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. 2022 Feb 28:12:720170.
doi: 10.3389/fphar.2021.720170. eCollection 2021.

Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia

Affiliations

Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia

Peter Natesan Pushparaj et al. Front Pharmacol. .

Abstract

Introduction: Alzheimer's disease (AD) is a major cause of the development of cognitive decline and dementia. AD and associated dementias (ADRD) are the major contributors to the enormous burden of morbidity and mortality worldwide. To date, there are no robust therapies to alleviate or cure this debilitating disease. Most drug treatments focus on restoring the normal function of neurons and the cells that cause inflammation, such as microglia in the brain. However, the role of astrocytes, the brain's housekeeping cells, in the development of AD and the initiation of dementia is still not well understood. Objective: To decipher the role of astrocytes in the entorhinal cortex of AD patients using single nuclear RNA sequencing (snRNASeq) datasets from the Single Cell RNA-seq Database for Alzheimer's Disease (scREAD). The datasets were originally derived from astrocytes, isolated from the entorhinal cortex of AD brain and healthy brain to decipher disease-specific signaling pathways as well as drugs and natural products that reverse AD-specific signatures in astrocytes. Methods: We used snRNASeq datasets from the scREAD database originally derived from astrocytes isolated from the entorhinal cortex of AD and healthy brains from the Gene Expression Omnibus (GEO) (GSE138852 and GSE147528) and analyzed them using next-generation knowledge discovery (NGKD) platforms. scREAD is a user-friendly open-source interface available at https://bmbls.bmi.osumc.edu/scread/that enables more discovery-oriented strategies. snRNASeq data and metadata can also be visualized and downloaded via an interactive web application at adsn.ddnetbio.com. Differentially expressed genes (DEGs) for each snRNASeq dataset were analyzed using iPathwayGuide to compare and derive disease-specific pathways, gene ontologies, and in silico predictions of drugs and natural products that regulate AD -specific signatures in astrocytes. In addition, DEGs were analyzed using the L1000FWD and L1000CDS2 signature search programming interfaces (APIs) to identify additional drugs and natural products that mimic or reverse AD-specific gene signatures in astrocytes. Results: We found that PI3K/AKT signaling, Wnt signaling, neuroactive ligand-receptor interaction pathways, neurodegeneration pathways, etc. were significantly impaired in astrocytes from the entorhinal cortex of AD patients. Biological processes such as glutamate receptor signaling pathway, regulation of synapse organization, cell-cell adhesion via plasma membrane adhesion molecules, and chylomicrons were negatively enriched in the astrocytes from the entorhinal cortex of AD patients. Gene sets involved in cellular components such as postsynaptic membrane, synaptic membrane, postsynapse, and synapse part were negatively enriched (p < 0.01). Moreover, molecular functions such as glutamate receptor activity, neurotransmitter receptor activity, and extracellular ligand-gated ion channels were negatively regulated in the astrocytes of the entorhinal cortex of AD patients (p < 0.01). Moreover, the application of NGKD platforms revealed that antirheumatic drugs, vitamin-E, emetine, narciclasine, cephaeline, trichostatin A, withaferin A, dasatinib, etc. can potentially reverse gene signatures associated with AD. Conclusions: The present study highlights an innovative approach to use NGKD platforms to find unique disease-associated signaling pathways and specific synthetic drugs and natural products that can potentially reverse AD and ADRD-associated gene signatures.

Keywords: alzheimer’s disease and dementia; anti-rheumatic agents; astrocytes; dasatinib; in silico tools; natural products; scREAD; single-nucleus RNA sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Pathology of Alzheimer’s Disease (Created using Biorender.com).
FIGURE 2
FIGURE 2
Venn diagram showing the DEGs obtained using the scREAD analysis of snRNASeq data from astrocytes of AD groups (AD00203, AD00205, and AD00206) compared to astrocytes of the healthy control group (AD00201) were 739, 241, and 639 respectively after filtering with a p-value cut off of 0.05 and log2 fold change (Log2Fc) of ±0.3. Further analysis of DEGs using iPathwayGuide software showed that 93 DEGs were commonly regulated in all the disease groups.
FIGURE 3
FIGURE 3
iPathwayGuide analysis shows the differentially regulated genes in the KEGG Alzheimer’s disease pathway in astrocytes from the AD group (AD00203) compared to astrocytes from the healthy control group (AD00201).
FIGURE 4
FIGURE 4
iPathwayGuide analysis shows the differentially regulated genes in the KEGG Alzheimer’s disease pathway in astrocytes from the AD group (AD00205) compared to astrocytes from the healthy control group (AD00201).
FIGURE 5
FIGURE 5
iPathwayGuide analysis shows the differentially regulated genes in the KEGG Alzheimer’s disease pathway in astrocytes from the AD group (AD00206) compared to astrocytes from the healthy control group (AD00201).
FIGURE 6
FIGURE 6
iPathwayGuide analysis shows the differentially regulated genes in the KEGG neurodegeneration pathway (multiple diseases) in the astrocytes of the AD group (AD00203) compared to the astrocytes of the healthy control group (AD00201).
FIGURE 7
FIGURE 7
iPathwayGuide analysis shows the differentially regulated genes in the KEGG neurodegeneration pathway (multiple diseases) in the astrocytes of the AD group (AD00205) compared to the astrocytes of the healthy control group (AD00201).
FIGURE 8
FIGURE 8
iPathwayGuide analysis shows the differentially regulated genes in the KEGG neurodegeneration pathway (multiple diseases) in the astrocytes of the AD group (AD00206) compared to the astrocytes of the healthy control group (AD00201).

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