Оглавление
Группа авторов. Genomic and Epigenomic Biomarkers of Toxicology and Disease
Genomic and Epigenomic Biomarkers of Toxicology and Disease. Clinical and Therapeutic Actions
Contents
List of Illustrations
List of Tables
Guide
Pages
Dedication
Preface
Acknowledgements
List of Contributors
1 Genomic and Epigenomic Biomarkers for Predictive Toxicity and Disease
Toxicity Testing in the Twenty-First Century
Biomarkers
Genomic Biomarkers
Epigenomic Biomarkers
MicroRNAs
Circular RNAs
The Need for a Book on Genomic and Epigenomic Biomarkers for Predictive Toxicity and Disease
References
2 MicroRNAs as Non-invasive Biomarkers of Toxicity and Chemical Hazard Genomic and Epigenomic Biomarkers of Toxicology and Disease
Introduction
Mechanisms that Contribute to Extracellular miRNA Release
Packaging into Vesicles and Mechanisms of Release
Biological Interpretations Due to Mechanisms of Release
MicroRNAs as Bioindicators of Toxicity and Disease
Application
Challenges and Future Focus
Conclusions
Acknowledgements
References
3 EV (Extracellular Vesicle)-associated miRNAs as Biomarkers of Toxicity
Introduction
The Classification of Extracellular Vesicles (EVs)
Components of Exosomes (EVs) RNAs
Proteins
Physiological and Cellular Functions of EVs
Cancer Biomarkers
Toxicology Biomarkers
Isolation and Characterization of EVs from Mouse Blood
Carbon Tetrachloride (CCl4) Administration and Histology
Identification of Differentially Expressed miRNAs by RNA-Seq
Conclusion
Acknowledgments
Competing Interests
Funding
References
4 Circulating miRNAs as Biomarkers of Toxic Heavy Metal Exposure
Metals and the Focus of This Chapter
Exposure to Metals
Biomarkers
Biomarkers of Heavy Metal Exposure
miRNA Biogenesis
Circulating miRNAs as Biomarkers for Disease
Circulating miRNAs Associated with Arsenic Exposure
Circulating miRNAs Associated with Lead Exposure
Circulating miRNAs Associated with Mercury Exposure
Circulating miRNAs Associated with Cadmium Exposure
Circulating miRNAs Associated with Chromium Exposure
Circulating miRNAs Associated with Mixed Metals Exposure
Summary of Potential Circulating miRNA Biomarkers for Heavy Metals
Future Avenues of Research
Techniques and Challenges for Identifying Circulating miRNAs
Acknowledgement
References
5 MicroRNA Biomarkers of Malignant Mesothelioma
Methods for Detecting the Expression of miRNAs
Early Screening for Malignant Mesothelioma
Diagnosis of Malignant Mesothelioma
Differential Expression of miRNAs in Cancer Tissues
Differential Expression of MicroRNAs in Serum and Plasma
Differential Expression of miRNAs in Pleural Effusion
MicroRNAs Associated with Malignant Mesothelioma Tissue Subtypes
Differential Diagnosis
MicroRNAs Related to the Occurrence and Development of Mesothelioma
MicroRNAs Related to Cell Cycle Regulation
MicroRNAs Related to Proliferation and Clone Formation
MicroRNAs Associated with Migration and Invasion
Apoptosis-related miRNAs
Inhibition of miRNAs Associated with Explant Tumor
Exosomal miRNA as a Target for Malignant Mesothelioma
MicroRNAs Related to Prognosis of Malignant Mesothelioma
References
6 Role of Non-coding RNAs in Innate Immune Responses Perturbed by Environmental Arsenic Exposure
Introduction
The Innate Immune System
Negative Impacts of Arsenic on Human Health
Negative Impacts of Arsenic on the Immune Function
The Zebrafish Model for Toxicological Responses to Arsenic
The Zebrafish Model of Innate Immune Responses
Role of Non-coding RNAS in Innate Immunity. Overview of Non-coding RNAs
MiRNAs Regulate Response to Injury and Infection Involving Multiple Cell Types
MiRNAs Regulate Macrophage Function
MiRNAs Regulate Neutrophil Function
The Expression of Non-coding RNAs Altered by Arsenic
Discussion
Gene-by-Environment Interactions
Functional Studies of Non-coding RNAs Using the Zebrafish Model
Future Studies on Gene-by-Environment Interactions
Acknowledgments
References
7 Transcriptomics Applications in Toxicology and Medicine
Introduction
Transcriptomics: Technical Aspects
Superior Sensitivity of Gene Expression Changes to Detect Target Organ Toxicity
Silica Exposure and Toxicity
In Vitro Cell Culture Studies
In Vivo Animal Studies
