Multifaceted Roles of CD5L in Infectious and Sterile Inflammation
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Systems and Chemical Biology Approaches to Study Cell Function and Response to Toxins
Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by MSc. Yingying Jiang born in Shandong, China Oral-examination: Systems and chemical biology approaches to study cell function and response to toxins Referees: Prof. Dr. Rob Russell Prof. Dr. Stefan Wölfl CONTRIBUTIONS The chapter III of this thesis was submitted for publishing under the title “Drug mechanism predominates over toxicity mechanisms in drug induced gene expression” by Yingying Jiang, Tobias C. Fuchs, Kristina Erdeljan, Bojana Lazerevic, Philip Hewitt, Gordana Apic & Robert B. Russell. For chapter III, text phrases, selected tables, figures are based on this submitted manuscript that has been originally written by myself. i ABSTRACT Toxicity is one of the main causes of failure during drug discovery, and of withdrawal once drugs reached the market. Prediction of potential toxicities in the early stage of drug development has thus become of great interest to reduce such costly failures. Since toxicity results from chemical perturbation of biological systems, we combined biological and chemical strategies to help understand and ultimately predict drug toxicities. First, we proposed a systematic strategy to predict and understand the mechanistic interpretation of drug toxicities based on chemical fragments. Fragments frequently found in chemicals with certain toxicities were defined as structural alerts for use in prediction. Some of the predictions were supported with mechanistic interpretation by integrating fragment- chemical, chemical-protein, protein-protein interactions and gene expression data. Next, we systematically deciphered the mechanisms of drug actions and toxicities by analyzing the associations of drugs’ chemical features, biological features and their gene expression profiles from the TG-GATEs database. -
UNIVERSITY of CALIFORNIA, SAN DIEGO Towards an Understanding of Inflammation in Macrophages a Dissertation Submitted in Partial
UNIVERSITY OF CALIFORNIA, SAN DIEGO Towards an Understanding of Inflammation in Macrophages A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Dawn Xiaobin Zhang Committee in charge: Professor Christopher L. Glass, Chair Professor Jack Bui Professor Ronald M. Evans Professor Richard L. Gallo Professor Joseph L. Witztum 2014 Copyright Dawn Xiaobin Zhang, 2014 All rights reserved. This Dissertation of Dawn Xiaobin Zhang is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2014 iii DEDICATION To my family and the love of my life, Matthew. iv EPIGRAPH How often have I said to you that when you have eliminated the impossible, whatever remains, however improbable, must be the truth? -Sherlock Holmes, From The Sign of the Four, Sir Arthur Conan Doyle v TABLE OF CONTENTS Signature Page ……………………………………………………………….. iii Dedication ……………………………………………………….…………….. iv Epigraph ……………………………………………………………………….. v Table of Contents ………………………………………………………….….. vi List of Figures ………………………………………………………….………. viii List of Tables ………………………………………………………….…….…. x Acknowledgements …………………………………….…………………..…. xi Vita …………………………………….……………………………………..…. xiii Abstract of the Dissertation ………………………………..…………………. xv Chapter I: Introduction: Towards an Understanding of Cell-Specific Function of Signal-Dependent Transcription Factors ……....…....…... 1 A. Abstract ……....…....………………………………...…………….. 2 B. Introduction -
Cellular Entry and Uncoating of Naked and Quasi-Enveloped Human
