Search

Knowledge about the molecular mechanisms driving Alzheimer's disease (AD) is still limited. To learn more about AD biology, we performed whole transcriptome sequencing on the hippocampus of 20 AD cases and 10 age- and sex-matched cognitively healthy controls. We observed 2716 differentially expressed genes, of which 48% replicated in a second data set of 84 AD cases and 33 controls. We used an integrative network-based approach for combining transcriptomic and protein-protein interaction data to find differentially expressed gene modules that may reflect key processes in AD biology. A total of 735 differentially expressed genes were clustered into 33 modules, of which 82% replicated in a second data set, highlighting the robustness of this approach. These 27 modules were enriched for signal transduction, transport, response to stimulus, and several organic and cellular metabolic pathways. Ten modules interacted with previously described AD genes. Our study indicates that analyzing RNA-expression data based on annotated gene modules is more robust than on individual genes. We provide a comprehensive overview of the biological processes involved in AD, and the detected differentially expressed gene modules may provide a molecular basis for future research into mechanisms underlying AD.

Objective To analyse LRP10 variants, recently associated with the development of Parkinson's disease (PD), Parkinson's disease dementia (PDD) and dementia with Lewy bodies (DLB), in a series of patients and controls from the South-West of the Netherlands (Walcheren). Methods A series of 130 patients with PD, PDD or DLB were clinically examined, and a structured questionnaire used to collect information about family history of PD and dementia. The entire LRP10 coding region was sequenced by Sanger methods in all patients, and haplotype analysis was performed for one recurrent LRP10 variant. The fragments containing possibly pathogenic LRP10 variants were sequenced in 62 unaffected control subjects from the same region. Other known PD-associated genes were analyzed by exome sequencing and gene dosage in the carriers of LRP10 variants. Results Four patients were carriers of a rare heterozygous, possibly pathogenic LRP10 variant: p.Arg151Cys, p.Arg263His, and p.Tyr307Asn. None of these variants was detected among the controls, nor were additional mutations identified in known PD-associated genes in the four LRP10 variant carriers. The previously reported p.Tyr307Asn variant was identified in two patients (with PD and PDD), who are connected genealogically within six generations, and in one of their relatives with cognitive decline. Haplotype analysis suggests a common founder for the p.Tyr307Asn variant carriers analyzed. Discussion We report three possibly pathogenic LRP10 variants in patients with PD and PDD from a local Dutch population. The identification of additional patients carrying the p.Tyr307Asn variant provides some further evidence that this variant is pathogenic for PD and PDD.

Next-generation sequencing has contributed to our understanding of the genetics of Alzheimer's disease (AD) and has explained a substantial part of the missing heritability of familial AD. We sequenced 19 exomes from 8 Dutch families with a high AD burden and identified EIF2AK3, encoding for protein kinase RNA-like endoplasmic reticulum kinase (PERK), as a candidate gene. Gene-based burden analysis in a Dutch AD exome cohort containing 547 cases and 1070 controls showed a significant association of EIF2AK3 with AD (OR 1.84 [95% CI 1.07-3.17], p-value 0.03), mainly driven by the variant p.R240H. Genotyping of this variant in an additional cohort from the Rotterdam Study showed a trend toward association with AD (p-value 0.1). Immunohistochemical staining with pPERK and peIF2 alpha of 3 EIF2AK3 AD carriers showed an increase in hippocampal neuronal cells expressing these proteins compared with nondemented controls, but no difference was observed in AD noncarriers. This study suggests that rare variants in EIF2AK3 may be associated with disease risk in AD. (C) 2018 The Authors. Published by Elsevier Inc.

Mutations in presenilin 1 (PSEN1), presenilin 2 (PSEN2), and amyloid precursor protein (APP) are major genetic causes of early-onset Alzheimer's disease (EOAD). Clinical heterogeneity is frequently observed in patients with PSEN1 and PSEN2 mutations. Using whole exome sequencing, we screened a Dutch cohort of 68 patients with EOAD for rare variants in Mendelian Alzheimer's disease, frontotemporal dementia, and prion disease genes. We identified 3 PSEN1 and 2 PSEN2 variants. Three variants, 1 in PSEN1 (p.H21Profs*2) and both PSEN2 (p.A415S and p.M174I), were novel and absent in control exomes. These novel variants can be classified as probable pathogenic, except for PSEN1 (p.H21Profs*2) in which the pathogenicity is uncertain. The initial clinical symptoms between mutation carriers varied from behavioral problems to memory impairment. Our findings extend the mutation spectrum of EOAD and underline the clinical heterogeneity among PSEN1 and PSEN2 mutation carriers. Screening for Alzheimer's disease–causing genes is indicated in presenile dementia with an overlapping clinical diagnosis.

