Computer-Based Design of an HLA-Haplotype and HIV-Clade Independent Cytotoxic T-Lymphocyte (CTL) Assay for Monitoring HIV-Specific Immunity

Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences

In 2019, 38 million people lived with HIV-1 infection resulting in 690,000 deaths. Over 50% of this infection and its associated deaths occurred in Sub-Saharan Africa. The West African region is a known hotspot of the HIV-1 epidemic. There is a need to develop an HIV-1 vaccine if the HIV epidemic would be effectively controlled. Few protective cytotoxic T Lymphocytes (CTL) epitopes within the HIV-1 GAG (HIV_gagconsv) have been previously identified to be functionally conserved among the HIV-1 M group. These epitopes are currently the focus of universal HIV-1 T cell-based vaccine studies. However, these epitopes' phenotypic and genetic properties have not been observed in natural settings for HIV-1 strains circulating in the West African region. This information is critical as the usefulness of universal HIV-1 vaccines in the West African region depends on these epitopes' occurrence in strains circulating in the area. This study describes non-synonymous substitutions within and without HIV_gagconsv genes isolated from 10 infected Nigerians at the early stages of HIV-1 infection. Furthermore, we analyzed these substitutions longitudinally in five infected individuals from the early stages of infection till after seroconversion. We identified three non-synonymous substitutions within HIV_gagconsv genes isolated from early HIV infected individuals. Fourteen and nineteen mutations outside the HIV_gagconsv were observed before and after seroconversion, respectively, while we found four mutations within the HIV_gagconsv. These substitutions include previously mapped CTL epitope immune escape mutants. CTL immune pressure likely leaves different footprints on HIV-1 GAG epitopes within and outside the HIV_gagconsv. This information is crucial for universal HIV-1 vaccine designs for use in the West African region.

An IL-15 Dependent CD8 T Cell Response to Selected HIV Epitopes is Related to Viral Control in Early-Treated HIV-Infected Subjects

In some early-treated HIV+ patients, Structured Treatment Interruption (STI) is associated to spontaneous control of viral rebound. Thus, in this clinical setting, we analyzed the immunological parameters associated to viral control. Two groups of early treated patients who underwent STI were retrospectively defined, according to the ability to spontaneously control HIV replication (Controller and Non-controller). Plasma cytokine levels were analyzed by multiplex analysis. CD8 T cell differentiation was determined by polychromatic flow cytometry. Antigen-specific IFN-Γ production was analyzed by ELISpot and intracellular staining after stimulation with HIV-peptides. Long-term Elispot assays were performed in the presence or absence of IL-15. Plasma IL-15 was found decreased over a period of time in Non-Controller patients, whereas a restricted response to Gag (aa.167–202 and 265–279) and Nef (aa.86–100 and 111–138) immunodominant epitopes was more frequently observed in Controller patients. Interestingly, in two Non-Controller patients the CD8-mediated T cells response to immunodominant epitopes could be restored in vitro by IL-15, suggesting a major role of cytokine homeostasis on the generation of protective immunity. In early-treated HIV+ patients undergoing STI, HIV replication control was associated to CD8 T cell maturation and sustained IL-15 levels, leading to HIV-specific CD8 T cell responses against selected Gag and Nef epitopes.

Quantitative prediction of peptide binding to HLA-DP1 protein

The exogenous proteins are processed by the host antigen-processing cells. Peptidic fragments of them are presented on the cell surface bound to the major hystocompatibility complex (MHC) molecules class II and recognized by the CD4+ T lymphocytes. The MHC binding is considered as the crucial prerequisite for T-cell recognition. Only peptides able to form stable complexes with the MHC proteins are recognized by the T-cells. These peptides are known as T-cell epitopes. All T-cell epitopes are MHC binders, but not all MHC binders are T-cell epitopes. The T-cell epitope prediction is one of the main priorities of immunoinformatics. In the present study, three chemometric techniques are combined to derive a model for in silico prediction of peptide binding to the human MHC class II protein HLA-DP1. The structures of a set of known peptide binders are described by amino acid z-descriptors. Data are processed by an iterative self-consisted algorithm using the method of partial least squares, and a quantitative matrix (QM) for peptide binding prediction to HLA-DP1 is derived. The QM is validated by two sets of proteins and showed an average accuracy of 86 percent.

T-cell epitope vaccine design by immunoinformatics

Vaccination is generally considered to be the most effective method of preventing infectious diseases. All vaccinations work by presenting a foreign antigen to the immune system in order to evoke an immune response. The active agent of a vaccine may be intact but inactivated ('attenuated') forms of the causative pathogens (bacteria or viruses), or purified components of the pathogen that have been found to be highly immunogenic. The increased understanding of antigen recognition at molecular level has resulted in the development of rationally designed peptide vaccines. The concept of peptide vaccines is based on identification and chemical synthesis of B-cell and T-cell epitopes which are immunodominant and can induce specific immune responses. The accelerating growth of bioinformatics techniques and applications along with the substantial amount of experimental data has given rise to a new field, called immunoinformatics. Immunoinformatics is a branch of bioinformatics dealing with in silico analysis and modelling of immunological data and problems. Different sequence- and structure-based immunoinformatics methods are reviewed in the paper.

