Selective Androgen Receptor Modulators (Sarms) And

Total Page:16

File Type:pdf, Size:1020Kb

Selective Androgen Receptor Modulators (Sarms) And (19) TZZ ¥6B_T (11) EP 2 222 636 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C07D 207/08 (2006.01) C07D 207/09 (2006.01) 10.04.2013 Bulletin 2013/15 C07D 498/04 (2006.01) A61K 31/402 (2006.01) A61P 5/26 (2006.01) (21) Application number: 08865188.0 (86) International application number: (22) Date of filing: 12.12.2008 PCT/US2008/013657 (87) International publication number: WO 2009/082437 (02.07.2009 Gazette 2009/27) (54) SELECTIVE ANDROGEN RECEPTOR MODULATORS (SARMS) AND USES THEREOF SELEKTIVE ANDROGENREZEPTORMODULATOREN (SARMS) UND IHRE VERWENDUNG MODULATEURS SÉLECTIFS DU RÉCEPTEUR ANDROGÈNE (SARM) ET LEURS UTILISATIONS (84) Designated Contracting States: (74) Representative: Baldock, Sharon Claire AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Boult Wade Tennant HR HU IE IS IT LI LT LU LV MC MT NL NO PL PT Verulam Gardens RO SE SI SK TR 70 Gray’s Inn Road Designated Extension States: London WC1X 8BT (GB) AL BA MK RS (56) References cited: (30) Priority: 21.12.2007 US 8731 P WO-A-02/068427 WO-A-03/090672 WO-A-2005/090282 WO-A-2006/124447 (43) Date of publication of application: WO-A-2007/015567 01.09.2010 Bulletin 2010/35 • HIGUCHI ET AL: "Potent, nonsteroidal selective (60) Divisional application: androgen receptor modulators (SARMs) based 12168231.4 / 2 489 656 on 8H-[1,4]oxazino[2,3-f]quinolin-8-ones" BIOORGANIC & MEDICINAL CHEMISTRY (73) Proprietor: Ligand Pharmaceuticals Inc. LETTERS, PERGAMON, ELSEVIER SCIENCE, San Diego, CA 92037 (US) GB, vol. 17, no. 19, 14 September 2007 (2007-09-14), pages 5442-5446, XP022249734 (72) Inventor: ZHI, Lin ISSN: 0960-894X San Diego, CA 92130 (US) Remarks: Thefile contains technical information submitted after the application was filed and not included in this specification Note: Within nine months of the publication of the mention of the grant of the European patent in the European Patent Bulletin, any person may give notice to the European Patent Office of opposition to that patent, in accordance with the Implementing Regulations. Notice of opposition shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention). EP 2 222 636 B1 Printed by Jouve, 75001 PARIS (FR) EP 2 222 636 B1 Description Related Applications 5 [0001] Benefit of priority is claimed to U.S. Provisional Patent Application Serial No. 61/008,731, to Lin Zhi, filed on December 21, 2007, entitled "SELECTIVE ANDROGEN RECEPTOR MODULATORS (SARMs) AND USES THEREOF." Field 10 [0002] Provided herein are selective androgen receptor modulator (SARM) compounds that bind to androgen receptors and/or modulate activity of androgen receptors, and to methods for making and using such compounds. Also provided are compositions including such compounds and methods for making and using such compositions. Background 15 [0003] Certain intracellular receptors (IRs) have been shown to regulate transcription of certain genes (e.g., see R. M. Evans, Science 240:889 (1988)). Certain of such IRs are steroid receptors, such as androgen receptors, estrogen receptors, mineralocorticoid receptors, and progesterone receptors. Gene regulation by such receptors typically involves binding of an IR by a ligand. 20 [0004] In certain instances, a ligand binds to an IR, forming a receptor/ligand complex. Such a receptor/ligand complex can then translocate to the nucleus of a cell, where it binds to the DNA of one or more gene regulatory regions. Once bound to the DNA of a particular gene regulatory region, a receptor/ ligand complex can modulate the production of the protein encoded by that particular gene. In certain instances, an androgen receptor/ ligand complex regulates expression of certain proteins. In certain instances, an androgen receptor/ligand complex can interact directly with the DNA of a 25 particular gene regulatory region or with other transcription factors. In certain instances, such interactions result in modulation of transcriptional activation. [0005] Androgen therapy has been used to treat a variety of male disorders such as reproductive disorders and primary or secondary male hypogonadism. A number of natural or synthetic AR agonists have been investigated for the treatment of musculoskeletal disorders, such as bone disease, hematopoietic disorders, neuromuscular disease, rheumatological 30 disease, wasting disease, and for hormone