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Epigenomes
Special Issues
Complex Disease Epigenetics
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Complex Disease Epigenetics

A special issue of Epigenomes (ISSN 2075-4655).

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 19399

Special Issue Editors

Dr. Miina Ollikainen

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Guest Editor
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00100 Helsinki, Finland
Interests: epigenetics; genetics; complex traits; twin study; early development; obesity; smoking; alcohol use
Special Issues, Collections and Topics in MDPI journals
Dr. Riikka Lund

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Guest Editor
Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
Interests: Epigenomics; genomics; transcriptomics; pluripotent stem cells; biomedicine; development; aging; molecular mechanisms of diseases; next-generation sequencing; genome-wide methods
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Complex diseases and traits have a genetic background, yet the final phenotypic outcome largely depends on an individual’s environment and lifestyle. Epigenetic modifications link these environmental factors to ontogenesis and disease development by dynamically altering gene expression.

In recent years, an increasing number of epigenome-wide association studies (EWAS) have been conducted, identifying thousands of associations between DNA methylation and diseases or traits. However, understanding the direction of these associations remains challenging. Mendelian randomization has become a powerful tool to infer causality in epigenetic modifications associated with disease outcomes. Furthermore, family and twin studies have shown that variation in epigenetic patterns is partly heritable, with disease-discordant monozygotic twins proving to be particularly informative. Despite the growing evidence of the impact of environmental exposures on epigenetic changes and subsequent disease development, we are far from fully understanding the underlying molecular mechanisms of complex disease onset and progression.

This Special Issue will focus on assembling our current knowledge of epigenetic changes in complex human diseases and traits. We will consider review, research or methods manuscripts of exceptional interest on the following topics:

  • Robust epigenetic associations and inferring causality
  • Epigenetic disease markers, risk predictors, and intervention targets
  • Interactions between the genome and epigenome
  • Novel study designs applied to epigenetic data
  • Methodological developments in epigenetics research

Dr. Miina Ollikainen
Dr. Riikka Lund
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Epigenomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Epigenetics
  • Epigenomics
  • Epigenome-wide association study
  • DNA methylation
  • Causality
  • Complex disease
  • Histone modifications
  • Noncoding RNAs

Published Papers (4 papers)

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Research

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11 pages, 627 KiB  
Article
Genome-Wide DNA Methylation and LncRNA-Associated DNA Methylation in Metformin-Treated and -Untreated Diabetes
by Wendy L. Solomon, Stanton B. E. Hector, Shanel Raghubeer, Rajiv T. Erasmus, Andre P. Kengne and Tandi E. Matsha
Epigenomes 2020, 4(3), 19; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4030019 - 01 Sep 2020
Cited by 7 | Viewed by 4109
Abstract
Metformin, which is used as a first line treatment for type 2 diabetes mellitus (T2DM), has been shown to affect epigenetic patterns. In this study, we investigated the DNA methylation and potential lncRNA modifications in metformin-treated and newly diagnosed adults with T2DM. Genome-wide [...] Read more.
Metformin, which is used as a first line treatment for type 2 diabetes mellitus (T2DM), has been shown to affect epigenetic patterns. In this study, we investigated the DNA methylation and potential lncRNA modifications in metformin-treated and newly diagnosed adults with T2DM. Genome-wide DNA methylation and lncRNA analysis were performed from the peripheral blood of 12 screen-detected and 12 metformin-treated T2DM individuals followed by gene ontology (GO) and KEGG pathway analysis. Differentially methylated regions (DMRs) observed showed 22 hypermethylated and 11 hypomethylated DMRs between individuals on metformin compared to screen-detected subjects. Amongst the hypomethylated DMR regions were the SLC gene family, specifically, SLC25A35 and SLC28A1. Fifty-seven lncRNA-associated DNA methylation regions included the mitochondrial ATP synthase-coupling factor 6 (ATP5J). Functional gene mapping and pathway analysis identified regions in the axon initial segment (AIS), node of Ranvier, cell periphery, cleavage furrow, cell surface furrow, and stress fiber. In conclusion, our study has identified a number of DMRs and lncRNA-associated DNA methylation regions in metformin-treated T2DM that are potential targets for therapeutic monitoring in patients with diabetes. Full article
(This article belongs to the Special Issue Complex Disease Epigenetics)
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Review