Lung Response to Crystalline Silica Exposure in Rats
Lung Gene Expression Changes in Response to Crystalline Silica Exposure
Blood Gene Expression Changes in Response to Crystalline Silica Exposure
Blood Gene Expression Signature to Predict/Detect Silica Exposure/Lung Toxicity
Molecular Mechanisms of Lung Response to Silica Exposure
Crystalline Silica and Lung Fibrosis
Transcriptomics and Alzeimer’s Disease
References
8 Network Biology for Biomarker Discovery and Therapy in Cancer
Introduction
Categories of Graphs in Biology
Molecular Networks and Their Role in Cancer Biomarker Discovery
Protein–Protein Interaction Network
Co-expression Network
Gene Transcriptional Regulatory Networks
Metabolic Network
Network Medicine and Drug Design
Conclusion
References
9 Epigenetic Biomarkers Link to Maternal Exposure and Offspring Health Outcomes
Introduction
Alterations in the Epigenetic Markers of Pregnancy or Birth Outcomes and Childhood Disease
Preeclampsia
Small for Gestational Age and Preterm Birth
Allergic Diseases
Metabolic Syndrome
Neurodevelopmental Disorders
Exposure to Prenatal Insults and Epigenetic Changes
Air Pollution and Smoking
Metals
Organic Pollutants
Maternal Diet
New Challenges and Future Directions
References
10 The Role of Dynamic Epigenetic Changes in Modulating Homeostasis after Exposure to Low-dose Environmental Chemicals
Introduction
Dynamic Epigenetic Changes after Environmental Exposure
DNA Methylation as a Potential Epigenetic Memory of Past Exposure Events
Histone Heterochromatin Markers and Their Modulators, Which Reshape the Epigenetic Landscape in Response to Past Exposure Events
The Epigenetic Regulation of Homeostasis. The Epigenetic Regulation of Metabolic Homeostasis
A Major Hypothesis in the Histone Acetylation Regulation of Metabolism
Histone Methylation-Regulated Metabolic Enzymes are Cell Type-Dependent
DNA Methylation Connects the Epigenome in the Nucleus and the Epigenome in Mitochondria
Epigenetic Regulation of Autophagy
Epigenetic Regulation of Calcium Signaling
Epigenetic Alterations Enriched in Homeostasis Pathways as a Potential Biomarker after Environmental Exposure
Conclusions
References
11 Emerging Non-invasive Molecular Biomarkers for Early Cancer Detection
Introduction
Conventional Methods of Early Cancer Diagnosis
Emerging Non-invasive Cancer Biomarkers. Diagnostic ctDNA Markers
MiRNAs as Biomarkers for Early Cancer Diagnosis
Exosomes as Cancer Biomarkers
Concluding Remarks
References
12 Aberrant DNA Methylation of Tumor Suppressor Genes and Oncogenes as Cancer Biomarkers
Introduction
Aberrant DNA Methylation of Tumor Suppressor Genes. P53
RASSF1A
Cadherin-1
Aberrant DNA Methylation of Oncogenes. Ras
ONECUT2
BORIS
Future Perspectives
References
13 SMYD Protein Family as Promising Biomarkers for Cancer Diagnosis and Prognosis
Introduction
SMYD Proteins as Cancer Biomarkers. Genetic Alterations as Biomarkers
Abnormal Expression as Biomarkers
SMYD Protein-mediated Lysine Methylation as a Cancer Biomarker. Functional Impacts of Protein Lysine Methylation
Histone Lysine Methylation as a Biomarker
Non-histone Lysine Methylation as a Biomarker
The RTK-RAS Signaling Pathway
Wnt Signaling Pathway
Cell Cycle Regulation
Concluding Remarks
References
14 Toward Precision Medicine Epigenetic Alterations in Human Melanoma
Introduction
Epigenetic Alterations in Melanoma
DNA Methylation
Histone Modifications
Non-coding RNAs as Epigenetic Regulators
Pathogenesis and Molecular Biology of Melanoma
Current Therapeutic Approaches
Therapeutic Implications of Epigenetic Changes in Melanoma
Conclusion
References
15 Currents Trends and Future Perspectives in Our Epigenetic Signatures What a Diet Can Trigger
How Epigenetics Influences Life: Short Overview
Diet-induced Epigenetic Alterations: Transgenerational Effects and Early Life Nutrition
Exposure to Chemicals through Food Chain
Nutritional Genomic Approaches in Cancers
Epigenetics and Prebiotics, Probiotics, and Postbiotics
Conclusion and Future Perspectives
References
16 Genetic and Epigenetic Biomarkers of Organophosphate Compounds, Dialkyl Phosphate Exposure, and Their Relation to Biological Effects
Introduction
Organophosphate Compounds
