MethylModes is an R package and Shiny application to identify multimodal distributions in human DNA methylation at individual CpG sites. Multimodal distributions, which can be the result of nearby genetic variation, environmental exposures or assay artifacts, are susceptible to confounding and important to identify for methylation analysis. MethylModes is easily incorporated into existing quality control pipelines of array-based DNA methylation data. The underlying algorithm uses kernel smoothing of probe-level data to locate the number and location of peaks. The algorithm can be parallelized across probes for efficient implementation at genome-scale. We provide a case study implementation of MethylModes in the Health and Retirement Study as well as the Airwave Health Monitoring Study. MethylModes is available on GitHub at https://github.com/lutiffan/methylModes as an R package wrapping an R Shiny application. We include a toy dataset to validate installation. The codebase is also published on Zenodo at https://doi.org/10.5281/zenodo.17448517. Supplementary data are available at Bioinformatics online.

Background Vascular cognitive impairment (VCI) is a group of cognitive disorders caused by cerebrovascular disease and is the second leading cause of dementia. VCI prevalence has significantly increased over the past decade. However, the molecular mechanisms underlying VCI remain unclear. Objective This review summarizes recent reports on the critical roles of hippocampal synaptic plasticity and epigenetic changes in VCI and vascular dementia (VaD) by incorporating findings from neuroimaging and molecular biology. Methods We reviewed studies employing molecular, electrophysiological, and neuroimaging approaches, conducted over the last two decades. Key targets of investigation included cerebral blood flow regulation, synaptic transmission, and epigenetic mechanisms such as DNA methylation, histone modification, and noncoding RNA regulation. Results Growing evidence suggests that chronic cerebral hypoperfusion and microvascular injury cause deficits in hippocampal synaptic plasticity, leading to long-term potentiation and memory formation deficits. Aberrant epigenetic changes, such as dysregulated DNA methylation, histone acetylation, and miRNA expression, contribute to neuroinflammatory and neurodegenerative processes. Electroencephalography and functional magnetic resonance imaging studies reflect changes in neural connectivity and network dynamics, and molecular imaging provides molecular-level evidence of these changes. Conclusion VCI is caused by the complex interaction of vascular dysfunction, synaptic dysregulation, and epigenetic modification. Identification of these convergent mechanisms may pave the way for new diagnostic biomarkers and therapeutic targets. Future studies on neuroimaging, molecular profiling, and epigenetic modifications could facilitate the early detection and precision-based treatment of VCI and VaD.

Introduction Glycolytic reprogramming has been implicated in rheumatoid arthritis (RA) pathogenesis, yet the underlying causal genes and epigenetic mechanisms remain unclear. This study aimed to systematically identify glycolysis-related genes and their methylation-regulated expression that may causally influence RA susceptibility. Methods We conducted a multi-omics Mendelian randomization (MR) analysis integrating genome-wide association study (GWAS) summary statistics for RA (FinnGen, UK Biobank, GCST90129453) with quantitative trait loci (QTLs) for blood-derived methylation (mQTL), expression (eQTL), and protein abundance (pQTL). Summary-data-based Mendelian randomization (SMR) and colocalization analyses were used to identify causal molecular signatures linking DNA methylation, gene expression, and protein abundance with RA risk. Replication was performed in independent RA cohorts. In addition, qPCR validation was conducted in an independent whole-blood cohort (30 RA patients and 30 healthy controls). Results SMR identified 129 CpG sites (75 genes), 28 transcripts, and 9 proteins significantly associated with RA risk. Seven glycolytic genes—PKD1, SLC2A4, ALAS1, ALDH7A1, LRFN3, PFKFB2, and PYGB—showed consistent evidence across methylation, expression, and GWAS datasets. Notably, hypomethylation at cg07036112 (PKD1; OR = 0.68, 95% CI: 0.59–0.78) and cg06891043 (SLC2A4; OR = 0.92, 95% CI: 0.89–0.96) was associated with increased gene expression and increased RA susceptibility. Colocalization supported shared causal variants at these loci (PP.H4 > 0.5). Additional signals included cg13241645 (ALAS1; OR = 0.72, 95% CI: 0.65–0.80) and cg01380361 (PFKFB2; OR = 1.33, 95% CI: 1.17–1.51). qPCR confirmed increased PKD1 and SLC2A4 mRNA expression in RA compared with healthy controls. Discussion This integrative multi-omics MR framework supports an epigenetically mediated contribution of glycolysis-related regulation to RA susceptibility and nominates PKD1 and SLC2A4 as robust genetically supported candidate genes. These findings highlight methylation-linked transcriptional changes in glycolysis-related pathways implicated in RA and suggest potential biomarkers and therapeutic targets.

