Advances in epigenetics link genetics to the environment and disease

Targeting ferroptosis offers therapy choice in sepsis-associated acute lung injury

Sepsis-associated acute lung injury (SALI) is a common complication of sepsis, consisting of a dysfunctional host response to infection-mediated heterogenous complexes. SALI is reported in up to 50 % of patients with sepsis and causes poor outcomes. Despite high incidence, there is a lack of understanding in its pathogenesis and optimal treatment. A better understanding of the molecular mechanisms underlying SALI may help produce better therapeutics. The effects of altered cell-death mechanisms, such as non-apoptotic regulated cell death (RCD) (i.e., ferroptosis), on the development of SALI are beginning to be discovered, while targeting ferroptosis as a meaningful target in SALI is increasingly being recognized. Here, we outline how a susceptible lung alveoli may develop SALI. Then we discuss the general mechanisms underlying ferroptosis, and how it contributes to SALI. We then outline the chemical structures of the emerging agents or compounds that can protect against SALI by inhibiting ferroptosis, summarizing their potential pharmacological effects. Finally, we highlight key limitations and possible strategies to overcome them. This review suggests that a detailed mechanistic and biological understanding of ferroptosis can foster the development of pharmacological antagonists in the treatment of SALI.

Histone deacetylase 8 in focus: Decoding structural prerequisites for innovative epigenetic intervention beyond hydroxamates

Histone deacetylase 8 (HDAC8) inhibitors play a pivotal role in epigenetic regulation. Numerous HDAC8 inhibitors (HDAC8is), that are non-hydroxamates have been identified to date, and a few of them exhibit antiproliferative activity that is on par with hydroxamates. While many non-hydroxamate-based HDAC8is have demonstrated selectivity, hydroxamate-based HDAC8is, like Vorinostat and TSA, have a tendency of non-specificity among the different HDAC isoforms. Moreover, because of the unfavorable toxic side effects, there are significant concerns surrounding the use of hydroxamate derivatives as therapeutic agents in cancer as well as other chronic diseases. Consequently, the research on non-hydroxamate-based HDAC8is is of utmost priority. In the present study, a comprehensive study was presented to unravel the structural requirements of non-hydroxamate-based HDAC8is from a diverse set of 866 compounds. The study utilized Classification-based Quantitative Structure-Activity Relationship (QSAR) analysis, incorporating Bayesian classification, Recursive partitioning, and other machine learning methods to pinpoint the key structural features essential for HDAC8 inhibition. To underscore and gain deeper insights into the identified structural features, molecular docking, and molecular dynamic (MD) simulation studies were conducted. The integration of these computational approaches unveiled key structural motifs essential for potent HDAC8 inhibitory activity, shedding light on the molecular basis of HDAC8 inhibition using non-hydroxamates.

Fine particulate matter‑induced cardiac developmental toxicity (Review)

Fine particulate matter (PM2.5) has become an important risk factor threatening human health. Epidemiological and toxicological investigations have revealed that PM2.5 not only leads to cardiovascular dysfunction, but it also gives rise to various adverse health effects on the human body, such as cardiovascular and cerebrovascular diseases, cancers, neurodevelopmental disorders, depression and autism. PM2.5 is able to penetrate both respiratory and placental barriers, thereby resulting in negative effects on fetal development. A large body of epidemiological evidences has suggested that gestational exposure to PM2.5 increases the incidence of congenital diseases in offspring, including congenital heart defects. In addition, animal model studies have revealed that gestational exposure to PM2.5 can disrupt normal heart development in offspring, although the potential molecular mechanisms have yet to be fully elucidated. The aim of the present review was to provide a brief overview of what is currently known regarding the molecular mechanisms underlying cardiac developmental toxicity in offspring induced by gestational exposure to PM2.5.

Systems biology of dry eye: Unraveling molecular mechanisms through multi-omics integration

Dry eye disease (DED) is a multifactorial condition with complex and incompletely understood molecular mechanisms. Advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and microbiomics, have provided new insights into the pathophysiology of DED. Genomic analyses have identified key genetic variants linked to immune regulation and lacrimal gland function. Transcriptomic studies reveal upregulated inflammatory pathways in ocular surface tissues, implicating these as core drivers of chronic inflammation. Proteomic research highlights significant alterations in tear protein composition, especially proteins involved in inflammation and tissue repair. Metabolomics studies focus on disrupted lipid metabolism and oxidative stress, which are crucial in maintaining tear film stability. Furthermore, microbiome research has demonstrated reduced microbial diversity and increased pathogenic bacteria, exacerbating inflammatory responses. The integration of multi-omics data allows for the identification of novel biomarkers and therapeutic targets, enabling precision diagnostics and personalized treatments. Therefore, this review highlights the critical importance of multi-omics approaches in deepening our understanding of DED's complex molecular mechanisms and their potential to transform clinical management and therapeutic innovations in this challenging field.

