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The Epigenetic Regulation of microRNA Genes and Their Role in Cell Invasion and Motility in Human Melanomas
Sandford Burnham Medical Research Institute

MicroRNAs have joined the ranks of important regulatory molecules known to control human cell fate in normal and diseased states. This is also true of cancer cells, including melanoma cells, which are known to undergo progressive epigenetic changes during disease manifestation.   We have identified a group of epigenetically regulated miRNA genes in melanoma cells, and employing direct DNA bisulphite and immunoprecipitated methylated DNA (methyl-DIP) deep-sequencing we have confirmed that the upstream CpG island sequences of several such miRNA genes are hypermethylated in cell lines derived from different stages of melanoma but not in melanocytes and keratinocytes.  Abnormalities in CpG island methylation were also seen in distinct melanoma patient samples classified as primary in situ, regional metastatic, distant metastatic, and nodal metastatic.  The cell line WM1552C derived from a stage 3 melanoma was engineered to artificially express one such epigenetically modified miRNA, miR-34b. This caused a reduction in cell invasion and proliferation rates, suggesting that reduced expression of miR-34b is related to invasiveness and high cell division rate of WM1552C.  RNA samples isolated from WM1552C with or without a miR-34b expression construct were subjected to deep sequencing to identify gene networks around miR-34b. Network modules potentially regulated by miR-34b are related to cytoskeletal remodeling, cell invasion and cell mortality functions, suggesting a mechanism for the role of miR-34b in regulating normal cell motility and cytokinesis.

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