Identification of Estradiol/Era-Regulated Genes in the Mouse Pituitary
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Independence of Hif1a and Androgen Signaling Pathways in Prostate Cancer
bioRxiv preprint doi: https://doi.org/10.1101/848424; this version posted November 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Independence of HIF1a and androgen signaling pathways in prostate cancer Maxine GB Tran1, 2*, Becky AS Bibby3†*, Lingjian Yang3, Franklin Lo1, Anne Warren1, Deepa Shukla1, Michelle Osborne1, James Hadfield1, Thomas Carroll1, Rory Stark1, Helen Scott1, Antonio Ramos-Montoya1, Charlie Massie1, Patrick Maxwell1, Catharine ML West3, 4, Ian G. Mills5,6** and David E. Neal1** 1Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, United Kingdom 2UCL division of Surgery and Interventional Science, Royal Free Hospital, Pond Street, London NW3 2QG 3Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Trust, Manchester, M20 4BX, United Kingdom 4Manchester Biomedical Research Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom. 5Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, BT9 7AE, United Kingdom 6Nuffield Department of Surgical Sciences, University of Oxford, OX3 9DU, UK *These authors contributed equally to this work **These authors contributed equally to this work †Corresponding author email: Becky Bibby, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Trust, Manchester, M20 4BX, United Kingdom, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/848424; this version posted November 26, 2019. -
Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug
cancers Article Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug Response Genes in Pediatric Acute Myeloid Leukemia David G.J. Cucchi 1 , Costa Bachas 1 , Marry M. van den Heuvel-Eibrink 2,3, Susan T.C.J.M. Arentsen-Peters 3, Zinia J. Kwidama 1, Gerrit J. Schuurhuis 1, Yehuda G. Assaraf 4, Valérie de Haas 3 , Gertjan J.L. Kaspers 3,5 and Jacqueline Cloos 1,* 1 Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; [email protected] (D.G.J.C.); [email protected] (C.B.); [email protected] (Z.J.K.); [email protected] (G.J.S.) 2 Department of Pediatric Oncology/Hematology, Erasmus MC–Sophia Children’s Hospital, 3015 CN Rotterdam, The Netherlands; [email protected] 3 Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; [email protected] (S.T.C.J.M.A.-P.); [email protected] (V.d.H.); [email protected] (G.J.L.K.) 4 The Fred Wyszkowski Cancer Research, Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003 Haifa, Israel; [email protected] 5 Emma’s Children’s Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology, 1081 HV Amsterdam, The Netherlands * Correspondence: [email protected] Received: 21 April 2020; Accepted: 12 May 2020; Published: 15 May 2020 Abstract: Novel treatment strategies are of paramount importance to improve clinical outcomes in pediatric AML. Since chemotherapy is likely to remain the cornerstone of curative treatment of AML, insights in the molecular mechanisms that determine its cytotoxic effects could aid further treatment optimization. -
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. -
RING1 Antibody (N-Term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP14560A
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 RING1 Antibody (N-term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP14560A Specification RING1 Antibody (N-term) - Product Information Application WB,E Primary Accession Q06587 Other Accession Q6MGB6, O35730, NP_002922.2 Reactivity Human Predicted Mouse, Rat Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Antigen Region 95-123 RING1 Antibody (N-term) - Additional Information RING1 Antibody (N-term) (Cat. #AP14560a) Gene ID 6015 western blot analysis in MDA-MB453 cell line lysates (35ug/lane).This demonstrates the Other Names RING1 antibody detected the RING1 protein E3 ubiquitin-protein ligase RING1, 632-, (arrow). Polycomb complex protein RING1, RING finger protein 1, Really interesting new gene 1 protein, RING1, RNF1 RING1 Antibody (N-term) - Background Target/Specificity This gene belongs to the RING finger family, This RING1 antibody