Evaluation of Epstein–Barr virus DNA methylation and load in saliva in the management of individuals at high risk of nasopharyngeal carcinoma

Introduction Chinese Hamster Ovary (CHO) cells are widely used for the production of recombinant therapeutics due to their ability to carry out human-like post-translational modifications. Media adaptation represents a key step in large-scale production to ensure optimal safety and cost efficiency. As DNA methylation is a central epigenetic mechanism underlying adaptive modulation of gene expression, we report here, for the first time, the use of high-coverage whole-genome bisulfite sequencing to generate single-base-resolution maps of CHO cells at different phases of growth in a fed-batch culture and undergoing media adaptation across four different media. Methods A CHO cell line was adapted to four commercially available media, and their growth rates and productivity were compared with those obtained using the control medium in a 7-day batch culture. This approach resulted in the generation of n = 57 high-quality whole-genome DNA methylation datasets, which were subjected to differential DNA methylation and gene association analyses. In addition, we developed a novel DNA methylation array comprising more than 63,000 CpG methylation sites across the CHO genome, enabling streamlined and efficient DNA methylation profiling of CHO cells. Results Analysis of n = 57 high-quality DNA methylation datasets revealed altered DNA methylation patterns across different phases of growth in a fed-batch culture and in response to distinct media adaptations. Specifically, adaptation to four different media resulted in highly specific methylation changes that were associated with distinct functional outcomes, including protein productivity. Finally, the customized DNA methylation microarray platform was used to validate all media adaptation-dependent epigenetic changes identified by whole-genome bisulfite sequencing (WGBS). Conclusion These findings identify and characterize dynamic DNA methylation changes occurring during media adaptation and support their potential use as predictive indicators of CHO cell phenotypic changes in response to a dynamic culture environment. Furthermore, this work represents a valuable resource for the development of DNA methylation-based biomarkers for the optimization of CHO cell culture.

Besides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. Here, we explore mammalian imprinted domains, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony-which is parent-of-origin dependent and lost upon neural differentiation-at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons. Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome. Moreover, we find no evidence that RT and organisation into TADs are linked in this domain. The combined replication timing, DNA methylation, 3D chromatin structure, and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.

Developing non-invasive prognostic biomarkers remains critical to improving personalized cancer care. Growth differentiation factor-15 (GDF-15), a TGF-β family cytokine, plays a key role in tumorigenesis and immune evasion. Circulating GDF-15 serves as a biomarker for cancer prognosis, and DNA methylation (DNAm)-predicted GDF-15 has been linked to mortality risk in the general population. However, the association between DNAm-predicted GDF-15 and mortality risk in cancer survivors remains unexplored. We analyzed the association between DNAm-predicted GDF-15 and all-cause, long-term all-cause, and cancer mortality risks using a cohort of 343 cancer survivors from the National Health and Nutrition Examination Survey (NHANES) 1999-2002 with a median follow-up of 138 months. Multivariable Cox regression reporting hazard ratios (HRs) and 95% confidence intervals (CIs) demonstrated that each 1-standard deviation (SD) increment in DNAm-predicted GDF-15 was associated with a 60% higher all-cause mortality risk adjusted with model 1 of age and sex, and a 54% greater all-cause mortality risk in model 2 adjusted additionally for ethnicity, education, smoking, and coronary heart disease. Participants in the high GDF-15 tertile showed a 201% and 166% higher mortality risk in model 1 and model 2, respectively (both p for trend < 0.0001) compared to the low tertile. Its association with long-term mortality risk remains unchanged. Stratified analyses indicated consistent relationships across multiple subgroups. Kaplan-Meier and competing risk analyses revealed a graded increase in cancer mortality risk across ascending GDF-15 tertiles; Cox models confirmed a significant positive association per 1-SD increment in the unadjusted model and model 1, which remained consistent in direction and magnitude in model 2, with a marginally significant (p = 0.052). The current study provided evidence that DNAm-predicted GDF-15, an alternative and precise estimate of GDF-15 based on DNA methylation, is positively associated with all-cause and long-term all-cause mortality risks and showed a trend of positive association with cancer mortality among cancer survivors. Future larger longitudinal studies with serial DNAm-predicted GDF-15 assessments are needed to verify potential causal links.

