Immunoinformatics and modeling perspective of t cell epitope-based cancer immunotherapy: A holistic picture

Journal of Biomolecular Structure and Dynamics

Volumn 27, Issue 3, 2009, Pages 293-305

  Mishra, Seema ^a   Sinha, Subrata ^a  

^a ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

Altered Peptide Ligands; Cancer Immunotherapy; Computer Aided Vaccine Design; Cryptic Epitopes; Immunoinformatics; Molecular Dynamics; Molecular Modeling; Promiscuous Epitopes; Systems Biology; T Cell Epitope

Indexed keywords

CANCER VACCINE; EPITOPE;

CANCER CELL; CANCER IMMUNOTHERAPY; GENETIC POLYMORPHISM; HELPER CELL; IMMUNE RESPONSE; IMMUNOGENICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN PROCESSING; REGULATORY T LYMPHOCYTE; REVIEW; T LYMPHOCYTE;

HARNESS;

EID: 70349912672     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2009.10507317     Document Type: Article

References (104)

1. Lizée, G., Cantu, M. A., and Hwu, P., 2007. Clin Cancer Res, 13:5250–5255.
2. Lizée, G., Radvanyi, L. G., Overwijk, W. W., and Hwu, P., 2006. Clin Cancer Res, 12:4794–4803.
3. Knutson, K. L., Schiffman, K., Cheever, M. A., and Disis, M. L., 2002. Clin Cancer Res, 8:1014–1018.
4. Coulie, P. G., and van der Bruggen, P., 2003. Curr Opin Immunol, 15:131–137.
5. Odunsi, K., Qian, F., Matsuzaki, J., Mhawech-Fauceglia, P., Andrews, C., and et al. 2007. Proc Natl Acad Sci USA, 104:12837–12842.
6. Bocchia, M., Gentili, S., Abruzzese, E., Fanelli, A., Iuliano, F., and et al. 2005. Lancet, 365:657–662.
7. Mishra, S., and Sinha, S., 2006. J Biomol Struct Dyn, 24:109–121.
8. Kobayashi, H., Lu, J., and Celis, E., 2001. Cancer Res, 61:7577–7584.
9. Lu, J., and Celis, E., 2000. Cancer Res, 60:5223–5227.
10. Consogno, G., Manici, S., Facchinetti, V., Bachi, A., Hammer, J., and et al. 2003. Blood, 101:1038–1044.
11. Asemissen, A. M., Keilholz, U., Tenzer, S., Müller, M., Walter, S., Stevanovic, S., and et al. 2006. Clin Cancer Res, 12:7476–7482.
12. Kobayashi, H., Nagato, T., Sato, K., Aoki, N., Kimura, S., and et al. 2007. Cancer Res, 67:5498–5504.
13. Panina-Bordignon, P., Tan, A., Termijtelen, A., Demotz, S., Corradin, G., and Lanzavecchia, A., 1989. Eur J Immunol, 19:2237–2242.
14. Parker, K. C., Bednarek, M. A., and Coligan, J. E., 1994. J Immunol, 152:163–175.
15. Rammensee, H. G., Friede, T., and Stevanoviíc, S., 1995. Immunogenetics, 41:178–228.
16. Singh, H., and Raghava, G. P., 2003. Bioinformatics, 19:1009–1014.
17. Singh, H., and Raghava, G. P., 2001. Bioinformatics, 17:1236–1237.
18. Zhang, G. L., Khan, A. M., Srinivasan, K. N., August, J. T., and Brusic, V., 2005. Nucleic Acids Res, 33:W172–W179.
19. Buus, S., Lauemoller, S. L., Worning, P., Kesmir, C., Frimurer, T., and et al. 2003. Tissue Antigens, 62:378–384.
20. Nielsen, M., Lundegaard, C., Worning, P., Lauemoller, S. L., Lamberth, K., and et al. 2003. Protein Sci, 12:1007–1017.
21. Nielsen, M., Lundegaard, C., Worning, P., Hvid, C. S., Lamberth, K., and et al. 2004. Bioinformatics, 20:1388–1397.
22. Guan, P., Hattotuwagama, C. K., Doytchinova, I. A., and Flower, D. R., 2006. Appl Bioinformatics, 5:55–61.
23. Bhasin, M., and Raghava, G. P., 2003. Hybrid Hybridomics, 22:229–234.
24. Nielsen, M., Lundegaard, C., Blicher, T., Lamberth, K., Harndahl, M., and et al. 2007. PLoS ONE, 2 (8):e796 (a)
25. Schueler-Furman, O., Altuvia, Y., Sette, A., and Margalit, H., 2000. Protein Sci, 9:1838–1846.
26. Schiewe, A. J., and Haworth, I. S., 2007. J Mol Graph Model, 26:667–675.
27. Tong, J. C., Zhang, Z. H., August, J. T., Brusic, V., Tan, T. W., and Ranganathan, S., 2007. Immunome Res, 3:7
28. Nussbaum, A. K., Kuttler, C., Hadeler, K. P., Rammensee, H. G., and Schild, H., 2001. Immunogenetics, 53:87–94.
29. Holzhütter, H. G., and Kloetzel, P. M., 2000. Biophys J, 79:1196–1205.
30. Holzhütter, H. G., Frömmel, C., and Kloetzel, P. M., 1999. J Mol Biol, 286:1251–1265.
31. Keşmir, C., Nussbaum, A. K., Schild, H., Detours, V., and Brunak, S., 2002. Protein Eng, 15:287–296.
32. Bhasin, M., and Raghava, G. P., 2005. Nucleic Acids Res, 33:W202–W207.
33. Bhasin, M., and Raghava, G. P., 2004. Protein Sci, 13:596–607.
34. Zhang, G. L., Petrovsky, N., Kwoh, C. K., August, J. T., and Brusic, V., 2006. Immunome Res, 2 (1):3
35. Ressing, M. E., Sette, A., Brandt, R. M., Ruppert, J., Wentworth, P. A., and et al. 1995. J Immunol, 154:5934–5943.
36. Yang, S., Linette, G. P., Longerich, S., Roberts, B. L., and Haluska, F. G., 2000. Cell Immunol, 204:29–37.
37. Sette, A., Vitiello, A., Reherman, B., Fowler, P., Nayersina, R., and et al. 1994. J Immunol, 153:5586–5592.
38. Madden, D. R., Garboczi, D. N., and Wiley, D. C., 1993. Cell, 75:693–708.
39. Doytchinova, I. A., Walshe, V. A., Jones, N. A., Gloster, S. E., Borrow, P., and Flower, D. R., 2004. J Immunol, 172:7495–7502.
40. Fagerberg, T., Cerottini, J. C., and Michielin, O., 2006. J Mol Biol, 356:521–546.
41. Hakenberg, J., Nussbaum, A. K., Schild, H., Rammensee, H. G., Kuttler, C., and et al. 2003. Appl Bioinformatics, 2:155–158.
42. Doytchinova, I. A., Guan, P., and Flower, D. R., 2006. BMC Bioinformatics, 7:131
43. Larsen, M. V., Lundegaard, C., Lamberth, K., Buus, S., Brunak, S., and et al. 2005. Eur J Immunol, 35:2295–2303.
44. Florea, L., Halldorsson, B., Kohlbacher, O., Schwartz, R., Hoffman, S., and Istrail, S., 2003. “ IEEE Computer Society ”. In Proceedings of the Computational Systems Bioinformatics (CSB'03)
45. De Groot, A. S., and Berzofsky, J. A., 2004. Methods, 34:425–428.
46. Peters, B., Bui, H. H., Frankild, S., Nielson, M., Lundegaard, C., and et al. 2006. PLoS Comput Biol, 2 (6):e65
47. Korber, B., LaBute, M., and Yusim, K., 2006. PloS Comput Biol, 2 (6):e71
48. Trost, B., Bickis, M., and Kusalik, A., 2007. Immunome Res, 3:5
49. Peters, B., Sidney, J., Bourne, P., Bui, H. H., Buus, S., and et al. 2005. PLoS Biol, 3:e91
50. Lefranc, M-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., and et al. 2005. Nucleic Acids Res, 33:D593–D597.
51. Toseland, C. P., Clayton, D. J., McSparron, H., Hemsley, S. L., Blythe, M. J., and et al. 2005. Immunome Res, 1:4
52. Reche, P. A., Zhang, H., Glutting, J. P., and Reinherz, E. L., 2005. Bioinformatics, 21:2140–2141.
53. Bhasin, M., Singh, H., and Raghava, G. P., 2003. Bioinformatics, 19:665–666.
54. Heckerman, D., Kadie, C., and Listgarten, J., 2007. J Comput Biol, 14:736–746.
55. Slingluff, C. L., Jr., Petroni, G. R., Chianese-Bullock, K. A., Smolkin, M. E., Hibbitts, S., and et al. 2007. Clin Cancer Res, 13:6386–6395.
56. Eggers, M., Boes-Fabian, B., Ruppert, T., Kloetzel, P. M., and Koszinowski, U. H., 1995. J Exp Med, 182:1865–1870.
57. van Endert, P. M., Riganelli, D., Greco, G., Fleischhauer, K., Sidney, J., and et al. 1995. J Exp Med, 182:1883–1895.
58. Uebel, S., Kraas, W., Kienle, S., Wiesmüller, K. H., Jung, G., and Tampé, R., 1997. Proc Natl Acad Sci USA, 94:8976–8981.
59. Hennecke, J., and Wiley, D. C., 2001. Cell, 104:1–4.
60. Stuge, T. B., Holmes, S. P., Saharan, S., Tuettenberg, A., Roederer, M., and et al. 2004. PLoS Med, 1:e28
61. Clay, T. M., Custer, M. C., McKee, M. D., Parkhurst, M., Robbins, P. F., and et al. 1999. J Immunol, 162:1749–1755.
62. Iero, M., Squarcina, P., Romero, P., Guillaume, P., Scarselli, E., and et al. 2007. Cancer Immunol Immunother, 56:1979–1991.
63. Parkhurst, M. R., Salgaller, M. L., Southwood, S., Robbins, P. F., Sette, A., and et al. 1996. J Immunol, 157:2539–2548.
64. Trojan, A., Witzens, M., Schultze, J. L., Vonderheide, R. H., Harig, S., and et al. 2001. Cancer Res, 61:4761–4765.
65. Tangri, S., Ishioka, G. Y., Huang, X., Sidney, J., Southwood, S., and et al. 2001. J Exp Med, 194:833–846.
66. Tang, Y., Lin, Z., Ni, B., Wei, J., Han, J., and et al. 2007. Cancer Immunol Immunother, 56:319–329.
67. Chen, J. L., Stewart-Jones, G., Bossi, G., Lissin, N. M., Wooldridge, L., and et al. 2005. J Exp Med, 201:1243–1255.
68. Powell, D. J., Jr. and Rosenberg, S. A., 2004. J Immunother (1997), 27:36–47.
69. Romero, P., Gervois, N., Schneider, J., Escobar, P., Valmori, D., and et al. 1997. J Immunol, 159:2366–2374.
70. Valmori, D., Gervois, N., Rimoldi, D., Fonteneau, J. F., Bonelo, A., and et al. 1998. J Immunol, 161:6956–6962. (a)
71. Valmori, D., Fonteneau, J. F., Lizana, C. M., Gervois, N., and et al. 1998. J Immunol, 160:1750–1758. (b)
72. Salazar, E., Zaremba, S., Arlen, P. M., Tsang, K. Y., and Schlom, J., 2000. Int J Cancer, 85:829–838.
73. Kittlesen, D. J., Thompson, L. W., Gulden, P. H., Skipper, J. C., and et al. 1998. J Immunol, 160:2099–2106.
74. Rivoltini, L., Squarcina, P., Loftus, D. J., Castelli, C., Tarsini, P., and et al. 1999. Cancer Res, 59:301–306.
