Signal Adaptor DAP10 Associates with MDL-1 and Triggers Osteoclastogenesis in Cooperation with DAP12
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An Interface-Based Prediction of Membrane Protein-Protein Interactions
bioRxiv preprint doi: https://doi.org/10.1101/871590; this version posted July 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. TransINT: an interface-based prediction of membrane protein-protein interactions Khazen, G.1,*, Gyulkhandanian, A.2, Issa, T.1 and Maroun, R.C. 2,* 1 Computer Science and Mathematics Department, Lebanese American University, Byblos-Lebanon 2 Inserm U1204/ Université d’Evry/Université Paris-Saclay/ Structure-Activité des Biomolécules Normales et Pathologiques 91025 Evry France. ABSTRACT Membrane proteins account for about one-third of the proteomes of organisms and include structural proteins, channels, and receptors. The mutual interactions they establish in the membrane play crucial roles in organisms, as they are behind many processes such as cell signaling and protein function. Because of their number and diversity, these proteins and their macromolecular complexes, along with their physical interfaces represent potential pharmacological targets par excellence for a variety of diseases, with very important implications for the design and discovery of new drugs or peptides modulating or inhibiting the interaction. Yet, structural data coming from experiments is very scarce for this family of proteins and the study of those proteins at the molecular level goes necessarily through extraction from cell membranes, a step that reveals itself noxious/harmful for their structure and function. To overcome this problem, we propose a computational approach for the prediction of alpha-helical transmembrane protein higher-order structures through data mining, sequence analysis, motif search, extraction, identification and characterization of the amino acid residues at the interface of the complexes. -
Distinct Gene Expression Pathways in Islets from Individuals with Short- and Long
Mastracci Teresa (Orcid ID: 0000-0003-1956-1951) Distinct Gene Expression Pathways in Islets from Individuals with Short- and Long- Duration Type 1 Diabetes Teresa L. Mastracci1,2*, Jean-Valery Turatsinze3, Benita K. Book4, Ivan A. Restrepo5, Michael J. Pugia1, Eric A. Wiebke4, Mark D. Pescovitz4, Decio L. Eizirik3 and Raghavendra G. Mirmira2,5,6,7 1 Indiana Biosciences Research Institute, Indianapolis, IN, USA. 2 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA. 3 ULB Center for Diabetes Research, Universite Libre de Bruxelles, Brussels, Belgium. 4 Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA. 5 Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA. 6 Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA. 7 Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. * Corresponding Author: Teresa L. Mastracci, 1345 W. 16th St., Suite 300, Indianapolis, IN 46202 USA. E-mail: [email protected] Running Title: Functional Genomics Analysis of T1D Islets Abstract word count: 272 This is the author's manuscript of the article published in final edited form as: Mastracci, T. L., Turatsinze, J.-V., Book, B. K., Restrepo, I. A., Pugia, M. J., Wiebke, E. A., … Mirmira, R. G. (n.d.). Distinct Gene Expression Pathways in Islets from Individuals with Short‐ and Long‐Duration Type 1 Diabetes. Diabetes, Obesity and Metabolism. https://doi.org/10.1111/dom.13298 Main text word count: 2730 References: 27; Tables: 2; Figures: 3 Abstract Aims: Our current understanding of the pathogenesis of type 1 diabetes (T1D) arose in large part from studies using the non-obese diabetic (NOD) mouse model. -
Supplementary Materials
Supplementary Materials Supplemental Figure S1. Distinct difference in expression of 576 sensome genes comparing cortex versus microglia. (A) This heatmap shows all 576 sensome candidate genes ordered by DE and with the left column shows if the gene is present in the “Hickman et al. sensome” Supplemental Figure S2. Mouse sensome and human sensome genes categorized by group. (A) Bar graph showing the number of mouse and human sensome genes per group (Cell-Cell Interactions, Chemokine and related receptors, Cytokine receptors, ECM receptors, Endogenous ligands receptors, sensors and transporters, Fc receptors, Pattern recognition and related receptors, Potential sensors but no known ligands and Purinergic and related receptors). Supplementary Figure S3. Overlap of ligands recognized by microglia sensome (A) Overlap between the ligands of the receptors from respectively human and mouse core sensome was shown using Venn Diagrams. (B) Ligands of human and mouse receptors categorized in groups (Glycoproteins, Cytokines, Immunoglobulin, Amino acids, Carbohydrates, Electrolytes, Lipopeptides, Chemokines, Neuraminic acids, Nucleic acids, Receptors, Lipids, Fatty acids, Leukotrienes, Hormones, Steroids and Phospholipids) and spread of different groups shown as parts of whole again highlighting that the distribution of ligands what the human and mouse sensome genes can sense (Categorization of ligands in Supplementary Table S1). Supplementary Figure S4. Microglia core sensome expression during aging. (A) Two-log fold change of microglia core sensome genes in aging mice derived from Holtman et al. [12]. (B) Accelerated aging model (ERCC1), with impaired DNA repair mechanism, shows changes of microglia core sensome expression [12]. (C) Microglia core sensome expression during aging in human derived from Olah et al. -
A Transcriptomic Atlas of Aged Human Microglia
ARTICLE DOI: 10.1038/s41467-018-02926-5 OPEN A transcriptomic atlas of aged human microglia Marta Olah1,2, Ellis Patrick 3, Alexandra-Chloe Villani2,4, Jishu Xu 2, Charles C. White2, Katie J. Ryan5, Paul Piehowski 6, Alifiya Kapasi6, Parham Nejad2, Maria Cimpean 5, Sarah Connor1,2, Christina J. Yung1, Michael Frangieh5, Allison McHenry5, Wassim Elyaman1,2, Vlad Petyuk 6, Julie A. Schneider7, David A. Bennett7, Philip L. De Jager 1,2 & Elizabeth M. Bradshaw1,2 With a rapidly aging global human population, finding a cure for late onset neurodegenerative diseases has become an urgent enterprise. However, these efforts are hindered by the lack of 1234567890():,; understanding of what constitutes the phenotype of aged human microglia—the cell type that has been strongly implicated by genetic studies in the pathogenesis of age-related neuro- degenerative disease. Here, we establish the set of genes that is preferentially expressed by microglia in the aged human brain. This HuMi_Aged gene set captures a unique phenotype, which we confirm at the protein level. Furthermore, we find this gene set to be enriched in susceptibility genes for Alzheimer’s disease and multiple sclerosis, to be increased with advancing age, and to be reduced by the protective APOEε2 haplotype. APOEε4 has no effect. These findings confirm the existence of an aging-related microglial phenotype in the aged human brain and its involvement in the pathological processes associated with brain aging. 1 Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York City, NY 10032, USA. 2 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA. -
Transcriptomic Gene Signatures Associated with Persistent Airflow Limitation
Hekking et al Revised manuscript ERJ-02298-2016 Transcriptomic gene signatures associated with persistent airflow limitation in patients with severe asthma P.P. Hekking1, M.J. Loza2, S. Pavlidis3, B. De Meulder4, D. Lefaudeux4, F. Baribaud2, C. Auffray4, A.H. Wagener1, P. Brinkman1, R. Lutter1, A.T. Bansal5, A.R. Sousa6, S. Bates6, Y. Pandis3, L.J. Fleming3, D.E. Shaw7, S.J. Fowler8, Y. Guo3, A. Meiser3, K. Sun3, J. Corfield9, P. Howarth10, E.H. Bel1, I.M. Adcock11, K.F. Chung11, R. Djukanovic10, P.J. Sterk1, and the U-BIOPRED Study Group* 1: Respiratory Medicine, Academic Medical Centre, Amsterdam, the Netherlands; 2: Janssen research and development; Johnsen & Johnsen, Springhouse, US; 3: Data Science Institute, Imperial College, London, UK; 4: European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS- UCBL-INSERM, Université de Lyon, France; 5: Acclarogen Ltd, Cambridge, UK; 6: Discovery Medicine, GlaxoSmithKline, Brentford, UK; 7: Respiratory Research Unit, University of Nottingham, UK; 8: Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester Academic Health Sciences Centre, UK; 9: Areteva, Nottingham, UK; 10: NIHR Southampton Centre for Biomedical Research, University of Southampton, UK; 11: National Heart & Lung institute - Imperial College, London, UK;*A list of the U-BIOPRED study group can be found in the online supplement Corresponding author: Pieter-Paul Hekking, Academic Medical Centre (AMC), Department of Respiratory Medicine, F5-260 1105 AZ, Amsterdam, the Netherlands Telephone: +31 (0) 20 566 1660 Fax: +31 (0) 20 566 9001 E-mail: [email protected] 1 Hekking et al Take home message Persistent airflow limitation in severe asthma is associated with a mechanism in which IL-13 and remodeling are involved. -
Supplementary Figure 1. Network Map Associated with Upregulated Canonical Pathways Shows Interferon Alpha As a Key Regulator
Supplementary Figure 1. Network map associated with upregulated canonical pathways shows interferon alpha as a key regulator. IPA core analysis determined interferon-alpha as an upstream regulator in the significantly upregulated genes from RNAseq data from nasopharyngeal swabs of COVID-19 patients (GSE152075). Network map was generated in IPA, overlaid with the Coronavirus Replication Pathway. Supplementary Figure 2. Network map associated with Cell Cycle, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair shows relationships among significant canonical pathways. Significant pathways were identified from pathway analysis of RNAseq from PBMCs of COVID-19 patients. Coronavirus Pathogenesis Pathway was also overlaid on the network map. The orange and blue colors in indicate predicted activation or predicted inhibition, respectively. Supplementary Figure 3. Significant biological processes affected in brochoalveolar lung fluid of severe COVID-19 patients. Network map was generated by IPA core analysis of differentially expressed genes for severe vs mild COVID-19 patients in bronchoalveolar lung fluid (BALF) from scRNA-seq profile of GSE145926. Orange color represents predicted activation. Red boxes highlight important cytokines involved. Supplementary Figure 4. 10X Genomics Human Immunology Panel filtered differentially expressed genes in each immune subset (NK cells, T cells, B cells, and Macrophages) of severe versus mild COVID-19 patients. Three genes (HLA-DQA2, IFIT1, and MX1) were found significantly and consistently differentially expressed. Gene expression is shown per the disease severity (mild, severe, recovered) is shown on the top row and expression across immune cell subsets are shown on the bottom row. Supplementary Figure 5. Network map shows interactions between differentially expressed genes in severe versus mild COVID-19 patients. -
NKG2D Ligands in Tumor Immunity
Oncogene (2008) 27, 5944–5958 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $32.00 www.nature.com/onc REVIEW NKG2D ligands in tumor immunity N Nausch and A Cerwenka Division of Innate Immunity, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany The activating receptor NKG2D (natural-killer group 2, activated NK cells sharing markers with dendritic cells member D) and its ligands play an important role in the (DCs), which are referred to as natural killer DCs NK, cd þ and CD8 þ T-cell-mediated immune response to or interferon (IFN)-producing killer DCs (Pillarisetty tumors. Ligands for NKG2D are rarely detectable on the et al., 2004; Chan et al., 2006; Taieb et al., 2006; surface of healthy cells and tissues, but are frequently Vosshenrich et al., 2007). In addition, NKG2D is expressed by tumor cell lines and in tumor tissues. It is present on the cell surface of all human CD8 þ T cells. evident that the expression levels of these ligands on target In contrast, in mice, expression of NKG2D is restricted cells have to be tightly regulated to allow immune cell to activated CD8 þ T cells (Ehrlich et al., 2005). In activation against tumors, but at the same time avoid tumor mouse models, NKG2D þ CD8 þ T cells prefer- destruction of healthy tissues. Importantly, it was recently entially accumulate in the tumor tissue (Gilfillan et al., discovered that another safeguard mechanism controlling 2002; Choi et al., 2007), suggesting that the activation via the receptor NKG2D exists. It was shown NKG2D þ CD8 þ T-cell population comprises T cells that NKG2D signaling is coupled to the IL-15 receptor involved in tumor cell recognition. -
COVID-19: a Drug Repurposing and Biomarker Identification by Using Comprehensive Gene-Disease Associations Through Protein-Protein Interaction Network Analysis
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 30 March 2020 doi:10.20944/preprints202003.0440.v1 COVID-19: A drug repurposing and biomarker identification by using comprehensive gene-disease associations through protein-protein interaction network analysis Suresh Kumar* Department of Diagnostic and Allied Health Science, Faculty of Health & Life Sciences, Management & Science University, 40100 Shah Alam, Selangor, Malaysia *Corresponding author Suresh Kumar, PhD Department of Diagnostic and Allied Health Science, Faculty of Health & Life Sciences Management & Science University, 40100 Shah Alam, Selangor, Malaysia Email: [email protected] Abstract COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. -
During Intestinal Inflammation Functions Contributes to Regulatory
