Druggable Genome in Attention Deficit/Hyperactivity Disorder and Its
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Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
NISCH Antibody Order 021-34695924 [email protected] Support 400-6123-828 50Ul [email protected] 100 Ul √ √ Web
TD13185 NISCH Antibody Order 021-34695924 [email protected] Support 400-6123-828 50ul [email protected] 100 uL √ √ Web www.ab-mart.com.cn Description: Acts either as the functional imidazoline-1 receptor (I1R) candidate or as a membrane- associated mediator of the I1R signaling. Binds numerous imidazoline ligands that induces initiation of cell-signaling cascades triggering to cell survival, growth and migration. Its activation by the agonist rilmenidine induces an increase in phosphorylation of mitogen- activated protein kinases MAPK1 and MAPK3 in rostral ventrolateral medulla (RVLM) neurons that exhibited rilmenidine-evoked hypotension (By similarity). Blocking its activation with efaroxan abolished rilmenidine-induced mitogen-activated protein kinase phosphorylation in RVLM neurons (By similarity). Acts as a modulator of Rac-regulated signal transduction pathways (By similarity). Suppresses Rac1-stimulated cell migration by interacting with PAK1 and inhibiting its kinase activity (By similarity). Also blocks Pak- independent Rac signaling by interacting with RAC1 and inhibiting Rac1-stimulated NF-kB response element and cyclin D1 promoter activation (By similarity). Inhibits also LIMK1 kinase activity by reducing LIMK1 'Tyr-508' phosphorylation (By similarity). Inhibits Rac- induced cell migration and invasion in breast and colon epithelial cells (By similarity). Inhibits lamellipodia formation, when overexpressed (By similarity). Plays a role in protection against apoptosis. Involved in association with IRS4 in the enhancement -
Allantoin Activates Imidazoline I-3 Receptors to Enhance Insulin
Tsai et al. Nutrition & Metabolism 2014, 11:41 http://www.nutritionandmetabolism.com/content/11/1/41 RESEARCH Open Access Allantoin activates imidazoline I-3 receptors to enhance insulin secretion in pancreatic β-cells Cheng-Chia Tsai1, Li-Jen Chen2,3, Ho-Shan Niu3, Kun-Ming Chung4, Juei-Tang Cheng5* and Kao-Chang Lin4,6 Abstract Background: Imidazoline I3 receptors (I-3R) can regulate insulin secretion in pancreatic β-cells. It has been indicated that allantoin ameliorates hyperglycemia by activating imidazoline I2 receptors (I-2R). Thus, the effect of allantoin on I-3R is identified in the present study. Methods: We used male Wistar rats to screen allantoin’s ability for lowering of blood glucose and stimulation of insulin secretion. Chinese hamster ovary-K1 cells transfected with imidazoline receptors (NISCH-CHO-K1 cells) were also applied to characterize the direct effect of allantoin on this receptor. Additionally, KU14R as specific antagonist was treated to block I-3R in rats and in the cultured pancreatic β-cells named Min 6 cells. Results: In rats, allantoin decreased blood sugar with an increase in plasma insulin. Also, allantoin enhanced calcium influx into NISCH-CHO-K1 cells in a way similar to agmatine, an I-R agonist. Moreover, KU14R dose-dependently blocked allantoin-induced insulin secretion both in Min 6 cells and in Wistar rats. Conclusion: Allantoin can activate I-3R to enhance insulin secretion for lowering of blood sugar in Wistar rats. Thus, allantoin may provide beneficial effects as a supplement for diabetic patients after clinical trials. Keywords: Allantoin, Insulin secretion, Imidazoline I3 receptor, CHO-K1, NISCH Background is mentioned to reduce blood glucose [11,12]. -
The Mineralocorticoid Receptor Leads to Increased Expression of EGFR
www.nature.com/scientificreports OPEN The mineralocorticoid receptor leads to increased expression of EGFR and T‑type calcium channels that support HL‑1 cell hypertrophy Katharina Stroedecke1,2, Sandra Meinel1,2, Fritz Markwardt1, Udo Kloeckner1, Nicole Straetz1, Katja Quarch1, Barbara Schreier1, Michael Kopf1, Michael Gekle1 & Claudia Grossmann1* The EGF receptor (EGFR) has been extensively studied in tumor biology and recently a role in cardiovascular pathophysiology was suggested. The mineralocorticoid receptor (MR) is an important efector of the renin–angiotensin–aldosterone‑system and elicits pathophysiological efects in the cardiovascular system; however, the underlying molecular mechanisms are unclear. Our aim was to investigate the importance of EGFR for MR‑mediated cardiovascular pathophysiology because MR is known to induce