Factors influencing brain recovery from stroke via possible epigenetic changes

Aim: To examine epigenetic changes leading to functional repair after damage to the central motor system.Data sources: A literature search was conducted using medical and health science electronic databases (PubMed, MEDLINE, Scopus) up to July 2023.Study selection: Data were summarized for type of intervention, study design, findings including human and animal studies.Data extraction: Data were extracted and double-checked independently for methodological quality. By means of the influence of environmental (calorie restriction or physical exercise) and other factors, epigenetic instructions were found to increase levels of BDNF and enhance synaptic neurotransmission, possibly leading to larger scale changes in structural and functional assets, which may end up to cognitive and motor repair after stroke.

Chromatin-based memory as a self-stabilizing influence on cell identity

Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states. Through pervasive, local, feedback loops, chromatin memory enables cell states that were initially unstable to become stable. Deeper appreciation of this self-stabilizing role for chromatin broadens our perspective of Waddington's epigenetic landscape from a static surface with islands of stability shaped by evolution, to a plasticine surface molded by experience. With implications for the evolution of cell types, stabilization of resistant states in cancer, and the widespread plasticity of complex life.

Epigenetic inheritance of PCOS by developmental programming and germline transmission

Polycystic ovary syndrome (PCOS) is a prevalent endocrine and metabolic disorder, affecting approximately 11-13% of women of reproductive age. Women with PCOS experience a higher prevalence of infertility, pregnancy complications, and cardiometabolic disorders such as obesity, insulin resistance, and type 2 diabetes mellitus. Furthermore, psychiatric comorbidities, including depression and anxiety, significantly impact the quality of life in this population. Although obesity exacerbates these health risks, the exact etiology and pathophysiology of PCOS remain complex and only partially understood. Emerging research suggests potential transgenerational inheritance through genetic and epigenetic mechanisms, highlighting the possibility of PCOS-related risks affecting subsequent generations, including sons. This review synthesizes recent findings on PCOS inheritance patterns and underscores areas for future clinical and research exploration.

The plasticity of epithelial cells and its potential in the induced differentiation of gastric cancer

Cell plasticity refers to the deviation of cells from normal terminal differentiation states when faced with environmental and genetic toxic stresses, resulting in the phenomenon of transforming into other cell or tissue phenotypes. Unlocking phenotype plasticity has been defined as a hallmark of malignant tumors. The stomach is one of the organs in the body with the highest degree of self-renewal and exhibits significant cell plasticity. In this paper, based on the review of the characteristics of normal differentiation of gastric epithelial cells and their markers, the four main phenotypes of gastric epithelial cell remodeling and their relationship with gastric cancer (GC) are drawn. Furthermore, we summarize the regulatory factors and mechanisms that affect gastric epithelial cell plasticity and outline the current status of research and future prospection for the treatment targeting gastric epithelial cell plasticity. This study has important theoretical reference value for the in-depth exploration of epithelial cell plasticity and the tumor heterogeneity caused by it, as well as for the precise treatment of GC.

Epigenetic alterations and memory: key players in the development/progression of chronic kidney disease promoted by acute kidney injury and diabetes

