Biology subjects

Andrews, S. J.

Publications and source records attributed to Andrews, S. J..

10 recordsLinked to original sources

bioRxiv2021

Genome-wide association study and functional validation implicates JADE1 in tauopathy

Primary age-related tauopathy (PART) is a neurodegenerative tauopathy with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-{beta} (A{beta}) deposition in plaques. The pathogenesis of PART is unknown, but evidence suggests it is associated with genes that promote tau pathology as well as others that protect from A{beta} toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n=647) using Braak neurofibrillary tangle stage as a quantitative trait adjusting for sex, age, genotyping platform, and principal components. We found significant associations with some candidate loci associated with AD and progressive supranuclear palsy, a primary tauopathy (SLC24A4, MS4A6A, HS3ST1, MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brain from tauopathies containing isoforms with four microtubule-binding domain repeats (4R) and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation revealed a direct and specific binding of JADE1 protein to tau containing four (4R) and no N-terminal inserts (0N4R) in post-mortem human PART brain tissue. Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a mediator of neurofibrillary degeneration.

neuroscience↗

bioRxiv2020

Mitochondrial pathway polygenic risk scores are associated with Alzheimer's Disease

INTRODUCTIONGenetic, animal and epidemiological studies involving biomolecular and clinical endophenotypes implicate mitochondrial dysfunction in Alzheimers disease (AD) pathogenesis. Polygenic risk scores (PRS) provide a novel approach to assess biological pathway-associated disease risk by combining the effects of variation at multiple, functionally related genes. METHODSWe investigated associations of PRS for genes involved in 12 mitochondrial pathways (pathway-PRS) related to AD in 854 participants from Alzheimers Disease Neuroimaging Initiative. RESULTSPathway-PRS for four mitochondrial pathways are significantly associated with increased AD risk: (i) response to oxidative stress (OR: 2.01 [95% Cl: 1.71, 2.37]); (ii) mitochondrial transport (OR: 1.81 [95% Cl: 1.55, 2.13]); (iii) hallmark oxidative phosphorylation (OR: 1.23 [95% Cl: 1.07, 1.41]); and (iv) mitochondrial membrane potential regulation (OR: 1.18 [95% Cl: 1.03, 1.36]). DISCUSSIONTherapeutic approaches targeting these pathways may have potential for modifying AD pathogenesis. Further investigation is required to establish a causal role for these pathways in AD pathology.

neuroscience↗

bioRxiv2020

The variant call format provides efficient and robust storage of GWAS summary statistics

Genome-wide association study (GWAS) summary statistics are a fundamental resource for a variety of research applications 1-6. Yet despite their widespread utility, no common storage format has been widely adopted, hindering tool development and data sharing, analysis and integration. Existing tabular formats 7,8 often ambiguously or incompletely store information about genetic variants and their associations, and also lack essential metadata increasing the possibility of errors in data interpretation and post-GWAS analyses. Additionally, data in these formats are typically not indexed, requiring the whole file to be read which is computationally inefficient. To address these issues, we propose an adaptation of the variant call format9 (GWAS-VCF) and have produced a suite of open-source tools for using this format in downstream analyses. Simulation studies determine GWAS-VCF is 9-46x faster than tabular alternatives when extracting variant(s) by genomic position. Our results demonstrate the GWAS-VCF provides a robust and performant solution for sharing, analysis and integration of GWAS data. We provide open access to over 10,000 complete GWAS summary datasets converted to this format (available from: https://gwas.mrcieu.ac.uk).

genetics↗

bioRxiv2020

Genetic Variants and Functional Pathways Associated with Resilience to Alzheimer's Disease

Approximately 30% of older adults exhibit the neuropathologic features of Alzheimers disease (AD) without signs of cognitive impairment. Yet, little is known about the genetic factors that allow these potentially resilient individuals to remain cognitively normal in the face of substantial neuropathology. We performed a large, genome-wide association study (GWAS) of two previously validated metrics of cognitive resilience quantified using a latent variable modeling approach and representing better-than-predicted cognitive performance for a given level of neuropathology. Data were harmonized across 5,108 participants from a clinical trial of AD and three longitudinal cohort studies of cognitive aging. All analyses were run across all participants and repeated restricting the sample to individuals with normal cognition to identify variants at the earliest stages of disease. As expected, all resilience metrics were genetically correlated with cognitive performance and education attainment traits (p-values<2.5x10-20), and we observed novel correlations with neuropsychiatric conditions (p-values<7.9x10-4). Notably, neither resilience metric was genetically correlated with clinical AD (p-values>0.42) nor associated with APOE (p-values>0.13). In single variant analyses, we observed a genome-wide significant locus among participants with normal cognition on chromosome 18 upstream of ATP8B1 (index SNP rs2571244, MAF=0.08, p=2.3x10-8). The top variant at this locus (rs2571244) was significantly associated with methylation in prefrontal cortex tissue at multiple CpG sites, including one just upstream of ATPB81 (cg19596477; p=2x10-13). Overall, this comprehensive genetic analysis of resilience implicates a putative role of vascular risk, metabolism, and mental health in protection from the cognitive consequences of neuropathology, while also providing evidence for a novel resilience gene along the bile acid metabolism pathway. Furthermore, the genetic architecture of resilience appears to be distinct from that of clinical AD, suggesting that a shift in focus to molecular contributors to resilience may identify novel pathways for therapeutic targets.

