Prediction of CD8+ Epitopes in Leishmania braziliensis Proteins Using EPIBOT: In Silico Search and In Vivo Validation

Abstract

BackgroundLeishmaniasis is caused by intracellular Leishmania parasites that induce a T-cell mediated response associated with recognition of CD4+ and CD8+ T cell Line 1Lineepitopes. Identification of CD8+ antigenic determinants is crucial for vaccine and therapy development. Herein, we developed an open-source software dedicated to search and compile data obtained from currently available on line prediction algorithms.Methodology/Principal FindingsWe developed a two-phase algorithm and implemented in an open source software called EPIBOT, that consolidates the results obtained with single prediction algorithms, generating a final output in which epitopes are ranked. EPIBOT was initially trained using a set of 831 known epitopes from 397 proteins from IEDB. We then screened 63 Leishmania braziliensis vaccine candidates with the EPIBOT trained tool to search for CD8+ T cell epitopes. A proof-of-concept experiment was conducted with the top eight CD8+ epitopes, elected by EPIBOT. To do this, the elected peptides were synthesized and validated for their in vivo cytotoxicity. Among the tested epitopes, three were able to induce lysis of pulsed-target cells.ConclusionOur results show that EPIBOT can successfully search across existing prediction tools, generating a compiled list of candidate CD8+ epitopes. This software is fast and a simple search engine that can be customized to search over different MHC alleles or HLA haplotypes.

Assessment of Protection Induced by DNA and Live Vaccine Encoding Leishmania MHC Class I Restricted Epitopes against L. major Challenge in Balb/c Mice Model

“…Most of them are at pre-vaccine in silico prediction-in vivo validation stage to predict potential MHC class I/II restricted peptides from known [51][52][53][54][55] or genome wide vaccine candidates [18,56,57].…”

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

“…There are also existing software tools (IEDB [ 16 ], EpiBot [ 17 ], EpiToolKit [ 18 ]) that compile the results generated from individual epitope prediction algorithms to improve the prediction accuracy with consensus methods or a unified final ranking. The current implementation of EpiToolKit (v2.0) also has the added functionality of incorporating sequencing variants in its Galaxy-like epitope prediction workflow (via its Polymorphic Epitope Prediction plugin).…”

VianniaTopes: a database of predicted immunogenic peptides forLeishmania(Viannia) species

“…For a more comprehensive analysis, we compared our predicted peptides with those reported in studies conducted with Leishmania species in the IEDB database. This database stores results from only two studies that exclusively performed experimental assays with peptides derived from species of the Viannia subgenus, one in L. braziliensis ( 42 ) and the other one in L. panamensis ( 43 ). These studies collectively reported 14 peptides as potential T cell epitopes, all of which have associated prediction data in VianniaTopes ( Table S4 ).…”