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The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects.

Kok DE, Dhonukshe-Rutten RA, Lute C, Heil SG, Uitterlinden AG, van der Velde N, van Meurs JB, van Schoor NM, Hooiveld GJ, de Groot LC, Kampman E, Steegenga WT - Clin Epigenetics (2015)

Bottom Line: The aim of this study was to identify effects of long-term supplementation with folic acid and vitamin B12 on genome-wide DNA methylation in elderly subjects.Pronounced changes were found for regions in the DIRAS3, ARMC8, and NODAL genes, implicated in carcinogenesis and early embryonic development.Long-term supplementation with folic acid and vitamin B12 in elderly subjects resulted in effects on DNA methylation of several genes, among which genes implicated in developmental processes.

View Article: PubMed Central - PubMed

Affiliation: Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands.

ABSTRACT

Background: Folate and its synthetic form folic acid function as donor of one-carbon units and have been, together with other B-vitamins, implicated in programming of epigenetic processes such as DNA methylation during early development. To what extent regulation of DNA methylation can be altered via B-vitamins later in life, and how this relates to health and disease, is not exactly known. The aim of this study was to identify effects of long-term supplementation with folic acid and vitamin B12 on genome-wide DNA methylation in elderly subjects. This project was part of a randomized, placebo-controlled trial on effects of supplemental intake of folic acid and vitamin B12 on bone fracture incidence (B-vitamins for the PRevention Of Osteoporotic Fractures (B-PROOF) study). Participants with mildly elevated homocysteine levels, aged 65-75 years, were randomly assigned to take 400 μg folic acid and 500 μg vitamin B12 per day or a placebo during an intervention period of 2 years. DNA was isolated from buffy coats, collected before and after intervention, and genome-wide DNA methylation was determined in 87 participants (n = 44 folic acid/vitamin B12, n = 43 placebo) using the Infinium HumanMethylation450 BeadChip.

Results: After intervention with folic acid and vitamin B12, 162 (versus 14 in the placebo group) of the 431,312 positions were differentially methylated as compared to baseline. Comparisons of the DNA methylation changes in the participants receiving folic acid and vitamin B12 versus placebo revealed one single differentially methylated position (cg19380919) with a borderline statistical significance. However, based on the analyses of differentially methylated regions (DMRs) consisting of multiple positions, we identified 6 regions that differed statistically significantly between the intervention and placebo group. Pronounced changes were found for regions in the DIRAS3, ARMC8, and NODAL genes, implicated in carcinogenesis and early embryonic development. Furthermore, serum levels of folate and vitamin B12 or plasma homocysteine were related to DNA methylation of 173, 425, and 11 regions, respectively. Interestingly, for several members of the developmental HOX genes, DNA methylation was related to serum levels of folate.

Conclusions: Long-term supplementation with folic acid and vitamin B12 in elderly subjects resulted in effects on DNA methylation of several genes, among which genes implicated in developmental processes.

No MeSH data available.


Related in: MedlinePlus

The effect of folic acid and vitamin B12 on DNA methylation of HOX genes. Mean DNA methylation changes after a 2-year intervention with folic acid and vitamin B12 (red, n = 44) or placebo (black, n = 43) for the 1052 positions located within one of the 39 HOX (homeobox) genes located on cluster A (chromosome 7), cluster B (chromosome 17), cluster C (chromosome 12), or cluster D (chromosome 2). Only positions annotated to one of these HOX genes were depicted; intergenic regions were not included in this figure. Bars are superimposed, meaning that red (folic acid and vitamin B12) and black (placebo) bars are presented together, whenever applicable behind each other, and both reflect the actual values on the y-axis
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Fig5: The effect of folic acid and vitamin B12 on DNA methylation of HOX genes. Mean DNA methylation changes after a 2-year intervention with folic acid and vitamin B12 (red, n = 44) or placebo (black, n = 43) for the 1052 positions located within one of the 39 HOX (homeobox) genes located on cluster A (chromosome 7), cluster B (chromosome 17), cluster C (chromosome 12), or cluster D (chromosome 2). Only positions annotated to one of these HOX genes were depicted; intergenic regions were not included in this figure. Bars are superimposed, meaning that red (folic acid and vitamin B12) and black (placebo) bars are presented together, whenever applicable behind each other, and both reflect the actual values on the y-axis

