Epigenomics最新文献_第4页

Increased methylation levels of the MTHFR gene promoter in Down syndrome. 唐氏综合征中MTHFR基因启动子甲基化水平升高。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-19 DOI: 10.1080/17501911.2025.2563501

Dijana Majstorović, Andrea Stoccoro, Anita Barišić, Alena Buretić Tomljanović, Marianna Giangreco, Vanessa Nicolì, Fabio Coppedè, Jadranka Vraneković

{"title":"Increased methylation levels of the MTHFR gene promoter in Down syndrome.","authors":"Dijana Majstorović, Andrea Stoccoro, Anita Barišić, Alena Buretić Tomljanović, Marianna Giangreco, Vanessa Nicolì, Fabio Coppedè, Jadranka Vraneković","doi":"10.1080/17501911.2025.2563501","DOIUrl":"https://doi.org/10.1080/17501911.2025.2563501","url":null,"abstract":"Aims: MTHFR is a key enzyme in the one-carbon metabolic pathway, whose activity has been implicated in Down syndrome (DS) and in the development of congenital heart defects (CHDs). The main aim was to assess promoter methylation levels of the MTHFR gene in DS individuals, including those with congenital heart defects (DS-CHD+), and those without (DS-CHD-), as well as control subjects. We also investigated if common MTHFR polymorphisms, namely 677C > T and 1298A > C correlate with MTHFR promoter methylation levels.Patients and methods: The study included 118 participants: 59 individuals with DS, 25 of which with CHD, and 59 age and gender matched controls. Genomic DNA was extracted from peripheral blood. Methylation-sensitive high-resolution melting and PCR - RFLP were used to assess methylation and genotyping.Results: DS individuals showed significantly higher MTHFR methylation levels than controls (p < 0.0001). No difference in MTHFR methylation levels between DS-CHD+ and DS-CHD- individuals was observed (p = 0.38). MTHFR 677TT carriers showed higher mean MTHFR methylation levels than 677CC carriers (p < 0.05).Conclusion: We observed a significant increase in MTHFR promoter methylation levels in DS individuals compared to controls. Folate metabolism could influence MTHFR methylation levels as shown indirectly by the association of the MTHFR 677C > T polymorphism.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-11"},"PeriodicalIF":2.6,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085461","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 DNA methylation in directing treatment in medulloblastoma. DNA甲基化在指导髓母细胞瘤治疗中的作用。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-04 DOI: 10.1080/17501911.2025.2554570

Mohammed A H Alsaedi, Gordon Strathdee

引用次数: 0

DNA methylation profile to aid in the diagnosis of pancreatic ductal adenocarcinoma and its role in disease progression. DNA甲基化谱有助于胰腺导管腺癌的诊断及其在疾病进展中的作用。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-03 DOI: 10.1080/17501911.2025.2554571

Elena Grafenhorst, Teodor G Calina, Mihnea P Dragomir

引用次数: 0

High-throughput assessment of FMR1 and SNRPN methylation-based newborn screening using IsoPure and QIAcube HT systems. 使用IsoPure和QIAcube HT系统高通量评估基于FMR1和SNRPN甲基化的新生儿筛查

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-01 Epub Date: 2025-08-13 DOI: 10.1080/17501911.2025.2544530

Caleb Cartagena, Mohammed Alshawsh, Minh Q Bui, Dinusha Gamage, Rajvi P Thakor, James Pitt, Ronda F Greaves, Meg Wall, Richard Saffery, David J Amor, David E Godler

