Keratin 12-Deficient Mice Have Fragile Corneal Epithelia
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Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
140503 IPF Signatures Supplement Withfigs Thorax
Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network. -
75 2. INTRODUCTION Triple-Negative Breast Cancer (TNBC)
[Frontiers in Bioscience, Scholar, 11, 75-88, March 1, 2019] The persisting puzzle of racial disparity in triple negative breast cancer: looking through a new lens Chakravarthy Garlapati1, Shriya Joshi1, Bikram Sahoo1, Shobhna Kapoor2, Ritu Aneja1 1Department of Biology, Georgia State University, Atlanta, GA, USA, 2Department of Chemistry, Indian Institute of Technology Bombay, Powai, India TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Dissecting the TNBC racially disparate burden 3.1. Does race influence TNBC onset and progression? 3.2. Tumor microenvironment in TNBC and racial disparity 3.3. Differential gene signatures and pathways in racially distinct TNBC 3.4. Our Perspective: Looking racial disparity through a new lens 4. Conclusion 5. Acknowledgement 6. References 1. ABSTRACT 2. INTRODUCTION Triple-negative breast cancer (TNBC) Triple-negative breast cancer (TNBC), is characterized by the absence of estrogen a subtype of breast cancer (BC), accounts for and progesterone receptors and absence 15-20% of all BC diagnoses in the US. It has of amplification of human epidermal growth been recognized that women of African descent factor receptor (HER2). This disease has no are twice as likely to develop TNBC than approved treatment with a poor prognosis women of European descent (1). As the name particularly in African-American (AA) as foretells, TNBCs lack estrogen, progesterone, compared to European-American (EA) and human epidermal growth factor receptors. patients. Gene ontology analysis showed Unfortunately, TNBCs are defined by what they specific gene pathways that are differentially “lack” rather than what they “have” and thus this regulated and gene signatures that are negative nomenclature provides no actionable differentially expressed in AA as compared to information on “druggable” targets. -
A Novel Keratin 12 Mutation in a German Kindred with Meesmann's
Br J Ophthalmol 2000;84:527–530 527 A novel keratin 12 mutation in a German kindred Br J Ophthalmol: first published as 10.1136/bjo.84.5.527 on 1 May 2000. Downloaded from with Meesmann’s corneal dystrophy L D Corden, O Swensson, B Swensson, R Rochels, B Wannke, H J Thiel, W H I McLean Abstract inherited disorder aVecting the corneal epithe- Aim—To study a kindred with Mees- lium of both eyes.1–3 It manifests in early child- mann’s corneal dystrophy (MCD) to de- hood and is characterised by myriads of termine if a mutation within the cornea intraepithelial microcysts of variable distribu- specific K3 or K12 genes is responsible for tion and density. The microcysts are best seen the disease phenotype. by retroillumination and slit lamp Methods—Slit lamp examination of the examination.45 Further clinical signs of the cornea in four members of the kindred disease are recurrent punctate erosions with lacrimation and photophobia. Symptoms in- Epithelial Genetics was carried out to confirm the diagnosis Group, Human of MCD. The region encoding the helix clude blurred vision and foreign body sensa- Genetics Unit, initiation motif (HIM) of the K12 polypep- tion. Histologically, the corneal epithelium Department of tide was polymerase chain reaction (PCR) appears irregularly thickened and contains Molecular and Cellular amplified from genomic DNA derived numerous vacuolated suprabasal cells.6–8 In Pathology, Ninewells addition, there is intraepithelial cyst formation Medical School, from aVected individuals in the kindred. Dundee DD1 9SY PCR products generated were subjected to with accumulated periodic acid SchiV (PAS) L D Corden direct automated sequencing. -
Proteomic Expression Profile in Human Temporomandibular Joint
