Microglial Subsets Research Articles

A cross-disease resource of living human microglia identifies disease-enriched subsets and tool compounds recapitulating microglial states.

Human microglia play a pivotal role in neurological diseases, but we still have an incomplete understanding of microglial heterogeneity, which limits the development of targeted therapies directly modulating their state or function. Here, we use single-cell RNA sequencing to profile 215,680 live human microglia from 74 donors across diverse neurological diseases and CNS regions. We observe a central divide between oxidative and heterocyclic metabolism and identify microglial subsets associated with antigen presentation, motility and proliferation. Specific subsets are enriched in susceptibility genes for neurodegenerative diseases or the disease-associated microglial signature. We validate subtypes in situ with an RNAscope-immunofluorescence pipeline and high-dimensional MERFISH. We also leverage our dataset as a classification resource, finding that induced pluripotent stem cell model systems capture substantial in vivo heterogeneity. Finally, we identify and validate compounds that recapitulate certain subtypes in vitro, including camptothecin, which downregulates the signature of disease-enriched subtypes and upregulates a signature previously associated with Alzheimer's disease.

Neonatal inflammation impairs developmentally-associated microglia and promotes a highly reactive microglial subset

Microglia and border-associated macrophages play critical roles in both immunity and neurodevelopment. The disruption of microglial development trajectories by neonatal inflammation is an important issue in research on neurodevelopmental disorders (NDDs), as models have suggested a strong association between inflammation and cognitive deficits. Here, we explored by single-cell RNA sequencing and flow cytometry the impact of neonatal inflammation in a mouse NDD model on brain myeloid cell subsets. A specific subset of microglia expressing the complement receptor C5ar1 has been identified, in which inflammatory pathways are most strongly activated. Based on transcriptional similarity, this subset appears to originate from the most mature and “homeostatic“ microglia at this stage of development and demonstrated hypersensitivity to inflammation. Besides that, Spp1-microglia supporting oligodendrocyte differentiation, primitive and proliferative microglia were reduced by inflammation. These findings suggest major changes in microglial subsets developmental trajectories and reactivity contributing to NDDs induced by neonatal inflammation.

The embryonic zebrafish brain is exclusively colonized by pu.1-dependent and lymphatic-independent population of microglia.

Microglia, the crucial immune cells inhabiting the central nervous system (CNS), perform a range of vital functions, encompassing immune defense and neuronal regulation. Microglia subsets with diverse functions and distinct developmental regulations have been identified recently. It is generally accepted that all microglia originate from hematopoiesis and depend on the myeloid transcription factor PU.1. However, a recent study reported the existence of mrc1+ microglia in zebrafish embryos, which are seemingly independent of Pu.1 and reliant on lymphatic vessels, sparking great interest in the possibility of lymphatic-originated microglia. To address this, we took advantage of a pu.1 knock-in zebrafish allele for a detailed investigation. Our results conclusively showed that almost all zebrafish embryonic microglia (~95% on average) express pu.1. Further, lineage tracing and mutant analysis revealed that these microglia neither emerged from nor depended on lymphatic vessels. In essence, our study refutes the presence of pu.1-independent but lymphatic-dependent microglia.

Galectin-9 Mediates the Functions of Microglia in the Hypoxic Brain Tumor Microenvironment.

Galectin-9 (Gal-9) is a multifaceted regulator of various pathophysiologic processes that exerts positive or negative effects in a context-dependent manner. In this study, we elucidated the distinctive functional properties of Gal-9 on myeloid cells within the brain tumor microenvironment (TME). Gal-9-expressing cells were abundant at the hypoxic tumor edge in the tumor-bearing ipsilateral hemisphere compared with the contralateral hemisphere in an intracranial mouse brain tumor model. Gal-9 was highly expressed in microglia and macrophages in tumor-infiltrating cells. In primary glia, both the expression and secretion of Gal-9 were influenced by tumors. Analysis of a human glioblastoma bulk RNA sequencing dataset and a single-cell RNA sequencing dataset from a murine glioma model revealed a correlation between Gal-9 expression and glial cell activation. Notably, the Gal-9high microglial subset was functionally distinct from the Gal-9neg/low subset in the brain TME. Gal-9high microglia exhibited properties of inflammatory activation and higher rates of cell death, whereas Gal-9neg/low microglia displayed a superior phagocytic ability against brain tumor cells. Blockade of Gal-9 suppressed tumor growth and altered the activity of glial and T cells in a mouse glioma model. Additionally, glial Gal-9 expression was regulated by hypoxia-inducible factor-2α in the hypoxic brain TME. Myeloid-specific hypoxia-inducible factor-2α deficiency led to attenuated tumor progression. Together, these findings reveal that Gal-9 on myeloid cells is an immunoregulator and putative therapeutic target in brain tumors. Significance: Galectin-9 serves as an immune checkpoint molecule that modulates the functional properties of microglia in the brain tumor microenvironment and could potentially be targeted to effectively treat brain tumors.

