DNA hydroxymethylation age of human blood determined by capillary hydrophilic-interaction liquid chromatography/mass spectrometry

Clinical Epigenetics

Bi-Feng Yuan²  Yu-Qi Feng²  Fang Zheng¹  Huan Zeng²  Meng-Dan Lan²  Qian-Yun Deng¹  Chun-Yan Peng¹  Han-Peng Jiang²  Jun Xiong² 

[1] Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of education), Department of Chemistry, Wuhan University, Wuhan 430072, China

关键词: Mass spectrometry;    Hydrophilic-interaction liquid chromatography;    Aging;    5-hydroxymethylcytosine;    5-methylcytosine;   

Others  :  1221398
DOI  :  10.1186/s13148-015-0109-x

 received in 2015-04-08, accepted in 2015-07-03,  发布年份 2015

【 摘 要 】

Background

Aging is a complex phenomenon and characterized by a progressive decline in physiology and function of adult tissues. However, it hasn’t been well established of the correlation between aging and global DNA methylation and hydroxymethylation that regulate the growth and development of higher organisms.

Results

We developed an on-line trapping/capillary hydrophilic-interaction liquid chromatography/electrospray ionization-mass spectrometry method for ultra-sensitive and simultaneous quantification of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in genomic DNA from human blood. Limits of detection for 5-mC and 5-hmC were 0.04 and 0.13 fmol, respectively. The imprecision and recovery of the method were determined with the relative standard deviations (RSDs) and relative errors being <11.2 and 14.0 %, respectively. We analyzed the contents of 5-mC and 5-hmC in genomic DNA of blood from 238 healthy people aged from 1 to 82 years. The results showed that 5-hmC content was significantly decreased and highly correlated with aging process, while 5-mC only showed slight correlation with age. We then established a DNA hydroxymethylation age model according to 5-hmC content with a mean absolute deviation (MAD) of approximate 8.9 years. We also calculated the mean relative error (MRE) using the predicted ages based on the age model and the chronological ages. The results showed that the MRE was 18.3 % for samples with ages from 20 to 82 years (95 % confidence interval, N = 190).

Conclusions

The global DNA hydroxymethylation represents a strong and reproducible mark of chronological age, which could be potentially applied in health assessment and prevention of diseases. The identification of biological or environmental factors that influence DNA hydroxymethylation aging rate may permit quantitative assessments of their impacts on health.