Prospective cohort study. Determine whether epigenetic age (EA), calculated via DNA methylation analysis, is associated with early postoperative complications in adult spinal deformity (ASD) surgery. ASD is increasingly prevalent in the aging population, with postoperative complication rates ranging from 37% to 71%. While chronological age (CA) and frailty scores are known predictors of poor outcomes, they may not fully capture biological vulnerability. EA, derived from DNA methylation patterns, may better reflect a patient's physiological reserve and stress response capacity. Thirty patients undergoing ASD surgery were prospectively enrolled and provided peripheral blood samples on the day of surgery. DNA methylation of peripheral blood mononuclear cells (PBMCs) was analyzed using the Illumina EPIC v2.0 array. EA was computed using the Horvath DNAmAge algorithm. Associations between EA, CA, and the Edmonton Frailty Index (EFI) with postoperative complications at 30 days were assessed using appropriate parametric and non-parametric statistical tests. Differentially methylated positions (DMPs) were identified between complication and non-complication group. Of the 30 enrolled patients (mean CA: 68.4y, 21 female), 14 (47%) experienced postoperative complications. Sixty-three DMPs were found between the two groups, with 35 hypomethylated and 28 hypermethylated CpG sites in the complication group. Genes affected were linked to immune response, including LRBA and NFACT2. Regulators of EGFR and WNT pathways were also differentially methylated. Patients with EA greater than CA were significantly more likely to experience complications (86% vs. 14%, P=0.038). The difference between EA and CA was greater in the complication group (5.07 vs. 0.87y, P=0.029). No significant differences were found in mean CA, EA, or EFI alone between the groups. Postoperative complications in ASD patients were associated with epigenetic alterations and elevated EA relative to CA. These findings suggest EA may be a novel biomarker for preoperative risk stratification in ASD surgery.

The prenatal period is a critical window for cardiovascular development in offspring. Accumulating evidence demonstrates that maternal nutritional imbalances during pregnancy—encompassing undernutrition, overnutrition, and specific nutrient deficiencies—elicit adverse adaptations in fetal vascular systems, thereby predisposing offspring to cardiovascular disease (CVD) in later life. This review synthesizes current knowledge on the impact of macronutrient (e.g., high-sugar, high-fat diets) and micronutrient (e.g., vitamin D, folate) imbalances, as well as exposures to alcohol and caffeine, on offspring cardiovascular health. Key mechanisms such as epigenetic regulation (e.g., DNA methylation, histone modifications), oxidative stress, and endothelial dysfunction are discussed. Furthermore, we highlight future research directions and potential early nutritional interventions aimed at mitigating long-term cardiovascular risks and breaking the cycle of intergenerational metabolic disease. By integrating mechanistic insights and epidemiological evidence, this review underscores the importance of optimizing maternal nutrition as a pivotal public health strategy for preventing offspring CVD.

