Abstract
Background Many HIV databases and applications focus on a limited domain of HIV knowledge. Since even a “simple” organism like HIV represents a very complex system with many interacting elements, the fractured structure of existing databases and applications likely limits our ability to investigate and understand HIV. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and presents the data in an interactive web application. HIVToolbox allows quick and convenient hypotheses generation, experiment interpretation, and potential new drug structure creation. Methods HIVToolbox was built as a standard three-tier J2EE web application, consisting of 1) an underlying relational MySQL database, 2) a set of standard Java data access objects that pull data from the database, and 3) a set of dynamic web pages the user interacts with. HIV-1 data from external sources such as the Protein Data Bank, NCBI, Los Alamos, etc. was collected, curated, and stored in the HIVToolbox database. Additional data, such as homology and position statistics matrices, was generated from existing data. Since version 1, drug binding site and drug resistant mutation data has also been added. Results HIVToolbox was used to create several new hypotheses about HIV-1 integrase, including predicting the location of a CK2 phosphorylation site, which was later confirmed by experiment. A new version of HIVToolbox support display of the 3D locations of drug resistant mutations on surface plots of HIV proteins and the drug binding sites for structures of complexes of HIV proteins with drugs. Conclusion HIVToolbox is an open-access web application that allows virologists and structural biologists to access detailed information about HIV-1 proteins, such as sequence, structure, functional sites and relationships, homology, drug binding sites, and drug resistant mutations, and to immediately see the relationships between any or all of them. Weblink: [http://hivtoolbox.bio-toolkit.com]
Background Analysis of human monoclonal antibodies (mAbs) developed from HIV-1 infected donors have enormously contributed to the identification of neutralization sensitive epitopes on the HIV-1 envelope glycoprotein. The third variable region (V3) is a crucial target on gp120, primarily due to its involvement in co-receptor (CXCR4 or CCR5) binding and presence of epitopes recognized by broadly neutralizing antibodies. Methods Thirty-three HIV-1 seropositive drug naive patients (18 males and 15 females) within the age range of 20-57 years (median=33 years) were recruited in this study for mAb production. The mAbs were selected from EBV transformed cultures with conformationally constrained Cholera-toxin-B containing V3C (V3C-CTB) fusion protein. We tested the mAbs for their binding with HIV-1 derived proteins and peptides by ELISA and for neutralization against HIV-1 viruses by TZM-bl assays. Results We isolated three anti-V3 mAbs, 277, 903 and 904 from the cells of different individuals. The ELISA binding revealed a subtype-C and subtype-A specific binding of antibody 277 and 903 while 904 exhibited cross reactivity also with subtype-B V3. Epitope mapping of mAbs with overlapping V3 peptides showed exclusive binding to V3 crown. The antibodies displayed high and low neutralizing activity against 2/5 tier 1 and 1/6 tier 2 viruses respectively. Overall, we observed a resistance of the tier 2 viruses to neutralization by the anti-V3 mAbs, despite exposure of the epitopes recognized by these antibodies on the native viruses, as determined by intact virion binding assay with two representative subtype-C and B viruses (Du156.12 and JRFL). Conclusion Our study suggests that the anti-V3 antibodies derived from subtype-C infected Indian patients display neutralization potential against tier 1 viruses. Defining the epitope specificities of these mAbs and further experimental manipulations will be helpful in identification of epitopes, unique to clade C or shared with non-clade C viruses, for immunogen design.
Background One major obstacle to induce bNAbs resides in the high variability of the viral envelope and structural mechanisms hiding crucial epitopes. Besides, maturation of bNAbs against HIV represents a difficult process that can be impaired by the immunodeficiency associated with HIV infection. We have explored the hypothesis that preserved B cell function in LTNPs could result in the production of bNAbs at higher frequency and increased affinity in comparison with HIV progressors. Methods Samples (142) from the cohort of LTNPs (median RNA copies/ml: 87, median CD4+: 802 cells/µl) were kindly provided by the HIV BioBank integrated in the Spanish AIDS Research Network (RIS). A control population of 191 untreated patients (median RNA copies/ml: 10,241, median CD4+: 567 cells/µl) from Hospital Clinic, Barcelona, was analyzed. Sera at 1/200 and 1/2000 dilutions were preincubated with Env recombinant viruses harboring a luciferase gene and then added to U87.CD4.CXCR4/CCR5. bNAbs specificities were studied by ELISA using mutated gp120 that abrogates antibody binding, competition ELISA with biotinylated antibodies, neutralization assays with mutated viruses and peptide competition neutralization assays. Results The percentage of elite neutralizers was higher in the LTNPs (9.3%) than in the control population (3.7%). Broadly neutralizing sera were screened for the presence of epitope-specific antibodies. CD4 binding site antibodies were detected in several sera. To determine whether these antibodies were responsible for broad neutralization, competition neutralization assays using RSC3 (antigenically resurfaced glycoprotein containing the CD4bs) were performed. RSC3 addition inhibited neutralization mediated by 16.7% of sera in LTNPs and 12.5% sera of the control population. Anti-MPER antibodies were detected in 50% individuals of both populations, including several sera with 4E10-like antibodies. Glycan-dependent HIV-1 NAbs were more abundant in LTNPs (66%) than in control population (37%). Conclusion Broad humoral immune responses against HIV-1 were more common among LTNP than a control population of untreated HIV-1-infected donors.