EGFR expression. We identifed a SNP within the EGFR promoter that modulates MR‑induced EGFR expression. In RNA‑sequencing and qPCR experiments in heart tissue of EGFR KO and WT mice, changes in EGFR abundance led to diferential expression of cardiac ion channels, especially of the T‑type calcium channel CACNA1H. Accordingly, CACNA1H expression was increased in WT mice after in vivo MR activation by aldosterone but not in respective EGFR KO mice. Aldosterone‑ and EGF‑responsiveness of CACNA1H expression was confrmed in HL‑1 cells by Western blot and by measuring peak current density of T‑type calcium channels. Aldosterone‑induced CACNA1H protein expression could be abrogated by the EGFR inhibitor AG1478. Furthermore, inhibition of T‑type calcium channels with mibefradil or ML218 reduced diameter, volume and BNP levels in HL‑1 cells. In conclusion the MR regulates EGFR and CACNA1H expression, which has an efect on HL‑1 cell diameter, and the extent of this regulation seems to depend on the SNP‑216 (G/T) genotype. -
Potassium Channels in Epilepsy
Downloaded from http://perspectivesinmedicine.cshlp.org/ on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Potassium Channels in Epilepsy Ru¨diger Ko¨hling and Jakob Wolfart Oscar Langendorff Institute of Physiology, University of Rostock, Rostock 18057, Germany Correspondence: [email protected] This review attempts to give a concise and up-to-date overview on the role of potassium channels in epilepsies. Their role can be defined from a genetic perspective, focusing on variants and de novo mutations identified in genetic studies or animal models with targeted, specific mutations in genes coding for a member of the large potassium channel family. In these genetic studies, a demonstrated functional link to hyperexcitability often remains elusive. However, their role can also be defined from a functional perspective, based on dy- namic, aggravating, or adaptive transcriptional and posttranslational alterations. In these cases, it often remains elusive whether the alteration is causal or merely incidental. With 80 potassium channel types, of which 10% are known to be associated with epilepsies (in humans) or a seizure phenotype (in animals), if genetically mutated, a comprehensive review is a challenging endeavor. This goal may seem all the more ambitious once the data on posttranslational alterations, found both in human tissue from epilepsy patients and in chronic or acute animal models, are included. We therefore summarize the literature, and expand only on key findings, particularly regarding functional alterations found in patient brain tissue and chronic animal models. INTRODUCTION TO POTASSIUM evolutionary appearance of voltage-gated so- CHANNELS dium (Nav)andcalcium (Cav)channels, Kchan- nels are further diversified in relation to their otassium (K) channels are related to epilepsy newer function, namely, keeping neuronal exci- Psyndromes on many different levels, ranging tation within limits (Anderson and Greenberg from direct control of neuronal excitability and 2001; Hille 2001). -
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. -
Supplemental Data-Ms. 72723-RG-3
Supplemental Data ALS Mutation FUS-R521C Causes DNA Damage and RNA Splicing Defects Haiyan Qiu, Sebum Lee, Yulei Shang, Wen-Yuan Wang, Kin Fai Au, Sherry Kamiya, Sami J. Barmada, Hansen Lui, Steven Finkbeiner, Caitlin E. Carlton, Amy A. Tang, Michael C. Oldham, Hejia Wang, James Shorter, Anthony J. Filiano, Erik D. Roberson, Warren G. Tourtellotte, Bin Chen, Li-Huei Tsai, Eric J. Huang 1 Supplemental Figure 1. Strategy to Propagate FUS-R521C Transgenic Mice and the Kaplan- Meir Curves for Disease Onset and Survival in N1F1, N2F2 and N2F3 FUS-R521C Mice. (A) A schematic diagram showing the strategy to expand and propagate FUS-R521C transgenic mice from founders to N1F1, N2F2 and N2F3 generations. In brief, the FUS-R521C founder was mated with C57BL6 females to generate N1F1 mice. The surviving N1F1 mice (3-6 months old) are intercrossed to generate N1F2 mice, which were mated with C57BL6 to generate N2F2 mice. To maintain the FUS-R521C colony, N2F2 mice were intercrossed for N2F3 mice. (B) Kaplan-Meier survival curve for the disease onset and survival in N1F1 FUS-R521C mice (n=103) and non- transgenic littermate controls (n=182). (C-D) The disease onset and survival curves for N2F2 and N2F3 FUS-R521C mice were similar, supporting the successful propagation of the transgene and the reproducibility of FUS-R521C phenotype. 2 Supplemental Figure 2. Expression of the Endogenous FUS Proteins and FLAG-tagged FUS- R521C Transgenic Proteins in Glial Cells Within Spinal Cord. (A-B’’) Confocal microscopy shows no expression of FUS in Iba-1+ microglial in control spinal cord from wild type mice. -
