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 DOI: 10.1177/1091581813488063

2013 32: 314International Journal of ToxicologyRochelle W. Tyl

Book Review: Toxicology and Epigenetics  

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Book Reviews

Book Reviews

Saura C. Sahu, EditorToxicology and Epigenetics. West Sussex, UK: John Wiley & SonsLimited, 2012. 658 pp. $200.00 USD. ISBN: 978-1-119-97609-7 (cloth)

Reviewed by: Rochelle W. Tyl, Developmental and ReproductiveToxicology, Research Triangle Institute (RTI International), ResearchTriangle Park, NC, USA.DOI: 10.1177/1091581813488063

This is an extraordinary international book with 33 chapters

contributed by 84 researchers from the United States, Canada,

India, Switzerland, Japan, Czech Republic, and Singapore,

from universities, medical schools, governmental agencies

(US Food and Drug Administration), research institutes, com-

mercial entities (Novartis Institutes for Biomedical Research

and Amgen), academies of science, and foundations. It is edited

by Dr Saura C. Sahu from the Division of Toxicology, Center

for Food Safety and Applied Nutrition, Food and Drug Admin-

istration, Laurel, Maryland, USA.

In the preface, Dr Sahu boldly states that the new epige-

netics revolution has transformed toxicology, ‘‘an old disci-

pline of science’’ and that this book ‘‘builds a bridge between

toxicology and epigenetics’’ at the forefront of this research

area. This book is a collaborative effort by international experts

to present ‘‘up-to-date, state-of-the-art’’ information on ‘‘toxico-

epigenetics’’ for scientists in this field as well as toxicologists,

geneticists, medical practitioners, pharmacologists, drug and

food scientists, and ‘‘federal regulators and safety assessors

of drugs, food, environmental, and consumer products.’’

This is the first edition of a book essentially introducing

toxico-epigenomics to (likely) graduate students and research-

ers and experts in other branches of toxicology, so a brief

introduction is warranted. As Dr Sahu indicates ‘‘Genetics is

defined as the study of heritable changes in gene expression,

caused by modifications in the base sequence of the gene

itself.’’ But ‘‘genetics, environmental factors, and xenobiotics

(all) contribute to toxicology and human disease.’’ Toxicoge-

nomics integrates ‘‘traditional’’ toxicology and genomics,

which results in consequences from the changes in genomic

DNA. However, heritable gene expression is altered by modi-

fications to DNA, which do not directly alter the genomic DNA

base sequence itself; that is, epigenetics. These heritable

epigenetic modifications include DNA methylation/demethyla-

tion, histone modifications, and noncoding small RNAs, that is,

toxico-epigenomics. This is not a book for neophytes but for

‘‘investigators . . . actively engaged in this rapidly developing

emerging new field of research’’ (chapter 1, Introduction).

The 33 chapters are eclectic and variable, focused or gen-

eral, short or long, detailed, dense, and well referenced, with

varying success, definitions, known mechanisms, such as life-

time epigenetic changes, transgenerational inheritance, epige-

netic reprogramming, and elucidation of the known (or

suspected or proposed) mechanisms of action of metals, che-

micals such as diethylstilbestrol, bisphenol A, and/or carcino-

genic metals. The mechanisms of DNA/cell transformation are

not fully understood but likely include DNA adducts, DNA

damage, oxidative stress, hormonal imbalance, altered cell

growth, and disruption of cell/tissue/organ function (chapter

2). Other chapters cover DNA methylation and toxicogenomics

(chapter 3), epigenetic marks on chromatin, with roles in diag-

nosis, treatment, therapy, and involving great complexity and

flexibility (chapter 4), molecular epigenetic changes caused by

environmental pollutants (chapter 5), epigenetic mediation of

environmental exposures to polycyclic aromatic hydrocarbons

(PAH; chapter 6), epigenetic changes from arsenic and arseni-

cals (chapters 7, 8, and 17), environmental epigenetics and

asthma and allergy (chapter 9), microRNAs (miRNAs) in pros-

tate cancer (chapter 10), epigenetics in cardiovascular health

(chapter 11), epigenetics in autoimmunity (chapter 12), epige-

netics in lupus (chapter 13), ocular epigenomics (chapter 14),

nuclear RNA silencing (chapter 15), epigenetic biomarkers in

cancer detection and diagnosis (chapter 16), DES and

endocrine-disrupting chemicals (chapter 18), epigenomics and

drug safety (chapter 19), archival toxico-epigenetics (chapter

20), nanoparticles and toxico-epigenomics (chapter 21), global

epigenomic profiling (chapter 22), transcriptomics (chapter

23), histone tail modifications (chapter 24), epigenetic effects

after radiation exposure (chapter 25), developmentally regulated

gene expression (chapter 26), chromatin insulators (chapter

27), bioinformatics for high-throughput studies (chapter 28),

computational methods in toxico-epigenomics (chapter 29),

databases (chapter 30), epigenetics and carcinogenic risk

assessment (chapter 31), epigenetic modification in chemical

carcinogenesis (chapter 32), and application of cancer toxico-

epigenomics in identifying high-risk populations (chapter 33).

Comments by individual chapter are as follows.

Chapter 1 by S. C. Sahu, as mentioned earlier, is an excellent

introduction to toxico-epigenomics. Chapter 2 by Y. A. S.

Cheng and W-y Tang on environment, epigenetics, and disease

provides a definition of epigenetics and mechanisms of action

and then focuses on environmental epigenetics and human

disease from exposure to metals (chromium, cadmium, arsenic,

nickel, lead, mercury), diethylstilbestrol (DES), bisphenol A

(BPA), 2, 3, 7, 8-tetrachlorodobenzo-pdioxin, phthalate esters,

polychlorinated biphenyls, disinfection byproducts, PAHs, and

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diet or living style. Finally, the authors discuss implications

and future prospects for environmental epigenetics and present

key questions to be answered (excellent idea and excellent

question choices!).Chapter 3 by D. Deobagkar, entitled DNA Methylation and

Toxicogenomics is difficult to read in places and has gramma-

tical errors that may be from those with written English

language difficulties, but the content is still understandable and

important. Dr Deobagkar makes the case for the use of toxico-

genomics in identifying and elucidating adverse biological

effects from environmental stressors, toxins, drugs, and other

chemicals and the use of functional genomics, which directly

measures phenotype, to provide a direct link between a specific

gene and its expression and modification by exposures. One

comment on chapter 3 content, in the discussion of dose and

exposure (section 3.2 Toxicology), Dr Deobagkar does not

include the necessity for providing the specifics of sex, age

(stage of development), of the exposed organism, the timing,

and the duration of the exposure or even the route of exposure.

A toxicologist would be disappointed and surprised.

Chapter 4 by D. Quenet et al discusses epigenetic marks on

chromatin with extensive detail in section 4.1.1 on DNA

methylation, including a very complex figure 4.2 (section

4.1.2) on posttranslational histone modifications; figure 4.6 is

also very detailed and complex.

Chapter 5 by S.S. Lewis et al on molecular epigenetic

changes caused by environmental pollution was very good,

with an excellent figure (figure 5.1), tracking environmental

exposure to altered gene expression and chromatin remodel-

ing, to epigenetic changes, to the physiological and to genetic

consequences of these epigenetic changes. A number of che-

micals are evaluated, including BPA, DDT, dioxin, 17alpha-

ethinylestradiol, hexabromocyclododecane, methoxychlor,

organochlorine pesticide mixtures, polybrominated diphenyl

ethers, phthalates, vinclozolin, and metals, including cadmium,

chromium, lead, methyl mercury, nickel, tungsten alloy, and

zinc (note redundancy with chapter 2).