Background HIV/SIV primarily infect activated CD4+ T cells, but can infect macrophages. Because of the relatively small percentage of infected macrophages, the interaction between antigen-specific CD8+ T cells and infected macrophages in HIV/SIV infection has been poorly studied. We, therefore, sought to determine whether SIV-specific CD8+ T cells could control viral replication in infected macrophages. Methods We wanted to ascertain whether ex vivo tetramer-sorted SIV-specific CD8+ T cells could suppress viral replication in SIVmac239/316e- and SIVsmE660-infected macrophages using a recently developed 48-hour viral suppression assay. We reasoned that freshly sorted CD8+ T cells might be more representative of the in vivo properties of CD8+ T cells than in vitro cultured cell lines and clones. Results Surprisingly, both ex vivo tetramer-sorted SIV-specific CD8+ T cells and bulk CD8+ T cells that eliminated and suppressed viral replication in SIV-infected CD4+ T cells were inefficient at controlling viral replication in SIV-infected macrophages. Our data suggest that macrophages may be an important reservoir for SIV because it may be difficult for SIV-specific CD8+ T cells to suppress viral replication in this particular cell type. Conclusion It is possible, therefore, that while AIDS virus-infected macrophages only constitute a small percentage of all virus-infected cells, they may be relatively resistant to CD8+ T cell-mediated lysis and continue to produce virus over long periods of time. Thus, macrophages could actually be contributing significantly to viral production. Induction of HIV/SIV-specific CD8+ T cells capable of killing infected macrophages or preventing establishment of the macrophage reservoir HIV might be critical for controlling viral replication.
Background The potential role of ADCC in prevention of infection is suggested by the RV144 HIV vaccine trial where non-neutralizing antibodies contributed to protection against infection with HIV. Studies from Kenya showed that HIV specific IgA in cervical fluid was present in uninfected sex workers. We aimed to analyze cervicovaginal lavage fluid(CVL) from 2 seroconverters (SC) and 10 highly exposed seronegative women who had unprotected sex with known positive partners. Methods A 51Cr-release assay with natural killer cells or monocytes as effectors was used to measure IgG or IgA mediated ADCC against clade specific gp120 coupled target cells. We analyzed CVL from ESN at one visit, and SC at intervals from one yr pre-seroconversion (PSC) to 6.5 yr after seroconversion (ASC). We evaluated activity at 4, 10 fold serial dilutions starting with a 1/10 dilution. Results Figure 1 (top)shows shows minimal to no activity of IgG mediated ADCC in the CVL of 10 ESN. Figure 1(bottom) shows IgA mediated ADCC in the CVL of the same 10 ESN. 4 patients show significant activity above background activity. At the peak dilution, patient 4 shows 27.3% Specific Release (SR), patient 6 shows 14.5 %SR, patient 8 shows 17.9 %SR and patient 10 shows 17.6 %SR. Figure 2 and 3 shows no IgA mediated ADCC activity in CVL of 2 seroconverters from PSC to 6.5 years ASC even while IgG activity is present in later visits. Conclusion HIV IgA in CVL samples was associated with ADCC and lack of HIV infection in exposed women, indicating that genital HIV IgA may contribute to protection from infection. Further studies need to be done to determine if IgA mediated ADCC antibodies may be protective in ESN.
Background CD4+ T-cells from gut-associated lymphoid tissues (GALT) are major HIV-1 targets. Recruitment of excess effector CD8+ T-cells in the proximity of target cells is critical for the control of viral replication. We investigated the colocalization potential o