{"title":"MDM2 and DNMT1 inhibitors induce neuroblastoma cell death through p53-dependent and independent pathways.","authors":"Shyam Sundar Jaganathan, Umamaheswari Natarajan, Appu Rathinavelu","doi":"10.1080/17501911.2025.2558497","DOIUrl":"https://doi.org/10.1080/17501911.2025.2558497","url":null,"abstract":"<p><strong>Introduction: </strong>Neuroblastoma, a highly aggressive pediatric cancer, presents significant treatment challenges due to its rapid proliferation, and resistance to conventional therapies. Growing evidence emphasizes the critical role of epigenetic modifications in tumor progression.</p><p><strong>Research design and methods: </strong>In this study, we explored the therapeutic potential of the MDM2 inhibitor RG-7388 alongside the DNMT inhibitors CM-272 and SGI-1027 in SK-N-SH and IMR-32 neuroblastoma cells. We hypothesized that RG-7388, CM-272, and SGI-1027 would induce p21 upregulation, leading to cell cycle arrest and activation of cell death pathways.</p><p><strong>Results: </strong>Cells treated with the above listed drug exhibited significant cell death, as determined by cell viability and caspase-3/7 activation assays. qRT-PCR and Western blot analyses revealed increased expression of p21 and pro-apoptotic BAX, along with decreased levels of the anti-apoptotic protein BCL-XL. Notably, RG-7388 treatment induced substantial PARP cleavage, consistent with activation of apoptosis.These findings suggest that MDM2 and DNMT1 inhibition promotes apoptosis through a p21-driven mechanism. Importantly, DNMT1 inhibition could provide a therapeutic alternative for neuroblastomas with p53 mutations, where p53 dependent mechanism is ineffective.</p><p><strong>Conclusion: </strong>Our results suggest that, if validated further, RG-7388, CM-272, and SGI-1027 could become effective therapeutic agents for treating aggressive neuroblastoma that may become resistant to first or second line of treatment.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-12"},"PeriodicalIF":2.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074538","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}
EpigenomicsPub Date : 2025-09-10DOI: 10.1080/17501911.2025.2558496
Chia-Hsuan Li, Bao-Yu Chen, Chih-Wei Lin, Shulan Hsieh, Cheng-Ta Yang, Joshua Oon Soo Goh, Yun-Hsuan Chang, Sheng-Hsiang Lin
{"title":"MicroRNAs signatures in small extracellular vesicles for psychological resilience in young adults using machine learning.","authors":"Chia-Hsuan Li, Bao-Yu Chen, Chih-Wei Lin, Shulan Hsieh, Cheng-Ta Yang, Joshua Oon Soo Goh, Yun-Hsuan Chang, Sheng-Hsiang Lin","doi":"10.1080/17501911.2025.2558496","DOIUrl":"https://doi.org/10.1080/17501911.2025.2558496","url":null,"abstract":"<p><strong>Aims: </strong>Psychological resilience refers to an individual's capacity to adapt to adverse events. MicroRNAs (miRNAs) play a crucial role in regulating post-transcriptional processes, while small extracellular vesicles (sEVs) act as transport vehicles. This study aimed to employ genome-wide profiling to identify and validate differences in the expression of resilience-associated sEV-miRNAs between low resilience (LR) and high resilience (HR) in young adults.</p><p><strong>Methods: </strong>Eighty participants were divided into LR or HR based on the Connor - Davidson Resilience Scale (CD-RISC). The expression levels of the target sEV-miRNAs in LR and HR were compared and analyzed.</p><p><strong>Results: </strong>Expression analyses demonstrated significant differences in let-7b, miR-151b, miR-335, and miR-193a between LR and HR (<i>p</i> < 0.01), with let-7b showing the highest discriminative ability. The AUC values for each sEV-miRNA ranged from 0.74 to 0.94, based on logistic regression and three machine learning models: random forest, support vector machine, and eXtreme gradient boosting. Based on leave-one-out cross-validation in different models, the combined four sEV-miRNAs demonstrated strong performance for detecting LR (AUC = 0.87-0.90). Sex-specific differences were also observed, with female participants showing more pronounced resilience signatures in targeted sEV-miRNAs.</p><p><strong>Conclusions: </strong>These findings suggest that sEV-miRNAs hold potential as biomarkers for psychological resilience in young adults.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-13"},"PeriodicalIF":2.6,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145029180","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}
EpigenomicsPub Date : 2025-09-09DOI: 10.1080/17501911.2025.2557186
Yahui Yang, Zhiyuan Sun, Fengshu Zhu, Aiguo Chen
