G Protein-Coupled Receptor Systems As Crucial Regulators of DNA Damage Response Processes
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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. -
Comprehensive Assessment of the Association of WNK4
OPEN Comprehensive Assessment of the SUBJECT AREAS: Association of WNK4 Polymorphisms GENETICS RESEARCH RENOVASCULAR HYPERTENSION with Hypertension: Evidence from a EPIDEMIOLOGY Meta-Analysis Received Xiao-gang Guo1, Jie Ding1, Hui Xu1,2, Tian-ming Xuan1, Wei-quan Jin1, Xiang Yin1, Yun-peng Shang1, 22 April 2014 Fu-rong Zhang1, Jian-hua Zhu1 & Liang-rong Zheng1 Accepted 15 September 2014 1Department of Cardiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China, Published 2Xiuzhou District, Gaozhao Street Community Health Service Center, Jiaxing 314031, China. 30 September 2014 The relationship between with-no-lysine [K] kinase 4 (WNK4) gene polymorphisms and hypertension has been widely investigated, However, the studies yielded contradictory results. To evaluate these inconclusive Correspondence and findings comprehensively, we therefore performed a meta-analysis. Ten articles encompassing 16 requests for materials independent case-control studies with 6089 hypertensive cases and 4881 normotensive controls were should be addressed to selected for this meta-analysis. Four WNK4 gene polymorphisms were identified (G1155942T, G1156666A, X.-G.G. (gxg22222@ T1155547C, and C6749T). The results showed statistically significant associations of G1155942T polymorphism (allelic genetic model: odds ration or OR51.62, 95% confidence interval or CI: 1.11–2.38, zju.edu.cn) P50.01; dominant model: OR51.85, 95% CI: 1.07–3.19, P50.03) and C6749T polymorphism (allele contrast: OR52.04, 95% CI: 1.60–2.59, P,0.01; dominant model: OR52.04, 95%CI: 1.59–2.62, P,0.01; and homozygous model: OR55.01, 95% CI: 1.29–19.54, P50.02) with hypertension risk. However, neither C1155547T nor G1156666A was associated significantly with hypertension susceptibility. -
Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum
SUPPLEMENTARY MATERIAL Comprehensive assessment of Indian variations in the druggable kinome landscape highlights distinct insights at the sequence, structure and pharmacogenomic stratum Gayatri Panda1‡, Neha Mishra1‡, Disha Sharma2,3, Rahul C. Bhoyar3, Abhinav Jain2,3, Mohamed Imran2,3, Vigneshwar Senthilvel2,3, Mohit Kumar Divakar2,3, Anushree Mishra3, Priyanka Banerjee4, Sridhar Sivasubbu2,3, Vinod Scaria2,3, Arjun Ray1* 1 Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India. 2 Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India. 3 CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi-110020, India. 4 Institute for Physiology, Charite-University of Medicine, Berlin, 10115 Berlin, Germany. ‡These authors contributed equally to this work. * [email protected] TABLE OF CONTENTS Name Title Supplemental_Figure_S1 Fauchere and Pliska hydrophobicity scale for variations in structure data Supplemental_Figure_S2 Phenotypic drug-drug correlogram Supplemental_Table_S1 545 kinase coding genes used in the study Supplemental_Table_S2 Classes and count of kinase coding genes Supplemental_Table_S3 Allele frequency Indian v/s other populations from 1000 genome data(1000g2015). Supplemental_Table_S4 IndiGen Structure Data- consisting of 12 genes and their 22 variants Supplemental_Table_S5 Genes, PDB ids, mutations in IndiGen data and associated drugs (FDA approved) Supplemental_Table_S6 Data used for docking and binding pocket similarity analysis Supplemental_Table_S7 -
G Protein-Coupled Receptor Kinase 4 Gene Variants in Human Essential Hypertension
