The baboon apolipoprotein E gene: structure, expression, and linkage with the gene for apolipoprotein C-1

From beta amyloid to altered proteostasis in Alzheimer's disease

Alzheimer's disease (AD) is an age related neurodegenerative disorder causing severe disability and important socio-economic burden, but with no cure available to date. To disentangle this puzzling disease genetic studies represented an important way for the comprehension of pathogenic mechanisms. Abnormal processing and accumulation of amyloid-β peptide (Aβ) has been considered the main cause and trigger factor of the disease. The amyloid cascade theory has fallen into crisis because the failure of several anti-amyloid drugs trials and because of the simple equation AD = abnormal Aβ deposition is not always the case. We now know that multiple neurodegenerative diseases share common pathogenic mechanisms leading to accumulation of misfolded protein species. Genome Wide Association studies (GWAS) led to the identification of large numbers of DNA common variants (SNPs) distributed on different chromosomes and modulating the Alzheimer's risk. GWAS genes fall into several common pathways such as immune system and neuroinflammation, lipid metabolism, synaptic dysfunction and endocytosis, all of them addressing to novel routes for different pathogenic mechanisms. Other hints could be derived from epidemiological and experimental studies showing some lifestyles may have a major role in the pathogenesis of many age-associated diseases by modifying cell metabolism, proteostasis and microglia mediated neuroinflammation.

A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward

Alzheimer's disease (AD) is considered a polygenic disorder. This view is clouded, however, by lingering uncertainty over how to treat the quasi "monogenic" role of apolipoprotein E (APOE). The APOE4 allele is not only the strongest genetic risk factor for AD, it also affects risk for cardiovascular disease, stroke, and other neurodegenerative disorders. This review, based mostly on data from human studies, ranges across a variety of APOE-related pathologies, touching on evolutionary genetics and risk mitigation by ethnicity and sex. The authors also address one of the most fundamental question pertaining to APOE4 and AD: does APOE4 increase AD risk via a loss or gain of function? The answer will be of the utmost importance in guiding future research in AD.

Association of GSTT1/GSTM1 and ApoE variants with left ventricular diastolic dysfunction in thalassaemia major patients

BACKGROUND

Cardiomyocytes are particularly susceptible to complications from iron loading. The blood transfusions in thalassaemia major create loading of iron that cannot be naturally excreted. Apolipoprotein E and Glutathione S-transferase act as the scavenger of free radicals, which are generated due to excess iron. The variants of Apolipoprotein E (ApoE) and Glutathione S-transferase (GST) may play a role in oxidative damage-induced cardiomyopathy, so we aimed to study the association of genetic variants of these genes on diastolic dysfunction in our patients.

MATERIALS AND METHODS

One hundred and five β-thalassaemia patients older than 10 years were enrolled for the study. Two-dimensional and M-mode echocardiography analysis was done in all patients. Genotyping of the genetic variants of aforementioned genes was done using the PCR-RFLP method. Serum Glutathione S-transferase levels were estimated by ELISA.

RESULTS

Diastolic dysfunction was observed in 24 (22.8%) patients, whereas left ventricular hypertrophy was present in 37(35.2%) patients. There was a significant association of GSTM1 null allele with diastolic dysfunction only. Serum GST levels were also positively correlated with e/a and e/e' ratio. Positive association of ApoE E2 allele with the diastolic dysfunction was also seen.

CONCLUSIONS

Patients having Glutathione S-transferase M1 allele and Apolipoprotein E E2 allele are predisposed to oxidative stress-induced cardiac injury.

Understanding the cause of sporadic Alzheimer's disease

The increasing prevalence of Alzheimer's disease (AD) and a lack of effective prevention or disease-modifying therapies are global challenges with devastating personal, social and economic consequences. The amyloid β (Aβ) hypothesis posits that cerebral β-amyloidosis is a critical early event in AD pathogenesis. However, failed clinical trials of Aβ-centric drug candidates have called this hypothesis into question. Whereas we acknowledge that the Aβ hypothesis is far from disproven, we here re-visit the links between Aβ, tau and neurodegeneration. We review the genetics, epidemiology and pathology of sporadic AD and give an updated account of what is currently known about the molecular pathogenesis of the disease.

