IF 3 4区医学

Epigenomics Pub Date : 2025-02-02 DOI: 10.1080/17501911.2025.2459552

Lauren Frazer, Tianjiao Chu, Patricia Shaw, Camille Boufford, Lucas Tavares Naief, Michaela Ednie, Laken Ritzert, Caitlin P Green, Misty Good, David Peters

{"title":"Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis.","authors":"Lauren Frazer, Tianjiao Chu, Patricia Shaw, Camille Boufford, Lucas Tavares Naief, Michaela Ednie, Laken Ritzert, Caitlin P Green, Misty Good, David Peters","doi":"10.1080/17501911.2025.2459552","DOIUrl":"https://doi.org/10.1080/17501911.2025.2459552","url":null,"abstract":"Background: Necrotizing enterocolitis (NEC) is an often fatal intestinal injury that primarily affects preterm infants for which screening tools are lacking. We performed a pilot analysis of DNA methylation in peripheral blood samples from preterm infants with and without NEC to identify potential NEC biomarkers.Methods: Peripheral blood samples were collected from infants at NEC diagnosis (n = 15) or from preterm controls (n = 13). Targeted genome-wide analysis was performed to identify DNA methylation differences between cases and controls.Results: Broad differences between NEC cases and controls were identified in distinct genomic elements. Differences between surgical NEC cases and controls were frequently associated with inflammation. Deconvolution analysis to identify cell type-specific DNA signatures revealed increases in ileal, vascular endothelial, and cardiomyocyte cell type proportions and decreases in colonic and neuronal cell type proportions in blood from NEC cases relative to controls.Conclusions: We identified marked differences in DNA methylation of peripheral blood samples from preterm infants with and without NEC. Increased ileal cell-specific methylation signatures in the blood of infants with NEC relative to controls, with a marked increase seen in surgical cases, provides rationale for further analysis of intestinal DNA methylation signatures as biomarkers of NEC.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-11"},"PeriodicalIF":3.0,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143079135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Predictive power of epigenetic age - opportunities and cautions. 表观遗传年龄的预测能力--机遇与警示。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-11-24 DOI: 10.1080/17501911.2024.2433409

Christine Nardini, Pietro Di Lena

引用次数: 0

The triple code model for advancing research in rare and undiagnosed diseases beyond the base pairs. 推进罕见和未确诊疾病研究的三重密码模型。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-12-04 DOI: 10.1080/17501911.2024.2436837

Gwen Lomberk, Raul Urrutia

引用次数: 0

Evaluation of agreement between common clustering strategies for DNA methylation-based subtyping of breast tumours. 评估基于DNA甲基化的乳腺肿瘤亚型的常见聚类策略之间的一致性。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-12-23 DOI: 10.1080/17501911.2024.2441653

Elaheh Zarean, Shuai Li, Ee Ming Wong, Enes Makalic, Roger L Milne, Graham G Giles, Catriona McLean, Melissa C Southey, Pierre-Antoine Dugué

{"title":"Evaluation of agreement between common clustering strategies for DNA methylation-based subtyping of breast tumours.","authors":"Elaheh Zarean, Shuai Li, Ee Ming Wong, Enes Makalic, Roger L Milne, Graham G Giles, Catriona McLean, Melissa C Southey, Pierre-Antoine Dugué","doi":"10.1080/17501911.2024.2441653","DOIUrl":"10.1080/17501911.2024.2441653","url":null,"abstract":"Aims: Clustering algorithms have been widely applied to tumor DNA methylation datasets to define methylation-based cancer subtypes. This study aimed to evaluate the agreement between subtypes obtained from common clustering strategies.Materials & methods: We used tumor DNA methylation data from 409 women with breast cancer from the Melbourne Collaborative Cohort Study (MCCS) and 781 breast tumors from The Cancer Genome Atlas (TCGA). Agreement was assessed using the adjusted Rand index for various combinations of number of CpGs, number of clusters and clustering algorithms (hierarchical, K-means, partitioning around medoids, and recursively partitioned mixture models).Results: Inconsistent agreement patterns were observed for between-algorithm and within-algorithm comparisons, with generally poor to moderate agreement (ARI <0.7). Results were qualitatively similar in the MCCS and TCGA, showing better agreement for moderate number of CpGs and fewer clusters (K = 2). Restricting the analysis to CpGs that were differentially-methylated between tumor and normal tissue did not result in higher agreement.Conclusion: Our study highlights that common clustering strategies involving an arbitrary choice of algorithm, number of clusters and number of methylation sites are likely to identify different DNA methylation-based breast tumor subtypes.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"105-114"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of excess sugar on the whole genome DNA methylation pattern in human sperm. 过量糖对人类精子全基因组DNA甲基化模式的影响。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-12-20 DOI: 10.1080/17501911.2024.2439782

