Publications by authors named "Matthias Heinig"

46 Publications

Asc-1 regulates white versus beige adipocyte fate in a subcutaneous stromal cell population.

Nat Commun 2021 03 11;12(1):1588. Epub 2021 Mar 11.

RG Adipocytes & Metabolism, Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany.

Adipose tissue expansion, as seen in obesity, is often metabolically detrimental causing insulin resistance and the metabolic syndrome. However, white adipose tissue expansion at early ages is essential to establish a functional metabolism. To understand the differences between adolescent and adult adipose tissue expansion, we studied the cellular composition of the stromal vascular fraction of subcutaneous adipose tissue of two and eight weeks old mice using single cell RNA sequencing. We identified a subset of adolescent preadipocytes expressing the mature white adipocyte marker Asc-1 that showed a low ability to differentiate into beige adipocytes compared to Asc-1 negative cells in vitro. Loss of Asc-1 in subcutaneous preadipocytes resulted in spontaneous differentiation of beige adipocytes in vitro and in vivo. Mechanistically, this was mediated by a function of the amino acid transporter ASC-1 specifically in proliferating preadipocytes involving the intracellular accumulation of the ASC-1 cargo D-serine.
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http://dx.doi.org/10.1038/s41467-021-21826-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7952576PMC
March 2021

Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice.

Life Sci Alliance 2021 01 30;4(1). Epub 2020 Nov 30.

Research Group Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany

Brown adipose tissue (BAT) plays an important role in the regulation of body weight and glucose homeostasis. Although increasing evidence supports white adipose tissue heterogeneity, little is known about heterogeneity within murine BAT. Recently, UCP1 high and low expressing brown adipocytes were identified, but a developmental origin of these subtypes has not been studied. To obtain more insights into brown preadipocyte heterogeneity, we use single-cell RNA sequencing of the BAT stromal vascular fraction of C57/BL6 mice and characterize brown preadipocyte and adipocyte clonal cell lines. Statistical analysis of gene expression profiles from brown preadipocyte and adipocyte clones identify markers distinguishing brown adipocyte subtypes. We confirm the presence of distinct brown adipocyte populations in vivo using the markers EIF5, TCF25, and BIN1. We also demonstrate that loss of enhances UCP1 expression and mitochondrial respiration, suggesting that BIN1 marks dormant brown adipocytes. The existence of multiple brown adipocyte subtypes suggests distinct functional properties of BAT depending on its cellular composition, with potentially distinct functions in thermogenesis and the regulation of whole body energy homeostasis.
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http://dx.doi.org/10.26508/lsa.202000924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723269PMC
January 2021

Cells of the adult human heart.

Nature 2020 12 24;588(7838):466-472. Epub 2020 Sep 24.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.
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http://dx.doi.org/10.1038/s41586-020-2797-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7681775PMC
December 2020

Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation.

Comput Struct Biotechnol J 2020 31;18:1330-1341. Epub 2020 May 31.

Institute for Diabetes and Cancer IDC, Helmholtz Zentrum Muenchen (HMGU) and German Center for Diabetes Research (DZD), Munich 85764, Neuherberg, Germany.

Advancements in the field of next generation sequencing lead to the generation of ever-more data, with the challenge often being how to combine and reconcile results from different OMICs studies such as genome, epigenome and transcriptome. Here we provide an overview of the standard processing pipelines for ChIP-seq and RNA-seq as well as common downstream analyses. We describe popular multi-omics data integration approaches used to identify target genes and co-factors, and we discuss how machine learning techniques may predict transcriptional regulators and gene expression.
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http://dx.doi.org/10.1016/j.csbj.2020.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306512PMC
May 2020

Inflammatory macrophage memory in nonsteroidal anti-inflammatory drug-exacerbated respiratory disease.

J Allergy Clin Immunol 2021 Feb 12;147(2):587-599. Epub 2020 Jun 12.

Center of Allergy and Environment, Technical University of Munich and Helmholtz Zentrum München, Munich, Germany. Electronic address:

Background: Nonsteroidal anti-inflammatory drug-exacerbated respiratory disease (N-ERD) is a chronic inflammatory condition, which is driven by an aberrant arachidonic acid metabolism. Macrophages are major producers of arachidonic acid metabolites and subject to metabolic reprogramming, but they have been neglected in N-ERD.

Objective: This study sought to elucidate a potential metabolic and epigenetic macrophage reprogramming in N-ERD.

Methods: Transcriptional, metabolic, and lipid mediator profiles in macrophages from patients with N-ERD and healthy controls were assessed by RNA sequencing, Seahorse assays, and LC-MS/MS. Metabolites in nasal lining fluid, sputum, and plasma from patients with N-ERD (n = 15) and healthy individuals (n = 10) were quantified by targeted metabolomics analyses. Genome-wide methylomics were deployed to define epigenetic mechanisms of macrophage reprogramming in N-ERD.

Results: This study shows that N-ERD monocytes/macrophages exhibit an overall reduction in DNA methylation, aberrant metabolic profiles, and an increased expression of chemokines, indicative of a persistent proinflammatory activation. Differentially methylated regions in N-ERD macrophages included genes involved in chemokine signaling and acylcarnitine metabolism. Acylcarnitines were increased in macrophages, sputum, nasal lining fluid, and plasma of patients with N-ERD. On inflammatory challenge, N-ERD macrophages produced increased levels of acylcarnitines, proinflammatory arachidonic acid metabolites, cytokines, and chemokines as compared to healthy macrophages.

Conclusions: Together, these findings decipher a proinflammatory metabolic and epigenetic reprogramming of macrophages in N-ERD.
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http://dx.doi.org/10.1016/j.jaci.2020.04.064DOI Listing
February 2021

Cistromic Reprogramming of the Diurnal Glucocorticoid Hormone Response by High-Fat Diet.

Mol Cell 2019 11 6;76(4):531-545.e5. Epub 2019 Nov 6.

Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Metabolic Programming, School of Life Sciences Weihenstephan, Gregor Mendel Str. 2, 85354 Freising, Technische Universitaet Muenchen (TUM), Munich, Germany. Electronic address:

The glucocorticoid receptor (GR) is a potent metabolic regulator and a major drug target. While GR is known to play integral roles in circadian biology, its rhythmic genomic actions have never been characterized. Here we mapped GR's chromatin occupancy in mouse livers throughout the day and night cycle. We show how GR partitions metabolic processes by time-dependent target gene regulation and controls circulating glucose and triglycerides differentially during feeding and fasting. Highlighting the dominant role GR plays in synchronizing circadian amplitudes, we find that the majority of oscillating genes are bound by and depend on GR. This rhythmic pattern is altered by high-fat diet in a ligand-independent manner. We find that the remodeling of oscillatory gene expression and postprandial GR binding results from a concomitant increase of STAT5 co-occupancy in obese mice. Altogether, our findings highlight GR's fundamental role in the rhythmic orchestration of hepatic metabolism.
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http://dx.doi.org/10.1016/j.molcel.2019.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7928064PMC
November 2019

Inferring Interaction Networks From Multi-Omics Data.

Front Genet 2019 12;10:535. Epub 2019 Jun 12.

Institute of Computational Biology, HelmholtzZentrum München, Munich, Germany.

A major goal in systems biology is a comprehensive description of the entirety of all complex interactions between different types of biomolecules-also referred to as the interactome-and how these interactions give rise to higher, cellular and organism level functions or diseases. Numerous efforts have been undertaken to define such interactomes experimentally, for example yeast-two-hybrid based protein-protein interaction networks or ChIP-seq based protein-DNA interactions for individual proteins. To complement these direct measurements, genome-scale quantitative multi-omics data (transcriptomics, proteomics, metabolomics, etc.) enable researchers to predict novel functional interactions between molecular species. Moreover, these data allow to distinguish relevant functional from non-functional interactions in specific biological contexts. However, integration of multi-omics data is not straight forward due to their heterogeneity. Numerous methods for the inference of interaction networks from homogeneous functional data exist, but with the advent of large-scale paired multi-omics data a new class of methods for inferring comprehensive networks across different molecular species began to emerge. Here we review state-of-the-art techniques for inferring the topology of interaction networks from functional multi-omics data, encompassing graphical models with multiple node types and quantitative-trait-loci (QTL) based approaches. In addition, we will discuss Bayesian aspects of network inference, which allow for leveraging already established biological information such as known protein-protein or protein-DNA interactions, to guide the inference process.
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http://dx.doi.org/10.3389/fgene.2019.00535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582773PMC
June 2019

Association of Human Promoter Variants with the Occurrence of Knee-Osteoarthritis in a Case Control Association Study.

Int J Mol Sci 2019 Mar 19;20(6). Epub 2019 Mar 19.

Experimental Rheumatology Unit, Department of Orthopedics, Jena University Hospital, Waldkrankenhaus 'Rudolf Elle', 07607 Eisenberg, Germany.

Our aim was to analyse (i) the presence of single nucleotide polymorphisms (SNPs) in the and core promoters in patients with rheumatoid arthritis (RA), knee-osteoarthritis (OA), and normal controls (NC); (ii) their functional influence on / transcription levels; and (iii) their associations with the occurrence of RA or knee-OA. and promoter SNPs were identified in an initial screening population using the Non-Isotopic RNase Cleavage Assay (NIRCA); their functional influence was analysed using reporter gene assays. Genotyping was done in RA ( = 298), knee-OA ( = 277), and NC ( = 484) samples. For replication, significant associations were validated in a Finnish cohort (OA: = 72, NC: = 548). Initially, two SNPs were detected in the promoter and two additional SNPs in the promoter in perfect linkage disequilibrium (LD). promoter SNP rs4647009 caused significant downregulation of reporter gene expression, whereas reporter gene expression was significantly upregulated in the presence of the promoter SNPs. The homozygous genotype of promoter SNPs showed an association with the susceptibility for knee-OA (odds ratio (OR) 2.12, 95% confidence interval (CI) 1.2⁻3.7, = 0.0086). This association was successfully replicated in the Finnish Health 2000 study cohort (allelic OR 1.72, 95% CI 1.2⁻2.5, = 0.006). Promoter variants may represent relevant susceptibility markers for knee-OA.
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http://dx.doi.org/10.3390/ijms20061382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6471183PMC
March 2019

Systems Genetics Approaches in Rat Identify Novel Genes and Gene Networks Associated With Cardiac Conduction.

