Model of stimulation-responsive splicing and strategies in identification of immunogenic isoforms of tumor antigens and autoantigens

Clinical Immunology

Volumn 121, Issue 2, 2006, Pages 121-133

  Yang, Fan ^a   Chen, Irene H ^a   Xiong, Zeyu ^a   Yan, Yan ^a   Wang, Hong ^a   Yang, Xiao Feng ^a  

^a TEMPLE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Alternative splicing; Autoantigens; Database mining; SEREX cloning; Stimulation responsive splicing; Tumor antigens

Indexed keywords

ALPHA INTERFERON; AUTOANTIGEN; CD44V ANTIGEN; FODRIN; INTERLEUKIN 13; INTERLEUKIN 14; KU ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MELANOMA ANTIGEN; MYELOBLASTIN; RNA; RO ANTIBODY; SMALL NUCLEAR RIBONUCLEOPROTEIN; TUMOR ANTIGEN;

ALTERNATIVE RNA SPLICING; ANTIBODY RESPONSE; ANTIGEN DETECTION; ANTIGEN SPECIFICITY; AUTOIMMUNE DISEASE; AUTOIMMUNITY; CANCER CELL DESTRUCTION; CANCER IMMUNOLOGY; CANCER INHIBITION; CANCER SCREENING; CANCER SUSCEPTIBILITY; CD4+ CD25+ T LYMPHOCYTE; CELL DESTRUCTION; CHRONIC MYELOID LEUKEMIA; CYTOTOXICITY; DOWN REGULATION; ENZYME LINKED IMMUNOSORBENT ASSAY; GENBANK; GENE OVEREXPRESSION; HUMAN; IMMUNOGENICITY; IMMUNOMODULATION; IMMUNOSTIMULATION; IMMUNOSURVEILLANCE; INSULIN DEPENDENT DIABETES MELLITUS; INTRON; LEUKEMIA REMISSION; MICROARRAY ANALYSIS; MOLECULAR MIMICRY; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; POLYMYOSITIS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN VARIANT; REFERENCE DATABASE; SCREENING TEST; SEQUENCE DATABASE; SHORT SURVEY; SOMATIC HYPERMUTATION; SOMATIC MUTATION; SYSTEMIC LUPUS ERYTHEMATOSUS; UPREGULATION; VITILIGO; WEGENER GRANULOMATOSIS;

ALTERNATIVE SPLICING; ANTIGENS, NEOPLASM; AUTOANTIGENS; DATABASES, GENETIC; DOWN-REGULATION; EPITOPES; GENOMIC INSTABILITY; HUMANS; MODELS, GENETIC; MODELS, IMMUNOLOGICAL; NEOPLASMS; PROTEIN ISOFORMS; PROTEOME; TRANSCRIPTION, GENETIC; UP-REGULATION;

EID: 33750098860     PISSN: 15216616     EISSN: 15217035     Source Type: Journal    
DOI: 10.1016/j.clim.2006.06.007     Document Type: Short Survey

References (130)

1. Rosenberg S.A. Progress in human tumour immunology and immunotherapy. Nature 411 (2001) 380-384
2. Boon T., and Van den Eynde B.J. Cancer vaccines: cancer antigens. Shared tumor-specific antigens. In: Rosenberg III S. (Ed). Principles and Practice of the Biologic Therapy of Cancer (2000), Lippincott Williams and Wilkins, Philadelphia 493-504
