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Astrocytes, a type of glia, are abundant and morphologically complex cells. Here, we report astrocyte molecular profiles, diversity, and morphology across the mouse central nervous system (CNS). We identified shared and region-specific astrocytic genes and functions and explored the cellular origins of their regional diversity. We identified gene networks correlated with astrocyte morphology, several of which unexpectedly contained Alzheimer’s disease (AD) risk genes. CRISPR/Cas9–mediated reduction of candidate genes reduced astrocyte morphological complexity and resulted in cognitive deficits. The same genes were down-regulated in human AD, in an AD mouse model that displayed reduced astrocyte morphology, and in other human brain disorders. We thus provide comprehensive molecular data on astrocyte diversity and mechanisms across the CNS and on the molecular basis of astrocyte morphology in health and disease. Description Astrocyte diversity and morphology Astrocytes are the major type of glia, displaying complex bushy morphologies as their defining feature. Endo et al. studied astrocyte similarities, diversity, and morphology across the mouse central nervous system (CNS) (see the Perspective by Baldwin). They identified gene networks related to astrocyte morphology between CNS regions, several of which unexpectedly included genes related to risk of Alzheimer’s disease (AD). When expression of these genes was reduced in mice, astrocyte morphological complexity was diminished, and mice exhibited impairments in a cognitive test. Remarkably, the same genes are down-regulated in both a mouse model of AD and in human AD and several other CNS disorders. These findings suggest that loss of astrocyte morphology may be therapeutically targetable in diverse CNS disorders. —SMH The molecular basis of astrocyte diversity and of their complex morphology in health and disease states is elucidated. INTRODUCTION The central nervous system (CNS) comprises a large population of non-neuronal cells called glia. The predominant type of glia are astrocytes, which were discovered ~140 years ago. Astrocytes tile the entire CNS, serve critical homeostatic functions, and display complex, “bushy” morphologies—their defining feature. Unlike CNS neurons, which are highly diverse, astrocytes have historically been considered largely homogenous, serving as a type of omnipresent glue that is equivalent between CNS areas. Although recent studies have challenged this belief, there has been no broad assessment of astrocyte diversity, similarity, or morphology across the CNS of any species. An important goal, therefore, is to rigorously understand the molecular similarities and differences between astrocytes in the CNS, to determine how they affect astrocyte morphology, and to determine how these properties relate to normal and disease conditions. RATIONALE It is critical to understand all cell types of the CNS in detail as part of our quest to explore fundamental biology and to develop new therapeutic strategies to treat CNS disorders. We studied astrocyte regional diversity and major signaling pathways using whole-brain imaging, astrocyte-neuron density, marker expression, astrocyte-specific and bulk tissue gene expression, single-cell gene expression, astrocyte morphology, and interrelationships between gene expression and morphology using bioinformatic methods across the CNS. The data were mined to identify genes and pathways related to astrocyte morphological complexity, which we explored experimentally using gene knockdowns. We then compared these morphology-related genes with astrocytic differentially expressed genes from an Alzheimer’s disease (AD) mouse model displaying reduced astrocyte morphology, as well as in relation to gene expression in AD and other CNS disorders. RESULTS We found several hundred genes that were enriched within and shared among astrocytes in the CNS, with functions related to metabolism, cholesterol, and neurotransmitter uptake and biosynthesis. These genes represent the core functions of astrocytes, but little is known about approximately a third of them, implying that understanding the fundamental physiology of astrocytes across CNS areas is an important ongoing experimental goal. Our data also reveal that astrocytes have molecular features and functions specific to CNS regions, and that these region-specific functions arise from the local tissue environment and by variable representation of seven distinct astrocyte subclusters. We mined our data to identify gene networks related to astrocyte morphology, and unexpectedly discovered several AD risk genes. We developed astrocyte-specific CRISPR/Cas9–based gene knockdown to reduce the expression of such genes in the hippocampus. We found a reduction of astrocyte morphology with changes in a cognitive task after knockdown of key morphology-related genes, indicating that astrocyte morphological changes affect neural circuit function. In addition to AD risk genes that were astrocyte morphology related, we found a significant association between morphology-related genes and those related to several other common CNS disorders. CONCLUSION We provide comprehensive molecular data that will allow many new types of experiments to explore core features of astrocytes across the CNS, in particular, those unique to specific regions and how they relate to the dynamics and biophysics of neural circuits in specific CNS regions. We used our data to identify the molecular underpinnings of astrocyte morphology between CNS regions and to show that reduced astrocyte morphological complexity, and the attendant loss of tissue support, is common to diverse CNS disorders. This raises the prospect that restoring astrocyte morphology, and thus the ensuing neuronal and tissue support functions, may be therapeutically beneficial in disease. Our findings provide the molecular basis to explore such strategies and to unravel the nascent underlying biology determining how astrocytes contribute to CNS function and dysfunction. Astrocyte diversity and morphology across the CNS. (1) Astrocyte morphology and gene expression was measured across CNS regions. (2) Gene expression data revealed the molecular signatures of astrocyte diversity and its origins. (3) Gene expression and morphological data identified gene networks related to complex morphology. Causal roles were explored. (4) Several astrocyte morphology genes were Alzheimer’s disease risk genes, a disorder in which astrocytes displayed reduced morphology.