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Epigenetic Regulation in Human Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 4242

Special Issue Editor


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Guest Editor
Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
Interests: clinical epigenetics (diagnostic and prognostic epi-signatures); EWAS; epigenetic editing (dCAS); epigenetics and machine learning; single-cell analyses
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Special Issue Information

Dear Colleagues,

Epigenetics comprises crucial mechanisms governing chromatin architecture and genome stability. In addition, these epigenetic mechanisms, in turn, regulate the expression of genes in different settings, such as in early development and cell differentiation, in response to environmental (external) factors or in response to/interaction with genetic (internal) variation. The epigenome is thus a highly dynamic regulatory system, and over the last decade the scientific interest in this field has increased tremendously. DNA methylation and histone modifications are, to date, the most commonly studied epigenetic features. Epigenetic regulation is controlled by a complex system of proteins involving epigenetic writers, readers, remodelers, and erasers. Genetic variation in genes encoding for such proteins often leads to severe diseases or syndromes. In many cases, specific epigenetic signatures are associated with particularly rare Mendelian disorders. Since the epigenome can be affected by external and environmental factors, it may also be associated with other classes of disease, including neuro-degenerative diseases, autoimmune diseases, cancer, and non-communicable as well as multi-factorial diseases. Recent progress in statistical methodologies, e.g., machine learning, network analysis, (integrative) multi-omics analyses, and other translational research (e.g., dCAS-based epigenetic editing), has paved the way towards a deeper understanding of the regulatory role of epigenetics within the pathophysiology of disease. In this Special Issue we invite you to submit an original research report or review article deciphering the role of the regulatory mechanism(s) of epigenetics in relation to disease and malignancies, (early) development, aging, or differentiation.

Dr. Peter Henneman
Guest Editor

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Keywords

  • epigenetics
  • integrative analysis
  • regulatory mechanism
  • multi-omics
  • chromatin

Published Papers (3 papers)

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Research

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15 pages, 3706 KiB  
Communication
Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature
by Liselot van der Laan, Kathleen Rooney, Sadegheh Haghshenas, Ananília Silva, Haley McConkey, Raissa Relator, Michael A. Levy, Irene Valenzuela, Laura Trujillano, Amaia Lasa-Aranzasti, Berta Campos, Neus Castells, Eline A. Verberne, Saskia Maas, Mariëlle Alders, Marcel M. A. M. Mannens, Mieke M. van Haelst, Bekim Sadikovic and Peter Henneman
Int. J. Mol. Sci. 2023, 24(18), 14240; https://doi.org/10.3390/ijms241814240 - 18 Sep 2023
Cited by 1 | Viewed by 1036
Abstract
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved [...] Read more.
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22–p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22–p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22–p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost. Full article
(This article belongs to the Special Issue Epigenetic Regulation in Human Disease)
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Review

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28 pages, 968 KiB  
Review
Role of microRNAs in Immune Regulation with Translational and Clinical Applications
by Zsuzsanna Gaál
Int. J. Mol. Sci. 2024, 25(3), 1942; https://doi.org/10.3390/ijms25031942 - 5 Feb 2024
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Abstract
MicroRNAs (miRNAs) are 19–23 nucleotide long, evolutionarily conserved noncoding RNA molecules that regulate gene expression at the post-transcriptional level. In this review, involvement of miRNAs is summarized in the differentiation and function of immune cells, in anti-infective immune responses, immunodeficiencies and autoimmune diseases. [...] Read more.
MicroRNAs (miRNAs) are 19–23 nucleotide long, evolutionarily conserved noncoding RNA molecules that regulate gene expression at the post-transcriptional level. In this review, involvement of miRNAs is summarized in the differentiation and function of immune cells, in anti-infective immune responses, immunodeficiencies and autoimmune diseases. Roles of miRNAs in anticancer immunity and in the transplantation of solid organs and hematopoietic stem cells are also discussed. Major focus is put on the translational clinical applications of miRNAs, including the establishment of noninvasive biomarkers for differential diagnosis and prediction of prognosis. Patient selection and response prediction to biological therapy is one of the most promising fields of application. Replacement or inhibition of miRNAs has enormous therapeutic potential, with constantly expanding possibilities. Although important challenges still await solutions, evaluation of miRNA fingerprints may contribute to an increasingly personalized management of immune dysregulation with a remarkable reduction in toxicity and treatment side effects. More detailed knowledge of the molecular effects of physical exercise and nutrition on the immune system may facilitate self-tailored lifestyle recommendations and advances in prevention. Full article
(This article belongs to the Special Issue Epigenetic Regulation in Human Disease)
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15 pages, 2953 KiB  
Review
Genetic and Epigenetic Factors in Gestational Diabetes Mellitus Pathology
by Łukasz Ustianowski, Jakub Udzik, Joanna Szostak, Anna Gorący, Klaudia Ustianowska and Andrzej Pawlik
Int. J. Mol. Sci. 2023, 24(23), 16619; https://doi.org/10.3390/ijms242316619 - 22 Nov 2023
Cited by 1 | Viewed by 1384
Abstract
Gestational diabetes (GDM) is the carbohydrate intolerance occurring during pregnancy. The risk factors of GDM include obesity, advanced maternal age, polycystic ovary syndrome, multigravidity, a sedentary lifestyle, and pre-existing hypertension. Additionally, complex genetic and epigenetic processes are also believed to play a crucial [...] Read more.
Gestational diabetes (GDM) is the carbohydrate intolerance occurring during pregnancy. The risk factors of GDM include obesity, advanced maternal age, polycystic ovary syndrome, multigravidity, a sedentary lifestyle, and pre-existing hypertension. Additionally, complex genetic and epigenetic processes are also believed to play a crucial role in the development of GDM. In this narrative review, we discuss the role of genetic and epigenetic factors in gestational diabetes mellitus pathogenesis. Full article
(This article belongs to the Special Issue Epigenetic Regulation in Human Disease)
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