Androgen-Dependent Pathology Demonstrates Myopathic
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
P53 Regulates Myogenesis by Triggering the Differentiation
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central p53 Regulates Myogenesis by Triggering the Differentiation Activity of pRb Alessandro Porrello, Maria Antonietta Cerone, Sabrina Coen, Aymone Gurtner, Giulia Fontemaggi, Letizia Cimino, Giulia Piaggio, Ada Sacchi, and Silvia Soddu Molecular Oncogenesis Laboratory, Regina Elena Cancer Institute, Center for Experimental Research, 00158 Rome, Italy Abstract. The p53 oncosuppressor protein regulates mary myoblasts, pRb is hypophosphorylated and prolif- cell cycle checkpoints and apoptosis, but increasing evi- eration stops. However, these cells do not upregulate dence also indicates its involvement in differentiation pRb and have reduced MyoD activity. The transduction and development. We had previously demonstrated of exogenous TP53 or Rb genes in p53-defective myo- that in the presence of differentiation-promoting stim- blasts rescues MyoD activity and differentiation poten- uli, p53-defective myoblasts exit from the cell cycle but tial. Additionally, in vivo studies on the Rb promoter do not differentiate into myocytes and myotubes. To demonstrate that p53 regulates the Rb gene expression identify the pathways through which p53 contributes at transcriptional level through a p53-binding site. to skeletal muscle differentiation, we have analyzed Therefore, here we show that p53 regulates myoblast the expression of a series of genes regulated during differentiation by means of pRb without affecting its myogenesis in parental and dominant–negative p53 cell cycle–related functions. (dnp53)-expressing C2C12 myoblasts. We found that in dnp53-expressing C2C12 cells, as well as in p53Ϫ/Ϫ pri- Key words: p53 • Rb • MyoD • differentiation • muscle Introduction The differentiation of skeletal myoblasts is characterized review, see Wright, 1992). -
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. -
Cellular and Developmental Control of O2 Homeostasis by Hypoxia-Inducible Factor 1␣
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Cellular and developmental control of O2 homeostasis by hypoxia-inducible factor 1a Narayan V. Iyer,1,5 Lori E. Kotch,1,5 Faton Agani,1 Sandra W. Leung,1 Erik Laughner,1 Roland H. Wenger,2 Max Gassmann,2 John D. Gearhart,3 Ann M. Lawler,3 Aimee Y. Yu,1 and Gregg L. Semenza1,4 1Center for Medical Genetics, Departments of Pediatrics and Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-3914 USA; 2Institute of Physiology, University of Zurich-Irchel, 8057 Zurich, Switzerland; 3Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 USA Hypoxia is an essential developmental and physiological stimulus that plays a key role in the pathophysiology of cancer, heart attack, stroke, and other major causes of mortality. Hypoxia-inducible factor 1 (HIF-1) is the only known mammalian transcription factor expressed uniquely in response to physiologically relevant levels −/− of hypoxia. We now report that in Hif1a embryonic stem cells that did not express the O2-regulated HIF-1a subunit, levels of mRNAs encoding glucose transporters and glycolytic enzymes were reduced, and cellular proliferation was impaired. Vascular endothelial growth factor mRNA expression was also markedly decreased in hypoxic Hif1a−/− embryonic stem cells and cystic embryoid bodies. Complete deficiency of HIF-1a resulted in developmental arrest and lethality by E11 of Hif1a−/− embryos that manifested neural tube defects, cardiovascular malformations, and marked cell death within the cephalic mesenchyme. In Hif1a+/+ embryos, HIF-1a expression increased between E8.5 and E9.5, coincident with the onset of developmental defects and cell death in Hif1a−/− embryos. -
The MCK Enhancer Contains a P53 Responsive Element (P53/Anti-Oncogene/Trans-Activation) HAROLD WEINTRAUB*, STEPHEN Hauschkat, and STEPHEN J
