Review Article
Proteomics technologies for the study of autoimmune disease
William H. Robinson,
Lawrence Steinman,
Paul J. Utz,
Corresponding Author
William H. Robinson
Stanford University School of Medicine, Stanford, California
Stanford University School of Medicine, Beckman Center Room B-002, Stanford, CA 94305Search for more papers by this authorLawrence Steinman
Stanford University School of Medicine, Stanford, California
Search for more papers by this authorPaul J. Utz
Stanford University School of Medicine, Stanford, California
Search for more papers by this authorWilliam H. Robinson,
Lawrence Steinman,
Paul J. Utz,
Corresponding Author
William H. Robinson
Stanford University School of Medicine, Stanford, California
Stanford University School of Medicine, Beckman Center Room B-002, Stanford, CA 94305Search for more papers by this authorLawrence Steinman
Stanford University School of Medicine, Stanford, California
Search for more papers by this authorPaul J. Utz
Stanford University School of Medicine, Stanford, California
Search for more papers by this author
REFERENCES
- 1 Jacobson DL, Gange SJ, Rose NR, Graham NM. Epidemiology and estimated population burden of selected autoimmune diseases in the United States. Clin Immunol Immunopathol 1997; 84: 223–43.
- 2 Khan J, Bittner M, Chen Y, Meltzer P, Trent J. DNA microarray technology: the anticipated impact on the study of human disease. Biochim Biophys Acta 1999; 1423: M17–28.
- 3 Futcher B, Latter G,Monardo P, McLaughlin C, Garrels J. A sampling of the yeast proteome. Mol Cell Biol 1999; 19: 7357–68.
- 4 Varshavsky A. The N-end rule: functions, mysteries, uses. Proc Natl Acad Sci U S A 1996; 93: 12142–9.
- 5 Jiang Z, Wu J. Alternative splicing and apoptosis. Proc Soc Exp Biol Med 1999; 220: 64–72.
- 6 Jackson R, Standart N. Do the poly(A) tail and 3′ untranslated region control mRNA translation? Cell 1990; 62: 15–24.
- 7 Sheets M, Fox C, Hunt T, van de Woude G, Wickens M. The 3′-untranslated regions of c-mos and cyclin mRNAs stimulate translation by regulating cytoplasmic polyadenylation. Genes Dev 1994; 8: 926–38.
- 8 Kontoyiannis D, Pasparakis M, Pizarro TT, Cominelli F, Kollias G. Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AU-rich elements: implications for joint and gut-associated immunopathologies. Immunity 1999; 10: 387–98.
- 9 Pandey A, Mann M. Proteomics to study genes and genomes. Nature 2000; 405: 837–46.
- 10
Rohlff C.
Proteomics in molecular medicine: applications in central nervous system disorders.
Electrophoresis
2000;
21:
1227–34.
10.1002/(SICI)1522-2683(20000401)21:6<1227::AID-ELPS1227>3.0.CO;2-L CAS PubMed Web of Science® Google Scholar
- 11 Borrebaeck C. Antibodies in diagnostics: from immunoassays to protein chips. Immunol Today 2000; 21: 379–82.
- 12 Emili A, Cagney G. Large-scale functional analysis using peptide or protein arrays. Nature Biotech 2000; 18: 393–7.
- 13 Walter G, Büssow K, Cahill D, Lueking A, Lehrach H. Protein arrays for gene expression and molecular interaction screening. Curr Opin Microbiol 2000; 3: 298–302.
- 14 Gygi S, Corthals G, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci U S A 2000; 97: 9390–5.
- 15 Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989; 340: 245–6.
- 16 Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, et al. A comprehensive analysis of protein-protein interactions in Saccaromyces cerevisiae. Nature 2000; 403: 623-627.
- 17 Von Mühlen CA, Tan EM. Autoantibodies in the diagnosis of systemic rheumatic diseases. Semin Arthritis Rheum 1995; 24: 323–58.
- 18 Meinhart CD, Wereley ST, Santiago JG. A PIV algorithm for estimating time-averaged velocity fields. J Fluids Engineering 2000; 122: 285–9.
- 19 Santiago JG, Wereley ST, Meinhart CD. A velocimetry technique for microfabricated fluidic systems. J Microelectromechanical Systems. In press.
- 20 Kawaoka J, Gomez F. Use of mobility ratios to estimate binding constants of ligands to proteins in affinity capillary electrophoresis. J Chromatograph 1998; 715: 203–10.
- 21 Beebe D, Moore J, Yu Q, Liu R, Kraft M, Jo B-H, et al. Microfluidic tectonics: a comprehensive construction platform for microfluidics systems. Proc Natl Acad Sci U S A 2000; 97: 13488–93.
- 22 Fulton RJ, McDade RL, Smith PL, Kienker LJ, Kettman JR Jr. Advanced multiplexed analysis with the FlowMetrix system. Clin Chem 1997; 43: 1749–56.
- 23 Walt DR. Techview: molecular biology—bead-based fiber-optic arrays. Science 2000; 287: 451–2.
- 24 Del Rincon I, Zeidel M, Rey E, Harley J, James J, Fischbach M, et al. Delineation of human systemic lupus erythematosus anti-Smith antibody response using phage display combinatorial libraries. J Immunol 2000; 165: 7011–6.
- 25 Ekins RP. Multianalyte immunoassay. J Pharm Biomed Anal 1987: 155–68.
- 26 Ekins R, Chu F. Multianalyte microspot immunoassay: the microanalytical “compact disk” of the future. Ann Biol Clin 1992; 50: 337–53.
- 27 Ekins R, Chu F, Micallef J. High specific activity chemiluminescent and fluorescent markers: their potential application to high sensitivity and ‘multianalyte’ immunoassays. J Biolumin Chemilumin 1989; 4: 59–78.
- 28 Mendoza L, McQuary P, Mongan A, Gangadharan R, Brignac S, Eggers M. High-throughput microarray-based enzyme-linked immunosorbant assay (ELISA). Biotechniques 1999; 27: 778–88.
- 29 Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991; 251: 767–73.
- 30 Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, et al. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 1999; 17: 974–8.
- 31 Blanchard AP, Friend SH. Cheap DNA arrays: it's not all smoke and mirrors. Nat Biotechnol 1999; 17: 953.
- 32 Ge H. UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA, and protein-ligand interactions. Nucleic Acids Res 2000; 28: e3.
- 33 Meheus L, van Venrooij WJ, Wiik A, Charles PJ, Tzioufas AG, Meyer O, et al. Multicenter validation of recombinant, natural and synthetic antigens used in a single multiparameter assay for the detection of specific anti-nuclear autoantibodies in connective tissue disorders. Clin Exp Rheumatol 1999; 17: 205–14.
- 34 Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995; 270: 467–70.
- 35 Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2001; 2: Research 0004.1–.13.
- 36 MacBeath G, Schreiber S. Printing proteins as microarrays for high-throughput function determination. Science 2000; 289: 1760–3.
- 37
Joos T,
Schrenk M,
Hopfl P,
Kroger K,
Chowdhury U,
Stoll D, et al.
A microarray enzyme-linked immunosorbent assay for autoimmune diagnostics.
Electrophoresis
2000;
21:
2641–50.
10.1002/1522-2683(20000701)21:13<2641::AID-ELPS2641>3.0.CO;2-5 CAS PubMed Web of Science® Google Scholar
- 38 Robinson W, DiGennaro C, Hueber W, Haab B; Kamachi M, Dean E, et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nature Med. In press.
- 39 Casciola-Rosen LA, Miller DK, Anhalt GJ, Rosen A. Specific cleavage of the 70 kDa protein component of the U1 small nuclear riboprotein is a characteristic biochemical feature of apoptotic cell death. J Biol Chem 1994; 269: 30757–60.
- 40 Casciola-Rosen L, Andrade F, Ulanet D, Wong W, Rosen A. Cleavage by granzyme B is strongly predictive of autoantigen status: implications for initiation of autoimmunity. J Exp Med 1999; 190: 815–26.
- 41 Utz PJ, Gensler TJ, Anderson P. Death, autoantigen modifications, and tolerance. Arthritis Res 2000; 2: 101–14.
- 42 Utz PJ, Anderson P. Posttranslational modifications, apoptosis, and the bypass of tolerance to autoantigens. Arthritis Rheum 1998; 41: 1152–60.
- 43 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science 2001; 291: 1304–51.
- 44 Lueking A, Horn M, Eickhoff H, Büssow K, Lehrach H, Walter G. Protein microarrays for gene expression and antibody screening. Anal Biochem 1999; 270: 103–11.
- 45 Büssow K, Cahill D, Nietfeld W, Bancroft D, Scherzinger E, Lehrach H, et al. A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Res 1998; 26: 5007–8.
- 46 Craft J, Fatenejad S. Self antigens and epitope spreading in systemic autoimmunity. Arthritis Rheum 1997; 40: 1374–82.
- 47 James J, Harley J. B-cell epitope spreading in autoimmunity. Immunol Rev 1998; 164: 185–200.
- 48 Abbas A, Murphy K, Sher A. Functional diversity of helper T lymphocytes. Nature 1996; 383: 789–93.