replacement therapy (HRT), such as female androgen deficiency. In addition, AR antagonists, such as flutamide and bicalutamide, are used to treat prostate cancer. The effectiveness of known modulators of steroid receptors is often tempered by their undesired side-effect profile, particularly during long-term administration. For example, potential side effects of androgen therapy for women include acne, weight gain, excess facial and body hair, permanent lowering of the voice, and adverse lipid changes. In men, adverse effects can include 35 disordered sleep and breathing, polycythemia, and repression of high density lipoprotein. Thus there is a need for compounds that do not exhibit the adverse side-effects. It is among the objects herein to provide such compounds that modulate the activity of androgen receptor. Summary 40 [0006] Compounds for use in compositions and methods for modulating the activity of androgen receptor are provided. The compounds provided herein are non-steroidal Selective Androgen Receptor Modulators or SARMs. In particular, non-steroidal SARMs display therapeutic benefit but generally do not display adverse androgenic effects, such as prostate enlargement, acne, hirsutism, virilization and masculinization. The compounds selectively modulate (agonize or antag- 45 onize) the function of the AR, such as in a tissue- selective manner, to produce the effects of androgens without or with reduced negative or undesired androgenic properties. Among the compounds provided herein are agonists of androgen receptor. Among the compounds provided herein are antagonists of androgen receptor. Among the compounds provided herein are androgen receptor partial agonists. [0007] Among the compounds provided herein are tissue specific selective androgen receptor modulators. They can 50 be used for oral testosterone replacement therapy. Compounds provided herein display agonist activity with EC 50 values generally less than 1 micromolar. Compounds provided herein display antagonist activity with IC 50 values generally less than 2 micromolar. SARMs provided herein generally target anabolic tissue, such as connective tissue, including bone and muscle, and can be used to increase the mass ofa connective tissue in a subject and to reverse connective tissue loss in a subject. Among the disorders that can be treated are muscle wasting, cachexia, frailty and osteoporosis and 55 other muscle and bone disorders, including those enumerated below. [0008] Compounds provided herein have a structure of Formula I: 2 EP 2 222 636 B1 5 10 1 2 3 where R is CF3, F, or Cl; R hydrogen or methyl; R is hydrogen or methyl; also described are compounds having a 4 structure of Formula II or Formula III, where R is halogen or lower haloalkyl, particularly CF 3 or halogen, and in particular 5 Cl or CF3; and R is lower alkyl or lower haloalkyl, particularly C1 to C4 alkyl or C1 to C4 haloalkyl, and in particular methyl, ethyl or CF3. Also provided are a pharmaceutically acceptable salt, ester or an acetate, formate or benzoate derivative of an alcohol functional group of compound of formula I. 15 [0009] In some embodiments, the compounds provided herein exhibit tissue selective androgen receptor agonist activity. In some embodiments, the compounds provided herein exhibit tissue selective androgen receptor antagonist activity. also described herein are androgen receptor selective binding compounds. [0010] Compounds provided herein are effective for treating one or more androgen receptor mediated diseases or conditions. Such conditions and diseases include those caused by androgen deficiency and/or those that can be amel- 20 iorated by androgen administration. In certain embodiments, compounds provided herein are effective for treating one or more diseases or conditions responsive to an androgen receptor agonist. In certain embodiments, compounds provided herein are effective in treating one or more conditions whose etiology involves hypoactivity or subsensitivity of androgen receptor. In other embodiments, compounds provided herein are effective for treating one or more diseases or conditions responsive to an androgen receptor antagonist. In other embodiments, compounds provided herein are effective in 25 treating one or more conditions whose etiology involves hyperactivity of androgen receptor. [0011] In some tissues, the compounds provided herein can exhibit AR agonist activity and can be used to treat conditions that