in yeast. Importantly, co-expression with the Nef-SF2 allele activated HckYEEI, resulting in growth arrest. This effect was dependent on the conserved Nef proline-rich motif essential for Hck binding through its SH3 domain. However, Nef-SF2 did not activate FynYEEI, consistent with our previous data that the Fyn tyrosine kinase is not activated by Nef in mammalian cells. We then tested several additional laboratory HIV-1 Nef alleles for their ability to activate HckYEEI. Consensus, Lai, NL4.3, SF2, and YU-2 Nef alleles activated HckYEEI to varying degrees, as reflected by yeast growth inhibition. In contrast, Nef-Eli failed to suppress growth in the presence of HckYEEI, consistent with its inability to bind the Hck SH3 domain in vitro. Growth inhibition paralleled tyrosine phosphorylation of yeast proteins on anti-phosphotyrosine immunoblots. The differential effects of these Nef alleles on Hck activation correlated closely with previous results in mammalian cells. Taken together, these studies validate the use of yeast to reconstitute Nef-Hck interactions in a system amenable to screens of clinical Nef isolates, which may have predictive value in terms of AIDS progression.

Nef and Transcription

STKE The Nef protein encoded by human immunodeficiency virus (HIV) appears to function in pathogenesis through interactions in a signaling complex associated with the T cell receptor. Witte et al. identified an unexpected interaction partner of Nef: the protein Eed (embryonic ectodermal development factor). Eed is a member of the Polycomb group of proteins that regulate differentiation and proliferation of lymphocytes by inhibiting transcription. Expression of Nef caused a transient localization of Eed at the plasma membrane. This recruitment of Eed away from the nucleus might relieve its effects on transcriptional activity. Eed can also associate with the cytoplasmic domain of integrins, and stimulation of integrins causes Eed to move to the plasma membrane. Thus, the HIV Nef protein may function in part by coopting a mechanism for control of transcriptional repression that is normally associated with integrin signaling. — LBR Mol. Cell 13 , 179 (2004).

Relationship of Nef-positive and GFAP-reactive astrocytes to drug use in early and late HIV infection.

Reactive astrocytosis is a well-documented feature of HIV encephalitis (HIVE), but it is unclear whether restricted infection of astrocytes contributes to this phenomenon. In addition, the part played by reactive and/or infected astrocytes in AIDS-related dementia is not fully understood. In this study of patients at different stages of the human immunodeficiency virus (HIV) infection, who had been treated at most with one antiretroviral drug, reactive astrocytes were identified by immunopositivity for glial fibrillary acidic protein (GFAP) and infected astrocytes by positivity for HIV Nef protein. Results were compared for drug-using AIDS patients with (n=9) and without (n=7) HIVE, for presymptomatic HIV-positive drug users (n=12) and for control HIV-negative subjects (n=20), including a group who used drugs (n=10). GFAP-reactive astrocytes in both grey and white matter were significantly more numerous in HIVE subjects than in each of the other groups but did not correlate with viral load. Nef-positive astrocytes were confined to HIVE cases and to white matter, but were numerous in only one subject who was treatment-naive. Nef-positive microglia were identified in all HIVE cases and in occasional AIDS and presymptomatic subjects who did not have HIVE. The results suggest that astrocytes may form an additional viral reservoir in late HIV infection and may contribute to HIVE. However, the number of GFAP-positive astrocytes was neither increased in pre-AIDS nor in drug abuse, in contrast with microglia which we have shown previously to be up-regulated in both states.

