Expression of Capn6 During Osteoclast Differentiation in Wild-Type and HDAC4 Knockout Mice a THESIS SUBMITTED to the FACULTY OF

Total Page:16

File Type:pdf, Size:1020Kb

Expression of Capn6 During Osteoclast Differentiation in Wild-Type and HDAC4 Knockout Mice a THESIS SUBMITTED to the FACULTY OF Expression of Capn6 During Osteoclast Differentiation in Wild-type and HDAC4 Knockout Mice A THESIS SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Molly Kopf IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF DENTISTRY Kim Mansky, PhD; Amy Tasca, DDS, PhD; and John Beyer, DDS, PhD June 2019 © Molly Kopf 2019 Acknowledgements First, I would like to thank my thesis committee chair Dr. Kim Mansky for her time and dedication to this project. It would not have been successful without her support and guidance. I would also like to thank my other committee members Dr. Amy Tasca and Dr. John Beyer for all their help and input for my master’s thesis. I greatly appreciate the time they committed to reviewing and shaping this thesis. Additionally, I would like to express my gratitude to those individuals working in the Mansky lab at the University of Minnesota. They taught me several lab procedures, contributed to the study by providing samples, and created a fun yet productive environment for completing my research. These individuals include but are not limited to Dr. Eric Jensen, Bora Faulkner, Kristina Astleford, Andrew Norton and Emily Campbell. Furthermore, I’d like to thank the full-time and part-time faculty members of the orthodontic clinic for their commitment to my education over the last two years. I’m eager to use the wisdom and knowledge I gleaned from them in my future career. Lastly, I’d like to acknowledge my fellow orthodontic co-residents. I value their support and will always cherish the memorable experience of our orthodontic residency. i Dedication I dedicate my master’s thesis to my husband Blake. Even though we were separated by hundreds of miles, you were there supporting me through it all. ii Abstract Introduction: The process of osteoclast differentiation and function consists of a network of complex signaling pathways with multiple negative and positive regulators. Previous studies suggest histone deacetylase (HDAC) proteins play a suppressive role in osteoclast differentiation; however, not much is known about the specific role of HDAC4. Expression of calpain 6 (Capn6) has been linked to increased organization of osteoclast microtubules for bone resorption. In this study, we observe the expression of Capn6 in wild-type and HDAC4 knockout osteoclasts. Methods: qRT-PCR was preformed to assess Capn6 expression in wild-type and HDAC4 knockout mice over days 0 to 4 of osteoclast differentiation. Immunoblot analysis was used to assess CAPN6 levels in both groups. Results: Levels of Capn6 expression increased later in osteoclast differentiation in the wild-type osteoclasts, though the results were not significant. There was a significant increase in Capn6 in osteoclasts from HDAC4 knockout mice after 3 days of RANKL stimulation. This was also significant when comparing HDAC4 knockout to wild-type osteoclasts. Conclusion: HDAC4 may be a negative regulator of osteoclast function, suppressing the expression of Capn6. More studies are indicated to understand the interaction of HDAC4 and Capn6 in the regulation of osteoclast activity. iii Table of Contents List of Tables v List of Figures vi Introduction 1 Materials and Methods 12 Results 15 Discussion 21 Conclusions 24 References 25 iv List of Tables Table 1. Capn6:Hprt expression in ten biologically independent wild-type 17 mice samples Table 2. Capn6:Hprt expression in five biologically independent HDAC 4 19 knockout mice samples v List of Figures Figure 1. Stimulation of osteoclast precursor by RANKL and M-CSF 3 Figure 2. The signaling pathways involved in the activation of NFATc1 5 Figure 3. Process of osteoclast resorption with HCl acid and 7 Cathepsin K Figure 4. Expression of RNA sequencing genes in wild-type vs. knockout 16 mice on day 2 of osteoclast differentiation Figure 5. A) Immunoblot analysis of Capn6 in wild-type mice B) Mean 18 Capn6:Hprt expression in wild-type mice over four days of differentiation Figure 6. Mean Capn6:Hprt expression over days of differentiation 19 between wild-type and HDAC4 knockout mice Figure 7. Mean Capn6:Hprt expression over days of differentiation 20 between wild-type (black) and HDAC4 knockout mice (white) vi Introduction Bone is often thought of as the strong, rigid supporting structure of the bodies of various organisms. It is necessary for the vitality of those organisms allowing for mobility, protection of significant organs, production of blood cells, and storage of minerals like calcium. Bone tissue is made up of a collagenous matrix, inorganic elements, and cells. Even though bone is strong and rigid, it is not static. Throughout a lifetime, bone is constantly being reshaped, remodeled, and repaired. This