Explore the vast range of titles available.

Noncoding genetic variation is a major driver of phenotypic diversity, but functional interpretation is challenging. To better understand common genetic variation associated with brain diseases, we defined noncoding regulatory regions for major cell types of the human brain. Whereas psychiatric disorders were primarily associated with variants in transcriptional enhancers and promoters in neurons, sporadic Alzheimer’s disease (AD) variants were largely confined to microglia enhancers. Interactome maps connecting disease-risk variants in cell-type–specific enhancers to promoters revealed an extended microglia gene network in AD. Deletion of a microglia-specific enhancer harboring AD-risk variants ablated BIN1 expression in microglia, but not in neurons or astrocytes. These findings revise and expand the list of genes likely to be influenced by noncoding variants in AD and suggest the probable cell types in which they function.

Spalt-like transcription factor 1 (SALL1) is a critical regulator of organogenesis and microglia identity. Here we demonstrate that disruption of a conserved microglia-specific super-enhancer interacting with the Sall1 promoter results in complete and specific loss of Sall1 expression in microglia. By determining the genomic binding sites of SALL1 and leveraging Sall1 enhancer knockout mice, we provide evidence for functional interactions between SALL1 and SMAD4 required for microglia-specific gene expression. SMAD4 binds directly to the Sall1 super-enhancer and is required for Sall1 expression, consistent with an evolutionarily conserved requirement of the TGFβ and SMAD homologs Dpp and Mad for cell-specific expression of Spalt in the Drosophila wing. Unexpectedly, SALL1 in turn promotes binding and function of SMAD4 at microglia-specific enhancers while simultaneously suppressing binding of SMAD4 to enhancers of genes that become inappropriately activated in enhancer knockout microglia, thereby enforcing microglia-specific functions of the TGFβ–SMAD signaling axis. Glass and colleagues show that the transcription factor SALL1-associated super-enhancer is exclusively activated in microglia, in part through SMAD4-mediated signaling, and that SALL1 subsequently enforces microglia-specific functions of SMAD4.

Background Growing evidence suggests that distal regulatory elements are essential for cellular function and states. The sequences within these distal elements, especially motifs for transcription factor binding, provide critical information about the underlying regulatory programs. However, cooperativities between transcription factors that recognize these motifs are nonlinear and multiplexed, rendering traditional modeling methods insufficient to capture the underlying mechanisms. Recent development of attention mechanism, which exhibit superior performance in capturing dependencies across input sequences, makes them well-suited to uncover and decipher intricate dependencies between regulatory elements. Result We present Transcription factors cooperativity Inference Analysis with Neural Attention (TIANA), a deep learning framework that focuses on interpretability. In this study, we demonstrated that TIANA could discover biologically relevant insights into co-occurring pairs of transcription factor motifs. Compared with existing tools, TIANA showed superior interpretability and robust performance in identifying putative transcription factor cooperativities from co-occurring motifs. Conclusion Our results suggest that TIANA can be an effective tool to decipher transcription factor cooperativities from distal sequence data. TIANA can be accessed through: https://github.com/rzzli/TIANA .

Macrophage-derived insulin-like growth factor enhances the uptake of microvesicles by non-professional phagocytes, such as airway epithelial cells and fibroblasts, thereby dampening tissue inflammation. Tissue inflammation control by non-professional phagocytes Our bodies clear billions of cells every day through the actions of both tissue-resident and recruited 'professional' phagocytes such as macrophages, and neighbouring 'non-professional' phagocytes such as epithelial cells or fibroblasts. The relative contributions of each phagocyte type to phagocytosis and tissue homeostasis in general are not well understood. Kodi Ravichandran and colleagues provide evidence for a role of macrophage-derived insulin like growth factor in enhancing the uptake of microvesicles by non-professional phagocytes, such as airway epithelial cells and fibroblasts, thereby dampening tissue inflammation. Professional phagocytes (such as macrophages 1 ) and non-professional phagocytes 2 , 3 , 4 , 5 , 6 , 7 , 8 (such as epithelial cells) clear billions of apoptotic cells and particles on a daily basis 9 . Although professional and non-professional macrophages reside in proximity in most tissues, whether they communicate with each other during cell clearance, and how this might affect inflammation, is not known 10 . Here we show that macrophages, through the release of a soluble growth factor and microvesicles, alter the type of particles engulfed by non-professional phagocytes and influence their inflammatory response. During phagocytosis of apoptotic cells or in response to inflammation-associated cytokines, macrophages released insulin-like growth factor 1 (IGF-1). The binding of IGF-1 to its receptor on non-professional phagocytes redirected their phagocytosis, such that uptake of larger apoptotic cells was reduced whereas engulfment of microvesicles was increased. IGF-1 did not alter engulfment by macrophages. Macrophages also released microvesicles, whose uptake by epithelial cells was enhanced by IGF-1 and led to decreased inflammatory responses by epithelial cells. Consistent with these observations, deletion of IGF-1 receptor in airway epithelial cells led to exacerbated lung inflammation after allergen exposure. These genetic and functional studies reveal that IGF-1- and microvesicle-dependent communication between macrophages and epithelial cells can critically influence the magnitude of tissue inflammation in vivo .

