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
prolekare.web.journal.doi_sk:
https://doi.org/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:
Gene expression – Messenger RNA – Immune response – Blood – Apoptosis – Microarrays – Gene ontologies – Cell binding assay
Zdroje
1. Opitz L, Salinas-Riester G, Grade M, Jung K, Jo P, Emons G, et al. Impact of RNA degradation on gene expression profiling. BMC Med Genomics. 2010;3:36. Epub 2010/08/11. doi: 10.1186/1755-8794-3-36 20696062; PubMed Central PMCID: PMC2927474.
2. Debey S, Schoenbeck U, Hellmich M, Gathof BS, Pillai R, Zander T, et al. Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J. 2004;4(3):193–207. Epub 2004/03/24. doi: 10.1038/sj.tpj.6500240 15037859.
3. Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol. 2014;12:42. Epub 2014/06/03. doi: 10.1186/1741-7007-12-42 24885439; PubMed Central PMCID: PMC4071332.
4. Thach DC, Lin B, Walter E, Kruzelock R, Rowley RK, Tibbetts C, et al. Assessment of two methods for handling blood in collection tubes with RNA stabilizing agent for surveillance of gene expression profiles with high density microarrays. J Immunol Methods. 2003;283(1–2):269–79. Epub 2003/12/09. doi: 10.1016/j.jim.2003.10.004 14659918
5. Augello; FA, Rainen; L, Uwe Oelmiller E, Ralf Wyrich G, Helge Bastian M, inventorsMethod and device for collecting and stabilizing biological sample. patent US 6,617,170 B2. 2003.
6. HORLITZ M, SCHUBERT A, SPRENGER-HAUSSELS M, GUNTHER K, WYRICH R, OELMULLER U, inventorsSTABILISATION OF BIOLOGICAL SAMPLES" patent WO 2014/049022 Al. 2004 3 April 2014.
7. Asare AL, Kolchinsky SA, Gao Z, Wang R, Raddassi K, Bourcier K, et al. Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation. BMC Genomics. 2008;9:474–. doi: 10.1186/1471-2164-9-474 18847473.
8. Menke A, Rex-Haffner M, Klengel T, Binder EB, Mehta D. Peripheral blood gene expression: it all boils down to the RNA collection tubes. BMC Res Notes. 2012;5:1. Epub 2012/01/05. doi: 10.1186/1756-0500-5-1 22214347; PubMed Central PMCID: PMC3280191.
9. Nikula T, Mykkanen J, Simell O, Lahesmaa R. Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl Res. 2013;161(3):181–8. Epub 2012/11/10. doi: 10.1016/j.trsl.2012.10.003 23138105.
10. Hantzsch M, Tolios A, Beutner F, Nagel D, Thiery J, Teupser D, et al. Comparison of whole blood RNA preservation tubes and novel generation RNA extraction kits for analysis of mRNA and MiRNA profiles. PLoS One. 2014;9(12):e113298. Epub 2014/12/04. doi: 10.1371/journal.pone.0113298 25469788; PubMed Central PMCID: PMC4254602.
11. Meyer A, Paroni F, Gunther K, Dharmadhikari G, Ahrens W, Kelm S, et al. Evaluation of Existing Methods for Human Blood mRNA Isolation and Analysis for Large Studies. PLoS One. 2016;11(8):e0161778. Epub 2016/08/31. doi: 10.1371/journal.pone.0161778 27575051; PubMed Central PMCID: PMC5004844.
12. Kang JE, Hwang SH, Lee JH, Park DY, Kim HH. Effects of RBC removal and TRIzol of peripheral blood samples on RNA stability. Clin Chim Acta. 2011;412(19–20):1883–5. Epub 2011/06/28. doi: 10.1016/j.cca.2011.06.016 21704608.
13. Barnes MG, Grom AA, Griffin TA, Colbert RA, Thompson SD. Gene Expression Profiles from Peripheral Blood Mononuclear Cells Are Sensitive to Short Processing Delays. Biopreserv Biobank. 2010;8(3):153–62. Epub 2011/07/12. doi: 10.1089/bio.2010.0009 21743826; PubMed Central PMCID: PMC3129811.
14. Beekman JM, Reischl J, Henderson D, Bauer D, Ternes R, Pena C, et al. Recovery of microarray-quality RNA from frozen EDTA blood samples. J Pharmacol Toxicol Methods. 2009;59(1):44–9. Epub 2008/11/26. doi: 10.1016/j.vascn.2008.10.003 19028589.
15. Carrol ED, Salway F, Pepper SD, Saunders E, Mankhambo LA, Ollier WE, et al. Successful downstream application of the Paxgene Blood RNA system from small blood samples in paediatric patients for quantitative PCR analysis. BMC Immunol. 2007;8:20. Epub 2007/09/14. doi: 10.1186/1471-2172-8-20 17850649; PubMed Central PMCID: PMC2031894.
16. Krawiec JA, Chen H, Alom-Ruiz S, Jaye M. Modified PAXgene method allows for isolation of high-integrity total RNA from microlitre volumes of mouse whole blood. Lab Anim. 2009;43(4):394–8. Epub 2009/06/09. doi: 10.1258/la.2008.0070157 19502296.
17. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1–13. Epub 2008/11/27. doi: 10.1093/nar/gkn923 19033363; PubMed Central PMCID: PMC2615629.
18. Bayatti N, Cooper-Knock J, Bury JJ, Wyles M, Heath PR, Kirby J, et al. Comparison of blood RNA extraction methods used for gene expression profiling in amyotrophic lateral sclerosis. PLoS One. 2014;9(1):e87508. Epub 2014/01/30. doi: 10.1371/journal.pone.0087508 24475299; PubMed Central PMCID: PMC3903649.
19. Bondar G, Cadeiras M, Wisniewski N, Maque J, Chittoor J, Chang E, et al. Comparison of whole blood and peripheral blood mononuclear cell gene expression for evaluation of the perioperative inflammatory response in patients with advanced heart failure. PLoS One. 2014;9(12):e115097. Epub 2014/12/18. doi: 10.1371/journal.pone.0115097 25517110; PubMed Central PMCID: PMC4269402.
20. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207–10. Epub 2001/12/26. doi: 10.1093/nar/30.1.207 11752295; PubMed Central PMCID: PMC99122.
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