Astrocytes are ubiquitous in the brain and are widely held to be largely identical. However, this view has not been fully tested, and the possibility that astrocytes are neural circuit specialized ...remains largely unexplored. Here, we used multiple integrated approaches, including RNA sequencing (RNA-seq), mass spectrometry, electrophysiology, immunohistochemistry, serial block-face-scanning electron microscopy, morphological reconstructions, pharmacogenetics, and diffusible dye, calcium, and glutamate imaging, to directly compare adult striatal and hippocampal astrocytes under identical conditions. We found significant differences in electrophysiological properties, Ca2+ signaling, morphology, and astrocyte-synapse proximity between striatal and hippocampal astrocytes. Unbiased evaluation of actively translated RNA and proteomic data confirmed significant astrocyte diversity between hippocampal and striatal circuits. We thus report core astrocyte properties, reveal evidence for specialized astrocytes within neural circuits, and provide new, integrated database resources and approaches to explore astrocyte diversity and function throughout the adult brain.
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•Multiple approaches were used to assess astrocyte diversity in two neural circuits•Physiological and anatomical studies showed evidence for astrocyte functional diversity•RNA-seq, proteomic, and cell marker analyses confirmed diversity•Evidence is provided for brain neural-circuit-specialized astrocytes
The Khakh lab used state-of-the-art optical, anatomical, electrophysiological, transcriptomic, and proteomic approaches to explore astrocyte similarities and differences in two neural circuits. Candid evaluation of the data across ten approaches provided not only strong evidence for astrocyte diversity but also an experimental workflow to explore astrocyte diversity across the brain.
Epigenetic reprogramming is a critical process of pathological gene induction during cardiac hypertrophy and remodeling, but the underlying regulatory mechanisms remain to be elucidated. Here we ...identified a heart-enriched long noncoding (lnc)RNA, named cardiac-hypertrophy-associated epigenetic regulator (Chaer), which is necessary for the development of cardiac hypertrophy. Mechanistically, Chaer directly interacts with the catalytic subunit of polycomb repressor complex 2 (PRC2). This interaction, which is mediated by a 66-mer motif in Chaer, interferes with PRC2 targeting to genomic loci, thereby inhibiting histone H3 lysine 27 methylation at the promoter regions of genes involved in cardiac hypertrophy. The interaction between Chaer and PRC2 is transiently induced after hormone or stress stimulation in a process involving mammalian target of rapamycin complex 1, and this interaction is a prerequisite for epigenetic reprogramming and induction of genes involved in hypertrophy. Inhibition of Chaer expression in the heart before, but not after, the onset of pressure overload substantially attenuates cardiac hypertrophy and dysfunction. Our study reveals that stress-induced pathological gene activation in the heart requires a previously uncharacterized lncRNA-dependent epigenetic checkpoint.
How chromatin accessibility and structure endow highly specialized cells with their unique phenotypes is an area of intense investigation. In the mammalian heart, an exclusive subset of cardiac cells ...comprise the conduction system. Many molecular components of this system are well studied and genetic variation in some of the components induces abnormal cardiac conduction. However, genetic risk for cardiac arrhythmias in human populations also occurs in noncoding regions. A study by Bhattacharyya, Kollipara, et al. in this issue of the JCI examines how chromatin accessibility and structure may explain the mechanisms by which noncoding variants increase susceptibility to cardiac arrhythmias. We discuss the implications of these findings for cell type-specific gene regulation and highlight potential therapeutic strategies to engineer locus-specific epigenomic remodeling in vivo.
Endothelial cells contribute to a subset of cardiac fibroblasts by undergoing endothelial-to-mesenchymal transition, but whether cardiac fibroblasts can adopt an endothelial cell fate and directly ...contribute to neovascularization after cardiac injury is not known. Here, using genetic fate map techniques, we demonstrate that cardiac fibroblasts rapidly adopt an endothelial-cell-like phenotype after acute ischaemic cardiac injury. Fibroblast-derived endothelial cells exhibit anatomical and functional characteristics of native endothelial cells. We show that the transcription factor p53 regulates such a switch in cardiac fibroblast fate. Loss of p53 in cardiac fibroblasts severely decreases the formation of fibroblast-derived endothelial cells, reduces post-infarct vascular density and worsens cardiac function. Conversely, stimulation of the p53 pathway in cardiac fibroblasts augments mesenchymal-to-endothelial transition, enhances vascularity and improves cardiac function. These observations demonstrate that mesenchymal-to-endothelial transition contributes to neovascularization of the injured heart and represents a potential therapeutic target for enhancing cardiac repair.
