Epigenomics最新文献

Background: Preterm birth and very low birth weight (VLBW; <1500 g) increase risks for poor health outcomes, potentially mediated by epigenetic modifications such as DNA methylation (DNAm). We hypothesized that DNAm differs between VLBW adults and their siblings in blood and adipose tissue.

Methods: We studied 75 adults born preterm with VLBW and 73 same-sex sibling controls from the Adults Born Preterm Sibling Study. DNAm at cytosine-guanine dinucleotide (CpG) sites in blood and adipose tissue was assessed using Illumina EPIC 850K at a mean age of 29 years. Biological pathways were investigated with QIAGEN ingenuity pathway analysis (IPA).

Results: No differences were observed in blood DNAm. In adipose tissue, 458 CpG sites were differentially methylated (FDR p < 0.05) between VLBW and siblings. Top sites were annotated to genes related to lipid metabolism (cg00264176 (FADS2), 0.077 (0.007), FDR p = 3.24 × 10^-14) and neural development (cg08277679 (KIF26A), 0.053 (0.005), FDR p = 8.22 × 10^-12). IPA identified enrichment for 81 pathways (FDR p < 0.05).

Conclusion: Our results suggest tissue-specific DNAm differences in VLBW adults compared to their siblings. The changes cluster in pathways related to lipid metabolism, neurodevelopment, and cardiometabolic regulation, suggesting lasting tissue-specific epigenetic modifications in VLBW adults.

Rapid methodological breakthroughs over the past ten years have transformed epigenomics from bulk, population-averaged assays into single-cell, multi-omic, and intracellular spatial investigations. This review surveys the interconnected technology pillars that now map the epigenome with unprecedented breadth and resolution. First, advances in next-generation and long-read sequencing empower investigators to chart chromatin accessibility, histone and DNA modifications, and three-dimensional higher-order chromatin structure in thousands of individual cells while retaining allele-specific information across kilobase-long molecules. Second, live-cell fluorescence probes and multiplexed chromatin tracing enable visualizing the dynamic organization of epigenetic marks and genome architecture of intact nuclei and tissues. Third, integrative platforms merge base-level reads with their native 3D coordinates, providing a holistic view of gene regulation in physiologic context. We distill key biological insights yielded by each methodology, discuss unresolved and persistent limitations, and outline future directions toward routine, cost-effective investigations. Together, these innovations are redefining how we interrogate chromatin biology in health and disease.

The integration of genetic and epigenetic information is essential for a comprehensive understanding of genome function and regulation. Traditional sequencing methods often fall short in capturing both genetic variants and epigenetic modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) simultaneously. Recent advances in 6-base sequencing have enabled the simultaneous, base-resolution detection of canonical bases and key cytosine modifications in a single workflow. This review explores the biological significance of 5mC and 5hmC, discusses current methods to achieve 6-base sequencing, and highlights recent applications in academic and clinical settings.

Brain disorders are among the most debilitating, costly and therapeutically challenging conditions worldwide. Therefore, there is a growing need for identification of biomarkers to support diagnostic, prognostic and therapeutic procedures. Technological advances are enabling increasingly precise, high-throughput profiling of epigenetic modifications, and the potential reversibility of epigenetic marks makes them a promising target for therapeutic intervention. Recent research on in-vitro models, post-mortem brain samples and peripheral tissues from living individuals has suggested that epigenetic mechanisms are involved in the pathogenesis of chronic mental illnesses, functioning as distal or proximal risk factors and mediating the long-term effects of environmental stressors on brain function. In brain cancers, including the highly lethal glioblastoma, epigenetic dysregulation (especially DNA methylation patterns) is already implicated in tumor classification as it contributes to cellular heterogeneity and may drive tumor progression. This review examines the multifaceted role of epigenomic regulation of brain gene expression, focusing on psychiatric disorders and primary brain malignancies such as glioblastoma. We summarize the technological advances that have enabled high-throughput and high-resolution exploration of the epigenome. Furthermore, we present the current knowledge of epigenomic signatures that may contribute to brain pathology and discuss their potential for biomarker discovery and the advancement of personalized medicine.

Aims: Environmental factors can alter DNA methylation (DNAm) levels, influence gene expression, and then change fasting glucose (FG) or hemoglobin A1c (HbA1c).

Methods: Through analyzing DNAm data of 2366 Taiwan Biobank individuals aged between 30 and 70 years, I evaluated the role of DNAm in mediating the associations of seven non-genetic factors (BMI, chronological age, sex, smoking, drinking alcoholic beverages, education, and regular exercise) with FG and HbA1c.

Results: Among 846,232 Cytosine-phosphate-Guanine (CpG) sites, the single-mediator model explored that 21, 15, 10, 3, 3, and 1 CpGs significantly mediated (p < 6.6E-9) the BMI-HbA1c, BMI-FG, sex-FG, age-FG, age-HbA1c, and drinking-HbA1c associations, respectively. The multiple-mediator model considered all significant mediators and selected the model with the smallest Akaike Information Criterion, and identified 8 CpGs that linked exposures (BMI, sex, age, and drinking) to diabetes indicators. Seven out of the 8 CpGs have been reported to be associated with diabetes, FG, HbA1c, or insulin resistance in previous epigenome-wide association studies.

Conclusion: Four of the 8 CpGs (cg19693031, cg04816311, cg00574958, and cg11024682) were associated with the expression of genes implicated in diabetes and metabolism, including the TXNIP, GPR146, CPT1A, and SREBF1 genes. These findings highlight the underlying epigenetic mechanism linking non-genetic factors with diabetes.

