Characterization of the melanoma miRNAome by deep sequencing

MicroRNAs are 18-23 nucleotide non-coding RNAs that regulate gene expression in a sequence specific manner. Little is known about the repertoire and function of miRNAs in melanoma or the melanocytic lineage. We therefore undertook a comprehensive analysis of the miRNAome in a diverse range of pigment cells including: melanoblasts, melanocytes, congenital nevocytes, acral, mucosal, cutaneous and uveal melanoma cells. We sequenced 12 small RNA libraries using Illumina's GAII platform. This massively parallel sequencing approach revealed a total of 539 known mature and mature-star sequences, along with the prediction of 389 novel miRNA candidates. Using the relative proportion of the total unique read counts against total number of reads, hierarchal clustering of all novel candidates plus known miRNAs gave good separation of the different histological subtypes. Some of the novel miRNAs may be specific to the melanocytic lineage and as such could be used as biomarkers to assist in the early detection of distant metastasises by measuring the circulating levels in blood. Follow up studies of the functional roles of these pigment cell miRNAs and the identification of their targets should shed further light on their role in the development and progression of melanoma. Illumina GAII deep sequencing of 12 melanoma and pigment cell lines