3. Y. Chen, SEREX review, Cancer Immunity http://www.cancerimmunity.org/SEREX/(2004).
4. Preuss K.D., Zwick C., Bormann C., Neumann F., and Pfreundschuh M. Analysis of the B-cell repertoire against antigens expressed by human neoplasms. Immunol. Rev. 188 (2002) 43-50
5. van der Bruggen P., Traversari C., Chomez P., Lurquin C., De Plaen E., Van den Eynde B., Knuth A., and Boon T. A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science 254 (1991) 1643-1647
6. Boon T., and van der Bruggen P. Human tumor antigens recognized by T lymphocytes. J. Exp. Med. 183 (1996) 725-729
7. Traversari C., van der Bruggen P., Luescher I.F., Lurquin C., Chomez P., Van Pel A., De Plaen E., Amar-Costesec A., and Boon T. A nonapeptide encoded by human gene MAGE-1 is recognized on HLA-A1 by cytolytic T lymphocytes directed against tumor antigen MZ2-E. J. Exp. Med. 176 (1992) 1453-1457
8. Sahin U., Tureci O., Schmitt H., Cochlovius B., Johannes T., Schmits R., Stenner F., Luo G., Schobert I., and Pfreundschuh M. Human neoplasms elicit multiple specific immune responses in the autologous host. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 11810-11813
9. Sahin U., Tureci O., and Pfreundschuh M. Serological identification of human tumor antigens. Curr. Opin. Immunol. 9 (1997) 709-716
10. Tureci O., Sahin U., and Pfreundschuh M. Serological analysis of human tumor antigens: molecular definition and implications. Mol. Med. Today 3 (1997) 342-349
11. Yang F., and Yang X.F. New concepts in tumor antigens: their significance in future immunotherapies for tumors. Cell Mol. Immunol. 2 (2005) 331-341
12. Schreiber R.D. Cancer vaccines 2004 opening address: the molecular and cellular basis of cancer immunosurveillance and immunoediting. Cancer Immun. 5 Suppl. 1 (2005) 1
13. Hisatomi H., Nagao K., Kawakita M., Matsuda T., Hirata H., Yamamoto S., Nakamoto T., Harasawa H., Kaneko N., Hikiji K., and Tsukada Y. Detection of circulating prostate tumor cells: alternative spliced variant of PSM induced false-positive result. Int. J. Mol. Med. 10 (2002) 619-622
14. Khong H.T., and Restifo N.P. Natural selection of tumor variants in the generation of "tumor escape" phenotypes. Nat. Immunol. 3 (2002) 999-1005
15. Dunn G.P., Old L.J., and Schreiber R.D. The three Es of cancer immunoediting. Annu. Rev. Immunol. 22 (2004) 329-360
16. Matlin A.J., Clark F., and Smith C.W. Understanding alternative splicing: towards a cellular code. Nat. Rev., Mol. Cell Biol. 6 (2005) 386-398
17. Venables J.P. Unbalanced alternative splicing and its significance in cancer. BioEssays 28 (2006) 378-386
18. Sanford J.R., Ellis J., and Caceres J.F. Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem. Soc. Trans. 33 (2005) 443-446
19. Lewin B. Nuclear splicing. In: Lewin B. (Ed). Genes VII. VII edn. (2000), Oxford Univ. Press Inc., New York
20. Wang Z., Lo H.S., Yang H., Gere S., Hu Y., Buetow K.H., and Lee M.P. Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res. 63 (2003) 655-657
21. Will C.L., Schneider C., Reed R., and Luhrmann R. Identification of both shared and distinct proteins in the major and minor spliceosomes. Science 284 (1999) 2003-2005
22. Lynch M., and Richardson A.O. The evolution of spliceosomal introns. Curr. Opin. Genet. Dev. 12 (2002) 701-710
23. Modrek B., and Lee C. A genomic view of alternative splicing. Nat. Genet. 30 (2002) 13-19
24. Black D.L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. (2003)