genetics↗

bioRxiv2019

Causal associations between potentially modifiable risk factors and the Alzheimer’s phenome: A Mendelian randomization study

ObjectiveTo evaluate the causal association of 22 previously reported risk factors for Alzheimers disease (AD) on the "AD phenome": AD, AD age of onset (AAOS), hippocampal volume, cortical surface area and thickness, cerebrospinal fluid (CSF) levels of A{beta}42, tau, and ptau181, and the neuropathological burden of neuritic plaques, neurofibrillary tangles, and vascular brain injury (VBI). MethodsPolygenic risk scores (PRS) for the 22 risk factors were computed in 26,431 AD cases/controls and the association with AD was evaluated using logistic regression. Two-sample Mendelian randomization was used to evaluate the causal effect of risk factors on the AD phenome. ResultsPRS for increased education and diastolic blood pressure were associated with reduced risk for AD. PRS for increased total cholesterol and moderate-vigorous physical activity were associated with an increased risk of AD. MR indicated that only Education was causally associated with reduced risk of AD, delayed AAOS, and increased cortical surface area and thickness. Total-and LDL-cholesterol levels were causally associated with increased neuritic plaque burden, while diastolic blood pressure and pulse pressure are causally associated with increased risk of VBI. Furthermore, total cholesterol was associated with decreased hippocampal volume; smoking initiation and BMI with decreased cortical thickness; and sleep duration with increased cortical thickness. InterpretationOur comprehensive examination of the genetic evidence for the causal roles of previously reported risk factors in AD using PRS and MR, supports a causal role for education, blood pressure, cholesterol levels, smoking, and BMI with the AD phenome.

genetics↗

bioRxiv2019

Mendelian randomization indicates that TNF is not causally associated with Alzheimer’s disease

INTRODUCTIONEpidemiological research has suggested that inhibition of tumor necrosis factor (TNF)- in patients with rheumatoid arthritis (RA) reduces the overall risk of Alzheimers disease (AD). TNF- antagonists have been suggested as a potential treatment for AD.\n\nMETHODSWe used a two-sample Mendelian randomization design to examine the causal relationship between blood TNF expression, serum TNF- levels, and RA on AD risk.\n\nRESULTSOur results do not support a causal relationship between TNF expression, serum TNF- levels or RA on AD risk.\n\nDISCUSSIONThese results suggest that TNF- antagonists are unlikely to reduce the risk of AD.

genetics↗

bioRxiv2019

Mitonuclear interactions influence Alzheimer’s disease risk

We examined the associations between mitochondrial DNA haplogroups (MT-hg) and their interactions with a polygenic risk score based on nuclear-encoded mitochondrial genes (nMT-PRS) with risk of dementia and age of onset of dementia (AOO). Logistic regression was used to determine the effect of MT-hgs and nMT-PRS on dementia at baseline (332 controls / 204 cases). Cox proportional hazards models were used to model dementia AOO (n=1047; 433 incident cases). Additionally, we tested for interactions between MT-hg and nMT-PRS in the logistic and Cox models. MT-hg K and a one SD larger nMT-PRS were associated with elevated odds of dementia. Significant antagonistic interactions between the nMT-PRS and MT-hg K and T were observed. Individual MT-hg were not associated with AOO; however, a significant antagonistic interactions was observed between the nMT-PRS and MT-hg T and a synergistic interaction between the nMT-PRS and MT-hg V. These results suggest that MT-hgs influence dementia risk, and that variants in the nuclear and mitochondrial genome interact to influence the age of onset of dementia.\n\nHighlightsO_LIMitochondrial dysfunction has been proposed to influence dementia risk\nC_LIO_LIMT-hg K and T interacted with a genetic risk score to reduce dementia risk\nC_LIO_LIMT-hg T and V interacted with a genetic risk score to influence dementia age of onset\nC_LI

genetics↗

bioRxiv2019

MitoImpute: A Snakemake pipeline for imputation of mitochondrial genetic variants

BackgroundVariation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phylogenetic lineages or haplogroups. This lack of resolution can limit functional and clinical interpretation of a substantial body of existing mtDNA data. To address this limitation, we developed and evaluated a method for imputing missing mtDNA single nucleotide variants (mtSNVs) that uses a large reference alignment of complete mtDNA sequences. The method and reference alignment are combined into a pipeline, which we call MitoImpute. ResultsWe aligned the sequences of 36,960 complete human mitochondrial genomes downloaded from GenBank, filtered and controlled for quality. These sequences were reformatted for use in imputation software, IMPUTE2. We assessed the imputation accuracy of MitoImpute by measuring haplogroup and genotype concordance in data from the 1,000 Genomes Project and the Alzheimers Disease Neuroimaging Initiative (ADNI). The mean improvement of haplogroup assignment in the 1,000 Genomes samples was 42.7% (Matthews correlation coefficient = 0.64). In the ADNI cohort, we imputed missing single nucleotide variants. ConclusionsThese results show that our reference alignment and panel can be used to impute missing mtSNVs in exiting data obtained from using microarrays, thereby broadening the scope of functional and clinical investigation of mtDNA. This improvement may be particularly useful in studies where participants have been recruited over time and mtDNA data obtained using different methods, enabling better integration of early data collected using less accurate methods with more recent sequence data.

