Single cell RNA sequencing of human microglia uncovers a subset that is associated with Alzheimer’s disease

AbstractThe extent of microglial heterogeneity in humans remains a central yet poorly explored question in light of the development of therapies targeting this cell type. Here, we investigate the population structure of live microglia purified from human cerebral cortex samples obtained at autopsy and during neurosurgical procedures. Using single cell RNA sequencing, we find that some subsets are enriched for disease-related genes and RNA signatures. We confirm the presence of four of these microglial subpopulations histologically and illustrate the utility of our data by characterizing further microglial cluster 7, enriched for genes depleted in the cortex of individuals with Alzheimer’s disease (AD). Histologically, these cluster 7 microglia are reduced in frequency in AD tissue, and we validate this observation in an independent set of single nucleus data. Thus, our live human microglia identify a range of subtypes, and we prioritize one of these as being altered in AD.

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The interplay between microglial states and major risk factors in Alzheimer’s disease through the eyes of single-cell RNA-sequencing: beyond black and white

Journal of Neurophysiology ◽

10.1152/jn.00395.2019 ◽

2019 ◽

Vol 122 (4) ◽

pp. 1291-1296 ◽

Cited By ~ 2

Author(s):

Djuna von Maydell ◽

Mehdi Jorfi

Keyword(s):

Risk Factors ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Single Cell ◽

Rna Sequencing ◽

Cellular Mechanisms ◽

Black And White ◽

Single Cell Rna Sequencing ◽

Sequencing Studies ◽

Integral Role

Microglia constitute ~10–20% of glial cells in the adult human brain. They are the resident phagocytic immune cells of the central nervous system and play an integral role as first responders during inflammation. Microglia are commonly classified as “HM” (homeostatic), “M1” (classically activated proinflammatory), or “M2” (alternatively activated). Multiple single-cell RNA-sequencing studies suggest that this discrete classification system does not accurately and fully capture the vast heterogeneity of microglial states in the brain. In fact, a recent single-cell RNA-sequencing study showed that microglia exist along a continuous spectrum of states. This spectrum spans heterogeneous populations of homeostatic and neuropathology-associated microglia in both healthy and Alzheimer’s disease (AD) mouse brains. Major risk factors, such as sex, age, and genes, modulate microglial states, suggesting that shifts along the trajectory might play a causal role in AD pathogenesis. This study provides important insight into the cellular mechanisms of AD and underlines the potential of novel cell-based therapies for AD.

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Single-cell RNA sequencing reveals B cell–related molecular biomarkers for Alzheimer’s disease

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00714-8 ◽

2021 ◽

Author(s):

Liu-Lin Xiong ◽

Lu-Lu Xue ◽

Ruo-Lan Du ◽

Rui-Ze Niu ◽

Li Chen ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

B Cells ◽

B Cell ◽

Single Cell ◽

Rna Sequencing ◽

Early Stage ◽

Diagnostic Process ◽

Sequencing Analysis ◽

Single Cell Rna Sequencing

AbstractIn recent years, biomarkers have been integrated into the diagnostic process and have become increasingly indispensable for obtaining knowledge of the neurodegenerative processes in Alzheimer’s disease (AD). Peripheral blood mononuclear cells (PBMCs) in human blood have been reported to participate in a variety of neurodegenerative activities. Here, a single-cell RNA sequencing analysis of PBMCs from 4 AD patients (2 in the early stage, 2 in the late stage) and 2 normal controls was performed to explore the differential cell subpopulations in PBMCs of AD patients. A significant decrease in B cells was detected in the blood of AD patients. Furthermore, we further examined PBMCs from 43 AD patients and 41 normal subjects by fluorescence activated cell sorting (FACS), and combined with correlation analysis, we found that the reduction in B cells was closely correlated with the patients’ Clinical Dementia Rating (CDR) scores. To confirm the role of B cells in AD progression, functional experiments were performed in early-stage AD mice in which fibrous plaques were beginning to appear; the results demonstrated that B cell depletion in the early stage of AD markedly accelerated and aggravated cognitive dysfunction and augmented the Aβ burden in AD mice. Importantly, the experiments revealed 18 genes that were specifically upregulated and 7 genes that were specifically downregulated in B cells as the disease progressed, and several of these genes exhibited close correlation with AD. These findings identified possible B cell-based AD severity, which are anticipated to be conducive to the clinical identification of AD progression.

