Abstract: Diabetic cardiomyopathy (DbCM), a significant chronic complication of diabetes, manifests as myocardial hypertrophy, fibrosis, and other pathological alterations that substantially impact cardiac function and elevate the risk of cardiovascular diseases and patient mortality. Myocardial energy metabolism disturbances in DbCM, encompassing glucose, fatty acid, ketone body and lactate metabolism, are crucial factors that contribute to the progression of DbCM. In recent years, novel protein post-translational modifications (PTMs) such as lactylation, β-hydroxybutyrylation, and succinylation have been demonstrated to be intimately associated with the myocardial energy metabolism process, and in conjunction with acetylation, they participate in the regulation of protein activity and gene expression activity in cardiomyocytes. This review examines the epigenetic pathogenesis of DbCM, primarily focusing on myocardial energy metabolism perturbations and novel PTMs associated with them. It provides a detailed analysis of the mechanisms of these novel PTMs in DbCM to enhance the understanding of DbCM pathophysiology and establish a theoretical foundation for the development of new treatment strategies for DbCM.

Abstract: Abstract Background/objective There is limited knowledge on how diet affects the epigenome of children. Ultra-processed food (UPF) consumption is emerging as an important factor impacting health, but mechanisms need to be uncovered. We therefore aimed to assess the association between UPF consumption and DNA methylation in children. Methods We conducted a meta-analysis of epigenome-wide association studies (EWAS) from a total of 3152 children aged 5–11 years from four European studies (HELIX, Generation XXI, ALSPAC, and Generation R). UPF consumption was defined applying the Nova food classification system (group 4), and DNA methylation was measured in blood with Illumina Infinium Methylation arrays. Associations were estimated within each cohort using robust linear regression models, adjusting for relevant covariates, followed by a meta-analysis of the resulting EWAS estimates. Results Although no CpG was significant at FDR level, we found suggestive associations ( p -value < 10 –5 ) between UPF consumption and methylation at seven CpG sites. Three of them, cg00339913 (PHYHIP), cg03041696 (intergenic), and cg03999434 (intergenic), were negatively associated, whereas the other four, cg14665028 (NHEJ1), cg18968409 (intergenic), cg24730307 (intergenic), and cg09709951 (ATF7), were positively associated with UPF intake. These CpGs have been previously associated with health outcomes such as carcinomas, and the related genes are mainly involved in pathways related to thyroid hormones and liver function. Conclusion We only found suggestive changes in methylation at 7 CpGs associated with UPF intake in a large EWAS among children: although this shows a potential impact of UPF intake on DNAm, this might not be a key mechanism underlying the health effects of UPFs in children. There is a need for more detailed dietary assessment in children studies and of intervention studies to assess potential epigenetic changes linked to a reduction in UPF in the diet. Graphical abstract

Abstract: Endometriosis appears to have a multilayered etiology, with genetic and epigenetic factors each contributing half of the pathogenesis. The molecular processes that underlie the onset of endometriosis are yet unclear, but it is assumed that an important contributor in the etiopathology of the disease is DNA methylation. We conducted a systematic review of the literature regarding DNA methylation in endometriosis following PRISMA guidelines. Records were obtained from PubMed and Web of Science on May 31, 2024. Original research articles analyzing regional or genome-wide DNA methylation in patients with confirmed endometriosis (by surgery and/or histological examination) were given consideration for inclusion. Only human studies were included, and there were no restrictions on the types of tissue that was analyzed (i.e., endometrium, blood, or fetal tissue). The study selection process was run by two manual reviewers. In parallel, an adapted virtual artificial intelligence-powered reviewer operated study selection and results were compared with the manual reviewers’ selection. Studies were divided into targeted (e.g., single gene or region level) and epigenome-wide association studies. For each, we extracted a list of genes studied with precise location of CpGs analyzed and the DNA methylation status according to the groups compared. Quality assessment of studies was performed following the Newcastle–Ottawa scale. Quality of evidence was graded following the Grading of Recommendations Assessment, Development and Evaluation. A total of 955 studies were screened, and 70 were identified as relevant for systematic review. Our analyses displayed that endometriosis could be polyepigenetic and with alterations in specific genes implicated in major signaling pathways contributing to the disease etiopathology (cell proliferation, differentiation, and division [PI3K-Akt and Wnt-signaling pathway], cell division [MAPK pathway], cell adhesion, cell communication, developmental processes, response to hormone, apoptosis, immunity, neurogenesis, and cancer). Our systematic review indicates that endometriosis is associated with DNA methylation modifications at specific genes involved in key endometrial biological processes, particularly in the ectopic endometrium. As DNA methylation appears to be an integral component of the pathogenesis of endometriosis, the identification of DNA methylation biomarkers would likely help better understand its causes and aggravating factors as well as potentially facilitate its diagnosis and support the development of new therapeutic approaches. DNA methylation modifications are observed in both eutopic and ectopic endometrium in endometriosis compared to the healthy endometrium, and their localization may influence important biological pathways of the female reproductive system. DMP: Differentially methylated position. DMR: Differentially methylated region.

