Ben A Barres

Stanford Medicine | Stanford · Department of Neurobiology

Microglia take on an altered morphology during chronic opioid treatment. This morphological change is broadly used to identify the activated microglial state associated with opioid side effects, including tolerance and opioid-induced hyperalgesia (OIH). Microglia display similar morphological responses in the spinal cord after peripheral nerve inju...

Background The important contribution of glia to mechanisms of injury and repair of the nervous system is increasingly recognized. In stark contrast to the central nervous system (CNS), the peripheral nervous system (PNS) has a remarkable capacity for regeneration after injury. Schwann cells are recognized as key contributors to PNS regeneration, b...

The ability to slow or reverse biological ageing would have major implications for mitigating disease risk and maintaining vitality1. Although an increasing number of interventions show promise for rejuvenation2, their effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplo...

Astrocytes regulate the response of the central nervous system to disease and injury and have been hypothesized to actively kill neurons in neurodegenerative disease1–6. Here we report an approach to isolate one component of the long-sought astrocyte-derived toxic factor5,6. Notably, instead of a protein, saturated lipids contained in APOE and APOJ...

Retrotransposons can cause somatic genome variation in the human nervous system, which is hypothesized to have relevance to brain development and neuropsychiatric disease. However, the detection of individual somatic mobile element insertions presents a difficult signal-to-noise problem. Using a machine-learning method (RetroSom) and deep whole-gen...

Reactive astrocytes have been implicated in the pathogenesis of neurodegenerative diseases, including a non-cell autonomous effect on motor neuron survival in ALS. We previously defined a mechanism by which microglia release three factors, IL-1α, TNFα, and C1q, to induce neurotoxic astrocytes. Here we report that knocking out these three factors ma...

Ageing is the single greatest cause of disease and death worldwide, and understanding the associated processes could vastly improve quality of life. Although major categories of ageing damage have been identified—such as altered intercellular communication, loss of proteostasis and eroded mitochondrial function¹—these deleterious processes interact...

Ageing is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death1. Despite rapid advances over recent years, many of the molecular and cellular processes that underlie the progressive loss of healthy physiology are poorly understood2. To gain a better insight into these proc...

The tumor microenvironment (TME) is critical for tumor progression. However, the establishment and function of the TME remain obscure because of its complex cellular composition. Using a mouse genetic system called mosaic analysis with double markers (MADMs), we delineated TME evolution at single-cell resolution in sonic hedgehog (SHH)-activated me...

Oligodendrocytes extend elaborate microtubule arbors that contact up to 50 axon segments per cell, then spiral around myelin sheaths, penetrating from outer to inner layers. However, how they establish this complex cytoarchitecture is unclear. Here, we show that oligodendrocytes contain Golgi outposts, an organelle that can function as an acentroso...

Active retrotransposons in the human genome (L1, Alu and SVA elements) can create genomic mobile element insertions (MEIs) in both germline and somatic tissue ¹ . Specific somatic MEIs have been detected at high levels in human cancers ² , and at lower to medium levels in human brains ³ . Dysregulation of somatic retrotransposition in the human bra...

Microglia, the brain’s immune cells, maintain homeostasis and sense pathological changes by continuously surveying the parenchyma with highly motile large processes. Here, we demonstrate that microglia also use thin actin-dependent filopodia that allow fast nanoscale sensing within discrete regions. Filopodia are distinct from large processes by th...

Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes1,2,3,4,5,6,7,8,9,10,11, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far12,13. Although single splicing events have been...

Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to...

Chemotherapy results in a frequent yet poorly understood syndrome of long-term neurological deficits. Neural precursor cell dysfunction and white matter dysfunction are thought to contribute to this debilitating syndrome. Here, we demonstrate persistent depletion of oligodendrocyte lineage cells in humans who received chemotherapy. Developing a mou...

Microglia are increasingly recognized for their major contributions during brain development and neurodegenerative disease. It is currently unknown whether these functions are carried out by subsets of microglia during different stages of development and adulthood or within specific brain regions. Here, we performed deep single-cell RNA sequencing...

Nervous system function depends on proper myelination for insulation and critical trophic support for axons. Myelination is tightly regulated spatially and temporally, but how it is controlled molecularly remains largely unknown. Here, we identified key molecular mechanisms governing the regional and temporal specificity of CNS myelination. We show...