Identifying the molecular targets for the beneficial or detrimental effects of small-molecule drugs is an important and currently unmet challenge. We have developed a method, drug affinity responsive ...target stability (DARTS), which takes advantage of a reduction in the protease susceptibility of the target protein upon drug binding. DARTS is universally applicable because it requires no modification of the drug and is independent of the mechanism of drug action. We demonstrate use of DARTS to identify known small-molecule-protein interactions and to reveal the eukaryotic translation initiation machinery as a molecular target for the longevity-enhancing plant natural product resveratrol. We envisage that DARTS will also be useful in global mapping of protein-metabolite interaction networks and in label-free screening of unlimited varieties of compounds for development as molecular imaging agents.
Eukaryotes must balance the metabolic and cell death actions of mitochondria via control of gene expression and cell fate by chromatin, thereby functionally binding the metabolome and epigenome. This ...interaction has far-reaching implications for chronic diseases in humans, the most common of which are those of the cardiovascular system. The most devastating consequence of cardiovascular disease, heart failure, is not a single disease, diagnosis, or endpoint. Human and animal studies have revealed that, regardless of etiology and symptoms, heart failure is universally associated with abnormal metabolism and gene expression – to frame this as cause or consequence, however, may be to wrongfoot the question. This essay aims to challenge current thinking on metabolic–epigenetic crosstalk in heart failure, presenting hypotheses for how chronic diseases arise, take hold, and persist. We unpack assumptions about the order of operations for gene expression and metabolism, exploring recent findings in noncardiac systems that link metabolic intermediates directly to chromatin remodeling. Lastly, we discuss potential mechanisms by which chromatin may serve as a substrate for metabolic memory, and how changes in cellular transcriptomes (and hence in cellular behavior) in response to stress correspond to global changes in chromatin accessibility and structure.
Heart failure is a ruinous destination for many afflicted with cardiovascular disease and is not a single condition or single set of diagnostic criteria; instead, it manifests through an intricate series of molecular and systemic malfunctions ranging from the suborganelle level to the multiple organ systems of the body.Regardless of the etiology, humans with, and animal models of, heart failure are characterized by abnormal metabolism and gene expression, some aspects of which are compensatory responses to the disease whereas others promulgate injury.Close communication between the metabolome and the epigenome sets basal susceptibility to various heart failure symptoms. This communication entrains detrimental conditions in metabolic–epigenetic memory and thus may be a target for novel treatments.
Abstract
Heart failure with preserved ejection fraction (HFpEF) exhibits a sex bias, being more common in women than men, and we hypothesize that mitochondrial sex differences might underlie this ...bias. As part of genetic studies of heart failure in mice, we observe that heart mitochondrial DNA levels and function tend to be reduced in females as compared to males. We also observe that expression of genes encoding mitochondrial proteins are higher in males than females in human cohorts. We test our hypothesis in a panel of genetically diverse inbred strains of mice, termed the Hybrid Mouse Diversity Panel (HMDP). Indeed, we find that mitochondrial gene expression is highly correlated with diastolic function, a key trait in HFpEF. Consistent with this, studies of a “two-hit” mouse model of HFpEF confirm that mitochondrial function differs between sexes and is strongly associated with a number of HFpEF traits. By integrating data from human heart failure and the mouse HMDP cohort, we identify the mitochondrial gene
Acsl6
as a genetic determinant of diastolic function. We validate its role in HFpEF using adenoviral over-expression in the heart. We conclude that sex differences in mitochondrial function underlie, in part, the sex bias in diastolic function.
Abstract
The response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered ...heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
The study of epigenomics has advanced in recent years to span the regulation of a single genetic locus to the structure and orientation of entire chromosomes within the nucleus. In this review, we ...focus on the challenges and opportunities of clinical epigenomics in cardiovascular disease. As an integrator of genetic and environmental inputs, and because of advances in measurement techniques that are highly reproducible and provide sequence information, the epigenome is a rich source of potential biosignatures of cardiovascular health and disease. Most of the studies to date have focused on the latter, and herein we discuss observations on epigenomic changes in human cardiovascular disease, examining the role of protein modifiers of chromatin, noncoding RNAs and DNA modification. We provide an overview of cardiovascular epigenomics, discussing the challenges of data sovereignty, data analysis, doctor-patient ethics and innovations necessary to implement precision health.
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•Changes in epigenetic features have been measured in blood and cardiovascular tissues in human disease•Epigenetic changes can serve as powerful biomarkers of human cardiovascular health and disease•Validation of epigenetic biomarkers comes from cohort studies in humans as well as preclinical studies in animals•Data acquisition, analysis and integration with medical records are evolving areas necessary for clinical implementation•Data sovereignty, clinical education, and machine learning are key opportunities to bridge discoveries to the clinic
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