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23 pages, 2100 KiB  
Review
An Epigenetics-Based Hypothesis of Autoantigen Development in Systemic Lupus Erythematosus
by Wesley Brooks
Epigenomes 2020, 4(2), 6; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4020006 - 23 Apr 2020
Cited by 5 | Viewed by 3801
Abstract
Currently, we have a limited understanding of mechanisms leading to systemic lupus erythematosus, but we know that genetics, environmental factors, and epigenetics contribute to the disease. One common aspect of the various environmental triggers is that they can cause cellular stress. When extraordinary [...] Read more.
Currently, we have a limited understanding of mechanisms leading to systemic lupus erythematosus, but we know that genetics, environmental factors, and epigenetics contribute to the disease. One common aspect of the various environmental triggers is that they can cause cellular stress. When extraordinary stress occurs, such as viral activation, a cell’s response can include increased nucleolar volume and activity to produce more machinery (e.g., ribosomes) to help the cell recover. However, nucleolar expansion can disrupt the epigenetic control in neighboring heterochromatin that comprises the nucleolar shell. This disruption can open underlying vulnerabilities that provoke an autoimmune reaction. Here, we review the “X chromosome-nucleolus nexus” hypothesis, which explains how nucleolar stress can disrupt epigenetically silenced chromatin, especially the neighboring inactive X chromosome (aka the nucleolar satellite). Chromatin disruption can lead to the expression of sequestered DNA, such as Alu elements and fully functional LINE-1 reverse transcriptase genes. In addition, Alu transcripts can disrupt the nucleolar structural integrity, leading to nucleolar disintegration. Such disintegration can leave nucleolar components and products in autoantigenic forms, such as abnormal conformations or incomplete macromolecular assemblies. Recent research on DNA sensing pathways can now be incorporated into the hypothesis to provide further details explaining how autoantibodies to endogenous nucleic acids arise. Full article
(This article belongs to the Special Issue Complex Disease Epigenetics)
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25 pages, 1455 KiB  
Review
Targeting HDAC Complexes in Asthma and COPD
by Martijn R. H. Zwinderman, Sander de Weerd and Frank J. Dekker
Epigenomes 2019, 3(3), 19; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes3030019 - 07 Sep 2019
Cited by 31 | Viewed by 5967
Abstract
Around three million patients die due to airway inflammatory diseases each year. The most notable of these diseases are asthma and chronic obstructive pulmonary disease (COPD). Therefore, new therapies are urgently needed. Promising targets are histone deacetylases (HDACs), since they regulate posttranslational protein [...] Read more.
Around three million patients die due to airway inflammatory diseases each year. The most notable of these diseases are asthma and chronic obstructive pulmonary disease (COPD). Therefore, new therapies are urgently needed. Promising targets are histone deacetylases (HDACs), since they regulate posttranslational protein acetylation. Over a thousand proteins are reversibly acetylated, and acetylation critically influences aberrant intracellular signaling pathways in asthma and COPD. The diverse set of selective and non-selective HDAC inhibitors used in pre-clinical models of airway inflammation show promising results, but several challenges still need to be overcome. One such challenge is the design of HDAC inhibitors with unique selectivity profiles, such as selectivity towards specific HDAC complexes. Novel strategies to disrupt HDAC complexes should be developed to validate HDACs further as targets for new anti-inflammatory pulmonary treatments. Full article
(This article belongs to the Special Issue Complex Disease Epigenetics)
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18 pages, 567 KiB  
Review
Epigenetic Modifications in Generalized Autoimmune Epithelitis: Sjögren’s Syndrome and Primary Biliary Cholangitis
by Pinelopi Arvaniti, Kalliopi Zachou, Aggeliki Lyberopoulou, Nikolaos K. Gatselis, Wesley H. Brooks, George N. Dalekos and Yves Renaudineau
Epigenomes 2019, 3(3), 15; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes3030015 - 08 Aug 2019
Cited by 6 | Viewed by 4830
Abstract
Sjögren’s syndrome (SjS) and primary biliary cholangitis (PBC) can be classified as a model of generalized autoimmune epithelitis based on their frequent coexistence in clinical practice and the highly specific immune mediated injury of target epithelial cells. Both of these autoimmune diseases are [...] Read more.
Sjögren’s syndrome (SjS) and primary biliary cholangitis (PBC) can be classified as a model of generalized autoimmune epithelitis based on their frequent coexistence in clinical practice and the highly specific immune mediated injury of target epithelial cells. Both of these autoimmune diseases are characterized by female predominance, highly specific circulating autoantibodies, and immune-mediated destruction of the salivary and lachrymal glands and the biliary epithelial cells, respectively. Although the genetic predisposition has been well described for both diseases, genetic studies have failed to completely elucidate their pathogenesis. The recent integration of epigenetic data, analyzing the different cellular partners, opens new perspectives and allows for better understanding of these complex and still incurable diseases. Epigenetic studies on SjS have elucidated the role of DNA methylation alterations in disease pathogenesis, while epigenetic changes that influence expression of genes on the X chromosome have been implicated in the geo-variability and occurrence of PBC. The aim of this review is to describe the advances in epigenetics in the field of autoimmune epithelitis as well as to highlight how epigenetic changes could contribute to better understanding of disease pathogenesis and progression. These advances could yield insights on novel therapeutic interventions. Full article
(This article belongs to the Special Issue Complex Disease Epigenetics)
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