- 49 Liblau R, Singer S, McDevitt H. Th1 and Th2 CD4+ T cells in the pathogenesis of organ-specific autoimmune diseases. Immunol Today 1995; 16: 34–8.
- 50 Harris D, Haynes L, Sayles P, Duso D, Eaton S, Lepak N, et al. Reciprocal regulation of polarized cytokine production by effector B and T cells. Nature Immunol 2000; 1: 475–82.
- 51 Whitney L, Becker K, Tresser N, Caballero-Ramos C, Munson P, Prabhu V, et al. Analysis of gene expression in multiple sclerosis lesions using cDNA microarrays. Ann Neurol 1999; 46: 425–8.
- 52 Zanders ED, Goulden MG, Kennedy TC, Kempsell KE. Analysis of immune system gene expression in small rheumatoid arthritis biopsies using a combination of subtractive hybridization and high-density cDNA arrays. J Immunol Methods 2000; 233: 131–40.
- 53
Ungethum U,
Haupl T,
Zacher J,
Gursche A,
Forster P,
Reutermann P, et al.
Patterns of differentially expressed genes in synovial tissue from RA and OA patients and from normal joints [abstract].
Arthritis Res
2001;
3:
A16.
10.1186/ar214 Google Scholar
- 54 Lock C, Hermans G, Pedotti R, Garren H, Langer-Gould A, Brendolan A, et al. Harvest of gene microarray analysis of recently inflamed acute/active versus non-inflamed chronic silent multiple sclerosis lesions yields seven new targets validated in an animal model. Submitted for publication.
- 55 Weiner HL, Friedman A, Miller A, Khoury SJ, al-Sabbagh A, Santos L, et al. Oral tolerance: immunologic mechanisms and treatment of animal and human organ-specific autoimmune diseases by oral administration of autoantigens. Annu Rev Immunol 1994; 12: 809–37.
- 56 Gaur A, Wiers B, Liu A, Rothbard J, Fathman CG. Amelioration of autoimmune encephalomyelitis by myelin basic protein synthetic peptide-induced anergy. Science 1992; 258: 1491–4.
- 57 Warren KG, Catz I, Wucherpfennig KW. Tolerance induction to myelin basic protein by intravenous synthetic peptides containing epitope P85 VVHFFKNIVTP96 in chronic progressive multiple sclerosis. J Neurol Sci 1997; 152: 31–8.
- 58 Brocke S, Gijbels K, Allegretta M, Ferber I, Piercy C, Blankenstein T, et al. Treatment of experimental encephalomyelitis with a peptide analogue of myelin basic protein. Nature 1996; 379: 343–6.
- 59 Critchfield JM, Racke MK, Zuniga-Pflucker JC, Cannella B, Raine CS, Goverman J, et al. T cell deletion in high antigen dose therapy of autoimmune encephalomyelitis. Science 1994; 263: 1139–43.
- 60 Furie RA, Cash JM, Cronin ME, Katz RS, Weisman MH, Aranow C, et al. Treatment of systemic lupus erythematosus with LJP 394. J Rheumatol 2001; 28: 257–65.
- 61 Ruiz P, Garren H, Urbanek-Ruiz I, Hirschberg D, Nguyen L, Karpuj M, et al. Suppressive immunization with DNA encoding a self-protein prevents autoimmune disease: modulation of T cell costimulation. J Immunol 1999; 162: 3336–41.
- 62 Garren H, Steinman L. DNA vaccination in the treatment of autoimmune disease. Curr Dir Autoimmun 2000; 2: 203–16.
- 63 Garren H, Ruiz PJ, Watkins TA, Fontoura P, Nguyen LT, Estline ER, et al. Combination of gene delivery and DNA vaccination to protect from and reverse Th1 autoimmune disease via deviation to the Th2 pathway. Immunity 2001; 15: 15–22.
- 64 Robinson WH, Garren H, Utz PJ, Steinman L. Proteomics for the development of DNA tolerizing vaccines to treat autoimmune disease. Clin Immunol. In press.
- 65 Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, et al. Global analysis of protein activities using proteome chips. Science 2001; 293: 210–5.
- 66 He M, Taussig MJ. Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res 2001; 29: e73:1–6.
- 67 Ziauddin J, Sabatini DM. Microarrays of cells expressing defined cDNAs. Nature 2001; 411: 107–10.
- 68 Utz P, Hottelet M, Schur P, Anderson P. Proteins phosphorylated during stress-induced apoptosis are common targets for autoantibody production in patients with systemic lupus erythematosus. J Exp Med 1997; 185: 843–54.