Comparison of blood RNA extraction methods used for gene expression profiling in amyotrophic lateral sclerosis

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Bayatti, Nadhim ^a   Cooper Knock, Johnathan ^a   Bury, Joanna J ^a   Wyles, Matthew ^a   Heath, Paul R ^a   Kirby, Janine ^a   Shaw, Pamela J ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBIN; MESSENGER RNA;

ADULT; AGED; AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; BIOGENESIS; CELL POPULATION; CLINICAL ARTICLE; CONTROLLED STUDY; DENSITY GRADIENT CENTRIFUGATION; EARLY DIAGNOSIS; ELECTROPHORESIS; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; NUCLEOTIDE METABOLISM; PRINCIPAL COMPONENT ANALYSIS; PROTEIN DEGRADATION; PROTEIN DEPLETION; PROTEIN LOCALIZATION; PROTEIN TRANSPORT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; RNA ISOLATION; SIGNAL TRANSDUCTION; VALIDATION PROCESS;

AMYOTROPHIC LATERAL SCLEROSIS; DNA PRIMERS; GENE EXPRESSION PROFILING; GENE ONTOLOGY; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; REAL-TIME POLYMERASE CHAIN REACTION; RNA;

EID: 84900298821     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0087508     Document Type: Article

References (26)

1. Kiernan MC, Vucic S, Cheah BC, Turner MR, Eisen A, et al. (2011) Amyotrophic lateral sclerosis. Lancet 377: 942-955.
2. Ferraiuolo L, Kirby J, Grierson AJ, Sendtner M, Shaw PJ (2011) Molecular pathways of motor neuron injury in amyotrophic lateral sclerosis. Nat Rev Neurol 7: 616-630.
3. Sharp FR, Xu H, Lit L, Walker W, Apperson M, et al. (2006) The future of genomic profiling of neurological diseases using blood. Arch Neurol 63: 1529-1536. (Pubitemid 44748794)
4. Cooper-Knock J, Kirby J, Ferraiuolo L, Heath PR, Rattray M, et al. (2012) Gene expression profiling in human neurodegenerative disease. Nat Rev Neurol 8: 518-530.
5. Kudo LC, Parfenova L, Vi N, Lau K, Pomakian J, et al. (2010) Integrative gene-tissue microarray-based approach for identification of human disease biomarkers: application to amyotrophic lateral sclerosis. Hum Mol Genet 19: 3233-3253.
6. Rollins B, Martin MV, Morgan L, Vawter MP (2010) Analysis of whole genome biomarker expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet 153B: 919-936.
7. Wright C, Bergstrom D, Dai H, Marton M, Morris M, et al. (2008) Characterization of globin RNA interference in gene expression profiling of whole-blood samples. Clin Chem 54: 396-405. (Pubitemid 351302623)
8. Rainen L, Oelmueller U, Jurgensen S, Wyrich R, Ballas C, et al. (2002) Stabilization of mRNA expression in whole blood samples. Clin Chem 48: 1883-1890. (Pubitemid 35222745)
9. Vartanian K, Slottke R, Johnstone T, Casale A, Planck SR, et al. (2009) Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 10: 2.
10. Matheson LA, Duong TT, Rosenberg AM, Yeung RS (2008) Assessment of sample collection and storage methods for multicenter immunologic research in children. J Immunol Methods 339: 82-89.
11. Asare AL, Kolchinsky SA, Gao Z, Wang R, Raddassi K, et al. (2008) Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation. BMC Genomics 9: 474.
12. Oster M, Pollinger JP, Stahler DR, Wayne RK (2012) Optimization of RNA isolation and leukocyte viability in canid RNA expression studies. Conservation Genetics Resources 4: 27-29.
13. Hammerle-Fickinger A, Riedmaier I, Becker C, Meyer HH, Pfaffl MW, et al. (2010) Validation of extraction methods for total RNA and miRNA from bovine blood prior to quantitative gene expression analyses. Biotechnol Lett 32: 35-44.
14. Mougeot JL, Li Z, Price AE, Wright FA, Brooks BR (2011) Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway. BMC Med Genomics 4: 74.
15. Prezeau N, Silvy M, Gabert J, Picard C (2006) Assessment of a new RNA stabilizing reagent (Tempus Blood RNA) for minimal residual disease in oncohematology using the EAC protocol. Leuk Res 30: 569-574. (Pubitemid 43374586)
16. Debey-Pascher S, Hofmann A, Kreusch F, Schuler G, Schuler-Thurner B, et al. (2011) RNA-stabilized whole blood samples but not peripheral blood mononuclear cells can be stored for prolonged time periods prior to transcriptome analysis. J Mol Diagn 13: 452-460.
17. Nikula T, Mykkanen J, Simell O, Lahesmaa R (2013) Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl Res 161: 181-188.
18. Menke A, Rex-Haffner M, Klengel T, Binder EB, Mehta D (2012) Peripheral blood gene expression: it all boils down to the RNA collection tubes. BMC Res Notes 5: 1.
19. Field LA, Jordan RM, Hadix JA, Dunn MA, Shriver CD, et al. (2007) Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples. Clin Biochem 40: 499-502. (Pubitemid 46483331)
20. Sankaran VG, Xu J, Orkin SH (2010) Advances in the understanding of haemoglobin switching. Br J Haematol 149: 181-194.
21. Pearson RD, Liu XJ, Sanguinetti G, Milo M, Lawrence ND, et al. (2009) puma: a Bioconductor package for propagating uncertainty in microarray analysis. BMC Bioinformatics 10.
22. Wolozin B (2012) Regulated protein aggregation: stress granules and neurodegeneration. Mol Neurodegener 7: 56.
23. Kim EK, Choi EJ (2010) Pathological roles of MAPK signaling pathways in human diseases. Biochim Biophys Acta 1802: 396-405.
24. Kirby J, Ning K, Ferraiuolo L, Heath PR, Ismail A, et al. (2011) Phosphatase and tensin homologue/protein kinase B pathway linked to motor neuron survival in human superoxide dismutase 1-related amyotrophic lateral sclerosis. Brain 134: 506-517.
25. Loucks FA, Le SS, Zimmermann AK, Ryan KR, Barth H, et al. (2006) Rho family GTPase inhibition reveals opposing effects of mitogen-activated protein kinase kinase/extracellular signal-regulated kinase and Janus kinase/signal transducer and activator of transcription signaling cascades on neuronal survival. J Neurochem 97: 957-967.
26. Huang da W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.