Systems analysis identifies miR-29b regulation of invasiveness in melanoma.
BACKGROUND
In many cancers, microRNAs (miRs) contribute to metastatic progression by modulating phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. This can be driven by miRs targeting multiple mRNA transcripts, inducing regulated changes across large sets of genes. The miR-target databases TargetScan and DIANA-microT predict putative relationships by examining sequence complementarity between miRs and mRNAs. However, it remains a challenge to identify which miR-mRNA interactions are active at endogenous expression levels, and of biological consequence.


METHODS
We developed a workflow to integrate TargetScan and DIANA-microT predictions into the analysis of data-driven associations calculated from transcript abundance (RNASeq) data, specifically the mutual information and Pearson's correlation metrics. We use this workflow to identify putative relationships of miR-mediated mRNA repression with strong support from both lines of evidence. Applying this approach systematically to a large, published collection of unique melanoma cell lines - the Ludwig Melbourne melanoma (LM-MEL) cell line panel - we identified putative miR-mRNA interactions that may contribute to invasiveness. This guided the selection of interactions of interest for further in vitro validation studies.


RESULTS
Several miR-mRNA regulatory relationships supported by TargetScan and DIANA-microT demonstrated differential activity across cell lines of varying matrigel invasiveness. Strong negative statistical associations for these putative regulatory relationships were consistent with target mRNA inhibition by the miR, and suggest that differential activity of such miR-mRNA relationships contribute to differences in melanoma invasiveness. Many of these relationships were reflected across the skin cutaneous melanoma TCGA dataset, indicating that these observations also show graded activity across clinical samples. Several of these miRs are implicated in cancer progression (miR-211, -340, -125b, -221, and -29b). The specific role for miR-29b-3p in melanoma has not been well studied. We experimentally validated the predicted miR-29b-3p regulation of LAMC1 and PPIC and LASP1, and show that dysregulation of miR-29b-3p or these mRNA targets can influence cellular invasiveness in vitro.


CONCLUSIONS
This analytic strategy provides a comprehensive, systems-level approach to identify miR-mRNA regulation in high-throughput cancer data, identifies novel putative interactions with functional phenotypic relevance, and can be used to direct experimental resources for subsequent experimental validation. Computational scripts are available: http://github.com/uomsystemsbiology/LMMEL-miR-miner.
['Andrews|Miles C|MC|', 'Cursons|Joseph|J|', 'Hurley|Daniel G|DG|', 'Anaka|Matthew|M|', 'Cebon|Jonathan S|JS|', 'Behren|Andreas|A|', 'Crampin|Edmund J|EJ|']
D000465:Algorithms D045744:Cell Line, Tumor D002465:Cell Movement D019295:Computational Biology D018450:Disease Progression D020869:Gene Expression Profiling D015972:Gene Expression Regulation, Neoplastic D006801:Humans D008545:Melanoma D035683:MicroRNAs D009361:Neoplasm Invasiveness D010641:Phenotype D034622:RNA Interference D012323:RNA Processing, Post-Transcriptional D020871:RNA Stability D012333:RNA, Messenger D059467:Transcriptome D057188:Workflow
Melanoma Cancer TargetScan Statistical association DIANA-microT CDS Phenotypic switching Systems biology micro-RNA