G protein-coupled receptor kinase 4 gene variants in human essential hypertension Robin A. Felder*, Hironobu Sanada*†, Jing Xu‡, Pei-Ying Yu‡, Zheng Wang‡, Hidetsuna Watanabe*, Laureano D. Asico*, Wei Wang‡, Shaopeng Zheng‡, Ikuyo Yamaguchi‡, Scott M. Williams§, James Gainer¶, Nancy J. Brown¶, Debra Hazen-Martinʈ, Lee-Jun C. Wong**, Jean E. Robillard††, Robert M. Carey‡‡, Gilbert M. Eisner‡, and Pedro A. Jose‡ *Department of Pathology, University of Virginia Health Sciences Center, Charlottesville, VA 22908; ‡Department of Pediatrics and Physiology and Biophysics, Georgetown University Medical Center, Washington, DC 20007; §Department of Microbiology, Meharry Medical College, Nashville, TN 37208; ¶Department of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232; ʈDepartment of Pathology, Medical University of South Carolina, Charleston, SC 29403; **Institute for Molecular and Human Genetics, Georgetown University Medical Center, Washington, DC 20007; ††Department of Pediatrics, University of Michigan College of Medicine, Ann Arbor, MI 48109; and ‡‡Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908 Communicated by Maria Iandolo New, Weill Medical College of Cornell University, New York, NY, December 21, 2001 (received for review August 10, 2001) Essential hypertension has a heritability as high as 30–50%, but its abnormal renal sodium transporters (3, 8, 13, 17). Also, the genetic cause(s) has not been determined despite intensive inves- coding region of the D1 receptor is unchanged in hypertensive tigation. The renal dopaminergic system exerts a pivotal role in subjects (16), as well as in rodents with genetic hypertension maintaining fluid and electrolyte balance and participates in the (unpublished studies). pathogenesis of genetic hypertension. -
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 -
Cells Receptor-Evoked Responses of Human Mast RGS13 Controls G
RGS13 Controls G Protein-Coupled Receptor-Evoked Responses of Human Mast Cells This information is current as Geetanjali Bansal, Jeffrey A. DiVietro, Hye Sun Kuehn, of September 25, 2021. Sudhir Rao, Karl H. Nocka, Alasdair M. Gilfillan and Kirk M. Druey J Immunol 2008; 181:7882-7890; ; doi: 10.4049/jimmunol.181.11.7882 http://www.jimmunol.org/content/181/11/7882 Downloaded from References This article cites 65 articles, 27 of which you can access for free at: http://www.jimmunol.org/content/181/11/7882.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 25, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2008 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology RGS13 Controls G Protein-Coupled Receptor-Evoked Responses of Human Mast Cells1 Geetanjali Bansal,2* Jeffrey A. DiVietro,* Hye Sun Kuehn,† Sudhir Rao,3‡ Karl H. Nocka,4‡ Alasdair M. Gilfillan,4† and Kirk M. -
GRK4 Protein Recombinant Human Protein Expressed in Sf9 Cells
Catalog # Aliquot Size G02-31G-20 20 µg G02-31G-50 50 µg GRK4 Protein Recombinant human protein expressed in Sf9 cells Catalog # G02-31G Lot # P1749-5 Product Description Purity Recombinant human GRK4 (140-end) was expressed by baculovirus in Sf9 insect cells using an N-terminal GST tag. The gene accession number for GRK4 is BC117320. The purity of GRK4 was determined to be >70% by densitometry, GRK4 Gene Aliases approx. MW 75kDa. GPRK2L, GPRK4, GRK4a, IT11 Formulation Recombinant protein stored in 50mM Tris-HCl, pH 7.5, 150mM NaCl, 10mM glutathione, 0.1mM EDTA, 0.25mM DTT, 0.1mM PMSF, 25% glycerol. Storage and Stability o Store product at –70 C. For optimal storage, aliquot target into smaller quantities after centrifugation and store at recommended temperature. For most favorable performance, avoid repeated handling and multiple freeze/thaw cycles. Scientific Background GRK4 or G protein-coupled receptor kinase 4 is a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase subfamily of the Ser/Thr protein kinase family which phosphorylates the activated forms of G protein-coupled receptors thus initiating its deactivation and it also play an important role in receptor desensitization. GRK4 protein has kinase activity GRK4 Protein and that it interacts with and is inhibitable by calmodulin Recombinant human protein expressed in Sf9 cells (1).GRK4 has been linked to both genetic and acquired Catalog # hypertension. GRK4 is highly expressed in testis (2). G02-31G Lot # P1749-5 References Purity >70% Concentration 0.05 µg/µl Stability 1yr at –70oC from date of shipment 1. -