continual dynamic process of resorption (bone degradation) and apposition (bone formation) is completed at such a rate that in one year, approximately 10% of the bone content is replaced in a human adult.1 Bone remodeling cycle The process of resorption and apposition is facilitated by specific cells called osteoclasts and osteoblasts, respectively. Through various signaling pathways, bone remolding occurs first by osteoclasts recruitment to the site of repair. Resorption creates Howship’s lacunae on the bony surface. Once these lacunae get to a depth of about 50µm, certain signals recruit mesenchymal cells to differentiate into osteoblasts at the site and start bone apposition.2 A disruption in the process of removing and adding bone can cause harmful effects in humans.2,3 For example, an increase in osteoclastic activity will lead to an imbalance where more bone will be resorbed. This will weaken the bone and cause bone disorders such as osteoporosis, rheumatoid arthritis, periodontal disease, multiple myeloma, and certain metastatic cancers.1–5 A decrease in 1 resorption processes by osteoclasts leads to an increase in the amount of bone and cause diseases such as osteopetrosis.5,6 Osteoclast differentiation Since osteoclasts play a key role in most bone disorders, studies have been conducted to learn more about their origin and differentiation process.4,5 Osteoclasts are multinuclear giant cells derived from hematopoietic precursors of the monocyte and macrophage lineage that surround the bone.3 Original studies looked at failed osteoclast recruitment leading to osteopetrosis to determine transcription factors involved in differentiation. One of the first transcription factors that plays a role in osteoclastogenesis is PU.1.4,5,7 This is a positive regulator of transcription involved in the generation of the common progenitors for both osteoclasts and macrophages; therefore, a deletion of PU.1 will cause a lack of both of those cell types, and knockout mice exhibit an osteopetrotic phenotype.1,7 In addition, many genes required for osteoclast and macrophage differentiation have PU.1 binding sites in their promoters.7 Studies have shown that there are two main factors that stimulate osteoclastogensis in vitro: macrophage colony stimulating factor (M-CSF) and receptor activator of nuclear factor (NF)-κB ligand (RANKL)1–3. RANKL is a membrane-bound cytokine derived from the tumor necrosis factor (TNF) family.1– 3 Osteoprotegerin (OPG), another TNF-derived receptor, was used to discover the importance of RANKL in osteoclast differentiation.4 OPG was simultaneously discovered by two groups: Amgen and Snow Brand Milk Group.6 It is a secreted 2 protein and was found to be a decoy receptor competing with RANK to bind RANKL, and thus inhibiting osteoclast differentiation and inducing osteopetrosis in vitro and in vivo. 2,5,8 Both RANK and RANKL are found in other organs of the body such as skeletal muscle, thymus, liver, colon, adrenal glands, lungs, brain and kidneys.6 The OPG/RANK/RANKL regulation system is important in the regulation of resorption by negatively and positively controlling the activation of RANK on osteoclasts. Figure 12: Stimulation of osteoclast precursor by RANKL and M-CSF PU.1 stimulates expression of colony-stimulating factor 1 receptor (CSF1R) on macrophage progenitors. This is a receptor for CSF1, also known as M-CSF which causes proliferation of osteoclast precursor cells as well as upregulates RANK. Again, M-CSF knockout mice have a lack of proliferating osteoclast cells, leading to an increase in bone density.7 M-CSF also activates microphthalmia-associated transcription factor (MITF), which plays a key role in 3 later stages of osteoclastogensis. MITF regulates the expression of anti-apoptotic protein Bcl-2 and promotes the survival of osteoclasts and macrophages.1,5,7 RANKL leads to osteoclast differentiation through its complex signaling pathway9. Both osteoblasts and osteocytes have been shown to be the source of RANKL that binds to RANK in osteoclasts.10,11 In vivo, it was demonstrated that a direct contact with osteoblasts or osteocytes is not needed for RANKL to bind to their receptors on the osteoblast progenitor cells.3,12 Additionally, it has been discovered that vesicular RANK secreted by osteoclasts exhibits a reverse signaling pathway that in turn upregulates osteoblast differentiation.12 This shows the unique coupling of bone formation and bone apposition. Therefore, therapies that inhibit osteoclast differentiation will also decrease the amount of bone formation due to this coupling phenomenon. Once RANK and RANKL bind, RANK has the ability to bind TRAF6 in osteoclasts, which has a major role in signal transduction for osteoclast differentiation.1,2,13 TRAF6 activates NF-κB and mitogen-activated kinases (MAPKs) pathway which led to activations
Recommended publications
  • Universidade Estadual De Campinas Instituto De Biologia
    UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso.
