David Gosselin

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

Rev-Erb-α and Rev-Erb-β are nuclear receptors that regulate the expression of genes involved in the control of circadian rhythm, metabolism and inflammatory responses. Rev-Erbs function as transcriptional repressors by recruiting nuclear receptor co-repressor (NCoR)–HDAC3 complexes to Rev-Erb response elements in enhancers and promoters of target genes, but the molecular basis for cell-specific programs of repression is not known. Here we present evidence that in mouse macrophages Rev-Erbs regulate target gene expression by inhibiting the functions of distal enhancers that are selected by macrophage-lineage-determining factors, thereby establishing a macrophage-specific program of repression. Remarkably, the repressive functions of Rev-Erbs are associated with their ability to inhibit the transcription of enhancer-derived RNAs (eRNAs). Furthermore, targeted degradation of eRNAs at two enhancers subject to negative regulation by Rev-Erbs resulted in reduced expression of nearby messenger RNAs, suggesting a direct role of these eRNAs in enhancer function. By precisely defining eRNA start sites using a modified form of global run-on sequencing that quantifies nascent 5′ ends, we show that transfer of full enhancer activity to a target promoter requires both the sequences mediating transcription-factor binding and the specific sequences encoding the eRNA transcript. These studies provide evidence for a direct role of eRNAs in contributing to enhancer functions and suggest that Rev-Erbs act to suppress gene expression at a distance by repressing eRNA transcription.

Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by an extended polyglutamine repeat in the N terminus of the Huntingtin protein (HTT). Reactive microglia and elevated cytokine levels are observed in the brains of HD patients, but the extent to which neuroinflammation results from extrinsic or cell-autonomous mechanisms in microglia is unknown. Using genome-wide approaches, we found that expression of mutant Huntingtin (mHTT) in microglia promoted cell-autonomous pro-inflammatory transcriptional activation by increasing the expression and transcriptional activities of the myeloid lineage-determining factors PU.1 and C/EBPs. We observed elevated levels of PU.1 and its target genes in the brains of mouse models and individuals with HD. Moreover, mHTT-expressing microglia exhibited an increased capacity to induce neuronal death ex vivo and in vivo in the presence of sterile inflammation. These findings suggest a cell-autonomous basis for enhanced microglia reactivity that may influence non-cell-autonomous HD pathogenesis.

An environment-dependent transcriptional network specifies human microglia identity

Of mice and mens microglia Microglia are immune system cells that function in protecting and maintaining the brain. Gosselin et al. examined the epigenetics and RNA transcripts from single microglial cells and observed consistent profiles among samples despite differences in age, sex, and diagnosis. Mouse and human microglia demonstrated similar microglia-specific gene expression profiles, as well as a shared environmental response among microglia collected either immediately after surgery (ex vivo) or after culturing (in vitro). Interestingly, those genes exhibiting differences in expression between humans and mice or after culturing were often implicated in neurodegenerative diseases. Science, this issue p. eaal3222 Single-cell sequencing of brain microglia reveals ex vivo and in vitro differences in transcription. INTRODUCTION Microglia play essential roles in central nervous system homeostasis and influence diverse aspects of neuronal function, including refinement of synaptic networks and elaboration of neuromodulatory factors for memory and motor learning. Many lines of evidence indicate that dysregulation of microglial functions contributes to the pathogenesis of neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease. Emerging evidence from mouse and human studies also suggests that microglia influence neurodevelopmental and psychiatric disorders such as schizophrenia and depression. Most disease risk alleles associated with neurodegenerative diseases reside in noncoding regions of the genome, requiring the delineation of functional genomic elements in the relevant human cell types to establish mechanisms of causation. The recent observation that mouse brain environment strongly influences microglia-specific gene expression has implications for understanding pathogenic responses of microglia in diseases and disorders and modeling their phenotypes in vitro. RATIONALE Although dysregulation of microglial activity is genetically linked to neurodegenerative diseases and psychiatric disorders, no systematic evaluations of human microglia gene expression or regulatory landscapes are currently available. In addition, the extent to which mice provide suitable models for human microglia is unclear. The major goals of this study were to define the transcriptomes and DNA regulatory elements of human microglia ex vivo and in vitro in comparison to the mouse and to systematically relate these features to expression of genes associated with genome-wide association study (GWAS) risk alleles or exhibiting altered expression in neurodegenerative diseases and psychiatric disorders. RESULTS We used RNA sequencing, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin sequencing to characterize the transcriptomes and epigenetic landscapes of human microglia isolated from surgically resected brain tissue in excess of that needed for diagnosis. Although some effects of underlying disease cannot be excluded, the overall pattern of gene expression was markedly consistent. Microglia-enriched genes were found to overlap significantly with genes exhibiting altered expression in neurodegenerative diseases and psychiatric disorders and with genes associated with a wide spectrum of disease-specific risk alleles. Human microglia gene expression was well correlated with mouse microglia gene expression, but numerous species-specific differences were also observed that included genes linked to human disease. More than half of the genes associated with noncoding GWAS risk alleles for Alzheimer’s disease are preferentially expressed in microglia. DNA recognition motifs enriched at active enhancers and expression of the corresponding lineage-determining transcription factors were very similar for human and mouse microglia. Transition of human and mouse microglia from the brain to tissue culture revealed remodeling of their respective enhancer landscapes and extensive down-regulation of genes that are induced in primitive mouse macrophages following migration into the fetal brain. Treatment of microglia in vitro with transforming growth factor β1 (TGF-β1) had relatively modest effects in maintaining the ex vivo pattern of gene expression. A significant subset of the genes up- or down-regulated in vitro exhibited altered expression in neurodegenerative diseases and psychiatric disorders. CONCLUSION These studies identify core features of human microglial transcriptomes and epigenetic landscapes. Intersection of the microglia-specific gene signature with GWAS and transcriptomic data supports roles of microglia as both responders and contributors to disease phenotypes. The identification of an environment-sensitive program of gene expression and corresponding regulatory elements enables inference of a conserved and dynamic transcription factor network that maintains microglia identity and function. The combinations of signaling factors in the brain necessary to maintain microglia phenotypes remain largely unknown. In concert, these findings will inform efforts to generate microglia-like cells in simple and complex culture systems and understand gene-environment interactions that influence homeostatic and pathogenic functions of microglia in the human brain. Brain environment specifies gene expression in microglia. Human microglia transcriptomes and enhancer landscapes were defined ex vivo following purification from surgically resected brain tissue and in vitro after transfer to a tissue culture environment. Dynamic changes in these features enabled delineation of transcription factors controlling an environment-dependent program of gene expression that overlaps with genes that are dysregulated in brain pathologies. Microglia play essential roles in central nervous system (CNS) homeostasis and influence diverse aspects of neuronal function. However, the transcriptional mechanisms that specify human microglia phenotypes are largely unknown. We examined the transcriptomes and epigenetic landscapes of human microglia isolated from surgically resected brain tissue ex vivo and after transition to an in vitro environment. Transfer to a tissue culture environment resulted in rapid and extensive down-regulation of microglia-specific genes that were induced in primitive mouse macrophages after migration into the fetal brain. Substantial subsets of these genes exhibited altered expression in neurodegenerative and behavioral diseases and were associated with noncoding risk variants. These findings reveal an environment-dependent transcriptional network specifying microglia-specific programs of gene expression and facilitate efforts to understand the roles of microglia in human brain diseases.

Phospholipase A2 regulates eicosanoid class switching during inflammasome activation

Significance Group IVA cytosolic phospholipase A2 (GIVA cPLA2) is widely viewed as the primary enzyme responsible for inflammatory arachidonic acid (AA) release and with high specificity. Our results demonstrate dual, phase-specific release of AA and 15-hydroxyeicosatetraenoic (15-HETE) acid by GIVA cPLA2 in primary and immortalized macrophages during a receptor-mediated program required for complete inflammatory commitment. These dual actions by GIVA cPLA2 were necessary for biosynthesis of proresolving lipoxins, providing a unique, upstream example of an enzyme linked to both the initiation and resolution of inflammation. Further, our results demonstrate a single-cell mechanism of lipoxin synthesis that is more efficient than the established transcellular biosynthetic mechanisms, underscoring the importance of enzyme coupling and the possibility of proresolution therapies at the membrane level. Initiation and resolution of inflammation are considered to be tightly connected processes. Lipoxins (LX) are proresolution lipid mediators that inhibit phlogistic neutrophil recruitment and promote wound-healing macrophage recruitment in humans via potent and specific signaling through the LXA4 receptor (ALX). One model of lipoxin biosynthesis involves sequential metabolism of arachidonic acid by two cell types expressing a combined transcellular metabolon. It is currently unclear how lipoxins are efficiently formed from precursors or if they are directly generated after receptor-mediated inflammatory commitment. Here, we provide evidence for a pathway by which lipoxins are generated in macrophages as a consequence of sequential activation of toll-like receptor 4 (TLR4), a receptor for endotoxin, and P2X7, a purinergic receptor for extracellular ATP. Initial activation of TLR4 results in accumulation of the cyclooxygenase-2–derived lipoxin precursor 15-hydroxyeicosatetraenoic acid (15-HETE) in esterified form within membrane phospholipids, which can be enhanced by aspirin (ASA) treatment. Subsequent activation of P2X7 results in efficient hydrolysis of 15-HETE from membrane phospholipids by group IVA cytosolic phospholipase A2, and its conversion to bioactive lipoxins by 5-lipoxygenase. Our results demonstrate how a single immune cell can store a proresolving lipid precursor and then release it for bioactive maturation and secretion, conceptually similar to the production and inflammasome-dependent maturation of the proinflammatory IL-1 family cytokines. These findings provide evidence for receptor-specific and combinatorial control of pro- and anti-inflammatory eicosanoid biosynthesis, and potential avenues to modulate inflammatory indices without inhibiting downstream eicosanoid pathways.

