Scott M. Williams

New strategies for identifying gene-gene interactions in hypertension

Essential hypertension is a common disease that has complex multifactorial etiology. For this reason, it is not surprising that studies of the effects of single genes on hypertension have often failed to replicate the original findings. We propose, as a working hypothesis, that the failure to replicate some single locus results is because the impact of single alleles on the risk of hypertension is dependent on genetic variations at other loci (i.e. gene-gene interactions) and on environmental factors (i.e. gene-environment interactions). Thus, studies that do not consider the appropriate genetic and/or environmental contexts may not identify important susceptibility loci. The identification and characterization of such gene-gene and gene-environment interactions have been limited by lack of powerful statistical methods and/or a lack of large enough sample sizes. Here, we review the general problem of identifying gene-gene interactions and describe several traditional and several newer methods that are being used to assess complex genetic interactions in essential hypertension.

DC-SIGN (CD209), pentraxin 3 and vitamin D receptor gene variants associate with pulmonary tuberculosis risk in West Africans.

We investigated the role of DC-SIGN (CD209), long pentraxin 3 (PTX3) and vitamin D receptor (VDR) gene single nucleotide polymorphisms (SNPs) in susceptibility to pulmonary tuberculosis (TB) in 321 TB cases and 347 healthy controls from Guinea-Bissau. Five additional, functionally relevant SNPs within toll-like receptors (TLRs) 2, 4 and 9 were typed but found, when polymorphic, not to affect host vulnerability to pulmonary TB. We did not replicate an association between SNPs in the DC-SIGN promoter and TB. However, we found that two polymorphisms, one in DC-SIGN and one in VDR, were associated in a nonadditive model with disease risk when analyzed in combination with ethnicity (P=0.03 for DC-SIGN and P=0.003 for VDR). In addition, PTX3 haplotype frequencies significantly differed in cases compared to controls and a protective effect was found in association with a specific haplotype (OR 0.78, 95% CI 0.63–0.98). Our findings support previous data showing that VDR SNPs modulate the risk for TB in West Africans and suggest that variation within DC-SIGN and PTX3 also affect the disease outcome.

Data simulation software for whole-genome association and other studies in human genetics.

Genome-wide association studies have become a reality in the study of the genetics of complex disease. This technology provides a wealth of genomic information on patient samples, from which we hope to learn novel biology and detect important genetic and environmental factors for disease processes. Because strategies for analyzing these data have not kept pace with the laboratory methods that generate the data it is unlikely that these advances will immediately lead to an improved understanding of the genetic contribution to common human disease and drug response. Currently, no single analytical method will allow us to extract all information from a whole-genome association study. Thus, many novel methods are being proposed and developed. It will be vital for the success of these new methods, to have the ability to simulate datasets consisting of polymorphisms throughout the genome with realistic linkage disequilibrium patterns. Within these datasets, we can embed genetic models of disease whereby we can evaluate the ability of novel methods to detect these simulated effects. This paper describes a new software package, genomeSIM, for the simulation of large-scale genomic data in population based case-control samples. It allows for single SNP, as well as gene-gene interaction models to be associated with disease risk. We describe the algorithm and demonstrate its utility for future genetic studies of whole-genome association.

Diagnostic tools for hypertension and salt sensitivity testing

Purpose of reviewOne-third of the worlds population has hypertension and it is responsible for almost 50% of deaths from stroke or coronary heart disease. These statistics do not distinguish salt-sensitive from salt-resistant hypertension or include normotensives who are salt-sensitive even though salt sensitivity, independent of blood pressure, is a risk factor for cardiovascular and other diseases, including cancer. This review describes new personalized diagnostic tools for salt sensitivity. Recent findingsThe relationship between salt intake and cardiovascular risk is not linear, but rather fits a J-shaped curve relationship. Thus, a low-salt diet may not be beneficial to everyone and may paradoxically increase blood pressure in some individuals. Current surrogate markers of salt sensitivity are not adequately sensitive or specific. Tests in the urine that could be surrogate markers of salt sensitivity with a quick turn-around time include renal proximal tubule cells, exosomes, and microRNA shed in the urine. SummaryAccurate testing of salt sensitivity is not only laborious but also expensive, and with low patient compliance. Patients who have normal blood pressure but are salt-sensitive cannot be diagnosed in an office setting and there are no laboratory tests for salt sensitivity. Urinary surrogate markers for salt sensitivity are being developed.

