Ever since eukaryotes subsumed the bacterial ancestor of mitochondria, the nuclear and mitochondrial genomes have had to closely coordinate their activities, as each encode different subunits of the ...oxidative phosphorylation (OXPHOS) system. Mitochondrial dysfunction is a hallmark of aging, but its causes are debated. We show that, during aging, there is a specific loss of mitochondrial, but not nuclear, encoded OXPHOS subunits. We trace the cause to an alternate PGC-1α/β-independent pathway of nuclear-mitochondrial communication that is induced by a decline in nuclear NAD+ and the accumulation of HIF-1α under normoxic conditions, with parallels to Warburg reprogramming. Deleting SIRT1 accelerates this process, whereas raising NAD+ levels in old mice restores mitochondrial function to that of a young mouse in a SIRT1-dependent manner. Thus, a pseudohypoxic state that disrupts PGC-1α/β-independent nuclear-mitochondrial communication contributes to the decline in mitochondrial function with age, a process that is apparently reversible.
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•A specific decline in mitochondrially encoded genes occurs during aging in muscle•Nuclear NAD+ levels regulate mitochondrial homeostasis independently of PGC-1α/β•Declining NAD+ during aging causes pseudohypoxia, which disrupts OXPHOS function•Raising nuclear NAD+ in old mice reverses pseudohypoxia and metabolic dysfunction
Aging disrupts an NAD+-dependent nuclear-mitochondrial communication pathway, causing a decline in the mitochondrially encoded oxidative phosphorylation components relative to nuclear-encoded components. Raising NAD+ levels in old mice alleviates the pseudohypoxic conditions that disrupt the communication pathway, reversing this mitochondrial defect.
Mutations in ADAR, which encodes the ADAR1 RNA-editing enzyme, cause Aicardi-Goutières syndrome (AGS), a severe autoimmune disease associated with an aberrant type I interferon response. How ADAR1 ...prevents autoimmunity remains incompletely defined. Here, we demonstrate that ADAR1 is a specific and essential negative regulator of the MDA5-MAVS RNA sensing pathway. Moreover, we uncovered a MDA5-MAVS-independent function for ADAR1 in the development of multiple organs. We showed that the p150 isoform of ADAR1 uniquely regulated the MDA5 pathway, whereas both the p150 and p110 isoforms contributed to development. Abrupt deletion of ADAR1 in adult mice revealed that both of these functions were required throughout life. Our findings delineate genetically separable roles for both ADAR1 isoforms in vivo, with implications for the human diseases caused by ADAR mutations.
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•ADAR1 is a specific negative regulator of the MDA5-MAVS antiviral response•A substantial fraction of ADAR1-controlled gene expression is MAVS independent•ADAR1 is essential for multi-organ development•ADAR1 isoforms independently contribute to regulation of MDA5 and developmental pathways
ADAR mutations cause Aicardi-Goutières syndrome, a severe human autoimmune disease, but how ADAR1 regulates autoimmunity remains unknown. Stetson and colleagues reveal two functions for ADAR1: prevention of MDA5- and MAVS-dependent autoimmunity and control of multi-organ development.
Exposure to arsenic in contaminated drinking water is an emerging public health problem that impacts more than 200 million people worldwide. Accumulating lines of evidence from epidemiological ...studies revealed that chronic exposure to arsenic can result in various human diseases including cancer, type 2 diabetes, and neurodegenerative disorders. Arsenic is also classified as a Group I human carcinogen. In this review, we survey extensively different modes of action for arsenic-induced carcinogenesis, with focus being placed on arsenic-mediated impairment of DNA repair pathways. Inorganic arsenic can be bioactivated by methylation, and the ensuing products are highly genotoxic. Bioactivation of arsenicals also elicits the production of reactive oxygen and nitrogen species (ROS and RNS), which can directly damage DNA and modify cysteine residues in proteins. Results from recent studies suggest zinc finger proteins as crucial molecular targets for direct binding to As3+ or for modifications by arsenic-induced ROS/RNS, which may constitute a common mechanism underlying arsenic-induced perturbations of DNA repair.
