Deciphering microRNA targets in pancreatic cancer using miRComb R package

Oncotarget
Maria Vila-CasadesúsMeritxell Gironella

Abstract

MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression. They play important roles in cancer but little is known about the specific functions that each miRNA exerts in each type of cancer. More knowledge about their specific targets is needed to better understand the complexity of molecular networks taking part in cancer. In this study we report the miRNA-mRNA interactome occurring in pancreatic cancer by using a bioinformatic approach called miRComb, which combines tissue expression data with miRNA-target prediction databases (TargetScan, miRSVR and miRDB). MiRNome and transcriptome of 12 human pancreatic tissues (9 pancreatic ductal adenocarcinomas and 3 controls) were analyzed by next-generation sequencing and microarray, respectively. Analysis confirmed differential expression of both miRNAs and mRNAs in cancerous tissue versus control, and unveiled 17401 relevant miRNA-mRNA interactions likely to occur in pancreatic cancer. They were sorted according to the degree of negative correlation between miRNA and mRNA expression. Results highlighted the importance of miR-148a and miR-21 interactions among others. Two components of the Notch signaling pathway, ADAM17 and EP300, were confirmed as miR-14...Continue Reading

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Citations

Dec 29, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Urszula DoughertyMarc Bissonnette
Jan 9, 2021·International Journal of Genomics·Javad BehrooziHabibollah Mahmoodzadeh

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Datasets Mentioned

BETA
U219

Methods Mentioned

BETA
dissection
transfection
PCR
Assay

Software Mentioned

DESeq
miRComb R
GOstats R package
miRNome
miRComb
R package
TargetScan

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