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Volumn 2, Issue 2, 2013, Pages 185-200

Reference genes selection for transcriptional profiling in blood of HD patients and R6/2 mice

Author keywords

Blood; Huntington s disease; Reference genes selection; RT qPCR

Indexed keywords

ANIMAL; ARTICLE; BLOOD; CASE CONTROL STUDY; DNA MICROARRAY; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS; HUMAN; HUNTINGTON CHOREA; MALE; METHODOLOGY; MOUSE; REFERENCE GENES SELECTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RT-QPCR; STANDARD;

EID: 84908043213     PISSN: 18796397     EISSN: 18796400     Source Type: Journal    
DOI: 10.3233/JHD-120042     Document Type: Article
Times cited : (8)

References (46)
  • 1
    • 69949102831 scopus 로고    scopus 로고
    • Huntington’s disease: The current state of research with peripheral tissues
    • Sassone J, Colciago C, Cislaghi G, Silani V, Ciammola A. Huntington’s disease: The current state of research with peripheral tissues. Exp Neurol. 2009;219(2): 385-97.
    • (2009) Exp Neurol , vol.219 , Issue.2 , pp. 385-397
    • Sassone, J.1    Colciago, C.2    Cislaghi, G.3    Silani, V.4    Ciammola, A.5
  • 2
    • 67650095269 scopus 로고    scopus 로고
    • Beyond the brain: Widespread pathology in Huntington’s disease
    • van der Burg JM, Bjorkqvist M, Brundin P. Beyond the brain: Widespread pathology in Huntington’s disease. Lancet Neurol. 2009;8(8): 765-74.
    • (2009) Lancet Neurol , vol.8 , Issue.8 , pp. 765-774
    • van der Burg, J.M.1    Bjorkqvist, M.2    Brundin, P.3
  • 3
    • 81955162960 scopus 로고    scopus 로고
    • What have we learned from gene expression profiles in Huntington’s disease?
    • Seredenina T, Luthi-Carter R. What have we learned from gene expression profiles in Huntington’s disease? Neurobiol Dis. 2012;45(1): 83-98.
    • (2012) Neurobiol Dis. , vol.45 , Issue.1 , pp. 83-98
    • Seredenina, T.1    Luthi-Carter, R.2
  • 4
    • 35348877164 scopus 로고    scopus 로고
    • Transcriptional signatures in Huntington’s disease
    • Cha JH. Transcriptional signatures in Huntington’s disease. Prog Neurobiol. 2007;83(4): 228-48.
    • (2007) Prog Neurobiol , vol.83 , Issue.4 , pp. 228-248
    • Cha, J.H.1
  • 5
    • 84860476261 scopus 로고    scopus 로고
    • Candidate Proteins, Metabolites and Transcripts in the Biomarkers for Spinal Muscular Atrophy (BforSMA) Clinical Study
    • Finkel RS, Crawford TO, Swoboda KJ, Kaufmann P, Juhasz P, Li X, et al. Candidate Proteins, Metabolites and Transcripts in the Biomarkers for Spinal Muscular Atrophy (BforSMA) Clinical Study. PLoS One. 2012;7(4): e35462.
    • (2012) PLoS One. , vol.7 , Issue.4 , pp. e35462
    • Finkel, R.S.1    Crawford, T.O.2    Swoboda, K.J.3    Kaufmann, P.4    Juhasz, P.5    Li, X.6
  • 6
    • 55349087953 scopus 로고    scopus 로고
    • Discovery and implementation of transcriptional biomarkers of synthetic LXR agonists in peripheral blood cells
    • Blasio-Smith EA, Arai M, Quinet EM, Evans MJ, Kornaga T, Basso MD, et al. Discovery and implementation of transcriptional biomarkers of synthetic LXR agonists in peripheral blood cells. J Transl Med. 2008;6: 59.
