2018 European Cystic Fibrosis Society 15Th ECFS Basic Science Conference
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PROTEOMIC ANALYSIS of HUMAN URINARY EXOSOMES. Patricia
ABSTRACT Title of Document: PROTEOMIC ANALYSIS OF HUMAN URINARY EXOSOMES. Patricia Amalia Gonzales Mancilla, Ph.D., 2009 Directed By: Associate Professor Nam Sun Wang, Department of Chemical and Biomolecular Engineering Exosomes originate as the internal vesicles of multivesicular bodies (MVBs) in cells. These small vesicles (40-100 nm) have been shown to be secreted by most cell types throughout the body. In the kidney, urinary exosomes are released to the urine by fusion of the outer membrane of the MVBs with the apical plasma membrane of renal tubular epithelia. Exosomes contain apical membrane and cytosolic proteins and can be isolated using differential centrifugation. The analysis of urinary exosomes provides a non- invasive means of acquiring information about the physiological or pathophysiological state of renal cells. The overall objective of this research was to develop methods and knowledge infrastructure for urinary proteomics. We proposed to conduct a proteomic analysis of human urinary exosomes. The first objective was to profile the proteome of human urinary exosomes using liquid chromatography-tandem spectrometry (LC- MS/MS) and specialized software for identification of peptide sequences from fragmentation spectra. We unambiguously identified 1132 proteins. In addition, the phosphoproteome of human urinary exosomes was profiled using the neutral loss scanning acquisition mode of LC-MS/MS. The phosphoproteomic profiling identified 19 phosphorylation sites corresponding to 14 phosphoproteins. The second objective was to analyze urinary exosomes samples isolated from patients with genetic mutations. Polyclonal antibodies were generated to recognize epitopes on the gene products of these genetic mutations, NKCC2 and MRP4. The potential usefulness of urinary exosome analysis was demonstrated using the well-defined renal tubulopathy, Bartter syndrome type I and using the single nucleotide polymorphism in the ABCC4 gene. -
Zebrafish Mutants Calamity and Catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism Erik C
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2008 Zebrafish mutants calamity and catastrophe define critical pathways of gene–nutrient interactions in developmental copper metabolism Erik C. Madsen Washington University School of Medicine in St. Louis Jonathan D. Gitlin Washington University School of Medicine in St. Louis Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Part of the Medicine and Health Sciences Commons Recommended Citation Madsen, Erik C. and Gitlin, Jonathan D., ,"Zebrafish mutants calamity and catastrophe define critical pathways of gene–nutrient interactions in developmental copper metabolism." PLoS Genetics.,. e1000261. (2008). https://digitalcommons.wustl.edu/open_access_pubs/892 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Zebrafish Mutants calamity and catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism Erik C. Madsen, Jonathan D. Gitlin¤* Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America Abstract Nutrient availability is an important environmental variable during development that has significant effects on the metabolism, health, and viability of an organism. To understand these interactions for the nutrient copper, we used a chemical genetic screen for zebrafish mutants sensitive to developmental copper deficiency. In this screen, we isolated two mutants that define subtleties of copper metabolism. The first contains a viable hypomorphic allele of atp7a and results in a loss of pigmentation when exposed to mild nutritional copper deficiency. -
Theranostics Deficiency of ATP6V1H Causes Bone Loss by Inhibiting
