HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires

Abstract

Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.

Keywords: HLA association; Leishmania; antigen presentation; human leukocyte antigen; immunogenetics; immunoinformatics; leishmaniasis; vaccine candidates.

Figure 1

A multiple sequence alignment of the risk-associated HLA-DRB1 alleles (top 5) versus the protection-associated HLA-DRB1 alleles (bottom 5). Non-similar positions were colored using the physicochemical properties of the respective amino acids. Rose = hydrophobic/aliphatic; Orange = aromatic; Blue = positively charged; Red = negatively charged; Green = hydrophilic; Purple = conformationally special; Yellow = Cysteine.

Figure 2

Consensus sequence logos of the 9 mer binding cores of predicted epitopes across HLA class II alleles. This plot shows the sequence conservation level (in bits) of an amino acid occurring at a certain position in the binding core. Protection and risk-associated HLA alleles have been separated in a 2-column matrix.

Figure 3

Upset Plot of strong-binding epitopes that are 1) unique to protection-associated alleles and 2) conserved across two major VL- (L. infantum and L. donovani) and two major CL-causing Leishmania species (L. braziliensis and L. mexicana). The set size denotes the total number of strong-binding epitopes predicted for each species, while the intersection size denotes the number of strong-binding epitopes shared across the species.

Figure 4

Upset Plots showing unique strong-binding epitopes of the CL-causing species (L. braziliensis and L. mexicana) that bind across the protection-associated alleles known for these species. The set size denotes the total number of strong-binding epitopes predicted for each species, while the intersection size denotes the number of strong-binding epitopes shared across the species.

Figure 5

Upset Plots showing unique strong-binding epitopes of the VL-causing species (L. donovani and L. infantum) that bind across the protection-associated alleles known for these species. The set size denotes the total number of strong-binding epitopes predicted for each species, while the intersection size denotes the number of strong-binding epitopes shared across the species.