Identification of CTL epitopes in hepatitis C virus by a genome-wide computational scanning and a rational design of peptide vaccine

Immunogenetics

Volumn 59, Issue 3, 2007, Pages 197-209

  Mashiba, Toshie ^a   Udaka, Keiko ^b,c   Hirachi, Yasuko ^b,c   Hiasa, Yoichi ^a   Miyakawa, Tomoya ^d   Satta, Yoko ^e   Osoda, Tsutomu ^d   Kataoka, Sayo ^b,c   Kohara, Michinori ^f   Onji, Morikazu ^a  

^a EHIME UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b KOCHI MEDICAL SCHOOL   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d NEC CORPORATION   (Japan)

^e GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^f TOKYO METROPOLITAN INSTITUTE OF MEDICAL SCIENCE   (Japan)

Author keywords

Cytotoxic T lymphocyte; Hepatitis C virus; HLA; Peptide; Vaccine

Indexed keywords

CORE PROTEIN; HLA A ANTIGEN; PEPTIDE DERIVATIVE; VIRUS VACCINE;

ANTIGEN PRESENTATION; ARTICLE; CD8+ T LYMPHOCYTE; CELLULAR IMMUNITY; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; DRUG BINDING; DRUG DESIGN; HEPATITIS C VIRUS; HUMAN; HUMAN CELL; HUMAN TISSUE; MATHEMATICAL COMPUTING; NUCLEOTIDE SEQUENCE; PERIPHERAL BLOOD MONONUCLEAR CELL; PRIORITY JOURNAL; VIRUS GENOME;

AMINO ACID SEQUENCE; ANTIGEN PRESENTATION; CELL LINE, TUMOR; CELLS, CULTURED; COMPUTER SIMULATION; CYTOSOL; EPITOPES, T-LYMPHOCYTE; GENOME; HEPACIVIRUS; HLA-A ANTIGENS; HUMANS; JAPAN; MOLECULAR SEQUENCE DATA; PHYLOGENY; T-LYMPHOCYTES, CYTOTOXIC; VACCINES, SUBUNIT;

HEPATITIS C VIRUS;

EID: 33846781213     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-006-0185-3     Document Type: Article

References (43)

