Effect of SORT1, APOB and APOE polymorphisms on LDL-C and coronary heart disease in Pakistani subjects and their comparison with Northwick Park Heart Study II

Missense variants in SORT1 are associated with LDL-C in an Amish population

Common noncoding variants at the human 1p13.3 locus associated with SORT1 expression are among those most strongly associated with low-density lipoprotein cholesterol (LDL-C) in human genome-wide association studies. However, validation studies in mice and cell lines have produced variable results regarding the directionality of the effect of SORT1 on LDL-C. This, together with the fact that the 1p13.3 variants are associated with expression of several genes, has raised the question of whether SORT1 is the causal gene at this locus. Using whole exome sequencing in members of an Amish population, we identified coding variants in SORT1 that are associated with increased (rs141749679, K302E) and decreased (rs149456022, Q225H) LDL-C. Further, analysis of plasma lipoprotein particle subclasses by ion mobility in a subset of rs141749679 (K302E) carriers revealed higher levels of large LDL particles compared to noncarriers. In contrast to the effect of these variants in the Amish, the sortilin K302E mutation introduced into a C57BL/6J mouse via CRISPR/Cas9 resulted in decreased non-high-density lipoprotein cholesterol, and the sortilin Q225H mutation did not alter cholesterol levels in mice. This is indicative of different effects of these mutations on cholesterol metabolism in the two species. To our knowledge, this is the first evidence that naturally occurring coding variants in SORT1 are associated with LDL-C, thus supporting SORT1 as the gene responsible for the association of the 1p13.3 locus with LDL-C.

Effect of APOB gene polymorphisms on body mass index, blood pressure, and total cholesterol levels: A cross-sectional study in Mexican population

APOB gene polymorphisms are considered risk factors for the development of dyslipidemia, hypertension, and cardiovascular disease (CVD) in several populations. In Mexico, these pathologies are frequent and studies regarding this gene are scarce. The aim of this cross-sectional study was to determined genotype, allele, and haplotype frequencies of APOB polymorphisms and performed analyses of association among the biochemical, hemodynamic, anthropometrical, and genetic variables. Blood samples were taken from 361 subjects from unselected Mexican population for biochemical analysis and for deoxyribonucleic acid extraction; besides blood pressure and body mass index (BMI) were measured. APOB polymorphisms rs934197, rs533617, rs693, and rs1042031 were genotyped by polymerase chain reaction (PCR)-restriction fragment length polymorphism; whereas, rs17240441 and c.66_67insCTGCTG were genotyped by PCR followed by electrophoresis. Genotype and allele frequencies were obtained by simple counting and deviations from Hardy-Weinberg equilibrium (HWE) were calculated by chi-square test. The effect of the polymorphisms on the quantitative variables was determined using analysis of variance, Student's t test, Pearson's and Spearman's correlations and multiple linear regression models. All the polymorphisms were within HWE. Frequencies of mutated alleles were highly heterogeneous: rs934197-T 33.6%, rs17240441-D 39.3%, c.66_67insCTGCTG-I 3.9%, rs533617-G 0.9%, rs693-T 40.5%, and rs1042031-G 17.3%. Chronic degenerative diseases were frequent in the studied population: overweight-obesity 55.1%, dyslipidemia 45.8%, and hypertension 23.5%. The association analyses showed that despite adjustments for age and sex the mutated alleles rs934197-T, rs1042031G, c.66_67-insCTGCTG-I, and rs533617-G, were related to lower values of BMI, total cholesterol (TC), systolic blood pressure, and diastolic blood pressure, respectively. All polymorphisms analyzed except rs533517 and c.66_67insCTGCTG showed high frequencies of the mutated allele, making them useful for association studies. Our results revealed that, APOB gene polymorphisms could be contributing to the development of several chronic diseases, such as essential hypertension, dyslipidemias, obesity, among others. However, specific studies with each pathology are needed to know the possible implications of the polymorphisms.

