Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods


Autoři: Duncan E. Donohue aff001;  Aarti Gautam aff001;  Stacy-Ann Miller aff001;  Seshamalini Srinivasan aff001;  Duna Abu-Amara aff003;  Ross Campbell aff001;  Charles R. Marmar aff003;  Rasha Hammamieh aff001;  Marti Jett aff001
Působiště autorů: Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America aff001;  The Geneva Foundation, Fort Detrick, MD, United States of America aff002;  Steven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury, Department of Psychiatry, NYU School of Medicine, New York, NY, United States of America aff003;  Advanced Biomedical Computing Center, Frederick, MD, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223065

Souhrn

Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. In the current study, we tested two recently introduced whole blood collection methods, RNAgard® and PAXgene® RNA, in addition to the traditional method of peripheral blood mononuclear cells (PBMCs) separated from whole blood and preserved in Trizol reagent. Study results revealed striking differences in the transcriptomic profiles from the three different methods that imply ex vivo changes in gene expression occurred during the blood collection, preservation, and mRNA extraction processes. When comparing the ability of the three preservation methods to accurately capture individuals’ expression differences, RNAgard® outperformed PAXgene® RNA, and both showed better individual separation of transcriptomic profiles than PBMCs. Hence, our study recommends using a single blood collection platform, and strongly cautions against combining methods during the course of a defined study.

Klíčová slova:

Apoptosis – Blood – Cell binding assay – Gene expression – Gene ontologies – Immune response – Messenger RNA – Microarrays


Zdroje

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PLOS One


2019 Číslo 10

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