No evidence for association of MTHFR 677C>T and 1298A>C variants with placental DNA methylation

Abstract

Background5,10-Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in one-carbon metabolism that ensures the availability of methyl groups for methylation reactions. Two single-nucleotide polymorphisms (SNPs) in the MTHFR gene, 677C>T and 1298A>C, result in a thermolabile enzyme with reduced function. These variants, in both the maternal and/or fetal genes, have been associated with pregnancy complications including miscarriage, neural tube defects (NTDs), and preeclampsia (PE), perhaps due to altered capacity for DNA methylation (DNAm). In this study, we assessed the association between MTHFR 677TT and 1298CC genotypes and risk of NTDs, PE, or normotensive intrauterine growth restriction (nIUGR). Additionally, we assessed whether these high-risk genotypes are associated with altered DNAm in the placenta.ResultsIn 303 placentas screened for this study, we observed no significant association between the occurrence of NTDs (N = 55), PE (early-onset: N = 28, late-onset: N = 20), or nIUGR (N = 21) and placental (fetal) MTHFR 677TT or 1298CC genotypes compared to healthy pregnancies (N = 179), though a trend of increased 677TT genotype in PE/IUGR together was observed (OR 2.53, p = 0.048). DNAm was profiled in 10 high-risk 677 (677TT + 1298AA), 10 high-risk 1298 (677CC + 1298CC), and 10 reference (677CC + 1298AA) genotype placentas. Linear modeling identified no significantly differentially methylated sites between high-risk 677 or 1298 and reference placentas at a false discovery rate < 0.05 and Δβ ≥ 0.05 using the Illumina Infinium HumanMethylation450 BeadChip. Using a differentially methylated region analysis or separating cytosine-guanine dinucleotides (CpGs) by CpG density to reduce multiple comparisons also did not identify differential methylation. Additionally, there was no consistent evidence for altered methylation of repetitive DNA between high-risk and reference placentas.ConclusionsWe conclude that large-scale, genome-wide disruption in DNAm does not occur in placentas with the high-risk MTHFR 677TT or 1298CC genotypes. Furthermore, there was no evidence for an association of the 1298CC genotype and only a tendency to higher 677TT in pregnancy complications of PE/IUGR. This may be due to small sample sizes or folate repletion in our Canadian population attenuating effects of the high-risk MTHFR variants. However, given our results and the conflicting results in the literature, investigations into alternative mechanisms that may explain the link between MTHFR variants and pregnancy complications, or in populations at risk of folate deficiencies, are warranted.Electronic supplementary materialThe online version of this article (10.1186/s13148-018-0468-1) contains supplementary material, which is available to authorized users.

Accurate ethnicity prediction from placental DNA methylation data

“…In a subset of C5 (n = 27) and 10 additional samples, high density SNP array genotypes 417 were collected. DNA samples from one site from the fetal side of each placenta were collected as 418 previously described [45] and quality was checked using a NanoDrop ND-1000 (Thermo 419 Scientific) as well as by electrophoresis on a 1% agarose gel. Genotyping at ~2.3 million SNPs 420 was done on the Illumina Infinium Omni2.5-8 (Omni2.5) array at the Centre for Applied 421 Genomics, Hospital for Sick Kids, Toronto, Canada.…”

“…[65-67]. Results from cohort C5 have been published elsewhere [45], and genotyping data was 435 collected for cohort C4 in the same manner. Briefly, these markers were measured in placental 436 villus DNA using the Sequenom iPlex Gold platform (Génome Québec Innovation Centre, 437…”

“…Montréal, Canada). Genetic ancestry inferred from 50 AIMs markers was computed using multi-438 dimensional scaling after combining with the same 50 AIMs from the 1000 Genomes Project 439 samples, as previously described [45]. 440…”

“…To test the ability of PlaNET to identify individuals of mixed ancestry, we examined 169 whether samples classified as 'ambiguous' were also intermediate with respect to genetically-170 defined ancestry. Genetic ancestry was inferred from 50 ancestry informative genotyping 171 markers (AIMs) in samples from cohorts C4 and C5 (n = 109), using 1000 Genomes Project 172 samples as reference populations [44,45]. These 50 markers were previously selected based on 173 their ability to differentiate between African, European, East Asian, and South Asian populations 174 [45].…”

“…Genetic ancestry was inferred from 50 ancestry informative genotyping 171 markers (AIMs) in samples from cohorts C4 and C5 (n = 109), using 1000 Genomes Project 172 samples as reference populations [44,45]. These 50 markers were previously selected based on 173 their ability to differentiate between African, European, East Asian, and South Asian populations 174 [45]. Plotting the first two multi-dimensional scaling coordinates calculated on the 50 AIMs in 175 To evaluate our hypothesis that a placental-specific approach to population inference 200 would outperform existing methods developed in other tissues, we compared the performance of 201…”