1. Agnello V, Abel G, Knight G, Muchmore E (1998) Detection of widespread hepatocyte infection in chronic hepatitis C. Hepatology 28:573-584
2. Appay V, Nixon D, Donahoe S, Gillespie G, Dong T, King A, Ogg G, Spiegel H, Conlon C, Spina C, Havlir D, Richman D, Waters A, Easterbrook P, McMichael A, Rowland-Jones S (2000) HIV-specific CD8(+) T cells produce antiviral cytokines but are impaired in cytolytic function. J Exp Med 192:63-75
3. Battergay M, Fikes J, Di-Bisceglie A, Wentworth P, Sette A, Celis E, Ching W, Grakoui A, Rice C, Kurokohchi K, Berzofsky J, Hoofnagle J, Feinstone S, Akatsuka T (1995) Patients with chronic hapatitis C have circulating cytotoxic T cells which recognize hepatitis C virus-encoded peptides binding to HLA-A2.1 molecules. J Virol 69:2462-2470
4. Boettler T, Spangenberg H, Neumann-Haefelin C, Panther E, Urbani S, Ferrari C, Blum H, von Weizsaecker F, Thimme R (2005) T cells with a CD4+CD25+ regulatory phenotype suppress in vitro proliferation of virus-specific CD8+ T cells during chronic hepatitis C virus infection. J Virol 79:7860-7867
5. Cerny A, McHutchinson J, Pasquinelli C, Brown M, Brothers M, Grabsheid B, Fowler P, Houghton M, Chisari F (1995) Cytotoxic T lymphocyte response to hepatitis C virus-derived peptides containing the HLA A2.1 binding motif. J Clin Invest 95:521-530
6. Chang K, Rehermann B, McHutchison J, Pasquinelli C, Southwood S, Sette A, Chisari F (1997) Immunological significance of cytotoxic T lymphocyte epitope variants in patients chronically infected by the hepatitis C virus. J Clin Invest 100:2376-2385
7. Cox A, Mosbruger T, Mao Q, Liu Z, Wang X, Yang H, Sidney J, Sette A, Pardoll D, Thomas D, Ray S (2005) Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med 201:1741-1752
8. Day C, Seth N, Lucas M, Appel H, Gauthier L, Lauer G, Robbins G, Szczepiorkowski Z, Casson D, Chung R, Bell S, Harcourt G, Walker B, Klenerman P, Wucherpfennig K (2003) Ex vivo analysis of human memory CD4 T cells specific for hepatitis C virus using MHC class II tetramers. J Clin Invest 112:831-842
9. Edwards P, Smith C, Neville A, O'Hare M (1982) A human-human hybridoma system based on a fast-growing mutant of the ARH-77 plasma cell leukemia-derived line. Eur J Immunol 12:641-648
10. Erickson A, Kimura Y, Igarashi S, Eichelberger J, Houghton M, Sidney J, McKinney D, Sette A, Hughes, A Walker C (2001) The outcome of hepatitis C virus infection is predicted by escape mutations in epitopes targeted by cytotoxic T lymphocytes. Immunity 15:883-895
11. Feld J, Hoofnagle J (2005) Mechanism of action of interferon and ribavirin in treatment of hepatitis C. Nature 436:967-972
12. Grakoui A, Shoukry N, Woolland D, Han J, Hanson H, Ghrayeb J, Murthy K, Rice C, Walker C (2003) HCV persistence and immune evasion in the absence of memory T cell help. Science 302:659-662
13. Huang Y, BObholzer N, Fayad R, Qiao L (2005) Turning on/off tumor-specific CTL response during progressive tumor growth. J Immunol 175:3110-3116
14. Imanishi T, Akaza T, Kimura A, Tokunaga K Gojobori T (1992) Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds) The Eleventh International Histocompatibility Workshop and Conference Yokohama Japan. Oxford University Press
15. Kaneko T, Moriyama T, Udaka K, Hiroishi K, Kita H, Okamoto H, Yagita H, Okumura K, Imawari M (1997) Impaired induction of cytotoxic T lymphocytes by antagonism of a weak agonist borne by a variant hepatitis C virus epitope. Eur J Immunol 27:1782-1787
16. Karaki S, Kariyone A, Kato N, Kano K, Iwakura Y, Takiguchi M (1993) HLA-B51 transgenic mice as recipients for production of polymorphic HLA-A B-specific antibodies. Immunogenetics 37:139-142
17. Kimura Y, Gushima T, Rawale S, Kaumaya P, Walker C (2005) Escape mutations alter proteasome processing of major histocompatibility complex class I-restricted epitopes in persistent hepatitis C virus infection. J Virol 79:4870-4876
18. Kurokohchi K, Arima K, Nishioka M (2001) A novel cytotoxic T-cell epitope presented by HLA-A24 molecule in hepatitis C virus infection. J Hepatol 34:930-935
19. Lie W, Myers N, Gorka J, Rubocki R, Connolly J, Hansen T (1990) Peptide ligand-induced conformation and surface expression of the Ld class I MHC molecule. Nature 344:439-441
20. Nakamoto Y, Kaneko S, Takizawa H, Kikumoto Y, Takano M, Himeda Y (2003) Analysis of the CD8-positive T cell response in Japanese patients with chronic hepatitis C using HLA-A*2402 peptide tetramers. J Med Virol 70:51-61
21. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous substitutions. Mol Biol Evol 3:418-426