Abstract: Cuproptosis, a form of cell death associated with copper ions, has been linked to the pathogenesis of various cancers, including gastric cancer. Investigating the role of cuproptosis-related genes through multi-omics analysis can enhance our understanding of disease mechanisms and improve prognosis prediction. This study aims to elucidate the role of cuproptosis-related genes in gastric cancer from a multi-omics perspective. We utilized multi-omics sequencing data from TCGA and GEO databases to explore the relationships between cuproptosis genes and gastric carcinogenesis, clinical phenotypes, and prognosis. This analysis encompassed mutation, copy number variation, methylation, mRNA expression, alternative splicing, and APA alterations. Additionally, we examined the regulatory roles of cuproptosis genes in gastric cancer through ceRNA interactions, gene mutations, and DNA methylation. A multi-omics prognostic model for gastric cancer was subsequently constructed. Our findings revealed that CDKN2A was the most frequently mutated gene in gastric cancer. Overall mutations in cuproptosis genes and copy number alterations of PDHB significantly impacted gastric cancer prognosis. Methylation, alternative splicing, and APA alterations of CDKN2A also influenced patient outcomes. Notably, MTF1, a key gene in cuproptosis, was found to affect apoptosis and invasion in gastric cancer cell lines. We successfully developed a multi-omics prognostic model for gastric cancer that offers significant predictive value for patient outcomes.

Abstract: Bisulfite conversion (BC) has been the gold standard in DNA methylation profiling for decades. During this chemical process, non-methylated cytosines are converted into uracils, while methylated cytosines remain intact. Despite its popularity, BC has major drawbacks when used for sensitive applications with low-quality and -quantity DNA samples, such as the required large amount of DNA input, the caused DNA fragmentation and loss, and the resulting reduced sequence complexity. Lately, to account for BC-related disadvantages the first commercial enzymatic conversion (EC) kit was launched. While EC follows the same conversion principle as BC it uses two enzymatic steps instead of one chemical step with BC. In this study, we validated and compared the conversion performance of the most widely used BC and EC kits using a multiplex qPCR assay (qBiCo) we recently developed, which provides several indexes: conversion efficiency, converted DNA recovery and fragmentation. Firstly, we implemented and standardized both DNA conversion methods. Secondly, using qBiCo, we performed a developmental validation for both conversion approaches, including testing the following parameters: repeatability, reproducibility, sensitivity and robustness. Regarding conversion efficiency, both methods performed similarly, with the limit of reproducible conversion being 5 ng and 10 ng for BC and EC, respectively. The recovery, however, is structurally overestimated for BC: 2.3 ± 0.7 and 0.7 ± 0.2 for EC. In contrast, degraded DNA input resulted in high fragmentation values after BC and low-medium values for EC (14.4 ± 1.2 and 3.3 ± 0.4, respectively). Finally, we converted 10 ng of 22 genomic DNA samples using both methods. We observed an overestimation of the BC DNA recovery (130%) and a low recovery for EC (40%). Our findings indicate that both DNA conversion methods have strengths and weaknesses. BC shows a high recovery, whereas EC does not cause extensive fragmentation that is characteristic to BC. EC is, therefore, more robust to the analysis of degraded DNA such as forensic-type or cell-free DNA, at least for the genomic DNA inputs tested here. We believe that the low recovery of EC could be improved by further optimizing and automating the bead-based cleanup steps. Overall, our study provides the first independent benchmarking of bisulfite- and enzyme-based conversion kits.

