Publications by authors named "Mario Looso"

56 Publications

Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction.

Nat Commun 2021 01 29;12(1):681. Epub 2021 Jan 29.

Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Germany.

Endothelial cells play a critical role in the adaptation of tissues to injury. Tissue ischemia induced by infarction leads to profound changes in endothelial cell functions and can induce transition to a mesenchymal state. Here we explore the kinetics and individual cellular responses of endothelial cells after myocardial infarction by using single cell RNA sequencing. This study demonstrates a time dependent switch in endothelial cell proliferation and inflammation associated with transient changes in metabolic gene signatures. Trajectory analysis reveals that the majority of endothelial cells 3 to 7 days after myocardial infarction acquire a transient state, characterized by mesenchymal gene expression, which returns to baseline 14 days after injury. Lineage tracing, using the Cdh5-CreERT2;mT/mG mice followed by single cell RNA sequencing, confirms the transient mesenchymal transition and reveals additional hypoxic and inflammatory signatures of endothelial cells during early and late states after injury. These data suggest that endothelial cells undergo a transient mes-enchymal activation concomitant with a metabolic adaptation within the first days after myocardial infarction but do not acquire a long-term mesenchymal fate. This mesenchymal activation may facilitate endothelial cell migration and clonal expansion to regenerate the vascular network.
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http://dx.doi.org/10.1038/s41467-021-20905-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846794PMC
January 2021

Mapping the Endothelial Cell -Sulfhydrome Highlights the Crucial Role of Integrin Sulfhydration in Vascular Function.

Circulation 2021 Mar 14;143(9):935-948. Epub 2020 Dec 14.

Institute for Vascular Signalling (S-I.B., J.H., J.W., M.K.D., V.R., F.D.L., B.F., S.Z., A.K., A.F.O.J., I.F.), Goethe University, Frankfurt am Main, Germany.

Background: In vascular endothelial cells, cysteine metabolism by the cystathionine γ lyase (CSE), generates hydrogen sulfide-related sulfane sulfur compounds (HS), that exert their biological actions via cysteine -sulfhydration of target proteins. This study set out to map the "-sulfhydrome" (ie, the spectrum of proteins targeted by HS) in human endothelial cells.

Methods: Liquid chromatography with tandem mass spectrometry was used to identify -sulfhydrated cysteines in endothelial cell proteins and β3 integrin intraprotein disulfide bond rearrangement. Functional studies included endothelial cell adhesion, shear stress-induced cell alignment, blood pressure measurements, and flow-induced vasodilatation in endothelial cell-specific CSE knockout mice and in a small collective of patients with endothelial dysfunction.

Results: Three paired sample sets were compared: (1) native human endothelial cells isolated from plaque-free mesenteric arteries (CSE activity high) and plaque-containing carotid arteries (CSE activity low); (2) cultured human endothelial cells kept under static conditions or exposed to fluid shear stress to decrease CSE expression; and (3) cultured endothelial cells exposed to shear stress to decrease CSE expression and treated with solvent or the slow-releasing HS donor, SG1002. The endothelial cell "-sulfhydrome" consisted of 3446 individual cysteine residues in 1591 proteins. The most altered family of proteins were the integrins and focusing on β3 integrin in detail we found that -sulfhydration affected intraprotein disulfide bond formation and was required for the maintenance of an extended-open conformation of the β leg. β3 integrin -sulfhydration was required for endothelial cell mechanotransduction in vitro as well as flow-induced dilatation in murine mesenteric arteries. In cultured cells, the loss of -sulfhydration impaired interactions between β3 integrin and Gα13 (guanine nucleotide-binding protein subunit α 13), resulting in the constitutive activation of RhoA (ras homolog family member A) and impaired flow-induced endothelial cell realignment. In humans with atherosclerosis, endothelial function correlated with low HS generation, impaired flow-induced dilatation, and failure to detect β3 integrin -sulfhydration, all of which were rescued after the administration of an HS supplement.

Conclusions: Vascular disease is associated with marked changes in the -sulfhydration of endothelial cell proteins involved in mediating responses to flow. Short-term HS supplementation improved vascular reactivity in humans highlighting the potential of interfering with this pathway to treat vascular disease.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.120.051877DOI Listing
March 2021

multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets.

Life Sci Alliance 2020 11 9;3(11). Epub 2020 Sep 9.

Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany

Targeting the coding genome to introduce nucleotide deletions/insertions via the CRISPR/Cas9 technology has become a standard procedure. It has quickly spawned a multitude of methods such as prime editing, APEX proximity labeling, or homology directed repair, for which supporting bioinformatics tools are, however, lagging behind. New CRISPR/Cas9 applications often require specific gRNA design functionality, and a generic tool is critically missing. Here, we introduce multicrispr, an R/bioconductor tool, intended to design individual gRNAs and complex gRNA libraries. The package is easy to use; detects, scores, and filters gRNAs on both efficiency and specificity; visualizes and aggregates results per target or CRISPR/Cas9 sequence; and finally returns both genomic ranges and sequences of gRNAs. To be generic, multicrispr defines and implements a genomic arithmetic framework as a basis for facile adaptation to techniques recently introduced such as prime editing or yet to arise. Its performance and design concepts such as target set-specific filtering render multicrispr a tool of choice when dealing with screening-like approaches.
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http://dx.doi.org/10.26508/lsa.202000757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494814PMC
November 2020

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation.

