Interleukin‑6 Signalling As a Valuable Cornerstone for Molecular Medicine (Review)
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
BIOINFORMATICS DOI: 10.1093/Bioinformatics/Btg1030
Vol. 19 Suppl. 1 2003, pages i222–i224 BIOINFORMATICS DOI: 10.1093/bioinformatics/btg1030 GeneLoc: exon-based integration of human genome maps Naomi Rosen, Vered Chalifa-Caspi, Orit Shmueli, Avital Adato, Michal Lapidot, Julie Stampnitzky, Marilyn Safran ∗ and Doron Lancet Weizmann Institute of Science, Rehovot, Israel Received on January 6, 2003; accepted on February 20, 2003 ABSTRACT to provide a comprehensive gene list, NCBI’s LocusLink Motivation: Despite the numerous available whole- contains thousands of model genes, categorized by level genome mapping resources, no comprehensive, inte- and type of support. Even known genes appearing in every grated map of the human genome yet exists. database may have different names in each database. The Results: GeneLoc, software adjunct to GeneCards and biologist must move among databases to figure out which UDB, integrates gene lists by comparing genomic coordi- genes are the same, and which could be a novel gene nates at the exon level and assigns unique and meaningful sought. UCSC’s Genome Browser website maps genes identifiers to each gene. from several sources on the same scale, but the maps are Availability: http://bioinfo.weizmann.ac.il/genecards and not integrated, making it difficult to relate genes from http://genecards.weizmann.ac.il/udb different sources. As stated (Jongeneel, 2000),‘there is an Supplementary information: http://bioinfo.weizmann.ac. urgent need for a human gene index that can be used to il/cards-bin/AboutGCids.cgi, http://genecards.weizmann. identify transcripts unambiguously.’ The author contends ac.il/GeneLocAlg.html that this index should have, among others, the following Contact: [email protected] qualities: comprehensiveness, uniqueness, and stability. -
Genome Analysis and Knowledge
Dahary et al. BMC Medical Genomics (2019) 12:200 https://doi.org/10.1186/s12920-019-0647-8 SOFTWARE Open Access Genome analysis and knowledge-driven variant interpretation with TGex Dvir Dahary1*, Yaron Golan1, Yaron Mazor1, Ofer Zelig1, Ruth Barshir2, Michal Twik2, Tsippi Iny Stein2, Guy Rosner3,4, Revital Kariv3,4, Fei Chen5, Qiang Zhang5, Yiping Shen5,6,7, Marilyn Safran2, Doron Lancet2* and Simon Fishilevich2* Abstract Background: The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient’s phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants. Results: We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform, with remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex’s main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex’s broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards’ recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. -
(CS-ⅣA-Be), a Novel IL-6R Antagonist, Inhibits IL-6/STAT3
Author Manuscript Published OnlineFirst on February 29, 2016; DOI: 10.1158/1535-7163.MCT-15-0551 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Chikusetsusaponin Ⅳa butyl ester (CS-Ⅳa-Be), a novel IL-6R antagonist, inhibits IL-6/STAT3 signaling pathway and induces cancer cell apoptosis Jie Yang 1, 2, Shihui Qian 2, Xueting Cai 1, 2, Wuguang Lu 1, 2, Chunping Hu 1, 2, * Xiaoyan Sun1, 2, Yang Yang1, 2, Qiang Yu 3, S. Paul Gao 4, Peng Cao 1, 2 1. Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China 2. Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, China 3. Shanghai Institute of Materia Medical, Chinese Academy of Sciences, Shanghai, 201203, China 4. Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY10065, USA Running title: CS-Ⅳa-Be, a novel IL-6R antagonist, inhibits IL-6/STAT3 Keywords: Chikusetsusaponin Ⅳ a butyl ester (CS- Ⅳ a-Be), STAT3, IL-6R, antagonist, cancer Grant support: P. Cao received Jiangsu Province Funds for Distinguished Young Scientists (BK20140049) grant, J. Yang received National Natural Science Foundation of China (No. 81403151) grant, and X.Y. Sun received National Natural Science Foundation of China (No. 81202576) grant. Corresponding author: Peng Cao Institute: Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, Jiangsu, China Mailing address: 100#, Shizi Street, Hongshan Road, Nanjing, Jiangsu, China Tel: +86-25-85608666 Fax: +86-25-85608666 Email address: [email protected] The first co-authors: Jie Yang and Shihui Qian The authors disclose no potential conflicts of interest. -
Full Review Molecular Disease Presentation in Diabetic Nephropathy