Valosin-containing protein (VCP) is involved in multiple cellular activities. Mutations in VCP lead to heterogeneous clinical presentations including inclusion body myopathy with Paget's disease of the bone, frontotemporal dementia and amyotrophic lateral sclerosis, even in patients carrying the same mutation. We screened a cohort of 48 patients with familial frontotemporal dementia (FTD) negative for MAPT, GRN, and C9orf72 mutations for other known FTD genes by using whole exome sequencing. In addition, we carried out targeted sequencing of a cohort of 37 patients with frontotemporal lobar degeneration with Transactive response DNA-binding protein 43 (TDP-43) subtype from the Netherlands Brain bank. Two novel (p.Thr262Ser and p.Arg159Ser) and one reported (p.Met158Val) VCP mutations in three patients with a clinical diagnosis of FTD were identified, and were absence in population-match controls. All three patients presented with behavioral changes, with additional semantic deficits in one. No signs of Paget or muscle disease were observed. Pathological examination of the patient with VCP p.Arg159Ser mutation showed numerous TDP-43 immunoreactive (IR) neuronal intranuclear inclusions (NIT) and dystrophic neurites (DN), while a lower number of NII and DN were observed in the patient with the VCP p.Thr262Ser mutation. Pathological findings of both patients were consistent with FTLD-TDP subtype D. Furthermore, only rare VCP-IR NII was observed in both cases. Our study expands the clinical heterogeneity of VCP mutations carriers, and indicates that other additional factors, such as genetic modifiers, may determine the clinical phenotype.

Genetic factors are important in all forms of dementia, especially in early onset dementia. The frequency of major gene defects in dementia has not been investigated in the Netherlands. Furthermore, whether the recently in a FTD family identified PRKAR1B gene is associated with an Alzheimer's disease (AD) like phenotype, has not been studied. With this study, we aimed to investigate the mutation frequency of the major AD and FTD genes and the PRKAR1B gene in a well-defined Dutch cohort of patients with early onset dementia. Mutation analysis of the genes PSEN1, APP, MAPT, GRN, C9orf72 and PRKAR1B was performed on DNA of 229 patients with the clinical diagnosis AD and 74 patients with the clinical diagnosis FTD below the age of 70 years. PSEN1 and APP mutations were found in, respectively 3.5 and 0.4 % of AD patients, and none in FTD patients. C9orf72 repeat expansions were present in 0.4 % of AD and in 9.9 % of FTD patients, whereas MAPT and GRN mutations both were present in 0.4 % in AD patients, and in 1.4 % resp. 2.7 % in FTD patients. We did not find any pathogenic mutations in the PRKAR1B gene. PSEN1 mutations are the most common genetic cause in Dutch AD patients, whereas MAPT and GRN mutations were found in less than 5 percent. C9orf72 repeat expansions were the most common genetic defect in FTD patients. No pathogenic PRKAR1B mutations were found in the early onset AD and FTD patients of our study.

International audience; Objectives: We describe the largest series of patients with TARDBP mutations presenting with frontotemporal dementia (FTD) and review the cases in the literature to precisely characterize FTD diseases associated with this genotype.Methods: The phenotypic characteristics of 29 TARDBP patients, including 10 new French and Dutch cases and 19 reviewed from the literature, were evaluated.Results: The most frequent phenotype was a behavioral variant frontotemporal dementia (bvFTD), but a significant proportion (40%) of our patients had semantic (svFTD) or nonfluent variants (nfvFTD) at onset; and svFTD was significantly more frequent in TARDBP carriers than in other FTD genotypes (p < 0.001). Remarkably, only a minority (40%) of our patients secondarily developed amyotrophic lateral sclerosis (ALS). Two patients carried a homozygous mutation but strikingly different phenotypes (bvFTD and ALS) indicating that homozygosity does not result in a specific phenotype. Earlier age at onset in children than parent's generations, mimicking an apparent “anticipation” (21.8 ± 9.3 years, p = 0.001), and possible reduced penetrance were present in most families.Conclusions: This study enlarges the phenotypic spectrum of TARDBP and will have important clinical implications: (1) FTD can be the only clinical manifestation of TARDBP mutations; (2) Initial language or semantic disorders might be indicative of a specific genotype; (3) Mutations should be searched in all FTD phenotypes after exclusion of major genes, even in the absence of ALS in the proband or in family history; (4) reduced penetrance and clinical variability should be considered to deliver appropriate genetic counseling.

