Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing

Emerging role of microglia in the developing dopaminergic system: Perturbation by early life stress

Early life stress correlates with a higher prevalence of neurological disorders, including autism, attention-deficit/hyperactivity disorder, schizophrenia, depression, and Parkinson's disease. These conditions, primarily involving abnormal development and damage of the dopaminergic system, pose significant public health challenges. Microglia, as the primary immune cells in the brain, are crucial in regulating neuronal circuit development and survival. From the embryonic stage to adulthood, microglia exhibit stage-specific gene expression profiles, transcriptome characteristics, and functional phenotypes, enhancing the susceptibility to early life stress. However, the role of microglia in mediating dopaminergic system disorders under early life stress conditions remains poorly understood. This review presents an up-to-date overview of preclinical studies elucidating the impact of early life stress on microglia, leading to dopaminergic system disorders, along with the underlying mechanisms and therapeutic potential for neurodegenerative and neurodevelopmental conditions. Impaired microglial activity damages dopaminergic neurons by diminishing neurotrophic support (e.g., insulin-like growth factor-1) and hinders dopaminergic axon growth through defective phagocytosis and synaptic pruning. Furthermore, blunted microglial immunoreactivity suppresses striatal dopaminergic circuit development and reduces neuronal transmission. Furthermore, inflammation and oxidative stress induced by activated microglia can directly damage dopaminergic neurons, inhibiting dopamine synthesis, reuptake, and receptor activity. Enhanced microglial phagocytosis inhibits dopamine axon extension. These long-lasting effects of microglial perturbations may be driven by early life stress-induced epigenetic reprogramming of microglia. Indirectly, early life stress may influence microglial function through various pathways, such as astrocytic activation, the hypothalamic-pituitary-adrenal axis, the gut-brain axis, and maternal immune signaling. Finally, various therapeutic strategies and molecular mechanisms for targeting microglia to restore the dopaminergic system were summarized and discussed. These strategies include classical antidepressants and antipsychotics, antibiotics and anti-inflammatory agents, and herbal-derived medicine. Further investigations combining pharmacological interventions and genetic strategies are essential to elucidate the causal role of microglial phenotypic and functional perturbations in the dopaminergic system disrupted by early life stress.

Inhibition of the cGAS-STING pathway: contributing to the treatment of cerebral ischemia-reperfusion injury

The cGAS-STING pathway plays an important role in ischemia-reperfusion injury in the heart, liver, brain, and kidney, but its role and mechanisms in cerebral ischemia-reperfusion injury have not been systematically reviewed. Here, we outline the components of the cGAS-STING pathway and then analyze its role in autophagy, ferroptosis, cellular pyroptosis, disequilibrium of calcium homeostasis, inflammatory responses, disruption of the blood-brain barrier, microglia transformation, and complement system activation following cerebral ischemia-reperfusion injury. We further analyze the value of cGAS-STING pathway inhibitors in the treatment of cerebral ischemia-reperfusion injury and conclude that the pathway can regulate cerebral ischemia-reperfusion injury through multiple mechanisms. Inhibition of the cGAS-STING pathway may be helpful in the treatment of cerebral ischemia-reperfusion injury.

Hippocampal microglial activation induces cognitive impairment and allodynia through neuronal plasticity changes in male mice with neuropathic pain

Clinical evidence indicates that cognitive impairment is a common comorbidity of chronic pain, including neuropathic pain, but the mechanism underlying this comorbidity remains unclear. Neuroinflammation plays a critical role in the development of both neuropathic pain and cognitive impairment. A previous study showed that minocycline, an inhibitor of microglia, ameliorated allodynia and cognitive impairment in partial sciatic nerve ligation (PSNL) mice. Therefore, the current study examined a potential role of brain microglia in allodynia and cognitive impairment in male mice with neuropathic pain due to PSNL. Immunohistochemistry of the microglial markers ionized calcium-binding adapter molecule 1 (Iba1), transmembrane protein 119 (TMEM119), and purinergic receptor P2Y12 (P2RY12) was performed to examine microglial status. Two weeks after PSNL, significant microglial activation was observed in the hippocampus and amygdala, but not in the perirhinal cortex. Inhibition of brain-region-specific microglia with a local microinjection of clodronate liposomes was examined to elucidate the involvement of these microglia in PSNL-induced allodynia and cognitive impairment. Local clodronate liposome microinjection to the hippocampus, but not the amygdala, ameliorated allodynia and cognitive impairment. Other changes in the hippocampus of PSNL mice, e.g., decreased hippocampal dendrite length and intersections number, were prevented by microinjection of clodronate liposomes. The current findings suggest hippocampal microglia are related to cognitive impairment and allodynia through neuronal plasticity changes observed in PSNL mice. Blocking hippocampal microglia-mediated neuroinflammation may be a novel approach for reducing comorbidities such as cognitive impairment associated with neuropathic pain.

Generation of an Inducible Destabilized-Domain Cre Mouse Line to Target Disease Associated Microglia

The function of microglia during progression of Alzheimer's disease (AD) can be investigated using mouse models that enable genetic manipulation of microglial subpopulations in a temporal manner. We developed mouse lines that express either Cre recombinase (Cre) for constitutive targeting, or destabilized-domain Cre recombinase (DD-Cre) for inducible targeting from the Cst7 locus (Cst7 DD-Cre) to specifically manipulate disease associated microglia (DAM) and crossed with Ai14 tdTomato cre-reporter line mice. Cst7Cre was found to target all brain resident myeloid cells, due to transient developmental expression of Cst7, but no expression was found in the inducible Cst7 DD-Cre mice. Further crossing of this line with 5xFAD mice combined with dietary administration of trimethoprim to induce DD-Cre activity produces long-term labeling in DAM without evidence of leakiness, with tdTomato-expression restricted to cells surrounding plaques. Using this model, we found that DAMs are a subset of plaque-associated microglia (PAMs) and their transition to DAM increases with age and disease stage. Spatial transcriptomic analysis revealed that tdTomato+ cells show higher expression of disease and inflammatory genes compared to other microglial populations, including non-labeled PAMs. These models allow either complete cre-loxP targeting of all brain myeloid cells (Cst7Cre), or inducible targeting of DAMs, without leakiness (Cst7 DD-Cre).

Drivers and shapers of macrophages specification in the developing brain

The brain harbors two major macrophage populations: microglia reside within the brain parenchyma, while border-associated macrophages (BAMs) are situated at central nervous system (CNS) interfaces. BAMs can be further classified into distinct subsets based on their localization: perivascular macrophages surround blood vessels, meningeal macrophages reside in the leptomeninges, dura macrophages in the dura mater, and choroid plexus macrophages are confined to the choroid plexus. The environmental factors and molecular mechanisms driving the specification of these macrophage populations are still being elucidated. Deciphering the communication pathways between CNS macrophages and their tissue niches during development, homeostasis, and pathologic conditions offers significant potential for treating a wide range of brain disorders, from neurodevelopmental and neuroinflammatory diseases to neurovascular and neurodegenerative conditions. With this short review, we will address the current understanding and knowledge gaps in the field, as well as the future directions for the upcoming years.

