Proteomic profiling of human liver biopsies: Hepatitis C virus-induced fibrosis and mitochondrial dysfunction

Hepatology

Volumn 46, Issue 3, 2007, Pages 649-657

  Diamond, Deborah L ^a   Jacobs, Jon M ^b   Paeper, Bryan ^a   Proll, Sean C ^a   Gritsenko, Marina A ^b   Carithers Jr , Robert L ^a   Larson, Anne M ^a   Yeh, Matthew M ^c   Camp II, David G ^b   Smith, Richard D ^b   Katze, Michael G ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIVER PROTEIN; REACTIVE OXYGEN METABOLITE;

ADULT; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE COURSE; DISORDERS OF MITOCHONDRIAL FUNCTIONS; DOWN REGULATION; FATTY ACID OXIDATION; FEMALE; GENOTYPE; HEPATITIS C; HUMAN; HUMAN TISSUE; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; LIVER BIOPSY; LIVER FIBROSIS; LIVER MITOCHONDRION; MALE; OXIDATIVE PHOSPHORYLATION; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ADULT; BIOPSY; FEMALE; HEPACIVIRUS; HUMANS; LIVER CIRRHOSIS; MALE; MIDDLE AGED; MITOCHONDRIA, LIVER; OXIDATIVE STRESS; PROTEINS; PROTEOMICS; SENSITIVITY AND SPECIFICITY;

EID: 34548788465     PISSN: 02709139     EISSN: None     Source Type: Journal    
DOI: 10.1002/hep.21751     Document Type: Article

References (35)

1. Alter MJ, Margolis HS, Ktawczynski K, Judson F, Mahres A, Alexander WJ, et al. The natural history of community-acquired hepatitis C in the United States. N Engl J Med 1992;321:1494-1500.
2. Jacobs JM, Diamond DL, Chan EY, Gritsenko MA, Qian W, Stastna M, et al. Proteome analysis of liver cells expressing a full-length hepatitis C virus (HCV) replicon and biopsy specimens of post transplantation liver from HCV-infected patients. J Virol 2005;79:7558-7569.
3. Fang C, Yi Z, Liu F, Lan S, Wang J, Lu H, Yang P, et al. Proteome analysis of human liver carcinoma Huh7 cells harboring hepatitis c virus subgenomic replicon. Proteomics 2005;6:519-527.
4. Mannova P, Fang R, Wang H, Deng B, McIntosh MW, Hanash SM, et al. Modification of host lipid raft proteome upon hepatitis C virus replication. Mol Cell Proteomics 2006;5:2319-2325.
5. Diamond DL, Proll SC, Jacobs JM, Chan EY, Camp DG II, Smith RD, et al. HepatoProteomics: applying proteomic technologies to the study of liver function and disease. HEPATOLOGY 2006;44:299-308.
6. 18O labeling and the accurate mass and time tag approach. Mol Cell Proteomics 2005;4:700-709.
7. Shen Y, Zhao R, Belov ME, Conrads TP, Anderson GA, Tang K, et al. Packed capillary reversed-phase liquid chromotaography with high-performance electrospray ionization fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal Chem 2001;73:1766-1775.
8. Eng JK, McCormack AL, Yates JR III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994;5:976-989.
9. Qian WJ, Liu T, Monroe ME, Strittmatter EF, Jacobs JM, Kangas LJ, et al. Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res 2005;4:53-62.
10. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003;75:4646-4658.
11. Petritis K, Kangas LJ, Ferguson PL, Anderson GA, Pasa-Tolic' L, Lipton MS, et al. Use of artificial neural networks for the prediction of peptide liquid chromatography elution times in proteome analyses. Anal Chem 2003;75:1039-1048.
12. Harkewicz R, Belov ME, Anderson DA, Pasa-Tolic L, Masselon CD, Prior DC, et al. ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation. J Am Soc Mass Spectrom 2002;13:144-154.
13. Horn DM, Zubarev RA, McLafferty FW. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom 2000;11:320-332.
14. Jacobs JM, Monroe ME, Qian WJ, Shen Y, Anderson GA, Smith RD. Ultra-sensitive, high throughput and quantitative proteomics measurements. Int J Mass Spectrom 2005;240:195-212.
15. Yao X, Freas A, Ramirez J, Demirev P, Fenselau C. Proteolytic 180 labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 2001;73:2836-2842.
16. Tian Q, Stephaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, et al. Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics 2004;3:960-969.
17. Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA. Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003;3:1912-1919.
18. Choe LH, Aggarwal K, Franck Z, Lee KH. A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis 2005;26:2437-2449.
19. Vascotto C, Cesaratto L, D'Ambrosio C, Scaloni A, Avellini C, Paron I, et al. Proteomic analysis of liver tissues subjected to early ischemia/reperfusion injury during human orthotopic liver transplantation. Proteomics 2006;6:3455-3465.
20. Zhang X, Guo Y, Song Y, Sun W, Yu C, Zhao X, et al. Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis. Proteomics 2006;6:5260-5268.
21. Regev A, Berho M, Jeffers LJ, Milikowski C, Molina EG, Pyrsopoulos NT, et al. Sampling error and intraobserver variation in liver biopsy patients with chronic HCV infection. Am J Gastroenterol 2002;97:2614-2618.
22. Batts KP, Ludwig J. An update on terminology and reporting. Am J Surg Pathol 1995;19:1409-1417.
23. Negro F. Mechanisms and significance of liver steatosis in hepatitis C virus infection. World J Gastroenterol 2006;12:6756-6765.
24. Dharancy S, Malapel M, Perlemuter G, Roskams T, Cheng Y, Dubuquoy L, et al. Impaired expression of the peroxisome proliferator-activated receptor alpha during hepatitis C virus infection. Gastroenterology 2005;128:334-342.
25. Cheng PL, Chang MH, Chao CH, Lee YHW. Hepatitis C viral proteins interact with Smad3 and differentially regulate TGF-β/Smad3-mediated transcriptional activation. Oncogene 2004;23:7821-7838.
26. Lee S, Park U, Lee YI. Hepatitis C virus core protein transactivates insulin-like growth factor II gene transcription through acting concurrently on Egr1 and Sp1 sites. Virology 2001;283:167-177.
27. Gong G, Waris G, Tanveer R, Siddiqui A. Human hepatitis C virus NS5A protein alters intracellular calcium levels, induces oxidative stress, and activates STAT-3 and NF-kappa B. Proc Natl Acad Sci 2001;98:9599-9604.
28. Choi J, Ou JHJ. Mechanisms of liver injury. III. Oxidative stress in the pathogenesis of hepatitis C virus. Am J Physiol Gastrointest Liver Physiol 2006;290:G847-G851.
29. Wang T, Weinman SA. Causes and consequences of mitochondrial reactive oxygen species generation in hepatitis C. J Gastroenterol Hepatol 2006;21:S34-S37.
30. Lonardo A, Adinolfi LE, Loria P, Carulli N, Ruggiero G, Day CP. Steatosis and hepatitis C virus: mechanisms and significance for hepatic and extrahepatic disease. Gastroenterology 2004;126:586-597.
31. Katze MG, He Y, Gale M Jr. Viruses and interferon: a fight for supremacy. Nat Rev Immunol 2002; 2:657-677.
32. Loo YM, Owen DM, Li K, Erickson AK, Johnson CL, Fish PM, et al. Viral and therapeutic control of IFN-β promoter stimulator 1 during hepatitis C virus infection. Proc Natl Acad Sci U S A 2006;103:6001-6006.
33. Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, et al. A mammalian organelle map by protein correlation profiling. Cell 2006;125:187-199.
34. Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 2006;125:173-186.
35. Qian WJ, Jacobs JM, Liu T, Camp DG II, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics 2006;5:1727-1744.