Novel, in-natural-infection subdominant HIV-1 CD8+ T-cell epitopes revealed in human recipients of conserved-region T-cell vaccines

Abstract

Background: Fine definition of targeted CD8+ T-cell epitopes and their human leucocyte antigen (HLA) class I restriction informs iterative improvements of HIV-1 T-cell vaccine designs and may predict early vaccine success or failure. Here, lymphocytes from volunteers, who had received candidate HIVconsv vaccines expressing conserved sub-protein regions of HIV-1, were used to define the optimum-length target epitopes and their HLA restriction. In HIV-1-positive patients, CD8+ T-cell responses predominantly recognize immunodominant, but hypervariable and therefore less protective epitopes. The less variable, more protective epitopes in conserved regions are typically subdominant. Therefore, induction of strong responses to conserved regions by vaccination provides an opportunity to discover novel important epitopes.

Methods: Cryopreserved lymphocytes from vaccine recipients were expanded by stimulation with 15-mer responder peptides for 10 days to establish short term-cell-line (STCL) effector cells. These were subjected to intracellular cytokine staining using serially truncated peptides and peptide-pulsed 721.221 cells expressing individual HLA class I alleles to define minimal epitope length and HLA restriction by stimulation of IFN-γ and TNF-α production and surface expression of CD107a.

Results: Using lymphocyte samples of 12 vaccine recipients, we defined 14 previously unreported optimal CD8+ T-cell HIV-1 epitopes and their four-digit HLA allele restriction (6 HLA-A, 7 HLA-B and 1 HLA-C alleles). Further 13 novel targets with incomplete information were revealed.

Conclusions: The high rate of discovery of novel CD8+ T-cell effector epitopes warrants further epitope mining in recipients of the conserved-region vaccines in other populations and informs development of HIV-1/AIDS vaccines.

Trial registration: ClinicalTrials.gov NCT01151319.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1. Conserved-region vaccine immunogen and the HIV-CORE 002 trial regimens.

(A) The box.A schematic representation of the chimaeric design of the first generation conserved immunogen HIVconsv. Capital letters above HIVconsv regions indicate the clade of origin, from which the consensus amino sequence for that region was derived. Individual HIV-1 proteins of region origin are colour coded. (B) The two vaccine regimens of the HIV-CORE 002 trial [18] that the volunteers analyzed in this study received. ChAdV–recombinant non-replicating simian (chimpanzee) adenovirus 63 ChAdV63.HIVconsv; MVA—recombinant non-replicating poxvirus modified vaccinia virus Ankara MVA.HIVconsv; and DNA–‘naked’ plasmid pSG2.HIVconsv DNA. (C and D) Optimal epitope mapping was performed using thawed vaccine-recipients’ PBMCs, which were in vitro expanded with the parental 15-mer peptides for 10 days to establish STCL. (C) Frequencies of vaccine-elicited, HIV-1-specific, in vitro 15-mer peptide (x-axis)-expanded sequential PBMC samples of several volunteers from 5 (black) and 12 (grey) months after the last vaccine administration. Specific cells were enumerated in an IFN-γ ELISPOT assay. Panel (D) overviews the frequencies of peptide-specific CD8+ STCLs over the volunteers and peptides used. Frequencies of specific cells from all tested volunteers expanded by the same 15-mer peptide are shown next to each other above each peptide given on the x-axis. Top and bottom graphs show frequencies of CD8+ T cells producing IFN-γ and TNF-α, respectively. S2 Table for the list of peptides and responding volunteers.