Abstract: Recent studies have demonstrated that patients with stage IB-IIIA non-small cell lung cancer (NSCLC) harboring EGFR mutations (EGFRm) can significantly benefit from adjuvant therapy with EGFR-TKIs. Nevertheless, there remains controversial in clinical practice about the use of EGFR-TKI adjuvant therapy for patients with stage IB EGFRm NSCLC. This retrospective cohort study was conducted at the Second Xiangya Hospital of Central South University. From January 2011 to December 2020, completely resected stage IA-IB NSCLC (8th TNM staging) patients with sensitive EGFR mutation were included. FFPE tumor and lymph node specimens were collected and subjected to the 8-gene methylation panel using modified MOB-qMSP approach. We employed stepwise regression to select variables and logistic regression to establish the predictive model. Cross-validation and decision curve analysis were performed. A total of 242 patients with IA2-IB EGFRm NSCLC were included in the study. Among these patients, 86 constituted the recurrence (Rec) group, while 156 formed the non-recurrence (Non-Rec) group. Through stepwise logistic regression, seven crucial feature variables were identified, including five-gene methylation variables (CDO1, TAC1, p16, CDH13, and APC) and two clinical variables (tumor invasion and differentiation). The ROC analysis revealed an AUC of 0.873 for the model with these seven variables. Internal cross-validation demonstrated a model accuracy exceeding 77%. The nomogram and decision curve analysis underscored the clinical utility of the model. We calculated the total score for each patient based on the nomogram and divided the patients into high-risk and low-risk groups. The cumulative risk curves for both groups evidenced that the recurrence risk in the high-risk group was significantly higher than in the low-risk group. We further divided the dataset into two cohorts—stage IA2-IA3 patients and stage IB patients. The model maintained a high AUC value (0.879) in stage IA2-A3 patients. Our study demonstrates that the methylation of five genes—CDO1, TAC1, p16, CDH13, and APC—in N2 lymph nodes represents a strong biomarker panel for predicting recurrence in stage IB EGFRm NSCLC after curative resection. This approach also shows exceptional predictive accuracy for postoperative recurrence in stage IA2-IA3 EGFRm NSCLC.

Abstract: Background Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide, but its pathophysiological mechanisms remain elusive. It is a progressive disease, encompassing hepatic steatosis, steatohepatitis with (out) fibrosis, and ultimately cirrhosis and hepatocellular carcinoma. DNA methylation (DNAm) is dysregulated in MASLD and may play a central role in its pathogenesis. Additionally, aging is associated with MASLD and shares common processes of chronic inflammation and oxidative stress. Therefore, this study focuses on DNAm changes in relation to MASLD progression and epigenetic age acceleration (EAA). Results Liver biopsies from 22 individuals with varying MASLD status were analyzed using Infinium MethylationEPIC BeadChip arrays. Strikingly, progression of MASLD was characterized by gradual DNAm changes, revealing multiple associated KEGG pathways. Additionally, Horvath’s EAA significantly correlated with MASLD stage and individual histological MASLD parameters while LiverClock’s EAA correlated only with MASLD stage. In contrast, both Horvath’s intrinsic EAA and HepClock’s EAA showed no significant correlations. Integrative analyses, leveraging both gradual MASLD and Horvath’s EAA DNAm signatures, gene expression (n = 118), and a MASLD-specific transcriptional regulatory network, identified (regulon-specific) transcription factors implicated in MASLD and EAA progression, representing a transcription factor-network of redox (ferroptosis), immune, and metabolic/endocrine related epigenetic processes. Conclusion Gradual DNAm changes were found to align with progression of MASLD and EAA, with EAA a potential nonbiased quantitative biomarker for MASLD. Integrative analysis highlighted potential new therapeutic transcription factor targets, with special emphasis on AEBP1 and emerging nuclear receptors including CAR(NR1I3), MR(NR3C2), GR(NR3C1), and ESRRG, underscoring the potential of epigenetic redox-metabolic therapies for MASLD. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1186/s13148-025-01945-6.