Aims: Adverse childhood experiences (ACEs), especially in early life, can affect psychosocial development and increase lifelong risk for mental disorders. ACEs are also known to induce persistent epigenetic changes. This study aimed to explore ACE-associated DNA methylation signatures using an epigenome-wide association study (EWAS) targeting inter-individual differentially methylated regions (DMRs).

Methods: We developed a targeted capture probe system covering ~1.3 million CpG sites within inter-individual DMRs. This system was applied to salivary DNA from drug-naïve children aged 6-12 years with exposure to multiple early-life ACEs (n = 23) or who had no ACEs (n = 21).

Results: We identified 15 novel DMRs significantly associated with ACEs. A cluster of six CpG sites within an exon of the EIF4G2 gene showed consistently increased methylation in children with ACEs, with strong inter-site correlations. Enrichment analysis indicated that genes near these DMRs are involved in neurodevelopmental disorders, suggesting that early adversity may influence brain development through epigenetic mechanisms.

Conclusion: Our findings suggest that early adversity may contribute to lasting epigenetic modifications in children. The identified DMRs may serve as noninvasive biomarkers for retrospective ACE assessment and provide insights into the biological embedding of early-life stress.

Epigenetics as a composite language capable of translating signals from the environment into heritable DNA modifications is revolutionizing the approach to biology and medicine. In the field of human reproductive physiology, many epigenetic marks have been decoded in the different stages of development, from gametogenesis to embryo development, pregnancy and its maintenance. These epigenetics marks are mainly ascribable to DNA methylation/demethylation processes, histone modifications, and non-coding RNAs mediated signals. Epigenetic modifiers such as DNA methyltransferases (DNMTs) and Ten-eleven translocation (TET) enzymes are involved in gene expression regulation by modifying the DNA methylation landscape, the first and best characterized epigenetic mark. In the context of human reproduction, epigenetics signals depict the mother-fetus crosstalk in which the maternal milieu dialogs with the growing embryo to establish an appropriate placental-fetal interface for a successful pregnancy. We here outline key features of the epigenetic crosstalk during the early embryo development and pregnancy establishment. The potential of inter- and trans-generational inheritance of specific epigenetic traits in response to environmental hints is also discussed. Finally, we move forward into future translational developments of epigenetics by discussing the potential use of epigenetic-based treatments (epidrugs) as upcoming therapeutic approaches in advanced personalized reproductive medicine.

Cardiovascular disease (CVD) is the leading cause of death among women globally. Pregnancy complications, such as hypertensive disorders of pregnancy (HDP), are known to increase the risk of developing CVD. Over 10% of pregnancies globally are affected by HDP, a condition characterized by increased blood pressure and a multiorgan disorder (preeclampsia) associated with a 2- to 8-fold higher risk of hypertension, ischemic heart disease, stroke, and heart failure. Altered epigenetic regulation of angiogenesis, endothelial function, and gene expression may help explain the link between HDP and later-life CVD risk. However, studies investigating how epigenetic modifications mediate the progression from HDP to CVD remain limited. This review provides an overview on how epigenetic mechanisms may influence the long-term cardiovascular consequences of HDP. It also highlights key research gaps, including the need for long-term longitudinal studies to show causality. Further research on this topic may result in better screening, prevention strategies, and personalized therapies for women's cardiovascular health. However, epigenetic markers should be viewed as complementary to established clinical predictors, with near-term value in mechanistic risk refinement rather than as replacements for current approaches.

Background: The effects of conventional cigarette (c-cig) use on DNA methylation are well established, but the impact of electronic cigarettes (e-cigs) remains unclear. Objective: This scoping review aimed to map and synthesize available evidence regarding the effects of e-cig use on DNA methylation profiles in human studies. Methods: PubMed, Lilacs, Scopus, Web of Science and Cochrane were searched using terms related to e-cigs and DNA methylation up to April 2025.

Results: Seven studies were included, analyzing samples from saliva, peripheral blood, and bronchial epithelial tissue. The findings indicate that e-cig use is associated with changes in DNA methylation profiles compared to nonsmokers, with alterations observed in global methylation, specific sites, and epigenetic aging markers (GrimAge). Some methylation changes were shared with c-cig users, while others appeared unique to e-cig exposure. The heterogeneity of study designs, exposure duration, and biological samples precludes definitive conclusions regarding the magnitude and clinical relevance of these changes.

Conclusion: E-cig use is associated with distinct alterations in DNA methylation in multiple human tissues, some of which are unique compared to conventional cigarettes. Further research is needed to clarify the long-term implications and potential health risks of these epigenetic changes.

Aim: Non-small cell lung cancer (NSCLC) has caused a heavy social and economic burden worldwide. DNA methylation, as an emerging blood biomarker, has great potential for early detection of NSCLC.

Methods: Seven CpG sites of the S100P gene were detected quantitatively using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry in 845 NSCLC patients (91.4% at stage I) and 1007 controls. Logistic regression was used to calculate covariate-adjusted ORs and 95% CIs.

Results: The logistic regression-based quartile analysis (Q1 lowest vs. Q4 highest) disclosed the association between hypomethylation of six CpG sites in the S100P gene and NSCLC (ORs ranged from 1.51 to 2.32, p and p for trend ≤0.004 for all), and even in NSCLC at stage I (ORs ranged from 1.53 to 2.26, p and p for trend ≤0.004 for all). The subgroup analyses suggested enhanced association in male gender and older age. Additionally, decreased methylation of S100P_CpG_5 was markedly relevant with advanced tumor size and tumor stage (p = 0.003 and p = 0.007, respectively).

Conclusions: Using quantitative mass spectrometry, we investigated an association between S100P hypomethylation in peripheral blood and NSCLC and suggested the great potential of DNA methylation signatures in whole blood for early detection of NSCLC.