Nephrol Dial Transplant (2015) 30: iv17–iv25 doi: 10.1093/ndt/gfv267 Full Review Molecular disease presentation in diabetic nephropathy Downloaded from https://academic.oup.com/ndt/article/30/suppl_4/iv17/2324968 by guest on 25 September 2021 Andreas Heinzel1, Irmgard Mühlberger1, Gil Stelzer2, Doron Lancet2, Rainer Oberbauer3, Maria Martin4 and Paul Perco1 1emergentec biodevelopment GmbH, Vienna, Austria, 2Weizmann Institute of Science, Rehovot, Israel, 3Medical University of Vienna, Vienna, Austria and 4EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK Correspondence and offprint requests to: Paul Perco; E-mail: [email protected] ABSTRACT INTRODUCTION Diabetic nephropathy, as the most prevalent chronic disease of Kidney disease is a common problem in patients with diabetes. the kidney, has also become the primary cause of end-stage Depending on the degree of GFR impairment and/or albumin- renal disease with the incidence of kidney disease in type 2 dia- uria, roughly 30% of subjects are affected. As with most betics continuously rising. As with most chronic diseases, the diabetes-associated comorbidities, the pathophysiology is pathophysiology is multifactorial with a number of deregulated multifactorial and the molecular pathways involved in the ini- molecular processes contributing to disease manifestation and tiation and progression constitute a wide and complex as well as progression. Current therapy mainly involves interfering in the redundant network of regulators. Considerable success has renin–angiotensin–aldosterone -
Causal Varian Discovery in Familial Congenital Heart Disease - an Integrative -Omic Approach Wendy Demos Marquette University
Marquette University e-Publications@Marquette Master's Theses (2009 -) Dissertations, Theses, and Professional Projects Causal Varian discovery in Familial Congenital Heart Disease - An Integrative -Omic Approach Wendy Demos Marquette University Recommended Citation Demos, Wendy, "Causal Varian discovery in Familial Congenital Heart Disease - An Integrative -Omic Approach" (2012). Master's Theses (2009 -). 140. https://epublications.marquette.edu/theses_open/140 CAUSAL VARIANT DISCOVERY IN FAMILIAL CONGENITAL HEART DISEASE – AN INTEGRATIVE –OMIC APPROACH by Wendy M. Demos A Thesis submitted to the Faculty of the Graduate School, Marquette University, in Partial Fulfillment of the Requirements for the Degree of Master of Science Milwaukee, Wisconsin May 2012 ABSTRACT CAUSAL VARIANT DISCOVERY IN FAMILIAL CONGENITAL HEART DISEASE – AN INTEGRATIVE –OMIC APPROACH Wendy M. Demos Marquette University, 2012 Background : Hypoplastic left heart syndrome (HLHS) is a congenital heart defect that leads to neonatal death or compromised quality of life for those affected and their families. This syndrome requires extensive medical intervention for the affected to survive. It is characterized by significant underdevelopment or non-existence of the components of the left heart and the aorta, including the left ventricular cavity and mass. There are many factors ranging from genetics to environmental relationships hypothesized to lead to the development of the syndrome, including recent studies suggesting a link between hearing impairment and congenital heart defects (CHD). Although broadly characterized those factors remain poorly understood. The goal of this project is to systematically utilize bioinformatics tools to determine the relationships of novel mutations found in exome sequencing to a familial congenital heart defect. Methods A systematic genomic and proteomic approach involving exome sequencing, pathway analysis, and protein modeling was implemented to examine exome sequencing data of a patient with HLHS. -
A New Cerkl Mouse Model Generated by CRISPR-Cas9 Shows
Retina ANewCerkl Mouse Model Generated by CRISPR-Cas9 Shows Progressive Retinal Degeneration and Altered Morphological and Electrophysiological Phenotype Elena B. Domènech,1,2 Rosa Andrés,1,2 M. José López-Iniesta,1 Serena Mirra,1,2 Rocío García-Arroyo,1 Santiago Milla,3 Florentina Sava,1 Jordi Andilla,4 Pablo Loza-Álvarez,4 Pedro de la Villa,3,5 Roser Gonzàlez-Duarte,1,2,6 and Gemma Marfany1,2,6,7 1Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain 2CIBERER/ISCIII, University of Barcelona, Barcelona, Spain 3Department of Systems Biology, University of Alcalá, Madrid, Spain 4ICFO–The Institute of Photonic Sciences, Barcelona Institute of Science and Technology, Barcelona, Spain 5Ramón y Cajal Institute for Health Research, Madrid, Spain 6DBGen Ocular Genomics, Barcelona, Spain 7Institute of Biomedicine, University of Barcelona, Barcelona, Spain Correspondence: Gemma Marfany, PURPOSE. Close to 100 genes cause retinitis pigmentosa, a Mendelian rare disease that Avinguda Diagonal, 643, edifici affects 1 out of 4000 people worldwide. Mutations in the ceramide kinase-like gene Prevosti, planta 1, 08028 Barcelona, (CERKL) are a prevalent cause of autosomal recessive cause retinitis pigmentosa and Spain; cone–rod dystrophy, but the functional role of this gene in the retina has yet to be fully [email protected]. determined. We aimed to generate a mouse model that resembles the phenotypic traits of Received: January 20, 2020 patients carrying CERKL mutations to undertake functional studies and assay therapeutic Accepted: June 14, 2020 approaches. Published: July 13, 2020 METHODS. The Cerkl locus has been deleted (around 97 kb of genomic DNA) by gene Citation: Domènech EB, Andrés R, editing using the CRISPR-Cas9 D10A nickase. -
