Carbohydrates 2018
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
(Glut1ds): Methylxanthines Potentiate GLUT1 Haploinsufficiency in Vitro
0031-3998/01/5002-0254 PEDIATRIC RESEARCH Vol. 50, No. 2, 2001 Copyright © 2001 International Pediatric Research Foundation, Inc. Printed in U.S.A. Glucose Transporter Type 1 Deficiency Syndrome (Glut1DS): Methylxanthines Potentiate GLUT1 Haploinsufficiency In Vitro YUAN-YUAN HO, HONG YANG, JÖRG KLEPPER, JORGE FISCHBARG, DONG WANG, AND DARRYL C. DE VIVO Department of Neurology, Columbia University, New York, New York 10032, U.S.A. [Y.Y.H., H.Y., D.W., D.C.D.]; Department of Pediatrics, University of Essen, Essen, Germany 45122 [J.K.]; and Departments of Physiology and Cellular Biophysics, and Ophthalmology, Columbia University, New York, New York 10032, U.S.A. [J.F.] ABSTRACT Methylxanthines such as caffeine and theophylline are known substrate for Glut1. The combined effects of caffeine (3 mM) and to inhibit glucose transport. We have studied such inhibition in phenobarbital (10 mM) on glucose transport, as determined in the glucose transporter type 1 deficiency syndrome (Glut1DS) by patient 15 and the maternal control, show no additive or syner- erythrocyte glucose transport assays. Data from four patients gistic inhibition. These data indicate that caffeine and phenobar- with individual mutations in the GLUT1 gene are discussed: bital have similar Glut1 inhibitory properties in these two sub- patient 1 (hemizygosity), 3 (S66F), 15 (368Ins23), and 17 jects. Our study suggests that Glut1DS patients may have a (R333W). Zero-trans influx of 14C-labeled 3-O-methyl glucose reduced safety margin for methylxanthines. Consumption of (3-OMG) into erythrocytes of patients is reduced (patient 1, 51%; methylxanthine-containing products may aggravate the neuro- 3, 45%; 15, 31%; 17, 52%) compared with maternal controls. -
Regulation of Myocardial Glucose Transporters GLUT1 and GLUT4 in Chronically Anemic Fetal Lambs
0031-3998/05/5804-0713 PEDIATRIC RESEARCH Vol. 58, No. 4, 2005 Copyright © 2005 International Pediatric Research Foundation, Inc. Printed in U.S.A. Regulation of Myocardial Glucose Transporters GLUT1 and GLUT4 in Chronically Anemic Fetal Lambs J. CARTER RALPHE, PETER N. NAU, CHRISTOPHER E. MASCIO, JEFFREY L. SEGAR, AND THOMAS D. SCHOLZ Department of Pediatrics [J.C.R., P.N.N., J.L.S., T.D.S.], Department of Surgery [C.E.M.], University of Iowa, Iowa City, Iowa 52242 ABSTRACT Little is known about the chronic adaptations that take place steady state, GLUT4 protein localized to the sarcolemma mem- in the fetal heart to allow for increased substrate delivery in brane. These findings suggest that the glucose transporters are response to chronic stress. Because glucose is an important fuel post-transcriptionally regulated in myocardium of chronically for the fetal cardiomyocytes, we hypothesized that myocardial anemic fetal sheep with changes that mimic normal postnatal glucose transporters 1 and 4 (GLUT1 and GLUT4, respectively) development. Unlike the postnatal heart, localization of GLUT4 are up-regulated in the fetal sheep heart that is chronically to the cell membrane suggests the importance of GLUT4 in basal stressed by anemia. Fetal sheep at 128 d gestation underwent glucose uptake in the stressed fetal heart. (Pediatr Res 58: daily isovolumic hemorrhage and determination of myocardial 713–718, 2005) blood flow, oxygen consumption, and substrate utilization. At the endof3or7dofanemia, myocardial levels of GLUT1 and Abbreviations GLUT4 mRNA and protein were measured and subcellular ERK, extracellular-regulated kinase localization was determined. Despite stable heart rate and blood GLUT1(4), glucose transporter 1 (4) pressure, anemia caused a nearly 4-fold increase in right and left HIF-1␣, hypoxia-inducible factor 1␣ ventricular (RV and LV) free wall blood flow. -
Multivalent Carbohydrate-Lectin Interactions: How Synthetic Chemistry Enables Insights Into Nanometric Recognition
molecules Review Multivalent Carbohydrate-Lectin Interactions: How Synthetic Chemistry Enables Insights into Nanometric Recognition René Roy 1,*, Paul V. Murphy 2 and Hans-Joachim Gabius 3 1 Pharmaqam and Nanoqam, Department of Chemistry, University du Québec à Montréal, P. O. Box 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada 2 School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland; [email protected] 3 Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, München 80539, Germany; [email protected] * Correspondence: [email protected]; Tel.: +1-514-987-3000 (ext. 2546) Academic Editor: Trinidad Velasco-Torrijos Received: 7 April 2016; Accepted: 10 May 2016; Published: 13 May 2016 Abstract: Glycan recognition by sugar receptors (lectins) is intimately involved in many aspects of cell physiology. However, the factors explaining the exquisite selectivity of their functional pairing are not yet fully understood. Studies toward this aim will also help appraise the potential for lectin-directed drug design. With the network of adhesion/growth-regulatory galectins as therapeutic targets, the strategy to recruit synthetic chemistry to systematically elucidate structure-activity relationships is outlined, from monovalent compounds to glyco-clusters and glycodendrimers to biomimetic surfaces. The versatility of the synthetic procedures enables to take examining structural and spatial parameters, alone and in combination, to its limits, for example with the aim to produce inhibitors for distinct galectin(s) that exhibit minimal reactivity to other members of this group. Shaping spatial architectures similar to glycoconjugate aggregates, microdomains or vesicles provides attractive tools to disclose the often still hidden significance of nanometric aspects of the different modes of lectin design (sequence divergence at the lectin site, differences of spatial type of lectin-site presentation). -
Is Retinal Metabolic Dysfunction at the Center of the Pathogenesis of Age-Related Macular Degeneration?
International Journal of Molecular Sciences Review Is Retinal Metabolic Dysfunction at the Center of the Pathogenesis of Age-related Macular Degeneration? Thierry Léveillard 1,*, Nancy J. Philp 2 and Florian Sennlaub 3 1 . Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France 2 . Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; [email protected] 3 . Department of Therapeutics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; fl[email protected] * Correspondence: [email protected]; Tel.: +33-1-5346-2548 Received: 21 December 2018; Accepted: 5 February 2019; Published: 11 February 2019 Abstract: The retinal pigment epithelium (RPE) forms the outer blood–retina barrier and facilitates the transepithelial transport of glucose into the outer retina via GLUT1. Glucose is metabolized in photoreceptors via the tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS) but also by aerobic glycolysis to generate glycerol for the synthesis of phospholipids for the renewal of their outer segments. Aerobic glycolysis in the photoreceptors also leads to a high rate of production of lactate which is transported out of the subretinal space to the choroidal circulation by the RPE. Lactate taken up by the RPE is converted to pyruvate and metabolized via OXPHOS. Excess lactate in the RPE is transported across the basolateral membrane to the choroid. The uptake of glucose by cone photoreceptor cells is enhanced by rod-derived cone viability factor (RdCVF) secreted by rods and by insulin signaling. Together, the three cells act as symbiotes: the RPE supplies the glucose from the choroidal circulation to the photoreceptors, the rods help the cones, and both produce lactate to feed the RPE. -
Disease-Induced Modulation of Drug Transporters at the Blood–Brain Barrier Level
International Journal of Molecular Sciences Review Disease-Induced Modulation of Drug Transporters at the Blood–Brain Barrier Level Sweilem B. Al Rihani 1 , Lucy I. Darakjian 1, Malavika Deodhar 1 , Pamela Dow 1 , Jacques Turgeon 1,2 and Veronique Michaud 1,2,* 1 Tabula Rasa HealthCare, Precision Pharmacotherapy Research and Development Institute, Orlando, FL 32827, USA; [email protected] (S.B.A.R.); [email protected] (L.I.D.); [email protected] (M.D.); [email protected] (P.D.); [email protected] (J.T.) 2 Faculty of Pharmacy, Université de Montréal, Montreal, QC H3C 3J7, Canada * Correspondence: [email protected]; Tel.: +1-856-938-8697 Abstract: The blood–brain barrier (BBB) is a highly selective and restrictive semipermeable network of cells and blood vessel constituents. All components of the neurovascular unit give to the BBB its crucial and protective function, i.e., to regulate homeostasis in the central nervous system (CNS) by removing substances from the endothelial compartment and supplying the brain with nutrients and other endogenous compounds. Many transporters have been identified that play a role in maintaining BBB integrity and homeostasis. As such, the restrictive nature of the BBB provides an obstacle for drug delivery to the CNS. Nevertheless, according to their physicochemical or pharmacological properties, drugs may reach the CNS by passive diffusion or be subjected to putative influx and/or efflux through BBB membrane transporters, allowing or limiting their distribution to the CNS. Drug transporters functionally expressed on various compartments of the BBB involve numerous proteins from either the ATP-binding cassette (ABC) or the solute carrier (SLC) superfamilies. -
Crystal Structure of a Glucose/H Symporter and Its Mechanism of Action
+ Crystal structure of a glucose/H symporter and its mechanism of action Cristina V. Iancua, Jamillah Zamoonb, Sang Bum Wooa, Alexander Aleshinc, and Jun-yong Choea,1 aDepartment of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago,IL 60064; bDepartment of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City 13060, Kuwait; and cDepartment of Infectious Diseases, Sanford Burnham Medical Research Institute, La Jolla, CA 92037 Edited* by H. Ronald Kaback, University of California, Los Angeles, CA, and approved September 26, 2013 (received for review June 25, 2013) + Glucose transporters are required to bring glucose into cells, of a Staphylococcus epidermidis glucose/H symporter (GlcPSe) where it is an essential energy source and precursor in protein by single anomalous dispersion methods. GlcPSe shares high se- and lipid synthesis. These transporters are involved in important quence identity (27–34%) and homology (49–58%) with the hu- common diseases such as cancer and diabetes. Here, we report the man GLUTs (Table S1), is highly specific for glucose, and is + crystal structure of the Staphylococcus epidermidis glucose/H sym- inhibited by the well-characterized inhibitors of human GLUTs porter in an inward-facing conformation at 3.2-Å resolution. The phloretin, cytochalasin B, and forskolin. In contrast to GlcP , + Se Staphylococcus epidermidis glucose/H symporter is homologous XylE transports xylose but not glucose, which is an inhibitor, and is to human glucose transporters, is very specific and has high avidity impervious to inhibition by cytochalasin B (13, 24). On the basis of for glucose, and is inhibited by the human glucose transport inhib- the GlcPSe structure and functional studies of wild-type and mu- itors cytochalasin B, phloretin, and forskolin. -
Downloaded from the App Store and Nucleobase, Nucleotide and Nucleic Acid Metabolism 7 Google Play
Hoytema van Konijnenburg et al. Orphanet J Rare Dis (2021) 16:170 https://doi.org/10.1186/s13023-021-01727-2 REVIEW Open Access Treatable inherited metabolic disorders causing intellectual disability: 2021 review and digital app Eva M. M. Hoytema van Konijnenburg1†, Saskia B. Wortmann2,3,4†, Marina J. Koelewijn2, Laura A. Tseng1,4, Roderick Houben6, Sylvia Stöckler‑Ipsiroglu5, Carlos R. Ferreira7 and Clara D. M. van Karnebeek1,2,4,8* Abstract Background: The Treatable ID App was created in 2012 as digital tool to improve early recognition and intervention for treatable inherited metabolic disorders (IMDs) presenting with global developmental delay and intellectual disabil‑ ity (collectively ‘treatable IDs’). Our aim is to update the 2012 review on treatable IDs and App to capture the advances made in the identifcation of new IMDs along with increased pathophysiological insights catalyzing therapeutic development and implementation. Methods: Two independent reviewers queried PubMed, OMIM and Orphanet databases to reassess all previously included disorders and therapies and to identify all reports on Treatable IDs published between 2012 and 2021. These were included if listed in the International Classifcation of IMDs (ICIMD) and presenting with ID as a major feature, and if published evidence for a therapeutic intervention improving ID primary and/or secondary outcomes is avail‑ able. Data on clinical symptoms, diagnostic testing, treatment strategies, efects on outcomes, and evidence levels were extracted and evaluated by the reviewers and external experts. The generated knowledge was translated into a diagnostic algorithm and updated version of the App with novel features. Results: Our review identifed 116 treatable IDs (139 genes), of which 44 newly identifed, belonging to 17 ICIMD categories. -
Frontiersin.Org 1 April 2015 | Volume 9 | Article 123 Saunders Et Al
ORIGINAL RESEARCH published: 28 April 2015 doi: 10.3389/fnins.2015.00123 Influx mechanisms in the embryonic and adult rat choroid plexus: a transcriptome study Norman R. Saunders 1*, Katarzyna M. Dziegielewska 1, Kjeld Møllgård 2, Mark D. Habgood 1, Matthew J. Wakefield 3, Helen Lindsay 4, Nathalie Stratzielle 5, Jean-Francois Ghersi-Egea 5 and Shane A. Liddelow 1, 6 1 Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC, Australia, 2 Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark, 3 Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia, 4 Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland, 5 Lyon Neuroscience Research Center, INSERM U1028, Centre National de la Recherche Scientifique UMR5292, Université Lyon 1, Lyon, France, 6 Department of Neurobiology, Stanford University, Stanford, CA, USA The transcriptome of embryonic and adult rat lateral ventricular choroid plexus, using a combination of RNA-Sequencing and microarray data, was analyzed by functional groups of influx transporters, particularly solute carrier (SLC) transporters. RNA-Seq Edited by: Joana A. Palha, was performed at embryonic day (E) 15 and adult with additional data obtained at University of Minho, Portugal intermediate ages from microarray analysis. The largest represented functional group Reviewed by: in the embryo was amino acid transporters (twelve) with expression levels 2–98 times Fernanda Marques, University of Minho, Portugal greater than in the adult. In contrast, in the adult only six amino acid transporters Hanspeter Herzel, were up-regulated compared to the embryo and at more modest enrichment levels Humboldt University, Germany (<5-fold enrichment above E15). -
Hereditary Xerocytosis Revisited
SOLVING CLINICAL PROBLEMS IN BLOOD DISEASES AJH AJH Educational Material A physician or group of physicians considers presentation and evolution of a real clinical case, reacting to clinical information and data (boldface type). This is followed by a discussion/commentary Hereditary xerocytosis revisited Natasha M. Archer,1,2 Boris E. Shmukler,3,4 Immacolata Andolfo,5,6 David H. Vandorpe,3,4 Radhakrishnan Gnanasambandam,7 John M. Higgins,8,9 Alicia Rivera,10,11 Mark D. Fleming,11 Frederick Sachs,7 Philip A. Gottlieb,7 Achille Iolascon,5,6 Carlo Brugnara,10,11 Seth L. Alper,3,4,12* and David G. Nathan1,2,13* A 21-year-old male student presented in 1980 as an Olympic ath- corpuscular hemoglobin (MCH), increased osmotic fragility, and mis- lete with a 12-year history of jaundice, pallor, and darkened urine sense mutations in the red cell membrane gene products SLC4A1/ induced by the atraumatic exercise of swimming [1]. Physical AE1, SLC2A1/GLUT1, and RHAG. HX, sometimes referred to as examination at that time was remarkable only for moderate scleral dehydrated stomatocytosis (DHSt), is caused by missense mutations icterus without hepatosplenomegaly. Hematological examination in the ATP binding cassette transporter ABCB6 [4] and in the red revealed moderate macrocytosis (mean corpuscular volume (MCV) cell membrane mechanosensitive cation channel, PIEZO1 [5–7]. Fam- 102 fL) without anemia (Hct 50%, Hb 17 g/dL, 9% reticulocytes). ilial pseudohyperkalemia, a related benign condition, is characterized The peripheral blood smear showed occasional target cells. Red cell by temperature-dependent loss of erythrocyte K, and is an incom- osmotic fragility was decreased. -
Bioisosteres of Carbohydrate Functional Groups in Glycomimetic Design
biomimetics Review Bioisosteres of Carbohydrate Functional Groups in Glycomimetic Design Rachel Hevey Molecular Pharmacy, Department Pharmaceutical Sciences, University of Basel, Klingelbergstr. 50, 4056 Basel, Switzerland; [email protected] Received: 30 June 2019; Accepted: 26 July 2019; Published: 28 July 2019 Abstract: The aberrant presentation of carbohydrates has been linked to a number of diseases, such as cancer metastasis and immune dysregulation. These altered glycan structures represent a target for novel therapies by modulating their associated interactions with neighboring cells and molecules. Although these interactions are highly specific, native carbohydrates are characterized by very low affinities and inherently poor pharmacokinetic properties. Glycomimetic compounds, which mimic the structure and function of native glycans, have been successful in producing molecules with improved pharmacokinetic (PK) and pharmacodynamic (PD) features. Several strategies have been developed for glycomimetic design such as ligand pre-organization or reducing polar surface area. A related approach to developing glycomimetics relies on the bioisosteric replacement of carbohydrate functional groups. These changes can offer improvements to both binding affinity (e.g., reduced desolvation costs, enhanced metal chelation) and pharmacokinetic parameters (e.g., improved oral bioavailability). Several examples of bioisosteric modifications to carbohydrates have been reported; this review aims to consolidate them and presents different possibilities for enhancing core interactions in glycomimetics. Keywords: bioisostere; carbohydrate; drug design; glycomimetic; lectin 1. Introduction The interaction of carbohydrates with proteins and cells is well established to play important roles in biology, from the maintenance of healthy tissue to the progression of diseases. The majority of cell types have a thick layer of carbohydrates at their surface which is approximately 10–100 Å thick, referred to as the glycocalyx [1,2]. -
In the Search of Glycoside-Based Molecules As Antidiabetic Agents
Topics in Current Chemistry (2019) 377:19 https://doi.org/10.1007/s41061-019-0243-6 REVIEW In the Search of Glycoside‑Based Molecules as Antidiabetic Agents Aleksandra Pałasz, et al. [full author details at the end of the article] Received: 20 December 2018 / Accepted: 14 May 2019 / Published online: 5 June 2019 © The Author(s) 2019 Abstract This review is an efort to summarize recent developments in synthesis of O-glyco- sides and N-, C-glycosyl molecules with promising antidiabetic potential. Articles published after 2000 are included. First, the O-glycosides used in the treatment of diabetes are presented, followed by the N-glycosides and fnally the C-glycosides constituting the largest group of antidiabetic drugs are described. Within each group of glycosides, we presented how the structure of compounds representing poten- tial drugs changes and when discussing chemical compounds of a similar structure, achievements are presented in the chronological order. C-Glycosyl compounds mim- icking O-glycosides structure, exhibit the best features in terms of pharmacody- namics and pharmacokinetics. Therefore, the largest part of the article is concerned with the description of the synthesis and biological studies of various C-glycosides. Also N-glycosides such as N-(β-D-glucopyranosyl)-amides, N-(β-D-glucopyranosyl)- ureas, and 1,2,3-triazolyl derivatives belong to the most potent classes of antidia- betic agents. In order to indicate which of the compounds presented in the given sec- tions have the best inhibitory properties, a list of the best inhibitors is presented at the end of each section. In summary, the best inhibitors were selected from each of the summarizing fgures and the results of the ranking were placed.