Mechanism of HIV Pathogenesis: Role of Superantigens in Disease

Initial infection with human immunodeficiency virus (HIV) results in a burst of viremia and an ensuing spread of virus to secondary lymphoid organs, after which a “latency” period occurs with little or no virus detectable in the circulation. The term latent period has been shown to be a misnomer, because substantial viral replication occurs during this time in lymph nodes, although clinically there appears to be few symptoms of disease. However, a telling indicator of active infection during this period is the initiation of decline in CD4+ T‐cell numbers. A number of hypotheses have been postulated for the mechanism(s), as of yet not fully elucidated, by which T cells are depleted. Although quiescent cells can be infected, it has been shown that replication of HIV in CD4+ T cells requires cellular activation. The levels of viremia early in infection indicate that a large number of cells are actively infected, further suggesting that a mechanism must exist by which HIV activates a large pool of cells and ultimately causes their depletion. One possible mechanism for activation would be the presence of an HIV‐encoded superantigen. Superantigens are proteins that are polyclonal stimulators of CD4+ T lymphocytes. This occurs as a result of their ability to form a trimo‐lecular complex with MHC class II molecules on antigen‐presenting cells and the Vβ‐specific region on the T‐cell receptor. Thus, superantigen activation of T cells is antigen‐nonspecific. The prototype superantigens are the staphylococcal enterotoxins. Putative viral superantigens include a protein from mouse mammary tumor virus and related retroviruses, rabies nucleocapsid, and the Nef protein of HIV. Nef is required for optimal HIV pathogenesis, and this may be due to its superantigen properties, where CD4 cells are transformed to the activated state for virus replication.

Screening Assay for the Detection of the Protein-Protein Interaction Between HIV-1 Nef Protein and the SH3 Domain of Hck

The interaction between the Human Immunodeficiency Virus Nef protein (HIV-1 Nef) and the Src Homology Region 3 (SH3) domain of Hck was studied using scintillation proximity assay (SPA). SPA is a quick and sensitive method that does not require a separation step, thus allowing assays to be performed in a homogeneous environment. In contrast to most conventional techniques, SPA may also be used to detect low affinity protein-protein interactions. In this study, the assay was configured using biotinylated Hck SH3 domain expressed both as a GST fusion protein and synthesized chemically in its' native form. Biotinylated Hck protein was immobilized to streptavidin-coated fluoromicrosphere SPA beads and the binding of [3H]Nef was detected by scintillation counting. Analysis of binding yielded an average equilibrium dissociation constant (KD) of 183 ± 30 nM for the interaction in line with reported values by other methods. The data presented demonstrates that using SPA, protein-protein interactions of relatively low affinity can be detected with a high degree of sensitivity and screening studies of inhibitors of these associations could be facilitated by the high sample throughput achievable with SPA.

Mechanism of HIV pathogenesis: role of superantigens in disease.

Initial infection with human immunodeficiency virus (HIV) results in a burst of viremia and an ensuing spread of virus to secondary lymphoid organs, after which a "latency" period occurs with little or no virus detectable in the circulation. The term latent period has been shown to be a misnomer, because substantial viral replication occurs during this time in lymph nodes, although clinically there appears to be few symptoms of disease. However, a telling indicator of active infection during this period is the initiation of decline in CD4+ T-cell numbers. A number of hypotheses have been postulated for the mechanism(s), as of yet not fully elucidated, by which T cells are depleted. Although quiescent cells can be infected, it has been shown that replication of HIV in CD4+ T cells requires cellular activation. The levels of viremia early in infection indicate that a large number of cells are actively infected, further suggesting that a mechanism must exist by which HIV activates a large pool of cells and ultimately causes their depletion. One possible mechanism for activation would be the presence of an HIV-encoded superantigen. Superantigens are proteins that are polyclonal stimulators of CD4+ T lymphocytes. This occurs as a result of their ability to form a trimolecular complex with MHC class II molecules on antigen-presenting cells and the Vbeta-specific region on the T-cell receptor. Thus, superantigen activation of T cells is antigen-nonspecific. The prototype superantigens are the staphylococcal enterotoxins. Putative viral superantigens include a protein from mouse mammary tumor virus and related retroviruses, rabies nucleocapsid, and the Nef protein of HIV. Nef is required for optimal HIV pathogenesis, and this may be due to its superantigen properties, where CD4 cells are transformed to the activated state for virus replication.

HIV-1 Nef protein: purification, crystallizations, and preliminary X-ray diffraction studies.

Human immunodeficiency virus Nef protein accelerates virulent progression of AIDS by its interaction with specific cellular proteins involved in cellular activation and signal transduction. Here we report the purification and crystallization of the conserved core of HIV-1LAI Nef protein in the unliganded form and in complex with the wild-type SH3 domain of the P59fyn protein-tyrosine kinase. One-dimensional NMR experiments show that full-length protein and truncated fragment corresponding to the product of HIV-1 protease cleavage have a well-folded compact tertiary structure. The ligand-free HIV-1 Nefcore protein forms cubic crystals belonging to space group P23 with unit cell dimensions of a = b = c = 86.4 A. The Nef-Fyn SH3 cocrystals belong to the space group P6(1)22 or its enantiomorph, P6(5)22, with unit cell dimensions of a = b = 108.2 A and c = 223.7 A. Both crystal forms diffract to a resolution limit of 3.0 A resolution using synchrotron radiation, and are thus suitable for X-ray structure determination.