are caused by androgen deficiency or hypoactivity or subsensitivity of androgen receptor, or that can be ameliorated by androgen replacement or are responsive to treatment with an AR agonist. Such conditions, include, but not limited to, aging skin; Alzheimer’s disease; anemias, such as for example, aplastic anemia; anorexia; arthritis, 30 including inflammatory arthritis, rheumatoid arthritis, osteoarthritis and gout; arteriosclerosis; atherosclerosis; bone dis- ease, including metastatic bone disease; bone damage or fracture, such as by accelerating bone fracture repair and/or stimulation of osteoblasts and/or stimulation of bone remodeling and/or stimulation of cartilage growth; distraction
Recommended publications
  • The Potential Role of Necroptosis in Clinical Diseases (Review)
    INTERNATIONAL JOURNAL OF MOleCular meDICine 47: 89, 2021 The potential role of necroptosis in clinical diseases (Review) WENLI DAI1*, JIN CHENG1*, XI LENG2, XIAOQING HU1 and YINGFANG AO1 1Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing 100191; 2Medical Imaging Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China Received November 19, 2020; Accepted March 8, 2021 DOI: 10.3892/ijmm.2021.4922 Abstract. As an important type of programmed cell death in 1. Introduction addition to apoptosis, necroptosis occurs in a variety of patho‑ physiological processes, including infections, liver diseases, Necroptosis, an emerging field closely related to apoptosis, is a kidney injury, neurodegenerative diseases, cardiovascular non‑caspase‑dependent cell death that has been implicated in diseases, and human tumors. It can be triggered by a variety the pathological processes of various diseases. It is regulated of factors, such as tumor necrosis factor receptor and Toll‑like by various genes that cause regular and ordered cell death. receptor families, intracellular DNA and RNA sensors, and Through activating specific death signaling pathways, it shares interferon, and is mainly mediated by receptor‑interacting typical characteristics of necrosis, including loss of metabolic protein kinase 1 (RIP1), RIP3, and mixed lineage kinase function and subcellular changes (1,2). Receptor‑interacting domain‑like protein. A better understanding of the mechanism protein kinase 1 (RIP1) was the first signaling molecule of necroptosis may be useful in the development of novel drugs identified in the necrosome (3). RIP1 and RIP3 interact for necroptosis‑related diseases.
    [Show full text]
  • Produktinformation
    Produktinformation Diagnostik & molekulare Diagnostik Laborgeräte & Service Zellkultur & Verbrauchsmaterial Forschungsprodukte & Biochemikalien Weitere Information auf den folgenden Seiten! See the following pages for more information! Lieferung & Zahlungsart Lieferung: frei Haus Bestellung auf Rechnung SZABO-SCANDIC Lieferung: € 10,- HandelsgmbH & Co KG Erstbestellung Vorauskassa Quellenstraße 110, A-1100 Wien T. +43(0)1 489 3961-0 Zuschläge F. +43(0)1 489 3961-7 [email protected] • Mindermengenzuschlag www.szabo-scandic.com • Trockeneiszuschlag • Gefahrgutzuschlag linkedin.com/company/szaboscandic • Expressversand facebook.com/szaboscandic PSMD10 Antibody, Biotin conjugated Product Code CSB-PA018899LD01HU Abbreviation 26S proteasome non-ATPase regulatory subunit 10 Storage Upon receipt, store at -20°C or -80°C. Avoid repeated freeze. Uniprot No. O75832 Immunogen Recombinant Human 26S proteasome non-ATPase regulatory subunit 10 protein (1-226AA) Raised In Rabbit Species Reactivity Human Tested Applications ELISA Relevance Acts as a chaperone during the assembly of the 26S proteasome, specifically of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD10:PSMC4:PSMC5:PAAF1 module which probably assembles with a PSMD5:PSMC2:PSMC1:PSMD2 module. Independently of the proteasome, regulates EGF-induced AKT activation through inhibition of the RHOA/ROCK/PTEN pahway, leading to prolonged AKT activation. Plays an important role in RAS-induced tumorigenesis. Acts as an proto-oncoprotein by being involved in negative regulation of tumor suppressors RB1 and p53/TP53. Overexpression is leading to phosphorylation of RB1 and proteasomal degradation of RB1. Regulates CDK4-mediated phosphorylation of RB1 by competing with CDKN2A for binding with CDK4. Facilitates binding of MDM2 to p53/TP53 and the mono- and polyubiquitination of p53/TP53 by MDM2 suggesting a function in targeting the TP53:MDM2 complex to the 26S proteasome.