{"title":"Blood-based DNA methylation markers for autism spectrum disorder identification using machine learning.","authors":"Yahui Yang, Zhiyuan Sun, Fengshu Zhu, Aiguo Chen","doi":"10.1080/17501911.2025.2557186","DOIUrl":"https://doi.org/10.1080/17501911.2025.2557186","url":null,"abstract":"<p><strong>Background: </strong>Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder lacking objective biomarkers for early diagnosis. DNA methylation is a promising epigenetic marker, and machine learning offers a data-driven classification approach. However, few studies have examined whole-blood, genome-wide DNA methylation profiles for ASD diagnosis in school-aged children.</p><p><strong>Methods: </strong>We analyzed genome-wide DNA methylation data from GEO dataset GSE113967, including 52 children with ASD and 48 typically developing (TD) controls. Differentially methylated positions (DMPs) were identified, and feature selection was performed using support vector machine-recursive feature elimination with cross-validation (SVM-RFECV). Classification models were developed using random forest (RF), extreme gradient boosting (XGBoost), and decision tree (DT) classifiers. A nomogram visualized feature contributions.</p><p><strong>Results: </strong>A total of 138 DMPs differentiated ASD from TD children. Eleven CpG sites selected by SVM-RFECV formed the basis for model construction. RF and XGBoost achieved the highest accuracy (75%), with DT reaching 70%. Functional annotation indicated enrichment in cell adhesion and immune-related pathways.</p><p><strong>Conclusions: </strong>This exploratory study demonstrates the feasibility of integrating peripheral blood DNA methylation data with machine learning to distinguish children with ASD. While limited by sample size and moderate accuracy, this study provides methodological insights into the feasibility of integrating epigenetic and computational approaches for ASD-related biomarker exploration.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-14"},"PeriodicalIF":2.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145023038","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}
EpigenomicsPub Date : 2025-09-05DOI: 10.1080/17501911.2025.2554569
Elizabeth DeSouza, Georgia Kruck, Corina Nagy
{"title":"Steroid hormone-mediated epigenetic programming during puberty: uncovering links to depression.","authors":"Elizabeth DeSouza, Georgia Kruck, Corina Nagy","doi":"10.1080/17501911.2025.2554569","DOIUrl":"https://doi.org/10.1080/17501911.2025.2554569","url":null,"abstract":"<p><p>DNA methylation (DNAm) is a key epigenetic modification that dynamically regulates eukaryotic development over time. DNAm has been found to influence a variety of biological processes in both normative and pathological states, such as depression. Since DNAm can serve as an interface between environmental influence and gene expression, it is a mechanism studied in the context of many pathologies, including psychiatric. Depression is a complex and heterogeneous disorder strongly influenced by puberty, as evidenced by increased rates in both sexes after sexual maturation. However, this effect is more pronounced in females, contributing to its twofold increased lifetime prevalence compared to males. Additionally, depression is consistently associated with altered DNAm at specific genomic sites. In this review, we discuss how DNAm programming can affect functional pathways during puberty and in turn, influence disease outcomes. Here, we highlight the bidirectional relationship of steroid hormone surges during this sensitive period and DNAm, adding a layer of complexity and insight into the pathophysiology of depression. Specifically, we explore the extent of DNAm change throughout puberty, how it contributes to individual and sex-specific differences in puberty, and how it may influence the risk for depression.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-13"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999927","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}
EpigenomicsPub Date : 2025-09-04DOI: 10.1080/17501911.2025.2554570
Mohammed A H Alsaedi, Gordon Strathdee
{"title":"The role of DNA methylation in directing treatment in medulloblastoma.","authors":"Mohammed A H Alsaedi, Gordon Strathdee","doi":"10.1080/17501911.2025.2554570","DOIUrl":"https://doi.org/10.1080/17501911.2025.2554570","url":null,"abstract":"<p><p>Medulloblastoma is the most common malignant childhood brain tumor. The disease exhibits significant clinical and molecular heterogeneity which leads to significant differences in outcome. Although survival rates have improved in recent years, outcome for patients with high-risk disease remains poor and survival is associated with significant treatment associated morbidity. Traditional risk stratification was established largely on the basis of clinical and histological factors, but these are not sufficient to capture the full biologic complexity of the disease. Recent advances have underscored the role of DNA methylation as a powerful epigenetic biomarker for precise subgroup stratification and prognostic classification of medulloblastoma into four primary molecular subtypes: WNT, SHH, Group 3, and Group 4. This review summarizes mechanisms of DNA methylation in cancer biology, methylation profiling analytical approaches, and their application in delineating medulloblastoma subtypes. Specific attention is placed on the clinical utility of methylation-based classifiers for guiding therapeutic decisions and clinical trial design.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-12"},"PeriodicalIF":2.6,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991470","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}