J Am Heart Assoc 2018 11;7(21):e009243

1 Department of Experimental Cardiology Heart Centre Academic Medical Center Amsterdam Amsterdam The Netherlands.

Background Electrocardiographic ( ECG ) parameters are regarded as intermediate phenotypes of cardiac arrhythmias. Insight into the genetic underpinnings of these parameters is expected to contribute to the understanding of cardiac arrhythmia mechanisms. Here we used HXB / BXH recombinant inbred rat strains to uncover genetic loci and candidate genes modulating ECG parameters. Methods and Results RR interval, PR interval, QRS duration, and QT c interval were measured from ECG s obtained in 6 male rats from each of the 29 available HXB / BXH recombinant inbred strains. Genes at loci displaying significant quantitative trait loci (QTL) effects were prioritized by assessing the presence of protein-altering variants, and by assessment of cis expression QTL ( eQTL ) effects and correlation of transcript abundance to the respective trait in the heart. Cardiac RNA -seq data were additionally used to generate gene co-expression networks. QTL analysis of ECG parameters identified 2 QTL for PR interval, respectively, on chromosomes 10 and 17. At the chromosome 10 QTL , cis- eQTL effects were identified for Acbd4, Cd300lg, Fam171a2, and Arhgap27; the transcript abundance in the heart of these 4 genes was correlated with PR interval. At the chromosome 17 QTL , a cis- eQTL was uncovered for Nhlrc1 candidate gene; the transcript abundance of this gene was also correlated with PR interval. Co-expression analysis furthermore identified 50 gene networks, 6 of which were correlated with PR interval or QRS duration, both parameters of cardiac conduction. Conclusions These newly identified genetic loci and gene networks associated with the ECG parameters of cardiac conduction provide a starting point for future studies with the potential of identifying novel mechanisms underlying cardiac electrical function.
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http://dx.doi.org/10.1161/JAHA.118.009243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404199PMC
November 2018

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model.

Cell Syst 2018 12 28;7(6):567-579.e6. Epub 2018 Nov 28.

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany; Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching 85748, Germany. Electronic address:

Mechanistic models are essential to deepen the understanding of complex diseases at the molecular level. Nowadays, high-throughput molecular and phenotypic characterizations are possible, but the integration of such data with prior knowledge on signaling pathways is limited by the availability of scalable computational methods. Here, we present a computational framework for the parameterization of large-scale mechanistic models and its application to the prediction of drug response of cancer cell lines from exome and transcriptome sequencing data. This framework is over 10 times faster than state-of-the-art methods, which enables modeling at previously infeasible scales. By applying the framework to a model describing major cancer-associated pathways (>1,200 species and >2,600 reactions), we could predict the effect of drug combinations from single drug data. This is the first integration of high-throughput datasets using large-scale mechanistic models. We anticipate this to be the starting point for development of more comprehensive models allowing a deeper mechanistic insight.
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http://dx.doi.org/10.1016/j.cels.2018.10.013DOI Listing
December 2018

Unilateral temporal interictal epileptiform discharges correctly predict the epileptogenic zone in lesional temporal lobe epilepsy.

Epilepsia 2018 08 15;59(8):1577-1582. Epub 2018 Jul 15.

Epilepsy Center, Department of Neurology, University Hospital, Ludwig-Maximilians-University, Munich, Germany.

Objective: To evaluate the necessity of recording ictal electroencephalography (EEG) in patients with temporal lobe epilepsy (TLE) considered for resective surgery who have unilateral temporal interictal epileptiform discharges (IEDs) and concordant ipsitemporal magnetic resonance imaging (MRI) pathology. To calculate the necessary number of recorded EEG seizure patterns (ESPs) to achieve adequate lateralization probability.

Methods: In a retrospective analysis, the localization and lateralization of interictal and ictal EEG of 304 patients with lesional TLE were analyzed. The probability of further contralateral ESPs was calculated based on a total of 1967 recorded ESPs, using Bayes' theorem.

Results: Two hundred seventy-one patients had unilateral TLE, and in 98% of them (265 of 271), IEDs were recorded during video-EEG monitoring. Purely unilateral temporal IEDs were present in 61% (166 of 271 patients). Ipsilateral temporal MRI pathology was found in 83% (138 of 166). Ictal EEG was concordant with the clinical side of TLE in 99% (136 of 138) of these patients. Two patients had discordant ictal EEG with both ipsilateral and contralateral ESPs. Epilepsy surgery with resection in the lesioned temporal lobe was still performed, and both patients remain seizure-free. Probability calculations demonstrate that at least 6 recorded unilateral ESPs result in a >95% probability for a concordance of >0.9 of any further ESPs.

Significance: The combination of purely unilateral temporal IED with ipsitemporal MRI pathology is sufficient to identify the epileptogenic zone, and the recording of ictal ESP did not add any surgically relevant information in these 138 patients. Rarely, discordant ESPs might be recorded, but the surgical outcome remains excellent after surgery on the lesioned side.
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http://dx.doi.org/10.1111/epi.14514DOI Listing
August 2018

Using Gene Expression to Annotate Cardiovascular GWAS Loci.