S41467-020-18249-3.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible. -
Kcnorman 1.Pdf
A Computational Systems Approach to Elucidate New Mechanisms Involved in Progressive Lung Disease by Katy Norman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biomedical Engineering) in the University of Michigan 2020 Doctoral Committee: Assistant Professor Kelly Arnold, Chair Professor Jeffrey Curtis Professor Jennifer Linderman Professor Bethany Moore Professor David Sept Katy C. Norman [email protected] ORCID iD: 0000-0001-8841-0212 © Katy C. Norman 2020 Acknowledgements When I look back on myself in 2015 as I just entered the PhD program, I have to give a little laugh about all the surprises and changes that have happened along the way. I have grown more than I could ever have imagined – I have become so much more comfortable and confident in my communication skills, in my scientific skills, and in myself. These changes and this growth could not have happened without my huge support network, and I am honored to have the chance to thank everyone for what they have given me and for what they have helped me achieve. I would first like to thank my adviser, Kelly Arnold, for giving me a chance to try out computational systems biology research when I had absolutely no background in the field coming in. I appreciate how you were easily able to create a space where I felt comfortable to learn, to ask questions, and to make mistakes as I worked towards gaining expertise in this field. Thank you for always being there for me with extra support when my nerves were getting the best of me before big presentations or before a big deadline, and for supporting my involvement in activities outside of the lab as well. -
GP130 Cytokines in Breast Cancer and Bone
cancers Review GP130 Cytokines in Breast Cancer and Bone Tolu Omokehinde 1,2 and Rachelle W. Johnson 1,2,3,* 1 Program in Cancer Biology, Vanderbilt University, Nashville, TN 37232, USA; [email protected] 2 Vanderbilt Center for Bone Biology, Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA 3 Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA * Correspondence: [email protected]; Tel.: +1-615-875-8965 Received: 14 December 2019; Accepted: 29 January 2020; Published: 31 January 2020 Abstract: Breast cancer cells have a high predilection for skeletal homing, where they may either induce osteolytic bone destruction or enter a latency period in which they remain quiescent. Breast cancer cells produce and encounter autocrine and paracrine cytokine signals in the bone microenvironment, which can influence their behavior in multiple ways. For example, these signals can promote the survival and dormancy of bone-disseminated cancer cells or stimulate proliferation. The interleukin-6 (IL-6) cytokine family, defined by its use of the glycoprotein 130 (gp130) co-receptor, includes interleukin-11 (IL-11), leukemia inhibitory factor (LIF), oncostatin M (OSM), ciliary neurotrophic factor (CNTF), and cardiotrophin-1 (CT-1), among others. These cytokines are known to have overlapping pleiotropic functions in different cell types and are important for cross-talk between bone-resident cells. IL-6 cytokines have also been implicated in the progression and metastasis of breast, prostate, lung, and cervical cancer, highlighting the importance of these cytokines in the tumor–bone microenvironment. This review will describe the role of these cytokines in skeletal remodeling and cancer progression both within and outside of the bone microenvironment. -
Due to Interleukin-6 Type Cytokine Redundancy Only Glycoprotein 130 Receptor Blockade Efficiently Inhibits Myeloma Growth