EpigenomicsPub Date : 2025-09-03DOI: 10.1080/17501911.2025.2554571
Elena Grafenhorst, Teodor G Calina, Mihnea P Dragomir
{"title":"DNA methylation profile to aid in the diagnosis of pancreatic ductal adenocarcinoma and its role in disease progression.","authors":"Elena Grafenhorst, Teodor G Calina, Mihnea P Dragomir","doi":"10.1080/17501911.2025.2554571","DOIUrl":"10.1080/17501911.2025.2554571","url":null,"abstract":"<p><p>There is no immunohistochemical or molecular marker to confirm the histologic diagnosis of pancreatic ductal adenocarcinoma (PDAC). This is particularly important in a scenario of unknown primary. Molecularly, PDAC is characterized by a limited set of driver mutations, and new predictive and prognostic markers are needed to guide novel therapies. Recent data show that DNA methylation profiles combined with complex machine learning algorithms are ideal tools to improve the diagnosis of PDAC. In addition, DNA methylation can be used to gain a deeper understanding of PDAC pathogenesis and further stratify this entity. Furthermore, exciting technologies have emerged, such as nanopore sequencing, which can be used to move these diagnostic tools from the postoperative to the intraoperative setting, or even as a liquid biopsy approach.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-10"},"PeriodicalIF":2.6,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144947563","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}
EpigenomicsPub Date : 2025-09-01Epub Date: 2025-08-13DOI: 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 <i>FMR1</i> and <i>SNRPN</i> 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":"<p><strong>Aim: </strong>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.</p><p><strong>Methods: </strong>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 (<i>n</i> = 20), fragile X syndrome (FXS, <i>n</i> = 20), or chromosome 15 imprinting disorders (<i>n</i> = 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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>","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}
EpigenomicsPub Date : 2025-09-01Epub Date: 2025-07-16DOI: 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":"<p><p>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.</p>","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}
EpigenomicsPub Date : 2025-09-01Epub Date: 2025-08-01DOI: 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":"<p><strong>Background: </strong>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.</p><p><strong>Methods: </strong>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.</p><p><strong>Results: </strong>SOM identified four clusters: Cluster 1 (<i>n</i> = 196; 21.3%) had high levels of all psychosocial factors; Cluster 2 (<i>n</i> = 250; 27.1%) exhibited chronic, traumatic, and childhood stress; Cluster 3 (<i>n</i> = 250; 27.1%) showed mental health symptoms, low social support, and high perceived stress; and Cluster 4 (<i>n</i> = 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.</p><p><strong>Conclusions: </strong>These findings highlight the cumulative impact of psychosocial factors on EAA and how stressors can get \"under the skin\" and contribute to health disparities.</p>","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}
EpigenomicsPub Date : 2025-09-01Epub Date: 2025-08-06DOI: 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":"<p><strong>Background: </strong>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.</p><p><strong>Methods: </strong>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 (<i>n</i> = 109) taken at the time of enrollment.</p><p><strong>Results: </strong>When adjusting for age, verbal IQ scores, and global DNAm signature, cg10331779 near <i>CTNND2</i> (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 <i>MLIP</i> (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 <i>SLC6A11</i>, <i>PRKG1/CSTF2T</i>, and <i>FAM3B</i> for processing speed, and regions in/near <i>PI4KB</i> and <i>SGCE/PEG10</i> 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.</p><p><strong>Conclusions: </strong>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.</p><p><strong>Clinical trial registration: </strong>www.clinicaltrials.gov identifier is NCT02793921.</p>","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}