Special Issue "DNA Methylation in Health and Diseases"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 1 November 2019.

Special Issue Editor

Guest Editor
Prof. Dr. Maurizio D'Esposito Website E-Mail
Institute of Genetics and Biophysics, Adriano Buzzati Traverso, 80131 Naples, Italy
Interests: epigenetics; DNA methylation; MECP2; Rett syndrome; chromatin diseases

Special Issue Information

Dear Colleagues,

The completion of the human genome project produced a comprehensive list of all genes necessary to build a human organism. However, years of extensive research have demonstrated that the situation is far more complex than a simple list of genes. There is an additional system encoding spatio-temporal information that cells use to determine when and where a particular gene will be expressed during development. This information is overlaid upon the DNA in the form of epigenetic marks, which are heritable during cell division but do not involve changes in the DNA sequence. One of the best characterized epigenetic modification of DNA in mammalian cells is the methylation of cytosines belonging to CpG doublets.

Here we review the impact of the studies on DNA methylation, the “primadonna” in the epigenetic scenario, on the understanding of basic processes and pathological conditions that bring the so-called Chromatin Diseases.

This Special Issue will thus be subdivided into contributions focused on the role of DNA methylation in biological processes, such as imprinting, the establishment of pluripotency, the impact of nutrients in brain epigenetics, and the changes of DNA methylation during brain development. The study of the DNA methylation changes in the diagnosis of genetic diseases will be discussed.

Conversely, the alteration of DNA methylation in genetic diseases will be thoroughly discussed, including relatively rare diseases (e.g., FSHD syndrome) and more common diseases, such as unstable repeat disorders as well as renal and immune diseases. Pathologies such as ischemic stroke, and its association to epigenetic deregulation and DNA methylation, will be also discussed.

Finally, we will give attention to the alterations in components of DNA methylation machinery (either writers or readers), which give rise to diseases such as Rett syndrome, mutated in the transcriptional modulator MECP2 and ICF syndrome, and mutated in the DNA methyltransferase DNMT3B.

Prof. Dr. Maurizio D'Esposito
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 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
  • DNA methylation
  • genome architecture
  • genomic imprinting
  • chromatin diseases
  • mechanisms of diseases
  • MECP2

Published Papers (2 papers)

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Research

Open AccessArticle
DNA Methylation Module Network-Based Prognosis and Molecular Typing of Cancer
Genes 2019, 10(8), 571; https://doi.org/10.3390/genes10080571 - 28 Jul 2019
Abstract
Achieving cancer prognosis and molecular typing is critical for cancer treatment. Previous studies have identified some gene signatures for the prognosis and typing of cancer based on gene expression data. Some studies have shown that DNA methylation is associated with cancer development, progression, [...] Read more.
Achieving cancer prognosis and molecular typing is critical for cancer treatment. Previous studies have identified some gene signatures for the prognosis and typing of cancer based on gene expression data. Some studies have shown that DNA methylation is associated with cancer development, progression, and metastasis. In addition, DNA methylation data are more stable than gene expression data in cancer prognosis. Therefore, in this work, we focused on DNA methylation data. Some prior researches have shown that gene modules are more reliable in cancer prognosis than are gene signatures and that gene modules are not isolated. However, few studies have considered cross-talk among the gene modules, which may allow some important gene modules for cancer to be overlooked. Therefore, we constructed a gene co-methylation network based on the DNA methylation data of cancer patients, and detected the gene modules in the co-methylation network. Then, by permutation testing, cross-talk between every two modules was identified; thus, the module network was generated. Next, the core gene modules in the module network of cancer were identified using the K-shell method, and these core gene modules were used as features to study the prognosis and molecular typing of cancer. Our method was applied in three types of cancer (breast invasive carcinoma, skin cutaneous melanoma, and uterine corpus endometrial carcinoma). Based on the core gene modules identified by the constructed DNA methylation module networks, we can distinguish not only the prognosis of cancer patients but also use them for molecular typing of cancer. These results indicated that our method has important application value for the diagnosis of cancer and may reveal potential carcinogenic mechanisms. Full article
(This article belongs to the Special Issue DNA Methylation in Health and Diseases)
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Open AccessArticle
Methylome-Wide Association Study in Peripheral White Blood Cells Focusing on Central Obesity and Inflammation
Genes 2019, 10(6), 444; https://doi.org/10.3390/genes10060444 - 11 Jun 2019
Abstract
Epigenetic signatures such as DNA methylation may be associated with specific obesity traits in different tissues. The onset and development of some obesity-related complications are often linked to visceral fat accumulation. The aim of this study was to explore DNA methylation levels in [...] Read more.
Epigenetic signatures such as DNA methylation may be associated with specific obesity traits in different tissues. The onset and development of some obesity-related complications are often linked to visceral fat accumulation. The aim of this study was to explore DNA methylation levels in peripheral white blood cells to identify epigenetic methylation marks associated with waist circumference (WC). DNA methylation levels were assessed using Infinium Human Methylation 450K and MethylationEPIC beadchip (Illumina) to search for putative associations with WC values of 473 participants from the Methyl Epigenome Network Association (MENA) project. Statistical analysis and Ingenuity Pathway Analysis (IPA) were employed for assessing the relationship between methylation and WC. A total of 669 CpGs were statistically associated with WC (FDR < 0.05, slope ≥ |0.1|). From these CpGs, 375 CpGs evidenced a differential methylation pattern between females with WC ≤ 88 and > 88 cm, and 95 CpGs between males with WC ≤ 102 and > 102 cm. These differentially methylated CpGs are located in genes related to inflammation and obesity according to IPA. Receiver operating characteristic (ROC) curves of the top four significant differentially methylated CpGs separated by sex discriminated individuals with presence or absence of abdominal fat. ROC curves of all the CpGs from females and one CpG from males were validated in an independent sample (n = 161). These methylation results add further insights about the relationships between obesity, adiposity-associated comorbidities, and DNA methylation where inflammation processes may be involved. Full article
(This article belongs to the Special Issue DNA Methylation in Health and Diseases)
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