Abstract: Currently, with the global aging of the population, inflammation, recognized as a hallmark in age-related diseases, has been studied and linked to cardiovascular diseases (CVD). However, limited evidence on whether inflammation modifies epigenetic aging and affects CVD risk. This study included 404 CVD patients and 1941 non-CVD individuals from the 1999–2002 National Health and Nutrition Examination Survey cross-sectional data. Low-grade systemic inflammation was assessed using C-reactive protein (CRP), neutrophil-to-lymphocyte ratio (NLR), and systemic inflammation response index (SIRI). Epigenetic age accelerations (EAAs) were calculated as the residuals between chronological and epigenetic ages: Horvath age acceleration (AgeAccel), AgeAccelHannum, and AgeAccelPheno. Weighted linear and logistic regression analyzed the associations between exposures and outcomes, with mediating effects assessed using the Sobel test. After adjusting confoundings, the log-transformed NLR and SIRI were positively associated with CVD risk, and the odds ratio (OR) ranges from 1.260 to 1.354 (all P < 0.05). Furthermore, the ln-transformed CRP was positively associated with AgeAccelHannum and AgeAccelPheno, and the coefficient (β) ranges from 0.505 to 1.304 (all P < 0.05); the ln-transformed NLR and SIRI were positively associated with all three EAAs, and the β ranges from 0.392 to 2.212 (all P < 0.005). Additionally, 1-unit increase in AgeAccelHannum and AgeAccelPheno was associated with 2.8% (OR: 1.028, 95% CI 1.007–1.049, P = 0.011) and 3.5% (OR: 1.035, 95% CI 1.014–1.056, P = 0.002) increase in CVD risk, respectively. After adjusting confoundings, mediation analysis showed that AgeAccelHannum mediates 10.44% (P = 0.046) of the association between NLR and CVD risk; and AgeAccelPheno mediates 24.03% (P = 0.009) and 18.16% (P = 0.015) of the NLR-CVD and SIRI-CVD risk associations, respectively. Our results demonstrate that EAAs mediate the association between systemic inflammation and CVD risk, highlighting the potential of a multi-target approach to inflammation and epigenetic modifications for personalized management to reduce CVD risk.

Abstract: Enriched environment (EE), as a non-pharmacological intervention, has garnered considerable attention for its potential to ameliorate neurodegenerative diseases (NDs). This review delineated the impact of EE on the biological functions associated with NDs, emphasizing its role in enhancing neural plasticity, reducing inflammation, and bolstering cognitive performance. We discussed the molecular underpinnings of the effects of EE, including modulation of key signaling pathways such as extracellular regulated kinase 1/2 (ERK1/2), mitogen-activated protein kinases (MAPK), and AMPK/SIRT1, which were implicated in neuroprotection and synaptic plasticity. Additionally, we scrutinized the influence of EE on epigenetic modifications and autophagy, processes pivotal to ND pathogenesis. Animal models, encompassing both rodents and larger animals, offer insights into the disease-modifying effects of EE, underscoring its potential as a complementary approach to pharmacological interventions. In summary, EE emerges as a promising strategy to augment cognitive function and decelerate the progression of NDs.

