Epigenetics in Human Development and Disease

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: 5 July 2024 | Viewed by 4824

Special Issue Editors

Centre of Exact and Natural Sciences, Molecular Biology Department, Federal University of Paraíba, Cidade Universitária—Campus I, João Pessoa, PB 58051-900, Brazil
Interests: epigenetic; DNA methylation; oral diseases; multifactorial diseases; genetic
Department of Cell Biology, University Federal of Paraná, Curitiba, PR, Brazil
Interests: genetic; epigenetic; human development and diseases; oral diseases; molecular biology

Special Issue Information

Dear Colleagues,

The molecular era has unraveled aspects of epigenetics in development and disease in humans. The great advance in this area mainly comes from data referring to tumor diseases; however, epigenetic aspects of human development and in inflammatory and mental diseases are still neglected in this regard. Epigenetic markers (DNA methylation, RNA methylation, histone modification and micro-RNAs) can be used as biomarkers, and since they are reversible, they can also be targets for treatments. In addition to genetic studies, the epigenetic approach can contribute to precision medicine, a healthcare model which advocates for the construction of biological databases for each individual based on concepts of classical genetics, epigenetic marks, metabolomics, and aspects of the patient's clinical phenotype, enabling the establishment of more accurate lines of diagnosis and treatment. This is a promising perspective that could be applied for reducing healthcare costs and lessening patient suffering.

The types of manuscripts we are interested in include original research, reviews, mini reviews, and case reports.

Specific themes include:

  1. DNA methylation and RNA methylation marks which are involved in human development and disease;
  2. Histone modification marks including methylation, acetylation, etc. which are involved in human development and disease;
  3. Non-coding RNA expression, including miRNA, lncRNA, etc. which are involved in human development and disease;
  4. Studies with epigenetic drugs will also be considered.

Dr. Naila Francis Paulo De Oliveira
Dr. Maria Cristina Leme Godoy dos Santos
Guest Editors

Manuscript Submission Information

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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. Genes 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

  • health development
  • inflammatory diseases
  • mental diseases
  • tumor diseases
  • epigenetic drugs

Published Papers (3 papers)

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Research

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21 pages, 6821 KiB  
Article
Analyzes In Silico Indicate the lncRNAs MIR31HG and LINC00939 as Possible Epigenetic Inhibitors of the Osteogenic Differentiation in PDLCs
by Rogério S. Ferreira, Rahyza I. F. Assis, Francesca Racca, Ana Carolina Bontempi, Rodrigo A. da Silva, Malgorzata Wiench and Denise C. Andia
Genes 2023, 14(8), 1649; https://doi.org/10.3390/genes14081649 - 18 Aug 2023
Viewed by 1068
Abstract
Chromatin conformation, DNA methylation pattern, transcriptional profile, and non-coding RNAs (ncRNAs) interactions constitute an epigenetic pattern that influences the cellular phenotypic commitment and impacts the clinical outcomes in regenerative therapies. Here, we investigated the epigenetic landscape of the SP7 transcriptor factor (SP7 [...] Read more.
Chromatin conformation, DNA methylation pattern, transcriptional profile, and non-coding RNAs (ncRNAs) interactions constitute an epigenetic pattern that influences the cellular phenotypic commitment and impacts the clinical outcomes in regenerative therapies. Here, we investigated the epigenetic landscape of the SP7 transcriptor factor (SP7) and Distal-Less Homeobox 4 (DLX4) osteoblastic transcription factors (TFs), in human periodontal ligament mesenchymal cells (PDLCs) with low (l-PDLCs) and high (h-PDLCs) osteogenic potential. Chromatin accessibility (ATAC-seq), genome DNA methylation (Methylome), and RNA sequencing (RNA-seq) assays were performed in l- and h-PDLCs, cultured at 10 days in non-induced (DMEM) and osteogenic (OM) medium in vitro. Data were processed in HOMER, Genome Studio, and edgeR programs, and metadata was analyzed by online bioinformatics tools and in R and Python environments. ATAC-seq analyses showed the TFs genomic regions are more accessible in l-PDLCs than in h-PDLCs. In Methylome analyses, the TFs presented similar average methylation intensities (AMIs), without differently methylated probes (DMPs) between l- and h-PDLCs; in addition, there were no differences in the expression profiles of TFs signaling pathways. Interestingly, we identified the long non-coding RNAs (lncRNAs), MIR31HG and LINC00939, as upregulated in l-PDLCs, in both DMEM and OM. In the following analysis, the web-based prediction tool LncRRIsearch predicted RNA:RNA base-pairing interactions between SP7, DLX4, MIR31HG, and LINC00939 transcripts. The machine learning program TriplexFPP predicted DNA:RNA triplex-forming potential for the SP7 DNA site and for one of the LINC00939 transcripts (ENST00000502479). PCR data confirmed the upregulation of MIR31HG and LINC00939 transcripts in l-PDLCs (× h-PDLCs) in both DMEM and OM (p < 0.05); conversely, SP7 and DLX4 were downregulated, confirming those results observed in the RNA-Seq analysis. Together, these results indicate the lncRNAs MIR31HG and LINC00939 as possible epigenetic inhibitors of the osteogenic differentiation in PDLCs by (post)transcriptional and translational repression of the SP7 and DLX4 TFs. Full article
(This article belongs to the Special Issue Epigenetics in Human Development and Disease)
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14 pages, 1082 KiB  
Article
DNA Methyltransferase Genes Are Associated with Oral Mucositis and Creatinine Levels in Oncopediatric Patients
by Beatriz Fernandes de Souza, José Maria Chagas Viana Filho, José Nunes de Queiroz Neto, Marina de Castro Coêlho, Ana Maria Gondim Valença, Darlene Camati Persuhn and Naila Francis Paulo de Oliveira
Genes 2023, 14(6), 1136; https://doi.org/10.3390/genes14061136 - 24 May 2023
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Abstract
The aim of this study was to investigate the association of single-nucleotide polymorphisms (SNPs) and the DNA methylation profiles of the DNA methyltransferase (DNMT) gene family with oral mucositis in children and adolescents with hematologic malignancies treated with methotrexate (MTX® [...] Read more.
The aim of this study was to investigate the association of single-nucleotide polymorphisms (SNPs) and the DNA methylation profiles of the DNA methyltransferase (DNMT) gene family with oral mucositis in children and adolescents with hematologic malignancies treated with methotrexate (MTX®). The population was comprised of healthy and oncopediatric patients aged between 4 and 19 years. An evaluation of oral conditions was performed using the Oral Assessment Guide. Demographic, clinical, hematological, and biochemical data were obtained from medical records. Genomic DNA extracted from oral mucosal cells was used for the analysis of polymorphisms in DNMT1 (rs2228611), DNMT3A (rs7590760), and DNMT3B (rs6087990) using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique (n = 102) and for DNA methylation using the methylation-specific PCR (MSP) technique (n = 85). The allele and genotypic frequencies of SNPs did not reveal any differences between patients with or without oral mucositis. An increase in the methylation frequency for DNMT1 in patients recovered from mucositis was detected. The DNMT3A methylated profile associated with the CC genotype (SNP rs7590760) appeared to be connected to higher values of creatinine. In addition, the DNMT3B unmethylated profile associated with the CC genotype (SNP rs6087990) appeared to be connected with higher values of creatinine. We conclude that the DNMT1 methylation profile is associated with the post-mucositis period and that the genetic and epigenetic profiles of DNMT3A and DNMT3B are associated with creatinine levels. Full article
(This article belongs to the Special Issue Epigenetics in Human Development and Disease)
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Review

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17 pages, 1036 KiB  
Review
A Review of the Epigenetic Clock: Emerging Biomarkers for Asthma and Allergic Disease
by Denitsa Vasileva, Celia M. T. Greenwood and Denise Daley
Genes 2023, 14(9), 1724; https://doi.org/10.3390/genes14091724 - 29 Aug 2023
Cited by 2 | Viewed by 1995
Abstract
DNA methylation (DNAm) is a dynamic, age-dependent epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma [...] Read more.
DNA methylation (DNAm) is a dynamic, age-dependent epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma and allergies. One method to study the role of DNAm is the epigenetic clock—an algorithm that uses DNAm levels at select age-informative Cytosine-phosphate-Guanine (CpG) dinucleotides to predict epigenetic age (EA). The difference between EA and calendar age (CA) is termed epigenetic age acceleration (EAA) and reveals information about the biological capacity of an individual. Associations between EAA and disease susceptibility have been demonstrated for a variety of age-related conditions and, more recently, phenotypes such as asthma and allergic diseases, which often begin in childhood and progress throughout the lifespan. In this review, we explore different epigenetic clocks and how they have been applied, particularly as related to childhood asthma. We delve into how in utero and early life exposures (e.g., smoking, air pollution, maternal BMI) result in methylation changes. Furthermore, we explore the potential for EAA to be used as a biomarker for asthma and allergic diseases and identify areas for further study. Full article
(This article belongs to the Special Issue Epigenetics in Human Development and Disease)
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