Cellular mechanisms that edit the immunopeptidome

Current Proteomics

Volumn 6, Issue 1, 2009, Pages 13-24

  Georgiadou, Dimitra ^a   Stratikos, Efstratios ^a  

^a INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 64749086370     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016409787847439     Document Type: Article

References (187)

1. Abele, R. and Tampe, R. (2006). Modulation of the antigen transport machinery TAP by friends and enemies. FEBS Lett. 580: 1156-63.
2. Ackerman, A.L. and Cresswell, P. (2004). Cellular mechanisms governing cross-presentation of exogenous antigens. Nat. Immunol. 5: 678-84.
3. Alfonso, C. and Karlsson, L. (2000). Nonclassical MHC class II molecules. Annu. Rev. Immunol. 18: 113-42.
4. Andersen, M.H., Schrama, D., Thor S.P. and Becker, J.C. (2006). Cytotoxic T cells. J. Invest. Dermatol. 126: 32-41.
5. Atkinson, E.A. and Bleackley, R.C. (1995). Mechanisms of lysis by cytotoxic T cells. Crit. Rev. Immunol. 15: 359-84.
6. Bangia, N., Lehner, P.J., Hughes, E.A., Surman, M. and Cresswell, P. (1999). The N-terminal region of tapasin is required to stabilize the MHC class I loading complex. Eur. J. Immunol. 29: 1858-70.
7. Barnden, M.J., Purcell, A.W., Gorman, J.J. and McCluskey, J. (2000). Tapasin-mediated retention and optimization of peptide ligands during the assembly of class I molecules. J. Immunol. 165: 322-30.
8. Beers, C., Burich, A., Kleijmeer, M.J., Griffith, J.M., Wong, P. and Rudensky, A.Y. (2005). Cathepsin S controls MHC class II-mediated antigen presentation by epithelial cells in vivo. J. Immunol. 174: 1205-12.
9. Belmares, M.P., Busch, R., Mellins, E.D. and McConnell, H.M. (2003). Formation of two peptide/MHC II isomers is catalyzed differentially by HLA-DM. Biochemistry 42: 838-47.
10. Belmares, M.P., Busch, R., Wucherpfennig, K.W., McConnell, H.M. and Mellins, E.D. (2002). Structural factors contributing to DM susceptibility of MHC class II/peptide complexes. J. Immunol. 169: 5109-17.
11. Bjorkman, P.J., Saper, M.A., Samraoui, B., Bennett, W.S., Strominger, J.L. and Wiley, D.C. (1987). Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329: 506-12.
12. Bouvier, M. and Wiley, D.C. (1994). Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules. Science 265: 398-402.
13. Brocke, P., Garbi, N., Momburg, F. and Hammerling, G.J. (2002). HLA- DM, HLA-DO and tapasin: functional similarities and differences. Curr. Opin. Immunol. 14: 22-9.
14. Brouwenstijn, N., Serwold, T. and Shastri, N. (2001). MHC class I molecules can direct proteolytic cleavage of antigenic precursors in the endoplasmic reticulum. Immunity 15: 95-104.
15. Bukulmez, H., Fife, M., Tsoras, M., Thompson, S.D., Twine, N.A., Woo, P., Olson, J.M., Elston, R.C., et al. (2005). Tapasin gene polymorphism in systemic onset juvenile rheumatoid arthritis: a family-based casecontrol study. Arthritis Res. Ther. 7: R285-90.
16. Burgdorf, S. and Kurts, C. (2008). Endocytosis mechanisms and the cell biology of antigen presentation. Curr. Opin. Immunol. 20: 89-95.
17. Burton, P.R., Clayton, D.G., Cardon, L.R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D.P., McCarthy, M.I., et al. (2007). Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat. Genet. 39: 1329-37.
18. Busch, D.H. and Pamer, E.G. (1998). MHC class I/peptide stability: implications for immunodominance, in vitro proliferation, and diversity of responding CTL. J. Immunol. 160: 4441-8.
19. Busch, R., Pashine, A., Garcia, K.C. and Mellins, E.D. (2002). Stabilization of soluble, low-affinity HLA-DM/HLA-DR1 complexes by leucine zippers. J. Immunol. Methods 263: 111-21.
20. Busch, R., Reich, Z., Zaller, D.M., Sloan, V. and Mellins, E.D. (1998). Secondary structure composition and pH-dependent conformational changes of soluble recombinant HLA-DM. J. Biol. Chem. 273: 27557-64.
21. Cabrera, C.M. (2007). The double role of the endoplasmic reticulum chaperone tapasin in peptide optimization of HLA class I molecules. Scand. J. Immunol. 65: 487-93.
22. Cascio, P., Hilton, C., Kisselev, A.F., Rock, K.L. and Goldberg, A.L. (2001). 26S proteasomes and immunoproteasomes produce mainly N- extended versions of an antigenic peptide. Embo. J. 20: 2357-66.
23. Chang, S.C., Momburg, F., Bhutani, N. and Goldberg, A.L. (2005). The ER aminopeptidase, ERAP1, trims precursors to lengths of MHC class I peptides by a "molecular ruler" mechanism. Proc. Natl. Acad. Sci. USA 102: 17107-12.
24. Chen, M. and Bouvier, M. (2007). Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection. EMBO J. 26: 1681-90.
25. Chou, C.L., Mirshahidi, S., Su, K.W., Kim, A., Narayan, K., Khoruzhenko, S., Xu, M. and Sadegh-Nasseri, S. (2008). Short peptide sequences mimic HLA-DM functions. Mol. Immunol. 45: 1935-43.
26. Chou, C.L. and Sadegh-Nasseri, S. (2000). HLA-DM recognizes the flexible conformation of major histocompatibility complex class II. J. Exp. Med. 192: 1697-706.
27. Cox, A.L., Skipper, J., Chen, Y., Henderson, R.A., Darrow, T.L., Shabanowitz, J., Engelhard, V.H., Hunt, D.F., et al. (1994). Identification of a peptide recognized by five melanoma-specific human cytotoxic T cell lines. Science 264: 716-9.
28. Cresswell, P. (1996). Invariant chain structure and MHC class II function. Cell 84: 505-7.
29. Cresswell, P., Ackerman, A.L., Giodini, A., Peaper, D.R. and Wearsch, P.A. (2005). Mechanisms of MHC class I-restricted antigen processing and cross-presentation. Immunol. Rev. 207: 145-57.
30. Davis, D.M. and Dustin, M.L. (2004). What is the importance of the immunological synapse? Trends Immunol. 25: 323-7.
31. Del Prete, G. (1998). The concept of type-1 and type-2 helper T cells and their cytokines in humans. Int. Rev. Immunol. 16: 427-55.
32. den Haan, J.M., Meadows, L.M., Wang, W., Pool, J., Blokland, E., Bishop, T.L., Reinhardus, C., Shabanowitz, J., Offringa, R., Hunt, D.F., Engelhard, V.H. and Goulmy, E. (1998). The minor histocompatibility antigen HA-1: a diallelic gene with a single amino acid polymorphism. Science 279: 1054-7.
33. den Haan, J.M., Sherman, N.E., Blokland, E., Huczko, E., Koning, F., Drijfhout, J.W., Skipper, J., Shabanowitz, J., et al. (1995). Identification of a graft versus host disease-associated human minor histocompatibility antigen. Science 268: 1476-80.
34. Dennert, G. (1997). Molecular mechanism of target lysis by cytotoxic T cells. Int. Rev. Immunol. 14: 133-52.
35. Denzin, L.K., Hammond, C. and Cresswell, P. (1996). HLA-DM interactions with intermediates in HLA-DR maturation and a role for HLA- DM in stabilizing empty HLA-DR molecules. J. Exp. Med. 184: 2153-65.
36. Denzin, L.K., Sant'Angelo, D.B., Hammond, C., Surman, M.J. and Cresswell, P. (1997). Negative regulation by HLA-DO of MHC class II-restricted antigen processing. Science 278: 106-9.
37. Deshaies, F., Brunet, A., Diallo, D.A., Denzin, L.K., Samaan, A. and Thibodeau, J. (2005). A point mutation in the groove of HLA-DO allows egress from the endoplasmic reticulum independent of HLA-DM. Proc. Natl. Acad. Sci. USA 102: 6443-8.
38. Dhiman, N., Ovsyannikova, I.G., Pinsky, N.A., Vierkant, R.A., Jacobsen, S.J., Jacobson, R.M. and Poland, G.A. (2003). Lack of association between transporter associated with antigen processing (TAP) and HLA- DM gene polymorphisms and antibody levels following measles vaccination. Eur. J. Immunogenet. 30: 195-200.
39. Dick, T. P., Bangia, N., Peaper, D.R. and Cresswell, P. (2002). Disulfide bond isomerization and the assembly of MHC class I-peptide complexes. Immunity 16: 87-98.
40. Everett, M.W. and Edidin, M. (2007). Tapasin increases efficiency of MHC I assembly in the endoplasmic reticulum but does not affect MHC I stability at the cell surface. J. Immunol. 179: 7646-52.
41. Evnouchidou, I., Momburg, F., Papakyriakou, A., Chron, A., Leondiadis, L., Chang, S.-C., Goldberg, A.L. and Stratikos, E. (2008). The internal sequence of the peptide-substrate intermediate determines its N-terminus trimming by ERAP1. PLoS ONE
42. Fahnestock, M.L., Tamir, I., Narhi, L. and Bjorkman, P.J. (1992). Thermal stability comparison of purified empty and peptide-filled forms of a class I MHC molecule. Science 258: 1658-62.
43. Falk, K., Lau, J., Santambrogio, L., Marin Esteban, V., Puentes, F., Strominger, J.L. and Rotzschke, O. (2001). Ligand-exchange of MHC class II proteins is triggered by H-bond donor groups of small molecules. J. Biol. Chem. 15: 15.
44. Falk, K., Lau, J.M., Santambrogio, L., Esteban, V.M., Puentes, F., Rotzschke, O. and Strominger, J.L. (2002). Ligand exchange of major histocompatibility complex class II proteins is triggered by H-bond donor groups of small molecules. J. Biol. Chem. 277: 2709-15.
45. Falk, K. and Rotzschke, O. (2002). The final cut: How ERAP1 trims MHC ligands to size. Nat. Immunol. 3: 1121-2.
46. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F. and Whitehouse, C.M. (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64-71.
47. Firat, E., Saveanu, L., Aichele, P., Staeheli, P., Huai, J., Gaedicke, S., Nil, A., Besin, G., et al. (2007). The role of endoplasmic reticulumassociated aminopeptidase 1 in immunity to infection and in crosspresentation. J. Immunol. 178: 2241-8.
48. Frelinger, J.A. and McMillan, M. (1996). The role of peptide specificity in MHC class I-restricted allogeneic responses. Immunol. Rev. 154: 45-58.
49. Friedl, P., den Boer, A.T. and Gunzer, M. (2005). Tuning immune responses: diversity and adaptation of the immunological synapse. Nat. Rev. Immunol. 5: 532-45.
50. Fruci, D., Niedermann, G., Butler, R.H. and van Endert, P.M. (2001). Efficient MHC class I-independent amino-terminal trimming of epitope precursor peptides in the endoplasmic reticulum. Immunity 15: 467-76.
51. Fung-Leung, W.P., Surh, C.D., Liljedahl, M., Pang, J., Leturcq, D., Peterson, P.A., Webb, S.R. and Karlsson, L. (1996). Antigen presentation and T cell development in H2-M-deficient mice. Science 271: 1278-81.
52. Furukawa, H., Kashiwase, K., Yabe, T., Ishikawa, Y., Akaza, T., Tadokoro, K., Tohma, S., Inoue, T., et al. (1998). Polymorphism of TAPASIN and its linkage disequilibria with HLA class II genes in the Japanese population. Tissue Antigens 52: 279-81.
53. Goto, Y., Hattori, A., Ishii, Y. and Tsujimoto, M. (2006). Reduced activity of the hypertension-associated Lys528Arg mutant of human adipocytederived leucine aminopeptidase (A-LAP)/ER-aminopeptidase-1. FEBS Lett. 580: 1833-8.
54. Groothuis, T.A., Griekspoor, A.C., Neijssen, J.J., Herberts, C.A. and Neefjes, J.J. (2005). MHC class I alleles and their exploration of the antigen-processing machinery. Immunol. Rev. 207: 60-76.
55. Guermonprez, P., Saveanu, L., Kleijmeer, M., Davoust, J., Van Endert, P. and Amigorena, S. (2003). ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells. Nature 425: 397-402.
56. Gulden, P.H., Fischer, P.3rd, Sherman, N.E., Wang, W., Engelhard, V.H., Shabanowitz, J., Hunt, D.F. and Pamer, E.G. (1996). A Listeria monocytogenes pentapeptide is presented to cytolytic T lymphocytes by the H2-M3 MHC class Ib molecule. Immunity 5: 73-9.
57. Hall, F.C., Rabinowitz, J.D., Busch, R., Visconti, K.C., Belmares, M., Patil, N.S., Cope, A.P., Patel, S., et al. (2002). Relationship between kinetic stability and immunogenicity of HLA- DR4/peptide complexes. Eur. J. Immunol. 32: 662-70.
58. Hammer, G.E., Gonzalez, F., Champsaur, M., Cado, D. and Shastri, N. (2006). The aminopeptidase ERAAP shapes the peptide repertoire displayed by major histocompatibility complex class I molecules. Nat. Immunol. 7: 103-12.
59. Hammer, G.E., Gonzalez, F., James, E., Nolla, H. and Shastri, N. (2007). In the absence of aminopeptidase ERAAP, MHC class I molecules present many unstable and highly immunogenic peptides. Nat. Immunol. 8: 101-8.
60. Hattori, A., Matsumoto, H., Mizutani, S. and Tsujimoto, M. (1999). Molecular cloning of adipocyte-derived leucine aminopeptidase highly related to placental leucine aminopeptidase/oxytocinase. J. Biochem. (Tokyo) 125: 931-8.
61. Henderson, R.A., Cox, A.L., Sakaguchi, K., Appella, E., Shabanowitz, J., Hunt, D.F. and Engelhard, V.H. (1993). Direct identification of an endogenous peptide recognized by multiple HLA-A2.1-specific cytotoxic T cells. Proc. Natl. Acad. Sci. USA 90: 10275-9.
62. Hershko, A. (2005). The ubiquitin system for protein degradation and some of its roles in the control of the cell-division cycle (Nobel lecture). Angew. Chem. Int. Ed. Engl. 44: 5932-43.
63. Houde, M., Bertholet, S., Gagnon, E., Brunet, S., Goyette, G., Laplante, A., Princiotta, M.F., Thibault, P., et al. (2003). Phagosomes are competent organelles for antigen cross-presentation. Nature 425: 402-6.
64. Howarth, M., Williams, A., Tolstrup, A.B. and Elliott, T. (2004). Tapasin enhances MHC class I peptide presentation according to peptide halflife. Proc. Natl. Acad. Sci. USA 101: 11737-42.
65. Hunt, D.F., Michel, H., Dickinson, T.A., Shabanowitz, J., Cox, A.L., Sakaguchi, K., Appella, E., Grey, H.M., et al. (1992). Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. Science 256: 1817-20.
66. Hunt, D.F., Yates, J.R.3rd, Shabanowitz, J., Winston, S. and Hauer, C.R. (1986). Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83: 6233-7.
67. Irvine, D.J., Purbhoo, M.A., Krogsgaard, M. and Davis, M.M. (2002). Direct observation of ligand recognition by T cells. Nature 419: 845-9.
68. Janeway, C.A.Jr. (1992). The immune system evolved to discriminate infectious nonself from noninfectious self. Immunol. Today 13: 11-6.
69. Jardetzky, T. (1997). Not just another Fab: the crystal structure of a TcR- MHC-peptide complex. Structure 5: 159-63.
70. Jardetzky, T.S., Lane, W.S., Robinson, R.A., Madden, D.R. and Wiley, D.C. (1991). Identification of self peptides bound to purified HLA-B27. Nature 353: 326-9.
71. Jensen, P.E. (1998). Antigen processing: HLA-DO-a hitchhiking inhibitor of HLA-DM. Curr. Biol. 8: R128-31.
72. Joshi, R.V., Zarutskie, J.A. and Stern, L.J. (2000). A three-step kinetic mechanism for peptide binding to MHC class II proteins. Biochemistry 39: 3751-62.
