Cover Image

Epigenetics in human disease /

Show other versions (4)

Epigenetics in Human Disease, Third Edition examines the diseases and conditions on which we have advanced knowledge of epigenetic mechanisms, such as cancer, autoimmune disorders, aging, metabolic disorders, neurobiological disorders and cardiovascular disease. From molecular mechanisms and epigene...

Full description

Bibliographic Details
Corporate Author: ScienceDirect (Online service)
Other Authors: Tollefsbol, Trygve O. (Editor)
Format: eBook
Language:English
Published: London, United Kingdom ; San Diego, CA, United States ; Cambridge, MA, United States ; Kidlington, Oxford, United Kingdom : Elsevier, Academic Press, an Imprint of Elsevier, [2024]
Edition:Third edition.
Series:Translational epigenetics series.
Subjects:
Medical genetics.
Epigenetics.
Genetics, Medical
Génétique médicale.
Épigénétique.
Epigenetics
Medical genetics
Electronic books.
Online Access:Connect to the full text of this electronic book
Table of Contents:
  • 9780443218125v1_WEB
  • Front Cover
  • Epigenetics in Human Disease
  • Translational Epigenetics Series
  • Epigenetics in Human Disease
  • Copyright
  • Volume 1 Contents
  • Contributors
  • Preface
  • 1- Introduction
  • 1
  • An overview of epigenetics of human disease
  • 1.1 Introduction
  • 1.2 Methodology
  • 1.3 Human cancer
  • 1.4 Neurological disease
  • 1.5 Autoimmunity and epigenetics
  • 1.6 Metabolic disorders
  • 1.7 Other disorders/diseases
  • 1.8 Development, aging, and transgenerational effects
  • 1.9 Future research
  • 1.10 Conclusion
  • Acknowledgement
  • References
  • 2
  • Methodology
  • 2
  • Profiling histone posttranslational modifications and chromatin-modifying proteins by high-throughput reverse p ...
  • 2.1 Introduction
  • 2.2 RPPA platform for detection of histone PTMs and modifying proteins
  • 2.2.1 Sample preparation
  • 2.2.1.1 Whole cell lysate sample preparation
  • 2.2.1.2 Histone sample preparation
  • 2.2.2 Antibody validation
  • 2.2.2.1 Antibody validation for histone- and chromatin-modifying proteins
  • 2.2.2.2 Antibody validation for histone PTMs
  • 2.2.2.2.1 Antibody validation with synthetic peptides corresponding to histone PTMs by peptide array
  • 2.2.2.2.2 Validation of histone PTM profiling with inhibitors of enzymatic histone-modifying protein
  • 2.2.3 RPPA design and slide printing
  • 2.2.4 RPPA total protein staining and antibody labeling
  • 2.2.4.1 Total protein staining
  • 2.2.4.2 Antibody labeling
  • 2.2.5 Slide scanning and image analysis
  • 2.2.6 Data normalization and analysis
  • 2.3 Comparison of histone PTM profiles by RPPA and mass spectrometry analyses
  • 2.4 Epigenetic RPPA application-detection of histone PTMs and their modifiers during somatic cell reprogramming
  • 2.5 Perspective and conclusion
  • Acknowledgments
  • References.
  • 3
  • Bioinformatics of epigenetic data generated from next-generation sequencing
  • 3.1 Introduction
  • 3.2 Preprocessing data from next-generation sequencing
  • 3.3 Read alignment
  • 3.4 Profiling genome-wide DNA methylation
  • 3.4.1 DNA methylation
  • 3.4.2 Experimental approaches for measuring DNA methylation
  • 3.4.3 Calling methylation from BS-seq and EM-seq
  • 3.4.4 Postalignment analysis of methylation data
  • 3.4.5 Protocol for BS-seq and EM-seq data analysis
  • 3.4.5.1 Key resources table
  • 3.4.5.2 Equipment
  • 3.4.5.3 Step-by-step method
  • 3.4.5.3.1 Preprocessing
  • 3.4.5.3.2 Read alignment and methylation calling
