Toxicology and Epigenetics

By Saura C. Sahu

Epigenetics is the study of both heritable and non-heritable changes in the regulation of gene activity and expression that occur without an alteration in the DNA sequence. This dynamic and rapidly developing discipline is making its impact across the biomedical sciences, in particular in toxicology where epigenetic differences can mean that different individuals respond differently to the same drug or chemical.

Toxicology and Epigenetics reflects the multidimensional character of this emerging area of toxicology, describing cutting-edge molecular technologies to unravel epigenetic changes, the use of in vivo and in vitro models, as well as the potential use of toxicological epigenetics in regulatory environments. An international team of experts consider the interplay between epigenetics and toxicology in a number of areas, including environmental, nutritional, pharmacological, and computational toxicology, nanomaterials, proteomics and metabolomics, and cancer research.

Topics covered include:

• environment, epigenetics and diseases
• DNA methylation and toxicogenomics
• chromatin at the intersection of disease and therapy
• epigenomic actions of environmental arsenicals
• environment, epigenetics and cardiovascular health
• toxicology, epigenetics and autoimmunity
• ocular epigenomics: potential sites of environmental impact in development and disease
• nuclear RNA silencing and related phenomena in animals
• epigenomics – impact for drug safety sciences
• methods of global epigenomic profiling
• transcriptomics: applications in epigenetic toxicology

Toxicology and Epigenetics is an essential insight into the current trends and future directions of research in this rapidly expanding field for investigators, toxicologists, risk assessors and regulators in academia, industry and government.

• Language: English
• Publisher: Wiley
• Release date: Aug 23, 2012
• ISBN: 9781118349069

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This edition first published 2012

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Library of Congress Cataloging-in-Publication Data

Toxicology and epigenetics / editor, Saura C. Sahu.

p. cm.

Includes bibliographical references and index.

ISBN 978-1-119-97609-7 (cloth)

1. Genetic toxicology. 2. Environmental toxicology. 3. Epigenetics. I. Sahu, Saura C.

RA1224.3.T698 2012

615.9′02–dc23

Dedicated to

My parents, Gopinath and Ichhamoni, for their gift of life, love and living example.

My wife, Jharana, for her lifelong friendship, love and support.

My children, Megha, Sudhir and Subir, for their love and care.

Saura C. Sahu

Preface

Toxicology, an old discipline of science, is undergoing a rapid transformation in recent years following the new ‘epigenetic’ revolution. ‘Epigenetics’, an emerging major scientific discipline, is growing rapidly. This monograph builds a bridge between toxicology and epigenetics at a level designed to take the reader to the forefront of research in this area. The importance of this field of research is evidenced by the increasing number of contributions published each year. It becomes increasingly clear that developments in this field are moving so rapidly that new means are needed to report the status of ongoing research activities. The contributions presented in this monograph represent a collaborative effort by international experts working in this emerging field of science.

The main purpose of this book is to assemble up-to-date, state-of-the-art information on toxicoepigenetics presented by internationally recognized experts in a single edition. Therefore, I sincerely hope that this book will provide an authoritative source of current information in this area of research and prove useful to the scientists interested in this scientific discipline throughout the world. However, it should be of interest to a variety of other scientific disciplines including toxicology, genetics, medicine and pharmacology, as well as drug and food sciences. Also, it should be of interest to federal regulators and safety assessors of drugs, food, environment, and consumer products.

Saura C. Sahu

Laurel, Maryland, USA

Acknowledgments

I express my sincere gratitude to the following individuals, who have influenced me directly or indirectly, for writing this book.

I must admit that writing this book was a challenge. I am indebted to the internationally recognized experts, who shared my enthusiasm for this field of science and contributed generously to this book. Their work speaks for itself and I am grateful to them for their cooperation and excellent contributions in their own areas of expertise.

I thank Dr Thomas A. Cebula, Dr Joseph E. LeClerc, Dr Daniel A. Casciano, Dr Philip W. Harvey, Dr Harry Salem and Dr Tohru Inoue for their encouragement, inspiration and support.

Finally, I thank my publishers; Paul Deards, Rebecca Ralf and Sarah Tilley of the publishing company, John Wiley & Sons, Ltd, for their cooperation and excellent support in the timely publication of this book.

List of Contributors

Ernest K. Amankwah Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA

Kathryn A. Bailey Environmental Sciences and Engineering, The University of North Carolina Gillings School of Global Public Health, UNC-Chapel Hill, Chapel Hill, NC, USA

Andrea Baccarelli Environmental Health, Harvard School of Public Health, Boston, MA, USA

Krishna K. Banaudha Biochemistry and Molecular Biology Department, The George Washington University, Washington, DC, USA

Frederick A. Beland Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, USA

Federico Bolognani Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Marjorie Brand Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Departments of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada

Michael W.Y. Chan Department of Life Science and Human Epigenomics Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC

Robert Y.S. Cheng Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

Yana Chervona Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA

Angela O. Choi Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada

William B. Coleman Department of Pathology and Laboratory Medicine, Curriculum in Toxicology, Program in Translational Medicine, UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA

Craig A. Cooney Research and Development, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA

Victor G. Corces Department of Biology, Emory University, Atlanta, GA, USA

Max Costa Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA

Philippe Couttet Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Yamini Dalal Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA

Deepti Deobagkar Center of Advanced Studies, Department of Zoology and Bioinformatics Center, University of Pune, Pune, India

F.J. Dilworth Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Departments of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada

Dana C. Dolinoy Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA

Jennifer L. Freeman School of Health Sciences, Purdue University, West Lafayette, IN, USA

Rebecca C. Fry Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina-Chapel Hill, NC, USA

Bernard W. Futscher Department of Pharmacology & Toxicology, College of Pharmacy and The University of Arizona Cancer Center, The University of Arizona, Tucson, AZ, USA

Sanjukta Ghosh Departments of Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA, USA

Kathleen M. Gilbert Arkansas Children's Hospital Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA

Olivier Grenet Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

S. Gurunathan Department of Bioinformatics, Faculty of Sciences and Humanities, SRM University, Chennai, India

David Heard Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Yoko Hirabayashi Division of Cellular and Molecular Toxicology, National Center for Biological Safety and Research, National Institute of Health Sciences, Setagaya, Tokyo, Japan

Katsuhide Igarashi Division of Cellular and Molecular Toxicology, National Center for Biological Safety and Research, National Institute of Health Sciences, Setagaya, Tokyo, Japan

Taisen Iguchi Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan

Tohru Inoue Department of Biological Function and Structural Medicine, Nihon University School of Medicine, Itabashi, Tokyo, Japan

Manasi P. Jain Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada

Pius Joseph Molecular Carcinogenesis Laboratory, Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA

Jun Kanno Division of Cellular and Molecular Toxicology, National Center for Biological Safety and Research, National Institute of Health Sciences, Setagaya, Tokyo, Japan

Igor Koturbash Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, USA

Harri Lempiäinen Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Solange S. Lewis Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA

Ying-Wei Li Division of Medical Technology, School of Allied Medical Professions; Molecular Biology and Cancer Genetics Program, College of Medicine, Comprehensive Cancer Center; The Ohio State University, Columbus, OH, USA

