Patterns of DNA Methylation Across the Leptin Core Promoter in Four Diverse Asian and North American Populations.

DNA methylation is the most widely studied of epigenetic mechanisms, with environmental effects recorded through patterned attachments of methyl groups along the DNA that are capable of modifying gene expression without altering the DNA sequencing. The degree to which these patterns of DNA methylation are heritable, the expected range of normality across populations, and the phenotypic relevance of pattern variation remain unclear. Genes regulating metabolic pathways appear to be vulnerable to ongoing nutritional programming over the life course, as dietary nutrients are significant environmental determinants of DNA methylation, supplying both the methyl groups and energy to generate the methylation process. Here we examine methylation patterns along a region of the metabolic gene leptin (LEP). LEP's putative functions include regulation of energy homeostasis, with its signals affecting energy intake and expenditure, adipogenesis and energy storage, lipid and glucose metabolism, bone metabolism, and reproductive endocrine function. A pattern of differential methylation across CpG sites of the LEP core promoter has been previously identified; however, any consistency of pattern or its phenotypic significance is not fully elucidated among populations. Using DNA extracted from unfractionated white blood cells of peripheral blood samples, our pilot study, divided into two parts, examined the significance of variation in DNA methylation patterns along the leptin core promoter in four populations (phase 1) and used biomarkers reflecting leptin's functional process in two of those populations, western Buryat of Siberia and the Mennonite of central Kansas, to investigate the relevance of the ethnic variation identified in the DNA methylation (phase 2). LEP's core promoter region contains both the binding site for C/EBPα (CCAAT/enhancer binding protein alpha), which tempers the final step in adipocyte maturity and capacity to synthesize leptin, and the TATA motif controlling leptin synthesis. Previous studies report that increased methylation in this region is correlated to decreased gene expression, suggesting tissue-specific methylation variation at this region ( Melzner et al. 2002 ). We hypothesized that evidence of nutritional epigenetic programming would be identified through variation in patterns of DNA methylation and that functional relevance of that variation among populations would be identified through biomarkers that reflect leptin's metabolic signals: serum leptin levels, lipoproteins of the lipid transport system, and anthropometric measures. In phase 1, our combined analyses of 313 individuals documented a distinct and consistent overall pattern of differential DNA methylation across seven CpG sites of LEP core promoter in all ethnicities and both sexes. This pattern replicates those identified in previous studies, suggesting a conserved core promoter region across populations. Phase 2 analyses of two of the four populations (n = 239), correlating methylation at the C/EBPα transcription binding site (TBS) with metabolic and anthropometric biomarkers reflecting LEP roles, showed that stature, which reflects bone growth and remodeling, was significantly and inversely correlated with the percentage of DNA methylation at this site in both sexes. We suggest that variation in DNA methylation along the LEP core promoter plays a substantial role in energy signals affecting both adipogenesis and bone metabolism.

Paternal Genetic Structure in Contemporary Mennonite Communities from the American Midwest.

Over the last 35 years, researchers from the Laboratory of Biological Anthropology at the University of Kansas have been working with Mennonite communities to better understand evolutionary patterns of fission-fusion in relationship to their genetic history and population structure. In this study, short tandem repeat (STR) markers from the nonrecombining region of the Y chromosome (NRY) provided increased resolution of the molecular population structure for these groups. NRY is known to be informative for determining paternal genetic ancestral patterns in recently derived human populations. Mennonites represent a branch of the Anabaptist movement that began in northern and central Europe in the 16th century and maintain a well-documented migration and genealogical history. Provided this historical information, we investigated the genetic relationship of 15 NRY STR loci within five Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, and Meridian) and Nebraska (Henderson). We sought to determine if patterns of fission/fusion along familial lines persisted with paternal genetic information as evidenced through other classical genetic polymorphisms and molecular markers. NRY haplotype information was obtained for 94 individuals, and genetic variation was analyzed and compared across the five study populations and comparative Anabaptist and European populations. NRY haplogroups were assigned using a Bayesian allele frequency approach with 14 STR loci. A total of 92 NRY haplotypes were detected, with none shared across these communities. The most prevalent NRY haplogroup was R1b, which occurred in 56% of the entire sample. Eight additional NRY haplogroups (E1b1b, G2a, I1, I2, J2a1, L, Q, and R1a) were detected in smaller frequencies. Principal component analysis of NRY data, in contrast to mitochondrial DNA data, displayed no patterns of population subdivision of these congregations into communities. These NRY genetic profiles provide additional information regarding the recent migratory history of Mennonite communities and additional evidence for fission along paternal lines after migration to the United States.