    [Show full text]
  • Cancer Vulnerabilities Unveiled by Genomic Loss
    Cancer Vulnerabilities Unveiled by Genomic Loss The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Nijhawan, Deepak, Travis I. Zack, Yin Ren, Matthew R. Strickland, Rebecca Lamothe, Steven E. Schumacher, Aviad Tsherniak, et al. “Cancer Vulnerabilities Unveiled by Genomic Loss.” Cell 150, no. 4 (August 2012): 842–854. © 2012 Elsevier Inc. As Published http://dx.doi.org/10.1016/j.cell.2012.07.023 Publisher Elsevier B.V. Version Final published version Citable link http://hdl.handle.net/1721.1/91899 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Cancer Vulnerabilities Unveiled by Genomic Loss Deepak Nijhawan,1,2,7,9,10 Travis I. Zack,1,2,3,9 Yin Ren,5 Matthew R. Strickland,1 Rebecca Lamothe,1 Steven E. Schumacher,1,2 Aviad Tsherniak,2 Henrike C. Besche,4 Joseph Rosenbluh,1,2,7 Shyemaa Shehata,1 Glenn S. Cowley,2 Barbara A. Weir,2 Alfred L. Goldberg,4 Jill P. Mesirov,2 David E. Root,2 Sangeeta N. Bhatia,2,5,6,7,8 Rameen Beroukhim,1,2,7,* and William C. Hahn1,2,7,* 1Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA 2Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA 3Biophysics Program, Harvard University, Boston, MA 02115, USA 4Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA 5Harvard-MIT Division of Health Sciences and Technology 6David H.
    [Show full text]
  • PSMD10 Antibody (Center) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AW5126
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 PSMD10 Antibody (Center) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AW5126 Specification PSMD10 Antibody (Center) - Product Information Application IF, WB, IHC-P,E Primary Accession O75832 Other Accession Q9Z2X2 Reactivity Human Predicted Mouse Host Rabbit Clonality Polyclonal Calculated MW H=24,16;M=25;Ra t=25 KDa Isotype Rabbit Ig Antigen Source HUMAN PSMD10 Antibody (Center) - Additional Information Gene ID 5716 Fluorescent image of Hela cells stained with PSMD10 Antibody (Center)(Cat#AW5126). Antigen Region AW5126 was diluted at 1:25 dilution. An 43-76 Alexa Fluor 488-conjugated goat anti-rabbit lgG at 1:400 dilution was used as the Other Names secondary antibody (green). Cytoplasmic 26S proteasome non-ATPase regulatory subunit 10, 26S proteasome regulatory actin was counterstained with Alexa Fluor® subunit p28, Gankyrin, p28(GANK), PSMD10 555 conjugated with Phalloidin (red). Dilution IF~~1:25 WB~~ 1:1000 IHC-P~~1:25 Target/Specificity This PSMD10 antibody is generated from a rabbit immunized with a KLH conjugated synthetic peptide between 43-76 amino acids from the Central region of human PSMD10. Format Purified polyclonal antibody supplied in PBS with 0.09% (W/V) sodium azide. This antibody is purified through a protein A column, followed by peptide affinity purification. Western blot analysis of lysates from MCF-7, PC-3, K562 cell line (from left to right), using Storage PSMD10 Antibody (Center)(Cat. #AW5126). Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Maintain refrigerated at 2-8°C for up to 2 AW5126 was diluted at 1:1000 at each lane.
    [Show full text]
  • Inactive USP14 and Inactive UCHL5 Cause Accumulation of Distinct Ubiquitinated Proteins In
    bioRxiv preprint doi: https://doi.org/10.1101/479758; this version posted November 26, 2018. 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. Inactive USP14 and inactive UCHL5 cause accumulation of distinct ubiquitinated proteins in mammalian cells Jayashree Chadchankar, Victoria Korboukh, Peter Doig, Steve J. Jacobsen, Nicholas J. Brandon, Stephen J. Moss, Qi Wang AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Tufts University, Boston, MA (J.C., S.J.M.) Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, MA (S.J.J., N.J.B., Q.W.) Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA (V.K., P.D.) Department of Neuroscience, Tufts University School of Medicine, Boston, MA (S.J.M.) Department of Neuroscience, Physiology and Pharmacology, University College, London, WC1E, 6BT, UK (S.J.M.) 1 bioRxiv preprint doi: https://doi.org/10.1101/479758; this version posted November 26, 2018. 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. Running title: Effects of inactive USP14 and UCHL5 in mammalian cells Keywords: USP14, UCHL5, deubiquitinase, proteasome, ubiquitin, β‐catenin Corresponding author: Qi Wang Address: Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, MA 02451 Email address: [email protected] 2 bioRxiv preprint doi: https://doi.org/10.1101/479758; this version posted November 26, 2018. 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.
