A Method to Assess Genomic DNA Methylation Using High-Performance Liquid Chromatography/Electrospray Ionization Mass Spectrometry

Friso, Simonetta; Choi, Sang‐Woon; Dolnikowski, Gregory G.; Selhub, Jacob

doi:10.1021/ac020050h

Cited by 220 publications

(159 citation statements)

References 41 publications

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“…Another intriguing example of disease susceptibility related to methyl donor diet was illustrated in a population study reporting an association between folate status and a mutation in the gene encoding methylenetetrahydrofolate reductase, a key enzyme in determining genomic DNA methylation. This study suggests an interplay between nutritional epigenetics and genetic susceptibility in the modulation of gene expression [51]. Collectively, these findings offer valuable insights into the pathophysiology of diseases associated with nutritional epigenetics.…”

Section: Dietary Factorsmentioning

confidence: 65%

Epigenetic reprogramming and imprinting in origins of disease

Tang

2007

Rev Endocr Metab Disord

216

134

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The traditional view that gene and environment interactions control disease susceptibility can now be expanded to include epigenetic reprogramming as a key determinant of origins of human disease. Currently, epigenetics is defined as heritable changes in gene expression that do not alter DNA sequence but are mitotically and trans-generationally inheritable. Epigenetic reprogramming is the process by which an organism's genotype interacts with the environment to produce its phenotype and provides a framework for explaining individual variations and the uniqueness of cells, tissues, or organs despite identical genetic information. The main epigenetic mediators are histone modification, DNA methylation, and non-coding RNAs. They regulate crucial cellular functions such as genome stability, X-chromosome inactivation, gene imprinting, and reprogramming of non-imprinting genes, and work on developmental plasticity such that exposures to endogenous or exogenous factors during critical periods permanently alter the structure or function of specific organ systems. Developmental epigenetics is believed to establish "adaptive" phenotypes to meet the demands of the later-life environment. Resulting phenotypes that match predicted later-life demands will promote health, while a high degree of mismatch will impede adaptability to later-life challenges and elevate disease risk. The rapid introduction of synthetic chemicals, medical interventions, environmental pollutants, and lifestyle choices, may result in conflict with the programmed adaptive changes made during early development, and explain the alarming increases in some diseases. The recent identification of a significant number of epigenetically regulated genes in various model systems has prepared the field to take on the challenge of characterizing distinct epigenomes related to various diseases. Improvements in human health could then be redirected from curative care to personalized, preventive medicine based, in part, on epigenetic markings etched in the "margins" of one's genetic make-up. NIH Public Access Author ManuscriptRev Endocr Metab Disord. Author manuscript; available in PMC 2014 June 13. Epigenetics meets genetics in disease susceptibilityIn the past, susceptibility of disease was believed to be determined solely by inheritable information carried on the primary sequence of the DNA. Individuals are endowed with different genotypes that dictate how they respond to endogenous factors such as development cues, hormones, and cytokines or to exogenous influences, including nutrient availability, infection, physical activities, social behavior, and other environmental factors. Over time, these responses form the basis of genetic variability to disease susceptibility. Aberrant changes in linear DNA sequence result in mutations, deletions, gene fusion, tandem duplications, or gene amplifications causing dysregulation of gene expression that underlies the genesis of disease [1][2][3][4][5][6][7]. Recently, however, it has become clear that epigenetic disr...

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Section: Dietary Factorsmentioning

confidence: 65%

Epigenetic reprogramming and imprinting in origins of disease

Tang

2007

Rev Endocr Metab Disord

216

134

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“…Genomic DNA methylation was determined in 1 µg DNA by enzymatic hydrolysis of DNA followed by LC-MS using the method of Friso et al [49].…”

Section: Methodsmentioning

confidence: 99%

Moderate folate depletion modulates the expression of selected genes involved in cell cycle, intracellular signaling and folate uptake in human colonic epithelial cell lines

Crott

Liu

Keyes

et al. 2008

The Journal of Nutritional Biochemistry

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Folate deficiency may affect gene expression by disrupting DNA methylation patterns or by inducing base substitution, DNA breaks, gene deletions and gene amplification. Changes in expression may explain the inverse relationship observed between folate status and risk of colorectal cancer. Three cell lines derived from the normal human colon, HCEC, NCM356 and NCM460, were grown for 32-34 days in media containing 25, 50, 75 or 150 nM folic acid, and the expression of genes involved in cell-cycle checkpoints, intracellular signaling, folate uptake and cell adhesion and migration was determined. Expression of Folate Receptor 1 was increased with decreasing media folate in all cell lines, as was p53, p21, p16 and β-catenin. With decreasing folate, the expression of both E-cadherin and SMAD-4 was decreased in NCM356. APC was elevated in NCM356 but unchanged in the other lines. No changes in global methylation were detected. A significant increase in p53 exon 7-8 strand breaks was observed with decreasing folate in NCM460 cells. The changes observed are consistent with DNA damage-induced activation of cell-cycle checkpoints and cellular adaptation to folate depletion. Folate-depletion-induced changes in the Wnt/APC pathway as well as in genes involved in cell adhesion, migration and invasion may underlie observed relationships between folate status and cancer risk.

