BIN1 rs744373 variant shows different association with Alzheimer’s disease in Caucasian and Asian populations

Abstract Background The association between BIN1 rs744373 variant and Alzheimer’s disease (AD) had been identified by genome-wide association studies (GWASs) as well as candidate gene studies in Caucasian populations. But in East Asian populations, both positive and negative results had been identified by association studies. Considering the smaller sample sizes of the studies in East Asian, we believe that the results did not have enough statistical power. Results We conducted a meta-analysis with 71,168 samples (22,395 AD cases and 48,773 controls, from 37 studies of 19 articles). Based on the additive model, we observed significant genetic heterogeneities in pooled populations as well as Caucasians and East Asians. We identified a significant association between rs744373 polymorphism with AD in pooled populations (P = 5 × 10− 07, odds ratio (OR) = 1.12, and 95% confidence interval (CI) 1.07–1.17) and in Caucasian populations (P = 3.38 × 10− 08, OR = 1.16, 95% CI 1.10–1.22). But in the East Asian populations, the association was not identified (P = 0.393, OR = 1.057, and 95% CI 0.95–1.15). Besides, the regression analysis suggested no significant publication bias. The results for sensitivity analysis as well as meta-analysis under the dominant model and recessive model remained consistent, which demonstrated the reliability of our finding. Conclusions The large-scale meta-analysis highlighted the significant association between rs744373 polymorphism and AD risk in Caucasian populations but not in the East Asian populations.

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Fast Algorithms for Conducting Large-Scale GWAS of Age-at-Onset Traits Using Cox Mixed-Effects Models

Genetics ◽

10.1534/genetics.119.302940 ◽

2020 ◽

Vol 215 (1) ◽

pp. 41-58 ◽

Cited By ~ 4

Author(s):

Liang He ◽

Alexander M. Kulminski

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Statistical Power ◽

Large Scale ◽

Cox Model ◽

Association Studies ◽

Age At Onset ◽

Mixed Effects ◽

Mixed Effects Models ◽

Genome Wide Association Studies

Age-at-onset is one of the critical traits in cohort studies of age-related diseases. Large-scale genome-wide association studies (GWAS) of age-at-onset traits can provide more insights into genetic effects on disease progression and transitions between stages. Moreover, proportional hazards (or Cox) regression models can achieve higher statistical power in a cohort study than a case-control trait using logistic regression. Although mixed-effects models are widely used in GWAS to correct for sample dependence, application of Cox mixed-effects models (CMEMs) to large-scale GWAS is so far hindered by intractable computational cost. In this work, we propose COXMEG, an efficient R package for conducting GWAS of age-at-onset traits using CMEMs. COXMEG introduces fast estimation algorithms for general sparse relatedness matrices including, but not limited to, block-diagonal pedigree-based matrices. COXMEG also introduces a fast and powerful score test for dense relatedness matrices, accounting for both population stratification and family structure. In addition, COXMEG generalizes existing algorithms to support positive semidefinite relatedness matrices, which are common in twin and family studies. Our simulation studies suggest that COXMEG, depending on the structure of the relatedness matrix, is orders of magnitude computationally more efficient than coxme and coxph with frailty for GWAS. We found that using sparse approximation of relatedness matrices yielded highly comparable results in controlling false-positive rate and retaining statistical power for an ethnically homogeneous family-based sample. By applying COXMEG to a study of Alzheimer’s disease (AD) with a Late-Onset Alzheimer’s Disease Family Study from the National Institute on Aging sample comprising 3456 non-Hispanic whites and 287 African Americans, we identified the APOE ε4 variant with strong statistical power (P = 1e−101), far more significant than that reported in a previous study using a transformed variable and a marginal Cox model. Furthermore, we identified novel SNP rs36051450 (P = 2e−9) near GRAMD1B, the minor allele of which significantly reduced the hazards of AD in both genders. These results demonstrated that COXMEG greatly facilitates the application of CMEMs in GWAS of age-at-onset traits.

