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PubMed2005

Targeting epigenetic changes in acute myeloid leukemia.

Recent advances in the understanding of acute myeloid leukemia (AML) and myeloid leukemogenesis have begun to narrow the focus of therapy to specific molecular aberrations that characterize subsets of this disease. Rather than embracing "one-fits-all" cytarabine-based chemotherapy as a standard approach for all patients, ongoing clinical research in AML focuses on drugs that target unique genomic aberrations, protein structure/functional alterations, or dysregulated cellular pathways that are specific for molecular subgroups of patients. Epigenetic modifications causing gene transcriptional repression have been associated with malignant transformation and are intriguing new targets in the treatment of AML. In contrast to genetic deletions causing irreversible loss of gene function, epigenetic gene silencing mediated by DNA methylation and histone deacetylation can be reversed via pharmacologic inhibition of DNA methyltransferases and histone deacetylases, respectively. When this occurs, normal patterns of gene expression, hematopoietic differentiation, and apoptosis may be restored and disease response obtained. In this review, we focus on the clinical applicability of epigenetic targeting in the treatment of patients with AML.

Acetylation↗

PubMed2006

[Epigenetic modification in human leukemia].

Epigenetic modification, which involve DNA methylation, RNA-associated silencing and histone modification, is implicated in cell proliferation, differentiation, survival, apoptosis and malignant transformation. Some leukemogenesis has been shown to be aberrance of epigenetic modification. This paper discussed the potential causes of some of leukemias correlating with the methylation of cell cycle regulation genes, small interference RNA and modification abnormality of histone after translation. The study on epigenetic modification abnormality of leukemia cells provides a new strategy for treatment of leukemia.

DNA Methylation↗

PubMed2007

Genetic and epigenetic changes induced by chronic low dose exposure to arsenic of mouse testicular Leydig cells.

Arsenic is an important environmental carcinogen that affects millions of people worldwide through contaminated water supplies. Genotoxicity of arsenic has been a topic of controversy. Both genetic alterations (mutations) and epigenetic changes (methylation) have been shown to play a crucial role in environmental carcinogenesis. Chronic exposure to arsenic has been shown to induce malignant transformation of mammalian cells. However, the genetic aberrations induced by arsenic in this process are unclear. The purpose of this study was to determine if both lower (1 pg/ml) and higher concentrations (100 ng/ml) of arsenic induces either mutations or methylation changes that could lead to the development of genomic instability in TM3 cells, immortalized Leydig cells derived from normal mouse testis. Two independent exposure times were used in this study which resulted in cells of 33 and 100 generations in age. Arsenic-induced genetic and epigenetic changes were screened at a genome-wide level by random amplified polymorphic DNA (RAPD), also known as AP-PCR method with undigested DNA as well as DNA digested by the methylation sensitive isosizomeric restriction enzymes MSPI and HpaII and untreated controls. Changes in the DNA fingerprint of both, the restriction enzyme digested DNA (indicating methylation changes) as well as undigested DNA (indicating mutations) from arsenic-treated (low as well as high dose) samples were observed as compared to their controls. Thus, this study provides the first evidence at DNA sequence level for mutagenic potential of arsenic. Further characterization of these altered genomic regions is underway. The understanding of these genetic and epigenetic changes in arsenic-induced carcinogenesis will provide a basis for better interventional approaches in both the treatment and prevention of arsenic-induced cancer.

Animals↗

PubMedDate not supplied

[Decoding common mechanisms of cellular genetic-epigenetic control in eukaryotes].