RESEARCH ARTICLE Cellular entry and uncoating of naked and quasi-enveloped human hepatoviruses Efraı´nE Rivera-Serrano1,2, Olga Gonza´ lez-Lo´ pez1,2, Anshuman Das2, Stanley M Lemon2,3* 1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 2Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 3Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, United States Abstract Many ‘non-enveloped’ viruses, including hepatitis A virus (HAV), are released non- lytically from infected cells as infectious, quasi-enveloped virions cloaked in host membranes. Quasi-enveloped HAV (eHAV) mediates stealthy cell-to-cell spread within the liver, whereas stable naked virions shed in feces are optimized for environmental transmission. eHAV lacks virus- encoded surface proteins, and how it enters cells is unknown. We show both virion types enter by clathrin- and dynamin-dependent endocytosis, facilitated by integrin b1, and traffic through early and late endosomes. Uncoating of naked virions occurs in late endosomes, whereas eHAV undergoes ALIX-dependent trafficking to lysosomes where the quasi-envelope is enzymatically degraded and uncoating ensues coincident with breaching of endolysosomal membranes. Neither virion requires PLA2G16, a phospholipase essential for entry of other picornaviruses. Thus naked and quasi-enveloped virions enter via similar endocytic pathways, but uncoat in different compartments and release their genomes to the cytosol in a manner mechanistically distinct from other Picornaviridae. DOI: https://doi.org/10.7554/eLife.43983.001 *For correspondence: [email protected] Competing interests: The Introduction authors declare that no The presence or absence of an external lipid envelope has featured strongly in the systematic classi- competing interests exist. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice. -
The Viral Oncoproteins Tax and HBZ Reprogram the Cellular Mrna Splicing Landscape
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. 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. The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape Charlotte Vandermeulen1,2,3, Tina O’Grady3, Bartimee Galvan3, Majid Cherkaoui1, Alice Desbuleux1,2,4,5, Georges Coppin1,2,4,5, Julien Olivet1,2,4,5, Lamya Ben Ameur6, Keisuke Kataoka7, Seishi Ogawa7, Marc Thiry8, Franck Mortreux6, Michael A. Calderwood2,4,5, David E. Hill2,4,5, Johan Van Weyenbergh9, Benoit Charloteaux2,4,5,10, Marc Vidal2,4*, Franck Dequiedt3*, and Jean-Claude Twizere1,2,11* 1Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.2Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.3Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.4Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. 5Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.6Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France.7Department of Pathology and Tumor Biology, Kyoto University, Japan.8Unit of Cell and Tissue Biology, GIGA Institute, University of Liege, Liege, Belgium.9Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven, Leuven, Belgium.10Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium.11Lead Contact. *Correspondence: [email protected]; [email protected]; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. -
Pinaud-2021-Frontimmunol-New.P
New insights into biomphalysin gene family diversification in the vector snail Biomphalaria glabrata Silvain Pinaud, Guillaume Tetreau, Pierre Poteaux, Richard Galinier, Cristian Chaparro, Damien Lassalle, Anaïs Portet, Elodie Simphor, Benjamin Gourbal, David Duval To cite this version: Silvain Pinaud, Guillaume Tetreau, Pierre Poteaux, Richard Galinier, Cristian Chaparro, et al.. New insights into biomphalysin gene family diversification in the vector snail Biomphalaria glabrata. Fron- tiers in Immunology, Frontiers, 2021, 12, 10.3389/fimmu.2021.635131. hal-03219003 HAL Id: hal-03219003 https://hal.archives-ouvertes.fr/hal-03219003 Submitted on 6 May 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ORIGINAL RESEARCH published: 01 April 2021 doi: 10.3389/fimmu.2021.635131 New Insights Into Biomphalysin Gene Family Diversification in the Vector Edited by: Roberta Lima Caldeira, Snail Biomphalaria glabrata Oswaldo Cruz Foundation (Fiocruz), Brazil Silvain Pinaud 1,2†‡, Guillaume Tetreau 1,2‡, Pierre Poteaux 1,2, Richard Galinier 1,2, Reviewed by: Cristian Chaparro 1,2, Damien Lassalle 1,2, Anaïs Portet 1,2†, Elodie Simphor 1,2, Coenraad Adema, Benjamin Gourbal 1,2 and David Duval 1,2* University of New Mexico, United States 1 IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France, 2 CNRS, IFREMER, University of Maria G. -
Combined DNA Methylation and Transcriptomic Assessments to Determine a Prognostic Model for PD-1-Negative Hepatocellular Carcinoma
