Our research group recently reported that aorto-radial (radial) and aorto-dorsalis-pedis (foot) pulse wave velocity (PWV) as proxies of arterial stiffness are substantially heritable in healthy youth. This paper aimed at uncovering the genetic contributions of adhesion molecules, key members in the inflammatory process, to PWV in these young individuals.
Radial and foot PWV were non-invasively measured with applanation tonometry in 702 black and white subjects (42% blacks, mean age 17.7 ±3.3 years) from the Georgia Cardiovascular Twin Study. Eight functional polymorphisms from genes for E-selectin (SELE), P-selectin (SELP), intercellular adhesion molecules-1 (ICAM1), and vascular cell adhesion molecules-1 (VCAM1) were genotyped.
Youth with Ser290Asn or Asn290Asn genotype (SELP) compared to those with Ser290Ser had an increase in both radial and foot PWV (6.61±0.07 vs. 6.41±0.05 m/s, p=0.026; 7.22±0.05 vs. 7.04±0.04 m/s, p=0.007). TT homozygotes of rs2244529 (SELP) had higher foot PWV (7.28±0.07 vs. 7.06±0.03 m/s, p=0.002) than CT heterozygotes and CC homozygotes. There appeared to be a decrease in foot PWV in youth with the 241Arg allele (ICAM1) as compared to those without (6.96±0.08 vs. 7.14±0.03 m/s, p=0.005). For the Asp693Asp (C to T) polymorphism (VCAM1), CC genotype had higher foot PWV than CT and TT genotypes (7.18±0.04 vs. 6.95±0.06 m/s, p<0.0001). There was an epistatic interaction between Ser290Asn, Gly241Arg, and Asp693Asp on foot PWV (p=0.017), explaining 3.6% variance of the foot PWV.
Genetic variation of adhesion molecules may be implicated in the development of arterial stiffness. Screening for adhesion molecule polymorphisms may help identify high-risk youth.
adhesion molecules; polymorphisms; PWV; arterial stiffness; youth
Genetic contribution to left ventricular (LV) structure is generally recognized, but whether and how this influence varies by ethnicity or with age is unknown.
Design and methods
Participants were 517 European American (EA) and African American (AA) twin pairs (mean age: 14.6 ± 3.0) at visit 1 and 422 EA and AA at follow-up 4.1 years later. Echocardiograms were obtained on both visits. Data were analyzed using structural equation modeling software Mx.
Body mass index (BMI) was a strong predictor for all LV measures at both visit 1 and 2, accounting for 3.5-24.2% of the total variance. Hemodynamics explained up to 4.5% additional LV measures variance. After adjusting for BMI, LV measures showed substantial heritability (range: 21%-71%). Best-fitting longitudinal models revealed considerable novel genetic effects on the interventricular septum, posterior wall and relative wall thickness (but not LV inner diameter), accounting for 32-41% of the phenotypic variance at visit 2, with no significant gender and ethnic effects. There was a gender difference for LV mass index in AA (P < 0.01), with a significant influence of novel genetic effects in males (47%), but not in females. No gender difference was seen in EA, with 34% of the phenotypic variance at visit 2 attributable to novel genetic effects.
The heritability of cardiac structure and geometry was equally substantial in both AA and EA. Significant novel genetic influences were detected for all measures but LV inner diameter and LV mass index in AA females. Further developmental genetic studies are warranted to elucidate the nature of the emerging gene effects during the transition from adolescence into adulthood.
heritability; left ventricular mass; ethnicity
Blood pressure variability (BPV) and its reduction in response to antihypertensive treatment are predictors of clinical outcomes; however, little is known about its heritability. In this study, we examined the relative influence of genetic and environmental sources of variance of BPV and the extent to which it may depend on race or sex in young twins.
Twins were enrolled from two studies. One study included 703 white twins (308 pairs and 87 singletons) aged 18–34 years, whereas another study included 242 white twins (108 pairs and 26 singletons) and 188 black twins (79 pairs and 30 singletons) aged 12–30 years. BPV was calculated from 24-h ambulatory blood pressure recording.
Twin modeling showed similar results in the separate analysis in both twin studies and in the meta-analysis. Familial aggregation was identified for SBP variability (SBPV) and DBP variability (DBPV) with genetic factors and common environmental factors together accounting for 18–40% and 23–31% of the total variance of SBPV and DBPV, respectively. Unique environmental factors were the largest contributor explaining up to 82–77% of the total variance of SBPV and DBPV. No sex or race difference in BPV variance components was observed. The results remained the same after adjustment for 24-h blood pressure levels.