  • 3.4.5.3.3 Downstream analysis
  • 3.4.6 DNA methylation analysis in cancer research
  • 3.4.7 Conclusion
  • 3.5 Assessing DNA-protein interactions via chromatin-ChIP-seq
  • 3.5.1 Library preparation for ChIP-seq
  • 3.5.2 Identifying DNA sequences associated with proteins or histone modifications
  • 3.5.3 Quality assessment of ChIP-seq data
  • 3.5.4 ChIP-seq in disease research
  • 3.5.5 Conclusion
  • 3.6 Analysis of the small RNA component of the epigenome
  • 3.6.1 Biogenesis of small RNA classes
  • 3.6.2 Next-generation sequencing of small RNA
  • 3.6.3 Profiling microRNAs
  • 3.6.4 Quality assessment of sRNA-seq data
  • 3.6.5 Prediction of microRNA in the genome
  • 3.6.6 Prediction of microRNA targets
  • 3.6.7 miRNA-seq in cancer research
  • 3.6.8 Conclusion
  • 3.7 Profiling chromatin accessibility using ATAC-seq
  • 3.7.1 Investigating chromatin accessibility using next-generation sequencing
  • 3.7.2 Preparing ATAC-seq samples
  • 3.7.3 Determining open chromatin regions using ATAC-seq
  • 3.7.4 Quality assessment of ATAC-seq data
  • 3.7.5 Data analysis for ATAC-seq
  • 3.7.5.1 Visualization of ATAC-seq peaks and surrounding genes
  • 3.7.5.2 Postalignment analyses
  • 3.7.6 ATAC-seq in cancer research
  • 3.7.7 Conclusion.
  • 3.8 Chromosome conformation capture
  • 3.9 Predicting transcriptional factor-binding sites with epigenomics data
  • 3.9.1 Epigenomic regulation
  • 3.9.2 Hit-based transcription factor-binding site prediction
  • 3.9.3 Site-centric transcription factor-binding site prediction
  • 3.9.4 Segmentation-based transcription factor-binding site prediction
  • 3.10 Integration of epigenome data
  • 3.10.1 Epigenomic profile of enhancers and their role in human diseases
  • 3.11 Summary
  • Glossary
  • Acknowledgments
  • References
  • 3
  • Human cancer
  • 4
  • Alterations of histone modifications in cancer
  • 4.1 Introduction
  • 4.2 Chromatin organization
  • 4.3 Histone modifications
  • 4.3.1 Histone acetylation
  • 4.3.2 Histone methylation
  • 4.3.3 Histone phosphorylation
  • 4.3.4 Histone ubiquitination
  • 4.3.5 Mode of action of histone modifications
  • 4.3.6 Histone crosstalk
  • 4.4 Histone modifications and cancer
  • 4.4.1 Alterations in the pattern of histone H3 modifications
  • 4.4.1.1 H3 oncohistones
  • 4.4.2 Alterations in the pattern of histone H4 modifications
  • 4.4.2.1 H4 oncohistones
  • 4.5 Mechanisms underlying alterations of histone modifications in cancer
  • 4.5.1 Alteration of histone acetylation network
  • 4.5.2 Alteration of the histone methylation network
  • 4.5.2.1 Alteration of histone lysine methylation
  • 4.5.2.1.1 Histone H3K4 methylation
  • 4.5.2.1.2 Mixed-lineage leukemia gene
  • 4.5.2.1.3 SET and MYND domain-containing (SMYD) gene
  • 4.5.2.1.4 Histone H3K9 methylation
  • 4.5.2.1.5 Histone H3K27 methylation
  • 4.5.2.1.5.1 Polycomb repressive complex and EZH2
  • 4.5.2.1.6 Histone H3K36 methylation
  • 4.5.2.2 Other H3 methylation
  • 4.5.2.2.1 Histone H3K79 methylation
  • 4.5.2.3 Modification of HISTONE H4 methylation
  • 4.5.2.3.1 Histone H4K20 methylation
  • 4.5.2.4 Alteration of histone arginine methylation network.
  • 4.5.2.4.1 Histone H3R8me2s and H4R3me2s
  • 4.5.2.4.2 Histone H4R3me2a
  • 4.5.2.4.3 Histone H3R17me2a and H3R26me2a
  • 4.5.2.5 Alteration of histone demethylation
  • 4.5.3 Alterations of histone phosphorylation and ubiquitination
  • 4.6 Conclusions
  • Case study
  • Title
  • Objective
  • Scope
  • Audience
  • Rationale
