Magnetic nanoparticles versus a commercial kit for apolipoprotein E gene polymorphism analysis

doi:10.3969/j.issn.2095-4344.2013.38.016

Abstract

Abstract:

BACKGROUND: Relative to blood samples, mouth swab samples are more beneficial for apolipoprotein E gene polymorphism analysis among large cohorts. However, agreement has not yet been reached about how to extract genomic DNA form mouth swab samples.
OBJECTIVE: To develop an appropriate method to extract genomic DNA form mouth swab samples, which are suitable for apolipoprotein E gene polymorphism analysis.
METHODS: Fifty mouth swab samples from patients with sporadic Alzheimer’s disease were collected. Magnetic nanoparticles and PicoDNA trace nucleic acid extraction kit were used to extract genomic DNA form mouth swab samples. And the purity and concentration of the genomic DNA extracted by the two methods were analyzed. Then PCR amplifications and DNA electrophoresis were performed to confirm whether the genomic DNA was able to amplify desired DNA fragments. DNA sequencing was applied to analyze apolipoprotein E gene polymorphisms.
RESULTS AND CONCLUSION: Genomic DNA extracted by the two methods was of high purity. The concentration of genomic DNA extracted by magnetic nanoparticles was higher than by PicoDNA trace nucleic acid extraction kit, and the difference had statistical significance (P < 0.05). All the genomic DNA were able to performed PCR amplifications to obtain desired PCR products, but results of DNA electrophoresis showed that DNA fragments were more clear by nanoparticles method. The results of DNA sequencing were the same by the
two methods. The distribution of ε2, ε3, ε4 genotypes of apolipoprotein E gene was 6%, 71%, 23%, respectively. Magnetic nanoparticles were better than PicoDNA trace nucleic acid extraction kit for extracting genomic DNA form mouth swab samples for apolipoprotein E gene polymorphism analysis.

Key words: genes, nanoparticles, apolipoproteins E, Alzheimer disease

CLC Number:

R318

Wu Ting, Yi Li, Huang Ying, Wu Jun. Magnetic nanoparticles versus a commercial kit for apolipoprotein E gene polymorphism analysis[J]. Chinese Journal of Tissue Engineering Research, doi: 10.3969/j.issn.2095-4344.2013.38.016.

