DNA Methylation and Complex Human Disease - 1st Edition - ISBN: 9780124201941, 9780127999203

DNA Methylation and Complex Human Disease

1st Edition

Authors: Michel Neidhart
Hardcover ISBN: 9780124201941
eBook ISBN: 9780127999203
Imprint: Academic Press
Published Date: 3rd September 2015
Page Count: 552
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Table of Contents

  • Preface
  • About the Author
  • Chapter 1. DNA Methylation – Introduction
    • 1.1 Epigenetics
    • 1.2 Histone Modifications
    • 1.3 DNA Methylation
    • 1.4 Methyl-Binding Domain Proteins
    • 1.5 DNA Demethylation
    • 1.6 DNA Hydroxymethylation
    • 1.7 Differentially Methylated Regions
    • 1.8 Nutriepigenomics
    • References
  • Chapter 2. DNA Methylation and Epigenetic Biomarkers in Cancer
    • 2.1 Introduction
    • 2.2 Cancerogenesis
    • 2.3 Epimutations in Cancer
    • 2.4 Conclusion
    • References
  • Chapter 3. DNA Methylation and Epigenetic Biomarkers in Non-Neoplastic Diseases
    • 3.1 Introduction
    • 3.2 Autoimmunity
    • 3.3 Metabolic Diseases
    • 3.4 Developmental Diseases
    • 3.5 Psychiatric Diseases
    • 3.6 Conclusion
    • References
  • Chapter 4. DNA Methylation and Environmental Factors
    • 4.1 Introduction
    • 4.2 Impact of the Environment in Early Life
    • 4.3 Nutritional Factors
    • 4.4 Adverse Environmental Factors
    • 4.5 Immune Activation
    • 4.6 Maternal Mood and Experience in Early Life
    • 4.7 Physical Exercise
    • 4.8 Conclusion
    • References
  • Chapter 5. DNA Methylation and Epidemiology
    • 5.1 Introduction
    • 5.2 Endocrine Disrupting Chemicals
    • 5.3 Epigenomics and Breast Cancer
    • 5.4 Tobacco Smoking
    • 5.5 Conclusion
    • References
  • Chapter 6. DNA Methylation and Viral Infections
    • 6.1 Introduction
    • 6.2 Virus Infection and Methylation Changes
    • 6.3 Virus Infections, Dna Methylation, and Cancer
    • 6.4 Endogenous Retroviruses
    • 6.5 Conclusion
    • References
  • Chapter 7. DNA Methylation and Cancer
    • 7.1 Introduction
    • 7.2 Maintenance and Plasticity of the Epigenome
    • 7.3 DNA Methylation, CpG Islands and CpG Shores
    • 7.4 Aberrant DNA Methylation in Cancer
    • 7.5 Epimutations, Heritable Alterations in Cancer
    • 7.6 Epimutations of Epigenetic Regulators
    • 7.7 Epigenetic Interplays
    • 7.8 Reactivation of Silenced Tumor Suppressor Genes
    • 7.9 Conclusion
    • References
  • Chapter 8. DNA Methylation in Breast and Ovarian Carcinomas
    • 8.1 Introduction
    • 8.2 Hormonal Receptors
    • 8.3 Hypomethylated Genes
    • 8.4 Hypermethylated Genes
    • 8.5 Conclusion
    • References
  • Chapter 9. DNA Methylation in Acquired Drug Resistance
    • 9.1 Introduction
    • 9.2 DNA Methylation and Acquired Drug Resistance
    • 9.3 Mechanisms of Acquired Drug Resistance
    • 9.4 Conclusion
    • References
  • Chapter 10. DNA Methylation and Endocrinology
    • 10.1 Introduction
    • 10.2 Imprinted Disorders
    • 10.3 Rapid Promoter Methylation/Demethylation Processes
    • 10.4 Exposure to Stress
    • 10.5 Maternal and Sexual Behavior
    • 10.6 Exposure to Endocrine Disruptors