25. Stamm S., Ben-Ari S., Rafalska I., Tang Y., Zhang Z., Toiber D., Thanaraj T.A., and Soreq H. Function of alternative splicing. Gene 344 (2005) 1-20
26. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F., and Kornblihtt A.R. A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol. Cell 19 (2005) 393-404
27. Stamm S. Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Hum. Mol. Genet. 11 (2002) 2409-2416
28. Faustino N.A., and Cooper T.A. Pre-mRNA splicing and human disease. Genes Dev. 17 (2003) 419-437
29. Kalnina Z., Zayakin P., Silina K., and Line A. Alterations of pre-mRNA splicing in cancer. Genes Chromosomes Cancer 42 (2005) 342-357
30. Yang X.F., Wu C.J., McLaughlin S., Chillemi A., Wang K.S., Canning C., Alyea E.P., Kantoff P., Soiffer R.J., Dranoff G., and Ritz J. CML66, a broadly immunogenic tumor antigen, elicits a humoral immune response associated with remission of chronic myelogenous leukemia. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 7492-7497
31. Wu C.J., Yang X.F., McLaughlin S., Neuberg D., Canning C., Stein B., Alyea E.P., Soiffer R.J., Dranoff G., and Ritz J. Detection of a potent humoral response associated with immune-induced remission of chronic myelogenous leukemia. J. Clin. Invest. 106 (2000) 705-714
32. Yan Y., Phan L., Yang F., Talpaz M., Yang Y., Xiong Z., Ng B., Timchenko N.A., Wu C.J., Ritz J., Wang H., and Yang X.F. A novel mechanism of alternative promoter and splicing regulates the epitope generation of tumor antigen CML66-L. J. Immunol. 172 (2004) 651-660
33. Streilein J.W. Ocular immune privilege: therapeutic opportunities from an experiment of nature. Nat. Rev., Immunol. 3 (2003) 879-889
34. Ali Eldib A.M., Ono T., Shimono M., Kaneko M., Nakagawa K., Tanaka R., Noguchi Y., and Nakayama E. Immunoscreening of a cDNA library from a lung cancer cell line using autologous patient serum: identification of XAGE-1b as a dominant antigen and its immunogenicity in lung adenocarcinoma. Int. J. Cancer 108 (2004) 558-563
35. Line A., Slucka Z., Stengrevics A., Li G., and Rees R.C. Altered splicing pattern of TACC1 mRNA in gastric cancer. Cancer Genet. Cytogenet. 139 (2002) 78-83
36. Line A., Slucka Z., Stengrevics A., Silina K., Li G., and Rees R.C. Characterisation of tumour-associated antigens in colon cancer. Cancer Immunol. Immunother. 51 (2002) 574-582
37. Yuki D., Lin Y.M., Fujii Y., Nakamura Y., and Furukawa Y. Isolation of LEM domain-containing 1, a novel testis-specific gene expressed in colorectal cancers. Oncol. Rep. 12 (2004) 275-280
38. Wang H.C., Su Y.R., Han K.J., Pang X.W., Peng J.R., Liang B., Wang S., and Chen W.F. Multiple variants and a differential splicing pattern of kinectin in human hepatocellular carcinoma. Biochem. Cell Biol. 82 (2004) 321-327
39. Lin J., Lin L., Thomas D.G., Greenson J.K., Giordano T.J., Robinson G.S., Barve R.A., Weishaar F.A., Taylor J.M., Orringer M.B., and Beer D.G. Melanoma-associated antigens in esophageal adenocarcinoma: identification of novel MAGE-A10 splice variants. Clin. Cancer Res. 10 (2004) 5708-5716
40. Schmid B.C., Rudas M., Fabjani G., Speiser P., Kaserer K., Leodolter S., and Zeillinger R. Evaluation of MUC1 splice variants as prognostic markers in patients with ductal carcinoma in situ of the breast. Oncol. Rep. 10 (2003) 1981-1985
41. Schmittgen T.D., Teske S., Vessella R.L., True L.D., and Zakrajsek B.A. Expression of prostate specific membrane antigen and three alternatively spliced variants of PSMA in prostate cancer patients. Int. J. Cancer 107 (2003) 323-329