  • Expected results and deliverables
  • Safety considerations
  • The process, workflow, and actions taken
  • Tools and materials used
  • Results
  • Challenges and solutions
  • Learning and knowledge outcomes
  • Citation
  • List of abbreviations
  • References
  • Further reading
  • 5
  • miRNAs as biomarkers breast cancer and their influence on tumor epigenetics
  • 5.1 Introduction
  • 5.2 Molecular profiling-breast cancer heterogeneity
  • 5.2.1 Subgroup discovery
  • 5.2.2 Multigene expression assays
  • 5.3 miRNAs in breast cancer
  • 5.3.1 Discovery of miRNAs
  • 5.3.2 miRNA biogenesis
  • 5.3.3 Tumor subclassification by miRNAs
  • 5.3.4 Enhancing breast cancer diagnostics using MiRNA
  • 5.4 miRNAs in determining prognosis
  • 5.4.1 miRNAs in predicting clinicopathological data
  • 5.4.2 miRNAs in predicting recurrence and survival
  • 5.5 Potential use of microRNAs for breast cancer therapeutics
  • 5.5.1 Therapeutic strategies
  • 5.5.2 Oncomir inhibition
  • 5.5.3 miRNA replacement therapies
  • 5.5.4 Challenges to miRNA-based therapeutics
  • 5.5.5 Predicting response to neoadjuvant therapies
  • 5.6 miRNAs in breast cancer epigenetics
  • 5.6.1 Breast cancer epigenome
  • 5.6.2 miRNAs regulate breast cancer epigenetics
  • 5.6.3 Epi-miRNAs targeting DNA methyltransferases and demethylases
  • 5.6.4 Epi-miRNAs targeting histone-modifying methyltransferases and demethylases
  • 5.7 Limitations of miRNA use in bioanalytics
  • 5.7.1 Reproducibility and relative quantification
  • 5.7.2 miRNA measurement
  • 5.7.3 Endogenous controls.
  • 5.7.4 Host and environment issues
  • 5.7.5 Future directions
  • 5.8 Conclusion
  • References
  • 6
  • Epigenetic biomarkers: Where are we in cancer therapy
  • 6.1 Introduction
  • 6.2 DNA methylation
  • 6.3 Histone modifications
  • 6.3.1 Histone acetylation and deacetylation
  • 6.3.2 Histone methylation
  • 6.3.3 Histone demethylation
  • 6.4 Nonhistone protein modifications
  • 6.4.1 Acetylation
  • 6.4.2 Methylation
  • 6.4.3 Phosphorylation
  • 6.4.4 Sumoylation
  • 6.4.5 Ubiquitination
  • 6.5 MicroRNAs
  • 6.6 Long noncoding RNAs
  • 6.7 Exosomes
  • 6.8 Future directions
  • 6.9 Chapter summary
  • A case of a phase III clinical trial combining an HDAC inhibitor with steroidal hormonal therapy
  • Objective
  • Scope
  • Audience
  • Rationale
  • Results, deliverables, and safety considerations
  • The process, workflow, and actions taken
  • Efficacy results
  • Biomarker changes
  • Challenges and solutions
  • Learning and knowledge outcomes
  • Acknowledgments
  • References
  • 4
  • Neurological disease
  • 7
  • Epigenetics in neurobehavioral disease
  • 7.1 Introduction
  • 7.2 Epigenetic mechanisms in neurobehavioral disease
  • 7.2.1 DNA methylation
  • 7.2.2 Noncoding RNA
  • 7.2.2.1 Long noncoding RNA
  • 7.2.2.2 Micro RNA
  • 7.2.3 Histone modifications
  • 7.3 Neurotransmitters
  • 7.4 Mood-based disorders
  • 7.5 Addiction
  • 7.6 Psychotic disorders
  • 7.7 Anxiety, fear, and stress disorders
  • 7.8 Sleep and circadian rhythm disorders
  • 7.9 Methodological challenges
  • 7.10 Conclusion
  • Case study
  • Objective
  • Scope
  • Audience
  • Rationale
  • Expected results and deliverables
  • Safety considerations
  • The process, workflow, and actions taken
  • Tools and materials used
  • Results
  • Challenges and solutions
  • Learning and knowledge outcomes
  • Acknowledgments
  • References
  • 8
  • Emerging role of epigenetics in human neurodevelopmental disorders.