Chapter 6, by B. Sadikovic and D.I. Rodenhiser, examines

epigenetic effects of PAHs (see also chapter 2).

Chapter 7 on epigenetic/epigenomic effects of environmen-

tal arsenicals, by P. L Severson and B. W. Futscher, focused on

urothelial effects. Arsenic-induced changes to the epigenome

by K. A. Bailey and R. C. Fry (chapter 8) focused on DNA

methylation patterns. Both chapters were excellent, clear, thor-

ough, and enlightening.

Chapter 17 also focused on arsenic but on the histone

changes. If the book was meant to be an overview, 3 chapters

on arsenic appear to be a bit excessive, although each focused

on a different aspect, and there is a large amount of information

available on arsenic poisoning.

Chapters 9 to 13 focus on human epigenetics/epigenomics

and asthma and allergy (chapter 9 by S. Lovinsky-Desir and R.

L. Miller), prostate cancer (chapter 10, by E. K. Amankwah and

J. K. Park), cardiovascular health (chapter 11 by S. Ghosh

and A. Baccarelli), autoimmunity (chapter 12 by C. A. Cooney

and K. M. Gilbert), and lupus (chapter 13, by D. Ray and B. C.

Richardson). The clinical importance of epigenetics/epige-

nomics for diagnosis, tracking of outcomes of treatments, and

long-term outcome for all of these adverse effects is striking.

This body of work documents the movement of this new

scientific area from fascinating theoretical construct to patient

treatment regimens.

Chapter 14 (by K. P. Mitton) focuses on ocular epigenomics

as potential sites of environmental impact on development and

disease, using disruption of DNA methylation and inhibition of

histone acetylation in zebrafish eye development.

Chapter 15 (by R. Malik and P. Svoboda) discusses nuclear

RNA silencing and related phenomena in animals. The authors

begin by describing RNA silencing; small RNAs (20-30

nucleotides long) function as specific guides for ribonuclopro-

tein complexes to silence transcription and thereby translation.

The silencing mechanism has 3 basic steps (1) production of

these small RNAs that typically uses RNase III and/or RNA-

dependent RNA polymerase, (2) formation of an effector com-

plex, involving loading the small RNAs on argonaute (AGO)

proteins, and (3) sequence-specific target recognition and

induction of silencing. RNA silencing involves posttranscrip-

tional mechanisms such as RNA interference (RNAi) or

miRNA pathways at the level of transcriptional repression.

Genes that regulate chromatin structure are directly or indirectly

regulated by miRNAs. The miRNAs also mediate transcrip-

tional regulation (activation or repression). These processes

are well documented and understood in Arabidopsis and

Shizosaccharomyces and are well described in this chapter,

but the role of miRNA in mammals still remains enigmatic.

Chapter 16 (by A. G. Rivenbark and W. B. Coleman) dis-

cusses epigenetic markers (DNA methylation) in detection and

diagnosis of various cancers in humans. Chapter 17 (by J. F.

Reichard and A. Puga), already mentioned, discusses the

epigenetic histone changes in the toxicologic mode (not yet

mechanism) of action of arsenic.

Chapter 18, by S. Miyagawa et al, discusses the irreversible

effects of DES on reproductive organs and the argument for

epigenetic effects of endocrine disrupting chemicals. They also

discuss the challenges in integrating epigenetic analysis into

‘‘traditional’’ toxicity testing.

In a shift of focus, chapter 19, by H. Kempiannan, et al.,

entitled Epigenomics-Impact for Drug Safety Science, exam-

ines this relatively new area from the perspective of the

dynamic epigenome and perturbations of disease. The 3 tables

and 2 figures are excellent, informative, detailed, clear, and

thorough. The thrust and conclusion of this chapter is that

epigenomic profiling technologies have great potential for pro-

viding novel mechanistic insight and candidate biomarkers for

drug efficacy and safety assessment during both preclinical and

clinical phases of drug development.

