TY - JOUR
T1 - 18O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma
AU - Chaerkady, Raghothama
AU - Thuluvath, Paul J.
AU - Kim, Min Sik
AU - Nalli, Anuradha
AU - Vivekanandan, Perumal
AU - Simmers, Jessica
AU - Torbenson, Michael
AU - Pandey, Akhilesh
N1 - Funding Information:
We thank Svenni Valdimarsson and Geoff Baxter for help with the design and construction of tanks, Mike Miles for providing the fish, John Laurie for fish husbandry and two anonymous referees for their useful comments on the manuscript. A.H. was funded by a Natural Environment Research Council, Co-operative Awards in Science and Engineering studentship supported by the Fisheries Research Services Freshwater Laboratory. S.W.G. received financial support from a Natural Environment Research Council Postdoctoral Fellowship in Freshwater Biology.
PY - 2008/12
Y1 - 2008/12
N2 - Introduction: Quantitative proteomics using tandem mass spectrometry is an attractive approach for identification of potential cancer biomarkers. Fractionation of complex tissue samples into subproteomes prior to mass spectrometric analyses increases the likelihood of identifying cancer-specific proteins that might be present in low abundance. In this regard, glycosylated proteins are an interesting class of proteins that are already established as biomarkers for several cancers. Materials and Methods: In this study, we carried out proteomic profiling of tumor and adjacent non-cancer liver tissues from hepatocellular carcinoma (HCC) patients. Glycoprotein enrichment from liver samples using lectin affinity chromatography and subsequent 18O/ 16O labeling of peptides allowed us to obtain relative abundance levels of lectin-bound proteins. As a complementary approach, we also examined the relative expression of proteins in HCC without glycoprotein enrichment. Lectin affinity enrichment was found to be advantageous to quantitate several interesting proteins, which were not detected in the whole proteome screening approach. We identified and quantitated over 200 proteins from the lectin-based approach. Interesting among these were fetuin, cysteine-rich protein 1, serpin peptidase inhibitor, leucine-rich alpha-2-glycoprotein 1, melanoma cell adhesion molecule, and heparan sulfate proteoglycan-2. Using lectin affinity followed by PNGase F digestion coupled to 18O labeling, we identified 34 glycosylation sites with consensus sequence N-X-T/S. Western blotting and immunohistochemical staining were carried out for several proteins to confirm mass spectrometry results. Conclusion: This study indicates that quantitative proteomic profiling of tumor tissue versus non-cancerous tissue is a promising approach for the identification of potential biomarkers for HCC.
AB - Introduction: Quantitative proteomics using tandem mass spectrometry is an attractive approach for identification of potential cancer biomarkers. Fractionation of complex tissue samples into subproteomes prior to mass spectrometric analyses increases the likelihood of identifying cancer-specific proteins that might be present in low abundance. In this regard, glycosylated proteins are an interesting class of proteins that are already established as biomarkers for several cancers. Materials and Methods: In this study, we carried out proteomic profiling of tumor and adjacent non-cancer liver tissues from hepatocellular carcinoma (HCC) patients. Glycoprotein enrichment from liver samples using lectin affinity chromatography and subsequent 18O/ 16O labeling of peptides allowed us to obtain relative abundance levels of lectin-bound proteins. As a complementary approach, we also examined the relative expression of proteins in HCC without glycoprotein enrichment. Lectin affinity enrichment was found to be advantageous to quantitate several interesting proteins, which were not detected in the whole proteome screening approach. We identified and quantitated over 200 proteins from the lectin-based approach. Interesting among these were fetuin, cysteine-rich protein 1, serpin peptidase inhibitor, leucine-rich alpha-2-glycoprotein 1, melanoma cell adhesion molecule, and heparan sulfate proteoglycan-2. Using lectin affinity followed by PNGase F digestion coupled to 18O labeling, we identified 34 glycosylation sites with consensus sequence N-X-T/S. Western blotting and immunohistochemical staining were carried out for several proteins to confirm mass spectrometry results. Conclusion: This study indicates that quantitative proteomic profiling of tumor tissue versus non-cancerous tissue is a promising approach for the identification of potential biomarkers for HCC.
KW - Hepatocellular carcinoma
KW - Lectin affinity enrichment
KW - Mass spectrometry
KW - Quantitative proteomics
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U2 - 10.1007/s12014-008-9013-0
DO - 10.1007/s12014-008-9013-0
M3 - Article
AN - SCOPUS:62549126875
SN - 1542-6416
VL - 4
SP - 137
EP - 155
JO - Clinical Proteomics
JF - Clinical Proteomics
IS - 3-4
ER -