    [Show full text]
  • Functional Gene Clusters in Global Pathogenesis of Clear Cell Carcinoma of the Ovary Discovered by Integrated Analysis of Transcriptomes
    International Journal of Environmental Research and Public Health Article Functional Gene Clusters in Global Pathogenesis of Clear Cell Carcinoma of the Ovary Discovered by Integrated Analysis of Transcriptomes Yueh-Han Hsu 1,2, Peng-Hui Wang 1,2,3,4,5 and Chia-Ming Chang 1,2,* 1 Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan; [email protected] (Y.-H.H.); [email protected] (P.-H.W.) 2 School of Medicine, National Yang-Ming University, Taipei 112, Taiwan 3 Institute of Clinical Medicine, National Yang-Ming University, Taipei 112, Taiwan 4 Department of Medical Research, China Medical University Hospital, Taichung 440, Taiwan 5 Female Cancer Foundation, Taipei 104, Taiwan * Correspondence: [email protected]; Tel.: +886-2-2875-7826; Fax: +886-2-5570-2788 Received: 27 April 2020; Accepted: 31 May 2020; Published: 2 June 2020 Abstract: Clear cell carcinoma of the ovary (ovarian clear cell carcinoma (OCCC)) is one epithelial ovarian carcinoma that is known to have a poor prognosis and a tendency for being refractory to treatment due to unclear pathogenesis. Published investigations of OCCC have mainly focused only on individual genes and lack of systematic integrated research to analyze the pathogenesis of OCCC in a genome-wide perspective. Thus, we conducted an integrated analysis using transcriptome datasets from a public domain database to determine genes that may be implicated in the pathogenesis involved in OCCC carcinogenesis. We used the data obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) DataSets. We found six interactive functional gene clusters in the pathogenesis network of OCCC, including ribosomal protein, eukaryotic translation initiation factors, lactate, prostaglandin, proteasome, and insulin-like growth factor.
    [Show full text]
  • Genome-Wide Transcript and Protein Analysis Reveals Distinct Features of Aging in the Mouse Heart
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.28.272260; this version posted April 21, 2021. 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-NC-ND 4.0 International license. Genome-wide transcript and protein analysis reveals distinct features of aging in the mouse heart Isabela Gerdes Gyuricza1, Joel M. Chick2, Gregory R. Keele1, Andrew G. Deighan1, Steven C. Munger1, Ron Korstanje1, Steven P. Gygi3, Gary A. Churchill1 1The Jackson Laboratory, Bar Harbor, Maine 04609 USA; 2Vividion Therapeutics, San Diego, California 92121, USA; 3Harvard Medical School, Boston, Massachusetts 02115, USA Corresponding author: [email protected] Key words for online indexing: Heart Aging Transcriptomics Proteomics eQTL pQTL Stoichiometry ABSTRACT Investigation of the molecular mechanisms of aging in the human heart is challenging due to confounding factors, such as diet and medications, as well limited access to tissues. The laboratory mouse provides an ideal model to study aging in healthy individuals in a controlled environment. However, previous mouse studies have examined only a narrow range of the genetic variation that shapes individual differences during aging. Here, we analyzed transcriptome and proteome data from hearts of genetically diverse mice at ages 6, 12 and 18 months to characterize molecular changes that occur in the aging heart. Transcripts and proteins reveal distinct biological processes that are altered through the course of natural aging. Transcriptome analysis reveals a scenario of cardiac hypertrophy, fibrosis, and reemergence of fetal gene expression patterns.
    [Show full text]
  • A KMT2A-AFF1 Gene Regulatory Network Highlights the Role of Core Transcription Factors and Reveals the Regulatory Logic of Key Downstream Target Genes
    Downloaded from genome.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press Research A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes Joe R. Harman,1,7 Ross Thorne,1,7 Max Jamilly,2 Marta Tapia,1,8 Nicholas T. Crump,1 Siobhan Rice,1,3 Ryan Beveridge,1,4 Edward Morrissey,5 Marella F.T.R. de Bruijn,1 Irene Roberts,3,6 Anindita Roy,3,6 Tudor A. Fulga,2,9 and Thomas A. Milne1,6 1MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; 2MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; 3MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 9DS, United Kingdom; 4Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, United Kingdom; 5Center for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom; 6NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, OX3 9DS, United Kingdom Regulatory interactions mediated by transcription factors (TFs) make up complex networks that control cellular behavior. Fully understanding these gene regulatory networks (GRNs) offers greater insight into the consequences of disease-causing perturbations than can be achieved by studying single TF binding events in isolation. Chromosomal translocations of the lysine methyltransferase 2A (KMT2A) gene produce KMT2A fusion proteins such as KMT2A-AFF1 (previously MLL-AF4), caus- ing poor prognosis acute lymphoblastic leukemias (ALLs) that sometimes relapse as acute myeloid leukemias (AMLs).
    [Show full text]
  • Differential Network As an Indicator of Osteoporosis with Network Entropy
    328 EXPERIMENTAL AND THERAPEUTIC MEDICINE 16: 328-332, 2018 Differential network as an indicator of osteoporosis with network entropy LILI MA, HONGMEI DU and GUANGDONG CHEN Department of Orthopaedics, Hebei Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China Received October 20, 2017; Accepted May 10, 2018 DOI: 10.3892/etm.2018.6169 Abstract. Osteoporosis is a common skeletal disorder charac- of osteoporosis (2,3). It is regarded that an increase of PBM terized by a decrease in bone mass and density. The peak bone by one standard deviation would reduce the fracture risk by mass (PBM) is a significant determinant of osteoporosis. To 50% (4). gain insights into the indicating effect of PBM to osteoporosis, Peripheral blood monocytes can serve as early precursors of this study focused on characterizing the PBM networks and osteoclasts (5-7). A growing body of literature has explored that identifying key genes. One biological data set with 12 mono- blood monocytes deliver many kinds of factors for bone metab- cyte low PBM samples and 11 high PBM samples was derived olism, such as interleukin-1 and tumor necrosis factor-α (8). to construct protein-protein interaction networks (PPINs). Osteoclasts in peripheral skeleton (9) and the central skeleton Based on clique-merging, module-identification algorithm was come from circulating monocytes (10). Substantial research used to identify modules from PPINs. The systematic calcu- has focused on the effect of circulating monocytes on patho- lation and comparison were performed to test whether the genesis of osteoporosis in young and middle aged adults. network entropy can discriminate the low PBM network from Research in systems biology has shown that variety in the high PBM network.
    [Show full text]
  • Bioinformatics Analysis of the CDK2 Functions in Neuroblastoma
    MOLECULAR MEDICINE REPORTS 17: 3951-3959, 2018 Bioinformatics analysis of the CDK2 functions in neuroblastoma LIJUAN BO1*, BO WEI2*, ZHANFENG WANG2, DALIANG KONG3, ZHENG GAO2 and ZHUANG MIAO2 Departments of 1Infections, 2Neurosurgery and 3Orthopaedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China Received December 20, 2016; Accepted November 14, 2017 DOI: 10.3892/mmr.2017.8368 Abstract. The present study aimed to elucidate the poten- childhood cancer mortality (1,2). Despite intensive myeloabla- tial mechanism of cyclin-dependent kinase 2 (CDK2) in tive chemotherapy, survival rates for neuroblastoma have not neuroblastoma progression and to identify the candidate substantively improved; relapse is common and frequently genes associated with neuroblastoma with CDK2 silencing. leads to mortality (3,4). Like most human cancers, this child- The microarray data of GSE16480 were obtained from the hood cancer can be inherited; however, the genetic aetiology gene expression omnibus database. This dataset contained remains to be elucidated (3). Therefore, an improved under- 15 samples: Neuroblastoma cell line IMR32 transfected standing of the genetics and biology of neuroblastoma may with CDK2 shRNA at 0, 8, 24, 48 and 72 h (n=3 per group; contribute to further cancer therapies. total=15). Significant clusters associated with differen- In terms of genetics, neuroblastoma tumors from patients tially expressed genes (DEGs) were identified using fuzzy with aggressive phenotypes often exhibit significant MYCN C-Means algorithm in the Mfuzz package. Gene ontology and proto-oncogene, bHLH transcription factor (MYCN) amplifi- pathway enrichment analysis of DEGs in each cluster were cation and are strongly associated with a poor prognosis (5).
