Vitamin B12 drives epigenetic reprogramming and leukemia progression through metabolic rewiring in AML

DNA methylation variability in pediatric aplastic anemia contributes to T cell differentiation

Phenotyping of ex vivo expanded NK cells reveals unique transcriptomic and epigenetic signatures

Hypermethylation of the ribosomal DNA coding sequence and disordered transcription factor binding as hallmarks of acute myeloid leukemia

ABSTRACT Background and Aims Perioperative anaphylaxis (POA) is a rare but life‐threatening complication with significant risks to patient health. Our previous national epidemiologic survey indicates regional differences in the incidence of suspected POA in China, which may be related to environmental and genetic factors. Therefore, this study aims to explore epigenetic alterations in Chinese patients with POA. Methods This case‐control study will involve patients with POA reported on the National Perioperative Anaphylaxis Safety Initiative (NPASI) platform and patients visiting the anesthesia consultation clinic at the China‐Japan Friendship Hospital (CJFH). Forty patients and twenty healthy controls will be enrolled in this study, and the POA patients will undergo allergen tests, including skin tests (STs) and/or the basophil activation test (BAT). Demographic information and details of POA events will be collected, and their peripheral blood mononuclear cells (PBMCs) will be isolated for DNA methylation detection. The fragmented DNA, after extraction and quality control, will be subjected to enzymatic conversion followed by whole‐genome bisulfite sequencing (WGBS) using high‐throughput sequencing. Data filtering and alignment will be performed using the BSMAP tool to map the reads to the reference genome. Differential methylation regions and functional gene pathways will be analyzed between POA patients and controls, aiming to identify epigenetically regulated genes linked to POA. The findings will be validated within the original data set to enhance result robustness. Conclusions This study aims to comprehensively investigate the epigenetic alterations associated with POA in Chinese patients. The results are expected to provide fundamental insights into the molecular mechanisms underlying POA, potentially guiding future research and informing preventive strategies in clinical practice. A schematic diagram for the recruitment and epigenetics study of POA patients can be seen in Figure . Schematic diagram for recruitment and epigenetics study of POA patients. image The research was registered on the Chinese Clinical Trial Registry and the registration number is ChiCTR2400089345.

DNA methylation-regulated DDX27 promotes colorectal cancer progression through EZH2.

Both absolute and presumably active rDNA (with a hypomethylated promoter region) copy number (CN) in the haploid human sperm genome are highly variable among individuals. Using a combination of droplet digital PCR and deep bisulfite sequencing, we have quantified absolute and presumably active rDNA CN in sperm samples (N = 190) with normal (NSPs) vs. abnormal semen parameters (ASPs), as well as in samples leading or not leading to a clinical pregnancy. ASP samples had a significantly lower presumably active CN (104 ± 31) than normozoospermic samples (115 ± 31). The loss of presumably active rDNA copies is explained by an increased promoter methylation (13.9% in ASP vs. 12.1% in NSP). When correcting for confounding factors, most importantly semen quality, samples not leading to a clinical pregnancy after IVF/ICSI displayed a significantly lower absolute (225 ± 51) and presumably active CN (103 ± 30) than samples with pregnancy (249 ± 62 and 115 ± 31, respectively). This between-group difference was most noticeable in normozoospermic males: absolute CN 220 ± 54; presumably active CN 107 ± 32 in samples without pregnancy and absolute CN 246 ± 63; presumably active CN 120 ± 28 in samples with pregnancy. We propose that absolute/active rDNA CN in sperm is a modulating factor contributing to idiopathic male infertility. In NSP samples, presumably active CN increases with absolute CN, which may have a positive impact on fertility and ART outcome. Our results suggest that approximately 60 active sperm rDNA copies are sufficient to establish a pregnancy.

Early postnatal overnutrition as a contributor to metabolic dysregulation: Insights into hepatic epigenetic mechanisms.

Whole genome bisulfite sequencing reveals epigenetic drivers of chronic chlorpyrifos exposure induced liver cell neoplasia.

Epigenetic transgenerational effects of prenatal exposure to 2,2',4,4'-tetrabromodiphenyl ether on sperm function and DNA methylation in rat offspring.

Vitamin C Promotes Epidermal Proliferation by Promoting DNA Demethylation of Proliferation-Related Genes in Human Epidermal Equivalents.

Functional characterization and epigenetic regulation of Tcf3a and Tcf3b during IgM+ B cell activation in large yellow croaker (Larimichthys crocea).

