Immunoinformatics analysis of H5N1 proteome for designing an epitope-derived vaccine and predicting the prevalence of pre-existing cellular-mediated immunity toward bird flu virus in Indonesian population

Immunome Research

Volumn 7, Issue 3, 2011, Pages

  Gustiananda, Marsia ^a  

^a EIJKMAN INSTITUTE FOR MOLECULAR BIOLOGY   (Indonesia)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; PROTEOME;

ALLELE; AMINO ACID SEQUENCE; AUTOIMMUNITY; AVIAN INFLUENZA; B LYMPHOCYTE; BACTERIAL STRAIN; BINDING AFFINITY; CELLULAR IMMUNITY; CONFERENCE PAPER; HLA SYSTEM; HUMAN; IMMUNOASSAY; INDONESIA; INFLUENZA VIRUS A H5N1; NONHUMAN; PREDICTIVE VALUE; PREVALENCE; VACCINATION;

AVES; INFLUENZA A VIRUS;

EID: 84866986274     PISSN: None     EISSN: 17457580     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (50)

1. McMichael AJ, Gotch FM, Noble GR, Beare PAS: Cytotoxic T-cell immunity to influenza. N. Engl. J. Med 1983, 309:13-17. (Pubitemid 13062888)
2. Epstein SL: Prior H1N1 influenza infection and susceptibility of Cleveland Family Study participants during the H2N2 pandemic of 1957: an experiment of nature. J Infect Dis 2006, 193:49-53.
3. Jameson J, Cruz J, Terajima M, Ennis FA: Human CD8+ and CD4+ T Lymphocyte Memory to Influenza A Viruses of Swine and Avian Species. The Journal of Immunology 1999, 162:7578-7583. (Pubitemid 29277740)
4. Gioia C, Castilletti C, Tempestilli M, Piacentini P, Bordi L, Chiappini R, Agrati C, Squarcione S, Ippolito G, Puro V, Capobianchi MR, Poccia F: Cross-subtype immunity against avian influenza in persons recently vaccinated for influenza. Emerg Infect Dis 2008, 14:121-128.
5. Kreijtz JH, de Mutsert G, van Baalen CA, Fouchier RA, Osterhaus AD, Rimmelzwaan GF: Cross-recognition of avian H5N1 influenza virus by human cytotoxic T-lymphocyte populations directed to human influenza A virus. J Virol 2008, 82:5161-5166. (Pubitemid 351705225)
6. Roti M, Yang J, Berger D, Huston L, James EA, Kwok WW: Healthy Human Subjects Have CD4+ T-cells Directed Against H5N1 Influenza Virus. The Journal of Immunology 2008, 180:1758-1768.
7. Lee LY, Ha Do LA, Simmons C, de Jong MD, Chau NV, Schumacher R, Peng YC, McMichael AJ, Farrar JJ, Smith GL, Townsend AR, Askonas BA, Rowland-Jones S, Dong T: Memory T-cells established by seasonal human influenza A infection cross-react with avian influenza A (H5N1) in healthy individuals. J Clin Invest 2008, 118:3478-3490.
8. Tu W, Mao H, Zheng J, Liu Y, Chiu SS, Qin G, Chan PL, Lam KT, Guan J, Zhang L, Guan Y, Yuen KY, Peiris JS, Lau YL: Cytotoxic T lymphocytes established by seasonal human influenza cross-react against 2009 pandemic H1N1 influenza virus. J Virol 2010, 84:6527-6535.
9. Ge X, Tan V, Bollyky PL, Standifer NE, James EA, Kwok WW: Assessment of seasonal influenza A virus-specific CD4 T-cell responses to 2009 pandemic H1N1 swine-origin influenza A virus. J Virol 2010, 84:3312-3319.
10. Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B: Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A 2009, 106:20365-20370.
11. De Groot AS, Ardito M, McClaine EM, Moise L, Martin WD: Immunoinformatic comparison of T-cell epitopes contained in novel swine -origin influenza A (H1N1) virus with epitopes in 2008-2009 conventional influenza vaccine. Vaccine 2009, 27:5740-5747.
12. De Jong MD, Tran TT, Truong HK, Vo MH, Smith GJ, Nguyen VC, Bach VC, Phan TQ, Do QH, Guan Y, Peiris JS, Tran TH, Farrar J: Oseltamivir resistance during treatment of influenza A (H5N1) infection. N Engl J Med. 2005, 353:2667-2672. (Pubitemid 41817715)
13. Kandun IN, Tresnaningsih E, Purba WH, Lee V, Samaan G, Harun S, Soni E, Septiawati C, Setiawati T, Sariwati E, Wandra T: Factors associated with case fatality of human H5N1 virus infections in Indonesia: a case series. Lancet 2008, 372:744-749.