Authors:
Matthias Heinig

Front Cardiovasc Med 2018 5;5:59. Epub 2018 Jun 5.

Institute of Computational Biology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany.

Genetic variants at hundreds of loci associated with cardiovascular phenotypes have been identified by genome wide association studies. Most of these variants are located in intronic or intergenic regions rendering the functional and mechanistic follow up difficult. These non-protein-coding regions harbor regulatory sequences. Thus the study of genetic variants associated with transcription-so called expression quantitative trait loci-has emerged as a promising approach to identify regulatory sequence variants. The genes and pathways they control constitute candidate causal drivers at cardiovascular risk loci. This review provides an overview of the expression quantitative trait loci resources available for cardiovascular genetics research and the most commonly used approaches for candidate gene identification.
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http://dx.doi.org/10.3389/fcvm.2018.00059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996083PMC
June 2018

Cadm2 regulates body weight and energy homeostasis in mice.

Mol Metab 2018 02 22;8:180-188. Epub 2017 Nov 22.

Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, 13125 Berlin, Germany. Electronic address:

Objective: Obesity is strongly linked to genes regulating neuronal signaling and function, implicating the central nervous system in the maintenance of body weight and energy metabolism. Genome-wide association studies identified significant associations between body mass index (BMI) and multiple loci near Cell adhesion molecule2 (CADM2), which encodes a mediator of synaptic signaling enriched in the brain. Here we sought to further understand the role of Cadm2 in the pathogenesis of hyperglycemia and weight gain.

Methods: We first analyzed Cadm2 expression in the brain of both human subjects and mouse models and subsequently characterized a loss-of-function mouse model of Cadm2 for alterations in glucose and energy homeostasis.

Results: We show that the risk variant rs13078960 associates with increased CADM2 expression in the hypothalamus of human subjects. Increased Cadm2 expression in several brain regions of Lep mice was ameliorated after leptin treatment. Deletion of Cadm2 in obese mice (Cadm2/ob) resulted in reduced adiposity, systemic glucose levels, and improved insulin sensitivity. Cadm2-deficient mice exhibited increased locomotor activity, energy expenditure rate, and core body temperature identifying Cadm2 as a potent regulator of systemic energy homeostasis.

Conclusions: Together these data illustrate that reducing Cadm2 expression can reverse several traits associated with the metabolic syndrome including obesity, insulin resistance, and impaired glucose homeostasis.
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http://dx.doi.org/10.1016/j.molmet.2017.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985021PMC
February 2018

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy.

Genome Biol 2017 09 14;18(1):170. Epub 2017 Sep 14.

Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands.

Background: Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases.

Results: Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls. We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls, affecting known as well as novel dilated cardiomyopathy genes. Moreover, we show a widespread effect of genetic variation on the regulation of transcription, isoform usage, and allele-specific expression. Systematic annotation of genome-wide association SNPs identifies 60 functional candidate genes for heart phenotypes, representing 20% of all published heart genome-wide association loci. Focusing on the dilated cardiomyopathy phenotype we found that eQTL variants are also enriched for dilated cardiomyopathy genome-wide association signals in two independent cohorts.

Conclusions: RNA transcription, splicing, and allele-specific expression are each important determinants of the dilated cardiomyopathy phenotype and are controlled by genetic factors. Our results represent a powerful resource for the field of cardiovascular genetics.
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http://dx.doi.org/10.1186/s13059-017-1286-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598015PMC
September 2017

Regulation of body weight and energy homeostasis by neuronal cell adhesion molecule 1.

Nat Neurosci 2017 Aug 19;20(8):1096-1103. Epub 2017 Jun 19.

Max Delbrück Center for Molecular Medicine, Berlin, Germany.

Susceptibility to obesity is linked to genes regulating neurotransmission, pancreatic beta-cell function and energy homeostasis. Genome-wide association studies have identified associations between body mass index and two loci near cell adhesion molecule 1 (CADM1) and cell adhesion molecule 2 (CADM2), which encode membrane proteins that mediate synaptic assembly. We found that these respective risk variants associate with increased CADM1 and CADM2 expression in the hypothalamus of human subjects. Expression of both genes was elevated in obese mice, and induction of Cadm1 in excitatory neurons facilitated weight gain while exacerbating energy expenditure. Loss of Cadm1 protected mice from obesity, and tract-tracing analysis revealed Cadm1-positive innervation of POMC neurons via afferent projections originating from beyond the arcuate nucleus. Reducing Cadm1 expression in the hypothalamus and hippocampus promoted a negative energy balance and weight loss. These data identify essential roles for Cadm1-mediated neuronal input in weight regulation and provide insight into the central pathways contributing to human obesity.
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http://dx.doi.org/10.1038/nn.4590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533218PMC
August 2017

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.