Chronic kidney disease (CKD) is a highly prevalent global public health issue and can progress to renal failure. Survivors of acute kidney injury (AKI) have an increased risk of progressing to CKD by 8.8-fold and kidney failure by 3.1-fold. Further, 20%‒40% of individuals with diabetes will develop CKD, also known as diabetic kidney disease (DKD). Thus, preventing these kidney diseases can positively impact quality-of-life and life-expectancy outcomes for affected individuals. Frequent episodes of hyperglycemia and renal hypoxia are implicated in the pathophysiology of CKD. Prior periods of hyperglycemia/uncontrolled diabetes can result in development/progression of DKD even after achieving normoglycemia, a phenomenon known as metabolic memory or legacy effect. Similarly, in AKI, hypoxic memory is stored in renal cells even after recovery from the initial AKI episode and can transition to CKD. Epigenetic mechanisms involving DNA methylation, chromatin histone post-translational modifications and non-coding RNAs are implicated in both metabolic and hypoxic memory, collectively known as "epigenetic memory." This epigenetic memory is generally reversible and provides a therapeutic avenue to ameliorate persistent disease progression due to hyperglycemia and hypoxia and prevent/ameliorate CKD progression. Indeed, therapeutic strategies targeting epigenetic memory are effective at preventing CKD development/progression in experimental models of AKI and DKD. Here, we review the latest in-depth evidence for epigenetic features in DKD and AKI, and in epigenetic memories of AKI-to-CKD transition or DKD development and progression, followed by translational and clinical implications of these epigenetic changes for the treatment of these widespread kidney disorders.

HEK-omics: The promise of omics to optimize HEK293 for recombinant adeno-associated virus (rAAV) gene therapy manufacturing

Gene therapy is poised to transition from niche to mainstream medicine, with recombinant adeno-associated virus (rAAV) as the vector of choice. However, robust, scalable, industrialized production is required to meet demand and provide affordable patient access, which has not yet materialized. Closing the chasm between demand and supply requires innovation in biomanufacturing to achieve the essential step change in rAAV product yield and quality. Omics provides a rich source of mechanistic knowledge that can be applied to HEK293, the most commonly used cell line for rAAV production. In this review, the findings from a growing number of diverse studies that apply genomics, epigenomics, transcriptomics, proteomics, and metabolomics to HEK293 bioproduction are explored. Learnings from CHO-Omics, application of omics approaches to improve CHO bioproduction, provide a framework to explore the potential of "HEK-Omics" as a multi-omics-informed approach providing actionable mechanistic insights for improved transient and stable production of rAAV and other recombinant products in HEK293.

Food Allergy Genetics and Epigenetics: A Review of Genome-Wide Association Studies

In this review, we provide an overview of food allergy genetics and epigenetics aimed at clinicians and researchers. This includes a brief review of the current understanding of genetic and epigenetic mechanisms, inheritance of food allergy, as well as a discussion of advantages and limitations of the different types of studies in genetic research. We specifically focus on the results of genome-wide association studies in food allergy, which have identified 16 genetic variants that reach genome-wide significance, many of which overlap with other allergic diseases, including asthma, atopic dermatitis, and allergic rhinitis. Identified genes for food allergy are mainly involved in epithelial barrier function (e.g., FLG, SERPINB7) and immune function (e.g., HLA, IL4). Epigenome-wide significant findings at 32 loci are also summarized as well as 14 additional loci with significance at a false discovery of < 1 × 10-4. Integration of epigenetic and genetic data is discussed in the context of disease mechanisms, many of which are shared with other allergic diseases. The potential utility of genetic and epigenetic discoveries is deliberated. In the future, genetic and epigenetic markers may offer ways to predict the presence or absence of clinical IgE-mediated food allergy among sensitized individuals, likelihood of development of natural tolerance, and response to immunotherapy.

Maternal high-fat diet orchestrates offspring hepatic cholesterol metabolism via MEF2A hypermethylation-mediated CYP7A1 suppression

BACKGROUND

Maternal overnutrition, prevalent among women of childbearing age, significantly impacts offspring health throughout their lifetime. While DNA methylation of metabolic-related genes mediates the transmission of detrimental effects from maternal high-fat diet (HFD), its role in programming hepatic cholesterol metabolism in offspring, particularly during weaning, remains elusive.

METHODS

Female C57BL/6 J mice were administered a HFD or control diet, before and during, gestation and lactation. Hepatic cholesterol metabolism genes in the liver of offspring were evaluated in terms of their expression. The potential regulator of cholesterol metabolism in the offspring's liver was identified, and the function of the targeted transcription factor was evaluated through in vitro experiments. The methylation level of the target transcription factor was assessed using the MassARRAY EpiTYPER platform. To determine whether transcription factor expression is influenced by DNA methylation, in vitro experiments were performed using 5-azacitidine and Lucia luciferase activity assays.