    • 10.7 Obesity and Type 2 Diabetes
    • 10.8 Conclusion
    • References
  • Chapter 11. DNA Methylation in Metabolic Diseases
    • 11.1 Introduction
    • 11.2 Obesity
    • 11.3 Type 2 Diabetes
    • 11.4 Epigenome-Metabolism Crosstalk
    • 11.5 Conclusion
    • References
  • Chapter 12. DNA Methylation in Pituitary Diseases
    • 12.1 Introduction
    • 12.2 Hypothalamo-Pituitary Axis
    • 12.3 Pituitary Development
    • 12.4 Pituitary Adenoma
    • 12.5 Pro-Opiomelanocortin Gene
    • 12.6 Prolactin and Growth Hormone
    • 12.7 Gonadotropins (Luteinizing Hormone, Follicle Stimulating Hormone)
    • 12.8 Thyroid Stimulating Hormone
    • 12.9 Arginine Vasopressin and Atrial Natriuretic Peptide
    • 12.10 Conclusion
    • References
  • Chapter 13. DNA Methylation and Development
    • 13.1 Introduction
    • 13.2 Different Embryonic Lineages
    • 13.3 Mesoderm Development
    • 13.4 Ectoderm Development
    • 13.5 Endoderm Development
    • 13.6 Hematopoietic Stem Cells
    • 13.7 Conclusion
    • References
  • Chapter 14. DNA Methylation in Growth Retardation
    • 14.1 Introduction
    • 14.2 Silver-Russell Syndrome
    • 14.3 Beckwith-Wiedemann Syndrome
    • 14.4 Transient Neonatal Diabetes Mellitus
    • 14.5 Pseudohypoparathyroidism Type 1b (PHP1b)
    • 14.6 Prader-Willi and Angelman Syndromes
    • 14.7 Syndromes Mimicking Uniparental Disomy 14 (UPD14)
    • 14.8 Familial Biparental Hydratidiform Mole
    • 14.9 Conclusion
    • References
  • Chapter 15. DNA Methylation in Cardiology
    • 15.1 Introduction
    • 15.2 Atherosclerosis
    • 15.3 Arrhythmia
    • 15.4 Ischemic Heart Disease
    • 15.5 Hypertension
    • 15.6 Conclusion
    • References
  • Chapter 16. DNA Methylation and Neurology
    • 16.1 Introduction
    • 16.2 Co-Adaptation of Imprinted Genes
    • 16.3 Memory
    • 16.4 Alcoholism
    • 16.5 Drug Addiction
    • 16.6 Schizophrenia
    • 16.7 Conclusion
    • References
  • Chapter 17. DNA Methylation in Psychiatric Diseases
    • 17.1 Introduction
    • 17.2 Major Psychosis
    • 17.3 Alzheimer’s Disease
    • 17.4 Autism
    • 17.5 Parkinson’s Disease
    • 17.6 Huntington’s Disease
    • 17.7 Amyotrophic Lateral Sclerosis
    • 17.8 Conclusion
    • References
  • Chapter 18. DNA Methylation in Cellular Mechanisms of Neurodegeneration
    • 18.1 Introduction
    • 18.2 Protein Misfolding
    • 18.3 Protein Degradation
    • 18.4 Membrane Damage
    • 18.5 Mitochondrial Dysfunction
    • 18.6 Axonal Transport
    • 18.7 Programmed Cell Death
    • 18.8 Early Life Experiences
    • 18.9 Conclusion
    • References
  • Chapter 19. DNA Methylation and Autoimmunity
    • 19.1 Introduction
    • 19.2 Environmental Factors
    • 19.3 Changes in DNA Methylation
    • 19.4 Conclusion
    • References
  • Chapter 20. DNA Methylation in Lymphocyte Development
    • 20.1 Introduction
    • 20.2 Hematopoietic Cells
    • 20.3 T-cell Subpopulations
    • 20.4 T-cell Functions
    • 20.5 B-cell Development
    • 20.6 Infection and Inflammation
    • 20.7 Tumor Clearance
    • 20.8 Environmental Factors and Autoimmunity
    • 20.9 Conclusion
    • References
  • Chapter 21. DNA Methylation in Stem Cell Diseases
