Toxicology and Epigenetics

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.

Dr. Saura C. Sahu, Research Chemist, Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration.
Dr. Sahu is the US Editor for the Journal of Applied Toxicology and the editor of Hepatotoxicity (Wiley, 2007), Toxicogenomics (Wiley, 2008), Nanotoxicity (Wiley, 2009), and Handbook of Systems Toxicology (Wiley, 2011).

Preface xxi

Acknowledgment xxiii

List of Contributors xxv

1 Introduction 1

Saura C. Sahu

References 2

2 Environment, Epigenetics, and Diseases 5

Robert Y.S. Cheng and Wan-yee Tang

2.1 Perceptions of epigenetics 5

2.2 Environmental epigenetics and human diseases 8

2.3 Implications of environmental epigenetics and future prospects 16

2.4 Key questions to be answered 17

Acknowledgments 17

References 17

3 DNA Methylation and Toxicogenomics 25

Deepti Deobagkar and Dileep Deobagkar

3.1 Introduction 25

3.2 Toxicology 26

3.3 Toxicogenomics 27

3.4 Epigenetics 29

3.5 DNA methylation 30

3.6 DNA methyltransferases 34

3.7 Techniques of methylation detection 34

3.8 Toxicogenomics and epigenetics 40

3.9 Hydroxymethyl cytosine and toxicogenomics 42

3.10 MicroRNAs 42

3.11 DNA methylation in cancer 42

3.12 Bioinformatics approach 44

3.13 Summary 45

Acknowledgements 46

References 46

4 Chromatin at the Intersection of Disease and Therapy 51

Delphine Qu

4.1 Epigenetic marks on chromatin: a complex pathway with high flexibility 51

4.3 Epigenetic modifications and potential therapy in other diseases 60

4.4 Conclusion 66

References 66

5 Molecular Epigenetic Changes Caused by Environmental Pollutants 73

Solange S. Lewis, Gregory J. Weber, Jennifer L. Freeman, and Maria S. Sepulveda

5.1 Introduction 73

5.2 DNA methylation 75

5.3 Histone modifications 75

5.4 Small non-coding RNAs 76

5.5 Epigenetic assays 76

5.6 Bisphenol A (BPA) 78

5.7 Dichlorodiphenyltrichloroethane (DDT) 83

5.8 Dioxin (TCDD or 2,3,7,8-tetrachlorodibenzo-p-dioxin) 84

5.9 17

5.10 Hexabromocyclododecane (HBCD) 85

5.11 Methoxychlor 86

5.12 Mixture of polychlorinated biphenyls, methyl mercury, and organochlorine pesticides 87

5.13 Polybrominated diphenyl ethers (PBDEs) 88

5.14 Phthalate (di-2-ethylhexyl phthalate or DEHP) 88

5.15 Vinclozolin 88

5.16 Epigenetic changes induced by metals 90

5.17 Concluding remarks 101

References 102

6 Epigenetic Mediation of Environmental Exposures to Polycyclic Aromatic Hydrocarbons 111

Bekim Sadikovic and David I. Rodenhiser

6.1 Introduction 111

6.2 Epigenetic modifications: DNA methylation 112

6.3 DNA methylation and cancer 113

6.4 Epigenetic histone modifications 114

6.5 Benzo(a)pyrene–a prototype PAH and environmental carcinogen 115

6.6 Molecular mechanisms of benzopyrene carcinogenicity: geno- and epigeno-toxicity 115

6.7 Epigenetic effects of multiple/synergistic carcinogen exposures 120

6.8 Summary and future considerations 122

Acknowledgements 123

References 123

7 Epigenomic Actions of Environmental Arsenicals 129

Paul L. Severson and Bernard W. Futscher

7.1 Introduction 129

7.2 Arsenicals in relation to human health 130

7.3 Arsenical mechanisms of action 131

7.4 Models to study arsenical action 133

7.5 Models used to study epigenetic action 134

7.6 Epigenetic effects of arsenicals 135

7.7 Perspectives 140

References 141

8 Arsenic-Induced Changes to the Epigenome 149

Kathryn A. Bailey and Rebecca C. Fry

8.1 Introduction 149

8.2 Arsenic exposure and DNA methylation 152

8.3 DNA methylation changes associated with arsenic exposure 168

8.4 Histone modifications associated with arsenic exposure 178

8.5 MicroRNA (miRNA) alterations associated with arsenic exposure 181