Proc. Natl. Acad. Sci. USA Vol. 88, pp. 4570-4571, June 1991 Biochemistry The MCK enhancer contains a p53 responsive element (p53/anti-oncogene/trans-activation) HAROLD WEINTRAUB*, STEPHEN HAUSCHKAt, AND STEPHEN J. TAPSCOTT* *Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1124 Columbia Street, Seattle, WA 98104; and tDepartment of Biochemistry, University of Washington, Seattle, WA 98195 Contributed by Harold Weintraub, March 4, 1991 ABSTRACT p53 is an antioncogene that is defective or suggesting that activation may be species specific; however, absent in a large number of human tumors. Its function in levels ofprotein produced by the expression vectors were not normal cells is not known. We show that co-transfection of directly assayed in these experiments. By using an MCK- mouse p53 with muscle-specific creatine kinase-chloramphen- specific antibody, we have not been able to demonstrate icol acetyltransferase reporter gene, containing 3.3 kilobase of activation of the endogenous MCK gene in 10T1/2 cells upstream control sequence for the muscle-specfic creatine transfected with p53; in contrast 10T'/2 cells transfected with kinase gene, results in a 10- to 80-fold activation. The p53 MyoD express endogenous MCK immunoreactivity. responsive element maps to a region disinguhed from the Table 2 shows that a transforming mutant of murine p53 known MyoD binding region. Identification ofa p53 responsive (Ala -3 Val at position 135) fails to activate MCK-CAT in element should allow a more focused analysis of the effects of CV1 cells. A related mutation has lost its capacity for p53 in controlling gene activity. transactivation when fused to the DNA binding domain of GaI4 (5, 6). -
Role of the Nuclear Receptor Rev-Erb Alpha in Circadian Food Anticipation and Metabolism Julien Delezie
Role of the nuclear receptor Rev-erb alpha in circadian food anticipation and metabolism Julien Delezie To cite this version: Julien Delezie. Role of the nuclear receptor Rev-erb alpha in circadian food anticipation and metabolism. Neurobiology. Université de Strasbourg, 2012. English. NNT : 2012STRAJ018. tel- 00801656 HAL Id: tel-00801656 https://tel.archives-ouvertes.fr/tel-00801656 Submitted on 10 Apr 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE CNRS UPR 3212 · Institut des Neurosciences Cellulaires et Intégratives THÈSE présentée par : Julien DELEZIE soutenue le : 29 juin 2012 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Neurosciences Rôle du récepteur nucléaire Rev-erbα dans les mécanismes d’anticipation des repas et le métabolisme THÈSE dirigée par : M CHALLET Etienne Directeur de recherche, université de Strasbourg RAPPORTEURS : M PFRIEGER Frank Directeur de recherche, université de Strasbourg M KALSBEEK Andries -
Myod-Cre Driven Alterations in K-Ras and P53 Lead to a Mouse Model
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.15.448607; this version posted June 15, 2021. 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. MyoD-Cre driven alterations in K-Ras and p53 lead to a mouse model with histological and molecular characteristics of human rhabdomyosarcoma with direct translational applications Kengo Nakahata1, Brian W. Simons2, Enrico Pozzo3, Ryan Shuck1, Lyazat Kurenbekova1, Cristian Coarfa4,6 Tajhal D. Patel1, and Jason T. Yustein*1,5,6 1Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030 2Center for Comparative Medicine, Baylor College of Medicine, Houston, TX 77030 3Translational Cardiomyology Laboratory, Stem Cell Research Institute, Stem Cell Biology and Embryology Unit, Department of Development and Regeneration, KU Leuven, Leuven, Belgium. 4Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 5Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX 77030 6Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, TX 77030 *Corresponding Author Corresponding Author: Jason T. Yustein, MD, PhD 1102 Bates St., Suite 1025.07 Houston, Texas 77030 832-824-4601 (Office) [email protected] ORCID: https://orcid.org/0000-0002-2052-0527 - 1 - bioRxiv preprint doi: https://doi.org/10.1101/2021.06.15.448607; this version posted June 15, 2021. 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. -
Hypoxia and Aging Eui-Ju Yeo1
