title: HLA-B molecules target more conserved regions of the HIV-1 proteome.
abstract: BACKGROUND
  HLA-B alleles of HIV-infected individuals have been shown to have a major impact on their rate of progression toward AIDS, and the T-cell responses they restrict are immunodominant.
  
  
  OBJECTIVE
  We sought to identify whether the association of HLA-B alleles with rate of progression toward AIDS is due to targeting of more restricted and thus more conserved regions of the HIV-1 proteome.
  
  
  METHODS
  Each residue of the HIV-1 consensus subtype B sequence was coded according to the presence/absence of an epitope, using the compiled epitope data available in the HIV-LANL immunology database. The Shannon entropy for each HXB2 position was calculated using pre-aligned HIV-1 clade B sequences as a measure of its degree of conservation. We then compared the entropy of empty versus epitope-containing positions and HLA-B-restricted versus HLA-A-restricted positions.
  
  
  RESULTS
  Positions containing CD8 epitopes were significantly more conserved than corresponding empty positions. Moreover, residues targeted by HLA-B alleles in the HIV-1 proteome were significantly more conserved than the ones targeted by HLA-A alleles. Analysing a recent dataset, we found that B epitope regions contain significantly more escape mutations and reversions, which might be the reason why we find them to be more conserved.
  
  
  CONCLUSIONS
  Our results suggest that epitopes in HIV-1 targeted by HLA-B alleles lie in more constrained regions of its proteins, in which mutations might have a higher fitness cost and tend to revert. Consequently, HLA-B-restricted cytotoxic T-lymphocyte (CTL) responses may persist longer. This may be one of the factors contributing to the immunodominance and impact of HLA-B-restricted CTL responses on disease progression.
authors.affiliation: Department of Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands.
authors.forename: Ana I
authors.initials: AI
authors.lastname: Fontaine Costa
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Rao
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lechenadec
authors.forename: Debbie
authors.initials: D
authors.lastname: van Baarle
authors.forename: Can
authors.initials: C
authors.lastname: Keşmir
mesh_terms: D017124:Conserved Sequence; D018450:Disease Progression; D019277:Entropy; D018984:Epitopes, T-Lymphocyte / Q000235:genetics* / Q000276:immunology; D015658:HIV Infections / Q000235:genetics* / Q000276:immunology; D015497:HIV-1 / Q000235:genetics*; D015235:HLA-B Antigens / Q000235:genetics* / Q000276:immunology; D006801:Humans; D016056:Immunodominant Epitopes / Q000235:genetics* / Q000276:immunology; D020543:Proteome / Q000235:genetics
chemical_list: D018984:Epitopes, T-Lymphocyte; D015235:HLA-B Antigens; D016056:Immunodominant Epitopes; D020543:Proteome