title: Identification of novel consensus CD4 T-cell epitopes from clade B HIV-1 whole genome that are frequently recognized by HIV-1 infected patients.
abstract: OBJECTIVE
  To identify promiscuous and potentially protective human CD4 T-cell epitopes in most conserved regions within the protein-coding genome of HIV-1 clade B consensus sequence.
  
  
  METHODS
  We used the TEPITOPE algorithm to screen the most conserved regions of the whole genome of the HIV-1 subtype B consensus sequence to identify promiscuous human CD4 T-cell epitopes in HIV-1. The actual promiscuity of HLA binding of the 18 selected peptides was assessed by binding assays to nine prevalent HLA-DR molecules. Synthetic peptides were tested with interferon-gamma ELISPOT assays on peripheral blood mononuclear cells (PBMC) from 38 HIV-1 infected patients and eight uninfected controls.
  
  
  RESULTS
  Most peptides bound to multiple HLA-DR molecules. PBMC from 91% of chronically HIV-1 infected patients recognized at least one of the promiscuous peptides, while none of the healthy controls recognized peptides. All 18 peptides were recognized, and each peptide was recognized by at least 18% of patients; 44% of the patients recognized five or more peptides. This response was not associated to particular HLA-DR alleles. Similar responses were obtained in CD8 T-cell-depleted PBMC.
  
  
  CONCLUSIONS
  In silico prediction of promiscuous epitopes led to the identification of naturally immunodominant CD4 T-cell epitopes recognized by PBMC from a significant proportion of a genetically heterogeneous patient population exposed to HIV-1. This combination of CD4 T-cell epitopes - 11 of them not described before - may have the potential for inclusion in a vaccine against HIV-1, allowing the immunization of genetically distinct populations.
authors.affiliation: Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, Brazil.
authors.forename: Simone G
authors.initials: SG
authors.lastname: Fonseca
authors.forename: Adriana
authors.initials: A
authors.lastname: Coutinho-Silva
authors.forename: Luiz Augusto M
authors.initials: LA
authors.lastname: Fonseca
authors.forename: Aluisio C
authors.initials: AC
authors.lastname: Segurado
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Moraes
authors.forename: Hélcio
authors.initials: H
authors.lastname: Rodrigues
authors.forename: Juergen
authors.initials: J
authors.lastname: Hammer
authors.forename: Esper G
authors.initials: EG
authors.lastname: Kallás
authors.forename: John
authors.initials: J
authors.lastname: Sidney
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette
authors.forename: Jorge
authors.initials: J
authors.lastname: Kalil
authors.forename: Edecio
authors.initials: E
authors.lastname: Cunha-Neto
mesh_terms: D000328:Adult; D000368:Aged; D000465:Algorithms; D018791:CD4 Lymphocyte Count; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology*; D016384:Consensus Sequence; D004797:Enzyme-Linked Immunosorbent Assay / Q000379:methods; D000939:Epitopes / Q000276:immunology*; D005260:Female; D016679:Genome, Viral / Q000235:genetics / Q000276:immunology; D015658:HIV Infections / Q000276:immunology*; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology; D006684:HLA-DR Antigens / Q000276:immunology; D006801:Humans; D007371:Interferon-gamma; D007963:Leukocytes, Mononuclear / Q000276:immunology; D008297:Male; D008875:Middle Aged; D010455:Peptides / Q000276:immunology; D014764:Viral Proteins / Q000276:immunology
chemical_list: D000939:Epitopes; D006684:HLA-DR Antigens; D010455:Peptides; D014764:Viral Proteins; D007371:Interferon-gamma