Dysbetalipoproteinaemia: a mixed hyperlipidaemia of remnant lipoproteins due to mutations in apolipoprotein E

Atherosclerosis is strongly associated with dyslipoproteinaemia, and especially with increasing concentrations of low-density lipoprotein and decreasing concentrations of high-density lipoproteins. Its association with increasing concentrations of plasma triglyceride is less clear but, within the mixed hyperlipidaemias, dysbetalipoproteinaemia (Fredrickson type III hyperlipidaemia) has been identified as a very atherogenic entity associated with both premature ischaemic heart disease and peripheral arterial disease. Dysbetalipoproteinaemia is characterized by the accumulation of remnants of chylomicrons and of very low-density lipoproteins. The onset occurs after childhood and usually requires an additional metabolic stressor. In women, onset is typically delayed until menopause. Clinical manifestations may vary from no physical signs to severe cutaneous and tendinous xanthomata, atherosclerosis of coronary and peripheral arteries, and pancreatitis when severe hypertriglyceridaemia is present. Rarely, mutations in apolipoprotein E are associated with lipoprotein glomerulopathy, a condition characterized by progressive proteinuria and renal failure with varying degrees of plasma remnant accumulation. Interestingly, predisposing genetic causes paradoxically result in lower than average cholesterol concentration for most affected persons, but severe dyslipidaemia develops in a minority of patients. The disorder stems from dysfunctional apolipoprotein E in which mutations result in impaired binding to low-density lipoprotein (LDL) receptors and/or heparin sulphate proteoglycans. Apolipoprotein E deficiency may cause a similar phenotype. Making a diagnosis of dysbetalipoproteinaemia aids in assessing cardiovascular risk correctly and allows for genetic counseling. However, the diagnostic work-up may present some challenges. Diagnosis of dysbetalipoproteinaemia should be considered in mixed hyperlipidaemias for which the apolipoprotein B concentration is relatively low in relation to the total cholesterol concentration or when there is significant disparity between the calculated LDL and directly measured LDL cholesterol concentrations. Genetic tests are informative in predicting the risk of developing the disease phenotype and are diagnostic only in the context of hyperlipidaemia. Specialised lipoprotein studies in reference laboratory centres can also assist in diagnosis. Fibrates and statins, or even combination treatment, may be required to control the dyslipidaemia.

The forgotten APOE allele: a review of the evidence and suggested mechanisms for the protective effect of APOE ɛ2

Ongoing efforts to improve survival, and enhance quality of life have led biomedical research to focus on disease and the mechanisms that increase risk for disease. The other side of that coin may be as important, i.e. examining the protective factors that allow some individuals to enjoy long, healthy lives. One of the best examples of a gene that positively influences cognitive health is the apolipoprotein (APOE) ɛ2 allele. The APOE ɛ4 allele is a well-established risk factor for Alzheimer's disease (AD) and has thus dominated the APOE literature, with the putative protective role of ɛ2 receiving little attention. This review describes the effects of APOE ɛ2 on the structure and function of the brain. With a focus on neurodegeneration, we discuss evidence for APOE ɛ2's protective effects, explore some key mechanisms through which this protection may be conferred, and address a few inconsistencies in the literature. Understanding the mechanisms that underlie the association between APOE ɛ2, cognition and longevity may provide new targets for research on promoting life-long health.

Genotype-by-diet effects on co-variation in Lp-PLA2 activity and LDL-cholesterol concentration in baboons fed an atherogenic diet

Both lipoprotein-associated phospholipase A(2) (Lp-PLA(2)) activity, a biomarker of inflammation, and concentration of its primary associated lipoprotein, LDL, are correlated with adverse coronary outcomes. We previously reported a quantitative trait locus (QTL) corresponding to HSA2p24.3-p23.2 with pleiotropic effects on Lp-PLA(2) activity and LDL-cholesterol (LDL-C) concentration in baboons fed a basal diet. Here, our goal was to locate pleiotropic QTLs influencing both traits in the same baboons fed a high-cholesterol, high-fat (HCHF) diet, and to assess whether shared genetic effects on these traits differ between diets. We assayed Lp-PLA(2) activity and LDL-C concentration in 683 baboons fed the HCHF diet. We used a bivariate maximum likelihood-based variance components approach in whole-genome linkage screens to locate a QTL [logarithm of odds (LOD) = 3.13, genome-wide P = 0.019] corresponding to HSA19q12-q13.2 with pleiotropic effects on Lp-PLA(2) activity and LDL-C levels in the HCHF diet. We additionally found significant evidence of genetic variance in response to diet for Lp-PLA(2) activity (P = 0.0017) and for LDL-C concentration (P = 0.00001), revealing a contribution of genotype-by-diet interaction to covariation in these two traits. We conclude that the pleiotropic QTLs detected at 2p24.3-p23.2 and 19q12-q13.2 on the basal and HCHF diets, respectively, exert diet-specific effects on covariation in Lp-PLA(2) activity and LDL-C concentration.

A primate model for Alzheimer's disease: investigation of the apolipoprotein E profile of the vervet monkey of St. Kitts

The apolipoprotein E4 allele has been previously associated with late onset Alzheimer's disease (AD). The major neuropathology of AD, senile (amyloid) plaques, and neurofibrillary tangles, has been observed in the vervet monkey (Chlorocebus aethiops). To further assess the suitability of the vervet as a model for AD, we undertook to determine the sequence of the vervet apoE exon 4 and to genotype an unrelated group of 30 aged animals raging from 15 to 28 years of age. All 30 animals were homozygous for the E4 allele.

Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism

Three common protein isoforms of apolipoprotein E (apoE), encoded by the epsilon2, epsilon3, and epsilon4 alleles of the APOE gene, differ in their association with cardiovascular and Alzheimer's disease risk. To gain a better understanding of the genetic variation underlying this important polymorphism, we identified sequence haplotype variation in 5.5 kb of genomic DNA encompassing the whole of the APOE locus and adjoining flanking regions in 96 individuals from four populations: blacks from Jackson, MS (n=48 chromosomes), Mayans from Campeche, Mexico (n=48), Finns from North Karelia, Finland (n=48), and non-Hispanic whites from Rochester, MN (n=48). In the region sequenced, 23 sites varied (21 single nucleotide polymorphisms, or SNPs, 1 diallelic indel, and 1 multiallelic indel). The 22 diallelic sites defined 31 distinct haplotypes in the sample. The estimate of nucleotide diversity (site-specific heterozygosity) for the locus was 0.0005+/-0.0003. Sequence analysis of the chimpanzee APOE gene showed that it was most closely related to human epsilon4-type haplotypes, differing from the human consensus sequence at 67 synonymous (54 substitutions and 13 indels) and 9 nonsynonymous fixed positions. The evolutionary history of allelic divergence within humans was inferred from the pattern of haplotype relationships. This analysis suggests that haplotypes defining the epsilon3 and epsilon2 alleles are derived from the ancestral epsilon4s and that the epsilon3 group of haplotypes have increased in frequency, relative to epsilon4s, in the past 200,000 years. Substantial heterogeneity exists within all three classes of sequence haplotypes, and there are important interpopulation differences in the sequence variation underlying the protein isoforms that may be relevant to interpreting conflicting reports of phenotypic associations with variation in the common protein isoforms.

Conserved protein motifs and structural organization of a fish gene homologous to mammalian apolipoprotein E

Apolipoprotein E (apoE) plays a central role in lipid metabolism from its ability to interact with lipoprotein receptors. Besides its role in cardiovascular diseases, apoE polymorphism contributes to susceptibility to neurodegenerative diseases, such as Alzheimer's disease. The statistical significance of the combined match scores obtained after apoE motif-based protein sequence database searches, the structural features of the deduced protein, and the phylogenetic analysis, support the evidence that a homologue to mammalian apoE can be found in teleost fish. Isolation and characterization of the first nonmammalian APOE revealed that the zebrafish gene spans 2555/2692 bp instead of 3597 bp in human and has the same splice junctions and exon/intron organization as found in mammals, except that there is an additional intron that splits the last exon (exon 4) into two exons (exons 4 and 5). Enlargement of APOE size in the mammalian lineage occurs mainly by Alu repeats insertion. The additional intron found in zebrafish gene was also identified at the same splicing site in trout APOE and is located in the corresponding linker region following the conserved low density lipoprotein receptor binding domain. Primer extension and reverse transcriptase PCR (RT-PCR) assays demonstrated that two transcription start sites are located 26 and 28 bp upstream of the first intron and 22 or 24 bp downstream from a canonical TATA box. Sequence inspection of the 5'-flanking region upstream of the TATA box revealed potential regulatory DNA elements. These results will serve as a basis for comparative studies on transcriptional and post-transcriptional mechanisms of APOE regulation in vertebrates.

