Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases
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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Review Article Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases
Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 601361, 16 pages http://dx.doi.org/10.1155/2013/601361 Review Article Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases Hsiang Cheng Chi,1 Cheng-Yi Chen,1 Ming-Ming Tsai,2 Chung-Ying Tsai,1 and Kwang-Huei Lin1 1 Department of Biochemistry, School of Medicine, Chang-Gung University, Taoyuan 333, Taiwan 2 Department of Nursing, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan Correspondence should be addressed to Kwang-Huei Lin; [email protected] Received 4 February 2013; Revised 14 May 2013; Accepted 28 May 2013 Academic Editor: Elena Orlova Copyright © 2013 Hsiang Cheng Chi et al. This 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. Thyroid hormones (THs) are potent mediators of several physiological processes, including embryonic development, cellular differentiation, metabolism, and cell growth. Triiodothyronine3 (T ) is the most biologically active TH form. Thyroid hormone receptors (TRs) belong to the nuclear receptor superfamily and mediate the biological functions of T3 via transcriptional regulation. TRs generally form heterodimers with the retinoid X receptor (RXR) and regulate target genes upon T3 stimulation. Research over the past few decades has revealed that disruption of cellular TH signaling triggers chronic liver diseases, including alcoholic or nonalcoholic fatty liver disease and hepatocellular carcinoma (HCC). Animal model experiments and epidemiologic studies to date imply close associations between high TH levels and prevention of liver disease. -
UC San Francisco Electronic Theses and Dissertations
UCSF UC San Francisco Electronic Theses and Dissertations Title Protease-activated receptor-2 (PAR2) in epithelial biology Permalink https://escholarship.org/uc/item/2b49z9sm Author Barker, Adrian Publication Date 2013 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California ii To my nephews for being the light of my life To my parents for showing me the way To Philip, your love knows no bounds iii ACKNOWLEDGEMENTS Wow, what a journey! First, I’d like to thank my mentor and advisor, Dr. Shaun Coughlin, for giving me the encouragement and wisdom that I needed to succeed in your lab. One thing I will take away from this experience is how powerful collaboration can be. Having encountered labs that have not been willing to collaborate, you are an inspiration and role-model in your willingness to share your resources and knowledge with the scientific community and the academic world is a better place because of it. To my thesis committee members, Dr. Charly Craik & Dr. Zena Werb. Thank you for the conversations and encouragement. You have given me motivation and kind words in pivotal moments in my career and they have helped me tremendously; more than you’ll ever know. To all the members of the Coughlin lab. We’ve been through so much together, and many of you have been around since the first day I stepped foot into the lab. Extra special thanks to: Dr. Hilary Clay, for help with the zebrafish work and for fighting for my project when it felt like no one else cared; Dr. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
The Study of TMPRSS-ERG Gene Fusion in Prostate Cancer in Pakistan
CAPITAL UNIVERSITY OF SCIENCE AND TECHNOLOGY, ISLAMABAD The Study of TMPRSS-ERG Gene Fusion in Prostate Cancer in Pakistan by Samra Manzoor A thesis submitted in partial fulfillment for the degree of Master of Science in the Faculty of Health and Life Sciences Department of Biosciences 2018 i Copyright c 2018 by Samra Manzoor All rights reserved. No part of this thesis may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, by any information storage and retrieval system without the prior written permission of the author. ii This thesis is dedicated to my husband Atif Mansoor Khan and my brother Naeem Ahmad who's support, encouragement, and constant love have sustained me throughout my life. I would like to dedicate this thesis to my best friend, Anila Sajjad and my kids (Shanzay and Aniq). Thank you for always believing in me, even when I did not, and cheering me on until the end. Words cannot express how much I love you all and appreciate everything you all have done for me. CAPITAL UNIVERSITY OF SCIENCE & TECHNOLOGY ISLAMABAD CERTIFICATE OF APPROVAL The Study of TMPRSS-ERG Gene Fusion in Prostate Cancer in Pakistan by Samra Manzoor MBS 163004 THESIS EXAMINING COMMITTEE S. No. Examiner Name Organization (a) External Examiner Dr. Maria Shabbir NUST, Islamabad (b) Internal Examiner Dr. Shaukat Iqbal Malik CUST, Islamabad (c) Supervisor Dr. Sahar Fazal CUST, Islamabad Dr. Sahar Fazal Thesis Supervisor October, 2018 Dr. Sahar Fazal Dr. Muhammad Abdul Qadir Head Dean Dept. of Biosciences Faculty of Health and Life Sciences October, 2018 October, 2018 iv Author's Declaration I, Samra Manzoor hereby state that my MS thesis titled \The Study of TMPRSS-ERG Gene Fusion in Prostate Cancer in Pakistan" is my own work and has not been submitted previously by me for taking any degree from Capital University of Science and Technology, Islamabad or anywhere else in the country/abroad. -
A Genomic Analysis of Rat Proteases and Protease Inhibitors