Abstract: Silver-Russell syndrome (SRS) is a complex multisystem condition requiring timely diagnosis for appropriate management. A clinical diagnosis is made in individuals scoring ≥ 4 Netchine-Harbison Clinical Scoring System (NH-CSS) criteria, with (epi)genetic investigations undertaken in those with NH-CSS ≥ 3 and strong clinical suspicion. Monogenic variants in imprinted (CDKN1C and IGF2) and non-imprinted (HMGA2 and PLAG1) genes are recognised as rare causes of SRS. The frequency of associated phenotypes is unclear. We evaluated the suitability of SRS as an umbrella term for these (epi)genotypes by identifying key clinical features and assessing the validity of NH-CSS. An extensive literature search identified 22 IGF2, 18 HMGA2, 11 CDKN1C and 11 PLAG1 published reports. Clinical phenotypes including the NH-CSS criteria were interrogated to assess (dis)similarity between the molecular subgroups of SRS. Strict adherence to the NH-CSS identified clinical SRS in 91% IGF2, 82% CDKN1C, 78% HMGA2 and 45% PLAG1 affected individuals. Relative macrocephaly was observed in 82% IGF2, 82% CDKN1C, 44% HMGA2, and 27% PLAG1 affected individuals. Prominent forehead was reported in 100% CDKN1C, 91% IGF2, 72% HMGA2, and 64% PLAG1 and body asymmetry in 23% IGF2 and 11% HMGA2 affected individuals. Clinical features not typically associated with SRS included: microcephaly, challenging behaviour, cardiac abnormalities, cleft palate, and asthma. The NH-CSS missed 9–55% of monogenic SRS. The diverse phenotypes of PLAG1, CDKN1C, HMGA2 and IGF2 variants may hinder a clinical diagnosis of SRS. These rarer (epi)genotypes could be considered as distinct entities.

Abstract: Fetal growth restriction (FGR) is associated with perinatal complications and potential neurodevelopmental risks, yet mechanistic understanding of metabolic dysregulation remains incomplete. We investigated amniotic fluid metabolites as potential functional biomarkers of fetal-placental dysfunction and explored the possibility of folic acid-mediated epigenetic remediation of metabolic imbalances in FGR. In FGR amniotic fluid, hypoxanthine was significantly upregulated, valproic acid (VPA) was significantly downregulated, and arginine/proline metabolism pathways were markedly enriched. Folic acid intervention significantly improved fetal growth parameters (crown–rump length, body weight, and placental weight; all P < 0.001). Compensatory labyrinth zone (Lb) hyperplasia was observed in FGR placenta, with a 40% increase in Lb/Jz ratio, while folic acid supplementation reduced Lb proportion by 10% and appeared to restore placental architecture. Epigenetically, folic acid supplementation suppressed histone deacetylases1 (HDAC1) expression, elevated H3K9ac levels and enhanced trophoblast proliferation. Our research suggests that dysregulation of the VPA-hypoxanthine axis may serve as a hallmark of FGR-associated metabolic stress. Folic acid may exerts potential dual therapeutic effects by correcting placental architecture through Lb normalization and initiating epigenetic reprogramming via HDAC1 inhibition and acetylation at lysine 9 of histone H3 (H3K9ac). These findings indicate that folate metabolism could play a regulatory role in placental gene transcription and fetal growth trajectories.

Abstract: Our results indicate that pathogenic PLAG1 variants leading to stable aberrant PLAG1 proteins and possibly acting in a dominant-negative manner influence methylation of the MEG8 locus. This study suggests a new pathogenetic mechanism of the PLAG1 gene in SRS, involving imprinted genes in the chr14q32 cluster through deregulation of the MEG8:Int2-DMR and provides an epigenetic signature that may be used to assess the damaging potential of the PLAG1 variants.