Figures/Tables 4

References

[1] Lauderback CM,Kanski J,Hackett JM,et al.Apolipoprotein E modulates Alzheimer's Abeta(1-42)-induced oxidative damage to synaptosomes in an allele-specific manner.Brain Res.2002;924(1):90-97.
[2] Raffai RL,Dong LM,Farese RV Jr,et al.Introduction of human apolipoprotein E4 "domain interaction" into mouse apolipoprotein E. Proc Natl Acad Sci U S A. 2001;98(20): 11587-11591.
[3] Li L,Thompson PA,Kitchens RL.Infection induces a positive acute phase apolipoprotein E response from a negative acute phase gene: a role of hepatic LDL receptors. J Lipid Res. 2008; 49(8):1782-1793.
[4] Laffont I,Takahashi M,Shibukawa Y,et al.Apolipoprotein E activates Akt pathway in neuron-2a in an isoform-specific manner. Biochem Biophys Res Commun. 2002;292(1):83-87.
[5] Huang Y.Aβ-independent roles of apolipoprotein E4 in the pathogenesis of Alzheimer’s disease. Trends Mol Med.2010; 16(6): 287-294.
[6] Luchsinger JA,Mayeux R.Cardiovascular risk factors and Alzheimer’s disease. Curr Atheroscler Rep.2004;6(4)：261-266.
[7] Lahiri DK.Apolipoprotein E as a target for developing new therapeutics for Alzheimer's disease based on studies from protein, RNA, and regulatory region of the gene.J Mol Neurosci. 2004;23(3):225-233.
[8] Mahley RW,Weisgraber KH,Huang Y.Apolipoprotein E4: a causative factor and therapeutic target in neuropathology, including Alzheimer's disease. Proc Natl Acad Sci U S A.2006; 103(15):5644-5651.
[9] Kline A.Apolipoprotein E,amyloid-ß clearance and therapeutic opportunities in Alzheimer's disease.Alzheimers Res Ther. 2012; 4(4):32.
[10] Ferri CP,Prince M,Brayne C,et al. Global prevalence of dementia :a Delphi consensus study.Lancet.2005; 366(9503): 2112-2117.
[11] Lasser RA,Dukoff R,Levy J,et al. Apolipoprotein E epsilon 4 allele in association with global cognitive performance and CSF markers in Alzheimer's disease. Int J Geriatr Psychiatry. 1998;13(11):767-774.
[12] Ewers M,Zhong Z,Bürger K,et al.Increased CSF-BACE 1 activity is associated with ApoE-epsilon 4 genotype in subjects with mild cognitive impairment and Alzheimer's disease.Brain.2008;131(Pt 5):1252-1258.
[13] Kim J,Basak J,Holtzman DM.The Role of Apolipoprotein E in Alzheimer’s Disease. Neuron.2009;63(3):287-303.
[14] Lahiri DK,Schnabel B. DNA isolation by a rapid method from human blood samples: effects of MgCl2,EDTA, storage time, and temperature on DNA yield and quality. Biochem Genet. 1993;31(7-8):321-328.
[15] Maloney B,Ray B,Hayden E,et al.Development and validation of the high-quality ‘Rapid Method for Swab’ (RMS) to genotype the HTTLPR serotonin transporter (SLC6A4) promoter polymorphism.Psychiatr Genet. 2009;19(2):72-82.
[16] Ilveskoski E,Lehtimäki T,Erkinjuntti T,et al.Rapid apolipoprotein E genotyping from mailed buccal swabs.J Neurosci Meth.1998;79(1):5-8.
[17] Walker AH,Najarian D,White DL,et al.Collection of genomic DNA by buccal swabs for polymerase chain reaction-based biomarker assays. Environ Health Perspect.1999;107 (7): 517-520.
[18] Rogers NL,Cole SA,Lan HC,et al.New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies. Am J Hum Biol 2007;19(3):319-326.
[19] Andrisin TE,Humma LM,Johnson JA.Collection of genomic DNA by the noninvasive mouthwash method for use in pharmacogenetic studies.Pharmacotherapy. 2002;22(8): 954-960.
[20] Rusanen P,Siikala E,Uittamo J,et al.A novel method for sampling the microbiota from the oral mucosa.Clin Oral Investig.2009;13(2):243-246.
[21] Badulli C,Sbarsi I,Di Giorgio D,et al.A new approach to safely type for HLA the HIV infected people eligible to abacavir therapy: saliva or buccal swab as reliable DNA sources.Clin Chim Acta.2011;412(21-22):1995-1998.
[22] McKhann G,Drachman D,Folstein M,et al.Clinical diagnosis of Alzheimer’s disease: report of the NINCDS-ADRDA Work Group under the auspices of Department of Health and Human Services Task Force on Alzheimer’s Disease. Neurology. 1984;34(7) :939-944.
[23] Jack CR Jr,Barkhof F,Bernstein MA,et al.Steps to standardization and validation of hippocampal volumetry as a biomarker in clinical trials and diagnostic criterion for Alzheimer's disease.Alzheimers Dement. 2011;7(4):474-485.
[24] Koch W, Ehrenhaft A,Griesser K,et al.TaqMan systems for genotyping of disease-related polymorphisms present in the gene encoding apolipoprotein E. Clin Chem Lab Med.2002; 40(11):1123-1131.
[25] Wijnen PA,Drent M,van Dieijen-Visser MP,et al. Pharmacogenetic testing after a simple DNA isolation method on buccal swab samples.Pharmacogenomics. 2009; 10(6):983-987.