Cruchaga et al.1 report that rare genetic variants in PLD3(phospholipase D3) are associated with increased Alzheimer’s disease(AD) risk. They showed that PLD3 is involved in amyloid-β precursor protein (APP) processing and overexpressed in brain tissue from AD patients. However, even the key variant PLD3-Val232Met, did not pass genome wide significance. This observation raises the question if the genetic association of PLD3 with AD replicates. We associated PLD3-Val232Met with AD in 3 large population-based studies and 3 case-control studies. In total, we meta-analyzed results from 1914 AD cases and 8021 controls of European descent. Additionally we searched for other coding PLD3-variants in sequence data of 1067 AD cases and 1553 controls. Carrier frequencies of PLD3-Val232Met in controls ranged from 0.34-1.42%, consistent with 0-1.17% reported by Cruchaga et al.1 (Table 1). Likewise, the frequencies of PLD3-Val232Met in cases ranged from 0.66-2.19% compared to 0.7-2.6%.1 We note that the range of carrier frequencies overlaps between cases and controls, such that in some population based cohorts, the carrier frequency in controls (e.g., 1.28% in FHS) is higher than that of cases in other cohorts (e.g., 0.68% in AGES). Within each cohort frequencies of PLD3-Val232Met were higher in cases than controls (Table 1), but in none of the populations the case carrier frequency for PLD3-Val232Met was significantly increased. However, pooled analyses showed a 1.94 fold increased risk of AD of carriers compared to non-carriers (Odds Ratio [OR] 1.94, adjusted for age and sex, 95% confidence interval=1.05 to 3.57) that was marginally significant (p-value = 0.03)(Table 1). Of note, the crude ORs often differed considerably from the age and sex adjusted estimates. With the exception of ADNI, the ORs were higher after adjustment for age and sex, suggesting that many a-symptomatic carriers were relatively young compared to cases and age needs to be controlled for in the analyses as a putative confounder. Table 1 Association of PLD3-Val232Met with Alzheimer’s disease We further associated other coding variants in PLD3 with AD and performed a gene-based test using sequence data from two studies encompassing 1067 AD cases and 1553 controls. We meta-analyzed results of whole genome sequence data of the ADNI study, 499 AD cases and 293 controls, with results of a combined cohort of 568 Dutch AD cases and 1260 Dutch controls. We observed 21 rare polymorphic coding variants and 1 splice site variant. Of the 20 observed PLD3-variants detected by Cruchaga et al.1, we observed 9 (S63G, P76A, V232M, N284S, C300Y, A442A, G452E, D447G and R488C). Five variants showed the same direction of effect as seen by Cruchaga et al.1. PLD3-A442A was one of the variants that showed a same direction of effect(Odds Ratio [OR] 1.24, 95% confidence interval = 0.74 to 2.06, p-value = 0.41). After correcting the p-value for multiple testing, none of the variants observed in our study conferred a significant increase in AD risk. Gene-based analysis also did not show significant association of PLD3-variants with AD risk (SKAT-O p-value = 0.61 and burden test OR 1.27 95% confidence interval [CI] =0.85 to 1.9, p-value = 0.24). In conclusion, the carrier frequencies of PLD3-Val232Met in our data set are consistent with those reported by Cruchaga et al.1 and we showed a nominally significant association of PLD3-Val232Met with AD. This is in contrast to findings presented in companion papers by Heilmann et al., Lambert et al. and Hooli et al. However, in contrast to Cruchaga et al.1 we found no significant association of other PLD3-variants with AD in the single variant or gene based analyses. Therefore, in our analyses PLD3 does not yet meet the criteria proposed by MacArthur et al.2 to be implicated in AD. Hence, our data do not strongly support an important contribution of rare PLD3-variants in the etiology of AD. The most notable findings in our study are the need to control for age as a confounder in rare variant analyses and the high variability of the frequency of PLD3-Val232Met across populations. The latter finding highlights the need for careful matching of cases and controls for ethnic background when investigating rare variants.

Sir, We thank Pottier et al. , 2014 for their interest in our recent study, reporting the identification of a novel mutation in the PRKAR1B gene in a family with cases of FUS-negative neuronal intermediate filament inclusion disease (NIFID) …

as a useful quantitative phenotype for GWAS and other "omics" analyses. Methods:We included non-Hispanic White participants from four prospective community-based cohort studies (ROS, MAP, CHAP, EAS) who were non-demented at study entry and have at least two repeatedmeasures of cognition.Within each cohort, individual cognitive tests were combined to form aggregate measures of global cognition and episodic memory. Genotype data from each cohort was quality controlled and imputed using 1000Genomes reference panel. We used linear mixed effects models to characterize individual paths of change in cognition, modeling age, sex and education as fixed effects and intercept and slope as random effects. For initial screen, we extracted individual residual cognitive slope estimates from the models and fit a linear regression model for each single nucleotide polymorphism (SNP), adjusting for population stratification. Results were meta-analyzed across cohorts. SNPs with p< 5x10 -8 were considered genome-wide significant and p < 5x10 -5 were considered suggestive. Results: A total of 3534 subjects were included. The average age at enrollment in each study ranged from 72 to 81, follow-up ranged from 2-18 years and incidence of clinical diagnosis of AD ranged from 19% to 34%. The most significant loci for decline in both global cognition and episodic memory was APOE (p1⁄43.1x10 -34 and p1⁄42.1x10 -24, respectively). Although no other nonAPOE locus reached genome-wide significance, we found highly suggestive results at two other regions. First, for global cognition, near the EDAR gene with the top locus reaching a p1⁄48.9x10 -8 and second, on the RAB3GAP2 genewith the top locus reaching a p1⁄41.3x10 -7. Results were similar for episodic memory. We are currently analyzing data from two other cohort studies for validation. Top hits will be further investigated with full mixed effects models for all SNPs with p < 5x10 -4. Conclusions: Our findings to date suggest that cognitive decline may be a useful phenotype for identifying genomic variation associated with AD or other factors influencing cognitive decline.