Chapter 20 (by B. A. Merrick) examines the molecular anal-

ysis of modified DNA from preserved tissues in toxicology

studies, although fixed tissues have not been viewed as partic-

ularly useful for biochemical or molecular analysis(the prefer-

ence has been to use frozen tissues for retrospective molecular

analyses). The improvements in extraction of intact DNA,

Book Reviews 315

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RNA, miRNA, and protein from paraffinized tissues and use of

amplification technologies have enabled use of fixed tissue

archives to detect epigenetic modifications (‘‘toxicomethylo-

mics’’). This chapter mainly discusses the processes to extract

DNA, RNA, and protein and methods of analysis, a very

different chapter from the others.

Nanoparticles and toxicoepigenomics are the topics of chap-

ter 21 (by M. P. Jain et al). These nanoparticles include natu-

rally occurring nanoparticles, anthropogenic (man-made)

ultrafine particles, and synthetic-engineered nanoparticles.

These particles are ubiquitous in the environment and have

always been resulting in widespread exposure and ‘‘potential

ecotoxicological effects.’’ The chapter discusses nanoparticles

with respect to their presence in the environment and their

subsequent biological and pathological consequences. Nano-

particles in soil, water, and air, medicine, biomedial research,

and toxicology (nanotoxicology) can affect humans and experi-

mental animals (as well as other organisms), thereby compli-

cating nanotoxicological studies, from molecular mechanisms

of nanoparticle toxicity and cellular (intracellular) defense

mechanisms. Induction of reactive oxygen species and there-

fore oxidative stress by nanoparticles occurs early in the expo-

sure and can instigate normal protective cellular effects (the

first tier); in the second tier, oxidative stress overwhelms the

cellular antioxidant system, and the resulting oxidative injury

can result in activation of proinflammatory transcription

factors early in inflammation. In the third tier, oxidative stress

is so great that cytotoxicity and cell death occur. A fascinating

chapter!Chapter 22 (by M. W. Y. Chan et al) examines modulation

of developmentally regulated gene expression through target-

ing of polycomb and bithorax group proteins in Drosophila.

This is a very different chapter using the fruit fly (the ‘‘work-

horse’’ of genetics) and the recognition that all cell types (in the

fruit fly and everything else) may have (must have) originated

from the initial identical primary DNA sequence but gives rise

to cell-specific gene expression programs and differentiated

cells. These cell-specific patterns of gene expression are estab-

lished through hormone-, growth factor-, and cytokine-initiated

signaling cascades transduced through transcription factors to

regulate the expression of specific subsets of genes within the

genome, within specific times, and spaces. These changes are

transmitted to daughter cells, so cellular memory is maintained

epigenetically through specific chromatin modifications. The

authors suggest that targeting the polycomb and bithorax genes

and their protein products and developing specific inhibitors to

modulate these proteins in (first normal and then) diseased cells

will enable therapeutic intervention (excellent chapter!).Chapter 23 (by P. Joseph) discusses transcriptomics and its

applications in epigenetic toxicology. He notes that if the intent

is to determine the expression of a single gene or a limited

number of genes in a biological sample, then use quantitative

reverse transcriptase–polymerase chain reaction analysis; how-

ever, if the objective is to determine the expression of ‘‘several

hundreds or thousands or all of the genes’’ expressed in a

biological sample, then the microarray analysis is the method

of choice. The chapter continues with descriptions of the

microarray analysis process, study designs, isolation of the

RNA, synthesis of the complementary DNA, target synthesis,

hybridization, washing, image acquisition, data generation and

analysis, and so on. This chapter is a clear, thorough description

of the process, results, various analyses, interpretations, and the

translation of transcriptomics data from experimental animals

to humans.