Mentions: Changes in serum levels of folate or vitamin B12 and plasma homocysteine after the 2-year intervention period were fairly subjected to interindividual variation resulting in an “overlap” between the intervention and placebo group (Fig. 2). In addition to the comparisons for the DNA methylation changes between these two groups, we therefore explored the relation between DNA methylation and serum folate, vitamin B12 or plasma homocysteine levels in a continuous manner. Applying the conservative threshold for significance of BH-adjusted p values <0.05 revealed no statistically significant positions related to folate levels. Exploration, however, of the top-35 positions for which DNA methylation tends to be related to serum folate levels showed a probe (cg24973150, p = 5.15E-05) located within a CpG island in the promoter region (TSS200) of the HOXB7 gene, which has been recently associated with the risk of neural tube defects [31]. Most (32 of the top-35 positions) of the observed positions were positively related to serum levels of folate, indicating that DNA methylation increased with higher levels of serum folate. In addition to the identification of individual positions, we subsequently identified 173 DMRs that were related to folate levels. One of the most prominent regions, consisting of 22 probes and a mean BH-adjusted p value of 0.001, belongs to the promoter region of HOXA4, another member of the homeobox family. An overview of DNA methylation changes in HOXB7, HOXA4, and the other HOX genes in one of the four HOX gene clusters is presented in Fig. 5, showing that mean DNA methylation for the majority of these HOX genes tends to be increased after intervention with folic acid and vitamin B12, whereas it mostly remained stable or decreased in the placebo group.Fig. 5


The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects.

Kok DE, Dhonukshe-Rutten RA, Lute C, Heil SG, Uitterlinden AG, van der Velde N, van Meurs JB, van Schoor NM, Hooiveld GJ, de Groot LC, Kampman E, Steegenga WT - Clin Epigenetics (2015)

The effect of folic acid and vitamin B12 on DNA methylation of HOX genes. Mean DNA methylation changes after a 2-year intervention with folic acid and vitamin B12 (red, n = 44) or placebo (black, n = 43) for the 1052 positions located within one of the 39 HOX (homeobox) genes located on cluster A (chromosome 7), cluster B (chromosome 17), cluster C (chromosome 12), or cluster D (chromosome 2). Only positions annotated to one of these HOX genes were depicted; intergenic regions were not included in this figure. Bars are superimposed, meaning that red (folic acid and vitamin B12) and black (placebo) bars are presented together, whenever applicable behind each other, and both reflect the actual values on the y-axis
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4644301&req=5