{"title":"High-throughput assessment of FMR1 and SNRPN methylation-based newborn screening using IsoPure and QIAcube HT systems.","authors":"Caleb Cartagena, Mohammed Alshawsh, Minh Q Bui, Dinusha Gamage, Rajvi P Thakor, James Pitt, Ronda F Greaves, Meg Wall, Richard Saffery, David J Amor, David E Godler","doi":"10.1080/17501911.2025.2544530","DOIUrl":"10.1080/17501911.2025.2544530","url":null,"abstract":"Aim: This study compared methylation-specific quantitative melt analysis of FMR1 and SNRPN methylation (mDNA) using automated bisulfite conversion by the magnetic-bead-based IsoPure and column-based QIAcube HT systems.Methods: Two bisulfite conversion methods were assessed on 3.2 mm punches from the same archival blood spots stored at room temperature for >10 years of individuals with FMR1 premutation (n = 20), fragile X syndrome (FXS, n = 20), or chromosome 15 imprinting disorders (n = 50) and freshly made blood spots from 184 newborns from the general population. Performance criteria were: (i) diagnostic sensitivity and specificity for the conditions screened; (ii) reaction failure rate; (iii) variability in mDNA between groups.Results: Both methods showed 100% sensitivity and specificity for differentiating FXS and individual chromosome 15 imprinting disorders. IsoPure showed reaction failure rates of 0.365% for SNRPN and 0.74% for FMR1 compared to 19.34% and 2.56%, for QIAcube HT, respectively, with most failed reactions originating from archival blood spots. IsoPure showed lower variability in mDNA values in the neurotypical and condition-specific ranges.Conclusion: The IsoPure system showed superior performance especially on archival samples, with broader applications for screening and diagnostic testing requiring high-throughput mDNA analyses on materials of limited quantity and quality.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"851-863"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Placental DNA methylation key topics: sex- and cell-type specificity, mediation, multi-omics, and biomarker discovery. 胎盘DNA甲基化关键主题：性别和细胞类型特异性，中介，多组学和生物标志物的发现。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-01 Epub Date: 2025-07-16 DOI: 10.1080/17501911.2025.2533115

Nathan J Cohen, Corina Lesseur, Andres Cardenas, Cavin K Ward-Caviness, Allison C Spring, Julia E Rager, Rebecca C Fry, Lauren A Eaves

{"title":"Placental DNA methylation key topics: sex- and cell-type specificity, mediation, multi-omics, and biomarker discovery.","authors":"Nathan J Cohen, Corina Lesseur, Andres Cardenas, Cavin K Ward-Caviness, Allison C Spring, Julia E Rager, Rebecca C Fry, Lauren A Eaves","doi":"10.1080/17501911.2025.2533115","DOIUrl":"10.1080/17501911.2025.2533115","url":null,"abstract":"The placenta is a dynamic organ that serves numerous purposes for fostering a successful pregnancy and the delivery of a healthy infant in humans. It performs critical functions in nutrient and oxygen transport, immune modulation, and hormonal regulation. DNA methylation, a key epigenetic mechanism of transcriptional regulation, plays a key role in the underlying etiologies of placenta-related health complications. Therefore, assessing placental DNA methylation is essential for understanding how adverse prenatal exposures may impact both short-term and long-term health outcomes in women and children. In this review, we summarize current knowledge on the effects of prenatal exposures on placental DNA methylation and their implications for maternal and child health, focused on human population studies. We also outline five critical directions for human placental DNA methylation research: (1) Investigating sex-specific DNA methylation patterns, (2) Assessing cell type-specific DNA methylation signatures, (3) Applying causal inference methods, (4) Integrating multi-omics approaches, and (5) Using DNA methylation as a biomarker for environmental exposures and developmental outcomes. Advancing research in these areas will enhance our understanding of the biological underpinnings of the developmental origins of health and disease (DOHaD) hypothesis and maximize the potential of placental samples to inform DOHaD-related research.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"905-921"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cumulative psychosocial factors and epigenetic age acceleration in the Hispanic Community Health Study/Study of Latinos. 西班牙裔社区健康研究/拉丁裔研究中的累积心理社会因素和表观遗传年龄加速

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-01 Epub Date: 2025-08-01 DOI: 10.1080/17501911.2025.2540260

Sarina Abrishamcar, Jasmine K Aqua, Christian Dye, Rebecca Jones-Antwi, Yinxian Chen, Linda C Gallo, Maria M Llabre, Krista M Perreira, Martha L Daviglus, Maria Argos, Bharat Thyagarajan, Anke Hüls, Andrea Baccarelli, Jianwen Cai, Carmen R Isasi, Robert C Kaplan, Karen N Conneely, Shakira F Suglia