Prediction of metabolic changes that result from genetic or environmental perturbations has several important applications, including diagnosing metabolic disorders and discovering novel drug ...targets. A cardinal challenge in obtaining accurate predictions is the integration of transcriptional regulatory networks with the corresponding metabolic network. We propose a method called probabilistic regulation of metabolism (PROM) that achieves this synthesis and enables straightforward, automated, and quantitative integration of high-throughput data into constraint-based modeling, making it an ideal tool for constructing genome-scale regulatory-metabolic network models for less-studied organisms. PROM introduces probabilities to represent gene states and gene-transcription factor interactions. By using PROM, we constructed an integrated regulatory-metabolic network for the model organism, Escherichia coli, and demonstrated that our method based on automated inference is more accurate and comprehensive than the current state of the art, which is based on manual curation of literature. After validating the approach, we used PROM to build a genome-scale integrated metabolic-regulatory model for Mycobacterium tuberculosis, a critically important human pathogen. This study incorporated data from more than 1,300 microarrays, 2,000 transcription factor-target interactions regulating 3,300 metabolic reactions, and 1,905 KO phenotypes for E. coli and M. tuberculosis. PROM identified KO phenotypes with accuracies as high as 95%, and predicted growth rates quantitatively with correlation of 0.95. Importantly, PROM represents the successful integration of a top-down reconstructed, statistically inferred regulatory network with a bottom-up reconstructed, biochemically detailed metabolic network, bridging two important classes of systems biology models that are rarely combined quantitatively.
Abstract
Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and ...host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions.
Alterations in circulating lipids and ectopic lipid deposition impact on the risk of developing cardiovascular and metabolic diseases. Lipoprotein lipase (LPL) hydrolyzes fatty acids (FAs) from ...triglyceride (TAG)-rich lipoproteins including very low density lipoproteins (VLDLs) and chylomicrons, and regulates their distribution to peripheral tissues. Angiopoietin-like 4 (ANGPTL4) mediates the inhibition of LPL activity under different circumstances. Accumulating evidence associates ANGPTL4 directly with the risk of atherosclerosis and type 2 diabetes (T2D). This review focuses on recent findings on the role of ANGPTL4 in metabolic and cardiovascular diseases. We highlight human and murine studies that explore ANGPTL4 functions in different tissues and how these effect disease development through possible autocrine and paracrine forms of regulation.
ANGPTL4 controls lipoprotein catabolism and energy distribution across different tissues by inhibiting LPL. Excessive lipid storage in adipose tissues and ectopic lipid accumulation in muscle and liver predispose to T2D.Accelerated catabolism of TAG-rich lipoproteins (VLDL and chylomicrons) is associated with decreased risk of coronary artery disease.Recent GWAS findings have shown that genetic variants in the ANGPTL4 locus are associated with protection against T2D and coronary artery disease.Although ANGPTL4 is a secreted protein, ANGPTL4 also controls lipoprotein metabolism and energy homeostasis as well as LPL-independent functions in the tissues where it is expressed.Targeting ANGPTL4 and other negative regulators of LPL (APOCIII and ANGPTL3) are novel therapeutic targets for treating dyslipidemia and cardiovascular diseases.
Anti-inflammatory strategies are proposed to have beneficial effects in Alzheimer’s disease. To explore how anti-inflammatory cytokine signaling affects Aβ pathology, we investigated the effects of ...adeno-associated virus (AAV2/1)-mediated expression of Interleukin (IL)-10 in the brains of APP transgenic mouse models. IL-10 expression resulted in increased Aβ accumulation and impaired memory in APP mice. A focused transcriptome analysis revealed changes consistent with enhanced IL-10 signaling and increased ApoE expression in IL-10-expressing APP mice. ApoE protein was selectively increased in the plaque-associated insoluble cellular fraction, likely because of direct interaction with aggregated Aβ in the IL-10-expressing APP mice. Ex vivo studies also show that IL-10 and ApoE can individually impair glial Aβ phagocytosis. Our observations that IL-10 has an unexpected negative effect on Aβ proteostasis and cognition in APP mouse models demonstrate the complex interplay between innate immunity and proteostasis in neurodegenerative diseases, an interaction we call immunoproteostasis.
