Genetic Effects on DNA Methylation and Its Potential Relevance for Obesity in Mexican Americans

<div><p>Several studies have identified effects of genetic variation on DNA methylation patterns and associated heritability, with research primarily focused on Caucasian individuals. In this paper, we examine the evidence for genetic effects on DNA methylation in a Mexican American cohort, a population burdened by a high prevalence of obesity. Using an Illumina-based platform and following stringent quality control procedures, we assessed a total of 395 CpG sites in peripheral blood samples obtained from 183 Mexican American individuals for evidence of heritability, proximal genetic regulation and association with age, sex and obesity measures (i.e. waist circumference and body mass index). We identified 16 CpG sites (∼4%) that were significantly heritable after Bonferroni correction for multiple testing and 27 CpG sites (∼6.9%) that showed evidence of genetic effects. Six CpG sites (∼2%) were associated with age, primarily exhibiting positive relationships, including CpG sites in two genes that have been implicated in previous genome-wide methylation studies of age (<i>FZD9</i> and <i>MYOD1</i>). In addition, we identified significant associations between three CpG sites (∼1%) and sex, including DNA methylation in <i>CASP6</i>, a gene that may respond to estradiol treatment, and in <i>HSD17B12</i>, which encodes a sex steroid hormone. Although we did not identify any significant associations between DNA methylation and the obesity measures, several nominally significant results were observed in genes related to adipogenesis, obesity, energy homeostasis and glucose homeostasis (<i>ARHGAP9</i>, <i>CDKN2A</i>, <i>FRZB</i>, <i>HOXA5</i>, <i>JAK3</i>, <i>MEST</i>, <i>NPY</i>, <i>PEG3</i> and <i>SMARCB1</i>). In conclusion, we were able to replicate several findings from previous studies in our Mexican American cohort, supporting an important role for genetic effects on DNA methylation. In addition, we found a significant influence of age and sex on DNA methylation, and report on trend-level, novel associations between DNA methylation and measures of obesity.</p></div

Most highly significant associations between DNA methylation and obesity measures.

<p>Note: all significance values are nominal.</p>#<p>CpG sites are annotated according to <i>GENE_Position_Strand</i>, as outlined in the methods section.</p>*<p>A positive value for beta indicates increased methylation is associated with increased obesity measures (i.e. increased waist circumference or increased BMI).</p

Significant age and sex associations with DNA methylation.

<p>P-values that are significant after correction for multiple testing are given in <b>bold.</b></p>#<p>CpG sites are annotated according to <i>GENE_Position_Strand</i>, as outlined in the methods section.</p>*<p>Note: a positive value for beta indicates increased methylation is associated with increased age and females.</p

Heritability and genetic regulation of DNA methylation.

<p>P-values that are significant after correction for multiple testing are given in <b>bold.</b></p>#<p>CpG sites are annotated according to <i>GENE_Position_Strand</i>, as outlined in the methods section.</p><p><a href="mailto:@Indicates" target="_blank">@Indicates</a> probe sequences containing SNPs with a MAF>5%.</p>*<p>MAF: Minor allele frequency; minor allele is reported second.</p

The genome-wide distribution of asymptotic p-values for each of the quality control filtered SNPs in the Australian cohort (n = 648,175).

<p>Our adjusted genome-wide significant and suggestive thresholds were set at p<5.11483×10⁻⁷ and p<1.02297×10⁻⁶, respectively.</p

Genome-wide joint linkage and association analysis results for EBNA-1 antibody traits for SAFHS.

<p>(A) Quantitative antibody titer. (B) Discrete serostatus.</p

<i>INHBB</i> locus variants identified in a sample of the Australian cohort (n = 96).

<p>Identified variants were genotyped in Australian individuals passing GWAS quality control criteria (n = 1,078). Novel variants submitted to dbSNP are assigned with their ‘ss’ submission ID number.</p>*<p>Fisher's exact test p-value.</p>1<p>Major allele/Minor allele.</p>2<p>Hardy-Weinberg equilibrium p-value.</p>3<p>Preeclampsia dataset allele discordant to reference template allele.</p

Association (conditional on linkage) results for 12 comparative pathogens.

<p>Focus is on the independent EBNA-1 associated SNPs rs477515/rs2516049 and rs2854275. There is no significant association of the top EBV SNPs with any of the other pathogens, after applying a Bonferroni correction to account for multiple testing (<i>p</i>≤0.05/12≈0.004).</p

<i>P</i>-values for EBNA-1 association, conditional on linkage, analysis for top systemic lupus erythematosus SNPs.

<p>Bold = <i>p</i>-value significant after Bonferoni correction for multiple testing (0.05/47≈1.06×10⁻³).</p

Heritability estimates of EBNA-1 quantitative antibody and discrete serostatus traits, with and without household effects.

a<p>Intermediate antibody titers were coded as unknown (indeterminate), thereby reducing the number of individuals included in analyses of the dichotomous serostatus trait.</p