The Camp-Binding Popdc Proteins Have a Redundant Function in the Heart
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Transcriptional Control of Tissue-Resident Memory T Cell Generation
Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. -
Tibbo, Amy J. (2020) Compartmentalized Camp Signaling Via the PDE4- Popeye Protein Complex
Tibbo, Amy J. (2020) Compartmentalized cAMP Signaling via the PDE4- Popeye Protein Complex. PhD thesis. http://theses.gla.ac.uk/81454/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] 1 Compartmentalized cAMP Signaling via the PDE4-Popeye Protein Complex Amy Jane Tibbo (BSc Hons) Thesis submitted in fulfilment of the requirements for Degree of Doctor of Philosophy Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow April 2020 2 Abstract The Popeye domain containing (POPDC) protein family are a unique family of transmembrane proteins with several proposed functions that are not fully understood. POPDC proteins are abundantly expressed in cardiac and skeletal muscle. Within the heart, POPDC1 has been shown to be highly expressed in the pace making centres and at moderate to low levels in the atria and ventricles. Given this localisation, a role for POPDC1 was hypothesised to be in the maintenance of normal heartbeat rhythm. Studies involving POPDC1 mutant mice and zebrafish provided evidence for this proposed function as the genetically modified model animals displayed cardiac arrhythmias as the predominant phenotype. -
(Popdc2). Generation and Functional Characterization of a Null Mutant in Mice and Promoter Analysis
The Popeye domain containing gene 2 (Popdc2). Generation and functional characterization of a null mutant in mice and promoter analysis. Dissertation For completion of the Doctorate degree in Natural Sciences at the Bayerische Julius-Maximilians-Universität Würzburg Alexander Froese from Dushanbe Würzburg 2007 Declaration: I hereby declare that the submitted dissertation was completed by myself and no other. I have not used any sources or materials other than those enclosed. Moreover I declare that the following dissertation has not been submitted further in this form or any other form, and has not been used to obtain any other equivalent qualifications at any other organisation/institution. Additionally, I have not applied for, nor will I attempt to apply for any other degree or qualification in relation to this work. Würzburg, den 21.12.2007 Alexander Froese The hereby submitted thesis was completed from January 2001 until April 2005 at the Cell and Molecular Biology Department, Technical University Braunschweig, Braunschweig and from May 2005 until December 2007 at the Department of Cell and Developmental Biology, University of Würzburg, under the supervision of Professor Dr. T. Brand. Members of the thesis committee: Chairman: Professor Dr. M. Müller Examiner: Professor Dr. T. Brand Examiner: PD Dr. S. Maier Submitted on: 21.12.2007 Date of oral exam: 20.02.2008 Wahrlich, wahrlich, ich sage euch: Wenn das Weizenkorn nicht in die Erde fällt und stirbt, bleibt es allein; wenn es aber stirbt, bringt es viel Frucht. Johannes 12;23-25 Истинно, истинно говорю вам: если пшеничное зерно, падши в землю, не умрёт, то останется одно; а если умрёт, то принесёт много плода. -
The Popeye Domain Containing Genes and Their Function in Striated Muscle
Journal of Cardiovascular Development and Disease Review The Popeye Domain Containing Genes and Their Function in Striated Muscle Roland F. R. Schindler 1, Chiara Scotton 2, Vanessa French 1, Alessandra Ferlini 2 and Thomas Brand 1,* 1 Developmental Dynamics, Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Hill End Road, Harefield UB9 6JH, UK; [email protected] (R.F.R.S.); [email protected] (V.F.) 2 Department of Medical Sciences, Medical Genetics Unit, University of Ferrara, Ferrara 44121, Italy; [email protected] (C.S.); fl[email protected] (A.F.) * Correspondence: [email protected]; Tel.: +44-189-582-8900 Academic Editors: Robert E. Poelmann and Monique R.M. Jongbloed Received: 26 April 2016; Accepted: 13 June 2016; Published: 15 June 2016 Abstract: The Popeye domain containing (POPDC) genes