Huey-Jen L. Lin Division of Medical Technology, School of Allied Medical Professions; Molecular Biology and Cancer Genetics Program, Comprehensive Cancer Center; The Ohio State University, Columbus, Ohio; Department of Medical Technology, University of Delaware, Newark, DE, USA

Stephanie Lovinsky-Desir Division of Pediatric Pulmonary, Department of Pediatrics, Columbia University College of Physicians and Surgeons; Children's Hospital of New York Presbyterian, New York City, NY, USA

Raphaëlle Luisier Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Radek Malik Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic

Philippe Marc Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Jennifer Marlowe Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Dusica Maysinger Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada

B. Alex Merrick Molecular Toxicology and Informatics Group, Biomolecular Screening Branch, National Toxicology Program Division, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

Rachel L. Miller Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine; Division of Pediatric Pulmonary, Department of Pediatrics; Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University College of Physicians and Surgeons, Columbia University, New York City, NY, USA

Kenneth P. Mitton Eye Research Institute, Control of Gene Expression Laboratory and the Pediatric Retinal Research Laboratory, Oakland University, Rochester, MI, USA

Shinichi Miyagawa Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan

Jonathan Moggs Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Pierre Moulin Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Arne Müller Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Paul Nioi Amgen Inc, Thousand Oaks, California, CA, USA

Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, Medical School; Department of Internal Medicine, Human Genetics and School of Public Health, Medical School, University of Michigan, Ann Arbor, MI, USA

Jong Y. Park Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Center and Research Institute, Tampa; College of Medicine, University of Florida, FL, USA

Zhengang Peng Division of Medical Technology, School of Allied Medical Professions; Molecular Biology and Cancer Genetics Program, College of Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA

Igor P. Pogribny Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, USA

Alvaro Puga Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, USA

Delphine Quénet Laboratory of Receptor Biology & Gene Expression, National Cancer Institute, Bethesda, MD, USA

Donna Ray Department of Medicine; School of Public Health, University of Michigan, Ann Arbor, MI, USA

John F. Reichard Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, USA

Bruce Richardson Department of Medicine; Veteran Affairs, Ann Arbor Healthcare System, University of Michigan, Ann Arbor, MI, USA

Ashley G. Rivenbark Department of Pathology and Laboratory Medicine, UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA

David I. Rodenhiser Departments of Paediatrics, Biochemistry and Oncology, University of Western Ontario; The EpiGen Western Research Group at The Children's Health Research Institute; London Regional Cancer Program at the London Health Sciences Centre, London, Ontario, Canada

Laura S. Rozek Department of Environmental Health Sciences, School of Public Health; Department of Otolaryngology, Medical School, University of Michigan, Ann Arbor, MI, USA

Bekim Sadikovic Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA

Saura C. Sahu Division of Toxicology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA

Maureen A. Sartor Department of Computational Medicine and Bioinformatics, Medical School; Department of Biostatistics, School of Public Health, University of Michigan, MI, USA

Maria S. Sepúlveda Department of Forestry and Natural Resources and School of Health Sciences, Purdue University, West Lafayette, IN, USA

Paul L. Severson Department of Pharmacology and Toxicology, College of Pharmacy and The University of Arizona Cancer Center, The University of Arizona, Tucson, AR, USA

Tamotsu Sudo Section of Translational Research and Development of Gynecological Oncology, Hyogo Cancer Center, Akashi, Hyogo, Japan

Petr Svoboda Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic

Wan-yee Tang Division of Molecular and Translational Toxicology, Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

Rémi Terranova Novartis Institutes for BioMedical Research, Preclinical Safety, Discovery and Investigative Safety, Basel, Switzerland

Joo Chuan Tong Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Data Mining Department, Institute for Infocomm Research, Connexis, Singapore

V. Umashanker Center for Bioinformatics, Vision Research Foundation, Sankara Nethralaya, Chennai, India

Mukesh Verma Methods and Technologies Branch, Epidemiology and Genetics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA

Marcin Walkiewicz Laboratory of Receptor Biology & Gene Expression, National Cancer Institute, Bethesda, MD, USA

Gregory J. Weber School of Health Sciences, Purdue University, West Lafayette, IN, USA

Jennifer Chao Weber College of Medicine, University of Arizona, Phoenix, AZ, USA

Jingping Yang Department of Biology, Emory University, Atlanta, GA, USA

Ryohei Yatsu Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan

Matthew T. Zuzolo Division of Medical Technology, School of Allied Medical Professions; Molecular Biology and Cancer Genetics Program, College of Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA

Chapter 1

Introduction

Saura C. Sahu

Division of Toxicology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA

Toxicoepigenomics is a rapidly developing new branch of toxicology. Currently it is a hot discipline of toxicological sciences (Trosko and Chang, 2010; Csoka and Szyf, 2009; Goldberg, Allis, and Bernstein, 2007; Watson and Goodman, 2002). Genetics is defined as heritable changes in the gene expression profiles caused by the modification of genomic DNA due to the alterations in sequence of its bases. It is long accepted that aging and various human diseases including cancer are caused by the changes in the genomic DNA sequence. This long-held ‘genetic’ mechanism of human diseases focuses on the genetic changes induced by the direct alterations in the genomic DNA sequence itself. Genetics, environmental factors, and xenobiotics contribute to toxicity and human disease. Recent ‘omics’ technologies opened the way to a systemic understanding of toxicology and pathogenesis (Waters and Fostel, 2004). Thus, they gave birth to a new branch of toxicology called toxicogenomics. Toxicogenomics is the integration of traditional toxicology and genomics leading to toxicity and pathogenicity induced by the heritable changes in the genomic DNA sequence itself. However, recent discoveries show that this is not always the case. It has been demonstrated that heritable gene expression, both in the disease states and induced by environmental exposures, is also altered by the DNA modifications without any direct alteration in genomic DNA sequence itself. Environmental factors such as diet, smoking, alcohol intake, environmental toxicants, and stress are capable of altering gene expression profiles that can be inherited by the future generations and such genes altered by the environmental factors without any alteration in the genomic DNA sequence can cause human diseases. This observation led to the discovery of an alternate complementary mechanism of human inheritance and disease called ‘epigenetic’ mechanism that does not involve any change in the genomic DNA sequence itself. Therefore, a new scientific discipline ‘epigenetics’ was born with the definition that it is the heritable changes in the expression of the gene without any direct alteration in the DNA sequence itself (Egger et al., 2004). The heritable epigenetic modifications induced by environmental factors involve DNA, histone, and chromosomes. The most common observations reported in the epigenetic inheritance process are DNA methylation, histone modification, and noncoding small RNAs (Bonasio, Tu, and Reinberg, 2010). These discoveries led to the increasing recognition of the importance of epigenetics in the mechanisms of toxicity. Therefore, another new branch of toxicology called toxicoepigenomics was born. Toxicoepigenomics is the integration of traditional toxicology and epigenetics leading to toxicity and pathogenicity induced by heritable alterations in the gene expression without any direct changes in the genomic DNA sequence itself.

An increasing body of evidence demonstrates that epigenetic patterns, altered by environmental factors, are associated with human diseases such as cancer, neurodevelopmental disorders, cardiovascular diseases, type-2 diabetes, obesity, and infertility (Meaney, 2010; Csoka and Szyf, 2009; Nicholls, 2000). Epigenetic changes have been observed in virus-associated human cancers (Li, Leu, and Chang, 2005). It is believed that early epigenetic molecular events lead to cancer development (Herceg, 2007). Epigenetic drug therapy has become an increased focus in the treatment of complex diseases including cancer (Jian, 2011). Understanding of epigenetic pathways and rapid development of sensitive detection technologies will help the development of drug therapies for these diseases, especially cancers. A systems-biology approach employing microarray analyses of epigenetic gene expression patterns have been suggested for the safety assessment of drugs (Csoka and Szyf, 2009; Trosko and Upham, 2010). More and more this approach is being used for epigenetic toxicological studies (Lefèvre and Mann, 2008; Chernov et al., 2010). Computational epigenomics, an emerging new discipline, will make significant contributions to toxicoepigenomics research. Chromatin immunoprecipitation (ChIP) is a useful tool for epigenetic studies. Recent technical advances such as ChIP-on-chip and ChIP-seq convert epigenetic research into a high-throughput endeavor (Bock and Lengauer, 2008). Bioinformatic methods will be useful in these efforts. Understanding the role of toxicity in pathogenesis is important. Control of the epigenetic diseases requires the identification of chemical and biological modulators of epigenetic targets. However, very little information on the potential toxicological consequence of such modulations is currently available and, therefore, requires further investigations. Better understanding of the epigenetic mechanism of human diseases, caused by environmental exposures, holds great promise for the future treatment of human diseases.

As the Editor of this monograph, Toxicology and Epigenetics, it gives me great pride to introduce a unique book which encompasses many aspects of toxicoepigenomics never published together before. It is only recently that epigenetic research has attracted the attention of toxicologists. The toxicoepigenomic research work, actively pursued throughout the world, will lead to major discoveries of fundamental importance and of great clinical significance. This monograph brings together the ideas and work of investigators of international reputation who have pioneered in this area of research. This book reflects the remarkable blossoming of the discipline of toxicoepigenetics in recent years. New ideas and new approaches are being brought to bear on explorations of epigenetic mechanisms in toxicology. Therefore, exciting times are ahead for the future research on toxicoepigenomics. I sincerely hope that this book will stimulate the creativity of all the investigators who are actively engaged in this rapidly developing emerging new field of research.

References

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Bonasio, R., Tu, S., and Reinberg, D. (2010) Molecular signals of epigenetic states. Science, 330, 612–616.

Chernov, A.V., Baranovskaya, S., Golubkov, V.S. et al. (2010) Microarray-based transcriptional and epigenetic profiling of matrix metalloproteinases, collagens, and related genes in cancer. J. Biol. Chem., 285, 19647–19659.

Csoka, A.B. and Szyf, M. (2009) Epigenetic side-effects of common pharmaceuticals: a potential new field in medicine and pharmacology. Med. Hypotheses, 73, 770–780.

Egger, G., Liang, G., Aparicio, A., and Jones, P.A. (2004) Epigenetics in human disease and prospects for epigenetic therapy: a review. Nature, 429, 457–463.

Goldberg, A.D., Allis, C.D., and Bernstein, E. (2007) Epigenetics: a landscape takes shape. Cell, 128, 635–638.

Herceg, Z. (2007) Epigenetics and cancer: towards an evaluation of the impact of environmental and dietary factors. Mutagenesis, 22, 91–103.

Jian, T. (2011) DNA methylation topology: potential of a chromatin landmark for epigenetic drug toxicology. Epigenomics, 3, 761–770.

Lefèvre, C. and Mann, J.R. (2008) RNA expression microarray analysis in mouse prospermatogonia: identification of candidate. Dev. Dyn., 237, 1082–1089.

Li, H.P., Leu, Y.W., and Chang, Y.S. (2005) Epigenetic changes in virus-associated human cancers. Cell Res., 15, 262–271.

Meaney, M.J. (2010) Epigenetics and the biological definition of gene x environment interactions. Child Dev., 81, 41–79.

Nicholls, R.D. (2000) The impact of genomic imprinting for neurobehavioural and developmental disorders. J. Clin. Invest., 105, 413–418.

Trosko, J.E. and Chang, C.C. (2010) Factors to consider in the use of stem cells for pharmaceutic drug development and for chemical safety assessment. Toxicology, 270, 18–34.

Trosko, J.E. and Upham, B.L. (2010) A paradigm shift is required for the risk assessment of potential human health after exposure to low level chemical exposures: a response to the toxicity testing in the 21st century report. Int. J. Toxicol., 29, 344–357.

Waters, M.D. and Fostel, J.M. (2004) Toxicogenomics and systems toxicology: aims and prospects. Nat. Rev. Genet., 5, 936–948.

Watson, R.E. and Goodman, J.I. (2002) Epigenetics and DNA methylation come of age. Toxicol. Sci., 67, 11–16.

Chapter 2

Environment, Epigenetics, and Diseases

Robert Y.S.¹ Cheng and Wan-yee Tang²

¹Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

²Division of Molecular and Translational Toxicology, Johns Hopkins Bloomberg School of Public Health, Department of Environmental Health Sciences, Baltimore, MD, USA

2.1 Perceptions of epigenetics

2.1.1 Definition of epigenetics

Disease susceptibility has now been recognized as a complex interplay between one's genetic make-up and epigenetic modulations induced by endogenous or exogenous environmental factors (Ho and Tang, 2007; Tang and Ho, 2007). Epigenetic disruption of gene expression has been shown to play an equally important role as genetic predisposition (such as polymorphisms, mutations, deletions, and insertions) in the development of disease (Dolinoy, Weidman, and Jirtle, 2007b; Godfrey et al., 2007; Jiang, Bressler, and Beaudet, 2004). ‘Epigenetics’ itself is defined as ‘outside conventional genetics’ (Jaenisch and Bird, 2003). Epigenetic changes are reversible, heritable modifications that are mitotically stable (Skinner, Manikkam, and Guerrero-Bosagna, 2010) and do not involve alterations in the primary DNA sequence (Bird, 2007; Rakyan et al., 2003; Whitelaw and Whitelaw, 2006). This dynamic nature makes the epigenome more responsive to environmental stimuli (Aguilera et al., 2010; Foley et al., 2009; Skinner, 2011; Tang and Ho, 2007). There are three distinct and intertwined mechanisms that are now known to regulate the epigenome: non-coding RNAs (ncRNAs), DNA methylation, and histone modifications (Cheung and Lau, 2005; Esteller, 2005; Morris, 2005). These processes singularly or jointly affect transcript stability, DNA folding, nucleosome positioning, chromatin compaction, and ultimately nuclear organization. They determine whether a gene is silenced or activated and when and where this occurs. Hence, they are known to be essential for normal cell development, maintenance of tissue-specific gene expression patterns in mammals, regulation of genome stability, X-chromosome inactivation, and gene imprinting (Bernstein, Meissner, and Lander, 2007).

2.1.2 DNA methylation

DNA methylation refers to the covalent addition of a methyl group derived from S-adenosyl-L-methionine to the fifth carbon of the cytosine ring to form the fifth base, 5-methyl cytosine (5meC) (Costello and Plass, 2001). This reaction is catalyzed by DNA methyltransferases (DNMT1, 3A, 3B, and 3L) and methylated DNA binding proteins (Methyl-CpG-Binding Domain or MBD1-4, MeCP1-2) (Gronbaek, Hother, and Jones, 2007). Across eukaryotic species, methylation occurs predominantly in cytosines located 5′ of guanines, known as CpG dinucleotides (CpGs). The methyl group of the 5meC inhibits binding of transcription factors (TFs) to their CpG-containing recognition site, resulting in gene suppression. Furthermore, DNA methylation enzymes mediate complex histone modifications and result in the establishment of repressive chromatin structures that permanently silence gene transcription (Wysocka et al., 2006).

2.1.3 Histone modifications and chromatin remodeling

The nucleosome is composed of five histone proteins (H1, H2A, B, H3, and H4). The N-terminus of these histone proteins are subject to covalent modifications such as methylation, phosphorylation, acetylation, and ubiquitination by a group of histone-modifying enzymes (Lee, Smith, and Shilatifard, 2010; Shilatifard, 2006). Alterations in these proteins contribute to the accessibility and compactness of the chromatin, and result in activation or suppression of particular genes (Marmorstein and Trievel, 2009). In addition to histone modifying enzymes, chromatin remodeling ATPase plays an important role in assisting gene transcription machinery by unwrapping the nucleosomal DNA or sliding the nucleosome itself along the DNA (Fry and Peterson, 2002; Harikrishnan et al., 2005; Mavrich et al., 2008; Smith and Peterson, 2005).

2.1.4 Non-coding RNAs

Evidence is rapidly emerging for the role of miRNAs in gene regulation (Matzke and Birchler, 2005; Verdel et al., 2004), demonstrating that miRNAs influence diverse biological functions including cell differentiation and proliferation during normal development and pathological responses (Bushati and Cohen, 2007; Kloosterman and Plasterk, 2006; Xu et al., 2009). miRNAs regulate gene expression at the post transcriptional level by means of RNA-induced silencing complex (RISC) (Flynt and Lai, 2008). A number of miRNAs were shown to bind to specific regions in the 3′ untranslated region (UTR) and block the translation of the messenger RNA (mRNA) of proto-oncogenes and tumor suppressors (Hammond, 2006). A single miRNA can target tens to hundreds of mRNAs because of the imperfect base pairing between miRNAs and mRNA (Baek et al., 2008; Friedman et al., 2009). Alteration of the expression of miRNAs is believed to contribute to the progression of tumorigenesis (Davis-Dusenbery and Hata, 2011) and other diseases (Dai and Ahmed, 2011; Guay et al., 2011; Kerr, Korenblat, and Davidson, 2011).

2.1.5 Lifetime epigenetics changes

DNA methylation patterns are established through defined phases during the development of an organism. Gamete methylation patterns, with the exception of ‘imprinted genes,’ are erased by a genome-wide demethylation at the eight-cell stage of mammalian blastocyst formation (Maclean and Wilkinson, 2005). During the implantation stage, methylation patterns are established via de novo methylation by means of DNA methyltransferases (DNMTs) (Okano et al., 1999). During adulthood, the amount and pattern of methylation is maintained and remains tissue- and cell-type specific. Disruption of these preset patterns of DNA methylation in adult life has been linked to aging and disease development (Casillas et al., 2003; Esteller, 2005; Issa, 2000; Kafri et al., 1992). On the other hand, ncRNAs have been established in a number of different cell types including human embryonic stem cells (Chen et al., 2004) during normal cell development. Both DNA methylation marks and ncRNA of the DNA sequence can be replicated during mitosis and permanently affect cell differentiation and functions of the somatic cells (Chen and Riggs, 2005). Therefore, it is believed that the epigenome can be altered by maternal factors or environmental mimics early in life and persist in later life. Data regarding the mechanism of how histone marks and chromatin remodeling are maintained during DNA replication remains elusive. Nevertheless, changes in histone modifications or histone modifying enzyme expression are observed during cell transformation and aging (Calvanese et al., 2009). Specific modifications at histone tails contribute in the development of human germ cells (Flanagan et al., 2006) and especially in sperm cells (Jenkins and Carrell, 2011). Aberrant expression of histone deacetylases (HDACs) was also found during aging and cancer (Sasaki et al., 2006), while trimethyl histone H4 lysine 20 (H4K20M3) expression level was found to be increased in aging animals (Fraga and Esteller, 2007; Sarg et al., 2002).

2.1.6 Transgenerational inheritance of the epigenome

Germ line transmission of epigenetic marks between generations has been recently demonstrated in animals exposed to environmental factors only once during germ line development (Anway et al., 2005; Bruner-Tran and Osteen, 2011; Matthews and Phillips, 2011). These marks can continuously transmit to subsequent generations without additional environmental exposure. This has indeed raised the question as to how these ‘reprogrammed’ marks are being inherited. DNA methylation is well-characterized as epigenetic machinery that functions in genomic imprinting during germ cell development (Kelsey, 2007). Gamete imprinting is reported as establishment of epigenetic patterns for future generations (Trasler, 2006). Imprinted genes are mostly regulated by DNA methylation at distinct regions called differential methylated regions (DMRs), where DNA methylation differs between maternal and paternal alleles. DNMT1 is postulated to maintain the methylation on imprinted genes and help to the gene to escape from erasure of allelic-specific methylation patterns through global demethylation during pre-implantation development (Howell et al., 2001). Other groups have suggested that a ‘reprogrammed’ epigenome may increase genomic instability, and thus allow genetic predispositions to pass through subgenerations (Skinner, 2011). More studies on the underlying mechanisms of how environmental factors ‘imprint’ the genome via epigenetic modification in germ cells are required in the future. The reversible and responsive nature of epigenetic modifications toward the environment leads us to wonder whether this reprogramming will persist or be further modified throughout the course of life of the organism.

2.1.7 Epigenetic reprogramming and inter-individual variations in human disease risk

Inter-individual phenotypic variations in the human population are now known as the result of epigenetic reprogramming in addition to genetic polymorphisms (Tang and Ho, 2007). These epigenetic marks are shown to be established during embryonic development (Chong and Whitelaw, 2004; Monk, Boubelik, and Lehnert, 1987) and thought to persistent throughout life. In utero exposure to hypoxia, hypo- or hypernourishment, infection, specific hormones, drugs, or toxins contributes to low birth weight and a greater risk of coronary heart disease, hypertension, stroke, depression, type 2 diabetes, and osteoporosis in later life (Chong and Whitelaw, 2004; Garg, 2006; Kroll, 2004; Liu and Freedman, 2005; Moore, 2005; Scher and Sawyers, 2005; Soussi et al., 2006; Tusie Luna, 2005). Epigenetic reprogramming has been speculated as the origin of fetal-based adult diseases (Tang and Ho, 2007). Environmental exposure to synthetic chemicals, medical interventions, environmental pollutants, and lifestyle choices at critical windows during early development (such as fetal or postnatal periods) may alter the epigenetic modifications in the genome. If these changes conflict with the programmed ‘adaptive changes’ made during early development, they may impede adaptability to later-life challenges and elevate disease risk (Bredfeldt et al., 2010; Ho et al., 2006; McLachlan et al., 2001; Meaney and Szyf, 2005; Perera et al., 2009; Tang et al., 2008). On the other hand, evidence has emerged to demonstrate that epigenetic variations could be established during adult life and in specific tissues or cell types in response to environmental exposure from the home environment or workplace, or life-choices such as diet, alcohol or tobacco use and pharmacologic treatments (Aguilera et al., 2010; Szyf, 2007).

2.2 Environmental epigenetics and human diseases

Environmental Epigenetics is the study of the molecular mechanisms of environmental factors interacting with the epigenome and impacting the biology in specific organs, tissues and cells, resulted in adaptive evolutionary changes or disease development (Figure 2.1). Both epidemiological and in vitro/vivo studies illustrated the association between disease risks and chronic exposure to particular metals and chemicals such as chromium (Cr), cadmium (Cd), inorganic arsenic (As), nickel (Ni), diethylstilbestrol (DES), bisphenol A (BPA), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), phthalate esters, polychlorinated biphenyls (PCBs), and chlorine disinfection by-products (DBPs). Sources of potential exposure to these toxic and/or carcinogenic metals/chemicals include consuming contaminated shellfish or water, living or working in a contaminated area, handling unsafe plastics, and exposure to metal-containing waste which is improperly handled. It is believed that heavy metals exert their carcinogenic effects in tissues by forming DNA adducts and inducing oxidative stress and DNA damage. However, their ability to transform normal cells to the neoplastic stage is not fully understood. Some of these heavy metals are even weak mutagens. Therefore, understanding the mechanism underlying pathogenesis and carcinogenesis induced by the heavy metals is extremely important. Other than heavy metals, environmental exposure of various chemical compounds have been reported to induce hormonal imbalance, promote cell growth, and disrupt organ functions through epigenetic modifications of genes in specific cells/tissues/organs. Herein, we review recent literature and provide evidence that heavy metals and chemical compounds not only exert toxic and carcinogenic effects in tissues, but also alter the epigenome and result in disease development. We also discuss the findings of how diets and lifestyles alter epigenetic machinery.

Figure 2.1 Epigenetic seesaw in determining disease risk

2.1

2.2.1 Chromium (Cr)

Cr is naturally occurring in rocks, animals, plants, soil, and volcanic dust and gases. In our environment, Cr primarily exists in two valence states, trivalent (Cr III) or hexavalent (Cr VI) along with the less common metallic Cr (Cr 0), and is commonly produced by industrial processes. Occupational exposure to Cr has been identified mostly in the industries producing ferrochrome. Ore refining, chemical and refractory processing, cement-producing plants, automobile brake lining and catalytic converters for automobiles, leather tanneries, and chrome pigments also contribute to the occupational exposure to Cr. Human populations are exposed to Cr (generally Cr [III]) through eating food, drinking water, inhaling air, or by direct contact with consumer products containing Cr (http://www.epa.gov). Cr has been shown to play a role in disease and cancer development by exerting its epigenetic effects in specific genes. Promoter methylation of p16INK4a, Adenomatous Polyposis Coli (APC), O-6-methylguanine-DNA methyltransferase (MGMT) and human MutL Homolog 1 (hMLH1) were observed in lung cancers from chromate-exposed workers (Ali et al., 2011; Kondo et al., 2006; Takahashi et al., 2005). Chromate exposure to lung cancer cells was shown to silence the hMLH1 promoter by altering the global levels of histone methyltransferases and demethylateases (Sun et al., 2009). In addition, short-term exposure to Cr(III) chloride in mouse liver cells was demonstrated to cross-link histone-modifying enzymes and DNMT1 at the CYP1A1 promoter and suppress benzo[a]pyrene-inducible aryl hydrocarbon receptor (AhR) gene expression by reducing levels of histone methyltransferase (H3K4me3) and HDAC (H3/H4Ac). This resulted in reduced CYP1a1 expression and dysregulation of xenobiotic metabolism (Sun et al., 2009). Importantly, paternal exposure to Cr(III) was shown to modify the epigenome and genome and to induce transgenerational carcinogenesis (Cheng et al., 2002, 2004a,b). Follow-up studies on this model demonstrated an allele-specific methylation of the 45S rRNA spacer promoter in sperm germ cells, leading to speculation that this epimutation may increase tumor risk in offspring (Shiao et al., 2005, 2011). Although Cr(III) is not classified as a human carcinogen by the EPA, these studies have alerted the public because of the availability of the non-regulated Cr(III) picolinate as in supplements.

2.2.2 Cadmium (Cd)

Cd has been designated a probable human carcinogen by the EPA and a human carcinogen by both the International Agency for Cancer Research (IACR) and the National Toxicology Program (NTP). Epidemiological studies linked Cd exposure with pulmonary disorders including bronchiolitis and emphysema, and cancers of the lung, bladder, prostate, and pancreas. The long half-life and poor excretion rate from the body make Cd a cumulative toxin, suggesting that previous exposures to Cd may lead to detrimental effects during the lifetime of exposed individuals. Airborne Cd is commonly found in the burning of fossil fuels such as coal or oil, and incineration of municipal waste materials. Smoking is another source of Cd exposure. Smokers have approximately twice as much Cd in their bodies compared to nonsmokers. For nonsmokers, food is generally the major source of Cd exposure due to the application of phosphate fertilizers or sewage sludge on farm fields (http://www.epa.gov). Cd was shown to induce cell transformation through the disruption of zinc-dependent cellular processes (Waalkes, 2003). However, Cd is known as a weak mutagen and has a weak DNA binding affinity (Arita and Costa, 2009). It leads to the speculation that Cd may promote carcinogenesis through epigenetic mechanisms. Ten weeks of Cd exposure induced malignant transformation of prostate epithelial cells and inactivated tumor suppressor genes, p16INK4a and RASSF1A, by altering DNMTs expression and activity (Benbrahim-Tallaa et al., 2007). Recently, evidence has indicated that global DNA methylation is affected by short-term Cd exposure in chick embryos (Doi et al., 2011). The inhibitory effects of Cd on DNMT3A/B expressions during the critical period of embryogenesis may contribute to the pathogenesis of ventral body wall defects in the chick embryo. Cd was also shown to induce histone modifications at the metallothionein 3 (MT-3) promoter in order to establish and maintain the bivalent chromatin structure for gene transcriptions during transformation of urothelial cells (Somji et al., 2011). Therefore, from an epigenetic standpoint, these data indicate that Cd may establish DNA methylation machinery and stably maintain chromatin structures for rapid gene transcription contributing to cells transformation.

2.2.3 Arsenic (As)

As is a semi-metal and exists naturally in rocks, soils, water, air, plants, and animals. As is also used in fertilizers, paints, dyes, metals, drugs, soaps, and semi-conductors. Industry practices such as copper smelting, mining, and coal burning also contribute to environmental exposure of As to human populations (http://www.epa.gov). Inorganic arsenite (As(III)) is more toxic than arsenate (As(V)) since it is better absorbed into the body and accumulates in many cell types. Arsenic exposure induces thickening and discoloration of skin lesions, and skin, lung, liver, bladder, nasal passage, prostate, and kidney tumors. It is also associated with diabetes, cardiovascular, and neurological diseases (Tchounwou, Patlolla, and Centeno, 2003; Tchounwou, Centeno, and Patlolla, 2004). It is well established that arsenic disrupts global and specific gene expression (Andrew et al., 2008; Bourdonnay et al., 2009; Somji et al., 2011; Su et al., 2006), supporting that arsenic-induced health effects could be mediated by epigenetic mechanisms (Reichard and Puga, 2010; Ren et al., 2011; Smeester et al., 2011). Both DNA methylation and arsenic metabolism require S-adenosylmethionine (SAM) as the methyl donor. This competitive demand between arsenic metabolism and DNA methylation for SAM may affect the percentage of methylated CpG dinucleotides throughout the genome. Experimental evidence in animals and cellular systems suggests that arsenic may induce hyper- and hypomethylation on a gene-specific basis, with an overall trend toward global hypomethylation (Reichard and Puga, 2010). Exposure of human lung adenocarcinoma A549 cells to arsenite results in increased hypermethylation in the p53 promoter (Mass and Wang, 1997). Significant hypermethylation of the gene p16 was also observed in cases of arsenicosis caused by high levels of arsenic (Chanda et al., 2006). There are very few studies that have evaluated the association of arsenic exposure with DNA methylation in humans. In populations exposed to high arsenic levels in drinking water such as West Bengal and Bangladesh, increasing arsenic exposure was associated with global DNA hypermethylation in leukocytes (Pilsner et al., 2007) and mononuclear cells (Majumdar et al., 2010), in contrast to the findings based on experimental studies and proposed mechanisms. These results suggest that more studies evaluating the association of arsenic exposure with global DNA methylation are needed to evaluate the consistency of those findings, especially in populations exposed to low to moderate levels of arsenic.

2.2.4 Nickel (Ni)

Ni is a nonessential, toxic, and carcinogenic metal (Costa et al., 2005; Kasprzak, Sunderman, and Salnikow, 2003) but it is very widely used in our environment in things such as Ni-Cd batteries, nickel plating merchandise, stainless steel, jewelry, and coins (Salnikow and Zhitkovich, 2008). Nickel can cause bronchitis, pulmonary fibrosis, asthma, pulmonary edema, cardiovascular, kidney diseases, and allergic dermatitis. In addition, the carcinogenic activity of Ni poses a serious threat to human health (Salnikow and Zhitkovich, 2008). Epidemiological studies have clearly implicated Ni(II) compounds as human carcinogens on the basis of increased mortality from respiratory tract malignancies in refinery workers chronically exposed to nickel-containing dusts and fumes (Scand. J. Work Environ. Health, 1990). Direct targeted mutagenesis induced by Ni was not considered as the primary cause in Ni-induced carcinogenesis (Trott et al., 1995). On the other hand, truncation, deamination, and oxidation of histone H2B has been reported in cells exposed to Ni(II) (Karaczyn, Golebiowski, and Kasprzak, 2005; Karaczyn et al., 2009), suggesting epigenetic machinery appeared to be involved Ni-carcinogenesis. Epigenetic modifications including changes in histone acetylation, methylation, or ubiquitination levels, chromatin remodeling, and alterations in DNA methylation as well as the activation or suppression of a number of TFs were found in cells/animals exposed to Ni (Broday et al., 2000; Cangul et al., 2002; Karaczyn, Golebiowski, and Kasprzak, 2005; Karaczyn et al., 2009). Over a decade ago, exposure of Ni compounds to the transgenic Chinese hamster (G12 model) was shown to alter the status of DNA methylation (Lee et al., 1995). Tumor suppressor gene Fhit was found to be silenced by promoter hypermethylation in response to Ni (Kowara et al., 2004). Moreover, Ni can suppress histone acetylation, demethylation, and ubiquitination in vitro (Broday et al., 2000; Golebiowski and Kasprzak, 2005). Taken together, these data suggest that epigenetic modifications by Ni appeared to be more influential than gene mutations in causing toxic and carcinogenic effects. It is also notable that Ni induces carcinogenesis as well as epigenetic effects in a tissue, strain, and species-dependent manner.

2.2.5 Lead (Pb)

Pb is a toxic metal naturally found in our environment and is commonly used in paints and other household products. Airborne Pb comes from industrial sources and leaded aviation gasoline. Pb can even be found in drinking water. Pb has been shown to cause a range of health effects, from behavioral problems and learning disabilities to seizures and death (http://www.epa.gov). A recent study demonstrated a global decline of gene expression levels of DNMTs and proteins involved in DNA methylation (MeCP2) and histone modifications in aging primates that received Pb treatment after birth. This data indicated that the epigenetic modifications in early life may contribute to an enhancement in neurodegeneration at old age (Bihaqi et al., 2011). Epigenetic effects induced by Pb were also observed in the human population. Prenatal Pb exposure was shown to be inversely associated with genomic DNA methylation in umbilical cord blood, suggesting the epigenome of the developing fetus can be influenced by maternal cumulative Pb burden, and long-term epigenetic programming may affect disease susceptibility (Pilsner et al., 2009). Similarly, Wright et al. reported the association between Pb exposure and DNA methylation of long interspersed nuclear elements-1 (LINE-1) and suggested changes in DNA methylation may represent a biomarker of past Pb exposure in human (Wright et al., 2010). Epigenetic studies on Pb can improve our understanding of the role of Pb on early events during development as well as late life abnormalities of the nervous system.

2.2.6 Mercury (Hg)

Hg is a naturally occurring element found in air, water, soil, rocks, and coal. It can also be released into the environment through burning coal or hazardous wastes, producing chlorine, breaking mercury products, spilling mercury, as well as improper treatment and disposal of mercury containing products. Larger quantities of these compounds are generated as byproducts from pollution control activities at gold mines or in waste in the United States. Hg exposure at high levels can exert harmful effects on the brain, heart, kidneys, lungs, and immune system of people of all ages. High levels of methylmercury (MeHg) in the bloodstream of unborn babies and young children may affect their developing nervous system and learning ability. Birds and mammals that eat fish contaminated with mercury showed reduced reproduction, slower growth, abnormal behavior, and death (http://www.epa.gov). Onishchenko et al. was the first group to show perinatal exposure to MeHg caused persistent changes in learning and motivational behavior in mice and induced epigenetic gene silencing of brain-derived neurotrophic factor (BDNF) in the hippocampus (Onishchenko et al., 2008). Recently, an inverse relationship between brain Hg exposure levels and DNA methylation levels has been demonstrated in polar bears (Pilsner et al., 2010). These findings imply Pb may disrupt epigenetic components in turn to affect the neural functions of animals, especially during the early development stage.

2.2.7 Diethylstilbestrol (DES)

DES is a synthetic estrogen that was used by women to prevent miscarriages during late 1930s to early 1970s. It took years before people became aware of the increased incidence of reproductive tract cancers in ‘DES daughters and sons.’ The link between in utero exposure to the DES-induced cancer was then established (Veurink, Koster, and Berg, 2005). DES was reported to cause various diseases in the human population, such as vaginal adenosis, gonadal dysgenesis, thrombocytopenia, gynecomastia, and breast cancer. DES is also known as a potent endocrine disruptor (ED) as it has a long-acting estrogenic effect. Exposure to DES in early development disrupts the differentiation of the reproductive tract and results in a high incidence of structural and functional abnormalities, as well as tumors in hormone-sensitive organs (Newbold, 2004). In animal studies, pre- and neonatal DES exposure induced high incidences of endometrial cancer in intact mice and altered a wide range of gene expression profiles and epigenetic modifications. Neonatal exposure of mice to DES induced demethylation of a single CpG site in the promoter of the lactoferrin (Li et al., 1997) and demethylation in exon 4 of c-fos (Li et al., 2003) in the uteri of the exposed animals. Furthermore, neonatal exposure to DES or genistein prevented the ovarian steroid-induced silencing of Nsbp1 gene in the uteri of intact mice after the onset of puberty, via DNA hypermethylation (Tang et al., 2008). These findings provide direct evidence that a xenoestrogen, such as DES is capable of disrupting epigenetic machinery to cause various unwanted effects in both human and animal populations.

2.2.8 Bisphenol A (BPA)

BPA, first synthesized in 1891, is now used as a cross-linking chemical to manufacture polycarbonate plastics and epoxy resins contained in a variety of consumer products including food and beverage containers, baby bottles, and dental sealants. Leakage of BPA from these consumer products led this xenoestrogen to be found ubiquitously at significant levels in the environment. Unlike other synthetic estrogens such as DES, BPA is a mimic of estrogen and has a lower binding activity to estrogen receptors (ERs) when compared to DES or 17β-estradiol (E2) (Kuiper et al., 1998). BPA remained less of a concern to the public until a breakthrough finding by Wade Welshons in the late 1990s. BPA at relatively low levels showed bioactivity in human and mice (Nagel et al., 1997). BPA also showed an equivalent activating capacity of the non-classical membrane ERs (Quesada et al., 2002; Wozniak, Bulayeva, and Watson, 2005) as E2. Their results have shown that BPA exerts its effect at a concentration far beneath the level used to establish the current EPA safety threshold. Importantly, BPA is found in higher concentrations not only in amniotic fluid as compared to maternal serum (Kawahata et al., 2004), but also in placental and fetal tissue (Ikezuki et al., 2002; Yamada et al., 2002). Thus, it is now believed that BPA is a toxicant for developing human tissues, particularly in estrogen sensitive reproductive organs. Fetal exposure to environmentally relevant doses of BPA has been shown to advance puberty, alter pubertal mammary gland development, and permanently change the morphology and functionality of female reproductive organs in mice (Maffini et al., 2006). These processes may involve epigenetic reprogramming of the genome.

Maternal exposure to BPA in rat was shown to modify methylation of the metastable loci, the viable yellow agouti (Avy), and CDK5 activator-binding protein (CabpIAP). Interestingly, this effect on DNA methylation and the associated change in coat color of the exposed animals were prevented by a maternal dietary supplementation with folic acid or genistein (Dolinoy, Huang, and Jirtle, 2007a). On the other hand, neonatal exposure to BPA in rat was found to induce adverse effects in spermatogenesis and fertility and aberrant DNA methylation in the testis (Salian, Doshi, and Vanage, 2009). In utero and early postnatal exposure to BPA results in alteration of DNA methylation status and development of malignancies of the breast and prostate. Our previous studies showed that DNA methylation might be one of the mechanisms for reprogramming the rat prostate in early life. Hypomethylation of the phosphodiesterase type IV variant 4 (PDE4D4) promoter was found in the rat prostate after neonatal exposure to an environmentally relevant dose of BPA, and this was associated with an increase in susceptibility of prostate carcinogenesis (Ho et al., 2006). Though there is emerging evidence to support the role of BPA in epigenetic reprogramming of the genome, further studies are required to examine the correlation between BPA-induced epigenetic alterations, changes in gene expression, and phenotypic outcomes (Vom Saal and Welshons, 2006; Welshons, Nagel, and Vom Saal, 2006). Of particular importance will be the exploration of molecular and behavioral changes that occur in response to environmentally relevant low doses of BPA in animals and humans.

2.2.9 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)

TCDD belongs to the family of dioxins which have been characterized by the EPA as probable human carcinogens at background levels of exposure. TCDD is an unintentional by-product of incomplete combustion from fossil fuels and wood, and released during the incineration of municipal and industrial wastes. TCDD can also be found in food, mainly meat, dairy products, and fish, and counts as the major source of human exposure. TCDD is known to be a developmental toxicant in animals, causing skeletal deformities, kidney defects, and weakened immune responses in the offspring of animals exposed to TCDD during pregnancy. Human studies have shown an association between TCDD and soft-tissue sarcomas, lymphomas, and stomach carcinomas (http://www.epa.gov). TCDD exerts its toxicity through binding to dioxin response elements (DREs) to activate gene expression of the AhR that works through xenobiotic metabolism machinery (Dere et al., 2011; Kerkvliet, 2009). Exposure of mouse embryos to TCDD inhibits fetal growth, and is strongly associated with changes in the methylation status of the imprinted genes H19 and Igf2 (Wu et al., 2004). Furthermore, TCDD showed its ability to induce histone modifications in normal human mammary epithelial cells and interfere with chromosomal positioning through the AhR (Oikawa et al., 2008). A recent study has demonstrated that TCDD altered Treg/Th17 differentiation, and consequent suppression of colitis through epigenetic reprogramming (Singh et al., 2011). TCDD levels in the environment have been declining since the early 1970s and after the clean-up actions from federal and state regulations; however, it is still important to investigate and monitor TCDD action because of its ability to induce epigenetic effects.

2.2.10 Phthalate ester

Phthalate esters including diethyl phthalate (DEP), dimethyl phthalate (DMP), di-n-octyl phthalate, butyl benzyl phthalate (BBP), di-n-butyl phthalate (DBP), di-2-(ethylhexyl) phthalate (DEHP), and bis(2-ethylhexyl) phthalate are commonly used as plasticizers in producing consumable plastic products Phthalates cause cleft lip and palate, an exposed brain, or incomplete formation of the skull or spine in the developing embryo or neonate, although this mechanism is still unknown. It is proposed that phthalates are EDs and toxic to cells by interfering with testosterone formation (http://www.epa.gov). Maternal exposure to DEHP in mice induced testicular dysgenesis syndrome (TDS) in fetuses and pups and significantly increased global DNA methylation levels and DNMTs expression (Wu et al., 2010a,b). These results suggest that DEHP may influence male reproductive tract development via epigenetic reprogramming.

2.2.11 Polychlorinated biphenyls (PCBs)

PCBs belong to a broad family of man-made organic chemicals, chlorinated hydrocarbons. They have a range of toxicity and vary in consistency from light-colored liquids to yellow or black waxy solids. PCBs are used in hundreds of industrial and commercial applications including electrical, heat transfer, and hydraulic equipment; as plasticizers in paints, plastics, and rubber products; and in pigments, dyes, and carbonless copy paper. The EPA has classified PCBs as probable human carcinogens, and while PCBs are chemically stable, they remain for long periods of time in air, water, and soil. PCBs increase the risk of non-Hodgkin's lymphoma by disrupting the immune system, cause adverse reproductive effects in both monkeys and humans, and impair visual recognition and short-term memory and learning in newborn baby monkeys. They can act as an ED to alter thyroid hormone levels in animals and humans (http://www.epa.gov). A number of epidemiological studies also demonstrated workers exposed to PCBs showed increased incidence of rare liver cancers and malignant melanomas (Knerr and Schrenk, 2006; Loomis et al., 1997). Transgenerational prenatal PCB exposure induced aberrant detrimental physiological and behavioral effects in the neuroendocrine systems in mice, although specific epigenetic effects were not investigated (Walker and Gore, 2011). However, other reports have shown that early life exposure to PCBs alters expression of DNMT1 in the hypothalamus, and DNMT1, 3a and 3b in rat liver (Desaulniers et al., 2005, 2009). Together, these findings indicate PCBs may interfere with DNA methylation machinery in animals, resulting in long-term effects in gene expression and organ function.

2.2.12 Disinfection by-products (DBPs)

Water suppliers often add a disinfectant, such as chlorine, to drinking water. Disinfectants themselves can react with naturally occurring materials in the water to form byproducts such as trihalomethanes, dichloroacetic acid (DCA), and trichloroacetic acid (TCA). Chlorite is a byproduct formed when chlorine dioxide is used to disinfect water (http://www.epa.gov). Chlorite has been shown to cause adverse reproductive or developmental effects in laboratory animals (Narotsky et al., 2008; Rice et al., 2008; Tardiff, Carson, and Ginevan, 2006). However, there is considerable uncertainty in toxicological studies of these byproducts that occur in disinfected drinking water. Currently, the EPA says there is no causal link between exposure to the DBPs and reproductive/development effects. Chlorinate methane exerts epigenetic carcinogenicity in rodent livers and kidneys and attributes to regenerative hyperplasia (Miyagawa et al., 1998). Tao et al. found that DCA and TCA promoted liver tumors in mice and were associated with an increase in global hypomethylation (Tao et al., 1998). They further reported that chlorine DBPs induced renal carcinogenicity and DNA hypomethylation in mice and rats (Tao et al., 2005). Overall, there is a great need for more evidence elucidating the epigenetic mechanisms induced by DBPs.

2.2.13 Polycyclic aromatic hydrocarbons (PAHs)

Polycyclic Aromatic Hydrocarbons (PAHs) are semi-volatile organic compounds and belong to a family called ‘polycyclic organic matter (POM).’ Benzo[a]pyrene (BaP) is also known as PAHs. Airborne POM compounds are primarily formed from the combustion of organic fuels and emissions from cigarette smoke, vehicle exhaust, home heating, laying tar, and grilling meat. The EPA has classified seven PAHs (BaP, benz[a]anthracene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, dibenz[a,h]anthracene, and indeno[1,2,3-cd]pyrene) as Group B2, which are probable human carcinogens (http://www.epa.gov). Epidemiologic studies have reported an increase in lung cancer in humans exposed to coke oven emissions, roofing tar emissions, and cigarette smoke (Agency for Toxic Substances and Disease Registry (ATSDR), 1995; U.S. Department of Health and Human Services, 1993). Animal studies have reported respiratory tract tumors from inhalation exposure to BaP and fore-stomach tumors, leukemia, and lung tumors from oral exposure to BaP (Agency for Toxic Substances and Disease Registry (ATSDR), 1995; U.S. EPA, 1999a and 1999b). Over two decades ago, scientists demonstrated mice exposed to 7,12-dimethylbenz[a]anthracene (DMBA) developed persistent immunosuppression, tumor outgrowth, and metastasis via alteration of the epigenetic machinery (Ward et al., 1986). Recently, scientists have found that genetic reactivation of LINE-1 by BaP involves nucleosomal histone modifications and alterations in DNMT1 recruitment to the LINE-1 promoter (Teneng et al., 2011). Moreover, the epigenetic effect of PAHs was found to be associated with childhood asthma. Perera et al. showed that methylation of a 5′CGI (CpG island) in acyl-CoA synthetase long-chain family member 3 (ACSL3), a gene that encodes a key enzyme in fatty acid metabolism, was significantly associated with the level of maternal PAH exposure, as well as with reported childhood asthma through to the age of five (Perera et al., 2009).

2.2.14 Diet or living style

There is growing evidence that numerous dietary factors, including micronutrients and non-nutrients like genistein and polyphenols, can modify epigenetic marks. Dietary factors such as folate, methionine, choline, and vitamin B12, are known as methyl donors and cofactors involved in SAM-substrated methylation and their epigenetic effects have been implied in human health (McKay and Mathers, 2011). Waterland et al. first demonstrated that supplementation of the diets of female mice with methyl donors before and after pregnancy permanently increased DNA methylation at Avy in their offspring (Waterland and Jirtle, 2003). Aging leads to progressive epigenetic silencing of the entire Hnf4a locus in islets in rats exposed to a poor maternal diet (Sandovici et al., 2011). Several population studies have also demonstrated a strong correlation between folate status and coronary artery disease. Patients with atherosclerotic vascular disease often exhibit higher homocysteine and S-adenosylhomocysteine (SAHC) levels and a lower genomic DNA methylation status (Castro et al., 2003).

Additionally, unhealthy lifestyles that involve consuming high-fat diets, alcohol, or cigarette use are highly associated with chronic diseases and are now believed to induce epigenetic changes in the genome. High-fat diets during pregnancy or in adults are associated with obesity (Milagro et al., 2009; Vucetic et al., 2010) and a higher incidence of mammary cancer (Yenbutr, Hilakivi-Clarke, and Passaniti, 1998) with changes in the epigenome. Alcohol consumption causes cellular injury in the liver, kidney, colon, and brain by altering epigenetic modifications, particularly hyper- and hypomethylation of DNA (Biermann et al., 2009; Schouten et al., 2008) as well as the acetylation and methylation of histones (Wang et al., 2010). Epigenetic changes induced by cigarette smoking are now widely investigated in several human diseases including asthma, chronic obstructive pulmonary disease (COPD), lung, and bladder cancers (Adcock et al., 2007; Georgiou et al., 2007). Huang Y. et al. has recently reported a direct link of cigarette smoking and DNA methylation in human immortalized, non-tumorigenic esophageal epithelial cell lines (Huang et al., 2011). The promoter of sequence-specific single-stranded DNA-binding protein 2 (SSBP2) was methylated in tumor tissues from esophageal squamous cell carcinoma patients. Collectively, these findings offer valuable insights into the pathophysiology of diseases associated with nutritional epigenetics. This knowledge may help in designing prevention strategies by modifying the nutritional status/lifestyles of at-risk populations.

2.3 Implications of environmental epigenetics and future prospects

Tracking epigenetic changes may help to understand disease etiology. With an advance of ‘omic’ profiling techniques and bioinformatics database search, epigenetic marks can be discovered at every stage of cell development or in response to any environmental exposure. Identification of the ‘modified’ genome/epigenome will give an insight into the ‘resetting’ and ‘programming’ in disease development. Epigenetic modulators of DNA methylation and histone modifying enzymes (Kaminskas et al., 2005; Zelent et al., 2005) have already been introduced and approved for epigenetic therapies. Knockdown or over-expression of particular miRNAs will be another very attractive target for the development and implementation of new therapeutic approaches to treat diseases such as cancer (Kota et al., 2009). All in all, the reversible nature of epigenetic reprogramming has led to the development of epigenome modulators in cancer therapy. Combinational therapy of epigenome modulators and chemotherapy/radiotherapy on cancer or other complex diseases must be further validated.

Establishment of epigenetic marks can provide a new generation of biomarkers for disease diagnosis. Taking prostate cancer (PCa) as an example, aberrant DNA methylation marks or differential miRNA expression were