Nat Commun 2020 08 26;11(1):4267. Epub 2020 Aug 26.

Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.

While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.
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http://dx.doi.org/10.1038/s41467-020-18035-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449963PMC
August 2020

Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System.

Mol Cell Proteomics 2020 09 24;19(9):1523-1532. Epub 2020 Jun 24.

CECAD Research Center Institute for Genetics, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. Electronic address:

Communication between individuals via molecules, termed chemosignaling, is widespread among animal and plant species. However, we lack knowledge on the specific functions of the substances involved for most systems. The femoral gland is an organ that secretes a waxy substance involved in chemical communication in lizards. Although the lipids and volatile substances secreted by the femoral glands have been investigated in several biochemical studies, the protein composition and functions of secretions remain completely unknown. Applying a proteomic approach, we provide the first attempt to comprehensively characterize the protein composition of femoral gland secretions from the Galápagos marine iguana. Using samples from several organs, the marine iguana proteome was assembled by next-generation sequencing and MS, resulting in 7513 proteins. Of these, 4305 proteins were present in the femoral gland, including keratins, small serum proteins, and fatty acid-binding proteins. Surprisingly, no proteins with discernible roles in partner recognition or inter-species communication could be identified. However, we did find several proteins with direct associations to the innate immune system, including lysozyme C, antileukoproteinase (ALP), pulmonary surfactant protein (SFTPD), and galectin (LGALS1) suggesting that the femoral glands function as an important barrier to infection. Furthermore, we report several novel anti-microbial peptides from the femoral glands that show similar action against and such as oncocin, a peptide known for its effectiveness against Gram-negative pathogens. This proteomics data set is a valuable resource for future functional protein analysis and demonstrates that femoral gland secretions also perform functions of the innate immune system.
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http://dx.doi.org/10.1074/mcp.RA120.001947DOI Listing
September 2020

The endocannabinoid anandamide has an anti-inflammatory effect on CCL2 expression in vascular smooth muscle cells.

Basic Res Cardiol 2020 04 22;115(3):34. Epub 2020 Apr 22.

Fachbereich Medizin, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.

Endocannabinoids are important lipid-signaling mediators. Both protective and deleterious effects of endocannabinoids in the cardiovascular system have been reported but the mechanistic basis for these contradicting observations is unclear. We set out to identify anti-inflammatory mechanisms of endocannabinoids in the murine aorta and in human vascular smooth muscle cells (hVSMC). In response to combined stimulation with cytokines, IL-1β and TNFα, the murine aorta released several endocannabinoids, with anandamide (AEA) levels being the most significantly increased. AEA pretreatment had profound effects on cytokine-induced gene expression in hVSMC and murine aorta. As revealed by RNA-Seq analysis, the induction of a subset of 21 inflammatory target genes, including the important cytokine CCL2 was blocked by AEA. This effect was not mediated through AEA-dependent interference of the AP-1 or NF-κB pathways but rather through an epigenetic mechanism. In the presence of AEA, ATAC-Seq analysis and chromatin-immunoprecipitations revealed that CCL2 induction was blocked due to increased levels of H3K27me3 and a decrease of H3K27ac leading to compacted chromatin structure in the CCL2 promoter. These effects were mediated by recruitment of HDAC4 and the nuclear corepressor NCoR1 to the CCL2 promoter. This study therefore establishes a novel anti-inflammatory mechanism for the endogenous endocannabinoid AEA in vascular smooth muscle cells. Furthermore, this work provides a link between endogenous endocannabinoid signaling and epigenetic regulation.
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http://dx.doi.org/10.1007/s00395-020-0793-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176595PMC
April 2020

AP-1 Contributes to Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion During Zebrafish Heart Regeneration.

Circ Res 2020 Jun 21;126(12):1760-1778. Epub 2020 Apr 21.

From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.

Rationale: The adult human heart is an organ with low regenerative potential. Heart failure following acute myocardial infarction is a leading cause of death due to the inability of cardiomyocytes to proliferate and replenish lost cardiac muscle. While the zebrafish has emerged as a powerful model to study endogenous cardiac regeneration, the molecular mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Furthermore, we are far from understanding the regulation of the chromatin landscape and epigenetic barriers that must be overcome for cardiac regeneration to occur.

Objective: To identify transcription factor regulators of the chromatin landscape, which promote cardiomyocyte regeneration in zebrafish, and investigate their function.

Methods And Results: Using the Assay for Transposase-Accessible Chromatin coupled to high-throughput sequencing (ATAC-Seq), we first find that the regenerating cardiomyocyte chromatin accessibility landscape undergoes extensive changes following cryoinjury, and that activator protein-1 (AP-1) binding sites are the most highly enriched motifs in regions that gain accessibility during cardiac regeneration. Furthermore, using bioinformatic and gene expression analyses, we find that the AP-1 response in regenerating adult zebrafish cardiomyocytes is largely different from the response in adult mammalian cardiomyocytes. Using a cardiomyocyte-specific dominant negative approach, we show that blocking AP-1 function leads to defects in cardiomyocyte proliferation as well as decreased chromatin accessibility at the and loci, which regulate sarcomere disassembly and cardiomyocyte protrusion into the injured area, respectively. We further show that overexpression of the family members and can promote changes in mammalian cardiomyocyte behavior in vitro.