Manuscrit De Thèse
MANUSCRIT DE THÈSE En vue de l’obtention du titre de Docteur en Sciences du vivant de l’université Paris Descartes Julien Fregeac Rôle du microARN 146a dans le développement cérébral et pertinence pour les maladies du neurodéveloppement Défense de thèse devant le jury composé de Docteur Alessandra Pierani Présidente Docteur Marion Coolen Rapporteure Docteur Frédéric Laumonnier Rapporteur Professeur Pierre Gressens Examinateur Professeur Christophe Lefebvre Examinateur Docteur Laurence Colleaux Directrice de thèse 1 2 Do not take life too seriously. You will never get out of it alive. Elbert Hubbard 3 4 REMERCIEMENTS À mon jury Mes premiers remerciements vont au Dr Marion Coolen et au Dr Frédéric Laumonnier pour le temps qu’ils ont pris afin d'évaluer mon manuscrit, au Pr Pierre Gressens et au Pr Christophe Lefebvre pour avoir accepté d’être mes examinateurs et au Dr Alessandra Pierani pour me faire l’honneur de présider mon jury. Enfin, je remercie l’ensemble de mon jury de m'offrir l'opportunité de discuter de mon projet de thèse avec des experts. Au Dr Laurence Colleaux J'aimerais adresser mes plus grands remerciements à ma directrice de thèse. J'aimerais te remercier Laurence pour m'avoir recruté et cru en moi alors même qu'on n'avait pas encore de financement de thèse, pour m'avoir encadré tout au long de ces quatre années de la meilleure des manières et encore plus pour ton soutien dans les moments difficiles de ces deux dernières années. Tu es une grande scientifique et une chef avec qui c'est un plaisir de travailler mais tu es avant tout une personne formidable. -
Systems Vaccinology for a Live Attenuated Tularemia Vaccine Reveals Unique Transcriptional Signatures That Predict Humoral and Cellular Immune Responses"’ Version 1.0
Supplementary Text Manuscript Appendix "‘Systems vaccinology for a live attenuated tularemia vaccine reveals unique transcriptional signatures that predict humoral and cellular immune responses"’ Version 1.0 December 23, 2019 Table of Contents 1 Introduction 8 2 Supplemental methods 8 2.1 Study Design . 8 2.2 Microarray experiment . 8 2.3 Cell mediated immunity experiments . 9 2.4 Microarray data preprocessing . 10 2.5 Differential gene analysis . 11 2.6 Determination of robust gene clusters . 11 2.7 Gene set enrichment analysis . 11 2.8 Regularized logistic regression analysis . 12 2.9 Regularized canonical correlation analysis . 13 2.10 Comparisons with viral vaccine microarray studies . 14 2.11 Cell mediated immunity analysis . 15 3 Supplemental results 15 4 References 84 1 List of Tables Table 1 Descriptive summary statistics of percent monocyte cells of live PBMCs fold change from baseline by treatment. 16 Table 2 Descriptive summary statistics of percent monocyte cells (CD16+) of live PBMCs fold change from baseline by treatment. 16 Table 3 Descriptive summary statistics of percent monocyte cells (CD16-) of live PBMCs fold change from baseline by treatment. 16 Table 4 Descriptive summary statistics of percent T-cells of live PBMCs fold change from baseline by treatment. 16 Table 5 Descriptive summary statistics of percent T-cells (CD4+) of live PBMCs fold change from baseline by treatment. 16 Table 6 Descriptive summary statistics of percent T-cells (CD4-) of live PBMCs fold change from baseline by treatment. 17 Table 7 Descriptive summary statistics of percent natural killer cells (CD56 bright) of live PBMCs fold change from baseline by treatment. -
Function and Regulation of Heterotrimeric G Proteins During Chemotaxis Kamp, Marjon E; Liu, Youtao; Kortholt, Arjan
