scholarly journals Meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex

2020 ◽  
Author(s):  
Rebecca G. Smith ◽  
Ehsan Pishva ◽  
Gemma Shireby ◽  
Adam R. Smith ◽  
Janou A.Y. Roubroeks ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Association Studies ◽  
Meta Analysis ◽  
Brain Regions ◽  
Braak Stage ◽  
Combine Data ◽  
Online Data ◽  
Data Resource ◽  
Significance Threshold

ABSTRACTEpigenome-wide association studies of Alzheimer’s disease have highlighted neuropathology-associated DNA methylation differences, although existing studies have been limited in sample size and utilized different brain regions. Here, we combine data from six DNA methylomic studies of Alzheimer’s disease (N=1,453 unique individuals) to identify differential methylation associated with Braak stage in different brain regions and across cortex. We identified 236 CpGs in the prefrontal cortex, 95 CpGs in the temporal gyrus and ten CpGs in the entorhinal cortex at Bonferroni significance, with none in the cerebellum. Our cross-cortex meta-analysis (N=1,408 donors) identified 220 CpGs associated with neuropathology, annotated to 121 genes, of which 84 genes had not been previously reported at this significance threshold. We have replicated our findings using two further DNA methylomic datasets consisting of a > 600 further unique donors. The meta-analysis summary statistics are available in our online data resource (www.epigenomicslab.com/ad-meta-analysis/).

scholarly journals A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rebecca G. Smith ◽  
Ehsan Pishva ◽  
Gemma Shireby ◽  
Adam R. Smith ◽  
Janou A. Y. Roubroeks ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Association Studies ◽  
Meta Analysis ◽  
Brain Regions ◽  
Braak Stage ◽  
Combine Data ◽  
Online Data ◽  
Data Resource ◽  
Significance Threshold

AbstractEpigenome-wide association studies of Alzheimer’s disease have highlighted neuropathology-associated DNA methylation differences, although existing studies have been limited in sample size and utilized different brain regions. Here, we combine data from six DNA methylomic studies of Alzheimer’s disease (N = 1453 unique individuals) to identify differential methylation associated with Braak stage in different brain regions and across cortex. We identify 236 CpGs in the prefrontal cortex, 95 CpGs in the temporal gyrus and ten CpGs in the entorhinal cortex at Bonferroni significance, with none in the cerebellum. Our cross-cortex meta-analysis (N = 1408 donors) identifies 220 CpGs associated with neuropathology, annotated to 121 genes, of which 84 genes have not been previously reported at this significance threshold. We have replicated our findings using two further DNA methylomic datasets consisting of a further >600 unique donors. The meta-analysis summary statistics are available in our online data resource (www.epigenomicslab.com/ad-meta-analysis/).

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

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.

scholarly journals Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Lanyu Zhang ◽  
Tiago C. Silva ◽  
Juan I. Young ◽  
Lissette Gomez ◽  
Michael A. Schmidt ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Dna Methylation ◽  
Prefrontal Cortex ◽  
Biomarker Discovery ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Braak Stage ◽  
Polycomb Repressive Complex 2 ◽  
Differentially Methylated Genes

AbstractDNA methylation differences in Alzheimer’s disease (AD) have been reported. Here, we conducted a meta-analysis of more than 1000 prefrontal cortex brain samples to prioritize the most consistent methylation differences in multiple cohorts. Using a uniform analysis pipeline, we identified 3751 CpGs and 119 differentially methylated regions (DMRs) significantly associated with Braak stage. Our analysis identified differentially methylated genes such as MAMSTR, AGAP2, and AZU1. The most significant DMR identified is located on the MAMSTR gene, which encodes a cofactor that stimulates MEF2C. Notably, MEF2C cooperates with another transcription factor, PU.1, a central hub in the AD gene network. Our enrichment analysis highlighted the potential roles of the immune system and polycomb repressive complex 2 in pathological AD. These results may help facilitate future mechanistic and biomarker discovery studies in AD.

scholarly journals 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)

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.

scholarly journals A Meta-Analysis of Alzheimer’s Disease Brain Transcriptomic Data

2018 ◽  
Author(s):  
Hamel Patel ◽  
Richard J.B Dobson ◽  
Stephen J Newhouse
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Frontal Lobe ◽  
Temporal Lobe ◽  
Parietal Lobe ◽  
Meta Analysis ◽  
Differential Expression Analysis ◽  
Brain Regions ◽  
Biological Pathways ◽  
Transcriptomic Changes

