Search Results (540)

Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, increasingly arising in patients with metabolic dysfunction-associated steatotic liver disease (MASLD). Epigenetic dysregulation, particularly DNA methylation, has been implicated in MASLD-HCC development, yet the roles that the principal DNA methylation precursor metabolites, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), play in this association are unclear. Objective: We investigated associations of circulating SAM, SAH, the SAM/SAH ratio, with MASLD-HCC. Methods: In a multi-center pilot case–control study, we evaluated 69 MASLD-HCC cases and 136 cancer-free MASLD controls. Plasma SAM and SAH levels were quantified by liquid chromatography–tandem mass spectrometry. Metabolite levels were categorized as greater than or less than the median based on distribution in controls. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for age, sex, body mass index, smoking status, and type 2 diabetes. Results: MASLD-HCC cases had significantly higher plasma SAM levels (mean 121 vs. 96 nmol/L; p = 0.001) and SAM/SAH ratios (2.09 vs. 1.48; p = 6.42 × 10⁻⁷) than MASLD controls. In multivariable-adjusted models, elevated SAM levels (OR_{≥median vs. <median} = 2.76; 95% CI: 1.38–5.72) and higher SAM/SAH ratio (OR_{≥median vs. <median} = 2.30; 95% CI: 1.15–4.73) were associated with higher odds of MASLD-HCC. SAH alone was associated with MASLD-HCC. Conclusions: Higher plasma SAM levels and SAM/SAH ratios are independently linked to MASLD-HCC development. These metabolites might serve as noninvasive markers for HCC risk stratification in patients with MASLD and improve early detection efforts for MASLD-HCC. Full article

Oral squamous cell carcinoma (OSCC) remains one of the most prevalent and aggressive malignancies worldwide, with late diagnosis contributing to poor survival rates. Recent evidence suggests that periodontitis may act as a co-factor in development of OSCC through persistent inflammation, microbial dysbiosis, and subsequent tissue remodeling. Identifying molecular signatures that link periodontitis with early oral cancerization is therefore of paramount importance for risk assessment, prevention, and timely intervention. This narrative review aims to provide an integrative overview of the current knowledge on molecular, genetic, and epigenetic biomarkers associated with oral cancer risk in patients with periodontitis. Specifically, periodontal pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum promote oral cancerization by modulating molecular, genetic, and epigenetic pathways, including p53, Cyclin D1, Ki-67, p16^INK4A, DNA methylation, histone modifications, and microRNA regulation. Therefore, this review provides a discussion about the role of inflammatory mediators, oxidative stress-related molecules, microbial-derived products, genetic markers and epigenetic mechanisms as early molecular signals of malignant transformation. The study of these salivary biomarkers (salivaomics) has emerged as a promising non-invasive diagnostic tool, although variability in sampling, biomarker stability, and confounding factors such as coexisting periodontal disease remain significant limitations. By synthesizing the available evidence, this review summarizes recent evidence linking periodontitis to oral cancerization, highlights potential salivary, proteomic, and inflammatory biomarkers, and considers the role of periodontal therapy in improving inflammatory profiles and modulating tumor-related biomarkers. Finally, it explores future perspectives, including the integration of Artificial Intelligence (AI) to enhance biomarker-based diagnosis and risk stratification in OSCC patients. Full article

Cell-free DNA (cfDNA) promoter hypermethylation shows promise as a blood-based biomarker for pancreatic cancer, and similar alterations may occur in acute pancreatitis (AP). This study investigated the cfDNA hypermethylation profile of AP patients over time, compared with healthy controls, and its association with AP severity markers. A prospective longitudinal study including hospitalized AP patients and healthy controls was conducted. Methylation-specific PCR of a 23-gene panel was performed on plasma collected at inclusion (T0), 6 weeks (T6W), 6 months (T6M), and 7–8 years (T8Y). Associations between gene hypermethylation and clinical markers of AP severity—CRP, leukocyte count, creatinine, hospital stay, and complications—were evaluated. AP patients had a significantly higher mean number of hypermethylated genes at T0 (7.4, 95% CI: 6.8–8.0) compared with the controls (3.3, 95% CI: 2.8–3.8; p < 0.01). The mean number decreased over time to 3.2 (95% CI: 2.4–4.1) at T8Y. Total hypermethylation was positively associated with CRP (ρ = 0.39; p = 0.0018), leukocytes (ρ = 0.35; p = 0.0052), and hospital stay (ρ = 0.27; p = 0.0375). AP patients exhibited significantly higher cfDNA hypermethylation at disease onset, which normalized over time. Total hypermethylation showed positive associations with several markers of AP severity. Full article

Heavy metal and metalloid stress, particularly from toxic elements like cadmium (Cd), poses a growing threat to plant ecosystems, crop productivity, and global food security. Elevated concentrations of these contaminants can trigger cytotoxic and genotoxic effects in plants, severely impairing growth, development, and reproduction. In recent years, epigenetic mechanisms have emerged as crucial regulators of plant responses to heavy metal stress, offering novel insights and strategies for enhancing plant resilience in contaminated environments. This review synthesises current advances in the field of plant epigenetics, focusing on key modifications such as DNA methylation, histone acetylation and remodelling, chromatin dynamics, and small RNA-mediated regulation. These processes not only influence gene expression under metal-induced stress but also hold promise for long-term adaptation through transgenerational epigenetic memory. Recent developments in high-throughput sequencing and functional genomics have accelerated the identification of epigenetic markers associated with stress tolerance, enabling the integration of these markers into breeding programs and targeted epigenome editing strategies. Special attention is given to cadmium stress responses, where specific epigenetic traits have been linked to enhanced tolerance. As plant epigenomic research progresses, its application in sustainable agriculture becomes increasingly evident offering environmentally friendly solutions to mitigate the impact of heavy metal pollution. This review provides a foundation for future research aimed at leveraging epigenetic tools to engineer crops capable of thriving under metal stress, thereby contributing to resilient agricultural systems and sustainable food production. Full article

Background/Objectives: Breast cancer is a heterogeneous disease, and the role of the transcription factor SPDEF remains controversial. We aimed to clarify the prognostic value of SPDEF, explore demographic and molecular correlates of its expression, and investigate potential regulatory mechanisms underlying its dysregulation. Methods: Genomic and clinical data for 1218 breast cancer tumors were obtained from The Cancer Genome Atlas (TCGA). SPDEF mRNA expression was compared across intrinsic subtypes, age, and race, and prognostic significance was evaluated by Kaplan–Meier analysis. Promoter methylation patterns and DNA methyltransferase (DNMT) expression were examined as potential regulatory drivers. Co-expression analysis was performed using gene panels representing luminal differentiation, basal identity, EMT, proliferation, DNA repair, and immune signaling. Results: Low SPDEF expression was significantly associated with worse overall, relapse-free, and metastasis-free survival across all breast cancers. Expression was lowest in Basal tumors, as well as among younger and Black or African American patients. Promoter methylation at six CpG islands correlated with both reduced SPDEF expression and inferior survival, and DNMT1, DNMT3A, and DNMT3B overexpression also aligned with poor prognosis and Basal enrichment. Co-expression analysis revealed that SPDEF downregulation coincided with loss of luminal markers and increased EMT, proliferation, DNA repair, and immune pathways. Conclusions: SPDEF functions as a tumor suppressor in breast cancer, with reduced expression linked to poor outcomes, aggressive molecular features, and epigenetic regulation. These findings highlight SPDEF and DNMT-driven methylation as potential prognostic biomarkers for enhanced risk stratification and targets for novel therapies, particularly in Basal breast cancers. Full article

Background: Obesity and gestational diabetes mellitus (GDM) are the most common metabolic conditions that have an unfavorable impact on maternal and fetal health. Maternal obesity and GDM are often associated with placental dysfunction and structural alterations. The apelin receptor (APLNR), vascular endothelial growth factor (VEGF), leptin, and DNA methylation play crucial roles in placental function. We aimed to investigate the placental volume and vascularization, and to determine the changes in these markers in obese and GDM mothers. Material and Methods: In our study, we investigated the human placenta (n = 48) at term. The placental structural analyses on volume and vascularization were conducted using three-dimensional ultrasound before labor. Placental APLNR expression was determined using RT-PCR, and leptin and VEGF concentrations using ELISA in placental tissues. Global DNA methylation was measured using colometric assay. Results: The age of GDM mothers was significantly higher than that of normal and obese mothers. The gestation length of GDM mothers was significantly shorter than that of normal and obese mothers. The placental volume was significantly higher in obese and GDM cases compared with normal cases. Vascularization indices (VI, FI, VFI) were significantly depressed in GDM and obesity. In the case of biomarker studies, APLNR, leptin, and VEGF showed similar decreases in obese and GDM placentas. Based on our results, the effect of GDM, not obesity, was more pronounced for these biomarkers. VEGF reduction correlates with three-dimensional placental vascularity studies. The DNA methylation was significantly elevated in both GDM and obese placental samples, while the GDM effect was more pronounced. Conclusions: This study is the first to demonstrate structural alterations of the placenta using placental tissue biomarkers in obesity and gestational diabetes mellitus (GDM). We found that both GDM and obesity affect placental volume and vascularity, as indicated by reduced leptin and VEGF levels, presumably mediated by epigenetic effects. Our findings may provide a novel therapeutic target for improving abnormal placental function caused by GDM and obesity. Full article

