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Originally published In Press as doi:10.1074/mcp.M700500-MCP200 on March 13, 2008.
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Molecular & Cellular Proteomics 7:1162-1173, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Discovery and Verification of Head-and-neck Cancer Biomarkers by Differential Protein Expression Analysis Using iTRAQ Labeling, Multidimensional Liquid Chromatography, and Tandem Mass Spectrometry*,S

Ranju Ralhan{ddagger},§,¶,||, Leroi V. DeSouza{ddagger},§, Ajay Matta,**, Satyendra Chandra Tripathi, Shaun Ghanny§,{ddagger}{ddagger}, Siddartha Datta Gupta§§, Sudhir Bahadur¶¶ and K. W. Michael Siu{ddagger},§,||||

From the Departments of {ddagger} Chemistry and {ddagger}{ddagger} Mathematics and Statistics and § Centre for Research in Mass Spectrometry, York University, Toronto, Ontario M2J 1P3, Canada and Departments of Biochemistry, §§ Pathology, and ¶¶ Otorhinolaryngology, All India Institute of Medical Sciences, New Delhi 110029, India

Multidimensional LC-MS/MS has been used for the analysis of biological samples labeled with isobaric mass tags for relative and absolute quantitation (iTRAQ) to identify proteins that are differentially expressed in human head-and-neck squamous cell carcinomas (HNSCCs) in relation to non-cancerous head-and-neck tissues (controls) for cancer biomarker discovery. Fifteen individual samples (cancer and non-cancerous tissues) were compared against a pooled non-cancerous control (prepared by pooling equal amounts of proteins from six non-cancerous tissues) in five sets by on-line and off-line separation. We identified 811 non-redundant proteins in HNSCCs, including structural proteins, signaling components, enzymes, receptors, transcription factors, and chaperones. A panel of proteins showing consistent differential expression in HNSCC relative to the non-cancerous controls was discovered. Some of the proteins include stratifin (14-3-3{sigma}); YWHAZ (14-3-3{zeta}); three calcium-binding proteins of the S100 family, S100-A2, S100-A7 (psoriasin), and S100-A11 (calgizarrin); prothymosin {alpha} (PTHA); L-lactate dehydrogenase A chain; glutathione S-transferase Pi; APC-binding protein EB1; and fascin. Peroxiredoxin2, carbonic anhydrase I, flavin reductase, histone H3, and polybromo-1D (BAF180) were underexpressed in HNSCCs. A panel of the three best performing biomarkers, YWHAZ, stratifin, and S100-A7, achieved a sensitivity of 0.92 and a specificity of 0.91 in discriminating cancerous from non-cancerous head-and-neck tissues. Verification of differential expression of YWHAZ, stratifin, and S100-A7 proteins in clinical samples of HNSCCs and paired and non-paired non-cancerous tissues by immunohistochemistry, immunoblotting, and RT-PCR confirmed their overexpression in head-and-neck cancer. Verification of YWHAZ, stratifin, and S100-A7 in an independent set of HNSCCs achieved a sensitivity of 0.92 and a specificity of 0.87 in discriminating cancerous from non-cancerous head-and-neck tissues, thereby confirming their overexpressions and utility as credible cancer biomarkers.

|| Recipient of the NCI, National Institutes of Health-Novartis Translational Cancer Research Fellowship Award of the International Union Against Cancer (UICC) at York University. To whom correspondence may be addressed: Dept. of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele St., Toronto, Ontario M2J 1P3, Canada. Tel.: 416-650-8021; Fax: 416-736-5936; E-mail: ralhanr{at}yorku.ca

|||| To whom correspondence may be addressed: Dept. of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele St., Toronto, Ontario M2J 1P3, Canada. Tel.: 416-650-8021; Fax: 416-736-5936; E-mail: kwmsiu{at}yorku.ca


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