Epigenomics of macrophages.

Macrophages play essential roles in tissue homeostasis, pathogen elimination, and tissue repair. A defining characteristic of these cells is their ability to efficiently adapt to a variety of abruptly changing and complex environments. This ability is intrinsically linked to a capacity to quickly alter their transcriptome, and this is tightly associated with the epigenomic organization of these cells and, in particular, their enhancer repertoire. Indeed, enhancers are genomic sites that serve as platforms for the integration of signaling pathways with the mechanisms that regulate mRNA transcription. Notably, transcription is pervasive at active enhancers and enhancer RNAs (eRNAs) are tightly coupled to regulated transcription of protein‐coding genes. Furthermore, given that each cell type possesses a defining enhancer repertoire, studies on enhancers provide a powerful method to study how specialization of functions among the diverse macrophage subtypes may arise. Here, we review recent studies providing insights into the distinct mechanisms that contribute to the establishment of enhancers and their role in the regulation of transcription in macrophages.

Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells

Affinity and dose of T cell receptor (TCR) interaction with antigens govern the magnitude of CD4+ T cell responses, but questions remain regarding the quantitative translation of TCR engagement into downstream signals. We find that while the response of mouse CD4+ T cells to antigenic stimulation is bimodal, activated cells exhibit analog responses proportional to signal strength. Gene expression output reflects TCR signal strength, providing a signature of T cell activation. Expression changes rely on a pre-established enhancer landscape and quantitative acetylation at AP-1 binding sites. Finally, we show that graded expression of activation genes depends on ERK pathway activation, suggesting that an ERK-AP-1 axis plays an important role in translating TCR signal strength into proportional activation of enhancers and genes essential for T cell function. DOI: http://dx.doi.org/10.7554/eLife.10134.001

Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages

Although macrophages can be polarized to distinct phenotypes in vitro with individual ligands, in vivo they encounter multiple signals that control their varied functions in homeostasis, immunity, and disease. Here, we identify roles of Rev-erb nuclear receptors in regulating responses of mouse macrophages to complex tissue damage signals and wound repair. Rather than reinforcing a specific program of macrophage polarization, Rev-erbs repress subsets of genes that are activated by TLR ligands, IL4, TGFβ, and damage-associated molecular patterns (DAMPS). Unexpectedly, a complex damage signal promotes co-localization of NF-κB, Smad3, and Nrf2 at Rev-erb-sensitive enhancers and drives expression of genes characteristic of multiple polarization states in the same cells. Rev-erb-sensitive enhancers thereby integrate multiple damage-activated signaling pathways to promote a wound repair phenotype. DOI: http://dx.doi.org/10.7554/eLife.13024.001

Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers

Macrophages populate every tissue of the body and play vital roles in homeostasis, pathogen elimination, and tissue healing. These cells possess the ability to adapt to a multitude of abruptly changing and complex environments. Furthermore, different populations of resident tissue macrophages each show their own defining gene signatures. The enhancer repertoire of these cells underlies both the cellular identity of a given subset of resident macrophage population and their ability to dynamically alter, in an efficient manner, their gene expression programs in response to internal and external signals. Notably, transcription is pervasive at active enhancers and enhancer RNAs, or eRNAs, are tightly correlated to regulated transcription of protein-coding genes. Furthermore, selection and establishment of enhancers is a dynamic and plastic process in which activation of intracellular signaling pathways by factors present in a macrophages environment play a determining role. Here, we review recent studies providing insights into the distinct mechanisms that contribute to the selection and function of enhancers in macrophages and the relevance of studying these mechanisms to gain a better understanding of complex human diseases.