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Novel Insight into Epigenomic Studies of Human Disease
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Novel Insight into Epigenomic Studies of Human Disease

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: 30 November 2024 | Viewed by 1564

Special Issue Editors

Prof. Dr. Mitsuko Masutani

E-Mail Website
Guest Editor
1. Department of Molecular and Genomic Biomedicine, Center for Bioinformatics and Molecular Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
2. Visiting Scientist, Central Radioisotope Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
Interests: radiation oncology; biology in anti-cancer treatment; polyADP-ribosylation; anti-tumor therapeutic; mouse; boron neutron capture therapy
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Takashi Ito

E-Mail Website
Guest Editor
Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
Interests: life sciences; medical biochemistry; primary mouse hepatocytes; biochemistry; apoptosis

Special Issue Information

Dear Colleagues,

Various types of epigenomic regulation system are involved in ontogenetic and disease development, including DNA methylation, histone codes such as protein methylation, and acetylation. Other types of post-translational protein modification systems also interact with epigenetic regulations. Chromatin structures and various stimuli affect epigenetic states. The dysregulation of these epigenetic systems cause diseases including cancers, as well as neurological and immunological disorders. In this Special Issue, we call for the submission of articles and reviews on all aspects of epigenetic regulations in diseases.

Prof. Dr. Mitsuko Masutani
Prof. Dr. Takashi Ito
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 regulation
  • DNA methylation
  • protein methylation
  • protein acetylation
  • histone modification
  • noncoding RNAs (ncRNAs)
  • post-translational modifications (PTMs)
  • chromatin
  • human disease

Published Papers (2 papers)

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Research

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17 pages, 10343 KiB  
Article
Understanding Hypoxia-Driven Tumorigenesis: The Interplay of HIF1A, DNA Methylation, and Prolyl Hydroxylases in Head and Neck Squamous Cell Carcinoma
by Julia Ostapowicz, Kamila Ostrowska, Agnieszka A. Rawłuszko-Wieczorek, Bartosz Wojtera, Sabina Koczot, Wojciech Golusiński and Wiktoria M. Suchorska
Int. J. Mol. Sci. 2024, 25(12), 6495; https://doi.org/10.3390/ijms25126495 - 12 Jun 2024
Viewed by 608
Abstract
Hypoxia-inducible factor 1-alpha (HIF1A) is a key transcription factor aiding tumor cells’ adaptation to hypoxia, regulated by the prolyl hydroxylase family (EGLN1-3) by directing toward degradation pathways. DNA methylation potentially influences EGLN and HIF1A levels, impacting cellular responses to hypoxia. We examined 96 [...] Read more.
Hypoxia-inducible factor 1-alpha (HIF1A) is a key transcription factor aiding tumor cells’ adaptation to hypoxia, regulated by the prolyl hydroxylase family (EGLN1-3) by directing toward degradation pathways. DNA methylation potentially influences EGLN and HIF1A levels, impacting cellular responses to hypoxia. We examined 96 HNSCC patients and three cell lines, analyzing gene expression of EGLN1-3, HIF1A, CA9, VEGF, and GLUT1 at the mRNA level and EGLN1 protein levels. Methylation levels of EGLNs and HIF1A were assessed through high-resolution melting analysis. Bioinformatics tools were employed to characterize associations between EGLN1-3 and HIF1A expression and methylation. We found significantly higher mRNA levels of EGLN3, HIF1A, GLUT1, VEGF, and CA9 (p = 0.021; p < 0.0001; p < 0.0001; p = 0.004, and p < 0.0001, respectively) genes in tumor tissues compared to normal ones and downregulation of the EGLN1 mRNA level in tumor tissues (p = 0.0013). In HNSCC patients with hypermethylation of HIF1A in normal tissue, we noted a reduction in HIF1A mRNA levels compared to tumor tissue (p = 0.04). In conclusion, the differential expression of EGLN and HIF1A genes in HNSCC tumors compared to normal tissues influences patients’ overall survival, highlighting their role in tumor development. Moreover, DNA methylation could be responsible for HIF1A suppression in the normal tissues of HNSCC patients. Full article
(This article belongs to the Special Issue Novel Insight into Epigenomic Studies of Human Disease)
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Review

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24 pages, 2775 KiB  
Review
Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer
by Hejer Dhahri, Wesley N. Saintilnord, Darrell Chandler and Yvonne N. Fondufe-Mittendorf
Int. J. Mol. Sci. 2024, 25(12), 6788; https://doi.org/10.3390/ijms25126788 - 20 Jun 2024
Viewed by 596
Abstract
The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone–histone or histone–DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. [...] Read more.
The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone–histone or histone–DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. These structural modifications alter chromatin compaction and accessibility of DNA by transcription factors and other regulatory proteins to influence gene regulatory processes such as DNA damage and repair, as well as transcriptional activation or repression. Histone variants can also generate a unique interactome composed of histone chaperones and chromatin remodeling complexes. Any of these perturbations can contribute to cellular plasticity and the progression of human diseases. Here, we focus on a frequently overlooked group of histone variants lying within the four human histone gene clusters and their contribution to breast cancer. Full article
(This article belongs to the Special Issue Novel Insight into Epigenomic Studies of Human Disease)
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