C679X loss-of-function PCSK9 variant lowers fasting glucose levels in a black South African population: A longitudinal study.

AIMS: To determine the longitudinal association of the loss-of-function (LOF) PCSK9 variants (C679X and A443T), proxies of PCSK9 inhibitor drugs, with LDL-C, fasting glucose and glycated hemoglobin. METHODS: We conducted a five year, longitudinal study, nested within the Prospective Urban and Rural Epidemiology study, among 737 apparently healthy, male and female black South Africans of the North West province. Genotyping of the C679X and A443T PCSK9 variants was achieved using Taqman assays from Applied Biosystems. Generalized estimating equations were used to determine longitudinal association of the A443T and C679X PCSK9 variants with LDL-C, fasting glucose and glycated hemoglobin. RESULTS: C679X and A443T variant carriers were associated with significant reductions in LDL-C of -0.98(-1.29, -0.67) mmol/L; p < 0.001) and -0.39(-0.57, -0.20) mmol/L; p < 0.001) respectively, compared to the non-carriers. Only C679X variant was independently associated with reductions in fasting glucose of -0.37 (-0.61, -0.13) mmol/L; p = 0.002) compared to non-carriers. However, the association of the selected variants with glycated hemoglobin were not significant. C679X and A443T carriers were associated with -0.07 (-0.23, 0.09) %; p = 0.400), 0.05 (-0.13, 0.22) %; p = 0.599) of glycated haemoglobin respectively. CONCLUSION: Our results indicated that carriers of A443T and C679X variants exhibit sustained low LDL-C levels over 5 years and have varied effects on T2D biomarkers compared to non-carriers.

Nutrient Patterns Associated with Fasting Glucose and Glycated Haemoglobin Levels in a Black South African Population.

Type 2 diabetes (T2D) burden is increasing globally. However, evidence regarding nutrient patterns associated with the biomarkers of T2D is limited. This study set out to determine the nutrient patterns associated with fasting glucose and glycated haemoglobin the biomarkers of T2D. Factor analysis was used to derive nutrient patterns of 2010 participants stratified by urban/rural status and gender. Principal Component Analysis (PCA) was applied to 25 nutrients, computed from the quantified food frequency questionnaires (QFFQ). Three nutrient patterns per stratum, which accounted for 73% of the variation of the selected nutrients, were identified. Multivariate linear regression models adjusted for age, BMI, smoking, physical activity, education attained, alcohol intake, seasonality and total energy intake were computed. Starch, dietary fibre and B vitamins driven nutrient pattern was significantly associated with fasting glucose (ß = -0.236 (-0.458; -0.014); p = 0.037) and glycated haemoglobin levels (ß = -0.175 (-0.303; -0.047); p = 0.007) in rural women. Thiamine, zinc and plant protein driven nutrient pattern was associated with significant reductions in glycated haemoglobin and fasting glucose ((ß = -0.288 (-0.543; -0.033); p = 0.027) and (ß = -0.382 (-0.752; -0.012); p = 0.043), respectively) in rural men. Our results indicate that plant driven nutrient patterns are associated with low fasting glucose and glycated haemoglobin levels.

Predictive utility of a genetic risk score of common variants associated with type 2 diabetes in a black South African population.

AIMS: To determine the predictive utility of polygenic risk scores of common variants associated with type 2 diabetes derived from the European and Asian ethnicities among a black South African population. METHOD: Our study was a case-control study nested within the Prospective Urban and Rural Epidemiological (PURE) study of 178 male and female cases, matched for age and gender with 178 controls. Four types of genetic risk scores (GRS) were developed from 66 selected SNPs. These comprised of beta cell related variants (GRSb), variants which had significant associations with T2D in our study (GRSn), variants from the trans-ethnic meta-analysis (GRStrans) and all the 66 selected SNPs (GRSt). RESULTS: Of the GRS's, only GRSn was associated with increased risk of T2D as indicated by an OR (95CI) of 1.21 (1.02-1.43) p-value=0.015. Stratified analysis of age and BMI, indicated the GRSn to be significantly associated with T2D among the non-obese and participants less than 50years. The area under the ROC of the T2D risk factors only was 0.652 (p value<0.001) and with the addition of GRSn it was 0.665 (p value<0.001). CONCLUSIONS: The GRS of European and Asian derived variants have limited clinical utility in the black South African population. The inclusion of population specific variants in the GRS is pivotal.

Common Variants Associated with Type 2 Diabetes in a Black South African Population of Setswana Descent: African Populations Diverge.

