(12) Patent Application Publication (10) Pub. No.: US 2011/001412.6 A1 Evans Et Al
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Supplementary Data
Figure 2S 4 7 A - C 080125 CSCs 080418 CSCs - + IFN-a 48 h + IFN-a 48 h + IFN-a 72 h 6 + IFN-a 72 h 3 5 MRFI 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 7 B 13 080125 FBS - D 080418 FBS - + IFN-a 48 h 12 + IFN-a 48 h + IFN-a 72 h + IFN-a 72 h 6 080125 FBS 11 10 5 9 8 4 7 6 3 MRFI 5 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 Molecule Molecule FIGURE 4S FIGURE 5S Panel A Panel B FIGURE 6S A B C D Supplemental Results Table 1S. Modulation by IFN-α of APM in GBM CSC and FBS tumor cell lines. Molecule * Cell line IFN-α‡ HLA β2-m# HLA LMP TAP1 TAP2 class II A A HC§ 2 7 10 080125 CSCs - 1∞ (1) 3 (65) 2 (91) 1 (2) 6 (47) 2 (61) 1 (3) 1 (2) 1 (3) + 2 (81) 11 (80) 13 (99) 1 (3) 8 (88) 4 (91) 1 (2) 1 (3) 2 (68) 080125 FBS - 2 (81) 4 (63) 4 (83) 1 (3) 6 (80) 3 (67) 2 (86) 1 (3) 2 (75) + 2 (99) 14 (90) 7 (97) 5 (75) 7 (100) 6 (98) 2 (90) 1 (4) 3 (87) 080418 CSCs - 2 (51) 1 (1) 1 (3) 2 (47) 2 (83) 2 (54) 1 (4) 1 (2) 1 (3) + 2 (81) 3 (76) 5 (75) 2 (50) 2 (83) 3 (71) 1 (3) 2 (87) 1 (2) 080418 FBS - 1 (3) 3 (70) 2 (88) 1 (4) 3 (87) 2 (76) 1 (3) 1 (3) 1 (2) + 2 (78) 7 (98) 5 (99) 2 (94) 5 (100) 3 (100) 1 (4) 2 (100) 1 (2) 070104 CSCs - 1 (2) 1 (3) 1 (3) 2 (78) 1 (3) 1 (2) 1 (3) 1 (3) 1 (2) + 2 (98) 8 (100) 10 (88) 4 (89) 3 (98) 3 (94) 1 (4) 2 (86) 2 (79) * expression of APM molecules was evaluated by intracellular staining and cytofluorimetric analysis; ‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α; # β-2 microglobulin; § β-2 microglobulin-free HLA-A heavy chain; ∞ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). -
Suitability of Immobilized Systems for Microbiological Degradation of Endocrine Disrupting Compounds
molecules Review Suitability of Immobilized Systems for Microbiological Degradation of Endocrine Disrupting Compounds Danuta Wojcieszy ´nska , Ariel Marchlewicz and Urszula Guzik * Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Science, University of Silesia in Katowice, Jagiello´nska28, 40-032 Katowice, Poland; [email protected] (D.W.); [email protected] (A.M.) * Correspondence: [email protected]; Tel.: +48-3220-095-67 Academic Editors: Urszula Guzik and Danuta Wojcieszy´nska Received: 10 September 2020; Accepted: 25 September 2020; Published: 29 September 2020 Abstract: The rising pollution of the environment with endocrine disrupting compounds has increased interest in searching for new, effective bioremediation methods. Particular attention is paid to the search for microorganisms with high degradation potential and the possibility of their use in the degradation of endocrine disrupting compounds. Increasingly, immobilized microorganisms or enzymes are used in biodegradation systems. This review presents the main sources of endocrine disrupting compounds and identifies the risks associated with their presence in the environment. The main pathways of degradation of these compounds by microorganisms are also presented. The last part is devoted to an overview of the immobilization methods used for the purposes of enabling the use of biocatalysts in environmental bioremediation. Keywords: EDCs; hormones; degradation; immobilization; microorganisms 1. Introduction The development of modern tools for the separation and identification of chemical substances has drawn attention to the so-called micropollution of the environment. Many of these contaminants belong to the emergent pollutants class. According to the Stockholm Convention they are characterized by high persistence, are transported over long distances in the environment through water, accumulate in the tissue of living organisms and can adversely affect them [1]. -
Identification and Developmental Expression of the Full Complement Of
Goldstone et al. BMC Genomics 2010, 11:643 http://www.biomedcentral.com/1471-2164/11/643 RESEARCH ARTICLE Open Access Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish Jared V Goldstone1, Andrew G McArthur2, Akira Kubota1, Juliano Zanette1,3, Thiago Parente1,4, Maria E Jönsson1,5, David R Nelson6, John J Stegeman1* Abstract Background: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Results: Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. -
Genetic Disruption of 21-Hydroxylase in Zebrafish Causes Interrenal Hyperplasia
