Genetics, Epigenetics and Cancer. Cancer Therapy
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ESRRB Regulates Glucocorticoid Gene Expression in Mice and Patients with Acute Lymphoblastic Leukemia
University of Massachusetts Medical School eScholarship@UMMS Open Access Articles Open Access Publications by UMMS Authors 2020-07-13 ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia Kayleigh M. Gallagher University of Massachusetts Medical School Et al. Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/oapubs Part of the Cancer Biology Commons, and the Neoplasms Commons Repository Citation Gallagher KM, Roderick JE, Tan SH, Tan TK, Murphy L, Yu J, Li R, O'Connor K, Zhu LJ, Green MR, Sanda T, Kelliher MA. (2020). ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia. Open Access Articles. https://doi.org/10.1182/bloodadvances.2020001555. Retrieved from https://escholarship.umassmed.edu/oapubs/4285 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in Open Access Articles by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. REGULAR ARTICLE ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia Downloaded from https://ashpublications.org/bloodadvances/article-pdf/4/13/3154/1748491/advancesadv2020001555.pdf by UNIV OF MASSACHUSETTS user on 10 August 2020 Kayleigh M. Gallagher,1 Justine E. Roderick,1 Shi Hao Tan,2 Tze King Tan,2 Leonard Murphy,1 Jun Yu,1 Rui Li,1 Kevin W. O’Connor,1 Julie Zhu,1 Michael R. Green,1 Takaomi Sanda,2 and Michelle A. Kelliher1 1Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and 2Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore Synthetic glucocorticoids (GCs), such as dexamethasone and prednisone, remain key Key Points components of therapy for patients with lymphoid malignancies. -
Intelligent Design, Abiogenesis, and Learning from History: Dennis R
Author Exchange Intelligent Design, Abiogenesis, and Learning from History: Dennis R. Venema A Reply to Meyer Dennis R. Venema Weizsäcker’s book The World View of Physics is still keeping me very busy. It has again brought home to me quite clearly how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don’t know; God wants us to realize his presence, not in unsolved problems but in those that are solved. Dietrich Bonhoeffer1 am thankful for this opportunity to nature, is the result of intelligence. More- reply to Stephen Meyer’s criticisms over, this assertion is proffered as the I 2 of my review of his book Signature logical basis for inferring design for the in the Cell (hereafter Signature). Meyer’s origin of biological information: if infor- critiques of my review fall into two gen- mation only ever arises from intelli- eral categories. First, he claims I mistook gence, then the mere presence of Signature for an argument against bio- information demonstrates design. A few logical evolution, rendering several of examples from Signature make the point my arguments superfluous. Secondly, easily: Meyer asserts that I have failed to refute … historical scientists can show that his thesis by not providing a “causally a presently acting cause must have adequate alternative explanation” for the been present in the past because the origin of life in that the few relevant cri- proposed candidate is the only known tiques I do provide are “deeply flawed.” cause of the effect in question. -
Identification of GA-Binding Protein Transcription Factor Alpha Subunit
International Journal of Molecular Sciences Article Identification of GA-Binding Protein Transcription Factor Alpha Subunit (GABPA) as a Novel Bookmarking Factor Shunya Goto 1, Masashi Takahashi 1, Narumi Yasutsune 1, Sumiki Inayama 1, Dai Kato 2, Masashi Fukuoka 3, Shu-ichiro Kashiwaba 1 and Yasufumi Murakami 1,2,* 1 Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; [email protected] (S.G.); [email protected] (M.T.); [email protected] (N.Y.); [email protected] (S.I.); [email protected] (S.K.) 2 Order-MadeMedical Research Inc., 208Todai-Kashiwa VP, 5-4-19 Kashiwanoha, Kashiwa-shi, Chiba-ken 277-0882, Japan; [email protected] 3 Department of Molecular Pharmacology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-3-5876-1717 (ext. 1919); Fax: +81-3-5876-1470 Received: 7 February 2019; Accepted: 27 February 2019; Published: 4 March 2019 Abstract: Mitotic bookmarking constitutes a mechanism for transmitting transcriptional patterns through cell division. Bookmarking factors, comprising a subset of transcription factors (TFs), and multiple histone modifications retained in mitotic chromatin facilitate reactivation of transcription in the early G1 phase. However, the specific TFs that act as bookmarking factors remain largely unknown. Previously, we identified the “early G1 genes” and screened TFs that were predicted to bind to the upstream region of these genes, then identified GA-binding protein transcription factor alpha subunit (GABPA) and Sp1 transcription factor (SP1) as candidate bookmarking factors. -
The Interactions of DNA Repair, Telomere Homeostasis, and P53 Mutational Status in Solid Cancers: Risk, Prognosis, and Prediction
cancers Review The Interactions of DNA Repair, Telomere Homeostasis, and p53 Mutational Status in Solid Cancers: Risk, Prognosis, and Prediction Pavel Vodicka 1,2,3, Ladislav Andera 4,5, Alena Opattova 1,2,3,† and Ludmila Vodickova 1,2,3,*,† 1 Institute of Experimental Medicine, AS CR, 142 20 Prague, Czech Republic; [email protected] (P.V.); [email protected] (A.O.) 2 First Medical Faculty, Charles University, 121 08 Prague, Czech Republic 3 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 301 00 Pilsen, Czech Republic 4 Institute of Biotechnology, AS CR, 252 50 Vestec, Czech Republic; [email protected] 5 Institute of Molecular Genetics, AS CR, 142 20 Prague, Czech Republic * Correspondence: [email protected] † These authors contribured eaqually to this paper. Simple Summary: p53 is a nuclear transcription factor with a pro-apoptotic function. Somatic mutations in this gene represent one of the most critical events in human carcinogenesis. The disruption of genomic integrity due to the accumulation of various kinds of DNA damage, deficient DNA repair capacity, and alteration of telomere homeostasis constitute the hallmarks of malignant diseases. The main aim of our review was to accentuate a complex comprehension of the interactions between fundamental players in carcinogenesis of solid malignancies such as DNA damage response, telomere homeostasis and TP53. Abstract: The disruption of genomic integrity due to the accumulation of various kinds of DNA Citation: Vodicka, P.; Andera, L.; Opattova, A.; Vodickova, L. The damage, deficient DNA repair capacity, and telomere shortening constitute the hallmarks of malig- Interactions of DNA Repair, Telomere nant diseases. -
Chip Validated H4k5ac (Clone RM140) Antibody with Positive and Negative Primer Sets
www.chromatrap.com Clywedog Rd South Wrexham Industrial Estate Wrexham LL13 9XS, United Kingdom Tel: +44 (0) 1978 666239/40 Email: [email protected] ChIP Validated H4K5ac (Clone RM140) Antibody with Positive and Negative Primer Sets Catalogue no: 900029 Chromatrap®’s ChIP Validated H4K5ac Antibody with Positive Primer Set provides a complete set of tools to assist with a successful ChIP assay. Including: H4K5ac antibody, control rabbit IgG, and positive primer set. The ChIP Validated H4K5ac Antibody with Positive Primer Set is not suitable for use with non-human species. Background: Histone 4 (H4) is one of the five core histone proteins, comprising the protein component of chromatin. H4 is ubiquitous within chromosomes and can be found bound to most gene sequences throughout the genome. Acetylation of lysine 5 on histone 4 (H4K5ac) is associated with open chromatin and active gene transcription. H4K5ac has been shown to have roles in epigenetic bookmarking, a process where genetic information is passed onto daughter cells during cell division. A rabbit IgG is included in this Antibody Primer Set as a negative control for the ChIP experiment. The H4K5ac positive primer set recognises the promoter of the GAPDH gene, associated with active transcription and is a suitable target for this antibody. Suggested Usage: Component Suggested Dilution Figure H4K5ac 2:1 (antibody: chromatin) 1 Rabbit IgG 2:1 (antibody: chromatin) 1 Positive Primer Set Dilute from 4M (provided) to 1M working concentration Please note: Optimal dilutions should be determined by the user. These volumes are stated as guidelines only. Advancements in Epigenetics *This product is for research use only. -
Ecological Developmental Biology and Disease States CHAPTER 5 Teratogenesis: Environmental Assaults on Development 167
Integrating Epigenetics, Medicine, and Evolution Scott F. Gilbert David Epel Swarthmore College Hopkins Marine Station, Stanford University Sinauer Associates, Inc. • Publishers Sunderland, Massachusetts U.S.A. © Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the publisher. Brief Contents PART 1 Environmental Signals and Normal Development CHAPTER 1 The Environment as a Normal Agent in Producing Phenotypes 3 CHAPTER 2 How Agents in the Environment Effect Molecular Changes in Development 37 CHAPTER 3 Developmental Symbiosis: Co-Development as a Strategy for Life 79 CHAPTER 4 Embryonic Defenses: Survival in a Hostile World 119 PART 2 Ecological Developmental Biology and Disease States CHAPTER 5 Teratogenesis: Environmental Assaults on Development 167 CHAPTER 6 Endocrine Disruptors 197 CHAPTER 7 The Epigenetic Origin of Adult Diseases 245 PART 3 Toward a Developmental Evolutionary Synthesis CHAPTER 8 The Modern Synthesis: Natural Selection of Allelic Variation 289 CHAPTER 9 Evolution through Developmental Regulatory Genes 323 CHAPTER 10 Environment, Development, and Evolution: Toward a New Synthesis 369 CODA Philosophical Concerns Raised by Ecological Developmental Biology 403 APPENDIX A Lysenko, Kammerer, and the Truncated Tradition of Ecological Developmental Biology 421 APPENDIX B The Molecular Mechanisms of Epigenetic Change 433 APPENDIX C Writing Development Out of the Modern Synthesis 441 APPENDIX D Epigenetic Inheritance Systems: -
Cadmium Induced Cell Apoptosis, DNA Damage, De
Int. J. Med. Sci. 2013, Vol. 10 1485 Ivyspring International Publisher International Journal of Medical Sciences 2013; 10(11):1485-1496. doi: 10.7150/ijms.6308 Research Paper Cadmium Induced Cell Apoptosis, DNA Damage, De- creased DNA Repair Capacity, and Genomic Instability during Malignant Transformation of Human Bronchial Epithelial Cells Zhiheng Zhou1*, Caixia Wang2*, Haibai Liu1, Qinhai Huang1, Min Wang1 , Yixiong Lei1 1. School of public health, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China 2. Department of internal medicine of Guangzhou First People’s Hospital affiliated to Guangzhou Medical University, Guangzhou 510180, People’s Republic of China * These authors contributed equally to this work. Corresponding author: Yixiong Lei, School of public health, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, People’s Republic of China. Fax: +86-20-81340196. E-mail: [email protected] © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/ licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. Received: 2013.03.23; Accepted: 2013.08.12; Published: 2013.08.30 Abstract Cadmium and its compounds are well-known human carcinogens, but the mechanisms underlying the carcinogenesis are not entirely understood. Our study was designed to elucidate the mech- anisms of DNA damage in cadmium-induced malignant transformation of human bronchial epi- thelial cells. We analyzed cell cycle, apoptosis, DNA damage, gene expression, genomic instability, and the sequence of exons in DNA repair genes in several kinds of cells. -
Early-Life Experience, Epigenetics, and the Developing Brain
Neuropsychopharmacology REVIEWS (2015) 40, 141–153 & 2015 American College of Neuropsychopharmacology. All rights reserved 0893-133X/15 REVIEW ............................................................................................................................................................... www.neuropsychopharmacologyreviews.org 141 Early-Life Experience, Epigenetics, and the Developing Brain 1 ,1 Marija Kundakovic and Frances A Champagne* 1Department of Psychology, Columbia University, New York, NY, USA Development is a dynamic process that involves interplay between genes and the environment. In mammals, the quality of the postnatal environment is shaped by parent–offspring interactions that promote growth and survival and can lead to divergent developmental trajectories with implications for later-life neurobiological and behavioral characteristics. Emerging evidence suggests that epigenetic factors (ie, DNA methylation, posttranslational histone modifications, and small non- coding RNAs) may have a critical role in these parental care effects. Although this evidence is drawn primarily from rodent studies, there is increasing support for these effects in humans. Through these molecular mechanisms, variation in risk of psychopathology may emerge, particularly as a consequence of early-life neglect and abuse. Here we will highlight evidence of dynamic epigenetic changes in the developing brain in response to variation in the quality of postnatal parent–offspring interactions. The recruitment of epigenetic pathways for the -
Genetics, Epigenetics and Disease a Literature Review By: Anthony M
Genetics, Epigenetics and Disease A Literature Review By: Anthony M. Pasek Faculty Advisor: Rodger Tepe, PhD A senior research project submitted in partial requirement for the degree Doctor of Chiropractic August 11, 2011 Abstract Objective – This article provides an overview of the scientific literature available on the subject of genetic mechanisms of disease etiology as compared to epigenetic mechanisms of disease etiology. The effects of environmental influences on genetic expression and transgenerational inheritance will also be examined. Methods – Searches of the keywords listed below in the databases PubMed and EBSCO Host yielded referenced articles from indexed journals, literature reviews, pilot studies, longitudinal studies, and conference meeting reports. Conclusion – Although current research trends indicate a relationship between the static genome and the dynamic environment and offer epigenetics as a mechanism, further research is necessary. Epigenetic processes have been implicated in many diseases including diabetes mellitus, obesity, cardiovascular disease, metabolic disease, cancer, autism, Alzheimer’s disease, depression, and addiction. Keywords – genetics, central dogma of biology, genotype, phenotype, genomic imprinting, epigenetics, histone modification, DNA methylation, agouti mice, epigenetic drift, Överkalix, Avon Longitudinal Study of Parents and Children (ALSPAC). 2 Introduction Genetics has long been the central field of biology and it’s central dogma states that DNA leads to RNA, which leads to protein and ultimately determines human health or sickness1. The Human Genome Project marked a great triumph for humanity and researchers expected to solve the riddle of many complex diseases with the knowledge gleamed from this project. However, many more questions were raised than answered. Several rare genetic disorders including hemophilia and cystic fibrosis were explained by alterations in the genetic code but true genetic diseases only affect about one percent of the human population2. -
Botany Genetics Mendelian Inheritance
References 1. Elrod S., Stansfield W., 2002, Genetics, 4th Edition, Tata McGraw-Hill 2. Strickberger M. W., 1985, Genetics, 3rd Edition, Macmillan Publishing Company 3. Griffiths A. J., Wessler S.R., Lewontin R.C., Carrol S. B., 2008, Introduction to Genetic Analysis, 9th Edition, W. H. Freeman and Company 4. Klug W.S., Cumming M.R., Spencer C. A., Palladino M. A., 2009, Concepts of Genetics, 9th Edition, Benjamin Cummings Publication 5. Tamarin R. H., 2002, Principles of Genetics, 7th Edition, Tata McGraw-Hill 6. Hartwell L.H., Hood L., Goldberg M.L., Reynolds A.E., Silver L. M., Veres R. C., 2004, Genetics, 2nd Edition, McGraw-Hill 7. Pierce B.A., Genetics: A Conceptual Approach, 4th edition, W.H. Freeman 8. T.H. Noel Ellis, Julie M.I. Hofer, Gail M. Timmerman-Vaughan, Clarice J. Coyne and Roger P. Hellens, 2011, Mendel, 150 years on, Trends in Plant Science, Vol. 16, 590-596 Genetics Botany Mendelian Inheritance Learn More / Supporting Materials / Source of Further Reading 2.1 Glossary Starting Term Defination Related Term Character <Character> < Genotype > < Genotype of an organism is the gene combination it possesses. Genotype of phenotypically yellow seeded F1 may be YY or Yy.> <Character> < Phenotype > < Phenotype refers to the observable attributes of an organism. Plants with either of the two genotypes Yy or Yy are phenotypically yellow seeded.> <Character> < Homozygote > < A plant with a pair of identical alleles is called as Homozygote (Y/Y or y/y).> <Character> < Heterozygote > < a plant in which the <term2> allele of the pair differ is called as heterozygote (Y/y).> <Character> < locus > < A locus (plural: loci) is the location of a gene on a chromosome. -
From 1957 to Nowadays: a Brief History of Epigenetics
International Journal of Molecular Sciences Review From 1957 to Nowadays: A Brief History of Epigenetics Paul Peixoto 1,2, Pierre-François Cartron 3,4,5,6,7,8, Aurélien A. Serandour 3,4,6,7,8 and Eric Hervouet 1,2,9,* 1 Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; [email protected] 2 EPIGENEXP Platform, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France 3 CRCINA, INSERM, Université de Nantes, 44000 Nantes, France; [email protected] (P.-F.C.); [email protected] (A.A.S.) 4 Equipe Apoptose et Progression Tumorale, LaBCT, Institut de Cancérologie de l’Ouest, 44805 Saint Herblain, France 5 Cancéropole Grand-Ouest, Réseau Niches et Epigénétique des Tumeurs (NET), 44000 Nantes, France 6 EpiSAVMEN Network (Région Pays de la Loire), 44000 Nantes, France 7 LabEX IGO, Université de Nantes, 44000 Nantes, France 8 Ecole Centrale Nantes, 44300 Nantes, France 9 DImaCell Platform, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France * Correspondence: [email protected] Received: 9 September 2020; Accepted: 13 October 2020; Published: 14 October 2020 Abstract: Due to the spectacular number of studies focusing on epigenetics in the last few decades, and particularly for the last few years, the availability of a chronology of epigenetics appears essential. Indeed, our review places epigenetic events and the identification of the main epigenetic writers, readers and erasers on a historic scale. This review helps to understand the increasing knowledge in molecular and cellular biology, the development of new biochemical techniques and advances in epigenetics and, more importantly, the roles played by epigenetics in many physiological and pathological situations. -
Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine
biomolecules Review Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine Ryuji Hamamoto 1,2,*, Masaaki Komatsu 1,2, Ken Takasawa 1,2 , Ken Asada 1,2 and Syuzo Kaneko 1 1 Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; [email protected] (M.K.); [email protected] (K.T.); [email protected] (K.A.); [email protected] (S.K.) 2 Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan * Correspondence: [email protected]; Tel.: +81-3-3547-5271 Received: 1 December 2019; Accepted: 27 December 2019; Published: 30 December 2019 Abstract: To clarify the mechanisms of diseases, such as cancer, studies analyzing genetic mutations have been actively conducted for a long time, and a large number of achievements have already been reported. Indeed, genomic medicine is considered the core discipline of precision medicine, and currently, the clinical application of cutting-edge genomic medicine aimed at improving the prevention, diagnosis and treatment of a wide range of diseases is promoted. However, although the Human Genome Project was completed in 2003 and large-scale genetic analyses have since been accomplished worldwide with the development of next-generation sequencing (NGS), explaining the mechanism of disease onset only using genetic variation has been recognized as difficult. Meanwhile, the importance of epigenetics, which describes inheritance by mechanisms other than the genomic DNA sequence, has recently attracted attention, and, in particular, many studies have reported the involvement of epigenetic deregulation in human cancer.