Single-nucleus and spatial signatures of the brainstem in normal brain and mild traumatic brain injury in male mice

The mammalian brainstem is particularly vulnerable to mild traumatic brain injury (mTBI), which is associated with prolonged autonomic dysfunction and coma. The spatial cellular connections within the brainstem or the mechanisms underlying its response to injury have been underestimated. Here, we performed single-nucleus RNA sequencing with spatial transcriptome sequencing in both normal and mTBI brainstems in male mice, revealing thirty-five neuron and non-neuron clusters. Typically, we identified subtypes of neurons that co-release multiple neurotransmitters, especially in the sagittal midline of the brainstem. Spatially adjacent neurons sharing similar gene expression patterns. The brainstem's response to mTBI has two features: (1) Oligodendrocytes around the fourth ventricle exhibit widespread disconnection at 1-h post-injury, and (2) Injury-related noradrenergic neurons, particularly in their interaction with neurons located in theIRt and the Sol. These findings provides a reference for further integrative investigations of cellular and circuit functions of brainstem.

Early establishment and life course stability of sex biases in the human brain transcriptome

To elaborate on the origins of the established male-female differences in several brain-related phenotypes, we assessed the patterns of transcriptomic sex biases in the developing and adult human forebrain. We find an abundance of sex differences in expression (sex-DEs) in the prenatal brain, driven by both hormonal and sex-chromosomal factors, and considerable consistency in the sex effects between the developing and adult brain, with little sex-DE exclusive to the adult forebrain. Sex-DE was not enriched in genes associated with brain disorders, consistent with systematic differences in the characteristics of these genes (e.g., constraint). Yet, the genes with persistent sex-DE across the lifespan were overrepresented in disease gene co-regulation networks, pointing to their potential to mediate sex biases in brain phenotypes. Altogether, our work highlights prenatal development as a crucial time point for the establishment of brain sex differences.

A dynamic and multimodal framework to define microglial states

The widespread use of single-cell RNA sequencing has generated numerous purportedly distinct and novel subsets of microglia. Here, we challenge this fragmented paradigm by proposing that microglia exist along a continuum rather than as discrete entities. We identify a methodological over-reliance on computational clustering algorithms as the fundamental issue, with arbitrary cluster numbers being interpreted as biological reality. Evidence suggests that the observed transcriptional diversity stems from a combination of microglial plasticity and technical noise, resulting in terminology describing largely overlapping cellular states. We introduce a continuous model of microglial states, where cell positioning along the continuum is determined by biological aging and cell-specific molecular contexts. The model accommodates the dynamic nature of microglia. We advocate for a parsimonious approach toward classification and terminology that acknowledges the continuous spectrum of microglial states, toward a robust framework for understanding these essential immune cells of the CNS.

Revisiting the Pathogenesis of X-Linked Adrenoleukodystrophy

BACKGROUND

X-ALD is a white matter (WM) disease caused by mutations in the ABCD1 gene encoding the transporter of very-long-chain fatty acids (VLCFAs) into peroxisomes. Strikingly, the same ABCD1 mutation causes either devastating brain inflammatory demyelination during childhood or, more often, progressive spinal cord axonopathy starting in middle-aged adults. The accumulation of undegraded VLCFA in glial cell membranes and myelin has long been thought to be the central mechanism of X-ALD.

METHODS

This review discusses studies in mouse and drosophila models that have modified our views of X-ALD pathogenesis.

RESULTS

In the Abcd1 knockout (KO) mouse that mimics the spinal cord disease, the late manifestations of axonopathy are rapidly reversed by ABCD1 gene transfer into spinal cord oligodendrocytes (OLs). In a peroxin-5 KO mouse model, the selective impairment of peroxisomal biogenesis in OLs achieves an almost perfect phenocopy of cerebral ALD. A drosophila knockout model revealed that VLCFA accumulation in glial myelinating cells causes the production of a toxic lipid able to poison axons and activate inflammatory cells. Other mouse models showed the critical role of OLs in providing energy substrates to axons. In addition, studies on microglial changing substates have improved our understanding of neuroinflammation.

CONCLUSIONS

Animal models supporting a primary role of OLs and axonal pathology and a secondary role of microglia allow us to revisit of X-ALD mechanisms. Beyond ABCD1 mutations, pathogenesis depends on unidentified contributors, such as genetic background, cell-specific epigenomics, potential environmental triggers, and stochasticity of crosstalk between multiple cell types among billions of glial cells and neurons.

Direct microglia replacement reveals pathologic and therapeutic contributions of brain macrophages to a monogenic neurological disease

Krabbe disease, also named globoid cell (GC) leukodystrophy (GLD) for its distinct lipid-laden macrophages, is a severe leukodystrophy caused by galactosylceramidase (GALC) mutations. Hematopoietic stem cell transplant (HSCT) ameliorates disease and is associated with central nervous system (CNS) engraftment of GALC+ donor macrophages. Yet, the role of macrophages in GLD pathophysiology and HSCT remains unclear. Using single-cell sequencing, we revealed early interferon response signatures that preceded progressively severe macrophage dyshomeostasis and identified a molecular signature of GCs, which we validated in human brain specimens. Genetic depletion and direct microglia replacement by CNS monocyte injection rapidly replaced >80% of endogenous microglia with healthy macrophages in the twitcher (GalcW355∗) mouse model of GLD. Perinatal microglia replacement completely normalized transcriptional signatures, rescued histopathology, and doubled average survival. Overall, we uncovered distinct forms of microglial dysfunction and evidence that direct, CNS-limited microglia replacement improves a monogenic neurodegenerative disease, identifying a promising therapeutic target.

Microglia transcriptional states and their functional significance: Context drives diversity

In the brain, microglia are continuously exposed to a dynamic microenvironment throughout life, requiring them to adapt accordingly to specific developmental or disease-related demands. The advent of single-cell sequencing technologies has revealed the diversity of microglial transcriptional states. In this review, we explore the various contexts that drive transcriptional diversity in microglia and assess the extent to which non-homeostatic conditions induce context-specific signatures. We discuss our current understanding and knowledge gaps regarding the relationship between transcriptional states and microglial function, review the influence of complex microenvironments and prior experiences on microglial state induction, and highlight strategies to bridge the gap between mouse and human studies to advance microglia-targeting therapeutics.

Border-associated macrophages as gatekeepers of brain homeostasis and immunity

The brain's border tissues serve as essential hubs for neuroimmune regulation and the trafficking of biomaterials to and from the brain. These complex tissues-including the meninges, perivascular spaces, choroid plexus, and circumventricular organs-balance the brain's need for immune privilege with immune surveillance and blood-brain communication. Macrophages are integral components of these tissues, taking up key strategic positions within the brain's circulatory system. These border-associated macrophages, or "BAMs," are therefore emerging as pivotal for brain homeostasis and disease. BAMs perform trophic functions that help to support border homeostasis but also act as immune sentinels essential for border defense. In this review, we integrate recent findings on BAM origins, cell states, and functions, aiming to provide global insights and perspectives on the complex relationship between these macrophages and their border niche.