Selective deletion of interleukin-1 alpha in microglia does not modify acute outcome but regulates neurorepair processes after experimental ischemic stroke.

Inflammation is a key contributor to stroke pathogenesis and exacerbates brain damage leading to poor outcome. Interleukin-1 (IL-1) is an important regulator of post-stroke inflammation, and blocking its actions is beneficial in pre-clinical stroke models and safe in the clinical setting. However, the distinct roles of the two major IL-1 receptor type 1 agonists, IL-1α and IL-1β, and the specific role of IL-1α in ischemic stroke remain largely unknown. Here we show that IL-1α and IL-1β have different spatio-temporal expression profiles in the brain after experimental stroke, with early microglial IL-1α expression (4 h) and delayed IL-1β expression in infiltrated neutrophils and a small microglial subset (24-72 h). We examined for the first time the specific role of microglial-derived IL-1α in experimental permanent and transient ischemic stroke through microglial-specific tamoxifen-inducible Cre-loxP-mediated recombination. Microglial IL-1α deletion did not influence acute brain damage, cerebral blood flow, IL-1β expression, neutrophil infiltration, microglial nor endothelial activation after ischemic stroke. However, microglial IL-1α knock out (KO) mice showed reduced peri-infarct vessel density and reactive astrogliosis at 14 days post-stroke, alongside long-term impaired functional recovery. Our study identifies for the first time a critical role for microglial IL-1α on neurorepair and functional recovery after stroke, highlighting the importance of targeting specific IL-1 mechanisms in brain injury to develop more effective therapies.

S100A8-enriched microglia populate the brain of tau-seeded and accelerated aging mice.

Long considered to fluctuate between pro- and anti-inflammatory states, it has now become evident that microglia occupy a variegated phenotypic landscape with relevance to aging and neurodegeneration. However, whether specific microglial subsets converge in or contribute to both processes that eventually affect brain function is less clear. To investigate this, we analyzed microglial heterogeneity in a tauopathy mouse model (K18-seeded P301L) and an accelerated aging model (Senescence-Accelerated Mouse-Prone 8, SAMP8) using cellular indexing of transcriptomes and epitopes by sequencing. We found that widespread tau pathology in K18-seeded P301L mice caused a significant change in the number and morphology of microglia, but only a mild overrepresentation of disease-associated microglia. At the cell population-level, we observed a marked upregulation of the calprotectin-encoding genes S100a8 and S100a9. In 9-month-old SAMP8 mice, we identified a unique microglial subpopulation that showed partial similarity with the disease-associated microglia phenotype and was additionally characterized by a high expression of the same calprotectin gene set. Immunostaining for S100A8 revealed that this population was enriched in the hippocampus, correlating with the cognitive impairment observed in this model. However, incomplete colocalization between their residence and markers of neuronal loss suggests regional specificity. Importantly, S100A8-positive microglia were also retrieved in brain biopsies of human AD and tauopathy patients as well as in a biopsy of an aged individual without reported pathology. Thus, the emergence of S100A8-positive microglia portrays a conspicuous commonality between accelerated aging and tauopathy progression, which may have relevance for ensuing brain dysfunction.