【 授权许可】

   
2015 Xiong et al.

【 图 表 】

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

【 参考文献 】

• [1]Johnson FB, Sinclair DA, Guarente L: Molecular biology of aging. Cell. 1999, 96:291-302.
• [2]Vanyushin BF, Nemirovsky LE, Klimenko VV, Vasiliev VK, Belozersky AN: The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes induced by hydrocortisone and other agents. Gerontologia 1973, 19:138-52.
• [3]Smith ZD, Meissner A: DNA methylation: roles in mammalian development. Nat Rev Genet. 2013, 14:204-20.
• [4]Robertson KD: DNA methylation and human disease. Nat Rev Genet. 2005, 6:597-610.
• [5]Gibbs WW: Biomarkers and ageing: the clock-watcher. Nature. 2014, 508:168-70.
• [6]Richardson B: Impact of aging on DNA methylation. Ageing Res Rev. 2003, 2:245-61.
• [7]Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, et al.: Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 2010, 20:434-9.
• [8]Horvath S: DNA methylation age of human tissues and cell types. Genome Biol. 2013, 14:R115. BioMed Central Full Text
• [9]Bork S, Pfister S, Witt H, Horn P, Korn B, Ho AD, et al.: DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells. Aging Cell. 2010, 9:54-63.
• [10]Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, et al.: Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A. 2012, 109:10522-7.
• [11]Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, et al.: Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013, 49:359-67.
• [12]McClay JL, Aberg KA, Clark SL, Nerella S, Kumar G, Xie LY, et al.: A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet. 2014, 23:1175-85.
• [13]Thompson RF, Atzmon G, Gheorghe C, Liang HQ, Lowes C, Greally JM, et al.: Tissue-specific dysregulation of DNA methylation in aging. Aging Cell. 2010, 9:506-18.
• [14]Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, Zhang J, et al.: Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010, 20:332-40.
• [15]Munzel M, Globisch D, Carell T: 5-Hydroxymethylcytosine, the sixth base of the genome. Angew Chem Int Ed Engl. 2011, 50:6460-8.
• [16]Branco MR, Ficz G, Reik W: Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet. 2012, 13:7-13.
• [17]Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, et al.: Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 2011, 25:679-84.
• [18]Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, et al.: Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. 2011, 473:398-402.
• [19]Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE: 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 2011, 12:R54. BioMed Central Full Text
• [20]Kriukiene E, Liutkeviciute Z, Klimasauskas S: 5-Hydroxymethylcytosine—the elusive epigenetic mark in mammalian DNA. Chem Soc Rev. 2012, 41:6916-30.
• [21]Chen ML, Shen F, Huang W, Qi JH, Wang Y, Feng YQ, et al.: Quantification of 5-Methylcytosine and 5-Hydroxymethylcytosine in genomic DNA from hepatocellular carcinoma tissues by capillary hydrophilic-interaction liquid chromatography/quadrupole TOF mass spectrometry. Clin Chem. 2013, 59:824-32.
• [22]Yang H, Liu Y, Bai F, Zhang JY, Ma SH, Liu J, et al.: Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene. 2013, 32:663-9.
• [23]Jin SG, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, et al.: 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer Res. 2011, 71:7360-5.
• [24]Udali S, Guarini P, Moruzzi S, Ruzzenente A, Tammen SA, Guglielmi A et al. Global DNA methylation and hydroxymethylation differ in hepatocellular carcinoma and cholangiocarcinoma and relate to survival rate. Hepatology. 2015. doi:10.1002/hep.27823
• [25]Tang Y, Zheng SJ, Qi CB, Feng YQ, Yuan BF: Sensitive and simultaneous determination of 5-methylcytosine and its oxidation products in genomic DNA by chemical derivatization coupled with liquid chromatography-tandem mass spectrometry analysis. Anal Chem. 2015, 87:3445-52.
• [26]Yuan BF, Feng YQ: Recent advances in the analysis of 5-methylcytosine and its oxidation products. TrAC-Trend Anal Chem. 2014, 54:24-35.
• [27]Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, et al.: Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2011, 29:68-72.
• [28]van den Hove DL, Chouliaras L, Rutten BP: The role of 5-hydroxymethylcytosine in aging and Alzheimer's disease: current status and prospects for future studies. Curr Alzheimer Res. 2012, 9:545-9.
• [29]Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al.: Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011, 333:1300-3.
• [30]Chen ML, Zhang J, Zhang Z, Yuan BF, Yu QW, Feng YQ: Facile preparation of organic-silica hybrid monolith for capillary hydrophilic liquid chromatography based on "thiol-ene" click chemistry. J Chromatogr A. 2013, 1284:118-25.
• [31]Jiang HP, Zhu JX, Peng C, Gao J, Zheng F, Xiao YX, et al.: Facile one-pot synthesis of a aptamer-based organic-silica hybrid monolithic capillary column by "thiol-ene" click chemistry for detection of enantiomers of chemotherapeutic anthracyclines. Analyst. 2014, 139:4940-6.
• [32]Jiang HP, Qi CB, Chu JM, Yuan BF, Feng YQ: Profiling of cis-Diol-containing nucleosides and ribosylated metabolites by boronate-affinity organic-silica hybrid monolithic capillary liquid chromatography/mass spectrometry. Sci Rep. 2015, 5:7785.
• [33]Song LG, James SR, Kazim L, Karpf AR: Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Chem. 2005, 77:504-10.
• [34]Liu S, Wang J, Su YJ, Guerrero C, Zeng YX, Mitra D, et al.: Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA. Nucleic Acids Res. 2013, 41:6421-9.
• [35]Laird A, Thomson JP, Harrison DJ, Meehan RR: 5-hydroxymethylcytosine profiling as an indicator of cellular state. Epigenomics-Uk. 2013, 5:655-69.
• [36]Wilson VL, Smith RA, Ma S, Cutler RG: Genomic 5-methyldeoxycytidine decreases with age. J Biol Chem. 1987, 262:9948-51.
• [37]Bocklandt S, Lin W, Sehl ME, Sanchez FJ, Sinsheimer JS, Horvath S, et al.: Epigenetic predictor of age. PLoS One. 2011, 6:e14821.
• [38]Weidner CI, Lin Q, Koch CM, Eisele L, Beier F, Ziegler P, et al.: Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol. 2014, 15:R24. BioMed Central Full Text
• [39]Murgatroyd C, Patchev AV, Wu Y, Micale V, Bockmuhl Y, Fischer D, et al.: Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat Neurosci. 2009, 12:1559-66.
• [40]Inoue A, Zhang Y: Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science. 2011, 334:194.
• [41]Yuan BF: 5-methylcytosine and its derivatives. Adv Clin Chem. 2014, 67:151-87.
• [42]Fan Y, Feng YQ, Da SL, Shi ZG: Poly (methacrylic acid-ethylene glycol dimethacrylate) monolithic capillary for in-tube solid phase microextraction coupled to high performance liquid chromatography and its application to determination of basic drugs in human serum. Anal Chim Acta. 2004, 523:251-8.