Microglial and TREM2 dialogues in the developing brain

From the migration of precursor cells to the refinement of neural circuits, the immune system plays a critical role in the development of the central nervous system. As the brain resident macrophages, microglia are integral to these processes, influencing key developmental stages and contributing to circuit remodeling. Recent years have brought a wealth of new insights into how microglia regulate key stages of brain development, particularly through their continuous crosstalk with various brain cell types. In this review, we synthesize this growing body of literature on microglia and neurodevelopment, highlighting the involvement of the TREM2 receptor, known for its role in aging and neurodegeneration, which profoundly affects the state of microglia and guides target cells by shaping their transcriptional and functional fate. We examine microglial communication with four major cell types-neural precursors, neurons, astrocytes, and oligodendrocytes-also delving into the described mechanisms that underpin these interactions.

A single-cell transcriptomic atlas of all cell types in the brain of 5xFAD Alzheimer mice in response to dietary inulin supplementation

BACKGROUND

Alzheimer's disease (AD) is a progressive neurodegenerative disease that is a major threat to the aging population. Due to lack of effective therapy, preventive treatments are important strategies to limit AD onset and progression, of which dietary regimes have been implicated as a key factor. Diet with high fiber content is known to have beneficial effects on cognitive decline in AD. However, a global survey on microbiome and brain cell dynamics in response to high fiber intake at single-cell resolution in AD mouse models is still missing.

RESULTS

Here, we show that dietary inulin supplementation synergized with AD progression to specifically increase the abundance of Akkermansia muciniphila in gut microbiome of 5 × Familial AD (FAD) mice. By performing single-nucleus RNA sequencing on different regions of the whole brain with three independent biological replicates, we reveal region-specific changes in the proportion of neuron, astrocyte, and granule cell subpopulations upon inulin supplementation in 5xFAD mice. In addition, we find that astrocytes have more pronounced region-specific diversity than microglia. Intriguingly, such dietary change reduces amyloid-β plaque burden and alleviates microgliosis in the forebrain region, without affecting the spatial learning and memory.

CONCLUSIONS

These results provide a comprehensive overview on the transcriptomic changes in individual cells of the entire mouse brain in response to high fiber intake and a resourceful foundation for future mechanistic studies on the influence of diet and gut microbiome on the brain during neurodegeneration.

Insights into the intramembrane protease SPPL2b and its substrates: Functions and disease implications

Specialized intramembrane proteases, known as iCLiPs, regulate the processing of transmembrane proteins by releasing intracellular domains, which can function as transcriptional regulators. The signal peptide peptidase-like (SPPL) family of iCLiPs, particularly SPPL2b, has roles in immune regulation, neuronal function, and disease pathogenesis. In the brain, SPPL2b localizes mainly in the plasma membrane of neurons and microglia and is abundant in the cortex and hippocampus. Its known substrates regulate neuronal growth, inflammation, and synaptic function, and increased amounts of SPPL2b have been found in postmortem brain tissue from patients with Alzheimer's disease. In this review, we discuss the currently known roles of SPPL2b, its substrates, and its disease implications. Understanding the downstream effects of SPPL2b-cleaved substrates will provide clearer insights into the impact of SPPL2b on cellular homeostasis and disease, potentially leading to new therapeutic strategies.

Neuroinflammation in Alzheimer disease

Increasing evidence points to a pivotal role of immune processes in the pathogenesis of Alzheimer disease, which is the most prevalent neurodegenerative and dementia-causing disease of our time. Multiple lines of information provided by experimental, epidemiological, neuropathological and genetic studies suggest a pathological role for innate and adaptive immune activation in this disease. Here, we review the cell types and pathological mechanisms involved in disease development as well as the influence of genetics and lifestyle factors. Given the decade-long preclinical stage of Alzheimer disease, these mechanisms and their interactions are driving forces behind the spread and progression of the disease. The identification of treatment opportunities will require a precise understanding of the cells and mechanisms involved as well as a clear definition of their temporal and topographical nature. We will also discuss new therapeutic strategies for targeting neuroinflammation, which are now entering the clinic and showing promise for patients.

Aging and neurodegeneration: when systemic dysregulations affect brain macrophage heterogeneity

Microglia, the major population of brain resident macrophages, differentiate from yolk sac progenitors in the embryo and play multiple nonimmune roles in brain organization throughout development and life. Various microglia subtypes have been described by transcriptomic and proteomic signatures, involved metabolic pathways, morphology, intracellular complexity, time of residency, and ontogeny, both in development and in disease settings. Such macrophage heterogeneity increases with aging or neurodegeneration. Monocytes' infiltration and differentiation into monocyte-derived macrophages (MDMs) in the brain contribute to this diversity. Microbiota's role in brain diseases has been recently highlighted, revealing how microbial signals, such as metabolites, influence microglia and MDMs. In this brief review, we describe how these signals can influence microglia through their sensome and shape MDMs from their development in the bone marrow to their differentiation in the brain. Monocytes could then be a crucial player in the constitution of a dysbiotic gut-brain axis in neurodegenerative diseases and aging.

CD11c-Expressing Microglia Are Transient, Driven by Interactions With Apoptotic Cells

Microglia, the parenchymal macrophage of the central nervous system, serve crucial remodeling functions throughout development. Microglia are transcriptionally heterogenous, suggesting that distinct microglial states confer discrete roles. Currently, little is known about how dynamic these states are, the cues that promote them, or how they impact microglial function. In the developing retina, we previously found a significant proportion of microglia express CD11c (Integrin αX, Itgax, subunit of complement receptor 4) which has also been reported in other developmental and disease contexts. Here, we sought to understand the regulation and function of CD11c+ microglia. We found that CD11c+ microglia track with prominent waves of neuronal apoptosis in postnatal retina. Using genetic fate mapping, we provide evidence that microglia transition out of the CD11c state to return to homeostasis. We show that CD11c+ microglia have elevated lysosomal content and contribute to the clearance of apoptotic neurons, and found that acquisition of CD11c expression is partially dependent upon the TAM receptor AXL. Using selective ablation, we found CD11c+ microglia are not uniquely critical for phagocytic clearance of apoptotic cells. Together, our data suggest that CD11c+ microglia are a transient state induced by developmental apoptosis rather than a specialized subset mediating phagocytic elimination.

