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Biomolecules
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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 5670

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 (4 papers)

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Research

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19 pages, 6791 KiB  
Article
Hypermethylation of the Gene Body in SRCIN1 Is Involved in Breast Cancer Cell Proliferation and Is a Potential Blood-Based Biomarker for Early Detection and a Poor Prognosis
by Hsieh-Tsung Shen, Chin-Sheng Hung, Clilia Davis, Chih-Ming Su, Li-Min Liao, Hsiu-Ming Shih, Kuan-Der Lee, Muhamad Ansar and Ruo-Kai Lin
Biomolecules 2024, 14(5), 571; https://doi.org/10.3390/biom14050571 - 12 May 2024
Viewed by 474
Abstract
Breast cancer is a leading cause of cancer mortality in women worldwide. Using the Infinium MethylationEPIC BeadChip, we analyzed plasma sample methylation to identify the SRCIN1 gene in breast cancer patients. We assessed SRCIN1-related roles and pathways for their biomarker potential. To [...] Read more.
Breast cancer is a leading cause of cancer mortality in women worldwide. Using the Infinium MethylationEPIC BeadChip, we analyzed plasma sample methylation to identify the SRCIN1 gene in breast cancer patients. We assessed SRCIN1-related roles and pathways for their biomarker potential. To verify the methylation status, quantitative methylation-specific PCR (qMSP) was performed on genomic DNA and circulating cell-free DNA samples, and mRNA expression analysis was performed using RT‒qPCR. The results were validated in a Western population; for this analysis, the samples included plasma samples from breast cancer patients from the USA and from The Cancer Genome Atlas (TCGA) cohort. To study the SRCIN1 pathway, we conducted cell viability assays, gene manipulation and RNA sequencing. SRCIN1 hypermethylation was identified in 61.8% of breast cancer tissues from Taiwanese patients, exhibiting specificity to this malignancy. Furthermore, its presence correlated significantly with unfavorable 5-year overall survival outcomes. The levels of methylated SRCIN1 in the blood of patients from Taiwan and the USA correlated with the stage of breast cancer. The proportion of patients with high methylation levels increased from 0% in healthy individuals to 63.6% in Stage 0, 80% in Stage I and 82.6% in Stage II, with a sensitivity of 78.5%, an accuracy of 90.3% and a specificity of 100%. SRCIN1 hypermethylation was significantly correlated with increased SRCIN1 mRNA expression (p < 0.001). Knockdown of SRCIN1 decreased the viability of breast cancer cells. SRCIN1 silencing resulted in the downregulation of ESR1, BCL2 and various cyclin protein expressions. SRCIN1 hypermethylation in the blood may serve as a noninvasive biomarker, facilitating early detection and prognosis evaluation, and SRCIN1-targeted therapies could be used in combination regimens for breast cancer patients. Full article
(This article belongs to the Special Issue DNA Methylation in Human Diseases)
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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 - 8 Oct 2023
Viewed by 1911
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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14 pages, 1357 KiB  
Review
Biological Rhythms, Chrono-Nutrition, and Gut Microbiota: Epigenomics Insights for Precision Nutrition and Metabolic Health
by Nathalia Caroline de Oliveira Melo, Amanda Cuevas-Sierra, Vitória Felício Souto and J. Alfredo Martínez
Biomolecules 2024, 14(5), 559; https://doi.org/10.3390/biom14050559 - 6 May 2024
Viewed by 1022
Abstract
Circadian rhythms integrate a finely tuned network of biological processes recurring every 24 h, intricately coordinating the machinery of all cells. This self-regulating system plays a pivotal role in synchronizing physiological and behavioral responses, ensuring an adaptive metabolism within the environmental milieu, including [...] Read more.
Circadian rhythms integrate a finely tuned network of biological processes recurring every 24 h, intricately coordinating the machinery of all cells. This self-regulating system plays a pivotal role in synchronizing physiological and behavioral responses, ensuring an adaptive metabolism within the environmental milieu, including dietary and physical activity habits. The systemic integration of circadian homeostasis involves a balance of biological rhythms, each synchronically linked to the central circadian clock. Central to this orchestration is the temporal dimension of nutrient and food intake, an aspect closely interwoven with the neuroendocrine circuit, gut physiology, and resident microbiota. Indeed, the timing of meals exerts a profound influence on cell cycle regulation through genomic and epigenetic processes, particularly those involving gene expression, DNA methylation and repair, and non-coding RNA activity. These (epi)genomic interactions involve a dynamic interface between circadian rhythms, nutrition, and the gut microbiota, shaping the metabolic and immune landscape of the host. This research endeavors to illustrate the intricate (epi)genetic interplay that modulates the synchronization of circadian rhythms, nutritional signaling, and the gut microbiota, unravelling the repercussions on metabolic health while suggesting the potential benefits of feed circadian realignment as a non-invasive therapeutic strategy for systemic metabolic modulation via gut microbiota. This exploration delves into the interconnections that underscore the significance of temporal eating patterns, offering insights regarding circadian rhythms, gut microbiota, and chrono-nutrition interactions with (epi)genomic phenomena, thereby influencing diverse aspects of metabolic, well-being, and quality of life outcomes. Full article
(This article belongs to the Special Issue DNA Methylation in Human Diseases)
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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 1464
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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