The mechanism of genetic epigenetic operation at genomic and chromosomic levels within the limits of imitation model of eucaryotic cellular compartment is postulated, this compartment including left and right operators. Probable pattern of interactions during reproduction, determination and expression of genes as a manifestation of genetic, epigenetic memory and memory of water is shown. A specific character and rate of transformations of nucleotides and proteins are realized through different operation mechanisms over hierarchic processes directed on the preservation of DNA in the line of cellular generations and also determining dynamics of the genome with DNA variations. The mechanism of programmed provision of genetic-epigenetic interaction lies in the ways of control, regulation, adaptation and modulation of nucleotides and proteins transformations which occur on the basis of specific (complementary, kinetic and tunnel effects) choice of directions, place, time and aim of nucleotide-nucleotide, nucleotide-protein, protein-nucleotide and protein-protein interactions.

DNA↗

PubMedDate not supplied

Epigenetic grading and metastatic potential of carcinomas of the breast.

A series of breast tumours were tested by the epigenetic grading (EGG) method. In previous investigations, a number of animal tumours, nonmalignant ones as well as some of known metastatic ability, had been examined and these had confirmed that increasing grades on the epigenetic scale reflect increasing degrees of malignancy. Based on these studies, the EGG scale was therefore subdivided into Group I (non-malignant tumours), Group III (malignant tumours) and a narrow intermediate Group II (non-malignant and lowly malignant tumours). The majority of fibrocystic hyperplasias were found in Group I and II. Carcinomas encompassed a broad zone including all three groups. Of Group I carcinomas, 50% were localised tumours. The majority of those in Group II showed involvement of regional lymph nodes. Of Group III carcinomas, 67% had disseminated to regional lymph nodes or had formed bony metastases. The remainder, though localised, showed little or no stromal reaction, indicating poor immunological response by the host. The patients have been followed up in order to evaluate the metastatic outcome. A higher incidence of distant metastases appears to be associated with Group III A and B carcinomas than with Groups I and II. The data obtained from the current study suggests that the metastatic ability of histologically proven carcinomas may be reflected in their epigenetic grades.

Adenofibroma↗

PubMed1995

Biomarkers for low-level exposure causing epigenetic responses in stem cells.

Our current understanding of experimental in vitro and in vivo studies, as well as of epidemiological data, suggests that carcinogenesis is the result of many endogenous and exogenous factors interacting during a multi-step, multi-mechanism process. No single factor "causes" cancer. Carcinogenesis is known to involve both mutagenic and nonmutagenic processes. Therefore, the objective of this review is to examine how low dose exposure to ionizing radiation might contribute to the carcinogenic process and if measurable "biomarkers" might be used to monitor the susceptibility, exposure, biological consequence and clinical disease patterns attributable to ionizing radiation. While the primary biomarker for ionizing radiation has been DNA damage and genetic/chromosomal mutations, possible effects on apoptosis and epigenetic processes have been examined. The search for biomarkers of cytotoxic (apoptotic) and epigenetic events induced by low-level ionizing radiation was thought to be difficult in view of the fact that controlled apoptotic and epigenetic events occur constantly in a healthy body exposed to background radiation. In addition, if the stem cell is the target cell for low-level radiation exposure, detection of biomarkers in this small subpopulation of cells in any tissue places severe limitations on any practical noninvasive means to identify such biomarkers. Last, a critical re-examination of the cancer incidence data of the Hiroshima/Nagasaki A-bomb survivors is suggested in view of modifying factors such as caloric restriction and post-irradiation trauma/treatment that could affect the multi-stage nature of carcinogenesis.

Animals↗

PubMedDate not supplied

[Epigenetic variations and pathologic changes in the cervical vertebrae of the protoneolithic population in Panonia].

Epigenetic variations and pathological alterations of cervical vertebrae in adult individuals inhumated in the Lepenski Vir and Vlasac protoneolithic settlements (c. 7000-5500 years B.C.) are described in the article. These findings were observed in 13 paleopathologic examined skeletons. Degenerative changes, growth alterations and congenital anomalies were noted by a detailed analysis of the vertebrae. Unilateral and bilateral epigenetic variations of foramen transversarium were found in 10 (or 76%) skeletons, and this variance frequency was of particular importance. Variations were classified as follows: (1)-Foramen transversarium duplex; (2)-Foramen transversarium accessorius; (3)-Tuberositas intra foraminis transversarium; (4)-Important diversity of diameters between the left and the right foramen, and (5)-Ribs of vertebra cervicalis VII. The frequent appearance of foramen transversarium epigenetic variations in examined skeletons the author attributes to the process of micro-evolution (gracilization and Mediterranean antropological race forming) already found in this protoneolithic population.