diagnostics Article Proteomic Expression Profile in Human Temporomandibular Joint Dysfunction Andrea Duarte Doetzer 1,*, Roberto Hirochi Herai 1 , Marília Afonso Rabelo Buzalaf 2 and Paula Cristina Trevilatto 1 1 Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; [email protected] (R.H.H.); [email protected] (P.C.T.) 2 Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-41-991-864-747 Abstract: Temporomandibular joint dysfunction (TMD) is a multifactorial condition that impairs human’s health and quality of life. Its etiology is still a challenge due to its complex development and the great number of different conditions it comprises. One of the most common forms of TMD is anterior disc displacement without reduction (DDWoR) and other TMDs with distinct origins are condylar hyperplasia (CH) and mandibular dislocation (MD). Thus, the aim of this study is to identify the protein expression profile of synovial fluid and the temporomandibular joint disc of patients diagnosed with DDWoR, CH and MD. Synovial fluid and a fraction of the temporomandibular joint disc were collected from nine patients diagnosed with DDWoR (n = 3), CH (n = 4) and MD (n = 2). Samples were subjected to label-free nLC-MS/MS for proteomic data extraction, and then bioinformatics analysis were conducted for protein identification and functional annotation. The three Citation: Doetzer, A.D.; Herai, R.H.; TMD conditions showed different protein expression profiles, and novel proteins were identified Buzalaf, M.A.R.; Trevilatto, P.C. -
Transcriptional Correlates of Proximal-Distal Identify and Regeneration Timing in Axolotl Limbs S
University of Kentucky UKnowledge Neuroscience Faculty Publications Neuroscience 6-2018 Transcriptional Correlates of Proximal-Distal Identify and Regeneration Timing in Axolotl Limbs S. Randal Voss University of Kentucky, [email protected] David Murrugarra University of Kentucky, [email protected] Tyler B. Jensen Northeastern University James R Monaghan Northeastern University Right click to open a feedback form in a new tab to let us know how this document benefits oy u. Follow this and additional works at: https://uknowledge.uky.edu/neurobio_facpub Part of the Anatomy Commons, Biochemistry Commons, Comparative and Evolutionary Physiology Commons, Neuroscience and Neurobiology Commons, and the Pharmacology, Toxicology and Environmental Health Commons Repository Citation Voss, S. Randal; Murrugarra, David; Jensen, Tyler B.; and Monaghan, James R, "Transcriptional Correlates of Proximal-Distal Identify and Regeneration Timing in Axolotl Limbs" (2018). Neuroscience Faculty Publications. 54. https://uknowledge.uky.edu/neurobio_facpub/54 This Article is brought to you for free and open access by the Neuroscience at UKnowledge. It has been accepted for inclusion in Neuroscience Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Transcriptional Correlates of Proximal-Distal Identify and Regeneration Timing in Axolotl Limbs Notes/Citation Information Published in Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, v. 208, p. 53-63. © 2017 Elsevier Inc. All rights reserved. This manuscript version is made available under the CC‐BY‐NC‐ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/. The document available for download is the author's post-peer-review final draft of the ra ticle. -
S Epithelial Corneal Dystrophy Phenotype Due to A
Eye (2013) 27, 367–373 & 2013 Macmillan Publishers Limited All rights reserved 0950-222X/13 www.nature.com/eye 1 2 2 2 Severe Meesmann’s H Hassan , C Thaung , ND Ebenezer , G Larkin , CLINICAL STUDY AJ Hardcastle2 and SJ Tuft1;2 epithelial corneal dystrophy phenotype due to a missense mutation in the helix- initiation motif of keratin 12 Abstract Purpose To describe a severe phenotype of protein. The clinical effects are markedly Meesmann’s epithelial corneal dystrophy more severe than the phenotype usually (MECD) and to determine the underlying associated with the Arg135Thr mutation molecular cause. within this motif, most frequently seen in Methods We identified a 30-member family European patients with MECD. affected by MECD and examined 11 of the 14 Eye (2013) 27, 367–373; doi:10.1038/eye.2012.261; affected individuals. Excised corneal tissue published online 7 December 2012 from one affected individual was examined histologically. We used PCR and direct Keywords: corneal epithelium; Meesmann sequencing to identify mutation of the corneal dystrophy; human KRT12 protein coding regions of the KRT3 and KRT12 genes. Introduction Results Cases had an unusually severe phenotype with large numbers of Meesmann’s epithelial corneal dystrophy 1Corneal Service, Moorfields intraepithelial cysts present from infancy and (MECD; OMIM #122100) is an autosomal Eye Hospital NHS they developed subepithelial fibrosis in the dominant inherited change of the corneal Foundation Trust, London, second to third decade. In some individuals, epithelium of the eye characterized by the UK the cornea became superficially vascularized, bilaterally symmetric development of numerous 2 a change accompanied by the loss of intraepithelial cysts.1,2 The cysts are best Department of Ocular clinically obvious epithelial cysts. -