The increasing worldwide prevalence of type 2 diabetes mellitus (T2D) is a serious global health concern. Although T2D has a strong genetic etiology, limited knowledge exists about the common variants associated with it in the black South African population. This study set out to evaluate the association of previously reported common variants in other world populations with T2D susceptibility in a black South African population of Setswana descent. A case-control study design of 178 cases and 178 controls nested in the Prospective Urban Rural Epidemiology (PURE) study was conducted wherein we genotyped for 77 single nucleotide polymorphisms (SNPs). PLINK software was used to evaluate the standard genetic models of disease penetrance for the association of the common variants with impaired glucose tolerance (IGT) while adjusting for age, sex, and body mass index. Only rs1436955 significantly associated with an increase in T2D risk; three other variants, rs831571, rs8050136, and rs7542900, significantly associated with decreased risk of T2D. However, none of the four SNPs had significant associations after correcting for multiple testing (p<0.05). Although further studies are required to confirm these observations, the common variants associated with T2D risk among the Black South Africans of Setswana descent might likely be different than those in the Asian and European populations. This study supports the broader thesis that the genetic background of Africans is diverse and cannot be directly extrapolated using genetic variants from other ethnicities. Therefore there is a need to identify the population-specific variants linked with T2D in Africa.

Interactions between C-reactive protein genotypes with markers of nutritional status in relation to inflammation.

Inflammation, as indicated by C-reactive protein concentrations (CRP), is a risk factor for chronic diseases. Both genetic and environmental factors affect susceptibility to inflammation. As dietary interventions can influence inflammatory status, we hypothesized that dietary effects could be influenced by interactions with single nucleotide polymorphisms (SNPs) in the CRP gene. We determined 12 CRP SNPs, as well as various nutrition status markers in 2010 black South Africans and analyzed their effect on CRP. Interactions were observed for several genotypes with obesity in determining CRP. Lipid intake modulated the pro-inflammatory effects of some SNPs, i.e., an increase in both saturated fatty acid and monounsaturated fatty acid intake in those homozygous for the polymorphic allele at rs2808630 was associated with a larger increase in CRP. Those harboring the minor alleles at rs3093058 and rs3093062 presented with significantly higher CRP in the presence of increased triglyceride or cholesterol intake. When harboring the minor allele of these SNPs, a high omega-6 to -3 ratio was, however, found to be anti-inflammatory. Carbohydrate intake also modulated CRP SNPs, as HbA1C and fasting glucose levels interacted with some SNPs to influence the CRP. This investigation highlights the impact that nutritional status can have on reducing the inherent genetic susceptibility to a heightened systemic inflammatory state.

Common and rare single nucleotide polymorphisms in the LDLR gene are present in a black South African population and associate with low-density lipoprotein cholesterol levels.

The LDL receptor has an essential role in regulating plasma LDL-C levels. Genetic variation in the LDLR gene can be associated with either lower or moderately raised plasma levels of LDL-C, or may cause familial hypercholesterolemia. The prevalence of single-nucleotide polymorphisms (SNPs) in the LDLR in the black South African population is not known and therefore, we aimed to determine the genotypic variation of the LDLR in the study population as well as to define the association of the different genotypes with plasma LDL-C levels. A random selection of 1860 apparently healthy black South African volunteers aged 35-60 years was made in a cross-sectional study. Novel SNPs were identified in a subset of 30 individuals by means of automated sequencing before screening the entire cohort by means of the Illumina VeraCode GoldenGate Genotyping Assay on a BeadXpress Reader system. Twenty-five SNPs were genotyped, two of which were novel. A very rare SNP, rs17249141, in the promoter region was significantly associated with lower levels of LDL-C. Four other SNPs (rs2738447, rs14158, rs2738465 and rs3180023) were significantly associated with increased levels of LDL-C. We can conclude that some of the various SNPs identified do indeed associate with LDL-C levels.

In black South Africans from rural and urban communities, the 4G/5G PAI-1 polymorphism influences PAI-1 activity, but not plasma clot lysis time.

Data on genetic and environmental factors influencing PAI-1 levels and their consequent effect on clot lysis in black African populations are limited. We identified polymorphisms in the promoter area of the PAI-1 gene and determined their influence on PAI-1act levels and plasma clot lysis time (CLT). We also describe gene-environment interactions and the effect of urbanisation. Data from 2010 apparently healthy urban and rural black participants from the South African arm of the PURE study were cross-sectionally analysed. The 5G allele frequency of the 4G/5G polymorphism was 0.85. PAI-1act increased across genotypes in the urban subgroup (p = 0.009) but not significantly in the rural subgroup, while CLT did not differ across genotypes. Significant interaction terms were found between the 4G/5G polymorphism and BMI, waist circumference and triglycerides in determining PAI-1act, and between the 4G/5G polymorphism and fibrinogen and fibrinogen gamma prime in determining CLT. The C428T and G429A polymorphisms did not show direct relationships with PAI-1act or CLT but they did influence the association of other environmental factors with PAI-1act and CLT. Several of these interactions differed significantly between rural and urban subgroups, particularly in individuals harbouring the mutant alleles. In conclusion, although the 4G/5G polymorphism significantly affected PAI-1act, it contributed less than 1% to the PAI-1act variance. (Central) obesity was the biggest contributor to PAI-1act variance (12.5%). Urbanisation significantly influenced the effect of the 4G/5G polymorphism on PAI-1act as well as gene-environment interactions for the C428T and G429A genotypes in determining PAI-1act and CLT.