Abstract WP316: Single-Cell RNA Sequencing Reveals a Massive Alteration in the Molecular Landscape of Microglia After Ischemic Stroke

Introduction: Ischemic stroke, a prevalent and often devastating disease, remains poorly treated. Neuroinflammation is a key element of stroke pathophysiology and represents a promising therapeutic target. Among the central components driving neuroinflammation, microglia - the primary resident immune cells within the brain parenchyma - are key players in mediating the immune response in the stroke brain. However, how microglia respond to stroke is incompletely understood. In this study, we took advantage of a mouse genetic tool (ie, Tmem119-CreERT2), sorted microglia, and performed single-cell RNA sequencing (scRNA-seq) analysis using a mouse model of permanent stroke. Moreover, as stroke exhibits sexual dimorphism, we included both male and female mice. Methods: Young male and female Ai6/TMEM119-CreERT2;Ai6 (Tmem119-Ai6) mice with microglia labeled with ZsGreen underwent permanent middle cerebral artery occlusion (pMCAO) or sham surgery. On day 3 after stroke, ZsGreen+ cells (microglia) in the brain were isolated by FACS, and used for scRNA-seq analysis. Results: First, we confirmed that in Tmem119-Ai6 mice, expression of fluorescent ZsGreen was almost exclusively in microglia in the brain, with minimal presence in blood cells. Our unbiased scRNA-seq analysis of ZsGreen+ cells revealed 13 distinct microglial clusters after stroke. Importantly, 4 major stroke-related microglial clusters were identified. One cluster shared a gene signature with the reported disease-associated microglia (DAM) subset. The other 3 clusters were characterized by an interferon (IFN) response signature, a highly proliferative state, and a macrophage-like profile, respectively. RNA in situ hybridization analysis showed that cells from these clusters mainly resided within the stroke boundaries. Notably, our scRNA-seq data suggest no major sexual dimorphism in the microglial response to permanent stroke. Conclusions: This is the first scRNA-seq study with a focus on microglia in the context of sex and stroke. We propose that 4 microglial subsets may be deemed as common stroke-associated microglia. Future work will be designed to elucidate the functional significance of these subsets and their potential implications for stroke therapy.

Anti-inflammatory reprogramming of microglia cells by metabolic modulators to counteract neurodegeneration; a new role for Ranolazine

Microglia chronic activation is a hallmark of several neurodegenerative diseases, including the retinal ones, possibly contributing to their etiopathogenesis. However, some microglia sub-populations have anti-inflammatory and neuroprotective functions, thus making arduous deciphering the role of these cells in neurodegeneration. Since it has been proposed that functionally different microglia subsets also rely on different metabolic routes, we hypothesized that modulating microglia metabolism might be a tool to enhance their anti-inflammatory features. This would have a preventive and therapeutic potential in counteracting neurodegenerative diseases. For this purpose, we tested various molecules known to act on cell metabolism, and we revealed the anti-inflammatory effect of the FDA-approved piperazine derivative Ranolazine on microglia cells, while confirming the one of the flavonoids Quercetin and Naringenin, both in vitro and in vivo. We also demonstrated the synergistic anti-inflammatory effect of Quercetin and Idebenone, and the ability of Ranolazine, Quercetin and Naringenin to counteract the neurotoxic effect of LPS-activated microglia on 661W neuronal cells. Overall, these data suggest that using the selected molecules -also in combination therapies- might represent a valuable approach to reduce inflammation and neurodegeneration while avoiding long term side effects of corticosteroids.

Associations of cortical SPP1 and ITGAX with cognition and common neuropathologies in older adults.

The secreted phosphoprotein 1 (SPP1) gene expressed by CD11c+ cells is known to be associated with microglia activation and neuroinflammatory diseases. As most studies rely on mouse models, we investigated these genes and proteins in the cortical brain tissue of older adults and their role in Alzheimer's disease (AD) and related disorders. We leveraged protein measurements, single-nuclei, and RNASeq data from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) of over 1200 samples for association analysis. Expression ofSPP1and its encoded protein osteopontin were associated with faster cognitive decline and greater odds of common neuropathologies. At single-cell resolution, integrin subunit alpha X (ITGAX) was highly expressed in microglia, where specific subpopulations were associated with AD and cerebral amyloid angiopathy. The study provides evidence of SPP1andITGAXassociation with cognitive decline and common neuropathologies identifying a microglial subset associated with disease.

Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data

Advances in single-cell RNA sequencing (scRNA-seq) techniques have accelerated functional interpretation of disease-associated variants discovered from genome-wide association studies (GWASs). However, identification of trait-relevant cell populations is often impeded by inherent technical noise and high sparsity in scRNA-seq data. Here, we developed scPagwas, a computational approach that uncovers trait-relevant cellular context by integrating pathway activation transformation of scRNA-seq data and GWAS summary statistics. scPagwas effectively prioritizes trait-relevant genes, which facilitates identification of trait-relevant cell types/populations with high accuracy in extensive simulated and real datasets. Cellular-level association results identified a novel subpopulation of naive CD8+ Tcells related to COVID-19 severity and oligodendrocyte progenitor cell and microglia subsets with critical pathways by which genetic variants influence Alzheimer's disease. Overall, our approach provides new insights for the discovery of trait-relevant cell types and improves the mechanistic understanding of disease variants from a pathway perspective.

Innate immune activation and aberrant function in the R6/2 mouse model and Huntington's disease iPSC-derived microglia.

Huntington's disease (HD) is an inherited autosomal dominant neurodegenerative disease caused by CAG repeats in exon 1 of the HTT gene. A hallmark of HD along with other psychiatric and neurodegenerative diseases is alteration in the neuronal circuitry and synaptic loss. Microglia and peripheral innate immune activation have been reported in pre-symptomatic HD patients; however, what "activation" signifies for microglial and immune function in HD and how it impacts synaptic health remains unclear. In this study we sought to fill these gaps by capturing immune phenotypes and functional activation states of microglia and peripheral immunity in the R6/2 model of HD at pre-symptomatic, symptomatic and end stages of disease. These included characterizations of microglial phenotypes at single cell resolution, morphology, aberrant functions such as surveillance and phagocytosis and their impact on synaptic loss in vitro and ex vivo in R6/2 mouse brain tissue slices. To further understand how relevant the observed aberrant microglial behaviors are to human disease, transcriptomic analysis was performed using HD patient nuclear sequencing data and functional assessments were conducted using induced pluripotent stem cell (iPSC)-derived microglia. Our results show temporal changes in brain infiltration of peripheral lymphoid and myeloid cells, increases in microglial activation markers and phagocytic functions at the pre-symptomatic stages of disease. Increases in microglial surveillance and synaptic uptake parallel significant reduction of spine density in R6/2 mice. These findings were mirrored by an upregulation of gene signatures in the endocytic and migratory pathways in disease-associated microglial subsets in human HD brains, as well as increased phagocytic and migratory functions of iPSC-derived HD microglia. These results collectively suggest that targeting key and specific microglial functions related to synaptic surveillance and pruning may be therapeutically beneficial in attenuating cognitive decline and psychiatric aspects of HD.

ARG1-expressing microglia show a distinct molecular signature and modulate postnatal development and function of the mouse brain

Molecular diversity of microglia, the resident immune cells in the CNS, is reported. Whether microglial subsets characterized by the expression of specific proteins constitute subtypes with distinct functions has not been fully elucidated. Here we describe a microglial subtype expressing the enzyme arginase-1 (ARG1; that is, ARG1+ microglia) that is found predominantly in the basal forebrain and ventral striatum during early postnatal mouse development. ARG1+ microglia are enriched in phagocytic inclusions and exhibit a distinct molecular signature, including upregulation of genes such as Apoe, Clec7a, Igf1, Lgals3 and Mgl2, compared to ARG1– microglia. Microglial-specific knockdown of Arg1 results in deficient cholinergic innervation and impaired dendritic spine maturation in the hippocampus where cholinergic neurons project, which in turn results in impaired long-term potentiation and cognitive behavioral deficiencies in female mice. Our results expand on microglia diversity and provide insights into microglia subtype-specific functions.

Pathogenic Microglia Orchestrate Neurotoxic Properties of Eomes-Expressing Helper T Cells

In addition to disease-associated microglia (DAM), microglia with MHC-II and/or IFN-I signatures may form additional pathogenic subsets that are relevant to neurodegeneration. However, the significance of such MHC-II and IFN-I signatures remains elusive. We demonstrate here that these microglial subsets play intrinsic roles in orchestrating neurotoxic properties of neurotoxic Eomes+ Th cells under the neurodegeneration-associated phase of experimental autoimmune encephalomyelitis (EAE) that corresponds to progressive multiple sclerosis (MS). Microglia acquire IFN-signature after sensing ectopically expressed long interspersed nuclear element-1 (L1) gene. Furthermore, ORF1, an L1-encoded protein aberrantly expressed in the diseased central nervous system (CNS), stimulated Eomes+ Th cells after Trem2-dependent ingestion and presentation in MHC-II context by microglia. Interestingly, administration of an L1 inhibitor significantly ameliorated neurodegenerative symptoms of EAE concomitant with reduced accumulation of Eomes+ Th cells in the CNS. Collectively, our data highlight a critical contribution of new microglia subsets as a neuroinflammatory hub in immune-mediated neurodegeneration.