73. Karlsson, L. (2005). DM and DO shape the repertoire of peptide-MHC- class-II complexes. Curr. Opin. Immunol. 17: 65-70.
74. Kasahara, M., Klein, D., Fan, W.M. and Gutknecht, J. (1990). Evolution of the class II major histocompatibility complex alleles in higher primates. Immunol. Rev. 113: 65-82.
75. Kienast, A., Preuss, M., Winkler, M. and Dick, T.P. (2007). Redox regulation of peptide receptivity of major histocompatibility complex class I molecules by ERp57 and tapasin. Nat. Immunol. 8: 864-72.
76. Kisselev, A.F., Akopian, T., Woo, K.M. and Goldberg, A.L. (1999). The sizes of peptides generated from protein by mammalian 26 and 20S proteasomes. Implications for understanding the degradative mechanism and antigen presentation. J. Biol. Chem. 274: 3363-3371.
77. Krogsgaard, M. and Davis, M.M. (2005). How T cells 'see' antigen. Nat. Immunol. 6: 239-45.
78. Kropshofer, H., Arndt, S.O., Moldenhauer, G., Hammerling, G.J. and Vogt, A.B. (1997a). HLA-DM acts as a molecular chaperone and rescues empty HLA-DR molecules at lysosomal pH. Immunity 6: 293-302.
79. Kropshofer, H., Hammerling, G.J. and Vogt, A.B. (1997b). How HLA-DM edits the MHC class II peptide repertoire: survival of the fittest? Immunol. Today 18: 77-82.
80. Kropshofer, H., Vogt, A.B., Moldenhauer, G., Hammer, J., Blum, J.S. and Hammerling, G.J. (1996). Editing of the HLA-DR-peptide repertoire by HLA-DM. Embo. J. 15: 6144-54.
81. Kropshofer, H., Vogt, A.B., Thery, C., Armandola, E.A., Li, B.C., Moldenhauer, G., Amigorena, S. and Hammerling, G.J. (1998). A role for HLA-DO as a co-chaperone of HLA-DM in peptide loading of MHC class II molecules. Embo. J. 17: 2971-81.
82. Kuttler, C., Nussbaum, A.K., Dick, T.P., Rammensee, H.G., Schild, H. and Hadeler, K.P. (2000). An algorithm for the prediction of proteasomal cleavages. J. Mol. Biol. 298: 417-29.
83. Kuwata, S., Yanagisawa, M., Nakagawa, H., Saeki, H., Etoh, T., Miyamoto, M. and Juji, T. (1996). HLA-DM gene polymorphisms in atopic dermatitis. J. Allergy Clin. Immunol. 98: S192-200.
84. Lauvau, G., Kakimi, K., Niedermann, G., Ostankovitch, M., Yotnda, P., Firat, H., Chisari, F.V. and van Endert, P.M. (1999). Human transporters associated with antigen processing (TAPs) select epitope precursor peptides for processing in the endoplasmic reticulum and presentation to T cells. J. Exp. Med. 190: 1227-40.
85. Lehner, P.J., Surman, M.J. and Cresswell, P. (1998). Soluble tapasin restores MHC class I expression and function in the tapasin-negative cell line .220. Immunity 8: 221-31.
86. Lewis, J.W., Sewell, A., Price, D. and Elliott, T. (1998). HLA-A*0201 presents TAP-dependent peptide epitopes to cytotoxic T lymphocytes in the absence of tapasin. Eur. J. Immunol. 28: 3214-20.
87. Liljedahl, M., Kuwana, T., Fung-Leung, W.P., Jackson, M.R., Peterson, P.A. and Karlsson, L. (1996). HLA-DO is a lysosomal resident which requires association with HLA-DM for efficient intracellular transport. Embo. J. 15: 4817-24.
88. Liljedahl, M., Winqvist, O., Surh, C.D., Wong, P., Ngo, K., Teyton, L., Peterson, P.A., Brunmark, A., et al. (1998). Altered antigen presentation in mice lacking H2-O. Immunity 8: 233-43.
89. Ljunggren, H.G., Stam, N.J., Ohlen, C., Neefjes, J.J., Hoglund, P., Heemels, M.T., Bastin, J., Schumacher, T.N., et al. (1990). Empty MHC class I molecules come out in the cold. Nature 346: 476-80.
90. MacPherson, G., Kushnir, N. and Wykes, M. (1999). Dendritic cells, B cells and the regulation of antibody synthesis. Immunol. Rev. 172: 325-34.
91. Margulies, D.H., Corr, M., Boyd, L.F. and Khilko, S.N. (1993). MHC class I/peptide interactions: binding specificity and kinetics. J. Mol. Recognit. 6: 59-69.
92. Marrack, P., Scott-Browne, J.P., Dai, S., Gapin, L. and Kappler, J.W. (2008). Evolutionarily conserved amino acids that control TCR-MHC interaction. Annu. Rev. Immunol. 26: 171-203.
93. McCluskey, J., Kanaan, C. and Diviney, M. (2003). Nomenclature and serology of HLA class I and class II alleles. Curr. Protoc. Immunol. Appendix 1: Appendix 1S.
94. McFarland, B.J., Beeson, C. and Sant, A.J. (1999). Cutting edge: a single, essential hydrogen bond controls the stability of peptide-MHC class II complexes. J. Immunol. 163: 3567-71.