Sorting through the extensive and confusing roles of sortilin in metabolic disease

Sortilin is a post-Golgi trafficking receptor homologous to the yeast vacuolar protein sorting receptor 10 (VPS10). The VPS10 motif on sortilin is a 10-bladed β-propeller structure capable of binding more than 50 proteins, covering a wide range of biological functions including lipid and lipoprotein metabolism, neuronal growth and death, inflammation, and lysosomal degradation. Sortilin has a complex cellular trafficking itinerary, where it functions as a receptor in the trans-Golgi network, endosomes, secretory vesicles, multivesicular bodies, and at the cell surface. In addition, sortilin is associated with hypercholesterolemia, Alzheimer's disease, prion diseases, Parkinson's disease, and inflammation syndromes. The 1p13.3 locus containing SORT1, the gene encoding sortilin, carries the strongest association with LDL-C of all loci in human genome-wide association studies. However, the mechanism by which sortilin influences LDL-C is unclear. Here, we review the role sortilin plays in cardiovascular and metabolic diseases and describe in detail the large and often contradictory literature on the role of sortilin in the regulation of LDL-C levels.

Genetic Regulatory Networks of Apolipoproteins and Associated Medical Risks

Apolipoproteins (APO proteins) are the lipoprotein family proteins that play key roles in transporting lipoproteins all over the body. There are nearly more than twenty members reported in the APO protein family, among which the A, B, C, E, and L play major roles in contributing genetic risks to several disorders. Among these genetic risks, the single nucleotide polymorphisms (SNPs), involving the variation of single nucleotide base pairs, and their contributing polymorphisms play crucial roles in the apolipoprotein family and its concordant disease heterogeneity that have predominantly recurred through the years. In this review, we have contributed a handful of information on such genetic polymorphisms that include APOE, ApoA1/B ratio, and A1/C3/A4/A5 gene cluster-based population genetic studies carried throughout the world, to elaborately discuss the effects of various genetic polymorphisms in imparting various medical conditions, such as obesity, cardiovascular, stroke, Alzheimer's disease, diabetes, vascular complications, and other associated risks.

The association of apolipoprotein-E (APOE) gene polymorphisms with coronary artery disease: a systematic review and meta-analysis

Background

Numerous studies have investigated the role of apolipoprotein E (APOE) polymorphisms in coronary artery disease (CAD), but some controversies exist regarding the outcomes as the results were not consistent and remain uncertain. Therefore, the present meta-analysis was conducted to evaluate the association of APOE polymorphisms with coronary artery disease.

Methods

All the relevant studies published in English language till August 2020 were identified by searching through various electronic databases. The complete data was independently extracted by the two researchers. The data were analyzed by using the Comprehensive Meta-Analysis program and MetaGenyo program. The pooled odds ratio was used to check the associations between CAD and APOE polymorphisms. The following genetic models were used to calculate the odds ratio: ε2 vs. ε3 and ε4 vs. ε3.

Results

In the final analysis, we include 12 studies regarding the role of APOE polymorphism in CAD. The pooled odds ratio for ε4 allele was higher (OR 2.00; 95% and CI, 1.48–2.71). There is no statistical significant association for ε2 allele with CAD (OR 1.38; 95% CI, 1.18–1.62). This analysis showed no publication bias exists in the current meta-analysis.

Conclusions

Our findings suggest that the apolipoprotein ε4 allele appears as a significant genetic risk factor for coronary artery disease while the ε2 allele is beneficial to alleviate the CAD risk.

Trial registration

Registered with PROSPERO International Prospective Register of Systematic Reviews. PROSPERO registration number CRD42020190464

Lack of Association of LPA Gene Polymorphisms with Coronary Artery Disease in Pakistani Subjects

Coronary artery disease (CAD) is the leading cause of death worldwide. Pakistan faces a high epidemic of CAD, and the disease burden is increasing with the passage of time. Several genetic markers have been reported to be significantly associated with CAD; one of them is the lipoprotein A gene. The aim of the current investigation was to genotype the LPA gene SNPs, rs3798220 and rs10455872, in Pakistani subjects with CAD in a case control study design. The genotyping was done by TaqMan allelic discrimination assay. The results showed that the cases had significantly higher prevalence of diabetes (64.6%), hypertension (62.1%), and smoking habits (29.5%). The level of cholesterol in cases was higher than in controls (208.25 ± 54.11 vs. 175.34 ± 43.51, p ≤ 0.0001). The LDL-C was higher in cases than in controls (104.62 ± 37.94 vs. 77.05 ± 21.17, p ≤ 0.0001). Similarly, triglycerides were also higher in cases than in controls (214.51 ± 74.60 vs. 190.54 ± 70.26, p ≤ 0.0001), whereas HDL-C was lower in cases than in controls (45.13 ± 11.63 vs. 67.9 ± 17.57, p ≤ 0.0001). For rs3798220, the risk allele (C) frequency was 0.005 in cases and 0.002 in controls. For rs10455872, the risk allele (G) frequency was 0.017 in cases and 0.014 in controls. The risk allele frequencies were not significantly different between cases and controls (p > 0.05). In conclusion, these two LPA SNPs do not contribute significantly to CAD progression and cannot be used as independent risk factors for CAD in Pakistani population.

Plasma cholesterol in Alzheimer's disease and frontotemporal dementia

Background

The relationship between the apolipoprotein E (APOE)-ε4 allele, triglyceride (TG) level, and cholesterol level and an increased risk of developing Alzheimer's disease (AD) has been well established, but their relationship with behavioral-variant frontotemporal dementia (bvFTD) is not well-known.

Methodology

The levels of TGs, total cholesterol (TC), low-density lipoprotein (LDL), and high-density lipoprotein were measured in bvFTD and AD patients and in normal controls (NCs). DNA was extracted, and APOE was genotyped.

Results

The APOE-ε4 allele frequency was higher in the AD group than in the NC group, but no difference was found between the AD and the bvFTD groups. The bvFTD group had higher LDL than the AD group, and significant differences were also found for the cholesterol level in the dementia groups compared with the NC group. Elevated LDL level was positively correlated with appetite and eating score in the bvFTD group. Compared with the AD patients and NCs without the APOE-ε4 allele, those with the APOE-ε4 allele had higher TC, but its correlation with the bvFTD group was absent.

Conclusions

The bvFTD and the AD groups had higher cholesterol levels. The APOE-ε4 allele and eating behavior might modify lipid metabolism in dementia. TG and cholesterol analyses may offer a new opportunity for targeted treatments.

Role of sortilin in lipid metabolism

PURPOSE OF REVIEW

Sortilin, encoded SORT1 gene at chromosome 1p13.3, is a multiligand receptor that traffics protein from the Golgi to the endosomes, secretory vesicles, and the cell surface. Genome-wide association studies (GWAS) revealed an association between sortilin and reduced plasma LDL-cholesterol (LDL-C) as well as reduced coronary artery disease (CAD). This review explores the various lipid metabolism pathways that are affected by alterations in sortilin expression.

RECENT FINDINGS

The effects of increased hepatic sortilin on plasma LDL-C levels are mediated by increased clearance of LDL-C and decreased very LDL (VLDL) secretion because of increased autophagy-mediated lysosomal degradation of apolipoproteinB100. Sort1 knockout models have shown opposite VLDL secretion phenotypes as well as whole body lipid metabolism in response to diet challenges, leading to confusion about the true role of sortilin in the liver and other tissues.

SUMMARY

The regulation of VLDL secretion by hepatic sortilin is complex and remains incompletely understood. Further investigation to determine the specific conditions under which both hepatic sortilin and total body sortilin cause changes in lipid metabolism pathways is needed.

Associations of Genetic Variations in ABCA1 and Lifestyle Factors with Coronary Artery Disease in a Southern Chinese Population with Dyslipidemia: A Nested Case-Control Study