Race, African Ancestry, and Helicobacter pylori Infection in a Low-Income United States Population

Background: Gastric cancer incidence in African Americans is twice that of whites, and differing prevalence of Helicobacter pylori strain-specific isolates may help explain the disparity. Methods: Serum levels of antibodies to each of 15 H. pylori proteins were assessed using multiplex serology for a sample of 689 African American and white participants from the Southern Community Cohort Study. African and European admixture was estimated using a panel of 276 ancestry genetic markers, with “low,” “medium,” and “high” categories of African ancestry defined as <85%, 85% to 95%, and ≥95%. Results: The majority (79%) of our study population were sero-positive for H. pylori. African American race was associated with a two- to sixfold increased odds for sero-positivity to eight H. pylori proteins, including the cancer-associated virulence constituents CagA [odds ratio (OR), 6.4; 95% CI, 4.5–9.1], and VacA (OR, 2.3; 95% CI, 1.5–3.5). Compared to whites, African Americans of low, medium, and high African ancestry had 1.6-, 4.1-, and 5.2-fold increased odds of sero-positivity to H. pylori, primarily related to CagA sero-positive strains, for which increasing African ancestry led to 2.5-, 9.6-, and 13.1-fold increased odds. Among African Americans alone, compared to those of low African ancestry, African Americans of medium and high African ancestry had 2.5- and 3.4-fold increased odds of sero-positivity to H. pylori, and 3.5- and 4.9-fold increased odds of CagA sero-positive H. pylori strains. Conclusions: Host genetic variation and/or lifestyle factors associated with African ancestry contribute to the likelihood of infection with H. pylori, particularly its virulent strains, in this low-income U.S. southern population. Impact: Our findings that low-income African Americans of high African ancestry have a particularly high prevalence of antibodies against H. pylori provides a framework for further research into better detection and prevention of gastric cancer in this population. Cancer Epidemiol Biomarkers Prev; 20(5); 826–34. ©2011 AACR.

Beta-1-adrenoceptor genetic variants and ethnicity independently affect response to beta-blockade.

Objectives Black patients may be less responsive to &bgr;-blockers than whites. Genetic variants in the &bgr;1-adrenergic receptor (&bgr;1-AR) associated with lesser response to &bgr;-blockers are more common in blacks than in whites. The purpose of this study was to determine whether ethnic differences in response to &bgr;-blockade can be explained by differing distributions of functional genetic variants in the &bgr;1-AR. Methods We measured sensitivity to &bgr;-blockade by the attenuation of exercise-induced tachycardia in 165 patients (92 whites), who performed a graded bicycle exercise test before and 2.5 h after oral atenolol (25 mg). We determined heart rate at rest and at three exercise levels from continuous ECG recordings and calculated the area under the curve. We also measured plasma atenolol concentrations and determined genotypes for variants of the &bgr;1-AR (Ser49Gly, Arg389Gly) and &agr;2C-AR (del322-325). The effects of ethnicity, genotype, and other covariates on the heart rate reduction after atenolol were estimated in multiple regression analyses. Results Atenolol resulted in a greater reduction in exercise heart rate in whites than in blacks (P=0.006). &bgr;1-AR Arg389 (P=0.003), but not the &agr;2C-AR 322-325 insertion allele (P=0.31), was independently associated with a greater reduction in heart rate area under the curve. Ethnic differences in sensitivity to atenolol remained significant (P=0.006) after adjustment for &bgr;1-AR and &agr;2C-AR genotypes. Conclusion Ethnic differences in sensitivity to the &bgr;1-blocker atenolol persist even after accounting for different distributions of functional genetic &bgr;1-AR variants, suggesting that additional, as yet unidentified factors contribute to such ethnic differences.

Variation in the alpha2B-adrenergic receptor gene (ADRA2B) and its relationship to vascular response in vivo.