Abstract: Trichostatin A (TSA) is a strong epigenetic tool that promises to have the future in the field of immune reprogramming, but its mechanisms of action in patient-derived immune cells in colorectal cancer (CRC) are still poorly studied. We examined in this current study the molecular and functional immune phenotype of lymphocytes of CRC patients and healthy donors in response to low-dose (0.1 nM), short-term (12 h) treatment with TSA, which aims at narrowing cytotoxicity and retaining epigenetic regulation. The TSA potentiated pro-inflammatory cytokines (IFN-gamma, IL-12, TNF-alpha) and inhibited immunoregulatory interleukins (IL-4, IL-10, IL-17, CCL5, Granzyme B in CRC-derived immune cells). At the transcriptional level, TSA induced TBX21 and TP53 and repressed GATA3, FOXP3, RORC, and MYC. Epigenetic profiling showed H3K14ac and H3K4me3 markups, H3K27me3 and HDAC1 downregulation, promoter hypermethylation of immune territory, less R-loop formation, and higher methylation of m6A RNA-partaking in the recommendation that TSA promotes chromatin and transcriptome multilayered modification. The TSA pretreated lymphocytes elicited cytotoxic effect in HT-29 CRC cells and also showed redox disproportion via depletion of glutathione and increase in nitric oxide. Although previous research focuses on the direct impact of TSA on tumor cells, in our study, we exclusively highlight TSA ability to reprogram the immune cells epigenetically in a more inflammatory tumor-reactive phenotype. The findings justify the possibility of TSA as an epigenetic adjunct of low toxicity in immuno-oncology and form a basis to continue in vivo and translational study in CRC immunotherapy.

Abstract: We provide the first longitudinal assessment of genome-wide DNA methylation in a cohort of patient with CF and identify CpG sites that predict clinical traits of key importance for lung disease. The associated genes play a critical role in inflammation or pancreatic endocrine activity. Overall, our results underscore the emerging role of DNA methylation as a key modulator of disease severity in CF.

Abstract: Germline stem cells are critical for sustaining fertility by balancing self-renewal and differentiation, and are regulated by genetic and epigenetic programs. Although extensively investigated, the rare female germline stem cells (FGSCs) in mammalian ovaries hinder their application in regenerative medicine. The N6-methyladenosine (m6A) reader YTHDF2 is required for female germ cell competence. However, the mechanistic underpinnings of how YTHDF2 regulates FGSC proliferation remain elusive. Here, we show that knockout of Ythdf2 enhances FGSC proliferation in vitro. YTHDF2 binds m6A-modified Ets1 mRNA and facilitates its degradation in an m6A-dependent manner. ETS1 functions as a key downstream effector of YTHDF2, as suppression of ETS1 expression partially reverses the Ythdf2-KO-induced phenotype. Additionally, we demonstrate that YTHDF2/ETS1 axis participates in regulating FGSC proliferation by modulation of proliferation-related gene expression. Moreover, histone lactylation modification H3K18la activates the expression of YTHDF2 in FGSCs. Overall, our study reveals that YTHDF2 intrinsically restrains mouse FGSC proliferation and provides a potential strategy to increase FGSC abundance for its potential clinical application.

Abstract: Colorectal cancer (CRC) is commonly associated with epigenetic modifications, including altered DNA methylation. Recent studies suggest that tumour-resident bacteria may influence CRC development, yet the impact of bacteria on epigenetic regulation is not understood. This study investigates the effect of lipopolysaccharide (LPS) from Fusobacterium periodonticum and Bacteroides fragilis, bacteria that are abundant in CRC tumours with high CpG island methylator phenotype (CIMP), on DNA methylation in HT29 colorectal cancer cells. HT29 cells were treated with LPS from F. periodonticum, B. fragilis, or a combination of both. DNA methylation was assessed using reduced representation bisulfite sequencing (RRBS), followed by bioinformatic analysis to identify differentially methylated CpG sites. RT-qPCR was used to analyse the expression of selected genes with altered CpG promoter methylation. F. periodonticum LPS treatment induced both hypermethylation and hypomethylation in HT29 cells, with significant hypermethylation observed near specific promoter regions, including PEPD and VAV3, with associated decrease in gene expression of these genes. B. fragilis LPS treatment predominantly induced hypomethylation. Co-treatment with both LPS molecules resulted in distinct methylation patterns, with B. fragilis LPS attenuating F. periodonticum LPS-induced hypermethylation. Bacterial LPS can induce dynamic alterations in DNA methylation profiles in HT29 colorectal cancer cells, leading to changes in gene expression. These findings suggest a novel link between tumour-resident bacteria and DNA methylation in colorectal cancer, highlighting, for the first time, a potential mechanism by which bacteria may influence colorectal carcinogenesis.