Traumatic brain injury (TBI) represents a major global public health challenge. It is propelled by a cascade of secondary injuries. These injuries include inflammation, endothelial dysfunction, hypoxia, cerebral edema, and disruption of epigenetic homeostasis. These processes can precipitate necrosis and apoptosis. They also significantly heighten the risk of long-term cognitive deficits, dementia, and other neurodegenerative disorders. TBI progression is typically segmented into acute and chronic phases. Each phase is characterized by distinct pathological mechanisms and epigenetic alterations. The acute phase is dominated by direct tissue damage and robust inflammatory responses. In contrast, chronic TBI often evolves into long-term neurodegenerative conditions like chronic traumatic encephalopathy (CTE). CTE is marked by persistent neuroinflammation and cognitive decline. A critical gap exists in prior research. It lies in the frequent failure to disentangle the unique epigenetic reprogramming specific to each phase. This failure hinders the development of precisely timed interventions. This review systematically delineates the spatiotemporal dynamics of epigenetic regulation following TBI. It aims to construct a phase-specific framework for precision intervention. Acute-phase hallmarks involve DNA methylation. An example is DNMT3A-mediated silencing of homeostatic genes. They also include histone acetylation and m6A RNA methylation. The WTAP/YTHDF1-Lcn2 axis exemplifies this m6A regulation. Conversely, the chronic phase is defined by sustained neuroinflammation, tau hyperphosphorylation, and ferroptosis. These processes are modulated by noncoding RNAs. Examples include miR-29b and lncRNA 4933431K23Rik. Epigenetic drift also plays a regulatory role. Mitochondrial and endoplasmic reticulum stress further interact with these pathways. They amplify secondary damage. We underscore the clinical promise of time-stratified, personalized epigenetic interventions. These interventions aim to improve long-term outcomes. They forge a critical link between fundamental epigenetic discovery and precision management of neurotrauma. This work deepens the understanding of TBI pathophysiology. It also lays a conceptual and target-oriented groundwork. This groundwork advances neurotrauma care into an era of temporally tailored, individualized precision therapy.

While height is a highly heritable trait with strong polygenic prediction, previous studies have postulated that minimal variation of its individual differences can be captured by DNA methylation (DNAm). We investigated the role of blood-based genome-wide DNAm in capturing the variance in adult height in a large population-based cohort of 7,654 unrelated individuals from Generation Scotland using DNAm profiled on the Illumina EPIC array. The posterior DNAm probe effects were used to construct a DNAm profile score (Methylation Profile Score-MPS) which was evaluated in three independent cohorts. Genome-wide DNAm captures 25.0% (95% credible interval (CrI) 17.2-31.9) of the phenotypic variation in height when applying Bayesian penalised regression using BayesR + conditional on genetic effects. The total variation captured jointly by DNAm and genetic effects (80.3%, 95% CrI 70.1-87.2) is larger than the marginal estimate based on genetic effects only (56.3%, 95% CrI 45.8-66.8). Out-of-sample prediction shows that the MPS is weakly correlated with measured height (Pearson correlation ranging from 0.14-0.26), as well as being associated with several health and lifestyle factors in the LBC1936 that are established correlates of height. With the advent of larger sample sizes in epigenomics anticipated to improve the power to detect associations between DNAm and complex traits, we urge caution when making assumptions around "null traits" based solely on methylome-wide association study results and encourage the use of whole-genome methods to assess the proportion of variation in a trait that may be captured by DNAm.