14. Kreijtz JH, Bodewes R, van den Brand JM, de Mutsert G, Baas C, van Amerongen G, Fouchier RA, Osterhaus AD, Rimmelzwaan GF: Infection of mice with a human influenza A/H3N2 virus induces protective immunity against lethal infection with influenza A/H5N1 virus. Vaccine 2009, 27:4983-4989.
15. Epstein SL, Tumpey TM, Misplon JA, Lo CY, Cooper LA, Subbarao K, Renshaw M, Sambhara S, Katz JM: DNA vaccine expressing conserved influenza virus proteins protective against H5N1 challenge infection in mice. Emerg Infect Dis 2002, 8:796-801.
16. Lafuente EM, Reche PA: Prediction of MHC-peptide binding: a systematic and comprehensive overview. Curr Pharm Des 2009, 15:3209-3220.
17. Lalvani A, Brookes R, Wilkinson RJ, Malin AS, Pathan AA, Andersen P, Dockrell H, Pasvol G, Hill AV: Human cytolytic and interferon gamma-secreting CD8+ T lymphocytes specific for Mycobacterium tuberculosis. Proc Natl Acad Sci USA 1998, 95: 270-275. (Pubitemid 28103943)
18. Altman JD, Moss PA, Goulder PJ, Barouch DH, McHeyzer-Williams MG, Bell JI, McMichael AJ, Davis MM: Phenotypic analysis of antigen-specific T lymphocytes. Science 1996, 27:94-96. (Pubitemid 26332731)
19. Asemissen AM, Nagorsen D, Keilholz U, Letsch A, Schmittel A, Thiel E, Scheibenbogen C: Flow cytometric determination of intracellular or secreted IFN gamma for the quantification of antigen reactive T-cells. J. Immunol. Meth 2001, 251:101-108. (Pubitemid 32261061)
20. Sette A, Sidney J: HLA supertypes and supermotifs: a functional perspective on HLA polymorphism. Curr Opin Immunol 1998, 10:478-482. (Pubitemid 28393833)
21. Sidney J, Peters B, Frahm N, Brander C, Sette A: HLA class I supertypes: a revised and updated classification. BMC Immunol 2008, 9:1.
22. De Groot AS, Sbai H, Aubin CA, McMurry J, Martin W: Immunoinformatic: Mining genomes for vaccine components. Immunology and Cell Biology 2002, 80:255-269. (Pubitemid 34639376)
23. Khan AM, Miotto O, Heiny AT, Salmon J, Srinivasan KN, Nascimento E, Marques ET, Brusic V, Tan TW, and August JT. A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol 2006, 244:141-147. (Pubitemid 46733910)
24. Heiny AT, Miotto O, Srinivasan KN, Khan AM, Zhang GL, Brusic V, Tan TW, August JT: Evolutionarily conserved protein sequences of influenza A viruses, avian and human, as vaccine targets. Plos ONE 2007, 2:e1190.
25. Wang M, Lamberth K, Harndahl M, Røder G, Stryhn A, Larsen MV, Nielsen M, Lundegaard C, Tang ST, Dziegel MH, Rosenkvist J, Pedersen AE, Buus A, Claesson MH, Lund O: CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. Vaccine 2007, 25:2823-2831. (Pubitemid 46420615)
26. Parida R, Shaila MS, Mukherjee S, Chandra NR, Nayak R: Computational analysis of proteome of H5N1 avian influenza virus to define T-cell epitopes with vaccine potential. Vaccine 2007, 25:7530-7539. (Pubitemid 47503496)
27. Somvanshi P, Singh V, Seth PK: Prediction of epitopes in hemagglutinin and neuraminidase proteins of influenza A virus H5N1 strain: a clue for diagnostic and vaccine development. OMICS 2008, 12:61-69. (Pubitemid 351341557)
28. Khurana S, Suguitan AL Jr, Rivera Y, Simmons CP, Lanzavecchia A, Sallusto F, Manischewitz J, King LR, Subbarao K, Golding H: Antigenic fingerprinting of H5N1 avian influenza using convalescent sera and monoclonal antibodies reveals potential vaccine and diagnostic targets. PLoS Med 2009, 6:e1000049.
29. Sun L, Lu X, Li C, Wang M, Liu Q, Li Z, Hu X, Li J, Liu F, Li Q, Belser JA, Hancock K, Shu Y, Katz JM, Liang M, Li D: Generation, characterization and epitope mapping of two neutralizing and protective human recombinant antibodies against influenza A H5N1 viruses. PLoS One 2009, 4:e5476.