Circadian clock dysfunction is a common symptom of aging and neurodegenerative diseases, though its impact on brain health is poorly understood. Astrocyte activation occurs in response to diverse insults and plays a critical role in brain health and disease. We report that the core circadian clock protein BMAL1 regulates astrogliosis in a synergist...

Microglia are increasingly recognized for their major contributions during brain development and neurodegenerative disease. It is currently unknown if these functions are carried out by subsets of microglia during different stages of development and adulthood or within specific brain regions. Here, we performed deep single-cell RNA sequencing (scRN...

Activation of microglia by classical inflammatory mediators can convert astrocytes into a neurotoxic A1 phenotype in a variety of neurological diseases1,2. Development of agents that could inhibit the formation of A1 reactive astrocytes could be used to treat these diseases for which there are no disease-modifying therapies. Glucagon-like peptide-1...

Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing, we identified nine peripheral LN non-endothelial SC clusters. Included are the established subsets, Ccl19hi T-zone reticular...

Microglia, the brain's resident macrophages, are dynamic CNS custodians with surprising origins in the extra-embryonic yolk sac. The consequences of their distinct ontogeny are unknown but critical to understanding and treating brain diseases. We created a brain macrophage transplantation system to disentangle how environment and ontogeny specify m...

The decline of cognitive function occurs with aging, but the mechanisms responsible are unknown. Astrocytes instruct the formation, maturation, and elimination of synapses, and impairment of these functions has been implicated in many diseases. These findings raise the question of whether astrocyte dysfunction could contribute to cognitive decline...

Call to action The developing brain initially makes more synapses than it needs. With further development, excess synapses are pruned away, leaving mature circuits. Synapses can be eliminated by microglia, which engulf and destroy them. Vainchtein et al. found that the microglia are called into action by astrocytes, supportive cells on which neuron...

For many years, efforts to decipher the various cellular components that comprise the CNS were stymied by a lack of technical strategies for isolating and profiling the brain's resident cell types. The advent of transcriptional profiling, combined with powerful new purification schemes, changed this reality and transformed our understanding of the...

Circadian clock dysfunction is a common symptom of aging and neurodegenerative diseases, though its impact on brain health is poorly understood. Astrocyte activation occurs in response to diverse insults and plays a critical role in brain health and disease. We report that the core circadian clock protein BMAL1 regulates astrogliosis in a synergist...

Microglia and non-parenchymal macrophages in the brain are mononuclear phagocytes that are increasingly recognized to be essential players in the development, homeostasis and diseases of the central nervous system. With the availability of new genetic, molecular and pharmacological tools, considerable advances have been made towards our understandi...

Microglia are brain-resident macrophages with important, but insufficiently understood functions in development, health, and disease. In a new exciting study, Wlodarczyk and colleagues uncover a transient subset of CD11c⁺ microglia that regulate CNS myelination via IGF-1 expression. These findings represent not only the first evidence for a microgl...

Significance Oligodendrocytes in the brain insulate neuronal axons in layers of fatty myelin to facilitate fast electrical signaling. Myelin basic protein (MBP), an important myelin component, is transported as mRNA away from the cell body before being translated into protein. In zebrafish, the anterograde motor kinesin transports mbp mRNA away fro...

Glioblastoma (GBM) is the most common primary brain cancer in adults and is notoriously difficult to treat because of its diffuse nature. We performed single-cell RNA sequencing (RNA-seq) on 3,589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variat...

Significance Myelin is a potent inhibitor of axon regeneration. In the central nervous system, failure to clear myelin debris after injury presents a major roadblock to recovery. In contrast, rapid myelin clearance in the peripheral nervous system (PNS) contributes to this system’s remarkable regenerative capacity, but the mechanisms involved have...

APOE4 is the strongest genetic risk factor for late-onset Alzheimer disease. ApoE4 increases brain amyloid-β pathology relative to other ApoE isoforms¹. However, whether APOE independently influences tau pathology, the other major proteinopathy of Alzheimer disease and other tauopathies, or tau-mediated neurodegeneration, is not clear. By generatin...

In the developing brain, neurons expressing VEGF-A and blood vessels grow in close apposition, but many of the molecular pathways regulating neuronal VEGF-A and neurovascular system development remain to be deciphered. Here, we show that miR-9 links neurogenesis and angiogenesis through the formation of neurons expressing VEGF-A. We found that miR-...

