Conservation analysis of dengue virus T-cell epitope-based vaccine candidates using peptide block entropy

Abstract

Broad coverage of the pathogen population is particularly important when designing CD8+ T-cell epitope vaccines against viral pathogens. Traditional approaches are based on combinations of highly conserved T-cell epitopes. Peptide block entropy analysis is a novel approach for assembling sets of broadly covering antigens. Since T-cell epitopes are recognized as peptides rather than individual residues, this method is based on calculating the information content of blocks of peptides from a multiple sequence alignment of homologous proteins rather than using the information content of individual residues. The block entropy analysis provides broad coverage of variant antigens. We applied the block entropy analysis method to the proteomes of the four serotypes of dengue virus (DENV) and found 1,551 blocks of 9-mer peptides, which cover 99% of available sequences with five or fewer unique peptides. In contrast, the benchmark study by Khan et al. (2008) resulted in 165 conserved 9-mer peptides. Many of the conserved blocks are located consecutively in the proteins. Connecting these blocks resulted in 78 conserved regions. Of the 1551 blocks of 9-mer peptides 110 comprised predicted HLA binder sets. In total, 457 subunit peptides that encompass the diversity of all sequenced DENV strains of which 333 are T-cell epitope candidates.

FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses

“…These tools include a selection of keyword searching tools: MAFFT [ 14 ] for multiple sequence alignment (MSA) and BLAST [ 13 ] for sequence similarity search. Specialized tools for the analysis of variability include sequence conservation metrics and their visualization using block entropy analysis [ 34 ]. The T-cell epitope prediction tools for HLA Class I and Class II have been integrated within FluKB for vaccine-related analyses.…”

“…FluKB enables conservation analysis of single positions within protein sequences, of linear blocks of amino acids extracted from multiple sequence alignments (MSA) of proteins using block entropy [ 34 ]. In addition, virtual peptides can be constructed from discontinuous epitopes within MSA and can be analyzed using block entropy, enabling the variability analysis of B-cell epitopes [ 30 ].…”

Dengue virus specific dual HLA binding T cell epitopes induce CD8+T cell responses in seropositive individuals

“…Most attempts at identifying dengue virus specific MHC class I restricted T cell epitopes have utilized MHC binding motif prediction approaches followed by confirmation through screening of T cells derived from healthy or infected individuals. This method has identified a number of epitopes, primarily associated with HLA-A2 alleles 11,[28][29][30] and identified the NS3 and NS5 proteins as the most immunodominant regions for specific CD8 C T cell responses. 4,5,10 Despite their ability to activate PBMCs in vitro, these predicted peptides have not been demonstrated to be presented on the surface of infected cells; therefore, peptides identified by these methods may not accurately represent those epitopes presented on the surface of infected cells in vivo, which are the authentic and most relevant targets for vaccine stimulated T cells.…”

“…Further, a number of these proteins are well conserved between dengue virus subtypes, in particular the non-structural proteins, indicating that these regions are likely to contain multiple CD8 C T cell epitopes. 10,11,29,30 There are several significant advantages in using the immunoproteomic approach to identify dengue virus specific MHC class I T cell epitopes. First and foremost, this approach allows for the identification of T cell epitopes that are naturally processed and presented on the surface of virally infected cells.…”

“…A number of DENV specific T cell activating epitopes have been reported; 4,5,[28][29][30] however, these epitopes have been generated using peptide prediction algorithms and therefore may not accurately represent the natural peptides presented on MHC class I molecules of the infected cells. In addition, in order for a vaccine formulation to be universally applicable (i.e.…”