Genomic loci with pleiotropic effects on coronary artery calcification

Multiethnic Genome-Wide Association Study of Subclinical Atherosclerosis in Individuals With Type 2 Diabetes

BACKGROUND

Coronary artery calcification (CAC) and carotid artery intima-media thickness (cIMT) are measures of subclinical atherosclerosis in asymptomatic individuals and strong risk factors for cardiovascular disease. Type 2 diabetes (T2D) is an independent cardiovascular disease risk factor that accelerates atherosclerosis.

METHODS

We performed meta-analyses of genome-wide association studies in up to 2500 T2D individuals of European ancestry (EA) and 1590 T2D individuals of African ancestry with or without exclusion of prevalent cardiovascular disease, for CAC measured by cardiac computed tomography, and 3608 individuals of EA and 838 individuals of African ancestry with T2D for cIMT measured by ultrasonography within the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium.

RESULTS

We replicated 2 loci (rs9369640 and rs9349379 near PHACTR1 and rs10757278 near CDKN2B) for CAC and one locus for cIMT (rs7412 and rs445925 near APOE-APOC1) that were previously reported in the general EA populations. We identified one novel CAC locus (rs8000449 near CSNK1A1L/LINC00547/POSTN at 13q13.3) at P=2.0×10-8 in EA. No additional loci were identified with the meta-analyses of EA and African ancestry. The expression quantitative trait loci analysis with nearby expressed genes derived from arterial wall and metabolic tissues from the Genotype-Tissue Expression project pinpoints POSTN, encoding a matricellular protein involved in bone formation and bone matrix organization, as the potential candidate gene at this locus. In addition, we found significant associations (P<3.1×10-4) for 3 previously reported coronary artery disease loci for these subclinical atherosclerotic phenotypes (rs2891168 near CDKN2B-AS1 and rs11170820 near FLJ12825 for CAC, and rs7412 near APOE for cIMT).

CONCLUSIONS

Our results provide potential biological mechanisms that could link CAC and cIMT to increased cardiovascular disease risk in individuals with T2D.

Genetic variations in G-protein signal pathways influence progression of coronary artery calcification: Results from the Heinz Nixdorf Recall study

BACKGROUND AND AIMS

Coronary artery calcification (CAC) is one of the most sensitive and specific markers of coronary atherosclerosis and believed to be heritable. We hypothesized that functionally relevant single-nucleotide polymorphisms (SNPs) in the G-protein signal pathway, which have been previously related to coronary artery disease, are associated with CAC progression.

METHODS

3108 participants from the Heinz Nixdorf Recall study with CAC measurements at both baseline (CACb) and 5-year follow-up (CAC5y) were included. We genotyped SNPs rs1042714 (ADRB2), rs6026584 and rs12481583 (GNAS), and rs5443 (GNB3) and defined a priori risk alleles derived from literature data. Regression analyses were applied to measures of 5-year CAC progression, unadjusted, adjusted for age, sex, and adjusted for age, sex, log(CACb+1) as well as for cardiovascular risk factors.

RESULTS

The presence of one or more risk alleles was associated with a 26.9% (95% CI 5.5-52.4) increase in 5-year CAC progression (p = 0.011) and a 29.2% (95% CI 5.9-57.6) accelerated increase of CAC over the 5-year period compared to what was expected with respect to the baseline CAC percentile value (p = 0.012). Each of those risk alleles increased the 5-year CAC progression by 4.4% (95% CI 1.3-7.6, p = 0.006) and resulted in a 4.9% accelerated increase of CAC over the 5-year period (95% CI 1.6-8.4, p = 0.004). These unadjusted data did not change after adjustment.

CONCLUSIONS

Genetic variations in the G-protein signal pathway are associated with CAC progression in a cumulative fashion, indicating the importance of the pathway for genetic heritability in CAC progression and coronary artery disease.

Can antihypertensive medication interfere with the vicious cycle between hypertension and vascular calcification?