95. McFarland, B.J., Katz, J.F., Beeson, C. and Sant, A.J. (2001). Energetic asymmetry among hydrogen bonds in MHC class II*peptide complexes. Proc. Natl. Acad. Sci. USA 98: 9231-6.
96. McTernan, C.L., Mijovic, C.H., Cockram, C.S. and Barnett, A.H. (2000). The nucleotide sequence of a new DMB allele, DMB*0106. Tissue Antigens 55: 470-2.
97. Meadows, L., Wang, W., den Haan, J.M., Blokland, E., Reinhardus, C., Drijfhout, J.W., Shabanowitz, J., Pierce, R., et al. (1997). The HLA- A*0201-restricted H-Y antigen contains a posttranslationally modified cysteine that significantly affects T cell recognition. Immunity 6: 273-81.
98. Mehta, A.M., Jordanova, E.S., Kenter, G.G., Ferrone, S. and Fleuren, G.J. (2008). Association of antigen processing machinery and HLA class I defects with clinicopathological outcome in cervical carcinoma. Cancer Immunol. Immunother. 57: 197-206.
99. Mehta, A.M., Jordanova, E.S., van Wezel, T., Uh, H.W., Corver, W.E., Kwappenberg, K.M., Verduijn, W., Kenter, G.G., et al. (2007). Genetic variation of antigen processing machinery components and association with cervical carcinoma. Genes Chromosomes Cancer 46: 577-86.
100. Momburg, F. and Tan, P. (2002). Tapasin-the keystone of the loading complex optimizing peptide binding by MHC class I molecules in the endoplasmic reticulum. Mol. Immunol. 39: 217-33.
101. Morris, P., Shaman, J., Attaya, M., Amaya, M., Goodman, S., Bergman, C., Monaco, J.J. and Mellins, E. (1994). An essential role for HLA-DM in antigen presentation by class II major histocompatibility molecules. Nature 368: 551-4.
102. Narayan, K., Chou, C.L., Kim, A., Hartman, I.Z., Dalai, S., Khoruzhenko, S. and Sadegh-Nasseri, S. (2007). HLA-DM targets the hydrogen bond between the histidine at position beta81 and peptide to dissociate HLA- DR-peptide complexes. Nat. Immunol. 8: 92-100.
103. Neefjes, J., Gottfried, E., Roelse, J., Gromme, M., Obst, R., Hammerling, G.J. and Momburg, F. (1995). Analysis of the fine specificity of rat, mouse and human TAP peptide transporters. Eur. J. Immunol. 25: 1133-6.
104. Nicholson, M.J., Moradi, B., Seth, N.P., Xing, X., Cuny, G.D., Stein, R.L. and Wucherpfennig, K.W. (2006). Small molecules that enhance the catalytic efficiency of HLA-DM. J. Immunol. 176: 4208-20.
105. Norbury, C.C. and Tewalt, E.F. (2006). Upstream toward the "DRiP"-ing source of the MHC class I pathway. Immunity 24: 503-6.
106. Ortmann, B., Copeman, J., Lehner, P.J., Sadasivan, B., Herberg, J.A., Grandea, A.G., Riddell, S.R., Tampe, R., et al. (1997). A critical role for tapasin in the assembly and function of multimeric MHC class I-TAP complexes. Science 277: 1306-9.
107. Ortutay, C. and Vihinen, M. (2006). Immunome: a reference set of genes and proteins for systems biology of the human immune system. Cell Immunol. 244: 87-9.
108. Ovsyannikova, I.G., Jacobson, R.M. and Poland, G.A. (2004). Variation in vaccine response in normal populations. Pharmacogenomics 5: 417-27.
109. Park, B., Lee, S., Kim, E. and Ahn, K. (2003). A single polymorphic residue within the peptide-binding cleft of MHC class I molecules determines spectrum of tapasin dependence. J. Immunol. 170: 961-8.
110. Park, B., Lee, S., Kim, E., Cho, K., Riddell, S.R., Cho, S. and Ahn, K. (2006). Redox regulation facilitates optimal peptide selection by MHC class I during antigen processing. Cell 127: 369-82.
111. Pashine, A., Busch, R., Belmares, M.P., Munning, J.N., Doebele, R.C., Buckingham, M., Nolan, G.P. and Mellins, E.D. (2003). Interaction of HLA-DR with an acidic face of HLA-DM disrupts sequence-dependent interactions with peptides. Immunity 19: 183-92.
112. Pathak, S.S., Lich, J.D. and Blum, J.S. (2001). Cutting edge: editing of recycling class II:peptide complexes by HLA-DM. J. Immunol. 167: 632-5.
113. Peaper, D.R., Wearsch, P.A. and Cresswell, P. (2005). Tapasin and ERp57 form a stable disulfide-linked dimer within the MHC class I peptideloading complex. EMBO J. 24: 3613-23.
114. Peters, B., Sidney, J., Bourne, P., Bui, H.H., Buus, S., Doh, G., Fleri, W., Kronenberg, M., Kubo, R., et al. (2005). The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol. 3: e91.
115. Pieters, J., Bakke, O. and Dobberstein, B. (1993). The MHC class II- associated invariant chain contains two endosomal targeting signals within its cytoplasmic tail. J. Cell Sci. 106( Pt 3): 831-46.
116. Pinet, V., Combe, B., Avinens, O., Caillat-Zucman, S., Sany, J., Clot, J. and Eliaou, J.F. (1997). Polymorphism of the HLA-DMA and DMB genes in rheumatoid arthritis. Arthritis Rheum. 40: 854-8.