The variance in BPV is predominantly determined by unique environment in youth and young adults, although familial aggregation due to additive genetic and/or common environment influences was also identified explaining about 25% of the variance in BPV.
blacks; blood pressure variability; heritability; meta-analysis; twin study
Prostasin, a serine protease, is suggested to be a novel mechanism regulating the epithelial sodium channel expressed in the distal nephron. This study aimed to evaluate whether the human prostasin gene is a novel candidate gene underlying blood pressure (BP) elevation.
In a sample of healthy African American (AA) and European American (EA) twin subjects aged 17.6±3.3 years (n=920, 45% AAs), race-specific tagging single nucleotide polymorphisms (tSNPs) were identified to tag all the available SNPs ± 2Kb up- and downstream of the prostasin gene from HapMap at r2 of 0.8 – 1.0. Selection yielded four tSNPs in AAs and one in EAs, with one tSNP (rs12597511: C to T) present in both AAs and EAs.
For rs12597511, CT and TT genotypes exhibited higher systolic BP than CC genotype (115.9±1.1 mmHg vs. 113.7±0.6 mmHg, p=0.025 [AAs]; and 110.7±0.5 mmHg vs. 109.6±0.6 mmHg, p=0.115 [EAs]). CT and TT genotypes compared to CC genotype showed a significant increase in diastolic BP in both racial groups (62.5±0.7 mmHg vs. 60.4±0.4 mmHg, p=0.003 [AAs]; and 58.2±0.3 mmHg vs. 56.7±0.4 mmHg, p=0.007 [EAs]). Furthermore, there was an increase in radial pulse wave velocity (PWV) in subjects with CT and TT genotype as compared to those with CC genotype (6.5±0.1 vs. 6.1±0.1 m/s, p<0.0001) [EAs]; and 6.7±0.1 vs. 6.6±0.1 m/s, p=0.354 [AAs]). Analyses combining AAs and EAs consistently demonstrated a statistical significance of rs1259751 on all the phenotypes including systolic/diastolic BP, and PWV.
Genetic variation of the prostasin gene may be implicated in the development of hypertension in youths.
Prostasin; ENaC; Polymorphisms; Blood Pressure; Arterial stiffness
We tested whether the heritability of heart rate variability (HRV) under stress is different from rest and its dependency on ethnicity or gender. HRV indexed by root mean square of successive differences (RMSSD) and high-frequency (HF) power was measured at rest and during 3 stressors in 427 European and 308 African American twins. No ethnic or gender differences were found for any measures. There was a nonsignificant increase in heritability of RMSSD (from 0.48 to 0.58) and HF (from 0.50 to 0.58) under stress. Up to 81% and 60% of the heritabilities of RMSSD and HF under stress could be attributed to genes influencing rest levels. The heritabilities due to genes expressed under stress were 0.11 for RMSSD and 0.23 for HF. The findings suggest that, independent of ethnicity and gender, HRV regulation at rest and under stress is largely influenced by the same genes with a small but significant contribution of stress-specific genetic effects.
Heart rate variability; Stress; Ethnicity; Twin study
To determine to what extent the genetic influences on blood pressure (BP) measured in the office, under psychologically stressful conditions in the laboratory and during real life are different from each other. Office BP, BP during a video game challenge and a social stressor interview, and 24-h ambulatory BP were measured in 238 European American and 186 African American twins. BP values across the two tasks were averaged to represent stress levels. Genetic model fitting showed no ethnic or gender differences for any of the measures. The model fitting resulted in heritability estimates of 63, 75 and 71% for office, stress and 24-h systolic BP (SBP) and 59, 67 and 69% for diastolic BP (DBP), respectively. Up to 81% of the heritability of office SBP and 71% of office DBP were attributed to genes that also influenced stress BP. However, only 45% of the heritability of 24-h SBP and 49% of 24-h DBP were attributed to genes that also influence office BP. Similarly, about 39% of the heritability of 24-h SBP and 42% of 24-h DBP were attributed to genes that also influence stress BP. Substantial overlap exists between genes that influence BP measured in the office, under laboratory stress and during real life. However, significant genetic components specific to each BP measurement also exist. These findings suggest that partly different genes or sets of genes contribute to BP regulation in different conditions.