RESEARCH ARTICLE Genetic Disruption of 21-Hydroxylase in Zebrafish Causes Interrenal Hyperplasia Helen Eachus,1 Andreas Zaucker,2 James A. Oakes,1,3 Aliesha Griffin,2 Meltem Weger,2 T¨ulay Guran, ¨ 2 Angela Taylor,2 Abigail Harris,4 Andy Greenfield,4 Jonathan L. Quanson,5 Karl-Heinz Storbeck,5 Vincent T. Cunliffe,1 Ferenc Muller, ¨ 6 and Nils Krone1,3 1Department of Biomedical Science, The Bateson Centre, Sheffield S10 2TN, United Kingdom; 2Centre for Endocrinology, Diabetes, and Metabolism, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; 3Academic Unit of Child Health, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2TG, United Kingdom; 4Mammalian Genetics Unit, Medical Research Council, Harwell Institute, Oxfordshire OX11 0RD, United Kingdom; 5Department of Biochemistry, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa; and 6Institute of Cancer and Genomic Sciences, University of Birmingham, College of Medical and Dental Sciences, Birmingham B15 2TT, United Kingdom Congenital adrenal hyperplasia is a group of common inherited disorders leading to glucocorticoid deficiency. Most cases are caused by 21-hydroxylase deficiency (21OHD). The systemic consequences of imbalanced steroid hormone biosynthesis due to severe 21OHD remains poorly understood. Therefore, we developed a zebrafish model for 21OHD, which focuses on the impairment of glucocorticoid biosynthesis. A single 21-hydroxylase gene (cyp21a2) is annotated in the zebrafish genome based on sequence homology. Our in silico analysis of the 21-hydroxylase (Cyp21a2) protein sequence suggests a sufficient degree of similarity for the usage of zebrafish cyp21a2 to model aspects of human 21OHD in vivo. We determined the spatiotemporal expression patterns of cyp21a2 by whole-mount in situ hybridization and reverse transcription polymerase chain reaction throughout early development. -
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. -
Part I Biopharmaceuticals
1 Part I Biopharmaceuticals Translational Medicine: Molecular Pharmacology and Drug Discovery First Edition. Edited by Robert A. Meyers. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2018 by Wiley-VCH Verlag GmbH & Co. KGaA. 3 1 Analogs and Antagonists of Male Sex Hormones Robert W. Brueggemeier The Ohio State University, Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Columbus, Ohio 43210, USA 1Introduction6 2 Historical 6 3 Endogenous Male Sex Hormones 7 3.1 Occurrence and Physiological Roles 7 3.2 Biosynthesis 8 3.3 Absorption and Distribution 12 3.4 Metabolism 13 3.4.1 Reductive Metabolism 14 3.4.2 Oxidative Metabolism 17 3.5 Mechanism of Action 19 4 Synthetic Androgens 24 4.1 Current Drugs on the Market 24 4.2 Therapeutic Uses and Bioassays 25 4.3 Structure–Activity Relationships for Steroidal Androgens 26 4.3.1 Early Modifications 26 4.3.2 Methylated Derivatives 26 4.3.3 Ester Derivatives 27 4.3.4 Halo Derivatives 27 4.3.5 Other Androgen Derivatives 28 4.3.6 Summary of Structure–Activity Relationships of Steroidal Androgens 28 4.4 Nonsteroidal Androgens, Selective Androgen Receptor Modulators (SARMs) 30 4.5 Absorption, Distribution, and Metabolism 31 4.6 Toxicities 32 Translational Medicine: Molecular Pharmacology and Drug Discovery First Edition. Edited by Robert A. Meyers. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2018 by Wiley-VCH Verlag GmbH & Co. KGaA. 4 Analogs and Antagonists of Male Sex Hormones 5 Anabolic Agents 32 5.1 Current Drugs on the Market 32 5.2 Therapeutic Uses and Bioassays -
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. -
Evolution of the Bile Salt Nuclear Receptor FXR in Vertebrates
Supplemental Material can be found at: http://www.jlr.org/cgi/content/full/M800138-JLR200/DC1 Evolution of the bile salt nuclear receptor FXR in vertebrates † † † †† †† Erica J. Reschly,* Ni Ai, Sean Ekins, ,§,** William J. Welsh, Lee R. Hagey, Alan F. Hofmann, and Matthew D. Krasowski1,* † Department of Pathology,* University of Pittsburgh, Pittsburgh, PA 15261; Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854; Collaborations in Chemistry,§ Jenkintown, PA 19046; Department of Pharmaceutical Sciences,** †† University of Maryland, Baltimore, MD 21202; and Department of Medicine, University of California-San Diego, San Diego, CA 92093-0063 Abstract Bile salts, the