Cell Rep 2017 04;19(3):643-654

Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany; German Center for Diabetes Research (DZD), German Center for Environmental Health GmbH, Munich 85764, Germany. Electronic address:

Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes. This coincides with a genome-wide temporary slowdown in cotranscriptional splicing, even for polyadenylated mRNAs that are localized at the chromatin. Subsequent splicing optimization correlates with increasing Ser-2 phosphorylation of the RNA Pol II carboxy-terminal domain (CTD) and activation of the positive transcription elongation factor (pTEFb). Thus, rapid de novo recruitment of RNA Pol II dictates the course of events during T cell activation, particularly transcription, splicing, and consequently translation.
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http://dx.doi.org/10.1016/j.celrep.2017.03.069DOI Listing
April 2017

Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function.

PLoS One 2017 3;12(2):e0170458. Epub 2017 Feb 3.

Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America.

Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein. To focus the analysis on a medically-important condition with a strong yet incompletely understood mitochondrial component, candidates were cross-referenced with an MPET-enriched module independently generated via genome-wide co-expression network analysis of a human heart failure gene expression dataset. The strongest uncharacterized candidate in the analysis was Leucine Rich Repeat Containing 2 (LRRC2). LRRC2 was found to be localized to the mitochondria in human cells and transcriptionally-regulated by the mitochondrial master regulator Pgc-1α. We report that Lrrc2 transcript abundance correlates with that of β-MHC, a canonical marker of cardiac hypertrophy in humans and experimentally demonstrated an elevation in Lrrc2 transcript in in vitro and in vivo rodent models of cardiac hypertrophy as well as in patients with dilated cardiomyopathy. RNAi-mediated Lrrc2 knockdown in a rat-derived cardiomyocyte cell line resulted in enhanced expression of canonical hypertrophic biomarkers as well as increased mitochondrial mass in the context of increased Pgc-1α expression. In conclusion, our meta-analysis represents a simple yet powerful springboard for the nomination of putative mitochondrially-pertinent proteins relevant to cardiac function and enabled the identification of LRRC2 as a novel mitochondrially-relevant protein and regulator of the hypertrophic response.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170458PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291451PMC
August 2017

Epigenetics and Control of RNAs.

Methods Mol Biol 2017 ;1488:217-237

Helmholtz Zentrum München, Institute of Computational Biology (ICB), Neuherberg, 85764, Germany.

Histone modifications are epigenetic marks that fundamentally impact the regulation of gene expression. Integrating histone modification information in the analysis of gene expression traits (eQTL mapping) has been shown to significantly enhance the prediction of eQTLs. In this chapter, we describe (1) how to perform quantitative trait locus (QTL) analysis using histone modification levels as traits and (2) how to integrate these data with information on RNA expression for the elucidation of the epigenetic control of transcript levels. We will provide a comprehensive introduction into the topic, describe in detail how ChIP-seq data are analyzed and elaborate on how to integrate ChIP-seq and RNA-seq data from a segregating disease animal model for the identification of the epigenetic control of RNA expression.
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http://dx.doi.org/10.1007/978-1-4939-6427-7_9DOI Listing
January 2018

52 Genetic Loci Influencing Myocardial Mass.

J Am Coll Cardiol 2016 09;68(13):1435-1448

Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, the Netherlands.

Background: Myocardial mass is a key determinant of cardiac muscle function and hypertrophy. Myocardial depolarization leading to cardiac muscle contraction is reflected by the amplitude and duration of the QRS complex on the electrocardiogram (ECG). Abnormal QRS amplitude or duration reflect changes in myocardial mass and conduction, and are associated with increased risk of heart failure and death.

Objectives: This meta-analysis sought to gain insights into the genetic determinants of myocardial mass.

Methods: We carried out a genome-wide association meta-analysis of 4 QRS traits in up to 73,518 individuals of European ancestry, followed by extensive biological and functional assessment.

Results: We identified 52 genomic loci, of which 32 are novel, that are reliably associated with 1 or more QRS phenotypes at p < 1 × 10(-8). These loci are enriched in regions of open chromatin, histone modifications, and transcription factor binding, suggesting that they represent regions of the genome that are actively transcribed in the human heart. Pathway analyses provided evidence that these loci play a role in cardiac hypertrophy. We further highlighted 67 candidate genes at the identified loci that are preferentially expressed in cardiac tissue and associated with cardiac abnormalities in Drosophila melanogaster and Mus musculus. We validated the regulatory function of a novel variant in the SCN5A/SCN10A locus in vitro and in vivo.

Conclusions: Taken together, our findings provide new insights into genes and biological pathways controlling myocardial mass and may help identify novel therapeutic targets.
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http://dx.doi.org/10.1016/j.jacc.2016.07.729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478167PMC
September 2016

Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci.

Genetics 2016 08 3;203(4):1629-40. Epub 2016 Jun 3.

RNA Bioinformatics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany High Throughput Genomics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany.

Extensive work has been dedicated to study mechanisms of microRNA-mediated gene regulation. However, the transcriptional regulation of microRNAs themselves is far less well understood, due to difficulties determining the transcription start sites of transient primary transcripts. This challenge can be addressed using expression quantitative trait loci (eQTLs) whose regulatory effects represent a natural source of perturbation of cis-regulatory elements. Here we used previously published cis-microRNA-eQTL data for the human GM12878 cell line, promoter predictions, and other functional annotations to determine the relationship between functional elements and microRNA regulation. We built a logistic regression model that classifies microRNA/SNP pairs into eQTLs or non-eQTLs with 85% accuracy; shows microRNA-eQTL enrichment for microRNA precursors, promoters, enhancers, and transcription factor binding sites; and depletion for repressed chromatin. Interestingly, although there is a large overlap between microRNA eQTLs and messenger RNA eQTLs of host genes, 74% of these shared eQTLs affect microRNA and host expression independently. Considering microRNA-only eQTLs we find a significant enrichment for intronic promoters, validating the existence of alternative promoters for intragenic microRNAs. Finally, in line with the GM12878 cell line derived from B cells, we find genome-wide association (GWA) variants associated to blood-related traits more likely to be microRNA eQTLs than random GWA and non-GWA variants, aiding the interpretation of GWA results.
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http://dx.doi.org/10.1534/genetics.116.187153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981266PMC
August 2016

Comparison of Cox Model Methods in A Low-dimensional Setting with Few Events.

Genomics Proteomics Bioinformatics 2016 08 17;14(4):235-43. Epub 2016 May 17.

Department of General and Interventional Cardiology, University Heart Center Hamburg-Eppendorf, 20246 Hamburg, Germany; German Center for Cardiovascular Research (DZHK), Hamburg/Kiel/Luebeck, Germany.

Prognostic models based on survival data frequently make use of the Cox proportional hazards model. Developing reliable Cox models with few events relative to the number of predictors can be challenging, even in low-dimensional datasets, with a much larger number of observations than variables. In such a setting we examined the performance of methods used to estimate a Cox model, including (i) full model using all available predictors and estimated by standard techniques, (ii) backward elimination (BE), (iii) ridge regression, (iv) least absolute shrinkage and selection operator (lasso), and (v) elastic net. Based on a prospective cohort of patients with manifest coronary artery disease (CAD), we performed a simulation study to compare the predictive accuracy, calibration, and discrimination of these approaches. Candidate predictors for incident cardiovascular events we used included clinical variables, biomarkers, and a selection of genetic variants associated with CAD. The penalized methods, i.e., ridge, lasso, and elastic net, showed a comparable performance, in terms of predictive accuracy, calibration, and discrimination, and outperformed BE and the full model. Excessive shrinkage was observed in some cases for the penalized methods, mostly on the simulation scenarios having the lowest ratio of a number of events to the number of variables. We conclude that in similar settings, these three penalized methods can be used interchangeably. The full model and backward elimination are not recommended in rare event scenarios.
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http://dx.doi.org/10.1016/j.gpb.2016.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996851PMC
August 2016

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

Genome Med 2016 Mar 17;8(1):28. Epub 2016 Mar 17.

Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.

Background: NF-κB is widely involved in lymphoid malignancies; however, the functional roles and specific transcriptomes of NF-κB dimers with distinct subunit compositions have been unclear.

Methods: Using combined ChIP-sequencing and microarray analyses, we determined the cistromes and target gene signatures of canonical and non-canonical NF-κB species in Hodgkin lymphoma (HL) cells.

Results: We found that the various NF-κB subunits are recruited to regions with redundant κB motifs in a large number of genes. Yet canonical and non-canonical NF-κB dimers up- and downregulate gene sets that are both distinct and overlapping, and are associated with diverse biological functions. p50 and p52 are formed through NIK-dependent p105 and p100 precursor processing in HL cells and are the predominant DNA binding subunits. Logistic regression analyses of combinations of the p50, p52, RelA, and RelB subunits in binding regions that have been assigned to genes they regulate reveal a cross-contribution of p52 and p50 to canonical and non-canonical transcriptomes. These analyses also indicate that the subunit occupancy pattern of NF-κB binding regions and their distance from the genes they regulate are determinants of gene activation versus repression. The pathway-specific signatures of activated and repressed genes distinguish HL from other NF-κB-associated lymphoid malignancies and inversely correlate with gene expression patterns in normal germinal center B cells, which are presumed to be the precursors of HL cells.

Conclusions: We provide insights that are relevant for lymphomas with constitutive NF-κB activation and generally for the decoding of the mechanisms of differential gene regulation through canonical and non-canonical NF-κB signaling.
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http://dx.doi.org/10.1186/s13073-016-0280-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794921PMC
March 2016

Meta-analysis identifies seven susceptibility loci involved in the atopic march.

Nat Commun 2015 Nov 6;6:8804. Epub 2015 Nov 6.

Research Institute of Medical Genetics, Tomsk, Russia.

Eczema often precedes the development of asthma in a disease course called the 'atopic march'. To unravel the genes underlying this characteristic pattern of allergic disease, we conduct a multi-stage genome-wide association study on infantile eczema followed by childhood asthma in 12 populations including 2,428 cases and 17,034 controls. Here we report two novel loci specific for the combined eczema plus asthma phenotype, which are associated with allergic disease for the first time; rs9357733 located in EFHC1 on chromosome 6p12.3 (OR 1.27; P=2.1 × 10(-8)) and rs993226 between TMTC2 and SLC6A15 on chromosome 12q21.3 (OR 1.58; P=5.3 × 10(-9)). Additional susceptibility loci identified at genome-wide significance are FLG (1q21.3), IL4/KIF3A (5q31.1), AP5B1/OVOL1 (11q13.1), C11orf30/LRRC32 (11q13.5) and IKZF3 (17q21). We show that predominantly eczema loci increase the risk for the atopic march. Our findings suggest that eczema may play an important role in the development of asthma after eczema.
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http://dx.doi.org/10.1038/ncomms9804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667629PMC
November 2015

Complement receptor 2 is up regulated in the spinal cord following nerve root injury and modulates the spinal cord response.