A genomic analysis of rat proteases and protease inhibitors Xose S. Puente and Carlos López-Otín Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain Send correspondence to: Carlos López-Otín Departamento de Bioquímica y Biología Molecular Facultad de Medicina, Universidad de Oviedo 33006 Oviedo-SPAIN Tel. 34-985-104201; Fax: 34-985-103564 E-mail: [email protected] Proteases perform fundamental roles in multiple biological processes and are associated with a growing number of pathological conditions that involve abnormal or deficient functions of these enzymes. The availability of the rat genome sequence has opened the possibility to perform a global analysis of the complete protease repertoire or degradome of this model organism. The rat degradome consists of at least 626 proteases and homologs, which are distributed into five catalytic classes: 24 aspartic, 160 cysteine, 192 metallo, 221 serine, and 29 threonine proteases. Overall, this distribution is similar to that of the mouse degradome, but significatively more complex than that corresponding to the human degradome composed of 561 proteases and homologs. This increased complexity of the rat protease complement mainly derives from the expansion of several gene families including placental cathepsins, testases, kallikreins and hematopoietic serine proteases, involved in reproductive or immunological functions. These protease families have also evolved differently in the rat and mouse genomes and may contribute to explain some functional differences between these two closely related species. Likewise, genomic analysis of rat protease inhibitors has shown some differences with the mouse protease inhibitor complement and the marked expansion of families of cysteine and serine protease inhibitors in rat and mouse with respect to human. -
Transcriptional Profiling of the Murine Airway Response to Acute Ozone Exposure
bioRxiv preprint doi: https://doi.org/10.1101/660316; this version posted June 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Transcriptional profiling of the murine airway response to acute ozone exposure Adelaide Tovar,*,†,2 Gregory J. Smith,*,‡,2 Joseph M. Thomas,* Jack R. Harkema,§ and Samir N. P. Kelada*,†,‡,1 *Department of Genetics, †Curriculum in Genetics & Molecular Biology, ‡Curriculum in Toxicology & Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; §Department of Pathology & Diagnostic Investigation, Michigan State University, East Lansing, MI, USA. 1To whom correspondence should be addressed at Department of Genetics, The University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27599, USA. E-mail: [email protected]. 2These authors contributed equally to this study. bioRxiv preprint doi: https://doi.org/10.1101/660316; this version posted June 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Exposure to ambient ozone (O3) pollution causes airway inflammation, epithelial injury, and decreased lung function. Long-term exposure is associated with increased mortality and exacerbations of respiratory conditions. While the adverse health effects of O3 exposure have been thoroughly described, less is known about the molecular processes that drive these outcomes. -
Tgfβ Suppresses Type 2 Immunity to Cancer Ming Liu1
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.04.977629; this version posted March 5, 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. TGFβ Suppresses Type 2 Immunity to Cancer Ming Liu1, Fengshen Kuo2, Kristelle J. Capistrano1, Davina Kang1, Briana G. Nixon1,3, Wei Shi1, Chun Chou1, Mytrang H. Do1,3, Shun Li1, Efstathios G. Stamatiades1, Yingbei Chen4, James J. 3,5 3,6 7 2 1,3* Hsieh , A. Ari Hakimi , Ichiro Taniuchi , Timothy A. Chan , Ming O. Li 1Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065 2Immunogenomics & Precision Oncology Platform (IPOP), Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065 3Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA 10065 4Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065 5Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63110 6Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center New York, NY USA, 10065 7Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan 230-0045 * Correspondence: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.03.04.977629; this version posted March 5, 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. Summary The immune system employs two distinct defense strategies against infections: pathogen elimination typified by type 1 immunity, and pathogen containment exemplified by type 2 immunity in association with tissue repair. -
Sequence and Evolutionary Analysis of the Human Trypsin Subfamily of Serine Peptidases
Biochimica et Biophysica Acta 1698 (2004) 77–86 www.bba-direct.com Sequence and evolutionary analysis of the human trypsin subfamily of serine peptidases George M. Yousefa,b, Marc B. Elliotta, Ari D. Kopolovica, Eman Serryc, Eleftherios P. Diamandisa,b,* a Department of Pathology and Laboratory Medicine, Division of Clinical Biochemistry, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5 b Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5G 1L5 c Faculty of Medicine, Department of Medical Biochemistry, Menoufiya University, Egypt Received 3 June 2003; received in revised form 1 October 2003; accepted 27 October 2003 Abstract Serine peptidases (SP) are peptidases with a uniquely activated serine residue in the substrate-binding site. SP can be classified into clans with distinct evolutionary histories and each clan further subdivided into families. We analyzed 79 proteins representing the S1A subfamily of human SP, obtained from different databases. Multiple alignment identified 87 highly conserved amino acid residues. In most cases of substitution, a residue of similar character was inserted, implying that the overall character of the local region was conserved. We also identified several conserved protein motifs. 7–13 cysteine positions, potentially forming disulfide bridges, were also found to be conserved. Most members are secreted as inactive (pro) forms with a trypsin-like cleavage site for activation. Substrate specificity was predicted to be trypsin-like for most members, with few chymotrypsin-like proteins. Phylogenetic analysis enabled us to classify members of the S1A subfamily into structurally related groups; this might also help to functionally sort members of this subfamily and give an idea about their possible functions. -
