Digital Reconstruction of the Neuro-Glia-Vascular Architecture

Current evidence of synaptic dysfunction after stroke: Cellular and molecular mechanisms

BACKGROUND

Stroke is an acute cerebrovascular disease in which brain tissue is damaged due to sudden obstruction of blood flow to the brain or the rupture of blood vessels in the brain, which can prompt ischemic or hemorrhagic stroke. After stroke onset, ischemia, hypoxia, infiltration of blood components into the brain parenchyma, and lysed cell fragments, among other factors, invariably increase blood-brain barrier (BBB) permeability, the inflammatory response, and brain edema. These changes lead to neuronal cell death and synaptic dysfunction, the latter of which poses a significant challenge to stroke treatment.

RESULTS

Synaptic dysfunction occurs in various ways after stroke and includes the following: damage to neuronal structures, accumulation of pathologic proteins in the cell body, decreased fluidity and release of synaptic vesicles, disruption of mitochondrial transport in synapses, activation of synaptic phagocytosis by microglia/macrophages and astrocytes, and a reduction in synapse formation.

CONCLUSIONS

This review summarizes the cellular and molecular mechanisms related to synapses and the protective effects of drugs or compounds and rehabilitation therapy on synapses in stroke according to recent research. Such an exploration will help to elucidate the relationship between stroke and synaptic damage and provide new insights into protecting synapses and restoring neurologic function.

Computational modeling of neuron-glia signaling interactions to unravel cellular and neural circuit functioning

Glial cells have been shown to be vital for various brain functions, including homeostasis, information processing, and cognition. Over the past 30 years, various signaling interactions between neuronal and glial cells have been shown to underlie these functions. This review summarizes the interactions, particularly between neurons and astrocytes, which are types of glial cells. Some of the interactions remain controversial in part due to the nature of experimental methods and preparations used. Based on the accumulated data, computational models of the neuron-astrocyte interactions have been developed to explain the complex functions of astrocytes in neural circuits and to test conflicting hypotheses. This review presents the most significant recent models, modeling methods and simulation tools for neuron-astrocyte interactions. In the future, we will especially need more experimental research on awake animals in vivo and new computational models of neuron-glia interactions to advance our understanding of cellular dynamics and the functioning of neural circuits in different brain regions.

Mechanisms of Activation of Brain's Drainage during Sleep: The Nightlife of Astrocytes

The study of functions, mechanisms of generation, and pathways of movement of cerebral fluids has a long history, but the last decade has been especially productive. The proposed glymphatic hypothesis, which suggests a mechanism of the brain waste removal system (BWRS), caused an active discussion on both the criticism of some of the perspectives and our intensive study of new experimental facts. It was especially found that the intensity of the metabolite clearance changes significantly during the transition between sleep and wakefulness. Interestingly, at the cellular level, a number of aspects of this problem have been focused on, such as astrocytes-glial cells, which, over the past two decades, have been recognized as equal partners of neurons and perform many important functions. In particular, an important role was assigned to astrocytes within the framework of the glymphatic hypothesis. In this review, we return to the "astrocytocentric" view of the BWRS function and the explanation of its activation during sleep from the viewpoint of new findings over the last decade. Our main conclusion is that the BWRS's action may be analyzed both at the systemic (whole-brain) and at the local (cellular) level. The local level means here that the neuro-glial-vascular unit can also be regarded as the smallest functional unit of sleep, and therefore, the smallest functional unit of the BWRS.

Accurate classification of major brain cell types using in vivo imaging and neural network processing

Comprehensive analysis of tissue cell type composition using microscopic techniques has primarily been confined to ex vivo approaches. Here, we introduce NuCLear (Nucleus-instructed tissue composition using deep learning), an approach combining in vivo two-photon imaging of histone 2B-eGFP-labeled cell nuclei with subsequent deep learning-based identification of cell types from structural features of the respective cell nuclei. Using NuCLear, we were able to classify almost all cells per imaging volume in the secondary motor cortex of the mouse brain (0.25 mm3 containing approximately 25,000 cells) and to identify their position in 3D space in a noninvasive manner using only a single label throughout multiple imaging sessions. Twelve weeks after baseline, cell numbers did not change yet astrocytic nuclei significantly decreased in size. NuCLear opens a window to study changes in relative density and location of different cell types in the brains of individual mice over extended time periods, enabling comprehensive studies of changes in cell type composition in physiological and pathophysiological conditions.

