Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.

<h4>Background</h4>Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been s...

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Autores principales:	Maurizio Callari, Matteo Dugo, Valeria Musella, Edoardo Marchesi, Giovanna Chiorino, Maurizia Mello Grand, Marco Alessandro Pierotti, Maria Grazia Daidone, Silvana Canevari, Loris De Cecco
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/820ce79622ae4e14b4e6fc7d79307889
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spelling	oai:doaj.org-article:820ce79622ae4e14b4e6fc7d793078892021-11-18T07:05:37ZComparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.1932-620310.1371/journal.pone.0045105https://doaj.org/article/820ce79622ae4e14b4e6fc7d793078892012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23028787/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples.<h4>Methodology/principal findings</h4>We investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport.<h4>Conclusions</h4>Technical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs - gene expression integration approach.Maurizio CallariMatteo DugoValeria MusellaEdoardo MarchesiGiovanna ChiorinoMaurizia Mello GrandMarco Alessandro PierottiMaria Grazia DaidoneSilvana CanevariLoris De CeccoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45105 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maurizio Callari Matteo Dugo Valeria Musella Edoardo Marchesi Giovanna Chiorino Maurizia Mello Grand Marco Alessandro Pierotti Maria Grazia Daidone Silvana Canevari Loris De Cecco Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
description	<h4>Background</h4>Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples.<h4>Methodology/principal findings</h4>We investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport.<h4>Conclusions</h4>Technical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs - gene expression integration approach.
format	article
author	Maurizio Callari Matteo Dugo Valeria Musella Edoardo Marchesi Giovanna Chiorino Maurizia Mello Grand Marco Alessandro Pierotti Maria Grazia Daidone Silvana Canevari Loris De Cecco
author_facet	Maurizio Callari Matteo Dugo Valeria Musella Edoardo Marchesi Giovanna Chiorino Maurizia Mello Grand Marco Alessandro Pierotti Maria Grazia Daidone Silvana Canevari Loris De Cecco
author_sort	Maurizio Callari
title	Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
title_short	Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
title_full	Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
title_fullStr	Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
title_full_unstemmed	Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
title_sort	comparison of microarray platforms for measuring differential microrna expression in paired normal/cancer colon tissues.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/820ce79622ae4e14b4e6fc7d79307889
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Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.

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