Scott Smemo

Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms

BackgroundAnimal studies suggest that brain apolipoprotein E (apoE) levels influence amyloid-β (Aβ) deposition and thus risk for Alzheimers disease (AD). We have previously demonstrated that deletion of the ATP-binding cassette A1 transporter (ABCA1) in mice causes dramatic reductions in brain and cerebrospinal fluid (CSF) apoE levels and lipidation. To examine whether polymorphisms in ABCA1 affect CSF apoE levels in humans, we measured apoE in CSF taken from 168 subjects who were 43 to 91 years old and were either cognitively normal or who had mild AD. We then genotyped the subjects for ten previously identified ABCA1 single nucleotide polymorphisms (SNPs).ResultsIn all subjects, the mean CSF apoE level was 9.09 μg/ml with a standard deviation of 2.70 μg/ml. Levels of apoE in CSF samples taken from the same individual two weeks apart were strongly correlated (r2 = 0.93, p < 0.01). In contrast, CSF apoE levels in different individuals varied widely (coefficient of variation = 46%). CSF apoE levels did not vary according to AD status, APOE genotype, gender or race. Average apoE levels increased with age by ~0.5 μg/ml per 10 years (r2 = 0.05, p = 0.003). We found no significant associations between CSF apoE levels and the ten ABCA1 SNPs we genotyped. Moreover, in a separate sample of 1225 AD cases and 1431 controls, we found no association between the ABCA1 SNP rs2230806 and AD as has been previously reported.ConclusionWe found that CSF apoE levels vary widely between individuals, but are stable within individuals over a two-week interval. AD status, APOE genotype, gender and race do not affect CSF apoE levels, but average CSF apoE levels increase with age. Given the lack of association between CSF apoE levels and genotypes for the ABCA1 SNPs we examined, either these SNPs do not affect ABCA1 function or if they do, they do not have strong effects in the CNS. Finally, we find no evidence for an association between the ABCA1 SNP rs2230806 and AD in a large sample set.

Association studies between risk for late-onset Alzheimer's disease and variants in insulin degrading enzyme.

Linkage studies have suggested there is a susceptibility gene for late onset Alzheimers disease (LOAD) in a broad region of chromosome 10. A strong positional and biological candidate is the gene encoding the insulin‐degrading enzyme (IDE), a protease involved in the catabolism of Aβ. However, previous association studies have produced inconsistent results. To systematically evaluate the role of variation in IDE in the risk for LOAD, we genotyped 18 SNPs spanning a 276 kb region in and around IDE, including three “tagging” SNPs identified in an earlier study. We used four case‐control series with a total of 1,217 cases and 1,257 controls. One SNP (IDE_7) showed association in two samples (P‐value = 0.0066, and P = 0.026, respectively), but this result was not replicated in the other two series. None of the other SNPs showed association with LOAD in any of the tested samples. Haplotypes, constructed from the three tagging SNPs, showed no globally significant association. In the UK2 series, the CTA haplotype was over‐represented in cases (P = 0.046), and in the combined data set, the CCG haplotype was more frequent in controls (P = 0.015). However, these weak associations observed in our series were in the opposite direction to the results in previous studies. Although our results are not universally negative, we were unable to replicate the results of previous studies and conclude that common variants or haplotypes of these variants in IDE are not major risk factors for LOAD.

Alpha-T-catenin is expressed in human brain and interacts with the Wnt signaling pathway but is not responsible for linkage to chromosome 10 in Alzheimer's disease.

The gene encoding α-T-catenin, CTNNA3, is positioned within a region on chromosome 10, showing strong evidence of linkage to Alzheimer’s disease (AD), and is therefore a good positional candidate gene for this disorder. We have demonstrated that α-T-catenin is expressed in human brain, and like other α-catenins, it inhibits Wnt signaling and is therefore also a functional candidate. We initially genotyped two single-nucleotide polymorphisms (SNPs) in the gene, in four independent samples comprising over 1200 cases and controls but failed to detect an association with either SNP. Similarly, we found no evidence for association between CTNNA3 and AD in a sample of subjects showing linkage to chromosome 10, nor were these SNPs associated with Aβ deposition in brain. To comprehensively screen the gene, we genotyped 30 additional SNPs in a subset of the cases and controls (n>700). None of these SNPs was associated with disease. Although an excellent candidate, we conclude that CTNNA3 is unlikely to account for the AD susceptibility locus on chromosome 10.

Ubiquilin 1 polymorphisms are not associated with late-onset Alzheimer's disease

Several studies have reported evidence for linkage of late‐onset Alzheimers disease (LOAD) to chromosome 9. Recently, an intronic polymorphism affecting alternative splicing of exon 8 of ubiquilin 1 (UBQLN1) was reported to be associated with LOAD. We attempted to replicate this observation by genotyping this polymorphism, rs12344615 (also known as UBQ‐8i), in a large sample of 1,544 LOAD cases and 1,642 nondemented controls. We did not find any evidence that this single nucleotide polymorphism, or any of six others tested in UBQLN1, increases risk for LOAD. Ann Neurol 2005

Variation in the Urokinase-Plasminogen Activator Gene Does Not Explain the Chromosome 10 Linkage Signal for Late Onset AD

Linkage studies indicate that the same region of chromosome 10 contains a risk locus for late onset Alzheimer disease (LOAD) and a QTL for plasma Aβ42 levels suggesting that a single locus may influence risk for AD by elevating plasma Aβ42 [Ertekin‐Taner et al., 2000 ; Myers et al., 2000 ]. A strong positional and biological candidate is the urokinase‐plasminogen activator (PLAU) gene. Eight polymorphisms spanning the entire gene were examined using case control (CC) and family‐based association methods. No association was observed by any method making it unlikely that variation in PLAU explains our linkage data.

A multi-incident, Old-Order Amish family with PD

BackgroundPD is largely a sporadic condition of unknown etiology, but specific inherited mutations are a cause of PD. ObjectiveTo describe a large, multi-incident Amish pedigree with PD. MethodsCase ascertainment, calculation of population prevalence, and calculation of kinship coefficients (a measure of relatedness between two individuals) for affecteds and subjects in a large kindred with PD were conducted. Sequencing of genes with known mutations sufficient to cause PD and marker-by-marker haplotype analysis in chromosomal regions flanking previously described genes with known mutations were performed. ResultsThe authors have examined 113 members of this pedigree and classified 67 as normal (no evidence of PD), 17 as clinically definite PD, 6 as clinically probable PD, and 23 as clinically possible PD. The mean age at onset of the clinically definite subjects was 56.7 years. The phenotype in this family is typical of idiopathic PD, including rest tremor, rigidity, bradykinesia, postural instability, and response to levodopa. In addition, dementia occurred in six of the clinically definite subjects, and many subjects experienced levodopa-related motor complications including wearing off and dopa-induced dyskinesias. In the index Amish community, a minimum prevalence of PD in the population 40 years and older of 552/100,000 was calculated. The mean kinship coefficient in the subjects with PD and those with PD by history (0.036) was higher (p = 0.007) than in a group of age-matched normal Amish control subjects (0.016), providing evidence that PD is inherited in this family. Sequence analysis did not detect any mutations in known PD genes. No single haplotype cosegregates with the disease in any of the chromosomal regions previously found to be linked to PD, and no marker in these regions exhibits increased homozygosity among definite PD cases. ConclusionsPD in this community is more common than in the general population, and this increased prevalence may be due in part to a novel gene(s).

Association studies testing for risk for late-onset Alzheimer's disease with common variants in the β-amyloid precursor protein (APP)†‡

Linkage studies have suggested a susceptibility locus for late‐onset Alzheimers disease (LOAD) on chromosome 21. A functional candidate gene in this region is the β‐amyloid precursor protein (APP) gene. Previously, coding mutations in APP have been associated with early onset Alzheimers Disease (EOAD). Three copies of APP are associated with AD pathology in Downs syndrome and in EOAD, suggesting that overexpression of APP may be a risk factor for LOAD. Although APP is a strong functional and positional candidate, to date there has been no thorough investigation using a dense map of SNPs across the APP gene. In order to investigate the role of common variation in the APP gene in the risk of LOAD, we genotyped 44 SNPs, spanning 300 kb spanning the entire gene, in a large case‐control series of 738 AD cases and 657 healthy controls. The SNPs showed no association in genotypic or allelic tests, even after stratification for presence or absence of the APOE ϵ4 allele. Haplotype analysis also failed to reveal significant association with any common haplotypes. These results suggest that common variation in the APP gene is not a significant risk factor for LOAD. However, we cannot rule out the possibility that multiple rare variants that increase APP expression or Aβ production might influence the risk for LOAD.

O2-02-07: Genetic variants on chromosome 9 are associated with late-onset Alzheimer’s disease, variation in allele-specific gene expression, and differential apoptotic response

Yonghong Li, Andrew Grupe, Charles Rowland, Petra Nowotny, John S.K. Kauwe, Scott Smemo, Anthony Hinrichs, Kristina Tacey, Shirley Kwok, Joseph Catanese, John Sninsky, Thomas J. White, Paul Hollingworth, Sandra L. Harris, Arnold Levine, Fabienne Wavrant-De Vrieze, John Hardy, Michael O’Donovan, Simon Lovestone, John Morris, Leon J. Thal, Michael Owen, Julie Williams, Alison Goate, Celera Diagnostics, Alameda, CA, USA; Washington University, St. Louis, MO, USA; Cardiff University, Cardiff, United Kingdom; Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Institute for Advanced Study, Princeton, NJ, USA; National Institute on Aging, Bethesda, MD, USA; Institute of Psychiatry, London, United Kingdom; University of California, San Diego, San Diego, CA, USA. Contact e-mail: yonghong.li@celeradiagnostics.com