encode a novel class of cAMP effector proteins, which are abundantly expressed in heart and skeletal muscle. Here, we will review their role in striated muscle as deduced from work in cell and animal models and the recent analysis of patients carrying a missense mutation in POPDC1. Evidence suggests that POPDC proteins control membrane trafficking of interacting proteins. Furthermore, we will discuss the current catalogue of established protein-protein interactions. In recent years, the number of POPDC-interacting proteins has been rising and currently includes ion channels (TREK-1), sarcolemma-associated proteins serving functions in mechanical stability (dystrophin), compartmentalization (caveolin 3), scaffolding (ZO-1), trafficking (NDRG4, VAMP2/3) and repair (dysferlin) or acting as a guanine nucleotide exchange factor for Rho-family GTPases (GEFT). -
Based on Network Pharmacology and RNA Sequencing Techniques to Explore the Molecular Mechanism of Huatan Jiangzhuo Decoction for Treating Hyperlipidemia
Hindawi Evidence-Based Complementary and Alternative Medicine Volume 2021, Article ID 9863714, 16 pages https://doi.org/10.1155/2021/9863714 Research Article Based on Network Pharmacology and RNA Sequencing Techniques to Explore the Molecular Mechanism of Huatan Jiangzhuo Decoction for Treating Hyperlipidemia XiaowenZhou ,1 ZhenqianYan ,1 YaxinWang ,1 QiRen ,1 XiaoqiLiu ,2 GeFang ,3 Bin Wang ,4 and Xiantao Li 1 1Laboratory of TCM Syndrome Essence and Objectification, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China 2Guangzhou Sagene Tech Co., Ltd., Guangzhou 510006, China 3College of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha 410208, China 4Shenzhen Traditional Chinese Medicine Hospital, Shenzhen 518000, China Correspondence should be addressed to Xiantao Li; [email protected] Received 22 May 2020; Revised 12 March 2021; Accepted 18 March 2021; Published 12 April 2021 Academic Editor: Jianbo Wan Copyright © 2021 Xiaowen Zhou et al. +is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. Hyperlipidemia, due to the practice of unhealthy lifestyles of modern people, has been a disturbance to a large portion of population worldwide. Recently, several scholars have turned their attention to Chinese medicine (CM) to seek out a lipid-lowering approach with high efficiency and low toxicity. +is study aimed to explore the mechanism of Huatan Jiangzhuo decoction (HTJZD, a prescription of CM) in the treatment of hyperlipidemia and to determine the major regulation pathways and potential key targets involved in the treatment process. -
Gene Expression Networks in the Murine Pulmonary Myocardium Provide Insight Into the Pathobiology of Atrial Fibrillation
INVESTIGATION Gene Expression Networks in the Murine Pulmonary Myocardium Provide Insight into the Pathobiology of Atrial Fibrillation Jordan K. Boutilier,*,†,1 Rhonda L. Taylor,*,†,1,2 Tracy Mann,‡ Elyshia McNamara,*,† Gary J. Hoffman,‡ Jacob Kenny,‡ Rodney J. Dilley,§ Peter Henry,‡ Grant Morahan,*,† Nigel G. Laing,*,† and Kristen J. Nowak*,‡ § *Harry Perkins Institute for Medical Research, †Centre for Medical Research, ‡School of Biomedical Sciences, and Ear Sciences Centre, Faculty of Health and Medical Sciences, University of Western Australia, QEII Medical Centre, Nedlands, 6009, Australia ABSTRACT The pulmonary myocardium is a muscular coat surrounding the pulmonary and caval veins. KEYWORDS Although its definitive physiological function is unknown, it may have a pathological role as the source of pulmonary ectopic beats initiating atrial fibrillation. How the pulmonary myocardium gains pacemaker function is not myocardium clearly defined, although recent evidence indicates that changed transcriptional gene expression networks are eQTL at fault. The gene expression profile of this distinct cell type in situ was examined to investigate underlying atrial fibrillation molecular events that might contribute to atrial fibrillation. Via systems genetics, a whole-lung transcriptome gene network data set from the BXD recombinant inbred mouse resource was analyzed, uncovering a pulmonary cardio- myocyte gene network of 24 transcripts, coordinately regulated by chromosome 1 and 2 loci. Promoter enrichment analysis and interrogation of publicly available ChIP-seq data suggested that transcription of this gene network may be regulated by the concerted activity of NKX2-5, serum response factor, myocyte en- hancer factor 2, and also, at a post-transcriptional level, by RNA binding protein motif 20. -
