Profiling placental and fetal DNA methylation in human neural tube defects

Epigenetics & Chromatin, Feb 2016

Background The incidence of neural tube defects (NTDs) declined by about 40 % in Canada with the introduction of a national folic acid (FA) fortification program. Despite the fact that few Canadians currently exhibit folate deficiency, NTDs are still the second most common congenital abnormality. FA fortification may have aided in reducing the incidence of NTDs by overcoming abnormal one carbon metabolism cycling, the process which provides one carbon units for methylation of DNA. We considered that NTDs persisting in a folate-replete population may also occur in the context of FA-independent compromised one carbon metabolism, and that this might manifest as abnormal DNA methylation (DNAm). Second trimester human placental chorionic villi, kidney, spinal cord, brain, and muscle were collected from 19 control, 22 spina bifida, and 15 anencephalic fetuses in British Columbia, Canada. DNA was extracted, assessed for methylenetetrahydrofolate reductase (MTHFR) genotype and for genome-wide DNAm using repetitive elements, in addition to the Illumina Infinium HumanMethylation450 (450k) array. Results No difference in repetitive element DNAm was noted between NTD status groups. Using a false discovery rate <0.05 and average group difference in DNAm ≥0.05, differentially methylated array sites were identified only in (1) the comparison of anencephaly to controls in chorionic villi (n = 4 sites) and (2) the comparison of spina bifida to controls in kidney (n = 3342 sites). Conclusions We suggest that the distinctive DNAm of spina bifida kidneys may be consequent to the neural tube defect or reflective of a common etiology for abnormal neural tube and renal development. Though there were some small shifts in DNAm in the other tested tissues, our data do not support the long-standing hypothesis of generalized altered genome-wide DNAm in NTDs. This finding may be related to the fact that most Canadians are not folate deficient, but it importantly opens the field to the investigation of other epigenetic and non-epigenetic mechanisms in the etiology of NTDs.

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Profiling placental and fetal DNA methylation in human neural tube defects

Price et al. Epigenetics & Chromatin Profiling placental and fetal DNA methylation in human neural tube defects E. Magda Price 0 1 2 Maria S. Peñaherrera 0 2 Elodie Portales‑Casamar 0 Paul Pavlidis 4 5 Margot I. Van Allen 2 Deborah E. McFadden 2 3 Wendy P. Robinson 0 2 0 Child and Family Research Institute , 950 W 28th Ave, Vancouver, BC V5Z 4H4 , UK 1 Dept of Obstetrics and Gynaecology, University of British Columbia , C420‐4500 Oak St, Vancouver, BC V6H 3N1 , UK 2 Dept of Medical Genetics, University of British Columbia , C201‐4500 Oak St, Vancouver, BC V6H 3N1 , UK 3 Dept of Pathol‐ ogy and Laboratory Medicine , Rm G227‐2211, Wesbrook Mall, Vancouver, BC V6T 2B5 , UK 4 Dept of Psychiatry, University of British Columbia , 2255 Wesbrook Mall, Vancouver, BC V6T 2A1 , UK 5 Centre for HighT‐hroughput Biology, University of British Columbia , 2185 East Mall, Vancouver V6T 1Z4 , UK Background: The incidence of neural tube defects (NTDs) declined by about 40 % in Canada with the introduction of a national folic acid (FA) fortification program. Despite the fact that few Canadians currently exhibit folate deficiency, NTDs are still the second most common congenital abnormality. FA fortification may have aided in reducing the incidence of NTDs by overcoming abnormal one carbon metabolism cycling, the process which provides one carbon units for methylation of DNA. We considered that NTDs persisting in a folate‑ replete population may also occur in the context of FA‑ independent compromised one carbon metabolism, and that this might manifest as abnormal DNA methylation (DNAm). Second trimester human placental chorionic villi, kidney, spinal cord, brain, and muscle were collected from 19 control, 22 spina bifida, and 15 anencephalic fetuses in British Columbia, Canada. DNA was extracted, assessed for methylenetetrahydrofolate reductase (MTHFR) genotype and for genome‑ wide DNAm using repetitive elements, in addition to the Illumina Infinium HumanMethylation450 (450k) array. Results: No difference in repetitive element DNAm was noted between NTD status groups. Using a false discovery rate <0.05 and average group difference in DNAm ≥0.05, differentially methylated array sites were identified only in (1) the comparison of anencephaly to controls in chorionic villi (n = 4 sites) and (2) the comparison of spina bifida to controls in kidney (n = 3342 sites). Conclusions: We suggest that the distinctive DNAm of spina bifida kidneys may be consequent to the neural tube defect or reflective of a common etiology for abnormal neural tube and renal development. Though there were some small shifts in DNAm in the other tested tissues, our data do not support the long‑ standing hypothesis of generalized altered genome‑ wide DNAm in NTDs. This finding may be related to the fact that most Canadians are not folate deficient, but it importantly opens the field to the investigation of other epigenetic and non‑ epigenetic mechanisms in the etiology of NTDs. Neural tube defects (NTDs); Spina bifida; Anencephaly; Illumina HumanMethylation450 BeadChip; 450k array; Epigenome‑ wide association study (EWAS); DNA methylation (DNAm) Background Neural tube defects (NTDs) are a spectrum of severe and often lethal congenital abnormalities that arise in the first month of pregnancy from a failure of the flat neural plate to elevate, fold, and close in the developing embryo [ 1, 2 ]. Folic acid (FA, synthetic folate) fortification and supplementation programs in more than 80 countries around the world [3] were initiated in response to mounting evidence that the incidence of NTDs could be lowered by increasing maternal pre- and perinatal FA intake [ 4 ]. Despite a 40  % decline in the incidence of NTDs [ 5 ], a 2007 Canadian post FA fortification survey reported that the most common NTDs—spina bifida (SB, caudal failure of neural tube closure) and anencephaly (AN, cranial failure of neural tube closure)—were still prevalent at respective rates of 0.41 and 0.36 per 1000 live-and stillbirths [ 6 ]. NTDs remain one of Canada’s most common congenital abnormalities [ 5 ]. The mechanism through which FA helps to prevent NTDs is unclear. Folate is a substrate for the activation of methyl groups in one-carbon metabolism (OCM), a biochemical pathway comprising two intersecting cycles: the DNA cycle (producing nucleotide precursors) and the methylation cycle (producing methyl donors) [ 7 ]. A hypothesis of altered capacity for DNA methylation (DNAm) has been proposed as the mechanism underlying FA prevention of NTDs [ 8 ]. The basis of this hypothesis was the observation of increased incidence of NTDs in association with maternal and fetal SNPs in methylenetetrahydrofolate reductase (MTHFR) [ 9 ], the enzyme at the intersection of the DNA and methylation cycles. These MTHFR variants result in reduced enzymatic activity [ 10, 11 ] which is expected to shift OCM toward the DNA cycle, restricting methylation capacity and leading to abnormal (...truncated)


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E. Price, Maria Peñaherrera, Elodie Portales-Casamar, Paul Pavlidis, Margot Van Allen, Deborah McFadden, Wendy Robinson. Profiling placental and fetal DNA methylation in human neural tube defects, Epigenetics & Chromatin, 2016, pp. 6, 9, DOI: 10.1186/s13072-016-0054-8