Background:
Human leukocyte antigen (HLA) class Ia molecules present peptides derived from the ER for recognition by cytotoxic T lymphocytes. As such, HLA class Ia-restricted peptides are well characterised drug targets for infectious diseases. However, their clinical potential is limited by the high polymorphism of the HLA class I genes within the population. In contrast, the HLA class Ib molecule, HLA-E, has only two alleles and thus offers the potential to develop donor-unrestricted therapies. With only a few reported HIV-derived HLA-E restricted peptides, there is limited understanding of the composition and druggability of the HIV HLA-E ‘ligandome.’ We therefore sought to systematically interrogate the HIV HLA-E ligandome to identify stably presented peptides as drug targets for a potential HIV cure strategy.
Methods:
The HIV proteome of in vitro infected cells was interrogated for HLA-E presented peptides using both immunopeptidomic (mass spectrometry) and bioinformatic (predictive) approaches. Putative ligands were then ranked based on stability using a panel of biochemical assays as well as an HLA-E cell surface stabilization assay. The stability of the highest ranked peptide, Gag275-283, was further assessed using an affinity-enhanced T cell receptor bispecific molecule (ImmTAX). The ImmTAX was used as a probe for peptide-HLA-E complexes on antigen-presenting cells (peptide-pulsed targets or HIV-infected cells) in T cell redirection assays.
Results:
Tandem mass spectrometry analysis of 1 billion infected C8166 cells (19.4% Gag+ by intracellular staining) failed to identify any HIV HLA-E peptides. Of >80 bioinformatically predicted ligands, all were characterised by low or unmeasurable complex thermostability and half-lives and performed poorly in the cell surface stabilisation assay. In T cell redirection assays using the ImmTAX, consistent presentation of Gag275-283 by HLA-E was only demonstrated when peptide was supplied exogenously (peptide pulsing model). Only sporadic and inconsistent peptide presentation was detected when the peptide source was endogenously expressed HIV Gag protein (infected cells).
Conclusions:
This study provides biochemical and biological evidence for the failure of HIV-derived peptides to form a stable complex with HLA-E, highlighting a major challenge for HLA-E targeted drug or vaccine development.