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Characterization of Alzheimer’s Disease-Associated Excitatory Neurons via Single-Cell RNA Sequencing Analysis

Frontiers in Aging Neuroscience ◽

10.3389/fnagi.2021.742176 ◽

2021 ◽

Vol 13 ◽

Author(s):

Fanghong Shao ◽

Meiting Wang ◽

Qi Guo ◽

Bowen Zhang ◽

Xiangting Wang

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Single Cell ◽

Rna Sequencing ◽

Neuronal Cell ◽

Cell Populations ◽

Sequencing Analysis ◽

Single Cell Rna Sequencing ◽

Excitatory Neurons

The detailed characteristics of neuronal cell populations in Alzheimer’s disease (AD) using single-cell RNA sequencing have not been fully elucidated. To explore the characterization of neuronal cell populations in AD, this study utilized the publicly available single-nucleus RNA-sequencing datasets in the transgenic model of 5X familial Alzheimer’s disease (5XFAD) and wild-type mice to reveal an AD-associated excitatory neuron population (C3:Ex.Neuron). The relative abundance of C3:Ex.Neuron increased at 1.5 months and peaked at 4.7 months in AD mice. Functional pathways analyses showed that the pathways positively related to neurodegenerative disease progression were downregulated in the C3:Ex.Neuron at 1.5 months in AD mice. Based on the differentially expressed genes among the C3:Ex.Neuron, four subtypes (C3.1–4) were identified, which exhibited distinct abundance regulatory patterns during the development of AD. Among these subtypes, the C3.1 neurons [marked by netrin G1 (Ntng1)] exhibited a similar regulatory pattern as the C3:Ex.Neuron in abundance during the development of AD. In addition, our gene set variation analysis (GSEA) showed that the C3.1 neurons, instead of other subtypes of the C3:Ex.Neuron, possessed downregulated AD pathways at an early stage (1.5 months) of AD mice. Collectively, our results identified a previously unidentified subset of excitatory neurons and provide a potential application of these neurons to modulate the disease susceptibility.

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Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease

Genome Research ◽

10.1101/gr.272484.120 ◽

2021 ◽

pp. gr.272484.120 ◽

Cited By ~ 1

Author(s):

Jielin Xu ◽

Pengyue Zhang ◽

Yin Huang ◽

Yadi Zhou ◽

Yuan Hou ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Data Analysis ◽

Single Cell ◽

Rna Sequencing ◽

Cell Nucleus ◽

Drug Repurposing ◽

Molecular Networks ◽

Sequencing Data ◽

Sequencing Data Analysis

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Microglia in Alzheimer's disease at single-cell level. Are there common patterns in humans and mice?

Journal of Experimental Medicine ◽

10.1084/jem.20202717 ◽

2021 ◽

Vol 218 (9) ◽

Author(s):

Yun Chen ◽

Marco Colonna

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Single Cell ◽

Rna Sequencing ◽

Disease Model ◽

Amyloid Β ◽

Future Directions ◽

Mhc Ii ◽

Single Nucleus ◽

Microglial Response

Alzheimer’s disease (AD) is characterized by extracellular aggregates of amyloid β peptides, intraneuronal tau aggregates, and neuronal death. This pathology triggers activation of microglia. Because variants of genes expressed in microglia correlate with AD risk, microglial response to pathology plausibly impacts disease course. In mouse AD models, single-cell RNA sequencing (scRNA-seq) analyses delineated this response as progressive conversion of homeostatic microglia into disease-associated microglia (DAM); additional reactive microglial populations have been reported in other models of neurodegeneration and neuroinflammation. We review all of these microglial signatures, highlighting four fundamental patterns: DAM, IFN–microglia, MHC-II microglia, and proliferating microglia. We propose that all reported microglia populations are either just one or a combination, depending on the clustering strategy applied and the disease model. We further review single-nucleus RNA sequencing (snRNA-seq) data from human AD specimens and discuss reasons for parallels and discrepancies between human and mouse transcriptional profiles. Finally, we outline future directions for delineating the microglial impact in AD pathogenesis.