J Neuroinflammation 2015 Oct 26;12:192. Epub 2015 Oct 26.

Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden.

Background: Activation of the complement system has been implicated in both acute and chronic states of neurodegeneration. However, a detailed understanding of this complex network of interacting components is still lacking.

Methods: Large-scale global expression profiling in a rat F2(DAxPVG) intercross identified a strong cis-regulatory influence on the local expression of complement receptor 2 (Cr2) in the spinal cord after ventral root avulsion (VRA). Expression of Cr2 in the spinal cord was studied in a separate cohort of DA and PVG rats at different time-points after VRA, and also following sciatic nerve transection (SNT) in the same strains. Consequently, Cr2 (-/-) mice and Wt controls were used to further explore the role of Cr2 in the spinal cord following SNT. The in vivo experiments were complemented by astrocyte and microglia cell cultures.

Results: Expression of Cr2 in naïve spinal cord was low but strongly up regulated at 5-7 days after both VRA and SNT. Levels of Cr2 expression, as well as astrocyte activation, was higher in PVG rats than DA rats following both VRA and SNT. Subsequent in vitro studies proposed astrocytes as the main source of Cr2 expression. A functional role for Cr2 is suggested by the finding that transgenic mice lacking Cr2 displayed increased loss of synaptic nerve terminals following nerve injury. We also detected increased levels of soluble CR2 (sCR2) in the cerebrospinal fluid of rats following VRA.

Conclusions: These results demonstrate that local expression of Cr2 in the central nervous system is part of the axotomy reaction and is suggested to modulate subsequent complement mediated effects.
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http://dx.doi.org/10.1186/s12974-015-0413-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624364PMC
October 2015

High salt reduces the activation of IL-4- and IL-13-stimulated macrophages.

J Clin Invest 2015 Nov 20;125(11):4223-38. Epub 2015 Oct 20.

A high intake of dietary salt (NaCl) has been implicated in the development of hypertension, chronic inflammation, and autoimmune diseases. We have recently shown that salt has a proinflammatory effect and boosts the activation of Th17 cells and the activation of classical, LPS-induced macrophages (M1). Here, we examined how the activation of alternative (M2) macrophages is affected by salt. In stark contrast to Th17 cells and M1 macrophages, high salt blunted the alternative activation of BM-derived mouse macrophages stimulated with IL-4 and IL-13, M(IL-4+IL-13) macrophages. Salt-induced reduction of M(IL-4+IL-13) activation was not associated with increased polarization toward a proinflammatory M1 phenotype. In vitro, high salt decreased the ability of M(IL-4+IL-13) macrophages to suppress effector T cell proliferation. Moreover, mice fed a high salt diet exhibited reduced M2 activation following chitin injection and delayed wound healing compared with control animals. We further identified a high salt-induced reduction in glycolysis and mitochondrial metabolic output, coupled with blunted AKT and mTOR signaling, which indicates a mechanism by which NaCl inhibits full M2 macrophage activation. Collectively, this study provides evidence that high salt reduces noninflammatory innate immune cell activation and may thus lead to an overall imbalance in immune homeostasis.
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http://dx.doi.org/10.1172/JCI80919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4639967PMC
November 2015

Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).

Curr Protoc Hum Genet 2015 Oct 6;87:11.16.1-11.16.14. Epub 2015 Oct 6.

Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.

Thousands of alternative exons are spliced out of messenger RNA to increase protein diversity. High-throughput sequencing of short cDNA fragments (RNA-seq) generates a genome-wide snapshot of these post-transcriptional processes. RNA-seq reads yield insights into the regulation of alternative splicing by revealing the usage of known or unknown splice sites as well as the expression level of exons. Constitutive exons are never covered by split alignments, whereas alternative exonic parts are located within highly expressed splicing junctions. The ratio between reads including or excluding exons, also known as percent spliced in index (PSI), indicates how efficiently sequences of interest are spliced into transcripts. This protocol describes a method to calculate the PSI without prior knowledge of splicing patterns. It provides a quantitative, global assessment of exon usage that can be integrated with other tools that identify differential isoform processing. Novel, complex splicing events along a genetic locus can be visualized in an exon-centric manner and compared across conditions.
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http://dx.doi.org/10.1002/0471142905.hg1116s87DOI Listing
October 2015

Translational regulation shapes the molecular landscape of complex disease phenotypes.

Nat Commun 2015 May 26;6:7200. Epub 2015 May 26.

Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rossle-Strasse 10, 13125 Berlin, Germany.