Neuroprotective and plasticity promoting effects of repetitive transcranial magnetic stimulation (rTMS): A role for microglia

Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive brain stimulation technique used to modulate neocortical excitability, with expanding applications in neurological and psychiatric disorders. However, the cellular and molecular mechanisms underlying its effects, particularly the role of microglia -the resident immune cells of the central nervous system- remain poorly understood. This review synthesizes recent findings on how different rTMS protocols influence microglial function under physiological conditions and in disease models. Emerging evidence indicates that rTMS modulates microglial activation, promoting neuroprotective and plasticity-enhancing processes not only in models of brain disorders, such as Alzheimer's and Parkinson's disease, but also in healthy neural circuits. While much of the current research has focused on the inflammatory profile of microglia, critical aspects such as activity-dependent synaptic remodeling, phagocytic activity, and process motility remain underexplored. Given the substantial heterogeneity of microglial responses across brain regions, age, and sex, as well as their differential roles in health and disease, a deeper understanding of their involvement in rTMS-induced plasticity is essential. Future studies should integrate selective microglial manipulation and advanced structural, functional, and molecular profiling techniques to clarify their causal involvement. Addressing these gaps will be pivotal in optimizing rTMS protocols and maximizing its therapeutic potential across a spectrum of neurological and neuropsychiatric conditions.

Type I interferon signalling and interferon-responsive microglia in health and disease

Recent evidence suggests that type I interferon (IFN-I) signalling extends beyond its canonical roles in antiviral defence and immunomodulation. Over the past decade, dysregulated IFN-I signalling has been linked to genetic disorders and neurodegenerative diseases, where it may contribute to neurological impairments. Microglia have emerged as key mediators of IFN-I responses in the central nervous system. A distinct transcriptional state responsive to interferons has recently been identified in microglia. The activation of the IFN-I pathway in these cells is now recognised as pivotal in both development and neurodegeneration. This review is divided into two main sections: the first examines the broader role of IFN-I signalling in the central nervous system, particularly its contribution to neurological dysfunction; the second focuses on the specific state of interferon-responsive microglia, exploring its mechanisms and relevance in neurodegenerative conditions. Finally, we discuss how these areas intersect and their implications for both healthy and diseased states.

Microglia aging in the hippocampus advances through intermediate states that drive activation and cognitive decline

During aging, microglia - the resident macrophages of the brain - exhibit altered phenotypes and contribute to age-related neuroinflammation. While numerous hallmarks of age-related microglia have been elucidated, the progression from homeostasis to dysfunction during the aging process remains unresolved. To bridge this gap in knowledge, we undertook complementary cellular and molecular analyses of microglia in the mouse hippocampus across the adult lifespan and in the experimental aging model of heterochronic parabiosis. Single-cell RNA-Seq and pseudotime analysis revealed age-related transcriptional heterogeneity in hippocampal microglia and identified intermediate states of microglial aging that also emerge following heterochronic parabiosis. We tested the functionality of intermediate stress response states via TGFβ1 and translational states using pharmacological approaches in vitro to reveal their modulation of the progression to an activated state. Furthermore, we utilized single-cell RNA-Seq in conjunction with in vivo adult microglia-specific Tgfb1 conditional genetic knockout mouse models to demonstrate that microglia advancement through intermediate aging states drives transcriptional inflammatory activation and hippocampal-dependent cognitive decline.

Age-dependent glial heterogeneity and traumatic injury responses in a vertebrate brain structure

The progression of traumatic brain injury (TBI) pathology is significantly influenced by age and involves a complex interplay of glial cells. However, the influence of age on the glial dynamics and their TBI responses remains mostly unexplored. Here, we obtain a comprehensive single-cell transcriptome atlas of three major glial types under the physiological and TBI conditions across four post-embryonic life stages in the zebrafish midbrain optic tectum. We identify a library of glial subtypes and states with specific age-dependent patterns that respond distinctly to TBI. Combining the glial interactome analysis and CRISPR-Cas9-mediated gene disruption, we reveal the essential roles of dla-notch3 and cxcl12a-cxcr4b interactions in the early-larval-stage-specific unresponsiveness of radial astrocytes to TBI and the TBI-induced age-independent recruitment of microglia to injury sites, respectively. Overall, our findings provide the molecular and cellular framework of TBI-induced age-related glial dynamics in vertebrate brains.

Neutrophil infiltration and microglial shifts in sepsis induced preterm brain injury: pathological insights

Preterm sepsis is a major contributor to brain injury and long-term neurodevelopmental impairments, but its molecular mechanisms remain poorly understood. This study integrated clinical and experimental approaches to investigate the pathological changes linking systemic inflammation to brain injury in preterm infants. Transcriptomic analysis of septic preterm infants' peripheral blood revealed upregulated immune, metabolic, and inflammatory pathways, suggesting a link between systemic and brain inflammation. Using P2 mice, we established a preterm white matter injury model through multiple doses of lipopolysaccharide, observing dose-dependent developmental delays, brain inflammation, and long-term behavioral deficits. Integrative analyses of peripheral blood and brain samples from both mice and preterm infants revealed consistent chemokine alterations and immune cell infiltration across peripheral and central compartments, highlighting the significant involvement of neutrophil extracellular traps in preterm brain injury. Furthermore, microglia exhibited significant transcriptional changes during the acute phase, accompanied by metabolic reprogramming from oxidative phosphorylation to glycolysis, with suggested involvement of Pgk1 and Pgam1. This shift intensified with escalating inflammation, along with PANoptosis-related gene upregulation, ultimately associated with microglial cell death. Collectively, these findings provide pathological insights into the immunometabolic alterations underlying sepsis-induced preterm brain injury and suggest potential targets for future therapeutic interventions to mitigate long-term neurodevelopmental deficits.

The Complementary Role of Morphology in Understanding Microglial Functional Heterogeneity

A search of the PubMed database for publications on microglia reveals an intriguing shift in scientific interest over time. Dividing microglia into categories such as "resting" and "activated" or M1 versus M2 is nowadays obsolete, with the current research focusing on unraveling microglial heterogeneity. The onset of transcriptomics, especially single-cell RNA sequencing (scRNA-seq), has profoundly reshaped our understanding of microglia heterogeneity. Conversely, microglia morphology analysis can offer important insights regarding their activation state or involvement in tissue responses. This review explores microglial heterogeneity under homeostatic conditions, developmental stages, and disease states, with a focus on integrating transcriptomic data with morphological analysis. Beyond the core gene expression profile, regional differences are observed with cerebellar microglia exhibiting a uniquely immune-vigilant profile. During development, microglia express homeostatic genes before birth, yet the bushy appearance is a characteristic that appears later on. In neurodegeneration, microglia alternate between proinflammatory and neuroprotective roles, influenced by regional factors and disease onset. Understanding these structural adaptations may help identify specific microglial subpopulations for targeted therapeutic strategies.