fcell-09-708819 August 9, 2021 Time: 10:32 # 1 ORIGINAL RESEARCH published: 11 August 2021 doi: 10.3389/fcell.2021.708819 Combined DNA Methylation and Transcriptomic Assessments to Determine a Prognostic Model for PD-1-Negative Hepatocellular Carcinoma Lixu Zhu1,2,3,4 and Wenzhi Guo1,2,3,4* 1 Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China, 2 Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China, 3 Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China, 4 Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China Edited by: Ritu Kulshreshtha, Hepatocellular carcinoma (HCC) has the highest incidence and mortality of any Indian Institute of Technology Delhi, malignancy in the world. Immunotherapy has been a major breakthrough for HCC India treatment, but immune checkpoint inhibitors (ICIs) are effective in only a small Reviewed by: Hernando Lopez Bertoni, percentage of HCC patients. In the present study, we screened programmed cell death Johns Hopkins Medicine, protein 1 (PD-1) -negative HCC samples, which are frequently resistant to ICIs, and United States Jingying Zhou, identified their methylation and transcription characteristics through the assessment The Chinese University of Hong Kong, of differential gene methylation and gene expression. We also screened for potential China targeted therapeutic drugs using the DrugBank database. Finally, we used a LASSO *Correspondence: (least absolute shrinkage and selection operator) regression analysis to construct Wenzhi Guo [email protected] a prognostic model based on three differentially methylated and expressed genes (DMEGs). -
Mammalian NPC1 Genes May Undergo Positive Selection And
Al-Daghri et al. BMC Medicine 2012, 10:140 http://www.biomedcentral.com/1741-7015/10/140 RESEARCHARTICLE Open Access Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes Nasser M Al-Daghri1,2,3*, Rachele Cagliani4, Diego Forni4, Majed S Alokail1,2,3, Uberto Pozzoli4, Khalid M Alkharfy1,2,3,5, Shaun Sabico1,2,3, Mario Clerici6,7† and Manuela Sironi4† Abstract Background: The NPC1 gene encodes a protein involved in intracellular lipid trafficking; its second endosomal loop (loop 2) is a receptor for filoviruses. A polymorphism (His215Arg) in NPC1 was associated with obesity in Europeans. Adaptations to diet and pathogens represented powerful selective forces; thus, we analyzed the evolutionary history of the gene and exploited this information for the identification of variants/residues of functional importance in human disease. Methods: We performed phylogenetic analysis, population genetic tests, and genotype-phenotype analysis in a population from Saudi Arabia. Results: Maximum-likelihood ratio tests indicated the action of positive selection on loop 2 and identified three residues as selection targets; these were confirmed by an independent random effects likelihood (REL) analysis. No selection signature was detected in present-day human populations, but analysis of nonsynonymous polymorphisms showed that a variant (Ile642Met, rs1788799) in the sterol sensing domain affects a highly conserved position. This variant and the previously described His215Arg polymorphism were tested for association with obesity and type 2 diabetes (T2D) in a cohort from Saudi Arabia. Whereas no association with obesity was detected, 642Met allele was found to predispose to T2D. A significant interaction was noted with sex (P = 0.041), and stratification on the basis of gender indicated that the association is driven by men (P = 0.0021, OR = 1.5). -
TIMD4 Rs6882076 SNP Is Associated with Decreased Levels Of