    [Show full text]
  • Supplementary Table 4: the Association of the 26S Proteasome
    Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 Supplementary Table 4: The association of the 26S proteasome and tumor progression/metastasis Note: the associateion between cancer and the 26S proteasome genes has been manually checked in PubMed a) GSE2514 (Lung cancer, 20 tumor and 19 normal samples; 25 out of 43 26S proteasome genes were mapped on the microarray platform. FWER p-value: 0.02) Entrez GeneID Gene Symbol RANK METRIC SCORE* Genes have been reported in cancer 10213 PSMD14 0.288528293 5710 PSMD4 0.165639699 Kim et al., Mol Cancer Res., 6:426, 2008 5713 PSMD7 0.147187442 5721 PSME2 0.130215749 5717 PSMD11 0.128598183 Deng et al., Breast Cancer Research and Treatment, 104:1067, 2007 5704 PSMC4 0.123157509 5706 PSMC6 0.115970835 5716 PSMD10 0.112173758 Mayer et al., Biochem Society Transaction, 34:746, 2006 5700 PSMC1 0.0898761 Kim et al., Mol Cancer Res., 6:426, 2008 5701 PSMC2 0.081513479 Cui et al., Proteomics, 6:498, 2005 5709 PSMD3 0.071682706 5719 PSMD13 0.071118504 7415 VCP 0.060464829 9861 PSMD6 0.055711303 Ren et al., Oncogene, 19:1419, 2000 5720 PSME1 0.052469168 5714 PSMD8 0.047414459 Deng et al., Breast Cancer Research and Treatment, 104:1067, 2007 5702 PSMC3 0.046327863 Pollice et al., JBC, 279:6345, 2003 6184 RPN1 0.043426223 55559 UCHL5IP 0.041885283 5705 PSMC5 0.041615516 5715 PSMD9 0.033147983 5711 PSMD5 0.030562362 Deng et al., Breast Cancer Research and Treatment, 104:1067, 2007 10197 PSME3 0.015149679 Roessler et al., Molecular & Cellular Proteomics 5:2092, 2006 5718 PSMD12 -0.00983229 Cui et al., Proteomics, 6:498, 2005 9491 PSMF1 -0.069156095 *Positive rank metric score represent that a gene is highly expressed in tumors.
    [Show full text]
  • The Silence of PSMC6 Inhibits Cell Growth and Metastasis in Lung Adenocarcinoma
    Hindawi BioMed Research International Volume 2021, Article ID 9922185, 9 pages https://doi.org/10.1155/2021/9922185 Research Article The Silence of PSMC6 Inhibits Cell Growth and Metastasis in Lung Adenocarcinoma Jian-Yu Zhang, Ke-Zhi Shi, Xiang-Yu Liao, Shi-Jun Li, Dan Bao, Ying Qian, and Dao-Jun Li The First College of Clinical Medical Science, Three Gorges University & Yichang Central People’s Hospital, Yichang, China Correspondence should be addressed to Dao-Jun Li; [email protected] Received 8 March 2021; Revised 24 April 2021; Accepted 28 May 2021; Published 19 June 2021 Academic Editor: Tao Huang Copyright © 2021 Jian-Yu Zhang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The proteasome has been validated as an anticancer drug target, while the role of a subunit of proteasome, PSMC6, in lung adenocarcinoma (LUAD) has not been fully unveiled. In this study, we observed that both the RNA and protein of PSMC6 were highly upregulated in LUAD compared with the adjacent normal tissues. Moreover, a high PSMC6 expression was associated with poor prognosis. In accordance with this finding, PSMC6 was associated with poor tumor differentiation. Furthermore, the silence of PSMC6 by small interference RNAs (siRNAs) could significantly inhibit cell growth, migration, and invasion in lung cancer cell lines, suggesting that PSMC6 might serve as a promising therapeutic target in LUAD. To further explore the molecular mechanism of PSMC6 in LUAD, we observed that the proteasome subunits, such as PSMD10, PSMD6, PSMD9, PSMD13, PSMB3, PSMB1, PSMA4, PSMC1, PSMC2, PSMD7, and PSMD14, were highly correlated with PSMC6 expression.
    [Show full text]