30. Kashyap AK, Steel J, Oner AF, Dillon MA, Swale RE, Wall KM, Perry KJ, Faynboym A, Ilhan M, Horowitz M, Horowitz L, Palese P, Bhatt RR, Lerner RA: Combinatorial antibody libraries from survivors of the Turkish H5N1 avian influenza outbreak reveal virus neutralization strategies. Proc Natl Acad Sci USA 2008, 105:5986-5991. (Pubitemid 351758386)
31. Sun Y, Liu J, Yang M, Gao F, Zhou J, Kitamura Y, Gao B, Tien P, Shu Y, Iwamoto A, Chen Z, Gao GF: Identification and structural definition of H5-specific CTL epitopes restricted by HLA-A*0201 derived from the H5N1 subtype of influenza A viruses. J Gen Virol 2010, 91:919-930.
32. Yuliwulandari R, Kashiwase K, Nakajima H, Uddin J, Susmiarsih TP, Sofro AS, Tokunaga K: Polymorphisms of HLA genes in Western Javanese (Indonesia): close affinities to Southeast Asian populations. Tissue Antigens 2009, 73:46-53.
33. Lal G, Shaila MS, Nayak R: Activated mouse T-cells downregulate, process and present their surface TCR to cognate anti-idiotypic CD4+ T-cells. Immunol Cell Biol 2006, 84:145-153. (Pubitemid 43344668)
34. Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V: Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol 2008, 16:8.
35. Stranzl T, Larsen MV, Lundegaard C, Nielsen M: NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics 2010, 62:357-368.
36. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A: A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 2006, 24:817-819. (Pubitemid 44086622)
37. Assarsson E, Bui HH, Sidney J, Zhang Q, Glenn J, Oseroff C, Mbawuike IN, Alexander J, Newman MJ, Grey H, Sette A: Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans. J Virol 2008, 82:12241-12251.
38. Hiromoto Y, Yamazaki Y, Fukushima T, Saito T, Lindstrom SE, Omoe K, Nerome R, Lim W, Sugita S, Nerome K: Evolutionary characterization of the six internal genes of H5N1 human influenza A virus. J Gen Virol 2000, 81:1293-1303. (Pubitemid 30232715)
39. Garten RJ., Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ: Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009, 325:197-201.
40. Neumann G, Noda T, Kawaoka Y: Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 2009, 459:731-739.
41. Octaviani CP, Ozawa M, Yamada S, Goto H, Kawaoka Y: High genetic compatibility between swine-origin H1N1 and highly pathogenic avian H5N1 influenza viruses. J Virol 2010, 84:10918-10922.
42. Wang TT, Palese P. Universal epitopes of influenza virus hemagglutinins?. Nat Struct Mol Biol 2009, 16:233-234.
43. González S, Zürcher T, Ortín J: Identification of two separate domains in the influenza virus PB1 protein involved in the interaction with the PB2 and PA subunits: a model for the viral RNA polymerase structure. Nucleic Acids Research 1996, 24: 4456-4463.
44. Poole E, Elton D, Medcalf L, Digard P: Functional domains of the influenza A virus PB2 protein: identification of NP- and PB1-binding sites. Virology 2004, 321: 120-133. (Pubitemid 38368109)
45. Gomard E, Sitbon M, Toubert A, Begue B, Levy JP: HLA-B27, a dominant restricting element in antiviral responses?. Immunogenetics 1984, 20:197-204. (Pubitemid 14058353)
46. López de Castro JA: HLA-B27: portraying immunodominant viral epitopes. Eur J Immunol 2005, 35:336-340.
47. Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V: Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatic. 2008, 9 Suppl 12:S22.
48. Wang M, Larsen MV, Nielsen M, Harndahl M, Justesen S, Dziegiel MH, Buus S, Tang ST, Lund O, Claesson MH: HLA class I binding 9mer peptides from influenza A virus induce CD4 T-cell responses. PLoS One 2010, 5:e10533.
49. Tan PT, Heiny AT, Miotto O, Salmon J, Marques ET, Lemonnier F, August JT: Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLoS One 2010, 5:e8754.
50. Biddison WE, Martin R: Peptide binding motifs for MHC class I and II molecules. Curr Protoc Immunol 2001, Appendix 1: Appendix 1I.