| Nasopharyngeal carcinoma (NPC) is a human malignant tumor with high incidence in five provinces of Southern China and Southeastern Asia. The etiology of NPC is associated with Epstein-Barr virus (EBV) infection, environmental factors and genetic alterations. Because of its complex histological features, there exist different histopathological classifications. Clinically, 98% NPC patients suffer from poorly-differentiated squamous cell carcinoma, which leads radiotherapy to be the main therapy method for NPC However, patients with NPC have highly variable clinical course, and the five-year survival rate for NPC patients is under 60%. This clinical heterogeneity with NPC indicates that there are sub-types in nasopharyngeal poorly-differentiated squamous cell carcinoma.Molecular classification of tumor refers to screening several tumor markers for finding unknown human tumor subtypes and/or categorizing particular tumors to already-defined classes using relevant molecular techniques cooperated with bioinformatics based on gene expression patterns. This up-to-date classification system will facilitate the early diagnosis of tumors, promote the development of personalised therapy for tumor patients and improve the prognostic evaluations for therapy. Nowadays, the molecular classification of tumors is becoming one of the most important fields in molecular pathology.cDNA microarray techinique has high sensitivity to test the gene expression level in both quality and quantity, especially in simultaneously monitoring thousands of gene expression in the same tissues or parailelly analyzing the same gene among different tissues. cDNA microarray techinique has been widely regarded as a new high throughput method for gene expression analysis. It is one of the most important techniques used in molecular classification of tumors.In the experiments of molecular classification of NPC, 24 tumor samples that were diagnosed as nasopharyngeal poorly-differentiated squamous cell carcinoma and contained >75% cancer cells by analysis of corresponding H&E-stained sections, 24 normal nasopharyngeal tissues and 4 nasopharyngeal poorly-differentiated squamous cell lines were also used for study. The 32P-dCTP labeled cDNA probes prepared from total RNA extracted from 24 NPC samples respectively , pooled RNA equally from 24 normal nasopharyngeal tissue and 4 NPC cell lines was respectively hybridized to Human 'Named Genes' GeneFilters (Microarrays GF211, ResGen, USA) containing approximately 4000 known genes. By Pathways 4.0 software, the signal intensity in each microarrays was normalized and calculated, and the ratio of genes' intensities of NPC and normal nasopharyngeal tissue was calculated, too.By t-test of expression profiles among all of the samples, 1625 genes were identified with statistically significant difference (P<0.05) between poorly-differentiated carcinomas and normal nasopharyngeal tissues. 114 genes were found to be up-regulated in all of 24 nasopharyngeal poorly-differentiated carcinoma samples, including basic transcription factor 3, cyclin D1, and so on. 42 genes were down-regulated, including cell death-regulatory protein GRIM19, translational inhibitor protein p14.5, et al.And, comparing the two gene expression profiles of nasopharyngeal poorly-differentiated squamous cell carcinoma tissues and cell lines, 50 genesexpressed in NPC tissues but not in cell lines were identified, and regarded as the genes expressed in rumor stroma cells.Based on the expression profiling of 4132 genes and 1625 genes, 24 nasopharyngeal poorly-differentiated squamous cell carcinomas were classified into two subtypes using hierarchical clustering by Cluster software. Both results were consistent: Group one including NPC 101 , 105, 106, 110, 112, 113, 115 and 121,Group two including NPC 102, 103, 104, 107, 108, 109, 111, 114, 116, 117, 118, 119, 120, 122, 123 and 124. 78 genes were identified with statistically significant difference (P<0.05) between the two groups. The clustering result on the basis of the expression pattern of...
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