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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

Differentially methylated positions after the intervention with folic acid and vitamin B12. Volcano plots show the statistical significance versus the changes in DNA methylation after the intervention with (a) the placebo or (b) folic acid and vitamin B12. Dashed lines represent 2 % methylation changes and a p value of 1.0E-05. Features of the positions (n = 162) that were differentially methylated after the intervention with folic acid and vitamin B12 are presented in (c) percentages of positions expressed per relationship to CpG islands for the differentially methylated positions (n = 162) as well as for all considered positions on the Infinium HumanMethylation450 Beadchip (n = 431,312), and (d) percentage of positions expressed per relationship to the nearest gene(s). e Number of positions according to the presented categories for absolute changes in DNA methylation for the 162 positions that were differentially methylated after the intervention with folic acid and vitamin B12. f Individual changes in DNA methylation for probe cg06191076 located within DIRAS3. Horizontal lines represent median ± interquartile ranges of DNA methylation, which is expressed as a beta value (0–100 %). Abbreviations: TSS200 200 base pairs around the transcription start site, TSS1500 1500 base pairs around the transcription start site, 3′UTR 3′ untranslated region, 5′UTR 5′ untranslated region, IGR intergenic region
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Fig3: Differentially methylated positions after the intervention with folic acid and vitamin B12. Volcano plots show the statistical significance versus the changes in DNA methylation after the intervention with (a) the placebo or (b) folic acid and vitamin B12. Dashed lines represent 2 % methylation changes and a p value of 1.0E-05. Features of the positions (n = 162) that were differentially methylated after the intervention with folic acid and vitamin B12 are presented in (c) percentages of positions expressed per relationship to CpG islands for the differentially methylated positions (n = 162) as well as for all considered positions on the Infinium HumanMethylation450 Beadchip (n = 431,312), and (d) percentage of positions expressed per relationship to the nearest gene(s). e Number of positions according to the presented categories for absolute changes in DNA methylation for the 162 positions that were differentially methylated after the intervention with folic acid and vitamin B12. f Individual changes in DNA methylation for probe cg06191076 located within DIRAS3. Horizontal lines represent median ± interquartile ranges of DNA methylation, which is expressed as a beta value (0–100 %). Abbreviations: TSS200 200 base pairs around the transcription start site, TSS1500 1500 base pairs around the transcription start site, 3′UTR 3′ untranslated region, 5′UTR 5′ untranslated region, IGR intergenic region

Mentions: At baseline, there were no statistically significant differences in methylation between the placebo and the intervention group. After intervention with folic acid and vitamin B12, 162 positions (versus 14 in the placebo group) of the 431,312 positions were differentially methylated as compared to baseline (Benjamini-Hochberg (BH)-adjusted p value <0.05). Volcano plots showing the DNA methylation changes versus the statistical significance are presented in Fig. 3a, b. An overview of the top-100 of differentially methylated positions with corresponding p values and methylation changes is presented in Additional file 2: Table S1. Mean changes in DNA methylation, as a result of the intervention, for these differentially methylated positions ranged from −4 to 5 % (Fig. 3e). Overall, positions within the CpG islands and around the transcription start sites were overrepresented among the positions that were differentially methylated after the intervention with folic acid and vitamin B12 (Fig. 3c, d).Fig. 3


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)

Differentially methylated positions after the intervention with folic acid and vitamin B12. Volcano plots show the statistical significance versus the changes in DNA methylation after the intervention with (a) the placebo or (b) folic acid and vitamin B12. Dashed lines represent 2 % methylation changes and a p value of 1.0E-05. Features of the positions (n = 162) that were differentially methylated after the intervention with folic acid and vitamin B12 are presented in (c) percentages of positions expressed per relationship to CpG islands for the differentially methylated positions (n = 162) as well as for all considered positions on the Infinium HumanMethylation450 Beadchip (n = 431,312), and (d) percentage of positions expressed per relationship to the nearest gene(s). e Number of positions according to the presented categories for absolute changes in DNA methylation for the 162 positions that were differentially methylated after the intervention with folic acid and vitamin B12. f Individual changes in DNA methylation for probe cg06191076 located within DIRAS3. Horizontal lines represent median ± interquartile ranges of DNA methylation, which is expressed as a beta value (0–100 %). Abbreviations: TSS200 200 base pairs around the transcription start site, TSS1500 1500 base pairs around the transcription start site, 3′UTR 3′ untranslated region, 5′UTR 5′ untranslated region, IGR intergenic region
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Fig3: Differentially methylated positions after the intervention with folic acid and vitamin B12. Volcano plots show the statistical significance versus the changes in DNA methylation after the intervention with (a) the placebo or (b) folic acid and vitamin B12. Dashed lines represent 2 % methylation changes and a p value of 1.0E-05. Features of the positions (n = 162) that were differentially methylated after the intervention with folic acid and vitamin B12 are presented in (c) percentages of positions expressed per relationship to CpG islands for the differentially methylated positions (n = 162) as well as for all considered positions on the Infinium HumanMethylation450 Beadchip (n = 431,312), and (d) percentage of positions expressed per relationship to the nearest gene(s). e Number of positions according to the presented categories for absolute changes in DNA methylation for the 162 positions that were differentially methylated after the intervention with folic acid and vitamin B12. f Individual changes in DNA methylation for probe cg06191076 located within DIRAS3. Horizontal lines represent median ± interquartile ranges of DNA methylation, which is expressed as a beta value (0–100 %). Abbreviations: TSS200 200 base pairs around the transcription start site, TSS1500 1500 base pairs around the transcription start site, 3′UTR 3′ untranslated region, 5′UTR 5′ untranslated region, IGR intergenic region
Mentions: At baseline, there were no statistically significant differences in methylation between the placebo and the intervention group. After intervention with folic acid and vitamin B12, 162 positions (versus 14 in the placebo group) of the 431,312 positions were differentially methylated as compared to baseline (Benjamini-Hochberg (BH)-adjusted p value <0.05). Volcano plots showing the DNA methylation changes versus the statistical significance are presented in Fig. 3a, b. An overview of the top-100 of differentially methylated positions with corresponding p values and methylation changes is presented in Additional file 2: Table S1. Mean changes in DNA methylation, as a result of the intervention, for these differentially methylated positions ranged from −4 to 5 % (Fig. 3e). Overall, positions within the CpG islands and around the transcription start sites were overrepresented among the positions that were differentially methylated after the intervention with folic acid and vitamin B12 (Fig. 3c, d).Fig. 3

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