Nasopharyngeal carcinoma (NPC) is a serious public health problem in Hong Kong and Southern China. The comparison of the protein expression in NPC cells and normal nasopharyngeal (NP) epithelial cells would be valuable in understanding the biological mechanisms in NPC formation. In the present study, we compared the proteomic pattern between an Epstein-Barr virus positive NPC cell line C666-1 and an immortalized normal nasopharyngeal epithelial cell line NP69 using two-dimensional polyacrylamide gel electrophoresis (2D PAGE) combined with mass spectrometry for protein identification. We performed 2D PAGE to separate the protein lysates of each cell line in duplicate. The gels were silver stained and their proteomic patterns were compared using PDQuest software. Protein spots with intensities differed by 4-fold or more were excised from the gel and identified by peptide mass fingerprinting (PMF) using Mascot program followed by protein identification using the Swiss-Prot or NCBInr databases. A total of 120 protein spots were found to be differentially expressed by 4-fold or more between the two cell lines. Among them, 38 were up-regulated in the C666-1 cell line while 82 were down-regulated. Fifteen each of up and down-regulated spots were subjected to PMF and 7 of them were successfully identified. Up-regulated proteins include isoform H of calpain 10 (9.9 fold) and ATP synthase alpha chain (19.9 fold) whereas down-regulated proteins include annexin A2 (0.1 fold), annexin A5 (0.2 fold), β-tubulin (0.1 fold), isoform 2 of heat shock cognate 71 kDa protein (<0.1 fold) and profilin (0.1 fold). Those proteins were found to be involved in cell growth and apoptosis (annexin A2, A5), protein folding (isoform 2 of heat shock cognate 71 kDa protein), energy homeostasis (ATP synthase alpha chain, calpain 10) and cytoskeletal maintenance (β-tubulin, profilin) which may have important implications in the development of NPC. Acknowledgments: The Central Allocation Group Research Project, Research Grant Council, Hong Kong Special Administrative Region (CA03/04.SC01); Direct Grant, The Chinese University of Hong Kong

[Proc Amer Assoc Cancer Res, Volume 47, 2006]