Epigenomes最新文献

{"title":"Novel Epigenetics Control (EpC) Nanocarrier for Cancer Therapy Through Dual-Targeting Approach to DNA Methyltransferase and Ten-Eleven Translocation Enzymes.","authors":"Risa Mitsuhashi, Kiyoshi Sato, Hiroyoshi Kawakami","doi":"10.3390/epigenomes9010006","DOIUrl":"10.3390/epigenomes9010006","url":null,"abstract":"<p><strong>Background/objectives: </strong>Aberrant hypermethylation in the promoter regions of tumor suppressor genes facilitates the pathogenesis and progression of cancer. Therefore, inhibitors targeting DNA methyltransferase (DNMT) have been tested in clinical studies. However, the current monotherapy of DNMT inhibitors shows limited efficacy. Furthermore, the mechanism of action of DNMT inhibitors is DNA replication-dependent. To address these limitations, we developed a novel core-shell-type \"epigenetics control (EpC) nanocarrier\" that encapsulated decitabine (5-aza-dC) in the PLGA core nanoparticle and hybridized TET1 gene-encoding pDNA on the lipid shell surface. This study aimed to evaluate whether the dual delivery of DNMT inhibitors and pDNA of TET1 could synergistically enhance tumor suppressor gene expression and induce cell cycle arrest and/or apoptosis in cancer cells. Herein, we demonstrate the potential of the EpC carrier in HCT116 human colon cancer cells to upregulate tumor suppressor gene expression and rapidly achieve cell cycle arrest.</p><p><strong>Methods: </strong>PLGA core nanoparticles were prepared by the W/O/W double emulsion method. The formation of core-shell nanoparticles and complexation with pDNA were investigated and optimized by dynamic light scattering, zeta potential measurement, and agarose gel electrophoresis. The cellular uptake and transfection efficiency were measured by confocal laser scanning microscopy and a luciferase assay, respectively. The expression of p53 protein was detected by Western blotting. The anti-tumor effects of the EpC nanocarrier were evaluated by cell cycle analysis and an apoptosis assay.</p><p><strong>Results: </strong>The EpC nanocarrier delivered the DNMT inhibitor and TET gene-encoding pDNA into HCT116 cells. It promoted the expression of the tumor suppressor protein p53 and induced rapid cell cycle arrest in the G2/M phase in HCT116 cells.</p><p><strong>Conclusions: </strong>Our findings suggest that the dual-targeting of DNMT and TET enzymes effectively repairs aberrant DNA methylation and induces growth arrest in cancer cells, and the dual-targeting strategy may contribute to the advancement of epigenetic cancer therapy.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenomic Echoes-Decoding Genomic and Epigenetic Instability to Distinguish Lung Cancer Types and Predict Relapse.","authors":"Alexandra A Baumann, Zholdas Buribayev, Olaf Wolkenhauer, Amankeldi A Salybekov, Markus Wolfien","doi":"10.3390/epigenomes9010005","DOIUrl":"10.3390/epigenomes9010005","url":null,"abstract":"<p><p>Genomic and epigenomic instability are defining features of cancer, driving tumor progression, heterogeneity, and therapeutic resistance. Central to this process are epigenetic echoes, persistent and dynamic modifications in DNA methylation, histone modifications, non-coding RNA regulation, and chromatin remodeling that mirror underlying genomic chaos and actively influence cancer cell behavior. This review delves into the complex relationship between genomic instability and these epigenetic echoes, illustrating how they collectively shape the cancer genome, affect DNA repair mechanisms, and contribute to tumor evolution. However, the dynamic, context-dependent nature of epigenetic changes presents scientific and ethical challenges, particularly concerning privacy and clinical applicability. Focusing on lung cancer, we examine how specific epigenetic patterns function as biomarkers for distinguishing cancer subtypes and monitoring disease progression and relapse.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-Molecule Nanopore Sequencing of the CpG Island from the Promoter of O6-Methylguanine-DNA Methyltransferase Provides Insights into the Mechanism of De Novo Methylation of G/C-Rich Regions.","authors":"Alexander V Sergeev, Daniil P Malyshev, Adelya I Genatullina, Galina V Pavlova, Elizaveta S Gromova, Maria I Zvereva","doi":"10.3390/epigenomes9010004","DOIUrl":"10.3390/epigenomes9010004","url":null,"abstract":"<p><strong>Background: </strong>The methylation of cytosine residues at CpG sites within the O6-methylguanine-DNA methyltransferase (<i>MGMT</i>) promoter is a key biomarker in glioblastoma therapy. The <i>MGMT</i> promoter (MGMTp) contains multiple guanine-rich sequences capable of folding into G-quadruplexes (G4s), but their relevance for MGMTp methylation is poorly understood.