Disease-Associated Mutations of Claudin-19 Disrupt Retinal Neurogenesis and Visual Function
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Structural Basis for Disruption of Claudin Assembly in Tight Junctions
www.nature.com/scientificreports OPEN Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin Received: 11 May 2016 Takehiro Shinoda1,2, Naoko Shinya1,2, Kaori Ito1,2, Noboru Ohsawa1,2, Takaho Terada1,3, Accepted: 01 September 2016 Kunio Hirata4, Yoshiaki Kawano4, Masaki Yamamoto4, Tomomi Kimura-Someya1,2, Published: 20 September 2016 Shigeyuki Yokoyama1,3 & Mikako Shirouzu1,2 The food-poisoning bacterium Clostridium perfringens produces an enterotoxin (~35 kDa) that specifically targets human claudin-4, among the 26 human claudin proteins, and causes diarrhea by fluid accumulation in the intestinal cavity. The C-terminal domain of the Clostridium perfringens enterotoxin (C-CPE, ~15 kDa) binds tightly to claudin-4, and disrupts the intestinal tight junction barriers. In this study, we determined the 3.5-Å resolution crystal structure of the cell-free synthesized human claudin- 4•C-CPE complex, which is significantly different from the structure of the off-target complex of an engineered C-CPE with mouse claudin-19. The claudin-4•C-CPE complex structure demonstrated the mechanism underlying claudin assembly disruption. A comparison of the present C-CPE-bound structure of claudin-4 with the enterotoxin-free claudin-15 structure revealed sophisticated C-CPE- induced conformation changes of the extracellular segments, induced on the foundation of the rigid four-transmembrane-helix bundle structure. These conformation changes provide a mechanistic model for the disruption of the lateral assembly of claudin molecules. Furthermore, the present novel structural mechanism for selecting a specific member of the claudin family can be used as the foundation to develop novel medically important technologies to selectively regulate the tight junctions formed by claudin family members in different organs. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Mutations in the Tight-Junction Gene Claudin 19 (CLDN19) Are Associated with Renal Magnesium Wasting, Renal Failure, and Severe Ocular Involvement
Mutations in the Tight-Junction Gene Claudin 19 (CLDN19) Are Associated with Renal Magnesium Wasting, Renal Failure, and Severe Ocular Involvement Martin Konrad, Andre´ Schaller, Dominik Seelow, Amit V. Pandey, Siegfried Waldegger, Annegret Lesslauer, Helga Vitzthum, Yoshiro Suzuki, John M. Luk, Christian Becker, Karl P. Schlingmann, Marcel Schmid, Juan Rodriguez-Soriano, Gema Ariceta, Francisco Cano, Ricardo Enriquez, Harald Ju¨ppner, Sevcan A. Bakkaloglu, Matthias A. Hediger, Sabina Gallati, Stephan C. F. Neuhauss, Peter Nu¨rnberg, and Stefanie Weber Claudins are major components of tight junctions and contribute to the epithelial-barrier function by restricting free diffusion of solutes through the paracellular pathway. We have mapped a new locus for recessive renal magnesium loss on chromosome 1p34.2 and have identified mutations in CLDN19, a member of the claudin multigene family, in patients affected by hypomagnesemia, renal failure, and severe ocular abnormalities. CLDN19 encodes the tight-junction protein claudin-19, and we demonstrate high expression of CLDN19 in renal tubules and the retina. The identified mutations interfere severely with either cell-membrane trafficking or the assembly of the claudin-19 protein. The identification of CLDN19 mutations in patients with chronic renal failure and severe visual impairment supports the fundamental role of claudin-19 for normal renal tubular function and undisturbed organization and development of the retina. Tight junctions constitute cell-cell contacts by forming cir- calcium reabsorption -
Single Cell Transcriptional and Chromatin Accessibility Profiling Redefine Cellular Heterogeneity in the Adult Human Kidney
ARTICLE https://doi.org/10.1038/s41467-021-22368-w OPEN Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney Yoshiharu Muto 1,7, Parker C. Wilson 2,7, Nicolas Ledru 1, Haojia Wu1, Henrik Dimke 3,4, ✉ Sushrut S. Waikar 5 & Benjamin D. Humphreys 1,6 1234567890():,; The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC- seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney. We demonstrate that snATAC-seq is comparable to snRNA-seq in the assignment of cell identity and can further refine our understanding of functional heterogeneity in the nephron. The majority of differ- entially accessible chromatin regions are localized to promoters and a significant proportion are closely associated with differentially expressed genes. Cell-type-specific enrichment of transcription factor binding motifs implicates the activation of NF-κB that promotes VCAM1 expression and drives transition between a subpopulation of proximal tubule epithelial cells. Our multi-omics approach improves the ability to detect unique cell states within the kidney and redefines cellular heterogeneity in the proximal tubule and thick ascending limb. 1 Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA. 2 Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA. 3 Department of Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark. 4 Department of Nephrology, Odense University Hospital, Odense, Denmark. -
Differences in Gene Expression Profiles and Carcinogenesis Pathways Involved in Cisplatin Resistance of Four Types of Cancer
596 ONCOLOGY REPORTS 30: 596-614, 2013 Differences in gene expression profiles and carcinogenesis pathways involved in cisplatin resistance of four types of cancer YONG YANG1,2, HUI LI1,2, SHENGCAI HOU1,2, BIN HU1,2, JIE LIU1,3 and JUN WANG1,3 1Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Capital Medical University, Beijing 100069; 2Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020; 3Department of Physiology, Capital Medical University, Beijing 100069, P.R. China Received December 23, 2012; Accepted March 4, 2013 DOI: 10.3892/or.2013.2514 Abstract. Cisplatin-based chemotherapy is the standard Introduction therapy used for the treatment of several types of cancer. However, its efficacy is largely limited by the acquired drug Cisplatin is primarily effective through DNA damage and is resistance. To date, little is known about the RNA expression widely used for the treatment of several types of cancer, such changes in cisplatin-resistant cancers. Identification of the as testicular, lung and ovarian cancer. However, the ability RNAs related to cisplatin resistance may provide specific of cancer cells to become resistant to cisplatin remains a insight into cancer therapy. In the present study, expression significant impediment to successful chemotherapy. Although profiling of 7 cancer cell lines was performed using oligo- previous studies have identified numerous mechanisms in nucleotide microarray analysis data obtained from the GEO cisplatin resistance, it remains a major problem that severely database. Bioinformatic analyses such as the Gene Ontology limits the usefulness of this chemotherapeutic agent. Therefore, (GO) and KEGG pathway were used to identify genes and it is crucial to examine more elaborate mechanisms of cisplatin pathways specifically associated with cisplatin resistance. -
CLDN19 Monoclonal Antibody (M02), Clone 2F2
CLDN19 monoclonal antibody (M02), clone 2F2 Catalog # : H00149461-M02 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a full-length recombinant Western Blot (Recombinant protein) Description: CLDN19. Sandwich ELISA (Recombinant Immunogen: CLDN19 (AAH30524, 1 a.a. ~ 211 a.a) full-length recombinant protein protein) with GST tag. MW of the GST tag alone is 26 KDa. Sequence: MANSGLQLLGYFLALGGWVGIIASTALPQWKQSSYAGDAIITAVGLYEGL WMSCASQSTGQVQCKLYDSLLALDGHIQSARALMVVAVLLGFVAMVLS VVGMKCTRVGDSNPIAKGRVAIAGGALFILAGLCTLTAVSWYATLVTQEF FNPSTPVNARYEFGPALFVGWASAGLAVLGGSFLCCTCPEPERPNSSP QPYRPGPSAAAREYV enlarge Host: Mouse ELISA Reactivity: Human Isotype: IgG2a Kappa Quality Control Antibody Reactive Against Recombinant Protein. Testing: Western Blot detection against Immunogen (48.95 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Datasheet: Download Applications Western Blot (Recombinant protein) Protocol Download Sandwich ELISA (Recombinant protein) Page 1 of 2 2018/11/27 Detection limit for recombinant GST tagged CLDN19 is 0.1 ng/ml as a capture antibody. Protocol Download ELISA Gene Information Entrez GeneID: 149461 GeneBank BC030524 Accession#: Protein AAH30524 Accession#: Gene Name: CLDN19 Gene Alias: - Gene claudin 19 Description: Omim ID: 248190, 610036 Gene Ontology: Hyperlink Gene Summary: The product of this gene belongs to the claudin family. It plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity. Defects in this gene are the cause of hypomagnesemia renal with ocular involvement (HOMGO). HOMGO is a progressive renal disease characterized by primary renal magnesium wasting with hypomagnesemia, hypercalciuria and nephrocalcinosis associated with severe ocular abnormalities such as bilateral chorioretinal scars, macular colobomata, significant myopia and nystagmus. -
Ep 3039174 B1
(19) TZZ¥Z¥__T (11) EP 3 039 174 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/6886 (2018.01) C12Q 1/6883 (2018.01) 16.10.2019 Bulletin 2019/42 (86) International application number: (21) Application number: 14840036.9 PCT/US2014/053306 (22) Date of filing: 28.08.2014 (87) International publication number: WO 2015/031694 (05.03.2015 Gazette 2015/09) (54) OLIGONUCLEOTIDE PROBES AND USES THEREOF OLIGONUKLEOTIDSONDEN UND VERWENDUNGEN DAVON SONDES OLIGONUCLÉOTIDIQUES ET LEURS UTILISATIONS (84) Designated Contracting States: (74) Representative: Patent Boutique LLP AL AT BE BG CH CY CZ DE DK EE ES FI FR GB 10A Printing House Yard GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Hackney Road PL PT RO RS SE SI SK SM TR London E2 7PR (GB) (30) Priority: 28.08.2013 US 201361871107 P (56) References cited: 06.09.2013 US 201361874621 P WO-A1-2011/066589 WO-A2-2010/056337 06.11.2013 US 201361900975 P WO-A2-2011/088226 WO-A2-2013/022995 05.12.2013 US 201361912471 P 06.01.2014 US 201461924192 P • TERESA JANAS ET AL: "The selection of 06.03.2014 US 201461949216 P aptamers specific for membrane molecular 03.04.2014 US 201461974949 P targets", CELLULAR & MOLECULAR BIOLOGY 07.05.2014 US 201461990085 P LETTERS, vol. 16, no. 1, 1 March 2011 16.05.2014 US 201461994704 P (2011-03-01), pages 25-39, XP055001923, ISSN: 14.07.2014 US 201462024436 P 1425-8153, DOI: 10.2478/s11658-010-0023-3 • HENNING ULRICH ET AL: "Disease-specific (43) Date of publication of application: biomarkerdiscovery by aptamers", CYTOMETRY 06.07.2016 Bulletin 2016/27 PART A, vol. -
Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans
HIGHLIGHTED ARTICLE | INVESTIGATION Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans Chen-Yu Wang,*,† Harrison Brand,‡,§,**,†† Natalie D. Shaw,‡‡,§§ Michael E. Talkowski,‡,§,**,†† and Jeannie T. Lee*,†,1 *Department of Molecular Biology, ††Center for Human Genetic Research, and ‡‡Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, †Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, ‡Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, §Program in Medical and Population Genetics and **Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, §§National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 ORCID IDs: 0000-0002-3912-5113 (C.-Y.W.); 0000-0001-7786-8850 (J.T.L.) ABSTRACT Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex- specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromo- somes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. -
Enhancer Hubs and Loop Collisions Identified from Single-Allele Topologies
ARTICLES https://doi.org/10.1038/s41588-018-0161-5 Enhancer hubs and loop collisions identified from single-allele topologies Amin Allahyar1,2,7, Carlo Vermeulen 3,7, Britta A. M. Bouwman3, Peter H. L. Krijger3, Marjon J. A. M. Verstegen3, Geert Geeven3, Melissa van Kranenburg3, Mark Pieterse3, Roy Straver 1, Judith H. I. Haarhuis4, Kees Jalink5, Hans Teunissen6, Ivo J. Renkens1, Wigard P. Kloosterman1, Benjamin D. Rowland4, Elzo de Wit 6, Jeroen de Ridder 1* and Wouter de Laat3* Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot dis- cern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chro- matin loops is believed to reflect ‘cohesin traffic jams’. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning. he invention of chromatin conformation capture (3C) tech- matrices cannot distinguish clustered interactions from mutually nology1 and derived methods2 has greatly advanced our exclusive interactions that independently occur in different cells. -
The Pdx1 Bound Swi/Snf Chromatin Remodeling Complex Regulates Pancreatic Progenitor Cell Proliferation and Mature Islet Β Cell
Page 1 of 125 Diabetes The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Jason M. Spaeth1,2, Jin-Hua Liu1, Daniel Peters3, Min Guo1, Anna B. Osipovich1, Fardin Mohammadi3, Nilotpal Roy4, Anil Bhushan4, Mark A. Magnuson1, Matthias Hebrok4, Christopher V. E. Wright3, Roland Stein1,5 1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2 Present address: Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 3 Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 4 Diabetes Center, Department of Medicine, UCSF, San Francisco, California 5 Corresponding author: [email protected]; (615)322-7026 1 Diabetes Publish Ahead of Print, published online June 14, 2019 Diabetes Page 2 of 125 Abstract Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin remodeling coregulatory complex that physically associates with Pdx1, a diabetes- linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, was necessary to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed Swi/Snf-deficient β cells lost the ability to produce the mRNAs for insulin and other key metabolic genes without effecting the expression of many essential islet-enriched transcription factors. -
Thousands of Cpgs Show DNA Methylation Differences in ACPA-Positive Individuals
G C A T T A C G G C A T genes Article Thousands of CpGs Show DNA Methylation Differences in ACPA-Positive Individuals Yixiao Zeng 1,2, Kaiqiong Zhao 2,3, Kathleen Oros Klein 2, Xiaojian Shao 4, Marvin J. Fritzler 5, Marie Hudson 2,6,7, Inés Colmegna 6,8, Tomi Pastinen 9,10, Sasha Bernatsky 6,8 and Celia M. T. Greenwood 1,2,3,9,11,* 1 PhD Program in Quantitative Life Sciences, Interfaculty Studies, McGill University, Montréal, QC H3A 1E3, Canada; [email protected] 2 Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; [email protected] (K.Z.); [email protected] (K.O.K.); [email protected] (M.H.) 3 Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada 4 Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada; [email protected] 5 Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; [email protected] 6 Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada; [email protected] (I.C.); [email protected] (S.B.) 7 Division of Rheumatology, Jewish General Hospital, Montréal, QC H3T 1E2, Canada 8 Division of Rheumatology, McGill University, Montréal, QC H3G 1A4, Canada 9 Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada; [email protected] 10 Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108, USA 11 Gerald Bronfman Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada * Correspondence: [email protected] Citation: Zeng, Y.; Zhao, K.; Oros Abstract: High levels of anti-citrullinated protein antibodies (ACPA) are often observed prior to Klein, K.; Shao, X.; Fritzler, M.J.; Hudson, M.; Colmegna, I.; Pastinen, a diagnosis of rheumatoid arthritis (RA). -
Notate Human RPE-Specific Gene Expression
UvA-DARE (Digital Academic Repository) Function and pathology of the human retinal pigment epithelium Booij, J.C. Publication date 2010 Link to publication Citation for published version (APA): Booij, J. C. (2010). Function and pathology of the human retinal pigment epithelium. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:25 Sep 2021 A new strategy to identify and an- notate human RPE-specific gene expression 3 Judith C Booij, Jacoline B ten Brink, Sigrid MA Swagemakers, Annemieke JMH Verkerk, Anke HW Essing, Peter J van der Spek, Arthur AB Bergen. PlosOne 2010, 5(3) e9341 Chapter 3 Abstract Background: The aim of the study was to identify and functionally annotate cell type-spe- cific gene expression in the human retinal pigment epithelium (RPE), a key tissue involved in age-related macular degeneration and retinitis pigmentosa.