    • 21.1 Introduction
    • 21.2 Stem Cell Differentiation
    • 21.3 Induced Pluripotent Stem Cells
    • 21.4 Environmental Factors and Aging
    • 21.5 Disruption of Differentiation and Development
    • 21.6 Conclusion and Outlook
    • References
  • Chapter 22. DNA Methylation and Rheumatology
    • 22.1 Introduction
    • 22.2 Systemic Lupus Erythematosus
    • 22.3 Systemic Sclerosis
    • 22.4 Osteoarthritis
    • 22.5 Rheumatoid Arthritis
    • 22.6 Juvenile Rheumatoid Arthritis
    • 22.7 Dermatomyositis
    • 22.8 Hypermobility Syndromes
    • 22.9 Conclusion
    • References
  • Chapter 23. DNA Methylation in Synovial Fibroblasts
    • 23.1 Introduction
    • 23.2 Endogenous Retroviruses
    • 23.3 DNA Hypomethylation
    • 23.4 DNA Methyltransferase 1
    • 23.5 S-Adenosylmethionine and Adenosylhomocysteine
    • 23.6 Recycling Pathway of Polyamines
    • 23.7 Differential Methylation of Specific Promoters
    • 23.8 MicroRNAs Interfering with DNA Methylation
    • 23.9 Conclusion
    • References
  • Chapter 24. DNA Methylation in Osteoporosis
    • 24.1 Introduction
    • 24.2 Early Development
    • 24.3 Osteoblast Differentiation
    • 24.4 Variations in the Response to Vitamin D
    • 24.5 Conclusion
    • References
  • Chapter 25. Epigenetic Therapies
    • 25.1 Introduction
    • 25.2 Demethylating Agents
    • 25.3 Cancer Stem Cells – Targeted Therapies
    • 25.4 Methyl Donors
    • 25.5 Polyamine Recycling Inhibitors
    • 25.6 Conclusion
    • References
  • Chapter 26. Demethylating Agents
    • 26.1 Introduction
    • 26.2 Mechanism of Action
    • 26.3 New Drug Development
    • 26.4 Combination Therapies
    • 26.5 Stem Cell Differentiation
    • 26.6 Induction of Autoimmunity
    • 26.7 Conclusion
    • References
  • Chapter 27. Methyl Donors
    • 27.1 Introduction
    • 27.2 L-Methionine
    • 27.3 Betaine
    • 27.4 S-Adenosylmethionine
    • 27.5 Methionine Metabolism
    • 27.6 Polyamine Metabolism
    • 27.7 Conclusion
    • References
  • Chapter 28. Methylome Analysis of Complex Diseases
    • 28.1 Introduction
    • 28.2 Global DNA Methylation Analysis
    • 28.3 Gene-Specific Methylation Analysis
    • 28.4 Methylome-Wide Analysis
    • 28.5 Sequencing Approaches
    • 28.6 Conclusion
    • References
  • Chapter 29. Methylome Analysis in Cancer
    • 29.1 Introduction
    • 29.2 Bisulfite-Based Methods
    • 29.3 Non-Bisulfite Methods
    • 29.4 Methylated DNA Binding Column
    • 29.5 Combination with MeDiP-seq or RRBS
    • 29.6 DNA Methylation in Formalin-Fixed Paraffin-Embedded Tissues
    • 29.7 Conclusion
    • References
  • Chapter 30. Methylome Analysis in Non-Neoplastic Disease
    • 30.1 Introduction
    • 30.2 Environmental Factors
    • 30.3 Cardiovascular Diseases
    • 30.4 Inflammatory Skin Diseases
    • 30.5 Asthma
    • 30.6 Inflammatory Bowel Disease
    • 30.7 Rheumatic Diseases
    • 30.8 Metabolic Diseases
    • 30.9 Neurodegenerative Diseases
    • 30.10 Psychiatric Disorders
    • 30.11 Neurological Disorders
    • 30.12 Conclusion
    • References
  • Chapter 31. Outlook
    • Concluding Thoughts
    • References
  • Glossary
  • Index

