Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Small RNA sequencing of melanoma samples to deduce microRNA expression profiles

ABSTRACT: We report results on microRNA profiles revealing the distribution of "isomirs" of microRNA in a cancerous state. Deep sequencing was conducted at Stanford University and data analysis was conducted at the University of Connecticut Health Center. Small RNA profiling to deduce differential microRNA expression levels along various stages of melanoma. Deep sequencing was performed on formalin-fixed paraffin-embedded (FFPE) archived tissue samples, fresh frozen samples from melanomas, and cell lines.

ORGANISM(S): Homo sapiens

SUBMITTER: Sam Dadras

PROVIDER: E-GEOD-36236 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Although gain of chromosome-5p is one of the most frequent DNA copy number imbalances in cervical squamous cell carcinoma (SCC), the genes that drive its selection remain poorly understood. In a previous cross-sectional clinical study we showed that the microRNA processor Drosha (located on chromosome-5p) demonstrates frequent copy-number gain and over-expression in cervical SCC, associated with altered microRNA profiles. Here, we have conducted gene depletion/over-expression experiments to demonstrate the functional significance of up-regulated Drosha in cervical SCC cells. Drosha depletion by RNA-interference (RNAi) produced significant, specific reductions in cell motility/invasiveness in vitro, with a silent RNAi-resistant Drosha mutation providing phenotype rescue. Unsupervised hierarchical clustering following global profiling of 319 microRNAs in eighteen cervical SCC cell line specimens generated two groups according to Drosha expression levels. Altering Drosha levels in individual SCC lines changed the group into which the cells clustered, with gene depletion effects being rescued by the RNAi-resistant mutation. Forty-five microRNAs showed significant differential expression between the groups, including four of fourteen that were differentially-expressed in association with Drosha levels in clinical samples. miR-31 up-regulation in Drosha over-expressing samples/cell lines was the highest-ranked change (by adjusted p-value) in both analyses, an observation validated by Northern blotting. These functional data support the role of Drosha as an oncogene in cervical SCC, by affecting expression of cancer-associated microRNAs that have the potential to regulate numerous protein-coding genes. This SuperSeries is composed of the following subset Series: GSE26175: Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles [miRNA] GSE26176: Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles [mRNA] Refer to individual Series

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Small RNA sequencing of melanoma samples to deduce microRNA expression profiles

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