title: Distinct Escape Pathway by Hepatitis C Virus Genotype 1a from a Dominant CD8+ T Cell Response by Selection of Altered Epitope Processing.
abstract: Antiviral CD8(+) T cells are a key component of the adaptive immune response against HCV, but their impact on viral control is influenced by preexisting viral variants in important target epitopes and the development of viral escape mutations. Immunodominant epitopes highly conserved across genotypes therefore are attractive for T cell based prophylactic vaccines. Here, we characterized the CD8(+) T cell response against the highly conserved HLA-B*51-restricted epitope IPFYGKAI1373-1380 located in the helicase domain of NS3 in people who inject drugs (PWID) exposed predominantly to HCV genotypes 1a and 3a. Despite this epitope being conserved in both genotypes, the corresponding CD8(+) T cell response was detected only in PWID infected with genotype 3a and HCV-RNA negative PWID, but not in PWID infected with genotype 1a. In genotype 3a, the detection of strong CD8(+) T cell responses was associated with epitope variants in the autologous virus consistent with immune escape. Analysis of viral sequences from multiple cohorts confirmed HLA-B*51-associated escape mutations inside the epitope in genotype 3a, but not in genotype 1a. Here, a distinct substitution in the N-terminal flanking region located 5 residues upstream of the epitope (S1368P; P = 0.00002) was selected in HLA-B*51-positive individuals. Functional assays revealed that the S1368P substitution impaired recognition of target cells presenting the endogenously processed epitope. The results highlight that, despite an epitope being highly conserved between two genotypes, there are major differences in the selected viral escape pathways and the corresponding T cell responses.
  
  
  OBJECTIVE
  HCV is able to evolutionary adapt to CD8(+) T cell immune pressure in multiple ways. Beyond selection of mutations inside targeted epitopes, this study demonstrates that HCV inhibits epitope processing by modification of the epitope flanking region under T cell immune pressure. Selection of a substitution five amino acids upstream of the epitope underlines that efficient antigen presentation strongly depends on its larger sequence context and that blocking of the multistep process of antigen processing by mutation is exploited also by HCV. The pathways to mutational escape of HCV are to some extent predictable but are distinct in different genotypes. Importantly, the selected escape pathway of HCV may have consequences for the destiny of antigen-specific CD8(+) T cells.
authors.affiliation: Institute for Virology, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Walker
authors.affiliation: Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Skibbe
authors.affiliation: Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hanover and the Helmholtz Centre for Infection Research, Hanover, Germany.
authors.forename: Eike
authors.initials: E
authors.lastname: Steinmann
authors.affiliation: Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hanover and the Helmholtz Centre for Infection Research, Hanover, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Pfaender
authors.affiliation: Ragon Institute of MGH, MIT, and Harvard, Charlestown, Massachusetts, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kuntzen
authors.affiliation: Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Dominik A
authors.initials: DA
authors.lastname: Megger
authors.affiliation: Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
authors.forename: Svenja
authors.initials: S
authors.lastname: Groten
authors.affiliation: Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Sitek
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Georg M
authors.initials: GM
authors.lastname: Lauer
authors.affiliation: Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Arthur Y
authors.initials: AY
authors.lastname: Kim
authors.affiliation: Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hanover and the Helmholtz Centre for Infection Research, Hanover, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Pietschmann
authors.affiliation: Ragon Institute of MGH, MIT, and Harvard, Charlestown, Massachusetts, USA.
authors.forename: Todd M
authors.initials: TM
authors.lastname: Allen
authors.affiliation: Institute for Virology, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany joerg.timm@med.uni-duesseldorf.de.
authors.forename: Joerg
authors.initials: J
authors.lastname: Timm
mesh_terms: D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D015331:Cohort Studies; D005838:Genotype; D059949:HLA-B51 Antigen / Q000378:metabolism; D016174:Hepacivirus / Q000235:genetics / Q000276:immunology*; D006526:Hepatitis C / Q000276:immunology*; D006801:Humans; D057131:Immune Evasion; D016056:Immunodominant Epitopes / Q000235:genetics / Q000276:immunology*; D009154:Mutation; D015819:Substance Abuse, Intravenous / Q000150:complications; D017361:Viral Nonstructural Proteins / Q000235:genetics / Q000276:immunology*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D059949:HLA-B51 Antigen; D016056:Immunodominant Epitopes; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases