Candidate Gene For Alzheimer's Disease Research Articles

Investigation of the effect of brain-derived neurotrophic factor (BDNF) polymorphisms on the risk of late-onset Alzheimer's disease (AD) and quantitative measures of AD progression

BDNF is a functional candidate gene for AD, owing to its role in neuronal development and survival. The Val66Met (G196A), along with another C270T polymorphism has been associated with AD, however, the effects seem to be inconsistent across studies. We examined the association of the G196A and C270T polymorphisms with sporadic late-onset AD (LOAD) in a large American White cohort of 995 AD cases and 671 controls and an American Black cohort of 64 AD cases and 45 controls. We also examined the association of these polymorphisms with quantitative measures of AD progression, including age at onset (AAO), disease duration and Mini-Mental State Examination (MMSE) scores. No significant difference in allele, genotype or estimated haplotype frequencies was observed between AD cases and controls within the American White and Black cohorts for the G196A and C270T polymorphisms. However, the frequency of the 196 * A allele was significantly lower in American Black subjects compared to Whites. While MMSE scores were significantly lower in C270T/CT carriers compared to C270T/CC subjects only among American Blacks, no such effect was observed among American Whites. The BDNF polymorphisms did not affect AAO or disease duration measures in American Whites or Blacks. Our finding does not support any association between the BDNF/G196A or C270T polymorphism and the risk of sporadic LOAD among American Whites or Blacks. The significant effect of the C270T polymorphism observed on MMSE scores among American Blacks needs to be further explored in a larger cohort.

Exclusion of CYP46 and APOM as candidate genes for Alzheimer's disease in a French population

Alzheimer's disease (AD) is a complex, multifactorial disorder, probably resulting from an interaction between environmental and genetic factors. Increasing evidence points to a link between cholesterol turnover and AD, suggesting that genes implicated in brain cholesterol homeostasis may be potential candidate genes for AD. With this background, we tested the potential association of the CYP46, APOM and APOF genes with the risk of developing AD. CYP46 encodes the enzyme cholesterol 24-hydrolase, which plays a key role in brain cholesterol turnover, and APOF and APOM encode apolipoproteins belonging to the large lipocalin family, which also includes ApoE. In contrast to two previous reports but in accordance with one other, we were unable to detect an association between an intron 2 polymorphism of CYP46 and AD. We also searched for polymorphisms within the APOM and APOF by dHPLC. We were unable to detect any polymorphisms in the coding and exon/intron sequences of the APOF. Finally, we excluded APOM as a genetic determinant of AD in our large French case control population.

Partial Loss-of-Function Mutations in Insulin-Degrading Enzyme that Induce Diabetes also Impair Degradation of Amyloid β-Protein

The causes of cerebral accumulation of amyloid beta-protein (Abeta) in most cases of Alzheimer's disease (AD) remain unknown. We recently found that homozygous deletion of the insulin-degrading enzyme (IDE) gene in mice results in an early and marked elevation of cerebral Abeta. Both genetic linkage and allelic association in the IDE region of chromosome 10 have been reported in families with late-onset AD. For IDE to remain a valid candidate gene for late-onset AD on functional grounds, it must be shown that partial loss of function of IDE can still alter Abeta degradation, but without causing early, severe elevation of brain Abeta. Here, we show that naturally occurring IDE missense mutations in a well-characterized rat model of type 2 diabetes mellitus (DM2) result in decreased catalytic efficiency and a significant approximately 15 to 30% deficit in the degradation of both insulin and Abeta. Endogenously secreted Abeta(40) and Abeta(42) are significantly elevated in primary neuronal cultures from animals with the IDE mutations, but there is no increase in steady-state levels of rodent Abeta in the brain up to age 14 months. We conclude that naturally occurring, partial loss-of-function mutations in IDE sufficient to cause DM2 also impair neuronal regulation of Abeta levels, but the brain can apparently compensate for the partial deficit during the life span of the rat. Our findings have relevance for the emerging genetic evidence suggesting that IDE may be a late-onset AD-risk gene, and for the epidemiological relationships among hyperinsulinemia, DM2, and AD.

Scoring insertion-deletion polymorphisms by dynamic allele-specific hybridization.

Genome variation provides researchers with thousands of markers with which to study human demographic history and phenotypes. Insertion-deletion (indel) polymorphism is an important and abundant form of human genome variation, and convenient methods for genotyping indels are therefore needed. Here we evaluate dynamic allele-specific hybridization (DASH) for its ability to score indels. Evaluation of six model indel DASH assays based on synthetic oligonucleotides showed that length differences of 1-5 bp were accurately scored. Only single probes were required to assay indels of 3-4 bp or less, while longer indels tended to require the use of both allele probes serially. The best results were obtained by central placing of the probe over the indel. Model study findings were confirmed by running indel DASH assays upon PCR-amplified targets representing four polymorphisms from Alzheimer's disease candidate genes APBB1 and LRP1. These indels were genotyped in a set of 121 patients and 156 controls. While no disease association was found, the data quality confirmed that DASH is a robust and useful procedure for genotyping indels of the size range typically found in the human genome.

Sequence variation in the CHAT locus shows no association with late-onset Alzheimer's disease.

There is substantial evidence for a susceptibility gene for late-onset Alzheimer's disease (AD) on chromosome 10. One of the characteristic features of AD is the degeneration and dysfunction of the cholinergic system. The genes encoding choline acetyltransferase (ChAT) and its vesicular transporter (VAChT), CHAT and SLC18A3 respectively, map to the linked region of chromosome 10 and are therefore both positional and obvious functional candidate genes for late-onset AD. We have screened both genes for sequence variants and investigated each for association with late-onset AD in up to 500 late-onset AD cases and 500 control DNAs collected in the UK. We detected a total of 17 sequence variants. Of these, 14 were in CHAT, comprising three non-synonymous variants (D7N in the S exon, A120T in exon 5 and L243F in exon 8), one synonymous change (H547H), nine single-nucleotide polymorphisms in intronic, untranslated or promoter regions, and a variable number of tandem repeats in intron 7. Three non-coding SNPs were detected in SLC18A3. None demonstrated any reproducible association with late-onset AD in our samples. Levels of linkage disequilibrium were generally low across the CHAT locus but two of the coding variants, D7N and A120T, proved to be in complete linkage disequilibrium.

Increased frequency of a new polymorphism in the cell division cycle 2 (cdc2) gene in patients with Alzheimer's disease and frontotemporal dementia

Recent studies show linkage between Alzheimer's disease (AD) and two loci on chromosome 10. The cell division cycle 2 (cdc2) gene is located close to one of the chromosome 10 markers, and is a candidate gene for AD since it is involved in the pathogenesis of AD. We sequenced coding exons and flanking intronic sequences and the promoter region on the cdc2 gene and found three new single nucleotide polymorphisms (SNPs). We analyzed 272 Caucasian AD cases, 160 controls and 70 cases with frontotemporal dementia (FTD) for these SNPs. Homozygosity for one of the SNPs (Ex6+7I/D) was more frequent in both AD and FTD cases than in controls. In the combined tauopathy (AD and FTD) group the odds ratio (OR) was 1.77 (95% CI 1.19–2.63) for the Ex6+7II genotype. Our findings suggest that the Ex6+7I allele is associated with tauopathies, both AD and FTD.

Investigation of oxidized LDL-receptor 1 (OLR1) as the candidate gene for Alzheimer's disease on chromosome 12.

Late-onset Alzheimer's disease (AD) is a genetically heterogeneous neurodegenerative disorder. In addition to the apolipoprotein E (APOE) gene on chromosome 19, linkage studies suggest the existence of multiple susceptibility genes for late-onset AD. Genome-wide linkage and chromosome-12-specific linkage studies have identified a broad 50-cM pericentromeric region between 12p12 and 12q13 among non- APOE*4 carriers. Some studies have implicated the alpha2-macroglobulin (A2M) gene in 12p12 as being the chromosome 12 gene, but the results are equivocal. Because of its close proximity to the A2M gene and because it is abundantly expressed in the brain, we reasoned that the oxidized LDL-receptor 1 (OLR1) gene could be a candidate gene for AD. We screened all exons and intron-exon boundaries of the OLR1 gene for new mutations and identified three novel sequence variations in intron 4, intron 5, and the 3' untranslated region (UTR). Pair-wise comparisons between the three polymorphic sites revealed significant linkage disequilibrium ( P<0.0001). We screened more than 800 late-onset AD cases and more than 700 controls for the three OLR1 polymorphisms. All polymorphisms showed significant association with AD after stratification by APOE*4, with the strongest effect being observed for the 3'UTR polymorphism among non- APOE*4 (odds ratio 0.658; 95% confidence interval: 0.47-0.92; P=0.014) and APOE*4 (odds ratio 1.72; 95% confidence interval: 1.07-2.78; P=0.025) carriers. DNA-protein binding assay with nuclear protein extracts from neuroblastoma cells indicated that the OLR1/3'UTR polymorphism affects the binding of a transcription factor in an allele-dependent manner. Our data suggest that genetic variation in the OLR1 gene may modify the risk of AD in an APOE*4-dependent fashion.

Distribution of plasma α1-antichymotrypsin levels in Alzheimer disease patients and controls and their genetic controls

Alzheimer's disease (AD) is a complex multifactorial disease in which many genetic and environmental factors are involved. Recent studies have shown that alpha(1)-antichymotrypsin (ACT) is one of the candidate genes for AD. Elevated levels of ACT have been widely, but not universally reported in the cerebrospinal fluid and plasma of AD patients. The genetic association between the ACT/codon -17*A allele of the signal peptide polymorphism and AD has been shown in some studies. One hypothesis is that the ACT/codon -17*A allele is in linkage disequilibrium with unknown functional mutation(s) in the ACT gene. Alternatively, the more hydrophobic character of the alanine (codon -17*A) may enhance ACT translocation into the endoplasmic reticulum and the Golgi apparatus, thus being secreted at higher levels. Therefore, this study was undertaken to determine the distribution of ACT plasma levels in cases (n = 397) and controls (n = 118) and the impact of ACT polymorphisms, including codon -17, on plasma ACT levels. In our cohort, plasma ACT levels were significantly higher in AD patients than controls (542.13 +/- 7.11 mg/liter vs. 496.62 +/- 12.79 mg/liter; P = 0.002). The ACT/codon -17 polymorphism showed significant association with ACT levels in male AD patients, while the effect of the intron 4 polymorphism was significant in both male and female patients. Codon 227 polymorphism was associated with lower ACT levels in AD patients. In conclusion, ACT may play an important role in the AD pathogenesis and genetic variation in the ACT gene appears to have some effect on plasma ACT concentrations.

Confirmation of association between D10S583 and Alzheimer's disease in a case–control sample

Several independent studies have reported that loci on chromosome 10 are associated/linked with Alzheimer's disease (AD), including a family-based study demonstrating an association between the marker D10S583 and AD. We have examined the D10S583 polymorphic marker and apolipoprotein E (APOE) gene in a case–control study. We observed the expected association of the APOE allele ε4 with AD, and an inverse association between the D10S583 allele 209 and AD. These data support the original findings that suggest the presence of a candidate gene for AD in this region of chromosome 10. The nearby insulin degrading enzyme gene has been previously proposed as a candidate gene; however, a number of other putative candidate genes are also located in this region. The ongoing investigation of the genetic source of association and linkage in this region is clearly warranted.

Identification of sequence variants and analysis of the role of the glycogen synthase kinase 3 beta gene and promoter in late onset Alzheimer's disease.

Alzheimer's disease (AD) is a disorder characterised by a progressive deterioration in memory and other cognitive functions. Glycogen synthase kinase 3 beta (GSK3 beta) phosphorylates the microtubule associated protein tau at sites that are aberrantly phosphorylated in AD. GSK3 beta binds to presenilin 1 and plays a role in wnt and insulin signalling cascades, both of which have been proposed to be linked to AD. Moreover GSK3 beta activity may be altered in AD brain. These observations suggest a central role for GSK3 beta in AD and led us to investigate GSK3 beta as a candidate gene for AD. We sought to identify sequence variations in the gene and its promoter, as these could have an effect on activity and expression leading to abnormal function. Sequencing over 3000 bp of the GSK3 beta putative promoter revealed there to be five sequence variations, two of which were common (>10%). However on further examination none of these, either alone or in synergy, had any association with late onset AD. Stratification of the data by APOE epsilon 4 status also produced no significant association. Sequencing of the GSK3 beta coding region revealed no variations. This would suggest that the aberrant phosphorylation of tau by GSK3 beta in AD is not due to sequence variations in the gene or its promoter.

The BACE gene: genomic structure and candidate gene study in late-onset Alzheimer's disease.

Alzheimer's disease (AD) pathology is characterized by beta-amyloid plaques and neurofibrillary tangles. Studies of autosomal dominant early-onset AD mutations suggest that beta-amyloid overproduction is sufficient to cause AD. Recently, the BACE gene, which encodes beta-secretase, the rate limiting enzyme in beta-amyloid formation, has been identified. Since this gene is a strong candidate gene for late-onset AD because of its function, we have characterized its genomic organization and identified two polymorphisms. Neither of these polymorphisms were associated with AD risk in genetic association studies comparing autopsy-confirmed late-onset AD cases and age-matched non-demented controls. Thus, we find no evidence that this locus influences risk for late-onset AD.

Analysis of genetic polymorphisms in the transforming growth factor-beta1 gene and the risk of Alzheimer's disease.

Alzheimer's disease (AD) is a complex disease involving several genetic and environmental components. Genetic studies have yet to identify all the genes involved in the pathogenesis of AD. Transforming growth factor-beta1 (TGF-beta1) is a candidate gene for AD. It is a multifunctional cytokine whose overexpression has been shown to promote the deposition of amyloid-beta peptide. The goal of this study was to investigate the association of three polymorphisms in TGF-beta1 with the risk of AD. Two of the polymorphisms are located in the 5' region at positions -800 (G-->A) and -509 (C-->T), and the third is in exon 5 at codon 263 (Thr-->Ile). We screened DNA samples from 428 sporadic, late-onset patients and 421 controls by PCR-based assays. There was no statistically significant difference in genotype or allele frequency distributions between cases and controls for the -800 or codon 263 polymorphisms (P=0.38 and P=0.60, respectively). The overall genotype distribution at the -509 site was significantly different between cases and controls. (P=0.017). The frequency of the -509/TT genotype was significantly higher in AD patients than controls (P=0.015). We further tested whether this polymorphism may alter the regulation of the TGF-beta1 gene using dual luciferase reporter assay. We subcloned the 5' flanking region, which contained the -509 C/T polymorphic sites, in front of the firefly luciferase reporter gene in pGL-3 basic vector and co-transfected with the pRL-CMV vector containing Renilla luciferase gene as a control for transfection efficiency in COS-1 cells. The activity of each promoter allele was directly measured by the ratio of firefly luciferase activity to Renilla luciferase activity. The -509 T allele was associated with marginally higher transcriptional activity of TGF-beta compared with the -509 C allele (P=0.051). These data suggest that the -509 polymorphism of TGF-beta1 may be modestly associated with the risk of AD. However, these data should be interpreted with caution as the differences associated with the -509 alleles in both the genetic association and the transfection studies were modest.

The genetics of Alzheimer's disease.

Alzheimer's disease (AD) is a genetically complex disorder. Mutations in the amyloid precursor protein and presenilin 1 (PS1) genes are fully penetrant and cause early-onset AD. Mutations in presenilin 2, a PS1 homologue, cause partially penetrant autosomal dominant AD with onset age beginning at 40 years and extending past 75 years. A fourth gene, apolipoprotein E (ApoE) is a risk-factor for late-onset AD. Over 40 genes have been tested as AD candidate genes, yet none has been clearly established as an AD risk factor. Linkage studies have implicated a number of chromosome regions as possible sites for late-onset AD loci with the strongest evidence being for chromosome 12. Candidate genes in this region include alpha2-macroglobulin (A2M) and low-density lipoprotein receptor-related gene (LRP), although neither has been clearly established as an AD gene. Identification of additional late-onset genes will require larger samples, more sophisticated analysis methods, and large-scale positional cloning efforts.

No genetic association between the LRP receptor and sporadic or late-onset familial Alzheimer disease

The low-density lipoprotein receptor-related protein gene (LRP1) is often mentioned as a candidate gene for Alzheimer disease (AD) because of its role as a receptor for apolipoprotein E (apoE), a major genetic risk factor for late-onset familial and sporadic AD. A recent association study of a tetranucleotide repeat polymorphism located 5' to the LRP1 gene detected an increase in the 87 base pair allele in AD cases compared to unaffected controls. Additionally, an independent study involving a genomic screen for genes associated with late-onset AD identified a region as a possible location of a late-onset AD gene on chromosome 12p between D12S373 and D12S390, about 10 cM proximal to LRP1. We examined 144 late-onset multiplex AD families, 436 sporadic AD cases, and 240 controls and found no evidence of linkage or association of LRP1 and AD. Our data indicate that genetic variation of the LRP1 gene is not a major risk factor in the etiology of AD.

No association between c-fos gene polymorphisms and sporadic Alzheimer's disease.

Although ApoE epsilon 4 is a major risk factor for sporadic Alzheimer's disease (AD), 20-30% of sporadic AD patients do not have this allele. This indicates that other risk factors are involved in the pathogenesis of sporadic AD. Studies of the genetic association between AD and polymorphisms in the c-fos gene, a candidate gene for AD, were conducted. The polymorphisms of DsaI in exon 2 and Sau3 AI in intron 2 were examined in 89 patients diagnosed as sporadic cases of probable AD clinically and radiologically according to the NINCDS-ADRDA criteria. This was also undertaken in 96 controls. There was no significant difference between the groups in allele frequencies or genotype counts. Although c-fos gene as a locus conferring susceptibility to sporadic AD cannot be ruled out, these data could not support the hypothesis that a c-fos allele should be another risk factor for sporadic AD.

Genetic analysis of the cellular oncogene fos in patients with chromosome 14 encoded Alzheimer's disease.

A major gene for familial early-onset Alzheimer's disease (AD) has been localised to chromosome 14q24.3. The c-fos gene (FOS), localised to 14q24.3-q31, is a candidate for the AD gene since it may be involved in the transcription regulation of the amyloid precursor protein gene (APP). Part of APP codes for the beta A4 amyloid present in AD brain lesions. We analyzed linkage of AD in the 2 early-onset AD families. AD/A and AD/B, using a polymerase chain reaction (PCR) based assay for a restriction fragment length polymorphism (RFLP). The RFLP is detected in BstNI digested DNA and is located near the 3' end of FOS. No obligate recombinants were detected. The 4 exons of FOS were sequenced in one pathologically confirmed AD patient in each family. No exonic mutations were found. Two intronic sequence variations were observed, one in intron 2 and one in intron 3. The intron 2 variation did not segregate with AD. The intron 3 variation which is a single G insertion was used in linkage studies in families AD/A and AD/B and showed conclusive linkage in both families in the absence of recombinants. Therefore, FOS cannot yet be excluded as a candidate gene for AD in these families since mutations may be present in regulatory sequences.