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Life Course Adiposity and Alzheimer’s Disease: A Mendelian Randomization Study

Journal of Alzheimer s Disease ◽

10.3233/jad-210345 ◽

2021 ◽

pp. 1-10

Author(s):

Xian Li ◽

Yan Tian ◽

Yu-Xiang Yang ◽

Ya-Hui Ma ◽

Xue-Ning Shen ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Life Course ◽

Mendelian Randomization ◽

Association Studies ◽

Meta Analysis ◽

Genome Wide Association Studies ◽

Fat Percentage ◽

Regression Methods ◽

Weighted Median

Background: Several studies showed that life course adiposity was associated with Alzheimer’s disease (AD). However, the underlying causality remains unclear. Objective: We aimed to examine the causal relationship between life course adiposity and AD using Mendelian randomization (MR) analysis. Methods: Instrumental variants were obtained from large genome-wide association studies (GWAS) for life course adiposity, including birth weight (BW), childhood body mass index (BMI), adult BMI, waist circumference (WC), waist-to-hip ratio (WHR), and body fat percentage (BFP). A meta-analysis of GWAS for AD including 71,880 cases and 383,378 controls was used in this study. MR analyses were performed using inverse variance weighted (IVW), weighted median, and MR-Egger regression methods. We calculated odds ratios (ORs) per genetically predicted standard deviation (1-SD) unit increase in each trait for AD. Results: Genetically predicted 1-SD increase in adult BMI was significantly associated with higher risk of AD (IVW: OR = 1.03, 95% confidence interval [CI] = 1.01–1.05, p = 2.7×10–3) after Bonferroni correction. The weighted median method indicated a significant association between BW and AD (OR = 0.94, 95% CI = 0.90–0.98, p = 1.8×10–3). We also found suggestive associations of AD with WC (IVW: OR = 1.03, 95% CI = 1.00–1.07, p = 0.048) and WHR (weighted median: OR = 1.04, 95% CI = 1.00–1.07, p = 0.029). No association was detected of AD with childhood BMI and BFP. Conclusion: Our study demonstrated that lower BW and higher adult BMI had causal effects on increased AD risk.

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Genome-Wide Meta-Analysis of Late-Onset Alzheimer's Disease Using Rare Variant Imputation in 324,809 Subjects Identifies Novel Rare Variant Locus NCK2: The International Genomics of Alzheimer's Project (IGAP)

10.1101/2021.03.14.21253553 ◽

2021 ◽

Author(s):

Adam C. Naj ◽

Ganna Leonenko ◽

Xueqiu Jian ◽

Benjamin Grenier-Boley ◽

Maria Carolina Dalmasso ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Rare Variant ◽

Late Onset ◽

Sequence Data ◽

Association Studies ◽

Meta Analysis ◽

Genome Wide Association Studies ◽

Genome Wide ◽

The Uk

Risk for late-onset Alzheimer's disease (LOAD) is driven by multiple loci primarily identified by genome-wide association studies, many of which are common variants with minor allele frequencies (MAF)>0.01. To identify additional common and rare LOAD risk variants, we performed a GWAS on 25,170 LOAD subjects and 41,052 cognitively normal controls in 44 datasets from the International Genomics of Alzheimer's Project (IGAP). Existing genotype data were imputed using the dense, high-resolution Haplotype Reference Consortium (HRC) r1.1 reference panel. Stage 1 associations of P<10-5 were meta-analyzed with the European Alzheimer's Disease Biobank (EADB) (n=20,301 cases; 21,839 controls) (stage 2 combined IGAP and EADB). An expanded meta-analysis was performed using a GWAS of parental AD/dementia history in the UK Biobank (UKBB) (n=35,214 cases; 180,791 controls) (stage 3 combined IGAP, EADB, and UKBB). Common variant (MAF≥0.01) associations were identified for 29 loci in stage 2, including novel genome-wide significant associations at TSPAN14 (P=2.33×10-12), SHARPIN (P=1.56×10-9), and ATF5/SIGLEC11 (P=1.03[mult]10-8), and newly significant associations without using AD proxy cases in MTSS1L/IL34 (P=1.80×10-8), APH1B (P=2.10×10-13), and CLNK (P=2.24×10-10). Rare variant (MAF<0.01) associations with genome-wide significance in stage 2 included multiple variants in APOE and TREM2, and a novel association of a rare variant (rs143080277; MAF=0.0054; P=2.69×10-9) in NCK2, further strengthened with the inclusion of UKBB data in stage 3 (P=7.17×10-13). Single-nucleus sequence data shows that NCK2 is highly expressed in amyloid-responsive microglial cells, suggesting a role in LOAD pathology.

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Meta-analysis of genetic association with diagnosed Alzheimer’s disease identifies novel risk loci and implicates Abeta, Tau, immunity and lipid processing

10.1101/294629 ◽

2018 ◽

Cited By ~ 9

Author(s):

BW Kunkle ◽

B Grenier-Boley ◽

R Sims ◽

JC Bis ◽

AC Naj ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Rare Variants ◽

Late Onset ◽

Association Studies ◽

Meta Analysis ◽

The Elderly ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Load Risk

IntroductionLate-onset Alzheimer’s disease (LOAD, onset age > 60 years) is the most prevalent dementia in the elderly1, and risk is partially driven by genetics2. Many of the loci responsible for this genetic risk were identified by genome-wide association studies (GWAS)3–8. To identify additional LOAD risk loci, the we performed the largest GWAS to date (89,769 individuals), analyzing both common and rare variants. We confirm 20 previous LOAD risk loci and identify four new genome-wide loci (IQCK, ACE, ADAM10, and ADAMTS1). Pathway analysis of these data implicates the immune system and lipid metabolism, and for the first time tau binding proteins and APP metabolism. These findings show that genetic variants affecting APP and Aβ processing are not only associated with early-onset autosomal dominant AD but also with LOAD. Analysis of AD risk genes and pathways show enrichment for rare variants (P = 1.32 × 10−7) indicating that additional rare variants remain to be identified.

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Pleiotropy of Alzheimer’s Disease and Educational Attainment: Insights from the Summary Statistics

Innovation in Aging ◽

10.1093/geroni/igab046.3513 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. 986-986

Author(s):

Yury Loika ◽

Elena Loiko ◽

Irina Culminskaya ◽

Alexander Kulminski

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Educational Attainment ◽

Large Scale ◽

Association Studies ◽

Epidemiological Studies ◽

Genome Wide Association Studies ◽

Summary Statistics ◽

Nucleotide Polymorphisms ◽

Omnibus Test

Abstract Epidemiological studies report beneficial associations of higher educational attainment (EDU) with Alzheimer’s disease (AD). Prior genome-wide association studies (GWAS) also reported variants associated with AD and EDU separately. The analysis of pleiotropic predisposition to these phenotypes may shed light on EDU-related protection against AD. We examined pleiotropic predisposition to AD and EDU using Fisher’s method and omnibus test applied to summary statistics for single nucleotide polymorphisms (SNPs) associated with AD and EDU in large-scale univariate GWAS at suggestive-effect (5×10-8

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Possible Role of Activin in the Adiponectin Paradox-Induced Progress of Alzheimer’s Disease

Journal of Alzheimer s Disease ◽

10.3233/jad-210206 ◽

2021 ◽

pp. 1-8

Author(s):

Makoto Hashimoto ◽

Gilbert Ho ◽

Shuei Sugama ◽

Takato Takenouchi ◽

Masaaki Waragai ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Transforming Growth Factor ◽

