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8.3
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Journals
Biomolecules
Special Issues
DNA Methylation in Human Diseases
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DNA Methylation in Human Diseases

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Nucleic Acids".

Deadline for manuscript submissions: 15 August 2024 | Viewed by 3851

Special Issue Editors

Dr. Eleonora Loi

E-Mail Website
Guest Editor
Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy
Interests: DNA methylation alterations; bioinformatic analysis of genomic and epigenomic data; epigenome editing; 2D and 3D cellular models; epigenomics
Special Issues, Collections and Topics in MDPI journals
Dr. Patrizia Zavattari

E-Mail Website
Guest Editor
Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy
Interests: DNA methylation alterations; somatic mutations and epimutations in solid and blood cancers; genomics; epigenomics; genetics of complex traits; trace elements and multifactorial diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Ana Florencia Vega Benedetti

E-Mail Website
Guest Editor
Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy
Interests: DNA methylation alterations; iPSC generation and cellular differentiation; 3D cellular models; solid tumors; infectious diseases

Special Issue Information

Dear Colleagues,

DNA methylation plays a crucial role in many biological processes, contributing to gene expression regulation. A growing body of evidence underlines that DNA methylation alterations are associated with several human diseases, including cancer, imprinting disorders, metabolic disorders, infectious diseases, autoimmune diseases, neurological disorders and others. Defects in the machinery that regulates the establishment and the maintenance of DNA methylation pattern can give rise to gene expression changes, leading to the onset of human diseases and influence their clinical course. Therefore, DNA methylation changes can be used as biomarkers at all stages of clinical disease management, from risk assessment, early diagnosis, prognosis, treatment choice and relapse monitoring. Furthermore, given the reversible nature of epigenetic modifications, there is an increasing interest in developing methods to reverse DNA methylation aberrations.

This Special Issue welcomes contributions focused on the role of DNA methylation in human diseases, including, but not limited to, studies aimed at elucidating the mechanisms leading to DNA methylation aberrations, understanding the functional impact of DNA methylation changes, the discovery of potential DNA methylation biomarkers and the development of new therapies based on DNA methylation reprogramming.

Dr. Eleonora Loi
Dr. Patrizia Zavattari
Dr. Ana Florencia Vega Benedetti
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. Biomolecules is an international peer-reviewed open access monthly 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 2700 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

  • DNA methylation alterations
  • DNA methylation profiling
  • DNMT aberrations
  • TET aberrations
  • DNA methylation machinery
  • DNA methylation biomarkers
  • DNA methylation reprogramming

Published Papers (2 papers)

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Research

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16 pages, 5050 KiB  
Article
Nicotinic Acid-Mediated Modulation of Metastasis-Associated Protein 1 Methylation and Inflammation in Brain Arteriovenous Malformation
by Xinpeng Deng, Shengjun Zhou, Ziliang Hu, Fanyong Gong, Junjun Zhang, Chenhui Zhou, Wenting Lan, Xiang Gao and Yi Huang
Biomolecules 2023, 13(10), 1495; https://doi.org/10.3390/biom13101495 - 08 Oct 2023
Viewed by 1829
Abstract
We explored metastasis-associated protein 1 (MTA1) promoter methylation in the development of brain arteriovenous malformation (BAVM). The clinical data of 148 sex- and age-matched BAVMs and controls were collected, and the MTA1 DNA methylation in peripheral white blood cells (WBC) was [...] Read more.
We explored metastasis-associated protein 1 (MTA1) promoter methylation in the development of brain arteriovenous malformation (BAVM). The clinical data of 148 sex- and age-matched BAVMs and controls were collected, and the MTA1 DNA methylation in peripheral white blood cells (WBC) was assessed by bisulfite pyrosequencing. Among them, 18 pairs of case–control samples were used for WBC mRNA detection, 32 pairs were used for WBC MTA1 protein measurement, and 50 pairs were used for plasma inflammatory factor analysis. Lipopolysaccharide (LPS) treatment was used to induce an inflammatory injury cell model of human brain microvascular endothelial cells (BMECS). 5-Aza-2′-deoxycytidine (5-AZA), nicotinic acid (NA), and MTA1 siRNAs were used in functional experiments to examine BMECS behaviors. RT-qPCR, Western blot, and ELISA or cytometric bead arrays were used to measure the expression levels of MTA1, cytokines, and signaling pathway proteins in human blood or BMECS. The degree of MTA1 promoter methylation was reduced in BAVM compared with the control group and was inversely proportional to MTA1 expression. Plasma ApoA concentrations in BAVM patients were significantly lower than those in controls and correlated positively with MTA1 promoter methylation and negatively with MTA1 expression. The expression of cytokine was markedly higher in BAVM than in controls. Cell experiments showed that 5-AZA decreased the methylation level of MTA1 and increased the expression of MTA1 protein. LPS treatment significantly increased cytokine concentrations (p < 0.05). NA and MTA1 silencing could effectively reverse the LPS-mediated increase in IL-6 and TNF-α expression through the NF-κB pathway. Our study indicated that NA may regulate MTA1 expression by affecting promoter DNA methylation, improve vascular inflammation through the NF-κB pathway, and alleviate the pathological development of BAVM. Full article
(This article belongs to the Special Issue DNA Methylation in Human Diseases)
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Review

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21 pages, 6812 KiB  
Review
Transgenerational Epigenetic DNA Methylation Editing and Human Disease
by Joshua D. Tompkins
Biomolecules 2023, 13(12), 1684; https://doi.org/10.3390/biom13121684 - 22 Nov 2023
Viewed by 1344
Abstract
During gestation, maternal (F0), embryonic (F1), and migrating primordial germ cell (F2) genomes can be simultaneously exposed to environmental influences. Accumulating evidence suggests that operating epi- or above the genetic DNA sequence, covalent DNA methylation (DNAme) can be recorded onto DNA in response [...] Read more.
During gestation, maternal (F0), embryonic (F1), and migrating primordial germ cell (F2) genomes can be simultaneously exposed to environmental influences. Accumulating evidence suggests that operating epi- or above the genetic DNA sequence, covalent DNA methylation (DNAme) can be recorded onto DNA in response to environmental insults, some sites which escape normal germline erasure. These appear to intrinsically regulate future disease propensity, even transgenerationally. Thus, an organism’s genome can undergo epigenetic adjustment based on environmental influences experienced by prior generations. During the earliest stages of mammalian development, the three-dimensional presentation of the genome is dramatically changed, and DNAme is removed genome wide. Why, then, do some pathological DNAme patterns appear to be heritable? Are these correctable? In the following sections, I review concepts of transgenerational epigenetics and recent work towards programming transgenerational DNAme. A framework for editing heritable DNAme and challenges are discussed, and ethics in human research is introduced. Full article
(This article belongs to the Special Issue DNA Methylation in Human Diseases)
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