University of Groningen Function and Regulation of Heterotrimeric G Proteins during Chemotaxis Kamp, Marjon E; Liu, Youtao; Kortholt, Arjan Published in: International Journal of Molecular Sciences DOI: 10.3390/ijms17010090 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2016 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Kamp, M. E., Liu, Y., & Kortholt, A. (2016). Function and Regulation of Heterotrimeric G Proteins during Chemotaxis. International Journal of Molecular Sciences, 17(1), [90]. https://doi.org/10.3390/ijms17010090 Copyright Other than for strictly personal use, 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), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 26-09-2021 International Journal of Molecular Sciences Review Function and Regulation of Heterotrimeric G Proteins during Chemotaxis Marjon E. Kamp †, Youtao Liu † and Arjan Kortholt * Received: 28 November 2015; Accepted: 31 December 2015; Published: 14 January 2016 Academic Editor: Kathleen Van Craenenbroeck Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; [email protected] (M.E.K.); [email protected] (Y.L.) * Correspondence: [email protected]; Tel.: +31-50-363-4206 † These authors contributed equally to this work. -
Supplementary Table S1. Kinase Selectivity of MPI-0479605. (A)
A B In-house kinase profiling Invitrogen SelectScreen Profiling % % % Kinase IC50 ( M) Kinase IC50 ( M) inhibition inhibition inhibition AKT3 >5 IKK-epsilon >5 Kinase at 500 nM Kinase at 500 nM Kinase at 500 nM ALK 0.26 INSR 0.38 ABL1 7 GRK6 -7 PAK1 4 AUR-A >5 JAK1 >5 GRK2 4 HCK 7 PASK 6 AUR-B >5 JNK1 0.11 AKT1 2 HIPK2 9 PHKG1 8 AUR-C >5 MEK1 >5 AXL 6 HIPK4 -6 PRKCB1 -2 B-RAF 3.2 MST4 >5 BMX 14 IGF1R 37 PRKCE 0 CDK1 >5 NEK2 >5 BRSK1 -9 IRAK4 0 PRKCG 3 CDK2 >5 PDK1 >5 CAMK2D -1 ITK 9 PRKCI -2 CDK6 >5 PKA >5 CDC42 BPA 0 LCK 29 PRKCN 6 CHK1 >5 PKC-delta >5 CDK5/p25 -1 LIMK1 17 PRKCZ -5 CHK2 >5 PLK1 >5 CSF1R 82 MAP2K1 11 PRKG2 2 C-MET >5 PLK4 3.3 CSK 1 MAP2K6 2 PTK6 15 C-SRC >5 ROCK2 >5 CSNK1D 10 MAP3K3 17 RET 11 DYRK2 >5 RSK2 >5 CSNK1G1 -1 MAP3K5 -1 RPS6KA2 23 ERK2 3.9 STK33 1.1 CSNK2A2 33 MAP3K8 12 RPS6KA5 2 FAK1 2.7 TAK1 >5 DCAMKL2 2 MAPK1 0 SGK2 4 FER 0.59 TAO1 >5 DYRK1B 1 MAPK11 2 SNF1LK2 3 FLT3 0.080 TBK1 >5 EEF2K 2 MAPK12 5 SRPK2 -3 HGK >5 TRKB >5 EGFR 14 MAPK3 -2 STK22B 11 IKK-alpha >5 YES1 >5 EPHA1 6 MAPK9 61 STK23 -1 IKK-beta >5 EPHA4 -10 MAPKAPK2 9 STK24 -2 EPHB1 -33 MARK4 3 STK25 0 ERBB2 5 MELK 6 TEK 6 FGFR1 15 MERTK 7 TYK2 10 FGR 17 MKNK1 2 TYRO3 -2 FLT4 15 MST1R 3 ZAP70 5 FRAP1 7 NEK1 1 GRK4 3 NEK4 -6 Supplementary Table S1. -
A Loss-Of-Function Genetic Screening Identifies Novel Mediators of Thyroid Cancer Cell Viability
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 19 A loss-of-function genetic screening identifies novel mediators of thyroid cancer cell viability Maria Carmela Cantisani1, Alessia Parascandolo2, Merja Perälä3,4, Chiara Allocca2, Vidal Fey3,4, Niko Sahlberg3,4, Francesco Merolla5, Fulvio Basolo6, Mikko O. Laukkanen1, Olli Pekka Kallioniemi7, Massimo Santoro2,8, Maria Domenica Castellone8 1IRCCS SDN, Naples, Italy 2Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita’ Federico II, Naples, Italy 3Medical Biotechnology, VTT Technical Research Centre of Finland, Turku, Finland 4Center for Biotechnology, University of Turku, Turku, Finland 5Dipartimento di Scienze Biomediche Avanzate, Università Federico II, Naples, Italy 6Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy 7FIMM-Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland 8Istituto di Endocrinologia ed Oncologia Sperimentale “G. Salvatore” (IEOS), C.N.R., Naples, Italy Correspondence to: Maria Domenica Castellone, e-mail: [email protected] Keywords: kinases, screening, siRNA, thyroid carcinoma Received: October 01, 2015 Accepted: March 02, 2016 Published: April 4, 2016 ABSTRACT RET, BRAF and other protein kinases have been identified as major molecular players in thyroid cancer. To identify novel kinases required for the viability of thyroid carcinoma cells, we performed a RNA interference screening in the RET/PTC1(CCDC6- RET)-positive papillary thyroid cancer cell line TPC1 using a library of synthetic small interfering RNAs (siRNAs) targeting the human kinome and related proteins. We identified 14 hits whose silencing was able to significantly reduce the viability and the proliferation of TPC1 cells; most of them were active also in BRAF-mutant BCPAP (papillary thyroid cancer) and 8505C (anaplastic thyroid cancer) and in RAS-mutant CAL62 (anaplastic thyroid cancer) cells.