Coronary artery disease has become a major health concern over the past several decades. We aimed to explore the association of single nucleotide polymorphisms (SNPs) in the ATP-binding cassette subfamily A member 1 (ABCA1) and lifestyle factors with coronary artery disease (CAD) in dyslipidemia. This nested case-control study included 173 patients with CAD and 500 matched control individuals (1:3, case: control) from a district in southern China. We collected medical reports, lifestyle details, and blood samples of individuals with dyslipidemia and used the polymerase chain reaction-ligase detection reaction method to genotype the SNPs. The CC genotype of the additive and recessive models of rs4149339, together with regular intake of fried foods or dessert, increased the risk of CAD (adjusted odd ratio (OR) = 1.91, p = 0.030; adjusted OR = 1.97, p = 0.017; adjusted OR = 1.80, p = 0.002; adjusted OR = 1.98, p = 0.001). The AT + AA genotype of the dominant model of rs4743763 and moderate/heavy physical activity reduced the risk of CAD (adjusted OR = 0.66, p = 0.030; adjusted OR = 0.44, p = 0.001). The CT + CC genotype of the dominant model of rs2472386 reduced the risk of CAD only in males (adjusted OR = 0.36, p = 0.001). The interaction between rs4149339 and rs4743763 of ABCA1 and haplotype CTT (comprising rs4149339, rs4743763, and rs2472386) appeared to increase the risk of CAD (relative excess risk due to interaction (RERI) = 3.19, p = 0.045; OR = 1.49, p = 0.019). Polymorphisms of rs4149339, rs4743763 and rs2472386 in ABCA1 and three lifestyle factors (physical activity, fried food intake, and dessert intake) were associated with CAD in people with dyslipidemia in southern China. These results provide the theoretical basis for gene screening and the prevention of chronic cardiovascular diseases.

Genetic risk score (GRS) constructed from polymorphisms in the PON1, IL-6, ITGB3, and ALDH2 genes is associated with the risk of coronary artery disease in Pakistani subjects

Background

Coronary artery disease (CAD) is a major killer in today’s world. Pakistan is also affected by this non-communicable disease like other countries. It is a multifactorial disease and is influenced by many gene-gene and gene-environment interactions.

Methods

A total of 623 (219 controls, 404 cases) Pakistani subjects were genotyped for four SNPs, rs662 (PON1), rs5918 (ITGB3), rs671 (ALDH2), rs1800795 (IL-6) by PCR-RFLP. Various anthropometric parameters were noted and serum lipid profile was measured using commercially available kits. Statistical analysis was done by SPSS version 22. A Genetic Risk Score (GRS) was calculated from individual SNPs. The association of the SNPs and the GRS with CAD was checked using logistic regression.

Results

The results showed that the risk allele frequencies of all variants were higher in the cases than the controls, however the difference was not statistically significant association (p > 0.0125). The mean GRS in the controls was 3.99 ± 1.42 and in cases, it was 4.29 ± 1.39, the difference between the groups was significant (p = 0.0109). logistic regression of individual SNPs and GRS with the CAD showed that independent SNPs were not significantly associated with the CAD however, the GRS had a strong association (p = 1.4 × 10^− 4). The subjects were divided into three groups based on GRS (Gp 1 with GRS 0–2, Gp 2 with GRS 3–5 and Gp 3 with GRS 6–8). The analysis of the effect of the individual SNPs and GRS groups on different lipid profile parameters revealed no significant association of any of the tested SNPs with any lipid parameter, however, the GRS groups showed marginally significant for TC and highly significant association for TG, LDL-c and HDL-c.

Conclusion

In conclusion, use of a GRS can provide better information than individual SNPs. The larger the number of the SNPs included in the analysis, the better would be the risk prediction.

Exome-wide analysis identifies three low-frequency missense variants associated with pancreatic cancer risk in Chinese populations

Germline coding variants have not been systematically investigated for pancreatic ductal adenocarcinoma (PDAC). Here we report an exome-wide investigation using the Illumina Human Exome Beadchip with 943 PDAC cases and 3908 controls in the Chinese population, followed by two independent replicate samples including 2142 cases and 4697 controls. We identify three low-frequency missense variants associated with the PDAC risk: rs34309238 in PKN1 (OR = 1.77, 95% CI: 1.48–2.12, P = 5.35 × 10⁻¹⁰), rs2242241 in DOK2 (OR = 1.85, 95% CI: 1.50–2.27, P = 4.34 × 10⁻⁹), and rs183117027 in APOB (OR = 2.34, 95% CI: 1.72–3.16, P = 4.21 × 10⁻⁸). Functional analyses show that the PKN1 rs34309238 variant significantly increases the level of phosphorylated PKN1 and thus enhances PDAC cells' proliferation by phosphorylating and activating the FAK/PI3K/AKT pathway. These findings highlight the significance of coding variants in the development of PDAC and provide more insights into the prevention of this disease.

Pancreatic ductal adenocarcinoma is a lethal human cancer with a poor 5-year overall survival rate. Here the authors perform an exome-wide analysis in a cohort of PDAC patients to identify three novel missense variants in PKN1, DOK2, and APOB genes, that are associated with PDAC risk.