RESULTS

Here, we demonstrate that maternal HFD results in higher body weight and hypercholesterolemia in the offspring as early as weaning age. Maternal HFD feeding exacerbates hepatic cholesterol accumulation in offspring primarily by inhibiting cholesterol elimination to bile acids, with a significant decrease of hepatic cholesterol 7α-hydroxylase (CYP7A1). RNA-seq analysis identified myocyte enhancer factor 2A (MEF2A) as a key transcription factor in the offspring liver, which was significantly downregulated in offspring of HFD-fed dams. MEF2A knockdown led to CYP7A1 downregulation and lipid accumulation in HepG2 cells, while MEF2A overexpression reversed this effect. Dual luciferase reporter assays confirmed direct modulation of CYP7A1 transcription by MEF2A. Furthermore, the reduced MEF2A expression was attributed to DNA hypermethylation in the Mef2a promoter region. This epigenetic modification manifested as early as the fetal stage.

CONCLUSIONS

This study provides novel insights into how maternal HFD orchestrates hepatic cholesterol metabolism via MEF2A hypermethylation-mediated CYP7A1 suppression in offspring at weaning.

Neuroprotective potential of Epigenetic modulators, its regulation and therapeutic approaches for the management of Parkinson's disease

The progressive degeneration of dopaminergic neurons in the substantia nigra region of the brain leads to a deficiency of dopamine and, ultimately, the onset of Parkinson's disease (PD). Since there is currently no cure for PD, patients all around the world are dealing with symptomatic management. PD progression is influenced by multiple elements, such as environmental, biological, chemical, genetic, and epigenetic factors. Epigenetics is gaining increased attention due to its role in controlling the expression of genes that contribute to PD. Recent advancements in our understanding of the brain network and its related conditions have shown that alterations in gene expression may occur independently of genetic abnormalities. Therefore, a thorough investigation has been carried out to explore the significance of epigenetics in all degenerative disorders. Epigenetic modifications are essential for regulating cellular homeostasis. Therefore, a deeper understanding of these modifications might provide valuable insights into many diseases and potentially serve as targets for therapeutic interventions. This review article focuses on diverse epigenetic alterations linked to the progression of PD. These abnormalities are supported by numerous research on the control of gene expression and encompass all the epigenetic processes. The beginning of PD is intricately associated with aberrant DNA methylation mechanisms. DNA methyltransferases are the enzymes that create and preserve various DNA methylation patterns. Integrating epigenetic data with existing clinical methods for diagnosing PD may aid in discovering potential curative medicines and novel drug development approaches. This article solely addresses the importance of epigenetic modulators in PD, primarily the mechanisms of DNMTs, their roles in the development of PD, and their therapeutic approaches; it bypasses other PD therapies.

Phosphorylation-mediated disassembly of C-terminal binding protein 2 tetramer impedes epigenetic silencing of pluripotency in mouse embryonic stem cells

Cells need to overcome both intrinsic and extrinsic threats. Although pluripotency is associated with damage responses, how stem cells respond to DNA damage remains controversial. Here, we elucidate that DNA damage activates Chk2, leading to the phosphorylation of serine 164 on C-terminal binding protein 2 (Ctbp2). The phosphorylation of Ctbp2 induces the disruption of Ctbp2 tetramer, weakening interactions with zinc finger proteins, leading to the dissociation of phosphorylated Ctbp2 from chromatin. This transition to a monomeric state results in the separation of histone deacetylase 1 from Ctbp2, consequently slowing the rate of H3K27 deacetylation. In contrast to the nucleosome remodeling and deacetylase complex, phosphorylated Ctbp2 increased binding affinity to polycomb repressive complex (PRC)2, interacting through the N-terminal domain of Suz12. Through this domain, Ctbp2 competes with Jarid2, inhibiting the function of PRC2. Thus, the phosphorylation of Ctbp2 under stress conditions represents a precise mechanism aimed at preserving stemness traits by inhibiting permanent transcriptional shutdown.

Association of exposure to second-hand smoke during childhood with blood DNA methylation

INTRODUCTION

By recent estimates, 40% of children worldwide are exposed to second-hand smoke (SHS), which has been associated with adverse health outcomes. While numerous studies have linked maternal smoking during pregnancy (MSDP) to widespread differences in child blood DNA methylation (DNAm), research specifically examining postnatal SHS exposure remains sparse. To address this gap, we conducted epigenome-wide meta-analyses to identify associations of postnatal SHS and child blood DNAm.