The energy challenges of artificial superintelligence

We argue here that contemporary semiconductor computing technology poses a significant if not insurmountable barrier to the emergence of any artificial general intelligence system, let alone one anticipated by many to be "superintelligent". This limit on artificial superintelligence (ASI) emerges from the energy requirements of a system that would be more intelligent but orders of magnitude less efficient in energy use than human brains. An ASI would have to supersede not only a single brain but a large population given the effects of collective behavior on the advancement of societies, further multiplying the energy requirement. A hypothetical ASI would likely consume orders of magnitude more energy than what is available in highly-industrialized nations. We estimate the energy use of ASI with an equation we term the "Erasi equation", for the Energy Requirement for Artificial SuperIntelligence. Additional efficiency consequences will emerge from the current unfocussed and scattered developmental trajectory of AI research. Taken together, these arguments suggest that the emergence of an ASI is highly unlikely in the foreseeable future based on current computer architectures, primarily due to energy constraints, with biomimicry or other new technologies being possible solutions.

Astrocytes: new evidence, new models, new roles

Astrocytes have been in the limelight of active research for about 3 decades now. Over this period, ideas about their function and role in the nervous system have evolved from simple assistance in energy supply and homeostasis maintenance to a complex informational and metabolic hub that integrates data on local neuronal activity, sensory and arousal context, and orchestrates many crucial processes in the brain. Rapid progress in experimental techniques and data analysis produces a growing body of data, which can be used as a foundation for formulation of new hypotheses, building new refined mathematical models, and ultimately should lead to a new level of understanding of the contribution of astrocytes to the cognitive tasks performed by the brain. Here, we highlight recent progress in astrocyte research, which we believe expands our understanding of how low-level signaling at a cellular level builds up to processes at the level of the whole brain and animal behavior. We start our review with revisiting data on the role of noradrenaline-mediated astrocytic signaling in locomotion, arousal, sensory integration, memory, and sleep. We then briefly review astrocyte contribution to the regulation of cerebral blood flow regulation, which is followed by a discussion of biophysical mechanisms underlying astrocyte effects on different brain processes. The experimental section is closed by an overview of recent experimental techniques available for modulation and visualization of astrocyte dynamics. We then evaluate how the new data can be potentially incorporated into the new mathematical models or where and how it already has been done. Finally, we discuss an interesting prospect that astrocytes may be key players in important processes such as the switching between sleep and wakefulness and the removal of toxic metabolites from the brain milieu.

Primary Glial Cell and Glioblastoma Morphology in Cocultures Depends on Scaffold Design and Hydrogel Composition

3D cell cultures better replicate the in vivo environment compared to 2D models. Glioblastoma multiforme, a malignant brain tumor, highly profits from its cellular environment. Here, the U87 glioblastoma cell line in the presence/absence of primary astrocytes is studied. Thiolated hyaluronic acid (HA-SH) hydrogel reinforced with microfiber scaffolds is compared to Matrigel. Hyaluronic acid is a major extracellular matrix (ECM) component in the brain. Poly(ɛ-caprolactone) (PCL) scaffolds are written by meltelectrowriting in a box and triangular shaped design with pore sizes of 200 µm. Scaffolds are composed of 10-layers of PCL microfibers. It is found that scaffold design has an impact on cellular morphology in the absence of hydrogel. Moreover, the used hydrogels have profound influences on cellular morphology resulting in spheroid formation in HA-SH for both the tumor-derived cell line and astrocytes, while cell viability is high. Although cocultures of U87 and astrocytes exhibit cell-cell interactions, polynucleated spheroid formation is still present for U87 cells in HA-SH. Locally restricted ECM production or inability to secrete ECM proteins may underlie the observed cell morphologies. Thus, the 3D reinforced PCL-HA-SH composite with glioma-like cells and astrocytes constitutes a reproducible system to further investigate the impact of hydrogel modifications on cellular behavior and development.

CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations

Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.

Bi-allelic variants in the ESAM tight-junction gene cause a neurodevelopmental disorder associated with fetal intracranial hemorrhage

The blood-brain barrier (BBB) is an essential gatekeeper for the central nervous system and incidence of neurodevelopmental disorders (NDDs) is higher in infants with a history of intracerebral hemorrhage (ICH). We discovered a rare disease trait in thirteen individuals, including four fetuses, from eight unrelated families associated with homozygous loss-of-function variant alleles of ESAM which encodes an endothelial cell adhesion molecule. The c.115del (p.Arg39Glyfs∗33) variant, identified in six individuals from four independent families of Southeastern Anatolia, severely impaired the in vitro tubulogenic process of endothelial colony-forming cells, recapitulating previous evidence in null mice, and caused lack of ESAM expression in the capillary endothelial cells of damaged brain. Affected individuals with bi-allelic ESAM variants showed profound global developmental delay/unspecified intellectual disability, epilepsy, absent or severely delayed speech, varying degrees of spasticity, ventriculomegaly, and ICH/cerebral calcifications, the latter being also observed in the fetuses. Phenotypic traits observed in individuals with bi-allelic ESAM variants overlap very closely with other known conditions characterized by endothelial dysfunction due to mutation of genes encoding tight junction molecules. Our findings emphasize the role of brain endothelial dysfunction in NDDs and contribute to the expansion of an emerging group of diseases that we propose to rename as "tightjunctionopathies."

Analysis of Network Models with Neuron-Astrocyte Interactions

Neural networks, composed of many neurons and governed by complex interactions between them, are a widely accepted formalism for modeling and exploring global dynamics and emergent properties in brain systems. In the past decades, experimental evidence of computationally relevant neuron-astrocyte interactions, as well as the astrocytic modulation of global neural dynamics, have accumulated. These findings motivated advances in computational glioscience and inspired several models integrating mechanisms of neuron-astrocyte interactions into the standard neural network formalism. These models were developed to study, for example, synchronization, information transfer, synaptic plasticity, and hyperexcitability, as well as classification tasks and hardware implementations. We here focus on network models of at least two neurons interacting bidirectionally with at least two astrocytes that include explicitly modeled astrocytic calcium dynamics. In this study, we analyze the evolution of these models and the biophysical, biochemical, cellular, and network mechanisms used to construct them. Based on our analysis, we propose how to systematically describe and categorize interaction schemes between cells in neuron-astrocyte networks. We additionally study the models in view of the existing experimental data and present future perspectives. Our analysis is an important first step towards understanding astrocytic contribution to brain functions. However, more advances are needed to collect comprehensive data about astrocyte morphology and physiology in vivo and to better integrate them in data-driven computational models. Broadening the discussion about theoretical approaches and expanding the computational tools is necessary to better understand astrocytes' roles in brain functions.

Estimates of the permeability of extra-cellular pathways through the astrocyte endfoot sheath

BACKGROUND

Astrocyte endfoot processes are believed to cover all micro-vessels in the brain cortex and may play a significant role in fluid and substance transport into and out of the brain parenchyma. Detailed fluid mechanical models of diffusive and advective transport in the brain are promising tools to investigate theories of transport.

METHODS

We derive theoretical estimates of astrocyte endfoot sheath permeability for advective and diffusive transport and its variation in microvascular networks from mouse brain cortex. The networks are based on recently published experimental data and generated endfoot patterns are based on Voronoi tessellations of the perivascular surface. We estimate corrections for projection errors in previously published data.

RESULTS

We provide structural-functional relationships between vessel radius and resistance that can be directly used in flow and transport simulations. We estimate endfoot sheath filtration coefficients in the range [Formula: see text] to [Formula: see text], diffusion membrane coefficients for small solutes in the range [Formula: see text] to [Formula: see text], and gap area fractions in the range 0.2-0.6%, based on a inter-endfoot gap width of 20 nm.

CONCLUSIONS

The astrocyte endfoot sheath surrounding microvessels forms a secondary barrier to extra-cellular transport, separating the extra-cellular space of the parenchyma and the perivascular space outside the endothelial layer. The filtration and membrane diffusion coefficients of the endfoot sheath are estimated to be an order of magnitude lower than those of the extra-cellular matrix while being two orders of magnitude higher than those of the vessel wall.

How does neurovascular unit dysfunction contribute to multiple sclerosis?

Multiple sclerosis is an inflammatory demyelinating disease of the central nervous system (CNS) and the most common non-traumatic cause of neurological disability in young adults. Multiple sclerosis clinical care has improved considerably due to the development of disease-modifying therapies that effectively modulate the peripheral immune response and reduce relapse frequency. However, current treatments do not prevent neurodegeneration and disease progression, and efforts to prevent multiple sclerosis will be hampered so long as the cause of this disease remains unknown. Risk factors for multiple sclerosis development or severity include vitamin D deficiency, cigarette smoking and youth obesity, which also impact vascular health. People with multiple sclerosis frequently experience blood-brain barrier breakdown, microbleeds, reduced cerebral blood flow and diminished neurovascular reactivity, and it is possible that these vascular pathologies are tied to multiple sclerosis development. The neurovascular unit is a cellular network that controls neuroinflammation, maintains blood-brain barrier integrity, and tightly regulates cerebral blood flow, matching energy supply to neuronal demand. The neurovascular unit is composed of vessel-associated cells such as endothelial cells, pericytes and astrocytes, however neuronal and other glial cell types also comprise the neurovascular niche. Recent single-cell transcriptomics data, indicate that neurovascular cells, particular cells of the microvasculature, are compromised within multiple sclerosis lesions. Large-scale genetic and small-scale cell biology studies also suggest that neurovascular dysfunction could be a primary pathology contributing to multiple sclerosis development. Herein we revisit multiple sclerosis risk factors and multiple sclerosis pathophysiology and highlight the known and potential roles of neurovascular unit dysfunction in multiple sclerosis development and disease progression. We also evaluate the suitability of the neurovascular unit as a potential target for future disease modifying therapies for multiple sclerosis.

Cell morphologies in the nervous system: Glia steal the limelight

Neurons and glia have distinct yet interactive functions but are both characterized by branching morphology. Dendritic trees have been digitally traced for over 40 years in many animal species, anatomical regions, and neuron types. Recently, long-range axons also are being reconstructed throughout the brain of many organisms from invertebrates to primates. In contrast, less attention has been paid until lately to glial morphology. Thus, although glia and neurons are similarly abundant in the nervous systems of humans and most animal models, glia have traditionally been much less represented than neurons in morphological reconstruction repositories such as NeuroMorpho.Org. This is rapidly changing with the advent of high-throughput glia tracing. NeuroMorpho.Org introduced glial cells in 2017 and today they constitute nearly a third of the database content. It took NeuroMorpho.Org 10 years to collect the first 40,000 neurons and now that amount of data can be produced in a single publication. This not only demonstrates the spectacular technological progress in data production, but also demands a corresponding advancement in informatics processing. At the same time, these publicly available data also open new opportunities for quantitative analysis and computational modeling to identify universal or cell-type-specific design principles in the cellular architecture of nervous systems. As a first application, we demonstrated that supervised machine learning of tree geometry classifies neurons and glia with practically perfect accuracy. Furthermore, we discovered a new morphometric biomarker capable of robustly separating these cell classes across multiple species, brain regions, and experimental preparations, with only sparse sampling of branch measurements.

Astrocyte innate immune activation and injury amplification following experimental focal cerebral ischemia

Astrocytes are a distinct population of glial cells responsible for many homeostatic functions in normal neural architecture. In the healthy brain, astrocyte functions range from maintenance of the blood brain barrier to modulation of synaptic transmission and neuronal plasticity to glial scar formation post-ischemic injury. In humans, this group of cells exhibits far greater heterogeneity than previously thought-with distinct subpopulations that likely carry out specialized functions. Following ischemic injury, astrocytes take on a distinct phenotype-known as the reactive astrocyte. This phenotype is responsible for both the propagation and amelioration of neuronal injury during ischemia. Following ischemia, astrocytes undergo temporal and spatial-dependent changes in morphology, gene expression, hypertrophy and hyperplasia as a result of signaling within the local microenvironment of the penumbra compared to the core infarct. This elicits a cascade of downstream effects, including inflammation and activation of the innate immune system, which both propagates and ameliorates local injury within the brain parenchyma. This review will focus upon the double-edged sword-that are astrocytes and the innate immune system. We will discuss the role that astrocytes and the innate immune system play in amplifying secondary brain injury, as well as attenuating ischemic damage. Specifically, we will focus on molecular signaling and processes that could be targeted as potential therapeutic interventions.

Machine learning classification reveals robust morphometric biomarker of glial and neuronal arbors

Neurons and glia are the two main cell classes in the nervous systems of most animals. Although functionally distinct, neurons and glia are both characterized by multiple branching arbors stemming from the cell bodies. Glial processes are generally known to form smaller trees than neuronal dendrites. However, the full extent of morphological differences between neurons and glia in multiple species and brain regions has not yet been characterized, nor is it known whether these cells can be reliably distinguished based on geometric features alone. Here, we show that multiple supervised learning algorithms deployed on a large database of morphological reconstructions can systematically classify neuronal and glial arbors with nearly perfect accuracy and precision. Moreover, we report multiple morphometric properties, both size related and size independent, that differ substantially between these cell types. In particular, we newly identify an individual morphometric measurement, Average Branch Euclidean Length that can robustly separate neurons from glia across multiple animal models, a broad diversity of experimental conditions, and anatomical areas, with the notable exception of the cerebellum. We discuss the practical utility and physiological interpretation of this discovery.

Domino reaction of neurovascular unit in neuropathic pain after spinal cord injury

The mechanism of neuropathic pain after spinal cord injury is complex, and the communication between neurons, glia, and blood vessels in neurovascular units significantly affects the occurrence and development of neuropathic pain. After spinal cord injury, a domino chain reaction occurs in the neuron-glia-vessel, which affects the permeability of the blood-spinal cord barrier and jointly promotes the development of neuroinflammation. This article discusses the signal transduction between neuro-glial-endothelial networks from a multidimensional point of view and reviews its role in neuropathic pain after spinal cord injury.

The role of circadian clock in astrocytes: From cellular functions to ischemic stroke therapeutic targets

Accumulating evidence suggests that astrocytes, the abundant cell type in the central nervous system (CNS), play a critical role in maintaining the immune response after cerebral infarction, regulating the blood-brain barrier (BBB), providing nutrients to the neurons, and reuptake of glutamate. The circadian clock is an endogenous timing system that controls and optimizes biological processes. The central circadian clock and the peripheral clock are consistent, controlled by various circadian components, and participate in the pathophysiological process of astrocytes. Existing evidence shows that circadian rhythm controls the regulation of inflammatory responses by astrocytes in ischemic stroke (IS), regulates the repair of the BBB, and plays an essential role in a series of pathological processes such as neurotoxicity and neuroprotection. In this review, we highlight the importance of astrocytes in IS and discuss the potential role of the circadian clock in influencing astrocyte pathophysiology. A comprehensive understanding of the ability of the circadian clock to regulate astrocytes after stroke will improve our ability to predict the targets and biological functions of the circadian clock and gain insight into the basis of its intervention mechanism.

Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser).

SIGNIFICANCE

There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.

Astrocyte development in the cerebral cortex: Complexity of their origin, genesis, and maturation

In the mammalian brain, astrocytes form a heterogeneous population at the morphological, molecular, functional, intra-, and inter-region levels. In the past, a few types of astrocytes have been first described based on their morphology and, thereafter, according to limited key molecular markers. With the advent of bulk and single-cell transcriptomics, the diversity of astrocytes is now progressively deciphered and its extent better appreciated. However, the origin of this diversity remains unresolved, even though many recent studies unraveled the specificities of astroglial development at both population and individual cell levels, particularly in the cerebral cortex. Despite the lack of specific markers for each astrocyte subtype, a better understanding of the cellular and molecular events underlying cortical astrocyte diversity is nevertheless within our reach thanks to the development of intersectional lineage tracing, microdissection, spatial mapping, and single-cell transcriptomic tools. Here we present a brief overview describing recent findings on the genesis and maturation of astrocytes and their key regulators during cerebral cortex development. All these studies have considerably advanced our knowledge of cortical astrogliogenesis, which relies on a more complex mode of development than their neuronal counterparts, that undeniably impact astrocyte diversity in the cerebral cortex.

Direct vascular contact is a hallmark of cerebral astrocytes

Astrocytes establish extensive networks via gap junctions that allow each astrocyte to connect indirectly to the vasculature. However, the proportion of astrocytes directly associated with blood vessels is unknown. Here, we quantify structural contacts of cortical astrocytes with the vasculature in vivo. We show that all cortical astrocytes are connected to at least one blood vessel. Moreover, astrocytes contact more vessels in deeper cortical layers where vessel density is known to be higher. Further examination of different brain regions reveals that only the hippocampus, which has the lowest vessel density of all investigated brain regions, harbors single astrocytes with no apparent vascular connection. In summary, we show that almost all gray matter astrocytes have direct contact to the vasculature. In addition to the glial network, a direct vascular access may represent a complementary pathway for metabolite uptake and distribution.

The Specific Role of Reactive Astrocytes in Stroke

Astrocytes are essential in maintaining normal brain functions such as blood brain barrier (BBB) homeostasis and synapse formation as the most abundant cell type in the central nervous system (CNS). After the stroke, astrocytes are known as reactive astrocytes (RAs) because they are stimulated by various damage-associated molecular patterns (DAMPs) and cytokines, resulting in significant changes in their reactivity, gene expression, and functional characteristics. RAs perform multiple functions after stroke. The inflammatory response of RAs may aggravate neuro-inflammation and release toxic factors to exert neurological damage. However, RAs also reduce excitotoxicity and release neurotrophies to promote neuroprotection. Furthermore, RAs contribute to angiogenesis and axonal remodeling to promote neurological recovery. Therefore, RAs’ biphasic roles and mechanisms make them an effective target for functional recovery after the stroke. In this review, we summarized the dynamic functional changes and internal molecular mechanisms of RAs, as well as their therapeutic potential and strategies, in order to comprehensively understand the role of RAs in the outcome of stroke disease and provide a new direction for the clinical treatment of stroke.