is generated from members of rabbits immunized with a KLH conjugated synthetic peptide between 95-123 amino which encode proteins characterized by a RING acids from the N-terminal region of human domain, a RING1. zinc-binding motif related to the zinc finger domain. The gene Dilution product can bind DNA and can act as a WB~~1:1000 transcriptional repressor. It is associated with the multimeric polycomb Format group protein complex. Purified polyclonal antibody supplied in PBS The gene product interacts with the polycomb with 0.09% (W/V) sodium azide. This group proteins BMI1, antibody is purified through a protein A EDR1, and CBX4, and colocalizes with these column, followed by peptide affinity proteins in large purification. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
RING1 Proteins Contribute to Early Proximal-Distal Specification of The
© 2016. Published by The Company of Biologists Ltd | Development (2016) 143, 276-285 doi:10.1242/dev.127506 RESEARCH ARTICLE RING1 proteins contribute to early proximal-distal specification of the forelimb bud by restricting Meis2 expression Nayuta Yakushiji-Kaminatsui1,*,‡, Takashi Kondo1,2,3, Takaho A. Endo4, Yoko Koseki1,2, Kaori Kondo1,2,3, Osamu Ohara4, Miguel Vidal5 and Haruhiko Koseki1,2,‡ ABSTRACT subunits to catalyze histone H2A monoubiquitylation at lysine 119 Polycomb group (PcG) proteins play a pivotal role in silencing (H2AK119ub1). PRC1 also targets chromatin compaction by SAM developmental genes and help to maintain various stem and domain polymerization of PHC1 and PHC2, a mammalian PH precursor cells and regulate their differentiation. PcG factors also ortholog, via H3K27me3 recognition by chromodomain proteins regulate dynamic and complex regional specification, particularly in such as CBX7 and CBX2 (Cao et al., 2002; Endoh et al., 2012; mammals, but this activity is mechanistically not well understood. In Isono et al., 2013; Kuzmichev et al., 2002). Recent studies identified this study, we focused on proximal-distal (PD) patterning of the a variant PRC1 complex containing RYBP (Ring1 and YY1 mouse forelimb bud to elucidate how PcG factors contribute to a binding protein)/YAF (YY1-associated factor), RING1A/B and a regional specification process that depends on developmental distinct PCGF subunit (Gao et al., 2012; Tavares et al., 2012), and signals. Depletion of the RING1 proteins RING1A (RING1) and demonstrated that H2AK119ub1 mediated by this variant PRC1 RING1B (RNF2), which are essential components of Polycomb leads to the recruitment of PRC2 and placement of H3K27me3 to repressive complex 1 (PRC1), led to severe defects in forelimb initiate Polycomb repression (Blackledge et al., 2014). -
Ten Commandments for a Good Scientist
Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Wageningen 2010 Thesis committee Thesis supervisors Prof. dr. ir. Ivonne M.C.M. Rietjens Professor of Toxicology Wageningen University Prof. dr. Albertinka J. Murk Personal chair at the sub-department of Toxicology Wageningen University Thesis co-supervisor Dr. ir. Jacques J.M. Vervoort Associate professor at the Laboratory of Biochemistry Wageningen University Other members Prof. dr. Michael R. Muller, Wageningen University Prof. dr. ir. Huub F.J. Savelkoul, Wageningen University Prof. dr. Everardus J. van Zoelen, Radboud University Nijmegen Dr. ir. Toine F.H. Bovee, RIKILT, Wageningen This research was conducted under the auspices of the Graduate School VLAG Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 14 September 2010 at 4 p.m. in the Aula Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds. Ana María Sotoca Covaleda Thesis Wageningen University, Wageningen, The Netherlands, 2010, With references, and with summary in Dutch. ISBN: 978-90-8585-707-5 “Caminante no hay camino, se hace camino al andar. Al andar se hace camino, y al volver la vista atrás se ve la senda que nunca se ha de volver a pisar” - Antonio Machado – A mi madre. -
Human/Mouse/Rat HIF-1 Alpha/HIF1A Antibody