METHODS

Six cohorts from the Pregnancy And Childhood Epigenetics (PACE) Consortium (total N = 2,695), with SHS data and child blood DNAm (aged 7-9 years) measured with the Illumina 450K array were included in the meta-analysis. Linear regression models adjusted for covariates were fitted to examine the association between the number of household smokers in postnatal life (0, 1, 2+) and child blood DNAm. Sensitivity models without adjusting for MSDP and restricted to mothers who did not smoke during pregnancy were evaluated.

RESULTS

Our analysis revealed significant associations (False Discovery Rate < 0.05) between household postnatal SHS exposure and DNAm at 11 CpGs in exposed children. Nine CpGs were mapped to genes (MYO1G, FAM184B, CTDSPL2, LTBP3, PDE10A, and FIBCD1), while 2 CpGs were located in open sea regions. Notably, all except 2 CpGs (mapped to FIBCD1 and CTDSPL2) have previously been linked to either personal smoking habits or in utero exposure to smoking. The models restricted to non-smoking mothers provided similar results. Importantly, several of these CpGs and their associated genes are implicated in conditions exacerbated by or directly linked to SHS.

CONCLUSIONS

Our findings highlight the potential biological effects of SHS on blood DNAm. These findings support further research on epigenetic factors mediating deleterious effects of SHS on child health and call for public health policies aimed at reducing exposure, particularly in environments where children are present.

Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome

The orchestration of dynamic epigenetic and epitranscriptomic modifications is pivotal for the fine-tuning of gene expression. However, these modifications are traditionally examined independently. Recent compelling studies have disclosed an interesting communication and interplay between m6A RNA methylation (m6A epitranscriptome) and epigenetic modifications, enabling the formation of feedback circuits and cooperative networks. Intriguingly, the interaction between m6A and DNA methylation machinery, coupled with the crosstalk between m6A RNA and histone modifications shape the transcriptional profile and translational efficiency. Moreover, m6A modifications interact also with non-coding RNAs, modulating their stability, abundance, and regulatory functions. In the light of these findings, m6A imprinting acts as a versatile checkpoint, linking epigenetic and epitranscriptomic layers toward a multilayer and time-dependent control of gene expression and cellular homeostasis. The scope of the present review is to decipher the m6A-coordinated circuits with DNA imprinting, chromatin architecture, and non-coding RNAs networks in normal physiology and carcinogenesis. Ultimately, we summarize the development of innovative CRISPR-dCas engineering platforms fused with m6A catalytic components (m6A writers or erasers) to achieve transcript-specific editing of m6A epitranscriptomes that can create new insights in modern RNA therapeutics.

Decoding ferroptosis: transforming orthopedic disease management

As a mechanism of cell death, ferroptosis has gained popularity since 2012. The process is distinguished by iron toxicity and phospholipid accumulation, in contrast to autophagy, apoptosis, and other cell death mechanisms. It is implicated in the advancement of multiple diseases across the body. Researchers currently know that osteosarcoma, osteoporosis, and other orthopedic disorders are caused by NRF2, GPX4, and other ferroptosis star proteins. The effective relief of osteoarthritis symptoms from deterioration has been confirmed by clinical treatment with multiple ferroptosis inhibitors. At the same time, it should be reminded that the mechanisms involved in ferroptosis that regulate orthopedic diseases are not currently understood. In this manuscript, we present the discovery process of ferroptosis, the mechanisms involved in ferroptosis, and the role of ferroptosis in a variety of orthopedic diseases. We expect that this manuscript can provide a new perspective on clinical diagnosis and treatment of related diseases.

Pharmacodynamics (PD), Pharmacokinetics (PK) and PK-PD Modeling of NRF2 Activating Dietary Phytochemicals in Cancer Prevention and in Health

Purpose of Review

Dietary phytochemicals, bioactive compounds derived from plants, have gained increasing attention for their potential role in cancer prevention. Among these, NRF2 (nuclear factor erythroid 2-related factor 2) activating dietary phytochemicals such as curcumin, sulforaphane, ursolic acid, and cyanidin have demonstrated significant antioxidant and anti-inflammatory properties, making them promising agents in chemoprevention. This review examines the pharmacokinetic (PK) and pharmacodynamic (PD) profiles of these dietary phytochemicals, with a focus on their NRF2-mediated effects in cancer prevention.