African American; ambulatory blood pressure; heritability; stress; twin
This study evaluates the tracking stability of office blood pressure (BP), ambulatory BP (ABP), BP variability (BPV) and nocturnal BP drops (dipping) from childhood to early adulthood, and their dependence on ethnicity, gender and family history (FH) of essential hypertension (EH). Generalized estimating equations (GEEs) were used to estimate tracking coefficients for 295 European Americans and 252 African Americans, with a maximum of 12 measurements over a 15-year period. Office BP and ABP had moderate-to-relatively high tracking coefficients (r= 0.30–0.59; P≤0.001). Twenty-four hour readings tracked better than office readings for diastolic BP (DBP; 0.57 vs. 0.46, P=1.72×10−6) and pulse pressure (PP) (0.59 vs. 0.51, P=2.70×10−4), and equally well for systolic BP (SBP; 0.55 vs. 0.54, P=0.805). Daytime readings tracked better than their night-time counterparts for SBP (0.50 vs. 0.37, P=7.62×10−13), DBP (0.49 vs. 0.30, P=7.98×10−32) and PP (0.55 vs. 0.50, P=0.0061). All BPV (r=0.08–0.28; P≤0.001) and dipping measures (r=0.07–0.12; odds ratio, 1.60–1.73; P≤0.001) had low tracking coefficients. Males had significantly higher tracking stability for office SBP, DBP and ambulatory PP than females (P<0.01). Subjects with a positive FH of EH had significantly higher tracking stability for daytime and night-time DBP and dipping indexed by continuous variables than those with a negative FH (P<0.001). No significant ethnic differences were observed. The high tracking stability of 24-h ABP highlights the importance of using ambulatory BP monitoring in both research and clinical settings.
ambulatory blood pressure; blood pressure variability; dipping; longitudinal study; tracking
To examine whether the genetic influences on blood pressure (BP) during night-time are different from those during daytime and the extent to which they depend on ethnicity or sex.
Ambulatory BP was measured in 240 European–American and 190 African–American twins (mean ± SD age, 17.2 ± 3.4). Individuals with night-time BP falls more than 10% of the daytime values were defined as dippers. A bivariate analysis of the daytime and the night-time BP levels, as well as a liability-threshold model of dippers vs. nondippers were used.
Bivariate model fitting showed no ethnic or sex differences for any of the measures, with heritabilities of 0.70 and 0.68 for SBP and 0.70 and 0.64 for DBP at daytime and at night-time. The genetic influences on daytime and night-time were not significantly different for SBP or DBP. The bivariate analysis also indicated that about 56 and 33% of the heritabilities of night-time SBP and DBP could be attributed to genes that also influenced daytime levels. The specific heritabilities due to genetic effects only influencing night-time values were 0.30 for SBP and 0.43 for DBP. The heritabilities of systolic and diastolic dipping were 0.59 and 0.81, respectively.
Independent of ethnicity and sex, an overlap exists between genes that influence daytime and night-time BP, as well as a significant genetic component that is specific to the night-time BP. These findings suggest that different genes or sets of genes contribute to BP regulation at daytime and night-time.
ambulatory blood pressure monitoring; blacks; dipping; heritability; twin study
High blood pressure variability is increasingly used as a predictor of target-organ damage and cardiovascular events. However, little is known about blood pressure variability changes with age and its possible sociodemographic, anthropometric, and genetic moderators.
Twenty-four-hour ambulatory blood pressure was measured up to 12 times over a 15-year period in 344 European Americans and 297 African–Americans with an average age of 14 years at the initial visit. Blood pressure variability was indexed by the weighted 24-h standard deviation of ambulatory blood pressure recordings.
Both systolic and diastolic blood pressure variability increased with age and ambulatory blood pressure mean values. Men had higher levels of blood pressure variability (P<0.001) and showed steeper linear increase rates with age than women. African–Americans showed higher values of blood pressure variability (P<0.05) than European Americans. Body mass index and waist circumference were also associated with higher blood pressure variability levels (P< 0.001). Individuals with higher father’s education level showed lower blood pressure variability. In the full model which included all the above factors, ethnic difference in systolic blood pressure variability was no longer significant.
The results of the present study suggest that men and African–Americans have higher blood pressure variability than women and European Americans. Apart from these ethnicity and sex effects, blood pressure variability increases with increases in age (especially in men), ambulatory blood pressure mean values and adiposity as well as decreased socioeconomic status
blood pressure variability; ethnicity; longitudinal study; sex; youth
To examine the heritability of arterial stiffness measured as pulse wave velocity (PWV) and its dependence on ethnicity, gender and blood pressure (BP).