ABSTRACTCryopreservation of sperm is critical for livestock genetic improvement, yet its impact on epigenetic stability, especially the methylation of imprinted genes, remains unclear. This study aimed to compare the effects of soy lecithin (SLE) and egg yolk (EYE) extenders on sperm quality and the DNA methylation of the imprinted genes H19 and MEG3 following the cryopreservation process. We evaluated sperm motility parameters, membrane integrity and morphology using six Holstein‐Friesian bull sperm samples. Total motility (TM) showed significant reductions after cryopreservation, decreasing from 91.6% ± 1.52% in fresh sperm to 79.9% ± 1.52% in the SLE group and 77.3% ± 1.52% in the EYE group post‐thaw (p ≤ 0.05). Similarly, progressive motility (PM) decreased from 64.4% ± 1.8% in fresh sperm to 44.9% ± 1.8% in the (SLE) group and 39.6% ± 1.8% in the (EYE) group. Freezing and post‐thawing processes resulted in significant reductions (p ≤ 0.05) in other motility parameters, including linearity (LIN), curvilinear velocity (VCL), straight‐line velocity (VSL) and average path velocity (VAP). Following the freezing–thawing process, the SLE group exhibited a smaller reduction in PM and LIN compared to the EYE group. Notably, the SLE extender demonstrated a protective role in membrane integrity compared to the EYE extender (p ≤ 0.05). However, bisulphite sequencing revealed no significant differences in the methylation levels of H19 and MEG3 genes or in sperm morphology between the two extenders (p ≥ 0.05). This study highlights the importance of selecting appropriate extenders in cryopreservation protocols and their implications for future research on sperm quality and fertility.

BackgroundOral squamous cell carcinoma (OSCC) remains a major global health burden, often diagnosed at advanced stages, with limited survival improvement. Epigenetic dysregulation, particularly promoter hypermethylation, plays a significant role in OSCC pathogenesis. Previous study by Demokan et al. identified Gamma-Aminobutyric Acid Receptor Beta-2 (GABRB2) as a candidate gene subject to methylation-dependent transcriptional silencing. This study aimed to evaluate the methylation and expression profiles of GABRB2 in OSCC and to explore its potential as a diagnostic biomarker.MethodsTissue and serum samples from 48 OSCC patients and 15 healthy controls were analyzed for GABRB2 promoter methylation via quantitative methylation-specific PCR and for gene expression levels via quantitative real-time PCR. Relationships between methylation, expression levels, clinicopathological parameters, and patient outcomes were statistically assessed.ResultsGABRB2 promoter hypermethylation was detected in 14.6% of tumor samples, predominantly in floor of the mouth and buccal tumors. Decreased GABRB2 expression was observed in 52.1% of tumor tissues compared to matched-normal tissues, while 22.9% of tumors exhibited increased expression. Methylation-dependent expression loss was confirmed in 71.4% of methylated tumors. Notably, decreased expression and hypermethylation of GABRB2 were correlated with poor prognosis parameters (p < 0.05). ROC analysis showed moderate discrimination for GABRB2 expression in distinguishing tumor from normal tissues (AUC = 0.635, p = 0.022), while serum-based analysis demonstrated poor diagnostic performance. Survival analysis revealed no statistically significant prognostic impact of GABRB2 expression levels (p > 0.05). However, alcohol consumption (p = 0.006) and recurrence developed (p = 0.030) as independent predictors of poor prognosis in multivariate analysis.ConclusionOur study suggests that there was association between methylation-based expression loss of GABRB2 with OSCC’ subgroups. To our knowledge, this is the first study to investigate GABRB2 gene methylation and expression profiling in both invasive/non-invasive samples from OSCC patients. Hypermethylation in the newly identified candidate GABRB2 gene may play a role in the development of tumors originating from the mouth floor and buccal anatomical regions of the oral cavity. However, since the loss of expression seen in the majority of our patients, we thought that only methylation may not the inhibition mechanism for GABRB2 gene decreased expression. The new identified candidate gene may be specific for the OSCC’s subgroups.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12903-025-06899-y.