Josefine Jönsson, Alexander Perfilyev, Unn Kugelberg, Signe Skog, Axel Lindström, Sabrina Ruhrmann, Jones K Ofori, Karl Bacos, Tina Rönn, Anita Öst, Charlotte Ling

{"title":"Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.","authors":"Josefine Jönsson, Alexander Perfilyev, Unn Kugelberg, Signe Skog, Axel Lindström, Sabrina Ruhrmann, Jones K Ofori, Karl Bacos, Tina Rönn, Anita Öst, Charlotte Ling","doi":"10.1080/17501911.2024.2439782","DOIUrl":"10.1080/17501911.2024.2439782","url":null,"abstract":"Aims, patients & methods: Dietary factors may regulate the epigenome. We aimed to explore whether a diet intervention, including excess sugar, affects the methylome in human sperm, and to describe the sperm methylome. We used Whole Genome Bisulfite Sequencing (WGBS) to analyze DNA methylation in sperm taken at three time points from 15 males during a diet intervention; i) at baseline, ii) after one week on a standardized diet, and iii) after an additional week on a high-sugar diet providing 150% of their estimated total energy expenditure.Results: We identified seven nominal diet-associated differentially methylated regions in sperm (p < 0.05). The diet was nominally associated with methylation of 143 sites linked to fertility (e.g. AHRR, GNAS, and HDAC4), 313 sites in imprinted genes (e.g. GLIS3, PEG10, PEG3, and SNURF), and 42 sites in top 1%-expressed genes (e.g. CHD2) (p < 0.05). In sperm, 3'UTRs and introns had the highest levels of methylation, while 5'UTRs and CpG islands had the lowest levels. Non-expressed genes in human sperm were hypomethylated in exons compared with transcribed genes.Conclusions: In human sperm, DNA methylation levels were linked to gene expression, and excess sugar had modest effects on methylation on imprinted and highly expressed genes, and genes affecting fertility.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"89-104"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PX-12 modulates vorinostat-induced acetylation and methylation marks in CAL 27 cells. PX-12调节vorinostat诱导的CAL 27细胞乙酰化和甲基化标记。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-12-23 DOI: 10.1080/17501911.2024.2441652

Rafia Akhlaq, Tehmina Ahmed, Tajwali Khan, Syed Usama Yaseen Jeelani, Jazmine-Saskya N Joseph-Chowdhury, Simone Sidoli, Syed Ghulam Musharraf, Arslan Ali