Vascular calcification is a phenomenon of disturbed calcium deposition, as part of the calcium that is supposed to be deposited to our bones, is lodged to our vessels. There are two forms of vascular calcification, each with a distinct anatomical distribution and clinical relevance, namely the intimal and medial calcification. Studies have demonstrated that hypertension may cause vascular calcification but also that both types of calcification, especially medial, promote arterial rigidity and hence hypertension. Implications of this two-way road are largely unknown as there is no consensus yet on their exact clinical value. However, several antihypertensive medications seem to be able to interfere with the cycle of high blood pressure and vascular calcium deposits. The present review summarizes the up-to-date data regarding the effect of antihypertensive medication on vascular calcification.

Genome-wide association study of gene by smoking interactions in coronary artery calcification

Many GWAS have identified novel loci associated with common diseases, but have focused only on main effects of individual genetic variants rather than interactions with environmental factors (GxE). Identification of GxE interactions is particularly important for coronary heart disease (CHD), a major preventable source of morbidity and mortality with strong non-genetic risk factors. Atherosclerosis is the major cause of CHD, and coronary artery calcification (CAC) is directly correlated with quantity of coronary atherosclerotic plaque. In the current study, we tested for genetic variants influencing extent of CAC via interaction with smoking (GxS), by conducting a GxS discovery GWAS in Genetic Epidemiology Network of Arteriopathy (GENOA) sibships (N = 915 European Americans) followed by replication in Framingham Heart Study (FHS) sibships (N = 1025 European Americans). Generalized estimating equations accounted for the correlation within sibships in strata-specific groups of smokers and nonsmokers, as well as GxS interaction. Primary analysis found SNPs that showed suggestive associations (p≤10⁻⁵) in GENOA GWAS, but these index SNPs did not replicate in FHS. However, secondary analysis was able to replicate candidate gene regions in FHS using other SNPs (+/−250 kb of GENOA index SNP). In smoker and nonsmoker groups, replicated genes included TCF7L2 (p = 6.0×10⁻⁵) and WWOX (p = 4.5×10⁻⁶); and TNFRSF8 (p = 7.8×10⁻⁵), respectively. For GxS interactions, replicated genes included TBC1D4 (p = 6.9×10⁻⁵) and ADAMTS9 (P = 7.1×10⁻⁵). Interestingly, these genes are involved in inflammatory pathways mediated by the NF-κB axis. Since smoking is known to induce chronic and systemic inflammation, association of these genes likely reflects roles in CAC development via inflammatory pathways. Furthermore, the NF-κB axis regulates bone remodeling, a key physiological process in CAC development. In conclusion, GxS GWAS has yielded evidence for novel loci that are associated with CAC via interaction with smoking, providing promising new targets for future population-based and functional studies of CAC development.

Matrix gla protein gene polymorphism is associated with increased coronary artery calcification progression

OBJECTIVE

Matrix gla protein (MGP) inhibits arterial and cartilaginous calcification. A threonine to alanine (Thr83Ala) polymorphism (codon 83) in MGP is associated with myocardial infarction and femoral artery calcification. We examined the association of the MGP Thr83Ala polymorphism with quantity and progression of coronary artery calcification (CAC), a noninvasive measure of subclinical coronary atherosclerosis.

METHODS AND RESULTS

In 605 participants of the Epidemiology of Coronary Artery Calcification Study, generalized linear mixed models were fit to determine the association of MGP Thr83Ala with CAC quantity and progression. There was a significant additive relation between MGP Thr83Ala and CAC progression (P=0.001). In the fully adjusted model, every 1 Ala83 allele increase was associated with an estimated 1.9% (95% confidence interval, 0.7%-3.0%) per year since baseline larger increase in CAC quantity. A proxy single nucleotide polymorphism for MGP Thr83Ala (rs6488724) was similarly associated with CAC progression in an independent cohort from the Genetic Epidemiology Network of Arteriopathy (GENOA) study.

CONCLUSIONS

Increased risk of myocardial infarction associated with MGP ThrAla83 genotype observed elsewhere may be related to faster progression of subclinical coronary atherosclerosis. MGP genotype could be a potential candidate for identifying individuals at increased risk of atherosclerotic disease who would benefit from aggressive primary prevention strategies.