A large scale detection of MLH1 methylation is lacking in esophageal cancer. MLH1 is a well-known mismatch repair gene. The mechanism of MLH1 in DNA double strand break (DSB) repair remains unclear. Esophageal cancer cell lines and 1018 cases of primary cancer samples were employed. Methylation specific PCR, Western Blot, and CRISPR/Cas9 knockout technique were utilized. Methylation of MLH1 was detected in 3.93%. MLH1 methylation was significantly associated with tumor differentiation, male gender, smoking, and tumor size (all p < 0.05). The median overall survival (OS) was 24.7 months (95% CI 13.4-36.0) and 51.5 months (95% CI 40.4-62.5) in MLH1 methylated and unmethylated groups, respectively. OS was shorter in MLH1 methylated compared to unmethylated group patients (p < 0.01). Multivariate factor analysis indicated that MLH1 methylation is an independent poor prognosis marker (p < 0.05). MLH1 promotes ataxia telangiectasia mutated (ATM), ataxia telangiectasia and RAD3-related (ATR), and non-homologous end-joining repair (NHEJ), while inhibiting microhomology-mediated end joining (MMEJ) repair signaling pathways. Deletion of MLH1 sensitized esophageal cancer cells to novobiocin. MLH1 plays important roles in DSB repair and deletion of MLH1 sensitizes ESCC cells to Polθ inhibitor.

Background/ObjectivesEpstein-Barr Virus (EBV) is a ubiquitous virus associated with a variety of diseases including cancers. Evidence has emerged that the C promoter is methylated in many EBV-associated malignancies, whereas in free virion DNA it is unmethylated. We have developed and evaluated a methylation-specific PCR assay for the EBV C Promoter (MSPCP) that can be applied to human biological specimens to quantify EBV methylation.MethodsTwo sets of methylation-specific primers were designed to anneal to bisulfite-converted DNA sequences with 3 CpGs in the forward primer binding site, and 2 CpGs in the reverse primer binding site. We evaluated this method in synthetic oligonucleotides, DNA extracted from cell lines, virion supernatants, and a variety of clinical specimens. EBV methylation of Cp, as measured by MSPCP, was validated with two orthogonal methods in select samples.ResultsIn contrived samples, this method had a linear range between 0–100% methylation. Application of this assay to DNA extracted from 11 formalin-fixed paraffin-embedded biopsy specimens showed high-level C promoter methylation in EBV-associated tumors (94–100%) but not in EBV-associated lymphoid hyperplasia. High-level EBV methylation was also detected in cell-free DNA extracted from the plasma of 13 patients with EBV-associated Hodgkin lymphoma. In contrast, EBV methylation was either not-detected, or detected at very low levels, in saliva from 25 adults in a general university population consistent with the presence of virion DNA.ConclusionsMSPCP is a simple, rapid and accurate method that characterizes the methylation status of the EBV C promoter, which may be useful in a variety of research and clinical settings.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13027-025-00702-x.

Stress factors like variations in temperatures, salinity, hypoxia, and pollution are bad for the health and survival of aquatic life. Epigenetics has shown us that stress factors can leave lasting changes, such as DNA methylation, histone modifications, and non-coding RNA alterations, that do not equate to changes in the primary genetic sequence. Considering these changes helps in assessing the resilience of a species and broadening the survival options for the species in natural habitats as well as in aquaculture. The current research proposes an Epigenetic Stress Response Profiling (ESRP) approach, which combines methylation mapping in Whole-Genome Bisulfite Sequencing (WGBS), correlating the epigenome with RNA-Seq, and metabolomic fingerprinting to derive multi-omics whereby an individual is exposed to an environment and other factors are aberrated, and the individual responds adaptively. The ESRP approach uses model organisms, Oreochromis niloticus and Cyprinus carpio, exposed to thermal, hypoxic, and salinity stress. The acquired epigenomic signatures are interpreted through machine learning algorithms to determine candidate biosignatures correlated with/impacting stress and stress-related growth. The study outlines candidate stress-responsive gene networks and methylation hotspots that are actionable targets for stress tolerance and growth in selective breeding and conservation efforts. The integration of epigenetics with the management of aquaculture will aim to increase adaptive capacity, which will boost conservation of biodiversity and sustain fisheries. This will also aid in the conservation of biodiversity in aquaculture and fisheries in the face of changing environmental conditions.

