Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele.

Cellular immune response plays a central role in outcome of Hepatitis C Virus (HCV) infection. While specific T-cell responses are related to viral clearance, impaired responses can lead to chronic infection, turning HCV variability into a major obstacle for vaccine development. In a recent work, Fytili et al. (2008) studied the cross reactive potential of HCV specific CD8+ T-cells and observed a large variation in immunogenicity among 28 naturally occurring NS3(1073) variants. In this work, we intend to evaluate this immunogenic variation at molecular level, through bioinformatics approaches. The D1-EM-D2 strategy was used to build in silico MHC:peptide complexes (pMHC) of these HCV-derived peptides in the context of HLA-A*02:01 allele. The TCR-interacting surface of these complexes were evaluated using the GRASP2 program. Structural analysis indicated a sharing of topological and electrostatic features among complexes that induced strong response in vitro. Besides, complexes that induced low response presented an important positively charged spot in the center of TCR-interacting area. This spot was seen even in complexes with conservative amino acid changes and is consistent with the impairment of recognition by wild-type-specific T-cells, observed in vitro. Furthermore, the most remarkable difference in electrostatic potential was seen precisely in the only complex unable to induce in vitro stimulation. All these observations were confirmed by Principal Component Analysis (PCA) and this approach was also applied to a set of 45 non-related immunogenic viral epitopes, indicating possible new targets for cross-reactivity studies. Our results suggest structural in silico analysis of pMHC complexes as a reliable tool for vaccine development, affording to predict the impact of viral escape mutations and selection of epitopes with potential to induce cross-reactive immune responses.

[1]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[2]  R. Purcell,et al.  Viral and immunological determinants of hepatitis C virus clearance, persistence, and disease , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Ursula Esser,et al.  Mapping T-cell receptor–peptide contacts by variant peptide immunization of single-chain transgenics , 1992, Nature.

[4]  R. Bartenschlager,et al.  Relation between viral fitness and immune escape within the hepatitis C virus protease , 2005, Gut.

[5]  Fenglin Lv,et al.  Toward prediction of binding affinities between the MHC protein and its peptide ligands using quantitative structure-affinity relationship approach. , 2008, Protein and peptide letters.

[6]  Alessandro Sette,et al.  The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..

[7]  P. Klenerman,et al.  CD8+ T lymphocyte responses are induced during acute hepatitis C virus infection but are not sustained , 2000, European journal of immunology.

[8]  H. Wolfson,et al.  Principles of flexible protein–protein docking , 2008, Proteins.

[9]  Karina Yusim,et al.  Immunoinformatics Comes of Age , 2006, PLoS Comput. Biol..

[10]  R. Rappuoli.  Reverse vaccinology : Genomics , 2000 .

[11]  Robyn L Stanfield,et al.  How TCRs bind MHCs, peptides, and coreceptors. , 2006, Annual review of immunology.

[12]  M. Manns,et al.  Functional and phenotypic characterization of peptide-vaccine-induced HCV-specific CD8+ T cells in healthy individuals and chronic hepatitis C patients. , 2007, Vaccine.

[13]  M. Manns,et al.  Cross-genotype-reactivity of the immunodominant HCV CD8 T-cell epitope NS3-1073. , 2008, Vaccine.

[14]  M. Cucchiarini,et al.  Vigorous peripheral blood cytotoxic T cell response during the acute phase of hepatitis C virus infection. , 2000, Cellular immunology.

[15]  A. Canella,et al.  Effect of interferon‐α therapy on epitope‐specific cytotoxic T lymphocyte responses in hepatitis C virus‐infected individuals , 2002 .

[16]  Joo Chuan Tong,et al.  Immunoinformatics: Current trends and future directions , 2009, Drug Discovery Today.

[17]  Marc Bonneville,et al.  Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus Epitope1 , 2009, The Journal of Immunology.

[18]  Robert D Bremel,et al.  An integrated approach to epitope analysis II: A system for proteomic-scale prediction of immunological characteristics , 2010, Immunome research.

[19]  S. Green,et al.  Cross-subtype antibody and cellular immune responses induced by a polyvalent DNA prime-protein boost HIV-1 vaccine in healthy human volunteers. , 2008, Vaccine.

[20]  Barry Honig,et al.  GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. , 2003, Methods in enzymology.

[21]  R. Kaul,et al.  Characterization of Cross-Reactive CD8+ T-Cell Recognition of HLA-A2-Restricted HIV-Gag (SLYNTVATL) and HCV-NS5b (ALYDVVSKL) Epitopes in Individuals Infected with Human Immunodeficiency and Hepatitis C Viruses , 2010, Journal of Virology.

[22]  R. Schwendener,et al.  A liposomal peptide vaccine inducing CD8+ T cells in HLA-A2.1 transgenic mice, which recognise human cells encoding hepatitis C virus (HCV) proteins. , 2004, Vaccine.

[23]  B. Rehermann,et al.  Immunology of hepatitis B virus and hepatitis C virus infection , 2005, Nature Reviews Immunology.

[24]  A. Canella,et al.  Effect of interferon-alpha therapy on epitope-specific cytotoxic T lymphocyte responses in hepatitis C virus-infected individuals. , 2002, European Journal of Immunology.

[25]  A. Prince,et al.  Protection against chronic hepatitis C virus infection after rechallenge with homologous, but not heterologous, genotypes in a chimpanzee model. , 2005, The Journal of infectious diseases.

[26]  J. Chies,et al.  Immunodominant viral peptides as determinants of cross-reactivity in the immune system – Can we develop wide spectrum viral vaccines?☆ , 2005, Medical Hypotheses.

[27]  Maurício Menegatti Rigo,et al.  MHC: Peptide Analysis: Implications on the Immunogenicity of Hantaviruses' N protein , 2009, BSB.

[28]  J. Bennink,et al.  Cross-Reactivity between Hepatitis C Virus and Influenza A Virus Determinant-Specific Cytotoxic T Cells , 2001, Journal of Virology.

[29]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[30]  R. Rappuoli,et al.  Reverse vaccinology. , 2000, Current opinion in microbiology.

[31]  Marialva Sinigaglia,et al.  Structural Allele-Specific Patterns Adopted by Epitopes in the MHC-I Cleft and Reconstruction of MHC:peptide Complexes to Cross-Reactivity Assessment , 2010, PloS one.

[32]  P. Doherty,et al.  Structural determinants of T-cell receptor bias in immunity , 2006, Nature Reviews Immunology.

[33]  B. Chiang,et al.  A New Insight into Hepatitis C Vaccine Development , 2010, Journal of biomedicine & biotechnology.

[34]  H. Rammensee,et al.  SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.

[35]  M. Sakaki,et al.  Immune Response of Cytotoxic T Lymphocytes and Possibility of Vaccine Development for Hepatitis C Virus Infection , 2010, Journal of biomedicine & biotechnology.

[36]  Robert D Bremel,et al.  An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches , 2010, Immunome research.

[37]  T. Schumacher,et al.  The Impact of Self-Tolerance on the Polyclonal CD8+ T Cell Repertoire1 , 2004, The Journal of Immunology.