Recent Findings

Preclinical studies have highlighted the potential of these dietary phytochemicals to modulate oxidative stress and inflammation, key drivers of carcinogenesis. We explore the complexity of their PK/PD properties, influenced by factors such as bioavailability, metabolism, and drug interactions. While most of these phytochemicals follow two compartmental PK, their anti-oxidant and anti-inflammatory effects follow the indirect response (IDR) model. Furthermore, we discuss the application of physiologically based pharmacokinetic (PBPK) modeling to simulate the behavior of these compounds in humans, providing insights for clinical translation.

Summary

The integration of PK-PD analysis into the development of dietary phytochemical-based therapies offers a pathway to optimize dosing strategies, enhance therapeutic efficacy, and improve safety. This review underscores the importance of these compounds as part of cancer interception strategies, particularly in the early stages of cancer development, where they may offer a natural, less toxic alternative to conventional therapies.

Graphical Abstract

Characterization of an Activated Metabolic Transcriptional Program in Hepatoblastoma Tumor Cells Using scRNA-seq

Hepatoblastoma is the most common primary liver malignancy in children, with metabolic reprogramming playing a critical role in its progression due to the liver's intrinsic metabolic functions. Enhanced glycolysis, glutaminolysis, and fatty acid synthesis have been implicated in hepatoblastoma cell proliferation and survival. In this study, we screened for altered overexpression of metabolic enzymes in hepatoblastoma tumors at tissue and single-cell levels, establishing and validating a hepatoblastoma tumor expression metabolic score using machine learning. Starting from the Mammalian Metabolic Enzyme Database, bulk RNA sequencing data from GSE104766 and GSE131329 datasets were analyzed using supervised methods to compare tumors versus adjacent liver tissue. Differential expression analysis identified 287 significantly regulated enzymes, 59 of which were overexpressed in tumors. Functional enrichment in the KEGG metabolic database highlighted a network enriched in amino acid metabolism, as well as carbohydrate, steroid, one-carbon, purine, and glycosaminoglycan metabolism pathways. A metabolic score based on these enzymes was validated in an independent cohort (GSE131329) and applied to single-cell transcriptomic data (GSE180665), predicting tumor cell status with an AUC of 0.98 (sensitivity 0.93, specificity 0.94). Elasticnet model tuning on individual marker expression revealed top tumor predictive markers, including FKBP10, ATP1A2, NT5DC2, UGT3A2, PYCR1, CKB, GPX7, DNMT3B, GSTP1, and OXCT1. These findings indicate that an activated metabolic transcriptional program, potentially influencing epigenetic functions, is observed in hepatoblastoma tumors and confirmed at the single-cell level.

Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila

Non-genetic information can be inherited across generations in a process known as transgenerational epigenetic inheritance (TEI). In Drosophila, hemizygosity of the Fab-7 regulatory element triggers inheritance of the histone mark H3K27me3 at a homologous locus on another chromosome, resulting in heritable epigenetic differences in eye color. Here, by mutating transcription factor binding sites within the Fab-7 element, we demonstrate the importance of the proteins pleiohomeotic and GAGA factor in the establishment and maintenance of TEI. We show that these proteins function by recruiting the polycomb repressive complex 2 and by mediating interchromosomal chromatin contacts between Fab-7 and its homologous locus, respectively. Using an in vivo synthetic biology system to induce them, we then show that chromatin contacts alone can establish TEI, providing a mechanism by which hemizygosity of one locus can establish epigenetic memory at another distant locus in trans through chromatin contacts.

Unraveling genetic mysteries: A comprehensive review of GWAS and DNA insights in animal and plant pathosystems

DNA serves as the carrier of genetic information, with sequence variations playing a pivotal role in defining hereditary traits. Genome-Wide Association Studies (GWAS) facilitate the investigation of the links between genetic variations and phenotypes, significantly influencing biological research, particularly in animal and plant pathology. By identifying genetic markers associated with specific traits or diseases, GWAS enhances our understanding of host-pathogen interactions and improves disease-resistant breeding strategies. It has been vital in revealing the genetic basis of disease resistance, pinpointing key genes and DNA loci, which enrich genetic resources for breeding programs and deepen our knowledge of disease resistance mechanisms at the DNA level. Additionally, GWAS contributes to pathogen population genetics, facilitating a thorough exploration of pathogen virulence. Integrating GWAS with marker-assisted selection enhances breeding efficiency and precision in selecting for disease-resistant traits. While previous research has largely focused on host genetics, the genetic variation of pathogens is equally significant. Notably, reports integrating animal and plant pathosystems are still lacking. Given the importance of these systems, this review summarizes key advancements in this field, addresses current challenges, and proposes future directions, thereby offering a vital reference for ongoing research.