Cholangiocarcinoma (CC) is a highly lethal malignancy that urgently requires reliable prognostic biomarkers. Although MUC1 expression and promoter methylation have been implicated in CC, the clinical significance of promoter methylation pattern composition, beyond average methylation levels, remains unclear. Here, we investigated the relationship between MUC1 promoter methylation heterogeneity, MUC1 mRNA expression, and prognosis in CC. We analyzed bisulfite amplicon sequencing data and mRNA expression of MUC1, DNA methylation-related enzymes (TET1, TET2, TET3, Dnmt1, and Dnmt3a), and tumor microenvironment stress markers in 131 CC tissues. In the neoplastic region, high MUC1 mRNA expression was associated with poor overall survival (HR = 0.131, 95% CI: 0.02to0.95, p = 0.042) and correlated with the abundance of completely unmethylated promoter patterns (r = 0.386, p < 0.001). Among the enzymes analyzed, only TET3 expression significantly correlated with the abundance of completely unmethylated patterns in the neoplastic region (Cohen's f2 = 0.108, p = 0.009), suggesting a potential region-specific regulatory association. We visualized beta-diversity in methylation pattern composition using t-SNE and classified samples into two groups based on a linear decision boundary in the t-SNE space. This classification stratified prognosis independently of clinical factors (HR = 0.291, 95% CI: 0.06to0.94, p = 0.037; multivariate p = 0.021). These findings propose a novel, composition-based epigenetic stratification framework in CC, revealing that MUC1 promoter methylation pattern structure-rather than average methylation level-has prognostic relevance. Our results highlight the potential of pattern-resolved methylation profiling in the development of clinically applicable epigenetic biomarkers.

Introduction Nasopharyngeal carcinoma (NPC) is a serious cancer with a poor prognosis and a significant risk of metastasis. Although its epigenetic control mechanisms are still unknown, epigallocatechin-3-gallate (EGCG) exhibits strong anticancer properties. Promoter methylation in malignancies often silences PACRG, a putative tumor suppressor gene. This study aimed to determine whether EGCG suppresses cancer by altering PACRG gene expression in NPC cells. Material and methods NPC cells were subjected to EGCG or 5-aza-dC. Cellular functions were assessed by CCK-8, Transwell, and flow cytometry assays. Methylation-specific PCR (MSP) was used to identify PACRG promoter methylation, and gene expression was measured using quantitative real-time PCR (qRT-PCR) and Western blot (WB). The expression of DNA methyltransferase-related genes was evaluated. siRNA targeting PACRG was used to assess its functional involvement in the effects mediated by EGCG. Results EGCG exerted dose- and time-dependent effects on NPC cells by reducing proliferation and migration while inducing apoptosis and G2 phase cell cycle arrest. Mechanistically, EGCG significantly reduced the mRNA expression and enzymatic activity of DNMT1, DNMT3A, and DNMT3B, resulting in decreased PACRG promoter methylation and restored PACRG expression. Functional assays revealed that knockdown of PACRG diminished the inhibitory effect of EGCG on NPC cells, indicating that the epigenetic reactivation of PACRG partially mediates the tumor-suppressive function of EGCG. Conclusions Our results revealed that EGCG inhibits NPC progression by reducing PACRG promoter methylation, highlighting that PACRG demethylation and reactivation are a promising therapeutic strategy.

DNA methylation is a key epigenetic mechanism regulating gene expression during spermatogenesis. This study investigated the effects of experimental amebiasis induced by Entamoeba histolytica and its treatment with metronidazole (MTZ) on the methylation status of the Spermatogenesis Associated 6 (SPATA6) gene and male reproductive function. Twenty-four adult male rats were assigned to control, infected, and MTZ-treated groups. Following treatment, testicular tissues were analyzed for SPATA6 promoter methylation via bisulfite sequencing, infection confirmation by PCR, histopathological changes by hematoxylin and eosin (H&E) staining, Inhibin B and Androgen-Binding Protein (ABP) expression by immunohistochemistry, and sperm quality indices. The infected group exhibited distinct non-CpG methylation at a SPATA6 locus, confirmed reproductive tract infection, severe testicular damage, increased expression of Inhibin B and ABP, and significantly impaired sperm parameters. MTZ treatment successfully cleared the parasite and partially restored testicular architecture and sperm count; however, residual abnormalities in sperm motility, histology, and SPATA6 methylation persisted. While these findings suggest that parasitic infection and its treatment may induce epigenetic dysregulation in the testis, the direct functional link between the observed methylation change and reproductive outcomes remains inconclusive due to the limited scope of analysis. These results underscore the need for genome-wide methylation and transcriptomic profiling to better characterize the molecular basis of infection- and treatment-related reproductive effects. The study provides initial insights into infection-associated epigenetic modulation in male reproduction, with potential implications for fertility and reproductive health.