Abstract Background: Prognostication in metastatic castration-resistant prostate cancer (mCRPC) is based largely on non-specific proteins and clinical factors which cannot be targeted therapeutically for delaying cancer progression in lethal mCRPC. DNA methylation, which can capture tumor-specific epigenetic changes, shows promise as a platform for identifying biology-based prognostic markers. This study investigates plasma cell-free DNA (cfDNA) methylation to identify mCRPC prognostic markers and develops an integrated clinical-molecular nomogram model for risk stratification and potentially personalized treatment strategies. Methods: Plasma was prospectively collected from localized prostate cancer (PC) (n=19), metastatic hormone-sensitive PC (mHSPC) (n=28), and metastatic castration resistant PC (mCRPC) (n=48) patients (pts). Extracted cfDNA underwent enzymatic methylation sequencing (EM-seq) targeting 366 genomic regions implicated in PC biology. Whole genome sequencing libraries were captured with a Twist targeted methylome panel. Bismark was used for methylation calling. mHapSuite was used to identify methylation haplotype blocks (MHBs) and subsequently calculate methylation haplotype load (MHL), the successive methylation at each fragment length. Differentially methylated regions (DMRs) unique to mCRPC were identified with Welch’s t-tests by comparing PC to mHSPC and mCRPC states. mCRPC survival analysis was performed with Cox proportional hazards models, Kaplan-Meier analysis, and nomograms. Results: From 366 target genomic regions, we identified 316 MHBs (linkage disequilibrium r2&amp;gt;0.5, CpG sites≥5) across the 96 PC patients. Comparing PC to mHSPC, 29 DMRs were identified (p-value&amp;lt;0.05). Comparing mHPSC to mCRPC, 271 DMRs were identified, of which 28 were shared with the localized PC vs. mHSPC analysis (p-value&amp;lt;0.05). A MHB-based composite risk score of the top 22 MHBs was generated for DMRs restricted to mCRPC state which showed worse mCRPC survival in high-risk patients (median survival time=15.5 months) than in low-risk patients (median survival time=36.5 months) (log-rank p-value=0.00052). Combining the top significant clinical markers with the MHB-based composite risk score also demonstrated decreased survival probability in high-risk patients (median survival time=15.5 months) as compared to low-risk patients (median survival time=42.8 months) (log-rank p-value=0.00025). Incorporation of the MHB-based score with predicted ctDNA fraction and clinical biomarkers into a multi-modal nomogram model improved the prognostic performance (6-month AUC=0.99, 1-year AUC=0.90, 2-year AUC=0.87) over clinical biomarkers alone (6-month AUC=0.98, 1-year AUC=0.87, 2-year AUC=0.84). Conclusions: Our findings demonstrate that cfDNA methylation signatures can complement existing prognostic models, offering a tumor-biology based personalized approach to mCRPC prognostication, which also identify therapeutic targets in pts with short survival. These findings warrant further validation in a newly recruited patient cohort. Citation Format: Manish Kohli, Jodie Wong, Yijun Tian, ManishKumar S. Patel, Kapil Avasthi, Claire Hanson, Enos Ampaw, Rebekah Gutowski, Muhammad Zaki H. Fadlullah, Joseph Finklestein, Aik C. Tan, Jong Park, Brandon J. Manley, Chiang-Ching Huang, Liang Wang. Plasma cell-free DNA methylation-based prognosis in metastatic castrate-resistant prostate cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr A033.

Abstract Background DNA methylation is a fundamental regulator of chromatin architecture and transcriptional control. While numerous studies have focused on the role of hypermethylation in disease progression, the biological and therapeutic consequences of widespread DNA methylation loss remain poorly defined. We identified a distinct subset of prostate cancers (PC), termed DNA Hypomethylated Prostate Cancers (DHMPCs), which are characterized by profound reductions in global DNA methylation levels. These tumors display aggressive clinical behavior, highlighting the urgent need to define effective therapeutic strategies tailored to this epigenetically defined cancer state. Objective We hypothesized that the global loss of DNA methylation observed in DHMPCs disrupts epigenome homeostasis and creates specific molecular dependencies that can be exploited therapeutically. Our goal was to systematically define these vulnerabilities and to rationally design combination treatment strategies for effective targeting of DHMPCs, with a focus on advanced PC. Study Design To delineate the biology of DHMPCs, we measured changes in global methylation pattern using validated orthogonal methods in large representative cohorts of localized and metastatic prostate cancer. We determined tumor cell intrinsic therapeutic vulnerabilities in broad pharmacologic screens and further assessed the patterns of epigenetic and transcriptomic alterations induced upon targeting these vulnerabilities in DHMPCs. Results Drug screens revealed that DHMPCs are highly sensitive to pharmacological AKT inhibition (AKTi). We show that the degree of global hypomethylation correlated strongly with response to AKTi across a broad panel of cancers, independent of canonical PI3K pathway alterations, including PTEN loss. Moreover, pharmacological induction of global DNA hypermethylation increased AKTi sensitivity, providing functional evidence for a methylation-dependent mechanism of response. Mechanistic studies demonstrated that AKTi triggers widespread epigenomic perturbations in DHMPCs, including global depletion of core histones and compensatory enrichment of the polycomb repressive complex 2 (PRC2)–associated histone mark H3K27me3. Building on this dependency, combined inhibition of AKT with EZH2 or EED inhibitors resulted in highly synergistic therapeutic effects, producing robust tumor growth suppression in preclinical models. Conclusions Together, these findings uncover an unanticipated mechanistic link between AKT signaling and DNA methylation state in PC. They establish global hypomethylation as a predictive biomarker for therapeutic vulnerability and provide a strong rationale for biomarker-guided development of combination therapies that co-target AKT and PRC2. More broadly, this work demonstrates how integrating epigenomic context with signaling pathway biology can enable the design of rational, effective treatment strategies for epigenetically defined cancer subtypes. Citation Format: Pallabi Mustafi, Helen Richards, Brian Hanratty, Radhika Patel, Adil Mohamed, Ilsa Coleman, Erolcan Sayar, Peter S. Nelson, Colm Morrissey, Ming Lam, Eva Corey, Chitvan Mittal, Gavin Ha, Jay Sarthy, Michael C. Haffner. Epigenetically Informed Therapeutic Strategies for DNA-Hypomethylated Prostate Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr PR005.