The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation
International Journal of Molecular Sciences Article The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation Rachel Gingold-Belfer 1,2,3,* , Gania Kessler-Icekson 1,3, Sara Morgenstern 4, Lea Rath-Wolfson 3,4, Romy Zemel 1,3, Doron Boltin 2,3, Zohar Levi 2,3 and Michal Herman-Edelstein 1,3,5 1 The Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva 4941492, Israel; [email protected] (G.K.-I.); [email protected] (R.Z.); [email protected] (M.H.-E.) 2 Rabin Medical Center, Gastroenterology Division, Petah Tikva 4941492, Israel; [email protected] (D.B.); [email protected] (Z.L.) 3 Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; [email protected] 4 Rabin Medical Center, Department of Pathology, Petah Tikva 4941492, Israel; [email protected] 5 Rabin Medical Center, Department of Nephrology, Petah Tikva 4937211, Israel * Correspondence: [email protected]; Tel.: +972-52-2405895 Abstract: Intestinal metaplasia (IM) is an intermediate step in the progression from premalignant to malignant stages of gastric cancer (GC). The Popeye domain containing (POPDC) gene family encodes three transmembrane proteins, POPDC1, POPDC2, and POPDC3, initially described in muscles and later in epithelial and other cells, where they function in cell–cell interaction, and cell migration. POPDC1 and POPDC3 downregulation was described in several tumors, including colon and gastric cancers. We questioned whether IM-to-GC transition involves POPDC gene Citation: Gingold-Belfer, R.; dysregulation. Gastric endoscopic biopsies of normal, IM, and GC patients were examined for Kessler-Icekson, G.; Morgenstern, S.; expression levels of POPDC1-3 and several suggested IM biomarkers, using immunohistochemistry Rath-Wolfson, L.; Zemel, R.; Boltin, and qPCR. -
Discovery and Validation of Sub-Threshold Genome-Wide
RESEARCH ARTICLE Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures Xinchen Wang1,2,3, Nathan R Tucker4, Gizem Rizki1, Robert Mills4, Peter HL Krijger5,6, Elzo de Wit5,6, Vidya Subramanian1, Eric Bartell1, Xinh-Xinh Nguyen4, Jiangchuan Ye4, Jordan Leyton-Mange4, Elena V Dolmatova4, Pim van der Harst7,8, Wouter de Laat5,6, Patrick T Ellinor2,4, Christopher Newton-Cheh2,4,9, David J Milan4*, Manolis Kellis2,3*, Laurie A Boyer1* 1Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 2Broad Institute of MIT and Harvard, Cambridge, United States; 3Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, United States; 4Cardiovascular Research Center, Massachusetts General Hospital, Boston, United States; 5Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, Netherlands; 6University Medical Center Utrecht, Utrecht, Netherlands; 7Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands; 8Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands; 9Center for Human Genetic Research, Massachusetts General Hospital, Boston, United States *For correspondence: dmilan@ Abstract Genetic variants identified by genome-wide association studies explain only a modest mgh.harvard.edu (DJM); manoli@ proportion of heritability, suggesting that meaningful associations lie ’hidden’ below current mit.edu (MK); [email protected] thresholds. Here, we integrate information from association studies with epigenomic maps to (LAB) demonstrate that enhancers significantly overlap known loci associated with the cardiac QT interval and QRS duration. We apply functional criteria to identify loci associated with QT interval that do Competing interests: The not meet genome-wide significance and are missed by existing studies. -
The Popeye Domain Containing Genes and Camp Signaling