Int. J. Med. Sci. 2019, Vol. 16 864 Ivyspring International Publisher International Journal of Medical Sciences 2019; 16(6): 864-871. doi: 10.7150/ijms.31729 Research Paper TIMD4 rs6882076 SNP Is Associated with Decreased Levels of Triglycerides and the Risk of Coronary Heart Disease and Ischemic Stroke Eksavang Khounphinith1, Rui-Xing Yin1,2,3,, Xiao-Li Cao2,3,4, Feng Huang1,2,3, Jin-Zhen Wu1, Hui Li5 1. Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China. 2. Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning 530021, Guangxi, China. 3. Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning 530021, Guangxi, China. 4. Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China. 5. Clinical Laboratory of the Affiliated Cancer Hospital, Guangxi Medical University, 71 Hedi Road, Nanning 530021, Guangxi, China. Corresponding author: Rui-Xing Yin; [email protected] © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2018.11.22; Accepted: 2019.04.03; Published: 2019.06.02 Abstract Background: The T-cell immunoglobulin and mucin domain 4 gene (TIMD4) rs6882076 single nucleotide polymorphism (SNP) has been associated with serum total cholesterol, low-density lipoprotein cholesterol and triglycerides (TG) levels, but the results are inconsistent. -
Functionally Diverse Human T Cells Recognize Non-Microbial Antigens Presented By
RESEARCH ARTICLE Functionally diverse human T cells recognize non-microbial antigens presented by MR1 Marco Lepore1, Artem Kalinichenko1, Salvatore Calogero1, Pavanish Kumar2, Bhairav Paleja2, Mathias Schmaler1, Vipin Narang2, Francesca Zolezzi2, Michael Poidinger2,3, Lucia Mori1,2, Gennaro De Libero1,2* 1Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland; 2Singapore Immunology Network, A*STAR, Singapore, Singapore; 3Singapore Institute for Clinical Sciences, A*STAR, Singapore, Singapore Abstract MHC class I-related molecule MR1 presents riboflavin- and folate-related metabolites to mucosal-associated invariant T cells, but it is unknown whether MR1 can present alternative antigens to other T cell lineages. In healthy individuals we identified MR1-restricted T cells (named MR1T cells) displaying diverse TCRs and reacting to MR1-expressing cells in the absence of microbial ligands. Analysis of MR1T cell clones revealed specificity for distinct cell-derived antigens and alternative transcriptional strategies for metabolic programming, cell cycle control and functional polarization following antigen stimulation. Phenotypic and functional characterization of MR1T cell clones showed multiple chemokine receptor expression profiles and secretion of diverse effector molecules, suggesting functional heterogeneity. Accordingly, MR1T cells exhibited distinct T helper-like capacities upon MR1-dependent recognition of target cells expressing physiological levels of surface MR1. These data extend the role of -
Apoptosis Inhibitor of Macrophage (AIM) Is Required for Obesity-Associated Recruitment of Inflammatory Macrophages Into Adipose Tissue
Apoptosis inhibitor of macrophage (AIM) is required for obesity-associated recruitment of inflammatory macrophages into adipose tissue Jun Kurokawaa, Hiromichi Naganoa, Osamu Oharab, Naoto Kubotac, Takashi Kadowakic, Satoko Araia, and Toru Miyazakia,1 aLaboratory of Molecular Biomedicine for Pathogenesis, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan; bDepartment of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; and cDepartment of Internal Medicine, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan Edited* by Tadatsugu Taniguchi, University of Tokyo, Tokyo, Japan, and approved June 14, 2011 (received for review February 3, 2011) Infiltration of inflammatory macrophages into adipose tissues with macrophages against different types of apoptosis-inducing stimuli the progression of obesity triggers insulin resistance and obesity- (13). AIM is a direct target for regulation by nuclear receptor liver related metabolic diseases. We recently reported that macrophage- X receptor/retinoid X receptor (LXR/RXR) heterodimers (15, derived apoptosis inhibitor of macrophage (AIM) protein is in- 16) and is solely produced by tissue macrophages. As a secreted molecule, AIM is detected in both human and mouse blood at creased in blood in line with obesity progression and is incorporated – into adipocytes, thereby inducing lipolysis in adipose tissue. Here various levels (13, 16 19) and increases in blood with the pro- we show that such a response is required for the recruitment of gression of obesity in mice fed a high-fat diet (HFD) (14). The augmented blood AIM induced lipolysis, as evident by the fact adipose tissue macrophages.