Background: Posttraumatic growth (PTG) refers to positive psychological change following trauma. While its psychological aspects are well-documented, the biological mechanisms remain unclear. Epigenetic changes, such as DNA methylation (DNAm), may offer insight into PTG’s neurobiological basis. Aims: This study aimed to identify epigenetic markers associated with PTG using an epigenome-wide association study (EWAS), the first of its kind in a trauma-exposed population. Methods: A longitudinal EWAS design was used to assess DNAm before and after trauma exposure in first-year paramedicine students (n = 39). Genome-wide methylation data were analyzed for associations with PTG, applying epigenome-wide and gene-wise statistical thresholds. Pathway enrichment analysis was also conducted. Results: The study identified two CpGs (cg09559117 and cg05351447) within the PCDHA1/PCDHA2 and PDZD genes significantly associated with PTG at the epigenome-wide threshold (p < 9.42 × 10^–8); these were replicated in an independent sample. DNAm in 5 CpGs across known PTSD candidate genes ANK3, DICER1, SKA2, IL12B and TPH1 were significantly associated with PTG after gene-wise Bonferroni correction. Pathway analysis revealed that PTG-associated genes were overrepresented in the Adenosine triphosphate Binding Cassette (ABC) transporters pathway (p = 2.72 × 10⁻⁴). Conclusions: These results identify genes for PTG, improving our understanding of the neurobiological underpinnings of PTG. Full article

Background/Objectives: Epigenetics refers to heritable modifications in gene expression that do not involve changes to the DNA sequence. Among these, DNA methylation, histone modifications, and non-coding RNAs play a key role in regulating gene activity and are influenced by environmental factors, including exposure to psychoactive substances. In recent years, it has been hypothesized that such alterations may serve as molecular markers with forensic relevance. This systematic review aims to evaluate whether current evidence supports the use of drug-induced epigenetic changes as potential toxicological fingerprints in human subjects. Methods: A systematic literature search was conducted following PRISMA guidelines, including articles published on PubMed between 1 January, 2010, and 31 December, 2025. Only studies conducted on human samples and published in English were considered; animal studies and articles lacking epigenetic data were excluded. Results: Forty-two studies met the inclusion criteria. The most commonly investigated substances (alcohol, cocaine, methamphetamine, cannabis, and opioids) were found to induce specific and, in some cases, persistent epigenetic changes. These include alterations in CpG methylation in promoter regions, variations in miRNA expression, and modulation of epigenetic enzymes. Such changes were observed in brain tissue, blood cells, and semen, with evidence of persistence even after drug cessation. Conclusions: Current evidence confirms that psychoactive substance use is associated with specific epigenetic modifications. However, forensic application remains limited due to confounding factors such as age, co-exposures, and post-mortem interval. Further standardized research is necessary to validate their use as forensic biomarkers. Full article

Background: Cancer-associated fibroblasts (CAFs) are a key component of the prostate cancer (PCa) microenvironment, the abundance of which is often linked to poor prognosis. The surface markers for CAFs are mostly established, yet our current knowledge of epigenetic alterations in them remains limited. The aim of this study was to evaluate the relationship between CAF-specific DNA methylation, their abundance and the PCa prognosis. Methods: The study included 88 PCa patients with known presence or absence of a biochemical recurrence within a 6-year period. Resected PCa tissue was assessed for the surface expression of FAP, PDGFRb, CD90, and POST, and for the methylation of EDARADD, GATA6, and PITX2 genes using qPCR and ddPCR. Results: The surface expression of FAP, PDGFRb and CD90 was associated with a higher Gleason score (p < 0.05). The analytical sensitivity of ddPCR was superior to qPCR; results obtained using ddPCR demonstrated a more significant association with clinical features of PCa. EDARADD methylation and PDGFRb expression were associated with a risk of biochemical recurrence (HR–0.961 [95% CI: 0.931–0.991] and HR–2.313 [95% CI: 1.054–5.088]; p < 0.05, respectively). Conclusions: Upon further validation, the abundance of CAFs and their specific methylation might become a promising tool for the assessment of prognosis in PCa after radical treatment. Full article

Background/Objectives: Most cervical intraepithelial neoplasias (CINs) regress over time. Diagnostic screenings are limited and cannot identify the disease trend, which leads to the risk of overtreatment. Reliable methods are needed to preselect patients who will probably progress. The diagnostic GynTect^® assay offers sensitive and specific CIN identification from cervical scrapes, measuring the methylation of six marker genes. We studied the main marker (ZNF671) methylation on formalin-fixed paraffin-embedded (FFPE) material to determine if the kit provides prognostic information too. Methods: We tested 289 FFPE samples from 139 patients with varying CIN grades and disease trends, including regressive, persistent, progressive, and recurrent disease. Additionally, we correlated age and human papillomavirus (HPV) status with the results. Results: Although there are differences between FFPE material and cervical scrapes, we achieved a similar increase in ZNF671 methylation with increasing neoplasia grade (dysplasia-free: 0%, CIN 1: 8.20%, CIN 2: 26.73%, CIN 3: 32.43%, carcinoma: 100%). In addition, ZNF671 is more likely to detect recurring (27.12% of positives) and progressive (59.32% of positives) neoplasia. Patients with regressive (1.69% of positives) or persistent (11.86% of positives) trends less frequently show ZNF671 methylation. Interestingly, patients with HPV 16 infection (52.54% of positives) and >30 years (89.83% of positives) are more likely to appear ZNF671 methylation-positive. However, patients < 30 years with persistent neoplasia (42.86% of positives) also show methylation more frequently. Conclusions: The methylation of ZNF671 is measurable in cervical FFPE material and has prognostic value. Since ZNF671-methylated samples are most likely to be progressing, we recommend the closer monitoring of patients with GynTect^®-positive test results. Full article

The document is an updated review, starting from the Special Issue “Molecular Breeding for Abiotic Stress Tolerance in Crops” published in the Int. J. Mol. Sci. It reviews molecular breeding strategies to enhance abiotic stress tolerance in crops, addressing challenges like drought, salinity, temperature extremes, and waterlogging, which threaten global food security. Climate change intensifies these stresses, making it critical to develop resilient crop varieties. Plants adapt to stress through mechanisms such as hormonal regulation (e.g., ABA, ethylene), antioxidant defense (e.g., SOD, CAT), osmotic adjustment (e.g., proline accumulation), and gene expression regulation via transcription factors like MYB and WRKY. Advanced tools, such as CRISPR/Cas9 genome editing, enable precise modifications of stress-related genes, improving tolerance without compromising yield. Examples include rice (OsRR22, OsDST) and wheat (TaERF3, TaHKT1;5). Epigenetic regulation, including DNA methylation and histone modifications, also plays a role in stress adaptation. Specific studies focused on polyamine seed priming for improved germination and stress resistance, cadmium detoxification mechanisms, and genome-wide association studies (GWAS) to identify genetic markers for salt tolerance and yield. Research on salinity tolerance in wheat emphasizes sodium exclusion and tissue tolerance mechanisms. Future perspectives focus on genetic engineering, molecular markers, epigenetic studies, and functional validation to address environmental stress challenges, including the use of AI and machine learning to manage the large amount of data. The review underscores the importance of translating molecular findings into practical applications to ensure sustainable crop production under changing climates. Full article

Rett syndrome (RTT) and MECP2 duplication syndrome, a subtype of autism spectrum disorder (ASD), are neurodevelopmental disorders caused by MeCP2 loss and gain of function, respectively. While MeCP2 is known to regulate transcription through its interaction with methylated DNA and chromatin-associated factors such as topoisomerase IIβ (TOP2β), the downstream transcriptional consequences of MeCP2 dosage imbalance remain partially characterized. Here, we present a transcriptome-centered analysis of mouse primary cortical neurons subjected to MeCP2 knockdown (KD) or overexpression (OE), which model RTT and ASD-like conditions in parallel. Using a robust computational pipeline integrating generalized linear models with quasi-likelihood F-tests and Magnitude–Altitude Scoring (GLMQL-MAS), we identified differentially expressed genes (DEGs) in KD and OE relative to wild-type (WT) neurons. This study represents a computational analysis of secondary transcriptomic data aimed at nominating candidate genes for future experimental validation. Gene Ontology enrichment revealed both shared and condition-specific biological processes, with KD uniquely affecting neurodevelopmental and stress-response pathways, and OE perturbing extracellular matrix, calcium signaling, and neuroinflammatory processes. To prioritize robust and disease-relevant targets, we applied Cross-MAS and further filtered DEGs by correlation with MeCP2 expression and regulation directional consistency. This yielded 16 high-confidence dosage-sensitive genes that were capable of classifying WT, KD, and OE samples with 100% accuracy using PCA and logistic regression. Among these, RTT-associated candidates such as Plcb1, Gpr161, Mknk2, Rgcc, and Abhd6 were linked to disrupted synaptic signaling and neurogenesis, while ASD-associated genes, including Aim2, Mcm6, Pcdhb9, and Cbs, implicated neuroinflammation and metabolic stress. These findings establish a compact and mechanistically informative set of MeCP2-responsive genes, which enhance our understanding of transcriptional dysregulation in RTT and ASD and nominate molecular markers for future functional validation and therapeutic exploration. Full article