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scREAD: A single-cell RNA-Seq database for Alzheimer’s Disease

10.1101/2020.08.06.240044 ◽

2020 ◽

Author(s):

Jing Jiang ◽

Cankun Wang ◽

Ren Qi ◽

Hongjun Fu ◽

Qin Ma

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Single Cell ◽

Rna Sequencing ◽

Neurodegenerative Disorder ◽

Supplementary Information ◽

Cell Type ◽

Link Type ◽

Postmortem Brain Tissue ◽

The Brain

AbstractSummaryAlzheimer’s disease (AD) is a progressive neurodegenerative disorder of the brain and the most common form of dementia among the elderly. The single-cell RNA-sequencing (scRNA-Seq) and single-nucleus RNA-sequencing (snRNA-Seq) techniques are extremely useful for dissecting the function/dysfunction of highly heterogeneous cells in the brain at the single-cell level, and the corresponding data analyses can significantly improve our understanding of why particular cells are vulnerable in AD. We developed an integrated database named scREAD (single-cell RNA-Seq database for Alzheimer’s Disease), which is the first database dedicated to the management of all the existing scRNA-Seq and snRNA-Seq datasets from human postmortem brain tissue with AD and mouse models with AD pathology. scREAD provides comprehensive analysis results for 55 datasets from eight brain regions, including control atlas construction, cell type prediction, identification of differentially expressed genes, and identification of cell-type-specific regulons.Availability and ImplementationscREAD is a one-stop and user-friendly interface and freely available at https://bmbls.bmi.osumc.edu/scread/. The backend workflow can be downloaded from https://github.com/OSU-BMBL/scread/tree/master/script, to enable more discovery-driven [email protected] or [email protected] informationSupplementary data are available at Bioinformatics online.

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Multimodal single-cell/nucleus RNA-sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer’s disease

10.1101/2020.09.23.310466 ◽

2020 ◽

Author(s):

Jielin Xu ◽

Pengyue Zhang ◽

Yin Huang ◽

Lynn Bekris ◽

Justin Lathia ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cell ◽

Association Studies ◽

Molecular Networks ◽

Genome Wide Association Studies ◽

Sequencing Data ◽

Network Analyses

AbstractSystematic identification of molecular networks in disease relevant immune cells of the nervous system is critical for elucidating the underlying pathophysiology of Alzheimer’s disease (AD). Two key immune cell types, disease-associated microglia (DAM) and disease-associated astrocytes (DAA), are biologically involved in AD pathobiology. Therefore, uncovering molecular determinants of DAM and DAA will enhance our understanding of AD biology, potentially identifying novel therapeutic targets for AD treatment. Here, we present an integrative, network-based methodology to uncover conserved molecular networks between DAM and DAA. Specifically, we leverage single-cell and single-nucleus RNA sequencing data from both AD transgenic mouse models and AD patient brains, drug-target networks, metabolite-enzyme associations, and the human protein-protein interactome, along with large-scale patient data validation from the MarketScan Medicare Supplemental Database. We find that common and unique molecular network regulators between DAM (i.e, PAK1, MAPK14, and SYK) and DAA (i.e., NFKB1, FOS, and JUN) are significantly enriched by multiple neuro-inflammatory pathways and well-known genetic variants (i.e., BIN1) from genome-wide association studies. Further network analysis reveal shared immune pathways between DAM and DAA, including Fc gamma R-mediated phagocytosis, Th17 cell differentiation, and chemokine signaling. Furthermore, integrative metabolite-enzyme network analyses imply that fatty acids (i.e., elaidic acid) and amino acids (i.e., glutamate, serine, and phenylalanine) may trigger molecular alterations between DAM and DAA. Finally, we prioritize repurposed drug candidates for potential treatment of AD by agents that specifically reverse dysregulated gene expression of DAM or DAA, including an antithrombotic anticoagulant triflusal, a beta2-adrenergic receptor agonist salbutamol, and the steroid medications (fluticasone and mometasone). Individuals taking fluticasone (an approved anti-inflammatory and inhaled corticosteroid) displayed a significantly decreased incidence of AD (hazard ratio (HR) = 0.858, 95% confidence interval [CI] 0.829-0.888, P < 0.0001) in retrospective case-control validation. Furthermore, propensity score matching cohort studies also confirmed an association of mometasone with reduced incidence of AD in comparison to fluticasone (HR =0.921, 95% CI 0.862-0.984, P < 0.0001).

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