Analysis of differentially expressed genes and metabolic pathways in human uveal melanoma

Background Studies showed that there exsits differential gene expression in human uveal melanoma (UM). However, the researching results are somewhat inconsistently abroad, while relevant literature is still less in China.Few domestic researches have reported the abnormalities of gene transcription level or the pathways of these genes. Objective This study was to compare the gene expression profiles between human UM and normal uvea tissues and analyze the metabolic pathways involved in these differentially expressed genes. Methods Four human UM samples were collected in Beijing Tongren Eye Center, and 4 pieces of normal uveal tissues from 4 donors served as controls.The expression of genes was detected with Human Genome U133 Plus 2.0 chip, and the expression profiles were compared between two groups.The biological functions and active pathways of the genes were analyzed by Gene Ontology Enrichment Analysis Software Toolkit (GOEAST). Results Compared with the normal controls, 4 165 differential genes were screened in human UM (12.50%), including 1 236 up-regulated genes (3.71%) and 2 929 down-regulated genes (8.79%), in which the genes of raised more than 5-, 10-, 50- and 100-fold were 113, 21, 1 and 1, respectively, and the genes of reduced by 50%, 90%, 98% and 99% were 1 053, 422, 33 and 5, respectively.The functions of these differentially expressed genes were associated with cellular differentiation and growth, development, cell adhension, immun response, transcriptional contol, signal transduction and anti-apoptosis.The metabolic pathways of differentially expressed genes included angiogenesis pathway, cell-cycle related protein kinase pathway and immune regulatory pathway (involving B lymphocytes and T lymphocytes). Conclusions Gene expression profiles are evidently different between human UM and normal uveal tissue.The variation of the gene profiles in human UM leads to the changes of multiple biological functions including angiogenesis and kinase pathway even immun system.It is implied that the pathogenesis of human UM is a comprehensive effect of multiple genes and biological pathways. Key words: Melanoma/genetics; Uveal neoplasms; Gene expression profile; Gene expression regulation, neoplastic; Genomics/methods; Cluster analysis; Expression profiling microarray; Humans