Global DNA methylation has been associated with numerous traits and conditions; however, its relationship with inflammation and oxidative stress biomarkers has not been fully elucidated. The objective of this study is to determine the correlation between inflammatory and oxidative stress markers with global DNA methylation after adjusting for personal, psychological, biochemical, anthropometric, and physiological variables in a non-representative sample of the Mexican population. An adult Mexican population was invited to participate and complete a questionnaire with personal and psychological variables. Additionally, anthropometric variables and blood pressure were measured in all the participants. Finally, general blood tests, global DNA methylation analysis, and measurements of inflammatory and oxidative stress markers were performed. A total of 157 participants were included, of which 83 (52.8%) were women, with a median age of 24 years and an age range of 18–58 years. In the comparison between sexes, men showed higher levels of global DNA methylation. In addition, men showed a higher number of correlations with this variable. The bivariate correlations showed low positive correlations of IL-8, IL-10, TNF-α, and 8-isoprostane with global DNA methylation in the total sample. In addition, BMI showed low negative and significant correlations with global DNA methylation in the total, women’s, and men’s samples, while blood pressure showed low negative correlations with global DNA methylation in the men’s sample. Men showed low negative correlations with personal and biochemical variables that were not found in the women’s group. In the multivariate analyses, the psychological variables (SOC-13 comprehensibility, perceived stress, and assertiveness) correlated negatively either in the total, or in men’s or women’s samples, and the daily intake of drugs correlated negatively with methylation in the women’s sample in the bivariate and multivariate analyses. In conclusion, global DNA methylation seems to be related to many variables, including the inflammatory and oxidative stress biomarkers, and this relationship is different in each sex. Full article

The livestock sector, a crucial source of revenue and global food security, is facing serious challenges due to climate change driven by global warming. This leads to serious effects on animal health and productivity, making it difficult for the livestock industry to meet the global demand and sustain the livelihoods of farmers. The main factor affecting livestock’s productivity is heat stress. However, animals develop various adaptive mechanisms to cope with the effects of heat stress. Cellular and molecular responses act as key defense mechanisms, enabling animals adapt to environmental changes. The recent advancements in molecular biology have opened up opportunities for extensive research on epigenetics, which has a key role in regulating gene expression in animals in response to environmental stimuli. Such studies have gained considerable attention regarding heat acclimation in animals due to the fact that epigenetic mechanisms have been recognized as key players in long-term adaptation to high temperatures in farm animals. This review summarizes the different mechanisms and methodologies used to assess heat stress-associated epigenetic changes, including DNA methylation, which is an extensively studied epigenetic regulatory mechanism in relation to gene expression. The review also highlights the mechanisms and regulation of adaptation to heat stress in animals and collates information related to various epigenetic markers to assess the heat stress response, thereby aiding in improving thermal resilience in animals. Full article

Methyl CpG-binding protein 2 (MeCP2) is an epigenetic reader of DNA methylation with high abundance in the brain. While genetic mutations occur across different protein domains of MeCP2, the T158M mutation is amongst the most frequent MeCP2 mutations. MeCP2 is encoded by the MECP2/Mecp2 gene located on the X chromosome. In humans, MECP2 mutations cause Rett Syndrome, a debilitating neurodevelopmental disorder in females, with very rare cases presenting in males. Despite the generation of different transgenic mouse lines with MeCP2 mutations, the sex-dependent phenotypic and molecular impact of common MeCP2 mutations in mouse models of disease remains largely unexplored. Here, we focus on the MeCP2 T158M mutation using Mecp2^tm4.1Bird/J transgenic mice (referred to as Mecp2^T158M), and report that Mecp2^T158M mutant mice display sex-specific molecular, behavioural, and phenotypic characteristics when compared to wild-type controls. Our data indicates sex- and brain-region-dependent impacts on the expression of MeCP2, synaptic proteins, cytoskeletal markers, and autophagy factors. Our findings demonstrate that the phenotypic and molecular characteristics of this mouse model may relate to the clinical manifestation in human patients with Rett Syndrome. Full article