Conclusions: AP-1 transcription factors play an essential role in the cardiomyocyte response to injury by regulating chromatin accessibility changes, thereby allowing the activation of gene expression programs that promote cardiomyocyte dedifferentiation, proliferation, and protrusion into the injured area.
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http://dx.doi.org/10.1161/CIRCRESAHA.119.316167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274905PMC
June 2020

Pleiotropic effects of laminar flow and statins depend on the Krüppel-like factor-induced lncRNA MANTIS.

Eur Heart J 2019 08;40(30):2523-2533

Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany.

Aims: To assess the functional relevance and therapeutic potential of the pro-angiogenic long non-coding RNA MANTIS in vascular disease development.

Methods And Results: RNA sequencing, CRISPR activation, overexpression, and RNAi demonstrated that MANTIS, especially its Alu-element, limits endothelial ICAM-1 expression in different types of endothelial cells. Loss of MANTIS increased endothelial monocyte adhesion in an ICAM-1-dependent manner. MANTIS reduced the binding of the SWI/SNF chromatin remodelling factor BRG1 at the ICAM-1 promoter. The expression of MANTIS was induced by laminar flow and HMG-CoA-reductase inhibitors (statins) through mechanisms involving epigenetic rearrangements and the transcription factors KLF2 and KLF4. Mutation of the KLF binding motifs in the MANTIS promoter blocked the flow-induced MANTIS expression. Importantly, the expression of MANTIS in human carotid artery endarterectomy material was lower compared with healthy vessels and this effect was prevented by statin therapy. Interestingly, the protective effects of statins were mediated in part through MANTIS, which was required to facilitate the atorvastatin-induced changes in endothelial gene expression. Moreover, the beneficial endothelial effects of statins in culture models (spheroid outgrowth, proliferation, telomerase activity, and vascular organ culture) were lost upon knockdown of MANTIS.

Conclusion: MANTIS is tightly regulated by the transcription factors KLF2 and KLF4 and limits the ICAM-1 mediated monocyte adhesion to endothelial cells and thus potentially atherosclerosis development in humans. The beneficial effects of statin treatment and laminar flow are dependent on MANTIS.
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http://dx.doi.org/10.1093/eurheartj/ehz393DOI Listing
August 2019

A whole organism small molecule screen identifies novel regulators of pancreatic endocrine development.

Development 2019 07 24;146(14). Epub 2019 Jul 24.

Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, 61231 Bad Nauheim, Germany

An early step in pancreas development is marked by the expression of the transcription factor Pdx1 within the pancreatic endoderm, where it is required for the specification of all endocrine cell types. Subsequently, Pdx1 expression becomes restricted to the β-cell lineage, where it plays a central role in β-cell function. This pivotal role of Pdx1 at various stages of pancreas development makes it an attractive target to enhance pancreatic β-cell differentiation and increase β-cell function. In this study, we used a newly generated zebrafish reporter to screen over 8000 small molecules for modulators of expression. We found four hit compounds and validated their efficacy at different stages of pancreas development. Notably, valproic acid treatment increased pancreatic endoderm formation, while inhibition of TGFβ signaling led to α-cell to β-cell transdifferentiation. HC toxin, another HDAC inhibitor, enhances β-cell function in primary mouse and human islets. Thus, using a whole organism screening strategy, this study identified new expression modulators that can be used to influence different steps in pancreas and β-cell development.
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http://dx.doi.org/10.1242/dev.172569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6679364PMC
July 2019

Connect-four: genomic analyses of regenerating stem cells identifies zygotic Dux factors as tumor initiators.

Mol Cell Oncol 2019 8;6(2):1565469. Epub 2019 Feb 8.

Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.

How, if and in which cell types embryonic gene expression programs are elicited to induce tumor formation remains poorly understood. Through genomic analyses of regenerating, p53 deficient muscle stem cells we identified various oncogenomic amplifications, including but not limited to, the zygotic transcription factor / to initiate tumorigenic transformation.
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http://dx.doi.org/10.1080/23723556.2019.1565469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512926PMC
February 2019

MARMoSET - Extracting Publication-ready Mass Spectrometry Metadata from RAW Files.

Mol Cell Proteomics 2019 08 16;18(8):1700-1702. Epub 2019 May 16.

Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, Bad Nauheim, Germany; The German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main. Electronic address:

In the context of publishing data sets acquired by mass spectrometry or works based on such molecular screens, metadata documenting the instrument settings are of central importance to the evaluation and reproduction of results. A single experiment may be linked to hundreds of data acquisitions, which are frequently stored in proprietary file formats. Together with community-, repository-, as well as publisher-specific reporting standards, this state of affairs frequently leads to manual -and thus error prone-metadata extraction and formatting. Data extracted from a single file also often stand in for an entire file set, implying a risk for unreported parameter divergence. To support quality control and data reporting, the C# application MARMoSET extracts and reduces publication relevant metadata from Thermo Fischer Scientific RAW files. It is integrated with an R package for easy reporting. The tool is expected to be particularly useful to high throughput environments such as service facilities with large project numbers and/or sizes.
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http://dx.doi.org/10.1074/mcp.TIR119.001505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6683000PMC
August 2019

Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples - a proof-of-principle assessment.

BMC Microbiol 2019 04 8;19(1):75. Epub 2019 Apr 8.

Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany.

Background: The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question.

Results: For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis.

Conclusions: The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization.
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http://dx.doi.org/10.1186/s12866-019-1448-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454699PMC
April 2019

The histone demethylase PHF8 facilitates alternative splicing of the histocompatibility antigen HLA-G.