Abstract Androgen Receptor Pathway Inhibition (ARPI) is a cornerstone of prostate cancer treatment; however, therapeutic resistance often arises due to an AR-independent cell state emerging as a result of tumor plasticity. Dysregulation of epigenetic reprogramming factors, including Polycomb Repressive Complex 2 (PRC2), creates an environment conducive to lineage plasticity. Thus inhibiting PRC2 offers a promising strategy to overcome ARPI therapeutic resistance in prostate cancer. ORIC-944 is a potent, orally bioavailable, allosteric PRC2 inhibitor with potential best-in-class drug properties that is currently in Phase 1b clinical development. In preclinical studies, ORIC-944 in combination with ARPI demonstrated efficacy across various models including AR-mutant and -wildtype, ARPI-resistant and -sensitive, and castration-resistant and -sensitive prostate cancers. Despite the spectrum of resistance mechanisms in these AR positive models, ORIC-944 consistently enhanced signatures of luminal cell state and AR signaling. These preclinical observations reveal the potential for ORIC-944 to block prostate tumor adaptation and re-sensitize tumors to ARPI. In this study of clinical samples from the ORIC-944-01 Phase 1b clinical trial, we aimed to evaluate the mechanism of ORIC-944 in patients with prostate cancer. DNA methylation profiling from liquid biopsies was chosen as a non-invasive method for investigating the epigenetic landscape of circulating tumor DNA. We identified CpG-rich regions associated with prostate tumorigenesis and transcriptional subtypes based on publicly available DNA methylation data from 100 metastatic castration-resistant prostate cancer (mCRPC) tumors, 35 healthy blood samples, and 150+ normal tissues. These selected regions became the foundation of a custom panel utilized on liquid biopsies to profile the epigenetic states of tumors from mCRPC patients treated with single-agent ORIC-944. A new methodology for cell-free DNA methylation was established to detect and quantify changes in subtype-associated regions independently of tumor burden. This approach and the clinical DNA methylation data showed that following treatment with ORIC-944, tumors from most patients experienced a shift in methylation pattern that suggests an increase in AR signaling. Notably, this shift was detectable after one treatment cycle of single agent ORIC-944, consistent with preclinical studies. Conversely, no patients showed an increase in neuroendocrine-associated signals after one cycle of treatment. These findings suggest that a selected set of informative methylation regions evaluated in plasma can identify epigenetic-driven changes in transcriptional activity during the treatment of patients with advanced prostate cancer. This approach is a key step towards enabling non-invasive epigenomic profiling of transcriptional states of prostate cancer. Furthermore, this analysis confirms our preclinical mechanistic data and hypothesis that ORIC-944 treatment enhances AR signaling in prostate cancer. Citation Format: Amber W. Wang, Michal Pawlak, Eric Ariazi, Livia Ulicna, Anne Page, Rupal Patel, Edna Chow Maneval, Pratik S. Multani, Lori S. Friedman, Anneleen Daemen, Aleksandr Pankov. Circulating tumor DNA methylation captures epigenetic changes in patients induced by the PRC2 inhibitor ORIC-944 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr PR024.

ABSTRACT DNA methylation (DNAm), capturing chronological gestational age (GA) and epigenetic gestational age acceleration (EGAA), can be modified by environmental exposures. The Asthma&Allergy array is a new DNAm array developed with content focused on asthma and allergy loci. The association between content on the Asthma&Allergy array and chronological GA and EGAA has not been evaluated alone or in the context of prenatal/perinatal exposures. We performed an epigenome wide association study (EWAS) chronological GA at single CpG sites and regions in cord blood from 391 newborn children from a Detroit-based birth cohort. We further constructed a multi-CpG site methylation model to predict chronological GA. Also, associations between prenatal/perinatal environmental factors with GA, epigenetic gestational age (EGA), and EGAA were assessed. We identified 2,435 CpG sites associated with chronological GA, and CpGs within the HLA class II locus (HLA-DRB1, HLA-DQB1, HLA-DRB6) were among the most significantly associated with chronological GA. Our multi-CpG site model attained higher predictive accuracy (R2 = 0.88) comparable to other published methods. Using genes implicated in region-based analyses (n = 395 regions), the pathways most significantly enriched with chronological GA-associated CpGs included T helper 1(Th1) and 2(Th2) activation, B-cell development, and IL-10 signaling, which were also enriched in at least one of the other published epigenetic GA clocks. In multi-exposure models, infant’s first-born status and maternal parity were associated with EGAA. Our findings highlight enrichment for T cell modulated pathways and antigen presentation as biological processes associated with chronological GA, as well as prenatal/perinatal factors that may affect EGAA.

Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors primarily involving the adrenal medulla and its associated paraganglia, with heterogeneous clinical behavior and complex molecular drivers. This study aimed to characterize DNA methylation and gene expression patterns in PPGLs to understand the molecular differences between tumor subtypes and malignancy. We performed an integrative analysis of DNA methylation (Illumina EPIC 850K) and gene expression profiles (Affymetrix microarrays) in 24 PPGLs, comparing these with The Cancer Genome Atlas (TCGA) data, to delineate cluster- and malignancy-specific epigenetic patterns. Comparison between pseudohypoxic Cluster I and kinase-signaling Cluster II tumors revealed 13 differentially methylated CpG sites, with a specific CpG within DSCAML1 showing hypermethylation in Cluster II accompanied by increased expression, suggesting context-dependent gene body methylation effects. Benign versus malignant comparisons identified 101 differentially methylated CpGs, including hypermethylated CpG in BAIAP2L1 and hypomethylated CpG in SHANK1 in malignant tumors. Pathway enrichment of differentially methylated genes revealed alterations in Notch signaling, adherens junctions, cytoskeletal regulation, and intracellular transport. Gene expression analysis demonstrated partial overlap between clusters, with malignant tumors exhibiting distinct transcriptional profiles involving RNA processing, metabolism, and adhesion pathways. Correlation between methylation and expression was generally limited, emphasizing that methylation-dependent gene regulation is a locus-specific and context-dependent regulation. These findings illustrate a complex interplay between epigenetic modifications and transcriptional programs in PPGLs, enhancing our understanding of molecular heterogeneity and tumor classification, and identifying candidate biomarkers and therapeutic targets for malignant progression.

The Impact of Omega-3 Fatty Acids on DNA Methylation in Midlife Woman: Epigenetic Mechanisms of Anti-Inflammatory Effects

For decades, paternal health was considered largely irrelevant to pregnancy outcomes, with scientific and clinical attention focused almost exclusively on maternal physiology. This perspective has shifted markedly over the past fifteen years. A growing body of evidence now indicates that paternal diet, physical activity, metabolic status, and broader lifestyle factors exert measurable influences on embryonic development, placental function, and long-term offspring health. These effects are mediated through multiple biological pathways, including sperm DNA methylation, histone retention, small non-coding RNAs, seminal plasma signaling, and immune–metabolic interactions at the time of implantation. Human studies demonstrate that paternal obesity and poor metabolic health are associated with altered sperm epigenetic profiles, dysregulation of imprinted genes such as IGF2, and increased risks of adverse pregnancy outcomes. Experimental models further reveal that paternal dietary imbalance—both undernutrition and overnutrition—can impair placental vascularization, induce hypoxia, and program sex-specific metabolic phenotypes in offspring. Conversely, paternal physical activity appears capable of partially counteracting diet-induced epigenetic disruptions, improving offspring metabolic health via modifications of the sperm RNA payload. This narrative review synthesizes evidence from human observational studies, controlled animal experiments, and mechanistic epigenetic research to examine how paternal diet, exercise, and lifestyle shape placental development and offspring health. Particular attention is given to the relevance of these findings for sport science and public health, highlighting paternal preconception health as a modifiable determinant of developmental outcomes.

Introduction Glioma stem cells (GSCs) have been implicated in radio- and chemotherapeutic resistance of glioblastoma (GBM). Therapeutic targeting of GSCs has shown promise in immunocompromised rodent models but have not been translated into effective therapies for human patients. These failures underscore the translational limitations of rodent models and highlight the need for complementary models that accurately and reliably predict therapeutic translation for human HGG. Spontaneous canine high-grade gliomas (HGGs) may provide a complementary translational model for human therapeutic development. While described in canine HGGs, little is known about canine glioma stem cell biology. Methods Here, we evaluated cellular metabolism, cytosine modifications, gene expression, and functional tests of malignancy to interrogate differences between canine high-grade astrocytoma-derived glioma stem-cell like cells (GSLC) and a traditional non-stem cell glioma cell line following exposure to hypoxia. Results Hypoxia increased oxygen consumption rates in GSLCs and augmented features of malignancy in GSLCs. We observed variable cytosine modifications and mRNA expression across cell lines, and our data did not correlate cytosine modification patterns with oxygen consumption capacity following hypoxia. However, we did demonstrate a positive correlation between up-regulated genes in human GBM GSCs and hypomethylation of orthologous canine genes following hypoxia. Discussion Together, these data support that hypoxia enhances distinct stem-like traits in canine astrocytoma GSLCs, similar to human GSCs.

Abstract Background: Prostate cancer is genomically heterogeneous with few shared drivers. We characterized tumor-specific DNA methylation programs that define evolutionary subtypes, remodel the tumor–microenvironment ecosystem, and yield liquid-biopsy biomarkers. Methods: Illumina EPIC-seq methylation was profiled in matched benign/tumor tissues from the UK Prostate ICGC cohort. A covariance-based DMR caller identified robust tumor-specific regions that were intersected with bulk RNA-seq, network analyses, and single-cell/spatial transcriptomics to localize programs in situ. A FACS-sorted, cell-type methylome atlas (luminal, basal, endothelial, fibroblast, immune, smooth muscle) anchored cell-of-origin assignments. Cell-free DNA was deconvolved against this atlas to quantify luminal tumor DNA and circulating microenvironmental DNA (cmDNA). Prognostic associations used penalized Cox models. Results: Tumor-specific DMRs separated cancers into two “mevotypes” mirroring genomic evotypes (ERG-fusion vs SPOP-mutant), indicating genomic–epigenomic interplay in evolutionary commitment. Cell-resolved methylomes attributed most tumor DMRs to luminal epithelium and uncovered neuronal/plasticity pathways in luminal cells, while immune/endothelial-assigned DMRs converged on ECM remodeling, angiogenesis, TGF-β, and Rho-GTPase signaling. Single-cell pseudotime and spatial mapping localized neuronal-enriched luminal programs to late-trajectory regions and a CHGA/CHGB-positive duct-adjacent epithelial circuit interfacing with fibroblasts at tumor–stroma borders. Network analysis highlighted MYC-centric modules and EZH2-linked transcription factor contexts, consistent with epigenetic priming toward quasi-neuroendocrine states in treatment-naïve localized adenocarcinoma. In plasma, deconvolution detected both luminal ctDNA and cmDNA; luminal fractions tracked tumor burden in metastatic disease (ichorCNA-concordant), whereas cmDNA—predominantly attributable to immune compartments—suggested an early, tumor-specific microenvironmental response that can precede and is independent of luminal ctDNA shedding. Methylation signatures derived from neuronal and microenvironmental gene sets associated with inferior relapse-free survival. Conclusions: Epigenetic drivers in early prostate cancer encode luminal neuronal plasticity and reorganize the tumor niche. A cell-resolved atlas enables cfDNA deconvolution to reveal luminal ctDNA plus cmDNA, supporting liquid-biopsy biomarker strategies for earlier detection and improved risk stratification in prostate cancer. Citation Format: Harveer Dev, Toby Milne-Clark, Henson Lee Yu, CRUK-ICGC Prostate Cancer Group. Epigenetic Drivers of Localised Prostate Cancers Reveal Neuronal and Microenvironmental Reprogramming and inform Liquid Biopsy Biomarkers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr A015.