Kinetics of HIV-1 CTL Epitopes Recognized by HLA I Alleles in HIV-Infected Individuals at Times near Primary Infection: The Provir/Latitude45 Study

Abstract

In patients responding successfully to ART, the next therapeutic step is viral cure. An interesting strategy is antiviral vaccination, particularly involving CD8 T cell epitopes. However, attempts at vaccination are dependent on the immunogenetic background of individuals. The Provir/Latitude 45 project aims to investigate which CTL epitopes in proviral HIV-1 will be recognized by the immune system when HLA alleles are taken into consideration. A prior study (Papuchon et al, PLoS ONE 2013) showed that chronically-infected patients under successful ART exhibited variations of proviral CTL epitopes compared to a reference viral strain (HXB2) and that a generic vaccine may not be efficient. Here, we investigated viral and/or proviral CTL epitopes at different time points in recently infected individuals of the Canadian primary HIV infection cohort and assessed the affinity of these epitopes for HLA alleles during the study period. An analysis of the results confirms that it is not possible to fully predict which epitopes will be recognized by the HLA alleles of the patients if the reference sequences and epitopes are taken as the basis of simulation. Epitopes may be seen to vary in circulating RNA and proviral DNA. Despite this confirmation, the overall variability of the epitopes was low in these patients who are temporally close to primary infection.

Sanger and Next-Generation Sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA

“…Total whole blood was collected from the patients and DNA was extracted from the PBMC followed by amplification and Sanger sequencing as described previously [ 4 , 5 ]. Sanger sequences are available in GenBank under accession numbers MF580925 to MF580945.…”

“…Gag and Pol ultra-deep-sequencing were performed by using the Roche 454 technology. Amplicons for Gag (obtained with the same primers as for Sanger sequencing) and Pol [ 4 , 5 ] were pooled at equimolar concentrations. Clonal amplification on beads (EmPCR) was performed by using the 454 Life Science Reagents that enable bi-directional sequencing, composed of 30 cycles of PCR amplification.…”

“…The method used for the molecular characterization of HLA alleles A and B in the Bordeaux and Montreal cohorts has been described previously [ 4 , 5 ]. For the patients from Lima, high-resolution HLA typing was performed by Sequence-Based Typing (SBT) at the University of Oklahoma Health Science Center, a CLIA/ASHI-accredited HLA typing laboratory, using in-house methods.…”

“…This vaccination involves the stimulation of a cytotoxic CD8-positive T cell (CTL)-mediated immune response which should be able to target the virus within the latent viral reservoir [ 3 ]. CTL epitopes are Human Leucocyte Antigen (HLA)-restricted and must be presented by molecules encoded by HLA alleles, thereby introducing a genetic and individual parameter into the physiopathology of the immune response and the evolution of HIV disease [ 4 , 5 ]. Some studies have shown that the viruses recovered from archived DNA are different from pre-ART circulating viruses and [ 6 ].…”

Provir/Latitude 45 study: A step towards a multi-epitopic CTL vaccine designed on archived HIV-1 DNA and according to dominant HLA I alleles

“…Some comments can be made at this point: (i) most of the vaccine constructs, whether they are based on recombinant viruses, plasmid DNA or lipopeptides, are designed on generic HIV-1 viruses and circulating strains may exhibit variations (depending on subtypes or not) especially regarding the CTL epitopes (ii) the virus resuming after discontinuation of cART originates from the archived proviral DNA and our team [15,16] plus R. Siliciano ‘s group [17] have drawn attention to the discrepancy between archived CTL epitopes and CTL epitopes of the circulating viruses before initiation of cART; (iii) there exist extensive experimental data that underscore the importance of a high binding affinity of CTL epitopes to their restricting HLA class I molecule and the recognizing T cell receptor (TCR) [18,19].…”