major end metabolites of cho- Bile salts are water-soluble, amphipathic end metabolites lesterol, vary significantly in structure across vertebrate of cholesterol that facilitate intestinal absorption of lipids species, suggesting that nuclear receptors binding these (1), enhance proteolytic cleavage of dietary proteins (2), Downloaded from molecules may show adaptive evolutionary changes. We com- and have potent antimicrobial activity in the small intestine pared across species the bile salt specificity of the major (3). In addition, bile salt signaling via nuclear hormone re- transcriptional regulator of bile salt synthesis, the farnesoid X receptor (FXR). We found that FXRs have changed speci- ceptors (NHRs) is important for bile salt homeostasis (4). ficity for primary bile salts across species by altering the Bile salts have not been detected in invertebrate animals. shape and size of the ligand binding pocket. In particular, In contrast to steroid hormones and vitamins, whose struc- the ligand binding pockets of sea lamprey (Petromyzon marinus) tures tend to be strongly conserved, bile salts exhibit www.jlr.org and zebrafish (Danio rerio) FXRs, as predicted by homology marked structural diversity across species (5–7). -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes. -
Microarray-Based Analysis of Genes, Transcription Factors, and Epigenetic Modifications in Lung Cancer Exposed to Nitric Oxide
CANCER GENOMICS & PROTEOMICS 17 : 401-415 (2020) doi:10.21873/cgp.20199 Microarray-based Analysis of Genes, Transcription Factors, and Epigenetic Modifications in Lung Cancer Exposed to Nitric Oxide ARNATCHAI MAIUTHED 1, ORNJIRA PRAKHONGCHEEP 2,3 and PITHI CHANVORACHOTE 2,3 1Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand; 2Cell-based Drug and Health Product Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand; 3Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand Abstract. Background/Aim: Nitric oxide (NO) is recognized NO exposure of lung cancer cells resulted in a change in as an important biological mediator that exerts several transcription factors (TFs) and epigenetic modifications human physiological functions. As its nature is an aqueous (histone modification and miRNA). Interestingly, NO soluble gas that can diffuse through cells and tissues, NO treatment was shown to potentiate cancer stem cell-related can affect cell signaling, the phenotype of cancer and modify genes and transcription factors Oct4, Klf4, and Myc. surrounding cells. The variety of effects of NO on cancer cell Conclusion: Through this comprehensive approach, the biology has convinced researchers to determine the defined present study illustrated the scheme of how NO affects mechanisms of these effects and how to control this mediator molecular events in lung cancer cells. for a better understanding as well as for therapeutic gain. Materials and Methods: We used bioinformatics and Lung cancer is one of the leading causes of cancer-related pharmacological experiments to elucidate the potential deaths worldwide (1, 2). Since the aggressive phenotypes regulation and underlying mechanisms of NO in non-small and treatment failures have been frequently observed in lung a lung cancer cell model. -
1,25-Dihydroxyvitamin D3-Induced Genes in Osteoblasts
1,25-DIHYDROXYVITAMIN D3-INDUCED GENES IN OSTEOBLASTS: UNCOVERING NEW FUNCTIONS FOR MENINGIOMA 1 AND SEMAPHORIN 3B IN SKELETAL PHYSIOLOGY by XIAOXUE ZHANG Submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Thesis advisor: Paul N. MacDonald Department of Pharmacology CASE WESTERN RESERVE UNIVERSITY May 2009 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of _____________________________________________________ candidate for the ______________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. I dedicate this thesis to my mother and father for their lifelong love, encouragement and sacrifice TABLE OF CONTENTS Table of Contents ii List of Tables iii List of Figures iv Acknowledgements vii Abbreviations x Abstract xiii Chapter I Introduction 1 Chapter II Meningioma 1 (MN1) is a 1,25-dihydroxyvitamin D3- 44 induced transcription coactivator that promotes osteoblast proliferation, motility, differentiation, and function Chapter III Semaphorin 3B (SEMA3B) is a 1,25- 108 dihydroxyvitamin D3-induced gene in osteoblasts that promotes