{"title":"PX-12 modulates vorinostat-induced acetylation and methylation marks in CAL 27 cells.","authors":"Rafia Akhlaq, Tehmina Ahmed, Tajwali Khan, Syed Usama Yaseen Jeelani, Jazmine-Saskya N Joseph-Chowdhury, Simone Sidoli, Syed Ghulam Musharraf, Arslan Ali","doi":"10.1080/17501911.2024.2441652","DOIUrl":"10.1080/17501911.2024.2441652","url":null,"abstract":"Aim: The hypoxic tumor microenvironment (TME) in oral squamous cell carcinoma (OSCC) is primarily regulated by hypoxia-inducible factor-1 alpha (HIF-1α), impacting histone acetylation and methylation, which contribute to drug resistance. Vorinostat, a histone deacetylase inhibitor (HDACi), de-stabilizes HIF-1α, while PX-12, a thioredoxin-1 (Trx-1) inhibitor, prevents HIF-1α accumulation. Combining HDACi with a Trx-1 inhibitor may enhance efficacy and reduce resistance by increasing reactive oxygen species (ROS) in cancer cells. This study examines how PX-12 influences vorinostat-induced histone modifications under hypoxia in the OSCC cell line CAL 27 using mass spectrometry.Materials and methods: The OSCC cell line CAL 27 was used to assess histone post-translational modifications induced by PX-12 and Vorinostat under hypoxic conditions through mass spectrometry.Results: The proteomic analysis (ProteomeXchange identifier PXD053244) revealed several crucial histone marks, such as H3K4me1, H3K9ac, H3K9me, H3K14ac, H3K27me, H3K36me, H4K12Ac, and H4K16ac. Along with site-specific histone modifications, exposure of cells to vorinostat and PX-12 alone or in combination affects the global acetylation and methylation levels under hypoxia.Conclusion: Mass spectrometry-based proteomics highlighted the impact of vorinostat and PX-12 on histone acetylation and methylation, offering valuable insights into the epigenetic mechanisms in OSCC and paving a way for epigenetic-based oral cancer therapeutics.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"79-87"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of lncRNAs in the interplay of signaling pathways and epigenetic mechanisms in glioma. lncrna在胶质瘤中信号通路相互作用和表观遗传机制中的作用。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2025-01-19 DOI: 10.1080/17501911.2024.2442297

Can Bora Yildiz, Jian Du, K Naga Mohan, Geraldine Zimmer-Bensch, Sara Abdolahi

引用次数: 0

EZH2 inhibition enhances the activity of Carboplatin in aggressive-variant prostate cancer cell lines.

IF 3 4区医学

Epigenomics Pub Date : 2025-01-29 DOI: 10.1080/17501911.2025.2453419

Maryam Latarani, Perla Pucci, Mark Eccleston, Massimiliano Manzo, Priyadarsini Gangadharannambiar, Irene Fischetti, Ilaria Alborelli, Vera Mongiardini, Namra Mahmood, Mario Paolo Colombo, Benedetto Grimaldi, Sushila Rigas, Shusuke Akamatsu, Cheryl Hawkes, Yuzhuo Wang, Elena Jachetti, Francesco Crea

{"title":"EZH2 inhibition enhances the activity of Carboplatin in aggressive-variant prostate cancer cell lines.","authors":"Maryam Latarani, Perla Pucci, Mark Eccleston, Massimiliano Manzo, Priyadarsini Gangadharannambiar, Irene Fischetti, Ilaria Alborelli, Vera Mongiardini, Namra Mahmood, Mario Paolo Colombo, Benedetto Grimaldi, Sushila Rigas, Shusuke Akamatsu, Cheryl Hawkes, Yuzhuo Wang, Elena Jachetti, Francesco Crea","doi":"10.1080/17501911.2025.2453419","DOIUrl":"https://doi.org/10.1080/17501911.2025.2453419","url":null,"abstract":"Background: Aggressive Variant Prostate Cancers (AVPCs) are incurable malignancies. Platinum-based chemotherapies are used for the palliative treatment of AVPC. The Polycomb Repressive Complex 2 (PRC2) promotes prostate cancer progression via histone H3 Lysine 27 tri-methylation (H3K27me3). EZH2 encodes the catalytic subunit of PRC2. A recently developed nucleosome capture technology (Nu.QⓇ).measures H3K27me3 levels in biological fluids. EZH2 inhibitors (EZH2i) are being tested in clinical trials. We hypothesize that epigenetic reprogramming via EZH2i improves the efficacy of Carboplatin in AVPC and that EZH2i activity can be measured via both cellular- and cell-free nucleosomal H3K27me3 (cf-H3K27me3) levels.Methods: We studied the expression of PRC2 genes in clinical prostate cancer cohorts (bioinformatics). We determined the effect of EZH2i on cellular- and cf-H3K27me3 levels. We measured dose-dependent effects of Carboplatin with/without EZH2i on AVPC cell viability (IC50). We used RNA-Seq to study how EZH2i modulates gene expression in AVPC cells.Results: PRC2 genes were significantly up-regulated in AVPC vs other prostate cancer types. EZH2i reduced both cellular and cf-H3K27me3 levels. EZH2i significantly reduced Carboplatin IC50. EZH2i reduced the expression of DNA repair genes and increased the expression of p53-dependent pro-apoptotic factors.Conclusions: EZH2i plus Carboplatin is a promising combination treatment for AVPC.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-10"},"PeriodicalIF":3.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The eighth annual US DOHAD meeting: promising approaches in epigenetics research of early life exposures.

IF 3 4区医学

Epigenomics Pub Date : 2025-01-28 DOI: 10.1080/17501911.2025.2459550

Amy L Non

{"title":"The eighth annual US DOHAD meeting: promising approaches in epigenetics research of early life exposures.","authors":"Amy L Non","doi":"10.1080/17501911.2025.2459550","DOIUrl":"https://doi.org/10.1080/17501911.2025.2459550","url":null,"abstract":"The U.S. Developmental Origins of Health and Disease (DOHaD) meeting is an annual conference of primarily U.S. scientists who study early life programming of health and disease. The eighth annual symposium, entitled \"Exploring Translational DOHaD Science: From Cells to Communities\" was held at the Rizzo Conference Center in Chapel Hill, North Carolina, from October 14 to 16, 2024. The meeting was organized by US-DOHaD President Danielle Christifano and Vice President Kaela Varberg, and other Society Council Members. This year's meeting had record attendance, with 158 attendees from diverse disciplines, and featured 10 keynote speakers, 11 platform talks, and 84 poster presentations. Four major topics were covered: 1) Early nutrition and developmental outcomes, 2) Prenatal origins of child health, 3) Developmental impacts of toxicant exposures, and 4) Metabolic origins of health. Overall, the presented research highlighted the value of studying epigenetic effects of dietary and toxic exposures early in life. Various strategies emerged to address challenges facing the field, such as harnessing the power of nationwide longitudinal birth cohorts, new methods to integrate epigenetic and environmental data across various levels, and the emerging potential of organoids to identify the causal impact of early life exposures.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-3"},"PeriodicalIF":3.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association between epigenetic aging and atrioventricular block: a two-sample Mendelian randomization study. 表观遗传衰老与房室传导阻滞之间的关系：一项双样本孟德尔随机化研究。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-20 DOI: 10.1080/17501911.2025.2454894

Wanqian Pan, Chi Zhang, Xiaojiao Du, Xiong Su, Jia Lin, Tingbo Jiang, Weixiang Chen

{"title":"Association between epigenetic aging and atrioventricular block: a two-sample Mendelian randomization study.","authors":"Wanqian Pan, Chi Zhang, Xiaojiao Du, Xiong Su, Jia Lin, Tingbo Jiang, Weixiang Chen","doi":"10.1080/17501911.2025.2454894","DOIUrl":"10.1080/17501911.2025.2454894","url":null,"abstract":"Aims: Atrioventricular block (AVB) is a prevalent bradyarrhythmia. This study aims to investigate the causal effects of epigenetic aging, as inferred from DNA methylation profiles on the prevalence of AVB by Mendelian randomization (MR) analysis.Methods: Genetic instruments for epigenetic aging and AVB were obtained from genome-wide association study data in the Edinburgh DataShare and FinnGen biobanks. Univariable and multivariable MR analyses were conducted to evaluate causal associations. Additionally, we employed sensitivity tests to assess the robustness of the MR findings.Results: MR analysis showed that genetically predicted GrimAge acceleration was significantly associated with a higher risk of AVB (inverse variance-weighted: p = 0.010, 95% confidence interval (CI) = 1.024-1.196; weighted median: p = 0.031, 95% CI = 1.009-1.215). However, no evidence supported a causal relationship between AVB and epigenetic aging. The association between epigenetic aging and AVB was established using multivariate MR analysis after adjusting for various risk factors. Sensitivity analyses confirmed the reliability and robustness of the results.Conclusion: Our findings suggest that epigenetic aging in GrimAge may increase the risk of AVB, emphasizing the importance of addressing epigenetic aging in strategies for AVB prevention.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-12"},"PeriodicalIF":3.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epigenomics最新文献