</p><p><strong>Objectives: </strong>Our study explores the impact of potential G-quadruplex-forming sequences (PQS) in the <i>MGMT</i> promoter CpG island on the activity of de novo DNA methyltransferase Dnmt3a. Additionally, we investigate their influence on the accuracy of methylation pattern detection using nanopore sequencing.</p><p><strong>Methods: </strong>Nanopore sequencing was employed to analyze the methylation of 94 clinically significant CpG sites in the human MGMTp using an in vitro de novo methylation system. Circular dichroism spectroscopy was used to identify G4 structures within the MGMTp CpG island. Interactions between the catalytic domain of Dnmt3a and the PQS from the MGMTp were examined by biolayer interferometry.</p><p><strong>Results: </strong>Guanine-rich DNA strands of the PQSs in the MGMTp were hypomethylated, while the complementary cytosine-rich strands were methylated by DNA methyltransferase Dnmt3a with higher efficiency. The accuracy of detecting modified bases in the PQS was significantly lower compared to surrounding sequences. Single-stranded guanine-rich DNA sequences from the MGMTp exhibited strong binding to Dnmt3a-CD, with an affinity approximately 10 times higher than their cytosine-rich complements (<i>K</i>_d = 3 × 10^-8 M and 3 × 10^-7 M, respectively). By binding to Dnmt3a, G4-forming oligonucleotides from MGMTp effectively inhibited the methylation reaction (IC₅₀ 6 × 10^-7 M).</p><p><strong>Conclusions: </strong>The obtained data indicate the role of PQSs in establishing de novo methylation of the <i>MGMT</i> promoter. They also highlight the challenges of sequencing guanine-rich regions and the impact of specific de novo methylation patterns on clinical data interpretation.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetics in Skin Homeostasis and Ageing.","authors":"Iasonas Dermitzakis, Stella Aikaterini Kyriakoudi, Sofia Chatzianagnosti, Despoina Chatzi, Efstratios Vakirlis, Soultana Meditskou, Maria Eleni Manthou, Paschalis Theotokis","doi":"10.3390/epigenomes9010003","DOIUrl":"10.3390/epigenomes9010003","url":null,"abstract":"<p><p>The skin, the largest organ of the human body, plays numerous essential roles, including protection against environmental hazards and the regulation of body temperature. The processes of skin homeostasis and ageing are complex and influenced by many factors, with epigenetic mechanisms being particularly significant. Epigenetics refers to the regulation of gene expression without altering the underlying DNA sequence. The dynamic nature of the skin, characterized by constant cellular turnover and responsiveness to environmental stimuli, requires precise gene activity control. This control is largely mediated by epigenetic modifications such as DNA methylation, histone modification, and regulation by non-coding RNAs. The present review endeavours to provide a comprehensive exploration and elucidation of the role of epigenetic mechanisms in regulating skin homeostasis and ageing. By integrating our current knowledge of epigenetic modifications with the latest advancements in dermatological research, we can gain a deeper comprehension of the complex regulatory networks that govern skin biology. Understanding these mechanisms also presents promising avenues for therapeutic interventions aimed at improving skin health and mitigating age-related skin conditions.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11755608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA and RNA Methylation in Rheumatoid Arthritis-A Narrative Review.","authors":"Kajetan Kiełbowski, Estera Bakinowska, Anna Gorący-Rosik, Karolina Figiel, Roksana Judek, Jakub Rosik, Paweł Dec, Andrzej Modrzejewski, Andrzej Pawlik","doi":"10.3390/epigenomes9010002","DOIUrl":"10.3390/epigenomes9010002","url":null,"abstract":"<p><p>Rheumatoid arthritis (RA) is a progressive autoimmune disease leading to structural and functional joint damage and, eventually, to physical disability. The pathogenesis of the disease is highly complex and involves interactions between fibroblast-like synoviocytes (FLSs) and immune cells, which stimulate the secretion of pro-inflammatory factors, leading to chronic inflammation. In recent years, studies have demonstrated the importance of epigenetics in RA. Specifically, epigenetic alterations have been suggested to serve as diagnostic and treatment biomarkers, while epigenetic mechanisms are thought to be involved in the pathogenesis of RA. Epigenetic regulators coordinate gene expression, and in the case of inflammatory diseases, they regulate the expression of a broad range of inflammatory molecules. In this review, we discuss current evidence on the involvement of DNA and RNA methylation in RA.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11755448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two Clinically Implementable Digital PCR Assessments of DNA Methylation for Diagnosing Heavy Alcohol Consumption.","authors":"Robert Philibert, Steven R H Beach, Allan M Andersen","doi":"10.3390/epigenomes9010001","DOIUrl":"10.3390/epigenomes9010001","url":null,"abstract":"<p><strong>Background: </strong>Heavy alcohol consumption (HAC) has a profound adverse effect on human health. Unfortunately, there is a relative lack of tools that are easily implementable in clinical settings and that can be used to supplement self-reporting in the diagnosis and management of HAC. In part, this paucity is due to limitations of currently available biological measures and a mismatch between available biological measures and the needs of clinicians managing HAC.</p><p><strong>Objectives: </strong>We first review the pros and cons of existing biological measures. Next, we review the underlying theory and the performance characteristics of two recently developed methylation-sensitive digital PCR (MSdPCR) assays, referred to as the Alcohol T Score (ATS) and ZSCAN25, for the assessment of chronic and recent HAC, respectively. Finally, we outline a paradigm for improving the clinical diagnosis and management of alcohol use disorders by utilizing these new markers of alcohol consumption.</p><p><strong>Conclusions: </strong>We conclude that further studies to understand the test performance characteristics of each of these epigenetic tools in larger, diverse populations are in order.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11755464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenome-Wide and Methylation Risk Score Analysis of Body Mass Index Among People with HIV.","authors":"Nanzha Abi, Alexandra Young, Pradeep Tiwari, Junyu Chen, Chang Liu, Qin Hui, Kaku So-Armah, Matthew S Freiberg, Amy C Justice, Ke Xu, Marta Gwinn, Vincent C Marconi, Yan V Sun","doi":"10.3390/epigenomes8040046","DOIUrl":"10.3390/epigenomes8040046","url":null,"abstract":"<p><p><b>Background/Objectives:</b> People with HIV (PWH) on antiretroviral therapy (ART) often gain weight, which increases their risk of type 2 diabetes and cardiovascular disease. The role of DNA methylation (DNAm) markers in obesity among PWH is understudied. This research explores the relationship between body mass index (BMI) and epigenetic patterns to better understand and manage obesity-related risks in PWH. <b>Methods:</b> We conducted an epigenome-wide association study (EWAS) on 892 African American male PWH from the Veterans Aging Cohort Study, examining BMI associations with DNAm using linear mixed models, adjusting for covariates, including soluble CD14. We compared our results with BMI-associated DNAm markers from non-HIV individuals and developed a methylation risk score (MRS) for BMI using machine learning and a cross-validation approach. <b>Results:</b> We identified four epigenome-wide significant CpG sites, including one in the <i>RAP1B</i> gene, indicating shared and unique BMI-related epigenetic markers between PWH and non-HIV individuals. The constructed BMI MRS explained approximately 19% of the BMI variance in PWH. <b>Conclusions:</b> DNAm markers and MRS are significantly linked to BMI in PWH, suggesting shared and distinct molecular mechanisms with non-HIV populations. These insights could lead to targeted interventions to reduce cardiometabolic disease risks in PWH under ART.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11675887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA Imprinting and Differentially Expressed Genes in <i>Longissimus thoracis</i> Muscle of <i>Bos indicus</i> Submitted to Early Weaning Management.","authors":"Gustavo Tinoco, Gustavo Russo, Rogério Curi, Marcelo Vicari, Paloma Melo, Isabella Souza, Juliana Torrecilhas, Philipe Moriel, Welder Baldassini, Luis Chardulo, Otávio Neto, Guilherme Pereira","doi":"10.3390/epigenomes8040045","DOIUrl":"10.3390/epigenomes8040045","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Early weaning management followed by energy supplementation can lead to metabolic alterations in the calf that exert long-term effects on the animal's health and performance. It is believed that the main molecular basis underlying these metabolic adaptations are epigenetic mechanisms that regulate, activate, or silence genes at different stages of development and/or in response to different environmental stimuli. However, little is known about postnatal metabolic programming in <i>Bos indicus</i>. Therefore, this study aimed to compare the DNA methylation profile of Nellore animals submitted to conventional and early weaning and to correlate the findings with genes differentially expressed in the <i>Longissimus thoracis</i> skeletal muscle of <i>Bos indicus</i> cattle. <b>Methods:</b> For this, we used Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Sequencing techniques to prospect differentially methylated genes (DMGs). <b>Results:</b> A total of 481 differentially methylated regions were identified, with 52% (250) being hypermethylated and 48% (231) hypomethylated. Functional enrichment analysis of 53 differentially methylated and differentially expressed genes was performed. The main enriched terms and pathways were associated with 3'-5'-cyclic adenosine monophosphate (<i>cAMP</i>) signaling, which presents the upregulated adenylate cyclase 3 (<i>ADCY3</i>) gene and significatively hypomethylated in the promoter region. Alterations in cAMP signaling are involved in numerous processes, many of them related to lipid metabolism. The relative differential expression of key genes of this pathway demonstrates the relationship between cAMP signaling and de novo lipogenesis. <b>Conclusions</b>: These findings suggest an important role of postnatal metabolic programming through DNA methylation mechanisms in determining fat deposition in beef.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11675247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental Factor Index (EFI): A Novel Approach to Measure the Strength of Environmental Influence on DNA Methylation in Identical Twins.","authors":"Yoichi Takenaka, Osaka Twin Research Group, Mikio Watanabe","doi":"10.3390/epigenomes8040044","DOIUrl":"10.3390/epigenomes8040044","url":null,"abstract":"<p><strong>Background/objectives: </strong>The dynamic interaction between genomic DNA, epigenetic modifications, and phenotypic traits was examined in identical twins. Environmental perturbations can induce epigenetic changes in DNA methylation, influencing gene expression and phenotypes. Although DNA methylation mediates gene-environment correlations, the quantitative effects of external factors on DNA methylation remain underexplored. This study aimed to quantify these effects using a novel approach.</p><p><strong>Methods: </strong>A cohort study was conducted on healthy monozygotic twins to evaluate the influence of environmental stimuli on DNA methylation. We developed the Environmental Factor Index (EFI) to identify methylation sites showing statistically significant changes in response to environmental stimuli. We analyzed the identified sites for associations with disorders, DNA methylation markers, and CpG islands.</p><p><strong>Results: </strong>The EFI identified methylation sites that exhibited significant associations with genes linked to various disorders, particularly cancer. These sites were overrepresented on CpG islands compared to other genomic features, highlighting their regulatory importance.</p><p><strong>Conclusions: </strong>The EFI is a valuable tool for understanding the molecular mechanisms underlying disease pathogenesis. It provides insights into the development of preventive and therapeutic strategies and offers a new perspective on the role of environmental factors in epigenetic regulation.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Age-Dependent DNA Methylation Variability on the X-Chromosome in Male and Female Twins.","authors":"Qihua Tan, Hikmat Alo, Marianne Nygaard, Mette Sørensen, Alisa Saleh, Jonas Mengel-From, Kaare Christensen","doi":"10.3390/epigenomes8040043","DOIUrl":"10.3390/epigenomes8040043","url":null,"abstract":"<p><p>We aimed to explore the age-dependent epigenetic variability on the X-chromosome with consideration of X-chromosome inactivation by applying a sex-stratified regression analysis to DNA methylation array data on X-linked CpGs in aging identical twins. We found 13 X-linked CpGs showing age-related significant increase in variability in males (FDR < 0.05) but none in females. In females, we found a significantly higher proportion of CpGs showing increased variability with age among nominally significant (<i>p</i> < 0.05) CpGs under inactivation, but not among CpGs escaping inactivation. Survival analysis showed a slight trend of correlation by directional change in the variable CpGs with mortality in males. Compared with females, the male X-chromosome can be more vulnerable to epigenetic instability during aging.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11586961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}