Definition of the contribution of an Osteopontin-producing CD11c+ microglial subset to Alzheimer’s disease

Alzheimer's disease (AD) is the most common form of incurable dementia and represents a critical public health issue as the world's population ages. Although microglial dysregulation is a cardinal feature of AD, the extensive heterogeneity of these immunological cells in the brain has impeded our understanding of their contribution to this disease. Here, we identify a pathogenic microglial subset which expresses the CD11c surface marker as the sole producer of Osteopontin (OPN) in the 5XFAD mouse model of AD. OPN production divides Disease-Associated Microglia (DAM) into two functionally distinct subsets, i.e., a protective CD11c+OPN- subset that robustly ingests amyloid β (Aβ) in a noninflammatory fashion and a pathogenic CD11c+OPN+ subset that produces proinflammatory cytokines and fails to ingest significant amounts of Aβ. Genetic ablation of OPN or administration of monoclonal anti-OPN antibody to 5XFAD mice reduces proinflammatory microglia, plaque formation, and numbers of dystrophic neurites and results in improved cognitive function. Analysis of brain tissue from AD patients indicates that levels of OPN-producing CD11c+ microglia correlate strongly with the degree of cognitive deficit and AD neuropathology. These findings define an OPN-dependent pathway to disease driven by a distinct microglial subset, and identify OPN as a novel therapeutic target for potentially effective immunotherapy to treat AD.

Abstract TP225: Cell-type-based Pathway Analysis In Experimental Subarachnoid Hemorrhage

Introduction: Recently, increasing evidence points to a pivotal role of neuroinflammation in the pathogenesis of Subarachnoid hemorrhage (SAH). However, the pattern of cell interaction after SAH is not clear. Methods: Endovascular perforation (EVP) murine SAH model was established to reproduce experimental SAH. Post-SAH CD11b+ single-cell suspension was harvested at day 3 and sequenced using 10X single-cell RNA-sequencing platform. Then, the detailed single-cell information of post-SAH cells was analyzed with bioinformatics. The same pathways and related ligand-receptors in microglia and other cells were compared. Results: More than 51 pathways were found in the crosstalk of brain cells after SAH, these cells including: microglia (microglia worked in 25 pathways), CNS-associated macrophage, astrocyte, neuron, monocyte and macrophage and Oligodendrocyte. In the microglia subsets’ interaction, 15 pathways upregulated, of which four pathways were specific to microglia subsets, including amyloid-β precursor protein (APP), Tumor necrosis factor (TNF), growth differentiation factor (GDF) and oncostatin M (OSM) signaling pathways. We precisely distinguished the ligand-receptor pattern in which microglia differ with other cells in 7 pathways, including chemokine ligands (CCL), colony-stimulating factor (CSF), GALECTIN, growth arrest-specific (GAS), intercellular adhesion molecule (ICAM), junction adhesion molecule (JAM) and secreted phosphoprotein 1 (SPP1) signaling pathways. Gene ontology (GO) results showed that compared with non-microglia cells, post-SAH microglia with upregulated function like leukocyte, glia cell activation and migration, while have downregulated functions of protein-lipid complex remodeling. Conclusions: Collectively, we first systematically report the interaction patterns of seven brain cells after SAH. Further the cell type based ligand-receptor analysis of microglia and other cells in the same pathway was comparatively conducted. These results revealed the cellular mechanisms for neuroinflammation after SAH, and the ligand-receptor results provided a theoretical basis and opportunities for accurate monitoring and modulation of SAH in the future.

Microglial heterogeneity and complement component 3 elimination within emerging multisensory midbrain compartments during an early critical period.