•The anti-inflammatory cytokine, IL-10, increases Aβ accumulation in APP mouse brain•IL-10 exacerbates memory impairment in APP mice and reduces synaptic proteins•IL-10 increases ApoE, which, by binding aggregated Aβ, is sequestered in plaques•IL-10 and ApoE suppress microglial Aβ phagocytosis in vitro
Chakrabarty et al. show that Interleukin-10 increases Aβ plaque deposition and impairs cognition in APP mice. This is mechanistically linked to decreased microglial Aβ phagocytosis and increased ApoE expression and sequestration in plaques, consistent with ApoE’s role as a pathological chaperone.
Investigators have long suspected that pathogenic microbes might contribute to the onset and progression of Alzheimer’s disease (AD) although definitive evidence has not been presented. Whether such ...findings represent a causal contribution, or reflect opportunistic passengers of neurodegeneration, is also difficult to resolve. We constructed multiscale networks of the late-onset AD-associated virome, integrating genomic, transcriptomic, proteomic, and histopathological data across four brain regions from human post-mortem tissue. We observed increased human herpesvirus 6A (HHV-6A) and human herpesvirus 7 (HHV-7) from subjects with AD compared with controls. These results were replicated in two additional, independent and geographically dispersed cohorts. We observed regulatory relationships linking viral abundance and modulators of APP metabolism, including induction of APBB2, APPBP2, BIN1, BACE1, CLU, PICALM, and PSEN1 by HHV-6A. This study elucidates networks linking molecular, clinical, and neuropathological features with viral activity and is consistent with viral activity constituting a general feature of AD.
•Common viral species frequently detected in normal, aging brain•Increased HHV-6A and HHV-7 in brains of subjects with Alzheimer’s disease (AD)•Findings were replicated in two additional, independent cohorts•Multiscale networks reveal viral regulation of AD risk, and APP processing genes
Readhead et al. construct multiscale networks of the late-onset Alzheimer’s disease (AD)-associated virome and observe pathogenic regulation of molecular, clinical, and neuropathological networks by several common viruses, particularly human herpesvirus 6A and human herpesvirus 7.
Resveratrol induces mitochondrial biogenesis and protects against metabolic decline, but whether SIRT1 mediates these benefits is the subject of debate. To circumvent the developmental defects of ...germline SIRT1 knockouts, we have developed an inducible system that permits whole-body deletion of SIRT1 in adult mice. Mice treated with a moderate dose of resveratrol showed increased mitochondrial biogenesis and function, AMPK activation, and increased NAD+ levels in skeletal muscle, whereas SIRT1 knockouts displayed none of these benefits. A mouse overexpressing SIRT1 mimicked these effects. A high dose of resveratrol activated AMPK in a SIRT1-independent manner, demonstrating that resveratrol dosage is a critical factor. Importantly, at both doses of resveratrol no improvements in mitochondrial function were observed in animals lacking SIRT1. Together these data indicate that SIRT1 plays an essential role in the ability of moderate doses of resveratrol to stimulate AMPK and improve mitochondrial function both in vitro and in vivo.
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► Resveratrol's ability to improve mitochondrial function requires SIRT1 in vivo ► Moderate doses of resveratrol activate AMPK and raise NAD+ in a SIRT1-dependent manner ► Activation of AMPK in the absence of SIRT1 does not improve mitochondrial function ► Overexpression of SIRT1 mimics resveratrol's effects on AMPK and mitochondria
Obesity and metabolic disorders are a major health concern in all developed countries and a primary focus of current medical research is to improve our understanding treatment of metabolic diseases. ...One avenue of research that has attracted a great deal of recent interest focuses upon understanding the role of miRNAs in the development of metabolic diseases. miRNAs have been shown to be dysregulated in a number of different tissues under conditions of obesity and insulin resistance, and have been demonstrated to be important regulators of a number of critical metabolic functions, including insulin secretion in the pancreas, lipid and glucose metabolism in the liver, and nutrient signaling in the hypothalamus. In this review we will focus on the important role of miRNAs in regulating the differentiation and function of white and brown adipose tissue and the potential importance of this for maintaining metabolic function and treating metabolic diseases. This article is part of a Special Issue entitled: MicroRNAs and lipid/energy metabolism and related diseases edited by Carlos Fernández-Hernando and Yajaira Suárez.
•miRNAs are critical regulators of all phases of adipogenesis in WAT.•miRNAs regulate the differentiation and function of BAT and browning of WAT.•Therapeutic targeting of miRNAs in WAT and BAT may prevent obesity and metabolic dysfunction.
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