J. Cardiovasc. Dev. Dis. 2014, 1, 121-133; doi:10.3390/jcdd1010121 OPEN ACCESS Journal of Cardiovascular Development and Disease ISSN 2308-3425 www.mdpi.com/journal/jcdd Review The Popeye Domain Containing Genes and cAMP Signaling Thomas Brand *, Kar Lai Poon †, Subreena Simrick and Roland F. R. Schindler Harefield Heart Science Centre, National Heart and Lung Institute (NHLI), Imperial College London, Hill End Road, Harefield UB96JH, UK; E-Mails: [email protected] (K.L.P.); [email protected] (S.S.); [email protected] (R.F.R.S.) † Current affiliation: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +44-1895-453 (ext. 826); Fax: +44-1895-828-900. Received: 3 April 2014; in revised form: 6 May 2014 / Accepted: 7 May 2014 / Published: 21 May 2014 Abstract: 3'-5'-cyclic adenosine monophosphate (cAMP) is a second messenger, which plays an important role in the heart. It is generated in response to activation of G-protein-coupled receptors (GPCRs). Initially, it was thought that protein kinase A (PKA) exclusively mediates cAMP-induced cellular responses such as an increase in cardiac contractility, relaxation, and heart rate. With the identification of the exchange factor directly activated by cAMP (EPAC) and hyperpolarizing cyclic nucleotide-gated (HCN) channels as cAMP effector proteins it became clear that a protein network is involved in cAMP signaling. The Popeye domain containing (Popdc) genes encode yet another family of cAMP-binding proteins, which are prominently expressed in the heart. -
Predict AID Targeting in Non-Ig Genes Multiple Transcription Factor
Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 is online at: average * The Journal of Immunology published online 20 March 2013 from submission to initial decision 4 weeks from acceptance to publication Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke, Man Liu, Gur Yaari, Ashraf M. Khalil, Mary M. Tomayko, Mark J. Shlomchik, David G. Schatz and Steven H. Kleinstein J Immunol http://www.jimmunol.org/content/early/2013/03/20/jimmun ol.1202547 Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://www.jimmunol.org/content/suppl/2013/03/20/jimmunol.120254 7.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 26, 2021. Published March 20, 2013, doi:10.4049/jimmunol.1202547 The Journal of Immunology Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke,* Man Liu,†,1 Gur Yaari,‡ Ashraf M. Khalil,x Mary M. Tomayko,{ Mark J. Shlomchik,†,x David G. -
The Popeye Domain Containing Genes and Their Function in Striated Muscle
Journal of Cardiovascular Development and Disease Review The Popeye Domain Containing Genes and Their Function in Striated Muscle Roland F. R. Schindler 1, Chiara Scotton 2, Vanessa French 1, Alessandra Ferlini 2 and Thomas Brand 1,* 1 Developmental Dynamics, Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Hill End Road, Harefield UB9 6JH, UK; [email protected] (R.F.R.S.); [email protected] (V.F.) 2 Department of Medical Sciences, Medical Genetics Unit, University of Ferrara, Ferrara 44121, Italy; [email protected] (C.S.); fl[email protected] (A.F.) * Correspondence: [email protected]; Tel.: +44-189-582-8900 Academic Editors: Robert E. Poelmann and Monique R.M. Jongbloed Received: 26 April 2016; Accepted: 13 June 2016; Published: 15 June 2016 Abstract: The Popeye domain containing (POPDC) genes encode a novel class of cAMP effector proteins, which are abundantly expressed in heart and skeletal muscle. Here, we will review their role in striated muscle as deduced from work in cell and animal models and the recent analysis of patients carrying a missense mutation in POPDC1. Evidence suggests that POPDC proteins control membrane trafficking of interacting proteins. Furthermore, we will discuss the current catalogue of established protein-protein interactions. In recent years, the number of POPDC-interacting proteins has been rising and currently includes ion channels (TREK-1), sarcolemma-associated proteins serving functions in mechanical stability (dystrophin), compartmentalization (caveolin 3), scaffolding (ZO-1), trafficking (NDRG4, VAMP2/3) and repair (dysferlin) or acting as a guanine nucleotide exchange factor for Rho-family GTPases (GEFT). -
Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein