Quantitative Proteomic Analysis Of Diverse Differentiated Nasopharyngeal Carcinoma Tissues

Nasopharyngeal carcinoma (NPC) has a remarkably distinctive ethnic and geographic distribution. It is prevalent in southern China and Southeast Asia, where its incidence and lethality has remained top among head and neck squamous cell carcinomas (HNSCC). Compared with other HNSCCs, NPC tends to present at a more advanced stage of disease because of its deep location and vague symptoms. The WHO classification distinguishes three histopathological types of NPC based on the degree of differentiation, among which the nonkeratinizing carcinoma (WHO II type) and the undifferentiated carcinoma (WHOâ…¢type) account for more than 97% of the first diagnosed patients. Although numerous efforts have been made to reveal the molecular mechanism of NPC carcinogenesis, it remains poorly understood, which is affected by research strategies, techniques and the specimens investigated.Proteomics as a high-throughput technology aims at identifying differential expression proteins associated with the development and progression of cancer, providing new opportunities to uncover biomarkers and therapeutic targets for NPC as well as reveal the molecular mechanism underlying this disease. However, the traditional tissue proteomic research on NPC has been limited in fresh-frozen specimens. So it is a challenge to explore the molecular mechanisms underlying NPC differentiation partly owing to the deficiency of well-differentiated NPC tissue specimens in frozen form, whereas they are conventionally banked and enriched in formalin-fixed paraffin-embedded (FFPE) form.The potential of FFPE tissue collections as an alternative to fresh-frozen tissues for biomarker discovery has come into realization with the advantages of extensive case collections and detailed clinical data. Although still in its infancy, formalin-fixed tissue proteomics holds promise as a powerful tool for biomaker-driven translational research, especially for the diseases with low incidence.In this study, taking advantage of the large-scale collections of FFPE tissues, we performed the quntitative proteomic analysis of FFPE NPC with diverse differentiation degrees using iTRAQ labeling, two-dimensional liquid chromatography, and tandem mass spectrometry. This has been the first report that focused on the differentiation mechanism of NPC tissues using proteomic tools. We demonstrated that the proteome inventory of NPC FFPE tissues was highly similar to that of the matched fresh tissues and aquired 730 unique proteins from the FFPE tissues of three histological types of NPC with diverse differentiation degrees,531 of which were labled by iTRAQ covering various cellular process including proliferation, death, defense response, DNA repair and carbohydrate metabolic process.146 proteins with the quantification information were picked out by the Cytoscape software to constitute a protein-protein interacting map.141 up-regulated proteins and 140 down-regulated proteins were classified according to the choromosome locolization of their coding genes. Choromosome 12 was found to contain the most coding genes of the up-regulated proteinsIn summary, our results demonstrated that the application of quantitative proteomics based on iTRAQ technology was effective in evaluating FFPE tissues. We identified and quantified related proteins with differential expression levels in the diverse differentiation types of NPC tissues that constitute the basic data for revealing the molecular mechanism of NPC differentiation and for screening differentiation-related biomarkers.