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

• Published in: PloS one Vol. 14; no. 10; p. e0223065
• Main Authors: Donohue, Duncan E., Gautam, Aarti, Miller, Stacy-Ann, Srinivasan, Seshamalini, Abu-Amara, Duna, Campbell, Ross, Marmar, Charles R., Hammamieh, Rasha, Jett, Marti
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 10.10.2019; Public Library of Science (PLoS)
• Subjects: Apoptosis; Armed forces; Biochemistry; Biological markers; Biology; Biology and Life Sciences; Biomarkers; Biomarkers - blood; Blood; Blood banks; Blood Specimen Collection; Collection; Comparative analysis; Drug development; Environmental health; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation - genetics; Genes; Genomes; Humans; Immune response; Leukocytes (mononuclear); Leukocytes, Mononuclear - metabolism; Medical research; Medical schools; Medicine and Health Sciences; Messenger RNA; Methods; Oligonucleotide Array Sequence Analysis; Peripheral blood mononuclear cells; Preservation; Reagents; Research and Analysis Methods; Ribonucleic acid; RNA; RNA - blood; RNA - genetics; RNA, Messenger - blood; RNA, Messenger - genetics; Therapeutics; Transcriptome - genetics; Traumatic brain injury; California; New York; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0223065

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.