Set-Based Tests for the Gene–Environment Interaction in Longitudinal Studies

<p>We propose a generalized score type test for set-based inference for the gene–environment interaction with longitudinally measured quantitative traits. The test is robust to misspecification of within subject correlation structure and has enhanced power compared to existing alternatives. Unlike tests for marginal genetic association, set-based tests for the gene–environment interaction face the challenges of a potentially misspecified and high-dimensional main effect model under the null hypothesis. We show that our proposed test is robust to main effect misspecification of environmental exposure and genetic factors under the gene–environment independence condition. When genetic and environmental factors are dependent, the method of sieves is further proposed to eliminate potential bias due to a misspecified main effect of a continuous environmental exposure. A weighted principal component analysis approach is developed to perform dimension reduction when the number of genetic variants in the set is large relative to the sample size. The methods are motivated by an example from the Multi-Ethnic Study of Atherosclerosis (MESA), investigating interaction between measures of neighborhood environment and genetic regions on longitudinal measures of blood pressure over a study period of about seven years with four exams. Supplementary materials for this article are available online.</p

Gene-Specific DNA Methylation Association with Serum Levels of C-Reactive Protein in African Americans

<div><p>A more thorough understanding of the differences in DNA methylation (DNAm) profiles in populations may hold promise for identifying molecular mechanisms through which genetic and environmental factors jointly contribute to human diseases. Inflammation is a key molecular mechanism underlying several chronic diseases including cardiovascular disease, and it affects DNAm profile on both global and locus-specific levels. To understand the impact of inflammation on the DNAm of the human genome, we investigated DNAm profiles of peripheral blood leukocytes from 966 African American participants in the Genetic Epidemiology Network of Arteriopathy (GENOA) study. By testing the association of DNAm sites on CpG islands of over 14,000 genes with C-reactive protein (CRP), an inflammatory biomarker of cardiovascular disease, we identified 257 DNAm sites in 240 genes significantly associated with serum levels of CRP adjusted for age, sex, body mass index and smoking status, and corrected for multiple testing. Of the significantly associated DNAm sites, 80.5% were hypomethylated with higher CRP levels. The most significant Gene Ontology terms enriched in the genes associated with the CRP levels were immune system process, immune response, defense response, response to stimulus, and response to stress, which are all linked to the functions of leukocytes. While the CRP-associated DNAm may be cell-type specific, understanding the DNAm association with CRP in peripheral blood leukocytes of multi-ethnic populations can assist in unveiling the molecular mechanism of how the process of inflammation affects the risks of developing common disease through epigenetic modifications.</p> </div

Characteristics of study sample and bivariate associations with Urinary UA excretion and gene expression levels from uric acid absorption/secretion associated genes, n = 541.

<p>*statistically significant association at α = 0.05.</p><p>UA = uric acid; BMI = body mass index; Bivariate association results were obtained from linear mixed models accounting for sibship (n = 541). ABCG2 ENSG00000118777, SLC17A1 ENSG00000124568, SLC17A3 ENSG00000124564, SLC22A12 ENSG00000197891, SLC2A9 ENSG00000109667, SLC2A9-001 ENST00000506583, SLC2A9-201 ENST00000309065, SLC2A9-002 ENST00000264784.</p><p>β coefficients for association with gene expression were standardized.</p><p>Characteristics of study sample and bivariate associations with Urinary UA excretion and gene expression levels from uric acid absorption/secretion associated genes, n = 541.</p

Gene expression by dietary protein intake interaction associations for urinary uric acid.

<p>*statistically significant association at α = 0.05.</p><p>ABCG2 ENSG00000118777, SLC17A1 ENSG00000124568, SLC17A3 ENSG00000124564, SLC22A12 ENSG00000197891, SLC2A9 ENSG00000109667, SLC2A9-001 ENST00000506583, SLC2A9-201 ENST00000309065, SLC2A9-002 ENST00000264784.</p><p>Gene expression by dietary protein intake interaction associations for urinary uric acid.</p

Quantile-quantile plot of DNAm association with lnCRP adjusted for top three principal components of the DNAm data.

