microRNAs in Toxicology and Medicine

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), Handbook of Systems Toxicology (Wiley, 2011), and Toxicology and Epigenetics (Wiley, 2012).

• List of Contributors xixPreface xxiiiAcknowledgments xxvPART I microRNAs AND TOXICOLOGY 11 Introduction 3Saura C. SahuReferences 42 Environmental Toxicants and Perturbation of miRNA Signaling 5Kathryn A. Bailey and Rebecca C. Fry2.1 Introduction 52.2 miRNAs: Description and Biological Significance 82.2.1 miRNA Biosynthesis and Processing 82.2.2 Interaction of miRNAs with mRNA Targets 92.3 Environmental Toxicant-Associated miRNA Perturbations 102.3.1 Toxicant Class 1: Carcinogenic Metals (Arsenic and Cadmium) 102.3.1.1 Arsenic 102.3.1.2 Cadmium 122.3.2 Toxicant Class 2: Air Toxicants (Formaldehyde, Diesel Exhaust Particles, Cigarette Smoke) 132.3.2.1 Formaldehyde 132.3.2.2 Diesel Exhaust Particles (DEPs) 142.3.2.3 Cigarette Smoke 142.3.3 Toxicant Class 3: Polycyclic Aromatic Hydrocarbon (B(a)P) 172.3.4 Toxicant Class 4: Endocrine Disruptors (BPA, DDT, Fludioxonil, Fenhexamid, and Nonylphenol) 192.3.4.1 BPA, DDT, Fludioxonil, Fenhexamid 192.3.4.2 Nonylphenol (NP) 202.4 Conclusions and Future Directions 22Acknowledgments 22References 223 microRNAs in Drug-Induced Liver Toxicity 33Si Chen, Jiekun Xuan and Lei Guo3.1 Introduction 333.2 miRNA Tissue Distribution and Abundance 343.2.1 miRNA in Solid Tissues 343.2.2 microRNA in Body Fluids 353.3 miRNA and Drug-Induced Liver Toxicity 353.3.1 Acetaminophen 363.3.2 Carbon Tetrachloride (CCl4) 373.3.3 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) 373.3.4 Benzo[a]pyrene 373.3.5 Tamoxifen 383.3.6 Others 383.4 Circulating miRNAs as Potential Biomarkers for Drug-Induced Liver Toxicity 383.4.1 Introduction of Circulating miRNAs 383.4.1.1 Exosomes 393.4.1.2 HDL 393.4.1.3 Ago2 393.4.2 Blood miRNAs in Drug-Induced Liver Toxicity 393.4.3 Urine miRNAs in Drug-Induced Liver Toxicity 413.4.4 Technique Challenges 423.5 Mechanistic Studies and Perspectives 42Disclaimer 44References 444 Fishing for microRNAs in Toxicology 49Jennifer L. Freeman, Gregory J. Weber and Maria S. Sepulveda4.1 microRNAs in Toxicology 494.2 Fish Models in Toxicology 494.2.1 Small Fish Models in Toxicology 504.2.2 Large Fish Models in Toxicology 514.3 Fish as Models for Studying miRNA Function 514.3.1 miRNA Studies in Zebrafish 514.3.2 miRNA Studies in Other Fish Models 524.4 Application of Fish Models in Toxicity Studies of miRNA Alterations 524.4.1 Zebrafish in Toxicity Studies of miRNA Alterations 524.4.2 Other Fish Models in Toxicity Studies of miRNA Alterations 684.5 Summary 68Acknowledgments 68References 68PART II microRNAs AND DISEASE STATES 775 microRNAs and Inflammation 79Yan Huang, Samir N. Ghadiali and S. Patrick Nana-Sinkam5.1 Introduction 795.2 miRNA Biogenesis and Functions 805.3 miRNAs in Hematopoietic Systems 805.4 miRNA and Inflammatory Diseases 815.5 Regulation of the Immune System 865.5.1 Acquired Immunity 865.5.2 Innate Immunity 865.6 Regulation of miRNA Expression 875.6.1 Regulation of miRNA by Cytokines and Bacterial Toxins 875.6.2 Regulation of miRNA by Mechanical Stimuli 885.7 Select miRNA Regulation of Inflammation 895.7.1 miR-146a: Negative Regulator of Immune Response 895.7.2 Role of miR-155 in Mediating Inflammatory Responses 915.7.3 miR-125a/b 925.7.4 miR-181a 