The lateral cortex of the inferior colliculus (LCIC) is a midbrain shell region that receives multimodal inputs that target discrete zones of its compartmental (modular-matrix) framework. This arrangement emerges perinatally in mice (postnatal day, P0-P12) as somatosensory and auditory inputs segregate into their respective modular and matrix terminal patterns. Microglial cells (MGCs) perform a variety of critical functions in the developing brain, among them identifying areas of active circuit assembly and selectively pruning exuberant or underutilized connections. Recent evidence in other brain structures suggest considerable MGC heterogeneity across the lifespan, particularly during established developmental critical periods. The present study examines the potential involvement of classical complement cascade signaling (C3-CR3/CD11b) in refining early multisensory networks, and identifies several microglial subsets exhibiting distinct molecular signatures within the nascent LCIC. Immunostaining was performed in GAD67-green fluorescent protein (GFP) and CX3CR1-GFP mice throughout and after the defined LCIC critical period. GAD labeling highlights the emerging LCIC modularity, while CX3CR1 labeling depicts MGCs expressing the fractalkine receptor. C3 expression is widespread throughout the LCIC neuropil early on, prior to its conspicuous absence from modular zones at P8, and more global disappearance following critical period closure. CD11b-expressing microglia while homogeneously distributed at birth, are biased to modular fields at P8 and then the surrounding matrix by P12. Temporal and spatial matching of the disappearance of C3 by LCIC compartment (i.e., modules then matrix) with CD11b-positive MGC occupancy implicates complement signaling in the selective refinement of early LCIC connectivity. Multiple-labeling studies for a variety of established MGC markers (CD11b, CX3CR1, Iba1, TMEM119) indicate significant MGC heterogeneity in the LCIC as its compartments and segregated multisensory maps emerge. Marker colocalization was the exception rather than the rule, suggesting that unique MGC subpopulations exist in the LCIC and perhaps serve distinct developmental roles. Potential mechanisms whereby microglia sculpt early multisensory LCIC maps and how such activity/inactivity may underlie certain neurodevelopmental conditions, including autism spectrum disorder and schizophrenia, are discussed.

A multimodal atlas of the molecular and cellular changes to cortex driven by Alzheimer’s disease

AbstractBackgroundAlzheimer’s disease (AD) is the most common form of dementia, which can be detected early as mild cognitive impairment but has no broadly effective treatments to halt patients' yearslong decline. Histopathology studies have long noted dramatic, progressive, and stereotyped changes across numerous brain regions, including protein aggregate formation and even selective loss of molecularly defined neuronal populations. But the underlying molecular and cellular mechanisms that cause AD and facilitate its progression remain unknown or are only coarsely understood, hampering efforts to treat or cure the disease.MethodTo uncover these mechanisms, we characterized the transcriptomic and epigenetic landscapes of AD by applying single nucleus RNA and ATAC sequencing to ∼8 million nuclei isolated from 3 cortical regions (entorhinal cortex, middle temporal gyrus, and prefrontal cortex) in 84 aged donors that span the histopathological and cognitive disease spectrums (including unaffected controls) as part of a broader Seattle AD Brain Cell Atlas (SEA‐AD) effort. We identified ∼130 highly resolved transcriptional cell types from the BRAIN initiatives’ neurotypical references and leveraged recently developed machine learning approaches to integrate and hierarchically classify nuclei across donors. This enabled characterization of cell type abundance, gene expression, and chromatin accessibility differences that correlate with AD neuropathology, cognition decline, and genetic background with unprecedented precision.ResultOur comprehensive molecular atlas identified specific intratelencephalic excitatory neurons, inhibitory neurons, and microglia subsets that have altered abundances, gene expression, and/or chromatin accessibility as a function of cognitive decline and quantitative neuropathology, suggesting these populations may be selectively vulnerable to AD or involved in disease etiology. Their differentially expressed genes and accessible chromatin regions include both those found by previous atlasing efforts and genome wide association studies as well as novel ones, providing new clues to the molecular pathways that underpin AD. By comparing the SEA‐AD atlas with the neurotypical references, we also identified how expression patterns of genes, chromatin accessibility, and cell‐cell interactions associated with AD are more broadly altered by the disease.ConclusionThe cell types and molecular pathways identified by our atlas provide new targets for the rational development of therapeutic interventions and as biomarkers for earlier detection of the disease.