<p>Quantile-quantile plot of DNAm association with lnCRP adjusted for top three principal components of the DNAm data.</p

Urinary UA association results for 880 SNPs in the <i>SLC2A9</i> gene region.

<p>Left Y-axis:–log₁₀(p-value) from association between SNPs and urinary UA, adjusted for age, sex, BMI, and urinary sodium, and accounting for sibship; Right Y-axis: SNP recombination rate based on HapMap hg18 CEU; X-axis: chromosomal location and gene regions; r² color code: degree of linkage disequilibrium with index (most strongly associated) SNP, rs12509955 (purple diamond).</p

<i>SLC2A9</i> gene expression association results for 880 SNPs in the <i>SLC2A9</i> gene region.

<p>Left Y-axis:–log₁₀(p-value) from association between SNPs and <i>SLC2A9</i> gene expression, accounting for sibship; Right Y-axis: SNP recombination rate based on HapMap hg18 CEU; X-axis: chromosomal location and gene regions; r² color code: degree of linkage disequilibrium with index (most strongly associated) SNP, rs2240724 (purple diamond).</p

Quantile-quantile plot of DNAm association with logCRP.

<p>Quantile-quantile plot of DNAm association with logCRP.</p

<i>SLC2A9</i> Genotype Is Associated with <i>SLC2A9</i> Gene Expression and Urinary Uric Acid Concentration

<div><p>Objectives</p><p><i>SLC2A9</i> gene variants have been associated with urinary uric acid (UA) concentration, but little is known about the functional mechanism linking these gene variants with UA. <i>SLC2A9</i> encodes a UA transporter present in the proximal tubule of the kidney, and gene expression levels of <i>SLC2A9</i> and other genes in the uricosuric pathway (<i>ABCG2</i>, <i>SLC17A1</i>, <i>SLC17A3</i>, <i>and SLC22A12) </i> could potentially mediate the relationship between <i>SLC2A9</i> gene variants and urinary UA excretion.</p><p>Methods</p><p>The association between urinary UA concentrations and single nucleotide polymorphisms (SNPs) within the <i>SLC2A9</i> gene region, expression levels of genes in the uricosuric pathway, and dietary protein intake were analyzed for a sample of non-Hispanic white participants from the Genetic Epidemiology Network of Arteriopathy (GENOA) cohort. The <i>SLC2A9 </i> SNP most significantly associated with urinary UA concentration was then tested for associations with gene expression levels from uric acid absorption/secretion associated genes. Models including interactions between dietary protein (total, animal, and vegetable) and genetic factors were also assessed.</p><p>Results</p><p>The most significant <i>SLC2A9 </i> SNP associated with urinary UA (rs12509955, corrected p = 0.001) was also associated with <i>SLC2A9</i> gene expression levels (corrected p = 0.0084); however, <i>SLC2A9</i> gene expression levels were not significantly associated with urinary UA concentrations (p = 0.509). The interactions between rs12509955 and total dietary protein, and <i>SLC2A9 </i> gene-level gene expression and dietary vegetable protein on the outcome of urinary UA were marginally significant (p = 0.11 and p = 0.07, respectively). Gene expression level of one <i>SLC2A9</i> transcript had a significant interaction with dietary animal protein (<i>SLC2A9-001</i> ENST00000506583, p = 0.01) and a marginally significant interaction with total dietary protein (p = 0.07) on urinary UA.</p><p>Conclusion</p><p>Our results illustrate that SNPs in the <i>SLC2A9</i> gene influence <i>SLC2A9</i> gene expression as well as urinary UA excretion. Evidence is also suggestive that gene-by-diet interactions may disproportionately increase urinary UA in genetically susceptible individuals that consume higher amounts of protein.</p></div

Manhattan plot of methylome-wide association with log CRP in 966 African Americans, adjusted for age, gender, BMI and cigarette smoking.

<p>Manhattan plot of methylome-wide association with log CRP in 966 African Americans, adjusted for age, gender, BMI and cigarette smoking.</p