Reprogramming of Monocytes by GM-CSF Contributes to Regulatory Immune Functions during Intestinal Inflammation This information is current as Jan Däbritz, Toni Weinhage, Georg Varga, Timo Wirth, of October 2, 2021. Karoline Walscheid, Anne Brockhausen, David Schwarzmaier, Markus Brückner, Matthias Ross, Dominik Bettenworth, Johannes Roth, Jan M. Ehrchen and Dirk Foell J Immunol published online 4 February 2015 http://www.jimmunol.org/content/early/2015/02/04/jimmun ol.1401482 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2015/02/04/jimmunol.140148 Material 2.DCSupplemental http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on October 2, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published February 4, 2015, doi:10.4049/jimmunol.1401482 The Journal of Immunology Reprogramming of Monocytes by GM-CSF Contributes to Regulatory Immune Functions during Intestinal Inflammation Jan Da¨britz,*,†,‡,x,1 Toni Weinhage,*,1 Georg Varga,* Timo Wirth,* Karoline Walscheid,* Anne Brockhausen,{,‖ David Schwarzmaier,* Markus Bruckner,€ # Matthias Ross,# Dominik Bettenworth,# Johannes Roth,†,‖ Jan M. -
Program in Human Neutrophils Fails To
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 is online at: average * The Journal of Immunology Anaplasma phagocytophilum , 20 of which you can access for free at: 2005; 174:6364-6372; ; from submission to initial decision 4 weeks from acceptance to publication J Immunol doi: 10.4049/jimmunol.174.10.6364 http://www.jimmunol.org/content/174/10/6364 Insights into Pathogen Immune Evasion Mechanisms: Fails to Induce an Apoptosis Differentiation Program in Human Neutrophils Dori L. Borjesson, Scott D. Kobayashi, Adeline R. Whitney, Jovanka M. Voyich, Cynthia M. Argue and Frank R. DeLeo cites 28 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2005/05/03/174.10.6364.DC1 This article http://www.jimmunol.org/content/174/10/6364.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* • Why • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Insights into Pathogen Immune Evasion Mechanisms: Anaplasma phagocytophilum Fails to Induce an Apoptosis Differentiation Program in Human Neutrophils1 Dori L. -
A Noncanonical Function of the Telomerase RNA Component in Human Embryonic Stem Cells
Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Winter 12-15-2019 A Noncanonical Function of the Telomerase RNA Component in Human Embryonic Stem Cells Kirsten Ann Brenner Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Cell Biology Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Brenner, Kirsten Ann, "A Noncanonical Function of the Telomerase RNA Component in Human Embryonic Stem Cells" (2019). Arts & Sciences Electronic Theses and Dissertations. 1990. https://openscholarship.wustl.edu/art_sci_etds/1990 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Molecular Genetics and Genomics Dissertation Examination Committee: Luis Batista, Chair Sheila Stewart, Co-Chair Sergei Djuranovic Todd Fehniger James Skeath Christopher Sturgeon A Noncanonical Function of the Telomerase RNA Component in Human Embryonic Stem Cells by Kirsten Ann Brenner A dissertation presented to The Graduate School of Washington University in partial fulfillment of the requirements for -
Signalling Through C-Type Lectin Receptors
REVIEWS Signalling through C-type lectin receptors: shaping immune responses Teunis B. H. Geijtenbeek and Sonja I. Gringhuis Abstract | C‑type lectin receptors (CLRs) expressed by dendritic cells are crucial for tailoring immune responses to pathogens. Following pathogen binding, CLRs trigger distinct signalling pathways that induce the expression of specific cytokines which determine T cell polarization fates. Some CLRs can induce signalling pathways that directly activate nuclear factor‑κB, whereas other CLRs affect signalling by Toll‑like receptors. Dissecting these signalling pathways and their effects on host immune cells is essential to understand the molecular mechanisms involved in the induction of adaptive immune responses. In this Review we describe the role of CLR signalling in regulating adaptive immunity and immunopathogenesis and discuss how this knowledge can be harnessed for the development of innovative vaccination approaches. Dendritic cells (DCs) are located throughout the body Triggering of several PRRs simultaneously can induce T helper (TH) cell A T cell subset that secretes a to capture and internalize invading pathogens, and diverse innate immune responses, which provides the distinct set of cytokines after subsequently process and present antigen on MHC diversity that is required to shape an effective adaptive activation, which occurs class I and class II molecules to CD8+ and CD4+ T cells, immune response. Distinct pathogens express different through the ligation of the T cell respectively1. Antigen presentation by DCs is in itself PAMPs, and the combination of these PAMPs functions receptor with its cognate ligand (peptide–MHC complex), not sufficient to induce effective T cell responses against as a fingerprint that triggers a specific set of PRRs, lead‑ + together with the recognition of pathogens.