Equivalent T Cell Epitope Promiscuity in Ecologically Diverse Human Pathogens

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Wiens, Kirsten E ^a   Swaminathan, Harish ^b   Copin, Richard ^a   Lun, Desmond S ^b   Ernst, Joel D ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ANTIGEN; CLOSTRIDIUM TOXIN; EPITOPE; HLA A ANTIGEN; HLA B ANTIGEN; HLA DR ANTIGEN;

ALGORITHM; ALLELE; ANTIGEN BINDING; ANTIGENIC VARIATION; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL SURVIVAL; BACTERIAL VIABILITY; BINDING AFFINITY; CELLULAR IMMUNITY; CLOSTRIDIUM TETANI; COMPUTER MODEL; FACTUAL DATABASE; HOST PATHOGEN INTERACTION; HUMAN IMMUNODEFICIENCY VIRUS; IMMUNE EVASION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; STREPTOCOCCUS PYOGENES; T LYMPHOCYTE;

EID: 84881254746     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073124     Document Type: Article

References (42)

1. Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, et al. (2011) The IMGT/HLA database. Nucleic Acids Res 39: D1171-D1176. doi:10.1093/nar/gkq998. PubMed: 21071412.
2. Apanius V, Penn D, Slev PR, Ruff LR, Potts WK, (1997) The nature of selection on the major histocompatibility complex. Crit Rev Immunol 17: 179-224. doi:10.1615/CritRevImmunol.v17.i2.40. PubMed: 9094452.
3. Dean M, Carrington M, O'Brien SJ, (2002) Balanced polymorphism selected by genetic versus infectious human disease. Annu Rev Genomics Hum Genet 3: 263-292. doi:10.1146/annurev.genom.3.022502.103149. PubMed: 12142357.
4. Penn DJ, Damjanovich K, Potts WK, (2002) MHC heterozygosity confers a selective advantage against multiple-strain infections. Proc Natl Acad Sci U S A 99: 11260-11264. doi:10.1073/pnas.162006499. PubMed: 12177415.
5. Kubinak JL, Ruff JS, Hyzer CW, Slev PR, Potts WK, (2012) Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types. Proc Natl Acad Sci U S A 109: 3422-3427. doi:10.1073/pnas.1112633109. PubMed: 22323587.
6. Deitsch KW, Lukehart SA, Stringer JR, (2009) Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens. Nat Rev Microbiol 7: 493-503. doi:10.1038/nrmicro2145. PubMed: 19503065.
7. Johnson WE, Desrosiers RC, (2002) Viral persistence: HIV's strategies of immune system evasion. Annu Rev Med 53: 499-518. doi:10.1146/annurev.med.53.082901.104053. PubMed: 11818487.
8. Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, et al. (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 42: 498-503. doi:10.1038/ng.590. PubMed: 20495566.
9. O'Sullivan D, Arrhenius T, Sidney J, Del Guercio MF, Albertson M, et al. (1991) On the interaction of promiscuous antigenic peptides with different DR alleles. Identification of common structural motifs. J Immunol 147: 2663-2669. PubMed: 1717570.
10. Panina-Bordignon P, Tan A, Termijtelen A, Demotz S, Corradin G, et al. (1989) Universally immunogenic T cell epitopes: promiscuous binding to human MHC class II and promiscuous recognition by T cells. Eur J Immunol 19: 2237-2242. doi:10.1002/eji.1830191209. PubMed: 2481588.
11. Kaufmann DE, Bailey PM, Sidney J, Wagner B, Norris PJ, et al. (2004) Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides. J Virol 78: 4463-4477. doi:10.1128/JVI.78.9.4463-4477.2004. PubMed: 15078927.
12. Krüger S, Schroers R, Rooney CM, Gahn B, Chen SY, (2003) Identification of a naturally processed HLA-DR-restricted T-helper epitope in Epstein-Barr virus nuclear antigen type 1. J Immunother 26: 212-221. doi:10.1097/00002371-200305000-00005. PubMed: 12806275.
13. Doolan DL, Southwood S, Chesnut R, Appella E, Gomez E, et al. (2000) HLA-DR-promiscuous T cell epitopes from Plasmodium falciparum pre-erythrocytic-stage antigens restricted by multiple HLA class II alleles. J Immunol 165: 1123-1137. PubMed: 10878392.
14. Axelsson-Robertson R, Weichold F, Sizemore D, Wulf M, Skeiky YA, et al. (2010) Extensive major histocompatibility complex class I binding promiscuity for Mycobacterium tuberculosis TB10.4 peptides and immune dominance of human leucocyte antigen (HLA)-B*0702 and HLA-B*0801 alleles in TB10.4 CD8 T-cell responses. Immunology 129: 496-505. doi:10.1111/j.1365-2567.2009.03201.x. PubMed: 20002212.
15. Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, et al. (2007) Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol 37: 2419-2433. doi:10.1002/eji.200737365. PubMed: 17705138.
16. Nakagawa M, Kim KH, Gillam TM, Moscicki AB, (2007) HLA class I binding promiscuity of the CD8 T-cell epitopes of human papillomavirus type 16 E6 protein. J Virol 81: 1412-1423. doi:10.1128/JVI.01768-06. PubMed: 17108051.
17. Sabbaj S, Bansal A, Ritter GD, Perkins C, Edwards BH, et al. (2003) Cross-reactive CD8+ T cell epitopes identified in US adolescent minorities. J Acquir Immune Defic Syndr 33: 426-438. doi:10.1097/00126334-200308010-00003. PubMed: 12869831.
18. Masemola AM, Mashishi TN, Khoury G, Bredell H, Paximadis M, et al. (2004) Novel and promiscuous CTL epitopes in conserved regions of Gag targeted by individuals with early subtype C HIV type 1 infection from southern Africa. J Immunol 173: 4607-4617. PubMed: 15383595.
19. Malim MH, Emerman M, (2001) HIV-1 sequence variation: drift, shift, and attenuation. Cell 104: 469-472. doi:10.1016/S0092-8674(01)00234-3. PubMed: 11239404.
20. Fischetti VA, Jones KF, Hollingshead SK, Scott JR, (1988) Structure, function, and genetics of streptococcal M protein. Rev Infect Dis 10 (Suppl 2):: S356-S359. doi:10.1093/cid/10.Supplement_2.S356. PubMed: 3055203.
21. Cunningham MW, (2000) Pathogenesis of group A streptococcal infections. Clin Microbiol Rev 13: 470-511. doi:10.1128/CMR.13.3.470-511.2000. PubMed: 10885988.
22. Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, et al. (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61: 1-13. doi:10.1007/s00251-008-0341-z. PubMed: 19002680.
23. Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S, (2010) NetMHCIIpan-2.0- Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Res 6: 9. doi:10.1186/1745-7580-6-9. PubMed: 21073747.
24. Sidney J, Peters B, Frahm N, Brander C, Sette A, (2008) HLA class I supertypes: a revised and updated classification. BMC Immunol 9: 1. doi:10.1186/1471-2172-9-1. PubMed: 18211710.
25. Jones MC, (1993) Simple Boundary Correction for Kernel Density-Estimation. Statist Comput 3: 135-146. doi:10.1007/BF00147776.
26. Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, et al. (2006) A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLOS Comput Biol 2: e65. doi:10.1371/journal.pcbi.0020065. PubMed: 16789818.
27. Zhang H, Lundegaard C, Nielsen M, (2009) Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics 25: 83-89. doi:10.1093/bioinformatics/btn579. PubMed: 18996943.
28. Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V, (2008) Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol 9: 8. doi:10.1186/1471-2172-9-8. PubMed: 18366636.
29. Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V, (2008) Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics 9 (Suppl 12):: S22. doi:10.1186/1471-2105-9-S7-P22. PubMed: 19091022.
30. Goebel T, (2007) Anthropology. The missing years for modern humans. Science 315: 194-196. doi:10.1126/science.1137564. PubMed: 17218514.
31. Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, et al. (2008) High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLOS Biol 6: e311. doi:10.1371/journal.pbio.0060311. PubMed: 19090620.
32. Weichold FF, Mueller S, Kortsik C, Hitzler WE, Wulf MJ, et al. (2007) Impact of MHC class I alleles on the M. tuberculosis antigen-specific CD8+ T-cell response in patients with pulmonary tuberculosis. Genes Immun 8: 334-343. doi:10.1038/sj.gene.6364392. PubMed: 17429413.
33. Eisen HN, Hou XH, Shen C, Wang K, Tanguturi VK, et al. (2012) Promiscuous binding of extracellular peptides to cell surface class I MHC protein. Proc Natl Acad Sci U S A 109: 4580-4585. doi:10.1073/pnas.1201586109. PubMed: 22403068.
34. Tan PT, Heiny AT, Miotto O, Salmon J, Marques ET, et al. (2010) Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLOS ONE 5: e8754. doi:10.1371/journal.pone.0008754. PubMed: 20090904.
35. Ribeiro SP, Rosa DS, Fonseca SG, Mairena EC, Postól E, et al. (2010) A vaccine encoding conserved promiscuous HIV CD4 epitopes induces broad T cell responses in mice transgenic to multiple common HLA class II molecules. PLOS ONE 5: e11072. doi:10.1371/journal.pone.0011072. PubMed: 20552033.
36. Lamonaca V, Missale G, Urbani S, Pilli M, Boni C, et al. (1999) Conserved hepatitis C virus sequences are highly immunogenic for CD4(+) T cells: implications for vaccine development. Hepatology 30: 1088-1098. doi:10.1002/hep.510300435. PubMed: 10498664.
37. Fonseca SG, Coutinho-Silva A, Fonseca LA, Segurado AC, Moraes SL, et al. (2006) Identification of novel consensus CD4 T-cell epitopes from clade B HIV-1 whole genome that are frequently recognized by HIV-1 infected patients. AIDS 20: 2263-2273. doi:10.1097/01.aids.0000253353.48331.5f. PubMed: 17117012.
38. Bryson S, Julien JP, Hynes RC, Pai EF, (2009) Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications. J Virol 83: 11862-11875. doi:10.1128/JVI.01604-09. PubMed: 19740978.
39. Rao X, Hoof I, Costa AI, van Baarle D, Keşmir C, (2011) HLA class I allele promiscuity revisited. Immunogenetics 63: 691-701. doi:10.1007/s00251-011-0552-6. PubMed: 21695550.
40. Sanjuán R, Nebot MR, Peris JB, Alcamí J, (2013) Immune Activation Promotes Evolutionary Conservation of T-Cell Epitopes in HIV-1. PLOS Biol 11: e1001523. PubMed: 23565057.
41. Morris GP, Allen PM, (2012) How the TCR balances sensitivity and specificity for the recognition of self and pathogens. Nat Immunol 13: 121-128. doi:10.1038/ni.2190. PubMed: 22261968.
42. Croft NP, Smith SA, Wong YC, Tan CT, Dudek NL, et al. (2013) Kinetics of Antigen Expression and Epitope Presentation during Virus Infection. PLOS Pathog 9: e1003129. PubMed: 23382674.