22. Nielsen M, Lundegaard C, Lund O, Kesmir C (2005) The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 57:33-41
23. Nouri-Aria K, ASallie R, Mizokami M, Portmann B, Williams R (1995) Intrahepatic expression of hepatitis C virus antigens in chronic liver disease. J Pathol 175:77-83
24. Nussbaum A, Kuttler C, Hadeler K, Rammensee H, Schild H (2001) PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics 53:87-94
25. Ray S, Fanning L, Wang X, Netski D, Kenny-Walsh E, Thomas D (2005) Divergent and convergent evolution after a common-source outbreak of hepatitis C virus. J Exp Med 201:1753-1759
26. Rushbrook S, Ward S, Unitt E, Vowler S, Lucas M, Klenerman P, Alexander G (2005) Regulatory T cells suppress in vitro proliferation of virus-specific CD8+ T cells during persistent hepatitis C virus infection. J Virol 79:7852-7859
27. Seifert U, Liermann H, Racanelli V, Halenius A, Wiese M, Wedemeyer H, Ruppert T, Rispeter K, Henklein P, Sijts A, Hengel H, Kloetzel P, Rehermann B (2004) Hepatitis C virus mutation affects proteasomal epitope processing. J Clin Invest 114:250-259
28. Semmo N, Day C, Ward S, Lucas M, Harcourt G, Loughry A, Klenerman P (2005) Preferential loss of IL-2-secreting CD4+ T helper cells in chronic HCV infection. Hepatology 41:1019-1028
29. Sugimoto K, Ikeda F, Standanlick J, Nunes F, Alter H, Chang K (2003) Suppression of HCV-specific T cells without differential hierarchy demonstrated ex vivo in persistent HCV infection. Hepatology 38:1437-1448
30. Tahara T, Yang S, Khan R, Abish S, Haemmerling G, Haemmerling U (1990) HLA antibody responses in HLA class I transgenic mice. Immunogenetics 32:351-360
31. Tanaka H, Akaza T, Juji T (1996) Report of the Japanese central bone marrow data center. Clin Transpl 139-144
32. Tester I, Smyk-Pearson S, Wang P, Wertheimer A, Yao E, Lewinsohn D, Tavis J, Rosen H (2005) Immune evasion versus recovery after acute hepatitis C virus infection from a shared source. J Exp Med 201:1725-1731
33. Thimme R, Bukh J, Spangenberg H, Wieland S, Pemberton J, Steiger C, Govindarajan S, Purcell R, Chisari F (2002) Viral and immunological determinants of hepatitis C virus clearance persistence and disease. Proc Natl Acad Sci USA 99:15661-15668
34. Timm J, Lauer G, Kavanagh D, Sheridan I, Kim A, Lucas M, Pillay T, Ouchi K, Reyor L, Schulze zur Wiesch J, Gandhi R, Chung R, Bhardwaj N, Klenerman P, Walker B, Allen T (2004) CD8 epitope escape and reversion in acute HCV infection. J Exp Med 200:1593-1604
35. Tokunaga K, Ishikawa Y, Ogawa A, Wang H, Mitsunaga S, Moriyama S, Lin L, Bannnai M, Watanabe Y, Kashiwase K, Tankaa H, Akaza T, Tadokoro K, Juji T (1997) Sequence-based association analysis of hLA class I and II alleles in Japanese supports conservation of common haplotypes. Immunogenetics 46:199-205
36. Tsubota A, Arase Y, Suzuki F, Suzuki Y, Akuta N, Hosaka T, Someya T, Kobayashi M, Saitoh S, Ikeda K, Kumada H (2004) High-dose interferon alpha-2b induction therapy in combination with ribavirin for Japanese patients infected with hepatitis C virus genotype 1b with a high baseline viral load. J Gastroenterol 39:155-161
37. Tsukiyama-Kohara K, Tone S, Maruyama I, Inoue K, Katsume A, Nuriya H, Ohmori H, Ohkawa J, Taira K, Hoshikawa Y, Shibasaki F, Reth M, Minatogawa Y, Kohara M (2004) Activation of the CK1-CDK-Rb-E2F pathway in full genome hepatitis C virus-expressing cells. J Biol Chem 15:14531-14541
38. Udaka K, Wiesmueller K.-H, Kienle S, Jung G, Tamamura H, Yamagishi H, Okumura K, Walden P, Suto T, Kawasaki T (2000) An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics 51:816-828
39. Udaka K, Mamitsuka H, Nakaseko Y, Abe N (2002) Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides. J Immunol 169:5744-5753
40. Valitutti S, Mueller S, Dessing M, Lanzavecchia A (1996) Different responses are elicited in cytotoxic T lymphocytes by different levels of T cell receptor occupancy. J Exp Med 183:1917-1921
41. Weiner A, Erickson A, Kansopon J, Crawford K, Muchmore E, Hughes A, Houghton M, Walker C (1995) Persistent hepatitis C virus infection in a chimpanzee is associated with emergence of a cytotoxic T lymphocyte escape variant. Proc Natl Acad Sci USA 92:2755-2759
42. Wherry E, Blattman J, Murali-Krishna K, vander Most R, Ahmed R (2003) Viral persistance alters CD8 T-cell immunodominance and tissue distribution and results in distinct stages of functional impairment. J Virol 77:4911-4927
43. Zeh H III, Leder G, Lotze M, Salter R, Tector M, Stuber G, Modrow S, Storkus W (1994) Flow-cytometric determination of peptide-class I complex formation. Identification of p53 peptides that bind to HLA-A2. Hum Immunol 39:79-86