genomics↗

bioRxiv2018

Alzheimer’s environmental and genetic risk scores are differentially associated with ‘g’ and δ

IntroductionWe investigated the association of the Australian National University Alzheimers Disease Risk Index (ANU-ADRI) and an AD genetic risk score (GRS) with cognitive performance.\n\nMethodsThe ANU-ADRI (composed of 11 risk factors for AD) and GRS (composed of 25 AD risk loci) were computed in 1,061 community-dwelling older adults. Participants were assessed on 11 cognitive tests and activities of daily living. Structural equation modelling was used to evaluate the association of the ANU-ADRI and GRS with: 1) general cognitive ability (g) 2) dementia related variance in cognitive performance ({delta}) and 3) verbal ability, episodic memory, executive function and processing speed.\n\nResultsA worse ANU-ADRI score was associated with poorer performance in g, {delta}, and each cognitive domain. A worse GRS was associated with poorer performance in {delta} and episodic memory.\n\nDiscussionThe ANU-ADRI was broadly associated with worse cognitive performance, validating its further use in early dementia risk assessment.\n\nHighlightsO_LIAn environmental/lifestyle dementia risk index is broadly associated with cognitive performance\nC_LIO_LIAn Alzheimers genetic risk score is associated with dementia severity and episodic memory\nC_LIO_LIThe environmental risk index is more strongly associated with dementia severity than genetic risk\nC_LI\n\nResearch in ContextO_ST_ABSSystematic ReviewC_ST_ABSThe authors reviewed the literature using online databases (e.g. PubMed). Previous research has highlighted the need for dementia risk assessment tools to be evaluated on outcomes prior to dementia onset, such as cognitive performance. The relevant citations have been appropriately cited.\n\nInterpretationThe Australian National University Alzheimers Disease Risk Index (ANU-ADRI) was more broadly associated with cognitive performance than Alzheimers genetic risk. For the ANU-ADRI, stronger effects were observed for dementia-related variance in cognitive task performance that for variance in general cognitive function. This suggests that ANU-ADRI is more specifically associated with dementia-related processes and further validates its use in early risk assessment for dementia.\n\nFuture DirectionsAccordingly, future studies should seek to evaluate the association of the ANU-ADRI and genetic risk with AD biomarkers and longitudinal cognitive performance to evaluate differential trajectories in g and {delta}.

genetics↗

bioRxiv2017

Association between alcohol consumption and Alzheimer’s disease: A Mendelian Randomization Study

INTRODUCTIONObservational studies have suggested that light-moderate alcohol consumptions decreases the risk of Alzheimers disease, but it is unclear if this association is causal.\n\nMETHODSTwo-sample Mendelian randomization (MR) analysis was used to examine whether alcohol consumption, alcohol dependence or Alcohol Use Disorder Identification Test (AUDIT) scores were causally associated with the risk of Late Onset Alzheimers disease (LOAD) or Alzheimers disease age of onset survival (AAOS). Additionally, {gamma}-glutamyltransferase levels were included as a positive control.\n\nRESULTSThere was no evidence of a causal association between alcohol consumption, alcohol dependence or AUDIT and LOAD. Alcohol consumption was associated with an earlier AAOS and increased {gamma}-glutamyltransferase blood concentrations. Alcohol dependence was associated with a delayed AAOS.\n\nDISCUSSIONMR found robust evidence of a causal association between alcohol consumption and an earlier AAOS, but not alcohol intake and LOAD risk. The protective effect of alcohol dependence is potentially due to survivor bias.\n\nResearch in ContextO_ST_ABSSystematic ReviewC_ST_ABSThe authors reviewed the literature using online databases (e.g. PubMed). Previous research links light-moderate alcohol consumption to a decreased risk of Alzheimers disease (AD), however, prior studies based on observational study designs may be biased due to unmeasured confounders influencing both alcohol consumption and AD risk.\n\nInterpretationWe used a two-sample Mendelian randomization (MR) approach to evaluated the causal relationship between alcohol intake and AD. MR uses genetic variants as proxies for environmental exposures to provide an estimate of the causal association between an intermediate exposure and a disease outcome. MR found evidence of a causal association between alcohol consumption and an earlier AD age of onset, suggesting that light-moderate alcohol consumption does not reduce risk of Alzheimers disease.\n\nFuture DirectionsFuture studies should use alterative study designs and account for additional confounders when evaluating the causal relationship between alcohol consumption and AD.\n\nHighlightsO_LIWe evaluated causal relationships between alcohol intake and Alzheimers disease\nC_LIO_LIAlcohol consumption is causally associated with an earlier Alzheimers age of onset\nC_LIO_LINo evidence of causal assocations between alcohol intake and Alzheimers risk\nC_LI

genetics↗