Dialkyl Phosphates
Toxicokinetics
OP Exposure
Regulations
OP Biomarkers
DAPs
Cholinesterases
Adducts
OP Toxic Effects
Genotoxicity of OP Compounds
Suggested Mechanisms. Clastogenicity
Aneuploidy
Biomarkers of Genotoxicity
Epigenetic Effects of OP Compounds
Suggested Mechanisms. DNA Methylation
Histone Modification
Adduct Formation
Potential Epigenetic Biomarkers
Concluding Remarks
References
17 Genetic, Epigenetic, and Anatomical Factors in Agenesis and Development of Female Reproductive Tract
Introduction
The Dysregulation of Genomic Factors in the Development of the Müllerian Duct Causes MRKH Syndrome
The Relationship of Epigenomic and Anatomical Factors with MRKH Syndrome
Estrogen Receptors in the Developing Uterus Are Irreversibly Involved in Uterine Function and Disease
Conclusion
Acknowledgment
References
18 Cause or Consequence Epigenomic DNA Methylation Changes in Arsenic-Mediated in Vitro Transformation of Human Prostate Cells
Introduction
Materials and Methods. Cells and Cell Culture
RNA-seq and Differential Expression
BisDNA-seq
Validation of Methylated Sequences by Roche454 Sequencing
Results. Gene Expression by RNA-seq
DNA Base-pair Methylation and Methylation Clusters
Proximity of Hg19 DMCs to the Gene Structure
Correlation of DNA Methylation and Gene Expression
Discussion
Acknowledgment
Disclaimer
References
19 Epigenetic Regulation of Sex Determination and Toxicity in Non-mammalian Vertebrates
Introduction
DNA Methylation
Histone Modifications
Non-coding RNAs
Sex Determinig Cascades in Mammals and Non-mammals
Cyp19a1
Dmrt1
Sex Determination and Reversal in Fish. Sex Determination in Chondricthyan Fish
Diverse Sex Determination Mechanisms in Teleost Fish
Modes of Sex Determination and Reversal among Teleost Species
Genetic Sex Determination
Environmental Sex Determination
Epigenetic Regulation of Sex Determination and Reversal in Gonochorists
Epigenetic Regulation of Sex Reversal in Sequential Hermaphrodites
Primordial Germ Cell Maintenance and Its Effect on Sex Determination
Epigenetic Regulation of Sex Determination in Amphibians and Reptiles. Sex Determination and Reversal in Amphibians
Sex Determination in Reptiles
Epigenetic Regulation of Sex Determination in Reptiles
Differential Methylation of Genomes by Incubation Temperatures
Epigenetic Regulation of Sex Determination in Alligators and Turtles
Comparison between GSD and TSD Species
Epigenetic Machinery and Sex Reversal in an Australian Lizard
Epigenetic Regulation of Sex Determination in Birds. Sex Determination and Gonadal Differentiation in Birds
Hypotheses Regarding Sex Determination in Birds
Sex Steroids and Avian Sex Differentiation
The Epigenetic Regulation of Avian Sex Determination
DNA Methylation and Histone Modifications
Regulation of Dmrt1 Expression by Non-coding RNAs
Possible Effects of Epigenetic Toxicants on Sex Determination of Non-mammalian Vertebrates. Epigenetic Toxicants and Their Implications for Non-mammalian Vertebrates
Case Studies
Possible Application of Non-mammalian Vertebrates as Biomarkers for Epigenetic Toxicants
Acknowledgment
References
20 Characterization of Genomic and Epigenomic Biomarkers of Nanoparticle Toxicity Using the Zebrafish Model System
Zebrafish: A Popular Experimental Animal Model
The Zebrafish Genome. Important Features of the Zebrafish Genome
Zebrafish and “-omics” Approaches
General Molecular Determinants and Genomic and Epigenomic Biomarkers of Nanoparticle Toxicity in Zebrafish
Genome and Genetic Biomarkers of Nanoparticle Toxicity Associated with Different Systems in Zebrafish
Neuronal Lineage Genetic Biomarkers of Nanoparticle Toxicity
Immune Lineage Genetic Biomarkers Associated with Nanoparticle Toxicity
Genetic Biomarkers of Nanoparticle Toxicity Associated with Reproductive Health
Genetic Biomarkers of Nanoparticle Toxicity Associated with Embryonic Development
Future Directions of Zebrafish Research for Informing Genomic and Epigenomic Biomarkers of Nanoparticle Toxicity through Novel Genetic Models and Integrated -omic Approaches to Clinical and Therapeutic Action
Conclusions
Funding
References
Index
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