[26] Le Marchand L,Lum-Jones A,Saltzman B,et al.Feasibility of collecting buccal cell DNA by mail in a cohort study. Cancer Epidemiol Biomarkers Prev. 2001;10(6):701-703.
[27] Drobnik A,Judd C,Banach D,et al.Public health implications of rapid hepatitis C screening with an oral swab for community-based organizations serving high-risk populations.Am J Public Health.2011;101(11):2151-2155.
[28] Wijnen PA,Op den Buijsch RA,Cheung SC,et al.Genotyping with a dried blood spot method: a useful technique for application in pharmacogenetics. Clin Chim Acta.2008; 388(1-2):189-191.
[29] Gavriel G,Modi N,Stanier P,et al.Neonatal buccal cell collection for DNA analysis. Arch Dis Child Fetal Neonatal Ed.2005;90(2):F187.
[30] Mitsouras K,Faulhaber EA.Saliva as an alternative source of high yield canine genomic DNA for genotyping studies.BMC Res Notes. 2009;2:219.
[31] London SJ,Xia J,Lehman TA,et al.Collection of buccal cell DNA in seventh- grade children using water and a toothbrush. Cancer Epidemiol Biomarkers Prev.2001;10(11):1227-1230.
[32] Ng DP,Koh D,Choo S,et al.Saliva as a viable alternative source of human genomic DNA in genetic epidemiology.Clin Chim Acta.2006;367(1-2):81-85.
[33] Rogers NL,Cole SA,Lan HC,et al. New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies. Am J Hum Biol. 2007;19(3):319-326.
[34] Ng DP,Koh D,Choo SG,et al.Effect of storage conditions on the extraction of PCR-quality genomic DNA from saliva. Clin Chim Acta. 2004 ;343(1-2):191-194.
[35] Laskowitz DT,Thekdi AD,Thekdi SD,et al.Downregulation of microglial activation by apolipoprotein E and apoE-mimetic peptides.Exp Neurol. 2001;167(1):74-85.
[36] Brown CM,Wright E,Colton CA,et al.Apolipoprotein E isoform mediated regulation of nitric oxide release.Free Radic Biol Med. 2002;32(11):1071-1075.
[37] Agosta F,Vossel KA,Miller BL,et al.Apolipoprotein E epsilon4 is associated with disease-specific effects on brain atrophy in Alzheimer's disease and frontotemporal dementia.Proc Natl Acad Sci U S A. 2009;106(6):2018-2022.
[38] Thal DR,Rüb U,Orantes M,et al.Phases of A beta-deposition in the human brain and its relevance for the development of AD.Neurology. 2002;58(12):1791-800.
[39] Drzezga A,Grimmer T,Henriksen G,et al.Effect of APOE genotype on amyloid plaque load and gray matter volume in Alzheimer disease.Neurology. 2009;72(17):1487-1494.
[40] Solomon A,Kivipelto M,Wolozin B,et al.Midlife serum cholesterol and increased risk of Alzheimer's and vascular dementia three decades later. Dement Geriatr Cogn Disord. 2009;28(1):75-80.
[41] Wolozin B,Manger J,Bryant R,et al.Re-assessing the relationship between cholesterol, statins and Alzheimer's disease.Acta Neurol Scand Suppl. 2006;185:63-70.
[42] Bu G. Apolipoprotein E and its receptors in Alzheimer's disease: pathways, pathogenesis and therapy.Nat Rev Neurosci.2009;10(5):333-544.
[43] Prince JA,Zetterberg H,Andreasen N,et al.APOE epsilon4 allele is associated with reduced cerebrospinal fluid levels of Abeta42.Neurology. 2004;62(11):2116-2118.
[44] Lahiri DK,Sambamurti K,Bennett DA.Apolipoprotein gene and its interaction with the environmentally driven risk factors: molecular, genetic and epidemiological studies of Alzheimer's disease.Neurobiol Aging 2004;25(5):651-660.
[45] Parker GR,Cathcart HM,Huang R,et al.Apolipoprotein gene E4 allele promoter polymorphisms as risk factors for Alzheimer's disease.Psychiatr Genet. 2005;15(4):271-275.
[46] Vitek MP,Brown CM,Colton CA.APOE genotype-specific differences in the innate immune response.Neurobiol Aging. 2009;30(9):1350-1360.
[47] Khachaturian AS,Corcoran CD,Mayer LS,et al.Apolipoprotein E epsilon4 count affects age at onset of Alzheimer disease, but not lifetime susceptibility: The Cache County Study.Arch Gen Psychiatry.2004;61(5):518-524.
[48] Heun R,Gühne U,Luck T,et al.Apolipoprotein E allele 4 is not a sufficient or a necessary predictor of the development of Mild Cognitive Impairment. Eur Psychiatry.2010; 25(1):15-18.
[49] Wang G,Su X.A novel technology for the detection, enrichment, and separation of trace amounts of target DNA based on amino-modified fluorescent magnetic composite nanoparticles .Anal Bioanal Chem.2010;397(3):1251-1258.
[50] Shan Z,Zhou Z,Chen H,et al.PCR-ready human DNA extraction from urine samples using magnetic nanoparticles. J Chromatogr B Analyt Technol Biomed Life Sci.2012; 881-882: 63-68.
[51] Zhao X,Tapec-Dytioco R,Wang K,et al.Collection of trace amounts of DNA/mRNA molecules using genomagnetic nanocapturers.Anal Chem. 2003;75(14):3476-3483.