A genome-wide linkage scan identifies multiple quantitative trait loci for HDL-cholesterol levels in families with premature CAD and MI

Plasma HDL cholesterol levels (HDL-C) are an independent predictor of coronary artery disease (CAD). We have completed a genome-wide linkage scan for HDL-C in a US cohort consisting of 388 multiplex families with premature CAD (GeneQuest). The heritability of HDL-C in GeneQuest was 0.37 with gender and age as covariates (P = 5.1 x 10(-4)). Two major quantitative trait loci (QTL) for log-transformed HDL-C adjusted for age and gender were identified onto chromosomes 7p22 and 15q25 with maximum multipoint logarithm of odds (LOD) scores of 3.76 and 6.69, respectively. Fine mapping decreased the 7p22 LOD score to a nonsignificant level of 3.09 and split the 15q25 QTL into two loci, one minor QTL on 15q22 (LOD = 2.73) that spanned the LIPC gene, and the other at 15q25 (LOD = 5.63). A family-based quantitative transmission disequilibrium test (QTDT) revealed significant association between variant rs1800588 in LIPC and HDL-C in the GeneQuest population (P = 0.0067), which may account for the minor QTL on 15q22. The 15q25 QTL is the most significant locus identified for HDL-C to date, and these results provide a framework for the ultimate identification of the underlying HDL-C variant and gene on chromosomes 15q25, which will provide insights into novel regulatory mechanisms of HDL-C metabolism.

Common variants of four bilirubin metabolism genes and their association with serum bilirubin and coronary artery disease in Chinese Han population

OBJECTIVES

Studies have revealed an inverse relationship between serum total bilirubin (TBIL) levels and coronary artery disease (CAD). This study investigated the genetic variants of four bilirubin metabolism genes--heme oxygenase-1 (HMOX1), biliverdin reductase A (BLVRA), solute carrier organic anion transporter family member 1B1 (SLCO1B1), and uridine diphosphate glycosyltransferase 1A1 (UGT1A1)--in relation to TBIL levels and CAD.

METHODS AND RESULTS

Thirty-five common single nucleotide polymorphisms (SNPs) were genotyped in 2380 unrelated Han participants who underwent angiocardiography at hospitals in Shanghai, China. Only three genetic variants--rs4399719 (UGT1A1 T-2473G), rs887829 (UGT1A1 G-364A), and rs4148323 (UGT1A1 G211A)--were associated with TBIL levels (each P<0.001). Four significant associations with CAD were detected after controlling age and the false discovery rate at 15%: the recessive effect of SNP rs887829 (UGT1A1 G-364A) [age-adjusted odds ratio (OR): 0.24; 95% confidence interval (CI): 0.10-0.60; P=0.0014] and dominant effect of rs4149013 (SLCO1B1 A-12099G) (age-adjusted OR: 0.70; 95% CI: 0.55-0.91; P=0.0069) on male CAD, and the additive effects of rs2877262 (BLVRA G+1238/in6C) (age-adjusted OR: 0.73; 95% CI: 0.59-0.89; P=0.0021) and rs2690381 (BLVRA G+2613/in6A) (age-adjusted OR: 0.70; 95% CI: 0.56-0.86; P=0.0008) on female CAD. SNPs rs2877262 and rs2690381 were both in a linkage disequilibrium block within BLVRA with r greater than 0.750. Correspondingly, this block was identified to be associated with female CAD.

CONCLUSION

Our study provides genetic evidences for the difference in the impact of these four bilirubin metabolism genes on TBIL levels and CAD.

The association of coronary artery calcification and carotid artery intima-media thickness with distinct, traditional coronary artery disease risk factors in asymptomatic adults

Coronary artery calcification (CAC) and common carotid artery intima-media thickness (CIMT) are measures of subclinical vascular disease. This 2000-2006 study aimed to characterize the associations among coronary artery disease risk factors, CAC quantity, and CIMT and to estimate shared genetic and environmental contributions to both CAC and CIMT among 478 asymptomatic Amish adults in Lancaster County, Pennsylvania. Heritability for CAC quantity and CIMT, adjusted for age and sex, was 0.42 (P = 0.0001) and 0.29 (P = 0.003), respectively. CAC quantity and CIMT were modestly correlated (adjusted r = 0.14, P = 0.003) but showed little evidence of shared genetic or environmental factors. However, significant genetic correlations were found for CAC quantity and total cholesterol (0.44 (standard error, 0.19); P = 0.03), for CAC quantity and low density lipoprotein cholesterol (0.55 (standard error, 0.17); P = 0.005), and for CIMT and waist circumference (0.58 (standard error, 0.25); P = 0.046), suggesting shared genes for these risk factors and measures of subclinical disease. Results suggest that some of the same genes influence variation in CAC and low density lipoprotein cholesterol, whereas a different set of genes influences variation in CIMT and waist circumference.

Can genes for mammographic density inform cancer aetiology?

Mammographic density (MD) reflects variations in fat, stromal and epithelial tissues that are thought to be regulated by several genes. High MD is an established risk factor for breast cancer; therefore, genes that regulate MD may indirectly influence breast cancer. These genes might also be fewer in number and easier to identify than those for breast cancer risk outside of inherited predisposition syndromes. In this Perspective, we review the limited genetic studies of MD and propose future directions.

Genetic epidemiology of subclinical cardiovascular disease in the diabetes heart study

A genome-wide linkage scan of 357 European American (EA) and 72 African American (AA) pedigrees multiplex for type 2 diabetes mellitus (T2DM) was performed with multipoint nonparametric QTL linkage analysis. Four subclinical measures of cardiovascular disease (CVD): coronary artery (CCP), carotid artery (CarCP), and abdominal aortic calcified plaque (AACP) and carotid artery intima-media thickness (IMT) were mapped. Analyses were adjusted for age, gender, body mass index, and (if appropriate) ethnicity and diabetes status. Evidence for linkage was observed in EA T2DM subjects to CarCP near 16p13 (LOD=4.39 at 8.4 cM; P = 0.00001). When all EA subjects were included, the LOD score was 2.52, suggesting an amplification of the linkage by diabetes. Linkage analysis of a principal components measure of vascular calcium (LOD = 3.85 at 9.3 cM on 16p in EA T2DM subjects) and bivariate analysis of CarCP X IMT (LOD = 3.77 at 9.3 cM on 16p in EA T2DM subjects) were consistent with this linkage. In addition, evidence for linkage was observed with CCP near D15S1515 (LOD = 2.34) in EAs. Additional loci on chromosomes 1, 2, 7, 10, 13, and 21 had LODs > 2.0. The identification of trait-determining polymorphisms underlying these linkages will help delineate risk factors for CVD in T2DM and the general population.

Application of machine learning algorithms to predict coronary artery calcification with a sibship-based design

As part of the Genetic Epidemiology Network of Arteriopathy study, hypertensive non-Hispanic White sibships were screened using 471 single nucleotide polymorphisms (SNPs) to identify genes influencing coronary artery calcification (CAC) measured by computed tomography. Individuals with detectable CAC and CAC quantity > or =70th age- and sex-specific percentile were classified as having a high CAC burden and compared to individuals with CAC quantity <70th percentile. Two sibs from each sibship were randomly chosen and divided into two data sets, each with 360 unrelated individuals. Within each data set, we applied two machine learning algorithms, Random Forests and RuleFit, to identify the best predictors of having high CAC burden among 17 risk factors and 471 SNPs. Using five-fold cross-validation, both methods had approximately 70% sensitivity and approximately 60% specificity. Prediction accuracies were significantly different from random predictions (P-value<0.001) based on 1,000 permutation tests. Predictability of using 287 tagSNPs was as good as using all 471 SNPs. For Random Forests, among the top 50 predictors, the same eight tagSNPs and 15 risk factors were found in both data sets while eight tagSNPs and 12 risk factors were found in both data sets for RuleFit. Replicable effects of two tagSNPs (in genes GPR35 and NOS3) and 12 risk factors (age, body mass index, sex, serum glucose, high-density lipoprotein cholesterol, systolic blood pressure, cholesterol, homocysteine, triglycerides, fibrinogen, Lp(a) and low-density lipoprotein particle size) were identified by both methods. This study illustrates how machine learning methods can be used in sibships to identify important, replicable predictors of subclinical coronary atherosclerosis.

Genetic and genomic insights into the molecular basis of atherosclerosis

Atherosclerosis is a complex disease involving genetic and environmental risk factors, acting on their own or in synergy. Within the general population, polymorphisms within genes in lipid metabolism, inflammation, and thrombogenesis are probably responsible for the wide range of susceptibility to myocardial infarction, a fatal consequence of atherosclerosis. Genetic linkage studies have been carried out in both humans and mouse models to identify these polymorphisms. Approximately 40 quantitative trait loci for atherosclerotic disease have been found in humans, and approximately 30 in mice. Recently, genome-wide association studies have been used to identify atherosclerosis-susceptibility polymorphisms. Although discovering new atherosclerosis genes through these approaches remains challenging, the pace at which these polymorphisms are being found is accelerating due to rapidly improving bioinformatics resources and biotechnologies. The outcome of these efforts will not only unveil the molecular basis of atherosclerosis but also facilitate the discovery of drug targets and individualized medication against the disease.

Genome-wide scans meta-analysis for pulse pressure

Genome scans for identifying susceptibility loci for pulse pressure have produced inconclusive results. A heterogeneity-based genome search meta-analysis was applied to available genome-scan data on pulse pressure. A genome search meta-analysis divides the whole genome into 120 bins and identifies bins that rank high on average in terms of linkage statistics across genome scans unweighted or weighted by study size. The significance of each bin's average rank (right-sided test) and heterogeneity among studies (left-sided test) was calculated using a Monte Carlo test. The meta-analysis involved 7 genome scans, 3 consisting of subjects of European descent. Of the 120 bins, 5 bins had significant average rank (P(rank)<or=0.05) by either unweighted or weighted analyses, 4 of which (bins 21.2: 21q22.11 to 21q22.3, 18.3: 18q12.2 to 18q21.33, 18.4: 18q21.33 to 18q23, and 6.2: 6p22.3 to 6p21.1) were significant by both. In subjects of European descent, 3 bins (22.1: 22q11.1 to 22q12.3, 22.2: 22q12.3 to 22q13.3, 10.4: 10q22.1 to 10q23.32) had P(rank)<or=0.05 with both unweighted and weighted analyses. Bin 10.4 showed low heterogeneity (P(Q)=0.04). None of the bins showed low heterogeneity (P(Q)>0.05), indicating variation in the strength of association. Further investigation of these regions may help to direct the identification of candidate genes for pulse pressure variation.

Coronary Artery Calcification Progression Is Heritable

Background— Coronary artery calcification (CAC), a marker of coronary artery atherosclerosis, can be measured accurately and noninvasively with the use of electron beam computed tomography. Serial measures of CAC quantify progression of calcified coronary artery plaque. Little is known about the role of genetic factors in progression of CAC quantity.

Methods and Results— We quantified the relative contributions of measured risk factors and unmeasured genes to CAC progression measured by 2 electron beam computed tomography examinations an average of 7.3 years apart in 877 asymptomatic white adults (46% men) from 625 families in a community-based sample. After adjustment for baseline risk factors and CAC quantity, the estimated heritability of CAC progression was 0.40 ( P <0.001). Baseline risk factors and CAC quantity explained 64% of the variation in CAC progression. Thus, genetic factors explained 14% of the variation [(100−64)×(0.40)] in CAC progression. After adjustment for risk factors, the estimated genetic correlation (pleiotropy) between baseline CAC quantity and CAC progression was 0.80 and was significantly different than 0 ( P <0.001) and 1 ( P =0.037). The environmental correlation between baseline CAC quantity and CAC progression was 0.42 and was significantly different than 0 ( P =0.006).

Conclusions— Evidence was found that many but not all genetic factors influencing baseline CAC quantity also influence CAC progression. The identification of common and unique genetic influences on these traits will provide important insights into the genetic architecture of coronary artery atherosclerosis.

Comparison of subclinical coronary atherosclerosis and risk factors in unselected populations in Germany and US-America

BACKGROUND

On the basis of the Framingham risk algorithm, overestimation of clinical events has been reported in some European populations. Electron-beam computed tomography-derived quantification of coronary artery calcification (CAC) allows for non-invasive assessment of coronary atherosclerosis in the general population and may thus add important in vivo information on the path from risk factor exposure to formation of clinical events. The current study was undertaken to compare the relationship between risk factors and subclinical coronary atherosclerosis between non-Hispanic white cohorts in Germany and US-America, the hypothesis being that subclinical coronary atherosclerosis might be less prevalent in Europe at the same level of classical risk factor exposure.

METHODS

The Heinz Nixdorf Recall (HNR) study, conducted in the German Ruhr area and the Epidemiology of Coronary Calcification (ECAC) study, conducted in Olmsted County, Minnesota, both recruited large unselected cohorts, men and women aged 45-74 years, from the general population. All subjects with no history of coronary artery disease (CAD) or stroke were included (n=3120 in HNR, n=703 in ECAC). Coronary risk factors were assessed by personal and computer-assisted interviews and direct laboratory measurements. Cardiovascular medication use (antihypertensive, lipid-lowering, and anti-diabetic) was noted. CAC scores were determined using the Agatston method in an identical fashion in both studies.

RESULTS

Adverse levels of risk factors were more prevalent, and the Framingham risk score was higher (10.6+/-7.6 versus 9.3+/-7.1, p<0.001) in HNR than ECAC, respectively. There was no difference in body mass index (BMI). CAC scores were greater in HNR than in ECAC (mean values, 155.7+/-423.0 versus 107.2+/-280.0; median values, 11.9 versus 2.4; p<0.001, respectively). When subjects were matched on CAD risk factors, presence and quantity of CAC were similar in the 2 cohorts. Risk factors significantly associated with CAC score in both studies included: age, male sex, current and former smoking, systolic blood pressure, and non-HDL-cholesterol. Inferences were similar after excluding subjects using lipid- or blood pressure-lowering medications. Using the same risk factor variables for modelling, the predicted CAC scores were comparable in both cohorts.

CONCLUSIONS

In the higher-risk German cohort, presence and quantity of CAC were greater than in the lower-risk US-American cohort. Risk factor associations with CAC were very similar in both unselected populations. We could not demonstrate a relative increase in subclinical coronary atherosclerosis in the US-American cohort. It appears possible to compare CAC as a measure of subclinical coronary artery disease in different populations on different continents, and accordingly, scanning guidelines might be translated across these populations.

A genome-wide linkage scan for ankle-brachial index in African American and non-Hispanic white subjects participating in the GENOA study

Little is known about the genetics of peripheral arterial disease (PAD). We performed linkage analyses to identify genomic regions that influence ankle-brachial index (ABI), a measure of PAD, in 1310 African Americans (AA) (mean age 62+/-9 years) and 796 non-Hispanic whites (NHW) (mean age 58+/-9 years) belonging to hypertensive sibships. ABI was determined at two sites in each lower extremity and the lower of the two average ABIs was used in the analyses after adjustment for age, age(2), sex, weight, total cholesterol, HDL cholesterol, and ever-smoking. Genotypes were measured at microsatellite marker loci spaced approximately 10cM apart across the 22 autosomes. Heritability was assessed by SOLAR and linkage analyses performed using a variance components approach. Modest heritability (h(2)) was noted for the fully adjusted ABI in each ethnic group (h(2)=0.195, P=0.002 in AA; h(2)=0.212, P=0.006 in NHW). Univariate linkage analyses demonstrated tentative evidence of linkage (multipoint LOD=1.3-2.0) for ABI on chromosomes 1p, 6q, 7q, 10p, and 16p in AA and on chromosome 3p and 3q in NHW. In conclusion, ABI is a modestly heritable trait in AA and NHW hypertensive sibships. Quantitative trait linkage analyses identified several chromosomal regions that may harbor genes influencing ABI.