935.8 Conclusion 94References 946 Regulatory Role of microRNAs in Mutagenesis 101Fanxue Meng, Yang Luan, Jian Yan and Tao Chen6.1 Introduction 1016.2 miRNA Roles in Xenobiotic Metabolism 1026.3 miRNA Roles in the Cell Cycle 1056.4 miRNA Roles in DNA Repair 1066.5 Apoptosis 1076.6 miRNA Regulation and Mutation Formation 1086.7 Conclusions 109Disclaimer 109References 1107 microRNAs and Cancer 113Dongsheng Yan and Geir Skogerbø7.1 Introduction 1137.2 miRNAs are Deregulated in Cancer 1147.3 miRNAs Function as Oncogenes and Tumor Suppressor Genes 1167.4 miRNAs in Cancer Metastasis 1177.5 miRNAs in Cancer Stem Cells 1197.6 Mutations in miRNA Loci 1197.7 Mutations in miRNA Target Genes 1207.8 Prospective: miRNA as Biomarkers and Therapeutics 121References 1218 miRNAs in Cancer Invasion and Metastasis 133Brock Humphries and Chengfeng Yang8.1 Introduction 1338.2 miRNAs and Cancer Invasion and Metastasis 1368.2.1 miRNAs Involved in Angiogenesis 1368.2.2 miRNAs Involved in Cancer Cell Detachment, Migration, and Invasion 1388.2.3 miRNAs Involved in Cancer Cell Intravasation 1408.2.4 miRNAs Involved in Circulating Cancer Cell Survival 1428.2.5 miRNAs Involved in Cancer Cell Extravasation 1438.2.6 miRNAs Involved in Metastatic Colonization 1448.3 miRNAs as Useful Cancer Prognostic Markers 1468.4 Future Perspectives 147References 1489 The Role of microRNAs in Tumor Progression and Therapy 153Azfur S. Ali, Aamir Ahmad, Shadan Ali, Philip A. Philip and Fazlul H. Sarkar9.1 Introduction 1539.2 Tumor Progression 1549.3 Key Signaling Pathways 1549.3.1 Angiogenesis 1549.3.2 The Ras Pathway 1559.3.3 The Epidermal Growth Factor Receptor Pathway 1559.3.4 The PI3K/Akt Pathway 1569.4 The miRNAs as Regulators of Tumor Progression 1569.4.1 Current Therapies to Control Tumor Progression 1579.4.2 Tumor Promoter miRNAs 1589.4.2.1 miR-21 1589.4.2.2 miR-155 1599.4.3 Tumor Suppressor miRNAs 1599.4.3.1 The miR-200 Family 1599.4.3.2 miR-146a 1609.4.3.3 The let-7 Family 1609.5 Regulation of miRNAs by Novel Anticancer Compounds 1609.6 Conclusions and Perspectives 161References 16210 Current Understanding of microRNAs as Therapeutic Targets in Cancer 167Marion Gayral, Jérome Torrisani and Pierre Cordelier10.1 Introduction on the Rationale of Using miRNAs as Therapeutics in Cancer 16710.2 Current Approaches to Target miRNAs 16710.3 Evidence of Successful miRNA Targeting in Experimental Cancer Models 16810.4 Open Question: Targeting miRNA Processing in Cancer Cells 17010.5 Concluding Remarks 170References 17011 microRNAs, New Players in Cancer Chemoprevention 173Bin Yi and Yaguang Xi11.1 Introduction 17311.2 miRNA and the Natural Products 17511.2.1 Vitamin A 17511.2.2 Vitamin B 17611.2.3 Vitamin D 17611.2.4 Vitamin E 17611.2.5 Fatty Acids 17611.2.6 Curcumin 17711.2.7 Resveratrol 17711.2.8 Ellagitannin 17711.2.9 Genistein 17711.2.10 Catechins 17811.2.11 Indoles 17811.3 miRNA and Pharmaceuticals 17811.3.1 Nonsteroidal Anti-Inflammatory Drugs (NSAIDs) 17811.3.2 Estrogen Receptor Antagonist 18111.4 Perspectives 182Acknowledgments 183References 18312 microRNA and Neurodegenerative Diseases 189Josephine Malmevik, Malin Ákerblom and Johan Jakobsson12.1 Introduction 18912.2 miRNAs and Parkinson’s Disease 19112.3 miRNAs and Alzheimer’s Disease 19312.4 miRNAs and Huntington’s Disease 19512.5 Outlook 195Acknowledgements 