    [Show full text]
  • Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis
    Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing
    [Show full text]
  • Solutions to Detect Apoptosis and Pyroptosis
    Powerful Tools for In vitro Fluorescent Imaging in Cancer Research Jackie Carville May 11, 2016 About Us Products and Services • Custom Assay Services – Immunoassay design and development – Antibody purification/conjugation • Consumable Reagents – ELISA Solutions – Cell-permeant Fluorescent Probes for detection of cell death • Products for research use only. Not for use in diagnostic procedures. ELISA Solutions • ELISA Wash Buffer • PBS • Substrates • Stop Solutions • Plates • Coating Buffers • Blocking Buffers • Conjugate Stabilizers • Assay Diluents • Sample Diluents Custom Services • Antibody Conjugation • Immunoassay Design • Immunoassay Development • Lyophilization • Plate Coating Overview of ICT’s Fluorescent Probes FOR DETECTION OF: • Active caspases • Caspases/Cathepsins in real time • Mitochondrial Health • Cytotoxicity • Serine Proteases Today’s Agenda • FLICA • FLISP • Magic Red • Cell Viability • Mito PT • Oxidative Stress • Cytotoxicity FLICA • FLICA – Fluorescent Labeled Inhibitor of Caspases • In vitro, whole cell detection of caspase activity in apoptotic or caspase-positive cells • Available in green, red, and far red assays FLICA Cancer Research Applications • FLICA is the most accurate and sensitive method of apoptosis detection • Can identify four stages of cell death in one sample • Detect poly caspase activity or individual caspase enzymes How FLICA A. INACTIVE CASPASE (ZYMOGEN) works… prodomain B. CASPASE PROCESSING FMK Fluorescent Reporter YVAD tag C. ACTIVATED CASPASE (HETERO-TETRAMER) D. BINDING OF FLICA Sample
    [Show full text]
  • The Osteoclast-Associated Protease Cathepsin K Is Expressed in Human Breast Carcinoma1
    CANCER RESEARCH57. 5386-5390. December I, 19971 The Osteoclast-associated Protease Cathepsin K Is Expressed in Human Breast Carcinoma1 Amanda J. Littlewood-Evans,' Graeme Bilbe, Wayne B. Bowler, David Farley, Brenda Wlodarski, Toshio Kokubo, Tetsuya Inaoka, John Sloane, Dean B. Evans, and James A. Gallagher Novartis Pharina AG, CH-4002 Base!. Switzerland (A. I. L-E., G. B., D. F., D. B. El; Human Bone Cell Research Group, Department of Human Anatomy and Cell Biology 1W. B. B., B. W., J. A. G.J, and Department of Pathology If. S.), University of Liverpool, Liverpool 5.69 3BX, United Kingdom [W. B. B., B. W., J. S., J. A. G.]; and Takarazuka Research Institute, Novartis Pharma lid., Takarazuka 665, Japan IT. K., T. LI ABSTRACT (ZR75—l,Hs578Tduct, BT474, ZR75—30,BT549, and T-47D), adenocarci noma (MDA-MB-231, SK-BR3, MDA-MB-468, and BT2O), and breast car Human cathepsin K is a novel cysteine protease previously reported cinoma[MVLNandMTLN,transfectedMCF-7-derivedclonesobtainedfrom to be restricted in its expression to osteoclasts. Immunolocalization of Dr. J. C. Nicolas (Unit de Recherches sur Ia Biochemie des Steroides Insern cathepsin K in breast tumor bone metastases revealed that the invading U58, Montpelier, France), and MCF-7]. The MCF-7 cells were obtained from breast cancer cells expressed this protease, albeit at a lower intensity two different sources, ATCC and Dr. Roland Schuele (Tumor Klinik, Freiburg, than in osteoclasts. In situ hybridization and immunolocalization stud Germany). These are indicated in the figure legend as clone 1 (ATCC) and ies were subsequently conducted to demonstrate cathepsin K mRNA clone 2 (Dr.