Association of human immunodeficiency virus Nef protein with actin is myristoylation dependent and influences its subcellular localization.

Human immunodeficiency virus (HIV) Nef functions are thought to be mediated via interactions with cellular proteins. Utilizing zone velocity sedimentation in glycerol gradients we found that recombinant HIV-1 Nef non-covalently associates with actin forming a high-molecular-mass complex of 150-300 kDa. This Nef/actin complex was present in human B and T lymphocytes but not in insect cells and was dependent on the N-terminal myristoylation of Nef, whereas the SH3-binding proline motif of Nef was not involved. Despite being myristoylated, HIV-2 Nef did not associate with actin. This might reflect differences in the subcellular localization of Nef since cell-fractionation experiments revealed that HIV-1 Nef was virtually exclusively localized in the cytoskeletal (detergent-insoluble) fraction whereas HIV-2 Nef had significantly reduced affinity for the cytoskeleton. Colocalization experiments in HIV-1-infected CD4+ fibroblasts revealed that Nef/actin complexes may also exist in HIV-infected cells. This novel interaction of HIV-1 Nef with actin provides insight into the association of Nef with cellular structures and reveals general differences in the interactions of the Nef proteins from HIV-1 and HIV-2.

Vβ Activation by HIV Nef Protein: Detection by a Simple Amplification Procedure

We previously reported that Nef protein from human immunodeficiency virus (HIV) has superantigen properties. However,we were unable to consistently demonstrate Vβ-specific expansion by Nef using flow cytometry, possibly due to its lower mitogenic activity compared to prototypic superantigens. Therefore, we developed a simple amplification detection method using immobilized anti-Vβ antibodies. Human peripheral blood mononuclear cells from adult donors were treated for 24 h with Nef and restimulated with immobilized anti-Vβ antibodies for an additional 72 h. Significant expansion of Vβ5.3 and Vβ18 T-cells were detected in Nef-treated cultures, with expansion of Vβ18 occurring with all donors tested, and Vβ5.3 expansion occurring in 50% of the donors. Variable responses were obtained with Vβ2, Vβ3, and Vβ9. These results were confirmed using the more time-consuming method of reverse transcriptase-polymerase chain reaction (RT-PCR). Thus, this novel, reproducible, and relatively simple method can detect Vβ-specific expansion by weak superantigens.

Human immunodeficiency virus type 1 Nef associates with a member of the p21-activated kinase family.

Although human immunodeficiency virus (HIV) Nef is essential for the induction of AIDS, its biochemical function has remained an enigma. In this study, HIV Nef protein is shown to associate with a serine-threonine kinase that recognizes histone H4 as a substrate, is serologically related to rat p21-activated kinase (PAK), and is specifically activated by Rac and Cdc42. These characteristics define the Nef-associated kinase as belonging to the PAK family. PAKs initiate kinase cascades in response to environmental stimuli, and their identification as a target of Nef implicates these signaling molecules in HIV pathogenesis and provides a novel target for clinical intervention.

The HIV Nef Protein Associates with Protein Kinase C Theta

Expression of the human immunodeficiency virus (HIV) Nef protein has been linked to both decreased cell surface expression of CD4 and an impairment of signal transduction. The recently reported association of Nef with an unidentified serine kinase provides a clue as to how Nef might exert its effects. Considering the key role of protein kinase C (PKC) in T cell activation, we investigated the possibility that Nef interacts with PKC. Our results, using two approaches for detecting interactions between Nef and PKC isozymes in Jurkat cells, show that Nef interacts preferentially with thetaPKC. The interaction of Nef and thetaPKC is independent of calcium, enhanced by phospholipid activators of PKC and not affected by a PKC pseudosubstrate peptide. Phorbol 12-myristate 13-acetate and phytohemagglutinin stimulation of Jurkat cells expressing Nef fails to produce the usual translocation of thetaPKC from the cytosol to the particulate fraction; translocation of betaPKC and epsilonPKC was unaffected. Indeed, there appears to be a net loss of thetaPKC in Nef-expressing cells following stimulation. The loss of thetaPKC, which may be a result of inhibition of its binding to RACKs due to Nef binding, could contribute to the various impairments of T cell function associated with HIV infection and Nef expression.