As part of the Georgia Cardiovascular Twin Study, we measured aortoradial (radial) and aorto-dorsalis-pedis (foot) PWV in 702 twins (41% black, 49% male) aged 12 – 30 years (mean: 17.7 ± 3.3) including monozygotic and dizygotic pairs of same- as well as opposite-gender. Ethnicity and gender effects on genetic and environmental contributions to PWV were estimated by genetic model fitting.
Diastolic BP was the most important hemodynamic predictor. Best fitting models showed no ethnicity or gender differences in estimates of genetic and environmental influence and indicated substantial heritabilities of 0.43 (95% CI: 0.30–0.54) and 0.53 (95% CI: 0.42–0.62) for radial and foot PWV, respectively. Over a quarter of these heritabilities (0.19 for radial PWV, 0.14 for foot PWV) were due to genes in common with DBP as based on multivariate models.
Individual differences in arterial stiffness of youth and young adults are substantially heritable and more than 25% of this heritability is explained by genes that also influence DBP. Heritability estimates do not show any differences between blacks and whites or males and females.
Arterial Stiffness; Heritability; Twins; ethnicity
In type 1 diabetes, diabetes-associated autoantibodies, including islet cell antibodies (ICAs), reflect adaptive immunity, while increased serum Nε-carboxymethyl-lysine (CML), an advanced glycation end product, is associated with proinflammation. We assessed whether serum CML and autoantibodies predicted type 1 diabetes and to what extent they were determined by genetic or environmental factors. Of 7,287 unselected schoolchildren screened, 115 were ICA+ and were tested for baseline CML and diabetes autoantibodies and followed (for median 7 years), whereas a random selection (n = 2,102) had CML tested. CML and diabetes autoantibodies were determined in a classic twin study of twin pairs discordant for type 1 diabetes (32 monozygotic, 32 dizygotic pairs). CML was determined by enzyme-linked immunosorbent assay, autoantibodies were determined by radioimmunoprecipitation, ICA was determined by indirect immunofluorescence, and HLA class II genotyping was determined by sequence-specific oligonucleotides. CML was increased in ICA+ and prediabetic schoolchildren and in diabetic and nondiabetic twins (all P < 0.001). Elevated levels of CML in ICA+ children were a persistent, independent predictor of diabetes progression, in addition to autoantibodies and HLA risk. In twins model fitting, familial environment explained 75% of CML variance, and nonshared environment explained all autoantibody variance. Serum CML, a glycotoxin, emerged as an environmentally determined diabetes risk factor, in addition to autoimmunity and HLA genetic risk, and a potential therapeutic target.
Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common complex disease. We analyzed genome-wide methylation profiles of over 470,000 CpGs in peripheral blood samples from 48 obese and 48 lean African-American youth aged 14–20 y old. A substantial number of differentially variable CpG sites (DVCs), using statistics based on variances, as well as a substantial number of differentially methylated CpG sites (DMCs), using statistics based on means, were identified. Similar to the findings in cancers, DVCs generally exhibited an outlier structure and were more variable in cases than in controls. By randomly splitting the current sample into a discovery and validation set, we observed that both the DVCs and DMCs identified from the first set could independently predict obesity status in the second set. Furthermore, both the genes harboring DMCs and the genes harboring DVCs showed significant enrichment of genes identified by genome-wide association studies on obesity and related diseases, such as hypertension, dyslipidemia, type 2 diabetes and certain types of cancers, supporting their roles in the etiology and pathogenesis of obesity. We generalized the recent finding on methylation variability in cancer research to obesity and demonstrated that differential variability is also an important feature of obesity-related methylation changes. Future studies on the epigenetics of obesity will benefit from both statistics based on means and statistics based on variances.
African-Americans; epigenome-wide association study (EWAS); genome-wide association study (GWAS); methylation variation; obesity
There is emerging evidence from animal studies suggesting a key role for methylation in the pathogenesis of essential hypertension. However, to date, very few studies have investigated the role of methylation in the development of human hypertension, and none has taken a genome-wide approach. Based on the recent studies that highlight the involvement of inflammation in the development of hypertension, we hypothesize that changes in DNA methylation of leukocytes are involved in the pathogenesis of hypertension.