    • (2008) J Transl Med. , vol.6 , pp. 59
    • Blasio-Smith, E.A.1    Arai, M.2    Quinet, E.M.3    Evans, M.J.4    Kornaga, T.5    Basso, M.D.6
  • 8
    • 23344448837 scopus 로고    scopus 로고
    • Genome-wide expression profiling of human blood reveals biomarkers for Huntington’s disease
    • Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, Rosas HD, et al. Genome-wide expression profiling of human blood reveals biomarkers for Huntington’s disease. Proc Natl Acad Sci U S A. 2005;102(31): 11023-8.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.31 , pp. 11023-11028
    • Borovecki, F.1    Lovrecic, L.2    Zhou, J.3    Jeong, H.4    Then, F.5    Rosas, H.D.6
  • 9
    • 35448968328 scopus 로고    scopus 로고
    • Analysis of potential transcriptomic biomarkers for Huntington’s disease in peripheral blood
    • Runne H, Kuhn A, Wild EJ, Pratyaksha W, Kristiansen M, Isaacs JD, et al. Analysis of potential transcriptomic biomarkers for Huntington’s disease in peripheral blood. Proc Natl Acad Sci U S A. 2007;104(36): 14424-9.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.36 , pp. 14424-14429
    • Runne, H.1    Kuhn, A.2    Wild, E.J.3    Pratyaksha, W.4    Kristiansen, M.5    Isaacs, J.D.6
  • 10
    • 72849144063 scopus 로고    scopus 로고
    • Gene expression changes in blood as a putative biomarker for Huntington’s disease
    • Lovrecic L, Kastrin A, Kobal J, Pirtosek Z, Krainc D, Peterlin B. Gene expression changes in blood as a putative biomarker for Huntington’s disease. Mov Disord. 2009;24(15): 2277-81.
    • (2009) Mov Disord , vol.24 , Issue.15 , pp. 2277-2281
    • Lovrecic, L.1    Kastrin, A.2    Kobal, J.3    Pirtosek, Z.4    Krainc, D.5    Peterlin, B.6
  • 11
    • 80054742094 scopus 로고    scopus 로고
    • Transcriptional modulator H2A histone family, member Y (H2AFY) marks Huntington disease activity in man and mouse
    • Hu Y, Chopra V, Chopra R, Locascio JJ, Liao Z, Ding H, et al. Transcriptional modulator H2A histone family, member Y (H2AFY) marks Huntington disease activity in man and mouse. Proc Natl Acad Sci U S A. 2011;108(41): 17141-6.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , Issue.41 , pp. 17141-17146
    • Hu, Y.1    Chopra, V.2    Chopra, R.3    Locascio, J.J.4    Liao, Z.5    Ding, H.6
  • 12
    • 78449311670 scopus 로고    scopus 로고
    • ADPribosylation factor guanine nucleotide-exchange factor 2 (ARFGEF2): A new potential biomarker in Huntington’s disease
    • Lovrecic L, Slavkov I, Dzeroski S, Peterlin B. ADPribosylation factor guanine nucleotide-exchange factor 2 (ARFGEF2): A new potential biomarker in Huntington’s disease. J Int Med Res. 2010;38(5): 1653-62.
    • (2010) J Int Med Res , vol.38 , Issue.5 , pp. 1653-1662
    • Lovrecic, L.1    Slavkov, I.2    Dzeroski, S.3    Peterlin, B.4
  • 13
    • 77649302072 scopus 로고    scopus 로고
    • Expressed Alu repeats as a novel, reliable tool for normalization of real-time quantitativeRT-PCR data
    • Marullo M, Zuccato C, Mariotti C, Lahiri N, Tabrizi SJ, Di DS, et al. Expressed Alu repeats as a novel, reliable tool for normalization of real-time quantitativeRT-PCR data. Genome Biol. 2010;11(1): R9.
    • (2010) Genome Biol. , vol.11 , Issue.1 , pp. R9
    • Marullo, M.1    Zuccato, C.2    Mariotti, C.3    Lahiri, N.4    Tabrizi, S.J.5    Di, D.S.6
  • 14
    • 21344471138 scopus 로고    scopus 로고
    • Real-time RT-PCR normalisation; strategies and considerations
    • Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005;6(4): 279-84.
    • (2005) Genes Immun , vol.6 , Issue.4 , pp. 279-284
    • Huggett, J.1    Dheda, K.2    Bustin, S.3    Zumla, A.4
  • 15
    • 77649235913 scopus 로고    scopus 로고
    • How to do successful gene expression analysis using real-time PCR
    • Derveaux S, Vandesompele J, Hellemans J. How to do successful gene expression analysis using real-time PCR. Methods. 2010;50(4): 227-30.
    • (2010) Methods , vol.50 , Issue.4 , pp. 227-230
    • Derveaux, S.1    Vandesompele, J.2    Hellemans, J.3
  • 16
    • 27644563899 scopus 로고    scopus 로고
    • The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization
    • Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, et al. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem. 2005;344(1): 141-3.