Association of apolipoprotein E gene polymorphisms with blood lipids and their interaction with dietary factors

BACKGROUND

Several candidate genes have been identified in relation to lipid metabolism, and among these, lipoprotein lipase (LPL) and apolipoprotein E (APOE) gene polymorphisms are major sources of genetically determined variation in lipid concentrations. This study investigated the association of two single nucleotide polymorphisms (SNPs) at LPL, seven tagging SNPs at the APOE gene, and a common APOE haplotype (two SNPs) with blood lipids, and examined the interaction of these SNPs with dietary factors.

METHODS

The population studied for this investigation included 660 individuals from the Prevention of Cancer by Intervention with Selenium (PRECISE) study who supplied baseline data. The findings of the PRECISE study were further replicated using 1238 individuals from the Caerphilly Prospective cohort (CaPS). Dietary intake was assessed using a validated food-frequency questionnaire (FFQ) in PRECISE and a validated semi-quantitative FFQ in the CaPS. Interaction analyses were performed by including the interaction term in the linear regression model adjusted for age, body mass index, sex and country.

RESULTS

There was no association between dietary factors and blood lipids after Bonferroni correction and adjustment for confounding factors in either cohort. In the PRECISE study, after correction for multiple testing, there was a statistically significant association of the APOE haplotype (rs7412 and rs429358; E2, E3, and E4) and APOE tagSNP rs445925 with total cholesterol (P = 4 × 10^- 4 and P = 0.003, respectively). Carriers of the E2 allele had lower total cholesterol concentration (5.54 ± 0.97 mmol/L) than those with the E3 (5.98 ± 1.05 mmol/L) (P = 0.001) and E4 (6.09 ± 1.06 mmol/L) (P = 2 × 10^- 4) alleles. The association of APOE haplotype (E2, E3, and E4) and APOE SNP rs445925 with total cholesterol (P = 2 × 10^- 6 and P = 3 × 10^- 4, respectively) was further replicated in the CaPS. Additionally, significant association was found between APOE haplotype and APOE SNP rs445925 with low density lipoprotein cholesterol in CaPS (P = 4 × 10^- 4 and P = 0.001, respectively). After Bonferroni correction, none of the cohorts showed a statistically significant SNP-diet interaction on lipid outcomes.

CONCLUSION

In summary, our findings from the two cohorts confirm that genetic variations at the APOE locus influence plasma total cholesterol concentrations, however, the gene-diet interactions on lipids require further investigation in larger cohorts.

Q192R polymorphism in the PON1 gene and familial hypercholesterolemia in a Saudi population

BACKGROUND

Familial hypercholesterolemia (FH) is an autosomal dominant condition characterized by abnormal levels of low-density lipoprotein (LDL) in the blood. FH is a risk factor for atherosclerosis and cardiovascular disease. The relationship between the paraoxonase 1 (PON1) gene, atherosclerosis and coronary artery disease has not been studied in Saudi patients.

OBJECTIVE

To investigate the genetic associations of the Q192R polymorphism in the PON1 gene with FH in Saudi patients.

DESIGN

Case-control study.

SETTING

Tertiary care center, Riyadh.

METHODS

Two hundred Saudi patients were enrolled in this study, including 100 patients with FH and 100 healthy controls, during the period from January 2012 to March 2013. Serum was separated from coagulated blood (3 mL) and used for analysis of lipid profiles. Genomic DNA was isolated from anticoagulant-treated blood (2 mL). Genotyping for the Q192R polymorphism was performed by polymerase chain reaction-restriction fragment length polymorphism analysis, followed by 3% agarose gel electrophoresis.

MAIN OUTCOME MEASURE

The strength of association between the Q192R polymorphism and FH in the Saudi population.

RESULTS

We confirmed that QR versus QQ (odds ratio [OR]: 1.55; 95% confidence interval [CI]: 1.05-3.43; P=.03), QR+RR versus QQ (OR: 1.98; 95% CI: 1.13-3.49; P=.01), and R versus Q (OR: 1.68; 95% CI: 1.09- 2.59; P=.01) in the Q192R polymorphism were associated with FH in the Saudi population.

CONCLUSION

In conclusion, the Q192R polymorphism in the PON1 gene is associated with FH in the Saudi population. Our results confirmed that the R allele, QR, and dominant model genotypes were associated with FH.

LIMITATION

Only a single variant (Q192R) was analyzed, and the medical and family histories of the patients were not known.

Common variants in the genes of triglyceride and HDL-C metabolism lack association with coronary artery disease in the Pakistani subjects

Background

Serum Triglyceride (TG) and High Density Lipoprotein (HDL-C) levels are modifiable coronary artery disease (CAD) risk factors. Polymorphisms in the genes regulating TG and HDL-C levels contribute to the development of CAD. The objective of the current study was to investigate the effect of four such single nucleotide polymorphism (SNPs) in the genes for Lipoprotein Lipase (LPL) (rs328, rs1801177), Apolipoprotein A5 (APOA5) (rs66279) and Cholesteryl ester transfer protein (CETP) (rs708272) on HDL-C and TG levels and to examine the association of these SNPs with CAD risk.

Methods

A total of 640 subjects (415 cases, 225 controls) were enrolled in the study. The SNPs were genotyped by KASPar allelic discrimination technique. Serum HDL-C and TG were determined by spectrophotometric methods.

Results

The population under study was in Hardy Weinberg equilibrium and minor allele of SNP rs1801177 was completely absent in the studied subjects. The SNPs were association with TG and HDL-C levels was checked through regression analysis. For rs328, the effect size of each risk allele on TG and HDL-C (mmol/l) was 0.16(0.08) and −0.11(0.05) respectively. Similarly, the effect size of rs662799 for TG and HDL-C was 0.12(0.06) and −0.13(0.0.3) and that of rs708272 was 0.08(0.04) and 0.1(0.03) respectively. The risk allele frequencies of the SNPs were higher in cases than controls, but the difference was not significant (p > 0.05) and SNPs were not associated with CAD risk (p > 0.05). The combined gene score of four SNPs significantly raised TG and lowered HDL-C but did not increase CAD risk.

Conclusion

The studied SNPs were associated with TG and HDL-C levels, but not with CAD in Pakistani population under study.

Electronic supplementary material

The online version of this article (doi:10.1186/s12944-017-0419-4) contains supplementary material, which is available to authorized users.

Genetic risk analysis of coronary artery disease in Pakistani subjects using a genetic risk score of 21 variants

BACKGROUND AND AIMS

Conventional coronary artery disease (CAD) risk factors like age, gender, blood lipids, hypertension and smoking have been the basis of CAD risk prediction algorithms, but provide only modest discrimination. Genetic risk score (GRS) may provide improved discrimination over and above conventional risk factors. Here we analyzed the genetic risk of CAD in subjects from Pakistan, using a GRS of 21 variants in 18 genes and examined whether the GRS is associated with blood lipid levels.

METHODS

625 (405 cases and 220 controls) subjects were genotyped for variants, NOS3 rs1799983, SMAD3 rs17228212, APOB rs1042031, LPA rs3798220, LPA rs10455872, SORT1 rs646776, APOE rs429358, GLUL rs10911021, FTO rs9939609, MIA3 rs17465637, CDKN2Ars10757274, DAB2IP rs7025486, CXCL12 rs1746048, ACE rs4341, APOA5 rs662799, CETP rs708272, MRAS rs9818870, LPL rs328, LPL rs1801177, PCSK9 rs11591147 and APOE rs7412 by TaqMan and KASPar allele discrimination techniques.

RESULTS

Individually, the single SNPs were not associated with CAD except APOB rs1042031 and FTO rs993969 (p = 0.01 and 0.009 respectively). However, the combined GRS of 21 SNPs was significantly higher in cases than controls (19.37 ± 2.56 vs. 18.47 ± 2.45, p = 2.9 × 10^-5), and compared to the bottom quintile, CAD risk in the top quintile of the GRS was 2.96 (95% CI 1.71-5.13). Atherogenic blood lipids showed significant positive association with GRS.

CONCLUSIONS

The GRS was quantitatively associated with CAD risk and showed association with blood lipid levels, suggesting that the mechanism of these variants is likely to be, in part at least, through creating an atherogenic lipid profile in subjects carrying high numbers of risk alleles.