Genomics of Inherited Bone Marrow Failure and Myelodysplasia Michael
Genomics of inherited bone marrow failure and myelodysplasia Michael Yu Zhang A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2015 Reading Committee: Mary-Claire King, Chair Akiko Shimamura Marshall Horwitz Program Authorized to Offer Degree: Molecular and Cellular Biology 1 ©Copyright 2015 Michael Yu Zhang 2 University of Washington ABSTRACT Genomics of inherited bone marrow failure and myelodysplasia Michael Yu Zhang Chair of the Supervisory Committee: Professor Mary-Claire King Department of Medicine (Medical Genetics) and Genome Sciences Bone marrow failure and myelodysplastic syndromes (BMF/MDS) are disorders of impaired blood cell production with increased leukemia risk. BMF/MDS may be acquired or inherited, a distinction critical for treatment selection. Currently, diagnosis of these inherited syndromes is based on clinical history, family history, and laboratory studies, which directs the ordering of genetic tests on a gene-by-gene basis. However, despite extensive clinical workup and serial genetic testing, many cases remain unexplained. We sought to define the genetic etiology and pathophysiology of unclassified bone marrow failure and myelodysplastic syndromes. First, to determine the extent to which patients remained undiagnosed due to atypical or cryptic presentations of known inherited BMF/MDS, we developed a massively-parallel, next- generation DNA sequencing assay to simultaneously screen for mutations in 85 BMF/MDS genes. Querying 71 pediatric and adult patients with unclassified BMF/MDS using this assay revealed 8 (11%) patients with constitutional, pathogenic mutations in GATA2 , RUNX1 , DKC1 , or LIG4 . All eight patients lacked classic features or laboratory findings for their syndromes. -
UCLA Electronic Theses and Dissertations
UCLA UCLA Electronic Theses and Dissertations Title Proteomic Analysis of Cancer Cell Metabolism Permalink https://escholarship.org/uc/item/8t36w919 Author Chai, Yang Publication Date 2013 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Proteomic Analysis of Cancer Cell Metabolism A thesis submitted in partial satisfaction of the requirements of the degree Master of Science in Oral Biology by Yang Chai 2013 ABSTRACT OF THESIS Proteomic Analysis of Cancer Cell Metabolism by Yang Chai Master of Science in Oral Biology University of California, Los Angeles, 2013 Professor Shen Hu, Chair Tumor cells can adopt alternative metabolic pathways during oncogenesis. This is an event characterized by an enhanced utilization of glucose for rapid synthesis of macromolecules such as nucleotides, lipids and proteins. This phenomenon was also known as the ‘Warburg effect’, distinguished by a shift from oxidative phosphorylation to increased aerobic glycolysis in many types of cancer cells. Increased aerobic glycolysis was also indicated with enhanced lactate production and glutamine consumption, and has been suggested to confer growth advantage for proliferating cells during oncogenic transformation. Development of a tracer-based ii methodology to determine de novo protein synthesis by tracing metabolic pathways from nutrient utilization may certainly enhance current understanding of nutrient gene interaction in cancer cells. We hypothesized that the metabolic phenotype of cancer cells as characterized by nutrient utilization for protein synthesis is significantly altered during oncogenesis, and 13C stable isotope tracers may incorporate 13C into non-essential amino acids of protein peptides during de novo protein synthesis to reflect the underlying mechanisms in cancer cell metabolism. -
KRT3 Gene Keratin 3
KRT3 gene keratin 3 Normal Function The KRT3 gene provides instructions for making a protein called keratin 3. Keratins are a group of tough, fibrous proteins that form the structural framework of epithelial cells, which are cells that line the surfaces and cavities of the body. Keratin 3 is produced in a tissue on the surface of the eye called the corneal epithelium. This tissue forms the outermost layer of the cornea, which is the clear front covering of the eye. The corneal epithelium acts as a barrier to help prevent foreign materials, such as dust and bacteria, from entering the eye. The keratin 3 protein partners with another keratin protein, keratin 12, to form molecules known as intermediate filaments. These filaments assemble into strong networks that provide strength and resilience to the corneal