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.

How phagocytes keep their appetite When a phagocyte engulfs a dying cell, it essentially doubles its cellular contents, yet phagocytes are capable of ingesting several apoptotic cells one after the other. The factors regulating this impressive engulfment capacity are not well understood. Kodi Ravichandran and colleagues show here that the mitochondrial membrane protein Ucp2, which is known to be linked to metabolic diseases and atherosclerosis, is critically important to engulfment capacity. Rapid and efficient removal of apoptotic cells by phagocytes is important during development, tissue homeostasis and in immune responses 1 , 2 , 3 , 4 , 5 . Efficient clearance depends on the capacity of a single phagocyte to ingest multiple apoptotic cells successively, and to process the corpse-derived cellular material 6 . However, the factors that influence continued clearance by phagocytes are not known. Here we show that the mitochondrial membrane potential of the phagocyte critically controls engulfment capacity, with lower potential enhancing engulfment and vice versa. The mitochondrial membrane protein Ucp2, which acts to lower the mitochondrial membrane potential 7 , 8 , 9 , was upregulated in phagocytes engulfing apoptotic cells. Loss of Ucp2 reduced phagocytic capacity, whereas Ucp2 overexpression enhanced engulfment. Mutational and pharmacological studies indicated a direct role for Ucp2-mediated mitochondrial function in phagocytosis. Macrophages from Ucp2 -deficient mice 10 , 11 were impaired in phagocytosis in vitro , and Ucp2 -deficient mice showed profound in vivo defects in clearing dying cells in the thymus and testes. Collectively, these data indicate that mitochondrial membrane potential and Ucp2 are key molecular determinants of apoptotic cell clearance. As Ucp2 is linked to metabolic diseases and atherosclerosis 11 , 12 , this newly discovered role for Ucp2 in apoptotic cell clearance has implications for the complex aetiology and pathogenesis of these diseases.

Apoptotic neurons generated during normal brain development or secondary to pathologic insults are efficiently cleared from the central nervous system. Several soluble factors, including nucleotides, cytokines, and chemokines are released from injured neurons, signaling microglia to find and clear debris. One such chemokine that serves as a neuronal-microglial communication factor is fractalkine, with roles demonstrated in several models of adult neurological disorders. Lacking, however, are studies investigating roles for fractalkine in perinatal brain injury, an important clinical problem with no effective therapies. We used a well-characterized mouse model of ethanol-induced apoptosis to assess the role of fractalkine in neuronal-microglial signaling. Quantification of apoptotic debris in fractalkine-knockout (KO) and CX3CR1-KO mice following ethanol treatment revealed increased apoptotic bodies compared to wild type mice. Ethanol-induced injury led to release of soluble, extracellular fractalkine. The extracellular media harvested from apoptotic brains induces microglial migration in a fractalkine-dependent manner that is prevented by neutralization of fractalkine with a blocking antibody or by deficiency in the receptor, CX3CR1. This suggests fractalkine acts as a \"find-me\" signal, recruiting microglial processes toward apoptotic cells to promote their clearance. Next, we aimed to determine whether there are downstream alterations in cytokine gene expression due to fractalkine signaling. We examined mRNA expression in fractalkine-KO and CX3CR1-KO mice after alcohol-induced apoptosis and found differences in cytokine production in the brains of these KOs by 6 h after ethanol treatment. Collectively, this suggests that fractalkine acts as a \"find me\" signal released by apoptotic neurons, and subsequently plays a critical role in modulating both clearance and inflammatory cytokine gene expression after ethanol-induced apoptosis.

Germinal matrix hemorrhage (GMH) is a devastating neurodevelopmental condition affecting preterm infants, but why blood vessels in this brain region are vulnerable to rupture remains unknown. Here we show that microglia in prenatal mouse and human brain interact with nascent vasculature in an age-dependent manner and that ablation of these cells in mice reduces angiogenesis in the ganglionic eminences, which correspond to the human germinal matrix. Consistent with these findings, single-cell transcriptomics and flow cytometry show that distinct subsets of CD45 + cells from control preterm infants employ diverse signaling mechanisms to promote vascular network formation. In contrast, CD45 + cells from infants with GMH harbor activated neutrophils and monocytes that produce proinflammatory factors, including azurocidin 1, elastase and CXCL16, to disrupt vascular integrity and cause hemorrhage in ganglionic eminences. These results underscore the brain’s innate immune cells in region-specific angiogenesis and how aberrant activation of these immune cells promotes GMH in preterm infants. Chen et al. show that subtypes of immune cells in prenatal human brain promote angiogenesis in the germinal matrix. Conversely, in preterm infants, proinflammatory immune cells disrupt angiogenesis and promote germinal matrix hemorrhage.