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“…For HPLC separation of nucleosides, cells were split 1:3 into tracer medium in 100-cm 2 culture plates, grown to confluence, and harvested. DNA was digested to nucleosides prior to separation by HPLC, using procedures described elsewhere (28). Peaks corresponding to nucleosides were identified from standards, collected, and isotope levels quantified.…”

Section: Materials-[6s]-[mentioning

confidence: 99%

Regulation of Folate-mediated One-carbon Metabolism by 10-Formyltetrahydrofolate Dehydrogenase

Anguera

Field

Perry

et al. 2006

Journal of Biological Chemistry

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10-Formyltetrahydrofolate dehydrogenase (FDH) catalyzes the NADP؉ -dependent conversion of 10-formyltetrahydrofolate to CO 2 and tetrahydrofolate (THF) and is an abundant high affinity folatebinding protein. Although several activities have been ascribed to FDH, its metabolic role in folate-mediated one-carbon metabolism is not well understood. FDH has been proposed to: 1) inhibit purine biosynthesis by depleting 10-formyl-THF pools, 2) maintain cellular folate concentrations by sequestering THF, 3) deplete the supply of folateactivated one-carbon units, and 4) stimulate the generation of THFactivated one-carbon unit synthesis by channeling folate cofactors to other folate-dependent enzymes. The metabolic functions of FDH were investigated in neuroblastoma, which do not contain detectable levels of FDH. Both low and high FDH expression reduced total cellular folate concentrations by 60%, elevated rates of folate catabolism, and depleted cellular 5-methyl-THF and S-adenosylmethionine levels. Low FDH expression increased the formyl-THF/THF ratio nearly 10-fold, whereas THF accounted for nearly 50% of total folate in neuroblastoma with high FDH expression. FDH expression did not affect the enrichment of exogenous formate into methionine, serine, or purines and did not suppress de novo purine nucleotide biosynthesis. We conclude that low FDH expression facilitates the incorporation of one-carbon units into the one-carbon pool, whereas high levels of FDH expression deplete the folate-activated one-carbon pool by catalyzing the conversion of 10-formyl-THF to THF. Furthermore, FDH does not increase cellular folate concentrations by sequestering THF in neuroblastoma nor does it inhibit or regulate de novo purine biosynthesis. FDH expression does deplete cellular 5-methyl-THF and S-adenosylmethionine levels indicating that FDH impairs the folate-dependent homocysteine remethylation cycle. Tetrahydrofolate (THF)2 polyglutamates are cofactors that function as one-carbon donors and acceptors in a set of reactions known as folate-mediated one-carbon metabolism, which occurs both in the cytoplasm and in mitochondria (see Fig. 1) (1). THF cofactors carry onecarbon units at three oxidation states ranging from formate to methanol (2). The biologically active THF derivatives contain a reduced pteridine and a polyglutamate peptide consisting of five to eight glutamate residues linked by ␥-peptide bonds (3). Cytoplasmic folate-mediated onecarbon metabolism is required for the de novo synthesis of purines (supplies the carbon-2 and carbon-8 of the purine ring) and thymidylate (methylation of dUMP to dTMP), and also for remethylation of homocysteine to methionine (2, 3). Methionine can be converted to S-adenosylmethionine (SAM) and serve as a methyl donor for numerous methylation reactions, including the methylation of DNA, RNA, and proteins. Serine is a primary source of folate-activated one-carbon units (4). Cytoplasmic serine hydroxymethyltransferase (cSHMT) catalyzes the THF-dependent aldol cleavage of serine to methylene-THF and...

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A Method to Assess Genomic DNA Methylation Using High-Performance Liquid Chromatography/Electrospray Ionization Mass Spectrometry

Cited by 220 publications

References 41 publications

Epigenetic reprogramming and imprinting in origins of disease

Epigenetic reprogramming and imprinting in origins of disease

Moderate folate depletion modulates the expression of selected genes involved in cell cycle, intracellular signaling and folate uptake in human colonic epithelial cell lines

Regulation of Folate-mediated One-carbon Metabolism by 10-Formyltetrahydrofolate Dehydrogenase

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