    [Show full text]
  • Large-Scale Serum Protein Biomarker Discovery in Duchenne Muscular Dystrophy
    Large-scale serum protein biomarker discovery in Duchenne muscular dystrophy Yetrib Hathouta, Edward Brodyb, Paula R. Clemensc,d, Linda Cripee, Robert Kirk DeLisleb, Pat Furlongf, Heather Gordish- Dressmana, Lauren Hachea, Erik Henricsong, Eric P. Hoffmana, Yvonne Monique Kobayashih, Angela Lortsi, Jean K. Mahj, Craig McDonaldg, Bob Mehlerb, Sally Nelsonk, Malti Nikradb, Britta Singerb, Fintan Steeleb, David Sterlingb, H. Lee Sweeneyl, Steve Williamsb, and Larry Goldb,1 aResearch Center for Genetic Medicine, Children’s National Medical Center, Washington, DC 20012; bSomaLogic, Inc., Boulder, CO 80301; cNeurology Service, Department of Veteran Affairs Medical Center, Pittsburgh, PA 15240; dUniversity of Pittsburgh, Pittsburgh, PA 15213; eThe Heart Center, Nationwide Children’s Hospital, The Ohio State University, Columbus, OH 15213; fParent Project Muscular Dystrophy, Hackensack, NJ 07601; gDepartment of Physical Medicine and Rehabilitation, University of California Davis School of Medicine, Davis, CA 95618; hDepartment of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202; iThe Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; jDepartment of Pediatrics, University of Calgary, Alberta Children’s Hospital, Calgary, AB, Canada T3B 6A8; kDivision of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, CO 80045; and lDepartment of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL 32610 Contributed
    [Show full text]
  • To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants
    Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin.
    [Show full text]
  • Serine Proteases with Altered Sensitivity to Activity-Modulating
    (19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants.
    [Show full text]
  • Acemannan Stimulates Bone Sialoprotein, Osteocalcin, Osteopon- Tin and Osteonectin Expression in Periodontal Ligament Cells in V
    Original Article บ ท วิ ท ย า ก า ร Acemannan Stimulates Bone Sialoprotein, Osteocalcin, Osteopon- tin and Osteonectin Expression in Periodontal Ligament Cells in Vitro Pintu-on Chantarawaratit1,2,4, Polkit Sangvanich3 and Pasutha Thunyakitpisal2,4 1Department of Orthodontics, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand 2Dental Biomaterials Program, Graduate School, Chulalongkorn University, Bangkok, Thailand 3Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand 4Research Unit of Herbal Medicine and Natural Products of Dental Application, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand Correspondence to: Pasutha Thunyakitpisal, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, 34, Henri-Dunant Rd, Patumwan, Bangkok 10330, Thailand Email: [email protected] Abstract The periodontium is composed of both soft and hard tissues, thus hard tissue regeneration is one of the most important processes in periodontal regeneration. Bone sialoprotein, osteocalcin, osteopontin and osteonectin are non- collagenous matrix proteins which play vital roles in the mineralization of hard tissue. Recent studies have demonstrated that acemannan, a polysaccharide extracted from Aloe vera gel, upregulated the expression of proteins involved in hard tissue regeneration. This study investigated effect of acemannan on bone sialoprotein, osteocalcin, osteopontin and osteonectin expression in human periodontal ligament cells. Primary periodontal ligament cells were isolated from impacted third molars and then treated with acemannan in vitro. The mRNA expression of bone sialoprotein and osteocalcin and the protein levels of osteopontin and osteonectin were determined using reverse transcription-polymerase chain reaction and western blot analysis, respectively. One-way analysis of variance and Dunnett multiple comparisons were performed to analyze the data.
