Comparative analysis of the liver and plasma proteomes as a novel and powerful strategy for hepatocellular carcinoma biomarker discovery

Cancer Letters

Volumn 286, Issue 1, 2009, Pages 134-139

  Beretta, Laura ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Biomarker; Hepatocellular carcinoma; Liver cancer; Mouse model; Proteomics

Indexed keywords

BIOLOGICAL MARKER; LIVER PROTEIN; METHIONINE ADENOSYLTRANSFERASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PLASMA PROTEIN; PLATELET DERIVED GROWTH FACTOR C; PROTEOME;

ANIMAL TISSUE; CONTROLLED STUDY; DIAGNOSTIC PROCEDURE; DISEASE COURSE; DISEASE MODEL; HUMAN; HUMAN TISSUE; LIQUID CHROMATOGRAPHY; LIVER CELL CARCINOMA; LIVER CIRRHOSIS; LIVER FIBROSIS; MASS SPECTROMETRY; METHODOLOGY; MOUSE; NONALCOHOLIC FATTY LIVER; NONHUMAN; PATHOGENESIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; SHORT SURVEY; TANDEM MASS SPECTROMETRY;

EID: 70350567762     PISSN: 03043835     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.canlet.2009.01.025     Document Type: Review

References (35)

1. Beretta L. Proteomics from the clinical perspective: many hopes and much debate. Nat. Methods 4 (2007) 785-786
2. Conrads T.P., Hood B.L., Petricoin III E.F., Liotta L.A., and Veenstra T.D. Cancer proteomics: many technologies, one goal. Expert Rev. Proteomics 2 (2005) 693-703
3. Hanash S.M. Disease proteomics. Nature 422 (2003) 226-232
4. Massion P.P., and Caprioli R.M. Proteomic strategies for the characterization and the early detection of lung cancer. J. Thorac. Oncol. 1 (2006) 1027-1039
5. Marko-Varga G., Ogiwara A., Nishimura T., Kawamura T., Fujii K., Kawakami T., Kyono Y., Tu H.K., Anyoji H., Kanazawa M., Akimoto S., Hirano T., Tsuboi M., Nishio K., Hada S., Jiang H., Fukuoka M., Nakata K., Nishiwaki Y., Kunito H., Peers I.S., Harbron C.G., South M.C., Higenbottam T., Nyberg F., Kudoh S., and Kato H. Personalized medicine and proteomics: lessons from non-small cell lung cancer. J. Proteome Res. 6 (2007) 2925-2935
6. Fu Q., and Van Eyk J.E. Proteomics and heart disease: identifying biomarkers of clinical utility. Expert Rev. Proteomics 3 (2006) 237-249
7. Bergeron J.J., and Hallett M. Peptides you can count on. Nat. Biotechnol. 25 (2007) 61-62
8. Liu H., Sadygov R.G., and Yates III J.R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76 (2004) 4193-4201
9. States D.J., Omenn G.S., Blackwell T.W., Fermin D., Eng J., Speicher D.W., and Hanash S.M. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24 (2006) 333-338
10. Gilchrist A., Au C.E., Hiding J., Bell A.W., Fernandez-Rodriguez J., Lesimple S., Nagaya H., Roy L., Gosline S.J., Hallett M., Paiement J., Kearney R.E., Nilsson T., and Bergeron J.J. Quantitative proteomics analysis of the secretory pathway. Cell 127 (2006) 1265-1281
11. Ryan D.P., and Matthews J.M. Protein-protein interactions in human disease. Curr. Opin. Struct. Biol. 15 (2005) 441-446
12. Irish J.M., Kotecha N., and Nolan G.P. Mapping normal and cancer cell signalling networks: towards single-cell proteomics. Nat. Rev. Cancer 6 (2006) 146-155
13. Massoud T.F., Paulmurugan R., De A., Ray P., and Gambhir S.S. Reporter gene imaging of protein-protein interactions in living subjects. Curr. Opin. Biotechnol. 18 (2007) 31-37
14. Villalobos V., Naik S., and Piwnica-Worms D. Current state of imaging protein-protein interactions in vivo with genetically encoded reporters. Annu. Rev. Biomed. Eng. 9 (2007) 321-349
15. Weissleder R. Molecular imaging in cancer. Science 312 (2006) 1168-1171
16. Chignard N., and Beretta L. Proteomics for hepatocellular carcinoma marker discovery. Gastroenterology 127 (2004) S120-125
17. Feng J.T., Shang S., and Beretta L. Proteomics for the early detection and treatment of hepatocellular carcinoma. Oncogene 25 (2006) 3810-3817