{"title":"Cumulative psychosocial factors and epigenetic age acceleration in the Hispanic Community Health Study/Study of Latinos.","authors":"Sarina Abrishamcar, Jasmine K Aqua, Christian Dye, Rebecca Jones-Antwi, Yinxian Chen, Linda C Gallo, Maria M Llabre, Krista M Perreira, Martha L Daviglus, Maria Argos, Bharat Thyagarajan, Anke Hüls, Andrea Baccarelli, Jianwen Cai, Carmen R Isasi, Robert C Kaplan, Karen N Conneely, Shakira F Suglia","doi":"10.1080/17501911.2025.2540260","DOIUrl":"10.1080/17501911.2025.2540260","url":null,"abstract":"Background: Hispanics/Latinos in the United States experience disproportionately high psychosocial factors compared to non-Hispanic/Latino Whites. Psychosocial factors may accelerate biological aging, measured by epigenetic age acceleration (EAA), a DNA methylation biomarker predictive of morbidity and mortality.Methods: We investigated the cumulative impact of psychosocial factors on EAA over time in 922 adults from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Psychosocial exposure profiles were derived using self-organizing maps (SOM), an unsupervised clustering method. We calculated EAA from whole blood DNA methylation at two timepoints using GrimAge and DunedinPACE.Results: SOM identified four clusters: Cluster 1 (n = 196; 21.3%) had high levels of all psychosocial factors; Cluster 2 (n = 250; 27.1%) exhibited chronic, traumatic, and childhood stress; Cluster 3 (n = 250; 27.1%) showed mental health symptoms, low social support, and high perceived stress; and Cluster 4 (n = 238; 24.5%) had relatively low psychosocial stress. Adjusted weighted linear mixed models exhibited increased GrimAge in Cluster 1 (1.27 years, 95% CI: 0.57,1.97) and Cluster 2 (0.62 years, 95% CI: 0.01,1.23) compared to Cluster 4. DunedinPACE increased 3% (95% CI: 0.01,0.05) and 2% (95% CI: 0.001,0.04) in Clusters 1 and 3, respectively.Conclusions: These findings highlight the cumulative impact of psychosocial factors on EAA and how stressors can get \"under the skin\" and contribute to health disparities.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"865-877"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA methylation associations with cognitive function in early-stage hormone receptor-positive breast cancer patients. 早期激素受体阳性乳腺癌患者的DNA甲基化与认知功能的关系

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-01 Epub Date: 2025-08-06 DOI: 10.1080/17501911.2025.2542116

Shuwei Liu, Dongjing Liu, Catherine M Bender, Kirk I Erickson, Susan M Sereika, John R Shaffer, Daniel E Weeks, Yvette P Conley

{"title":"DNA methylation associations with cognitive function in early-stage hormone receptor-positive breast cancer patients.","authors":"Shuwei Liu, Dongjing Liu, Catherine M Bender, Kirk I Erickson, Susan M Sereika, John R Shaffer, Daniel E Weeks, Yvette P Conley","doi":"10.1080/17501911.2025.2542116","DOIUrl":"10.1080/17501911.2025.2542116","url":null,"abstract":"Background: Approximately one-third of breast cancer (BC) patients show poorer cognitive function (CF). Using DNA methylation (DNAm) data, here we aimed to identify genes and biological pathways associated with CF in postmenopausal women with early-stage hormone receptor-positive (HR+) BC.Methods: Epigenome-wide association studies (EWAS) and differentially methylated region analyses were performed for each CF phenotype (seven objective domains and one subjective phenotype) using DNAm data from whole blood samples (n = 109) taken at the time of enrollment.Results: When adjusting for age, verbal IQ scores, and global DNAm signature, cg10331779 near CTNND2 (p-value = <math><mn>9.65</mn><mo>×</mo><mrow><msup><mn>10</mn><mrow><mo>-</mo><mn>9</mn></mrow></msup></mrow></math>) and cg25906741 in MLIP (p-value = <math><mn>2.01</mn><mo>×</mo><mrow><msup><mn>10</mn><mrow><mo>-</mo><mn>8</mn></mrow></msup></mrow></math>) were associated with processing speed and subjective CF, respectively, while regions in/near SLC6A11, PRKG1/CSTF2T, and FAM3B for processing speed, and regions in/near PI4KB and SGCE/PEG10 for mental flexibility were differentially methylated. In addition, beta-estradiol was identified as a common upstream regulator for all the CF phenotypes, suggesting an essential role of estrogen in explaining variation in CF of HR+ BC patients.Conclusions: In our EWAS of 8 CF phenotypes, we found two epigenome-wide significant signals, one for processing speed and the other for subjective CF. We also found three differentially methylated regions associated with processing speed and two associated with mental flexibility.Clinical trial registration: www.clinicaltrials.gov identifier is NCT02793921.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"879-889"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bifaceted functions of histone methyltransferases. 组蛋白甲基转移酶的双面功能。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-01 Epub Date: 2025-07-13 DOI: 10.1080/17501911.2025.2530925

