AUTHOR=Lopes-Ribeiro Ágata , Araujo Franklin Pereira , Oliveira Patrícia de Melo , Teixeira Lorena de Almeida , Ferreira Geovane Marques , Lourenço Alice Aparecida , Dias Laura Cardoso Corrêa , Teixeira Caio Wilker , Retes Henrique Morais , Lopes Élisson Nogueira , Versiani Alice Freitas , Barbosa-Stancioli Edel Figueiredo , da Fonseca Flávio Guimarães , Martins-Filho Olindo Assis , Tsuji Moriya , Peruhype-Magalhães Vanessa , Coelho-dos-Reis Jordana Grazziela Alves 

TITLE=In silico and in vitro arboviral MHC class I-restricted-epitope signatures reveal immunodominance and poor overlapping patterns

JOURNAL=Frontiers in Immunology

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.1035515

DOI=10.3389/fimmu.2022.1035515

ISSN=1664-3224

ABSTRACT=The present work sought to identify MHC-I-restricted peptide signatures for arbovirus using in silico
and in vitro peptide microarray tools. First, an in-silico analysis of immunogenic epitopes restricted
to four of the most prevalent human MHC class-I was performed by identification of MHC affinity
score. For that, more than 10,000 peptide sequences from 5 Arbovirus and 8 different viral serotypes,
namely Zika (ZIKV), Dengue (DENV serotypes 1-4), Chikungunya (CHIKV), Mayaro (MAYV) and
Oropouche (OROV) viruses, in addition to YFV were analyzed. Haplotype HLA-A*02.01 was the
dominant human MHC for all arboviruses. Over one thousand HLA-A2 immunogenic peptides were
employed to build a comprehensive identity matrix, which allowed the identification of only three
overlapping peptides between two or more flavivirus sequences, suggesting poor overlapping of
virus-specific immunogenic peptides amongst arborviruses. Intending to assess HLA-A*02:01
reactivity of peptides in vitro, a peptide microarray was designed and generated using a dimeric
protein containing HLA-A*02:01. Global analysis of the fluorescence intensity for peptide-HLA-
A*02:01 binding indicated a dose-response effect in the array. Considering all assessed arboviruses,
the number of DENV-derived peptides with HLA-A*02:01 reactivity was the highest. Furthermore, a
lower number of YFV-17DD overlapping peptides presented reactivity when compared to non-
overlapping peptides. In addition, the assessment of HLA-A*02:01-reactive peptides across virus
polyproteins highlighted non-structural proteins as “hot-spots”. Data analysis supported these
findings showing the presence of major hydrophobic sites in the final segment of non-structural
protein 1 throughout 2a (Ns2a) and in non-structural proteins 2b (Ns2b), 4a (Ns4a) and 4b (Ns4b). To
our knowledge, these results provide the most comprehensive and detailed snapshot of the
immunodominant peptide signature for arbovirus with MHC-class I restriction, which may bring insight into the design of future virus-specific vaccines to arboviruses and for vaccination protocols
in highly endemic areas.