Epigenetic control of circadian clocks by environmental signals

Circadian clocks have evolved to enable organisms to respond to daily environmental changes. Maintaining a robust circadian rhythm under various perturbations and stresses is essential for the fitness of an organism. In the core circadian oscillator conserved in eukaryotes (from fungi to mammals), a negative feedback loop based on both transcription and translation drives circadian rhythms. The expression of circadian clock genes depends both on the binding of transcription activators at the promoter and on the chromatin state of the clock genes, and epigenetic modifications of chromatin are crucial for transcriptional regulation of circadian clock genes. Herein we review current knowledge of epigenetic regulation of circadian clock mechanisms and discuss how environmental cues can control clock gene expression by affecting chromatin states.

Implications for metabolic disturbances in myelodysplastic syndromes

The Myelodysplastic Syndromes (MDS) are heterogeneous stem cell malignancies clinically characterized by bone marrow dysplasia, peripheral blood cytopenias, and a high risk for transformation to acute myeloid leukemia. In early stages of disease, differentiation defects and maturation blocks result in deficient hematopoiesis. In higher risk disease, unrestricted proliferation of immature blast cells leads to leukemogenesis. Disease pathogenesis can be attributed to many factors including chronic inflammation that is driven in part by commonly found somatic gene mutations (SGM) fostering expansion of malignant clones while suppressing normal hematopoiesis. Cellular metabolism that both directly and indirectly regulates hematopoietic stem cell (HSC) fate, is intimately connected to the immune system, is altered by MDS somatic gene mutations and is likely is a major contributor to disease pathophysiology. Despite this likely role in pathobiology, there is an underwhelming depth of literature on the subject and the precise metabolic dysregulations in these myeloid malignancies have yet to be fully delineated. In this review, we will provide a general overview of several major metabolic processes and how each directs HSC fate, provide a summary of metabolic studies in MDS, discuss how common SGM and inflammation influence metabolic pathways to drive bone marrow failure, and end with a discussion of standards of care and how these should be carefully considered in the context of metabolic dysregulation.

Replication-coupled inheritance of chromatin states

During the development of eukaryote, faithful inheritance of chromatin states is central to the maintenance of cell fate. DNA replication poses a significant challenge for chromatin state inheritance because every nucleosome in the genome is disrupted as the replication fork passes. It has been found that many factors including DNA polymerases, histone chaperones, as well as, RNA Pol II and histone modifying enzymes coordinate spatially and temporally to maintain the epigenome during this progress. In this review, we provide a summary of the detailed mechanisms of replication-coupled nucleosome assembly and post-replication chromatin maturation, highlight the inheritance of chromatin states and epigenome during these processes, and discuss the future directions and challenges in this field.

Polycomb in female reproductive health: patterning the present and programming the future

Epigenetic modifications regulate chromatin accessibility, gene expression, cell differentiation and tissue development. As epigenetic modifications can be inherited via mitotic and meiotic cell divisions, they enable a heritable memory of cell identity and function and can alter inherited characteristics in the next generation. Tight regulation of epigenetic information is critical for normal cell function and is often disrupted in diseases including cancer, metabolic, neurological and inherited congenital conditions. The ovary performs critical functions in female reproductive health and fertility, including oocyte and sex-hormone production. Oocytes undergo extensive epigenetic programming including the establishment of maternal genomic imprints, which are critical for offspring health and development. Epigenetic modifiers also regulate ovarian somatic cells, such as granulosa and theca cells which support oocytes and produce hormones. While ovarian dysfunction contributes to serious ovarian conditions such as primary ovarian insufficiency (POI), polycystic ovary syndrome (PCOS) and ovarian cancers, the roles of epigenetic modifications in the ovary and their contribution to ovarian dysfunction are not properly understood. Here we review recent advancements in understanding Polycomb proteins, important epigenetic modifiers that have emerging roles in ovarian development and maternal epigenetic inheritance. Polycomb group proteins (PcGs) contribute to the faithful establishment of epigenetic information in oocytes, a process essential for normal offspring development in mice. Emerging evidence also indicates that PcGs regulate ovarian function and female fertility. Understanding these and similar mechanisms will provide greater insight into the epigenetic regulation of ovarian and oocyte function, and how its disruption can impact reproductive health and maternal inheritance.