Fig5: The effect of folic acid and vitamin B12 on DNA methylation of HOX genes. Mean DNA methylation changes after a 2-year intervention with folic acid and vitamin B12 (red, n = 44) or placebo (black, n = 43) for the 1052 positions located within one of the 39 HOX (homeobox) genes located on cluster A (chromosome 7), cluster B (chromosome 17), cluster C (chromosome 12), or cluster D (chromosome 2). Only positions annotated to one of these HOX genes were depicted; intergenic regions were not included in this figure. Bars are superimposed, meaning that red (folic acid and vitamin B12) and black (placebo) bars are presented together, whenever applicable behind each other, and both reflect the actual values on the y-axis
Mentions: Changes in serum levels of folate or vitamin B12 and plasma homocysteine after the 2-year intervention period were fairly subjected to interindividual variation resulting in an “overlap” between the intervention and placebo group (Fig. 2). In addition to the comparisons for the DNA methylation changes between these two groups, we therefore explored the relation between DNA methylation and serum folate, vitamin B12 or plasma homocysteine levels in a continuous manner. Applying the conservative threshold for significance of BH-adjusted p values <0.05 revealed no statistically significant positions related to folate levels. Exploration, however, of the top-35 positions for which DNA methylation tends to be related to serum folate levels showed a probe (cg24973150, p = 5.15E-05) located within a CpG island in the promoter region (TSS200) of the HOXB7 gene, which has been recently associated with the risk of neural tube defects [31]. Most (32 of the top-35 positions) of the observed positions were positively related to serum levels of folate, indicating that DNA methylation increased with higher levels of serum folate. In addition to the identification of individual positions, we subsequently identified 173 DMRs that were related to folate levels. One of the most prominent regions, consisting of 22 probes and a mean BH-adjusted p value of 0.001, belongs to the promoter region of HOXA4, another member of the homeobox family. An overview of DNA methylation changes in HOXB7, HOXA4, and the other HOX genes in one of the four HOX gene clusters is presented in Fig. 5, showing that mean DNA methylation for the majority of these HOX genes tends to be increased after intervention with folic acid and vitamin B12, whereas it mostly remained stable or decreased in the placebo group.Fig. 5

Bottom Line: The aim of this study was to identify effects of long-term supplementation with folic acid and vitamin B12 on genome-wide DNA methylation in elderly subjects.Pronounced changes were found for regions in the DIRAS3, ARMC8, and NODAL genes, implicated in carcinogenesis and early embryonic development.Long-term supplementation with folic acid and vitamin B12 in elderly subjects resulted in effects on DNA methylation of several genes, among which genes implicated in developmental processes.

View Article: PubMed Central - PubMed

Affiliation: Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands.

ABSTRACT

Background: Folate and its synthetic form folic acid function as donor of one-carbon units and have been, together with other B-vitamins, implicated in programming of epigenetic processes such as DNA methylation during early development. To what extent regulation of DNA methylation can be altered via B-vitamins later in life, and how this relates to health and disease, is not exactly known. The aim of this study was to identify effects of long-term supplementation with folic acid and vitamin B12 on genome-wide DNA methylation in elderly subjects. This project was part of a randomized, placebo-controlled trial on effects of supplemental intake of folic acid and vitamin B12 on bone fracture incidence (B-vitamins for the PRevention Of Osteoporotic Fractures (B-PROOF) study). Participants with mildly elevated homocysteine levels, aged 65-75 years, were randomly assigned to take 400 μg folic acid and 500 μg vitamin B12 per day or a placebo during an intervention period of 2 years. DNA was isolated from buffy coats, collected before and after intervention, and genome-wide DNA methylation was determined in 87 participants (n = 44 folic acid/vitamin B12, n = 43 placebo) using the Infinium HumanMethylation450 BeadChip.

Results: After intervention with folic acid and vitamin B12, 162 (versus 14 in the placebo group) of the 431,312 positions were differentially methylated as compared to baseline. Comparisons of the DNA methylation changes in the participants receiving folic acid and vitamin B12 versus placebo revealed one single differentially methylated position (cg19380919) with a borderline statistical significance. However, based on the analyses of differentially methylated regions (DMRs) consisting of multiple positions, we identified 6 regions that differed statistically significantly between the intervention and placebo group. Pronounced changes were found for regions in the DIRAS3, ARMC8, and NODAL genes, implicated in carcinogenesis and early embryonic development. Furthermore, serum levels of folate and vitamin B12 or plasma homocysteine were related to DNA methylation of 173, 425, and 11 regions, respectively. Interestingly, for several members of the developmental HOX genes, DNA methylation was related to serum levels of folate.

Conclusions: Long-term supplementation with folic acid and vitamin B12 in elderly subjects resulted in effects on DNA methylation of several genes, among which genes implicated in developmental processes.

No MeSH data available.


Related in: MedlinePlus