Microarray and Deep Sequencing Cross-platform Analysis of the MirRNome and IsomiR Variation in Response to Epidermal Growth Factor

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2013 Jun 4

PMID 23724959

Citations 22

Authors

Franc Llorens

Manuela Hummel

Lorena Pantano

Xavier Pastor

Ana Vivancos

Ester Castillo

Heidi Mattlin

Anna Ferrer

Matthew Ingham

Marc Noguera

Robert Kofler

Juliane C Dohm

Raquel Pluvinet

Monica Bayes

Heinz Himmelbauer

Jose Antonio Del Rio

Eulalia Marti

Lauro Sumoy

Affiliations

Soon will be listed here.

Abstract

Background: Epidermal Growth Factor (EGF) plays an important function in the regulation of cell growth, proliferation, and differentiation by binding to its receptor (EGFR) and providing cancer cells with increased survival responsiveness. Signal transduction carried out by EGF has been extensively studied at both transcriptional and post-transcriptional levels. Little is known about the involvement of microRNAs (miRNAs) in the EGF signaling pathway. miRNAs have emerged as major players in the complex networks of gene regulation, and cancer miRNA expression studies have evidenced a direct involvement of miRNAs in cancer progression.

Results: In this study, we have used an integrative high content analysis approach to identify the specific miRNAs implicated in EGF signaling in HeLa cells as potential mediators of cancer mediated functions. We have used microarray and deep-sequencing technologies in order to obtain a global view of the EGF miRNA transcriptome with a robust experimental cross-validation. By applying a procedure based on Rankprod tests, we have delimited a solid set of EGF-regulated miRNAs. After validating regulated miRNAs by reverse transcription quantitative PCR, we have derived protein networks and biological functions from the predicted targets of the regulated miRNAs to gain insight into the potential role of miRNAs in EGF-treated cells. In addition, we have analyzed sequence heterogeneity due to editing relative to the reference sequence (isomiRs) among regulated miRNAs.

Conclusions: We propose that the use of global genomic miRNA cross-validation derived from high throughput technologies can be used to generate more reliable datasets inferring more robust networks of co-regulated predicted miRNA target genes.

Citing Articles

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Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli.

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Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions.

Guo L, Zheng L, Zhao Y, Wang Q Biomed Res Int. 2018; 2018:8518563.

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Bioengineered Noncoding RNAs Selectively Change Cellular miRNome Profiles for Cancer Therapy.

Ho P, Duan Z, Batra N, Jilek J, Tu M, Qiu J J Pharmacol Exp Ther. 2018; 365(3):494-506.

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