epithelium. Health Conditions Related to Genetic Changes Meesmann corneal dystrophy At least three mutations in the KRT3 gene have been found to cause Meesmann corneal dystrophy, an eye disease characterized by the formation of tiny cysts in the corneal epithelium. All of the identified KRT3 gene mutations associated with Meesmann corneal dystrophy change single protein building blocks (amino acids) in the keratin 3 protein. These changes occur in a region of the protein that is critical for the formation and stability of intermediate filaments. The altered keratin 3 protein interferes with the assembly of intermediate filaments, weakening the structural framework of the corneal epithelium. As a result, this outer layer of the cornea is abnormally fragile and develops the cysts that characterize Meesmann corneal dystrophy. The cysts likely contain clumps of abnormal keratin proteins and other cellular debris. -
Sharon Carr Mphil Thesis
ADENOVIRUS AND ITS INTERACTION WITH HOST CELL PROTEINS Sharon Carr A Thesis Submitted for the Degree of MPhil at the University of St. Andrews 2007 Full metadata for this item is available in Research@StAndrews:FullText at: http://research-repository.st-andrews.ac.uk/ Please use this identifier to cite or link to this item: http://hdl.handle.net/10023/219 This item is protected by original copyright Adenovirus and its interaction with host cell proteins Sharon Carr School of Biomedical Sciences University of St Andrews A thesis submitted for the degree of Master of Philosophy September 2006 1 I, …………………., hereby certify that this thesis, which is approximately 75,000 words in length, has been written by me, that it is the record of work carried out by me and that it has not been submitted in any previous application for a higher degree. date…………… signature of candidate………………………… I was admitted as a research student in September 2002 and as a candidate for the degree of Doctor of Philosophy in September 2002; the higher study for which this is a record was carried out in the University of St Andrews between 2002 and 2005, and at the University of Dundee between 2005 and 2006. date…………… signature of candidate………………………… I hereby certify that the candidate has fulfilled the conditions of the Resolution and Regulations appropriated for the degree of Master of Philosophy in the University of St Andrews and that the candidate is qualified to submit this thesis in application for that degree. date…………… signature of supervisors………………………… ………………………… 2 In submitting this thesis to the University of St Andrews I understand that I am giving permission for it to be made available for use in accordance with the regulations of the University Library for the time being in force, subject to any copyright vested in the work not being affected thereby. -
Mass Spectrometry Analysis Reveals Dynamic Changes of Protein
Japanese Journal of Gastroenterology and Hepatology Research Article Mass Spectrometry Analysis Reveals Dynamic Changes of Protein Components in Lipid Rafts from Rat Liver after Partial Hepatectomy Zhu B1*, Li J1*, Yang C1, Jiang M1, Zhou Q1, Wang Y1, 2* and Chen P1, 2* 1Department of Gastroenterology, The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, P.R. China 2Department of Gastroenterology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China Received: 08 Apr 2020 1. Abstract Accepted: 27 Apr 2020 Lipid raft, as scaffolding platform for signal transduction, plays important role in the liver re- Published: 30 Apr 2020 generation. But the lipid raft protein expression pattern during liver regeneration has been not * Corresponding author: reported. In this study, lipid raft proteins from the liver of 72 h post partial hepatectomy and Ping Chen, Department of Gastroen- sham-operated group were identified by liquid chromatography-tandem mass spectrometry (LC- terology, The National & Local Joint MS/MS) combined with label-free semi-quantitative analysis. Totally 458 lipid raft proteins were Engineering Laboratory of Animal identified, and most of identified lipid raft proteins were mainly involved in transporter, signal Peptide Drug Development, College transduction, and metabolism. Moreover, label-free quantification analysis suggested that the level of Life Sciences, Hunan Normal Uni- of 46 plasma membrane-related proteins have changed obviously (with ratio≥2) after 72 h hepa- versity, Changsha 410081, P.R. China, tectomy. Several differently expressed proteins, including caveolin-1 and flotillin-1, were validated E-mail: [email protected] by western blotting.