The &agr;2B-adrenergic receptor (ADRA2B) plays an important role in vasoconstriction and blood pressure regulation. One common variant in the ADRA2B gene (del301–303) has been identified, and results in markedly decreased receptor desensitization in vitro but does not alter vascular sensitivity in vivo. Therefore, we fully characterized genetic variations in ADRA2B and related them to phenotype in vivo. We examined 5812 bp of contiguous sequence of ADRA2B (promoter, exonic, and 3′-untranslated region; 3′-UTR) using the polymerase chain reaction to amplify the genomic target followed by bidirectional sequencing (n=68). Haplotypes were inferred using an expectation maximization algorithm. Vasoconstriction in response to increasing doses of the highly selective &agr;2-adrenergic receptor agonist, dexmedetomidine (0.01–1000 ng/min) was measured in the dorsal hand vein using a linear variable differential transformer. The dose that produced 50% (ED50) of maximum venoconstriction (Emax) was determined for each subject from the individual dose–response curves. ED50 and Emax were compared in subjects with and without variant alleles and haplotypes of interest. We identified 24 variable sites, 12 in the promoter region, five in the coding region (including two previously described as non-synonymous variants) and seven in the 3′-UTR region. Four haplotypes were inferred, representing approximately 95% of the cohort. One haplotype, characterized by two single nucleotide polymorphisms in the promoter region, and one in the 3′-UTR, occurred in seven of 38 African-Americans, and was associated with a lower Emax, 61.3% [95% confidence interval (CI) 39.5–83.0, n=7] compared to 78.1% (CI 73.8–82.5) in wild-types (n=61) (P=0.02). There was no association between the nine common variants and dexmedetomidine ED50. We have described novel variants and haplotypes of the ADRA2B gene. These do not alter sensitivity to a selective &agr;2-adrenergic receptor agonist but some may decrease maximal venoconstriction in vivo.

G Protein–Coupled Receptor Kinase 4 Role in Blood Pressure Regulation

Nearly 30% of middle-aged Americans have hypertension, but the prevalence is higher in non-Hispanic blacks and individuals >60 years of age (65%).1 There is a direct and quantitative relationship between higher blood pressure values and mortality. Although 30% to 50% is thought to be heritable, the genetic cause(s) of essential hypertension has been difficult to identify. More than 1 gene is undoubtedly involved, because Mendelian dominant and recessive traits are not readily discernible in hypertensive subjects, except in those with monogenic forms of hypertension. Moreover, in any hypertensive individual, risk-predisposing genes are engaged in a complex network of gene-gene and gene-environment interactions.2,3 The kidney plays a major role in the long-term regulation of blood pressure, and abnormal sodium chloride metabolism is frequently encountered in hypertension. Therefore, many studies have focused on the abnormal renal handling of sodium chloride in the pathogenesis of essential hypertension.2,4 Approximately 50% of subjects with essential hypertension are sodium chloride sensitive.5 Indeed, humans with salt-sensitive hypertension have increased sodium transport in the renal proximal tubule and medullary thick ascending limb, although distal tubular mechanisms may also be involved.6 The sodium retention in hypertension is because of enhanced sodium transport, per se, and/or a failure to respond appropriately to signals that decrease sodium transport. Sodium transport is regulated by natriuretic and antinatriuretic hormones and humoral agents, such as dopamine and angiotensin, which exert their effects via G protein–coupled receptors (GPCRs). Activation of certain postjunctional dopamine receptor subtypes (D1R, D3R, D4R, and D5R) and the angiotensin type 2 receptor inhibit, whereas activation of the postjunctional D2R and angiotensin type 1 receptor (AT1R) increase sodium transport.2,7 The GPCR kinases (GRKs) are a 7-member family of serine/threonine protein kinases characterized by their …

Cytokine polymorphisms and gastric cancer risk: an evolving view.

More than 20 years after the identification of Helicobacter pylori as a human pathogen, gastric cancer continues to be a leading cause of cancer deaths worldwide. Genetic association studies have the potential for helping to identify those at greatest risk for developing gastric cancer subsequent to infection by H. pylori. IL1B promoter polymorphisms have been supported by several meta-analyses as being associated with gastric cancer risk. In this review, we discuss challenges in experimental design of gene association studies in gastric cancer, with attention to gene-environment interactions that may lead to inconsistency in findings across populations.

G6PD A- deficiency and severe malaria in The Gambia: heterozygote advantage and possible homozygote disadvantage.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is frequent in Africa, because it confers resistance to Plasmodium falciparum malaria; however, the nature of the protection and the genotypes associated with it have been controversial. In 1972, Bienzle and others described protection from malaria in West African females heterozygous for G6PD A-. They determined that G6PD A- heterozygotes had lower parasite counts than A- homozygotes, hemizygous males, and normal individuals. However, other studies have reached different conclusions about the protective genotypes. DNA samples from 135 children with severe malaria and 146 children with mild malaria from The Gambia were genotyped for the G6PD A- mutation that is most frequent among Gambians (G6PD 968 T->C); there was a marked deficiency of heterozygotes and an excess of homozygotes with severe malaria, producing a strong deviation from Hardy-Weinberg equilibrium. Our results support the protective effect in G6PD A- heterozygous females and suggest that homozygotes might be more susceptible to severe malaria attacks.