FEBS Lett 2019 03 27;593(5):487-498. Epub 2019 Feb 27.

Institute for Cardiovascular Physiology, Medical Faculty, Goethe University, Frankfurt, Germany.

Histone3-lysine9 (H3K9) residues not only control gene expression, but also contribute to RNA splicing. Here, the H3K9 histone demethylase PHF8 was investigated in endothelial cells for its involvement in alternative splicing. An angiogenic sprouting assay shows the importance of PHF8 for endothelial cells. Immunoprecipitation reveals that PHF8 interacts with U1 spliceosomal proteins, such as SRPK1 and snRNP70. We identify the histocompatibility antigen HLA-G as a target of PHF8. The inclusion of HLA-G intron 4, with concomitant RNA Polymerase II accumulation at this intron is controlled by PHF8 and H3K9. Soluble HLA-G is generated after PHF8 knockdown, which leads to reduced T-cell proliferation. Collectively, PHF8 knockdown generates the immunosuppressive alternative splice product soluble HLA-G, which is secreted by endothelial cells to elicit a potential inhibitory effect on inflammation.
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http://dx.doi.org/10.1002/1873-3468.13337DOI Listing
March 2019

aPKC controls endothelial growth by modulating c-Myc via FoxO1 DNA-binding ability.

Nat Commun 2018 12 17;9(1):5357. Epub 2018 Dec 17.

Laboratory for Cell Polarity and Organogenesis, Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.

Strict regulation of proliferation is vital for development, whereas unregulated cell proliferation is a fundamental characteristic of cancer. The polarity protein atypical protein kinase C lambda/iota (aPKCλ) is associated with cell proliferation through unknown mechanisms. In endothelial cells, suppression of aPKCλ impairs proliferation despite hyperactivated mitogenic signaling. Here we show that aPKCλ phosphorylates the DNA binding domain of forkhead box O1 (FoxO1) transcription factor, a gatekeeper of endothelial growth. Although mitogenic signaling excludes FoxO1 from the nucleus, consequently increasing c-Myc abundance and proliferation, aPKCλ controls c-Myc expression via FoxO1/miR-34c signaling without affecting its localization. We find this pathway is strongly activated in the malignant vascular sarcoma, angiosarcoma, and aPKC inhibition reduces c-Myc expression and proliferation of angiosarcoma cells. Moreover, FoxO1 phosphorylation at Ser218 and aPKC expression correlates with poor patient prognosis. Our findings may provide a potential therapeutic strategy for treatment of malignant cancers, like angiosarcoma.
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http://dx.doi.org/10.1038/s41467-018-07739-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297234PMC
December 2018

WIlsON: Web-based Interactive Omics VisualizatioN.

Bioinformatics 2019 03;35(6):1055-1057

Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany.

Motivation: High throughput (HT) screens in the omics field are typically analyzed by automated pipelines that generate static visualizations and comprehensive spreadsheet data for scientists. However, exploratory and hypothesis driven data analysis are key aspects of the understanding of biological systems, both generating extensive need for customized and dynamic visualization.

Results: Here we describe WIlsON, an interactive workbench for analysis and visualization of multi-omics data. It is primarily intended to empower screening platforms to offer access to pre-calculated HT screen results to the non-computational scientist. Facilitated by an open file format, WIlsON supports all types of omics screens, serves results via a web-based dashboard, and enables end users to perform analyses and generate publication-ready plots.

Availability And Implementation: We implemented WIlsON in R with a focus on extensibility using the modular Shiny and Plotly frameworks. A demo of the interactive workbench without limitations may be accessed at http://loosolab.mpi-bn.mpg.de. A standalone Docker container as well as the source code of WIlsON are freely available from our Docker hub https://hub.docker. com/r/loosolab/wilson, CRAN https://cran.r-project.org/web/packages/wilson/, and GitHub repository https://github.molgen.mpg.de/loosolab/wilson-apps, respectively.
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http://dx.doi.org/10.1093/bioinformatics/bty711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419899PMC
March 2019

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement.

Nat Commun 2018 11 19;9(1):4877. Epub 2018 Nov 19.

Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.

Formation and segregation of cell lineages forming the heart have been studied extensively but the underlying gene regulatory networks and epigenetic changes driving cell fate transitions during early cardiogenesis are still only partially understood. Here, we comprehensively characterize mouse cardiac progenitor cells (CPCs) marked by Nkx2-5 and Isl1 expression from E7.5 to E9.5 using single-cell RNA sequencing and transposase-accessible chromatin profiling (ATAC-seq). By leveraging on cell-to-cell transcriptome and chromatin accessibility heterogeneity, we identify different previously unknown cardiac subpopulations. Reconstruction of developmental trajectories reveal that multipotent Isl1 CPC pass through an attractor state before separating into different developmental branches, whereas extended expression of Nkx2-5 commits CPC to an unidirectional cardiomyocyte fate. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5. Our data provide a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.
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http://dx.doi.org/10.1038/s41467-018-07307-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242939PMC
November 2018

Oncogenic Amplification of Zygotic Dux Factors in Regenerating p53-Deficient Muscle Stem Cells Defines a Molecular Cancer Subtype.

Cell Stem Cell 2018 12 15;23(6):794-805.e4. Epub 2018 Nov 15.

Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany; German Center for Cardiovascular Research (DZHK), Rhine Main, Germany. Electronic address:

The identity of tumor-initiating cells in many cancer types is unknown. Tumors often express genes associated with embryonic development, although the contributions of zygotic programs to tumor initiation and formation are poorly understood. Here, we show that regeneration-induced loss of quiescence in p53-deficient muscle stem cells (MuSCs) results in rhabdomyosarcoma formation with 100% penetrance. Genomic analyses of purified tumor cells revealed spontaneous and discrete oncogenic amplifications in MuSCs that drive tumorigenesis, including, but not limited to, the amplification of the cleavage-stage Dux transcription factor (TF) Duxbl. We further found that Dux factors drive an early embryonic gene signature that defines a molecular subtype across a broad range of human cancers. Duxbl initiates tumorigenesis by enforcing a mesenchymal-to-epithelial transition, and targeted inactivation of Duxbl specifically in Duxbl-expressing tumor cells abolishes their expansion. These findings reveal how regeneration and genomic instability can interact to activate zygotic genes that drive tumor initiation and growth.
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http://dx.doi.org/10.1016/j.stem.2018.10.011DOI Listing
December 2018

Myh10 deficiency leads to defective extracellular matrix remodeling and pulmonary disease.

Nat Commun 2018 11 2;9(1):4600. Epub 2018 Nov 2.

Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.

Impaired alveolar formation and maintenance are features of many pulmonary diseases that are associated with significant morbidity and mortality. In a forward genetic screen for modulators of mouse lung development, we identified the non-muscle myosin II heavy chain gene, Myh10. Myh10 mutant pups exhibit cyanosis and respiratory distress, and die shortly after birth from differentiation defects in alveolar epithelium and mesenchyme. From omics analyses and follow up studies, we find decreased Thrombospondin expression accompanied with increased matrix metalloproteinase activity in both mutant lungs and cultured mutant fibroblasts, as well as disrupted extracellular matrix (ECM) remodeling. Loss of Myh10 specifically in mesenchymal cells results in ECM deposition defects and alveolar simplification. Notably, MYH10 expression is downregulated in the lung of emphysema patients. Altogether, our findings reveal critical roles for Myh10 in alveologenesis at least in part via the regulation of ECM remodeling, which may contribute to the pathogenesis of emphysema.
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http://dx.doi.org/10.1038/s41467-018-06833-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214918PMC
November 2018

The potassium channel KCNJ13 is essential for smooth muscle cytoskeletal organization during mouse tracheal tubulogenesis.

Nat Commun 2018 07 19;9(1):2815. Epub 2018 Jul 19.

Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.

Tubulogenesis is essential for the formation and function of internal organs. One such organ is the trachea, which allows gas exchange between the external environment and the lungs. However, the cellular and molecular mechanisms underlying tracheal tube development remain poorly understood. Here, we show that the potassium channel KCNJ13 is a critical modulator of tracheal tubulogenesis. We identify Kcnj13 in an ethylnitrosourea forward genetic screen for regulators of mouse respiratory organ development. Kcnj13 mutants exhibit a shorter trachea as well as defective smooth muscle (SM) cell alignment and polarity. KCNJ13 is essential to maintain ion homeostasis in tracheal SM cells, which is required for actin polymerization. This process appears to be mediated, at least in part, through activation of the actin regulator AKT, as pharmacological increase of AKT phosphorylation ameliorates the Kcnj13-mutant trachea phenotypes. These results provide insight into the role of ion homeostasis in cytoskeletal organization during tubulogenesis.
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http://dx.doi.org/10.1038/s41467-018-05043-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052067PMC
July 2018

Long noncoding RNA LISPR1 is required for S1P signaling and endothelial cell function.

J Mol Cell Cardiol 2018 03 3;116:57-68. Epub 2018 Feb 3.

Goethe-University, Institute for Cardiovascular Physiology, Frankfurt am Main, Germany; German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany. Electronic address:

Sphingosine-1-Phosphate (S1P) is a potent signaling lipid. The effects of S1P are mediated by the five S1P receptors (S1PR). In the endothelium S1PR1 is the predominant receptor and thus S1PR1 abundance limits S1P signaling. Recently, lncRNAs were identified as a novel class of molecules regulating gene expression. Interestingly, the lncRNA NONHSAT004848 (LISPR1, Long intergenic noncoding RNA antisense to S1PR1), is closely positioned to the S1P1 receptors gene and in part shares its promoter region. We hypothesize that LISPR1 controls endothelial S1PR1 expression and thus S1P-induced signaling in endothelial cells. In vitro transcription and translation as well as coding potential assessment showed that LISPR1 is indeed noncoding. LISPR1 was localized in both cytoplasm and nucleus and harbored a PolyA tail at the 3'end. In human umbilical vein endothelial cells, as well as human lung tissue, qRT-PCR and RNA-Seq revealed high expression of LISPR1. S1PR1 and LISPR1 were downregulated in human pulmonary diseases such as COPD. LISPR1 but also S1PR1 were induced by inflammation, shear stress and statins. Knockdown of LISPR1 attenuated endothelial S1P-induced migration and spheroid outgrowth of endothelial cells. LISPR1 knockdown decreased S1PR1 expression, which was paralleled by an increase of the binding of the transcriptional repressor ZNF354C to the S1PR1 promoter and a reduction of the recruitment of RNA Polymerase II to the S1PR1 5'end. This resulted in attenuated S1PR1 expression and attenuated S1P downstream signaling. Collectively, the disease relevant lncRNA LISPR1 acts as a novel regulatory unit important for S1PR1 expression and endothelial cell function.
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http://dx.doi.org/10.1016/j.yjmcc.2018.01.015DOI Listing
March 2018

The NADPH organizers NoxO1 and p47phox are both mediators of diabetes-induced vascular dysfunction in mice.