18. Chignard N., Shang S., Wang H., Marrero J., Brechot C., Hanash S.M., and Beretta L. Cleavage of endoplasmic reticulum proteins in hepatocellular carcinoma: Detection of generated fragments in patient sera. Gastroenterology 130 (2006) 2010-2022
19. Le Naour F., Brichory F., Misek D.E., Brechot C., Hanash S.M., and Beretta L. A distinct repertoire of autoantibodies in hepatocellular carcinoma identified by proteomic analysis. Mol. Cell. Proteomics 1 (2002) 197-203
20. Obeid M., Tesniere A., Ghiringhelli F., Fimia G.M., Apetoh L., Perfettini J.L., Castedo M., Mignot G., Panaretakis T., Casares N., Metivier D., Larochette N., van Endert P., Ciccosanti F., Piacentini M., Zitvogel L., and Kroemer G. Calreticulin exposure dictates the immunogenicity of cancer cell death. Nat. Med. 13 (2007) 54-61
21. Chen E.I., Hewel J., Felding-Habermann B., and Yates III J.R. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol. Cell. Proteomics 5 (2006) 53-56
22. Wang H., Clouthier S.G., Galchev V., Misek D.E., Duffner U., Min C.K., Zhao R., Tra J., Omenn G.S., Ferrara J.L., and Hanash S.M. Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol. Cell. Proteomics 4 (2005) 618-625
23. Liu T., Qian W.J., Gritsenko M.A., Camp II D.G., Monroe M.E., Moore R.J., and Smith R.D. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. J. Proteome Res. 4 (2005) 2070-2080
24. Plavina T., Wakshull E., Hancock W.S., and Hincapie M. Combination of abundant protein depletion and multi-lectin affinity chromatography (M-LAC) for plasma protein biomarker discovery. J. Proteome Res. 6 (2007) 662-671
25. Stahl-Zeng J., Lange V., Ossola R., Eckhardt K., Krek W., Aebersold R., and Domon B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6 (2007) 1809-1817
26. Lai K.K., Kolippakkam D., and Beretta L. Comprehensive and quantitative proteome profiling of the mouse liver and plasma. Hepatology 47 (2008) 1043-1051
27. Horie Y., Suzuki A., Kataoka E., Sasaki T., Hamada K., Sasaki J., Mizuno K., Hasegawa G., Kishimoto H., Iizuka M., Naito M., Enomoto K., Watanabe S., Mak T.W., and Nakano T. Hepatocyte-specific Pten deficiency results in steatohepatitis and hepatocellular carcinomas. J. Clin. Invest. 113 (2004) 1774-1783
28. Stiles B., Wang Y., Stahl A., Bassilian S., Lee W.P., Kim Y.J., Sherwin R., Devaskar S., Lesche R., Magnuson M.A., and Wu H. Liver-specific deletion of negative regulator Pten results in fatty liver and insulin hypersensitivity [corrected]. Proc. Natl. Acad. Sci. USA 101 (2004) 2082-2087
29. Watanabe S., Horie Y., and Suzuki A. Hepatocyte-specific Pten-deficient mice as a novel model for nonalcoholic steatohepatitis and hepatocellular carcinoma. Hepatol. Res. 33 (2005) 161-166
30. Xu X., Kobayashi S., Qiao W., Li C., Xiao C., Radaeva S., Stiles B., Wang R.H., Ohara N., Yoshino T., LeRoith D., Torbenson M.S., Gores G.J., Wu H., Gao B., and Deng C.X. Induction of intrahepatic cholangiocellular carcinoma by liver-specific disruption of Smad4 and Pten in mice. J. Clin. Invest. 116 (2006) 1843-1852
31. Martinez-Chantar M.L., Corrales F.J., Martinez-Cruz L.A., Garcia-Trevijano E.R., Huang Z.Z., Chen L., Kanel G., Avila M.A., Mato J.M., and Lu S.C. Spontaneous oxidative stress and liver tumors in mice lacking methionine adenosyltransferase 1A. FASEB J. 16 (2002) 1292-1294
32. Campbell J.S., Hughes S.D., Gilbertson D.G., Palmer T.E., Holdren M.S., Haran A.C., Odell M.M., Bauer R.L., Ren H.P., Haugen H.S., Yeh M.M., and Fausto N. Platelet-derived growth factor C induces liver fibrosis, steatosis, and hepatocellular carcinoma. Proc. Natl. Acad. Sci. USA 102 (2005) 3389-3394
33. Lee J.S., Chu I.S., Mikaelyan A., Calvisi D.F., Heo J., Reddy J.K., and Thorgeirsson S.S. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat. Genet. 36 (2004) 1306-1311
34. Thorgeirsson S.S., Lee J.S., and Grisham J.W. Functional genomics of hepatocellular carcinoma. Hepatology 43 (2006) S145-150
35. Beretta L. The Human liver proteome project. Mol. Cell. Proteomics 6 (2007) 2043