EcoRI-RFLP of the Apo B gene: a study in a sample group from south Italy

Apolipoprotein B Gene Polymorphisms and Dyslipidemia in HIV Infected Adult Zimbabweans

Background:

Dyslipidemia does not occur in all HIV-infected or antiretroviral therapy-experienced patients suggesting role of host genetic factors but there is paucity of data on association between dyslipidemia and gene polymorphisms in Zimbabwe.

Objective:

To determine association of lipoprotein levels and apolipoprotein B polymorphisms in HIV-infected adults.

Method:

Demographic data were collected from 103 consenting patients; lipoprotein levels were determined and blood samples were successfully genotyped for both apolipoprotein B 2488C>T Xba1 and apolipoprotein B 4154G>A p.Gln4154Lys EcoR1 polymorphisms by real time polymerase chain reaction.

Results:

Mean age of genotyped patients was 40.3 ± 10.1 years, 68% were female; prevalence of dyslipidemia was 67.4%. Of 103 samples genotyped for apolipoprotein B Xba1 polymorphism, 76 (74%) were homozygous C/C, 24 (23%) were heterozygous C/T and only three (3%) were homozygous T/T. Apolipoprotein B EcoR1 polymorphism showed little variability, one participant had rare genotype A/A, 68.3% had wild type genotype G/G.

Conclusion:

Observed frequencies of apolipoprotein B XbaI and EcoRI polymorphisms matched other African studies. In spite of low numbers of rare variants, there was positive association between both total cholestrol and high density lipoprotein with ECoR1 wild type G/G genotype, suggesting that ECoRI 4154 G allele could be more protective against coronary heart disease than EcoR1 4154 A allele. There is need for further research at population level to confirm whether apolipoprotein B ECoR1 genotyping is useful for predicting risk of dyslipidemia in HIV patients in our setting.

The APOB gene polymorphism in the pathogenesis of gallstone disease in pre- and postmenopausal women

Aim of the study

The decrease in estrogen levels in the postmenopausal period changes the lipid profile by the expression of hepatic genes related to metabolism of cholesterol and bile acid synthesis that could be important in the pathogenesis of cholelithiasis. The aim of the study was to determine the APOB gene 7673C>T and 12669G>A polymorphisms in the pathogenesis of gallstones and analysis of the composition of gallstones in pre- and postmenopausal women.

Material and methods

The study group consisted of 94 women qualified to the laparoscopic cholecystectomy while the control group consisted of 81 women in whom gallstones and other changes in the bile ducts were excluded. Gallstones composition analysis was performed using commercially available assays. The prevalence of the APOB gene polymorphisms was determined using the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP).

Results

When assessing the composition of gallstones in pre- and postmenopausal women, we observed differences in the studied parameters. Analysis of genetic variants of APOB gene 7673C>T and 12669G>A polymorphisms showed no significant statistical differences between studied groups and controls.

Conclusions

Analysis of 7673C>T and 12669G>A polymorphisms showed no relationship between specific genetic variants and the risk of gallstones in pre- and postmenopausal women, pointing to the fact that the investigated polymorphisms are not relevant as prognostic factors in gallstone disease in the Caucasian population. Because of the possible contribution of a variety of factors in gallstones pathogenesis the studies are required to take account of additional environmental factors, what may indicate different occurrence between investigated polymorphisms, gallstone disease development and gallstones composition in Caucasians.

Genetic association of APOB polymorphisms with variation in serum lipid profile among the Kuwait population

BACKGROUND

Several studies have identified APOB as a candidate gene predisposing individuals to dyslipidemia. Polymorphisms including the signal peptide (rs11279109), codon 2488 XbaI (rs1042031), codon 3611 MspI (rs693), codon 4154 EcoRI (rs1801701) and the 3' variable number of tandem repeats have been reported to be associated with dyslipidemia in several populations. With limited studies on Arabs, this study aimed to investigate the genetic association of APOB polymorphisms and assess the potential influence of minor and rare alleles on serum lipid levels in the Kuwaiti population.

METHODS

A total of 795 Kuwaiti subjects, documented with phenotypic data and fasting serum lipid levels, were genotyped for the five polymorphisms using PCR, PCR-RFLP and gene fragment analysis. Genotype and allele association with variation in serum lipid levels as well as haplotypes were analyzed using chi-square test, univariate and logistic regression analysis.

RESULTS

Analysis of the genotype and allele frequencies distribution revealed a significant positive association between the APOB signal peptide and 3611 MspI polymorphisms with increased levels of triglycerides (statistical power of 80%). Haplotype analysis further supported the findings by showing that carriers of haplotypes (IX-M-E+M) had significantly lower mean (SD) TG levels (0.86 ± 0.07) as compared to non-carriers (1.01 ± 0.02). Significance was also observed with regards to positive family history of hypercholesterolemia.

CONCLUSION

The results imply a "protective role" for two alleles (rs11279109 and rs1801701) in which logistic regression analysis showed a significant half-fold decrease in the risk for heterozygotes of rs11279109 and an 8.8 fold decrease in the risk for homozygous M-M- of rs1801701 of having lower TG levels (<1.70 mmol/L) in individuals. This suggests that genetic interaction between various polymorphisms at different gene loci act in linkage disequilibrium to affect serum TG levels. Apo B genotyping may be a useful adjunct for the identification of individuals at risk of developing dyslipidemia in order to provide them with lifestyle modifications and/or pharmacological intervention to mitigate the effects of gene interaction and environmental influence.

Polymorphism of the apolipoprotein B gene and association with plasma lipid and lipoprotein levels in the Mongolian Buryat

Allele frequencies at six RFLP sites (Ins/Del, ApaLI, AluI, XbaI, MspI, and EcoRI) of the apolipoprotein B gene (APOB) and the relationship of genotypes with plasma lipid and lipoprotein levels in the Mongolian Buryat were investigated. Common alleles at these sites in 110 Buryat subjects were I, G, A-, X-, M+, and E+; the frequencies of 0.809-0.991 differed strikingly from those of a few Asians and most Europeans. Five unambiguous haplotypes of all sites were revealed at 74%; haplotype IGA-X-M+E+ (000000) was the most frequent (67%), followed by IGA+X-M+E+ (001000) (19%). The frequency constitution differed significantly from the Chinese, Malaysians, and Caucasians but resembled the Indians. No APOB polymorphisms were associated with cholesterol levels (total, HDL and LDL). Significant associations of genotypes were shown with the triglyceride level only at the AluI and XbaI sites. The lipid level of A-A+ females or X-X+ males was higher than that of A-A- females or X-X- males, respectively.

Apolipoprotein B (APOB) Gene Polymorphism in Patients with Gallbladder Disease

Cholelithiasis is one of the most prevalent gastroenterological diseases, precipitated mainly by environmental factors. However, twin studies provided strong evidence for a role of genetic factors in the disease pathogenesis. An association between plasma lipoprotein levels and gallstone disease (GSD) was presented. Apolipoprotein B is an essential structural component of triglyceride-rich lipoprotein particles and plays an important role in the maintenance of cholesterol homeostasis in mammals. Various studies have shown a relationship between APOB gene polymorphisms and lipoprotein levels, but only few investigated a potential association between APOB polymorphism and GSD, giving contrary results. In the current study, an association between common polymorphisms in APOB gene (T2488T and E4154K) and cholesterol gallstone disease was examined. Two hundred and forty patients of Caucasian origin suffering from cholelithiasis, as well as 217 healthy individuals, were included in the study. Patients were genotyped for two single nucleotide polymorphisms (SNPs) in APOB gene: 2488C>T (XbaI), and 4154G>A (EcoRI) using PCR-RLFP method. The resulting analysis has shown that polymorphic loci in positions 2488 and 4154 in APOB gene are in full linkage in a Polish population and form only three haplotypes: 2488C-4154G, 2488T-4154G and 2488C-4154A. Frequency and distribution of 2488C>T alleles did not differ significantly between patients and controls. The 4154G allele has been found to be associated with GSD (p=0.001). A risk of gallstone formation was reduced in 4154AA homozygotes (OR=0.25, p=0.009) and heterozygous individuals (OR=0.63, p=0.03) as compared to 4154GG homozygotes. Additionally, 2488C-4154A haplotype was identified as a protective factor against GSD (p=0.04). Our results suggest that SNPs in APOB, potentially considered as one of lith genes as well as certain haplotypes, may be risk factors for GSD.

Exploration of multilocus effects in a highly polymorphic gene, the apolipoprotein (APOB) gene, in relation to plasma apoB levels

A detailed exploration of all the polymorphisms in candidate genes is required to better characterize the relationship between gene variability and complex traits. We propose a novel strategy for investigating the association between a highly polymorphic gene and a phenotype, by combining a multilocus genotype analysis and an haplotype analysis. For the multilocus genotype analysis, a data mining tool--termed DICE (Detection of Informative Combined Effects)--was developed to identify the best subset of polymorphisms that are associated--individually or in combination--with the phenotype. For the haplotype analysis, we used our recently developed method of haplotype-phenotype association to determine the most informative and parsimonious haplotype model fitting the data. We illustrate this strategy by investigating the association between twelve polymorphisms of the APOB gene and plasma apoB levels in 1442 European subjects. After exploring all main effects and interactions between polymorphisms, DICE identified the N4311S polymorphism as the most informative polymorphism in relation to apoB levels. Haplotype analysis led to the same conclusion. Additionally, DICE identified the E4154K (EcoRI) and the T2488T (XbaI) polymorphisms as potentially interesting. This selection was not modified by inclusion of the common APOE polymorphism in the analysis.

The effect of six polymorphisms in the Apolipoprotein B gene on parameters of lipid metabolism in a Danish population

Lipoproteins are vehicles for the distribution of plasma lipids and polymorphisms in the genes for apolipoproteins could influence the amount of lipid in plasma. We examined the effect of six single nucleotide polymorphisms in codons 71, 591, 2488, 2712, 3611, and 4154 of the apolipoprotein B gene on fasting levels of triglyceride, VLDL-, LDL-, HDL- and total cholesterol and on body mass index (BMI) in a cohort of 2656 Danes aged 40-70 years using a linear model correcting for the effects of gender, age, BMI, smoking, alcohol consumption and physical activity. The codon 2488 polymorphism was the most influential of the tested polymorphisms, significantly influencing triglyceride (P = 0.002), LDL-cholesterol (P < or = 0.0004), VLDL-cholesterol (P = 0.006) and total cholesterol (P = 0.0001). The codon 2712 polymorphism had an impact on triglyceride (P = 0.007) and VLDL-cholesterol (P = 0.001), while the codon 71 polymorphism influenced LDL- and total cholesterol (P = 0.04 and P = 0.02, respectively). An interaction between smoking and codon 591 (P = 0.03) and smoking and codon 3611 (P = 0.02) on BMI was observed, as well as modest interactions between codon 3611 and codons 2488 and 2712 on lipid parameters. All polymorphisms were in close linkage disequilibrium. The population was not in Hardy-Weinberg equilibrium in four of the six polymorphisms but the lack of equilibrium was restricted mainly to the 60-year olds.

Polymorphism of the apolipoprotein B gene and blood lipid concentrations in Japanese and Caucasian population samples

To examine whether a racial difference in apolipoprotein B (Apo B) gene polymorphism between Japanese and American Caucasians corresponds with the lower blood cholesterol concentrations in Japanese than in Americans, we examined the EcoRI polymorphism of the Apo B gene for 271 nonsmoking men and women aged 47-69 years in two population-based samples: rural Japanese living in Akita and Caucasians living in Minneapolis-St. Paul, Minnesota, USA. Mean values of serum cholesterol concentrations were significantly lower in Japanese than in Caucasians for both men and women (difference = 25-26 mg/dl). An allele-specific polymerase chain reaction was conducted to examine the Eco RI cutting site at the 12669 cDNA position of the Apo B gene. The allele R2 (absence of the cutting site) has been associated with lower cholesterol concentrations in two previous studies. The frequency of the R2 allele was 6% for Japanese and 17% for Caucasians (P < 0.001), and this race difference in allele frequency was identical for men and women. After controlling for age, body mass index, alcohol intake, and for women, menopausal status and hormone replacement therapy, the adjusted mean (SE) cholesterol level among Japanese was 204 (3) mg/dl for genotype R1R1 and 185 (7) mg/dl for genotype R1R2 or R2R2 combined (P = 0.01). The respective mean values among Caucasians were 224(5) mg/dl and 232(7) mg/dl (P = 0.36). The polymorphism had a similar effect on total cholesterol concentrations for both men and women. The observed lower prevalence of the R2 allele in Japanese than in Caucasians indicates that this variation in the Apo B gene does not explain the racial difference in blood cholesterol concentrations.

Apolipoprotein B gene DNA polymorphisms (EcoRI and MspI) and serum lipid levels in the Serbian healthy population: interaction of rare alleles and smoking and cholesterol levels

The frequency of restriction fragment length polymorphisms (RFLPs) of the apolipoprotein B (apo B) gene, detected by EcoRI and MspI, and their influence on serum lipids were studied in a total of 239 healthy subjects from the Belgrade area. The influence of interaction between different genotypes and smoking was also studied. The relative frequency of both rare R2 and M2 alleles (lacking the cutting site) was similar to that reported in other groups of Caucasians (0.16 and 0.11, respectively). No association was observed between the apo B genotypes and serum lipid levels adjusted for age, body mass index, and blood pressure either in the whole sample or in either women or men. When smokers and non-smokers were considered separately, smoking had a significant impact on total cholesterol variability in all individuals with genotype M1M2 and high density lipoprotein (HDL) cholesterol variability in women with genotype R1R2. The presence of the rare alleles of these two polymorphisms in smokers was associated with lower lipid levels in the whole sample and in both women and men analyzed separately, except for an increase of HDL cholesterol level in male smokers, heterozygous for EcoRI polymorphism (R1R2).

Phenotypic expression and frequency of familial defective apolipoprotein B-100 in Belgian hypercholesterolemics

DNA screening for apolipoprotein (apo) B mutations causing familial defective apolipoprotein B-100 (FDB) was performed in 87 hyperlipidemic Belgian individuals using heteroduplex analysis. Eighteen FDB heterozygotes from 5 unrelated families were identified. Three of the index cases reported an early family history of premature coronary heart disease (CHD). The frequency of the apo B3500 mutation was 8% in Belgians with type IIa hyperlipidemia, indicating that the prevalence of FDB may be as high as 1 in 250 in the general Belgian population. Plasma lipid levels of the patients identified in the present study are similar to those previously reported for FDB heterozygotes. We compared these data with results obtained in a genotype/phenotype correlation study of heterozygous familial hyper-cholesterolemia (FH) in the Afrikaner population of South Africa. Plasma cholesterol levels in FDB heterozygotes were similar to those reported for FH heterozygotes with defective receptors (Asp206-->Glu, approximately 20% normal receptor activity), but significantly lower than in FH heterozygotes with a mutant protein which virtually lacks receptor activity (Val408-->Met, < 2% normal receptor activity). FDB appears to be a significant genetic cause of hypercholesterolemia in Belgium.

Influence of polymorphisms for apolipoprotein B (ins/del, XbaI, EcoRI) and apolipoprotein E on serum lipids and apolipoproteins in a Javanese population

A total of 231 healthy subjects from a central Javanese population were investigated for the distribution of three apolipoprotein B (apo B) polymorphisms (ins/del, XbaI, and EcoRI), as well as apolipoprotein E (apo E) polymorphism in relation to serum lipid and apolipoprotein concentrations. The frequencies of the rarer alleles (del, 0.09; X+, 0.1; and R-, 0.06) were lower than have been found for some Asian and European populations. Distribution of genotypes was in Hardy-Weinburg equilibrium for all the polymorphisms. A linkage disequilibrium was observed only between the ins/del and XbaI site polymorphisms of apo B (chi 2(4)) = 25.3; P < 0.001) consistent with that observed in some other population studies. No polymorphism of the apo B gene had an association with serum lipid or apolipoprotein concentrations in this population except for XbaI, which appeared to be associated with serum TG (as the log transform: R2 = 8.3; F = 4.8; P < 0.01). The apo E4 allele was found to be associated with significantly higher serum total cholesterol (TC) and low-density lipoprotein cholesterol (LDLC). Apo E polymorphism explained 5.9% of the sample variance of serum LDLC (F = 5.4; P < 0.01).