Method & Results
We conducted a genome-wide methylation analysis on 8 hypertensive cases and 8 normotensive age-matched controls aged 14–23 years and performed validation of the most significant CpG sites in 2 genes in an independent sample of 36 hypertensive cases and 60 normotensive controls aged 14–30 years. Validation of the CpG sites in the SULF1 gene was further conducted in a second replication sample of 36 hypertensive cases and 34 controls aged 15.8–40 years. A CpG site in the SULF1 gene showed higher methylation levels in cases than in healthy controls in the genome-wide step (p = 6.2×10−5), which was confirmed in the validation step (p = 0.011) for subjects ≤30 years old but was not significant for subjects of all ages combined (p = 0.095).
The identification of a difference in a blood leukocyte DNA methylation site between hypertensive cases and normotensive controls suggests that changes in DNA methylation may play an important role in the pathogenesis of hypertension. The age dependency of the effect further suggests complexity of epigenetic regulation in this age-related disease.
The genomic region at 9p21 chromosome near the CDKN2A/CDKN2B genes is associated with type 2 diabetes(T2D) and cardiovascular disease(CVD). The effect of the 9p21 locus on long-term mortality in patients with T2D has yet to be determined.
We examined three single nucleotide polymorphisms (SNPs) on 9p21, consistently and independently associated with T2D (rs10811661) or CVD (rs10757278, rs2383206), in relation to the risk of total and cardiovascular mortality in diabetic patients. We also aimed to replicate the previously observed interaction between rs2383206 and glycemic control on mortality.
Genotypes for three SNPs were determined in 914 individuals from a prospective cohort of T2D patients of Dutch origin. Associations with mortality were assessed using Cox proportional hazard analyses.
After a median follow-up of 9.5 years, 358 out of 914 patients had died. The hazard ratio (HR) for total mortality among individuals homozygous for the T2D-risk allele of rs10811661 compared to non-homozygous individuals was 0.74(95%CI 0.59-0.93). For the carriers of both CVD-risk alleles of rs10757278, the HR for total mortality was 1.31(95%CI 1.01-1.70). We found a significant interaction between rs2383206 and HbA1c on mortality, which was higher among patients with two CVD-risk alleles in the two lowest HbA1c tertiles (HR 1.68(95%CI 1.08-2.63); HR 1.48(95%CI 1.01-2.18).
In conclusion, common variants on 9p21 were associated with mortality in patients with T2D in a Dutch population. The T2D SNP was inversely associated with mortality, while the CVD SNP increased the risk for mortality. We confirmed a possible, although different, synergistic relationship between HbA1c and rs2383206 on total mortality.
Type 2 Diabetes; CVD; Mortality; 9p21; Genetics; SNP
In recent genetic association studies, common variants including rs12917707 in the UMOD locus have shown strong evidence of association with eGFR, prevalent and incident chronic kidney disease and uromodulin urinary concentration in general population cohorts. The association of rs12917707 with end-stage renal disease (ESRD) in a recent case-control study was only nominally significant.
To investigate whether rs12917707 associates with ESRD, graft failure (GF) and urinary uromodulin levels in an independent cohort, we genotyped 1142 ESRD patients receiving a renal transplantation and 1184 kidney donors as controls. After transplantation, 1066 renal transplant recipients were followed up for GF. Urinary uromodulin concentration was measured at median [IQR] 4.2 [2.2-6.1] yrs after kidney transplantation.
The rs12917707 minor allele showed association with lower risk of ESRD (OR 0.89 [0.76-1.03], p = 0.04) consistent in effect size and direction with the previous report (Böger et al, PLoS Genet 2011). Meta-analysis of these findings showed significant association of rs12917707 with ESRD (OR 0.91 [0.85-98], p = 0.008). In contrast, rs12917707 was not associated with incidence of GF. Urinary uromodulin concentration was lower in recipients-carriers of the donor rs12917707 minor allele as compared to non-carriers, again consistent with previous observations in general population cohorts.
Our study thus corroborates earlier evidence and independently confirms the association between UMOD and ESRD.
UMOD; Uromodulin; Polymorphisms; SNP; End-stage renal disease; Kidney transplantation
Obesity is a complex multifaceted disease resulting from interactions between genetics and lifestyle. The proportion of phenotypic variance ascribed to genetic variance is 0.4 to 0.7 for obesity and recent years have seen considerable success in identifying disease-susceptibility variants. Although with the advent of genome-wide association studies the list of genetic variants predisposing to obesity has significantly increased the identified variants only explain a fraction of disease heritability. Studies of gene–environment interactions can provide more insight into the biological mechanisms involved in obesity despite the challenges associated with such designs. Epigenetic changes that affect gene function without DNA sequence modifications may be a key factor explaining interindividual differences in obesity, with both genetic and environmental factors influencing the epigenome. Disentangling the relative contributions of genetic, environmental and epigenetic marks to the establishment of obesity is a major challenge given the complex interplay between these determinants.
Gene–environment interaction; Lifestyle; Genetics; Environment; Epigenetics; Obesity; Epigenome
Chronic kidney disease (CKD) is a complex disorder. As genome-wide association studies identified cubilin gene CUBN as a locus for albuminuria, and urinary protein loss is a risk factor for progressive CKD, we tested the hypothesis that common genetic variants in CUBN are associated with end-stage renal disease (ESRD) and proteinuria. First, a total of 1142 patients with ESRD, admitted for renal transplantation, and 1186 donors were genotyped for SNPs rs7918972 and rs1801239 (case-control study). The rs7918972 minor allele frequency (MAF) was higher in ESRD patients comparing to kidney donors, implicating an increased risk for ESRD (OR 1.39, p = 0.0004) in native kidneys. Second, after transplantation recipients were followed for 5.8 [3.8–9.2] years (longitudinal study) documenting ESRD in transplanted kidneys – graft failure (GF). During post-transplant follow-up 92 (9.6%) cases of death-censored GF occurred. Donor rs7918972 MAF, representing genotype of the transplanted kidney, was 16.3% in GF vs 10.7% in cases with functioning graft. Consistently, a multivariate Cox regression analysis showed that donor rs7918972 is a predictor of GF, although statistical significance was not reached (HR 1.53, p = 0.055). There was no association of recipient rs7918972 with GF. Rs1801239 was not associated with ESRD or GF. In line with an association with the outcome, donor rs7918972 was associated with elevated proteinuria levels cross-sectionally at 1 year after transplantation. Thus, we identified CUBN rs7918972 as a novel risk variant for renal function loss in two independent settings: ESRD in native kidneys and GF in transplanted kidneys.
To examine the relations of race, sex, adiposity, adipokines and physical activity to telomere length in adolescents.
Leukocyte telomere length (T/S ratio) was assessed cross-sectionally in 667 adolescents (aged 14–18 years, 48% blacks, 51% girls) using a quantitative PCR method. Generalized Estimating Equations analyses were performed.
Black adolescents had longer telomeres than white adolescents (age and sex adjusted T/S ratio ± SE: 1.32 ± 0.01 vs. 1.27 ± 0.01, p=0.014) and girls had longer telomeres than boys (age and race adjusted T/S ratio ± SE: 1.31 ± 0.01 vs. 1.27 ± 0.01, p=0.007). None of the adiposity or adipokine measures explained a significant proportion of the variance in telomere length. Vigorous physical activity was positively associated with telomere length (adjusted R2=0.019, p=0.009) and accounted for 1.9% of the total variance only in girls.
This study, conducted in a biracial adolescent cohort, demonstrated that: (1) race and sex differences in telomere length have already emerged during adolescence; (2) adiposity and adipokines are not associated with telomere length at this age; and (3) the anti-aging effect of vigorous physical activity may begin in youth especially in girls.
Telomere length; race; sex; adiposity; adipokines; physical activity; adolescents
It is known that genetic variants can affect gene expression, but it is not yet completely clear through what mechanisms genetic variation mediate this expression. We therefore compared the cis-effect of single nucleotide polymorphisms (SNPs) on gene expression between blood samples from 1,240 human subjects and four primary non-blood tissues (liver, subcutaneous, and visceral adipose tissue and skeletal muscle) from 85 subjects. We characterized four different mechanisms for 2,072 probes that show tissue-dependent genetic regulation between blood and non-blood tissues: on average 33.2% only showed cis-regulation in non-blood tissues; 14.5% of the eQTL probes were regulated by different, independent SNPs depending on the tissue of investigation. 47.9% showed a different effect size although they were regulated by the same SNPs. Surprisingly, we observed that 4.4% were regulated by the same SNP but with opposite allelic direction. We show here that SNPs that are located in transcriptional regulatory elements are enriched for tissue-dependent regulation, including SNPs at 3′ and 5′ untranslated regions (P = 1.84×10−5 and 4.7×10−4, respectively) and SNPs that are synonymous-coding (P = 9.9×10−4). SNPs that are associated with complex traits more often exert a tissue-dependent effect on gene expression (P = 2.6×10−10). Our study yields new insights into the genetic basis of tissue-dependent expression and suggests that complex trait associated genetic variants have even more complex regulatory effects than previously anticipated.
Gene expression can be affected by genetic variation, e.g. single nucleotide polymorphisms (SNPs). These are called expression-affecting SNPs or eSNPs. Gene expression levels are known to vary across different tissues in the same individual, despite the fact that genetic variation is the same in these tissues. We explored the different mechanisms by which genetic variants can mediate tissue-dependent gene expression. We observed that the genetic variants that associated with complex traits are more likely to affect gene expression in a tissue-dependent manner. Our results suggest that complex traits are even more complex than we had anticipated, and they underline the great importance of using expression data from tissues relevant to the disease being studied in order to further the understanding of the biology underlying the disease association.
Genetic linkage and association methods have long been the most important tools for gene identification in humans. These approaches can either be hypothesis-based (i.e., candidate-gene studies) or hypothesis-free (i.e., genome-wide studies). The first part of this review offers an overview of the latest successes in gene finding for blood pressure (BP) and essential hypertension using these DNA sequence–based discovery techniques. We further emphasize the importance of post–genome-wide association study (post-GWAS) analysis, which aims to prioritize genetic variants for functional follow-up. Whole-genome next-generation sequencing will eventually be necessary to provide a more comprehensive picture of all DNA variants affecting BP and hypertension. The second part of this review discusses promising novel approaches that move beyond the DNA sequence and aim to discover BP genes that are differentially regulated by epigenetic mechanisms, including microRNAs, histone modification, and methylation.
Linkage analysis; Association analysis; Genome-wide association study; GWAS; Post-GWAS analysis; Next-generation sequencing; Epigenetics; microRNAs; Histone modification; Methylation; Hypertension; Blood pressure
The corrected QT (QTc) interval is a complex quantitative trait, believed to be influenced by several genetic and environmental factors. It is a strong prognostic indicator of cardiovascular mortality in patients with and without cardiac disease. More than 700 mutations have been described in 12 genes (LQT1-LQT12) involved in congenital long QT syndrome. However, the heritability (genetic contribution) of QTc interval in the general population cannot be adequately explained by these long QT syndrome genes. In order to further investigate the genetic architecture underlying QTc interval in the general population, genome-wide association studies, in which up to one million single nucleotide polymorphisms are assayed in thousands of individuals, are now being employed and have already led to the discovery of variants in seven novel loci and five loci that are known to cause congenital long or short QT syndrome. Here we show that a combined risk score using 11 of these loci explains about 10% of the heritability of QTc. Additional discovery of both common and rare variants will yield further etiological insight and accelerate clinical applications.
Recent genome-wide association (GWA) studies identified several common variants for obesity: rs9939609 in FTO, rs7566605 near INSIG2 and both rs17782313 and rs17700633 near the MC4R gene. This study aimed to assess the influence of these polymorphisms on development of adiposity in European– (EA) and African–American (AA) youth in two ongoing longitudinal studies including 986 and 606 participants with age ranges of 10–25.8 and 4.0–23.9 years, respectively. Individual growth curve modeling was conducted separately in the two studies. We tested the effect of the SNPs on levels and increase with age (i.e., slope) of weight, body mass index (BMI), waist circumference and skinfolds from childhood to adulthood, and potential moderation by ethnicity or gender. Beta coefficients computed in the two studies were pooled using meta-analysis. Rs9939609 was associated with logtransformed levels of BMI (β = 0.021, P = 0.01), weight (β = 0.019, P = 0.04) and waist circumference (β = 0.012, P = 0.04). Rs17782313 was associated with triceps (β = 0.05, P = 0.02). Significant interactions of rs17700633 with gender were observed on subscapular-, suprailiac- and sum of skinfolds, with significant associations limited to males (P < 0.05). No significant interactions with ethnicity were found. Only one effect on the slope was observed, rs17700633 showed a significant interaction with age on triceps (β = 0.004, P = 0.04). In two longitudinal studies of EA and AA youth, we replicated the effect of FTO and common variants near MC4R on general and central adiposity. These variants did not affect the increase with age of adiposity from childhood to adulthood with one exception. Common variants for obesity identified in GWA studies have detectable but modest effects on growth curves for adiposity in EA and AA youth.
Electronic supplementary material
The online version of this article (doi:10.1007/s10654-011-9583-4) contains supplementary material, which is available to authorized users.
Adiposity; Genetic; Growth curve model
Antipsychotic affinity for the histamine H1 receptor and the muscarinic M3 receptor have been associated with the side effects weight gain, and development of diabetes, respectively.