There is significant need to develop physiologically relevant models for investigating human astrocytes in health and disease. Here, we present an approach for generating astrocyte lineage cells in a three-dimensional (3D) cytoarchitecture using human cerebral cortical spheroids (hCSs) derived from pluripotent stem cells. We acutely purified astroc...

Glioblastoma is the most common primary brain cancer in adults and is notoriously difficult to treat due to its diffuse nature. We performed single-cell RNAseq on 3589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumor’s genome and...

Dietary excess triggers accumulation of pro-inflammatory microglia in the mediobasal hypothalamus (MBH), but the components of this microgliosis and its metabolic consequences remain uncertain. Here, we show that microglial inflammatory signaling determines the immunologic response of the MBH to dietary excess and regulates hypothalamic control of...

Astrocytes constitute approximately 30% of the cells in the mammalian central nervous system (CNS). They are integral to brain and spinal-cord physiology and perform many functions important for normal neuronal development, synapse formation, and proper propagation of action potentials. We still know very little, however, about how these functions...

Microglia, the resident macrophages of the CNS, engage in various CNS-specific functions that are critical for development and health. To better study microglia and the properties that distinguish them from other tissue macrophage populations, we have optimized serum-free culture conditions to permit robust survival of highly ramified adult microgl...

The actin cytoskeleton is essential for many fundamental biological processes, but tools for directly manipulating actin dynamics are limited to cell-permeable drugs that preclude single-cell perturbations. Here we describe DeActs, genetically encoded actin-modifying polypeptides, which effectively induce actin disassembly in eukaryotic cells. We d...

This work was supported by grants from the National Institutes of Health (R01 AG048814, B.A.B.; RO1 DA15043, B.A.B.; P50 NS38377, V.L.D. and T.M.D.) Christopher and Dana Reeve Foundation (B.A.B.), the Novartis Institute for Biomedical Research (B.A.B.), Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (B.A.B.), the JPB Foundation (B.A....

Reactive astrocytes are strongly induced by central nervous system (CNS) injury and disease, but their role is poorly understood. Here we show that a subtype of reactive astrocytes, which we termed A1, is induced by classically activated neuroinflammatory microglia. We show that activated microglia induce A1 astrocytes by secreting Il-1α, TNF and C...

Opioid pain medications have detrimental side effects including analgesic tolerance and opioid-induced hyperalgesia (OIH). Tolerance and OIH counteract opioid analgesia and drive dose escalation. The cell types and receptors on which opioids act to initiate these maladaptive processes remain disputed, which has prevented the development of therapie...

Significance Susceptibility to Alzheimer’s disease (AD) is strongly controlled by apolipoprotein E ( APOE ) genotype. The E4 allele greatly increases risk whereas the E2 allele decreases risk, but it is not known how the APOE allele controls AD risk. In this paper, we report a novel role for APOE by showing that APOE2 enhances and APOE4 decreases t...

The tumor suppressor protein adenomatous polyposis coli (APC) is multifunctional, participating in the canonical Wnt/β-catenin signal transduction pathway, as well as in modulating cytoskeleton function. Although expressed by Schwann cells, the role that APC plays in these cells and in the myelination of the peripheral nervous system (PNS) is unkno...

Glial cells are essential components of the nervous system. In this issue, Singhvi et al. uncover cellular and molecular mechanisms through which C. elegans glia shape sensory neuron terminals and thus control animal thermosensing behaviors.

After spinal-cord injury, cells called astrocytes form a scar that is thought to block neuronal regeneration. The finding that the scar promotes regrowth of long nerve projections called axons challenges this long-held dogma. See Article p.195

Significance Microglia are the tissue resident macrophages of the brain and spinal cord, implicated in important developmental, homeostatic, and disease processes, although our understanding of their roles is complicated by an inability to distinguish microglia from related cell types. Although they share many features with other macrophages, micro...

Long non-coding RNAs (lncRNAs) (> 200 bp) play crucial roles in transcriptional regulation during numerous biological processes. However, it is challenging to comprehensively identify lncRNAs, because they are often expressed at low levels and with more cell-type specificity than are protein-coding genes. In the present study, we performed ab initi...

lncRNA-TF expression correlation heatmap. Correlation analysis was carried out to identify any correlations between the expression of TFs with binding motifs inside the ENCODE promoter regions upstream of lncRNAs that are up-regulated during OPC formation and their target lncRNAs. The TFs with more binding motifs are listed toward the left side of...