Breast Cancer Tumor Suppressors: a Special Emphasis on Novel Protein Nischarin Mazvita Maziveyi and Suresh K
Published OnlineFirst September 21, 2015; DOI: 10.1158/0008-5472.CAN-15-1395 Cancer Review Research Breast Cancer Tumor Suppressors: A Special Emphasis on Novel Protein Nischarin Mazvita Maziveyi and Suresh K. Alahari Abstract Tumor suppressor genes regulate cell growth and prevent vast number of cellular processes, including neuronal protection spontaneous proliferation that could lead to aberrant tissue and hypotension. The NISCH promoter experiences hypermethy- function. Deletions and mutations of these genes typically lead lation in several cancers, whereas some highly aggressive breast to progression through the cell-cycle checkpoints, as well as cancer cells exhibit genomic loss of the NISCH locus. Further- increased cell migration. Studies of these proteins are important more, we discuss data illustrating a novel role of Nischarin as as they may provide potential treatments for breast cancers. In this a tumor suppressor in breast cancer. Analysis of this new para- review, we discuss a comprehensive overview on Nischarin, a digm may shed light on various clinical questions. Finally, the novel protein discovered by our laboratory. Nischarin, or imida- therapeutic potential of Nischarin is discussed. Cancer Res; 75(20); zoline receptor antisera-selected protein, is a protein involved in a 4252–9. Ó2015 AACR. Introduction (6, 7). It also interacts with LIM kinase (LIMK) in order to prevent cytoskeletal reorganization (8). Typically, scaffold proteins such Breast cancer initiation and progression involve several genetic as Nischarin are characterized as caretaker genes because their events that can activate oncogenes and/or abrogate the function of effects on tumor growth are indirect. tumor suppressor genes. Tumor suppressor genes are commonly lost or deleted in cancers, facilitating the initiation and progres- sion of cancer through several biological events, including cell Discovery of Nischarin proliferation, cell death, cell migration, and cell invasion. -
Discovery of the First Genome-Wide Significant Risk Loci for Attention Deficit/Hyperactivity Disorder
ARTICLES https://doi.org/10.1038/s41588-018-0269-7 Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder Ditte Demontis 1,2,3,69, Raymond K. Walters 4,5,69, Joanna Martin5,6,7, Manuel Mattheisen1,2,3,8,9,10, Thomas D. Als 1,2,3, Esben Agerbo 1,11,12, Gísli Baldursson13, Rich Belliveau5, Jonas Bybjerg-Grauholm 1,14, Marie Bækvad-Hansen1,14, Felecia Cerrato5, Kimberly Chambert5, Claire Churchhouse4,5,15, Ashley Dumont5, Nicholas Eriksson16, Michael Gandal17,18,19,20, Jacqueline I. Goldstein4,5,15, Katrina L. Grasby21, Jakob Grove 1,2,3,22, Olafur O. Gudmundsson13,23,24, Christine S. Hansen 1,14,25, Mads Engel Hauberg1,2,3, Mads V. Hollegaard1,14, Daniel P. Howrigan4,5, Hailiang Huang4,5, Julian B. Maller5,26, Alicia R. Martin4,5,15, Nicholas G. Martin 21, Jennifer Moran5, Jonatan Pallesen1,2,3, Duncan S. Palmer4,5, Carsten Bøcker Pedersen1,11,12, Marianne Giørtz Pedersen1,11,12, Timothy Poterba4,5,15, Jesper Buchhave Poulsen1,14, Stephan Ripke4,5,27, Elise B. Robinson4,28, F. Kyle Satterstrom 4,5,15, Hreinn Stefansson 23, Christine Stevens5, Patrick Turley4,5, G. Bragi Walters 23,24, Hyejung Won 17,18, Margaret J. Wright 29, ADHD Working Group of the Psychiatric Genomics Consortium (PGC)30, Early Lifecourse & Genetic Epidemiology (EAGLE) Consortium30, 23andMe Research Team30, Ole A. Andreassen 31, Philip Asherson32, Christie L. Burton 33, Dorret I. Boomsma34,35, Bru Cormand36,37,38,39, Søren Dalsgaard 11, Barbara Franke40, Joel Gelernter 41,42, Daniel Geschwind 17,18,19, Hakon Hakonarson43, Jan Haavik44,45, Henry R. -
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Nischarin inhibition alters energy metabolism by activating AMP-activated protein kinase Shengli Dong, Louisiana State University Somesh Baranwal, Louisiana State University AnaPatricia Garcia, Emory University Silvia J. Serrano-Gomez, Louisiana State University Steven Eastlack, Louisiana State University Tomoo Iwakuma, Kansas University Medical Center Donald Mercante, Louisiana State University Franck Mauvais-Jarvis, Tulane University School of Medicine Suresh K. Alahari, Louisiana State University Journal Title: Journal of Biological Chemistry Volume: Volume 292, Number 41 Publisher: American Society for Biochemistry and Molecular Biology | 2017-10-13, Pages 16833-16846 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.1074/jbc.M117.784256 Permanent URL: https://pid.emory.edu/ark:/25593/tdw0b Final published version: http://dx.doi.org/10.1074/jbc.M117.784256 Copyright information: © 2017 by The American Society for Biochemistry and Molecular Biology, Inc. Accessed October 1, 2021 8:18 PM EDT ARTICLE cro Nischarin inhibition alters energy metabolism by activating AMP-activated protein kinase Received for publication, March 2, 2017, and in revised form, August 22, 2017 Published, Papers in Press, August 24, 2017, DOI 10.1074/jbc.M117.784256 Shengli Dong‡, Somesh Baranwal‡§, Anapatricia Garcia¶, Silvia J. Serrano-Gomez‡ʈ, Steven Eastlack‡, Tomoo Iwakuma**, Donald Mercante‡‡, Franck Mauvais-Jarvis§§1, and Suresh K. Alahari‡2 From the ‡Department of Biochemistry and Molecular Biology, School of Medicine, and ‡‡Department of Biostatistics, -
Therapeutic Effect of Agmatine on Neurological Disease: Focus on Ion Channels and Receptors
Neurochemical Research (2019) 44:735–750 https://doi.org/10.1007/s11064-018-02712-1 REVIEW PAPER Therapeutic Effect of Agmatine on Neurological Disease: Focus on Ion Channels and Receptors Sumit Barua1 · Jong Youl Kim1 · Jae Young Kim1 · Jae Hwan Kim4 · Jong Eun Lee1,2,3 Received: 15 October 2018 / Revised: 19 December 2018 / Accepted: 24 December 2018 / Published online: 4 January 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract The central nervous system (CNS) is the most injury-prone part of the mammalian body. Any acute or chronic, central or peripheral neurological disorder is related to abnormal biochemical and electrical signals in the brain cells. As a result, ion channels and receptors that are abundant in the nervous system and control the electrical and biochemical environment of the CNS play a vital role in neurological disease. The N-methyl-D-aspartate receptor, 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl) propanoic acid receptor, kainate receptor, acetylcholine receptor, serotonin receptor, α2-adrenoreceptor, and acid-sensing ion channels are among the major channels and receptors known to be key components of pathophysiological events in the CNS. The primary amine agmatine, a neuromodulator synthesized in the brain by decarboxylation of L-arginine, can regu- late ion channel cascades and receptors that are related to the major CNS disorders. In our previous studies, we established that agmatine was related to the regulation of cell differentiation, nitric oxide synthesis, and murine brain endothelial cell migration, relief of chronic pain, cerebral edema, and apoptotic cell death in experimental CNS disorders. -
Ion Channels 3 1
r r r Cell Signalling Biology Michael J. Berridge Module 3 Ion Channels 3 1 Module 3 Ion Channels Synopsis Ion channels have two main signalling functions: either they can generate second messengers or they can function as effectors by responding to such messengers. Their role in signal generation is mainly centred on the Ca2 + signalling pathway, which has a large number of Ca2+ entry channels and internal Ca2+ release channels, both of which contribute to the generation of Ca2 + signals. Ion channels are also important effectors in that they mediate the action of different intracellular signalling pathways. There are a large number of K+ channels and many of these function in different + aspects of cell signalling. The voltage-dependent K (KV) channels regulate membrane potential and + excitability. The inward rectifier K (Kir) channel family has a number of important groups of channels + + such as the G protein-gated inward rectifier K (GIRK) channels and the ATP-sensitive K (KATP) + + channels. The two-pore domain K (K2P) channels are responsible for the large background K current. Some of the actions of Ca2 + are carried out by Ca2+-sensitive K+ channels and Ca2+-sensitive Cl − channels. The latter are members of a large group of chloride channels and transporters with multiple functions. There is a large family of ATP-binding cassette (ABC) transporters some of which have a signalling role in that they extrude signalling components from the cell. One of the ABC transporters is the cystic − − fibrosis transmembrane conductance regulator (CFTR) that conducts anions (Cl and HCO3 )and contributes to the osmotic gradient for the parallel flow of water in various transporting epithelia.