117. Pyo, C.W., Hur, S.S., Kim, Y.K., Kim, T.Y. and Kim, T.G. (2003). Association of TAP and HLA-DM genes with psoriasis in Koreans. J. Invest. Dermatol. 120: 616-22.
118. Rammensee, H., Bachmann, J., Emmerich, N.P., Bachor, O.A. and Stevanovic, S. (1999). SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50: 213-9.
119. Riberdy, J.M., Newcomb, J.R., Surman, M.J., Barbosa, J.A. and Cresswell, P. (1992). HLA-DR molecules from an antigen-processing mutant cell line are associated with invariant chain peptides. Nature 360: 474-7.
120. Rizvi, S.M. and Raghavan, M. (2006). Direct peptide-regulatable interactions between MHC class I molecules and tapasin. Proc. Natl. Acad. Sci. USA 103: 18220-5.
121. Rocha, N. and Neefjes, J. (2008). MHC class II molecules on the move for successful antigen presentation. EMBO J. 27: 1-5.
122. Roche, P.A. and Cresswell, P. (1990). Invariant chain association with HLA-DR molecules inhibits immunogenic peptide binding. Nature 345: 615-8.
123. Roche, P.A., Marks, M.S. and Cresswell, P. (1991). Formation of a ninesubunit complex by HLA class II glycoproteins and the invariant chain. Nature 354: 392-4.
124. Rock, K.L. (2006). Exiting the outside world for cross-presentation. Immunity 25: 523-5.
125. Rock, K.L. and Goldberg, A.L. (1999). Degradation of cell proteins and the generation of MHC classI-presented peptides. Annu. Rev. Immunol. 17: 739-779.
126. Rock, K.L. and Shen, L. (2005). Cross-presentation: underlying mechanisms and role in immune surveillance. Immunol. Rev. 207: 166-83.
127. Roelse, J., Gromme, M., Momburg, F., Hammerling, G. and Neefjes, J. (1994). Trimming of TAP-translocated peptides in the endoplasmic reticulum and in the cytosol during recycling. J. Exp. Med. 180: 1591-7.
128. Rudensky, A., Preston-Hurlburt, P., Hong, S.C., Barlow, A. and Janeway, C.A.Jr. (1991). Sequence analysis of peptides bound to MHC class II molecules. Nature 353: 622-7.
129. Sadegh-Nasseri, S., Chen, M., Narayan, K. and Bouvier, M. (2008). The convergent roles of tapasin and HLA-DM in antigen presentation. Trends Immunol. 29: 141-7.
130. Sadegh-Nasseri, S. and Germain, R.N. (1991). A role for peptide in determining MHC class II structure. Nature 353: 167-70.
131. Sadegh-Nasseri, S. and McConnell, H.M. (1989). A kinetic intermediate in the reaction of an antigenic peptide and I-Ek. Nature 337: 274-6.
132. Sadegh-Nasseri, S., Stern, L.J., Wiley, D.C. and Germain, R.N. (1994). MHC class II function preserved by low-affinity peptide interactions preceding stable binding. Nature 370: 647-50.
133. Sanchez, M.L., Katsumata, K., Atsumi, T., Romero, F.I., Bertolaccini, M.L., Funke, A., Amengual, O., Kondeatis, E., et al. (2004). Association of HLA-DM polymorphism with the production of antiphospholipid antibodies. Ann. Rheum. Dis. 63: 1645-8.
134. Sant, A.J., Beeson, C., McFarland, B., Cao, J., Ceman, S., Bryant, P.W. and Wu, S. (1999). Individual hydrogen bonds play a critical role in MHC class II: peptide interactions: implications for the dynamic aspects of class II trafficking and DM-mediated peptide exchange. Immunol. Rev. 172: 239-53.
135. Santambrogio, L., Sato, A.K., Fischer, F.R., Dorf, M.E. and Stern, L.J. (1999). Abundant empty class II MHC molecules on the surface of immature dendritic cells. Proc. Natl. Acad. Sci. USA 96: 15050-5.
136. Saric, T., Beninga, J., Graef, C.I., Akopian, T.N., Rock, K.L. and Goldberg, A.L. (2001). Major histocompatibility complex class I-presented antigenic peptides are degraded in cytosolic extracts primarily by thimet oligopeptidase. J. Biol. Chem. 276: 36474-81.
137. Saric, T., Chang, S.C., Hattori, A., York, I.A., Markant, S., Rock, K.L., Tsujimoto, M. and Goldberg, A.L. (2002). An IFN-gamma-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I- presented peptides. Nat. Immunol. 3: 1169-76.
138. Saveanu, L., Carroll, O., Lindo, V., Del Val, M., Lopez, D., Lepelletier, Y., Greer, F., Schomburg, L., et al. (2005). Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum. Nat. Immunol. 6: 689-97.
139. Schmitt, L., Boniface, J.J., Davis, M.M. and McConnell, H.M. (1999). Conformational isomers of a class II MHC-peptide complex in solution. J. Mol. Biol. 286: 207-18.
140. Schoenhals, G.J., Krishna, R.M., Grandea, A.G.3rd, Spies, T., Peterson, P.A., Yang, Y. and Fruh, K. (1999). Retention of empty MHC class I molecules by tapasin is essential to reconstitute antigen presentation in invertebrate cells. EMBO J. 18: 743-53.
141. Schomburg, L., Kollmus, H., Friedrichsen, S. and Bauer, K. (2000). Molecular characterization of a puromycin-insensitive leucyl-specific aminopeptidase, PILS-AP. Eur. J. Biochem. 267: 3198-207.