Cellular network perturbations point to a new microglia‐astrocyte community accelerating Alzheimer’s disease progression

AbstractBackgroundAlzheimer’s Disease (AD) is a fatal neurodegenerative disease where abnormal accumulation of amyloid‐β and tau aggregates drive neurodegeneration and leads to cognitive impairment, dementia and eventually death. Combining results from recent studies, each finding a novel AD‐associated cell state of different non‐neuronal cell types, suggests a system level change of the cellular environment of the AD brain and its potential role in disease outcome.MethodTo better understand the dynamics of the cellular environment in aging human brains and AD, we applied single‐nucleus RNA‐sequencing to profile 424 aging brains of individuals across different clinicopathological characteristics. We characterized the cellular diversity within the aging human prefrontal cortex, resulting in a detailed atlas of ∼1.7 million cells classified into 95 cellular subsets of different cell types, including rare populations of microglia and astrocytes.ResultsQuantifying variations across individuals, we uncovered multiple cell subsets associated with disease pathologies and cognitive impairment. Of these, we prioritize an uncommon Microglial subset 13 (Mic.13, average 3.2% of microglia) and Astrocyte subset 10 (Ast.10, average 3.8% of astrocytes). Mic.13 expresses AD risk gene TREM2 and microglial markers linked to AD (e.g. APOE, SPP1), and its proportion is strongly associated with AD pathologies, amyloid‐β plaques and neurofibrillary tangles, and cognitive decline. Applying a mediation model, we showed that Mic.13 partially mediates the effect of amyloid‐β on tau (proportion mediated [p.m.] = 18%). While the impact of Mic.13 on cognitive decline is largely mediated by tau (p.m. = 43%), an additional subset highlighted by our analysis Ast.10, associated with both tau and cognitive decline, partially mediates the impact of tau and Mic.13 on cognitive decline (p.m. = 7.2% and p.m. = 12% respectively). Integration of all cellular states revealed an intricate network of multi‐cellular communities, each composed of multiple states of different cell types. Investigating the dynamics of the cellular communities in the aging brain and along disease progression, uncovered unique trajectories spanning from a healthy to diseased brains.ConclusionOur charted atlas of the cellular environment and modelling of the cellular dynamics supports a system level change underlying AD, with an active role for multiple cell types in disease progression, and highlights novel research directions and potential therapeutic targets.

Integrative and comparative single-cell analysis reveals transcriptomic difference between human tumefactive demyelinating lesion and glioma

Tumefactive demyelinating lesion (TDL) is an immune-mediated disease which can be misdiagnosed as glioma. At present, there is no study comparing difference between the two disorders at the cellular level. Here, we perform integrative and comparative single-cell RNA sequencing (ScRNA-seq) transcriptomic analysis on TDL and glioma lesions. At single-cell resolution, TDL is comprised primarily of immune cells, which is completely different from glioma. The integrated analysis reveals a TDL-specific microglial subset involving in B cell activation and proliferation. Comparative analysis highlights remyelination function of glial cells and demyelination function of T cells in TDL. Subclustering and pseudotime trajectory analysis of T cells in TDL reveal their heterogeneity and diverse functions involving in TDL pathogenesis and recovery process. Our study identifies substantial differences between TDL and glioma at single-cell resolution. The observed heterogeneity and potentially diverse functions of cells in TDL may be critical in disease progression.

Microglial transcriptome diversity: The new milestone to reveal the neuroinflammation in subarachnoid haemorrhage

AbstractThe diversity of microglial transcriptome after subarachnoid haemorrhage (SAH) was analysed for the first time. By using single‐cell RNA sequencing (scRNA‐seq), microglia were found with diverse microglial substates and significant subgroups were defined. Microglia subsets were found to interact with each other and crosstalk with other kinds of brain cells, which ultimately affected the neuroinflammation in SAH. Microglia‐mediated neuroinflammation has been considered to be the key factor in the evolution of brain injury after SAH, but the pathophysiological mechanisms are still unclear. Under these circumstances, the study comprehensively analysed the changes of microglial transcriptome after SAH, and explored possible modes of activating the inflammatory pathways. This study expanded and systemically laid out the understanding of microglia‐mediated neuroinflammation after SAH and provided strong theoretical support for future microglia modulation research in SAH.