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Biomedicines
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Epigenetic Regulation and Its Impact for Medicine (2nd Edition)
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Epigenetic Regulation and Its Impact for Medicine (2nd Edition)

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (31 October 2025) | Viewed by 9013

Special Issue Editor

Dr. Marie Černá

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Guest Editor
Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic
Interests: epigenetics: DNA methylation, RNA interference, gene expression; immunogenetics of autoimmune multifactorial diseases; multiple sclerosis; celiac diseases; type 1 diabetes mellitus; rheumatologic diseases; etiopatogenesis; multifactorial diseases associated with metabolic syndrome X; type 2 diabetes mellitus and its complications (diabetic nephropathy); neurosciences; spinal muscular atrophy (SMA); tumors of the brain (glioblastoma); stroke; variability of genes and genomes; pharmacogenetics and population genetics (Caucasians, American Indians, Gypsies)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The term epigenetics was first introduced by Conrad Waddington in 1942. For half a century, its significance to gene expression, cell differentiation and heritability was unclear. However, modern technologies that emerged at the beginning of the 21st century have opened a new area of research. The epigenetic regulation of the genome allows cells to react to external signals caused by the alternation of gene activity by modifying gene expression. The epigenome controls the accessibility of DNA for transcription factors that regulate the level of gene expression. Therefore, epigenetic modifications are the collective heritable changes in phenotype caused by the processes that arise independent of primary DNA sequences.

A major driving force in epigenetics has been the development of new technology that has not only stimulated new discoveries, but also expanded this field by allowing for novel discoveries only possible through the use of these tools.

Plenty of studies have focused on the identification of possible biomarkers able to predict the onset of the disease, its activity degree, its progression phase and its response to disease-modifying drugs. Non-coding RNAs have the potential to serve as such biomarkers. These molecules can easily be detected in the peripheral blood or urine.

We encourage authors to submit articles and review papers about the role of epigenetic modulation in the etiopathology, prognosis and therapy of various diseases. We believe that this Special Issue will reflect the new era of epigenetics and show its important role in modern medicine.

Dr. Marie Černá
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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. Biomedicines 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 2600 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

  • gene expression
  • DNA methylation
  • histone modifications
  • non-coding RNAs
  • biomarkers

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Related Special Issue

Published Papers (6 papers)

