Guanidine to adenine (G/A) substitution in the promoter region of the apolipoprotein AI gene is associated with elevated serum apolipoprotein AI levels in Chinese non-smokers

Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group

Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.

Significant Implications of APOA1 Gene Sequence Variations and Its Protein Expression in Bladder Cancer

Apolipoprotein A1 (APOA1) is a potential biomarker because of its variable concentration in different types of cancers. The current study is the first of its kind to evaluate the association between the APOA1 genotypes of −75 G/A and +83 C/T in tandem with the APOA1 protein expression in urine samples to find out the risk and potential relationship for differentially expressed urinary proteins and APOA1 genotypes. The study included 108 cases of bladder tumors and 150 healthy controls that were frequency matched to cases with respect to age, sex, and smoking status. Genotyping was performed using PCR-RFLP and the urinary expression of the APOA1 protein was done using ELISA. Bladder tumor cases were significantly associated with the APOA1 −75 AA genotype (p < 0.05), while the APOA1 +83 C/T heterozygotes showed an association with cases (p < 0.05). The overall distribution of the different haplotypes showed a marked difference between the cases and controls in GT when compared with the wild type GC (p < 0.03). Bladder tumor cases that carried the variant genotype APOA1 −75AA were found more (70.0%) with a higher expression (≥20 ng/mL)of the APOA1 urinary protein and differed significantly against wild type GG (p = 0.03). Again, in low grade bladder tumors, urinary APOA1 protein was exhibited significantly more (52.4% vs. 15.4% high grade) with a higher expression (≥20 ng), while high grade tumor cases (84.6% vs. 47.5% low grade) showed a lower APOA1 expression (<20 ng/mL) (O.R = 6.08, p = 0.002). A strong association was observed between APOA1 −75G/A and risk for bladder tumor and its relation to urinary protein expression, which substantiates its possible role as a marker for the risk assessment of the disease and as a promising diagnostic marker for different grades of malignant bladder tumors.

Association of APOA1-75G/A and +83C/T polymorphic variation with acute coronary syndrome patients in Kashmir (India)

Introduction: Acute coronary syndrome (ACS) comes under the ambit of cardiovascular disease.APOA-1 gene plays a vital role in lipid metabolism and has been observed to have plausible role in ACS. This cross sectional case-control study was conducted to evaluate association between APOA 1-75G/A(rs1799837), +83C/T (rs5069) genotypes and risk for ACS. Methods: The current case-control study that included confirmed 90 ACS cases and 150 healthy controls were genotyped for APOA 1-75 G/A and +83 C/T by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLF) method. Results: APOA 1-75G/A distribution of genotypes/alleles among cases and controls was seen proportionally same with no association to ACS (P = 0.5). APOA 1+83 C/T variants showed protective effect with ACS where variant TT genotype presented more in controls (12%) than cases (1.6%) (P = 0.004) and likewise variant 'T' allele was found more in controls than ACS cases (9.4% vs.28.5% respectively: P < 0.05). Further, significantly high difference of CT genotype was seen among cases and controls 15% vs. 33% respectively (P = 0.002). The overall distribution of different haplotypes showed a marked difference in GT when compared with GC between cases and controls (P = 0.0001). Conclusion: The study shows that TT genotype and variant T allele of APOA 1 +83 C/T depicted a protective role with respect to ACS whereas APOA 1-75G>A showed no relation. Haplotype GT was observed to significantly over-represent in controls with its protective effect in ACS as against wild type haplotype GC.

Association of the Apolipoprotein A-I Gene Polymorphisms with Cardiovascular Disease Risk Factors and Atherogenic Indices in Patients from Assam, Northeast India

Cardiovascular disease (CVD) risk factors, and particularly decreased high density lipoprotein cholesterol (HDL-C) dyslipidemia are prevalent in Assam, India. This study was undertaken to investigate whether Apolipoprotein A-I (APOA1) gene polymorphisms (G-75A and C+83T) were associated with i) the risk for decreased HDL-C, and ii) other CVD risk factors, viz. serum lipids, atherogenic indices, obesity, and blood pressure (BP). A total of 649 subjects were screened, from which 200 eligible individuals, classified as case group with decreased HDL-C levels (100 subjects) and control group with normal HDL-C levels (100 subjects) were enrolled and genotyped using polymersase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing. Lipid fractions [HDL-C, total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), very low density lipoprotein cholesterol (VLDL-C), triglycerides (TG)] and atherogenic indices [Castelli's Risk Indices-I and -II (CRI-I and -II), non-HDL-C fraction, atherogenic index of plasma (AIP), atherogenic coefficient (AC)] were estimated. The G-75A and C+83T loci were not associated with decreased HDL-C risk. This was confirmed across different genetic models (dominant, recessive, additive and allelic). Association was also absent with BP and obesity. However, the G-75A locus was associated with LDL-C, whereas the C+83T locus was associated with TG and VLDL-C. Furthermore, these sites had effects on atherogenic indices. The rare A allele at the G-75A locus was associated with adverse CRI-I, CRI-II, non-HDL-C and AC values, while the major C allele at the C+83T locus was associated with adverse AIP values. Thus, the pro-atherogenic G-75A polymorphism and the anti-atherogenic C+83T polymorphism represent important genetic loci that modulate CVD risk factors in subjects from Assam.

Apolipoprotein A1 polymorphisms and risk of coronary artery disease: a meta-analysis

INTRODUCTION

It has been reported that APOA1 -75G/A polymorphism might be associated with susceptibility to coronary artery disease (CAD). Owing to mixed and inconclusive results, we conducted a meta-analysis to systematically summarize and clarify the association between APOA1-75G/A polymorphism and the risk of CAD.

MATERIAL AND METHODS

A systematic search of studies on the association of single nucleotide polymorphisms (SNP) with susceptibility to CAD was conducted. A total of 9 case-control studies (1864 cases and 1196 controls) on the APOA1-75G/A polymorphism were included.

RESULTS

We observed no statistically significant association between APOA1 -75G/A polymorphism and risk of CAD under the dominant genetic model (AA + AG vs. GG: OR = 1.03, 95% CI: 0.65-1.66), allelic contrast (A vs. G: OR = 0.88, 95% CI: 0.58-1.32), heterozygote model (AG vs. GG: OR = 1.24, 95% CI: 0.81-1.89) or homozygote model (AA vs. GG: OR = 0.52, 95% CI: 0.26-1.05). Significant heterogeneity between individual studies appears in all five models, but a strong association under the recessive genetic model (AA vs. AG + GG: OR = 0.51, 95% CI: 0.28-0.92). In the subgroup analysis by Hardy-Weinberg equilibrium (HWE; the presence or absence of HWE in controls), significantly decreased CAD risk and no significant heterogeneity were observed among controls consistent with HWE. Overall, the APOA1 A allele is one of the protective factors of CAD. A stronger association between APOA1-75G/A polymorphisms and CAD risk was present in the studies consistent with HWE.

CONCLUSIONS

The minor allele of the APOA1-75G/A polymorphism is a protective factor for CAD, especially in the studies consistent with HWE.

Apolipoprotein A1 -75 G/A and +83 C/T polymorphisms and renal cancer risk

Background

Apolipoprotein A1 (ApoA1) is the major apoprotein constituent of high-density lipoprotein that can play important roles in tumor invasion and metastasis. The objective of the present study was to evaluate the association of two genetic variants (−75 G/A and +83 C/T) of APOA1 with predisposition to renal cancer.

Methods

A total of 432 subjects, including 216 pathologically-proven renal cancer cases and 216 age- and gender-matched healthy controls, were recruited into this hospital-based case–control study. Genotyping of the APOA1 was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) combined with gel electrophoresis, and then confirmed by direct sequencing.

Results

Patients with renal cancer had a significantly higher frequency of APOA1 -75 AA genotype [odds ratio (OR) = 2.10, 95 % confidence interval (CI) = 1.18, 3.75; P = 0.01] and APOA1 -75 A allele (OR =1.40, 95 % CI = 1.05, 1.87; P = 0.02) than controls. When stratifying by the distant metastasis status, patients with distant metastasis had a significantly higher frequency of APOA1 -75 AA genotype genotype (OR =2.20, 95 % CI = 1.04, 4.68; P = 0.04).

Conclusion

This study is, to our knowledge, the first to examine prospectively an increased risk role of APOA1 -75 AA genotype and APOA1 -75 A allele in renal cancer susceptibility.

Effect of apolipoprotein A1 genetic polymorphisms on lipid profiles and the risk of coronary artery disease

Background

The disorder of lipid metabolism and genetic predisposition are major risk factors for coronary artery disease (CAD). Variants in the apolipoprotein A1 (APOA1) gene play an important role in the regulation of lipids. The objective of the present study was to investigate the effect of two polymorphisms (-75 G/A and +83 C/T) of APOA1 on lipid profiles and the risk of CAD.

Methods

A total number of 300 subjects with CAD and 300 age and sex matched healthy controls were enrolled for the study. Genotyping of the APOA1 was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) combined with gel electrophoresis, and then confirmed by direct sequencing.

Results

The frequencies of APOA1 -75 AA genotype [odds ratio (OR) =0.50, 95 % confidence interval (CI) = 0.28, 0.88; P = 0.02] and APOA1 -75 A allele (OR =0.76, 95 % CI = 0.59, 0.98; P = 0.04) were significantly lower in CAD than in controls. The APOA1 -75 A allele was significantly associated with increasing serum concentrations of ApoA1 and high-density lipoprotein cholesterol (HDL-C) (P < 0.001).

Conclusions

The individuals with the APOA1 -75 A allele were likely to have a lower risk of CAD as a result of its effect on higher serum concentrations of ApoA1 and HDL-C.

Association of apolipoprotein A1 -75 G/A polymorphism with susceptibility to the development of acute lung injury after cardiopulmonary bypass surgery

Introduction

Apolipoprotein A1 (apoA1) is the major apoprotein constituent of high density lipoprotein (HDL) which exerts innate protective effects in systemic inflammation. However, its role in the acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) has not been well studied. The objective of this study was to investigate the potential association between APOA1 -75 G/A polymorphism and the development of ALI after cardiopulmonary bypass (CPB) surgery.

Materials and methods

A hospital-based case–control study was conducted in patients with ALI (n = 300), patients without ALI (n = 300) and healthy controls (n = 300). Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assay was applied to assess the APOA1 -75 G/A genotypes.

Results

Patients with ALI had a significantly higher frequency of APOA1 -75 AA genotype [odds ratio (OR) =1.75, 95% confidence interval (CI) = 1.04, 2.92; P = 0.03] than patients without ALI. APOA1 -75 AA genotype (OR =3.47, 95% CI = 1.60, 7.52; P = 0.002) and A allele (OR =1.92, 95% CI = 1.24, 2.96; P = 0.003) were the significant independent prognostic factors for the 30-day survival rate of patients with ALI after CPB surgery.

Conclusion

Our study suggested that APOA1 -75 AA genotype was associated with a higher ALI risk after CPB surgery. Patients with the APOA1 -75 AA genotype and A allele had higher 30-day mortality of ALI after CPB surgery. Additional studies are needed to confirm this finding.

Interactions between the apolipoprotein a1/c3/a5 haplotypes and alcohol consumption on serum lipid levels

BACKGROUND

The interactions between apolipoprotein (Apo) A1/C3/A5 haplotypes and alcohol consumption on serum lipid profiles have not been previously explored. The present study was undertaken to detect the polymorphisms of ApoA1 -75 bp G>A (rs1799837), ApoC3 3238C>G (rs5128), ApoA5 -1131T>C (rs662799), ApoA5 c.553G>T (rs2075291), and ApoA5 c.457G>A (rs3135507) and the interactions between their haplotypes and alcohol consumption on serum lipid levels.

METHODS

Genotyping was performed in 1,030 unrelated subjects (516 nondrinkers and 514 drinkers) aged 15 to 89. The interactions between ApoA1/C3/A5 haplotypes and alcohol consumption on serum lipid levels were detected by factorial regression analysis after controlling for potential confounders.

RESULTS

The frequencies of ApoC3 3238 CG/GG genotypes and ApoA1 -75 bp A allele in nondrinkers were higher in females than in males (p < 0.05). The frequencies of ApoC3 3238 CG/GG genotypes and G allele in drinkers were higher in females than in males (p < 0.05). The frequencies of ApoA1 -75 bp GA/AA genotypes and A allele in males were higher, and those of ApoC3 3238 CG/GG genotypes were lower in drinkers than in nondrinkers (p < 0.05 to 0.01). The frequency of ApoC3 3238 GG genotype in male drinkers was also higher in ≥25 g/d than in <25 g/d subgroups (p < 0.05). There were 11 haplotypes with a frequency >1% in our study population. The haplotypes of G-G-T-C-G (in the order of c.553G>T, c.457G>A, -1131T>C, 3238C>G, and -75 bp G>A), G-G-T-C-A, and G-G-C-G-G were shown consistent interactions with alcohol consumption to increase serum total cholesterol, high-density lipoprotein cholesterol (HDL-C), and ApoA1 levels (p < 0.05 to 0.001). The interactions between G-G-T-G-G (HDL-C and ApoA1), G-G-C-C-A (ApoA1), G-A-T-C-G (triglyceride), G-G-T-C-G (ApoA1/ApoB ratio), and G-G-C-G-G (ApoB) haplotypes and alcohol consumption on serum lipid levels were also detected (p < 0.05 to 0.001); the levels of these serum lipid parameters were significantly higher in drinkers than in nondrinkers.

CONCLUSIONS

The differences in serum lipid parameters between drinkers and nondrinkers might partly result from different interactions between the ApoA1/C3/A5 haplotypes and alcohol consumption.

CYP4A11 variant is associated with high-density lipoprotein cholesterol in women

The ω-hydroxylase CYP4A11 catalyzes the transformation of epoxyeicosatrienoic acids to omega-hydroxylated-epoxyeicosatrienoic acids, endogenous peroxisome proliferator-activated receptor α (PPARα) agonists. PPARα activation increases high-density lipoprotein-cholesterol (HDL-C). A cytosine-for-thymidine (T8590C) variant of CYP4A11 encodes for a ω-hydroxylase with reduced activity. This study examined the relationship between CYP4A11 T8590C genotype and metabolic parameters in the Framingham Offspring Study and in a clinical practice-based biobank, BioVU. In women in the Framingham Offspring Study, the CYP4A11 8590C allele was associated with reduced HDL-C concentrations (54.2±0.9 mg/dL in CYP4A11 CC or CT genotype women versus 56.7±0.5 mg/dL in TT women, p=0.02), and with an increased prevalence of low HDL-C, defined categorically as ≤50mg/dL [odds ratio 1.39 (95% CI 1.02-1.90), p=0.04]. In the BioVU cohort, the CYP4A11 8590C allele was also associated with low HDL-C in women [odds ratio 1.69 (95% CI 1.03-2.77, p=0.04)]. There was no relationship between genotype and HDL-C in men in either cohort.

Studies of gene variants related to inflammation, oxidative stress, dyslipidemia, and obesity: implications for a nutrigenetic approach

Obesity is currently considered a serious public health issue due to its strong impact on health, economy, and quality of life. It is considered a chronic low-grade inflammation state and is directly involved in the genesis of metabolic disturbances, such as insulin resistance and dyslipidemia, which are well-known risk factors for cardiovascular disease. Furthermore, there is evidence that genetic variation that predisposes to inflammation and metabolic disturbances could interact with environmental factors, such as diet, modulating individual susceptibility to developing these conditions. This paper aims to review the possible interactions between diet and single-nucleotide polymorphisms (SNPs) in genes implicated on the inflammatory response, lipoprotein metabolism, and oxidative status. Therefore, the impact of genetic variants of the peroxisome proliferator-activated receptor-(PPAR-)gamma, tumor necrosis factor-(TNF-)alpha, interleukin (IL)-1, IL-6, apolipoprotein (Apo) A1, Apo A2, Apo A5, Apo E, glutathione peroxidases 1, 2, and 4, and selenoprotein P exposed to variations on diet composition is described.

Apolipoprotein A1 gene polymorphism (G-75A and C+83T) in patients with myocardial infarction: a pilot study in a north Indian population

The apolipoprotein A1 gene polymorphism (G-75A and C+83T) was studied in 100 subjects (50 patients diagnosed with myocardial infarction and 50 healthy subjects). Serum apolipoprotein (apo) A1 and apo B levels were estimated immunoturbidometrically. Extracted DNA from blood was amplified by polymerase chain reaction, digested with MspI restriction enzyme, run on 8% polyacrylamide gel, and restriction fragment length polymorphism was studied by using a gel documentation system. Serum (mean +/- SD) apo A1 levels were significantly higher in control subjects than the study group (100.80 +/- 7.06 mg/dL [1.0 +/- 0.07 g/L] and 72.56 +/- 9.86 mg/dL [0.73 +/- 0.1 g/L], respectively; P < .0001), whereas apo B levels were significantly lower (72.12 +/- 11.32 mg/dL [0.7 +/- 0.1 g/L] and 97.45 +/- 9.04 mg/dL [1.0 +/- 0.09 g/L], respectively; P < .0001). The G allele frequency at the -75-base-pair (bp) site was higher in the study group (79%) compared with the control group (58%). The T allele frequency at the +83-bp site was higher in the study group (56%) than in the control group (32%). G at -75 bp upstream from the start of transcription and T at +83 bp in the first intron may be susceptibility alleles for myocardial infarction.

Synergistic effect between apolipoprotein E and apolipoprotein A1 gene polymorphisms in the risk for coronary artery disease

Alterations in lipid metabolism and genetic predisposition are major risk factors for coronary artery disease (CAD). Variations in genes involved in lipid metabolism may act synergistically to confer risk or protection against CAD. The objective of the present study was to determine such interactions in variants of apolipoprotein E and apolipoprotein A1 genes. One hundred and forty subjects with clinically confirmed CAD and 100 unrelated normal subjects participated in the study. Multiple regression analysis was used to relate lipid and apolipoprotein profiles with genotypes. Odd ratios were calculated for various combinations of ApoE and ApoA1 genotypes. Prevalence of ApoE 'E4' and ApoA1 'A' and 'T' alleles was significantly higher in patients than controls. Serum apolipoprotein E and apolipoprotein A1 levels were significantly lower in CAD patients than controls. When lipid parameters were related to genotypes, the polymorphisms associated to various markers were in agreement with previous reports. ApoE 2/4 genotype in combination with either ApoA1 heterozygous GA or CT genotype conferred higher risk of CAD. E3 allele in homozygous or heterozygous state in combination with ApoA1+83 CC genotype conferred highest protection (P < 0.05). Thus, it appears that ApoE and ApoA1 gene variants may act synergistically to associate with risk and protection against CAD.

Genetic interactions with diet influence the risk of cardiovascular disease

Single-nucleotide polymorphisms are an integral component of the evolutionary process that over millennia have resulted from the interaction between the environment and the human genome. Relatively recent changes in diet have upset this interaction with respect to the nutritional environment, but nutritional science is beginning to better understand the interaction between genes and diet, with the resulting potential to influence cardiovascular disease risk by dietary modification. Single-nucleotide polymorphisms in several genes have been linked to differential effects in terms of lipid metabolism; however, even a simple model of benefit and risk is difficult to interpret in terms of dietary advice to carriers of the various alleles because of conflicting interactions between different genes. The n-3 family of polyunsaturated fatty acids is underrepresented in our modern diet; much of the benefit of polyunsaturated fatty acids found in studies of various polymorphisms seems to be linked to increased n-3 polyunsaturated fatty acid intake. The nascent science of nutrigenomics faces many challenges; more and better research is needed to clarify the picture, rebut scepticism, and re-invigorate the discussion concerning genetic polymorphism and its interaction with diet.

Association of two apolipoprotein A-I gene MspI polymorphisms with lipid and blood pressure levels

INTRODUCTION

Two MspI polymorphisms in the ApoA-I gene (G-75A and C83T) have been shown to be associated with plasma HDL-cholesterol levels.

METHODS

We used a PCR-based RFLP method to determine the association of these polymorphisms with lipid parameters in 271 non-diabetic, normotriglyceridaemic Chinese subjects, of whom 104 were patients with hypertension, with 10.2% having hypercholesterolaemia and the remainder were controls.

RESULTS

As expected, the hypertensive group had higher blood pressure and indices of obesity, and a more adverse lipid profile. No differences in the ApoA-I G-75A genotype or allele frequency distributions between the controls and patients were identified. However, there was a significantly lower frequency of the CT genotype (p=0.012) and T allele (p=0.011) in the affected subjects with hypercholesterolaemia or hypertension. Similarly, blood pressure and triglyceride levels were significantly lower and HDL-cholesterol levels significantly higher in the subjects with the CT genotype compared to those with the CC genotype (p<0.05). However, the G-75A genotypes did not appear to influence the lipid or blood pressure levels. The -75A allele frequency was higher in our healthy controls than an equivalent Caucasian population (31.1% vs. 18.3%, p<0.001), whereas the 83T allele frequency was similar between the healthy Chinese and Caucasian groups.

CONCLUSION

The 83T allele may be associated with a better lipid profile and blood pressure levels in this group of Chinese subjects.

Association between MspI polymorphism of the APO AI gene and Type 2 diabetes mellitus

AIMS

Genes of the Apo AI/CIII/AIV cluster on chromosome 11 have been related to plasma lipid patterns. The close relationship between carbohydrate metabolism and lipid metabolism warrants investigation of the association between this cluster and Type 2 diabetes mellitus. We therefore examined the possible association between polymorphisms of this cluster and Type 2 diabetes mellitus as part of a study of the prevalence of diabetes and the metabolic syndrome in southern Spain.

METHODS

A total of 1224 persons were selected randomly from the town of Pizarra in the province of Malaga, southern Spain. The sample errors for the prevalence of Type 2 diabetes mellitus and the three polymorphisms studied were all < or = 4%. All subjects underwent phenotyping after an oral glucose tolerance test (75 g) (WHO 1998 criteria) and the XmnI and MspI polymorphisms of Apo AI and the SstI polymorphism of Apo CIII were genotyped.

RESULTS

Those subjects with the mutated AA genotype of the MspI polymorphism (-75 G-->A) of Apo AI had a greater risk of impaired glucose tolerance [odds ratio (OR) = 1.95, CI = 1.02-3.8, P = 0.05], Type 2 diabetes mellitus, both known (OR = 7.38, CI = 1.3-39.7, P = 0.02) and unknown (OR = 3.7, CI = 1.4-9.9, P = 0.009). This risk was independent of age, sex, obesity, triglyceride level, HDL cholesterol and pattern of insulin resistance.

CONCLUSIONS

Pending confirmation in prospective studies, the AA genotype of the MspI polymorphism of the Apo AI gene, within the Apo A-I/C-III/A-IV cluster, seems to be a risk factor for Type 2 diabetes mellitus.

The APOA1/C3/A4/A5 gene cluster, lipid metabolism and cardiovascular disease risk

PURPOSE OF REVIEW

APOA1/C3/A4/A5 are key components modulating lipoprotein metabolism and cardiovascular disease risk. This review examines the evidence regarding linkage disequilibrium and haplotype structure within the A1/C3/A4/A5 cluster, and assesses its association with plasma lipids and cardiovascular disease risk. In addition, we use genomic information from several species to draw inferences about the location of functional variants within this cluster.

RECENT FINDINGS

The close physical distance of these genes and the interrelated functions of these apolipoproteins have encumbered attempts to determine the role of individual variants on lipid metabolism. Therefore, current research aims to define linkage disequilibrium and haplotype structure within this cluster. Functional variants in regulatory regions are most interesting as they are potentially amenable to therapy. Comparative genomics can contribute to the identification of such functional variants.

SUMMARY

Genetic variability at the APOA1/C3/A4/A5 cluster has been examined in relation to lipid metabolism and cardiovascular disease risk. However, the findings are inconsistent. This is partly due to the classic approach of studying single and mostly nonfunctional polymorphisms. Moreover, allelic expression may depend on the concurrent presence of environmental factors. Association studies using haplotypes should increase the power to detect true associations and interactions. We hypothesize that phenotypes observed in association with transcriptional regulatory variants can be readily modified by environmental factors. Therefore, studies focusing on regulatory variants may be more fruitful to locate/define future therapeutic targets.

APOA1 polymorphisms are associated with variations in serum triglyceride concentrations in hypercholesterolemic individuals

Background: Apolipoprotein A-I gene (

Methods:

Results: G–75A polymorphism was associated with differences in serum concentrations of triglyceride and very low-density lipoprotein (VLDL)-cholesterol (p=0.026) in HC men. After atorvastatin treatment, women carrying the

Conclusion: Our data suggest that

Association of two apolipoprotein A-I gene MspI polymorphisms with high density lipoprotein (HDL)-cholesterol levels and indices of obesity in selected healthy Chinese subjects and in patients with early-onset type 2 diabetes

OBJECTIVE

Previous studies have reported associations between two apolipoprotein A-I (apoA-I) gene MspI polymorphisms (G-75A and C83T) and high density lipoprotein (HDL)-cholesterol and/or apoA-I levels, but have not investigated the relationship with obesity.

METHODS

We determined the distribution of these polymorphisms in 482 early-onset (< or = 40 years) Type 2 Chinese diabetics and 167 Chinese selected healthy controls.

RESULTS

The -75A and 83T allele frequencies were similar in the diabetic and healthy subjects. In the healthy control subjects, HDL-cholesterol levels were significantly higher in the AA homozygotes than in the GG/GA carriers (1.74 +/- 0.58 vs. 1.45 +/- 0.58 mmol/l, P<0.001). Furthermore, analyses showed a significant relationship between increasing HDL-cholesterol tertiles and the AA genotype frequency in the selected healthy subjects (3.6, 8.9 and 16.1%, P=0.026). For the C83T polymorphism, healthy male CT carriers had higher HDL-cholesterol levels than CC homozygotes (1.71 +/- 0.57 vs. 1.25 +/- 0.30 mmol/l, P=0.001), but this was not found in females. No relationship between these polymorphisms and lipid levels was found in the diabetics, who had a more adverse lipid profile than the selected controls. In the diabetics, but not the controls, in CT carriers compared to CC homozygotes there were lower levels of body mass index (BMI; 23.8 +/- 3.9 vs. 25.4 +/- 4.7 kg/m2, P=0.048) and waist-to-height ratio (0.49 +/- 0.06 vs. 0.52 +/- 0.07, P=0.023), and this relationship was supported by tertile analysis.

CONCLUSIONS

The -75AA genotype was associated with higher HDL-cholesterol levels in the selected healthy, but not diabetic, subjects. The 83T allele was associated with greater indices of obesity in the diabetic patients, and with higher HDL-cholesterol in heterozygous healthy male subjects.

Polyunsaturated fatty acids modulate the effects of the APOA1 G-A polymorphism on HDL-cholesterol concentrations in a sex-specific manner: the Framingham Study

BACKGROUND

A common G-to-A substitution in the promoter area (-75 base pairs) of the apolipoprotein A-I gene (APOA1) has been described. The A allele was shown to be associated with higher HDL-cholesterol concentrations in some studies but not in others.

OBJECTIVE

We examined whether dietary fat modulates the association between this polymorphism and HDL-cholesterol concentrations.

DESIGN

We studied a population-based sample of 755 men and 822 women from the Framingham Offspring Study.

RESULTS

The frequency of the A allele was 0.165. No significant differences were observed between G/G subjects and carriers of the A allele for any lipid variables. In multivariate linear regression models, HDL-cholesterol concentrations in women were associated with a significant interaction between polyunsaturated fatty acid (PUFA) intake as a continuous variable and APOA1 genotype (P = 0.005). By using 3 categories of PUFA intake, we found a significantly different effect of APOA1 genotype across PUFA categories in women. When PUFA intake was <4% of energy, G/G subjects had approximately 14% higher HDL-cholesterol concentrations than did carriers of the A allele (P < 0.05). Conversely, when PUFA intake was >8%, HDL-cholesterol concentrations in carriers of the A allele were 13% higher than those of G/G subjects (P < 0.05). No significant allelic difference was observed for subjects in the range of PUFA intake of 4-8% of energy. These interactions were not significant in men.

CONCLUSIONS

We found a significant gene-diet interaction associated with the APOA1 G-A polymorphism. In women carriers of the A allele, higher PUFA intakes were associated with higher HDL-cholesterol concentrations, whereas the opposite effect was observed in G/G women.

Variations in the promoter region of the apolipoprotein A-1 gene influence plasma lipoprotein(a) levels in Asian Indian neonates from Singapore

We studied the influence of two DNA polymorphisms (-75 bp G/A and +83 bp C/T) in the promoter region of the apolipoprotein A-1 (apoA1) gene on cord plasma level of lipoprotein(a) [Lp(a)] in 1076 newborns of both genders from the three major ethnic groups in Singapore-Chinese, Malays, and Asian Indians. The frequency of the A: allele at -75 bp in the Indians was significantly lower than the Chinese and Malays. There was no linkage disequilibrium between the two sites studied. Both polymorphic sites were not significantly associated with any lipid factors except for Lp(a) levels in the Asian Indians. The AA and CC homozygotes were significantly associated with lower Lp(a) levels. These associations were specific only to the male Indian neonates. The genetic variations at the -75 and +83 bp explained 6.9% and 7.2%, respectively, of the total variability of plasma Lp(a) levels at birth in the Asian Indians. The Lp(a) levels were also significantly different between composite genotypes in the order GG/TT > GA/CT > GG/CT > GA/CC > GG/CC > AA/CC. The effects of the two polymorphisms seem to be additive as the composite genotypes were able to explain 14% of the Lp(a) variance, equivalent to the sum of the two constituent sites. Our results showed that there is significant ethnic- and gender-specific influence of the apoA1 gene on plasma Lp(a) levels at birth that is inherent and independent of known gene-environment interactions.

Genetic association of five apolipoprotein polymorphisms with serum lipoprotein-lipid levels in African blacks

Genetic studies carried out mainly in European and European-derived populations have shown that common polymorphisms in genes coding for apolipoproteins are significant determinants of serum lipoprotein-lipid levels variation. However, except for a few sporadic studies, the distribution of apolipoprotein polymorphisms and their association with serum lipoprotein-lipid levels have not been evaluated systematically in African or African-derived populations. In this investigation we have studied five apolipoprotein polymorphisms, including APOA1/MspI-75 bp, APOA1/MspI+83 bp, APOC3/PvuII, APOE, and APOH in 786 Africans (493 men, 293 women) from Nigeria. The sample is comprised of Nigerian civil servants consisting of 462 junior staff (less affluent) and 324 senior staff (more affluent) where staff status is a correlate of their socioeconomic status. We first examined genetic associations in the total sample stratified by gender to determine the role of apolipoprotein polymorphisms in affecting serum lipid profile in the general population, and then by staff status to evaluate possible gene-environment interactions. In the total sample, the APOC3/PvuII polymorphism showed significant effect on HDL-cholesterol (P = 0.029) and HDL3-cholesterol (P = 0.009) in women, and the APOE polymorphism was significantly associated with total cholesterol (P = 0.031) and LDL-cholesterol (P = 0.0006) in women. Multiple regression analyses showed that the APOC3/PvuII polymorphism accounts for about 2 and 3% of the variation in HDL-cholesterol and HDL3-cholesterol, respectively, in women; while the APOE polymorphism accounted for about 5 and 6% of the variation in total- and LDL-cholesterol, respectively, in women. Whereas the association of the APOE polymorphism was independent of the staff status, the significant affect of the APOC3/PvuII polymorphism on HDL- and HDL3-cholesterol was confined to senior staff women where it explained about 7% of their variation. We also observed an interaction between staff and the APOH polymorphism in affecting cholesterol levels. The APOH polymorphism showed significant association with total cholesterol (P = 0.010) and LDL-cholesterol (P = 0.016) in senior staff women and explained about 7 and 5% of their phenotypic variations, respectively. These data indicate that gene-environment interaction may play an important role in affecting serum lipid profile in African populations.

Variation at the lipoprotein lipase and apolipoprotein AI-CIII gene loci are associated with fasting lipid and lipoprotein traits in a population sample from Iceland: interaction between genotype, gender, and smoking status

The effects of polymorphisms in the lipoprotein lipase (LPL) gene (HindIII and S447X) and in the apolipoprotein (apo) AI-CIII gene cluster (G75A and C1100T) on levels of fasting plasma triglycerides, apoCIII, high density lipoprotein cholesterol (HDL-C), and apoAI were examined in 315 healthy men and women from Iceland. Non-smoking and smoking men and women were examined separately because of the strong effects of smoking status and gender on lipoproteins. For the LPL gene, there were no significant associations between plasma traits and genotypes of the S447X polymorphism, but the LPL-HindIII polymorphism was associated with significant effects on levels of all traits, with the effect of genotype on triglycerides and apoAI being modulated by smoking status, (genotype x smoking interaction, P < .02). The H- allele was generally associated with slightly lower levels of apoCIII, with a lowering effect on triglycerides only in smokers and with a raising effect on ApoAI in non-smoking and smoking men and in non-smoking women. For the apoCIII C1100T polymorphism, smoking and non-smoking men with one or more T alleles had levels of triglycerides roughly 10% higher than those with only the C allele; in contrast, the women with the T allele had lower levels of triglycerides (15.7% lower in non-smokers, P = .04; gender x genotype interaction, P = .02). In males and females and in smokers and non-smokers, the T allele was associated with levels of apoCIII that were 9-20% higher than those with only the C allele (P = .004 overall). In the non-smoking men, nonlinear additive effects were observed with combinations of genotypes at the LPL and apoAI-CIII loci, with the HDL-C and apoAI raising effect associated with the A75 allele and H- allele seen only in those men with both alleles, and the apoCIII raising effect associated with the H+ and T alleles seen only in those with both alleles. Thus, variations at both of the LPL and apoAI-apoCIII loci influence levels of triglycerides, apoCIII, HDL-C, and apoAI, but these effects are strongly modulated by smoking and are different between men and women. The mechanisms for these interactions between smoking or gender and genes are unknown, but future studies should take such interactions into account.

Segregation analysis of two-locus models regulating apolipoprotein-A1 levels

For quantitative traits associated with risk to complex diseases, such as heart disease, single major locus models are likely to be too simplistic. Currently, researchers have begun to use oligogenic models of inheritance, but the resolving power of these models remains to be determined. As the major apoprotein of high density lipoprotein (HDL), apolipoprotein A1 (apo-A1) is generally accepted as a protective factor for coronary artery disease. Although familial aggregation of apo-A1 levels has been reported, the mode of inheritance of apo-A1 remains ill defined. In the present study, we conducted a segregation analysis comparing a series of one-locus and two-locus univariate models for apo-A1 levels in a sample of 137 families ascertained through probands undergoing elective, diagnostic coronary angiography. A two-locus Mendelian model fit these data significantly better than any one-locus model. The incorporation of the second major locus into the model of inheritance leads to a significant improvement in the fit, and a significant decrease of the residual heritability. The best-fitting model included two loci with a reciprocal pattern of epistasis generating 4 distinct genotypic distributions. Taken together, these two major loci account for 58% of the variance of adjusted apo-A1 levels. This demonstration of a second major locus controlling apo-A1 levels may explain the equivocal results obtained from previous studies. This two-locus model may be more powerful for linkage analysis to map one or both of these quantitative trait loci.

The genetics of serum lipid responsiveness to dietary interventions

CHD is a multifactorial disease that is associated with non-modifiable risk factors, such as age, gender and genetic background, and with modifiable risk factors, including elevated total cholesterol and LDL-cholesterol levels. Lifestyle modification should be the primary treatment for lowering cholesterol values. The modifications recommended include dietary changes, regular aerobic exercise, and normalization of body weight. The recommended dietary changes include restriction in the amount of total fat, saturated fat and cholesterol together with an increase in the consumption of complex carbohydrate and dietary fibre, especially water-soluble fibre. However, nutrition scientists continue to question the value of these universal concepts and the public health benefits of low-fat diets, and an intense debate has been conducted in the literature on whether to focus on reduction of total fat or to aim efforts primarily towards reducing the consumption of saturated and trans fats. Moreover, it is well known that there is a striking variability between subjects in the response of serum cholesterol to diet. Multiple studies have examined the gene-diet interactions in the response of plasma lipid concentrations to changes in dietary fat and/or cholesterol. These studies have focused on candidate genes known to play key roles in lipoprotein metabolism. Among the gene loci examined, APOE has been the most studied, and the current evidence suggests that this locus might be responsible for some of the inter-individual variability in dietary response. Other loci, including APOA4, APOA1, APOB, APOC3, LPL and CETP have also been found to account for some of the variability in the fasting and fed states.

The A/G polymorphism in the -78 position of the apolipoprotein A-I promoter does not have a direct effect on transcriptional efficiency

A promoter polymorphism A/G at position 78 bp upstream of the transcription initiation site characterizes the human apolipoprotein A-I gene. Some studies correlated the higher Apo A-I levels or increased Apo A-I transcription efficiency with the A allele, while other studies did not confirm these results. We have investigated the in vitro effects of this transition on the transcriptional efficiency of ApoAI gene by creating two sets of identical constructs with the whole Apo A-I promoter, carrying the A or the G, linked to the complete ApoAI gene. The relative activity of the two promoter alleles was determined through a quantitative RT-PCR system after transient tranfections of human HepG2 cell line in basal state and after stimulation with retinoic acid or 17beta-estradiol. Our results exclude differences in promoter activity linked to the A or G promoter alleles either in basal or in stimulated conditions. The data suggest that the A/G polymorphism does not directly affect the transcriptional efficiency of ApoAI gene, although it may be in linkage disequilibrium with other regulatory sequences and the combination of these elements may explain the contradictory results of the ApoAI gene expression.

Human apolipoprotein A-I gene promoter mutation influences plasma low density lipoprotein cholesterol response to dietary fat saturation

Previous studies have shown that the A to G transition occurring at position -75 bp upstream of the transcriptional start site in the human apolipoprotein A-I gene may affect plasma high density lipoprotein cholesterol (HDL-C) levels and low density lipoprotein cholesterol (LDL-C) response to changes in amount of dietary fat. We have examined the response to dietary fat saturation as a function of this mutation in 50 men and women. Subjects were first fed a saturated (SAT) fat diet (35% fat, 17% SAT) for 28 days, followed by a diet rich in monounsaturated fatty (MUFA) acids (35% fat, 22% MUFA) for 35 days and a diet rich in polyunsaturated (PUFA) fat (35% fat, 13% PUFA) for 35 days. All meals were prepared and consumed at the study sites. Lipoproteins were measured at the end of each diet period. The allele frequency for the A allele was 0.13. Subjects carrying the A allele had higher plasma cholesterol, LDL-C and triglyceride levels than those homozygotes for the G allele. As compared to the SAT diet, a PUFA diet induced significantly greater plasma total (P = 0.003) and LDL-C decreases (P = 0.001) in G/A women (-1.62 and -1.32 mmol/l, respectively) than in G/G subjects (-0.87 and -0.74 mmol/l for plasma and LDL-C, respectively). Multiple regression analysis demonstrated that in women, the variability in LDL-C response from a diet rich in SAT fat to a diet rich in PUFA was primarily due to LDL-C levels (during the SAT phase), accounting for 55.1% of the variance, waist to hip ratio (W/H; 11.4%) and the G/A polymorphism (10%). Whereas in men the major determinant of this response was smoking (21.4%). In conclusion, the G/A polymorphism appears to have a small but significant effect on plasma LDL-C responsiveness to changes in dietary fat saturation specially in women.

Association of apolipoprotein genetic polymorphisms with plasma cholesterol in a Japanese rural population. The Shibata Study

The association between apolipoprotein (apo) genetic polymorphisms and lipid phenotypes remains to be determined because such studies have reported contradictory results. We have measured plasma total cholesterol (TC) and HDL cholesterol (HDL-C) in a cross-sectional sample of 1328 (462 men and 866 women) Japanese (aged 40 to 80 years) and analyzed their DNA for the following genotypes: apoA1-C3 Msp I and Sst I sites; apoB signal peptide insertion/deletion, Xba I site and 3' variable number of tandem repeats (VNTR); and apoE. Using multivariate analyses (ANOVA) we found that (1) the polymorphisms of apoA1-C3 and apoB genes are not significantly associated with TC or HDL-C and (2) the polymorphism of the apoE gene is significantly related with TC and the TC:HDL-C ratio. The epsilon 2 carriers have lower levels of TC and a lower TC:HDL-C ratio, epsilon 3 carriers have intermediate levels, and epsilon 4 carriers have higher levels. These findings held whether sexes were analyzed separately or together. Although an opposite trend in HDL-C levels was observed, it did not reach the level of statistical significance. Multiple regression analyses have shown that apoE polymorphism accounts for about 2.3% of the variation in TC and TC:HDL-C ratio irrespective of sex. When the subjects are divided into two groups according to their age (< or = 59 and > or = 60 years old), the effect of apoE alleles on serum cholesterols appears to be diluted in the younger age group whereas it appears to be accentuated in the older group for both sexes. Our findings suggest that among the apo genetic polymorphisms examined, the apoE gene may be considered as a possible candidate for the "high-risk" strategy of atherosclerosis prevention in the Japanese population.

Genetic polymorphism of paraoxonase and the risk of coronary heart disease

Recent studies have implicated paraoxonase, an HDL-associated enzyme, in providing protection against LDL oxidation, thus affecting the risk of coronary heart disease (CHD) in the general population. In this study, we evaluated the distribution of a biallelic PON polymorphism at codon 192 (A and B alleles) and its relationship with plasma lipids and CHD in two racial groups comprising Asian Indians and Chinese from Singapore. The frequency of the B allele was significantly higher in Chinese control subjects than in Indian control subjects (0.58 versus 0.33; P < .0001). With the exception of a marginal effect on apolipoprotein A-I levels in Indians, no other significant association was observed between the PON polymorphism and quantitative lipid traits in either racial group. However, there was a race-specific association of the B allele with CHD in Indians but not in Chinese. The Indian CHD patients had a significantly higher frequency of the B allele than control subjects (.43 versus .33; P = .014). The age- and sex-adjusted odds ratio for developing CHD with the B allele (BB+AB genotypes) was 2.01 (95% CI, 1.17 to 3.45; P = .011) compared with the A allele (AA genotype). When the Indian patients were stratified into subgroups, the association remained significant in nondiabetic patients (odds ratio, 2.29; P = .008), and it became stronger in patients with myocardial infarction (odds ratio, 2.94; P = .004) than in patients without myocardial infarction (odds ratio, 1.11; P = .76). These data indicate that a common polymorphism in the PON gene is an independent risk factor for CHD in populations with white ancestry.

Response to dietary fat and cholesterol and genetic polymorphisms

1. We examined common polymorphisms in the genes encoding the LDL receptor, lipoprotein lipase, apoAI, apoB, apoAIV and cholesteryl ester transfer protein and related them to changes in LDL and HDL cholesterol after high fat/high cholesterol diets. 2. The only significant association was seen with the apoIV polymorphism, which leads to a structural change in the protein. The response to fat and cholesterol in subjects with at least one apoAIV 2 allele was only 30% of that seen in subjects with the common apoIV 1 allele (P < 0.01), accounting for 6-7% of the variance in response. This confirms the results of two previous studies in which dietary cholesterol intake was changed. 3. No association were seen with polymorphisms of the other five genes examined.

Small genetic effects in complex diseases: a review of regulatory sequence variants in dyslipoproteinemia and atherosclerosis

OBJECTIVE

Most reported mutations that affect lipoprotein metabolism are found within the coding sequences of genes. Recently, a few mutations that occur within promoter sequences have been detected. These promoter sequence variants are the topic of the present review.

METHODS

Some of these variants are fairly common genomic variants in the promoter regions for candidate genes in lipoprotein metabolism, such as APOA1, APOC3, LPA, and LPL. It is possible that such regulatory sequence variants can result in chronic, modestly altered levels of expression of qualitatively normal gene products. This might have a cumulative effect on quantitative phenotypes, such as plasma lipoprotein concentrations, over the long term. Such an effect might not be detected by existing clinical, biochemical, and/or physiological assays.

RESULTS

At present, the most consistent evidence from several lines of experiments indicates that genomic variation in the APOC3 promoter creates slightly elevated plasma triglyceride concentrations within the physiologic range. This altered expression appears to predispose to hypertriglyceridemia in the presence of secondary factors. Genetic variants that produce small effects on promoter function might thus be one component of the predisposition to complex diseases.

CONCLUSION

The aggregate of many small effects may create or contribute to a background of susceptibility that, under appropriate conditions, leads to development of frank dyslipidemia and atherosclerosis.

The genetic basis of atherosclerosis

Atherogenesis is a complex process that involves the contributions of several pathophysiological sub-systems. The dissection of the genetic component of atherosclerosis has become possible using current molecular technologies and analytical methods. Genetic factors are considered to determine the limits under which atherosclerosis develops and environmental factors are considered to position an individual's risk within these limits. Atherosclerosis proceeds through a well-characterized series of pathological stages that involve key cell types and the expression of particular gene products. Reductionist experimental models have helped to produce a list of several hundred candidate genes for the study of the genetic component of atherosclerosis. Within certain families and isolated communities the effect of a single candidate gene upon atherosclerosis susceptibility may be profound, as in the case of mutations in the gene encoding the low-density lipoprotein receptor, which produce familial hypercholesterolemia and premature atherosclerosis. However, particular candidate genes have small effects on atherosclerosis or to one of its intermediate phenotypes, in whole populations. In addition, pleiotropy and epistasis can confound the identification of the genetic component of atherosclerosis. Despite these limitations, it might still be possible to use genetic information clinically in order to classify individuals who are susceptible to atherosclerosis, especially if as yet undiscovered candidate genes are found to be important determinants of disease. However, it will be impossible to predict the onset of a clinical manifestation of atherosclerosis in a particular person. This is due to the confounding influence of other forces, such as variations in interindividual environmental landscape, non-linear interactions between genes and environment, and even the possible influence of biological chaos.

Haplotype analysis of two APOA1/MspI polymorphisms in relation to plasma levels of apo A-I and HDL-cholesterol

A common MspI polymorphism (G/A) in the promoter region of the APOA1 gene (-75 bp) has been shown to be associated with plasma apo A-I and HDL-C variation in several, but not all, studies. Recently another MspI polymorphic site (+/-) in the 5'region of APOA1 (+83 bp) has been identified which may also be relevant to HDL metabolism. This study was undertaken to elucidate the individual and combined effects of these two polymorphisms on plasma apo A-I and HDL-C levels in a cohort of 534 normoglycemic US Whites from the San Luis Valley, Colorado. Both polymorphisms were in strong linkage disequilibrium (P < 0.005); of the expected four haplotypes (G+, G-, A+, A-) the A- was not observed in this sample. Single site RFLP analysis revealed an independent and significant effect associated with each polymorphism on plasma apo A-I variation but not on HDL-C variation. Further analyses showed that the genotype effects of both polymorphisms were confined to non-smokers only. Haplotype analysis, combining both RFLPs, was more informative as this explained almost twice the amount of phenotypic variation in plasma apo A-I compared to single RFLP analysis in non-smokers. Compared to the most common haplotype (G+), the A+ and G- haplotypes were associated with increased plasma apo A-I levels by 6.7 mg/dl and 22.0 mg/dl, respectively in non-smoking men, and by 4.6 mg/dl and 15.1 mg/dl in non-smoking women, respectively. These data indicate that haplotype analysis in this region may be important to elucidate the functional significance of the APOA1 gene in HDL metabolism.