Assay of cell proliferation by BrdU staining. The percentage of BrdU positive cells under each condition was calculated. No significant difference was observed between control and shRNA knockdowns. (TIF)

Master table of lncRNA expression. lncRNA expression level (FPKM) calculated using Cufflinks (version 1.3.0) [22]. All analyses were performed before the 5330416C01Rik cDNA annotation update when the 5330416C01Rik gene did not include lnc-OPC. (XLSX)

Visualizing gene co-expression network as a heatmap. The heatmap depicts the Topological Overlap Matrix (TOM) among all genes used in the analysis [69]. Light color indicates low overlap and darker red color represents higher overlap. Blocks of darker colors along the diagonal are the modules. The dendrogram and module assignment (labeled in differ...

The values for the expression of 5330416C01Rik in healthy and EAE mice were extracted from a previous study [59]. Fold changes in 5330416C01Rik expression in EAE mice compared to healthy mice are shown in glial progenitors and neuronal progenitors. (TIF)

WGCNA clusters of protein-coding genes and lncRNAs. Module assignment for each gene is presented in the ‘Label.Merged’ column. The membership values of each gene associated with each module (color coded by WGCNA) are presented in the table. (XLSX)

Differentially expressed genes called by DESeq after the depletion of lnc-OPC, and gene ontology (GO) functional term enrichment analysis. (XLSX)

A selected set of transcription factor footprints detected by DNase-DGF in ESCs and in Whole Brain E14.5 sample. Displayed is the aggregate signal of the DNase-DGF cutting profiles for the indicated transcription factors. The profiles were computed using CENTIPEDE on the genome-wide sets of sites that match the corresponding motif. DNase cutting si...

Specific TF binding sites in proximity to up-regulated lncRNAs (OPC compared with NSC). TF occupancy was examined for each lncRNA that is up-regulated in OPC compared to NSC. The presence of TF binding in proximity to a lncRNA is indicated as ‘1’. Binding sites for OLIG2 and ASCL1 from DNAse-DGF data are shown. Annotated ENCODE promoter regions con...

OLIG2 binding peaks called by MACS from OLIG2 ChIP-Seq experiment. (XLSX)

Choosing the soft-thresholding power for WGCNA analysis. The choice of soft thresholding power was based on the criterion of approximate scale-free topology [69]. We chose the power 10, which is the lowest power for which the scale-free topology fit index curve flattens out upon reaching a high value. The left panel shows the scale-free fit index (...

Assessing global effect of lnc-OPC knockdown using differential expression analysis. The R package DESeq was adopted to call differentially expressed genes. The left panel is the MA-plot showing normalized mean compared to log2-fold change for the control compared to lnc-OPC-depleted sample. Red dots represent genes called as differentially express...

Cell purity estimation. Signals from other cell types were estimated using established cell-type specific markers. (XLSX)

Gene Ontology (GO) enrichment analysis of co-expression modules identified by WGCNA. Each worksheet contains the analysis result calculated using the DAVID bioinformatics tool [70]. The worksheets are ordered by module size. (XLSX)

Supplementary methods. (DOCX)

The functional and molecular similarities and distinctions between human and murine astrocytes are poorly understood. Here, we report the development of an immunopanning method to acutely purify astrocytes from fetal, juvenile, and adult human brains and to maintain these cells in serum-free cultures. We found that human astrocytes have abilities s...

Glia account for more than half of the cells in the mammalian nervous system, and the past few decades have witnessed a flood of studies that detail novel functions for glia in nervous system development, plasticity and disease. Here, and in the accompanying poster, we review the origins of glia and discuss their diverse roles during development, i...

Synaptic dysfunction is a hallmark of many neurodegenerative and psychiatric brain disorders, yet we know little about the mechanisms that underlie synaptic vulnerability. Although neuroinflammation and reactive gliosis are prominent in virtually every CNS disease, glia are largely viewed as passive responders to neuronal damage rather than drivers...

Significance We investigated the molecular basis of Wallerian degeneration slow (WldS) axon protection by defining a spatial and temporal requirement of WldS activity to promote axonal survival. The findings carry clinical significance in showing that the cellular mechanisms governing degeneration of mammalian axons exhibit a latency period before...

Myelin is essential in vertebrates for the rapid propagation of action potentials, but the molecular mechanisms driving its formation remain largely unknown. Here we show that the initial stage of process extension and axon ensheathment by oligodendrocytes requires dynamic actin filament assembly by the Arp2/3 complex. Unexpectedly, subsequent myel...