Abstract: These findings highlight ESSH as a critical window where epigenetically driven immune changes facilitate ESCC progression. Targeting these early epigenetic-immune interactions may offer a novel strategy for ESCC early detection and combination therapy.

Abstract: Glaucoma represents a predominant cause of irreversible blindness globally, characterized by the association of elevated intraocular pressure (IOP) and retinal ganglion cell loss with dysfunction of the trabecular meshwork (TM), the principal tissue regulating conventional aqueous humor outflow. Emerging evidence suggests that this dysfunction is not exclusively driven by genetic variation or mechanical stress; rather, it is significantly influenced by epigenetic mechanisms that integrate factors such as aging, hypoxia/oxidative stress, glucocorticoid exposure, and other environmental challenges into enduring alterations in TM phenotype. This review synthesizes current understanding of the primary epigenetic mechanisms involved in glaucomatous TM remodeling, encompassing DNA methylation, histone modifications, non-coding RNAs (including microRNAs and long non-coding RNAs), and RNA N⁶-methyladenosine (m⁶A) methylation. In this study, we elucidate the role of aberrant DNA methylation in the regulation of profibrotic genes, such as TGF-β1 and GDF7, elasticity-modifying genes like LOXL1, and repetitive elements, which collectively contribute to extracellular matrix (ECM) accumulation, tissue stiffening, and increased outflow resistance. Furthermore, we explore how dysregulated miRNA-lncRNA networks and histone acetylation/methylation influence central signaling pathways, including TGF-β/BMP-Smad, Wnt/β-catenin, RhoA/ROCK, PI3K-Akt, and NF-κB. These pathways are crucial in orchestrating trabecular meshwork (TM) fibrosis, cytoskeletal remodeling, cellular senescence, and impaired stress responses. Additionally, we investigate the emerging roles of m⁶A regulators, such as METTL3, YTHDF2, and YTHDC2, at the intersection of outflow pathway fibrosis and retinal ganglion cell vulnerability. We propose that epigenetic modifiers, ncRNA-based therapies, and partial epigenetic reprogramming could offer innovative, TM-targeted, and neuroprotective strategies beyond conventional IOP-lowering treatments. Collectively, our findings support an integrated model wherein diverse epigenetic modifications converge to produce a stereotypical glaucomatous TM phenotype, thereby presenting novel opportunities for mechanism-based diagnosis and therapeutic intervention in glaucoma.

Abstract: Neonatal encephalopathy with suspected hypoxic ischaemic encephalopathy (NESHIE) is a neurological disorder caused by oxygen deprivation and limited blood flow to a neonate's brain. Although various antenatal and perinatal factors have been identified, their precise role in NESHIE pathogenesis remains unclear. The pathophysiology involves multiple molecular pathways that can be explored using a multi-omics approach, including epigenetics. Epigenetics involves heritable changes in gene expression without altering the DNA sequence, encompassing chemical modifications to DNA and histone proteins, as well as changes mediated by non-coding RNAs (ncRNAs). These epigenetic changes regulate gene expression and can be influenced by environmental factors, offering crucial insights into gene regulation and disease mechanisms. This review examines the role of epigenetic mechanisms in NESHIE, focusing on the modulation of hypoxia-inducible factor-1 alpha (HIF-1α) and ncRNA during hypoxic conditions. Additionally, epigenetic-mediated foetal programming may shed light on how maternal and antenatal risk factors contribute to NESHIE susceptibility. Understanding these epigenetic signatures could advance biomarker discovery and the development of novel therapeutic strategies for NESHIE.