Association Studies ◽

Meta Analysis ◽

Amyloid Β ◽

Activin A ◽

Antagonistic Pleiotropy ◽

Type I ◽

Genome Wide Association Studies

Accumulating evidence suggests that the adiponectin (APN) paradox might be involved in promoting aging-associated chronic diseases such as Alzheimer’s disease (AD). In human brain, APN regulation of the evolvability of amyloidogenic proteins (APs), including amyloid-β (Aβ) and tau, in developmental/reproductive stages, might be paradoxically manifest as APN stimulation of AD through antagonistic pleiotropy in aging. The unique mechanisms underlying APN activity remain unclear, a better understanding of which might provide clues for AD therapy. In this paper, we discuss the possible relevance of activin, a member of transforming growth factor β (TGFβ) superfamily of peptides, to antagonistic pleiotropy effects of APN. Notably, activin, a multiple regulator of cell proliferation and differentiation, as well as an endocrine modulator in reproduction and an organizer in early development, might promote aging-associated disorders, such as inflammation and cancer. Indeed, serum activin, but not serum TGFβ increases during aging. Also, activin/TGFβ signal through type II and type I receptors, both of which are transmembrane serine/threonine kinases, and the serine/threonine phosphorylation of APs, including Aβ 42 serine 8 and αS serine 129, may confer pathological significance in neurodegenerative diseases. Moreover, activin expression is induced by APN in monocytes and hepatocytes, suggesting that activin might be situated downstream of the APN paradox. Finally, a meta-analysis of genome-wide association studies demonstrated that two SNPs relevant to the activin/TGFβ receptor signaling pathways conferred risk for major aging-associated disease. Collectively, activin might be involved in the APN paradox of AD and could be a significant therapeutic target.

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Meta-Analysis of Aldehyde Dehydrogenase 2 Gene Polymorphism and Alzheimer's Disease in East Asians

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques ◽

10.1017/s0317167100011938 ◽

2011 ◽

Vol 38 (3) ◽

pp. 500-506 ◽

Cited By ~ 25

Author(s):

Pan-Pan Hao ◽

Yu-Guo Chen ◽

Jia-Li Wang ◽

Xing Li Wang ◽

Yun Zhang

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Aldehyde Dehydrogenase ◽

Meta Analysis ◽

East Asian ◽

Small Sample ◽

Aldehyde Dehydrogenase 2 ◽

Cross Sectional ◽

Asian Populations ◽

Aldehyde Dehydrogenase 2 Gene

Background:The association of genetic polymorphism of mitochondrial aldehyde dehydrogenase 2 (ALDH2) and Alzheimer's disease (AD) has been controversial and has been investigated only in several small-sample studies. In the present study, we performed a meta-analysis to evaluate the cross-sectional association ofALDH2variants and AD risk in East Asian populations.Methods:Trials were retrieved through MEDLINE, EMBASE, J-STAGE and the China National Knowledge Internet databases (from January 1, 1994 to November 1, 2010) without any restriction on language. Data were abstracted by a standardized protocol.Results:We found four studies of 821AD patients and 1380 healthy controls that qualified for the analysis. The variantALDH2genotype GA/AA was not associated with increased AD risk (odds ratio (OR) = 1.35; 95% confidence interval (CI) = 0.75-2.42; p = 0.32), even after stratification for the status of apolipoprotein E epsilon 4 allele. However, in the subgroup analyses, the association was significant for men (OR = 1.72; 95% CI = 1.10-2.67; p = 0.02).Conclusions:This study adds to the evidence thatALDH2GA/AA genotype increases the risk of AD among East Asian men, although the effect size is moderate.

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Functional biological paths altered in Alzheimer’s disease: from genes to bile acids

10.1101/2020.01.31.929554 ◽

2020 ◽

Author(s):

Priyanka Gorijala ◽

Kwangsik Nho ◽

Shannon L. Risacher ◽

Rima Kaddurah-Daouk ◽

Andrew J. Saykin ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Bile Acids ◽

