NF-Κb Signaling in Gastric Cancer
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
Molecular, Genetic, and Nutritional Aspects of Major and Trace Minerals
Molecular, Genetic, and Nutritional Aspects of Major and Trace Minerals Edited by James F. Collins AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW ORK • OFORD • PARIS SAN DIEGO • SAN FRANCISCO • SINGAPORE • SDNE • TOKO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1800, San Diego, CA 92101-4495, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom Copyright © 2017 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. -
THE ROLE of HOMEODOMAIN TRANSCRIPTION FACTOR IRX5 in CARDIAC CONTRACTILITY and HYPERTROPHIC RESPONSE by © COPYRIGHT by KYOUNG H
THE ROLE OF HOMEODOMAIN TRANSCRIPTION FACTOR IRX5 IN CARDIAC CONTRACTILITY AND HYPERTROPHIC RESPONSE By KYOUNG HAN KIM A THESIS SUBMITTED IN CONFORMITY WITH THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE DEPARTMENT OF PHYSIOLOGY UNIVERSITY OF TORONTO © COPYRIGHT BY KYOUNG HAN KIM (2011) THE ROLE OF HOMEODOMAIN TRANSCRIPTION FACTOR IRX5 IN CARDIAC CONTRACTILITY AND HYPERTROPHIC RESPONSE KYOUNG HAN KIM DOCTOR OF PHILOSOPHY GRADUATE DEPARTMENT OF PHYSIOLOGY UNIVERSITY OF TORONTO 2011 ABSTRACT Irx5 is a homeodomain transcription factor that negatively regulates cardiac fast transient + outward K currents (Ito,f) via the KV4.2 gene and is thereby a major determinant of the transmural repolarization gradient. While Ito,f is invariably reduced in heart disease and changes in Ito,f can modulate both cardiac contractility and hypertrophy, less is known about a functional role of Irx5, and its relationship with Ito,f, in the normal and diseased heart. Here I show that Irx5 plays crucial roles in the regulation of cardiac contractility and proper adaptive hypertrophy. Specifically, Irx5-deficient (Irx5-/-) hearts had reduced cardiac contractility and lacked the normal regional difference in excitation-contraction with decreased action potential duration, Ca2+ transients and myocyte shortening in sub-endocardial, but not sub-epicardial, myocytes. In addition, Irx5-/- mice showed less cardiac hypertrophy, but increased interstitial fibrosis and greater contractility impairment following pressure overload. A defect in hypertrophic responses in Irx5-/- myocardium was confirmed in cultured neonatal mouse ventricular myocytes, exposed to norepinephrine while being restored with Irx5 replacement. Interestingly, studies using mice ii -/- virtually lacking Ito,f (i.e. KV4.2-deficient) showed that reduced contractility in Irx5 mice was completely restored by loss of KV4.2, whereas hypertrophic responses to pressure-overload in hearts remained impaired when both Irx5 and Ito,f were absent. -
Activated Peripheral-Blood-Derived Mononuclear Cells
Transcription factor expression in lipopolysaccharide- activated peripheral-blood-derived mononuclear cells Jared C. Roach*†, Kelly D. Smith*‡, Katie L. Strobe*, Stephanie M. Nissen*, Christian D. Haudenschild§, Daixing Zhou§, Thomas J. Vasicek¶, G. A. Heldʈ, Gustavo A. Stolovitzkyʈ, Leroy E. Hood*†, and Alan Aderem* *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103; ‡Department of Pathology, University of Washington, Seattle, WA 98195; §Illumina, 25861 Industrial Boulevard, Hayward, CA 94545; ¶Medtronic, 710 Medtronic Parkway, Minneapolis, MN 55432; and ʈIBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598 Contributed by Leroy E. Hood, August 21, 2007 (sent for review January 7, 2007) Transcription factors play a key role in integrating and modulating system. In this model system, we activated peripheral-blood-derived biological information. In this study, we comprehensively measured mononuclear cells, which can be loosely termed ‘‘macrophages,’’ the changing abundances of mRNAs over a time course of activation with lipopolysaccharide (LPS). We focused on the precise mea- of human peripheral-blood-derived mononuclear cells (‘‘macro- surement of mRNA concentrations. There is currently no high- phages’’) with lipopolysaccharide. Global and dynamic analysis of throughput technology that can precisely and sensitively measure all transcription factors in response to a physiological stimulus has yet to mRNAs in a system, although such technologies are likely to be be achieved in a human system, and our efforts significantly available in the near future. To demonstrate the potential utility of advanced this goal. We used multiple global high-throughput tech- such technologies, and to motivate their development and encour- nologies for measuring mRNA levels, including massively parallel age their use, we produced data from a combination of two distinct signature sequencing and GeneChip microarrays. -
Relb Deficiency in Dendritic Cells Protects from Autoimmune
RelB Deficiency in Dendritic Cells Protects from Autoimmune Inflammation Due to Spontaneous Accumulation of Tissue T Regulatory Cells This information is current as of September 24, 2021. Nico Andreas, Maria Potthast, Anna-Lena Geiselhöringer, Garima Garg, Renske de Jong, Julia Riewaldt, Dennis Russkamp, Marc Riemann, Jean-Philippe Girard, Simon Blank, Karsten Kretschmer, Carsten Schmidt-Weber, Thomas Korn, Falk Weih and Caspar Ohnmacht Downloaded from J Immunol 2019; 203:2602-2613; Prepublished online 2 October 2019; doi: 10.4049/jimmunol.1801530 http://www.jimmunol.org/content/203/10/2602 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2019/10/01/jimmunol.180153 Material 0.DCSupplemental References This article cites 74 articles, 23 of which you can access for free at: http://www.jimmunol.org/content/203/10/2602.full#ref-list-1 by guest on September 24, 2021 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 *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 Author Choice Freely available online through The Journal of Immunology Author Choice option 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 © 2019 by The American Association of Immunologists, Inc. -
Assessment of NR4A Ligands That Directly Bind and Modulate the Orphan Nuclear Receptor Nurr1
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.22.109017; this version posted May 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Assessment of NR4A Ligands that Directly Bind and Modulate the Orphan Nuclear Receptor Nurr1 Paola Munoz-Tello 1, Hua Lin 2,3, Pasha Khan 2, Ian Mitchelle S. de Vera 1,4, Theodore M. Kamenecka 2, and Douglas J. Kojetin 1,2,* 1 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA 2 Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA 3 Current address: Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China 4 Current address: Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA * Correspondence: [email protected] as ligands that increase Nurr1 transcription in human neuroblastoma SK- ABSTRACT N-BE(2)-C cells (11). Amodiaquine improves behavioral alterations in a Nurr1/NR4A2 is an orphan nuclear receptor transcription factor im- Parkinson’s disease animal model (11) and improves neuropathology and plicated as a potential drug target for neurological disorders including memory impairment in an Alzheimer’s disease animal model (12). Alzheimer’s and Parkinson’s diseases. Previous studies identified small molecule modulators of NR4A nuclear receptors including Nurr1 and Amodiaquine is the most potent and efficacious Nurr1 agonist of the Nur77/NR4A1; it remains unclear whether these ligands affect Nurr1 4-amino-7-chloroquinoline compounds, but these compounds are not through direct binding or indirect non-binding mechanisms. -
Angiogenic Patterning by STEEL, an Endothelial-Enriched Long
Angiogenic patterning by STEEL, an endothelial- enriched long noncoding RNA H. S. Jeffrey Mana,b, Aravin N. Sukumara,b, Gabrielle C. Lamc,d, Paul J. Turgeonb,e, Matthew S. Yanb,f, Kyung Ha Kub,e, Michelle K. Dubinskya,b, J. J. David Hob,f, Jenny Jing Wangb,e, Sunit Dasg,h, Nora Mitchelli, Peter Oettgeni, Michael V. Seftonc,d,j, and Philip A. Marsdena,b,e,f,1 aInstitute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada; bKeenan Research Centre for Biomedical Science in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto, Toronto, ON M5B 1T8, Canada; cDonnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E2, Canada; dInstitute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; eDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; fDepartment of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; gArthur and Sonia Labatt Brain Tumour Research Institute, Hospital for SickKids, University of Toronto, Toronto, ON M5G 1X8, Canada; hDivision of Neurosurgery and Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada; iDepartment of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115; and jDepartment of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada Edited by Napoleone Ferrara, University of California, San Diego, La Jolla, CA, and approved January 24, 2018 (received for review August 28, 2017) Endothelial cell (EC)-enriched protein coding genes, such as endothelial formation in vitro and blood vessel formation in vivo. -
Off the Beaten Pathway: the Complex Cross Talk Between Notch and NF-Kb Clodia Osipo1,2, Todd E Golde3, Barbara a Osborne4 and Lucio a Miele1,2,5
Laboratory Investigation (2008) 88, 11–17 & 2008 USCAP, Inc All rights reserved 0023-6837/08 $30.00 PATHOBIOLOGY IN FOCUS Off the beaten pathway: the complex cross talk between Notch and NF-kB Clodia Osipo1,2, Todd E Golde3, Barbara A Osborne4 and Lucio A Miele1,2,5 The canonical Notch pathway that has been well characterized over the past 25 years is relatively simple compared to the plethora of recently published data suggesting non-canonical signaling mechanisms and cross talk with other pathways. The manner in which other pathways cross talk with Notch signaling appears to be extraordinarily complex and, not surprisingly, context-dependent. While the physiological relevance of many of these interactions remains to be estab- lished, there is little doubt that Notch signaling is integrated with numerous other pathways in ways that appear increasingly complex. Among the most intricate cross talks described for Notch is its interaction with the NF-kB pathway, another major cell fate regulatory network involved in development, immunity, and cancer. Numerous reports over the last 11 years have described multiple cross talk mechanisms between Notch and NF-kB in diverse experimental models. This article will provide a brief overview of the published evidence for Notch–NF-kB cross talk, focusing on vertebrate systems. Laboratory Investigation (2008) 88, 11–17; doi:10.1038/labinvest.3700700; published online 3 December 2007 KEYWORDS: Notch signaling; NF-kB cross talk; non-canonical signaling; IKK kinases CANONICAL NOTCH SIGNALING endocytosed into the ligand-expressing cell.10 This unmasks Canonical Notch signaling has been recently reviewed by the HD and triggers an extracellular cleavage in it by ADAM several authors,1–6 and the reader is referred to these reviews (a disintegrin and metalloproteinase) 10 or 17,1,2 followed by for detailed information and additional references. -
Expression and Regulation of Sex Determining Genes in the Mouse
Expression and regulation of sex determining genes in the mouse. Veronica Mercedes Narvaez Padilla A thesis submitted for the Degree of Doctor of Philosophy 1996 Department of Developmental Genetics Department of Biology National Institute for Medical Research, University College London The Ridgeway, Mill Hill, Gower Street, London, NW7 lAA London, WCIE GET ProQuest Number: 10016705 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest 10016705 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 In memory of Pepe and Arturo. ...Many times Fve been alone and many times Fve cried. Anyway you’ll never know the many ways Fve tried... (Lennon & M cC artney) Little darling, it’s being a long cold lonely winter. Little darling, it feels like years since it’s been here. Here comes the sun, here comes the sun and I say It’s alright! (G. Harrison) Contents Contents ...................................................................................................................................................4 -
1714 Gene Comprehensive Cancer Panel Enriched for Clinically Actionable Genes with Additional Biologically Relevant Genes 400-500X Average Coverage on Tumor
xO GENE PANEL 1714 gene comprehensive cancer panel enriched for clinically actionable genes with additional biologically relevant genes 400-500x average coverage on tumor Genes A-C Genes D-F Genes G-I Genes J-L AATK ATAD2B BTG1 CDH7 CREM DACH1 EPHA1 FES G6PC3 HGF IL18RAP JADE1 LMO1 ABCA1 ATF1 BTG2 CDK1 CRHR1 DACH2 EPHA2 FEV G6PD HIF1A IL1R1 JAK1 LMO2 ABCB1 ATM BTG3 CDK10 CRK DAXX EPHA3 FGF1 GAB1 HIF1AN IL1R2 JAK2 LMO7 ABCB11 ATR BTK CDK11A CRKL DBH EPHA4 FGF10 GAB2 HIST1H1E IL1RAP JAK3 LMTK2 ABCB4 ATRX BTRC CDK11B CRLF2 DCC EPHA5 FGF11 GABPA HIST1H3B IL20RA JARID2 LMTK3 ABCC1 AURKA BUB1 CDK12 CRTC1 DCUN1D1 EPHA6 FGF12 GALNT12 HIST1H4E IL20RB JAZF1 LPHN2 ABCC2 AURKB BUB1B CDK13 CRTC2 DCUN1D2 EPHA7 FGF13 GATA1 HLA-A IL21R JMJD1C LPHN3 ABCG1 AURKC BUB3 CDK14 CRTC3 DDB2 EPHA8 FGF14 GATA2 HLA-B IL22RA1 JMJD4 LPP ABCG2 AXIN1 C11orf30 CDK15 CSF1 DDIT3 EPHB1 FGF16 GATA3 HLF IL22RA2 JMJD6 LRP1B ABI1 AXIN2 CACNA1C CDK16 CSF1R DDR1 EPHB2 FGF17 GATA5 HLTF IL23R JMJD7 LRP5 ABL1 AXL CACNA1S CDK17 CSF2RA DDR2 EPHB3 FGF18 GATA6 HMGA1 IL2RA JMJD8 LRP6 ABL2 B2M CACNB2 CDK18 CSF2RB DDX3X EPHB4 FGF19 GDNF HMGA2 IL2RB JUN LRRK2 ACE BABAM1 CADM2 CDK19 CSF3R DDX5 EPHB6 FGF2 GFI1 HMGCR IL2RG JUNB LSM1 ACSL6 BACH1 CALR CDK2 CSK DDX6 EPOR FGF20 GFI1B HNF1A IL3 JUND LTK ACTA2 BACH2 CAMTA1 CDK20 CSNK1D DEK ERBB2 FGF21 GFRA4 HNF1B IL3RA JUP LYL1 ACTC1 BAG4 CAPRIN2 CDK3 CSNK1E DHFR ERBB3 FGF22 GGCX HNRNPA3 IL4R KAT2A LYN ACVR1 BAI3 CARD10 CDK4 CTCF DHH ERBB4 FGF23 GHR HOXA10 IL5RA KAT2B LZTR1 ACVR1B BAP1 CARD11 CDK5 CTCFL DIAPH1 ERCC1 FGF3 GID4 HOXA11 IL6R KAT5 ACVR2A -
Eda-Activated Relb Recruits an SWI/SNF (BAF) Chromatin-Remodeling Complex and Initiates Gene Transcription in Skin Appendage Formation
Eda-activated RelB recruits an SWI/SNF (BAF) chromatin-remodeling complex and initiates gene transcription in skin appendage formation Jian Simaa,1,2, Zhijiang Yana,1, Yaohui Chena, Elin Lehrmanna, Yongqing Zhanga, Ramaiah Nagarajaa, Weidong Wanga, Zhong Wangb, and David Schlessingera,2 aLaboratory of Genetics and Genomics, National Institute on Aging/NIH-Intramural Research Program, Baltimore, MD 21224; and bDepartment of Cardiac Surgery, Cardiovascular Research Center, University of Michigan, Ann Arbor, MI 48109 Edited by Elaine Fuchs, The Rockefeller University, New York, NY, and approved June 28, 2018 (received for review January 23, 2018) Ectodysplasin A (Eda) signaling activates NF-κB during skin ap- during organ development induce distinct BAF complexes to pendage formation, but how Eda controls specific gene transcrip- modulate gene expression. tion remains unclear. Here, we find that Eda triggers the formation Here, we report that skin-specific Eda signaling triggers the for- of an NF-κB–associated SWI/SNF (BAF) complex in which p50/RelB re- mation of a large BAF-containing complex that includes a BAF cruits a linker protein, Tfg, that interacts with BAF45d in the BAF com- complex, an NF-κB dimer of p50/RelB, and a specific linker pro- plex. We further reveal that Tfg is initially induced by Eda-mediated tein, Tfg (TRK-fusion gene). Thus, Eda/NF-κB signaling operates RelB activation and then bridges RelB and BAF for subsequent gene through a BAF complex to regulate specific gene expression in regulation. The BAF component BAF250a is particularly up-regulated in organ development, which may exemplify a more general paradigm skin appendages, and epidermal knockout of BAF250a impairs skin for gene-specific regulation in many other systems. -
Autoimmune-Mediated Thymic Atrophy Is Accelerated but Reversible in Relb-Deficient Mice
ORIGINAL RESEARCH published: 22 May 2018 doi: 10.3389/fimmu.2018.01092 Autoimmune-Mediated Thymic Atrophy Is Accelerated but reversible in relB-Deficient Mice Brendan J. O’Sullivan1, Suman Yekollu1, Roland Ruscher1, Ahmed M. Mehdi1, Muralidhara Rao Maradana1, Ann P. Chidgey 2 and Ranjeny Thomas1* 1 Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia, 2 Stem Cells and Immune Regeneration Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia Polymorphisms impacting thymic function may decrease peripheral tolerance and hasten autoimmune disease. The NF-κB transcription factor subunit, RelB, is essential for the development and differentiation of medullary thymic epithelial cells (mTECs): RelB-deficient mice have reduced thymic cellularity and markedly fewer mTECs, lack- ing AIRE. The precise mechanism of this mTEC reduction in the absence of RelB is Edited by: unclear. To address this, we studied mTECs and dendritic cells (DCs), which critically Antony Basten, regulate negative selection, and thymic regulatory T-cells (tTreg) in RelB−/− mice, which Garvan Institute of Medical / Research, Australia have spontaneous multiorgan autoimmune disease. RelB− − thymi were organized, with − + Reviewed by: medullary structures containing AIRE mTECs, DCs, and CD4 thymocytes, but fewer Mitsuru Matsumoto, tTreg. Granulocytes infiltrated the RelB−/− thymic cortex, capsule, and medulla, producing Tokushima University, Japan inflammatory thymic medullary atrophy, which could be treated by granulocyte depletion Lianjun Zhang, or RelB+ DC immunotherapy, with concomitant recovery of mTEC and tTreg numbers. Université de Lausanne, These data indicate that central tolerance defects may be accelerated by autoimmune Switzerland thymic inflammation where impaired RelB signaling impairs the medullary niche, and may *Correspondence: Ranjeny Thomas be reversible by therapies enhancing peripheral Treg or suppressing inflammation.