Mitochondrial DNA diversity in Mennonite communities from the midwestern United States.

We examined mitochondrial DNA (mtDNA) variation in six Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, Meridian, and Garden City) and Nebraska (Henderson) to determine their genetic structure and its relationship to population history. Mitochondrial DNA haplogroup and haplotype information were obtained from blood samples from 118 individuals. Molecular genetic variation was analyzed using diversity measures, neutrality test statistics, spatial analysis of molecular variance (SAMOVA), and multidimensional scaling plots. The Mennonite samples exhibited eight western European mtDNA haplogroups: H, HV0, I, J, K, T, U, and X. Comparable to other populations of European descent, haplogroup H was the most frequent in all six communities and ranged from 35% in Lone Tree to 75% in Old Order Mennonites from Garden City. Fifty-eight different mtDNA haplotypes were found in these groups with only one shared among all six populations. Haplotype diversities varied from 0.81 in Goessel to 0.96 in Henderson and Garden View. Multivariate statistical analysis of these populations indicates that these Anabaptist communities formed new congregations by fissioning along familial lines. Population subdivision of these communities into congregations supports previously documented patterns of fission-fusion. These haploid molecular data provide a more accurate reflection of biological relationships between midwestern Mennonite communities than evidence based on classical genetic markers.

Reduced fat oxidation and obesity risks among the Buryat of Southern Siberia.

Over the last 20 years, obesity and associated metabolic diseases have emerged as major global health problems. Among urbanizing populations of developing regions of the world, childhood undernutrition often coexists with adult overnutrition, a phenomenon known as the "dual nutritional burden". A recent work (Frisancho 2003: Am J Hum Biol 15:522-532) suggests that linear growth stunting in early childhood may contribute to adult obesity by reducing the body's ability to oxidize fat. We test central aspects of this model drawing on data from 112 adult Buryat herders (53 males; 59 females) from Southern Siberia. The results are consistent with the predictions of the model, but only for women. Shorter Buryat women (height-for-age Z-scores < or = -1) have significantly lower fasting fat oxidation levels compared to their taller counterparts. Shorter women are also significantly heavier and fatter, and have higher serum lipid levels. Among all Buryat women, reduced fat oxidation is significantly correlated with percent body fatness, serum triglyceride levels, and serum leptin levels, after controlling for relevant covariates. Additionally, Buryat women with high dietary fat intakes and low fat oxidation are significantly fatter and have higher lipid and leptin levels than those with low fat intakes and high fat oxidation. These results suggest that developmental changes in fat oxidation may play a role in the origins of obesity among populations with high rates of linear growth stunting. Further longitudinal research is necessary to elucidate the pathways through which early-life undernutrition may increase risks for adulthood obesity and cardiovascular disease.

Sex-specific interaction between APOE genotype and carbohydrate intake affects plasma HDL-C levels: the Strong Heart Family Study.

Low plasma levels of high-density lipoprotein cholesterol (HDL-C) are identified as a risk factor for cardiovascular disease (CVD). Sexual dimorphism, however, is widely reported in both HDL-C and CVD, with the underlying explanations of these sexual differences not fully understood. HDL-C is a complex trait influenced by both genes and dietary factors. Here we examine evidence for a sex-specific effect of APOE and the macronutrient carbohydrate on HDL-C, triglycerides (TG) and apoprotein A-1 (ApoA-1) in a sample of 326 male and 423 female participants of the Strong Heart Family Study (SHFS). Using general estimating equations in SAS to account for kinship correlations, stratifying by sex, and adjusting for age, body mass index (BMI) and SHS center, we examine the relationship between APOE genotype and carbohydrate intake on circulating levels of HDL-C, TG, and ApoA-1 through a series of carbohydrate-by-sex interactions and stratified analyses. APOE-by-carbohydrate intake shows significant sex-specific effects. All males had similar decreases in HDL-C levels associated with increased carbohydrate intake. However, only those females with APOE-4 alleles showed significantly lower HDL-C levels as their percent of carbohydrate intake increased, while no association was noted between carbohydrate intake and HDL-C in those females without an APOE-4 allele. These findings demonstrate the importance of understanding sex differences in gene-by-nutrient interaction when examining the complex architecture of HDL-C variation.

The influence of basal metabolic rate on blood pressure among indigenous Siberians.

Hypertension is an important global health issue and is currently increasing at a rapid pace in most industrializing nations. Although a number of risk factors have been linked with the development of hypertension, including obesity, high dietary sodium, and chronic psychosocial stress, these factors cannot fully explain the variation in blood pressure and hypertension rates that occurs within and between populations. The present study uses data collected on adults from three indigenous Siberian populations (Evenki, Buryat, and Yakut [Sakha]) to test the hypothesis of Luke et al. (Hypertension 43 (2004) 555-560) that basal metabolic rate (BMR) and blood pressure are positively associated independent of body size. When adjusted for body size and composition, as well as potentially confounding variables such as age, smoking status, ethnicity, and degree of urbanization, BMR was positively correlated with systolic blood pressure (SBP; P < 0.01) and pulse pressure (PP; P < 0.01); BMR showed a trend with diastolic blood pressure (DBP; P = 0.08). Thus, higher BMR is associated with higher SBP and PP; this is opposite the well-documented inverse relationship between physical activity and blood pressure. If the influence of BMR on blood pressure is confirmed, the systematically elevated BMRs of indigenous Siberians may help explain the relatively high blood pressures and hypertension rates documented among native Siberians in the post-Soviet period. These findings underscore the importance of considering the influence of biological adaptation to regional environmental conditions in structuring health changes associated with economic development and lifestyle change.

Functional COMT Val158Met polymorphism, risk of acute coronary events and serum homocysteine: the Kuopio ischaemic heart disease risk factor study.

BACKGROUND: The role of circulating levels of total homocysteine tHcy in the development of coronary heart disease (CHD) is still under debate. One reason for conflicting results between previous studies on homocysteine and heart diseases could be consequence of different interactions between homocysteine and genes in different study populations. Many genetic factors play a role in folate-homocysteine metabolism, like functional polymorphism (Val108Met) in the Catechol-O-methyltransferase (COMT) gene. METHODOLOGY AND FINDINGS: Our aim was to examine the role of COMT Val158Met polymorphism and interaction of this polymorphism with serum tHcy and folate concentration on the risk of acute coronary and events in middle-aged men from eastern Finland. A population-based prospective cohort of 792 men aged 46-64 years was examined as part of the Kuopio Ischaemic Heart Disease Risk Factor Study. During an average follow-up of 9.3 years, there were 69 acute coronary events in men with no previous history of CHD. When comparing the COMT low activity genotype with the others, we found an age and examination year adjusted hazard rate ratio (HRR) of 1.73 (95% confidence interval (CI), 1.07-2.79), and an age, examination year, serum LDL and HDL cholesterol, and triglyceride concentration, systolic blood pressure and smoking adjusted HRR of 1.77 (95% CI, 1.05-2.77). Although serum tHcy concentration was not statistically significantly associated with acute coronary events (HRR for the highest third versus others 1.52, 95% CI, 0.93-2.49), subjects with both high serum tHcy and the COMT low activity genotype had an additionally increased adjusted risk of HRR 2.94 (95% CI 1.50-5.76) as compared with other men. CONCLUSIONS: This prospective cohort study suggests that the functional COMT Val158Met polymorphism is associated with increased risk of acute coronary events and it may interact with high serum tHcy levels.

Apolipoproteins (apoproteins) and LPL variation in Mennonite populations of Kansas and Nebraska.