The evolution of Alzheimer disease, the reproductive schedule, and apoE isoforms

Alzheimer disease (AD)-like neuropathology increases progressively during aging in most primates, and, in some species, is concurrent with reproductive decline in females and cognitive impairments. We consider how the schedule of AD may have evolved in early humans in relation to the apolipoprotein E (apoE) allele system, which is not found in other primates, and to the increasing duration of postnatal care. The delay of independence and the increasing length of maturation required that the schedule of AD-like neurodegeneration be slowed, otherwise parental caregivers would already have become impaired. We hypothesize that the uniquely human apoE epsilon3 allele evolved from the epsilon4 of primate ancestors during human evolution in relation to the rapid increases of brain size and the emergence of grandmothering. In discussing theses possibilities, we review the diverse bioactivities of apoE, which include involvement in hormone systems. The evolution of menopause is also considered in relation to the protective effect of estrogen on AD.

Empirical evaluation of preservation methods for faecal DNA

We evaluate the relative effectiveness of four methods for preserving faecal samples for DNA analysis. PCR assays of fresh faecal samples collected from free-ranging baboons showed that amplification success was dependent on preservation method, PCR-product size, and whether nuclear or mitochondrial DNA was assayed. Storage in a DMSO/EDTA/Tris/salt solution (DETs) was most effective for preserving nuclear DNA, but storage in 70% ethanol, freezing at -20 degrees C and drying performed approximately equally well for mitochondrial DNA and short (< 200 bp) nuclear DNA fragments. Because faecal DNA is diluted and degraded, repeated extractions from faeces may be necessary and short nuclear markers should be employed for genotyping. A review of molecular scatology studies further suggests that three to six faeces per individual should be collected.

Recent polymorphic insertion of an Alu repeat in the baboon lipoprotein lipase (LPL) gene

We have identified a polymorphic insertion in the lipoprotein lipase (LPL) gene in a captive baboon colony. Mapping and nucleotide (nt) sequence analysis of the polymorphism showed that it is due to the presence or absence of an Alu repetitive element in intron 7 of the baboon LPL gene. This polymorphic Alu repeat has not been reported in humans, and we did not detect the repeat in a survey of the LPL intron 7 gene region in other non-human primates. Comparison of nt at diagnostic positions in this Alu insertion with different Alu subfamily consensus sequences showed that it most closely resembles the young AluY subfamily. These data suggest that this polymorphic Alu repeat inserted independently in the baboon lineage.

Cerebrovascular amyloidosis in squirrel monkeys and rhesus monkeys: apolipoprotein E genotype

Some neuropathological changes characteristic of aging and Alzheimer's disease (AD) in humans are present also in senescent non-human primates. The human apoE4 allele is associated with an increased risk of developing late-onset familial and sporadic AD. We found that rhesus monkeys and three subspecies of squirrel monkeys are homozygous for apoE phenotype with arginine at positions 112 and 158 as in human apoE4. However, in both species threonine replaces arginine at position 61 of human apoE. It was previously shown that arginine 61 was critical in determining apoE4 lipoprotein distribution in humans.

Arginine residues at codons 112 and 158 in the apolipoprotein E gene correspond to the ancestral state in humans

Apolipoprotein E is a secretory glycoprotein that associates with lipoprotein particles and is coded for by a single locus on chromosome 19. The three common allelic isoforms of this protein (apo E2, apo E3 and apo E4) are associated with distinct patterns of lipoprotein metabolism and variable risks for coronary artery disease. In addition, recent work has shown that the presence of the apo E4 isoform constitutes a major risk for developing late-onset Alzheimer's disease as well as hypercholesterolaemia. The only differences between these isoforms result from cysteine-arginine interchanges at codons 112 and 158. There is considerable disagreement in the literature concerning the identity of the ancestral allele. In order to resolve this, 24 chimpanzees and individuals from a number of other primate species were analysed. All were similar to apo E4. This suggests that apo E4 is the ancestral allele and that apo E2 and apo E3 arose after the split of the human and chimpanzee lineages.

Neuropathology and apolipoprotein E profile of aged chimpanzees: implications for Alzheimer disease

Neuropathological findings in three aged chimpanzees were compared with those in rhesus monkeys and individuals with Alzheimer disease. Senile plaques and blood vessels were immunoreactive for amyloid beta-protein and apolipoprotein E (apoE) in the nonhuman primates, recapitulating findings in human aging and Alzheimer disease. Neurofibrillary tangles, another hallmark of Alzheimer disease, were absent. PCR/restriction-enzyme analysis in chimpanzees revealed an APOE profile similar to the human APOE type 4 allele associated with an increased risk of Alzheimer disease. These findings militate against the hypothesis that the absence of APOE type 3 allele predisposes to neurofibrillary tangle formation and support the value of aged primates for exploring mechanisms of amyloid processing and the role of apoE.

Baboon apolipoprotein C-I: cDNA and gene structure and evolution

We have isolated and characterized cDNA and genomic clones for apolipoprotein C-I (apoC-I) encoded by the APOC1 locus in baboons. Baboon apoC-I cDNA is only 410 bp in size, but the gene spans 4.5 kb including four small exons and three introns containing a large number of Alu repeats. The coding sequences of apoC-I cDNA and genomic clones are identical, indicating that this genomic clone contains the functional gene for apoC-I rather than a pseudogene like human APOC1'. We also detected a second gene in Southern blots of baboon genomic DNA that may correspond to the human APOC1' pseudogene. Two start sites for baboon APOC1 transcription were mapped to nucleotides that are 7 and 9 bp downstream from the predominant start site for human APOC1 transcription. Alignment of Alu repeats showed that the 5' region of the baboon APOC1 gene is more similar to that of the human pseudogene APOC1', and the 3' region and coding sequences are more similar to those of human APOC1. These regions are separated by an Alu repeat that is present only in the baboon gene, perhaps reflecting its role in gene rearrangement or conversion. Sequence comparisons from baboon, human, dog, and rat showed extensive differences in apoC-I amino acid sequences, which are less conserved than nucleotide sequences. However, comparisons of hydrophilicity profiles show significant conservation of protein domains that may be important for apoC-I function.

Cloning and sequencing of bovine apolipoprotein E complementary DNA and molecular evolution of apolipoproteins E, C-I, and C-II

Apolipoprotein (apo) E, a major protein component of plasma lipoproteins, is a physiological ligand for the low density lipoprotein (LDL) receptor as well as for a specific apoE receptor; it is therefore an important modulator of lipoprotein metabolism. In this study we cloned and sequenced bovine apoE complementary DNA. Comparison of nucleotide substitution rates shows that apoE is less conservative than apoA-I and evolves about 30% faster than an average mammalian protein. Although apoE is not a conservative protein, several regions have been well conserved among all eight mammalian sequences now available. These include a 33-amino-acid block immediately upsteam from the third intron/exon junction and the LDL receptor binding region. We have also compared published apoC-I and apoC-II sequences. Both proteins are less conservative than apoE. In particular, apoC-I shows no well-conserved region except for a small region in the common 33-amino-acid block, suggesting that the function of apoC-I does not have stringent structural requirements. On the other hand, in apoC-II the region encoded by exon 4, which consists of the last 29 amino acids of the polypeptide, has been rather well conserved, probably because this region is important for the activation of lipoprotein lipase and chylomicron and very low density lipoprotein metabolism.

Metabolic regulation of plasma apolipoprotein E by estrogen and progesterone in the baboon (Papio sp)

Apolipoprotein (apo) E plays an important role in the metabolism of lipoproteins. To determine the effects of estrogen and progesterone on plasma levels and metabolism of apo E, we used 12 ovariectomized baboons fed a cholesterol- and fat-enriched diet. These baboons were divided into four groups and treated with estrogen, progesterone, estrogen + progesterone, and a placebo control. After 10 months, although the lipid levels were not different among the treatment groups, low-density lipoprotein (LDL)/high-density lipoprotein (HDL) ratios in the estrogen + progesterone group were significantly lower than those in the control and progesterone groups. Estrogen alone or in combination with progesterone decreased plasma apo E levels significantly compared with those in the control group. Plasma apo E levels in the progesterone group were similar to those in the control group. In all groups, most (greater than 60%) of the apo E was present in HDL. HDL apo E concentrations in the estrogen and estrogen + progesterone groups were significantly lower than those in the control and progesterone groups. To determine the metabolic mechanisms of these changes in apo E levels, turnover studies were conducted by injection of iodinated apo E-labeled very-low-density lipoprotein (VLDL) and HDL. Residence times were calculated using multicompartment modeling. Progesterone alone and in combination with estrogen decreased residence times of apo E injected in both HDL and VLDL compared with estrogen alone and control groups. Progesterone alone also increased the apo E production rate compared with other groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Isolation and characterization of several plasma apolipoproteins of common marmoset monkey

To explore the potential of the common marmoset monkey (Callithrix jacchus) as a model for human plasma lipoprotein metabolism, several marmoset apolipoproteins were isolated and characterized in this study. Based on several properties, including molecular weight, amino acid composition, and sequence, the marmoset apolipoproteins are strikingly similar to human apolipoprotein (apo) A-I, A-II, C-III, and A-IV. The first 54 residues of marmoset apo A-I showed 87% sequence identity with the corresponding region of human apo A-I. Amino-terminal sequence analysis of a minor basic apo A-I isoform revealed that it contained an amino-terminal hexapeptide extension (Arg-His-Phe-Gln-Gln-) identical to that found in human proapo A-I. Like apo A-II in most nonhuman primates, marmoset apo-A-II differed from human apo A-II in that it did not contain cysteine and therefore existed as a monomer. The complete amino acid sequence of marmoset apo A-II was deduced. The protein contains 77 amino acids, as does human apo A-II, and showed an 82% identity with its human equivalent. In both species, apo C-III and E had similar amino-terminal sequences and amino acid compositions. Like human apo E, marmoset apo E contained minor sialylated isoforms. However, unlike human apo C-III, no sialyated isoforms of marmoset apo C-III were observed. In addition, the marmoset possessed an apolipoprotein whose molecular weight and amino acid composition were similar to those of human apo A-IV. The close structural similarities between corresponding marmoset and human apolipoproteins indicate that the marmoset monkey will be useful as a model for human lipoprotein metabolism.

The baboon gene for apolipoprotein A-I: characterization of a cDNA clone and identification of DNA polymorphisms for genetic studies of cholesterol metabolism

We have isolated and sequenced a baboon apolipoprotein A-I (ApoA-I) clone from a liver cDNA library using a human cDNA hybridization probe. This baboon cDNA contains the entire ApoA-I coding region (801 bp, 267 aa), a 3' untranslated region, and a poly(A)tail. Among comparisons with apoAI sequences from other species, the baboon cDNA is most similar to that of the cynomolgus macaque (99.2% homologous) and least similar to the rat sequence (72.6% homologous). A high frequency of nonsynonymous substitutions are observed by alignment of baboon and human apoAI cDNAs, but comparisons of hydrophilicity profiles show that protein structure is conserved by substitutions of aa with similar properties. A polymorphic PstI cleavage site was identified by Southern blot analysis and subsequently mapped to the 5' end of the baboon apoAI gene. To identify effects of apoAI allelic variation on cholesterol metabolism, we used immunoblotting to compare the distributions of ApoA-I among lipoprotein size classes in baboons from each genotype under basal and atherogenic diets. We observed an increase of ApoA-I in high density lipoprotein (size class 1) particles after atherogenic diets in homozygotes for one allele, as compared to slight decreases in the other genotypes.