Cervical Vertebrae↗

PubMed2026

Epigenetic Regulation of the BDNF Gene by Molybdenum in 9 to 11-Year-Old Children: A Targeted Gene DNA Methylation Study.

While essential trace minerals are known to influence DNA methylation (DNAm), molybdenum's (Mo) role in epigenetic regulation remains largely unexplored. This study examined associations between Mo status and DNAm of the brain-derived neurotrophic factor (BDNF) gene, a critical regulator of neurogenesis, in children aged 9-11 years, focusing on 107 CpG sites across BDNF and its antisense transcript (BDNF-AS).BDNF and BDNF-AS methylation was analyzed in blood samples from 72 children randomly selected from a cohort of 292 participants. Dietary Mo intake was estimated from food records, and creatinine-adjusted urinary Mo levels were quantified. Higher urinary molybdenum was significantly associated with decreased methylation at five BDNF 5'UTR sites (p<.05) and increased methylation of BDNF-AS (p =  .0001), consistent with enhanced BDNF transcriptional activity. African American children exhibited lower urinary Mo excretion than European American children, suggesting greater retention, and showed cortisol-associated increases in BDNF methylation not observed in European American children.These findings demonstrate associations between molybdenum status and DNA methylation patterns at the BDNF locus in children. While functional validation through BDNF protein measurement is needed, results suggest molybdenum may influence neurotrophin gene regulation through epigenetic mechanisms, highlighting the importance of trace mineral nutrition during neurodevelopment.

Humans↗

PubMed2025

dCas-Based Tools to Visualize Chromatin or Modify Epigenetic Marks at Specific Plant Genomic Loci.

Development of locus-specific approaches targeting precise regions on chromatin, for locus/transcription visualization or transcription/epigenetic marks editing, is a critical challenge in functional genetics and epigenetics. Systems engineered from the clustered regularly interspaced short palindromic repeats (CRISPR) and its associated endonuclease (Cas) operate through DNA sequence-specific recognition by so-called guide RNAs, which provides high flexibility and modularity for precise chromatin visualization or edition. Here, we provide an overview of the CRISPR/Cas-derived tools developed for visualization of chromatin loci in live imaging or for effective modification of gene expression. These tools make use of effector modules that combine activators, repressors, and epigenetic modifiers with a deactivated Cas protein (dCas). We present how their use in plants brought advances in visualizing or manipulating the expression of loci involved in agronomically interesting traits such as flowering time and response to drought or heat. We also discuss the limitations and future improvements of the dCas-related technologies, such as more compact and combinatorial systems, spatiotemporal targeting for fine-tuning of gene expression, and live visualization of chromatin dynamics.

Chromatin↗

PubMed2026

Advanced High-Resolution and Super-Resolution Microscopy Techniques for Investigating Chromatin Structure and Epigenetics.

Fluorescence microscopy has emerged as an indispensable tool for investigating chromatin structure and epigenetic states. This technique not only enables super-resolution imaging to unveil detailed localizations and structures but also offers precise quantitative capabilities for comparing variations across multiple conditions. In this chapter, we present a comprehensive guide to immunofluorescence methods, detailing two primary fixation protocols. Additionally, we describe the application of super-resolution spinning disc microscopy, emphasizing its utility in detecting nuclear and epigenetic markers.

Chromatin↗

PubMed2026

Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology.

Understanding how genetic variants influence disease risk through molecular mechanisms remains a central challenge in complex disease genetics. Nonsyndromic orofacial clefts (OFCs) exemplify this challenge, with most risk loci residing in non-coding regions. We hypothesized that common genetic variants influence OFC risk by modulating DNA methylation at regulatory elements through methylation quantitative trait loci (meQTLs). We analyzed 10 OFC-associated SNPs against genome-wide DNA methylation profiles in 409 cases and 456 controls, identifying 23 potential meQTLs. Findings were validated using 358 cleft-discordant sibling pairs with MethyLight assays. We performed formal mediation analysis, genotype-tissue interaction and cross-referenced with the mQTL Database to assess developmental timing. Nine meQTLs were validated, including rs987525 (8q24)-cg16561172 (MYC) (P = 9.6 × 10⁻⁶), which mapped to a mesendoderm-active enhancer upstream of MYC. Genotype × tissue interaction confirmed tissue-specificity (P = 1.00 × 10- 3), with stronger effects in oral-derived tissue (saliva). Additional validated SNP-CpG associations involved MAFB-PLCG1, NOG-PPM1E, FOXE1-FRZB, and SPRY2-LGR4. While effect sizes correlated between tissues (r = 0.81), formal mediation analysis indicated individual CpG sites do not fully mediate SNP-phenotype relationships, suggesting coordinated epigenetic mechanisms. Most associations showed peak effects during childhood, while 8q24 showed unique adult-specific patterns. We identified genetic variants influencing methylation at craniofacial regulatory elements, and provided a mechanistic link for a major risk locus, 8q24, with tissue-specific effects in saliva. While individual CpG sites did not fully mediate the genetic risk, our findings identified specific regulatory regions where coordinated epigenetic changes may contribute to OFC susceptibility.

Humans↗

PubMed2026

A machine learning approach to identify key epigenetic transcripts for ageing research in human blood (Epitage).

DNA methylation is an established biomarker of human ageing and is used by a variety of tools to identify meaningful epigenetic signals. We investigated whether analysing CpGs grouped by transcript as functional units could generate a ranked list of transcripts most correlated with age that might otherwise be overlooked in genome-wide CpG-based studies. Here we present Epitage ( https://github.com/a00s/epitage ), a continuously updated ranked list of transcripts built from the GSE87571 dataset (714 whole-blood samples, ages 14-94 years) through intensive testing with machine-learning models. To support reproducible analyses, we developed ugPlot ( https://github.com/a00s/ugplot ), an open-source R/Shiny tool with a graphical user interface that automates model training, testing, and comparison. Initially, we identified 48 transcripts across 13 genes, with some transcripts from the genes OBSCN, PRRT1, and SPTBN4 showing better predictive performance when multiple associated CpGs were analysed together rather than individually. In contrast, for the majority of transcripts, a dominant individual CpG still showed a higher Spearman correlation with age, as seen in established ageing genes such as ELOVL2, FHL2, and TRIM59. Epitage is a transcript-ranking list based on the methylation patterns observed in the analysed dataset. It provides a reproducible framework for prioritising transcripts associated with human ageing and for guiding future epigenetic studies.

Humans↗

PubMed2026

Epigenetic regulation of fatty acid chain elongation in MAFLD and its implications in the liver-brain axis dysfunction.