    • (2005) Anal Biochem , vol.344 , Issue.1 , pp. 141-143
    • Dheda, K.1    Huggett, J.F.2    Chang, J.S.3    Kim, L.U.4    Bustin, S.A.5    Johnson, M.A.6
  • 17
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RTPCR data by geometric averaging of multiple internal control genes
    • RESEARCH0034
    • Vandesompele J, De PK, Pattyn F, Poppe B, Van RN, De PA, et al. Accurate normalization of real-time quantitative RTPCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3(7): RESEARCH0034.
    • (2002) Genome Biol. , vol.3 , Issue.7
    • Vandesompele, J.1    De, P.K.2    Pattyn, F.3    Poppe, B.4    Van, R.N.5    De, P.A.6
  • 18
    • 0034657845 scopus 로고    scopus 로고
    • The use of TaqMan RT-PCR assays for semiquantitative analysis of gene expression in CNS tissues and disease models
    • Medhurst AD, Harrison DC, Read SJ, Campbell CA, Robbins MJ, Pangalos MN. The use of TaqMan RT-PCR assays for semiquantitative analysis of gene expression in CNS tissues and disease models. J Neurosci Methods. 2000;98(1): 9-20.
    • (2000) J Neurosci Methods , vol.98 , Issue.1 , pp. 9-20
    • Medhurst, A.D.1    Harrison, D.C.2    Read, S.J.3    Campbell, C.A.4    Robbins, M.J.5    Pangalos, M.N.6
  • 19
    • 3442876969 scopus 로고    scopus 로고
    • Normalization of realtime quantitative reverse transcription-PCR data: A modelbased variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    • Andersen CL, Jensen JL, Orntoft TF. Normalization of realtime quantitative reverse transcription-PCR data: A modelbased variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004;64(15): 5245-50.
    • (2004) Cancer Res , vol.64 , Issue.15 , pp. 5245-5250
    • Andersen, C.L.1    Jensen, J.L.2    Orntoft, T.F.3
  • 20
    • 1842483281 scopus 로고    scopus 로고
    • Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excelbased tool using pair-wise correlations
    • Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excelbased tool using pair-wise correlations. Biotechnol Lett. 2004;26(6): 509-15.
    • (2004) Biotechnol Lett , vol.26 , Issue.6 , pp. 509-515
    • Pfaffl, M.W.1    Tichopad, A.2    Prgomet, C.3    Neuvians, T.P.4
  • 21
    • 64149083208 scopus 로고    scopus 로고
    • Interindividual and interethnic variation in genomewide gene expression: Insights into the biological variation of gene expression and clinical implications
    • FanHP, Di LC, Fu BY, Lam LC, Tang NL. Interindividual and interethnic variation in genomewide gene expression: Insights into the biological variation of gene expression and clinical implications. Clin Chem. 2009;55(4): 774-85.
    • (2009) Clin Chem , vol.55 , Issue.4 , pp. 774-785
    • Fan, H.P.1    Di, L.C.2    Fu, B.Y.3    Lam, L.C.4    Tang, N.L.5
  • 22
    • 7444226814 scopus 로고    scopus 로고
    • Equivalence test in quantitative reverse transcription polymerase chain reaction: Confirmation of reference genes suitable for normalization
    • Haller F, Kulle B, Schwager S, Gunawan B, von HA, Sultmann H, et al. Equivalence test in quantitative reverse transcription polymerase chain reaction: Confirmation of reference genes suitable for normalization. Anal Biochem. 2004;335(1): 1-9.
    • (2004) Anal Biochem , vol.335 , Issue.1 , pp. 1-9
    • Haller, F.1    Kulle, B.2    Schwager, S.3    Gunawan, B.4    von, H.A.5    Sultmann, H.6
  • 23
    • 56549119132 scopus 로고    scopus 로고
    • Optimisation of region-specific reference gene selection and relative gene expression analysis methods for pre-clinical trials of Huntington’s disease
    • Benn CL, Fox H, Bates GP. Optimisation of region-specific reference gene selection and relative gene expression analysis methods for pre-clinical trials of Huntington’s disease. Mol Neurodegener. 2008;3: 17.
    • (2008) Mol Neurodegener. , vol.3 , pp. 17
    • Benn, C.L.1    Fox, H.2    Bates, G.P.3
  • 24
    • 52949140212 scopus 로고    scopus 로고
    • Housekeeping genes revisited: Different expressions depending on gender, brain area and stressor
    • Derks NM, Muller M, Gaszner B, Tilburg-Ouwens DT, Roubos EW, Kozicz LT. Housekeeping genes revisited: Different expressions depending on gender, brain area and stressor. Neuroscience. 2008;156(2): 305-9.
