scholarly journals Molecular Networks and Key Regulators of the Dysregulated Neuronal System in Alzheimer’s Disease

2019 ◽  
Author(s):  
Minghui Wang ◽  
Aiqun Li ◽  
Michiko Sekiya ◽  
Noam D. Beckmann ◽  
Xiuming Quan ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Mechanisms ◽  
Late Onset ◽  
Brain Regions ◽  
Molecular Networks ◽  
Parahippocampal Gyrus ◽  
Specific Gene ◽  
Neuronal System ◽  
Full Spectrum

SUMMARYTo study the molecular mechanisms driving the pathogenesis and identify novel therapeutic targets of late onset Alzheimer’s Disease (LOAD), we performed an integrative network analysis of whole-genome DNA and RNA sequencing profiling of four cortical areas, including the parahippocampal gyrus, across 364 donors spanning the full spectrum of LOAD-related cognitive and neuropathological disease severities. Our analyses revealed thousands of molecular changes and uncovered for the first-time multiple neuron specific gene subnetworks most dysregulated in LOAD. ATP6V1A, a critical subunit of vacuolar-type H+-ATPase (v-ATPase), was predicted to be a key regulator of one neuronal subnetwork and its role in disease-related processes was evaluated through CRISPR-based manipulation of human induced pluripotent stem cell derived neurons and RNAi-based knockdown in transgenic Drosophila models. This study advances our understanding of LOAD pathogenesis by providing the global landscape and detailed circuits of complex molecular interactions and regulations in several key brain regions affected by LOAD and the resulting network models provide a blueprint for developing next generation therapeutics against LOAD.

scholarly journals Failure To Detect Chlamydia pneumoniaein the Late-Onset Alzheimer's Brain

2000 ◽  
Vol 38 (7) ◽  
pp. 2591-2594 ◽  
Author(s):  
Robert H. Ring ◽  
Joseph M. Lyons
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Chlamydia Pneumoniae ◽  
Late Onset ◽  
Brain Regions ◽  
Postmortem Brain ◽  
Respiratory Pathogen ◽  
Specific Gene ◽  
Tissue Samples ◽  
Postmortem Brain Tissue

Epidemiological studies have yet to identify a single cause for the most common late-onset form of Alzheimer's disease. The common respiratory pathogen Chlamydia pneumoniae recently has been implicated as a risk factor for this form of Alzheimer's disease. Were this true, there would be a dramatic shift in current paradigms of Alzheimer's disease research and treatment. In the absence of published confirmation, we obtained postmortem brain tissue from late-onset Alzheimer's disease patients (n = 15) and representative controls (n = 5) and extracted DNA from up to six separate brain regions in each instance, including those areas particularly relevant to Alzheimer's disease neuropathology. Each sample of DNA (n = 101) was assayed five times or more for the presence of C. pneumoniae DNA using a nested-PCR protocol targeting a species-specific gene sequence coding for the major outer membrane protein of this organism. We were unable unequivocally to detect C. pneumoniae in any of the 101 samples tested by PCR and failed to culture the organism from tissue samples. We conclude that C. pneumoniae is neither strongly nor uniquely associated with the neuropathology seen in late-onset Alzheimer's disease.

scholarly journals Differential Network Analyses of Alzheimer’s Disease Identify Early Events in Alzheimer’s Disease Pathology

2014 ◽  
Vol 2014 ◽  
pp. 1-18 ◽  
Author(s):  
Jing Xia ◽  
David M. Rocke ◽  
George Perry ◽  
Monika Ray
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Late Onset ◽  
Brain Regions ◽  
Posterior Cingulate Cortex ◽  
Renal Diseases ◽  
Middle Temporal Gyrus ◽  
Specific Gene ◽  
Network Analyses ◽  
Coexpression Networks

In late-onset Alzheimer’s disease (AD), multiple brain regions are not affected simultaneously. Comparing the gene expression of the affected regions to identify the differences in the biological processes perturbed can lead to greater insight into AD pathogenesis and early characteristics. We identified differentially expressed (DE) genes from single cell microarray data of four AD affected brain regions: entorhinal cortex (EC), hippocampus (HIP), posterior cingulate cortex (PCC), and middle temporal gyrus (MTG). We organized the DE genes in the four brain regions into region-specific gene coexpression networks. Differential neighborhood analyses in the coexpression networks were performed to identify genes with low topological overlap (TO) of their direct neighbors. The low TO genes were used to characterize the biological differences between two regions. Our analyses show that increased oxidative stress, along with alterations in lipid metabolism in neurons, may be some of the very early events occurring in AD pathology. Cellular defense mechanisms try to intervene but fail, finally resulting in AD pathology as the disease progresses. Furthermore, disease annotation of the low TO genes in two independent protein interaction networks has resulted in association between cancer, diabetes, renal diseases, and cardiovascular diseases.

scholarly journals Single-cell transcriptomic analysis elucidates APOE genotype specific changes across cell types in two brain regions in Alzheimer’s disease

2021 ◽  
Author(s):  
Stella Belonwu ◽  
Yaqiao Li ◽  
Daniel Bunis ◽  
Arjun Arkal Rao ◽  
Caroline Warly Solsberg ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Apoe Genotype ◽  
Cell Types ◽  
Brain Regions ◽  
Single Cell Level ◽  
Cell Level ◽  
Single Nucleus

Abstract Alzheimer’s Disease (AD) is a complex neurodegenerative disease that gravely affects patients and imposes an immense burden on caregivers. Apolipoprotein E4 (APOE4) has been identified as the most common genetic risk factor for AD, yet the molecular mechanisms connecting APOE4 to AD are not well understood. Past transcriptomic analyses in AD have revealed APOE genotype-specific transcriptomic differences; however, these differences have not been explored at a single-cell level. Here, we leverage the first two single-nucleus RNA sequencing AD datasets from human brain samples, including nearly 55,000 cells from the prefrontal and entorhinal cortices. We observed more global transcriptomic changes in APOE4 positive AD cells and identified differences across APOE genotypes primarily in glial cell types. Our findings highlight the differential transcriptomic perturbations of APOE isoforms at a single-cell level in AD pathogenesis and have implications for precision medicine development in the diagnosis and treatment of AD.

scholarly journals Linking the association between circRNAs and Alzheimer’s disease progression by multi-tissue circular RNA characterization

2020 ◽  
Author(s):  
IJu Lo ◽  
Jamie Hill ◽  
Bjarni J. Vilhjálmsson ◽  
Jørgen Kjems
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Inferior Frontal Gyrus ◽  
Circular Rna ◽  
Brain Regions ◽  
Parahippocampal Gyrus ◽  
Circular Rnas ◽  
Cognitive Disability ◽  
Anterior Prefrontal Cortex ◽  
Progressive Course

AbstractAlzheimer’s Disease (AD) has devastating consequences for patients during its slow, progressive course. It is important to understand the pathology of AD onset. Recently, circular RNAs (circRNAs) have been found to participate in many human diseases including cancers and neurodegenerative conditions. In this study, we mined the published dataset on the AMP-AD Knowledge Portal from the Mount Sinai Brain Bank (MSBB) to describe the circRNA profiles at different AD stage in brain samples from four AD patients brain regions, anterior prefrontal cortex, superior temporal lobe, parahippocampal gyrus, and inferior frontal gyrus. We found in total 147 circRNAs to be differentially expressed (DE) during AD progression in the four regions. We also characterized the mRNA-circRNA co-expression network and annotated the potential function of circRNAs based on the co-expressed modules. Based on our results, we propose that parahippocampal gyrus is the most circRNA-regulated region during the AD progression. The strongest negatively AD stage-correlated module in parahippocampal gyrus were enriched in cognitive disability and pathological-associated pathways such as synapse organization and regulation of membrane potential. Finally, the regression model based on the expression pattern of DE circRNAs in the module could help to distinguish the disease severity of patients, further supported the importance of circRNAs in AD pathology. In conclusion, our finding indicates that circRNAs in parahippocampal gyrus are possible regulators of AD progression and potentially be a therapeutic target or of AD.

scholarly journals PRECISION MEDICINE - THE GOLDEN GATE FOR DETECTION, TREATMENT AND PREVENTION OF ALZHEIMER’S DISEASE

2016 ◽  
pp. 1-17
Author(s):  
H. Hampel ◽  
S.E. O’Bryant ◽  
J.I. Castrillo ◽  
C. Ritchie ◽  
K. Rojkova ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Neurodegenerative Diseases ◽  
Precision Medicine ◽  
Molecular Mechanisms ◽  
Clinical Symptoms ◽  
Late Onset ◽  
Therapeutic Success ◽  
Preclinical Stage ◽  
Treatment And Prevention

