In silico predicted mycobacterial epitope elicits in vitro T-cell responses

Molecular Immunology

Volumn 61, Issue 1, 2014, Pages 16-22

  Khan, Md Kawsar ^a,b   Zaman, Shabnam ^a,b   Chakraborty, Sajib ^b   Chakravorty, Rajib ^c   Alam, Mohammad Murshid ^a   Bhuiyan, Taufiqur Rahman ^a   Rahman, Muhammad Jubayer ^d   Fernández, Carmen ^d   Qadri, Firdausi ^a   Seraj, Zeba I ^b  

^a INTERNATIONAL CENTRE FOR DIARRHOEAL DISEASE RESEARCH   (Bangladesh)

^b UNIVERSITY OF DHAKA   (Bangladesh)

^c CSIRO   (Australia)

^d STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Ag85B; Epitope vaccine; Immunoinformatics; Tuberculosis

Indexed keywords

AMINO ACID; BACTERIAL ANTIGEN; BACTERIAL PROTEIN; BCG VACCINE; CD45RO ANTIGEN; EPITOPE; HLA ANTIGEN CLASS 1; HLA ANTIGEN CLASS 2; SECRETORY PROTEIN; SECRETORY PROTEIN AG85B; UNCLASSIFIED DRUG;

ADULT; ALLELE; AMINO ACID SEQUENCE; ANTIGEN PRESENTATION; ARTICLE; BINDING AFFINITY; BIOINFORMATICS; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL PROLIFERATION; COMPUTER MODEL; DNA FLANKING REGION; HUMAN; HUMAN CELL; IMMUNE RESPONSE; IN VITRO STUDY; MEMORY T LYMPHOCYTE; MOLECULE; MYCOBACTERIUM TUBERCULOSIS; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; T LYMPHOCYTE;

AG85B; EPITOPE VACCINE; IMMUNOINFORMATICS; TUBERCULOSIS;

ACYLTRANSFERASES; AMINO ACID SEQUENCE; ANTIGENS, BACTERIAL; ANTIGENS, CD45; BACTERIAL PROTEINS; CD4-POSITIVE T-LYMPHOCYTES; CD8-POSITIVE T-LYMPHOCYTES; CELL PROLIFERATION; COMPUTER SIMULATION; CROSS REACTIONS; EPITOPE MAPPING; EPITOPES, T-LYMPHOCYTE; HLA ANTIGENS; HUMANS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PROTEIN BINDING; T-LYMPHOCYTES; TUBERCULOSIS VACCINES;

EID: 84900851672     PISSN: 01615890     EISSN: 18729142     Source Type: Journal    
DOI: 10.1016/j.molimm.2014.04.009     Document Type: Article

References (48)