Inactivation of microglial LXRβ in early postnatal mice impairs microglia homeostasis and causes long-lasting cognitive dysfunction

Microglia, the largest population of brain immune cells, play an essential role in regulating neuroinflammation by removing foreign materials and debris and in cognition by pruning synapses. Since liver X receptor β (LXRβ) has been identified as a regulator of microglial homeostasis, this study examined whether its removal from microglia affects neuroinflammation and cognitive function. We used a cell-specific tamoxifen-inducible Cre-loxP-mediated recombination to remove LXRβ from microglia specifically. We now report that ablation of LXRβ in microglia in early postnatal life led to a reduction in microglial numbers, distinct morphological changes indicative of microglial activation, and enhanced synapse engulfment accompanied by cognitive deficits. Removal of LXRβ from microglia in adult mice caused no cognitive defects. RNAseq analysis of microglia revealed that loss of LXRβ led to reduced expression of SAll1, a master regulator of microglial homeostasis, while increasing expression of genes associated with microglial activation and CNS disease. This study demonstrates distinctly different functions of microglial LXRβ in developing and adult mice and points to long-term consequences of defective LXRβ signaling in microglia in early life.

A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate

The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here, we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development.

Microglia heterogeneity, modeling and cell-state annotation in development and neurodegeneration

Within the CNS, microglia execute various functions associated with brain development, maintenance of homeostasis and elimination of pathogens and protein aggregates. This wide range of activities is closely associated with a plethora of cellular states, which may reciprocally influence or be influenced by their functional dynamics. Advancements in single-cell RNA sequencing have enabled a nuanced exploration of the intricate diversity of microglia, both in health and disease. Here, we review our current understanding of microglial transcriptional heterogeneity. We provide an overview of mouse and human microglial diversity encompassing aspects of development, neurodegeneration, sex and CNS regions. We offer an insight into state-of-the-art technologies and model systems that are poised to improve our understanding of microglial cell states and functions. We also provide suggestions and a tool to annotate microglial cell states on the basis of gene expression.

Lamin A/C regulates cerebellar granule cell maturation

Lamin A/C is a nuclear type V intermediate filament protein part of the meshwork structure underlying the inner nuclear membrane (nuclear lamina), which plays numerous roles, including maintenance of nuclear shape, heterochromatin organization, and transcriptional regulation. Our group has demonstrated the role of Lamin A/C in different pathophysiological conditions. Here, we investigated for the first time how Lamin A/C affects neuronal maturation in rat cerebellar granule cells (GCs). Primary rat cerebellar GCs where we silenced the Lmna gene constituted our key model; this provided a rather homogeneous cellular system showing a neuronal population in vitro. We then validated our findings in another in vivo murine model with knock-out of the Lmna gene and in an in vitro human neuronal model with silencing of the LMNA gene. We observed across three different models that Lamin A/C down-regulation affects neurons maturation by protecting the cells from glutamate-evoked excitotoxicity and correlates with an inhibition of calcium influxes and a down-regulation of pro-inflammatory cytokine pathways. Consistent with previous findings from our group, this study corroborates that Lamin A/C plays a key role in neural development and opens new significant implications for a better comprehension of the mechanisms involved in neurodegenerative diseases, where changes in the nuclear envelope are linked to neuroinflammatory processes and damage.

Central Nervous System Macrophages in Health and Disease

The central nervous system (CNS) has a unique set of macrophages that seed the tissue early during embryonic development. Microglia reside in the parenchyma, and border-associated macrophages are present in border regions, including the meninges, perivascular spaces, and choroid plexus. CNS-resident macrophages support brain homeostasis during development and steady state. In the diseased brain, however, the immune landscape is altered, with phenotypic and transcriptional changes in resident macrophages and the invasion of blood-borne monocytes, which differentiate into monocyte-derived macrophages upon entering the CNS. In this review, we focus on the fate and function of the macrophage compartment in health, neurodegenerative conditions such as amyloidosis, and neuroinflammation as observed in multiple sclerosis and infection. We discuss our current understanding that monocyte-derived macrophages contribute to neuropathology whereas native macrophages play a neuroprotective role in disease.

Depletion of Cell Adhesion Molecule L1 from Microglia and Macrophages Reduces Recovery After Spinal Cord Injury

The young mammalian central nervous system regenerates after spinal cord injury and recovers locomotion, whereas adult mice only show limited recovery that depends on the injury severity, genetic background, and physical therapy. At the molecular level, key regulators that contribute to recovery are cell adhesion molecules, such as L1CAM (L1). At the cell surface, L1 functions as a homotypic receptor that signal-transduces crucial functions in neuronal migration and survival, neurite outgrowth, myelination, formation of synapses, and synaptic plasticity. In the adult central nervous system, L1 is expressed only by neurons. We now show that L1 is unexpectedly also expressed by 26% microglia, freshly isolated from a 7-day-old mouse brain. At postnatal day 21, only 3% of microglia are L1-positive. Using a mouse mutant in which L1 is deleted specifically in monocytes of 10- to 14-week-old mice, functional recovery was reduced up to 4 weeks after injury at lower thoracic spinal levels. Also, NF200-immunoreactive and 5-HT-immunoreactive fibers were found decreased below the injury site as compared to wild-type mice. In conclusion, microglial cells that express L1 stimulate neurite outgrowth in vitro, improve functional recovery after spinal cord injury in adult mice, and increase fiber densities caudal to the lesion site.

Single-Nucleus RNA Sequencing Reveals Enduring Signatures of Acute Stress and Chronic Exercise in Striatal Microglia

Acute stress has enduring effects on the brain and motivated behavior across species. For example, acute stress produces persisting decreases in voluntary physical activity as well as molecular changes in the striatum, a brain region that regulates voluntary physical activity and other motivated behaviors. Microglia, the primary immune cells of the central nervous system, are positioned at the interface between neural responses to stress and neural coordination of voluntary activity in that they respond to stress, sense molecular changes in the striatum, and modulate neuronal activity. However, the role of striatal microglia in stress-induced long-term suppression of voluntary activity is unknown. Here, we employ single-nucleus RNA sequencing to investigate how stress and exercise impact the biology of microglia in the striatum. We find that striatal microglia display altered activation profiles 6 weeks after an acute stressor. Furthermore, we show that access to a running wheel is associated with an additional and distinct microglial activation profile characterized by upregulation of genes related to complement components and phagocytosis pathways. Finally, we find that distinct gene sets show expression changes associated with general access to a running wheel versus variation in running levels. Taken together, our results deepen our understanding of the diverse molecular states that striatal microglia assume in response to stress and exercise and suggest that microglia exhibit a broader range of functional states than previously thought.

Microglia efferocytosis: an emerging mechanism for the resolution of neuroinflammation in Alzheimer's disease

Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by significant neuroinflammatory responses. Microglia, the immune cells of the central nervous system, play a crucial role in the pathophysiology of AD. Recent studies have indicated that microglial efferocytosis is an important mechanism for clearing apoptotic cells and cellular debris, facilitating the resolution of neuroinflammation. This review summarizes the biological characteristics of microglia and the mechanisms underlying microglial efferocytosis, including the factors and signaling pathways that regulate efferocytosis, the interactions between microglia and other cells that influence this process, and the role of neuroinflammation in AD. Furthermore, we explore the role of microglial efferocytosis in AD from three perspectives: its impact on the clearance of amyloid plaques, its regulation of neuroinflammation, and its effects on neuroprotection. Finally, we summarize the current research status on enhancing microglial efferocytosis to alleviate neuroinflammation and improve AD, as well as the future challenges of this approach as a therapeutic strategy for AD.

Radial glia integrin avb8 regulates cell autonomous microglial TGFβ1 signaling that is necessary for microglial identity

Microglial diversity arises from the interplay between inherent genetic programs and external environmental signals. However, the mechanisms by which these processes develop and interact within the growing brain are not yet fully understood. Here, we show that radial glia-expressed integrin beta 8 (ITGB8) activates microglia-expressed TGFβ1 to drive microglial development. Domain-restricted deletion of Itgb8 in these progenitors results in regionally restricted and developmentally arrested microglia that persist into adulthood. In the absence of autocrine TGFβ1 signaling, microglia adopt a similar phenotype, leading to neuromotor symptoms almost identical to Itgb8 mutant mice. In contrast, microglia lacking the canonical TGFβ signal transducers Smad2 and Smad3 have a less polarized dysmature phenotype and correspondingly less severe neuromotor dysfunction. Our study describes the spatio-temporal regulation of TGFβ activation and signaling in the brain necessary to promote microglial development, and provides evidence for the adoption of microglial developmental signaling pathways in brain injury or disease.

Atg5 in microglia regulates sex-specific effects on postnatal neurogenesis in Alzheimer's disease

Female Alzheimer's disease (AD) patients display greater cognitive deficits and worse AD pathology as compared to male AD patients. In this study, we found that conditional knockout (cKO) of Atg5 in female microglia failed to obtain disease-associated microglia (DAM) gene signatures in familiar AD mouse model (5xFAD). Next, we analyzed the maintenance and neurogenesis of neural stem cells (NSCs) in the hippocampus and subventricular zone (SVZ) from 5xFAD mice with Atg5 cKO. Our data indicated that Atg5 cKO reduced the NSC number in hippocampus of female but not male 5xFAD mice. However, in the SVZ, Atg5 cKO only impaired NSCs in male 5xFAD mice. Interestingly, female 5xFAD;Fip200 cKO mice and 5xFAD;Atg14 cKO mice did not show NSC defects. These autophagy genes cKO 5xFAD mice exhibited a higher neurogenesis activity in their SVZ. Together, our data indicate a sex-specific role for microglial Atg5 in postnatal neurogenesis in AD mice.

A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate

The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development.

Age-dependent progression from clearance to vulnerability in the early response of periventricular microglia to α-synuclein toxic species

Cytoplasmic alpha-synuclein (αSyn) aggregates are a typical feature of Parkinson's disease (PD). Extracellular insoluble αSyn can induce pathology in healthy neurons suggesting that PD neurodegeneration may spread through cell-to-cell transfer of αSyn proteopathic seeds. Early pro-homeostatic reaction of microglia to toxic forms of αSyn remains elusive, which is especially relevant considering the recently uncovered microglial molecular diversity. Here, we show that periventricular microglia of the subependymal neurogenic niche monitor the cerebrospinal fluid and can rapidly phagocytize and degrade different aggregated forms of αSyn delivered into the lateral ventricle. However, this clearing ability worsens with age, leading to an increase in microglia with aggregates in aged treated mice, an accumulation also observed in human PD samples. We also show that exposure of aged microglia to aggregated αSyn isolated from human PD samples results in the phosphorylation of the endogenous protein and the generation of αSyn seeds that can transmit the pathology to healthy neurons. Our data indicate that while microglial phagocytosis rapidly clears toxic αSyn, aged microglia can contribute to synucleinopathy spreading.

Microglial Engulfment of Multisensory Terminals in the Midbrain Inferior Colliculus During an Early Critical Period

The lateral cortex of the inferior colliculus (LCIC) receives multisensory input arrays that preferentially target its compartmental organization. Inputs of somatosensory origin end within modular zones, while auditory inputs terminate throughout an encompassing matrix. Such discrete mapping emerges during an early postnatal critical period (birth to postnatal day 12, P12) via a process of segregation. Similar to other primitive brain maps, it appears an initial excess of connections may be pruned through a refinement process. Microglial cells (MGCs) are involved in a variety of systems in the selective removal and degradation of unnecessary contacts. Aberrations in map plasticity during early critical periods have been associated with certain neurodevelopmental conditions, including autism spectrum disorders (ASD). Despite evidence linking multisensory integration deficits with cognitive/behavioral disturbances associated with ASD, mechanisms that govern multimodal network modifications remain poorly understood. Thus, the present study combines novel tract-tracing approaches in living brain preparations and immunocytochemistry in CX3CR1-GFP knock-in mice to determine: (1) if fractalkine signaling (CX3CL1-CX3CR1) influences MGC engulfment of auditory afferents, (2) whether individual MGCs phagocytose endings of multisensory origin (auditory and somatosensory), and (3) whether consumed product is degraded via the MGC's lysosomal pathway. We demonstrate active MGC pruning of auditory endings at peak LCIC stages for projection shaping (P4, P8) that significantly decreases coincident with its critical period closure (P12). While developmentally regulated, auditory engulfment appears fractalkine signaling-independent. We also provide evidence that individual LCIC microglia engulf both auditory and somatosensory terminals that co-localize with the lysosomal marker, CD68. These results suggest a prominent role for microglia in the remodeling of early multisensory midbrain maps.

Multiple Sclerosis: Glial Cell Diversity in Time and Space

Multiple sclerosis (MS) is the most prevalent human inflammatory disease of the central nervous system with demyelination and glial scar formation as pathological hallmarks. Glial cells are key drivers of lesion progression in MS with roles in both tissue damage and repair depending on the surrounding microenvironment and the functional state of the individual glial subtype. In this review, we describe recent developments in the context of glial cell diversity in MS summarizing key findings with respect to pathological and maladaptive functions related to disease-associated glial subtypes. A particular focus is on the spatial and temporal dynamics of glial cells including subtypes of microglia, oligodendrocytes, and astrocytes. We contextualize recent high-dimensional findings suggesting that glial cells dynamically change with respect to epigenomic, transcriptomic, and metabolic features across the inflamed rim and during the progression of MS lesions. In summary, detailed knowledge of spatially restricted glial subtype functions is critical for a better understanding of MS pathology and its pathogenesis as well as the development of novel MS therapies targeting specific glial cell types.

Propagation of neuronal micronuclei regulates microglial characteristics

Microglia-resident immune cells in the central nervous system-undergo morphological and functional changes in response to signals from the local environment and mature into various homeostatic states. However, niche signals underlying microglial differentiation and maturation remain unknown. Here, we show that neuronal micronuclei (MN) transfer to microglia, which is followed by changing microglial characteristics during the postnatal period. Neurons passing through a dense region of the developing neocortex give rise to MN and release them into the extracellular space, before being incorporated into microglia and inducing morphological changes. Two-photon imaging analyses have revealed that microglia incorporating MN tend to slowly retract their processes. Loss of the cGAS gene alleviates effects on micronucleus-dependent morphological changes. Neuronal MN-harboring microglia also exhibit unique transcriptome signatures. These results demonstrate that neuronal MN serve as niche signals that transform microglia, and provide a potential mechanism for regulation of microglial characteristics in the early postnatal neocortex.

Integrative Genomics Approach Identifies Glial Transcriptomic Dysregulation and Risk in the Cortex of Individuals With Alcohol Use Disorder

BACKGROUND

Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Previous studies of AUD used underpowered single-cell analysis or bulk homogenates of postmortem brain tissue, which obscure gene expression changes in specific cell types. Therefore, we sought to conduct the largest-to-date single-nucleus RNA sequencing (snRNA-seq) postmortem brain study in AUD to elucidate transcriptomic pathology with cell type-specific resolution.

METHODS

Here, we performed snRNA-seq and high-dimensional network analysis of 73 postmortem samples from individuals with AUD (n = 36, nnuclei = 248,873) and neurotypical control individuals (n = 37, nnuclei = 210,573) in the dorsolateral prefrontal cortex from both male and female donors. Additionally, we performed analysis for cell type-specific enrichment of aggregate genetic risk for AUD as well as integration of the AUD proteome for secondary validation.

RESULTS

We identified 32 distinct cell clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glial populations. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and coexpression modules linked to AUD. Differential gene expression was secondarily validated by integration of a publicly available AUD proteome. Finally, analysis for aggregate genetic risk for AUD identified subtypes of glia as potential key players not only affected by but also causally linked to the progression of AUD.

CONCLUSIONS

These results highlight the importance of cell type-specific molecular changes in AUD and offer opportunities to identify novel targets for treatment on the single-nucleus level.

Prenatal Maternal Immune Activation with Lipopolysaccharide Accelerates the Developmental Acquisition of Neonatal Reflexes in Rat Offspring Without Affecting Maternal Care Behaviors

Maternal immune activation (MIA)-infection with an immunogen during pregnancy-is linked to an increased risk of neurodevelopmental disorders (NDDs) in offspring. Both MIA and NDDs are associated with developmental delays in offsprings' motor behavior. Therefore, the current study examined the effects of MIA on neonatal reflex development in male and female offspring. Sprague Dawley rats were administered lipopolysaccharide (LPS; 50 μg/mL/kg, i.p.) or saline on embryonic day (E)15 of gestation. The offspring were then tested daily from postnatal day (P)3-P21 to determine their neonatal reflex abilities. The maternal care behaviors of the dam were also quantified on P1-P5, P10, and P15. We found that, regardless of sex, the E15 LPS offspring were able to forelimb grasp, cliff avoid, and right with a correct posture at an earlier postnatal age than the E15 saline offspring did. The E15 LPS offspring also showed better performance of forelimb grasping, hindlimb grasping, righting with correct posture, and walking with correct posture than the E15 saline offspring did. There were no significant differences in maternal licking/grooming, arched-back nursing, non-arched-back nursing, or total nursing across the E15 groups. Overall, these findings suggest that MIA with LPS on E15 accelerates reflex development in offspring without affecting maternal care. This may be explained by the stress acceleration hypothesis, whereby early-life stress accelerates development to promote survival.

Microglia are Required for Developmental Specification of AgRP Innervation in the Hypothalamus of Offspring Exposed to Maternal High-Fat Diet During Lactation

Agouti-related peptide (AgRP) neurons in the arcuate nucleus of the hypothalamus respond to multiple metabolic signals and distribute neuroendocrine information to other brain regions such as the paraventricular hypothalamic nucleus (PVH), which plays a central role in metabolic homeostasis. Neural projections from AgRP neurons to the PVH form during the postnatal lactational period in mice and these projections are reduced in offspring of dams that consumed a high-fat diet (HFD) during lactation (MHFD-L). Here we used immunohistochemistry to visualize microglial morphology in MHFD-L offspring and identified changes that were regionally localized to the PVH and appeared temporally restricted to the period when AgRP neurons innervate this region. In addition, axon labeling experiments revealed that microglia engulf AgRP terminals in the PVH, and that the density of AgRP innervation to the PVH in MHFD-L offspring may be dependent on microglia, because microglial depletion blocked the decrease in PVH AgRP innervation observed in MHFD-L offspring, as well as prevented the increased body weight exhibited at weaning. Together, these findings suggest that microglia are activated by exposure to MHFD-L and interact directly with AgRP axons during postnatal development to permanently alter innervation of the PVH, with implications for developmental programming of metabolic phenotype.

Activity-dependent regulation of microglia numbers by pyramidal cells during development shape cortical functions

Beyond their role as immune sentinels, microglia are actively involved in establishing and maintaining cortical circuits. Alteration in microglial numbers has been associated with abnormal behaviors akin to those observed in neurodevelopmental disorders. Consequently, establishing the appropriate microglial numbers during development is crucial for ensuring normal cortical function. Here, we uncovered a dynamic relationship between pyramidal cells and microglia that tunes microglial numbers and development through distinct phases of mouse postnatal development. Changes in pyramidal cell activity during development induce differential release of activity-dependent proteins such as Activin A, which, in turn, adjusts microglial numbers accordingly. Decoupling of this relationship not only changes microglial numbers but has a long-term consequence on their role as synaptic organizers, which ultimately affects cortical function. Our findings reveal that microglia adapt their numbers to changes in pyramidal cell activity during a critical time window in development, consequently adjusting their numbers and function to the demands of the developing local circuits.

An increase in reactive oxygen species underlies neonatal cerebellum repair

The neonatal mouse cerebellum shows remarkable regenerative potential upon injury at birth, wherein a subset of Nestin-expressing progenitors (NEPs) undergoes adaptive reprogramming to replenish granule cell progenitors that die. Here, we investigate how the microenvironment of the injured cerebellum changes upon injury and contributes to the regenerative potential of normally gliogenic - NEPs and their adaptive reprogramming. Single cell transcriptomic and bulk chromatin accessibility analyses of the NEPs from injured neonatal cerebella compared to controls show a temporary increase in cellular processes involved in responding to reactive oxygen species (ROS), a known damage-associated molecular pattern. Analysis of ROS levels in cerebellar tissue confirm a transient increased one day after injury at postanal day 1, overlapping with the peak cell death in the cerebellum. In a transgenic mouse line that ubiquitously overexpresses human mitochondrial catalase (mCAT), ROS is reduced 1 day after injury to the granule cell progenitors, and we demonstrate that several steps in the regenerative process of NEPs are curtailed leading to reduced cerebellar growth. We also provide preliminary evidence that microglia are involved in one step of adaptive reprogramming by regulating NEP replenishment of the granule cell precursors. Collectively, our results highlight that changes in the tissue microenvironment regulate multiple steps in adaptative reprogramming of NEPs upon death of cerebellar granule cell progenitors at birth, highlighting the instructive roles of microenvironmental signals during regeneration of the neonatal brain.

Microglial Regulation of Neural Networks in Neuropsychiatric Disorders

Microglia serve as vital innate immune cells in the central nervous system, playing crucial roles in the generation and development of brain neurons, as well as mediating a series of immune and inflammatory responses. The morphologic transitions of microglia are closely linked to their function. With the advent of single-cell sequencing technology, the diversity of microglial subtypes is increasingly recognized. The intricate interactions between microglia and neuronal networks have significant implications for psychiatric disorders and neurodegenerative diseases. A deeper investigation of microglia in neurologic diseases such as Alzheimer disease, depression, and epilepsy can provide valuable insights in understanding the pathogenesis of diseases and exploring novel therapeutic strategies, thereby addressing issues related to central nervous system disorders.

A model-based factorization method for scRNA data unveils bifurcating transcriptional modules underlying cell fate determination

Manifold-learning is particularly useful to resolve the complex cellular state space from single-cell RNA sequences. While current manifold-learning methods provide insights into cell fate by inferring graph-based trajectory at cell level, challenges remain to retrieve interpretable biology underlying the diverse cellular states. Here, we described MGPfactXMBD, a model-based manifold-learning framework and capable to factorize complex development trajectories into independent bifurcation processes of gene sets, and thus enables trajectory inference based on relevant features. MGPfactXMBD offers a more nuanced understanding of the biological processes underlying cellular trajectories with potential determinants. When bench-tested across 239 datasets, MGPfactXMBD showed advantages in major quantity-control metrics, such as branch division accuracy and trajectory topology, outperforming most established methods. In real datasets, MGPfactXMBD recovered the critical pathways and cell types in microglia development with experimentally valid regulons and markers. Furthermore, MGPfactXMBD discovered evolutionary trajectories of tumor-associated CD8+ T cells and yielded new subtypes of CD8+ T cells with gene expression signatures significantly predictive of the responses to immune checkpoint inhibitor in independent cohorts. In summary, MGPfactXMBD offers a manifold-learning framework in scRNA-seq data which enables feature selection for specific biological processes and contributing to advance our understanding of biological determination of cell fate.

Microglial plasticity governed by state-specific enhancer landscapes

Single-cell transcriptomic studies have identified distinct microglial subpopulations with shared and divergent gene signatures across development, aging and disease. Whether these microglial subsets represent ontogenically separate lineages of cells, or they are manifestations of plastic changes of microglial states downstream of some converging signals is unknown. Furthermore, despite the well-established role of enhancer landscapes underlying the identity of microglia, to what extent histone modifications and DNA methylation regulate microglial state switches at enhancers have not been defined. Here, using genetic fate mapping, we demonstrate the common embryonic origin of proliferative-region-associated microglia (PAM) enriched in developing white matter, and track their dynamic transitions into disease-associated microglia (DAM) and white matter-associated microglia (WAM) states in disease and aging contexts, respectively. This study links spatiotemporally discrete microglial states through their transcriptomic and epigenomic plasticity, while revealing state-specific histone modification profiles that govern state switches in health and disease.

Mechanisms and environmental factors shaping the ecosystem of brain macrophages

Brain macrophages encompass two major populations: microglia in the parenchyma and border-associated macrophages (BAMs) in the extra-parenchymal compartments. These cells play crucial roles in maintaining brain homeostasis and immune surveillance. Microglia and BAMs are phenotypically and epigenetically distinct and exhibit highly specialized functions tailored to their environmental niches. Intriguingly, recent studies have shown that both microglia and BAMs originate from the same myeloid progenitor during yolk sac hematopoiesis, but their developmental fates diverge within the brain. Several works have partially unveiled the mechanisms orchestrating the development of microglia and BAMs in both mice and humans; however, many questions remain unanswered. Defining the molecular underpinnings controlling the transcriptional and epigenetic programs of microglia and BAMs is one of the upcoming challenges for the field. In this review, we outline current knowledge on ontogeny, phenotypic diversity, and the factors shaping the ecosystem of brain macrophages. We discuss insights garnered from human studies, highlighting similarities and differences compared to mice. Lastly, we address current research gaps and potential future directions in the field. Understanding how brain macrophages communicate with their local environment and how the tissue instructs their developmental trajectories and functional features is essential to fully comprehend brain physiology in homeostasis and disease.

Prenatal inflammation impairs early CD11c-positive microglia induction and delays myelination in neurodevelopmental disorders

Histological chorioamnionitis (HCA) is a form of maternal immune activation (MIA) linked to an increased risk of neurodevelopmental disorders in offspring. Our previous study identified neurodevelopmental impairments in an MIA mouse model mimicking HCA. Thus, this study investigated the role of CD11c+ microglia, key contributors to myelination through IGF-1 production, in this pathology. In the mouse model, the CD11c+ microglial population was significantly lower in the MIA group than in the control group on postnatal day 3 (PN3d). Furthermore, myelination-related protein levels significantly decreased in the MIA group at PN8d. In humans, preterm infants with HCA exhibited higher IL-6 and IL-17A cord-serum levels and lower IGF-1 levels than those without HCA, followed by a higher incidence of delayed myelination on magnetic resonance imaging at the term-equivalent age. In silico analysis revealed that the transient induction of CD11c+ microglia during early development occurred similarly in mice and humans. Notably, a lack of high CD11c+ microglial population has been observed in children with neurodevelopmental disorders. This study reports impaired induction of CD11c+ microglia during postnatal development in a mouse model of MIA associated with delayed myelination. Our findings may inform strategies for improving outcomes in infants with HCA.

The Human Microglia Atlas (HuMicA) unravels changes in disease-associated microglia subsets across neurodegenerative conditions

Dysregulated microglia activation, leading to neuroinflammation, is crucial in neurodegenerative disease development and progression. We constructed an atlas of human brain immune cells by integrating nineteen single-nucleus RNA-seq and single-cell RNA-seq datasets from multiple neurodegenerative conditions, comprising 241 samples from patients with Alzheimer's disease, autism spectrum disorder, epilepsy, multiple sclerosis, Lewy body diseases, COVID-19, and healthy controls. The integrated Human Microglia Atlas (HuMicA) included 90,716 nuclei/cells and revealed nine populations distributed across all conditions. We identified four subtypes of disease-associated microglia and disease-inflammatory macrophages, recently described in mice, and shown here to be prevalent in human tissue. The high versatility of microglia is evident through changes in subset distribution across various pathologies, suggesting their contribution in shaping pathological phenotypes. A GPNMB-high subpopulation was expanded in AD and MS. In situ hybridization corroborated this increase in AD, opening the question on the relevance of this population in other pathologies.