The extent of translational control of gene expression in mammalian tissues remains largely unknown. Here we perform genome-wide RNA sequencing and ribosome profiling in heart and liver tissues to investigate strain-specific translational regulation in the spontaneously hypertensive rat (SHR/Ola). For the most part, transcriptional variation is equally apparent at the translational level and there is limited evidence of translational buffering. Remarkably, we observe hundreds of strain-specific differences in translation, almost doubling the number of differentially expressed genes. The integration of genetic, transcriptional and translational data sets reveals distinct signatures in 3'UTR variation, RNA-binding protein motifs and miRNA expression associated with translational regulation of gene expression. We show that a large number of genes associated with heart and liver traits in human genome-wide association studies are primarily translationally regulated. Capturing interindividual differences in the translated genome will lead to new insights into the genes and regulatory pathways underlying disease phenotypes.
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http://dx.doi.org/10.1038/ncomms8200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455061PMC
May 2015

Quantitative interaction proteomics of neurodegenerative disease proteins.

Cell Rep 2015 May 7;11(7):1134-46. Epub 2015 May 7.

Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13092 Berlin, Germany. Electronic address:

Several proteins have been linked to neurodegenerative disorders (NDDs), but their molecular function is not completely understood. Here, we used quantitative interaction proteomics to identify binding partners of Amyloid beta precursor protein (APP) and Presenilin-1 (PSEN1) for Alzheimer's disease (AD), Huntingtin (HTT) for Huntington's disease, Parkin (PARK2) for Parkinson's disease, and Ataxin-1 (ATXN1) for spinocerebellar ataxia type 1. Our network reveals common signatures of protein degradation and misfolding and recapitulates known biology. Toxicity modifier screens and comparison to genome-wide association studies show that interaction partners are significantly linked to disease phenotypes in vivo. Direct comparison of wild-type proteins and disease-associated variants identified binders involved in pathogenesis, highlighting the value of differential interactome mapping. Finally, we show that the mitochondrial protein LRPPRC interacts preferentially with an early-onset AD variant of APP. This interaction appears to induce mitochondrial dysfunction, which is an early phenotype of AD.
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http://dx.doi.org/10.1016/j.celrep.2015.04.030DOI Listing
May 2015

histoneHMM: Differential analysis of histone modifications with broad genomic footprints.

BMC Bioinformatics 2015 Feb 22;16:60. Epub 2015 Feb 22.

Groningen Bioinformatics Center, University of Groningen, Nijenborgh 7, AG, Groningen, 9747, The Netherlands.

Background: ChIP-seq has become a routine method for interrogating the genome-wide distribution of various histone modifications. An important experimental goal is to compare the ChIP-seq profiles between an experimental sample and a reference sample, and to identify regions that show differential enrichment. However, comparative analysis of samples remains challenging for histone modifications with broad domains, such as heterochromatin-associated H3K27me3, as most ChIP-seq algorithms are designed to detect well defined peak-like features.

Results: To address this limitation we introduce histoneHMM, a powerful bivariate Hidden Markov Model for the differential analysis of histone modifications with broad genomic footprints. histoneHMM aggregates short-reads over larger regions and takes the resulting bivariate read counts as inputs for an unsupervised classification procedure, requiring no further tuning parameters. histoneHMM outputs probabilistic classifications of genomic regions as being either modified in both samples, unmodified in both samples or differentially modified between samples. We extensively tested histoneHMM in the context of two broad repressive marks, H3K27me3 and H3K9me3, and evaluated region calls with follow up qPCR as well as RNA-seq data. Our results show that histoneHMM outperforms competing methods in detecting functionally relevant differentially modified regions.

Conclusion: histoneHMM is a fast algorithm written in C++ and compiled as an R package. It runs in the popular R computing environment and thus seamlessly integrates with the extensive bioinformatic tool sets available through Bioconductor. This makeshistoneHMM an attractive choice for the differential analysis of ChIP-seq data. Software is available from http://histonehmm.molgen.mpg.de .
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http://dx.doi.org/10.1186/s12859-015-0491-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4347972PMC
February 2015

Cutaneous Na+ storage strengthens the antimicrobial barrier function of the skin and boosts macrophage-driven host defense.

Cell Metab 2015 Mar;21(3):493-501

Interdisciplinary Center for Clinical Research and Department of Nephrology and Hypertension, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Germany; Divison of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Immune cells regulate a hypertonic microenvironment in the skin; however, the biological advantage of increased skin Na(+) concentrations is unknown. We found that Na(+) accumulated at the site of bacterial skin infections in humans and in mice. We used the protozoan parasite Leishmania major as a model of skin-prone macrophage infection to test the hypothesis that skin-Na(+) storage facilitates antimicrobial host defense. Activation of macrophages in the presence of high NaCl concentrations modified epigenetic markers and enhanced p38 mitogen-activated protein kinase (p38/MAPK)-dependent nuclear factor of activated T cells 5 (NFAT5) activation. This high-salt response resulted in elevated type-2 nitric oxide synthase (Nos2)-dependent NO production and improved Leishmania major control. Finally, we found that increasing Na(+) content in the skin by a high-salt diet boosted activation of macrophages in a Nfat5-dependent manner and promoted cutaneous antimicrobial defense. We suggest that the hypertonic microenvironment could serve as a barrier to infection.
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http://dx.doi.org/10.1016/j.cmet.2015.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350016PMC
March 2015