Apoproteins (also known as apolipoproteins) have been studied extensively because of their role in lipid transport, association between specific genotypes and elevated serum lipid levels, and increased risk of heart disease. There is considerable genetic variation in the geographic distributions of these markers, with a north-south cline of the APOE*4 allele observed in Europe by Lucotte et al. ([1997] Hum Biol 69:253-262). This study compares the frequencies of seven APO (APOA1 -75 bp, APOA1 +83 bp, APOB Ins/Del, APOB XbaI, APOC3 SstI, and APOE) and LPL loci in Mennonite populations from Kansas and Nebraska. In total, 277 individuals were sampled from Goessel, Meridian, Garden View, and Lone Tree in 2002-2004. In addition, DNA samples that were collected in 1981 from Henderson, Nebraska, were genotyped for the seven APO and LPL loci. Of the seven APO and LPL loci tested, only one locus, APOB XbaI, departed significantly from Hardy-Weinberg equilibrium, with an unexpected excess of observed heterozygotes. The frequencies of the several APO loci are unique among the Mennonites, separating them from other European populations. A bidimensional scaling representation of Reynold's co-ancestry distances based on allelic frequencies of the seven APO and LPL markers in five Mennonite congregations fails to represent schematically the known patterns of fission. It is unclear whether the observed patterns are due to selection operating on these loci or whether genetic drift, small populations sizes, or a lack of statistical power of these biallelic loci distort the observed genetic relationship among congregations.

Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats.

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.

Genotype-by-sex interaction in the regulation of high-density lipoprotein: the Framingham Heart Study.

Low levels of high-density lipoprotein (HDL) are widely documented as a risk factor for cardiovascular disease (CVD). Furthermore, there is marked sexual dimorphism in both HDL levels and the prevalence of CVD. However, the extent to which genetic factors contribute to such dimorphism has been largely unexplored. We examined the evidence for genotype-by-sex effects on HDL in a longitudinal sample of 1562 participants from 330 families in the Framingham Heart Study at three times points corresponding approximately to 1971-1974, 1980-1983, and 1988-1991. Using a variance component method, we conducted a genome scan of HDL at each time point in males and females, separately and combined, and tested for genotype-by-sex interaction at a quantitative trait locus (QTL) at each time point. Consistent findings were noted only for females on chromosome 2 near marker D2S1328, with adjusted LOD scores of 2.6, 2.2, and 2.1 across the three time points, respectively. In males suggestive linkage was detected on chromosome 16 near marker D16S3396 at the second time point and on chromosome 18 near marker D18S851 at the third time point (adjusted LOD = 2.2 and 2.4, respectively). Although the heritability of HDL is similar in males and females, sex appears to exert a substantial effect on the QTL-specific variance of HDL. When genotype-by-sex interactions exist and are not modeled, the power to detect linkage is reduced; thus our results may explain in part the paucity of significant linkage findings for HDL.

Climatic influences on basal metabolic rates among circumpolar populations.

This article examines evidence for elevations in basal metabolic rate (BMR) among indigenous Northern (circumpolar) populations and considers potential mechanisms and the adaptive basis for such elevations. Data on BMR among indigenous (n = 109 males; 122 females) and nonindigenous (n = 15 males; 22 females) circumpolar groups of North America and Siberia are compiled and compared to predicted BMRs based on three different references: body surface area (Consolazio et al., 1963), body mass (Schofield, 1985), and fat-free mass (Poehlman and Toth, 1995). Regardless of which reference is used, indigenous circumpolar groups show systematic and statistically significant elevations in BMR ranging from +7% to +19% above predicted values for indigenous men and from +3 to +17% for indigenous women. Nonindigenous males also show elevations in BMR, although not to the same extent as in indigenous men (deviations = +3 to +14%), whereas nonindigenous females show no clear evidence of elevated BMRs (deviations = -7 to +5%). This pattern of variation between indigenous and nonindigenous groups suggests that both functional and genetic factors play a role in metabolic adaptation to northern climes. Recent studies on the ecology and genetics of thyroid function offer insights into the mechanisms through which indigenous circumpolar populations may regulate metabolic rates. Studies of seasonal variation in thyroid hormone levels suggest that indigenous circumpolar populations may have a greater capacity to elevate BMR during severe cold than nonindigenous groups. Recent twin studies indicate a significant genetic component of thyroid responses to environmental stressors. Further research exploring the genetics of seasonal variation in thyroid function and BMR among circumpolar groups would advance understanding of the role that selection may have played in shaping metabolic variation.