Intestinal transcription and synthesis of apolipoprotein AI is regulated by five natural polymorphisms upstream of the apolipoprotein CIII gene

Elevated interleukin-10: a new cause of dyslipidemia leading to severe HDL deficiency

BACKGROUND

Low high-density lipoprotein cholesterol (HDL-C) is a risk factor for coronary artery disease. Investigating mechanisms underlying acquired severe HDL deficiency in noncritically ill patients ("disappearing HDL syndrome") could provide new insights into HDL metabolism.

OBJECTIVE

To determine the cause of low HDL-C in patients with severe acquired HDL deficiency.

METHODS AND RESULTS

Patients with intravascular large B-cell lymphoma (n = 2), diffuse large B-cell lymphoma (n = 1), and autoimmune lymphoproliferative syndrome (n = 1) presenting with markedly decreased HDL-C, low low-density lipoprotein cholesterol (LDL-C), and elevated triglycerides were identified. The abnormal lipoprotein profile returned to normal after therapy in all 4 patients. All patients were found to have markedly elevated serum interleukin-10 (IL-10) levels that also normalized after therapy. In a cohort of autoimmune lymphoproliferative syndrome patients (n = 93), IL-10 showed a strong inverse correlation with HDL-C (R(2) = 0.3720, P < .0001). A direct causal role for increased serum IL-10 in inducing the observed changes in lipoproteins was established in a randomized, placebo-controlled clinical trial of recombinant human IL-10 in psoriatic arthritis patients (n = 18). Within a week of initiating subcutaneous recombinant human IL-10 injections, HDL-C precipitously decreased to near-undetectable levels. LDL-C also decreased by more than 50% (P < .0001) and triglycerides increased by approximately 2-fold (P < .005). All values returned to baseline after discontinuing IL-10 therapy.

CONCLUSION

Increased IL-10 causes severe HDL-C deficiency, low LDL-C, and elevated triglycerides. IL-10 is thus a potent modulator of lipoprotein levels, a potential new biomarker for B-cell disorders, and a novel cause of disappearing HDL syndrome.

Long-range regulatory polymorphisms affecting a GABA receptor constitute a quantitative trait locus (QTL) for social behavior in Caenorhabditis elegans

Aggregation is a social behavior that varies between and within species, providing a model to study the genetic basis of behavioral diversity. In the nematode Caenorhabditis elegans, aggregation is regulated by environmental context and by two neuromodulatory pathways, one dependent on the neuropeptide receptor NPR-1 and one dependent on the TGF-β family protein DAF-7. To gain further insight into the genetic regulation of aggregation, we characterize natural variation underlying behavioral differences between two wild-type C. elegans strains, N2 and CB4856. Using quantitative genetic techniques, including a survey of chromosome substitution strains and QTL analysis of recombinant inbred lines, we identify three new QTLs affecting aggregation in addition to the two known N2 mutations in npr-1 and glb-5. Fine-mapping with near-isogenic lines localized one QTL, accounting for 5%–8% of the behavioral variance between N2 and CB4856, 3′ to the transcript of the GABA neurotransmitter receptor gene exp-1. Quantitative complementation tests demonstrated that this QTL affects exp-1, identifying exp-1 and GABA signaling as new regulators of aggregation. exp-1 interacts genetically with the daf-7 TGF-β pathway, which integrates food availability and population density, and exp-1 mutations affect the level of daf-7 expression. Our results add to growing evidence that genetic variation affecting neurotransmitter receptor genes is a source of natural behavioral variation.

In both animals and humans, normal individuals can behave differently in the same environment. Natural variation in behavior is partly due to genetic differences between individuals and partly due to experience. Mapping studies have demonstrated that the genetic component of natural behavioral variation is complex, with many genes that each contribute a small amount to the observed behavior. This complexity has made it difficult to identify the causative genes for individual differences. Here we use the nematode worm C. elegans to dissect a social behavioral trait, the propensity to aggregate with other animals in the presence of food. We find that the behavioral differences between two wild-type worm strains result from at least five genetic differences between the strains, two of which were previously known. One of the three new loci affects a receptor for the neurotransmitter GABA, which regulates excitability in the brain. In the context of previous work, we suggest that a significant number of genes that generate behavioral variation encode neurotransmitter receptors. This analysis in a model animal may help guide discoveries of the genetic variants that affect common human behavioral traits by suggesting classes of genes to examine closely.

Association between the -455T>C promoter polymorphism of the APOC3 gene and the metabolic syndrome in a multi-ethnic sample

Background

Common polymorphisms in the promoter of the APOC3 gene have been associated with hypertriglyceridemia and may impact on phenotypic expression of the metabolic syndrome (MetS). The rs7566605 marker, located near the INSIG2 gene, has been found to be associated with obesity, making it also a potential genetic determinant for MetS. The objective of this study is to examine the APOC3 -455T>C and the INSIG2 rs7566605 polymorphisms as potential genetic determinants for MetS in a multi-ethnic sample.

Methods

Subjects were genotyped for both the APOC3 -455T>C and INSIG2 rs7566605 polymorphisms, and classified for the presence or absence of MetS (NCEP ATP III and IDF definitions). The total study population included 2675 subjects (≥18 years of age) from six different geographical ancestries.

Results

For the overall study population, the prevalence of MetS was 22.6% (NCEP ATP III definition). Carriers of ≥1 copy of APOC3 -455C were more likely to have MetS (NCEP ATP III definition) than noncarriers (carrier odds ratio 1.73, 95% CI 1.40 to 2.14, adjusting for age and study group). The basis of the association was related not only to a higher proportion of -455C carriers meeting the triglyceride and high-density lipoprotein cholesterol criteria, but also the blood pressure criteria compared with wild-type homozygotes. Plasma apo C-III concentrations were not associated with APOC3 -455T>C genotype. The INSIG2 rs7566605 polymorphism was not associated with MetS or measures of obesity.

Conclusion

Meta-analysis of the sample of multiple geographic ancestries indicated that the functional -455T>C promoter polymorphism in APOC3 was associated with an approximately 2-fold increased risk of MetS, whereas the INSIG2 rs7566605 polymorphism was not associated with MetS.

Apolipoprotein AI-CIII-AIV gene cluster polymorphisms in relation to cholesterol gallstone

OBJECTIVE

To investigate the frequency of variants at Xmn I, Msp I sites of apolipoprotein (Apo), A I-CIII-AIV gene cluster, and its relation to cholesterol gallstones in Chinese patients.

METHODS

Restriction fragment length polymorphisms (RFLP) at Xmn I, Msp I sites of ApoAI-CIII-AIV gene cluster were studied using a polymerase chain reaction (PCR) in 161 patients with cholesterol gallstones and 94 healthy subjects from a Chinese population in Sichuan Province.

RESULTS

In both the cholesterol gallstone group and the healthy control group, X1 and M1 alleles were the major alleles and homozygous X1X1 and M1M1 genotypes were the most frequent. However, the frequency of X2 allele mutation in female patients of the cholesterol gallstones group was significantly higher than that in women in the healthy control group (P<0.05), but no difference was found in the frequency of M2 alleles mutation (P>0.05).

CONCLUSION

The data showed that Xmn I RFLP of ApoAI-CIII-AIV gene cluster is associated to some extent with cholesterol gallstones in female Chinese patients.

Associations among race/ethnicity, ApoC-III genotypes, and lipids in HIV-1-infected individuals on antiretroviral therapy

BACKGROUND

Protease inhibitors (PIs) are associated with hypertriglyceridemia and atherogenic dyslipidemia. Identifying HIV-1-infected individuals who are at increased risk of PI-related dyslipidemia will facilitate therapeutic choices that maintain viral suppression while reducing risk of atherosclerotic diseases. Apolipoprotein C-III (apoC-III) gene variants, which vary by race/ethnicity, have been associated with a lipid profile that resembles PI-induced dyslipidemia. However, the association of race/ethnicity, or candidate gene effects across race/ethnicity, with plasma lipid levels in HIV-1-infected individuals, has not been reported.

METHODS AND FINDINGS

A cross-sectional analysis of race/ethnicity, apoC-III/apoA-I genotypes, and PI exposure on plasma lipids was performed in AIDS Clinical Trial Group studies (n = 626). Race/ethnicity was a highly significant predictor of plasma lipids in fully adjusted models. Furthermore, in stratified analyses, the effect of PI exposure appeared to differ across race/ethnicity. Black/non-Hispanic, compared with White/non-Hispanics and Hispanics, had lower plasma triglyceride (TG) levels overall, but the greatest increase in TG levels when exposed to PIs. In Hispanics, current PI antiretroviral therapy (ART) exposure was associated with a significantly smaller increase in TGs among patients with variant alleles at apoC-III-482, -455, and Intron 1, or at a composite apoC-III genotype, compared with patients with the wild-type genotypes.

CONCLUSIONS

In the first pharmacogenetic study of its kind in HIV-1 disease, we found race/ethnic-specific differences in plasma lipid levels on ART, as well as differences in the influence of the apoC-III gene on the development of PI-related hypertriglyceridemia. Given the multi-ethnic distribution of HIV-1 infection, our findings underscore the need for future studies of metabolic and cardiovascular complications of ART that specifically account for racial/ethnic heterogeneity, particularly when assessing candidate gene effects.

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.

Effect of glucosamine on apolipoprotein AI mRNA stabilization and expression in HepG2 cells

Previously published studies suggest that an alteration in hexosamine flux induces a state of insulin resistance in muscle, liver, and other cell types. Glucosamine also alters the expression of several genes through an effect on transcription factors such as Sp1. Since the anti-atherogenic protein apolipoprotein AI (apoAI) is positively regulated by insulin, at least partly through its effect on Sp1, we investigated the effect of glucosamine on apoAI gene expression in the hepatocyte cell line, HepG2. By 24 hours of treatment with 0.1, 1, or 3 mmol/L glucosamine, the amount of apoAI protein secreted into the culture media increased 1.8-fold, 5.5-fold, and 2.3-fold, respectively. The decline in apoAI secretion at the highest glucosamine levels may be due to toxicity since the percentage of cells able to exclude trypan blue was lower in this group than in control cells (98.5% +/- 1.5% in control cells v 89.2% +/- 2.1% in cells treated with 3 mmol/L glucosamine, P <.01). ApoAI mRNA levels increased 2.4-fold in hepatocytes treated with 1 mmol/L glucosamine for 24 hours (1,158.1 +/- 78.8 v 482.2 +/- 24.3 arbitrary integrator units [AIU], P <.02), suggesting that the increase in apoAI protein secretion was due, at least partly, to an increase in apoAI mRNA levels. However, glucosamine had no effect on apoAI gene transcription rate as measured by nuclear runoff analysis (3,155 +/- 46.0 in control cells v 3,181 +/- 30.0 AIU in glucosamine-treated cells). Similarly, apoAI promoter activity measured in HepG2 cell transfected with an apoAI reporter plasmid containing the full-length apoAI promoter including an insulin-responsive Sp1 binding site did not change with glucosamine addition. In this assay, the chloramphenicol acetyltransferase (CAT) activity was 12.4% +/- 3.1%, 10.1% +/- 2.4%, 9.8% +/- 2.0%, 9.7% +/- 2.2%, and 11.9% +/- 2.9% in cells treated with 0, 0.03, 0.1, 0.3, and 1 mmol/L glucosamine, respectively. The apoAI mRNA turnover studies showed that 1 mmol/L glucosamine treatment of HepG2 cells was associated with increased apoAI mRNA half-life, from 7.6 to 16.6 hours. These findings suggest that increases in apoAI gene expression by glucosamine occur primarily through stabilizing apoAI mRNA.

Abundant raw material for cis-regulatory evolution in humans

Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

Prevalence of the APOC3 promoter polymorphisms T-455C and C-482T in Asian-Indians

Potential mechanisms accounting for the high cardiovascular death rates observed in Asian-Indians are dyslipidemia and insulin resistance. Polymorphisms in the APOC3 promoter (-455 T/C and -482 C/T) were frequently encountered in young Asian-Indians and they correlated with reduced concentrations of apolipoprotein A-I.

Novel genes for familial combined hyperlipidemia

Familial combined hyperlipidemia (FCHL) is a complex genetic disorder of unknown etiology. Recently, 'modifier' genes of the FCHL phenotype, such as the apolipoprotein AI-CIII-AIV gene cluster and LPL, have been identified in several populations. A 'major' gene for FCHL has been identified in a Finnish isolate which maps to a region syntenic to murine chromosome 3 where a locus for combined hyperlipidemia has been identified. We review these and other recent studies which indicate that FCHL is genetically heterogeneous.

A bifunctional regulatory element of the human ApoA-I gene responsive to a distal enhancer

Promoter elements located up to 2 kb upstream of the apolipoprotein A-I (apoA-I) gene are necessary for apoA-I expression in liver and intestine cells in tissue culture. In transgenic mice, a distal enhancer located between the apoA-IV and apoC-III genes is additionally necessary for tissue-specific expression of apoA-I in liver and intestine. We have identified a previously uncharacterized regulatory element between 746 and 856 nucleotides 5' of the apoA-I transcription start site that differentially affects the expression of apoA-I reporter plasmids in intestine cells dependent on the presence of the distal apolipoprotein enhancer. Deletion of the -856/-746 sequence strongly repressed transcription in the presence of the apolipoprotein enhancer, but in the absence of the enhancer, deletion of the -856/-746 element increased transcription. By contrast, in liver cells, deletion of the -856/-746 element strongly repressed transcription in the presence of the distal enhancer but had no detectable effect on transcription in the absence of the distal enhancer. Electrophoretic mobility shift analysis revealed tissue-specific and sequence-specific protein-DNA complexes formed by the -856/-746 element in intestine, liver, and HeLa cell nuclear extracts. The complexes formed by extracts of intestinal cells differed from those of liver and HeLa cells by their sensitivity to DNase digestion and their pattern of protein footprints. Collectively, the data suggest that the -856/-746 sequence is a composite regulatory element that interacts with multiple proteins and the apolipoprotein distal enhancer to achieve tissue-specific expression of apoA-I.

The effect on transcription efficiency of the apolipoprotein AI gene of DNA variants at the 5' untranslated region

Elevated circulating levels of high-density lipoprotein and apolipoprotein AI are associated with reduced coronary artery disease risk. We have shown that a C to T substitution at +83 bp and a G to A substitution at -75 bp of the apolipoprotein AI gene are both related to increased high-density lipoprotein levels in a healthy population but not in a coronary population, among whom the same mutations are associated with increased disease severity. In the present study, we explored the effects of these base changes on transcriptional efficiency in vitro. We directionally cloned (using polymerase chain reaction) the 5' region of the apolipoprotein AI gene (-281 to +330 bp) with GC, GT, and AC haplotypes into a pGL3-luciferase reporter gene basic vector, and transfected the constructed vectors into HepG2 cells. The cells carrying the T allele at the +83 bp site (GT 112.3 +/- 12.4) had the same transcriptional efficiency as those bearing the C allele (GC 126.3 +/- 9.6). However, for cells with the A allele at -75 bp there was a twofold decrease in transcription (AC 63.1 +/- 9.3) accompanied by similar changes in Luc+ mRNA levels; this reduced transcription was only present if the apolipoprotein AI leader sequence was included in the insert. While the findings are inconsistent with the T or A allele being associated with higher high-density lipoprotein levels, they are consistent with the finding that the alleles are associated with an increased coronary artery disease risk, and demonstrate that the 5' leader region of the apolipoprotein AI gene participates in regulating apolipoprotein AI transcription. They also suggest that other regions of the apolipoprotein AI gene may have an active role in such regulation, and that environmental effects may influence allele-specific expression.

The human CC chemokine receptor 5 (CCR5) gene. Multiple transcripts with 5'-end heterogeneity, dual promoter usage, and evidence for polymorphisms within the regulatory regions and noncoding exons

Human CC chemokine receptor 5 (CCR5), mediates the activation of cells by the chemokines macrophage inflammatory protein-1alpha, macrophage inflammatory protein-1beta, and RANTES, and serves as a fusion cofactor for macrophage-tropic strains of human immunodeficiency virus type 1. To understand the molecular mechanisms that regulate human CCR5 gene expression, we initiated studies to determine its genomic and mRNA organization. Previous studies have identified a single CCR5 mRNA isoform whose open reading frame is intronless. We now report the following novel findings. 1) Complex alternative splicing and multiple transcription start sites give rise to several distinct CCR5 transcripts that differ in their 5'-untranslated regions (UTR). 2) The gene is organized into four exons and two introns. Exons 2 and 3 are not interrupted by an intron. Exon 4 and portions of exon 3 are shared by all isoforms. Exon 4 contains the open reading frame, 11 nucleotides of the 5'-UTR and the complete 3'-UTR. 3) The transcripts appear to be initiated from two distinct promoters: an upstream promoter (PU), upstream of exon 1, and a downstream promoter (PD), that includes the "intronic" region between exons 1 and 3. 4) PU and PD lacked the canonical TATA or CAAT motifs, and are AT-rich. 5) PD demonstrated strong constitutive promoter activity, whereas PU was a weak promoter in all three leukocyte cell environments tested (THP-1, Jurkat, and K562). 6) We provide evidence for polymorphisms in the noncoding sequences, including the regulatory regions and 5'-UTRs. The structure of CCR5 was strikingly reminiscent of the overall structure of other chemokine/chemoattractant receptors, underscoring an important evolutionarily conserved function for a prototypical gene structure. This is the first description of functional promoters for any CC chemokine receptor gene, and we speculate that the complex pattern of splicing events and dual promoter usage may function as a versatile mechanism to create diversity and flexibility in the regulation of CCR5 expression.