MOESM2 of Geographical and ethnic distribution of single nucleotide polymorphisms within genes of the folate/homocysteine pathway metabolism

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<em>VNN1</em> Gene Expression Levels and the G-137T Polymorphism Are Associated with HDL-C Levels in Mexican Prepubertal Children

<div><h3>Background</h3><p><em>VNN1</em> gene expression levels and the G-137T polymorphism have been associated with high density lipoprotein cholesterol (HDL-C) levels in Mexican American adults. We aim to evaluate the contribution of <em>VNN1</em> gene expression and the G-137T variant to HDL-C levels and other metabolic traits in Mexican prepubertal children.</p> <h3>Methodology/Principal Findings</h3><p><em>VNN1</em> mRNA expression levels were quantified in peripheral blood leukocytes from 224 unrelated Mexican-Mestizo children aged 6–8 years (107 boys and 117 girls) and were genotyped for the G-137T variant (rs4897612). To account for population stratification, a panel of 10 ancestry informative markers was analyzed. After adjustment for admixture, the TT genotype was significantly associated with lower <em>VNN1</em> mRNA expression levels (<em>P</em> = 2.9 × 10⁻⁵), decreased HDL-C levels (β = −6.19, <em>P</em> = 0.028) and with higher body mass index (BMI) z-score (β = 0.48, <em>P</em> = 0.024) in the total sample. In addition, <em>VNN1</em> expression showed a positive correlation with HDL-C levels (r = 0.220; <em>P</em> = 0.017) and a negative correlation with BMI z-score (r = −0.225; <em>P</em> = 0.015) only in girls.</p> <h3>Conclusion/Significance</h3><p>Our data suggest that <em>VNN1</em> gene expression and the G-137T variant are associated with HDL-C levels in Mexican children, particularly in prepubertal girls.</p> </div

Effect of G-137T variant on <i>VNN1</i> expression levels in Mexican prepubertal children.

<p>The results are presented as the global mean ± the standard error.</p

Correlation of <i>VNN1</i> mRNA levels in leukocytes with metabolic phenotypes.

<p>BMI, body mass index; FM, percent fat mass; TG, triglyceride; TC, total cholesterol; HDL-C, high-density lipoprotein cholesterol.</p>a<p><i>P</i>-values adjusted for admixture.</p>*<p>Significant after Bonferroni correction.</p

Association of G-137T variant with metabolic parameters stratified by gender.

<p>Effect values are presented as effect for two T copies (recessive model), standard error (SE). Genotype frequencies: all children (GG, 41.1%; GT, 47.7%; TT, 11.2%); boys (GG, 42.1%; GT, 49.5%; TT, 8.4%); girls (GG, 40.2%; GT, 46.1%; TT, 13.7%). BMI, body mass index; FM, percent fat mass; TG, triglyceride; TC, total cholesterol; HDL-C, high-density lipoprotein cholesterol.</p>a<p><i>P</i>-values adjusted for admixture in all tests and for BMI z-score when appropriate.</p>*<p>Significant after Bonferroni correction.</p

Anthropometric and biochemical parameters according to gender.

<p>Data are means ± s.d. or n (%). BMI, body mass index; FM, percent fat mass; TG, triglyceride; TC, total cholesterol; HDL-C, high-density lipoprotein cholesterol; HA, hypoalphalipoproteinemia.</p>a<p><i>P</i>-values were calculated by t-test;</p>b<p>X² test.</p

Genotypes, allele frequencies, and geographic locations of the Native American populations investigated.

1<p>Samples genotyped in present study  = 229;</p>2<p>Caution is needed regarding the classification of these modes of subsistence, since they are not stable over time and may not be unique. However, the two categories adopted here (agriculturalist and hunter-gatherer/forager) represent general pre-Columbian subsistence conditions of the investigated populations in accordance with what is known about them. AMOVA results: (a) Among the subdivisions (<i>F_CT</i>): 3.6% (<i>p</i> = 0.000); (b) Among populations within the Mesoamerican Agriculturalist subdivision (<i>F_ST):</i> 1.8% (<i>p</i> = 0.008); (c) Among populations within the South American hunter-gatherer/forager subdivision: 5.3% (<i>p</i> = 0.005); Among populations within the Andean Agriculturarist group: 0% (<i>p</i> = 0.36).</p

Plot of the joint <i>F_ST</i> and <i>He</i> distributions for the Mesoamerican agriculturalist <i>versus</i> South American (agriculturalists + hunter-gatherer/foraging) groups.

<p>Each dot indicates a SNP (listed in item c.2 in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038862#s2" target="_blank">Materials and Methods</a> section). The lines represent confidence intervals. Only the <i>ABCA1</i> locus showed significance at the 5% level (filled blue circle). Five selected SNPs were not plotted in the figure because of monomorphic sites in all subdivisions, missing data, and/or dot superposition.</p

Zea pollen relics ages and 230Cys*ABCA1 populations frequencies used for the regression analysis.

1<p>Located near the archeological sites of <i>Zea</i> pollen relics; 2 Conversion according to <a href="http://www.radiocarbon.ldeo.columbia.edu/radcarbcal.htm" target="_blank">www.radiocarbon.ldeo.columbia.edu/radcarbcal.htm</a>.</p>2<p>Data relative to archeological information were obtained from Blake (2006).</p

<i>ABCA1*</i>230Cys frequencies versus radiocarbon ages of maize domestication (<i>Zea</i> pollen relics; Blake [<b>42</b>]).

<p>Spearman’s rho value  = 0.936975 and <i>p</i> = 0.0019.</p