Large‐scale computational identification of HIV T‐cell epitopes

Bioinformatics‐driven T‐cell epitope‐identification methods can enhance vaccine target selection significantly. We evaluated three unrelated computational methods to screen Pol, Gag and Env sequences extracted from the Los Alamos HIV database for HLA‐A∗0201 and HLA‐B∗3501 T‐cell epitope candidates. The hidden Markov model predicted 389 HLA‐B∗3501‐restricted candidates from 374 HIV‐1 and 97 HIV‐2 sequences. The artificial neural network (ANN) model, and Bioinformatics and Molecular Analysis Section (BIMAS) quantitative matrix predictions for A∗0201 yielded 1122 HIV‐1 and 548 HIV‐2 candidates. The overall sequence coverage of the predicted A∗0201 T‐cell epitopes was 2.7% (HIV‐1) and 3.0% (HIV‐2). HLA‐B∗3501‐predicted epitopes covered 0.9% (HIV‐1) and 1.4% (HIV‐2) of the total sequence. Comparison of 890 ANN‐ and 397 BIMAS‐derived HIV‐1 A∗0201‐restricted epitope candidates showed that only 13‐19% of the predicted and 26% of the experimentally confirmed T‐cell epitopes were captured by both methods. Extrapolating these results, we estimated that at least 247 predicted HIV‐1 epitopes are yet to be discovered as active A∗0201‐restricted T‐cell epitopes. Adequate comparison and combined usage of various predictive bioinformatics methods, rather than uncritical use of any single prediction method, will enable cost‐effective and efficient T‐cell epitope screening.

[1]  A. D. De Groot,et al.  An interactive Web site providing major histocompatibility ligand predictions: application to HIV research. , 1997, AIDS research and human retroviruses.

[2]  A. Tolstrup,et al.  Functional screening of a retroviral peptide library for MHC class I presentation. , 2001, Gene.

[3]  M A Nowak,et al.  Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. , 1998, Science.

[4]  G. Shaw,et al.  Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection , 1994, Journal of virology.

[5]  R. Phillips,et al.  Patterns of Immunodominance in HIV-1–specific Cytotoxic T Lymphocyte Responses in Two Human Histocompatibility Leukocyte Antigens (HLA)-identical Siblings with HLA-A*0201 Are Influenced by Epitope Mutation , 1997, The Journal of experimental medicine.

[6]  S. Rowland-Jones,et al.  Cytotoxic T cell responses to multiple conserved HIV epitopes in HIV-resistant prostitutes in Nairobi. , 1998, The Journal of clinical investigation.

[7]  Vladimir Brusic,et al.  MHCPEP, a database of MHC-binding peptides: update 1996 , 1997, Nucleic Acids Res..

[8]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[9]  W. Blattner,et al.  Efficient Processing of the Immunodominant, HLA-A*0201-Restricted Human Immunodeficiency Virus Type 1 Cytotoxic T-Lymphocyte Epitope despite Multiple Variations in the Epitope Flanking Sequences , 1999, Journal of Virology.

[10]  H Mamitsuka,et al.  Predicting peptides that bind to MHC molecules using supervised learning of hidden markov models , 1998, Proteins.

[11]  Limsoon Wong,et al.  FIMM, a database of functional molecular immunology , 2000, Nucleic Acids Res..

[12]  P. Klenerman,et al.  The influence of antigenic variation on cytotoxic T lymphocyte responses in HIV-1 infection , 1998, Journal of Molecular Medicine.

[13]  K. Parker,et al.  Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. , 1994, Journal of immunology.

[14]  Michael A. Gonzalez,et al.  From genome to vaccine: in silico predictions, ex vivo verification. , 2001, Vaccine.

[15]  Mark Lindsey,et al.  Complexity among constituents of the HLA-B*1501 peptide motif , 1998, Immunogenetics.

[16]  John Sidney,et al.  Identification of Novel HLA-A2-Restricted Human Immunodeficiency Virus Type 1-Specific Cytotoxic T-Lymphocyte Epitopes Predicted by the HLA-A2 Supertype Peptide-Binding Motif , 2001, Journal of Virology.

[17]  C. Schönbach,et al.  Fine tuning of peptide binding to HLA-B*3501 molecules by nonanchor residues. , 1995, Journal of immunology.

[18]  D. Flower,et al.  Toward the quantitative prediction of T-cell epitopes: coMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201. , 2001, Journal of medicinal chemistry.

[19]  J Zeleznikow,et al.  Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding. , 2001, Journal of molecular graphics & modelling.

[20]  R. Phillips,et al.  Antagonism of cytotoxic T lymphocyte‐mediated lysis by natural HIV‐1 altered peptide ligands requires simultaneous presentation of agonist and antagonist peptides , 1997, European journal of immunology.

[21]  M. McElrath,et al.  CD8 CTL responses in vaccines: emerging patterns of HLA restriction and epitope recognition. , 2001, Immunology letters.

[22]  P. Sharp,et al.  Genetic diversity of HIV-1: the moving target. , 2000, AIDS.

[23]  L C Harrison,et al.  MHCPEP: a database of MHC-binding peptides. , 1994, Nucleic acids research.

[24]  B. Walker,et al.  HIV-specific cytotoxic T lymphocytes in seropositive individuals , 1987, Nature.

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

[26]  N. Nathanson,et al.  Biological considerations in the development of a human immunodeficiency virus vaccine. , 2000, The Journal of infectious diseases.

[27]  S. H. van der Burg,et al.  HIV-1 reverse transcriptase-specific CTL against conserved epitopes do not protect against progression to AIDS. , 1997, Journal of immunology.

[28]  Edward C. Holmes,et al.  Clustered Mutations in HIV-1 Gag Are Consistently Required for Escape from Hla-B27–Restricted Cytotoxic T Lymphocyte Responses , 2001, The Journal of experimental medicine.

[29]  V. Brusic,et al.  Neural network-based prediction of candidate T-cell epitopes , 1998, Nature Biotechnology.

[30]  R. J. Stonier,et al.  Complex Systems: Mechanism of Adaptation , 1994 .

[31]  Steven M. Wolinsky,et al.  Eventual AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes , 2002, Nature.