Redox Biol 2018 05 22;15:12-21. Epub 2017 Nov 22.

Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany; German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, Frankfurt, Germany. Electronic address:

Aim: NADPH oxidases are important sources of reactive oxygen species (ROS). Several Nox homologues are present together in the vascular system but whether they exhibit crosstalk at the activity level is unknown. To address this, vessel function of knockout mice for the cytosolic Nox organizer proteins p47phox, NoxO1 and a p47phox-NoxO1-double knockout were studied under normal condition and during streptozotocin-induced diabetes.

Results: In the mouse aorta, mRNA expression for NoxO1 was predominant in smooth muscle and endothelial cells, whereas p47phox was markedly expressed in adventitial cells comprising leukocytes and tissue resident macrophages. Knockout of either NoxO1 or p47phox resulted in lower basal blood pressure. Deletion of any of the two subunits also prevented diabetes-induced vascular dysfunction. mRNA expression analysis by MACE (Massive Analysis of cDNA ends) identified substantial gene expression differences between the mouse lines and in response to diabetes. Deletion of p47phox induced inflammatory activation with increased markers of myeloid cells and cytokine and chemokine induction. In contrast, deletion of NoxO1 resulted in an attenuated interferon gamma signature and reduced expression of genes related to antigen presentation. This aspect was also reflected by a reduced number of circulating lymphocytes in NoxO1-/- mice.

Innovation And Conclusion: ROS production stimulated by NoxO1 and p47phox limit endothelium-dependent relaxation and maintain blood pressure in mice. However, NoxO1 and p47phox cannot substitute each other despite their similar effect on vascular function. Deletion of NoxO1 induced an anti-inflammatory phenotype, whereas p47phox deletion rather elicited a hyper-inflammatory response.
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http://dx.doi.org/10.1016/j.redox.2017.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5723277PMC
May 2018

Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment.

Mol Cell Proteomics 2018 02 15;17(2):270-289. Epub 2017 Nov 15.

¶Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany 35043;

Ovarian cancer is characterized by early transcoelomic metastatic spread via the peritoneal fluid, where tumor cell spheroids (TU), tumor-associated T cells (TAT), and macrophages (TAM) create a unique microenvironment promoting cancer progression, chemoresistance, and immunosuppression. However, the underlying signaling mechanisms remain largely obscure. To chart these signaling networks, we performed comprehensive proteomic and transcriptomic analyses of TU, TAT, and TAM from ascites of ovarian cancer patients. We identify multiple intercellular signaling pathways driven by protein or lipid mediators that are associated with clinical outcome. Beyond cytokines, chemokines and growth factors, these include proteins of the extracellular matrix, immune checkpoint regulators, complement factors, and a prominent network of axon guidance molecules of the ephrin, semaphorin, and slit families. Intriguingly, both TU and TAM from patients with a predicted short survival selectively produce mediators supporting prometastatic events, including matrix remodeling, stemness, invasion, angiogenesis, and immunosuppression, whereas TAM associated with a longer survival express cytokines linked to effector T-cell chemoattraction and activation. In summary, our study uncovers previously unrecognized signaling networks in the ovarian cancer microenvironment that are of potential clinical relevance.
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http://dx.doi.org/10.1074/mcp.RA117.000400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5795391PMC
February 2018

Pulmonary endothelial cell DNA methylation signature in pulmonary arterial hypertension.

Oncotarget 2017 Aug 19;8(32):52995-53016. Epub 2017 May 19.

INSERM UMR_S 999, Hôpital Marie Lannelongue, Le Plessis Robinson, France.

Pulmonary arterial hypertension (PAH) is a severe and incurable pulmonary vascular disease. One of the primary origins of PAH is pulmonary endothelial dysfunction leading to vasoconstriction, aberrant angiogenesis and smooth muscle cell proliferation, endothelial-to-mesenchymal transition, thrombosis and inflammation. Our objective was to study the epigenetic variations in pulmonary endothelial cells (PEC) through a specific pattern of DNA methylation. DNA was extracted from cultured PEC from idiopathic PAH ( = 11), heritable PAH ( = 10) and controls ( = 18). DNA methylation was assessed using the Illumina HumanMethylation450 Assay. After normalization, samples and probes were clustered according to their methylation profile. Differential clusters were functionally analyzed using bioinformatics tools. Unsupervised hierarchical clustering allowed the identification of two clusters of probes that discriminates controls and PAH patients. Among 147 differential methylated promoters, 46 promoters coding for proteins or miRNAs were related to lipid metabolism. Top 10 up and down-regulated genes were involved in lipid transport including ABCA1, ABCB4, ADIPOQ, miR-26A, BCL2L11. NextBio meta-analysis suggested a contribution of ABCA1 in PAH. We confirmed ABCA1 mRNA and protein downregulation specifically in PAH PEC by qPCR and immunohistochemistry and made the proof-of-concept in an experimental model of the disease that its targeting may offer novel therapeutic options. In conclusion, DNA methylation analysis identifies a set of genes mainly involved in lipid transport pathway which could be relevant to PAH pathophysiology.
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http://dx.doi.org/10.18632/oncotarget.18031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581088PMC
August 2017

Single-cell profiling reveals GPCR heterogeneity and functional patterning during neuroinflammation.

JCI Insight 2017 Aug 3;2(15). Epub 2017 Aug 3.

Department of Pharmacology.

GPCR expression was intensively studied in bulk cDNA of leukocyte populations, but limited data are available with respect to expression in individual cells. Here, we show a microfluidic-based single-cell GPCR expression analysis in primary T cells, myeloid cells, and endothelial cells under naive conditions and during experimental autoimmune encephalomyelitis, the mouse model of multiple sclerosis. We found that neuroinflammation induces characteristic changes in GPCR heterogeneity and patterning, and we identify various functionally relevant subgroups with specific GPCR profiles among spinal cord-infiltrating CD4 T cells, macrophages, microglia, or endothelial cells. Using GPCRs CXCR4, S1P1, and LPHN2 as examples, we show how this information can be used to develop new strategies for the functional modulation of Th17 cells and activated endothelial cells. Taken together, single-cell GPCR expression analysis identifies functionally relevant subpopulations with specific GPCR repertoires and provides a basis for the development of new therapeutic strategies in immune disorders.
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http://dx.doi.org/10.1172/jci.insight.95063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543912PMC
August 2017

Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration.

Elife 2017 06 20;6. Epub 2017 Jun 20.

Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.

Zebrafish display a distinct ability to regenerate their heart following injury. However, this ability is not shared by another teleost, the medaka. In order to identify cellular and molecular bases for this difference, we performed comparative transcriptomic analyses following cardiac cryoinjury. This comparison points to major differences in immune cell dynamics between these models. Upon closer examination, we observed delayed and reduced macrophage recruitment in medaka, along with delayed neutrophil clearance. To investigate the role of immune responses in cardiac regeneration, we delayed macrophage recruitment in zebrafish and observed compromised neovascularization, neutrophil clearance, cardiomyocyte proliferation and scar resolution. In contrast, stimulating Toll-like receptor signaling in medaka enhanced immune cell dynamics and promoted neovascularization, neutrophil clearance, cardiomyocyte proliferation and scar resolution. Altogether, these data provide further insight into the complex role of the immune response during regeneration, and serve as a platform to identify and test additional regulators of cardiac repair.
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http://dx.doi.org/10.7554/eLife.25605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498136PMC
June 2017

UROPA: a tool for Universal RObust Peak Annotation.

Sci Rep 2017 06 1;7(1):2593. Epub 2017 Jun 1.

Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), Ludwigstrasse 43, 61231, Bad Nauheim, Germany.

The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.
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http://dx.doi.org/10.1038/s41598-017-02464-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453960PMC
June 2017

Promoter hypermethylation as a mechanism for Lamin A/C silencing in a subset of neuroblastoma cells.

PLoS One 2017 19;12(4):e0175953. Epub 2017 Apr 19.

Epigenetics of Cancer and Aging Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay.

Nuclear lamins support the nuclear envelope and provide anchorage sites for chromatin. They are involved in DNA synthesis, transcription, and replication. It has previously been reported that the lack of Lamin A/C expression in lymphoma and leukaemia is due to CpG island promoter hypermethylation. Here, we provide evidence that Lamin A/C is silenced via this mechanism in a subset of neuroblastoma cells. Moreover, Lamin A/C expression can be restored with a demethylating agent. Importantly, Lamin A/C reintroduction reduced cell growth kinetics and impaired migration, invasion, and anchorage-independent cell growth. Cytoskeletal restructuring was also induced. In addition, the introduction of lamin Δ50, known as Progerin, caused senescence in these neuroblastoma cells. These cells were stiffer and developed a cytoskeletal structure that differed from that observed upon Lamin A/C introduction. Of relevance, short hairpin RNA Lamin A/C depletion in unmethylated neuroblastoma cells enhanced the aforementioned tumour properties. A cytoskeletal structure similar to that observed in methylated cells was induced. Furthermore, atomic force microscopy revealed that Lamin A/C knockdown decreased cellular stiffness in the lamellar region. Finally, the bioinformatic analysis of a set of methylation arrays of neuroblastoma primary tumours showed that a group of patients (around 3%) gives a methylation signal in some of the CpG sites located within the Lamin A/C promoter region analysed by bisulphite sequencing PCR. These findings highlight the importance of Lamin A/C epigenetic inactivation for a subset of neuroblastomas, leading to enhanced tumour properties and cytoskeletal changes. Additionally, these findings may have treatment implications because tumour cells lacking Lamin A/C exhibit more aggressive behaviour.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175953PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397038PMC
April 2017

Long Noncoding RNA MANTIS Facilitates Endothelial Angiogenic Function.

Circulation 2017 Jul 28;136(1):65-79. Epub 2017 Mar 28.

