P53 Regulates Myogenesis by Triggering the Differentiation
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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. -
The Retinoblastoma Tumor-Suppressor Gene, the Exception That Proves the Rule
Oncogene (2006) 25, 5233–5243 & 2006 Nature Publishing Group All rights reserved 0950-9232/06 $30.00 www.nature.com/onc REVIEW The retinoblastoma tumor-suppressor gene, the exception that proves the rule DW Goodrich Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA The retinoblastoma tumor-suppressor gene (Rb1)is transmission of one mutationally inactivated Rb1 allele centrally important in cancer research. Mutational and loss of the remaining wild-type allele in somatic inactivation of Rb1 causes the pediatric cancer retino- retinal cells. Hence hereditary retinoblastoma typically blastoma, while deregulation ofthe pathway in which it has an earlier onset and a greater number of tumor foci functions is common in most types of human cancer. The than sporadic retinoblastoma where both Rb1 alleles Rb1-encoded protein (pRb) is well known as a general cell must be inactivated in somatic retinal cells. To this day, cycle regulator, and this activity is critical for pRb- Rb1 remains an exception among cancer-associated mediated tumor suppression. The main focus of this genes in that its mutation is apparently both necessary review, however, is on more recent evidence demonstrating and sufficient, or at least rate limiting, for the genesis of the existence ofadditional, cell type-specific pRb func- a human cancer. The simple genetics of retinoblastoma tions in cellular differentiation and survival. These has spawned the hope that a complete molecular additional functions are relevant to carcinogenesis sug- understanding of the Rb1-encoded protein (pRb) would gesting that the net effect of Rb1 loss on the behavior of lead to deeper insight into the processes of neoplastic resulting tumors is highly dependent on biological context. -
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. -
Elevated E2F1 Inhibits Transcription of the Androgen Receptor in Metastatic Hormone-Resistant Prostate Cancer
Research Article Elevated E2F1 Inhibits Transcription of the Androgen Receptor in Metastatic Hormone-Resistant Prostate Cancer Joanne N. Davis,1 Kirk J. Wojno,1 Stephanie Daignault,1 Matthias D. Hofer,2,3 Rainer Kuefer,3 Mark A. Rubin,3,4 and Mark L. Day1 1Department of Urology, University of Michigan, Ann Arbor, Michigan; 2Department of Urology, University of Ulm, Ulm, Germany; 3Department of Pathology, Brigham and Women’s Hospital; and 4Harvard University, School of Medicine, Boston, Massachusetts Abstract disease recurs in an estimated 15% to 30% of patients (2). The androgen receptor (AR) is the mediator of the physiologic effects of Activation of E2F transcription factors, through disruption of androgen. It regulates the growth of normal and malignant the retinoblastoma (Rb) tumor-suppressor gene, is a key event prostate epithelial cells. Upon ligand binding, AR translocates to in the development of many human cancers. Previously, we the nucleus, binds to DNA recognition sequences, and activates showed that homozygous deletion of Rb in a prostate tissue transcription of target genes, including genes involved in cell recombination model exhibits increased E2F activity, acti- proliferation, apoptosis, and differentiation (reviewed in ref. 3). vation of E2F-target genes, and increased susceptibility to Androgen ablation therapy is highly successful for the treatment of hormonal carcinogenesis. In this study, we examined the hormone-sensitive prostate cancer; however, hormone resistance expression of E2F1 in 667 prostate tissue cores and compared significantly limits its benefits. Hormonal ablation therapy will it with the expression of the androgen receptor (AR), a marker control metastatic disease for 18 to 24 months (4), but once of prostate epithelial differentiation, using tissue microarray metastatic prostate cancer ceases to respond to hormonal therapy, analysis. -
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 -
Androgen-Dependent Pathology Demonstrates Myopathic
Research article Androgen-dependent pathology demonstrates myopathic contribution to the Kennedy disease phenotype in a mouse knock-in model Zhigang Yu,1 Nahid Dadgar,1 Megan Albertelli,2 Kirsten Gruis,3 Cynthia Jordan,4 Diane M. Robins,2 and Andrew P. Lieberman1 1Department of Pathology, 2Department of Human Genetics, and 3Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan, USA. 4Department of Psychology and Neuroscience Program, Michigan State University, East Lansing, Michigan, USA. Kennedy disease, a degenerative disorder characterized by androgen-dependent neuromuscular weakness, is caused by a CAG/glutamine tract expansion in the androgen receptor (Ar) gene. We developed a mouse model of Kennedy disease, using gene targeting to convert mouse androgen receptor (AR) to human sequence while introducing 113 glutamines. AR113Q mice developed hormone and glutamine length–dependent neuromus- cular weakness characterized by the early occurrence of myopathic and neurogenic skeletal muscle pathology and by the late development of neuronal intranuclear inclusions in spinal neurons. AR113Q males unexpect- edly died at 2–4 months. We show that this androgen-dependent death reflects decreased expression of skeletal muscle chloride channel 1 (CLCN1) and the skeletal muscle sodium channel α-subunit, resulting in myotonic discharges in skeletal muscle of the lower urinary tract. AR113Q limb muscles show similar myopathic features and express decreased levels of mRNAs encoding neurotrophin-4 and glial cell line–derived neurotrophic fac- tor. These data define an important myopathic contribution to the Kennedy disease phenotype and suggest a role for muscle in non–cell autonomous toxicity of lower motor neurons. Introduction dent on the presence of androgen (13–16) and is regulated, in Kennedy disease, or spinal and bulbar muscular atrophy, is one part, by hormone-dependent retrograde transport (17, 18). -
DEK Is a Homologous Recombination DNA Repair Protein and Prognostic Marker for a Subset of Oropharyngeal Carcinomas
DEK is a homologous recombination DNA repair protein and prognostic marker for a subset of oropharyngeal carcinomas A dissertation submitted to the Graduate School Of the University of Cincinnati In partial fulfillment of the requirements to the degree of Doctor of Philosophy (Ph.D.) in the Department of Cancer and Cell Biology of the College of Medicine March 29, 2017 by ERIC ALAN SMITH B.S Rose-Hulman Institute of Technology, 2010 Dissertation Committee: Susanne I. Wells, Ph.D. (Chair) Paul R. Andreassen, Ph.D. Nancy Ratner, Ph.D. Peter J. Stambrook , Ph.D. Kathryn A. Wikenheiser-Brokamp, M.D., Ph.D. Abstract The DEK oncogene is currently under investigation as a therapeutic target and clinical biomarker for tumor progression, chemotherapy resistance and poor outcomes for multiple types of malignancies. With regard to most cancer types, the degree of DEK overexpression correlates with higher stage tumors and worse patient survival, marking this molecule as a promising prognostic factor. Prior to this work, the utility of DEK as a biomarker had not been assessed in oropharyngeal squamous cell carcinoma (OPSCC), an aggressive disease characterized by poor survival and high rates of treatment comorbidities. As discussed in chapter 1, OPSCC is comprised of two subtypes based on the presence or absence of human papillomavirus (HPV) infection. In general, HPV+ OPSCCs have improved therapy response and an overall better prognosis than their HPV- counterparts. This treatment sensitivity may be due in part to the HPV oncogenes, which inactivate and degrade tumor suppressors as discussed in chapter 2, removing the need for the development of mutations that promote radiation and chemotherapy resistance. -
Restrictions in Cell Cycle Progression of Adult Vestibular Supporting Cells in Response to Ectopic Cyclin D1 Expression
Restrictions in Cell Cycle Progression of Adult Vestibular Supporting Cells in Response to Ectopic Cyclin D1 Expression Heidi Loponen1, Jukka Ylikoski2, Jeffrey H. Albrecht3, Ulla Pirvola1* 1 Institute of Biotechnology, University of Helsinki, Helsinki, Finland, 2 Helsinki Ear Institute, Helsinki, Finland, 3 Division of Gastroenterology, Hennepin County Medical Center, Minneapolis, Minnesota, United States of America Abstract Sensory hair cells and supporting cells of the mammalian inner ear are quiescent cells, which do not regenerate. In contrast, non-mammalian supporting cells have the ability to re-enter the cell cycle and produce replacement hair cells. Earlier studies have demonstrated cyclin D1 expression in the developing mouse supporting cells and its downregulation along maturation. In explant cultures of the mouse utricle, we have here focused on the cell cycle control mechanisms and proliferative potential of adult supporting cells. These cells were forced into the cell cycle through adenoviral-mediated cyclin D1 overexpression. Ectopic cyclin D1 triggered robust cell cycle re-entry of supporting cells, accompanied by changes in p27Kip1 and p21Cip1 expressions. Main part of cell cycle reactivated supporting cells were DNA damaged and arrested at the G2/M boundary. Only small numbers of mitotic supporting cells and rare cells with signs of two successive replications were found. Ectopic cyclin D1-triggered cell cycle reactivation did not lead to hyperplasia of the sensory epithelium. In addition, a part of ectopic cyclin D1 was sequestered in the cytoplasm, reflecting its ineffective nuclear import. Combined, our data reveal intrinsic barriers that limit proliferative capacity of utricular supporting cells. Citation: Loponen H, Ylikoski J, Albrecht JH, Pirvola U (2011) Restrictions in Cell Cycle Progression of Adult Vestibular Supporting Cells in Response to Ectopic Cyclin D1 Expression. -
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. -
Functional Characterization of the Arabidopsis Retinoblastoma Related Protein
Research Collection Doctoral Thesis Functional characterization of the Arabidopsis retinoblastoma related protein Author(s): Gutzat, Ruben Publication Date: 2009 Permanent Link: https://doi.org/10.3929/ethz-a-006023141 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH Nr. 18446 FUNCTIONAL CHARACTERIZATION OF THE ARABIDOPSIS RETINOBLASTOMA RELATED PROTEIN ABHANDLUNG zur Erlangung des Titels DOKTOR DER WISSENSCHAFTEN der ETH ZÜRICH vorgelegt von RUBEN GUTZAT Dipl.-Biol. Univ. Konstanz geboren am 14.07.1977 aus Deutschland Angenommen auf Antrag von Prof. Dr. Wilhelm Gruissem Prof. Dr. Claudia Köhler Prof. Dr. Ueli Grossniklaus Prof. Dr. Ben Scheres 2009 Ruben Gutzat FUNCTIONAL CHARACTERIZATION OF THE ARABIDOPSIS RETINOBLASTOMA RELATED PROTEIN 2 Abstract The retinoblastoma protein (pRB) is a master regulator of cell cycle and differentiation in animal cells and as such an important tumor suppressor. It regulates the G1/S-phase transition via binding to E2F/DP transcription factors and therefore inhibiting expression of S-phase genes. Some studies provide evidence that pRB is also important for cell fate determination. However, whether this is an effect only on some specialized cell types or if pRB has a general effect on cell differentiation remains unresolved. The presence of retinoblastoma-related proteins (RBRs) in plants offers the opportunity to study the function of this protein in a completely different developmental context. For example, plant organs develop after embryogenesis, plants switch from heterotrophy to autotrophy during germination and plants do not develop tumors without infection of specialized pathogens.