Plasma Cell Disorders SUPPLEMENTARY APPENDIX Due to interleukin-6 type cytokine redundancy only glycoprotein 130 receptor blockade efficiently inhibits myeloma growth Renate Burger, 1 Andreas Günther, 1 Katja Klausz, 1 Matthias Staudinger, 1 Matthias Peipp, 1 Eva Maria Murga Penas, 2 Stefan Rose-John, 3 John Wijdenes 4 and Martin Gramatzki 1 1Division of Stem Cell Transplantation and Immunotherapy, Department of Internal Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany; 2Institute of Human Genetics, Christian-Albrechts-University Kiel and Uni - versity Medical Center Schleswig-Holstein, Kiel, Germany; 3Department of Biochemistry, Christian-Albrechts-University of Kiel, Medical Faculty, Germany and 4Gen-Probe/Diaclone SAS, Besançon, France ©2017 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2016.145060 Received: February 25, 2016. Accepted: September 14, 2016. Pre-published: September 22, 2016. Correspondence: [email protected] SUPPLEMENTARY METHODS Cell lines and culture Cell lines INA-6, INA-6.Tu1 and B9 were cultivated in RPMI-1640 with GlutaMax™-I, 25 mM HEPES (Gibco®/Life Technologies GmbH, Darmstadt, Germany), 10% (v/v) heat-inactivated fetal bovine serum (FBS) (HyClone; Perbio Science, Erembodegen, Belgium), and antibiotics (R10+ medium) supplemented with 2.5 ng/ml recombinant huIL-6 (Gibco®/Life Technologies GmbH, Darmstadt, Germany). The cell lines are routinely confirmed to be negative for mycoplasma contamination (Venor™GeM Mycoplasma Detection Kit, Sigma-Aldrich, St. Louis, MO). Cytokines and other reagents Recombinant huIL-6 was purchased from Gibco®/Life Technologies (Darmstadt, Germany), huLIF was from Reliatech (Wolfenbüttel, Germany). Recombinant muIL-6 was obtained from Peprotech (Rocky Hill, NJ), and soluble muIL-6R was from R&D Systems (Minneapolis, MN). -
The Regulation of Htert by Alternative Splicing
THE REGULATION OF HTERT BY ALTERNATIVE SPLICING APPROVED BY SUPERVISORY COMMITTEE First Name Last Name, credentials Jerry Shay, Ph.D. Woodring Wright, M.D., Ph.D. Hongtao Yu, Ph.D. Melanie Cobb, Ph.D. Beatriz Fontoura, Ph.D. DEDICATION I would like to thank the members of my Graduate Committee and mentors, Jerry Shay and Woodring Wright, all of the members of the Shay/Wright lab, my collaborators, the UTSW MSTP, my friends, my family, my significant other and my two cats, Kerrigan and Tofu. THE REGULATION OF HTERT BY ALTERLATIVE SPLICING by LAURA YU YUAN DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas May, 2019 Copyright by Laura Yu Yuan, 2019 All Rights Reserved THE REGULATION OF HTERT BY ALTERNATIVE SPLICING Publication No. Laura Yu Yuan, M.D., Ph.D. The University of Texas Southwestern Medical Center at Dallas, 2019 Supervising Professors: Jerry Shay, Ph.D., and Woodring Wright, M.D., Ph.D. Telomeres are non-coding DNA hexameric repeats (TTAGGG in mammals) located at the ends of linear chromosomes that, along with their associated proteins, protect against the loss of genomic material during cell division and prevent the recognition of chromosome ends as double-strand breaks. Human telomeres shorten with continued cell proliferation but are maintained by human telomerase reverse transcriptase (hTERT), an enzyme that synthesizes telomeric repeats using an RNA template. -
Identification of Differentially Expressed Genes in Human Bladder Cancer Through Genome-Wide Gene Expression Profiling
521-531 24/7/06 18:28 Page 521 ONCOLOGY REPORTS 16: 521-531, 2006 521 Identification of differentially expressed genes in human bladder cancer through genome-wide gene expression profiling KAZUMORI KAWAKAMI1,3, HIDEKI ENOKIDA1, TOKUSHI TACHIWADA1, TAKENARI GOTANDA1, KENGO TSUNEYOSHI1, HIROYUKI KUBO1, KENRYU NISHIYAMA1, MASAKI TAKIGUCHI2, MASAYUKI NAKAGAWA1 and NAOHIKO SEKI3 1Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8520; Departments of 2Biochemistry and Genetics, and 3Functional Genomics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan Received February 15, 2006; Accepted April 27, 2006 Abstract. Large-scale gene expression profiling is an effective CKS2 gene not only as a potential biomarker for diagnosing, strategy for understanding the progression of bladder cancer but also for staging human BC. This is the first report (BC). The aim of this study was to identify genes that are demonstrating that CKS2 expression is strongly correlated expressed differently in the course of BC progression and to with the progression of human BC. establish new biomarkers for BC. Specimens from 21 patients with pathologically confirmed superficial (n=10) or Introduction invasive (n=11) BC and 4 normal bladder samples were studied; samples from 14 of the 21 BC samples were subjected Bladder cancer (BC) is among the 5 most common to microarray analysis. The validity of the microarray results malignancies worldwide, and the 2nd most common tumor of was verified by real-time RT-PCR. Of the 136 up-regulated the genitourinary tract and the 2nd most common cause of genes we detected, 21 were present in all 14 BCs examined death in patients with cancer of the urinary tract (1-7).