We investigated polymorphisms of the histamine H1 (HRH1) and muscarinic acetylcholine receptor M3 (CHRM3) receptor genes for an association with body mass index (BMI) and glycated hemoglobin (HbA1c).
We included 430 Caucasian patients with a non-affective psychotic disorder using antipsychotics for at least 3 months. Primary endpoints of the study were cross-sectionally measured BMI and HbA1c; secondary endpoints were obesity and hyperglycaemia. Two single-nucleotide polymorphisms (SNPs) in the HRH1 gene, rs346074 and rs346070, and one SNP in the CHRM3 gene, rs3738435, were genotyped. Our primary hypothesis in this study was an interaction between genotype on BMI and antipsychotic affinity for the H1 and M3 receptor.
A significant association of interaction between haplotype rs346074–rs346070 and BMI (p value 0.025) and obesity (p value 0.005) in patients using high-H1 affinity antipsychotics versus patients using low-H1 affinity antipsychotics was found. There was no association of CHRM3 gene variant rs3738435 with BMI, and we observed no association with HbA1c or hyperglycaemia in any of the variants.
This study, for the first time, demonstrates a significant association between HRH1 variants and BMI in patients with a psychotic disorder using antipsychotics. In future, genotyping of HRH1 variants may help predicting weight gain in patients using antipsychotics.
Electronic supplementary material
The online version of this article (doi:10.1007/s00213-011-2211-x) contains supplementary material, which is available to authorized users.
Antipsychotics; BMI; HbA1c; Schizophrenia; Polymorphism; Histamine; Muscarine; Pharmacogenetics; Weight gain; Hyperglycaemia
Despite evidence linking obesity to impaired immune function, little is known about the specific mechanisms. Because of emerging evidence that immune responses are epigenetically regulated, we hypothesized that DNA methylation changes are involved in obesity induced immune dysfunction and aimed to identify these changes.
We conducted a genome wide methylation analysis on seven obese cases and seven lean controls aged 14 to 18 years from extreme ends of the obesity distribution and performed further validation of six CpG sites from six genes in 46 obese cases and 46 lean controls aged 14 to 30 years.
In comparison with the lean controls, we observed one CpG site in the UBASH3A gene showing higher methylation levels and one CpG site in the TRIM3 gene showing lower methylation levels in the obese cases in both the genome wide step (P = 5 × 10-6 and P = 2 × 10-5 for the UBASH3A and the TRIM3 gene respectively) and the validation step (P = 0.008 and P = 0.001 for the UBASH3A and the TRIM3 gene respectively).
Our results provide evidence that obesity is associated with methylation changes in blood leukocyte DNA. Further studies are warranted to determine the causal direction of this relationship as well as whether such methylation changes can lead to immune dysfunction.
See commentary: http://www.biomedcentral.com/1741-7015/8/88/abstract
Reduced heart rate variability (HRV) and increased C-reactive protein (CRP) levels are both predictors of coronary artery disease (CAD), and are correlated with each other. We examined whether these two phenotypes share a common genetic substrate and investigated the relations of the CRP gene polymorphisms with both CRP levels and HRV indices. We examined 236 male twins free of symptomatic CAD, with mean age (±SD) of 54 years (±2.9). Plasma CRP levels were measured and frequency domain measures of HRV were assessed using a 24-hour ECG recording, including ultra-low, very-low, low and high frequency power (ULF, VLF, LF, and HF). Three SNPs in the CRP gene were genotyped. Generalized estimating equations were used to examine the association between CRP and HRV, as well as the genotype-phenotype association. Bivariate structural equation modeling was performed to estimate the genetic and environmental correlations between CRP and HRV, and the explanatory effect of CRP gene polymorphisms on the CRP-HRV association. Both CRP (h2=0.76) and HRV indices (h2=0.56–0.64) showed high heritability. Higher CRP levels were significantly associated with lower HRV. A robust genetic correlation was found between CRP and ULF (rG=−0.3, P=0.001). One CRP SNP (rs1205) was significantly associated with both CRP (P=0.003) and ULF (P=0.005) and explained 11% of the genetic covariance between them. In conclusion, reduced HRV is significantly correlated with increased CRP plasma levels and this correlation is due, in large part, to common genetic influences. A polymorphism in the CRP gene contributes to both CRP levels and HRV.
C-reactive protein; heart rate variability; common genes; genetic polymorphisms