ABSTRACTBackgroundMicroarray technologies have identified imbalances in the expression of specific genes and biological pathways in Alzheimer’s disease (AD) brains. However, there is a lack of reproducibility across individual AD studies, and many related neurodegenerative and mental health disorders exhibit similar perturbations. We are yet to identify robust transcriptomic changes specific to AD brains.Methods and ResultsTwenty-two AD, eight Schizophrenia, five Bipolar Disorder, four Huntington's disease, two Major Depressive Disorder and one Parkinson’s disease dataset totalling 2667 samples and mapping to four different brain regions (Temporal lobe, Frontal lobe, Parietal lobe and Cerebellum) were analysed. Differential expression analysis was performed independently in each dataset, followed by meta-analysis using a combining p-value method known as Adaptively Weighted with One-sided Correction. This identified 323, 435, 1023 and 828 differentially expressed genes specific to the AD temporal lobe, frontal lobe, parietal lobe and cerebellum brain regions respectively. Seven of these genes were consistently perturbed across all AD brain regions with SPCS1 gene expression pattern replicating in RNA-seq data. A further nineteen genes were perturbed specifically in AD brain regions affected by both plaques and tangles, suggesting possible involvement in AD neuropathology. Biological pathways involved in the “metabolism of proteins” and viral components were significantly enriched across AD brains.ConclusionThis study solely relied on publicly available microarray data, which too often lacks appropriate phenotypic information for robust data analysis and needs to be addressed by future studies. Nevertheless, with the information available, we were able to identify specific transcriptomic changes in AD brains which could make a significant contribution towards the understanding of AD disease mechanisms and may also provide new therapeutic targets.

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

2018 ◽  
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.

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

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.

scholarly journals Multi-regional Neurodegeneration in Alzheimer’s disease: Meta-analysis and data integration of transcriptomics data

2018 ◽  
Author(s):  
Karbalaei Reza ◽  
Rezaei-Tavirani Mostafa ◽  
Torkzaban Bahareh ◽  
Azimzadeh Sadegh
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Metabolic Pathways ◽  
Analytical Study ◽  
Meta Analysis ◽  
Brain Regions ◽  
Regulatory Pathways ◽  
Transcriptomics Data ◽  
The Brain

AbstractAlzheimer’s disease (AD) is a complex neurodegenerative disease with various deleterious perturbations in regulatory pathways of various brain regions. Thus, it would be critical to understanding the role of different regions of the brain in initiation and progression of AD, However, owing to complex and multifactorial nature of this disease, the molecular mechanism of AD has yet to be fully elucidated. To confront with this challenge, we launched a meta-analytical study of current transcriptomics data in four different regions of the brain in AD (Entorhinal, Hippocampus, Temporal and Frontal) with systems analysis of identifying involved signaling and metabolic pathways. We found different regulatory patterns in Entorhinal and Hippocampus regions to be associated with progression of AD. We also identified shared versus unique biological pathways and critical proteins among different brain regions. ACACB, GAPDH, ACLY, and EGFR were the most important proteins in Entorhinal, Frontal, Hippocampus and Temporal regions, respectively. Moreover, eight proteins including CDK5, ATP5G1, DNM1, GNG3, AP2M1, ALDOA, GPI, and TPI1 were differentially expressed in all four brain regions, among which, CDK5 and ATP5G1 were enriched in KEGG Alzheimer’s disease pathway as well.

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

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.

scholarly journals Sex-specific DNA methylation changes in Alzheimer’s disease pathology

2021 ◽  
Author(s):  
Lanyu Zhang ◽  
Juan Young ◽  
Lissette Gomez ◽  
Tiago Silva ◽  
Michael Schmidt ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Dna Methylation ◽  
Epigenetic Modification ◽  
Association Studies ◽  
Specific Treatment ◽  
Type I ◽  
Braak Stage ◽  
Biological Processes ◽  
Specific Manner

Abstract Sex is an important factor that contributes to the clinical and biological heterogeneities in Alzheimer’s disease (AD), but the regulatory mechanisms underlying sex disparity in AD are still not well understood. DNA methylation is an important epigenetic modification that regulates gene transcription and is known to be involved in AD. We performed the first large-scale sex-specific meta-analysis of DNA methylation changes in AD, by re-analyzing four recent epigenome-wide association studies totaling more than 1000 postmortem prefrontal cortex brain samples using a uniform analytical pipeline. For each cohort we employed two complementary analytical strategies, a sex-stratified analysis that examined methylation-Braak stage associations in male and female samples separately, and a sex-by-Braak stage interaction analysis that compared the magnitude of these associations between different sexes. Our analysis uncovered 14 novel CpGs, mapped to genes such as TMEM39A and TNXB that are associated with AD in a sex-specific manner. TMEM39A is known to be involved in inflammation, dysregulated type I interferon responses, and other immune processes. TNXB encodes tenascin proteins, which are extracellular matrix glycoproteins demonstrated to modulate synaptic plasticity in the brain. Moreover, for many previously implicated AD genes, such as MBP and AZU1, our analysis provided the new insights that they were predominately driven by effects in only one sex. These sex-specific DNA methylation changes were enriched in divergent biological processes such as integrin activation in females and complement activation in males. Importantly, a number of drugs commonly prescribed for AD patients also targeted these genes with sex-specific DNA methylation changes. Our study implicated multiple new loci and biological processes that affected AD in a sex-specific manner and highlighted the importance of sex-specific treatment regimens for AD patients.

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