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

Menke, Andreas, Rex-Haffner, Monika, Klengel, Torsten, Binder, Elisabeth B. and Mehta, Divya (2012) Peripheral blood gene expression: it all boils down to the RNA collection tubes. BMC Research Notes, 2012 . doi:10.1186/1756-0500-5-1


Author Menke, Andreas
Rex-Haffner, Monika
Klengel, Torsten
Binder, Elisabeth B.
Mehta, Divya
Title Peripheral blood gene expression: it all boils down to the RNA collection tubes
Journal name BMC Research Notes   Check publisher's open access policy
ISSN 1756-0500
Publication date 2012-01-04
Year available 2012
Sub-type Article (original research)
DOI 10.1186/1756-0500-5-1
Open Access Status DOI
Volume 2012
Total pages 8
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
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.
Keyword RNA collection
Gene expression
Biomarker discovery
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article ID : 5:1

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Brain Institute Publications
 
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Created: Mon, 27 Oct 2014, 14:38:12 EST by Sylvie Pichelin on behalf of Queensland Brain Institute