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

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

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

Quantile-quantile plot of DNAm association with logCRP.

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

Polymorphisms in the vitamin D receptor gene are associated with reduced rate of sputum culture conversion in multidrug-resistant tuberculosis patients in South Africa

<div><p>Background</p><p>Vitamin D modulates the inflammatory and immune response to tuberculosis (TB) and also mediates the induction of the antimicrobial peptide cathelicidin. Deficiency of 25-hydroxyvitamin D and single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene may increase the risk of TB disease and decrease culture conversion rates in drug susceptible TB. Whether these VDR SNPs are found in African populations or impact multidrug-resistant (MDR) TB treatment has not been established. We aimed to determine if SNPs in the VDR gene were associated with sputum culture conversion among a cohort of MDR TB patients in South Africa.</p><p>Methods</p><p>We conducted a prospective cohort study of adult MDR TB patients receiving second-line TB treatment in KwaZulu-Natal province. Subjects had monthly sputum cultures performed. In a subset of participants, whole blood samples were obtained for genomic analyses. Genomic DNA was extracted and genotyped with Affymetrix Axiom Pan-African Array. Cox proportional models were used to determine the association between VDR SNPs and rate of culture conversion.</p><p>Results</p><p>Genomic analyses were performed on 91 MDR TB subjects enrolled in the sub-study; 60% were female and median age was 35 years (interquartile range [IQR] 29–42). Smoking was reported by 21% of subjects and most subjects had HIV (80%), were smear negative (57%), and had cavitary disease (55%). Overall, 87 (96%) subjects initially converted cultures to negative, with median time to culture conversion of 57 days (IQR 17–114). Of 121 VDR SNPs examined, 10 were significantly associated (p<0.01) with rate of sputum conversion in multivariable analyses. Each additional risk allele on SNP rs74085240 delayed culture conversion significantly (adjusted hazard ratio 0.30, 95% confidence interval 0.14–0.67).</p><p>Conclusions</p><p>Polymorphisms in the VDR gene were associated with rate of sputum culture conversion in MDR TB patients in this high HIV prevalence setting in South Africa.</p></div

Baseline participant characteristics and 2-month sputum culture status.

<p>Baseline participant characteristics and 2-month sputum culture status.</p

Principal component analysis of study participants compared to HapMap ethnic groups.

<p>Principal component analysis of study participants compared to HapMap ethnic groups.</p

Hazard of sputum culture conversion by vitamin D receptor gene single nucleotide polymorphism.

<p>Hazard of sputum culture conversion by vitamin D receptor gene single nucleotide polymorphism.</p

Poor tuberculosis treatment outcome by vitamin D receptor gene single nucleotide polymorphism, N = 88.

<p>Poor tuberculosis treatment outcome by vitamin D receptor gene single nucleotide polymorphism, N = 88.</p

Enrichment for functional annotations and cell-type groups using stratified LD score regression.

<p><b>A.</b> Enrichment estimates of 24 main annotations for each of four BP traits. Annotations are ordered by size. Error bars represent jackknife standard errors around the estimates of enrichment, and stars indicate significance at P < 0.05 after Bonferroni correction for 24 hypotheses tested and four BP traits. <b>B.</b> Significance of enrichment of 10 cell-type groups for four BP traits. Dotted line and stars indicate significance at P < 0.05 after Bonferroni correction for 10 hypotheses tested and four BP traits.</p