42. Heuze-Vourc'h N., Leblond V., and Courty Y. Complex alternative splicing of the hKLK3 gene coding for the tumor marker PSA (prostate-specific-antigen). Eur. J. Biochem. 270 (2003) 706-714
43. Stoilov P., Meshorer E., Gencheva M., Glick D., Soreq H., and Stamm S. Defects in pre-mRNA processing as causes of and predisposition to diseases. DNA Cell Biol. 21 (2002) 803-818
44. Ng B., Yang F., Huston D.P., Yan Y., Yang Y., Xiong Z., Peterson L.E., Wang H., and Yang X.F. Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes. J. Allergy Clin. Immunol. 114 (2004) 1463-1470
45. Sacchi S., Kantarjian H., O'Brien S., Cohen P.R., Pierce S., and Talpaz M. Immune-mediated and unusual complications during interferon alfa therapy in chronic myelogenous leukemia. J. Clin. Oncol. 13 (1995) 2401-2407
46. Wang R. The role of MHC class II-restricted tumor antigens and CD4T cells in antitumor immunity. TRENDS Immunol. 22 (2001) 269-276
47. Overwijk W.W., Lee D.S., Surman D.R., Irvine K.R., Touloukian C.E., Chan C.C., Carroll M.W., Moss B., Rosenberg S.A., and Restifo N.P. Vaccination with a recombinant vaccinia virus encoding a "self" antigen induces autoimmune vitiligo and tumor cell destruction in mice: requirement for CD4(+) T lymphocytes. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 2982-2987
48. Shevach E. Regulatory T cells in autoimmunity. Annu. Rev. Immunol. 18 (2000) 423-449
49. Antony P.A., and Restifo N.P. Do CD4+ CD25+ immunoregulatory T cells hinder tumor immunotherapy?. J. Immunother. 25 (2002) 202-206
50. Morris E., Hart D., Gao L., Tsallios A., Xue S.A., and Stauss H. Generation of tumor-specific T-cell therapies. Blood Rev. 20 (2006) 61-69
51. Yang X.F., Wu C.J., Chen L., Alyea E.P., Canning C., Kantoff P., Soiffer R.J., Dranoff G., and Ritz J. CML28 is a broadly immunogenic antigen, which is overexpressed in tumor cells. Cancer Res. 62 (2002) 5517-5522
52. Mahler M., Bluthner M., and Pollard K.M. Advances in B-cell epitope analysis of autoantigens in connective tissue diseases. Clin. Immunol. 107 (2003) 65-79
53. Renkvist N., Castelli C., Robbins P.F., and Parmiani G. A listing of human tumor antigens recognized by T cells. Cancer Immunol. Immunother. 50 (2001) 3-15
54. Agrawal S., Pilarski R., and Eng C. Different splicing defects lead to differential effects downstream of the lipid and protein phosphatase activities of PTEN. Hum. Mol. Genet. 14 (2005) 2459-2468
55. Vigneron N., Stroobant V., Chapiro J., Ooms A., Degiovanni G., Morel S., van der Bruggen P., Boon T., and Van den Eynde B.J. An antigenic peptide produced by peptide splicing in the proteasome. Science 304 (2004) 587-590
56. Hanada K., Yewdell J.W., and Yang J.C. Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature 427 (2004) 252-256
57. Cresswell P. Cell biology. Cutting and pasting antigenic peptides. Science 304 (2004) 525-527
58. Rammensee H.G. Immunology: protein surgery. Nature 427 (2004) 203-204
59. Horiuchi T., and Aigaki T. Alternative trans-splicing: a novel mode of pre-mRNA processing. Biol. Cell 98 (2006) 135-140
60. Liu X.Q. Protein-splicing intein: genetic mobility, origin, and evolution. Annu. Rev. Genet. 34 (2000) 61-76
61. Shastri N., Schwab S., and Serwold T. Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules. Annu. Rev. Immunol. 20 (2002) 463-493