Identification of Novel Tumor Suppressor Proteases by Degradome Profiling of Colorectal Carcinomas
www.impactjournals.com/oncotarget/ Oncotarget, November, Vol.4, No 11 Identification of novel tumor suppressor proteases by degradome profiling of colorectal carcinomas Julia M. Fraile1, Gonzalo R. Ordóñez1, Pedro M. Quirós1, Aurora Astudillo2, José A. Galván3, Dolors Colomer4, Carlos López-Otín1, José M.P. Freije1 and Xose S. Puente1 1 Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain, 2 Servicio de Anatomía Patológica, Instituto Universitario de Oncología, Hospital Universitario Central de Asturias, Oviedo, Spain, 3 Banco de Tumores, Instituto Universitario de Oncología, Hospital Universitario Central de Asturias, Oviedo, Spain, 4 Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain. Correspondence to: Xose S. Puente, email: [email protected] Correspondence to: Jose M.P. Freije , email: [email protected] Keywords: proteolysis, metastasis, invasion, cancer Received: August 20, 2013 Accepted: September 13, 2013 Published: September 15, 2013 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT: Proteolytic enzymes play important roles during tumor development and progression through their ability to promote cell growth or by facilitating the invasion of surrounding tissues. The human genome contains more than 570 protease-coding genes, many of them forming functional networks, which has forced the use of global strategies for the analysis of this group of enzymes. In this study, we have designed a new quantitative PCR-based device for profiling the entire degradome in human malignancies. We have used this method to evaluate protease expression levels in colorectal carcinomas with the finding that most proteases with altered expression in these tumors exert their function in the extracellular compartment. -
Microarray-Based Identification and RT-PCR Test
BMC Cancer BioMed Central Research article Open Access Microarray-based identification and RT-PCR test screening for epithelial-specific mRNAs in peripheral blood of patients with colon cancer Rossella Solmi*1, Giampaolo Ugolini2, Giancarlo Rosati2, Simone Zanotti2, Mattia Lauriola1, Isacco Montroni2, Marco del Governatore2, Antonello Caira2, Mario Taffurelli2, Donatella Santini4, Domenico Coppola3, Lia Guidotti1, Paolo Carinci1 and Pierluigi Strippoli1 Address: 1Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, I-40126 Bologna, Italy, 2Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy, 3"H.Lee Moffit" Cancer Center and Research Institute, University of South Florida, Tampa, FL, USA and 4Department of Pathology, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy Email: Rossella Solmi* - [email protected]; Giampaolo Ugolini - [email protected]; Giancarlo Rosati - [email protected]; Simone Zanotti - [email protected]; Mattia Lauriola - [email protected]; Isacco Montroni - [email protected]; Marco del Governatore - [email protected]; Antonello Caira - [email protected]; Mario Taffurelli - [email protected]; Donatella Santini - [email protected]; Domenico Coppola - [email protected]; Lia Guidotti - [email protected]; Paolo Carinci - [email protected]; Pierluigi Strippoli - [email protected] * Corresponding author Published: 20 October 2006 Received: 02 May 2006 Accepted: 20 October 2006 BMC Cancer 2006, 6:250 doi:10.1186/1471-2407-6-250 This article is available from: http://www.biomedcentral.com/1471-2407/6/250 © 2006 Solmi et al; licensee BioMed Central Ltd. -
Analyzing the Role of Genetics and Genomics in Cardiovascular Disease
IT'S COMPLICATED: ANALYZING THE ROLE OF GENETICS AND GENOMICS IN CARDIOVASCULAR DISEASE by JEFFREY HSU Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Adviser: Dr. Jonathan D Smith Department of Molecular Medicine CASE WESTERN RESERVE UNIVERSITY January 2014 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of: Jeffrey Hsu candidate for the Doctor of Philosophy degree*. Thomas LaFramboise Thesis Committee Chair Mina Chung David Van Wagoner David Serre Jonathan D Smith Date: 5/24/2013 We also certify that written approval has been obtained for any proprietary material contained therein. i Contents Abstract 1 Acknowledgments 3 1 Introduction 4 1.1 Heritability of cardiovascular diseases . .4 1.2 Genome wide era and complex diseases . .7 1.3 Functional genomics of disease associated loci . .8 1.4 Animal models for functional studies of CAD . 13 2 Genetic-Genomic Replication to Identify Candidate Mouse Atheroscle- rosis Modifier Genes 14 2.1 Introduction . 14 2.2 Methods . 15 2.2.1 Mouse and cell studies . 15 2.3 Results . 17 2.3.1 Atherosclerosis QTL replication in a new cross . 17 2.3.2 Protein coding differences between AKR and DBA mice resid- ing in ATH QTLs . 22 2.3.3 eQTL in bone marrow derived macrophages and endothelial cells 30 2.3.4 Macrophage eQTL replication between different crosses and dif- ferent platforms . 44 3 Transcriptome Analysis of Genes Regulated by Cholesterol Loading in Two Strains of Mouse Macrophages Associates Lysosome Pathway and ER Stress Response with Atherosclerosis Susceptibility 51 3.1 Introduction .