75. Rognan, D., Scapozza, L., Folkers, G., and Daser, A., 1995. Proc Natl Acad Sci USA, 92:753–757.
76. Bredenbeck, A., Losch, F. O., Sharav, T., Eichler-Mertens, M., Filter, M., and et al. 2005. J Immunol, 174:6716–6724.
77. Michielin, O., Luescher, I., and Karplus, M., 2000. J Mol Biol, 300:1205–1235.
78. Rognan, D., Stryhn, A., Fugger, L., Lyngbaek, S., Engberg, J., and et al. 2000. J Comput Aided Mol Des, 14:53–69.
79. Zoete, V., and Michielin, O., 2007. Proteins, 67:1026–1047.
80. Shimbara, N., Nakajima, H., Tanahashi, N., Ogawa, K., Niwa, S., and et al. 1997. Genes Cells, 2:785–800.
81. Paradela, A., García-Peydró, M., Vázquez, J., Rognan, D., and López de Castro, J. A., 1998. J Immunol, 161:5481–5490.
82. García, F., Rognan, D., Lamas, J. R., Marina, A., and López de Castro, J. A., 1998. Tissue Antigens, 51:1–9.
83. Scapozza, L., Rognan, D., Folkers, G., and Daser, A., 1995. Acta Crystallogr D Biol Crystallogr, 51:541–549.
84. Santegoets, S. J., Schreurs, M. W., Reurs, A. W., Lindenberg, J. J., Kueter, E. W., and et al. 2007. J Immunol, 179:2005–2012.
85. Flower, D. R., and Doytchinova, I. A., 2002. Appl Bioinformatics, 1:167–176.
86. Tung, C. W., and Ho, S. Y., 2007. Bioinformatics, 23:942–949.
87. Naz, R. K., and Dabir, P., 2007. Front Biosci, 12:1833–1844.
88. Wooldridge, L., Lissina, A., Vernazza, J., Gostick, E., Laugel, B., and et al. 2007. Eur J Immunol, 37:1323–1333.
89. May, R. J., Dao, T., Pinilla-Ibarz, J., Korontsvit, T., Zakhaleva, V., Zhang, R. H., and et al. 2007. Clin Cancer Res, 13:4547–4555.
90. Shastri, N., Schwab, S., and Serwold, T., 2002. Ann Rev Immunol, 20:463–493.
91. Ho, O., and Green, W. R., 2006. J Immunol, 177:8283–8289.
92. Scardino, A., Alimandi, M., Correale, P., Smith, S. G., Bei, R., and et al. 2007. Cancer Res, 67:7028–7036.
93. Hanada, K., Yewdell, J. W., and Yang, J. C., 2004. Nature, 427:252–256.
94. Nielsen, M., Lundegaard, C., and Lund, O., 2007. BMC Bioinformatics, 8:238 (b)
95. Wang, H. Y., Lee, D. A., Peng, G., Guo, Z., Li, Y., and et al. 2004. Immunity, 20:107–118.
96. Wang, H. Y., Peng, G., Guo, Z., Shevach, E. M., and Wang, R. F., 2005. J Immunol, 174:2661–2670.
97. Clarke, S. L., Betts, G. J., Plant, A., Wright, K. L., El-Shanawany, T. M., and et al. 2006. PLoS ONE 1, e129
98. Chiriva-Internati, M., Grizzi, F., Bright, R. K., and Kast, W. M., 2004. J Transl Med, 2:26
99. Weinzierl, A. O., Lemmel, C., Schoor, O., Müller, M., and et al. 2007. Mol Cell Proteom-ics, 6:102–113.
100. Celada, F., and Seiden, P. E., 1992. Immunol Today, 13:56–62.
101. Seiden, P. E., and Celada, F., 1992. J Theor Biol, 158:329–357.
102. Bernaschi, M., and Castiglione, F., 2001. Comput Biol Med, 31:303–331.
103. Lollini, P. L., Motta, S., and Pappalardo, F., 2006. BMC Bioinformatics, 7:352
104. Castiglione, F., Duca, K., Jarrah, A., Laubenbacher, R., Hochberg, D., and et al. 2007. Bioinformatics, 23:1371–1377.