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Molecular Research on Epigenetic Modifications
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Molecular Research on Epigenetic Modifications

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 February 2025 | Viewed by 8687

Special Issue Editors

Dr. Marco Miceli

E-Mail Website
Guest Editor
1. Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, 80131 Naples, Italy
2. CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
Interests: epigenetics; HDAC; HDAC inhibitors; human mesenchymal stem cells (hMSC); amniocytes and bone regeneration
Dr. Mariella Cuomo

E-Mail Website
Guest Editor
1. Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, 80131 Naples, Italy
2. CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
Interests: DNA methylation; brain tumors; stem cells
Dr. Rosa Della Monica

E-Mail Website
Guest Editor
1. Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, 80131 Naples, Italy
2. CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
Interests: DNA methylation; brain tumors; cell cycle
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Epigenetics generally refers to heritable changes in gene expression and in the organization of chromatin that are not caused by alterations in the DNA sequence. The complexity of the mammalian genome is regulated by heritable epigenetic mechanisms, which are the basis of cell differentiation, development and homeostasis. These mechanisms help to determine cell fate and phenotype and must be stably maintained during cell division to preserve their identity, as well as to react to intrinsic signals during development or those originating from external environmental factors. Aberrations in epigenetic modifications are essential protagonists in the genesis and progression of various diseases, including cancer, assuming a predominant role in the understanding and treatment of these diseases.

These aberrations can lead to inappropriate expression or activation of transcription factors associated with oncogenesis and/or inactivation or inability to express tumor suppressor genes. The molecular basis of epigenetics is very complex and the discovery of new molecular targets for new and more powerful drugs has led to the search for small modulating molecules that can revert an increasing number of diseases.

Led by Dr. Marco Miceli and assisted by our co-Guest editors, Dr. Mariella Cuomo and Dr. Rosa Della Monica, this Special Issue of IJMS, “Molecular Research on Epigenetic Modifications”, welcomes researchers to contribute to the scientific advancement of this promising new discipline.

Dr. Marco Miceli
Dr. Mariella Cuomo
Dr. Rosa Della Monica
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • epigenetic modifications
  • chromatin remodeling
  • transcription factors
  • RNA modification
  • histones
  • methylation
  • diseases
  • epigenetic drugs development

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Published Papers (4 papers)

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Research

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18 pages, 4484 KiB  
Article
Changes in Gut Microbial Composition and DNA Methylation in Obese Patients with NAFLD After Bariatric Surgery
by Antonella Agodi, Claudia Ojeda-Granados, Andrea Maugeri, Martina Barchitta, Ornella Coco, Salvatore Pezzino, Gaetano Magro, Gaetano La Greca, Francesco Saverio Latteri, Sergio Castorina and Stefano Puleo
Int. J. Mol. Sci. 2024, 25(21), 11510; https://doi.org/10.3390/ijms252111510 - 26 Oct 2024
Viewed by 735
Abstract
This study investigates the effects of bariatric surgery on non-alcoholic fatty liver disease (NAFLD) by examining the interplay between gut microbiota, epigenetics, and metabolic health. A cohort of 22 patients undergoing sleeve gastrectomy (SG) was analyzed for changes in gut microbial composition and [...] Read more.
This study investigates the effects of bariatric surgery on non-alcoholic fatty liver disease (NAFLD) by examining the interplay between gut microbiota, epigenetics, and metabolic health. A cohort of 22 patients undergoing sleeve gastrectomy (SG) was analyzed for changes in gut microbial composition and DNA methylation profiles before and six months after surgery. Correlations between gut microbial abundance and clinical markers at baseline revealed that certain genera were associated with worse metabolic health and liver markers. Following SG, significant improvements were observed in the clinical, anthropometric, and biochemical parameters of the NAFLD patients. Although alpha-diversity indices (i.e., Chao1, Simpson, Shannon) did not show significant changes, beta-diversity analysis revealed a slight shift in microbial composition (PERMANOVA, p = 0.036). Differential abundance analysis identified significant changes in specific bacterial taxa, including an increase in beneficial Lactobacillus species such as Lactobacillus crispatus and Lactobacillus iners and a decrease in harmful taxa like Erysipelotrichia. Additionally, DNA methylation analysis revealed 609 significant differentially methylated CpG sites between the baseline values and six months post-surgery, with notable enrichment in genes related to the autophagy pathway, such as IRS4 and ATG4B. The results highlight the individualized responses to bariatric surgery and underscore the potential for personalized treatment strategies. In conclusion, integrating gut microbiota and epigenetic factors into NAFLD management could enhance treatment outcomes, suggesting that future research should explore microbiome-targeted therapies and long-term follow-ups on liver health post-surgery. Full article
(This article belongs to the Special Issue Molecular Research on Epigenetic Modifications)
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14 pages, 2060 KiB  
Article
Unraveling the Role of JMJD1B in Genome Stability and the Malignancy of Melanomas
by Perla Cruz, Diego Peña-Lopez, Diego Figueroa, Isidora Riobó, Vincenzo Benedetti, Francisco Saavedra, Claudia Espinoza-Arratia, Thelma M. Escobar, Alvaro Lladser and Alejandra Loyola
Int. J. Mol. Sci. 2024, 25(19), 10689; https://doi.org/10.3390/ijms251910689 - 4 Oct 2024
Viewed by 820
Abstract
Genome instability relies on preserving the chromatin structure, with any histone imbalances threating DNA integrity. Histone synthesis occurs in the cytoplasm, followed by a maturation process before their nuclear translocation. This maturation involves protein folding and the establishment of post-translational modifications. Disruptions in [...] Read more.
Genome instability relies on preserving the chromatin structure, with any histone imbalances threating DNA integrity. Histone synthesis occurs in the cytoplasm, followed by a maturation process before their nuclear translocation. This maturation involves protein folding and the establishment of post-translational modifications. Disruptions in this pathway hinder chromatin assembly and contribute to genome instability. JMJD1B, a histone demethylase, not only regulates gene expression but also ensures a proper supply of histones H3 and H4 for the chromatin assembly. Reduced JMJD1B levels lead to the cytoplasmic accumulation of histones, causing defects in the chromatin assembly and resulting in DNA damage. To investigate the role of JMJD1B in regulating genome stability and the malignancy of melanoma tumors, we used a JMJD1B/KDM3B knockout in B16F10 mouse melanoma cells to perform tumorigenic and genome instability assays. Additionally, we analyzed the transcriptomic data of human cutaneous melanoma tumors. Our results show the enhanced tumorigenic properties of JMJD1B knockout melanoma cells both in vitro and in vivo. The γH2AX staining, Micrococcal Nuclease sensitivity, and comet assays demonstrated increased DNA damage and genome instability. The JMJD1B expression in human melanoma tumors correlates with a lower mutational burden and fewer oncogenic driver mutations. Our findings highlight JMJD1B’s role in maintaining genome integrity by ensuring a proper histone supply to the nucleus, expanding its function beyond gene expression regulation. JMJD1B emerges as a crucial player in preserving genome stability and the development of melanoma, with a potential role as a safeguard against oncogenic mutations. Full article
(This article belongs to the Special Issue Molecular Research on Epigenetic Modifications)
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Review

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26 pages, 2707 KiB  
Review
Basic Pathogenic Mechanisms and Epigenetic Players Promoted by Extracellular Vesicles in Vascular Damage
by Concetta Schiano, Carolina Balbi, Filomena de Nigris and Claudio Napoli
Int. J. Mol. Sci. 2023, 24(8), 7509; https://doi.org/10.3390/ijms24087509 - 19 Apr 2023
Cited by 5 | Viewed by 2052
Abstract
Both progression from the early pathogenic events to clinically manifest cardiovascular diseases (CVD) and cancer impact the integrity of the vascular system. Pathological vascular modifications are affected by interplay between endothelial cells and their microenvironment. Soluble factors, extracellular matrix molecules and extracellular vesicles [...] Read more.
Both progression from the early pathogenic events to clinically manifest cardiovascular diseases (CVD) and cancer impact the integrity of the vascular system. Pathological vascular modifications are affected by interplay between endothelial cells and their microenvironment. Soluble factors, extracellular matrix molecules and extracellular vesicles (EVs) are emerging determinants of this network that trigger specific signals in target cells. EVs have gained attention as package of molecules with epigenetic reversible activity causing functional vascular changes, but their mechanisms are not well understood. Valuable insights have been provided by recent clinical studies, including the investigation of EVs as potential biomarkers of these diseases. In this paper, we review the role and the mechanism of exosomal epigenetic molecules during the vascular remodeling in coronary heart disease as well as in cancer-associated neoangiogenesis. Full article
(This article belongs to the Special Issue Molecular Research on Epigenetic Modifications)
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15 pages, 1644 KiB  
Review
Methyl Donor Micronutrients: A Potential Dietary Epigenetic Target in Systemic Lupus Erythematosus Patients
by Karen Pesqueda-Cendejas, Bertha Campos-López, Paulina E. Mora-García, José M. Moreno-Ortiz and Ulises De la Cruz-Mosso
Int. J. Mol. Sci. 2023, 24(4), 3171; https://doi.org/10.3390/ijms24043171 - 6 Feb 2023
Cited by 3 | Viewed by 3755
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by an aberrant immune response and persistent inflammation. Its pathogenesis remains unknown; however, a complex interaction between environmental, genetic, and epigenetic factors has been suggested to cause disease onset. Several studies have demonstrated [...] Read more.
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by an aberrant immune response and persistent inflammation. Its pathogenesis remains unknown; however, a complex interaction between environmental, genetic, and epigenetic factors has been suggested to cause disease onset. Several studies have demonstrated that epigenetic alterations, such as DNA hypomethylation, miRNA overexpression, and altered histone acetylation, may contribute to SLE onset and the disease’s clinical manifestations. Epigenetic changes, especially methylation patterns, are modifiable and susceptible to environmental factors such as diet. It is well known that methyl donor nutrients, such as folate, methionine, choline, and some B vitamins, play a relevant role in DNA methylation by participating as methyl donors or coenzymes in one-carbon metabolism. Based on this knowledge, this critical literature review aimed to integrate the evidence in animal models and humans regarding the role of nutrients in epigenetic homeostasis and their impact on immune system regulation to suggest a potential epigenetic diet that could serve as adjuvant therapy in SLE. Full article
(This article belongs to the Special Issue Molecular Research on Epigenetic Modifications)
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