Human/Mouse/Rat HIF-1 alpha/HIF1A Antibody Monoclonal Mouse IgG1 Clone # 241809 Catalog Number: MAB1536 DESCRIPTION Species Reactivity Human/Mouse/Rat Specificity Detects human, mouse, and rat HIF-1 alpha/HIF1A. Source Monoclonal Mouse IgG1 Clone # 241809 Purification Protein A or G purified from hybridoma culture supernatant Immunogen E. coli-derived recombinant human HIF-1 alpha/HIF1A Arg575-Asn826 Accession # Q16665.1 Formulation Lyophilized from a 0.2 μm filtered solution in PBS with Trehalose. See Certificate of Analysis for details. *Small pack size (-SP) is supplied either lyophilized or as a 0.2 μm filtered solution in PBS. APPLICATIONS Please Note: Optimal dilutions should be determined by each laboratory for each application. General Protocols are available in the Technical Information section on our website. Recommended Sample Concentration Western Blot 1 µg/mL See Below Immunohistochemistry 5-25 µg/mL See Below Immunoprecipitation 1-3 µg/500 µg cell MCF‑7 human breast cancer cell line treated with CoCl2, see our available Western blot lysate detection antibodies Simple Western 10 µg/mL See Below Knockout Validated HIF-1 alpha/HIF1A is specifically detected in HeLa human cervical epithelial carcinoma parental cell line but is not detectable in HIF-1 alpha/HIF1A knockout HeLa cell line. DATA Western Blot Immunohistochemistry Detection of Human, Mouse, HIF-1 alpha/HIF1A in Human Kidney. and Rat HIF-1 alpha/HIF1A by HIF-1 alpha/HIF1A was detected in Western Blot. Western blot immersion fixed paraffin-embedded sections shows lysates of MCF-7 human of human kidney using Mouse Anti- breast cancer cell line, Balb-3T3 Human/Mouse/Rat HIF-1 alpha/HIF1A mouse embryonic fibroblast cell Monoclonal Antibody (Catalog # MAB1536) line, and PC-12 rat adrenal at 5 µg/mL for 1 hour at room temperature pheochromocytoma cell line followed by incubation with the Anti-Mouse untreated (-) or treated (+) with IgG VisUCyte™ HRP Polymer Antibody 150 μM CoCl2 for 8 hours. -
Vitamin D Genes & Exposure in Relation to Kidney Cancer by Sara
Vitamin D Genes & Exposure in Relation to Kidney Cancer by Sara Karami B.S., Biology, James Madison University, 2002 M.P.H, Epidemiology, The George Washington University, 2004 A Dissertation submitted to The Faculty of The Columbian College of Arts and Science of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 31, 2009 Dissertation directed by Katherine L. Hunting Professor of Environmental and Occupational Health and of Epidemiology and Biostatistics and Lee E. Moore Epidemiological Investigator, NIH, NCI The Columbian College of Arts and Science of The George Washington University certifies that Sara Karami has passed the Final Examination for the degree of Doctor of Philosophy as of August 12, 2009. This is the final and approved form of the dissertation. Vitamin D Genes & Exposure in Relation to Kidney Cancer Sara Karami Dissertation Research Committee: Katherine L. Hunting, Professor of Environmental and Occupational Health and of Epidemiology and Biostatistics, Dissertation Director Lee E. Moore, Epidemiological Investigator, NIH, NCI, Co-Director Paul H. Levine, Professor of Epidemiology and Biostatistics, Committee Member Yinglei Lai, Assistant Professor of Statistics, Committee Member ii © Copyright 2009 by Sara Karami All rights reserved iii Dedication The author wishes to thank everyone involved in the dissertation process for their guidance and support. Special thanks to Dr. Lee Moore, Dr. Katherine Hunting, Dr. Paul Levine, Dr. Yinglei Lai, Dr. Sean Cleary, and Dr. Donte Verme. iv Acknowledgement The author wishes to acknowledge the National Cancer Institute, the International Agency for Research on Cancer, and the School of Public Health and Health Services of The George Washington University for their assistance. -
Structural and Spatial Chromatin Features at Developmental Gene Loci in Human Pluripotent Stem Cells