From Institute for Cardiovascular Physiology (M.S.L., C.F., I.J., M.J.M., J.E., F.M., R.P.B.), Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine (F.M.R., J.H., I.W.), Institute of Vascular Signalling (J.H.), Institute of Cardiovascular Regeneration (P.H. Y.P., S.U., K.S., R.A.B., S.D.), Department of Neurosurgery (T.M.F.), Pharmazentrum Frankfurt, Institute of General Pharmacology and Toxicology (K.D.), Goethe University, Germany; ECCPS Bioinformatics and Sequencing Facility (J.P., S.G., C.K., M.L.) and Department of Lung Development and Remodeling (C.V., S.S.P.), Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany; Institute of Neurology (K.H.P., M.M., K.D.); Department of Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich, Germany (L.M.); Luxembourg Centre of Neuropathology (M.M.); Laboratoire National de Santé, Dudelange, Luxembourg (M.M.); Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette (M.M.); NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (M.M.); Cardiovascular Innovation Institute, University of Louisville, KY (S.U.); Department of Internal Medicine, Member of the German Center for Lung Research (DZL), Justus-Liebig University, Giessen, Germany (R.T.S., N.W., S.S.P.); Department of Medicine, Duke University and Durham VA Medical Center, NC (F.J.M.); and German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany (M.S.L., C.F., I.J., J.H., J.E., P.H., F.M., Y.P., K.H.P., K.S., I.W., R.A.B., S.D., R.P.B.).

Background: The angiogenic function of endothelial cells is regulated by numerous mechanisms, but the impact of long noncoding RNAs (lncRNAs) has hardly been studied. We set out to identify novel and functionally important endothelial lncRNAs.

Methods: Epigenetically controlled lncRNAs in human umbilical vein endothelial cells were searched by exon-array analysis after knockdown of the histone demethylase JARID1B. Molecular mechanisms were investigated by RNA pulldown and immunoprecipitation, mass spectrometry, microarray, several knockdown approaches, CRISPR-Cas9, assay for transposase-accessible chromatin sequencing, and chromatin immunoprecipitation in human umbilical vein endothelial cells. Patient samples from lung and tumors were studied for MANTIS expression.

Results: A search for epigenetically controlled endothelial lncRNAs yielded lncRNA n342419, here termed MANTIS, as the most strongly regulated lncRNA. Controlled by the histone demethylase JARID1B, MANTIS was downregulated in patients with idiopathic pulmonary arterial hypertension and in rats treated with monocrotaline, whereas it was upregulated in carotid arteries of subjected to atherosclerosis regression diet, and in endothelial cells isolated from human glioblastoma patients. CRISPR/Cas9-mediated deletion or silencing of MANTIS with small interfering RNAs or GapmeRs inhibited angiogenic sprouting and alignment of endothelial cells in response to shear stress. Mechanistically, the nuclear-localized MANTIS lncRNA interacted with BRG1, the catalytic subunit of the switch/sucrose nonfermentable chromatin-remodeling complex. This interaction was required for nucleosome remodeling by keeping the ATPase function of BRG1 active. Thereby, the transcription of key endothelial genes such as , , and was regulated by ensuring efficient RNA polymerase II machinery binding.

Conclusion: MANTIS is a differentially regulated novel lncRNA facilitating endothelial angiogenic function.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.116.026991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491227PMC
July 2017

A reverse signaling pathway downstream of Sema4A controls cell migration via Scrib.

J Cell Biol 2017 Jan 22;216(1):199-215. Epub 2016 Dec 22.

Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany

Semaphorins comprise a large family of ligands that regulate key cellular functions through their receptors, plexins. In this study, we show that the transmembrane semaphorin 4A (Sema4A) can also function as a receptor, rather than a ligand, and transduce signals triggered by the binding of Plexin-B1 through reverse signaling. Functionally, reverse Sema4A signaling regulates the migration of various cancer cells as well as dendritic cells. By combining mass spectrometry analysis with small interfering RNA screening, we identify the polarity protein Scrib as a downstream effector of Sema4A. We further show that binding of Plexin-B1 to Sema4A promotes the interaction of Sema4A with Scrib, thereby removing Scrib from its complex with the Rac/Cdc42 exchange factor βPIX and decreasing the activity of the small guanosine triphosphatase Rac1 and Cdc42. Our data unravel a role for Plexin-B1 as a ligand and Sema4A as a receptor and characterize a reverse signaling pathway downstream of Sema4A, which controls cell migration.
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http://dx.doi.org/10.1083/jcb.201602002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223600PMC
January 2017

LimiTT: link miRNAs to targets.

BMC Bioinformatics 2016 May 11;17(1):210. Epub 2016 May 11.

Group of Bioinformatics, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, D-61231, Bad Nauheim, Germany.

Background: MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation of miRNA target interactions (MTIs) by high throughput screenings is challenging, as frequently used in silico target prediction tools are prone to emit false positives. This issue is aggravated for niche model organisms, where validated miRNAs and MTIs both have to be transferred from well described model organisms. Even though DBs exist that contain experimentally validated MTIs, they are limited in their search options and they utilize different miRNA and target identifiers.

Results: The implemented pipeline LimiTT integrates four existing DBs containing experimentally validated MTIs. In contrast to other cumulative databases (DBs), LimiTT includes MTI data of 26 species. Additionally, the pipeline enables the identification and enrichment analysis of MTIs with and without species specificity based on dynamic quality criteria. Multiple tabular and graphical outputs are generated to permit the detailed assessment of results.

Conclusion: Our freely available web-based pipeline LimiTT ( https://bioinformatics.mpi-bn.mpg.de/ ) is optimized to determine MTIs with and without species specification. It links miRNAs and/or putative targets with high granularity. The integrated mapping to homologous target identifiers enables the identification of MTIs not only for standard models, but for niche model organisms as well.
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http://dx.doi.org/10.1186/s12859-016-1070-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866021PMC
May 2016