62. Bracco L., and Kearsey J. The relevance of alternative RNA splicing to pharmacogenomics. Trends Biotechnol. 21 (2003) 346-353
63. van der Houven van Oordt W., Diaz-Meco M.T., Lozano J., Krainer A.R., Moscat J., and Caceres J.F. The MKK(3/6)-p38-signaling cascade alters the subcellular distribution of hnRNP A1 and modulates alternative splicing regulation. J. Cell Biol. 149 (2000) 307-316
64. Tanabe M., Sasai N., Nagata K., Liu X.D., Liu P.C., Thiele D.J., and Nakai A. The mammalian HSF4 gene generates both an activator and a repressor of heat shock genes by alternative splicing. J. Biol. Chem. 274 (1999) 27845-27856
65. Sato N., Hori O., Yamaguchi A., Lambert J.C., Chartier-Harlin M.C., Robinson P.A., Delacourte A., Schmidt A.M., Furuyama T., Imaizumi K., Tohyama M., and Takagi T. A novel presenilin-2 splice variant in human Alzheimer's disease brain tissue. J. Neurochem. 72 (1999) 2498-2505
66. Wu J.Y., Tang H., and Havlioglu N. Alternative pre-mRNA splicing and regulation of programmed cell death. Prog. Mol. Subcell Biol. 31 (2003) 153-185
67. Akusjarvi G., and Stevenin J. Remodelling of the host cell RNA splicing machinery during an adenovirus infection. Curr. Top. Microbiol. Immunol. 272 (2003) 253-286
68. Klokov D., Criswell T., Leskov K.S., Araki S., Mayo L., and Boothman D.A. IR-inducible clusterin gene expression: a protein with potential roles in ionizing radiation-induced adaptive responses, genomic instability, and bystander effects. Mutat. Res. 568 (2004) 97-110
69. Xie J., and McCobb D.P. Control of alternative splicing of potassium channels by stress hormones. Science 280 (1998) 443-446
70. Z. Xiong, A. Shaibani, Y.-P. Li, Y. Yan, S. Zhang, Y. Yang, F. Yang, H. Wang, X.-F. Yang, The expression of alternative splicing factor ASF/SF2 is downregulated in inflamed muscle, J. Clin. Pathol. (in press).
71. Yang Y.Y., Yin G.L., and Darnell R.B. The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 13254-13259
72. Lipes B.D., and Keene J.D. Autoimmune epitopes in messenger RNA. RNA 8 (2002) 762-771
73. Kamachi M., Le T.M., Kim S.J., Geiger M.E., Anderson P., and Utz P.J. Human autoimmune sera as molecular probes for the identification of an autoantigen kinase signaling pathway. J. Exp. Med. 196 (2002) 1213-1225
74. Garcia-Blanco M.A., Baraniak A.P., and Lasda E.L. Alternative splicing in disease and therapy. Nat. Biotechnol. 22 (2004) 535-546
75. Xiong Z., Shaibani A., Li Y.P., Yan Y., Zhang S., Yang Y., Yang F., Wang H., and Yang X.F. Alternative splicing factor ASF/SF2 is downregulated in inflamed muscle. J. Clin. Pathol. (2006) (Electronic publication ahead of print)
76. Hassfeld W., Steiner G., Studnicka-Benke A., Skriner K., Graninger W., Fischer I., and Smolen J.S. Autoimmune response to the spliceosome. An immunologic link between rheumatoid arthritis, mixed connective tissue disease, and systemic lupus erythematosus. Arthritis Rheum. 38 (1995) 777-785
77. Monneaux F., and Muller S. Key sequences involved in the spreading of the systemic autoimmune response to spliceosomal proteins. Scand. J. Immunol. 54 (2001) 45-54
78. Ng B., Yan Y., Yang Y., Xiong Z., Phan L., Li Y., Huston D., Wang H., and Yang X.-F. Novel isoforms of RNA exosome autoantigens are modulated by proinflammatory cytokines through alternative splicing: role in enhancing antigen immunogenicity in idiopathic inflammatory myositis. Arthritis Rheum. 48 (2003) 3631
79. Burchert A., Wolfl S., Schmidt M., Brendel C., Denecke B., Cai D., Odyvanova L., Lahaye T., Muller M.C., Berg T., Gschaidmeier H., Wittig B., Hehlmann R., Hochhaus A., and Neubauer A. Interferon-alpha, but not the ABL-kinase inhibitor imatinib (STI571), induces expression of myeloblastin and a specific T-cell response in chronic myeloid leukemia. Blood 101 (2003) 259-264
80. Gullo C., Au M., Feng G., and Teoh G. The biology of Ku and its potential oncogenic role in cancer. Biochim. Biophys. Acta 1765 (2006) 223-234
81. Kelavkar U., Wang S., and Badr K. KU 70/80 lupus autoantigen is the transcription factor induced by interleukins (IL)-13 and - 4 leading to induction of 15-lipoxygenase (15-LO) in human cells. Adv. Exp. Med. Biol. 507 (2002) 469-481
82. Li X., and Manley J.L. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122 (2005) 365-378
83. Yeo G., Holste D., Kreiman G., and Burge C.B. Variation in alternative splicing across human tissues. Genome Biol. 5 (2004) R74
84. Ludewig B., Junt T., Hengartner H., and Zinkernagel R.M. Dendritic cells in autoimmune diseases. Curr. Opin. Immunol. 13 (2001) 657-662
85. Zinkernagel R.M., and Hengartner H. Regulation of the immune response by antigen. Science 293 (2001) 251-253
86. Saito E., Fujimoto M., Hasegawa M., Komura K., Hamaguchi Y., Kaburagi Y., Nagaoka T., Takehara K., Tedder T.F., and Sato S. CD19-dependent B lymphocyte signaling thresholds influence skin fibrosis and autoimmunity in the tight-skin mouse. J. Clin. Invest. 109 (2002) 1453-1462
87. Graham K.L., and Utz P.J. Sources of autoantigens in systemic lupus erythematosus. Curr. Opin. Rheumatol. 17 (2005) 513-517
88. Weg-Remers S., Ponta H., Herrlich P., and Konig H. Regulation of alternative pre-mRNA splicing by the ERK MAP-kinase pathway. EMBO J. 20 (2001) 4194-4203
89. Hanawa H., Abe S., Hayashi M., Yoshida T., Yoshida K., Shiono T., Fuse K., Ito M., Tachikawa H., Kashimura T., Okura Y., Kato K., Kodama M., Maruyama S., Yamamoto T., and Aizawa Y. Time course of gene expression in rat experimental autoimmune myocarditis. Clin. Sci. (Lond) 103 (2002) 623-632
90. Tanaka M., Kishimura M., Ozaki S., Osakada F., Hashimoto H., Okubo M., Murakami M., and Nakao K. Cloning of novel soluble gp130 and detection of its neutralizing autoantibodies in rheumatoid arthritis. J. Clin. Invest. 106 (2000) 137-144
91. Klein L., Klugmann M., Nave K.A., Tuohy V.K., and Kyewski B. Shaping of the autoreactive T-cell repertoire by a splice variant of self protein expressed in thymic epithelial cells. Nat. Med. 6 (2000) 56-61
92. Kralovicova J., Gaunt T.R., Rodriguez S., Wood P.J., Day I.N., and Vorechovsky I. Variants in the human insulin gene that affect pre-mRNA splicing: is -23HphI a functional single nucleotide polymorphism at IDDM2?. Diabetes 55 (2006) 260-264
93. Dogra R.S., Vaidyanathan P., Prabakar K.R., Marshall K.E., Hutton J.C., and Pugliese A. Alternative splicing of G6PC2, the gene coding for the islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP), results in differential expression in human thymus and spleen compared with pancreas. Diabetologia 49 (2006) 953-957
94. Park Y.S., Kawasaki E., Kelemen K., Yu L., Schiller M.R., Rewers M., Mizuta M., Eisenbarth G.S., and Hutton J.C. Humoral autoreactivity to an alternatively spliced variant of ICA512/IA-2 in Type I diabetes. Diabetologia 43 (2000) 1293-1301
95. Diez J., Park Y., Zeller M., Brown D., Garza D., Ricordi C., Hutton J., Eisenbarth G.S., and Pugliese A. Differential splicing of the IA-2 mRNA in pancreas and lymphoid organs as a permissive genetic mechanism for autoimmunity against the IA-2 type 1 diabetes autoantigen. Diabetes 50 (2001) 895-900
96. Gabanella F., Carissimi C., Usiello A., and Pellizzoni L. The activity of the spinal muscular atrophy protein is regulated during development and cellular differentiation. Hum. Mol. Genet. 14 (2005) 3629-3642
97. Casciola-Rosen L., Andrade F., Ulanet D., Wong W.B., and Rosen A. Cleavage by granzyme B is strongly predictive of autoantigen status: implications for initiation of autoimmunity. J. Exp. Med. 190 (1999) 815-826
98. Levin M.C., Lee S.M., Kalume F., Morcos Y., Dohan Jr. F.C., Hasty K.A., Callaway J.C., Zunt J., Desiderio D., and Stuart J.M. Autoimmunity due to molecular mimicry as a cause of neurological disease. Nat. Med. 8 (2002) 509-513
99. Matzinger P. The danger model: a renewed sense of self. Science 296 (2002) 301-305
100. Plotz P.H. The autoantibody repertoire: searching for order. Nat. Rev., Immunol. 3 (2003) 73-78
101. Yang X., Mirkovic D., Zhang S., Zhang Q.E., Yang Y., Xiong Z., Yang F., Chen I.H., Li L., and Wang H. Processing sites are different in the generation of HLA-A2.1-restricted T cell reactive tumor antigen epitopes and viral epitopes. International Journal of Immunopathology and Pharmacology 19 4 (2006)
102. Rock K.L., York I.A., and Goldberg A.L. Post-proteasomal antigen processing for major histocompatibility complex class I presentation. Nat. Immunol. 5 (2004) 670-677
103. Kloetzel P.M. Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII. Nat. Immunol. 5 (2004) 661-669
104. Uebel S., Kraas W., Kienle S., Wiesmuller K.H., Jung G., and Tampe R. Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 8976-8981
105. Daniel S., Brusic V., Caillat-Zucman S., Petrovsky N., Harrison L., Riganelli D., Sinigaglia F., Gallazzi F., Hammer J., and van Endert P.M. Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules. J. Immunol. 161 (1998) 617-624
106. Holzhutter H.G., Frommel C., and Kloetzel P.M. A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome. J. Mol. Biol. 286 (1999) 1251-1265
107. Tenzer S., Peters B., Bulik S., Schoor O., Lemmel C., Schatz M.M., Kloetzel P.M., Rammensee H.G., Schild H., and Holzhutter H.G. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell. Mol. Life Sci. 62 (2005) 1025-1037
108. Kesmir C., Nussbaum A.K., Schild H., Detours V., and Brunak S. Prediction of proteasome cleavage motifs by neural networks. Protein Eng. 15 (2002) 287-296
109. Tureci O., Usener D., Schneider S., and Sahin U. Identification of tumor-associated autoantigens with SEREX. Methods Mol. Med. 109 (2005) 137-154
110. Fernandez Madrid F., Tang N., Alansari H., Karvonen R.L., and Tomkiel J.E. Improved approach to identify cancer-associated autoantigens. Autoimmun. Rev. 4 (2005) 230-235
111. Uchida K., Akita Y., Matsuo K., Fujiwara S., Nakagawa A., Kazaoka Y., Hachiya H., Naganawa Y., Oh-Iwa I., Ohura K., Saga S., Kawai T., Matsumoto Y., Shimozato K., and Kozaki K. Identification of specific autoantigens in Sjogren's syndrome by SEREX. Immunology 116 (2005) 53-63
112. Krebs P., Kurrer M., Sahin U., Tureci O., and Ludewig B. Autoimmunity seen through the SEREX-scope. Autoimmun. Rev. 2 (2003) 339-345
113. Yang X.F., Weber G.F., and Cantor H. A novel Bcl-x isoform connected to the T cell receptor regulates apoptosis in T cells. Immunity 7 (1997) 629-639
114. Yang X.F., Milhiet P.E., Gaudoux F., Crine P., and Boileau G. Complete sequence of rabbit kidney aminopeptidase N and mRNA localization in rabbit kidney by in situ hybridization. Biochem. Cell Biol. 71 (1993) 278-287
115. Zappulla J.P., Wickham L., Bawab W., Yang X.F., Storozhuk M.V., Castellucci V.F., and DesGroseillers L. Cloning and characterization of Aplysia neutral endopeptidase, a metallo-endopeptidase involved in the extracellular metabolism of neuropeptides in Aplysia californica. J. Neurosci. 19 (1999) 4280-4292
116. Yang X.-F., Ye Q., Press B., Han R.Z., Bassing C.H., Sleckman B.P., Alt F.W., and Cantor H. Analysis of the complex genomic structure of Bcl-x and its relationship to Bcl-xgamma expression after CD28-dependent costimulation. Mol. Immunol. 39 (2002) 45-55
117. Sercarz E.E. Driver clones and determinant spreading. J. Autoimmun. 14 (2000) 275-277
118. Rodda S., Tribbick G., and Maeji N.J. Synthetic peptides in epitope mapping. In: Johnstone AaT M.W. (Ed). Immunochemistry 1 A Practical Approach (1997), IRL Press, Oxford 121-146
119. Margulies D. Induction of immune responses. In: Coligan J., Kruisbeek A.M., Margulies D.H., Shevach E.M., Strober W., and Hoboken (Eds). Current Protocols in Immunology (2000), John Wiley and Sons, Inc., New Jersey 2.0.1-2.14.19
120. Jameson B.A., and Wolf H. The antigenic index: a novel algorithm for predicting antigenic determinants. Comput. Appl. Biosci. 4 (1988) 181-186
121. Peters B., Sidney J., Bourne P., Bui H.H., Buus S., Doh G., Fleri W., Kronenberg M., Kubo R., Lund O., Nemazee D., Ponomarenko J.V., Sathiamurthy M., Schoenberger S.P., Stewart S., Surko P., Way S., Wilson S., and Sette A. The design and implementation of the immune epitope database and analysis resource. Immunogenetics 57 (2005) 326-336
122. Schlessinger A., Ofran Y., Yachdav G., and Rost B. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res. 34 (2006) D777-D780
123. Williams S.C., Badley R.A., Davis P.J., Puijk W.C., and Meloen R.H. Identification of epitopes within beta lactoglobulin recognised by polyclonal antibodies using phage display and PEPSCAN. J. Immunol. Methods 213 (1998) 1-17
124. Van Regenmortel M.H.V. Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. Methods 9 (1996) 465-472
125. Robinson W.H., DiGennaro C., Hueber W., Haab B.B., Kamachi M., Dean E.J., Fournel S., Fong D., Genovese M.C., de Vegvar H.E., Skriner K., Hirschberg D.L., Morris R.I., Muller S., Pruijn G.J., van Venrooij W.J., Smolen J.S., Brown P.O., Steinman L., and Utz P.J. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 8 (2002) 295-301
126. Robinson W.H., Garren H., Utz P.J., and Steinman L. Millennium award. Proteomics for the development of DNA tolerizing vaccines to treat autoimmune disease. Clin. Immunol. 103 (2002) 7-12
127. Moudgil K., and Sercarz E.E. Antigenic determinants involved in induction and propagation of autoimmunity. In: Rose N., and Mackay I.R. (Eds). The Autoimmune Diseases. 3rd edn. (1998), Academic Press, San Diego 45-58
128. Bach J.F., and Chatenoud L. Tolerance to islet autoantigens in type 1 diabetes. Annu. Rev. Immunol. 19 (2001) 131-161
129. Robinson W.H., Steinman L., and Utz P.J. Proteomics technologies for the study of autoimmune disease. Arthritis Rheum. 46 (2002) 885-893
130. Vacek M., Sazani P., and Kole R. Antisense-mediated redirection of mRNA splicing. Cell. Mol. Life Sci. 60 (2003) 825-833