Theranostics 2016, Vol. 6, Issue 12 2183 Ivyspring International Publisher Theranostics 2016; 6(12): 2183-2195. doi: 10.7150/thno.17140 Research Paper Deficiency of ATP6V1H Causes Bone Loss by Inhibiting Bone Resorption and Bone Formation through the TGF-β1 Pathway Xiaohong Duan1*, Jin Liu1*, Xueni Zheng1*, Zhe Wang1, Yanli Zhang1, Ying Hao1, Tielin Yang2, Hongwen Deng3 1. State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Oral Diseases, Department of Oral Biology, Clinic of Oral Rare and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, Xi’an, 710032, People’s Republic of China. 2. Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, People’s Republic of China. 3. School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA. *Contributed equally to this work. Corresponding author: Xiaohong Duan, State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Oral Diseases, Department of Oral Biology, Clinic of Oral Rare and Genetic Diseases, School of Stomatology, the Fourth Military Medical University, 145 West Changle Road, Xi’an 710032, P. R. China. Tel: 86-29-84776169; Fax: 86-29-84776169; E-mail: [email protected]. © Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions. Received: 2016.08.08; Accepted: 2016.08.15; Published: 2016.09.13 Abstract Vacuolar-type H +-ATPase (V-ATPase) is a highly conserved, ancient enzyme that couples the energy of ATP hydrolysis to proton transport across vesicular and plasma membranes of eukaryotic cells. -
Molecular Mechanism of Embryo Transport and Embryo
MOLECULAR MECHANISM OF EMBRYO TRANSPORT AND EMBRYO IMPLANTATION IN MICE By SHUO XIAO (Under the Direction of Xiaoqin Ye) ABSTRACT Embryo transport and embryo implantation are essential events in mammalian reproduction during pregnancy. This dissertation was conducted to investigate the effect of bisphenol A (BPA) on early pregnancy and the molecular mechanism (s) of embryo transport and embryo implantation. Timed pregnant female mice were treated subcutaneously with 0, 0.025, 0.5, 10, 40, and 100 mg/kg/day BPA from gestation day 0.5 (D0.5, mating night as D0) to D3.5. High dose of preimplantation BPA exposure resulted in delayed embryo transport and preimplantation embryo development, and delayed/failed embryo implantation, indicating the adverse effect of BPA on early pregnancy. Preimplantation 17β-estradiol (E2) exposure at 1 and 10 µg/kg/day from D0.5 to D2.5 delayed embryo transport in the ampulla-isthmus junction of oviduct in mice, which is associated with the oviductal epithelium hyperplasia. Microarray analysis revealed 53 differentially expressed genes in the oviduct upon 10 µg/kg/day E2 treatment, which may have potential function in embryo transport regulation. Embryo implantation is a process that the receptive uterus accepts an embryo to implant into the uterine wall. Microarray analysis of the preimplantation D3.5 and postimplantation D4.5 uterine luminal epithelium (LE) identified 627 differentially expressed genes and 21 significantly changed signaling pathways upon embryo implantation. 12 of these genes were newly characterized and showed spatiotemporal expression patterns in the mouse periimplantation uterine LE. The most upregulated gene in the D4.5 LE Atp6v0d2 (34.7x) is a subunit of vacuolar-type H+-ATPase (V-ATPase) that regulates the cell acidification through ATP hydrolysis and proton translocation. -
ELMO1 Signaling Is a Promoter of Osteoclast Function and Bone Loss ✉ Sanja Arandjelovic 1 , Justin S
ARTICLE https://doi.org/10.1038/s41467-021-25239-6 OPEN ELMO1 signaling is a promoter of osteoclast function and bone loss ✉ Sanja Arandjelovic 1 , Justin S. A. Perry 1, Ming Zhou 2, Adam Ceroi3, Igor Smirnov4, Scott F. Walk1, Laura S. Shankman1, Isabelle Cambré3, Suna Onengut-Gumuscu 5, Dirk Elewaut 3, Thomas P. Conrads 2 & ✉ Kodi S. Ravichandran 1,3 Osteoporosis affects millions worldwide and is often caused by osteoclast induced bone loss. 1234567890():,; Here, we identify the cytoplasmic protein ELMO1 as an important ‘signaling node’ in osteoclasts. We note that ELMO1 SNPs associate with bone abnormalities in humans, and that ELMO1 deletion in mice reduces bone loss in four in vivo models: osteoprotegerin deficiency, ovariectomy, and two types of inflammatory arthritis. Our transcriptomic analyses coupled with CRISPR/Cas9 genetic deletion identify Elmo1 associated regulators of osteoclast function, including cathepsin G and myeloperoxidase. Further, we define the ‘ELMO1 inter- actome’ in osteoclasts via proteomics and reveal proteins required for bone degradation. ELMO1 also contributes to osteoclast sealing zone on bone-like surfaces and distribution of osteoclast-specific proteases. Finally, a 3D structure-based ELMO1 inhibitory peptide reduces bone resorption in wild type osteoclasts. Collectively, we identify ELMO1 as a signaling hub that regulates osteoclast function and bone loss, with relevance to osteoporosis and arthritis. 1 Center for Cell Clearance, Department of Microbiology, Immunology, and Cancer Biology and Carter Immunology Center, University of Virginia, Charlottesville, VA, USA. 2 Inova Schar Cancer Institute, Inova Center for Personalized Health, Fairfax, VA, USA. 3 Inflammation Research Centre, VIB, and the Department of Biomedical Molecular Biology, Ghent Univeristy, Ghent, Belgium. -
Kidney V-Atpase-Rich Cell Proteome Database
A comprehensive list of the proteins that are expressed in V-ATPase-rich cells harvested from the kidneys based on the isolation by enzymatic digestion and fluorescence-activated cell sorting (FACS) from transgenic B1-EGFP mice, which express EGFP under the control of the promoter of the V-ATPase-B1 subunit. In these mice, type A and B intercalated cells and connecting segment principal cells of the kidney express EGFP. The protein identification was performed by LC-MS/MS using an LTQ tandem mass spectrometer (Thermo Fisher Scientific). For questions or comments please contact Sylvie Breton ([email protected]) or Mark A. Knepper ([email protected]). -
Molecular Architecture Underlying Fluid Absorption by the Developing Inner
RESEARCH ARTICLE Molecular architecture underlying fluid absorption by the developing inner ear Keiji Honda1†, Sung Huhn Kim2‡, Michael C Kelly3, Joseph C Burns3§, Laura Constance2, Xiangming Li2#, Fei Zhou2, Michael Hoa4, Matthew W Kelley3, Philine Wangemann2*, Robert J Morell5, Andrew J Griffith1* 1Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 2Anatomy and Physiology Department, Kansas State University, Manhattan, United States; 3Developmental Neuroscience Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 4Auditory Development and Restoration Program, National Institute on *For correspondence: Deafness and Other Communication Disorders, National Institutes of Health, [email protected] (PW); Bethesda, United States; 5Genomics and Computational Biology Core, National [email protected] (AJG) Institute on Deafness and Other Communication Disorders, National Institutes of Present address: Health, Bethesda, United States †Otolaryngology Department, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan; ‡Department of Abstract Mutations of SLC26A4 are a common cause of hearing loss associated with Otorhinolaryngology, Head and enlargement of the endolymphatic sac (EES). Slc26a4 expression in the developing mouse Neck Surgery, Yonsei University College of Medicine, Seoul, endolymphatic sac is required for acquisition of normal inner ear structure and function. Here, we Korea; §Decibel Therapeutics, show that the mouse endolymphatic sac absorbs fluid in an SLC26A4-dependent fashion. Fluid Cambridge, United States; absorption was sensitive to ouabain and gadolinium but insensitive to benzamil, bafilomycin and #Technique R and D-Drug S3226. Single-cell RNA-seq analysis of pre- and postnatal endolymphatic sacs demonstrates two Substance, GlaxoSmithKline types of differentiated cells. -
Robles JTO Supplemental Digital Content 1
Supplementary Materials An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma based on mRNA, microRNA and DNA Methylation Biomarkers Ana I. Robles1, Eri Arai2, Ewy A. Mathé1, Hirokazu Okayama1, Aaron Schetter1, Derek Brown1, David Petersen3, Elise D. Bowman1, Rintaro Noro1, Judith A. Welsh1, Daniel C. Edelman3, Holly S. Stevenson3, Yonghong Wang3, Naoto Tsuchiya4, Takashi Kohno4, Vidar Skaug5, Steen Mollerup5, Aage Haugen5, Paul S. Meltzer3, Jun Yokota6, Yae Kanai2 and Curtis C. Harris1 Affiliations: 1Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 2Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 3Genetics Branch, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 4Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 5Department of Chemical and Biological Working Environment, National Institute of Occupational Health, NO-0033 Oslo, Norway. 6Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona (Barcelona), Spain. List of Supplementary Materials Supplementary Materials and Methods Fig. S1. Hierarchical clustering of based on CpG sites differentially-methylated in Stage I ADC compared to non-tumor adjacent tissues. Fig. S2. Confirmatory pyrosequencing analysis of DNA methylation at the HOXA9 locus in Stage I ADC from a subset of the NCI microarray cohort. 1 Fig. S3. Methylation Beta-values for HOXA9 probe cg26521404 in Stage I ADC samples from Japan. Fig. S4. Kaplan-Meier analysis of HOXA9 promoter methylation in a published cohort of Stage I lung ADC (J Clin Oncol 2013;31(32):4140-7). Fig. S5. Kaplan-Meier analysis of a combined prognostic biomarker in Stage I lung ADC. -
Large-Scale Proteomics and Phosphoproteomics of Urinary Exosomes
JASN Express. Published on December 3, 2008 as doi: 10.1681/ASN.2008040406 BASIC RESEARCH www.jasn.org Large-Scale Proteomics and Phosphoproteomics of Urinary Exosomes Patricia A. Gonzales,*† Trairak Pisitkun,* Jason D. Hoffert,* Dmitry Tchapyjnikov,* ʈ Robert A. Star,‡ Robert Kleta,§ ¶ Nam Sun Wang,† and Mark A. Knepper* *Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, ‡Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases, §Section of Human ʈ Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, and Office of Rare Diseases, Office of the Director, National Institutes of Health, Bethesda, and †Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland; and ¶London Epithelial Group, Centre for Nephrology, University College London, London, United Kingdom ABSTRACT Normal human urine contains large numbers of exosomes, which are 40- to 100-nm vesicles that originate as the internal vesicles in multivesicular bodies from every renal epithelial cell type facing the urinary space. Here, we used LC-MS/MS to profile the proteome of human urinary exosomes. Overall, the analysis identified 1132 proteins unambiguously, including 177 that are represented on the Online Mendelian Inheritance in Man database of disease-related genes, suggesting that exosome analysis is a potential approach to discover urinary biomarkers. We extended the proteomic analysis to phospho- proteomic profiling using neutral loss scanning, and this yielded multiple novel phosphorylation sites, including serine-811 in the thiazide-sensitive Na-Cl co-transporter, NCC. To demonstrate the potential use of exosome analysis to identify a genetic renal disease, we carried out immunoblotting of exosomes from urine samples of patients with a clinical diagnosis of Bartter syndrome type I, showing an absence of the sodium-potassium-chloride co-transporter 2, NKCC2. -
Novel Gene Signatures for Stage Classification of the Squamous Cell
www.nature.com/scientificreports OPEN Novel gene signatures for stage classifcation of the squamous cell carcinoma of the lung Angel Juarez‑Flores, Gabriel S. Zamudio & Marco V. José* The squamous cell carcinoma of the lung (SCLC) is one of the most common types of lung cancer. As GLOBOCAN reported in 2018, lung cancer was the frst cause of death and new cases by cancer worldwide. Typically, diagnosis is made in the later stages of the disease with few treatment options available. The goal of this work was to fnd some key components underlying each stage of the disease, to help in the classifcation of tumor samples, and to increase the available options for experimental assays and molecular targets that could be used in treatment development. We employed two approaches. The frst was based in the classic method of diferential gene expression analysis, network analysis, and a novel concept known as network gatekeepers. The second approach was using machine learning algorithms. From our combined approach, we identifed two sets of genes that could function as a signature to identify each stage of the cancer pathology. We also arrived at a network of 55 nodes, which according to their biological functions, they can be regarded as drivers in this cancer. Although biological experiments are necessary for their validation, we proposed that all these genes could be used for cancer development treatments. As GLOBOCAN reported in 2018, lung cancer was the frst cause of deaths and new cases by cancer worldwide 1. Squamous cell carcinoma of the lung (SCC) is one type of lung cancer which comprises approximately 30% of all lung cancer cases. -
Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared Amongst Δγ T, Innate Lymphoid, and Th Cells
Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 δγ is online at: average * The Journal of Immunology , 10 of which you can access for free at: 2016; 197:1460-1470; Prepublished online 6 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600643 http://www.jimmunol.org/content/197/4/1460 Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst T, Innate Lymphoid, and Th Cells You Jeong Lee, Gabriel J. Starrett, Seungeun Thera Lee, Rendong Yang, Christine M. Henzler, Stephen C. Jameson and Kristin A. Hogquist J Immunol cites 41 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by 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://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2016/07/06/jimmunol.160064 3.DCSupplemental This article http://www.jimmunol.org/content/197/4/1460.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 © 2016 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. The Journal of Immunology Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst gd T, Innate Lymphoid, and Th Cells You Jeong Lee,* Gabriel J. -
Supplementary Table 3. Genes Specifically Regulated by Zol (Non-Significant for Fluva)
Supplementary Table 3. Genes specifically regulated by Zol (non-significant for Fluva). log2 Genes Probe Genes Symbol Genes Title Zol100 vs Zol vs Set ID Control (24h) Control (48h) 8065412 CST1 cystatin SN 2,168 1,772 7928308 DDIT4 DNA-damage-inducible transcript 4 2,066 0,349 8154100 VLDLR very low density lipoprotein 1,99 0,413 receptor 8149749 TNFRSF10D tumor necrosis factor receptor 1,973 0,659 superfamily, member 10d, decoy with truncated death domain 8006531 SLFN5 schlafen family member 5 1,692 0,183 8147145 ATP6V0D2 ATPase, H+ transporting, lysosomal 1,689 0,71 38kDa, V0 subunit d2 8013660 ALDOC aldolase C, fructose-bisphosphate 1,649 0,871 8140967 SAMD9 sterile alpha motif domain 1,611 0,66 containing 9 8113709 LOX lysyl oxidase 1,566 0,524 7934278 P4HA1 prolyl 4-hydroxylase, alpha 1,527 0,428 polypeptide I 8027002 GDF15 growth differentiation factor 15 1,415 0,201 7961175 KLRC3 killer cell lectin-like receptor 1,403 1,038 subfamily C, member 3 8081288 TMEM45A transmembrane protein 45A 1,342 0,401 8012126 CLDN7 claudin 7 1,339 0,415 7993588 TMC7 transmembrane channel-like 7 1,318 0,3 8073088 APOBEC3G apolipoprotein B mRNA editing 1,302 0,174 enzyme, catalytic polypeptide-like 3G 8046408 PDK1 pyruvate dehydrogenase kinase, 1,287 0,382 isozyme 1 8161174 GNE glucosamine (UDP-N-acetyl)-2- 1,283 0,562 epimerase/N-acetylmannosamine kinase 7937079 BNIP3 BCL2/adenovirus E1B 19kDa 1,278 0,5 interacting protein 3 8043283 KDM3A lysine (K)-specific demethylase 3A 1,274 0,453 7923991 PLXNA2 plexin A2 1,252 0,481 8163618 TNFSF15 tumor necrosis