Lipid metabolism plays a crucial role in cellular health and physiology by acting as an energy storehouse, cell membrane component, brain development and signaling molecules. Crucial steps to metabolize dietary fat take place within the hepatic tissue. Any abnormalities in the hepatic fatty metabolic pathways cause abnormal accumulation of lipid inside the liver, causing MAFLD, ranging from simple steatosis to more complex steatohepatitis and fibrosis. During high-fat-diet-induced hepatic inflammation, systemic proinflammatory cytokines disrupt the blood-brain barrier, resulting in neuroinflammation, cognitive impairment, brain damage and even neurodegeneration. Further, during this altered metabolic scenario, circulating metabolites pass through the impaired BBR and deregulate the epigenetic landscape of the central nervous system. Thus, it becomes crucial to understand the epi-metabolic crosstalk between two crucial organs of our body: the liver and the brain. Here in this chapter, we demonstrate the approach that we are using in our laboratory to study the epigenetic reprogramming in the context of metabolic gene expression in the liver, which is the causal for life style disorders like MAFLD. Remarkably, we intend to understand how liver dysfunction can have an implication in the brain function. Here, we discuss the concept of developing a diet-induced steatosis and steatohepatitis mouse model to understand the disease progression and its interconnection with brain physiology. Further, we also demonstrate 2D and 3D cell culture models to study the liver-brain cross-talk in greater molecular detail. Collectively, these approaches can provide a template for studying the role of epi-metabolic cross-talk in liver-guided brain dysfunction upon MAFLD.

Animals↗

PubMed2025

Epigenetic Regulation in Dilated Cardiomyopathy.

Dilated cardiomyopathy (DCM) is a nonischemic heart muscle disease characterized by impaired contractility, cardiac dilation, and heart failure, with both genetic and nongenetic causes. Emerging evidence highlights epigenetic mechanisms, including deoxyribonucleic acid methylation, histone modifications, chromatin remodeling, and noncoding RNAs, as critical regulators of gene expression in DCM pathogenesis. This article explores familial DCM linked to pathogenic variants in genes like lamin A/C and titin, as well as nongenetic forms such as diabetic and autoimmune DCM. By summarizing recent discoveries, it highlights the epigenetic factors in bridging genetic and environmental influences, offering potential biomarkers and therapeutic targets for improved DCM management.

Humans↗

PubMed2026

Multiscale Modeling Primer: Focus on Chromatin and Epigenetics.

A central challenge in modern biology is to understand how molecular interactions produce cellular and organismal functions across vast spatiotemporal scales. Nowhere is this challenge more apparent than in the study of chromatin, where meters of DNA compact into a micron-sized nucleus. How this polymer folds is a dynamic process, regulated by epigenetic modifications-chemical changes to DNA and histones that involve only a handful of atoms. These small changes cooperate to produce emergent, higher-order structures that define cellular identity and function. To explain this system, we must integrate static, high-resolution snapshots from techniques like cryo-EM with dynamic, lower-resolution data from microscopy and genomics. Multiscale computational models are essential tools that bridge these experimental gaps and reveal the mechanisms of emergent behavior. However, the communication divide between experimental biologists and quantitative modelers often hampers progress. This primer addresses that gap. It first introduces the fundamental biology of chromatin and epigenetics at an introductory level for non-biologists audiences. We then survey the landscape of computational approaches, from atomistic to systems-level models, and connect them to the experimental data that inform and validate them at an introductory level for non-computationalists. We argue that the next frontier will require us to build integrative models that can predict how molecular perturbations mechanistically alter cellular phenotypes, which will open a new era of chromatin-targeted therapeutics.

Chromatin Dynamics↗

PubMed2026

Gene-environment interaction between perinatal oxytocin exposure and Pten mutation shapes epigenetic reprogramming of oxytocin signaling and behavior in mice.

Synthetic oxytocin (Pitocin) is the most commonly used pharmacologic agent for induction and augmentation of labor. Beyond its uterotonic effects, oxytocin plays a critical role in neurodevelopment and social behavior. Dysregulated oxytocin signaling has been implicated in autism spectrum disorder (ASD), raising concern that perinatal exposure to exogenous oxytocin may have lasting neurodevelopmental consequences. This study aimed to determine whether offspring harboring a genetic predisposition for ASD are differentially impacted by perinatal oxytocin exposures, with a focus on long-term oxytocin signaling and autism-like behavior. Pregnant mice carrying offspring with heterozygous mutations in phosphatase and tensin homolog deleted on chromosome ten (Pten), a well-established monogenic risk factor for ASD, received continuous oxytocin versus phosphate-buffered saline (PBS) control via micro-osmotic pumps during late gestation. Wild-type (WT) offspring exposed to each treatment served as a secondary control. Adult offspring were assessed for oxytocin receptor (Oxtr) methylation in the frontal cortex and hippocampus, oxytocin expression in the hypothalamus, serum oxytocin levels, and were subject to a battery of social and anxiety-related behavior tests. Perinatal oxytocin exposure produced genotype-dependent effects in offspring. Epigenetic analyses revealed bidirectional remodeling of Oxtr methylation in the frontal cortex and hippocampus, with increased exon 1 methylation in WT mice and decreased methylation in Pten-mutant mice, resulting in significant genotype-treatment interactions. Hypothalamic oxytocin expression increased following treatment regardless of genotype, though baseline levels were higher in Pten-mutant mice. Neither oxytocin treatment nor genotype impacted long-term serum oxytocin levels. Behavioral outcomes were modest but context-specific: repetitive behaviors and cognition performance were unchanged, but oxytocin-treated Pten-mutant mice exhibited increased anxiety-like behavior alongside improved social memory. In contrast, oxytocin-treated WT mice showed reduced social novelty preference. Exploratory analyses suggested potential sex-dependent trends. Our findings support a model in which genetic susceptibility shapes the epigenetic encoding of early-life hormonal signals, thereby recalibrating oxytocin system function and downstream behavioral outcomes. Together, these data highlight the context-dependent effects of perinatal oxytocin exposure and argue against uniformly beneficial or detrimental effects, emphasizing the importance of gene-environment interactions in neurodevelopmental trajectories.

Animals↗

PubMed2025

Developmental timing of index trauma exposure and accelerated epigenetic aging in United States military veterans.

Trauma exposure has been linked to accelerated GrimAge, an epigenetic biomarker of premature morbidity and mortality. Building on this evidence, the present study examined whether the type and timing of index trauma exposure are differentially associated with accelerated GrimAge. Participants were 873 European American male United States military Veterans from the National Health and Resilience in Veterans Study. We investigated associations between self-reported age at index trauma, index trauma type (interpersonal violence, non-interpersonal trauma, or loss/instability/other), and accelerated GrimAge, operationalized as GrimAge exceeding chronological age by five or more years. Results revealed that interpersonal violence was associated with three-fold greater odds of accelerated GrimAge compared to other trauma types. Age at index trauma was not independently associated with accelerated GrimAge. However, we observed a significant interaction between trauma type and its developmental timing, even after adjusting for index trauma recency, cumulative trauma burden, and other potential confounders. Specifically, Veterans who were older at the time of exposure to interpersonal violence or trauma involving loss or instability had higher odds of accelerated GrimAge. In contrast, exposure to non-interpersonal trauma was more strongly associated with accelerated GrimAge when it occurred at younger ages. These results indicate that trauma type and timing jointly influence epigenetic aging in Veterans, highlighting the need for tailored interventions that address specific trauma characteristics to reduce associated long-term health risks in this population.

Humans↗

PubMed2025

HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury.

Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-cell ATAC-seq and identify YAP/TEAD activation as a key driver of chromatin remodeling. An in vivo CRISPR screen highlights the histone acetyltransferase HBO1 as a critical barrier to reprogramming. HBO1 is recruited by YAP to target loci, where it promotes histone H3 lysine 14 acetylation (H3K14ac) and engages the chromatin reader zinc-finger MYND-type containing 8 (ZMYND8) to suppress YAP/TEAD-driven transcription. Loss of HBO1 accelerates chromatin remodeling, enhances YAP binding, and enables a more complete hepatocyte-to-BEC transition. Our findings position HBO1 as an epigenetic brake that restrains YAP-mediated reprogramming, suggesting that targeting HBO1 may enhance hepatocyte plasticity for liver regeneration.

Hepatocytes↗