1. Aagaard C., Dietrich J., Doherty M., Andersen P. TB vaccines: current status and future perspectives. Immunol. Cell Biol. 2009, 87:279-286.
2. Arifuzzaman M., Rashu R., Leung D.T., Hosen M.I., Bhuiyan T.R., et al. Antigen-specific memory T cell responses after vaccination with an oral killed cholera vaccine in Bangladeshi children and comparison to responses in patients with naturally acquired cholera. Clin. Vaccine Immunol. 2012, 19:1304-1311.
3. Assarsson E., Sidney J., Oseroff C., Pasquetto V., Bui H.H., et al. A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection. J. Immunol. 2007, 178:7890-7901.
4. Beveridge N.E., Price D.A., Casazza J.P., Pathan A.A., Sander C.R., et al. Immunisation with BCG and recombinant MVA85A induces long-lasting, polyfunctional Mycobacterium tuberculosis-specific CD4+ memory T lymphocyte populations. Eur. J. Immunol. 2007, 37:3089-3100.
5. Boom W.H., Canaday D.H., Fulton S.A., Gehring A.J., Rojas R.E., et al. Human immunity to M. tuberculosis: T cell subsets and antigen processing. Tuberculosis (Edinb) 2003, 83:98-106.
6. Bourdette D.N., Edmonds E., Smith C., Bowen J.D., Guttmann C.R., et al. A highly immunogenic trivalent T cell receptor peptide vaccine for multiple sclerosis. Mult. Scler. 2005, 11:552-561.
7. Bui H.H., Sidney J., Peters B., Sathiamurthy M., Sinichi A., et al. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 2005, 57:304-314.
8. Bui H.H., Sidney J., Dinh K., Southwood S., Newman M.J., et al. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 2006, 7:153.
9. Burroughs N.J., de Boer R.J., Kesmir C. Discriminating self from nonself with short peptides from large proteomes. Immunogenetics 2004, 56:311-320.
10. Chakraborty S., Chakravorty R., Ahmed M., Rahman A., Waise T.M., et al. A computational approach for identification of epitopes in dengue virus envelope protein: a step towards designing a universal dengue vaccine targeting endemic regions. In Silico Biol. 2010, 10:235-246.
11. Chang S.T., Ghosh D., Kirschner D.E., Linderman J.J. Peptide length-based prediction of peptide-MHC class II binding. Bioinformatics 2006, 22:2761-2767.
12. Davila J., McNamara L.A., Yang Z. Comparison of the predicted population coverage of tuberculosis vaccine candidates Ag85B-ESAT-6, Ag85B-TB10.4, and Mtb72f via a bioinformatics approach. PLoS ONE 2012, 7:e40882.
13. De Groot A.S., Bosma A., Chinai N., Frost J., Jesdale B.M., et al. From genome to vaccine: in silico predictions, ex vivo verification. Vaccine 2001, 19:4385-4395.
14. Devasundaram S., Deenadayalan A., Raja A. In silico analysis of potential human T cell antigens from Mycobacterium tuberculosis for the development of subunit vaccines against tuberculosis. Immunol. Invest. 2014, 43:137-159.
15. Feng C.G., Bean A.G., Hooi H., Briscoe H., Britton W.J. Increase in gamma interferon-secreting CD8(+), as well as CD4(+), T cells in lungs following aerosol infection with Mycobacterium tuberculosis. Infect. Immun. 1999, 67:3242-3247.
16. Geluk A., van Meijgaarden K.E., Franken K.L., Drijfhout J.W., D'Souza S., et al. Identification of major epitopes of Mycobacterium tuberculosis AG85B that are recognized by HLA-A*0201-restricted CD8+ T cells in HLA-transgenic mice and humans. J. Immunol. 2000, 165:6463-6471.
17. Hartigan J.A. Clustering Algorithms 1975, 351. John Wiley & Sons, Inc.
18. Hoft D.F., Blazevic A., Abate G., Hanekom W.A., Kaplan G., et al. A new recombinant bacille Calmette-Guerin vaccine safely induces significantly enhanced tuberculosis-specific immunity in human volunteers. J. Infect. Dis. 2008, 198:1491-1501.
19. Jurcevic S., Travers P.J., Hills A., Agrewala J.N., Moreno C., et al. Distinct conformations of a peptide bound to HLA-DR1 or DRB5*0101 suggested by molecular modelling. Int. Immunol. 1996, 8:1807-1814.
20. Kaufmann S.H. Tuberculosis vaccine development: strength lies in tenacity. Trends Immunol. 2012, 33:373-379.
21. Kaufmann S.H., Hussey G., Lambert P.H. New vaccines for tuberculosis. Lancet 2010, 375:2110-2119.
22. Knutson K.L., Schiffman K., Disis M.L. Immunization with a HER-2/neu helper peptide vaccine generates HER-2/neu CD8 T-cell immunity in cancer patients. J. Clin. Invest. 2001, 107:477-484.
23. Korber B., LaBute M., Yusim K. Immunoinformatics comes of age. PLoS Comput. Biol. 2006, 2:e71.