Abstract: Cisplatin resistance remains a major challenge in the clinical treatment of bladder cancer (BC), and the epigenetic regulation of this resistance, particularly involving 5-hydroxymethylcytosine (5hmC), has not been fully elucidated. Here, we investigated the role of 5hmC and vitamin C (VC) in modulating cisplatin sensitivity in BC. Clinical analyses of 36 BC patients receiving cisplatin-based neoadjuvant chemotherapy showed that reduced 5hmC levels in pre-chemotherapy tumor tissues were significantly associated with cisplatin resistance (CR-BC) and poor prognosis, with low 5hmC correlating with shorter progression-free survival (PFS). In vitro, we established two cisplatin-resistant cell lines (T24-CR, UMUC-3-CR) that exhibited reduced 5hmC compared to parental cells. Treatment with 100 μM VC significantly restored 5hmC levels in CR-BC cells by activating TET enzymes, inhibited cell proliferation, and enhanced cisplatin sensitivity; these effects were abrogated by the TET inhibitor Bobcat339, confirming VC acts in a TET-dependent manner. Mechanistically, genome-wide 850 K methylation array and RNA-seq analyses revealed that VC upregulated methylation specifically at the promoter of ATF4, a downstream effector of the MAPK pathway, thereby downregulating ATF4 expression. ATF4 knockdown in CR-BC cells increasing cisplatin sensitivity, while Bobcat339 reversed VC-induced ATF4 downregulation. In vivo, VC combined with cisplatin significantly inhibited tumor growth in T24-CR xenografts, and co-treatment with ATF4 knockdown further enhanced this effect, accompanied by elevated 5hmC and reduced Ki67 in tumors. Collectively, our findings identify reduced 5hmC as a hallmark of cisplatin-resistant BC and reveal a novel mechanism by which VC enhances cisplatin sensitivity. VC activates TET enzymes to increase 5mC at the ATF4 promoter, downregulating ATF4 and modulating the MAPK pathway. This highlights VC as a potential epigenetic adjuvant to overcome cisplatin resistance in BC.

Abstract: Vitamin D is a fat-soluble vitamin that has a protective role in colorectal cancer. Several studies have identified the association between vitamin D and changes in DNA methylation in different types of tumours. Dickkopf-1 (DKK1) inhibits the Wnt/β-catenin signalling pathway, and 1,25(OH)2D3 can induce DKK1 expression in colorectal cancer. However, whether 1,25(OH)2D3 can affect DKK1 expression by regulating DNA methylation in colorectal cancer is not known. Fifty-seven colorectal cancer (CRC) patients and fifty-five healthy controls were included in this study. Serum DKK1 and 25(OH)D levels were measured via ELISA and liquid chromatography‒tandem mass spectrometry, respectively, and the associations of DKK1 with clinicopathological characteristics and 25(OH)D were analysed. A DKK1 expression plasmid was transfected into cells to assess the functional significance of DKK1 in CRC progression via CCK8, wound healing and migration assays. BiSulphite Amplicon Sequencing (BSAS) and methylation-specific PCR were used to detect the DKK1 methylation status of colorectal cancer cells and tissues. The effect of 1,25(OH)2D3 on DKK1 methylation was investigated by pyrosequencing. A dual-luciferase reporter assay was performed to investigate the influence of CpG island methylation on DKK1 transcriptional activity. A decreased serum DKK1 level was closely associated with nerve infiltration and 25(OH)D status in patients with colorectal cancer. Overexpression of DKK1 reduced the proliferative and migratory capabilities of colorectal cancer cells. The methylation patterns of DKK1 (− 195 to + 231), including 31 CpG sites, were assayed via BSAS in CRC cells and tissues. Compared with those in adjacent normal tissues, the methylation levels of multiple CpG sites located in the promoter, 5’UTR and exon 1 were increased in tumour tissues. DKK1 hypermethylation was associated with decreased DKK1 expression in colorectal cancer cells and tissues. 1,25(OH)2D3 induced DKK1 expression in colorectal cancer cells, and pyrosequencing revealed that 1,25(OH)2D3 treatment induced demethylation of CpG sites located in the promoter (− 97 to − 32) and 5’UTR (+ 39 to + 97). The dual-luciferase reporter assay further confirmed that CpG island methylation (-120 to + 225) directly represses DKK1 transcription. DKK1 functions as a tumour suppressor in colorectal cancer, and 1,25(OH)2D3 upregulates DKK1 expression by inducing demethylation of the DKK1 promoter and 5’UTR in specific colorectal cancer cell lines.

Abstract: The present study suggests three candidate DMPs and pathways that may explain the association between DNA methylation at birth and obesity at 12 years of age.