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Peripheral blood gene expression: it all boils down to the RNA collection tubes

BACKGROUND: Gene expression profiling from peripheral blood is a valuable tool for biomarker discovery in clinical studies. Different whole blood RNA collection and processing methods are highly variable and might confound comparisons of results across studies. The main aim of the study was to compa...

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Autores principales: Menke, Andreas, Rex-Haffner, Monika, Klengel, Torsten, Binder, Elisabeth B, Mehta, Divya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280191/
https://www.ncbi.nlm.nih.gov/pubmed/22214347
http://dx.doi.org/10.1186/1756-0500-5-1
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author Menke, Andreas
Rex-Haffner, Monika
Klengel, Torsten
Binder, Elisabeth B
Mehta, Divya
author_facet Menke, Andreas
Rex-Haffner, Monika
Klengel, Torsten
Binder, Elisabeth B
Mehta, Divya
author_sort Menke, Andreas
collection PubMed
description BACKGROUND: Gene expression profiling from peripheral blood is a valuable tool for biomarker discovery in clinical studies. Different whole blood RNA collection and processing methods are highly variable and might confound comparisons of results across studies. The main aim of the study was to compare genome-wide gene expression profiles obtained from the two widely used commercially available whole blood RNA collection systems - PAXgene™ and Tempus™ tubes. Comparisons of present call rates, variances, correlations and influence of globin reduction across the two collection systems was performed using in vivo glucocorticoid stimulation in 24 peripheral blood samples from three individuals. RESULTS: RNA quality, yield and numbers of detected transcripts from the two RNA collection systems was comparable, with no significant differences between the tube types. Globin reduction resulted in a significant increase in present call rates (p = 8.17 × 10(-5 )and p = 1.95 × 10(-3 )in PAXgene™ and Tempus™ tubes respectively) and significant decrease in gene expression variance in both RNA collection tubes (p = 0.0025 and p = 0.041 in PAXgene™ and Tempus™ tubes respectively). Comparisons of glucocorticoid receptor-stimulated gene expression profiles between the two collection tube systems revealed an overlap of only 17 to 54%, depending on the stringency level of the statistical thresholds. This overlap increased by 1-8% when the RNA samples were processed to remove the globin mRNA. CONCLUSION: RNA obtained from PAXgene™ and Tempus™ tubes was comparable in terms of quality and yield, however, detectable gene expression changes after glucocorticoid receptor stimulation were distinct, with an overlap of only up to 46% between the two collection systems. This overlap increased to 54% when the samples were depleted of globin mRNA and drastically reduced to 17-18% when only gene expression differences with a fold change greater than 2.0 were assessed. These results indicate that gene expression profiles obtained from PAXgene™ and Tempus™ differ drastically and should not be analyzed together. These data suggest that researchers must exert caution while interpreting expression profiles obtained through different RNA collection tubes.
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spelling pubmed-32801912012-02-16 Peripheral blood gene expression: it all boils down to the RNA collection tubes Menke, Andreas Rex-Haffner, Monika Klengel, Torsten Binder, Elisabeth B Mehta, Divya BMC Res Notes Research Article BACKGROUND: Gene expression profiling from peripheral blood is a valuable tool for biomarker discovery in clinical studies. Different whole blood RNA collection and processing methods are highly variable and might confound comparisons of results across studies. The main aim of the study was to compare genome-wide gene expression profiles obtained from the two widely used commercially available whole blood RNA collection systems - PAXgene™ and Tempus™ tubes. Comparisons of present call rates, variances, correlations and influence of globin reduction across the two collection systems was performed using in vivo glucocorticoid stimulation in 24 peripheral blood samples from three individuals. RESULTS: RNA quality, yield and numbers of detected transcripts from the two RNA collection systems was comparable, with no significant differences between the tube types. Globin reduction resulted in a significant increase in present call rates (p = 8.17 × 10(-5 )and p = 1.95 × 10(-3 )in PAXgene™ and Tempus™ tubes respectively) and significant decrease in gene expression variance in both RNA collection tubes (p = 0.0025 and p = 0.041 in PAXgene™ and Tempus™ tubes respectively). Comparisons of glucocorticoid receptor-stimulated gene expression profiles between the two collection tube systems revealed an overlap of only 17 to 54%, depending on the stringency level of the statistical thresholds. This overlap increased by 1-8% when the RNA samples were processed to remove the globin mRNA. CONCLUSION: RNA obtained from PAXgene™ and Tempus™ tubes was comparable in terms of quality and yield, however, detectable gene expression changes after glucocorticoid receptor stimulation were distinct, with an overlap of only up to 46% between the two collection systems. This overlap increased to 54% when the samples were depleted of globin mRNA and drastically reduced to 17-18% when only gene expression differences with a fold change greater than 2.0 were assessed. These results indicate that gene expression profiles obtained from PAXgene™ and Tempus™ differ drastically and should not be analyzed together. These data suggest that researchers must exert caution while interpreting expression profiles obtained through different RNA collection tubes. BioMed Central 2012-01-04 /pmc/articles/PMC3280191/ /pubmed/22214347 http://dx.doi.org/10.1186/1756-0500-5-1 Text en Copyright ©2011 Menke et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Menke, Andreas
Rex-Haffner, Monika
Klengel, Torsten
Binder, Elisabeth B
Mehta, Divya
Peripheral blood gene expression: it all boils down to the RNA collection tubes
title Peripheral blood gene expression: it all boils down to the RNA collection tubes
title_full Peripheral blood gene expression: it all boils down to the RNA collection tubes
title_fullStr Peripheral blood gene expression: it all boils down to the RNA collection tubes
title_full_unstemmed Peripheral blood gene expression: it all boils down to the RNA collection tubes
title_short Peripheral blood gene expression: it all boils down to the RNA collection tubes
title_sort peripheral blood gene expression: it all boils down to the rna collection tubes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280191/
https://www.ncbi.nlm.nih.gov/pubmed/22214347
http://dx.doi.org/10.1186/1756-0500-5-1
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