    • (2008) Neuroscience , vol.156 , Issue.2 , pp. 305-309
    • Derks, N.M.1    Muller, M.2    Gaszner, B.3    Tilburg-Ouwens, D.T.4    Roubos, E.W.5    Kozicz, L.T.6
  • 25
    • 34548822478 scopus 로고    scopus 로고
    • Effects of aging, dietary restriction and glucocorticoid treatment on housekeeping gene expression in rat cortex and hippocampus-evaluation by real time RT-PCR
    • Tanic N, Perovic M, Mladenovic A, Ruzdijic S, Kanazir S. Effects of aging, dietary restriction and glucocorticoid treatment on housekeeping gene expression in rat cortex and hippocampus-evaluation by real time RT-PCR. J Mol Neurosci. 2007;32(1): 38-46.
    • (2007) J Mol Neurosci , vol.32 , Issue.1 , pp. 38-46
    • Tanic, N.1    Perovic, M.2    Mladenovic, A.3    Ruzdijic, S.4    Kanazir, S.5
  • 26
    • 33747066769 scopus 로고    scopus 로고
    • Age-related changes in relative expression of real-time PCR housekeeping genes in human skeletal muscle
    • Touchberry CD, Wacker MJ, Richmond SR, Whitman SA, Godard MP. Age-related changes in relative expression of real-time PCR housekeeping genes in human skeletal muscle. J Biomol Tech. 2006;17(2): 157-62.
    • (2006) J Biomol Tech , vol.17 , Issue.2 , pp. 157-162
    • Touchberry, C.D.1    Wacker, M.J.2    Richmond, S.R.3    Whitman, S.A.4    Godard, M.P.5
  • 28
    • 0034694128 scopus 로고    scopus 로고
    • Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitativeRT-PCR
    • Schmittgen TD, Zakrajsek BA. Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitativeRT-PCR. J Biochem Biophys Methods. 2000;46(1-2): 69-81.
    • (2000) J Biochem Biophys Methods. , vol.46 , Issue.1-2 , pp. 69-81
    • Schmittgen, T.D.1    Zakrajsek, B.A.2
  • 29
    • 33644750203 scopus 로고    scopus 로고
    • Effects of Histone Deacetylase Inhibitor (HDACi); Trichostatin-A (TSA) on the expression of housekeeping genes
    • Mogal A, Abdulkadir SA. Effects of Histone Deacetylase Inhibitor (HDACi); Trichostatin-A (TSA) on the expression of housekeeping genes. Mol Cell Probes. 2006;20(2): 81-6.
    • (2006) Mol Cell Probes , vol.20 , Issue.2 , pp. 81-86
    • Mogal, A.1    Abdulkadir, S.A.2
  • 30
    • 21244499405 scopus 로고    scopus 로고
    • GAPDH as a housekeeping gene: Analysis of GAPDH mRNA expression in a panel of 72 human tissues
    • Barber RD, Harmer DW, Coleman RA, Clark BJ. GAPDH as a housekeeping gene: Analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics. 2005;21(3): 389-95.
    • (2005) Physiol Genomics , vol.21 , Issue.3 , pp. 389-395
    • Barber, R.D.1    Harmer, D.W.2    Coleman, R.A.3    Clark, B.J.4
  • 31
    • 16044373842 scopus 로고    scopus 로고
    • Exon 1 of theHDgene with an expanded CAG repeat is sufficient to cause a progressive neurological phenotype in transgenic mice
    • Mangiarini L, Sathasivam K, Seller M, Cozens B, Harper A, Hetherington C, et al. Exon 1 of theHDgene with an expanded CAG repeat is sufficient to cause a progressive neurological phenotype in transgenic mice. Cell. 1996;87(3): 493-506.
    • (1996) Cell , vol.87 , Issue.3 , pp. 493-506
    • Mangiarini, L.1    Sathasivam, K.2    Seller, M.3    Cozens, B.4    Harper, A.5    Hetherington, C.6
  • 32
    • 49549109150 scopus 로고    scopus 로고
    • Blood level of brain-derived neurotrophic factor mRNA is progressively reduced in rodent models of Huntington’s disease: Restoration by the neuroprotective compound CEP-1347
    • Conforti P, Ramos C, Apostol BL, Simmons DA, Nguyen HP, Riess O, et al. Blood level of brain-derived neurotrophic factor mRNA is progressively reduced in rodent models of Huntington’s disease: Restoration by the neuroprotective compound CEP-1347. Mol Cell Neurosci. 2008;39(1): 1-7.
