Deficient Mice: a Novel Murine Model for Primary Open Angle Glaucoma
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Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
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. -
Allosteric Activation of the Nitric Oxide Receptor Soluble Guanylate Cyclase
RESEARCH ARTICLE Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy Benjamin G Horst1†, Adam L Yokom2,3†, Daniel J Rosenberg4,5, Kyle L Morris2,3‡, Michal Hammel4, James H Hurley2,3,4,5*, Michael A Marletta1,2,3* 1Department of Chemistry, University of California, Berkeley, Berkeley, United States; 2Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; 3Graduate Group in Biophysics, University of California, Berkeley, Berkeley, United States; 4Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, United States; 5California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States Abstract Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71˚ rotation of the heme-binding b H-NOX and PAS domains. Repositioning of the b *For correspondence: H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to [email protected] (JHH); move the catalytic domains into an active conformation. YC-1 binds directly between the b H-NOX [email protected] (MAM) domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was †These authors contributed corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the equally to this work endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological Present address: ‡MRC London effects of NO. -
Purinergic Receptor Transactivation by the Β2-Adrenergic Receptor Increases Intracellular Ca2+ in Non-Excitable Cells
Molecular Pharmacology Fast Forward. Published on March 9, 2017 as DOI: 10.1124/mol.116.106419 This article has not been copyedited and formatted. The final version may differ from this version. MOLPHARM/2016/106419 Title page: Purinergic receptor transactivation by the β2-adrenergic receptor increases intracellular Ca2+ in non-excitable cells. Wayne Stallaert, Emma T van der Westhuizen, Anne-Marie Schönegge, Bianca Plouffe, Mireille Downloaded from Hogue, Viktoria Lukashova, Asuka Inoue, Satoru Ishida, Junken Aoki, Christian Le Gouill & Michel Bouvier. molpharm.aspetjournals.org Department of Biochemistry, Université de Montréal, Montréal, QC, Canada (WS, ETvdW, A- MS, BP, MB). Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada (WS, ETvdW, A-MS, BP, MH, VL, CLG, MB). Monash Institute for at ASPET Journals on September 30, 2021 Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (ETvdW). Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan (AI, SI, JA). Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan (AI). Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan (JA). 1 Molecular Pharmacology Fast Forward. Published on March 9, 2017 as DOI: 10.1124/mol.116.106419 This article has not been copyedited and formatted. The final version may differ from this version. MOLPHARM/2016/106419 Running title page: a) Running title: β2AR transactivation of purinergic receptors b) Corresponding author: Michel Bouvier, IRIC - Université de Montréal, P.O. Box 6128 Succursale Centre-Ville, Montréal, Qc. Canada, H3C 3J7. Tel: +1-514-343-6319. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
Cardiovascular and Pharmacological Implications of Haem-Deficient NO
ARTICLE Received 27 Feb 2015 | Accepted 27 Aug 2015 | Published 7 Oct 2015 DOI: 10.1038/ncomms9482 OPEN Cardiovascular and pharmacological implications of haem-deficient NO-unresponsive soluble guanylate cyclase knock-in mice Robrecht Thoonen1,2,w, Anje Cauwels1,2, Kelly Decaluwe3, Sandra Geschka4, Robert E. Tainsh5, Joris Delanghe6, Tino Hochepied1,2, Lode De Cauwer1,2, Elke Rogge1,2, Sofie Voet1,2, Patrick Sips1,2, Richard H. Karas7, Kenneth D. Bloch5, Marnik Vuylsteke8,9, Johannes-Peter Stasch4,10, Johan Van de Voorde3, Emmanuel S. Buys5,* & Peter Brouckaert1,2,* Oxidative stress, a central mediator of cardiovascular disease, results in loss of the prosthetic haem group of soluble guanylate cyclase (sGC), preventing its activation by nitric oxide (NO). Here we introduce Apo-sGC mice expressing haem-free sGC. Apo-sGC mice are viable and develop hypertension. The haemodynamic effects of NO are abolished, but those of the sGC activator cinaciguat are enhanced in apo-sGC mice, suggesting that the effects of NO on smooth muscle relaxation, blood pressure regulation and inhibition of platelet aggregation require sGC activation by NO. Tumour necrosis factor (TNF)-induced hypotension and mortality are preserved in apo-sGC mice, indicating that pathways other than sGC signalling mediate the cardiovascular collapse in shock. Apo-sGC mice allow for differentiation between sGC-dependent and -independent NO effects and between haem-dependent and -independent sGC effects. Apo-sGC mice represent a unique experimental platform to study the in vivo consequences of sGC oxidation and the therapeutic potential of sGC activators. 1 Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium. -
Antagonism of Forkhead Box Subclass O Transcription Factors Elicits Loss of Soluble Guanylyl Cyclase Expression S
Supplemental material to this article can be found at: http://molpharm.aspetjournals.org/content/suppl/2019/04/15/mol.118.115386.DC1 1521-0111/95/6/629–637$35.00 https://doi.org/10.1124/mol.118.115386 MOLECULAR PHARMACOLOGY Mol Pharmacol 95:629–637, June 2019 Copyright ª 2019 by The Author(s) This is an open access article distributed under the CC BY-NC Attribution 4.0 International license. Antagonism of Forkhead Box Subclass O Transcription Factors Elicits Loss of Soluble Guanylyl Cyclase Expression s Joseph C. Galley, Brittany G. Durgin, Megan P. Miller, Scott A. Hahn, Shuai Yuan, Katherine C. Wood, and Adam C. Straub Heart, Lung, Blood and Vascular Medicine Institute (J.C.G., B.G.D., M.P.M., S.A.H., S.Y., K.C.W., A.C.S.) and Department of Pharmacology and Chemical Biology (J.C.G., A.C.S.), University of Pittsburgh, Pittsburgh, Pennsylvania Received November 29, 2018; accepted March 31, 2019 Downloaded from ABSTRACT Nitric oxide (NO) stimulates soluble guanylyl cyclase (sGC) protein expression showed a concentration-dependent down- activity, leading to elevated intracellular cyclic guano- regulation. Consistent with the loss of sGC a and b mRNA and sine 39,59-monophosphate (cGMP) and subsequent vascular protein expression, pretreatment of vascular smooth muscle smooth muscle relaxation. It is known that downregulation of cells with the FoxO inhibitor decreased sGC activity mea- sGC expression attenuates vascular dilation and contributes to sured by cGMP production following stimulation with an NO molpharm.aspetjournals.org the pathogenesis of cardiovascular disease. However, it is not donor. -
Structure/Function of the Soluble Guanylyl Cyclase Catalytic Domain
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nitric Oxide Manuscript Author . Author manuscript; Manuscript Author available in PMC 2018 July 01. Published in final edited form as: Nitric Oxide. 2018 July 01; 77: 53–64. doi:10.1016/j.niox.2018.04.008. Structure/function of the soluble guanylyl cyclase catalytic domain Kenneth C. Childers and Elsa D. Garcin* University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA Abstract Soluble guanylyl cyclase (GC-1) is the primary receptor of nitric oxide (NO) in smooth muscle cells and maintains vascular function by inducing vasorelaxation in nearby blood vessels. GC-1 converts guanosine 5′-triphosphate (GTP) into cyclic guanosine 3′,5′-monophosphate (cGMP), which acts as a second messenger to improve blood flow. While much work has been done to characterize this pathway, we lack a mechanistic understanding of how NO binding to the heme domain leads to a large increase in activity at the C-terminal catalytic domain. Recent structural evidence and activity measurements from multiple groups have revealed a low-activity cyclase domain that requires additional GC-1 domains to promote a catalytically-competent conformation. How the catalytic domain structurally transitions into the active conformation requires further characterization. This review focuses on structure/function studies of the GC-1 catalytic domain and recent advances various groups have made in understanding how catalytic activity is regulated including small molecules interactions, Cys-S-NO modifications and potential interactions with the NO-sensor domain and other proteins. Keywords Soluble guanylyl cyclase; Adenylyl cyclase; Catalytic domain; Nitric oxide; S-nitrosation; Activation mechanism 1. -
A Rare Variant of ANK3 Is Associated with Intracranial Aneurysm
ORIGINAL RESEARCH published: 25 June 2021 doi: 10.3389/fneur.2021.672570 A Rare Variant of ANK3 Is Associated With Intracranial Aneurysm Junyu Liu 1, Xin Liao 2,3, Jilin Zhou 1, Bingyang Li 2, Lu Xu 1, Songlin Liu 1, Yifeng Li 1, Dun Yuan 1, Chongyu Hu 4, Weixi Jiang 1* and Junxia Yan 2,5* 1 Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China, 2 Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China, 3 The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China, 4 Department of Neurology, Hunan People’s Hospital, Changsha, China, 5 Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China Intracranial aneurysm (IA) is a cerebrovascular disorder in which abnormal dilation of a blood vessel results from weakening of the blood vessel wall. The aneurysm may rupture, leading to subarachnoid hemorrhage with severe outcomes. This study was conducted to identify the genetic factors involved in the etiology of IA. Whole-exome sequencing was performed in three IA-aggregate families to identify candidate variants. Further association studies of candidate variants were performed among sporadic cases Edited by: and controls. Bioinformatic analysis was used to predict the functions of candidate Osama O. Zaidat, genes and variants. Twenty variants were identified after whole-exome sequencing, Northeast Ohio Medical University, among which eight were selected for replicative association studies. ANK3 c.4403G>A United States (p.R1468H) was significantly associated with IA (odds ratio 4.77; 95% confidence interval Reviewed by: Basil Erwin Grüter, 1.94–11.67; p-value = 0.00019). -
GSE50161, (C) GSE66354, (D) GSE74195 and (E) GSE86574
Figure S1. Boxplots of normalized samples in five datasets. (A) GSE25604, (B) GSE50161, (C) GSE66354, (D) GSE74195 and (E) GSE86574. The x‑axes indicate samples, and the y‑axes represent the expression of genes. Figure S2. Volanco plots of DEGs in five datasets. (A) GSE25604, (B) GSE50161, (C) GSE66354, (D) GSE74195 and (E) GSE86574. Red nodes represent upregulated DEGs and green nodes indicate downregulated DEGs. Cut‑off criteria were P<0.05 and |log2 FC|>1. DEGs, differentially expressed genes; FC, fold change; adj.P.Val, adjusted P‑value. Figure S3. Transcription factor‑gene regulatory network constructed using the Cytoscape iRegulion plug‑in. Table SI. Primer sequences for reverse transcription‑quantitative polymerase chain reaction. Genes Sequences hsa‑miR‑124 F: 5'‑ACACTCCAGCTGGGCAGCAGCAATTCATGTTT‑3' R: 5'‑CTCAACTGGTGTCGTGGA‑3' hsa‑miR‑330‑3p F: 5'‑CATGAATTCACTCTCCCCGTTTCTCCCTCTGC‑3' R: 5'‑CCTGCGGCCGCGAGCCGCCCTGTTTGTCTGAG‑3' hsa‑miR‑34a‑5p F: 5'‑TGGCAGTGTCTTAGCTGGTTGT‑3' R: 5'‑GCGAGCACAGAATTAATACGAC‑3' hsa‑miR‑449a F: 5'‑TGCGGTGGCAGTGTATTGTTAGC‑3' R: 5'‑CCAGTGCAGGGTCCGAGGT‑3' CD44 F: 5'‑CGGACACCATGGACAAGTTT‑3' R: 5'‑TGTCAATCCAGTTTCAGCATCA‑3' PCNA F: 5'‑GAACTGGTTCATTCATCTCTATGG‑3' F: 5'‑TGTCACAGACAAGTAATGTCGATAAA‑3' SYT1 F: 5'‑CAATAGCCATAGTCGCAGTCCT‑3' R: 5'‑TGTCAATCCAGTTTCAGCATCA‑3' U6 F: 5'‑GCTTCGGCAGCACATATACTAAAAT‑3' R: 5'‑CGCTTCACGAATTTGCGTGTCAT‑3' GAPDH F: 5'‑GGAAAGCTGTGGCGTGAT‑3' R: 5'‑AAGGTGGAAGAATGGGAGTT‑3' hsa, homo sapiens; miR, microRNA; CD44, CD44 molecule (Indian blood group); PCNA, proliferating cell nuclear antigen; -
Disrupted Nitric Oxide Signaling Due to GUCY1A3 Mutations Increases Risk for Moyamoya Disease, Achalasia and Hypertension
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Clin Genet Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 October 01. Published in final edited form as: Clin Genet. 2016 October ; 90(4): 351–360. doi:10.1111/cge.12739. Disrupted Nitric Oxide Signaling due to GUCY1A3 Mutations Increases Risk for Moyamoya Disease, Achalasia and Hypertension Stephanie Wallace1, Dong-chuan Guo1, Ellen Regalado1, Lauren Mellor-Crummey1, Michael Banshad2, Deborah A. Nickerson2, Robert Dauser3, Neil Hanchard4, Ronit Marom4, Emil Martin1, Vladimir Berka1, Iraida Sharina1, Vijeya Ganesan5, Dawn Saunders6, Shaine Morris7, and Dianna M. Milewicz, MD1 1Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas 2Department of Genome Sciences, University of Washington, Seattle, Washington 3Department of Neurosurgery, Texas Children’s Hospital, Houston, Texas 4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 5Neuroscience Unit, University College of London Institute of Child Health, London, UK 6Department of Radiology, Great Ormond Street Hospital, London, UK 7Department of Pediatrics – Cardiology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas Abstract Moyamoya disease (MMD) is a progressive vasculopathy characterized by occlusion of the terminal portion of the internal carotid arteries and its branches, and the formation of compensatory moyamoya collateral vessels. Homozygous mutations in GUCY1A3 have been reported as a cause of MMD and achalasia. Probands (n = 96) from unrelated families underwent sequencing of GUCY1A3. Functional studies were performed to confirm the pathogenicity of identified GUCY1A3 variants. Two affected individuals from unrelated families were found to have compound heterozygous mutations in GUCY1A3.