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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 4553

Special Issue Editors


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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

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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

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Keywords

  • epigenetic regulation
  • DNA methylation
  • protein methylation
  • protein acetylation
  • histone modification
  • noncoding RNAs (ncRNAs)
  • post-translational modifications (PTMs)
  • chromatin
  • human disease

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Published Papers (5 papers)

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Research

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9 pages, 1071 KiB  
Communication
Epigenomic Alterations of the Human CYP11B Gene in Adrenal Zonation
by Yoshimichi Takeda, Masashi Demura, Takashi Yoneda, Shigehiro Karashima, Mitsuhiro Kometani, Daisuke Aono, Seigo Konishi, Shin-ichi Horike, Yasuhiro Nakamura, Yuto Yamazaki, Hironobu Sasano and Yoshiyu Takeda
Int. J. Mol. Sci. 2024, 25(22), 11956; https://doi.org/10.3390/ijms252211956 - 7 Nov 2024
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Abstract
The CYP11B2 gene is sporadically expressed in the zona glomerulosa (ZG), whereas the CYP11B1 gene is detected in the zona fasciculata (ZF)/reticularis (ZR), with predominant expression in the ZF. We studied the association between DNA methylation and adrenal zonation. Next, the CYP11B2 methylation [...] Read more.
The CYP11B2 gene is sporadically expressed in the zona glomerulosa (ZG), whereas the CYP11B1 gene is detected in the zona fasciculata (ZF)/reticularis (ZR), with predominant expression in the ZF. We studied the association between DNA methylation and adrenal zonation. Next, the CYP11B2 methylation statuses in the adrenal medulla (n = 4) and pheochromocytomas (n = 7) were examined. The expression of CYP11B2 in pheochromocytomas and non-functioning adenomas (NFAs) (n = 4) was also studied. Adrenals from five autopsy subjects were assessed for immunohistochemically defined adrenal zonation. We used laser capture microscopy to isolate DNA from each zone in adrenal tissues. CYP11B1 was predominantly unmethylated in the ZF but heavily methylated in the ZG and the ZR. In contrast, CYP11B2 was hypomethylated in the ZG compared with in the ZF and the ZR. In terms of the expression site and strength, the promoter methylation patterns for CYP11B2 and CYP11B1 showed capacities to express CYP11B enzymes. The DNA methylation patterns of the CYP11B2 and CYP11B1 promoters were closely associated with adrenal zonation. The unmethylated CpGs of CYP11B2 were found in the adrenal medulla and pheochromocytomas. Gene expression of CYP11B2 was detected in the pheochromocytomas. These results indicate the possibility that the synthesis of aldosterone occurs in the adrenal medulla. Further study is necessary to elucidate the pathophysiological roles for the synthesis of aldosterone in the adrenal medulla. Full article
(This article belongs to the Special Issue Novel Insight into Epigenomic Studies of Human Disease)
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17 pages, 5315 KiB  
Article
PRC1 Protein Subcomplexes Architecture: Focus on the Interplay between Distinct PCGF Subunits in Protein Interaction Networks
by Nayla Munawar, Kieran Wynne and Giorgio Oliviero
Int. J. Mol. Sci. 2024, 25(18), 9809; https://doi.org/10.3390/ijms25189809 - 11 Sep 2024
Viewed by 617
Abstract
The six PCGF proteins (PCGF1-6) define the biochemical identity of Polycomb repressor complex 1 (PRC1) subcomplexes. While structural and functional studies of PRC1 subcomplexes have revealed their specialized roles in distinct aspects of epigenetic regulation, our understanding of the variation in the protein [...] Read more.
The six PCGF proteins (PCGF1-6) define the biochemical identity of Polycomb repressor complex 1 (PRC1) subcomplexes. While structural and functional studies of PRC1 subcomplexes have revealed their specialized roles in distinct aspects of epigenetic regulation, our understanding of the variation in the protein interaction networks of distinct PCGF subunits in different PRC1 complexes is incomplete. We carried out an affinity purification mass spectrometry (AP-MS) screening of three PCGF subunits, PCGF1 (NSPC1), PCGF2 (MEL18), and PCGF4 (BMI1), to define their interactome and potential cellular function in pluripotent human embryonal carcinoma cell “NT2”. The bioinformatic analysis revealed that these interacting proteins cover a range of functional pathways, often involved in cell biology and chromatin regulation. We also found evidence of mutual regulation (at mRNA and protein level) between three distinct PCGF subunits. Furthermore, we confirmed that the disruption of these subunits results in reduced cell proliferation ability. We reveal an interplay between the compositional diversity of the distinct PCGF containing PRC1 complex and the potential role of PCGF proteins within the wider cellular network. Full article
(This article belongs to the Special Issue Novel Insight into Epigenomic Studies of Human Disease)
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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 1084
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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15 pages, 747 KiB  
Review
miRNAs as Epigenetic Biomarkers in the Study of the Bidirectional Relationship between Type 2 Diabetes Mellitus and Periodontitis: A Systematic Review
by María Mata-Monterde, Ana Serrano-Valcarce, Pedro José Almiñana-Pastor, Pablo Micó-Martínez and Andrés López-Roldán
Int. J. Mol. Sci. 2024, 25(19), 10723; https://doi.org/10.3390/ijms251910723 - 5 Oct 2024
Viewed by 691
Abstract
The objective of this study is to analyze the miRNA expression of oral fluids such as gingival crevicular fluid (GCF) in patients with periodontitis and Type 2 diabetes mellitus, and how these epigenetic biomarkers can influence the bidirectional relationship of these two inflammatory [...] Read more.
The objective of this study is to analyze the miRNA expression of oral fluids such as gingival crevicular fluid (GCF) in patients with periodontitis and Type 2 diabetes mellitus, and how these epigenetic biomarkers can influence the bidirectional relationship of these two inflammatory diseases. This review was conducted following the PRISMA criteria. PubMed, Scopus, Cochrane Library, Embase, and Web of Science databases were searched for clinical studies conducted on humans investigating, through GCF miRNA expression, the relationship between periodontal diseases and type 2 diabetes mellitus. In addition, the etiopathogenic pathways of the studied miRNAs were analyzed using the DIANA MIR path tool. A total of 1436 references were identified in the initial literature search, and seven articles were finally included in this review. Most of the articles included in this review were case–control studies and examined the expression of miRNAs in patients with periodontitis with or without diabetes. Due to their characteristics, miRNAs appear to be the ideal biomarkers for improving the understanding and knowledge of the etiopathogenic pathways that link both diseases. Among all the studied miRNAs, miR-146a, miR-155, miR-200b, miR-223, and miR-203 showed strong involvement in inflammatory and metabolic pathways, making them potential good diagnostic and prognostic biomarkers. Full article
(This article belongs to the Special Issue Novel Insight into Epigenomic Studies of Human Disease)
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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 1454
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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