Proteomic approaches in the search for biomarkers of liver fibrosis

Trends in Molecular Medicine

Volumn 16, Issue 4, 2010, Pages 171-183

  Cowan, Matthew L ^a   Rahman, Tony M ^b   Krishna, Sanjeev ^a  

^a University of London Cranmer Terrace   (United Kingdom)

^b ST GEORGE'S UNIVERSITY HOSPITALS NHS FOUNDATION TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE AMINOTRANSFERASE; ALBUMIN; ALKALINE PHOSPHATASE; ALPHA 1 ANTICHYMOTRYPSIN; ALPHA 1 MICROGLOBULIN; ALPHA 2 MACROGLOBULIN; ANGIOTENSINOGEN; APOLIPOPROTEIN A1; APOLIPOPROTEIN A4; APOLIPOPROTEIN C1; APOLIPOPROTEIN C2; APOLIPOPROTEIN D; ASPARTATE AMINOTRANSFERASE; BETA 2 MICROGLOBULIN; BETA2 GLYCOPROTEIN 1; BIOTINIDASE; CERULOPLASMIN; CLUSTERIN; COLLAGEN; COMPLEMENT COMPONENT C1S; COMPLEMENT COMPONENT C3; COMPLEMENT COMPONENT C4; HYALURONIC ACID; MATRIX METALLOPROTEINASE; PLATELET DERIVED GROWTH FACTOR; SOMATOMEDIN C; TISSUE INHIBITOR OF METALLOPROTEINASE; TRANSFORMING GROWTH FACTOR BETA; UNINDEXED DRUG;

AMINO ACID SEQUENCE; CHRONIC LIVER DISEASE; DISEASE MARKER; HEPATITIS C; HUMAN; LIVER BIOPSY; LIVER CELL CARCINOMA; LIVER FIBROSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEOMICS; PROTHROMBIN TIME; REVIEW; RISK ASSESSMENT; RISK FACTOR; THROMBOCYTE COUNT; TWO DIMENSIONAL GEL ELECTROPHORESIS; UNINDEXED SEQUENCE;

BIOLOGICAL MARKERS; CHRONIC DISEASE; DIAGNOSIS, DIFFERENTIAL; HUMANS; LIVER CIRRHOSIS; PROTEOMICS;

EID: 77950518456     PISSN: 14714914     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molmed.2010.01.006     Document Type: Review

References (103)

1. Friedman S.L. Liver fibrosis - from bench to bedside. J. Hepatol. 38 Suppl 1 (2003) S38-53
2. Poynard T., et al. Natural history of liver fibrosis progression in patients with chronic hepatitis C. The OBSVIRC, METAVIR, CLINIVIR, and DOSVIRC groups. Lancet 349 (1997) 825-832
3. D'Amico G., et al. Natural history and prognostic indicators of survival in cirrhosis: a systematic review of 118 studies. J. Hepatol. 44 (2006) 217-231
4. Afdhal N.H., and Nunes D. Evaluation of liver fibrosis: a concise review. Am. J. Gastroenterol. 99 (2004) 1160-1174
5. Fried M.W., et al. Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N. Engl. J. Med. 347 (2002) 975-982
6. Friedman S.L., and Bansal M.B. Reversal of hepatic fibrosis - fact or fantasy?. Hepatology 43 (2006) S82-88
7. Albanis E., and Friedman S.L. Antifibrotic agents for liver disease. Am. J. Transplant 6 (2006) 12-19
8. Bravo A.A., et al. Liver biopsy. N. Engl. J. Med. 344 (2001) 495-500
9. Akay S., et al. Liver biopsy: is the pain for real or is it only the fear of it?. Dig. Dis. Sci. 52 (2007) 579-581
10. Terjung B., et al. Bleeding complications after percutaneous liver biopsy. An analysis of risk factors. Digestion 67 (2003) 138-145
11. Cravatt B.F., et al. The biological impact of mass-spectrometry-based proteomics. Nature 450 (2007) 991-1000
12. Petricoin E.F., et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359 (2002) 572-577
13. Papadopoulos M.C., et al. A novel and accurate diagnostic test for human African trypanosomiasis. Lancet 363 (2004) 1358-1363
14. Agranoff D., et al. Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum. Lancet 368 (2006) 1012-1021
15. Liotta L.A., et al. Clinical proteomics: written in blood. Nature 425 (2003) 905
16. Brunt E.M., et al. Nonalcoholic steatohepatitis: a proposal for grading and staging the histological lesions. Am. J. Gastroenterol. 94 (1999) 2467-2474
17. Bedossa P., and Poynard T. An algorithm for the grading of activity in chronic hepatitis C. The METAVIR Cooperative Study Group. Hepatology 24 (1996) 289-293
18. Ishak K., et al. Histological grading and staging of chronic hepatitis. J. Hepatol. 22 (1995) 696-699
19. Westin J., et al. Interobserver study of liver histopathology using the Ishak score in patients with chronic hepatitis C virus infection. Liver 19 (1999) 183-187
20. Stanley A.J., et al. Assessment of liver histology in patients with hepatitis C and normal transaminase levels. Eur. J. Gastroenterol. Hepatol. 8 (1996) 869-872
21. Poynard T., and Bedossa P. Age and platelet count: a simple index for predicting the presence of histological lesions in patients with antibodies to hepatitis C virus. METAVIR and CLINIVIR Cooperative Study Groups. J. Viral. Hepat. 4 (1997) 199-208
22. Gressner A.M., et al. Non-invasive biomarkers for monitoring the fibrogenic process in liver: a short survey. World J. Gastroenterol. 15 (2009) 2433-2440
23. Imbert-Bismut F., et al. Biochemical markers of liver fibrosis in patients with hepatitis C virus infection: a prospective study. Lancet 357 (2001) 1069-1075
24. Parkes J., et al. Performance of serum marker panels for liver fibrosis in chronic hepatitis C. J. Hepatol. 44 (2006) 462-474
25. Wai C.T., et al. A simple noninvasive index can predict both significant fibrosis and cirrhosis in patients with chronic hepatitis C. Hepatology 38 (2003) 518-526
26. Forns X., et al. Identification of chronic hepatitis C patients without hepatic fibrosis by a simple predictive model. Hepatology 36 (2002) 986-992
27. Rosenberg W.M., et al. Serum markers detect the presence of liver fibrosis: a cohort study. Gastroenterology 127 (2004) 1704-1713
28. Haydon G.H., et al. Prediction of cirrhosis in patients with chronic hepatitis C infection by artificial neural network analysis of virus and clinical factors. J. Viral. Hepat. 5 (1998) 255-264
29. Jiang Z., et al. Support vector machine-based feature selection for classification of liver fibrosis grade in chronic hepatitis C. J. Med. Syst. 30 (2006) 389-394
30. Guha I.N. Back to the future with noninvasive biomarkers of liver fibrosis. Hepatology 49 (2009) 9-11
31. Sebastiani G., et al. Stepwise combination algorithms of non-invasive markers to diagnose significant fibrosis in chronic hepatitis C. J. Hepatol. 44 (2006) 686-693
32. Castera L., et al. Non-invasive evaluation of liver fibrosis using transient elastography. J. Hepatol. 48 (2008) 835-847
33. Lim A.K., et al. Hepatic vein transit times using a microbubble agent can predict disease severity non-invasively in patients with hepatitis C. Gut 54 (2005) 128-133
34. Rouviere O., et al. MR elastography of the liver: preliminary results. Radiology 240 (2006) 440-448
35. Lewin M., et al. Diffusion-weighted magnetic resonance imaging for the assessment of fibrosis in chronic hepatitis C. Hepatology 46 (2007) 658-665
36. Lim A.K., et al. The relationship of in vivo 31P MR spectroscopy to histology in chronic hepatitis C. Hepatology 37 (2003) 788-794
37. Diamond D.L., et al. HepatoProteomics: applying proteomic technologies to the study of liver function and disease. Hepatology 44 (2006) 299-308
38. Cheung K.J., et al. The HCV serum proteome: a search for fibrosis protein markers. J. Viral. Hepat. 16 (2009) 418-429
39. White I.R., et al. Serum proteomic analysis focused on fibrosis in patients with hepatitis C virus infection. J. Transl. Med. 5 (2007) 33
40. Gangadharan B., et al. Novel serum biomarker candidates for liver fibrosis in hepatitis C patients. Clin. Chem. 53 (2007) 1792-1799
41. Gray J., et al. A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease. BMC Cancer 9 (2009) 271
42. He Q.Y., et al. Serum biomarkers of hepatitis B virus infected liver inflammation: a proteomic study. Proteomics 3 (2003) 666-674
43. Trak-Smayra V., et al. Serum proteomic profiling of obese patients: correlation with pathology and evolution after bariatric surgery. Gut 58 (2008) 825-832
44. Younossi Z.M., et al. Hepatic gene expression in patients with obesity-related non-alcoholic steatohepatitis. Liver Int. 25 (2005) 760-771
45. Zhu X.D., et al. New serum biomarkers for detection of HBV-induced liver cirrhosis using SELDI protein chip technology. World J. Gastroenterol. 10 (2004) 2327-2329
46. Cui J., et al. Prediction of chronic hepatitis B, liver cirrhosis and hepatocellular carcinoma by SELDI-based serum decision tree classification. J. Cancer Res. Clin. Oncol. 133 (2007) 825-834
47. Schwegler E.E., et al. SELDI-TOF MS profiling of serum for detection of the progression of chronic hepatitis C to hepatocellular carcinoma. Hepatology 41 (2005) 634-642
48. Gobel T., et al. New multi protein patterns differentiate liver fibrosis stages and hepatocellular carcinoma in chronic hepatitis C serum samples. World J. Gastroenterol. 12 (2006) 7604-7612
49. Hu J., et al. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct. Genomic Proteomic 3 (2005) 322-331
50. Poon T.C., et al. Prediction of liver fibrosis and cirrhosis in chronic hepatitis B infection by serum proteomic fingerprinting: a pilot study. Clin. Chem. 51 (2005) 328-335
51. Morra R., et al. Diagnostic value of serum protein profiling by SELDI-TOF ProteinChip compared with a biochemical marker, FibroTest, for the diagnosis of advanced fibrosis in patients with chronic hepatitis C. Aliment Pharmacol. Ther. 26 (2007) 847-858
52. Jacobs J.M., et al. Proteome analysis of liver cells expressing a full-length hepatitis C virus (HCV) replicon and biopsy specimens of posttransplantation liver from HCV-infected patients. J. Virol. 79 (2005) 7558-7569
53. Sato S., et al. Proteomic profiling of lipid droplet proteins in hepatoma cell lines expressing hepatitis C virus core protein. J. Biochem. 139 (2006) 921-930
54. Kristensen D.B., et al. Proteome analysis of rat hepatic stellate cells. Hepatology 32 (2000) 268-277
55. Cheung K.J., et al. Proteomics in liver fibrosis is more than meets the eye. Eur. J. Gastroenterol. Hepatol. 20 (2008) 450-464
56. Low T.Y., et al. A proteomic analysis of thioacetamide-induced hepatotoxicity and cirrhosis in rat livers. Proteomics 4 (2004) 3960-3974
57. Xu X.Q., et al. Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics. Proteomics 4 (2004) 3235-3245
58. Diamond D.L., et al. Proteomic profiling of human liver biopsies: hepatitis C virus-induced fibrosis and mitochondrial dysfunction. Hepatology 46 (2007) 649-657
59. Cairns D.A., et al. Sample size determination in clinical proteomic profiling experiments using mass spectrometry for class comparison. Proteomics 9 (2009) 74-86
60. Molleken C., et al. Detection of novel biomarkers of liver cirrhosis by proteomic analysis. Hepatology 49 (2009) 1257-1266
61. Carr S.A., and Anderson L. Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?. Clin Chem 54 (2008) 1749-1752
62. Mischak H., et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clinical Applications 1 (2007) 148-156
63. Ransohoff D.F. Bias as a threat to the validity of cancer molecular-marker research. Nat. Rev. Cancer 5 (2005) 142-149
64. Ransohoff D.F. Rules of evidence for cancer molecular-marker discovery and validation. Nat. Rev. Cancer 4 (2004) 309-314
65. Banks R.E., et al. Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin. Chem. 51 (2005) 1637-1649
66. Sorace J.M., and Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 4 (2003) 24
67. Baggerly K.A., et al. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 20 (2004) 777-785
68. Semmes O.J., et al. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin. Chem. 51 (2005) 102-112
69. Verrills N.M. Clinical proteomics: present and future prospects. Clin. Biochem. Rev. 27 (2006) 99-116
70. Bjorhall K., et al. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 5 (2005) 307-317
71. Geho D.H., et al. The amplified peptidome: the new treasure chest of candidate biomarkers. Curr. Opin. Chem. Biol. 10 (2006) 50-55
72. Keshishian H., et al. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell Proteomics 6 (2007) 2212-2229
73. Diamandis E.P. Point: Proteomic patterns in biological fluids: do they represent the future of cancer diagnostics?. Clin. Chem. 49 (2003) 1272-1275
74. Bedossa P., et al. Sampling variability of liver fibrosis in chronic hepatitis C. Hepatology 38 (2003) 1449-1457
75. Colloredo G., et al. Impact of liver biopsy size on histological evaluation of chronic viral hepatitis: the smaller the sample, the milder the disease. J. Hepatol. 39 (2003) 239-244
76. Standish R.A., et al. An appraisal of the histopathological assessment of liver fibrosis. Gut 55 (2006) 569-578
77. Poynard T., et al. Biochemical surrogate markers of liver fibrosis and activity in a randomized trial of peginterferon alfa-2b and ribavirin. Hepatology 38 (2003) 481-492
78. Castera L., et al. Evolving practices of non-invasive markers of liver fibrosis in patients with chronic hepatitis C in France: Time for new guidelines?. J. Hepatol. 46 (2007) 528-529
79. Castera L., et al. Prospective comparison of transient elastography, Fibrotest, APRI, and liver biopsy for the assessment of fibrosis in chronic hepatitis C. Gastroenterology 128 (2005) 343-350
80. Naveau S., et al. Alpha-2-macroglobulin and hepatic fibrosis. Diagnostic interest. Dig. Dis. Sci. 39 (1994) 2426-2432
81. Leroy V., et al. Circulating matrix metalloproteinases 1, 2, 9 and their inhibitors TIMP-1 and TIMP-2 as serum markers of liver fibrosis in patients with chronic hepatitis C: comparison with PIIINP and hyaluronic acid. Am. J. Gastroenterol. 99 (2004) 271-279
82. Lok A.S., et al. Predicting cirrhosis in patients with hepatitis C based on standard laboratory tests: results of the HALT-C cohort. Hepatology 42 (2005) 282-292
83. Fontana R.J., et al. Modeling hepatic fibrosis in African American and Caucasian American patients with chronic hepatitis C virus infection. Hepatology 44 (2006) 925-935
84. Sterling R.K., et al. Development of a simple noninvasive index to predict significant fibrosis in patients with HIV/HCV coinfection. Hepatology 43 (2006) 1317-1325
85. Angulo P., et al. The NAFLD fibrosis score: a noninvasive system that identifies liver fibrosis in patients with NAFLD. Hepatology 45 (2007) 846-854
86. Koda M., et al. FibroIndex, a practical index for predicting significant fibrosis in patients with chronic hepatitis C. Hepatology 45 (2007) 297-306
87. Harrison S.A., et al. Development and validation of a simple NAFLD clinical scoring system for identifying patients without advanced disease. Gut 57 (2008) 1441-1447
88. Gravel P., et al. New alterations of serum glycoproteins in alcoholic and cirrhotic patients revealed by high resolution two-dimensional gel electrophoresis. Biochem. Biophys Res. Commun. 220 (1996) 78-85
89. Serpaggi J., et al. Direct and indirect evidence for the reversibility of cirrhosis. Hum. Pathol. 37 (2006) 1519-1526
90. Moreno M., et al. Long-term evolution of liver histopathology in patients with chronic hepatitis C and sustained response. Rev. Esp. Enferm. Dig. 97 (2005) 860-869
91. Hammel P., et al. Regression of liver fibrosis after biliary drainage in patients with chronic pancreatitis and stenosis of the common bile duct. N. Engl. J. Med. 344 (2001) 418-423
92. Kisseleva T., and Brenner D.A. Hepatic stellate cells and the reversal of fibrosis. J Gastroenterol Hepatol 21 Suppl 3 (2006) S84-87
93. Baroni G.S., et al. Interferon gamma decreases hepatic stellate cell activation and extracellular matrix deposition in rat liver fibrosis. Hepatology 23 (1996) 1189-1199
94. Pockros P.J., et al. Final results of a double-blind, placebo-controlled trial of the antifibrotic efficacy of interferon-gamma1b in chronic hepatitis C patients with advanced fibrosis or cirrhosis. Hepatology 45 (2007) 569-578
95. Issa R., et al. Spontaneous recovery from micronodular cirrhosis: evidence for incomplete resolution associated with matrix cross-linking. Gastroenterology 126 (2004) 1795-1808
96. Shi Z., et al. Strain-specific differences in mouse hepatic wound healing are mediated by divergent T helper cytokine responses. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 10663-10668
97. Geerts A., et al. Collagen type I and III occur together in hybrid fibrils in the space of Disse of normal rat liver. Hepatology 12 (1990) 233-241
98. Han Y.P. Matrix metalloproteinases, the pros and cons, in liver fibrosis. J. Gastroenterol. Hepatol. 21 Suppl 3 (2006) S88-91
99. Herbst H., et al. Temporal and spatial patterns of transin/stromelysin RNA expression following toxic injury in rat liver. Virchows Arch. B Cell Pathol. Incl. Mol. Pathol. 60 (1991) 295-300
100. Hong H., et al. Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) mass spectrometry (MS). BMC Bioinformatics 6 Suppl 2 (2005) S5
101. Honda M., et al. Different signaling pathways in the livers of patients with chronic hepatitis B or chronic hepatitis C. Hepatology 44 (2006) 1122-1138
102. Mehta S.H., et al. Exceeding the limits of liver histology markers. J. Hepatol. 50 (2009) 36-41
103. Gluud C., et al. Hepatology may have problems with putative surrogate outcome measures. J. Hepatol. 46 (2007) 734-742