8.6 Conclusions and future directions 182

Acknowledgments 183

References 183

9 Environmental Epigenetics, Asthma, and Allergy: Our Environment’s Molecular Footprints 191

Stephanie Lovinsky-Desir and Rachel L. Miller

9.1 Introduction 191

9.2 Asthma environmental toxicants associated with epigenetic regulation 193

9.3 Epigenetic changes and asthma phenotype 197

9.4 ‘Pharmacoepigenetics’ 200

9.5 Conclusion 200

References 201

10 miRNAs in Human Prostate Cancer 205

Ernest K. Amankwah and Jong Y. Park

10.1 Introduction 205

10.2 Biogenesis, function, and target of miRNA 206

10.3 miRNA and human cancer 208

10.4 miRNAs as oncogenes and tumor suppressors 209

10.5 Expression profile of miRNA in prostate cancer 210

10.6 miRNA as therapeutic targets for prostate cancer 213

10.7 Conclusion and future directions 213

References 213

11 Environment, Epigenetics, and Cardiovascular Health 219

Sanjukta Ghosh and Andrea Baccarelli

11.1 Introduction 219

11.2 Epidemiological evidence of environmental factors affecting

cardiovascular health 220

11.3 Cause and effect relation between environmental exposure

and cardiovascular diseases 222

11.4 Cardiovascular epigenetic signatures as risk factors and biomarkers for environmental exposure 232

11.5 Conclusion 233

References 233

12 Toxicology, Epigenetics, and Autoimmunity 241

Craig A. Cooney and Kathleen M. Gilbert

12.1 Introduction 241

12.2 Drugs and toxicants in epigenetics 243

12.3 Metabolic requirements for epigenetics 244

12.4 Autoimmunity and epigenetics 245

12.5 Conclusion 251

References 252

13 Toxicoepigenomics in Lupus 261

Donna Ray and Bruce Richardson

13.1 Introduction 261

13.2 Etiology of lupus 262

13.3 Epigenetics and lupus 264

13.4 Environmental contributions to lupus 267

13.5 Summary 270

References 270

14 Ocular Epigenomics: Potential Sites of Environmental Impact in Development and

Disease 275

Kenneth P. Mitton

14.1 Introduction 275

14.2 Gene expression in ocular development 277

14.3 Epigenetic regulation in ocular development 280

14.4 DNA-methylation changes in ocular disease 283

14.5 Inherited and age-related diseases of the eye 286

14.5.1 Genetic diseases 286

14.5.2 Diabetes: metabolic memory 287

14.5.3 Spinocerebellar ataxia type 7 (SCA7): histone acetylation 287

14.6 Pharmacological effects on retinal function 287

14.7 Future research 289

References 289

15 Nuclear RNA Silencing and Related Phenomena in Animals 297

Radek Malik and Petr Svoboda

15.1 Introduction 297

15.2 Conclusion 310

Acknowledgments 310

References 310

16 Epigenetic Biomarkers in Cancer Detection and Diagnosis 317

Ashley G. Rivenbark and William B. Coleman

16.1 DNA methylation 317

16.2 Epigenetics of cancer 319

16.3 Epigenetic biomarkers for cancer diagnostics: DNA methylation 320

16.4 Application of aberrant DNA methylation to cancer diagnostics 323

16.5 Epigenetic biomarkers in breast cancer 323

16.6 Epigenetic biomarkers in prostate cancer 324

16.7 Epigenetic biomarkers in lung cancer 325

16.8 Epigenetic biomarkers in colorectal cancer 326

16.9 Epigenetic biomarkers in liver cancer 328

16.10 Cancer detection and diagnosis 330

References 332

17 Epigenetic Histone Changes in the Toxicologic Mode of Action of Arsenic 339

John F. Reichard and Alvaro Puga

17.1 Introduction 339

17.2 Epigenetics and cancer 340

17.3 Epigenetics effects of arsenic 341

17.4 Conclusions 348

References 350

18 Irreversible Effects of Diethylstilbestrol on Reproductive Organs and a Current

Approach for Epigenetic Effects of Endocrine Disrupting Chemicals 357

Shinichi Miyagawa, Ryohei Yatsu, Tamotsu Sudo, Katsuhide Igarashi, Jun Kanno, and Taisen Iguchi