142. Schuler, M.M., Nastke, M.D. and Stevanovikc, S. (2007). SYFPEITHI: database for searching and T-cell epitope prediction. Methods Mol. Biol. 409: 75-93.
143. Schumacher, T.N., Heemels, M.T., Neefjes, J.J., Kast, W.M., Melief, C.J. and Ploegh, H.L. (1990). Direct binding of peptide to empty MHC class I molecules on intact cells and in vitro. Cell 62: 563-7.
144. Seliger, B., Ritz, U. and Ferrone, S. (2006). Molecular mechanisms of HLA class I antigen abnormalities following viral infection and transformation. Int. J. Cancer 118: 129-38.
145. Serwold, T., Gaw, S. and Shastri, N. (2001). ER aminopeptidases generate a unique pool of peptides for MHC class I molecules. Nat. Immunol. 2: 644-51.
146. Serwold, T., Gonzalez, F., Kim, J., Jacob, R. and Shastri, N. (2002). ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum. Nature 419: 480-3.
147. Sijts, A.J. and Pamer, E.G. (1997). Enhanced intracellular dissociation of major histocompatibility complex class I-associated peptides: a mechanism for optimizing the spectrum of cell surface-presented cytotoxic T lymphocyte epitopes. J. Exp. Med. 185: 1403-11.
148. Skipper, J.C., Hendrickson, R.C., Gulden, P.H., Brichard, V., Van Pel, A., Chen, Y., Shabanowitz, J., Wolfel, T., et al. (1996). An HLA-A2- restricted tyrosinase antigen on melanoma cells results from posttranslational modification and suggests a novel pathway for processing of membrane proteins. J. Exp. Med. 183: 527-34.
149. Stern, L.J., Brown, J.H., Jardetzky, T.S., Gorga, J.C., Urban, R.G., Strominger, J.L. and Wiley, D.C. (1994). Crystal structure of the human class
150. II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368: 215-21.
151. Stratikos, E., Mosyak, L., Zaller, D.M. and Wiley, D.C. (2002). Identification of the lateral interaction surfaces of human histocompatibility leukocyte antigen (HLA)-DM with HLA-DR1 by formation of tethered complexes that present enhanced HLA-DM catalysis. J. Exp. Med. 196: 173-83.
152. Stratikos, E., Wiley, D.C. and Stern, L.J. (2004). Enhanced catalytic action of HLA-DM on the exchange of peptides lacking backbone hydrogen bonds between their N-terminal region and the MHC class II alphachain. J. Immunol. 172: 1109-17.
153. Thayer, W.P., Ignatowicz, L., Weber, D.A. and Jensen, P.E. (1999). Class II-associated invariant chain peptide-independent binding of invariant chain to class II MHC molecules. J. Immunol. 162: 1502-9.
154. Thompson, S.J., Loftus, L.T., Ashley, M.D. and Meller, R. (2008). Ubiquitin-proteasome system as a modulator of cell fate. Curr. Opin. Pharmacol. 8: 90-5.
155. Toussirot, E., Sauvageot, C., Chabod, J., Ferrand, C., Tiberghien, P. and Wendling, D. (2000). The association of HLA-DM genes with rheumatoid arthritis in Eastern France. Hum. Immunol. 61: 303-8.
156. Ullrich, H.J., Doring, K., Gruneberg, U., Jahnig, F., Trowsdale, J. and van Ham, S.M. (1997). Interaction between HLA-DM and HLA-DR involves regions that undergo conformational changes at lysosomal pH. Proc. Natl. Acad. Sci. USA 94: 13163-8.
157. van der Burg, S.H., Visseren, M.J., Brandt, R.M., Kast, W.M. and Melief, C.J. (1996). Immunogenicity of peptides bound to MHC class I molecules depends on the MHC-peptide complex stability. J. Immunol. 156: 3308-14.
158. van der Merwe, P.A. and Davis, S.J. (2003). Molecular interactions mediating T cell antigen recognition. Annu. Rev. Immunol. 21: 659-84.
159. van Ham, M., van Lith, M., Griekspoor, A. and Neefjes, J. (2000). What to do with HLA-DO? Immunogenetics 51: 765-70.
160. van Ham, S.M., Gruneberg, U., Malcherek, G., Broker, I., Melms, A. and Trowsdale, J. (1996). Human histocompatibility leukocyte antigen (HLA)-DM edits peptides presented by HLA-DR according to their ligand binding motifs. J. Exp. Med. 184: 2019-24.
161. van Ham, S.M., Tjin, E.P., Lillemeier, B.F., Gruneberg, U., van Meijgaarden, K.E., Pastoors, L., Verwoerd, D., Tulp, A., et al. (1997). HLA-DO is a negative modulator of HLA-DM-mediated MHC class II peptide loading. Curr. Biol. 7: 950-7.
162. van Niel, G., Wubbolts, R. and Stoorvogel, W. (2008). Endosomal sorting of MHC class II determines antigen presentation by dendritic cells. Curr. Opin. Cell Biol. 20: 437-44.
163. Voges, D., Zwickl, P. and Baumeister, W. (1999). The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu. Rev. Biochem. 68: 1015-68.
164. Vogt, A.B., Kropshofer, H. and Hammerling, G.J. (1997a). How HLA-DM affects the peptide repertoire bound to HLA-DR molecules. Hum. Immunol. 54: 170-9.
165. Vogt, A.B., Moldenhauer, G., Hammerling, G.J. and Kropshofer, H. (1997b). HLA-DM stabilizes empty HLA-DR molecules in a chaperone-like fashion. Immunol. Lett. 57: 209-11.
166. Vukmanovic, S., Bevan, M.J. and Hogquist, K.A. (1993). The specificity of positive selection: MHC and peptides. Immunol. Rev. 135: 51-66.
167. Wearsch, P.A. and Cresswell, P. (2007). Selective loading of high-affinity peptides onto major histocompatibility complex class I molecules by the tapasin-ERp57 heterodimer. Nat. Immunol. 8: 873-81.
168. Weber, D.A., Evavold, B.D. and Jensen, P.E. (1996). Enhanced dissociation of HLA-DR-bound peptides in the presence of HLA- DM. Science 274: 618-20.
169. West, J.E. and Reed, A.M. (1999). Analysis of HLA-DM polymorphism in juvenile dermatomyositis (JDM) patients. Hum. Immunol. 60: 255-8.
170. Williams, A.P., Bevan, S., Bunce, M., Houlston, R., Welsh, K.I. and Elliott, T. (2000). Identification of novel Tapasin polymorphisms and linkage disequilibrium to MHC class I alleles. Immunogenetics 52: 9-11.
171. Williams, A.P., Peh, C.A., Purcell, A.W., McCluskey, J. and Elliott, T. (2002). Optimization of the MHC class I peptide cargo is dependent on tapasin. Immunity 16: 509-20.
172. Yabe, T., Kawamura, S., Sato, M., Kashiwase, K., Tanaka, H., Ishikawa, Y., Asao, Y., Oyama, J., et al. (2002). A subject with a novel type I bare lymphocyte syndrome has tapasin deficiency due to deletion of 4 exons by Alu-mediated recombination. Blood 100: 1496-8.
173. Yamao, F. (1999). Ubiquitin system: selectivity and timing of protein destruction. J. Biochem. 125: 223-9.
174. Yan, J., Parekh, V.V., Mendez-Fernandez, Y., Olivares-Villagomez, D., Dragovic, S., Hill, T., Roopenian, D.C., Joyce, S., et al. (2006). In vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules. J. Exp. Med. 203: 647-59.
175. Yewdell, J. (2002). To DRiP or not to DRiP: generating peptide ligands for MHC class I molecules from biosynthesized proteins. Mol. Immunol. 39: 139-46.
176. York, I.A., Brehm, M.A., Zendzian, S., Towne, C.F. and Rock, K.L. (2006). Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims MHC class I- presented peptides in vivo and plays an important role in immunodominance. Proc. Natl. Acad. Sci. USA 103: 9202-7.
177. York, I.A., Chang, S.C., Saric, T., Keys, J.A., Favreau, J.M., Goldberg, A.L. and Rock, K.L. (2002). The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat. Immunol. 3: 1177-84.
178. York, I.A., Goldberg, A.L., Mo, X.Y. and Rock, K.L. (1999). Proteolysis and class I major histocompatibility complex antigen presentation. Immunol. Rev. 172: 49-66.
179. York, I.A., Mo, A.X., Lemerise, K., Zeng, W., Shen, Y., Abraham, C.R., Saric, T., Goldberg, A.L., et al. (2003). The cytosolic endopeptidase, thimet oligopeptidase, destroys antigenic peptides and limits the extent of MHC class I antigen presentation. Immunity 18: 429-40.
180. Yost, R.A. and Enke, C.G. (1978). Selected ion fragmentation with a tandem quadrupole mass-spectrometer. J. Am. Chem. Soc. 100: 2274-2275.
181. Yue, F., Huang, H.L., Huang, J.X., Liang, L.Y., Huang, Z.L., Wei, Q.Y. and Chen, X.M. (2007). HLA-DM polymorphism and risk of trichloroethylene induced medicamentosa-like dermatitis. Biomed. Environ. Sci. 20: 506-11.
182. Zarling, A.L., Ficarro, S.B., White, F.M., Shabanowitz, J., Hunt, D.F. and Engelhard, V.H. (2000). Phosphorylated peptides are naturally processed and presented by major histocompatibility complex class I molecules in vivo. J. Exp. Med. 192: 1755-62.
183. Zarling, A.L., Luckey, C.J., Marto, J.A., White, F.M., Brame, C.J., Evans, A.M., Lehner, P.J., Cresswell, P., et al. (2003). Tapasin is a facilitator, not an editor, of class I MHC peptide binding. J. Immunol. 171: 5287-95.
184. Zarutskie, J.A., Busch, R., Zavala-Ruiz, Z., Rushe, M., Mellins, E.D. and Stern, L.J. (2001). The kinetic basis of peptide exchange catalysis by HLA-DM. Proc. Natl. Acad. Sci. USA 98: 12450-5.
185. Zarutskie, J.A., Sato, A.K., Rushe, M.M., Chan, I.C., Lomakin, A., Benedek, G.B. and Stern, L.J. (1999). A conformational change in the human major histocompatibility complex protein HLA-DR1 induced by peptide binding. Biochemistry 38: 5878-87.
186. Zhang, Q., Wang, P., Kim, Y., Haste-Andersen, P., Beaver, J., Bourne, P.E., Bui, H.H., Buus, S., et al. (2008). Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 36: W513-8.
187. Zwart, W., Griekspoor, A., Kuijl, C., Marsman, M., van Rheenen, J., Janssen, H., Calafat, J., van Ham, M., et al. (2005). Spatial separation of HLA-DM/HLA-DR interactions within MIIC and phagosome-induced immune escape. Immunity 22: 221-33.