    • (2008) Mol Cell Neurosci , vol.39 , Issue.1 , pp. 1-7
    • Conforti, P.1    Ramos, C.2    Apostol, B.L.3    Simmons, D.A.4    Nguyen, H.P.5    Riess, O.6
  • 33
    • 80051623323 scopus 로고    scopus 로고
    • Brain-derived neurotrophic factor in patients with Huntington’s disease
    • Zuccato C, Marullo M, Vitali B, Tarditi A, Mariotti C, Valenza M, et al. Brain-derived neurotrophic factor in patients with Huntington’s disease. PLoS One. 2011;6(8): e22966.
    • (2011) PLoS One. , vol.6 , Issue.8 , pp. e22966
    • Zuccato, C.1    Marullo, M.2    Vitali, B.3    Tarditi, A.4    Mariotti, C.5    Valenza, M.6
  • 34
    • 33644975004 scopus 로고    scopus 로고
    • RNA integrity and the effect on the realtime qRT-PCR performance
    • Fleige S, PfafflMW. RNA integrity and the effect on the realtime qRT-PCR performance. Mol Aspects Med. 2006;27(2-3): 126-39.
    • (2006) Mol Aspects Med. , vol.27 , Issue.2-3 , pp. 126-139
    • Fleige, S.1    Pfaffl, M.W.2
  • 36
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10): R80.
    • (2004) Genome Biol. , vol.5 , Issue.10 , pp. R80
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5    Dudoit, S.6
  • 38
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2): 185-93.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 39
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. 1995;57: 289-300.
    • (1995) Journal of the Royal Statistical Society , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 42
    • 80052606828 scopus 로고    scopus 로고
    • Identification of Phosphoglycerate Kinase 1 (PGK1) as a reference gene for quantitative gene expression measurements in human blood RNA
    • Falkenberg VR, Whistler T, Murray JR, Unger ER, Rajeevan MS. Identification of Phosphoglycerate Kinase 1 (PGK1) as a reference gene for quantitative gene expression measurements in human blood RNA. BMC Res Notes. 2011;4: 324.
    • (2011) BMC Res Notes. , vol.4 , pp. 324
    • Falkenberg, V.R.1    Whistler, T.2    Murray, J.R.3    Unger, E.R.4    Rajeevan, M.S.5
  • 43
    • 0037101835 scopus 로고    scopus 로고
    • Dysregulation of gene expression in the R6/2 model of polyglutamine disease: Parallel changes in muscle and brain
    • Luthi-Carter R, Hanson SA, Strand AD, BergstromDA, Chun W, Peters NL, et al. Dysregulation of gene expression in the R6/2 model of polyglutamine disease: Parallel changes in muscle and brain. Hum Mol Genet. 2002;11(17): 1911-26.
    • (2002) Hum Mol Genet , vol.11 , Issue.17 , pp. 1911-1926
    • Luthi-Carter, R.1    Hanson, S.A.2    Strand, A.D.3    Bergstrom, D.A.4    Chun, W.5    Peters, N.L.6
  • 45
    • 34447317536 scopus 로고    scopus 로고
    • Histones associated with downregulated genes are hypo-acetylated in Huntington’s disease models
    • Sadri-Vakili G, Bouzou B, Benn CL, Kim MO, Chawla P, Overland RP, et al. Histones associated with downregulated genes are hypo-acetylated in Huntington’s disease models. Hum Mol Genet. 2007;16(11): 1293-306.
    • (2007) Hum Mol Genet , vol.16 , Issue.11 , pp. 1293-1306
    • Sadri-Vakili, G.1    Bouzou, B.2    Benn, C.L.3    Kim, M.O.4    Chawla, P.5    Overland, R.P.6
  • 46
    • 25844526181 scopus 로고    scopus 로고
    • Gene expression in Huntington’s disease skeletal muscle: A potential biomarker
    • Strand AD, Aragaki AK, Shaw D, Bird T, Holton J, Turner C, et al. Gene expression in Huntington’s disease skeletal muscle: A potential biomarker. Hum Mol Genet. 2005;14(13): 1863-76.
    • (2005) Hum Mol Genet , vol.14 , Issue.13 , pp. 1863-1876
    • Strand, A.D.1    Aragaki, A.K.2    Shaw, D.3    Bird, T.4    Holton, J.5    Turner, C.6


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