Malaria antigens are presented to CD8 T cells via the non-classical HLA-E

CD8 T cells have long been known to target infected hepatocytes during the intracellular liver stages of Plasmodium—the causative agent of malaria. Current T cell vaccine strategies are limited by the inability to obtain sufficient amounts of Plasmodium-infected hepatocytes to identify peptides presented on MHC-I (“immunopeptidomics”). Recently, we demonstrated that the blood stages of Plasmodium vivax are also susceptible to CD8 T cell killing and performed immunopeptidomics on Pv-infected reticulocytes. Peptides mapped to proteins conserved across Plasmodium spp. and were common across volunteers. Furthermore, ~50% of the peptides detected are not predicted to bind classical HLA-I molecules and thus could be presented by non-classical HLA. In support of this, blocking HLA-E during in vitro stimulation of PBMCs with a pool of newly-identified peptides substantially reduced the CD8 T cell response. Mechanistic studies conducted in the rhesus macaque/P. cynomolgi malaria model demonstrated that CD8 T cell killing of infected reticulocytes is conserved in this model as are CD8 responses to the newly identified peptides. In vitrostimulation assays showed that CD8 T cell responses to at least 3 of 9 peptides tested are completely restricted to MHC-E. This is supported by in vitro binding assays showing peptide binding to HLA-E. In summary, we demonstrate for the first time that malaria infection induces HLA/MHC-E-restricted CD8 T cell responses to newly identified peptides that are conserved across host and parasite species. Given the extreme conservation of MHC-E, these results pave the way to explore a universal, species-transcending vaccine for malaria based on MHC-E presentation of novel antigens.

Mechanistic diversity in MHC class I antigen recognition

Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.

Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8+ T Cell Tolerance

The human immune system relies on the capability of CD8+ T cells to patrol body cells, spot infected cells and eliminate them. This cytotoxic response is supposed to be limited to infected cells to avoid killing of healthy cells. To enable this, CD8+ T cells have T Cell Receptors (TCRs) which should discriminate between self and non-self through the recognition of antigenic peptides bound to Human Leukocyte Antigen class I (HLA-I) complexes-i.e., HLA-I immunopeptidomes-of patrolled cells. The majority of these antigenic peptides are produced by proteasomes through either peptide hydrolysis or peptide splicing. Proteasome-generated cis-spliced peptides derive from a given antigen, are immunogenic and frequently presented by HLA-I complexes. Theoretically, they also have a very large sequence variability, which might impinge upon our model of self/non-self discrimination and central and peripheral CD8+ T cell tolerance. Indeed, a large variety of cis-spliced epitopes might enlarge the pool of viral-human zwitter epitopes, i.e., peptides that may be generated with the exact same sequence from both self (human) and non-self (viral) antigens. Antigenic viral-human zwitter peptides may be recognized by CD8+ thymocytes and T cells, induce clonal deletion or other tolerance processes, thereby restraining CD8+ T cell response against viruses. To test this hypothesis, we computed in silico the theoretical frequency of zwitter non-spliced and cis-spliced epitope candidates derived from human proteome (self) and from the proteomes of a large pool of viruses (non-self). We considered their binding affinity to the representative HLA-A*02:01 complex, self-antigen expression in Medullary Thymic Epithelial cells (mTECs) and the relative frequency of non-spliced and cis-spliced peptides in HLA-I immunopeptidomes. Based on the present knowledge of proteasome-catalyzed peptide splicing and neglecting CD8+ TCR degeneracy, our study suggests that, despite their frequency, the portion of the cis-spliced peptides we investigated could only marginally impinge upon the variety of functional CD8+ cytotoxic T cells (CTLs) involved in anti-viral response.