Limits...
Characterization of the Melanoma miRNAome by Deep Sequencing.

Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons PG, Schmidt C, Sturm RA, Hayward NK - PLoS ONE (2010)

Bottom Line: MicroRNAs (miRNAs) are 18-23 nucleotide non-coding RNAs that regulate gene expression in a sequence specific manner.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 Genome Analyzer II platform.

View Article: PubMed Central - PubMed

Affiliation: Oncogenomics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia.

ABSTRACT

Background: MicroRNAs (miRNAs) 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.

Methodology/principal findings: We sequenced 12 small RNA libraries using Illumina's Genome Analyzer II platform. This massively parallel sequencing approach of a diverse set of melanoma and pigment cell libraries revealed a total of 539 known mature and mature-star sequences, along with the prediction of 279 novel miRNA candidates, of which 109 were common to 2 or more libraries and 3 were present in all libraries.

Conclusions/significance: Some of the novel candidate miRNAs may be specific to the melanocytic lineage and as such could be used as biomarkers to assist in the early detection of distant metastases by measuring the circulating levels in blood. Follow up studies of the functional roles of these pigment cell miRNAs and the identification of the targets should shed further light on the development and progression of melanoma.

Show MeSH

Related in: MedlinePlus

Unsupervised hierarchical clustering using the Pearson's correlation between all expressed miRNAs.QF1160MB, melanoblasts; MELB, melanocytes; D10, acral melanoma; D11, mucosal melanoma; MEL202, uveal melanoma.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2837346&req=5

pone-0009685-g003: Unsupervised hierarchical clustering using the Pearson's correlation between all expressed miRNAs.QF1160MB, melanoblasts; MELB, melanocytes; D10, acral melanoma; D11, mucosal melanoma; MEL202, uveal melanoma.

Mentions: Using the relative proportion of the total unique read counts against total number of reads, a condition tree (Genespring 7.3.1, Agilent) of all novel candidates plus known miRNAs gave good separation of the different histological subtypes of sample (Figure 3).


Characterization of the Melanoma miRNAome by Deep Sequencing.

Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons PG, Schmidt C, Sturm RA, Hayward NK - PLoS ONE (2010)

Unsupervised hierarchical clustering using the Pearson's correlation between all expressed miRNAs.QF1160MB, melanoblasts; MELB, melanocytes; D10, acral melanoma; D11, mucosal melanoma; MEL202, uveal melanoma.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2837346&req=5

pone-0009685-g003: Unsupervised hierarchical clustering using the Pearson's correlation between all expressed miRNAs.QF1160MB, melanoblasts; MELB, melanocytes; D10, acral melanoma; D11, mucosal melanoma; MEL202, uveal melanoma.
Mentions: Using the relative proportion of the total unique read counts against total number of reads, a condition tree (Genespring 7.3.1, Agilent) of all novel candidates plus known miRNAs gave good separation of the different histological subtypes of sample (Figure 3).

Bottom Line: MicroRNAs (miRNAs) are 18-23 nucleotide non-coding RNAs that regulate gene expression in a sequence specific manner.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 Genome Analyzer II platform.

View Article: PubMed Central - PubMed

Affiliation: Oncogenomics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia.

ABSTRACT

Background: MicroRNAs (miRNAs) 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.

Methodology/principal findings: We sequenced 12 small RNA libraries using Illumina's Genome Analyzer II platform. This massively parallel sequencing approach of a diverse set of melanoma and pigment cell libraries revealed a total of 539 known mature and mature-star sequences, along with the prediction of 279 novel miRNA candidates, of which 109 were common to 2 or more libraries and 3 were present in all libraries.

Conclusions/significance: Some of the novel candidate miRNAs may be specific to the melanocytic lineage and as such could be used as biomarkers to assist in the early detection of distant metastases by measuring the circulating levels in blood. Follow up studies of the functional roles of these pigment cell miRNAs and the identification of the targets should shed further light on the development and progression of melanoma.

Show MeSH
Related in: MedlinePlus