18.1 Introduction 357

18.2 Adverse effects of perinatally-exposed DES on the mouse vagina 358

18.3 MeDIP-ChIP 359

18.4 Future research needs 362

Acknowledgments 363

References 363

19 Epigenomics–Impact for Drug Safety Sciences 365

Harri Lempi Pierre Moulin, Philippe Couttet, Olivier Grenet, Jennifer Marlowe, Jonathan Moggs, and Rainen, Raphaelle Luisier, Arne Muller, Philippe Marc, David Heard, Federico Bolognani, emi Terranova

19.1 Introduction the dynamic epigenome and perturbations in disease 365

19.2 Relevance of epigenetics for toxicology 370

19.3 Toward identifying epigenetic biomarkers of drug-induced toxicity 371

19.4 Challenges of integrating epigenetic analysis into toxicity testing 373

19.5 Practical considerations 374

19.6 Bioinformatics and modeling of epigenomic data 376

19.7 Case study: identification of early mechanism and biomarkers for non-genotoxic carcinogenesis (NGC) 378

19.8 Conclusions 379

Acknowledgments 380

References 380

20 Archival Toxicoepigenetics: Molecular Analysis of Modified DNA from Preserved Tissues in Toxicology Studies 387

B. Alex Merrick

20.1 Introduction 387

20.2 Preservation of tissue: effects on protein and nucleic acids 388

20.3 Extraction of nucleic acids from fixed or embedded tissues 391

20.4 Analysis of methylated DNA for epigenetics 394

20.5 Survey of epigenetic studies using formalin preserved tissues 395

20.6 Prospects for toxicoepigenetics in preserved tissues 401

20.7 Conclusion 402

References 403

21 Nanoparticles and Toxicoepigenomics 409

Manasi P. Jain, Angela O. Choi, and Dusica Maysinger

21.1 Nanoparticles 409

21.2 Particles and the environment 410

21.3 Nanoparticles in soil 412

21.4 Nanoparticles in water 412

21.5 Nanoparticles and air 413

21.6 Nanoparticles in medicine 414

21.7 Nanotoxicology 414

21.8 Nanotoxicology in humans and experimental animals 414

21.9 Complications with nanotoxicological studies 416

21.10 Molecular mechanisms of nanoparticle toxicity and cellular defense mechanisms 417

21.11 Molecular mechanisms of nanoparticle-induced cytotoxicity 418

21.12 Nano-epigenomcs and epigenetics 419

21.13 Conclusion 421

References 422

22 Methods of Global Epigenomic Profiling 427

Michael W.Y. Chan, Zhengang Peng, Jennifer R. Chao, Yingwei Li, Matthew T. Zuzolo, and Huey-Jen L. Lin

22.1 Introduction 427

22.2 DNA methylation 428

22.3 Histone modifications and chromatin remodeling 435

22.4 Noncoding RNA 439

22.5 Summary and discussion 440

Acknowledgments 440

References 440

23 Transcriptomics: Applications in Epigenetic Toxicology 445

Pius Joseph

23.1 Introduction 445

23.2 Microarray analysis of gene expression profiles 446

23.3 Gene expression studies–challenges 453

23.4 Conclusions 456

Acknowledgments 456

Disclaimer 457

References 457

24 Carcinogenic Metals Alter Histone Tail Modifications 459

Yana Chervona and Max Costa

24.1 Introduction 459

24.2 Epigenetics and histone tail modifications 460

24.3 Arsenic 462

24.4 Nickel 463

24.5 Hexavalent chromium (Cr [VI]) 466

24.6 Cadmium 468

24.7 Summary 470

References 470

25 Prediction of Epigenetic and Stochastic Gene Expression Profiles of Late Effects after Radiation Exposure 475

Yoko Hirabayashi and Tohru Inoue

25.1 Introduction–pathological profiling (diagnostic endpoint) and toxicological profiling (probabilistic endpoint) 475

25.2 Radiation exposure and dosimetric quantum biology 477

25.3 Common gene expression profiles after subacute and prolonged effects after radiation exposure 478

25.4 Stochastic expression gene profiles after radiation exposure 483

25.5 Conclusions 492

Appendix A 494

Appendix B 495

Appendix C 495

References 509

26 Modulation of Developmentally Regulated Gene Expression Programs through Targeting of Polycomb and Trithorax Group Proteins 511

Marjorie Brand and F.J. Dilworth

26.1 Introduction 511

26.2 Polycomb group (PcG) proteins 512

26.3 Trithorax group genes 516

26.4 Model for the transcriptional regulation of developmentally regulated genes by PcG and TrxG 526

26.5 PcG and TrxG proteins in disease 527

26.6 Targeting PcG and TrxG proteins in disease 528

References 529

27 Chromatin Insulators and Epigenetic Inheritance in Health and Disease 539

Jingping Yang and Victor G. Corces

27.1 Introduction 539

27.2 Structure and organization of insulators 540

27.3 Insulators and chromatin architecture 543

27.4 Regulation of insulator function 552

27.5 Insulators and the external/internal cellular environment 555

27.6 Insulators and disease 557

27.7 Concluding remarks 560

Acknowledgments 561

References 561

28 Bioinformatics for High-Throughput Toxico-Epigenomics Studies 569

Maureen A. Sartor, Dana C. Dolinoy, Laura S. Rozek, and Gilbert S. Omenn

28.1 Introduction 569

28.2 Evaluating environmental influences on the epigenome 570

28.3 Establishment of the field of environmental epigenomics 570

28.4 An evolutionary perspective: the case of genomic imprinting 571

28.5 Transitioning from epigenetics to epigenomics and related bioinformatics 572

28.6 Observational studies in epigenomics 576

28.7 Integrative analyses with epigenomics data 577

28.8 Gene set enrichment and concept tools for pathway analyses 578

28.9 Databases and resources 580

28.10 Illustrative applications from environmental exposures/perturbations 581

28.11 University of Michigan NIEHS P30 center approach 583

28.12 Future directions 584

Acknowledgments 584

References 584

29 Computational Methods in Toxicoepigenomics 589

Joo Chuan Tong

29.1 Introduction 589

29.2 Data sources 589

29.3 Computational tools 591

29.4 Conclusion 592

References 592

30 Databases and Tools for Computational Epigenomics 595

V. Umashankar and S. Gurunathan

30.1 Introduction 595

30.2 Epigenetics and Computational Epigenetics 596

30.3 Epigenomics and Computational Epigenomics 596

30.4 Human Epigenome Project (HEP) 596

30.5 Epigenome Prediction Mechanism 597

30.6 Epigenomics Databases 599

30.7 Tools Employed in Computational Epigenomics 606

30.8 Sophisticated Algorithms 611

30.9 Conclusion 612

References 613

Website References 613

31 Interface of Epigenetics and Carcinogenic Risk Assessment 615

Paul Nioi

31.1 Introduction 615

31.2 Key epigenetic changes implicated in carcinogenesis 616

31.3 DNA methylation changes in chemical carcinogenesis 617

31.4 Methods of detecting alterations in the genomic methylome 623

31.5 Conclusions 624

References 627

32 Epigenetic Modifications in Chemical Carcinogenesis 631

Igor P. Pogribny, Igor Koturbash, and Frederick A. Beland

32.1 Introduction 631

32.2 Epigenetic alterations in cancer cells 632

32.3 Role of epigenetic alterations in chemical carcinogenesis 634

32.4 Future perspectives: epigenetic alterations and cancer risk assessment 638

References 638

33 Application of Cancer Toxicoepigenomics in Identifying High-Risk Populations 645

Mukesh Verma and Krishna K. Banaudha

33.1 Introduction: epigenetic mechanisms and cancer 645

33.2 Toxicity and cancer epigenetics 646

33.3 Advantages of using a cohort consortia approach to studying toxicoepigenomics in cancer 649

33.4 Data integration 650

33.5 Challenges and future directions 650

References 651

Index 653

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