During this decade, breakthrough conceptual shifts have commenced to emerge in the field of Alzheimer’s disease (AD) recognizing risk factors and the non-linear dynamic continuum of complex pathophysiologies amongst a wide dimensional spectrum of multi-factorial brain proteinopathies/neurodegenerative diseases. As is the case in most fields of medicine, substantial advancements in detecting, treating and preventing AD will likely evolve from the generation and implementation of a systematic precision medicine strategy. This approach will likely be based on the success found from more advanced research fields, such as oncology. Precision medicine will require integration and transfertilization across fragmented specialities of medicine and direct reintegration of Neuroscience, Neurology and Psychiatry into a continuum of medical sciences away from the silo approach. Precision medicine is biomarker-guided medicine on systems-levels that takes into account methodological advancements and discoveries of the comprehensive pathophysiological profiles of complex multi-factorial neurodegenerative diseases, such as late-onset sporadic AD. This will allow identifying and characterizing the disease processes at the asymptomatic preclinical stage, where pathophysiological and topographical abnormalities precede overt clinical symptoms by many years to decades. In this respect, the uncharted territory of the AD preclinical stage has become a major research challenge as the field postulates that early biomarker guided customized interventions may offer the best chance of therapeutic success. Clarification and practical operationalization is needed for comprehensive dissection and classification of interacting and converging disease mechanisms, description of genomic and epigenetic drivers, natural history trajectories through space and time, surrogate biomarkers and indicators of risk and progression, as well as considerations about the regulatory, ethical, political and societal consequences of early detection at asymptomatic stages. In this scenario, the integrated roles of genome sequencing, investigations of comprehensive fluid-based biomarkers and multimodal neuroimaging will be of key importance for the identification of distinct molecular mechanisms and signaling pathways in subsets of asymptomatic people at greatest risk for progression to clinical milestones due to those specific pathways. The precision medicine strategy facilitates a paradigm shift in Neuroscience and AD research and development away from the classical “one-size-fits-all” approach in drug discovery towards biomarker guided “molecularly” tailored therapy for truly effective treatment and prevention options. After the long and winding decade of failed therapy trials progress towards the holistic systems-based strategy of precision medicine may finally turn into the new age of scientific and medical success curbing the global AD epidemic.

Features of molecule expression markers of insulin resistance in experimental Alzheimer’s disease

2015 ◽  
Vol 61 (4) ◽  
pp. 43-48
Author(s):  
Ya V Gorina ◽  
Yu K Komleva ◽  
O L Lopatina ◽  
V V Volkova ◽  
G E Gersog ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Insulin Resistance ◽  
Alzheimer's Disease ◽  
Molecular Markers ◽  
Molecular Mechanisms ◽  
Cognitive Disorders ◽  
Brain Regions ◽  
Significant Loss ◽  
Amyloid Accumulation ◽  
The Central Nervous System

Alzheimer’s Disease (AD) is characterized by a significant loss of neurons and synapses, especially in the hippocampus and cortex, the extracellular β-amyloid accumulation and formation of neurofibrillary tangles. Insulin resistance plays important role in neurodegeneration and cognitive disorders in the central nervous system, especially AD. However, the cellular and molecular mechanisms that connect insulin resistance and Alzheimer’s pathogenesis remain largely unexplained. Therefore, great importance is the identification of molecular markers that allow to define new approaches to targeted pharmacological correction of neurodegeneration. This article describes the study of the expression of molecular markers, namely, IRAP, GLUT4, and IL-18 in different brain regions (hippocampus, olfactory bulb) rats with experimental AD

scholarly journals Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities

2021 ◽  
Vol 17 (1) ◽  
pp. e1008517
Author(s):  
Marzia Antonella Scelsi ◽  
Valerio Napolioni ◽  
Michael D. Greicius ◽  
Andre Altmann ◽  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Rare Variants ◽  
Late Onset ◽  
Integrative Approach ◽  
Specific Gene ◽  
Tissue Specific ◽  
Association Testing ◽  
Wide Range ◽  
Network Propagation

State-of-the-art rare variant association testing methods aggregate the contribution of rare variants in biologically relevant genomic regions to boost statistical power. However, testing single genes separately does not consider the complex interaction landscape of genes, nor the downstream effects of non-synonymous variants on protein structure and function. Here we present the NETwork Propagation-based Assessment of Genetic Events (NETPAGE), an integrative approach aimed at investigating the biological pathways through which rare variation results in complex disease phenotypes. We applied NETPAGE to sporadic, late-onset Alzheimer’s disease (AD), using whole-genome sequencing from the AD Neuroimaging Initiative (ADNI) cohort, as well as whole-exome sequencing from the AD Sequencing Project (ADSP). NETPAGE is based on network propagation, a framework that models information flow on a graph and simulates the percolation of genetic variation through tissue-specific gene interaction networks. The result of network propagation is a set of smoothed gene scores that can be tested for association with disease status through sparse regression. The application of NETPAGE to AD enabled the identification of a set of connected genes whose smoothed variation profile was robustly associated to case-control status, based on gene interactions in the hippocampus. Additionally, smoothed scores significantly correlated with risk of conversion to AD in Mild Cognitive Impairment (MCI) subjects. Lastly, we investigated tissue-specific transcriptional dysregulation of the core genes in two independent RNA-seq datasets, as well as significant enrichments in terms of gene sets with known connections to AD. We present a framework that enables enhanced genetic association testing for a wide range of traits, diseases, and sample sizes.

scholarly journals Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease

2018 ◽  
Author(s):  
Stephen A. Semick ◽  
Rahul A. Bharadwaj ◽  
Leonardo Collado-Torres ◽  
Ran Tao ◽  
Joo Heon Shin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Dna Methylation ◽  
Neurodegenerative Disorder ◽  
Late Onset ◽  
Brain Regions ◽  
Epigenetic Mechanism ◽  
Novel Genes ◽  
Age Related

AbstractBackgroundLate-onset Alzheimer’s disease (AD) is a complex age-related neurodegenerative disorder that likely involves epigenetic factors. To better understand the epigenetic state associated with AD represented as variation in DNA methylation (DNAm), we surveyed 420,852 DNAm sites from neurotypical controls (N=49) and late-onset AD patients (N=24) across four brain regions (hippocampus, entorhinal cortex, dorsolateral prefrontal cortex and cerebellum).ResultsWe identified 858 sites with robust differential methylation, collectively annotated to 772 possible genes (FDR<5%, within 10kb). These sites were overrepresented in AD genetic risk loci (p=0.00655), and nearby genes were enriched for processes related to cell-adhesion, immunity, and calcium homeostasis (FDR<5%). We analyzed corresponding RNA-seq data to prioritize 130 genes within 10kb of the differentially methylated sites, which were differentially expressed and had expression levels associated with nearby DNAm levels (p<0.05). This validated gene set includes previously reported (e.g. ANK1, DUSP22) and novel genes involved in Alzheimer’s disease, such as ANKRD30B.ConclusionsThese results highlight DNAm changes in Alzheimer’s disease that have gene expression correlates, implicating DNAm as an epigenetic mechanism underlying pathological molecular changes associated with AD. Furthermore, our framework illustrates the value of integrating epigenetic and transcriptomic data for understanding complex disease.

scholarly journals PLCG2 as a Risk Factor for Alzheimer's Disease

2020 ◽  
Author(s):  
Andy Po-Yi Tsai ◽  
Chuanpeng Dong ◽  
Christoph Preuss ◽  
Miguel Moutinho ◽  
Peter Bor-Chian Lin ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Late Onset ◽  
Missense Variant ◽  
Parahippocampal Gyrus ◽  
Carrier Status ◽  
Eqtl Analysis ◽  
Expression Levels ◽  
Amyloid Pathology ◽  
The Brain

Abstract Background Alzheimer's disease (AD) is characterized by robust microgliosis and phenotypic changes that accompany disease pathogenesis. Indeed, genetic variants in microglial genes are linked to risk for late-onset AD (LOAD). Phospholipase C 𝛾 2 (PLCG2) participates in the transduction of signals emanating from immune cell-surface receptors that regulate the inflammatory response and is selectively expressed by microglia in the brain. A rare variant in PLCG2 (P522R) was previously found to be protective against LOAD. Here, we performed association analysis to identify a new genetic variation in PLCG2 that is associated with elevated risk for LOAD.Methods Using whole genome sequencing (N=1,894) and RNA-Seq (N=1,077) data from the AMP-AD cohort, we investigated whether a missense variant in PLCG2 (M28L) was associated with risk for LOAD. We have examined the homology model and space-filling model of PLCG2 generated with PyMOL to investigate the protein structure of PLCG2 with substitutions of LOAD risk and protective variants in PLCG2 . Gene expression analysis and expression quantitative trait loci (eQTL) of PLCG2 were conducted. We also evaluated the relationship between PLCG2 expression levels and amyloid plaque density and expression levels of microglia specific markers ( AIF1 and TMEM119 ). Age, sex, and APOE ε4 carrier status were used as covariates. Finally, we investigated the longitudinal changes PLCG2 expression in the 5XFAD mouse model of AD and it relationship to amyloid pathology progression.Results A rare missense variant in PLCG2 (M28L) confers increased AD risk ( p =0.047; OR=1.164 [95% CI=1.002-1.351]). PLCG2 is highly expressed in the brain and was significantly up-regulated in the parahippocampal gyrus, superior temporal gyrus, and inferior temporal gyrus in LOAD. Higher PLCG2 expression levels were associated with increased brain amyloid deposition. The findings were validated in 5xFAD mice, showing a disease progression-dependent increase in Plcg2 expression with amyloid pathology. Furthermore, eQTL analysis identified several variants as associated with increased PLCG2 expression levels in the brain and other organs.Conclusions Our results provide further evidence that PLCG2 and the M28L variant confers increase risk for LOAD and may play an important role in AD pathophysiology.

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