Chapter 24 (by Y. Chervona and M. Costa) discusses metal

carcinogenesis and makes a strong case for the carcinogenic

metals, such as arsenic, nickel, hexavalent chromium, and

cadmium, acting epigenetically by altering ‘‘normal’’ histone

tail modifications.

Chapter 25 (by Y. Hirabayashi and T. Inoue) discusses

prediction of epigenetic and stochastic gene expression profiles

of late effects after radiation exposure, initially by comparing

pathological profiling (diagnostic endpoint) and toxicological

profiling (probabilistic endpoint). This is a very complex and

detailed chapter.

Chapter 26 (by M. Brand and F. J. Dilworth) returns to

polycomb and trithorax (see chapter 22 on polycomb and

bithorax) and examines modulations of developmentally regu-

lated gene expression programs through targeting of the pro-

teins from this gene group. There is some overlap between this

chapter and chapter 22. This chapter, by Brand and Dilworth, is

a detailed meticulous description of the development of cell-

specific gene expression programs from primary DNA

sequences, regulated temporally and spatially by hormone-,

growth factor-, and cytokine-initiated signaling cascades that

are transduced through transcription factors to regulate specific

subsets of genes within the genome. These cell-specific gene

programs are also transmitted to daughter cells during pro-

liferation by cellular memory. This cellular memory is main-

tained epigenetically through specific chromatin modifications.

This chapter provides detailed and specific mechanisms for

enhancement and/or suppression of developmentally important

genes in Drosophila (such as Zeste and EED [extra sex comb])

through polycomb group proteins (table 26.1) and trithorax

group proteins (table 26.2). The authors also make the case

that, since the polycomb and trithorax proteins are defined by

mutations in Drosophila, which give rise to homeotic transfor-

mations, it is not surprising that somatic mutations in the genes

that code for these proteins are implicated in a number of dis-

eases in humans such as leukemia, solid cancers such as lym-

phomas, and myelodysplastic syndromes.

Chapter 27 (by J. Yang and V. G. Corces) on chromatin

insulators and epigenetic inheritance in health and disease

describes chromatin insulators as DNA-bound protein

complexes, originally discovered in Drosophila and later in

vertebrates, which can mediate intra- and inter-chromosome

interactions; they act by bringing together regulatory

sequences, originally located at great distances from each

other, and/or on separate chromosomes, to locations very close

together, and thereby affecting the expression of adjacent

genes. This can result in activation or repression of single gene

or large chromosome domains. The insulators ‘‘can alter’’ the

316 International Journal of Toxicology 32(4)

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status of the chromatin in these genes or domains and thereby

also modify patterns of epigenetic inheritance. These insulator-

mediated interactions are viewed as contributing to the estab-

lishment of the ‘‘3-dimensional organization’’ of the nuclear

DNA. Since this structure is directly related to gene expression,

the authors argue that ‘‘the organization of the genome in the

nucleus is in part a determinant and in part a consequence of the

transcriptional status of a cell.’’ Insulator function is itself

regulated by enhancing or preventing the establishment of a

functional loop between the 2 genetic sites (one termed an

enhancer and the other termed a promotor). This process is

affected by hormones, can regulate viral genomes, and defects

in its function will ‘‘likely’’ lead to abnormalities in gene

expression and disease, including neurological/neurodegenera-

tive disorders and cancer. A fascinating chapter!Chapter 28 (by M. A. Sartor et al) focuses on bioinformatics

for high-throughput toxico-epigenomics studies, with excellent

initial commentary on environmental genomics, genomic

imprinting, and a cogent evolutionary perspective.

Chapter 29 (by J. C. Tong) describes computational methods

in toxico-epigenomics. Chapter 30 (by U. Mashankar and

S. Gurunathan) describes databases and tools for computational

epigenomics. Chapter 31 (by P. Nioi) describes the interface of

epigenetics and carcinogenic risk assessment by reviewing case

studies of epigenetic changes, specifically DNA methylation,

reported in chemically induced cancers in humans and rodents

by agents with well-defined mechanisms and pathways. Chapter

32 (by I. P. Porgrbny et al) is a synergistic chapter (with chapter

31) on epigenetic modifications in chemical carcinogenesis.

Chapter 33 (by M. Verna and K. Banaudha), the last

brief chapter, introduces the application of cancer toxico-

epigenomics in identifying high-risk population. The authors

cogently argue that epigenetic marks are tissue specific and

that ‘‘aberrant DNA methylation is a hallmark of cancer.’’

Minor comments by this reviewer include the chapters are

very variable in size (small to huge) and scope (some are ‘‘how

to’’ while others are more broad, explanatory, and encompass-

ing). Not all areas of epigenetics/epigenomics are discussed,

while other areas are discussed in more than 1 chapter. There

are also numerous grammatical errors likely from the interna-

tional authors all writing in English. In addition, some

abbreviations are not defined when first used or ever (e.g.,

‘‘APL’’ on page 137, ‘‘DC’’ on page 199, etc.), and some

figures are very (too) complex and/or poorly explained.

After reading this book, this reviewer came cross an article

by MemczaK et al1 in Nature, March 21, 2013, introducing

circular RNA species in plants and animals, which act as post-

translational regulators. They are well-expressed, stable

transcripts with robust expression, which function as miRNA’s

sponges (letter from Hansen et al2); they are circularized using

splice genes. These circular RNAs can counteract the function

of regulatory miRNAs and counteract the actions of competing

endogenous RNAs. These circular RNAs can act as miRNA

mimics, competing with other RNAs for bonding with the

RNA-binding proteins or to miRNAs. The miRNAs are

approximately 21 nucleotides long, noncoding RNAs that

guide the effector protein AGO to messenger RNAs (mRNAs)

of coding genes to repress their protein synthesis. In humans,

miRNAs directly regulate expression of most mRNAs in a

large range of biological functions. This newly discovered

regulatory RNA adds another complex aspect to the RNA

world (in News & Views from K.S. Kosik3).

In the end, what is clearly emerging, based on this book (and

other articles), is the varied and complex ways a given fixed

genome in a given species is manipulated to result in very

different outcomes at different times under different circum-

stances, including the first moves toward a new and different

species, by various ingenious mechanisms.

All-in-all, this is an ambitious book covering a number of

important aspects of a very new and very exciting area in

toxicology, epigenetics, and epigenomics. I highly recommend

it (warts and all) and look forward to the second edition.

References

1. Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large

class of animal RNAs with regulatory potency. Nature. 2013;

495(7441):333-338.

2. Hansen TB, Jensen TI, Clausen BH, et al. RNA circles function as

efficient microRNA sponges. Nature. 2013;495(7441):384-388.

3. Kosik KS. Circles reshape the RNA world. Nature. 2013;

495(7441):322-324.

Kalipatnapu N. RaoForensic Toxicology—Medico-Legal Case Studies. Boca Raton, FL: CRCPress, 2012. 261 pp. $99.95. ISBN: 978-1-4398-1 (Hardback)

Reviewed by: John A. Budny, PharmaCal, Ltd, Westlake Village, CA91362, USADOI: 10.1177/1091581813492948

Forensic toxicology, in the broadest sense, is the application of

toxicology to support the implementation of laws. There are

certain criminal and civil adjudications that would not be pos-

sible or not be remotely or partially correct without the contri-

butions of a sage toxicologist. In fact, some criminal and civil

investigations, as a prelude to a trial, would not be productive

without contributions from forensic toxicology. It is, therefore,

reasonable to collect and report or publish historical legal mat-

ters that were resolved or at least resulted in a more enlightened

outcome, with the help of forensic toxicology so that the legal

community can understand the contributions that toxicology

can and does make to forensics. It is that purpose for which

Forensic Toxicology—Medico-Legal Case Studies was written.

Book Reviews 317

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