Jawad Akhtar, Vassiliki Saloura

引用次数: 0

The emerging role of multiomics in aging research. 多组学在衰老研究中的新作用。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-09-01 Epub Date: 2025-07-20 DOI: 10.1080/17501911.2025.2533111

Douglas M Ruden

{"title":"The emerging role of multiomics in aging research.","authors":"Douglas M Ruden","doi":"10.1080/17501911.2025.2533111","DOIUrl":"10.1080/17501911.2025.2533111","url":null,"abstract":"Aging is a complex biological process involving coordinated changes across multiple molecular systems. Traditional reductionist approaches, while valuable, are insufficient to capture the full scope of aging's systemic nature. Multiomics - integrating data from genomics, transcriptomics, epigenomics, proteomics, and metabolomics - provides a comprehensive framework to study aging as an interconnected network. In this Perspective, I explore how multiomic strategies, particularly those leveraging epigenomic and single-cell data, are reshaping our understanding of aging biology. Epigenetic alterations, including DNA methylation and histone modifications, are not only hallmarks but also powerful biomarkers of biological age. I discuss advances in multiomic aging clocks, cross-tissue atlases, and single-cell spatial technologies that decode aging at unprecedented resolution. I also build on a prior review I wrote with colleagues, Epigenomics. 2023;15(14):741-754, which introduced the concept of pathological epigenetic events that are reversible (PEERs) - epigenetic alterations linked to early-life exposures that predispose to aging and disease but may be therapeutically modifiable. This Perspective examines how PEERs and multiomics intersect to inform biomarkers, geroprotective interventions, and personalized aging medicine. Finally, I highlight integration challenges, ethical concerns, and the need for standardization to accelerate clinical translation. Together, these insights position multiomics as a central pillar in the future of aging research.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"897-904"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epigenetic silencing of JAM3 promoted progression in serous ovarian carcinoma through PI3K/AKT pathway. 表观遗传沉默JAM3通过PI3K/AKT通路促进浆液性卵巢癌的进展。

IF 2.6 4区医学

Epigenomics Pub Date : 2025-08-01 Epub Date: 2025-07-25 DOI: 10.1080/17501911.2025.2535942

Haiyan Wang, Chunlei Wen, Jiling Xie, Jiandong Wang, Wenxiu Yang

{"title":"Epigenetic silencing of JAM3 promoted progression in serous ovarian carcinoma through PI3K/AKT pathway.","authors":"Haiyan Wang, Chunlei Wen, Jiling Xie, Jiandong Wang, Wenxiu Yang","doi":"10.1080/17501911.2025.2535942","DOIUrl":"10.1080/17501911.2025.2535942","url":null,"abstract":"Background: Junctional adhesion molecule 3 (JAM3) is frequently epigenetically silenced in various cancers, but its role in serous ovarian carcinoma (SOC) was unclear.Research design and methods: This study evaluated JAM3 expression and methylation in SOC using immunohistochemistry (IHC), bisulfite sequencing PCR (BSP), and quantitative methylation-specific PCR (qMSP). Cell proliferation, apoptosis, migration, and invasion were examined using CCK8, flow cytometry, scratch-wound, and transwell assays. Pathways downstream of JAM3 were explored through RNA sequencing (RNA-seq) and Western Blot analysis, with rescue experiments using AKT inhibitor (MK2206) to validate pathway dependency.Results: Findings revealed that JAM3 expression is significantly reduced in SOC, correlating with advanced clinical stages and poor prognosis. Methylation levels of the JAM3 promoter were higher in SOC samples compared to normal tissues and were linked to increased Ki67 expression and clinical stages. Functionally, overexpressing JAM3 in SOC cells triggered apoptosis and hindered proliferation, migration, and invasion, whereas JAM3 knockdown produced opposite effects. Mechanism analysis demonstrated that JAM3 affects SOC cell proliferation through the PI3K/AKT signaling pathway.Conclusions: Conclusively, JAM3 acts as a tumor suppressor in SOC by modulating the PI3K/AKT pathway. These insights present JAM3 as a promising therapeutic target for SOC diagnosis and treatment.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"803-815"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144714983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0