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Research

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23 pages, 2780 KB  
Article
Prematurity and Epigenetic Regulation of SLC6A4: Longitudinal Insights from Birth to the First Month of Life
by Aline de Araújo Brasil, Leo Travassos Vieira Milone, Paulo Victor Barbosa Eleutério dos Santos, Stephanie Cristina Alves de Oliveira Saide, Vitor Barreto Paravidino, Georgia Chalfun, Letícia Santiago da Silva Ferreira, Mariana Berquó Carneiro Ferreira, Anna Beatriz Muniz Ferreira, Geovanna Barroso de Farias, Jaqueline Rodrigues Robaina, Mariana Barros Genuíno de Oliveira, Maria Clara de Magalhães-Barbosa, Arnaldo Prata-Barbosa and Antonio José Ledo Alves da Cunha
Biomedicines 2025, 13(11), 2753; https://doi.org/10.3390/biomedicines13112753 - 11 Nov 2025
Viewed by 469
Abstract
Background/Objectives: Prematurity is a significant global health concern, often associated with neurodevelopmental challenges. Solute Carrier Family 6 Member 4 (SLC6A4), the gene encoding the serotonin transporter, a key component in serotonin reuptake in the synaptic cleft, plays a key role in [...] Read more.
Background/Objectives: Prematurity is a significant global health concern, often associated with neurodevelopmental challenges. Solute Carrier Family 6 Member 4 (SLC6A4), the gene encoding the serotonin transporter, a key component in serotonin reuptake in the synaptic cleft, plays a key role in stress response and neurodevelopment. Epigenetic regulation of stress-related genes, such as SLC6A4, influences neonatal stress adaptation and developmental outcomes. This study aimed to quantify and compare DNA methylation levels at 13 CpG sites in the promoter region of the SLC6A4 gene between preterm and term neonates at three time points. Methods: A cohort of 46 preterm infants and a cohort of 49 full-term infants were analyzed. Blood samples collected at birth (D0), the fifth day (D5), and the thirtieth day (D30) were used to analyze DNA methylation, using bisulfite conversion and pyrosequencing. Results: Significant differences in SLC6A4 methylation were observed. At D0, CpGs 12 and 13 showed higher methylation in preterm infants. CpG 9 showed lower methylation in preterm infants at D5. Extremely preterm infants had the highest values of methylation at the three time points. Longitudinal mixed-effects analysis revealed distinct temporal patterns between groups. Total and site-specific methylation at CpGs 2, 8, and 9 increased over time in full-term infants, while methylation remained stable over time in very preterm and extremely preterm infants. Conclusions: This study reveals significant differences in SLC6A4 methylation between very preterm, extremely preterm, and full-term infants, highlighting the impact of prematurity and early-life stress on the epigenome. These findings contribute to improving our understanding of the epigenetic mechanisms shaping neurodevelopment and stress adaptation in neonates. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine (2nd Edition))
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21 pages, 7735 KB  
Article
MicroRNAs Associated with Parenchymal Hematoma After Endovascular Mechanical Reperfusion for Acute Ischemic Stroke in Rats
by Jin-Kun Zhuang, Zhong-Run Huang, Wang Qin, Chang-Luo Li, Qi Li, Chun Xiang, Yong-Hua Tuo, Zhong Liu, Qian-Yu Chen and Zhong-Song Shi
Biomedicines 2025, 13(2), 449; https://doi.org/10.3390/biomedicines13020449 - 12 Feb 2025
Viewed by 1447
Abstract
Background/Objectives: Hemorrhagic transformation after endovascular thrombectomy predicts poor outcomes in acute ischemic stroke with large-vessel occlusion. The roles of microRNAs (miRNAs) in the pathogenesis of parenchymal hematoma (PH) after endovascular thrombectomy still remain unclear. This study aimed to investigate the miRNA and mRNA [...] Read more.
Background/Objectives: Hemorrhagic transformation after endovascular thrombectomy predicts poor outcomes in acute ischemic stroke with large-vessel occlusion. The roles of microRNAs (miRNAs) in the pathogenesis of parenchymal hematoma (PH) after endovascular thrombectomy still remain unclear. This study aimed to investigate the miRNA and mRNA regulatory network associated with PH after mechanical reperfusion in an animal stroke model and an oxygen–glucose deprivation/reoxygenation (OGD/R) model. Methods: Twenty-five miRNAs were assessed in a mechanical reperfusion-induced hemorrhage transformation model in rats under hyperglycemic conditions receiving 5 h middle cerebral artery occlusion. The differentially expressed miRNAs associated with PH were assessed in a neuron, astrocyte, microglia, brain microvascular endothelial cell (BMEC), and pericyte model of OGD/R. The predicted target genes of the differentially expressed miRNAs were further assessed in the animal model. The miRNA-mRNA regulatory network of PH was established. Results: Thirteen down-regulated miRNAs (miRNA-29a-5p, miRNA-29c-3p, miRNA-126a-5p, miRNA-132-3p, miRNA-136-3p, miRNA-142-3p, miRNA-153-5p, miRNA-218a-5p, miRNA-219a-2-3p, miRNA-369-5p, miRNA-376a-5p, miRNA-376b-5p, and miRNA-383-5p) and one up-regulated miRNA (miRNA-195-3p) were found in the rat peri-infarct with PH after mechanical reperfusion. Of these 14 PH-related miRNAs, 10 were significantly differentially expressed in at least two of the five neuron, astrocyte, microglia, BMEC, and pericyte models after OGD/R, consistent with the animal stroke model results. Thirty-one predicted hub target genes were significantly differentially expressed in the rat peri-infarct with PH after mechanical reperfusion. Forty-nine miRNA-mRNA regulatory axes of PH were revealed, and they were related to the mechanisms of inflammation, immunity, oxidative stress, and apoptosis. Conclusions: Fourteen miRNAs were associated with PH after mechanical reperfusion in the rat stroke and the OGD/R models. Simultaneously differentially expressed miRNAs and related genes in several cells of the neurovascular unit may serve as valuable targets for PH after endovascular thrombectomy in acute ischemic stroke. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine (2nd Edition))
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Review

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38 pages, 2772 KB  
Review
The Role of NSUN Family Genes in m5C Methylation and Diseases
by Tao Jiang, Nili Jiang, Xuan Chen and Zuming Xiong
Biomedicines 2025, 13(12), 2951; https://doi.org/10.3390/biomedicines13122951 - 30 Nov 2025
Viewed by 318
Abstract
5-Methylcytosine (m5C) methylation is a widely present nucleic acid modification in various RNAs and is a reversible epigenetic modification that affects RNA stability, nuclear export, and translation processes. Methylation writers are responsible for adding methyl groups to RNA molecules, regulating gene expression and [...] Read more.
5-Methylcytosine (m5C) methylation is a widely present nucleic acid modification in various RNAs and is a reversible epigenetic modification that affects RNA stability, nuclear export, and translation processes. Methylation writers are responsible for adding methyl groups to RNA molecules, regulating gene expression and cellular function through catalyzing methyl transfer reactions. In order to more intuitively demonstrate the important value of NOL1/NOP2/SUN domain (NSUN) family genes in both tumor and non-tumor diseases, we conducted a relevant review. The NSUN family genes (NSUN1/NOP2, NSUN2, NSUN3, NSUN4, NSUN5, NSUN6, NSUN7) are the main writers of m5C methylation. These genes can regulate methylation and affect the expression of other genes and are important in tumor and non-tumor diseases. Pieces of research on 7 NSUN family genes regarding methylation, diagnostic value, inflammatory diseases, cancer, and other diseases were searched for and summarized separately. Differences in NSUN family genes have been observed in many cancers, which can affect tumor growth, metastasis, chemotherapy resistance, and m5C methylation. In addition to affecting cancer, NSUN family genes have also attracted widespread attention due to their involvement in diseases related to growth, development, and metabolism. NSUN2 is the most studied NSUN family gene, which exhibits cancer promoting effects in various cancers such as lung cancer, liver cancer, and colorectal cancer. This review provides an overview of the roles of NSUN family genes in methylation, diagnostic value, inflammatory diseases, cancer, and other diseases. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine (2nd Edition))
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24 pages, 1055 KB  
Review
Mass Spectrometry for Lysine Methylation: Principles, Progress, and Prospects
by Mackenzie G. Cumming and Kyle K. Biggar
Biomedicines 2025, 13(11), 2825; https://doi.org/10.3390/biomedicines13112825 - 19 Nov 2025
Viewed by 503
Abstract
Lysine methylation is a regulatory post-translational modification with diverse roles across both histone and non-histone proteins. Despite its biological relevance, comprehensive characterization of lysine methylation remains analytically challenging due to its low stoichiometry, subtle mass changes, and the absence of standardized, robust enrichment [...] Read more.
Lysine methylation is a regulatory post-translational modification with diverse roles across both histone and non-histone proteins. Despite its biological relevance, comprehensive characterization of lysine methylation remains analytically challenging due to its low stoichiometry, subtle mass changes, and the absence of standardized, robust enrichment strategies. Mass spectrometry (MS) has become the cornerstone of methylation analysis, supporting both targeted and proteome-wide investigations. In this review, we examine the evolution of MS-based workflows for lysine methylation, including advances in ionization and fragmentation techniques, high-resolution mass analyzers, and acquisition strategies such as data-independent acquisition (DIA) and parallel accumulation–serial fragmentation (PASEF). We evaluate bottom-up, middle-down, and top-down proteomic approaches and discuss enrichment methods ranging from immunoaffinity and chromatography to chemical derivatization. Particular attention is given to persistent challenges, including proteolytic constraints and isobaric interference, that complicate confident site-level resolution. Finally, we highlight emerging solutions and future directions aimed at improving the sensitivity, specificity, and reproducibility of lysine methylation profiling. Together, this synthesis provides a forward-looking roadmap for optimizing MS workflows in methyllysine proteomics. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine (2nd Edition))
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36 pages, 451 KB  
Review
From Petri Dish to Primitive Heart: How IVF Alters Early Cardiac Gene Networks and Epigenetic Landscapes
by Charalampos Voros, Georgios Papadimas, Marianna Theodora, Despoina Mavrogianni, Diamantis Athanasiou, Ioakeim Sapantzoglou, Kyriakos Bananis, Antonia Athanasiou, Aikaterini Athanasiou, Charalampos Tsimpoukelis, Ioannis Papapanagiotou, Dimitrios Vaitsis, Aristotelis-Marios Koulakmanidis, Maria Anastasia Daskalaki, Vasileios Topalis, Nikolaos Thomakos, Panagiotis Antsaklis, Fotios Chatzinikolaou, Dimitrios Loutradis and Georgios Daskalakis
Biomedicines 2025, 13(8), 2044; https://doi.org/10.3390/biomedicines13082044 - 21 Aug 2025
Cited by 1 | Viewed by 1746
Abstract
Numerous infants have been conceived by in vitro fertilization (IVF) and other assisted reproductive technologies (ART). Increasing evidence indicates that these approaches induce minor alterations in molecules during the initial phases of embryogenesis. This narrative review examines the molecular pathophysiology of embryonic cardiogenesis [...] Read more.
Numerous infants have been conceived by in vitro fertilization (IVF) and other assisted reproductive technologies (ART). Increasing evidence indicates that these approaches induce minor alterations in molecules during the initial phases of embryogenesis. This narrative review examines the molecular pathophysiology of embryonic cardiogenesis in the context of assisted reproductive technology, emphasizing transcriptional and epigenetic regulation. Essential transcription factors for cardiac development, including NKX2-5, GATA4, TBX5, ISL1, MEF2C, and HAND1/2, play a crucial role in mesodermal specification, heart tube formation, and chamber morphogenesis. Animal models and human preimplantation embryos have demonstrated that ART-related procedures, including gamete micromanipulation, supraphysiological hormone exposure, and extended in vitro culture, can alter the expression or epigenetic programming of these genes. Subsequent to ART, researchers have identified anomalous patterns of DNA methylation, alterations in histones, and modifications in chromatin accessibility in cardiogenic loci. These alterations indicate that errors occurred during the initial reprogramming process, potentially resulting in structural congenital heart abnormalities (CHDs) or modifications in cardiac function later in life. Analysis of the placental epigenome in babies conceived using assisted reproductive technology reveals that imprinted and developmental genes critical for cardiac development remain dysfunctional. This review proposes a mechanistic theory about the potential subtle alterations in the cardiogenic gene network induced by ART, synthesizing findings from molecular embryology, transcriptomics, and epigenomics. Understanding these molecular issues is crucial not only for enhancing ART protocols but also for evaluating the cardiovascular risk of children conceived by ART postnatally and for early intervention. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine (2nd Edition))

Other

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23 pages, 646 KB  
Systematic Review
Epigenetic Alterations in Ovarian Function and Their Impact on Assisted Reproductive Technologies: A Systematic Review
by Charalampos Voros, Antonia Varthaliti, Despoina Mavrogianni, Diamantis Athanasiou, Antonia Athanasiou, Aikaterini Athanasiou, Anthi-Maria Papahliou, Constantinos G. Zografos, Vasileios Topalis, Panagiota Kondili, Menelaos Darlas, Sophia Sina, Maria Anastasia Daskalaki, Marianna Theodora, Panos Antsaklis and Georgios Daskalakis
Biomedicines 2025, 13(3), 730; https://doi.org/10.3390/biomedicines13030730 - 17 Mar 2025
Cited by 6 | Viewed by 3795
Abstract
Background: Epigenetic modifications have an important role in controlling ovarian function, modulating ovarian response and implantation success in Assisted Reproductive Technologies (ART). The alterations, such as DNA methylation and non-coding RNA control, have been identified as key variables regulating ovarian physiology and [...] Read more.
Background: Epigenetic modifications have an important role in controlling ovarian function, modulating ovarian response and implantation success in Assisted Reproductive Technologies (ART). The alterations, such as DNA methylation and non-coding RNA control, have been identified as key variables regulating ovarian physiology and reproductive outcomes. This systematic review investigates the significance of epigenetic pathways in ovarian function, with an emphasis on their effect on ART success rates. Methods: A thorough search of the PubMed, Scopus, and EMBASE databases was performed to find articles published between 2015 and 2024 that investigated the connection between epigenetic changes and ovarian function in ART patients. Studies that examined miRNA expression, DNA methylation, and histone changes in follicular fluid, granulosa cells, and embryos were included. The study followed the PRISMA recommendations to guarantee scientific rigor and repeatability. The data were combined into a thorough study of epigenetic markers linked to ovarian aging, ovarian reserve, and implantation success. Results: A total of 15 studies satisfied the inclusion criteria, with substantial relationships found between distinct epigenetic markers and ovarian function. Changes in miRNA expression patterns in follicular fluid and granulosa cells were associated with oocyte maturation, ovarian reserve, and implantation potential. Women with low ovarian reserve and polycystic ovary syndrome (PCOS) have different DNA methylation patterns. MiR-27a-3p and miR-15a-5p were shown to be involved with granulosa cell malfunction and poor ovarian response, whereas global DNA hypomethylation was linked to ovarian aging and ART results. Conclusions: Epigenetic alterations affect ovarian function via pathways that control hormone signaling, follicular development, and implantation success. Further study is needed to determine the practical applicability of epigenetic biomarkers in predicting ART effectiveness and enhancing patient treatment procedures. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Its Impact for Medicine (2nd Edition))
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