ARTICLE DOI: 10.1038/s41467-017-01679-x OPEN Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells Hiroki Ikeda1, Masamitsu Sone1,2, Shinya Yamanaka1,3 & Takuya Yamamoto 1,2,4 Higher-order chromatin organization controls transcriptional programs that govern cell properties and functions. In order for pluripotent stem cells (PSCs) to appropriately respond 1234567890 to differentiation signals, developmental gene loci should be structurally and spatially regu- lated to be readily available for immediate transcription, even though these genes are hardly expressed in PSCs. Here, we show that both chromatin interaction profiles and nuclear positions at developmental gene loci differ between human somatic cells and hPSCs, and that changes in the chromatin interactions are closely related to the nuclear repositioning. Moreover, we also demonstrate that developmental gene loci, which have bivalent histone modifications, tend to colocalize in PSCs. Furthermore, this colocalization requires PRC1, PRC2, and TrxG complexes, which are essential regulatory factors for the maintenance of transcriptionally poised developmental genes. Our results indicate that higher-order chro- matin regulation may be an integral part of the differentiation capacity that defines pluripotency. 1 Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan. 2 Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan. 3 Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA. 4 AMED-CREST, AMED 1-7-1 Otemach, Chiyodaku, Tokyo 100-0004, Japan. Correspondence and requests for materials should be addressed to T.Y. -
Table S1. Identified Proteins with Exclusive Expression in Cerebellum of Rats of Control, 10Mg F/L and 50Mg F/L Groups
Table S1. Identified proteins with exclusive expression in cerebellum of rats of control, 10mg F/L and 50mg F/L groups. Accession PLGS Protein Name Group IDa Score Q3TXS7 26S proteasome non-ATPase regulatory subunit 1 435 Control Q9CQX8 28S ribosomal protein S36_ mitochondrial 197 Control P52760 2-iminobutanoate/2-iminopropanoate deaminase 315 Control Q60597 2-oxoglutarate dehydrogenase_ mitochondrial 67 Control P24815 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 1 84 Control Q99L13 3-hydroxyisobutyrate dehydrogenase_ mitochondrial 114 Control P61922 4-aminobutyrate aminotransferase_ mitochondrial 470 Control P10852 4F2 cell-surface antigen heavy chain 220 Control Q8K010 5-oxoprolinase 197 Control P47955 60S acidic ribosomal protein P1 190 Control P70266 6-phosphofructo-2-kinase/fructose-2_6-bisphosphatase 1 113 Control Q8QZT1 Acetyl-CoA acetyltransferase_ mitochondrial 402 Control Q9R0Y5 Adenylate kinase isoenzyme 1 623 Control Q80TS3 Adhesion G protein-coupled receptor L3 59 Control B7ZCC9 Adhesion G-protein coupled receptor G4 139 Control Q6P5E6 ADP-ribosylation factor-binding protein GGA2 45 Control E9Q394 A-kinase anchor protein 13 60 Control Q80Y20 Alkylated DNA repair protein alkB homolog 8 111 Control P07758 Alpha-1-antitrypsin 1-1 78 Control P22599 Alpha-1-antitrypsin 1-2 78 Control Q00896 Alpha-1-antitrypsin 1-3 78 Control Q00897 Alpha-1-antitrypsin 1-4 78 Control P57780 Alpha-actinin-4 58 Control Q9QYC0 Alpha-adducin 270 Control Q9DB05 Alpha-soluble NSF attachment protein 156 Control Q6PAM1 Alpha-taxilin 161 -
G Protein-Coupled Receptors
S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2015/16: G protein-coupled receptors. British Journal of Pharmacology (2015) 172, 5744–5869 THE CONCISE GUIDE TO PHARMACOLOGY 2015/16: G protein-coupled receptors Stephen PH Alexander1, Anthony P Davenport2, Eamonn Kelly3, Neil Marrion3, John A Peters4, Helen E Benson5, Elena Faccenda5, Adam J Pawson5, Joanna L Sharman5, Christopher Southan5, Jamie A Davies5 and CGTP Collaborators 1School of Biomedical Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK, 2Clinical Pharmacology Unit, University of Cambridge, Cambridge, CB2 0QQ, UK, 3School of Physiology and Pharmacology, University of Bristol, Bristol, BS8 1TD, UK, 4Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK, 5Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK Abstract The Concise Guide to PHARMACOLOGY 2015/16 provides concise overviews of the key properties of over 1750 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/ 10.1111/bph.13348/full. G protein-coupled receptors are one of the eight major pharmacological targets into which the Guide is divided, with the others being: ligand-gated ion channels, voltage-gated ion channels, other ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading.