Medical epigenetics 2nd edition trygve tollefsbol - Download the full ebook set with all chapters in

Page 1


Instant digital products (PDF, ePub, MOBI) ready for you

Download now and discover formats that fit your needs...

Handbook of Epigenetics : The New Molecular and Medical Genetics 3rd Edition Trygve O. Tollefsbol

https://ebookmass.com/product/handbook-of-epigenetics-the-newmolecular-and-medical-genetics-3rd-edition-trygve-o-tollefsbol/

ebookmass.com

Medical Terminology 2nd Edition Paula Bostwick

https://ebookmass.com/product/medical-terminology-2nd-edition-paulabostwick/

ebookmass.com

Epigenetics in Cardiovascular Disease Yvan Devaux

https://ebookmass.com/product/epigenetics-in-cardiovascular-diseaseyvan-devaux/

ebookmass.com

Vermicomposting for Sustainable Food Systems in Africa 1st Edition Hupenyu Allan Mupambwa

https://ebookmass.com/product/vermicomposting-for-sustainable-foodsystems-in-africa-1st-edition-hupenyu-allan-mupambwa/

ebookmass.com

Practical Petroleum Geochemistry for Exploration and Production Harry Dembicki

https://ebookmass.com/product/practical-petroleum-geochemistry-forexploration-and-production-harry-dembicki/

ebookmass.com

I is for INVOKING: The A, B C's of Witchery (Moonbeam Chronicles Book 9) Carolina Mac

https://ebookmass.com/product/i-is-for-invoking-the-a-b-cs-ofwitchery-moonbeam-chronicles-book-9-carolina-mac/

ebookmass.com

Protein Interactions: The Molecular Basis of Interactomics 1st Edition Volkhard Helms

https://ebookmass.com/product/protein-interactions-the-molecularbasis-of-interactomics-1st-edition-volkhard-helms/

ebookmass.com

French phrase book Teach Yourself Books

https://ebookmass.com/product/french-phrase-book-teach-yourself-books/

ebookmass.com

Practical Approaches to Biological Inorganic Chemistry 2nd Edition Robert R. Crichton (Editor)

https://ebookmass.com/product/practical-approaches-to-biologicalinorganic-chemistry-2nd-edition-robert-r-crichton-editor/

ebookmass.com

Scaling Impact. Finance and Investment for a Better World Kusisami Hornberger

https://ebookmass.com/product/scaling-impact-finance-and-investmentfor-a-better-world-kusisami-hornberger/ ebookmass.com

Medical Epigenetics

Second Edition

Translational Epigenetics Series

Trygve Tollefsbol - Series Editor

Transgenerational Epigenetics

Edited by Trygve O. Tollefsbol, 2014

Personalized Epigenetics

Edited by Trygve O. Tollefsbol, 2015

Epigenetic Technological Applications

Edited by Y. George Zheng, 2015

Epigenetic Cancer Therapy

Edited by Steven G. Gray, 2015

DNA Methylation and Complex Human Disease

By Michel Neidhart, 2015

Epigenomics in Health and Disease

Edited by Mario F. Fraga and Agustin F. Fernández, 2015

Epigenetic Gene Expression and Regulation

Edited by Suming Huang, Michael Litt and C. Ann Blakey, 2015

Epigenetic Biomarkers and Diagnostics

Edited by Jose Luis García-Giménez, 2015

Drug Discovery in Cancer Epigenetics

Edited by Gerda Egger and Paola Barbara Arimondo, 2015

Medical Epigenetics

Edited by Trygve O. Tollefsbol, 2016

Chromatin Signaling and Diseases

Edited by Olivier Binda and Martin Fernandez-Zapico, 2016

Genome Stability

Edited by Igor Kovalchuk and Olga Kovalchuk, 2016

Chromatin Regulation and Dynamics

Edited by Anita Göndör, 2016

Neuropsychiatric Disorders and Epigenetics

Edited by Dag H. Yasui, Jacob Peedicayil and Dennis R. Grayson, 2016

Polycomb Group Proteins

Edited by Vincenzo Pirrotta, 2016

Epigenetics and Systems Biology

Edited by Leonie Ringrose, 2017

Cancer and Noncoding RNAs

Edited by Jayprokas Chakrabarti and Sanga Mitra, 2017

Nuclear Architecture and Dynamics

Edited by Christophe Lavelle and Jean-Marc Victor, 2017

Epigenetic Mechanisms in Cancer

Edited by Sabita Saldanha, 2017

Epigenetics of Aging and Longevity

Edited by Alexey Moskalev and Alexander M. Vaiserman, 2017

The Epigenetics of Autoimmunity

Edited by Rongxin Zhang, 2018

Epigenetics in Human Disease, Second Edition

Edited by Trygve O. Tollefsbol, 2018

Epigenetics of Chronic Pain

Edited by Guang Bai and Ke Ren, 2018

Epigenetics of Cancer Prevention

Edited by Anupam Bishayee and Deepak Bhatia, 2018

Computational Epigenetics and Diseases

Edited by Loo Keat Wei, 2019

Pharmacoepigenetics

Edited by Ramón Cacabelos, 2019

Epigenetics and Regeneration

Edited by Daniela Palacios, 2019

Chromatin Signaling and Neurological Disorders

Edited by Olivier Binda, 2019

Transgenerational Epigenetics, Second Edition

Edited by Trygve Tollefsbol, 2019

Nutritional Epigenomics

Edited by Bradley Ferguson, 2019

Prognostic Epigenetics

Edited by Shilpy Sharma, 2019

Epigenetics of the Immune System

Edited by Dieter Kabelitz, 2020

Stem Cell Epigenetics

Edited by Eran Meshorer and Giuseppe Testa, 2020

Epigenetics Methods

Edited by Trygve Tollefsbol, 2020

Histone Modifications in Therapy

Edited by Pedro Castelo-Branco and Carmen Jeronimo, 2020

Environmental Epigenetics in Toxicology and Public Health

Edited by Rebecca Fry, 2020

Developmental Human Behavioral Epigenetics

Edited by Livio Provenzi and Rosario Montirosso, 2020

Epigenetics in Cardiovascular Disease

Edited by Yvan Devaux and Emma Robinson, 2021

Epigenetics of Exercise and Sports

Edited by Stuart M. Raleigh, 2021

Genome Stability, Second Edition

Edited by Igor Kovulchuk and Olga Kovulchuk, 2021

Twin and Family Studies of Epigenetics

Edited by Shuai Li and John L. Hopper, 2021

Epigenetics and Metabolomics

Edited by Paban K. Agrawala and Poonam Rana, 2021

Translational Epigenetics Series Medical Epigenetics

Second Edition

Volume 29

Distinguished Professor of Biology, Senior Scientist, Comprehensive Cancer Center, Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, AL, United States

Academic Press is an imprint of Elsevier

125 London Wall, London EC2Y 5AS, United Kingdom

525 B Street, Suite 1650, San Diego, CA 92101, United States

50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States

The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom

Copyright © 2021 Elsevier Inc. All rights reserved.

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions

This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein).

Notices

Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary.

Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.

To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein.

Library of Congress Cataloging-in-Publication Data

A catalog record for this book is available from the Library of Congress

British Library Cataloguing-in-Publication Data

A catalogue record for this book is available from the British Library

ISBN 978-0-12-823928-5

For information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals

Publisher: Andre Gerhard Wolff

Acquisitions Editor: Peter Linsley

Editorial Project Manager: Megan Ashdown

Production Project Manager: Sreejith Viswanathan

Cover Designer: Miles Hitchen

Typeset by STRAIVE, India

3.

4.

5. Behavioral medical epigenetics

6. Medical epigenetics and twins

7.

Epigenetic biomarkers of disease

Patricia Chaves, Juan Luis Onieva, and Isabel Barragán

Section C Epigenetics of system disorders

9. Autoimmune disease and epigenetics

Sarah J. Blossom

prognosis, and drug response

prognosis, and drug response

8. Prognostic epigenetics

Adriana Fodor, Adriana Rusu, Gabriela Roman, Ramona Suharoschi, Romana Vulturar, Adela Sitar-Taut, and Angela Cozma

10. Epigenetics of pulmonary diseases

Akshaya Thoutam and Narasaiah Kolliputi

11. Cardiovascular disorders and epigenetics

Charbel Abi Khalil

14. Epigenetics in bone and joint disorders

N. Altorok, V. Nagaraja, and B. Kahaleh

12. Epigenomics of intestinal disease

S. Hashimoto-Hill, D.R. Kelly, and T. Alenghat

13. Epigenetics of skin disorders

15. Epigenetics of muscle disorders

Elisa Oltra

Epigenetic

Pathophysiology,

Genetic

Epigenetic

16. Reproductive disease epigenetics

Maricarmen Colon-Diaz, Alexander J. Jaramillo, Edwin Y. Soto, and Perla M. Elosegui

Section D

Multi-system medical epigenetics

18. Pediatric diseases and epigenetics

syndromes and disorders whose genes are involved in the processes and mechanisms of epigenetic regulation of

17. Epigenetics in ocular medicine

Beckwith–Wiedemann syndrome (aka Wiedemann–Beckwith syndrome)

syndrome (aka Silver–Russell syndrome)

The

21. Epigenetics in acute myeloid leukemia

Carmela Dell’Aversana, Cristina Giorgio, Francesco Paolo Tambaro, Giulia Sgueglia, and Lucia Altucci

19. Epigenetics of infectious diseases

K.L. Seib and M.P. Jennings

Helicobacter pylori and altered DNA methylation in infection and gastric cancer

Epigenetic modifications in bacterial pathogens

of DNA in bacterial pathogens

Dam N6-Adenine DNA methyltransferase

22. Epigenetic regulation in cancer metastasis

Guanying Bianca Xu, Huan Wang, Shijia Alexia Chen, and Hong Chen

20. Clinical utility of solid tumor epigenetics

Engin Demirdizen, Julian Taranda, and Sevin Turcan

23. Epigenetics in exercise science and sports medicine

A. Schenk, S. Proschinger, and P. Zimmer

Section E

Bioinformatics of epigenetic medicine

24. Machine learning in epigenetic diseases

Karyn G. Robinson and Robert E. Akins

26. Pharmacoepigenomics in neurodegenerative diseases

Nicoletta Nuzziello and Maria Liguori

pharmacoepigenomic

methylation as a pharmacoepigenomic target for NDDs 563

Histone posttranslational modifications affecting chromatin remodeling as pharmacoepigenomic targets for NDDs 565

as pharmacoepigenomic targets for NDDs 565 Epigenetic-modifying drugs for NDDs 568

Section F

Pharmacology of epigenetics

25. Epigenetics in toxicology and drug development

J. Tajbakhsh and J. Singh

Section G

Therapeutic epigenetics

27. Therapeutics and DNA methylation inhibitors

Shyamala C. Navada

Solid tumors 590

Epigenetic agents in combination—DNMT and HDAC inhibitors 591

Other DNMT inhibitors 591

Novel nucleoside DNMT inhibitors 591

Orally available 5-aza and 5-azadC 592

Nonnucleoside DNMT inhibitors 592

Conclusions 592

References 593

28. Histone deacetylase inhibitors in medical therapeutics

P. Chun

Introduction 597

Classification of histone deacetylases 597

Classification of HDAC inhibitors 598

HDAC inhibitors for the treatment of cancer 599

HDACs and cancer 599

Role of HDAC inhibitors in cancer 599

HDAC inhibitors and clinical outcomes 601

Combination therapy with immune checkpoint inhibitors 603

Conclusions 605

HDAC inhibitors for the treatment of heart diseases 605

Effects of HDAC inhibition on cardiac hypertrophy 606

Effects of HDAC inhibition on cardiac hypertension 608

Effects of HDAC inhibition on myocardial infarction 608

Effects of HDAC inhibition on heart failure 609

Effects of HDAC inhibition on atrial fibrillation 609

HDAC inhibitors for the treatment of kidney disease 609

Effects of HDAC inhibition on renal fibrosis 609

Effects of HDAC inhibitors on renal inflammation 610

HDAC inhibitors for the treatment of idiopathic pulmonary fibrosis 610

HDAC inhibitors for the treatment of inflammatory bowel disease 612

HDAC inhibitors for the treatment of rheumatoid arthritis 613

HDAC inhibitors for the treatment of schizophrenia 615

HDAC inhibitors for the treatment of Parkinson’s disease 616

Suppression of nuclear α-synuclein 616

Inhibition of neuroinflammation and oxidative stress 616

Increase in GDNF and BDNF 617

HDAC inhibitors for the treatment of diabetes mellitus 617

Effects of HDAC inhibitors on the pancreatic β-cells in diabetes 617

Effects of HDAC inhibitors in diabetic kidneys 618

Safety issues with the use of HDAC inhibitors 619

29. Sirtuins as NAD+-dependent deacetylases and their potential in medical therapy

Ashok Kumar and Mona Dvir-Ginzberg

30. Experimental approaches toward histone acetyltransferase modulators as therapeutics

D. Chen, H. Wapenaar, and F.J. Dekker

Challenges in the development of HAT modulators 682

Therapeutic possibilities of HAT modulators 683

HAT modulators in cancers 683

HAT modulators in inflammatory diseases and neurological diseases 683

Conclusion 684

References 684

31. Histone methylation modifiers in medical therapeutics

P. Trojer

Introduction 693

Enhancer of zeste homolog 2 (EZH2, KMT6A) 697

EZH2 functions in transcriptional repression 697

Discovery of EZH2 inhibitors 699

Therapeutic application of EZH2 inhibitors in NHL 699

Therapeutic application of EZH2 inhibitors in other cancer types 700

Disruptor of telomeric silencing like (DOT1L, KMT4) 702

DOT1L functions in transcription elongation 702

Discovery of DOT1L inhibitors 704

Therapeutic application of DOT1L inhibitors in AML 704

Lysine-specific demethylase 1 (LSD1, KDM1A) 705

LSD1 functions in activation and repression of transcription 705

Discovery of LSD1 inhibitors 707

Therapeutic application of LSD1 inhibitors in AML and MPNs 707

Therapeutic application of LSD1 inhibitors in solid tumors 708

Targeting other histone methylation modifiers 708

Conclusions 710

Glossary 712 Abbreviations 712 References 712

32. Modulation of noncoding RNAs (ncRNAs) and their potential role as therapeutics

Luciano Pirola, Oskar Ciesielski, Marta Biesiekierska, and Aneta Balcerczyk Introduction

33. Nutrients and phytonutrients as promising epigenetic nutraceuticals

Anait S. Levenson

34. Epigenetics of pain management

T. Louwies, A.C. Johnson, C.O. Ligon, and B. Greenwood-Van Meerveld

35. Precision medical epigenetics

Chang Zeng, Zhou Zhang, Xiaolong Cui, and Wei Zhang

36. Epigenetics and regenerative medicine

Ehnes, Shiri Levy, and Hannele

853 Epigenetic defects in aged tissues 853 Epigenetics and aging from a muscle regeneration perspective: Satellite stem cells 853

New insights into epigenetics and aging in other tissues can inform nascent fields: The salivary gland 856

Epigenetic dysregulation in developmental plasticity and non-age-related brain diseases 859

Age-related decline in cognition is linked to the deregulation of epigenetic marks 859

Epigenetic remodeling tools used in regenerative medicine therapeutics 861

Epigenetic chemical inhibitors 861 Epigenetic noncoding RNA used in regenerative medicine 861 Novel targeted epigenetic remodeler tools 862

of epigenetic remodelers in regenerative medicine 863

Epigenetic application tools in hESC and iPSC 863

37. Stem cell epigenetics in medical therapy

Baoli Cheng, Liqi Shu, Emily G Allen, and Peng Jin

Introduction 873

Stem cells 873

Epigenetics of stem cells 875

DNA methylation 875

Histone modifications 877

Noncoding RNA 878

RNA modifications 878

Therapeutic prospects of stem cells 879

Summary 880

Glossary 880

Abbreviation 881

References 881

Section H

Medical epigenetics: Future prospects

39. Epigenetics: Future prospective in human disorders and therapeutics

Shriram N. Rajpathak, Vinayak S. Biradar, and Deepti D. Deobagkar

Introduction 903

Epigenetics in stress and related disorders 903

Early life events and stress biology 903

Oxidative stress as a mediator for epigenetic changes 904

Stress and epigenetics machinery 904

Stress-related disorders 905

Epigenetics in human chromosomal disorders 907

Outline for an association between aneuploidy and epigenetic machinery 907

38.

The clinical landscape of HDAC inhibitors

A. Ganesan

Nucleosome modification and transcriptional regulation 885

One to eleven: The human zinc-dependent HDACs 885

Nuclear protein deacetylases HDAC1, HDAC2, and HDAC3 885

Cytoplasmic protein deacetylase HDAC6 886

Protein fatty acid deacylases HDAC8 and HDAC11 886

Polyamine deacetylase HDAC10 886

Pseudoenzymes HDAC4, HDAC5, HDAC7, and HDAC9 886

HDAC inhibitors—A pharmacological classification 886

Nonselective HDAC inhibitors 887

Nuclear isoform selective HDAC inhibitors 889

HDAC6 and HDAC8 isoform selective inhibitors 890

Dual mechanism HDAC inhibitors 891

Advanced clinical trials—Hematological cancers 892

Advanced clinical trials—Non-blood cancers 893

Advanced clinical trials—Beyond cancer 894

Summary 895

References 896

Autosomal aneuploidy conditions 909

Sex chromosomal aneuploidy 909

Non-coding RNAs as regulators in X monosomy and trisomy 913

Future perspective 914 References 914

40. Prospective advances in medical epigenetics

Jiali Deng, Mengying Guo, and Junjie Xiao

Introduction 919

Prospective advances of DNA methylation in medical epigenetics 921

Prospective advances of DNA methylation in vitiligo 923

Prospective advances of DNA methylation in liver 923

Prospective advances of DNA methylation age 926

Prospective advances of DNA methylation in neuron 926

Prospective advances of histone modification in medical epigenetics 927

Prospective advances of noncoding RNAs in medical epigenetics 928

International Human Epigenome Consortium and epigenetical precision medicine 930

Limitations 931

Prospect 931

Acknowledgments 932 References 932

Index 937

Contributors

Numbers in parenthesis indicate the pages on which the authors’ contributions begin.

Charbel Abi Khalil  (197), Epigenetics Cardiovascular Lab, Research Department, Weill Cornell MedicineQatar, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medicine, New York, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, United States

Robert E. Akins  (513), Center for Pediatric Clinical Research and Development, Alfred I. duPont Hospital for Children, Nemours Children’s Health System, Wilmington, DE, United States

T. Alenghat (213), Division of Immunobiology and Center for Immunology and Tolerance, Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States

Emily G Allen  (873), Department of Human Genetics, Emory University, Atlanta, GA, United States

N. Altorok  (251), Division of Rheumatology and Immunology, Department of Internal Medicine, University of Toledo Medical Center, Toledo, OH, United States

Lucia Altucci  (447), Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy

Aneta Balcerczyk  (721), Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland

Isabel Barragán  (117), Medical Oncology Service, Section of Immuno-Oncology, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain; Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden

Marta Biesiekierska  (721), Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland

Vinayak S. Biradar  (903), Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India

Sarah J. Blossom  (171), Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Science Center, Albuquerque, NM, United States

Patricia Chaves (171), Medical Oncology Service, Section of Immuno-Oncology, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga (IBIMA); University of Málaga, Málaga, Spain

D. Chen (665), Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands

Hong Chen (471), Department of Food Science and Human Nutrition; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States

Shijia Alexia Chen  (471), Department of Food Science and Human Nutrition, University of Illinois at UrbanaChampaign, Urbana, IL, United States

Baoli Cheng (873), Department of Human Genetics, Emory University, Atlanta, GA, United States

P. Chun  (597), College of Pharmacy, Inje University, Gimhae, South Korea

Oskar Ciesielski  (721), Department of Molecular Biophysics, Faculty of Biology and Environmental Protection; The Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Lodz, Poland

Maricarmen Colon-Diaz (309), San Juan Bautista Medical School, Caguas, Puerto Rico

O.H. Cox (81), The Johns Hopkins Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States

Angela Cozma  (143), University of Medicine and Pharmacy; Department of 4th Internal Medicine, ClujNapoca, Romania

Xiaolong Cui  (839), Department of Chemistry, University of Chicago, Chicago, IL, United States

F.J. Dekker  (665), Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands

Carmela Dell’Aversana  (447), Institute for Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS) – National Research Council (CNR); Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy

Engin Demirdizen  (425), Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany

Jiali Deng  (919), Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong; Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China

Deepti D. Deobagkar  (903), Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India

Mona Dvir-Ginzberg  (633), Institute of Bio-Medical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel

Devon Ehnes  (853), Institute for Stem Cell and Regenerative Medicine; Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States

J.C. Eissenberg  (103), Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Doisy Research Center, St Louis, MO, United States

Perla M. Elosegui  (309), San Juan Bautista Medical School, Caguas, Puerto Rico

Adriana Fodor  (143), University of Medicine and Pharmacy; Department of Diabetes, Nutrition and Metabolic Diseases, Cluj-Napoca, Romania

A. Ganesan (885), School of Pharmacy, University of East Anglia, Norwich, United Kingdom

Cristina Giorgio (447), Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy

Mengying Guo  (919), Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong; Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China

J.G. Hall  (377), Department of Medical Genetics and Pediatrics, University of British Columbia; BC Children’s Hospital, Vancouver, BC, Canada

S. Hashimoto-Hill  (213), Division of Immunobiology and Center for Immunology and Tolerance, Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States

Mustapha Umar Imam  (33), Centre for Advanced Medical Research and Training; Department of Medical Biochemistry, Faculty of Basic Medical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria

Maznah Ismail (33), Laboratory of Molecular Biomedicine, Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia

Alexander J. Jaramillo  (309), San Juan Bautista Medical School, Caguas, Puerto Rico

M.P. Jennings  (407), Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia

Peng Jin  (873), Department of Human Genetics, Emory University, Atlanta, GA, United States

A.C. Johnson  (817), Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center; Veterans Affairs Health Care System; Department of Physiology, University of Oklahoma Health Sciences Center; Department of Neurology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States

B. Kahaleh  (251), Division of Rheumatology and Immunology, Department of Internal Medicine, University of Toledo Medical Center, Toledo, OH, United States

D.R. Kelly  (213), Division of Immunobiology and Center for Immunology and Tolerance, Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States

Alexander Koliada  (11), Molecular Genetic Laboratory Diagen, Kyiv, Ukraine

Narasaiah Kolliputi  (185), Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida, Tampa, FL, Unites States

Ashok Kumar  (633), Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, United States

R.S. Lee (81), The Johns Hopkins Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States

Anait S. Levenson  (741), Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States

Shiri Levy  (853), Institute for Stem Cell and Regenerative Medicine; Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States

C.O. Ligon  (817), Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States

Maria Liguori  (559), National Research Council, Institute of Biomedical Technologies, Bari Unit, Bari, Italy

Ji Liu  (347), Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, United States

T. Louwies  (817), Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States

Qianjin Lu  (231), Department of Dermatology, Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenetics, Changsha, Hunan, People’s Republic of China

Shuaihantian Luo  (231), Department of Dermatology, Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenetics, Changsha, Hunan, People’s Republic of China

Oleh Lushchak  (11), Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine

B. Greenwood-Van Meerveld  (817), Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center; Veterans Affairs Health Care System; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States

Rachel L. Miller (51), Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States

V. Nagaraja (251), Division of Rheumatology, Department of Internal Medicine University of Michigan, Ann Arbor, MI, United States

Shyamala C. Navada  (585), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States

Nicoletta Nuzziello  (559), National Research Council, Institute of Biomedical Technologies, Bari Unit, Bari, Italy

Jessica Oh  (51), Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States

Elisa Oltra  (279), Department of Pathology, School of Health Sciences, Catholic University of Valencia, Valencia, Spain

Juan Luis Onieva  (117), Medical Oncology Service, Section of Immuno-Oncology, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain

Der Jiun Ooi  (33), Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, MAHSA University, Jenjarom, Selangor, Malaysia

Luciano Pirola (721), Cardiology, Metabolism and Nutrition Laboratory, INSERM U1060, Lyon-1 University, South Lyon Medical Faculty, Pierre Benite, France

S. Proschinger  (491), Department for Molecular and Cellular Sports Medicine, German Sport University Cologne, Cologne, Germany

Shriram N. Rajpathak (903), Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India

Karyn G. Robinson  (513), Tissue Engineering and Regenerative Medicine Laboratory, Alfred I. duPont Hospital for Children, Nemours Children’s Health System, Wilmington, DE, United States

Gabriela Roman  (143), University of Medicine and Pharmacy; Department of Diabetes, Nutrition and Metabolic Diseases, Cluj-Napoca, Romania

Hannele Ruohola-Baker (853), Institute for Stem Cell and Regenerative Medicine; Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States

Adriana Rusu  (143), University of Medicine and Pharmacy; Department of Diabetes, Nutrition and Metabolic Diseases, Cluj-Napoca, Romania

Kamaldeen Olalekan Sanusi  (33), Department of Physiology, Faculty of Basic Medical Sciences; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria

A. Schenk  (491), Institute for Sport and Sport science, TU Dortmund University, Dortmund, Germany

K.L. Seib (407), Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia

Giulia Sgueglia  (447), Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy

Liqi Shu  (873), Department of Human Genetics, Emory University, Atlanta, GA, United States

J. Singh  (529), Forma Therapeutics, Watertown, MA, United States

Adela Sitar-Tăut  (143), University of Medicine and Pharmacy; Department of 4th Internal Medicine, ClujNapoca, Romania

Edwin Y. Soto  (309), San Juan Bautista Medical School, Caguas, Puerto Rico

Ramona Suharoschi  (143), University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca; Molecular Nutrition and Proteomics Research Laboratory, Cluj-Napoca, Romania

J. Tajbakhsh  (529), Cedars-Sinai Medical Center, Los Angeles, CA, United States

Francesco Paolo Tambaro (447), Center for Bone Marrow Transplant and Blood Transfusion, Children’s Hospital “Santobono-Pausilipon”, Naples, Italy

Julian Taranda  (425), Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany

Akshaya Thoutam  (185), Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida, Tampa, FL, Unites States

Trygve O. Tollefsbol  (3), Distinguished Professor, Department of Biology; O’Neal Comprehensive Cancer Center; Integrative Center for Aging Research; Nutrition Obesity Research Center; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States

P. Trojer  (693), Constellation Pharmaceuticals Inc., Cambridge, MA, United States

Sevin Turcan (425), Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany

Yaaqub Abiodun Uthman (33), Department of Physiology, Faculty of Basic Medical Sciences; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria

Alexander Vaiserman  (11), Laboratory of Epigenetics, D.F. Chebotarev Institute of Gerontology, NAMS, Kyiv, Ukraine

Romana Vulturar  (143), University of Medicine and Pharmacy; Department of Cell and Molecular Biology, Cluj-Napoca, Romania

Huan Wang (471), Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL; Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States

H. Wapenaar (665), Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom

R. Weksberg  (377), Division of Clinical and Metabolic Genetics and Genetics and Genome Biology Program, The Hospital for Sick Children; Department of Pediatrics and Institute of Medical Science, University of Toronto, Toronto, ON, Canada

Junjie Xiao  (919), Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong; Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China

Guanying Bianca Xu  (471), Department of Food Science and Human Nutrition, University of Illinois at UrbanaChampaign, Urbana, IL, United States

Chang Zeng  (839), Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States

Wei Zhang  (839), Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Institute of Precision Medicine, Jining Medical University, Jining, China; The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States

Zhou Zhang  (839), Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States

P. Zimmer (491), Institute for Sport and Sport science, TU Dortmund University, Dortmund, Germany

Preface

It has been several years since the first volume of Medical Epigenetics appeared, and a second volume is not only timely but also appropriate given the rapid developments in the areas covered in this field. The field of medical epigenetics has indeed undergone rapid growth, and the chapters contained in this new edition have been updated and revised to reflect these new changes. The first edition of Medical Epigenetics received Honorable Mention in the Clinical Medicine Award Category by the American Publishers Awards for Professional and Scholarly Excellence (PROSE) and also a “Highly Commended” Award by the British Medical Association, which attests to the high standards of this book. Many of the chapters in the second edition are authored by the same leaders in this field who contributed to the first edition of this award-winning book.

Medical Epigenetics, Second Edition provides a comprehensive analysis of the importance of epigenetics to health management. The purpose of this book is to fill a current need for a comprehensive volume on the medical aspects of epigenetics with a focus on human systems, epigenetic diseases that affect these systems, and modes of treating epigeneticbased disorders and diseases. The intent of this book is to provide a stand-alone comprehensive volume that will cover all human systems relevant to epigenetic maladies and all major aspects of medical epigenetics. The overall goal is to provide the leading book on medical epigenetics that will be useful not only to physicians, nurses, medical students, and many others directly involved with health care but also to investigators in life sciences, biotech companies, graduate students, and many others who are interested in more applied aspects of epigenetics. Research in the area of translational epigenetics is a cornerstone of this volume.

The first volume of Medical Epigenetics was published about 5 years ago, and many developments in the numerous areas of epigenetic involvement in medicine have taken place since that time. There has also been a surge of interest in precision medicine since 2015, and the second edition of Medical Epigenetics will cover this new and exciting area as well with a focus on epigenetics in precision medicine. A few areas that have not changed considerably over the 5 years or that were of lesser interest in the first edition have been removed from the second edition of Medical Epigenetics

The overall design of this book is to build from the fundamental mechanisms of epigenetics as they apply to humans to approaches for treating epigenetic-based diseases. The book begins with the basic tenets of epigenetics in human systems and progresses through general medical aspects of epigenetics, epigenetics of system disorders, multisystem medical epigenetics, pharmacology of epigenetics, and therapeutic epigenetics. The volume closes with two chapters on future prospects in medical epigenetics. It is intended that this book will be among the most comprehensive and leading books in the area of medical epigenetics and improve upon the award-winning first volume of this book.

Overview Section A

Chapter 1

Advances in medical epigenetics

aDistinguished Professor, Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States, bO’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States, cIntegrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL, United States, dNutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States, eComprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States

Introduction

Epigenetic processes consist of biochemical changes to the DNA or its associated proteins or RNA that does not change the DNA sequence itself but does impact the level of gene expression. Epigenetics in general has a highly important role in medicine that provides previously unimagined new opportunities to disease management that span from diagnosis to treatment and extend as well to prognosis [1]. Virtually all systems of the body are affected by epigenetic processes and in many cases, epigenetic processes impact many different biological systems [2]. DNA methylation, histone modifications, and noncoding RNA comprise three major components of the epigenetic machinery that has relevance to medical conditions [3–8]. All of these mechanisms are capable of regulating gene expression leading to many of the pathological features that are manifested by epigenetic aberrations.

Basic principles of epigenetics

The most studied of the major epigenetic mechanisms is DNA methylation and for many years led the way to our understanding of the power of epigenetics in many biological phenomena such as X chromosome inactivation and mitotic inheritance of epigenetics as well as many other processes. The study of DNA methylation also was critical in the developmental stages of the field of epigenetics in leading the way toward our realization that modifications of DNA, no matter how simple can have a major impact on health when these modifications are altered [9].

5-Methylcytosine (5mC), the product of the DNA methyltransferases (DNMTs) that catalyze DNA methylation, is amenable to further modifications and leads to a number of biological changes [6]. The ten-eleven translocase dioxygenases (TET enzymes) can modify 5mC to produce 5-hydroxymethylcytosine (5hmC) that can further become modified by the TET enzymes to produce 5-formylcytosine and 5-carboxylcytosine. Once corrected by the DNA repair mechanisms, one of the significant outcomes is an enzymatic conversion of 5mC to cytosine. Therefore, DNA methylation cannot only be placed enzymatically into the genome, but it can also be lost through an enzymatic demethylation process. This reversibility of DNA methylation could have many implications in medical diseases that have changes in gene expression secondary to fluctuations in DNA methylation. The histones also undergo reversible changes in their modifications during disease formation and progression and this is also driven by enzymatic processes. For example, histone acetyltransferases (HATs) add acetyl moieties to the N-terminal tails of histones that can often lead to an increase in gene expression. Also highly relevant are the histone deacetylases (HDACs) that remove acetyl groups from the histones. In fact, HDAC inhibitors may serve as an important therapeutic target with respect to cognitive decline as a component of neurodegenerative disease [6]. The noncoding RNAs (ncRNAs) comprise the third major mediator of epigenetic changes that occur in human cells and that appear to have considerable potential for impacting medical diagnosis, treatment, and prognosis [3]

Taken together, these three major mechanisms for mediating epigenetic changes result in a large percentage of epigenetic control of gene expression that is a major component of medical diseases. Perhaps even more important is that these epigenetic modifiers frequently do not act alone but often participate in a cross talk process. DNA methylation may interact with histone modifications to silence the expression of a gene as well as many other permutations on this theme that become possible between intraepigenetic interactions. Moreover, these epigenetic mechanisms also often interact with other important mediators of gene control such as transcription factors.

Epigenetics. https://doi.org/10.1016/B978-0-12-823928-5.00002-5

Copyright © 2021 Elsevier Inc. All rights reserved.

General medical aspects of epigenetics

Although much has been learned about epigenetics and its role in medicine, much less is known about the lifetime temporal aspects of epigenetic changes. For instance, as described in Chapter 2, there is evidence that epigenetic changes during sensitive stages of early life may be critical to the health of adults. One of the primary factors that can contribute to early-life epigenetic modifications is environmental insults that can result in epigenetic aberrations that may give rise to disease formation later in life. Moreover, lifestyle factors such as one’s diet, the quality or quantity of exercise, or environmental factors can result in epigenetic modifications that, depending on the type of lifestyle change, may either increase or decrease health in general (Chapter 3). Disease prevention and promotion of health are extremely important in medical care and collectively will greatly decrease the amount of human suffering from diseases as well as reduce spiraling health care costs. By focusing on the impact of epigenetic prevention of disease, we may be able to “get ahead of the curve” so to speak and to prevent many medically related diseases before they begin or at least slow their progression. Environmental exposures to air, food, and personal products can have a major effect on epigenetic mechanisms that can also occur at specific time windows of exposure. As discussed in Chapter 4, these environmental factors include dietary exposures, chemicals, allergens, and pollutants. Advances in this field are rapidly developing and the impact of the environment on epigenetic aspects of disease, although a classic aspect of the field of epigenetics, is still understudied and it is likely that major discoveries will continue to unfold in this area that is critical to medical epigenetics. In fact, early life experiences can greatly influence behavior and this can be mediated through epigenetic modifications. Factors such as stress and cortisol can alter epigenetic marks that may influence gene expression and subsequently lead to changes in behavior (Chapter 5). For example, genes of the hypothalamic-pituitary-adrenal axis have been implicated in glucocorticoid-related behavioral disorders and epigenetic mechanisms such as DNA methylation and histone modifications can be affected by glucocorticoids that subsequently affect neurotransmitter genes. These changes may precipitate or worsen behavioral aberrations and perhaps psychiatric disorders as well.

The proverbial nature vs nurture influence of disease has perplexed investigators for about as long as it has been known that each of these important factors can influence disease formation. Through the study of twins, especially monozygotic twins, we now know that phenotypic variation increases with aging of organisms and that this is due at least in part to environmental factors that alter the epigenetic machinery. In a fascinating review by Joel Eissenberg (Chapter 6), twin studies have tremendous potential to tether out the epigenetic roles in complex traits and multifactorial diseases. A major challenge in this endeavor, however, will be to fully resolve the mechanisms for age-related “epigenetic drift” and to deduce which of the epigenetic changes that are divergent in twins as they age are contributing to the etiology of diseases and which are by-products of pathology. This involves another major challenge in medicine besides the relative contribution of nature vs nurture, that is, cause and effect. Twin studies will likely reveal a wealth of information about the role of epigenetics in medicine and my estimate is that this field, although still in an early phase, has tremendous potential to answer many of the significant questions that persist with respect to medical epigenetics.

In addition to increasing our understanding, the mechanisms of epigenetics in medicine, on a more practical level we also need to enhance the ability to diagnose diseases and to better predict the outcomes of diseases. In fact, advances in medical epigenetics are contributing significantly to the development of epigenetic biomarkers useful for diagnosis (Chapter 7) as well as the prognosis (Chapter 8) of many diseases such as cancer. The identification of epigenetic aberrations in medical disorders opens important opportunities for the development of biomarkers for earlier diagnosis and perhaps prevention of diseases. Epigenetic biomarkers of interest include not only DNA methylation and histone modifications, but also noncoding RNAs (Chapter 7). Many of these epigenetic biomarkers are also greatly enhancing the predictive power of disease outcome that can be an important factor for monitoring and adjusting treatment regimens such as various disease progress (Chapter 8).

Epigenetics of system disorders

Since epigenetic mechanisms can have a significant impact on gene expression, it is not surprising that epigenetic aberrations influence virtually all systems of the body ranging from the disorders of the intestinal tract, to cardiovascular disorders to dermatological diseases. It is now apparent that immune-based disorders can occur secondary to epigenetic aberrations that involve both the initiation and perpetuation of these disorders (Chapter 9). Recent discoveries have suggested that the immune system may carry a “memory” of prior exposures to pathogens that are encoded in the maintenance of altered epigenetic marks. This new direction may lead to increased precision medicine for diseases of the immune system that has fascinating potential. The pulmonary system is also very prone to aberrations of an epigenetic nature (Chapter 10) and chronic obstructive pulmonary disease, asthma, interstitial lung diseases such as idiopathic pulmonary fibrosis and other

Turn static files into dynamic content formats.

Create a flipbook
Issuu converts static files into: digital portfolios, online yearbooks, online catalogs, digital photo albums and more. Sign up and create your flipbook.