Description

  • Preface
  • About the Author
  • Chapter 1. DNA Methylation – Introduction
    • 1.1 Epigenetics
    • 1.2 Histone Modifications
    • 1.3 DNA Methylation
    • 1.4 Methyl-Binding Domain Proteins
    • 1.5 DNA Demethylation
    • 1.6 DNA Hydroxymethylation
    • 1.7 Differentially Methylated Regions
    • 1.8 Nutriepigenomics
    • References
  • Chapter 2. DNA Methylation and Epigenetic Biomarkers in Cancer
    • 2.1 Introduction
    • 2.2 Cancerogenesis
    • 2.3 Epimutations in Cancer
    • 2.4 Conclusion
    • References
  • Chapter 3. DNA Methylation and Epigenetic Biomarkers in Non-Neoplastic Diseases
    • 3.1 Introduction
    • 3.2 Autoimmunity
    • 3.3 Metabolic Diseases
    • 3.4 Developmental Diseases
    • 3.5 Psychiatric Diseases
    • 3.6 Conclusion
    • References
  • Chapter 4. DNA Methylation and Environmental Factors
    • 4.1 Introduction
    • 4.2 Impact of the Environment in Early Life
    • 4.3 Nutritional Factors
    • 4.4 Adverse Environmental Factors
    • 4.5 Immune Activation
    • 4.6 Maternal Mood and Experience in Early Life
    • 4.7 Physical Exercise
    • 4.8 Conclusion
    • References
  • Chapter 5. DNA Methylation and Epidemiology
    • 5.1 Introduction
    • 5.2 Endocrine Disrupting Chemicals
    • 5.3 Epigenomics and Breast Cancer
    • 5.4 Tobacco Smoking
    • 5.5 Conclusion
    • References
  • Chapter 6. DNA Methylation and Viral Infections
    • 6.1 Introduction
    • 6.2 Virus Infection and Methylation Changes
    • 6.3 Virus Infections, Dna Methylation, and Cancer
    • 6.4 Endogenous Retroviruses
    • 6.5 Conclusion
    • References
  • Chapter 7. DNA Methylation and Cancer
    • 7.1 Introduction
    • 7.2 Maintenance and Plasticity of the Epigenome
    • 7.3 DNA Methylation, CpG Islands and CpG Shores
    • 7.4 Aberrant DNA Methylation in Cancer
    • 7.5 Epimutations, Heritable Alterations in Cancer
    • 7.6 Epimutations of Epigenetic Regulators
    • 7.7 Epigenetic Interplays
    • 7.8 Reactivation of Silenced Tumor Suppressor Genes
    • 7.9 Conclusion
    • References
  • Chapter 8. DNA Methylation in Breast and Ovarian Carcinomas
    • 8.1 Introduction
    • 8.2 Hormonal Receptors
    • 8.3 Hypomethylated Genes
    • 8.4 Hypermethylated Genes
    • 8.5 Conclusion
    • References
  • Chapter 9. DNA Methylation in Acquired Drug Resistance
    • 9.1 Introduction
    • 9.2 DNA Methylation and Acquired Drug Resistance
    • 9.3 Mechanisms of Acquired Drug Resistance
    • 9.4 Conclusion
    • References
  • Chapter 10. DNA Methylation and Endocrinology
    • 10.1 Introduction
    • 10.2 Imprinted Disorders
    • 10.3 Rapid Promoter Methylation/Demethylation Processes
    • 10.4 Exposure to Stress
    • 10.5 Maternal and Sexual Behavior
    • 10.6 Exposure to Endocrine Disruptors
    • 10.7 Obesity and Type 2 Diabetes
    • 10.8 Conclusion
    • References
  • Chapter 11. DNA Methylation in Metabolic Diseases
    • 11.1 Introduction
    • 11.2 Obesity
    • 11.3 Type 2 Diabetes
    • 11.4 Epigenome-Metabolism Crosstalk
    • 11.5 Conclusion
    • References
  • Chapter 12. DNA Methylation in Pituitary Diseases
    • 12.1 Introduction
    • 12.2 Hypothalamo-Pituitary Axis
    • 12.3 Pituitary Development
    • 12.4 Pituitary Adenoma
    • 12.5 Pro-Opiomelanocortin Gene
    • 12.6 Prolactin and Growth Hormone
    • 12.7 Gonadotropins (Luteinizing Hormone, Follicle Stimulating Hormone)
    • 12.8 Thyroid Stimulating Hormone
    • 12.9 Arginine Vasopressin and Atrial Natriuretic Peptide
    • 12.10 Conclusion
    • References
  • Chapter 13. DNA Methylation and Development
    • 13.1 Introduction
    • 13.2 Different Embryonic Lineages
    • 13.3 Mesoderm Development
    • 13.4 Ectoderm Development
    • 13.5 Endoderm Development
    • 13.6 Hematopoietic Stem Cells
    • 13.7 Conclusion
    • References
  • Chapter 14. DNA Methylation in Growth Retardation
    • 14.1 Introduction
    • 14.2 Silver-Russell Syndrome
    • 14.3 Beckwith-Wiedemann Syndrome
    • 14.4 Transient Neonatal Diabetes Mellitus
    • 14.5 Pseudohypoparathyroidism Type 1b (PHP1b)
    • 14.6 Prader-Willi and Angelman Syndromes
    • 14.7 Syndromes Mimicking Uniparental Disomy 14 (UPD14)
    • 14.8 Familial Biparental Hydratidiform Mole
    • 14.9 Conclusion
    • References
  • Chapter 15. DNA Methylation in Cardiology
    • 15.1 Introduction
    • 15.2 Atherosclerosis
    • 15.3 Arrhythmia
    • 15.4 Ischemic Heart Disease
    • 15.5 Hypertension
    • 15.6 Conclusion
    • References
  • Chapter 16. DNA Methylation and Neurology
    • 16.1 Introduction
    • 16.2 Co-Adaptation of Imprinted Genes
    • 16.3 Memory
    • 16.4 Alcoholism
    • 16.5 Drug Addiction
    • 16.6 Schizophrenia
    • 16.7 Conclusion
    • References
  • Chapter 17. DNA Methylation in Psychiatric Diseases
    • 17.1 Introduction
    • 17.2 Major Psychosis
    • 17.3 Alzheimer’s Disease
    • 17.4 Autism
    • 17.5 Parkinson’s Disease
    • 17.6 Huntington’s Disease
    • 17.7 Amyotrophic Lateral Sclerosis
    • 17.8 Conclusion
    • References
  • Chapter 18. DNA Methylation in Cellular Mechanisms of Neurodegeneration
    • 18.1 Introduction
    • 18.2 Protein Misfolding
    • 18.3 Protein Degradation
    • 18.4 Membrane Damage
    • 18.5 Mitochondrial Dysfunction
    • 18.6 Axonal Transport
    • 18.7 Programmed Cell Death
    • 18.8 Early Life Experiences
    • 18.9 Conclusion
    • References
  • Chapter 19. DNA Methylation and Autoimmunity
    • 19.1 Introduction
    • 19.2 Environmental Factors
    • 19.3 Changes in DNA Methylation
    • 19.4 Conclusion
    • References
  • Chapter 20. DNA Methylation in Lymphocyte Development
    • 20.1 Introduction
    • 20.2 Hematopoietic Cells
    • 20.3 T-cell Subpopulations
    • 20.4 T-cell Functions
    • 20.5 B-cell Development
    • 20.6 Infection and Inflammation
    • 20.7 Tumor Clearance
    • 20.8 Environmental Factors and Autoimmunity
    • 20.9 Conclusion
    • References
  • Chapter 21. DNA Methylation in Stem Cell Diseases
    • 21.1 Introduction
    • 21.2 Stem Cell Differentiation
    • 21.3 Induced Pluripotent Stem Cells
    • 21.4 Environmental Factors and Aging
    • 21.5 Disruption of Differentiation and Development
    • 21.6 Conclusion and Outlook
    • References
  • Chapter 22. DNA Methylation and Rheumatology
    • 22.1 Introduction
    • 22.2 Systemic Lupus Erythematosus
    • 22.3 Systemic Sclerosis
    • 22.4 Osteoarthritis
    • 22.5 Rheumatoid Arthritis
    • 22.6 Juvenile Rheumatoid Arthritis
    • 22.7 Dermatomyositis
    • 22.8 Hypermobility Syndromes
    • 22.9 Conclusion
    • References
  • Chapter 23. DNA Methylation in Synovial Fibroblasts
    • 23.1 Introduction
    • 23.2 Endogenous Retroviruses
    • 23.3 DNA Hypomethylation
    • 23.4 DNA Methyltransferase 1
    • 23.5 S-Adenosylmethionine and Adenosylhomocysteine
    • 23.6 Recycling Pathway of Polyamines
    • 23.7 Differential Methylation of Specific Promoters
    • 23.8 MicroRNAs Interfering with DNA Methylation
    • 23.9 Conclusion
    • References
  • Chapter 24. DNA Methylation in Osteoporosis
    • 24.1 Introduction
    • 24.2 Early Development
    • 24.3 Osteoblast Differentiation
    • 24.4 Variations in the Response to Vitamin D
    • 24.5 Conclusion
    • References
  • Chapter 25. Epigenetic Therapies
    • 25.1 Introduction
    • 25.2 Demethylating Agents
    • 25.3 Cancer Stem Cells – Targeted Therapies
    • 25.4 Methyl Donors
    • 25.5 Polyamine Recycling Inhibitors
    • 25.6 Conclusion
    • References
  • Chapter 26. Demethylating Agents
    • 26.1 Introduction
    • 26.2 Mechanism of Action
    • 26.3 New Drug Development
    • 26.4 Combination Therapies
    • 26.5 Stem Cell Differentiation
    • 26.6 Induction of Autoimmunity
    • 26.7 Conclusion
    • References
  • Chapter 27. Methyl Donors
    • 27.1 Introduction
    • 27.2 L-Methionine
    • 27.3 Betaine
    • 27.4 S-Adenosylmethionine
    • 27.5 Methionine Metabolism
    • 27.6 Polyamine Metabolism
    • 27.7 Conclusion
    • References
  • Chapter 28. Methylome Analysis of Complex Diseases
    • 28.1 Introduction
    • 28.2 Global DNA Methylation Analysis
    • 28.3 Gene-Specific Methylation Analysis
    • 28.4 Methylome-Wide Analysis
    • 28.5 Sequencing Approaches
    • 28.6 Conclusion
    • References
  • Chapter 29. Methylome Analysis in Cancer
    • 29.1 Introduction
    • 29.2 Bisulfite-Based Methods
    • 29.3 Non-Bisulfite Methods
    • 29.4 Methylated DNA Binding Column
    • 29.5 Combination with MeDiP-seq or RRBS
    • 29.6 DNA Methylation in Formalin-Fixed Paraffin-Embedded Tissues
    • 29.7 Conclusion
    • References
  • Chapter 30. Methylome Analysis in Non-Neoplastic Disease
    • 30.1 Introduction
    • 30.2 Environmental Factors
    • 30.3 Cardiovascular Diseases
    • 30.4 Inflammatory Skin Diseases
    • 30.5 Asthma
    • 30.6 Inflammatory Bowel Disease
    • 30.7 Rheumatic Diseases
    • 30.8 Metabolic Diseases
    • 30.9 Neurodegenerative Diseases
    • 30.10 Psychiatric Disorders
    • 30.11 Neurological Disorders
    • 30.12 Conclusion
    • References
  • Chapter 31. Outlook
    • Concluding Thoughts
    • References
  • Glossary
  • Index

Key Features

  • Discusses breaking biomarker research in major disease families of current health concern and research interest, including obesity, type II diabetes, schizophrenia, and autoimmunity
  • Summarizes advances not only relevant to cancer, but also in non-neoplastic disease, currently an emerging field
  • Describes wholly new concepts, including the linking of metabolic pathways with epigenetics
  • Provides translational researchers with the knowledge of both basic research and clinic applications of DNA methylation in human diseases

Readership

Basic biology and translational researchers above graduate level interested in developmental biology, genetics, health genomics, epigenesis in complex disease, and therapeutic possibilities


Details

No. of pages:
552
Language:
English
Copyright:
© Academic Press 2016
Published:
Imprint:
Academic Press
eBook ISBN:
9780127999203
Hardcover ISBN:
9780124201941

About the Authors

Michel Neidhart Author

Professor Neidhart is a senior scientist at the Center of Experimental Rheumatology, Centre for Clinical Research, Switzerland.

Affiliations and Expertise

Center of Experimental Rheumatology, Centre for Clinical Research, University Hospital, Zurich, Switzerland