196References 19613 Sleep and microRNAs (miRNAs) in Neurodegenerative Diseases 201Daniel B. Kay and Christopher J. Davis13.1 Sleep and microRNAs (miRNAs) in Neurodegenerative Diseases 20113.2 miRNAs and Sleep 20213.3 Aging 20313.4 Alzheimer’s Disease 20413.5 Parkinson’s Disease 20513.6 Creutzfeldt–Jakob Disease 20613.7 Huntington’s Disease 20713.8 Multiple Sclerosis 20813.9 Fronto-Temporal Dementia 20813.10 Summary 208Acknowledgments 209References 20914 Role of microRNA in Autism Spectrum Disorder 215Tewarit Sarachana and Valerie W. Hu14.1 Introduction 21514.2 Epidemiology of ASD 21614.3 Etiology of ASD: Genetic Associations 21614.4 ASD as Multigenic Systemic Disorders 21714.5 Evidence for Epigenetic Contributions 21814.6 The Role of microRNAs in Neurodevelopment 21814.7 microRNAs in Neurodevelopmental and Psychiatric Disorders: An Overview 21914.8 microRNA Expression Profiles in Autism Spectrum Disorder 22014.8.1 Evidence for Dysregulated miRNAs in Brain and Blood 22014.8.2 Identification of Novel Gene Targets of Differentially Expressed miRNAs in ASD 22014.8.3 Brain-Related miRNAs are Differentially Expressed in LCLs from Individuals with ASD 22214.8.4 Functional Associations of Confirmed Differentially Expressed miRNAs 22514.9 Conclusions 226Acknowledgments 227References 22715 The Emerging Function of Natural Products as Regulators of miRNAs in Human Diseases 237Keitaro Hagiwara, Luc Gailhouste, Nobuyoshi Kosaka and Takahiro Ochiya15.1 Introduction 23715.2 History of Natural Products as Drugs 23815.3 Functions of miRNAs in Human Diseases 23815.4 Regulation of miRNAs using Natural Products 23915.5 Resveratrol and miRNAs 23915.6 EGCG and miRNAs 24115.7 Curcumin and miRNAs 24215.8 Isoflavone and miRNAs 24215.9 Metformin miRNA 24215.10 Traditional Herbs and miRNAs 24315.11 Polyphenol and miRNAs 24315.12 Rice and miRNA 24315.13 Human Breast Milk and miRNAs 24415.14 Conclusion 245Acknowledgments 245References 245PART III microRNAs AND STEM CELLS 24916 Pluripotency and Early Cell Fate Decisions are Orchestrated by microRNAs 251Matthias Jung and Insa S. Schroeder16.1 Importance of microRNAs in ES and iPS Cells 25116.2 Biogenesis and Function of microRNAs 25216.3 microRNAs Mark ES Cell Identity 25316.3.1 ES Cell Identity is Characterized by Distinct miRs 25316.3.2 Mouse ES Cell-Specific miRs 25416.3.3 Human ES Cell-Specific miRs 25516.3.4 Self-Renewal of ES Cells is Regulated by Cell Cycle Regulating miRs 25516.3.5 Differentiation Capacity of ES Cells is Maintained by miRs 25616.3.6 Isoforms and 3 Variability in ES Cell-Specific miRs 25616.4 microRNAs Guide Induced Pluripotency 25716.4.1 Reprogramming Factors Regulate ES Cell-Associated miRs 25716.4.2 Differentiation of ES and iPS Cells is Prevented by miRs 25816.4.3 Reprogramming Requires ES Cell-Specific miRs 25816.5 microRNAs Manipulate Cell Fate Decision 25916.5.1 Induction of Early Differentiation is Regulated by miRs 25916.5.2 Major Signaling Pathways in ES Cells Regulated by miRs 26016.5.3 Differentiation of ES Cells Can be Manipulated by miRs 26016.5.4 Cell Fate Decisions are Influenced by miRs and RNA Binding Proteins (RBPs) 261References 26217 microRNAs in Cancer Stem Cells: Micromanagers of Malignancy 269Arun Bhardwaj, Sumit Arora, Seema Singh, and Ajay P. Singh17.1 Introduction 26917.2 Cancer Stem Cells 27017.2.1 Origin of Cancer Stem Cells 27017.2.2 Characteristics and Pathological Significance of Cancer Stem Cells 27117.3 microRNAs: Biology and Mechanism 27317.4 Role of microRNAs in the Regulation of Genes and Signaling Pathways Associated with Cancer Stem Cells 27317.4.1 HMGA2 27517.4.2 Bcl-2 27517.4.3 Bmi-1 27617.4.4 Wnt/β-Catenin 27617.4.5 Notch 27717.4.6 Hedgehog 27717.4.7 TGF-β 27817.5 Translational Implications and Future Perspectives 279References 279PART IV microRNAs AND GENOMICS 28518 microRNAs: Tiny Regulators of Great Potential for Gene Regulation 287Nahid Akhtar and Tariq M. Haqqi18.1 Introduction 28718.2 microRNAs: Biogenesis and Expression Criteria 28818.3 Mechanism of miRNA Mediated Regulation of Genes 28818.4 Complexities of miRNA Regulation 29018.5 microRNA and Epigenetics 29118.6 Role of miRNAs in Biological Processes 29518.7 microRNAs: Association with Disease Pathogenesis 29618.8 microRNAs: Another Way to Unravel Disease Pathogenesis 29718.9 microRNAs as Novel Therapeutic Targets 29818.10 Concluding Remarks 299Competing Interests 300Conflict of interest statement 300Acknowledgments 300References 30019 Exploration of microRNA Genomic Variation Associated with Common Human Diseases 309Joel Fontanarosa and Yang Dai19.1 Introduction 30919.2 Methods 31019.3 Results 31119.4 Discussion 313Acknowledgment 315References 315PART V microRNAs AND EPIGENOMICS 31720 Crosstalk between microRNAs and Epigenetics: From the Nutritional Perspective 319Zhenhua Liu, Stephanie A Tammen, Simonetta Friso and Sang-Woon Choi20.1 Introduction 31920.2 Epigenetic Regulation of microRNA Expression 32120.2.1 microRNA Biogenesis and Epigenetic Regulation 32120.2.2 Epigenetically-Regulated microRNAs 32320.2.2.1 microRNAs Controlled by Promoter Methylation 32320.2.2.2 microRNAs Controlled by Histone Modification 32420.3 Regulation of Epigenetic Machinery by microRNAs 32620.3.1 Epigenetic Machinery and its Regulation by microRNA 32620.3.2 epi-miRNAs 32720.4 microRNA and Epigenetics: Regulation by Nutrition 32920.4.1 Nutrition and Epigenetics 32920.4.1.1 One-Carbon Nutrients 32920.4.1.2 Dietary Bioactive Components 32920.4.2 Nutrition and microRNA 33120.4.2.1 One-Carbon Nutrients 33120.4.2.2 Dietary Bioactive Components 33120.4.3 Nutritional Modulation of the Epigenetics-microRNA Inter-Regulatory Network 33220.5 Summary 333References 334PART VI microRNAs AND BIOMARKERS 34121 Body Fluid microRNAs as Toxicological Biomarkers 343Zhishan Wang and Chengfeng Yang21.1 microRNA History, Biogenesis and Functions 34321.2 Differential Expression of miRNAs During Development and Diseases 34421.3 Alterations of miRNA Expressions by Toxicant Exposures 34521.4 Discovery of Body Fluid miRNAs 34621.5 Body Fluid miRNAs as Toxicological Biomarkers 34721.5.1 Plasma or Serum miRNAs as Toxicological Biomarkers 34721.5.1.1 Plasma or Serum miRNAs as Biomarkers for Liver Injuries 34721.5.1.2 Plasma or Serum miRNAs as Biomarkers for Heart Injuries 34921.5.1.3 Plasma or Serum miRNAs as Biomarkers for Kidney Injuries 35021.5.1.4 Plasma or Serum miRNAs as Biomarkers for Radiation Exposure 35121.5.1.5 Plasma or Serum miRNAs as Biomarkers for Drug Abuse 35321.5.2 Urinary miRNAs as Toxicological Biomarkers 35321.5.2.1 Urinary miRNAs as Biomarkers for Kidney Injuries 35321.5.2.2 Urinary miRNAs as Biomarkers for Liver Injuries 35421.5.3 Other Body Fluid miRNAs as Toxicological Biomarkers 35521.6 Challenges and the Future of Body Fluid miRNAs as Biomarkers 356References 35822 Cell-free microRNAs as Biomarkers in Human Diseases 363Xi Yang, William B. Mattes, Qiang Shi, Zuquan Weng and William F. Salminen22.1 Introduction 36322.2 Secretion and Transportation of Cell-Free miRNAs in Body Fluids 36522.3 Technical Challenges in the Analysis of Cell-Free miRNAs 36722.4 Cell-Free miRNAs as Novel Potential Biomarkers for Cancers and Tissue Injuries 36922.4.1 Acute Myeloid Leukemia and B-Cell Lymphoma 37022.4.2 Bladder Cancer 37022.4.3 Breast Cancer 37022.4.4 Colorectal Cancer 37322.4.5 Gastric Cancer 37322.4.6 Hepatocellular Carcinoma 37422.4.7 Lung Cancer 37422.4.8 Melanoma 37522.4.9 Oral and Squamous Cell Carcinoma 37522.4.10 Ovarian Cancer 37622.4.11 Pancreatic Cancer 37622.4.12 Prostate Cancer 37722.4.13 Cardiovascular Diseases 37722.4.14 Drug-Induced Liver Injury 37922.4.15 Kidney Injury 38022.5 Conclusion and Perspectives 380Disclaimer 380References 38123 Plasma microRNAs as Biomarkers of Human Diseases 389Katarina Cuk, Dharanija Madhavan, Andrey Turchinovich and Barbara Burwinkel23.1 Introduction 38923.2 Cancer 39023.2.1 Breast Cancer 39023.2.2 Prostate Cancer 39123.2.3 Lung Cancer 40623.2.4 Colorectal Cancer 40723.3 Cardiovascular Diseases and Disorders 40823.3.1 Acute Myocardial Infarction 40823.3.2 Other Cardiovascular Diseases 41023.4 Neurological Diseases and Disorders 41123.5 Diabetes Mellitus 41223.6 Infectious Diseases 41323.7 Standardization of Circulating miRNA Analysis 41323.7.1 Sample Processing and Handling 41323.7.2 Data Normalization 41523.8 Discovery, Origins and Functions of Circulating miRNAs 416References 41824 Circulating microRNAs as Biomarkers of Drug-Induced Pancreatitis 425Rodney Rouse, Barry A. Rosenzweig and Karol L. Thompson24.1 Introduction 42524.2 Pancreatic Injury and Serum Biomarkers 42624.3 Amylase and Lipase: Sensitivity and Specificity as Biomarkers of Pancreatic Injury 42724.4 Pancreas Selective microRNAs as Circulating Biomarkers 42824.4.1 Pancreas Selective Expression of microRNAs in Tissue 42824.4.2 Circulating microRNAs in Models of Pancreatitis 42924.4.3 Mouse Model of Acute Pancreatic Injury 43024.4.4 Time Course of Pancreas-Selective microRNAs in the Serum of Mice Treated with Caerulein 43024.4.5 Dose Response of Pancreas-Selective microRNAs in the Serum of Mice Treated with Caerulein 43224.4.6 Serum Lipase and Amylase in Mice Treated with Caerulein 43324.4.7 Receiver Operating Characteristic (ROC) Analysis of Serum microRNAs, Lipase, and Amylase 43324.5 Conclusions 43324.6 Future Directions 434Acknowledgments 434Disclaimer 434References 43525 microRNA Profiling: Strategies and Challenges 437Jiekun Xuan, Leming Shi and Lei Guo25.1 miRNA Biogenesis 43725.2 Challenges of miRNA Profiling 43725.3 miRNA Profiling Methodologies 43825.3.1 Northern Blotting 43825.3.2 Quantitative Reverse Transcription PCR 44025.3.3 Microarray 44125.3.4 Next Generation Sequencing 44125.3.4.1 Roche/454 44125.3.4.2 Illumina/Solexa 44225.3.4.3 Life Technologies/SOLiD 44225.3.4.4 cDNA Library Construction 44325.3.4.5 Multiplexing 44325.3.4.6 Bioinformatics Tools 44425.4 Technical Challenges of Circulating miRNA Profiling 44625.5 Quality Assessment and Data Normalization 446Disclaimer 448References 448Index 455