Biological Networks ◽

Large Scale ◽

Association Studies ◽

Underlying Mechanism ◽

Genome Wide Association Studies ◽

Functional Protein ◽

Age Related

AbstractLarge-scale genome wide association studies (GWASs) have been performed in search for risk genes for Alzheimer’s disease (AD). Despite the significant progress, replicability of genetic findings and their translation into targetable mechanisms related to the disease pathogenesis remains a challenge. Given that bile acids have been suggested in recent metabolic studies as potential age-related metabolic factors associated with AD, we integrated genomic and metabolomic data together with heterogeneous biological networks and investigated the potential cascade of effect of genetic variations to proteins, bile acids and ultimately AD brain phenotypes. Particularly, we leveraged functional protein interaction networks and metabolic networks and focused on the genes directly interacting with AD-altered bile acids and their functional regulators. We examined the association of all the SNPs located in those candidate genes with AD brain imaging phenotypes, and identified multiple AD risk SNPs whose downstream genes and bile acids were also found to be altered in AD. These AD related markers span from genetics to metabolomics, forming functional biological paths connecting across multiple-omics layers, and give valuable insights into the underlying mechanism of AD.

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Cross–trait analysis of Alzheimer’s disease and gastrointestinal tract disorders identifies shared loci highlighting immune-related and statin pathways

10.21203/rs.3.rs-757229/v1 ◽

2021 ◽

Author(s):

Emmanuel Adewuyi ◽

Eleanor O’Brien ◽

Dale Nyholt ◽

Tenielle Porter ◽

Simon Laws

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Gastrointestinal Tract ◽

Association Studies ◽

Meta Analysis ◽

Genome Wide Association Studies ◽

Ulcer Disease ◽

Genome Wide ◽

Underlying Mechanisms ◽

Irritable Bowel

Abstract Several observational studies suggest a relationship between Alzheimer’s disease (AD) and gastrointestinal tract (GIT) disorders; however, their underlying mechanisms remain unclear. Here, we analysed several genome-wide association studies (GWAS) summary statistics (N = 34,652 – 456,327) to assess AD and GIT disorders relationships. We found a significant genetic overlap and correlation between AD and each of gastroesophageal reflux disease (GERD), peptic ulcer disease (PUD), medications for GERD or PUD (PGM), gastritis-duodenitis, irritable bowel syndrome and diverticulosis, but not inflammatory bowel disease. Our analysis suggests a partial causal association between AD and gastritis-duodenitis, diverticulosis and medication for PUD. GWAS meta-analysis identified seven loci (P < 5 × 10-8, PDE4B, CD46, SEMA3F, HLA-DRA, MTSS2, PHB, and APOE) shared by AD and PGM, six of which are novel. These loci were replicated using GERD and PUD GWAS and reinforced in gene-based analyses. Lipid metabolism, autoimmune system, lipase inhibitors, PD-1 signalling, and statin pathways were significantly enriched for AD and GIT disorders. These findings support shared genetic susceptibility in AD and GIT disorders. Lipase inhibitors and statins may provide novel therapeutic avenues for AD, GIT disorders, or their comorbidity.

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Alzheimer’s disease risk SNPs show no strong effect on miRNA expression in human lymphoblastoid cell lines

10.1101/367318 ◽

2018 ◽

Author(s):

Inken Wohlers ◽

Colin Schulz ◽

Fabian Kilpert ◽

Lars Bertram

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Cell Lines ◽

Mirna Expression ◽

Large Scale ◽

Disease Risk ◽

Association Studies ◽

Lymphoblastoid Cell Lines ◽

Eqtl Analysis ◽

Genome Wide Association Studies

AbstractThe role of microRNAs (miRNAs) in the pathogenesis of Alzheimer’s disease (AD) is currently extensively investigated. In this study, we assessed the potential impact of AD genetic risk variants on miRNA expression by performing large-scale bioinformatic data integration. Our analysis was based on genetic variants from three AD genome-wide association studies (GWAS). Association with miRNA expression was tested by expression quantitative trait loci (eQTL) analysis using next-generation miRNA sequencing data generated in lymphoblastoid cell lines (LCL). While, overall, we did not identify a strong effect of AD GWAS variants on miRNA expression in this cell type we highlight two notable outliers, i.e. miR-29c-5p and miR-6840-5p. MiR-29c-5p was recently reported to be involved in the regulation of BACE1 and SORL1 expression. In conclusion, despite two exceptions our large-scale assessment provides only limited support for the hypothesis that AD GWAS variants act as miRNA eQTLs.

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