    [Show full text]
  • Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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 The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.
    [Show full text]
  • A Model for Profiling the Emolecular Effects of Alcohol
    The Pharmacogenomics Journal (2015) 15, 177–188 © 2015 Macmillan Publishers Limited All rights reserved 1470-269X/15 www.nature.com/tpj ORIGINAL ARTICLE The synaptoneurosome transcriptome: a model for profiling the emolecular effects of alcohol D Most1,2, L Ferguson1,2, Y Blednov1, RD Mayfield1 and RA Harris1 Chronic alcohol consumption changes gene expression, likely causing persistent remodeling of synaptic structures via altered translation of mRNAs within synaptic compartments of the cell. We profiled the transcriptome from synaptoneurosomes (SNs) and paired total homogenates (THs) from mouse amygdala following chronic voluntary alcohol consumption. In SN, both the number of alcohol-responsive mRNAs and the magnitude of fold-change were greater than in THs, including many GABA-related mRNAs upregulated in SNs. Furthermore, SN gene co-expression analysis revealed a highly connected network, demonstrating coordinated patterns of gene expression and highlighting alcohol-responsive biological pathways, such as long-term potentiation, long-term depression, glutamate signaling, RNA processing and upregulation of alcohol-responsive genes within neuroimmune modules. Alterations in these pathways have also been observed in the amygdala of human alcoholics. SNs offer an ideal model for detecting intricate networks of coordinated synaptic gene expression and may provide a unique system for investigating therapeutic targets for the treatment of alcoholism. The Pharmacogenomics Journal (2015) 15, 177–188; doi:10.1038/tpj.2014.43; published online 19 August 2014 INTRODUCTION mRNAs from SN15,16,18,19 and TH samples from mouse amygdala, a Alcohol dependence is a severe and widespread disease. Over 17 brain region known to be involved with the negative reinforce- 20 million Americans suffer from alcohol-related problems; total cost ment of alcohol and other drugs of abuse.
    [Show full text]
  • CHAPTER 41 Target Genes: Bone Proteins 719
    CHAPTER 41 Target Genes: Bone Proteins 719 45. Bellows CG, Reimers SM, Heersche JN 1999 Expression of 61. Price PA, Williamson MK, Lothringer JW 1981 Origin of the mRNAs for type-I collagen, bone sialoprotein, osteocalcin, vitamin K-dependent bone protein found in plasma and its and osteopontin at different stages of osteoblastic differentia- clearance by kidney and bone. J Biol Chem 256:12760–12766. tion and their regulation by 1,25-dihydroxyvitamin D3. Cell 62. Ducy P, Desbois C, Boyce B, Pinero G, Story B, Dunstan C, Tissue Res 297:249–259. Smith E, Bonadio J, Goldstein S, Gundberg C, Bradley A, 46. Broess M, Riva A, Gerstenfeld LC 1995 Inhibitory effects of Karsenty G 1996 Increased bone formation in osteocalcin- 1,25(OH)2 vitamin D3 on collagen type I, osteopontin, and deficient mice. Nature 382:448–452. osteocalcin gene expression in chicken osteoblasts. J Cell 63. Chenu C, Colucci S, Grano M, Zigrino P, Barattolo R, Biochem 57:440–451. Zambonin G, Baldini N, Vergnaud P, Delmas PD, Zallone AZ 47. Yoon K, Buenaga R, Rodan GA, Prince CW, Butler WT 1994 Osteocalcin induces chemotaxis, secretion of matrix pro- 1987 Tissue specificity and developmental expression of teins, and calcium-mediated intracellular signaling in human rat osteopontin. Biochem Biophys Res Commun 148: osteoclast-like cells. J Cell Biol 127:1149–1158. 1129–1136. 64. Watts NB 1999 Clinical utility of biochemical markers of bone 48. Beresford JN, Joyner CJ, Devlin C, Triffitt JT 1994 The effects remodeling. Clin Chem 45:1359–1368. of dexamethasone and 1,25-dihydroxyvitamin D3 on osteogenic 65.
    [Show full text]
  • 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
    [Show full text]