Proteomics on the diagnostic horizon: Lessons from rheumatology

American Journal of the Medical Sciences

Volumn 333, Issue 1, 2007, Pages 16-25

  Wu, Tianfu ^a   Mohan, Chandra ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

MS MS; Protein microarray; Proteomics; Rheumatology; Two dimensional gel electrophoresis

Indexed keywords

BIOLOGICAL MARKER;

CAPILLARY ELECTROPHORESIS; DIAGNOSTIC APPROACH ROUTE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; LUPUS ERYTHEMATOSUS NEPHRITIS; MASS SPECTROMETRY; MOLECULE; OSTEOARTHRITIS; PROTEIN MICROARRAY; REVIEW; RHEUMATIC DISEASE; RHEUMATOID ARTHRITIS; RHEUMATOLOGY; SJOEGREN SYNDROME; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; SYSTEMIC LUPUS ERYTHEMATOSUS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 33846245995     PISSN: 00029629     EISSN: None     Source Type: Journal    
DOI: 10.1097/00000441-200701000-00003     Document Type: Article

References (79)

1. Collins FS, Green ED, Guttmacher AE, et al. A vision for the future of genomics research. Nature 2003;422:835-47.
2. Greenbaum D, Colangelo C, Williams K, et al. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003;4:117.
3. Gygi SP, Rochon Y, Franza BR, et al. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999;19:1720-30.
4. Espina V, Mehta AI, Winters ME, et al. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 2003;3:2091-100.
5. Anderson KS, LaBaer J. The sentinel within: exploiting the immune system for cancer biomarkers. J Proteome Res 2005;4:1123-33.
6. Rogers MA, Clarke P, Noble J, et al. Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res 2003;63:6971-83.
7. Zhou G, Li H, DeCamp D, et al. 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol Cell Proteomics 2002;1:117-24.
8. Diamandis EP. Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol Cell Proteomics 2004;3:367-78.
9. Diamandis EP. Proteomic patterns to identify ovarian cancer: 3 years on Expert Rev Mol Diagn 2004;4:575-7.
10. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 2004;20:777-85.
11. Baggerly KA, Morris JS, Edmonson SR, et al. Signal in noise: evaluating reported reproducibility of serum proteomics tests for ovariancancer. J Natl Cancer Inst 2005;97:307-9.
12. Tolson J, Bogumil R, Brunst E, et al. Serum protein profiling by SELDI mass spectrometry: detection of multiple variants of serum amyloid alpha in renal cancer patients. Lab Invest 2004;84:845-56.
13. Vlahou A, Giannopoulos A, Gregory BW, et al. Urinary protein profiling of bladder cancer patients by decision tree classification of mass spectral data. Clin Chem 2004;50:1438-41.
14. Vlahou A, Laronga C, Wilson L, et al. A novel approach towards development of a rapid blood test for breast cancer. Clinical Breast Cancer 2003;4:203-9.
15. Vlahou A, Schellhammer PF, Mendrinos S, et al. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am J Pathol 2001;158:1491-502.
16. Grizzle W, Semmes OJ, Feng Z, et al. The EDRN SELDI prostate cancer detection study: a study in biomarker validation in GU oncology. Urol Oncol 2004;22:337-43.
17. Grizzle WE, Adam BL, Bigbee WL, et al. Serum protein expression profiling for cancer detection: validation of a SELDI-based approach for prostate cancer. Dis Markers 2004;19:185-95.
18. Wadsworth JT, Somers KD, Cazares LH, et al. Distinguishing healthy smokers from head and neck cancer. Arch Otolaryngol Head Neck Surg 2004;130:98-104.
19. Petricoin EF, Ardekani AM, Hitt BA, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572-7.
20. Laronga C, Becker S, Watson P, et al. SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers. Dis Markers 2003;19:229-38.
21. Adam BL, Qu Y, Davis JW, et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 2002;62:3609-14.
22. Xiao Z, Adam BL, Cazares LH, et al. Quantitation of serum prostate-specific membrane antigen by a novel protein biochip immunoassay discriminates benign from malignant prostate disease. Cancer Res 2001;61:6029-33.
23. Christoph SK, Tilman V, Edeltraud K, et al. Identification of tumor antigens in renal cell carcinoma by serological proteome analysis. Proteomics 2001;1:8908.
24. Woong-Shick A, Sung-Pil P, Su-Mi B, et al. Identification of hemoglobin-alpha and -beta subunits as potential serum biomarkers for the diagnosis and prognosis of ovarian cancer. Cancer Sci 2005;96:197-201.
25. Li J, Zhang Z, Rosenzweig J, et al. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002;48:1296-304.
26. Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 2005;5:845-56.
27. Fathman CG, Soares L, Chan SM, et al. An array of possibilities for the study of autoimmunity. Nature 2005;435:605-11.
28. Dumont D, Noben J, Raus J, et al. Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients. Proteomics 2004;4:2117-24.
29. Gilburd B, Abu-Shakra M, Shoenfeld Y, et al. Autoantibodies profile in the sera of patients with Sjogren's syndrome: the ANA evaluation - a homogeneous, multiplexed system. Clin Dev Immunol 2004;11:53-6.
30. Lorenz P, Ruschpler P, Koczan D, et al. From transcriptome to proteome: differentially expressed proteins identified in synovial tissue of patients suffering from rheumatoid arthritis and osteoarthritis by an initial screen with a panel of 791 antibodies. Proteomics 2003;3:991-1002.
31. Rus V, Atamas SP, Shustova V, et al. Expression of cytokine and chemokine related genes in peripheral blood mononuclear cells from lupus patients by cDNA array. Clin Immunol 2002;102:283-90.
32. Schaub S, Rush D, Wilkins J, et al. Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol 2004;15:219-27.
33. Stone JH, Rajapakse VN, Hoffman GS, et al. A serum proteomic approach to gauging the state of remission in Wegener's granulomatosis. Arthritis Rheum 2005;52:902-10.
34. Weissinger EM, Wittke S, Kaiser T, et al. Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int 2004;65:2426-34.
35. Rovin BH, Song H, Hebert LA, et al. Plasma, urine, and renal expression of adiponectin in human systemic lupus erythematosus. Kidney Int 2005;68:1825-33.
36. Hueber W, Kidd BA, Tomooka BH, et al. Antigen microarray profiling of autoantibodies in rheumatoid arthritis. Arthritis Rheum 2005;52:2645-55.
37. Chan S, Ermann J, Su L, et al. Protein microarrays for multiplex analysis of signaling pathways. Nature Med 2004;10:1390-6.
38. Drynda S, Ringel B, Kekow M, et al. Proteome analysis reveals disease-associated marker proteins to differentiate RA patients from other inflammatory joint diseases with the potential to monitor anti-TNF therapy. Pathol Res Pract 2004;200:165-71.
39. Pieper R, Gatlin CL, McGrath AM, et al. Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004;4:1159-74.
40. Spahr CS, Davis MT, McGinley MD, et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry I. Profiling an unfractionated tryptic digest. Proteomics 2001;1:93-107.
41. Tonge R, Shaw J, Middleton B, et al. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001;1:377-96.
42. Hoorn EJ, Hoffert JD, Knepper MA. The Application of DIGE-based proteomics to renal physiology. Nephron Physiol 2006;104:61-72.
43. Sinz A, Bantscheff M, Mikkat S, et al. Mass spectrometric proteome analyses of synovial fluids and plasmas from patients suffering from rheumatoid arthritis and comparison to reactive arthritis or osteoarthritis. Electrophoresis 2002;23:3445-56.
44. Oates JC, Varghese S, Bland AM, et al. Prediction of urinary protein markers in lupus nephritis. Kidney Int 2005;68:2588-92.
45. Link AJ, Eng J, Schieltz DM, et al. Direct analysis of protein complexes using mass spectrometry. Nat Biotech 1999;17:676-82.
46. Ashley L, McCormack DM, et al. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal Chem 1997;69:767-76.
47. Delahunty C, Yates JR 3rd. Protein identification using 2D-LC-MS/MS. Methods 2005;35:248-55.
48. Washburn MP, Ulaszek R, Deciu C, et al. Analysis of quantitative proteomic data generated via multidimensional protein identification technology . Anal Chem 2002;74:1650-7.
49. Gygi SP, Rist B, Gerber SA, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotech 1999;17:994-9.
50. Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3:1154-69.
51. DeSouza L, Diehl G, Rodrigues MJ, et al. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J Proteome Res 2005;4:377-86.
52. Hardt M, Witkowska HE, Webb S, et al. Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents. Anal Chem 2005;77:4947-54 .
53. Wu WW, Wang G, Baek SJ, et al. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J Proteome Res 2006;5:651-8.
54. Pang JX, Ginanni N, Dongre AR, et al. Biomarker discovery in urine by proteomics. J Proteome Res 2002;1:161-9.
55. Liao H, Wu J, Kuhn E, et al. Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis. Arthritis Rheum 2004;50:3792-803.
56. Coombes KR, Morris JS, Hu J, et al. Serum proteomics profiling: a young technology begins to mature. Nat Biotechnol 2005;23:291-2.
57. Chapman K. The ProteinChip® Biomarker System from Ciphergen Biosystems: a novel proteomics platform for rapid biomarker discovery and validation. Biochem Soc Trans 2002;30:82-7.
58. Coombes KR, Tsavachidis S, Morris JS, et al. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics 2005;5:4107-17.
59. Vidal BC, Bonventre JV, I-Hong H-S. Towards the application of proteomics in renal disease diagnosis. Clin Sci (Lond) 2005;109:421-30.
60. Miyamae T, Malehorn DE, Lemster B, et al. Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy. Arthritis Res Ther 2005;7:R746-55.
61. Tomosugi N, Kitagawa K, Takahashi N, et al. Diagnostic potential of tear proteomic patterns in Sjogren's syndrome. J Proteome Res 2005;4:820-5.
62. Fliser D, Wittke S, Mischak H. Capillary electrophoresis coupled to mass spectrometry for clinical diagnostic purposes. Electrophoresis 2005;26:2708-16.
63. Kaiser T, Hermann A, Kielstein JT, et al. Capillary electrophoresis coupled to mass spectrometry to establish polypeptide patterns in dialysis fluids. J Chromatogr A 2003;1013:157-71.
64. Wittke S, Fliser D, Haubitz M, et al. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A 2003;1013:173-81.
65. Mischak H, Kaiser T, Walden M, et al. Proteomic analysis for the assessment of diabetic renal damage in humans. Clin Sci (Lond) 2004;107:485-95.
66. Liotta LA, Espina V, Mehta AI, et al. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 2003;3:317-25.
67. Liotta LA, Ferrari M, Petricoin E. Clinical proteomics: written in blood. Nature 2003;425:905.
68. Hanash S. Disease proteomics. Nature 2003;422:226-32.
69. Robinson WH, DiGennaro C, Hueber W, et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med 2002;8:295-301.
70. Li QZ, Xie C, Wu T, et al. Glomerular proteome arrays: a novel approach to uncover autoantibody clusters that best predict disease activity in lupus. J Clin Invest 2005;115:3428-39.
71. Mohan C, Morel L, Yang P, et al. Genetic dissection of SLE pathogenesis: a recipe for nephrophilic autoantibodies. J Clin Invest 1999;103:1685-95.
72. Liang Z, Xie C, Chen C, et al. Pathogenic profiles and molecular signatures of ANAs derived from NZM2410 lupus mice. J Exp Med 2004;199:381-98.
73. Kader HA, Tchernev VT, Satyaraj E, et al. Protein microarray analysis of disease activity in pediatric inflammatory bowel disease demonstrates elevated serum PLGF, IL-7, TFG-1, and IL-12p40 levels in Crohn's disease and ulcerative colitis patients in remission versus active disease. Am J Gastroenterol 2005;100:414-23.
74. Patterson SD. How much of the proteome do we see with discovery-based proteomics methods and how much do we need to see? Curr Proteomics 2004;1:3-12.
75. Constans A. Improving lab-on-a-chip. The Scientist 2005;19:32.
76. Liotta LA, Kohn EC, Petricoin EF. Clinical proteomics: personalized molecular medicine. JAMA 2001;286:2211-4.
77. Mehta AI, Ross S, Lowenthal MS, et al. Biomarker amplification by serum carrier protein binding. Disease Markers 2003;19:1-10.
78. Han DK, Eng J, Zhou H, et al. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 2001;19:946-51.
79. Cutillas PR, Chalkley RJ, Hansen KC, et al. The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol 2004;287:F353-64.