24. Lopez J.A., Weilenman C., Audran R., Roggero M.A., Bonelo A., et al. A synthetic malaria vaccine elicits a potent CD8(+) and CD4(+) T lymphocyte immune response in humans. Implications for vaccination strategies. Eur. J. Immunol. 2001, 31:1989-1998.
25. Lundegaard C., Lamberth K., Harndahl M., Buus S., Lund O., et al. NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res. 2008, 36:W509-W512.
26. Maher D., Dye C., Floyd K., Pantoja A., Lonnroth K., et al. Planning to improve global health: the next decade of tuberculosis control. Bull. World Health Organ. 2007, 85:341-347.
27. Martin C. The dream of a vaccine against tuberculosis; new vaccines improving or replacing BCG?. Eur. Respir. J. 2005, 26:162-167.
28. Mohamud R., Azlan M., Yero D., Alvarez N., Sarmiento M.E., et al. Immunogenicity of recombinant Mycobacterium bovis bacille Calmette-Guerin clones expressing T and B cell epitopes of Mycobacterium tuberculosis antigens. BMC Immunol. 2013, 14(Suppl. 1):S5.
29. Mustafa A.S. Development of new vaccines and diagnostic reagents against tuberculosis. Mol. Immunol. 2002, 39:113-119.
30. Mustafa A.S., Shaban F.A., Abal A.T., Al-Attiyah R., Wiker H.G., et al. Identification and HLA restriction of naturally derived Th1-cell epitopes from the secreted Mycobacterium tuberculosis antigen 85B recognized by antigen-specific human CD4(+) T-cell lines. Infect. Immun. 2000, 68:3933-3940.
31. Mustafa A.S., Abal A.T., Shaban F., El-Shamy A.M., Amoudy H.A. HLA-DR binding prediction and experimental evaluation of T-cell epitopes of mycolyl transferase 85B (Ag85B), a major secreted antigen of Mycobacterium tuberculosis. Med. Princ. Pract. 2005, 14:140-146.
32. Nielsen M., Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 2009, 10:296.
33. Nielsen M., Lundegaard C., Worning P., Lauemoller S.L., Lamberth K., et al. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 2003, 12:1007-1017.
34. Nielsen M., Lundegaard C., Lund O. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 2007, 8:238.
35. O'Brien C., Flower D.R., Feighery C. Peptide length significantly influences in vitro affinity for MHC class II molecules. Immunol. Res. 2008, 4:6.
36. Peters B., Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 2005, 6:132.
37. Peters B., Bui H.H., Frankild S., Nielson M., Lundegaard C., et al. A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput. Biol. 2006, 2:e65.
38. Pym A.S., Brodin P., Majlessi L., Brosch R., Demangel C., et al. Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat. Med. 2003, 9:533-539.
39. Schellens I.M., Kesmir C., Miedema F., van Baarle D., Borghans J.A. An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs. AIDS 2008, 22:33-37.
40. Schmid B.V., Kesmir C., de Boer R.J. The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes. BMC Evol. Biol. 2009, 9:184.
41. Tan P.T., Heiny A.T., Miotto O., Salmon J., Marques E.T., et al. Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLoS ONE 2010, 5:e8754.
42. Tenzer S., Peters B., Bulik S., Schoor O., Lemmel C., et al. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell. Mol. Life Sci. 2005, 62:1025-1037.
43. van Dissel J.T., Soonawala D., Joosten S.A., Prins C., Arend S.M., et al. Ag85B-ESAT-6 adjuvanted with IC31(R) promotes strong and long-lived Mycobacterium tuberculosis specific T cell responses in volunteers with previous BCG vaccination or tuberculosis infection. Vaccine 2011, 29:2100-2109.
44. Vita R., Zarebski L., Greenbaum J.A., Emami H., Hoof I., et al. The immune epitope database 2.0. Nucleic Acids Res. 2010, 38:D854-D862.
45. Vordermeier H.M., Harris D.P., Moreno C., Ivanyi J. Promiscuous T cell recognition of an H-2 IA-presented mycobacterial epitope. Eur. J. Immunol. 1994, 24:2061-2067.
46. Wang J., Thorson L., Stokes R.W., Santosuosso M., Huygen K., et al. Single mucosal, but not parenteral, immunization with recombinant adenoviral-based vaccine provides potent protection from pulmonary tuberculosis. J. Immunol. 2004, 173:6357-6365.
47. Weil A.A., Arifuzzaman M., Bhuiyan T.R., LaRocque R.C., Harris A.M., et al. Memory T-cell responses to Vibrio cholerae O1 infection. Infect. Immun. 2009, 77:5090-5096.
48. Zvi A., Ariel N., Fulkerson J., Sadoff J.C., Shafferman A. Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses. BMC Med. Genomics 2008, 1:18.