HLA‐dependent variations in human immunodeficiency virus Nef protein alter peptide/HLA binding

In human immunodeficiency virus (HIV) infection, sequence variations within defined cytotoxic T lymphocyte (CTL) epitopes may lead to escape from CTL recognition. In a previous report, we have shown that the variable central region of HIV Nef protein (amino acids 73-144) that contains potential CTL epitopes, can escape the CTL response. We suggested that this non recognition occurs through a variety of mechanisms. In particular, we provided evidence that HIV Nef sequences recovered from HLA-A11-expressing individuals have alterations in the major anchor residues essential for binding of the two Nef epitopes (amino acids 73-82 and 84-92) to the HLA-A11 molecule. Here, we investigate in more detail whether variations in autologous Nef sequences affect HLA binding, leading to CTL escape. Potential epitopes were sought by testing Nef peptides containing the HLA-A11-specific motif or related motifs. We confirmed that only the two previously described epitopes identified in cytolysis tests have optimal reactivity with the HLA-A11 molecule. We then sequenced several viral variants from donors that do not express the HLA-A11 molecule and compared the variability of these epitopes with those obtained from HLA-A11-expressing individuals. One substitution (Leu85) found in the sequences isolated from both populations increase the reactivity of the HLA-A11-restricted epitope 84-92, and might explain the difference in immunogenicity observed between the two HLA-A11-restricted epitopes from HLA-A11+ individuals. In addition, selective variations were only detected in virus isolated from HLA-A11-expressing individuals. Furthermore, examination of the association of variant peptides with the HLA-A11 molecule demonstrated that a single substitution within the minimal epitope could not always completely abrogate HLA binding, suggesting that multiple alterations within a particular epitope may accumulate during disease progression, allowing the virus to escape CTL recognition.

Regulation of Human Immunodeficiency Virus Nef Protein by Phosphorylation

Human immunodeficiency virus isolates express a Nef protein with either an alanine or a threonine at amino acid residue 15. The threonine residue is a site for phosphorylation by protein kinase C. Jurkat T cells constitutively expressing the alanine variant of Nef exhibit the ability to downregulate the induction of transcription factors NF-kB and AP-1. In contrast, Jurkat cells with the threonine variant of Nef are at least partially restored in their ability to recruit NF-kB and AP-1.

Expression of the type 1 human immunodeficiency virus Nef protein in T cells prevents antigen receptor-mediated induction of interleukin 2 mRNA.

Stable transformants of the Jurkat T-cell line have been obtained that express either of two distinct forms of the type 1 human immunodeficiency virus nef gene: the nef-1-encoded protein (Nef-1) contains alanine, glycine, and valine at positions 15, 29, and 33, respectively; the protein specified by nef-2 (Nef-2) has threonine, arginine, and alanine at the corresponding positions. When Jurkat cells or their Nef-2-expressing transformants are treated with phorbol 12-myristate 13-acetate (PMA) plus either phytohemagglutinin (PHA) or antibodies against CD3 epsilon, T-cell receptor beta chain, or CD2, there is a prompt increase in interleukin 2 (IL-2) mRNA and intracellular calcium and in the IL-2 receptor alpha chain on the cell surface. Although cells expressing Nef-1 also induce calcium mobilization and the production of IL-2 receptor alpha chain, the formation of IL-2 mRNA is blocked in response to these stimuli. Moreover, Nef-1-expressing cells transfected with a plasmid in which the IL-2 promoter is fused to the chloramphenicol acetyltransferase (CAT) gene fail to induce CAT following treatment with PMA and PHA. By contrast, the parental and Nef-2-containing cells induce CAT normally. Nef-1-expressing cells can produce IL-2 mRNA in response to a combination of PMA and ionomycin, although much less efficiently than the parental Jurkat cells or Nef-2-expressing cells. These findings, and others described herein, suggest that the virally encoded Nef protein interferes with a signal emanating from the T-cell receptor complex that induces IL-2 gene transcription.