Yeo Experimental & Molecular Medicine (2019) 51:67 https://doi.org/10.1038/s12276-019-0233-3 Experimental & Molecular Medicine REVIEW ARTICLE Open Access Hypoxia and aging Eui-Ju Yeo1 Abstract Eukaryotic cells require sufficient oxygen (O2) for biological activity and survival. When the oxygen demand exceeds its supply, the oxygen levels in local tissues or the whole body decrease (termed hypoxia), leading to a metabolic crisis, threatening physiological functions and viability. Therefore, eukaryotes have developed an efficient and rapid oxygen sensing system: hypoxia-inducible factors (HIFs). The hypoxic responses are controlled by HIFs, which induce the expression of several adaptive genes to increase the oxygen supply and support anaerobic ATP generation in eukaryotic cells. Hypoxia also contributes to a functional decline during the aging process. In this review, we focus on the molecular mechanisms regulating HIF-1α and aging-associated signaling proteins, such as sirtuins, AMP-activated protein kinase, mechanistic target of rapamycin complex 1, UNC-51-like kinase 1, and nuclear factor κB, and their roles in aging and aging-related diseases. In addition, the effects of prenatal hypoxia and obstructive sleep apnea (OSA)- induced intermittent hypoxia have been reviewed due to their involvement in the progression and severity of many diseases, including cancer and other aging-related diseases. The pathophysiological consequences and clinical manifestations of prenatal hypoxia and OSA-induced chronic intermittent hypoxia are discussed in detail. Introduction chemoreceptors stimulates the neurotransmitter release 3 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Oxygen (O2) plays critical roles in aerobic respiration pathway and modulates the activity of a neutral endo- and metabolism as the final electron acceptor of the peptidase, neprilysin (NEP), which modifies the cellular mitochondrial electron transport chain, which is respon- response to hypoxia by hydrolyzing substance P4. -
Physical Interaction of the Retinoblastoma Protein with Human D Cyclins
Cell, Vol. 73, 499-511, May 7, 1993, Copyright 0 1993 by Cell Press Physical Interaction of the Retinoblastoma Protein with Human D Cyclins Steven F. Dowdy,* Philip W. Hinds,’ Kenway Louie,’ into Rb- tumor cells by microinjection, viral infection, or Steven I. Reed,t Andrew Arnold,* transfection can lead to the growth arrest of these recipient and Robert A. Weinberg” cells (Huang et al., 1988; Goodrich et al., 1991; Templeton *The Whitehead Institute for Biomedical Research et al., 1991; Hinds et al., 1992). and Department of Biology Oncoproteins specified by the SV40, adenovirus, and Massachusetts Institute of Technology papilloma DNA tumor viruses have been shown to associ- Cambridge, Massachusetts 02142 ate with pRb in virus-transformed cells (Whyte et al., 1988; tThe Scripps Research Institute DeCaprio et al., 1988; Dyson et al., 1989). Oncoprotein Department of Molecular Biology binding of pRb is presumed to lead to its sequestration 10666 North Torrey Pines Road and functional inactivation. Conserved region II mutants La Jolla, California 92037 of adenovirus ElA, SV40 large T antigen, human papil- *Endocrine Unit loma E7 viral oncoproteins that have lost their ability to and Massachusetts General Hospital Cancer Center bind pflb, and other pRb-related proteins exhibit signifi- Massachusetts General Hospital cantly reduced transforming potential (Moran et al., 1986; and Harvard Medical School Lillie et al., 1987; Cherington et al., 1988; DeCaprio et al., Boston, Massachusetts 02114 1988; Moran, 1988; Smith and Ziff, 1988; Whyte et al., 1989). This suggests that binding of pRb and related pro- teins by these oncoproteins is critical to their transforming abilities. -
The DEAD-Box Protein P72 Regulates ERΑ-&Sol;Oestrogen
Oncogene (2009) 28, 4053–4064 & 2009 Macmillan Publishers Limited All rights reserved 0950-9232/09 $32.00 www.nature.com/onc ORIGINAL ARTICLE The DEAD-box protein p72 regulates ERa-/oestrogen-dependent transcription and cell growth, and is associated with improved survival in ERa-positive breast cancer NC Wortham1,6, E Ahamed2,6, SM Nicol1, RS Thomas2, M Periyasamy2, J Jiang2,3, AM Ochocka2, S Shousha3, L Huson4, SE Bray5, RC Coombes2, S Ali2 and FV Fuller-Pace1 1Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; 2Department of Oncology, Imperial College London, Hammersmith Hospital Campus, London, UK; 3Department of Histopathology, Imperial College London, Charing Cross Hospital, London, UK; 4Statistical Advisory Service, Imperial College London, South Kensington Campus, London, UK and 5Tayside Tissue Bank, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK The DEAD-box RNA helicases p68 (DDX5) and p72 Introduction (DDX17) have been shown to act as transcriptional co- activators for a diverse range of transcription factors, The DEAD-box subfamily of RNA helicases, originally including oestrogen receptor-a (ERa). Here, we show that, so named on the basis of the presence of a conserved although both proteins interact with and co-activate ERa motif having the sequence Asp-Glu-Ala-Asp, have been in reporter gene assays, small interfering RNA-mediated implicated in cellular processes involving the regulation knockdown of p72, but not p68, results in a significant of RNA structure, including pre-mRNA processing, inhibition of oestrogen-dependent transcription of endo- RNA export, RNA degradation, ribosome assembly, genous ERa-responsive genes and oestrogen-dependent translation and miRNA maturation (Linder et al., 1989; growth of MCF-7 and ZR75-1 breast cancer cells. -
Daily Rhythmicity of Clock Gene Transcript Levels in Fast and Slow
Wu et al. BMC Genomics (2016) 17:1008 DOI 10.1186/s12864-016-3373-z RESEARCHARTICLE Open Access Daily rhythmicity of clock gene transcript levels in fast and slow muscle fibers from Chinese perch (Siniperca chuatsi) Ping Wu1†, Yu-Long Li1†, Jia Cheng1†, Lin Chen1, Xin Zhu1, Zhi-Guo Feng3, Jian-She Zhang1,2* and Wu-Ying Chu1,2* Abstract Background: Clock genes are considered to be the molecular core of biological clock in vertebrates and they are directly involved in the regulation of daily rhythms in vertebrate tissues such as skeletal muscles. Fish myotomes are composed of anatomically segregated fast and slow muscle fibers that possess different metabolic and contractile properties. To date, there is no report on the characterization of the circadian clock system components of slow muscles in fish. Results: In the present study, the molecular clock components (clock, arntl1/2, cry1/2/3, cry-dash, npas2, nr1d1/2, per1/2/3, rorα and tim genes) and their daily transcription levels were characterized in slow and fast muscles of Chinese perch (Siniperca chuatsi). Among the 15 clock genes, nrld2 and per3 had no daily rhythmicity in slow muscles, and cry2/3 and tim displayed no daily rhythmicity in fast muscles of the adult fish. In the slow muscles, the highest expression of the most clock paralogs occurred at the dark period except arntl1, nr1d1, nr1d2 and tim. With the exception of nr1d2 and tim, the other clock genes had an acrophase at the light period in fast muscles. The circadian expression of the myogenic regulatory factors (mrf4 and myf5), mstn and pnca showed either a positive or a negative correlation with the transcription pattern of the clock genes in both types of muscles. -
Myod Family: a Paradigm for Development?
Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press COMMENTARY MyoD family: a paradigm for development? Eric N. Olson Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030 USA The establishment of specialized cell types during devel- DNA linked to a neomycin-resistance gene, Emerson opment involves commitment of multipotential stem and co-workers obtained evidence for a genetic locus, cells to specific lineages and subsequent expression of myd, that was also sufficient to generate stable myo- distinct sets of cell type-specific genes. Several gene genic clones (Pinney et al. 1988). Southern analysis products that regulate cell fate have been identified in showed that myd does not correspond to MyoD or the DrosophiIa and Caenorhabditis elegans, however, the other known myogenic regulatory genes (see below). The mechanisms that establish complex cellular phenotypes observation that MyoD was expressed constitutively in in vertebrates have been more difficult to approach. The myd transfectants led to the proposal that these genes recent identification of a family of muscle-specific regu- may function sequentially in a dependent myogenic reg- latory factors that can convert fibroblasts to skeletal ulatory hierarchy. However, given the ability of MyoD muscle has contributed significant insight into the and other myogenic regulatory gene products to activate events that regulate myogenesis and has provided a one another's expression, it is equally likely that myd framework for understanding the mechanisms that may may lie at an equivalent level or even "downstream" of regulate the establishment of diverse cell types during MyoD in a regulatory hierarchy.