Phagocytes express multiple phosphatidylserine (PtdSer) receptors that recognize apoptotic cells. It is unknown whether these receptors are interchangeable or if they play unique roles during cell clearance. Loss of the PtdSer receptor Mertk is associated with apoptotic corpse accumulation in the testes and degeneration of photoreceptors in the eye. Both phenotypes are linked to impaired phagocytosis by specialized phagocytes: Sertoli cells and the retinal pigmented epithelium (RPE). Here, we overexpressed the PtdSer receptor BAI1 in mice lacking MerTK ( Mertk −/− Bai1 Tg ) to evaluate PtdSer receptor compensation in vivo . While Bai1 overexpression rescues clearance of apoptotic germ cells in the testes of Mertk −/− mice it fails to enhance RPE phagocytosis or prevent photoreceptor degeneration. To determine why MerTK is critical to RPE function, we examined visual cycle intermediates and performed unbiased RNAseq analysis of RPE from Mertk +/+ and Mertk −/− mice. Prior to the onset of photoreceptor degeneration, Mertk −/− mice had less accumulation of retinyl esters and dysregulation of a striking array of genes, including genes related to phagocytosis, metabolism, and retinal disease in humans. Collectively, these experiments establish that not all phagocytic receptors are functionally equal, and that compensation among specific engulfment receptors is context and tissue dependent.

BackgroundGlioblastoma Multiforme (GBM) is the most aggressive and treatment-resistant brain tumor. GBM progression is heavily influenced by non-malignant microglia, the brain resident macrophages, that get coerced into a symbiotic relationship with tumor cells causing them to adopt an immunosuppressive and tumor-protective state.1 2 GBM outcomes are also influenced by sex, with males having worse prognosis.3 Here, we investigate novel regulators of the GBM tumor-associated microglia (GBM-TAM) state and use male-biased gene expression to distinguish candidates most likely to drive GBM progression.MethodsHuman microglia were isolated from 18 GBM tumors, 10 intermediate/low-grade tumors, and 12 normal brain regions by FACS (CD11b+, CD45mid, CX3CR1mid, CD64+, and CCR2low). Microglia were processed for bulk RNA-seq followed by differential gene expression and pathway analysis using DESeq2 and GSEA algorithms, respectively. CRISPRi experiments were conducted by integrating MPP1 and non-targeting control guide RNAs into dCas9-KRAB-expressing stem cells followed by differentiation into microglia. Differentiated microglia were treated with LPS for 3 hours to trigger inflammation then processed for RNA-seq.ResultsIncreased abundance of immunosuppressive genes IL-10 and CD204, and decreased abundance of homeostatic genes P2RY12 and SALL1 was observed in GBM-TAMs compared to normal microglia, supporting the GBM-TAM state transition. Genes belonging to tumor-supportive pathways like cell proliferation, hypoxia, and glycolysis were also increased in GBM-TAMs. Since GBM is more aggressive in males, we distilled GBM-TAM genes to those most likely to promote tumor progression based on male-biased expression. Genes in inflammatory and cell proliferation pathways were male-biased, and none were female-biased. We used gene expression correlation analysis to find candidate regulators of the male-biased GBM-TAM pathways, prioritizing genes from the sex chromosomes given their role in establishing sex differences. X chromosome gene Membrane Palmitoylated Protein 1 (MPP1) was correlated with the GBM-TAM inflammatory pathway, and progressively increased in abundance with tumor grade. We tested the role of MPP1 in the inflammatory response using stem cell-derived microglia treated with LPS. MPP1 knockdown led to downregulation of genes involved in lipid metabolism, membrane composition, and the microtubule cytoskeleton, and upregulation of genes involved in inflammation, many belonging to the GBM-TAM inflammatory pathway.ConclusionsWe conclude that MPP1 is a novel regulator of the GBM-TAM state by mediating interactions and signaling between TAMs and tumor cells at the plasma membrane. Our results support an anti-tumor role for MPP1 by suppressing the TAM inflammatory program. Our ongoing work directly tests the function of MPP1 in tumor progression.ReferencesSørensen MD, Dahlrot RH, Boldt HB, Hansen S, Kristensen BW. Tumour-associated microglia/macrophages predict poor prognosis in high-grade gliomas and correlate with an aggressive tumour subtype. Neuropathology and Applied Neurobiology. 2018;44(2):185–206.Maas SLN, Abels ER, Van De Haar LL, et al. Glioblastoma hijacks microglial gene expression to support tumor growth. J Neuroinflammation. 2020;17(1):120.Ostrom QT, Cioffi G, Gittleman H, et al. CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2012–2016. Neuro Oncol. 2019;21(Suppl 5):v1-v100.