Delayed early antiretroviral treatment is associated with an HIV-specific long-term cellular response in HIV-1 vertically infected infants

Antiviral T-cell immune responses appear to be crucial to control HIV replication. Infants treated before the third month of life with highly active antiretroviral treatment (HAART) did not develop a persistent HIV-specific immune response. We evaluated how delayed initiation of HAART after 3 months of age influences the development of HIV-1-specific T-cell responses during long-term follow-up in 9 HIV-1 vertically infected infants. These data suggest that a longer antigenic stimulation, due to a larger window for therapeutic intervention with HAART, is associated with the establishment of a persistent specific HIV immune response resulting in a long-term viral control of vertically infected infants.

Differentiation of monocytes into CD1a- dendritic cells correlates with disease progression in HIV-infected patients

Monocyte differentiation into dendritic cells (DCs) depends on microenvironmental conditions. In this study, the capacity of human monocytes to differentiate into mature DCs and their ability to induce an antiviral immune response was investigated in HIV-infected patients. In healthy subjects, monocytes differentiate into CD1a+ DCs in the presence of granulocyte macrophage colony-stimulating factor and interleukin (IL)-4 and matured in the presence of lipopolysaccharide. Here, we found that in 30% and 45% of HIV-infected white and African subjects, respectively, monocytes gave rise to a homogeneous CD1a* DC population. In the patients who gave rise only to the CD1a* DCs, this population spontaneously produced IL-10 but not IL-12, and induced a T helper 2-like immune response when cultured with human T cells isolated from cord blood mononuclear cells. In patients with monocytes differentiated into CD1a* DCs, a high percentage of HIV-specific CD4 T cells producing IL-4 were seen in the peripheral blood. Furthermore, differentiation of monocytes into DCs with CD1a* phenotype correlated with low CD4 T-cell counts and high viral loads in HIV-infected subjects. These results suggest that the differentiation of monocytes into CD1a* DCs may be a phenotypic marker associated with progression of the disease.

Successful simplification of protease inhibitor-based HAART with triple nucleoside regimens in children vertically infected with HIV

OBJECTIVE

To assess the virological, immunological and metabolic effects of switching from an efficacious first-line protease inhibitor (PI)-based HAART to a simplified triple nucleoside reverse transcriptase inhibitor (NRTI) regimen in children vertically infected with HIV.

DESIGN

Prospective, open-label, before-after study of 20 vertically infected children with at least 12 consecutive months of undetectable viral load under a PI-based HAART and no previous history of NRTI treatment.

METHODS

At study entry, HAART was shifted to a triple-NRTI combination.

RESULTS

The children were aged 2 to 18 years (median, 7.9) and were followed for 96 weeks. All were receiving a PI-based regimen for an average duration of 4 years before enrollment. At study entry, 12 patients (60%) switched to abacavir, 5 (25%) to lamivudine; 2 (10%) to zidovudine and 2 to didanosine (10%). All but one patient maintained plasma HIV RNA < 50 copies/ml during the entire follow-up. No immunological failure was observed at week 96. A trend of normalization (P < 0.001) of T cell receptor Vbeta families of the CD8 cell subset was detected in 19/20 (95%), with an increased HIV-specific CD8 T cell response (P < 0.01) in 17/20 (85%). Dyslipidaemia significantly improved during the follow up (P < 0.001). No new cases of lipodystrophy were detected.

CONCLUSIONS

Switching to triple-NRTI regimens in selected HIV-infected children with an extremely low likelihood of harbouring nucleoside-associated mutations maintains viral suppression and immunological function, improving metabolic abnormalities and the effort to take medication for up to 96 weeks.

T-Cell response profiling to biological threat agents including the SARS coronavirus

The emergence of pathogens such as SARS and the increased threat of bioterrorism has stimulated the development of novel diagnostic assays for differential diagnosis. Rather than focusing on the detection of an individual pathogen component, we have developed a T cell profiling system to monitor responses to the pathogens in an array format. Using a matrix of antigens specific for different pathogens, a specific T cell profile was generated for each individual by monitoring the intracellular production of interferon-gamma by flow cytometry. This assay allows for the testing of multiple proteins or peptides at a single time and provides a quantitative and phenotypic assessment of CD4(+) and CD8(+) responding cells. We present profiling examples for several positive individuals, including those vaccinated with the smallpox and anthrax vaccines. We also show antigen optimization for the SARS-hCoV, as studies revealed that these proteins contain peptides which cross-react with more common coronaviruses, a cause of the common cold. The T cell array is an early and sensitive multiplex measure of active infection, exposure to a pathogen, or effective, recent vaccination.

Flow cytometry and T-cell response monitoring after smallpox vaccination

Orthopoxvirus zoonosis or smallpox as result of bioterrorism or biological warfare represents a risk for epidemic spread. By monitoring T-cell responses by flow cytometry, we observed a recall response after recent vaccination against smallpox. When the high similarity between the orthopoxviruses is considered, this rapid assay that uses vaccinia antigens could identify recently exposures.