The RNA Revolution in the Central Molecular Biology Dogma Evolution

Human genome projects in the 1990s identified about 20,000 protein-coding sequences. We are now in the RNA revolution, propelled by the realization that genes determine phenotype beyond the foundational central molecular biology dogma, stating that inherited linear pieces of DNA are transcribed to RNAs and translated into proteins. Crucially, over 95% of the genome, initially considered junk DNA between protein-coding genes, encodes essential, functionally diverse non-protein-coding RNAs, raising the gene count by at least one order of magnitude. Most inherited phenotype-determining changes in DNA are in regulatory areas that control RNA and regulatory sequences. RNAs can directly or indirectly determine phenotypes by regulating protein and RNA function, transferring information within and between organisms, and generating DNA. RNAs also exhibit high structural, functional, and biomolecular interaction plasticity and are modified via editing, methylation, glycosylation, and other mechanisms, which bestow them with diverse intra- and extracellular functions without altering the underlying DNA. RNA is, therefore, currently considered the primary determinant of cellular to populational functional diversity, disease-linked and biomolecular structural variations, and cell function regulation. As demonstrated by RNA-based coronavirus vaccines' success, RNA technology is transforming medicine, agriculture, and industry, as did the advent of recombinant DNA technology in the 1980s.

Epigenetics-targeted drugs: current paradigms and future challenges

Epigenetics governs a chromatin state regulatory system through five key mechanisms: DNA modification, histone modification, RNA modification, chromatin remodeling, and non-coding RNA regulation. These mechanisms and their associated enzymes convey genetic information independently of DNA base sequences, playing essential roles in organismal development and homeostasis. Conversely, disruptions in epigenetic landscapes critically influence the pathogenesis of various human diseases. This understanding has laid a robust theoretical groundwork for developing drugs that target epigenetics-modifying enzymes in pathological conditions. Over the past two decades, a growing array of small molecule drugs targeting epigenetic enzymes such as DNA methyltransferase, histone deacetylase, isocitrate dehydrogenase, and enhancer of zeste homolog 2, have been thoroughly investigated and implemented as therapeutic options, particularly in oncology. Additionally, numerous epigenetics-targeted drugs are undergoing clinical trials, offering promising prospects for clinical benefits. This review delineates the roles of epigenetics in physiological and pathological contexts and underscores pioneering studies on the discovery and clinical implementation of epigenetics-targeted drugs. These include inhibitors, agonists, degraders, and multitarget agents, aiming to identify practical challenges and promising avenues for future research. Ultimately, this review aims to deepen the understanding of epigenetics-oriented therapeutic strategies and their further application in clinical settings.

Unveiling the role of histone deacetylases in neurological diseases: focus on epilepsy

Epilepsy remains a prevalent chronic neurological disease that is featured by aberrant, recurrent and hypersynchronous discharge of neurons and poses a great challenge to healthcare systems. Although several therapeutic interventions are successfully utilized for treating epilepsy, they can merely provide symptom relief but cannot exert disease-modifying effect. Therefore, it is of urgent need to explore other potential mechanism to develop a novel approach to delay the epileptic progression. Since approximately 30 years ago, histone deacetylases (HDACs), the versatile epigenetic regulators responsible for gene transcription via binding histones or non-histone substrates, have grabbed considerable attention in drug discovery. There are also substantial evidences supporting that aberrant expressions and/activities of HDAC isoforms are reported in epilepsy and HDAC inhibitors (HDACi) have been successfully utilized for therapeutic purposes in this condition. However, the specific mechanisms underlying the role of HDACs in epileptic progression have not been fully understood. Herein, we reviewed the basic information of HDACs, summarized the recent findings associated with the roles of diverse HDAC subunits in epilepsy and discussed the potential regulatory mechanisms by which HDACs affected the development of epilepsy. Additionally, we also provided a brief discussion on the potential of HDACs as promising therapeutic targets for epilepsy treatment, serving as a valuable reference for basic study and clinical translation in epilepsy field.

Resolution of Chronic Inflammation, Restoration of Epigenetic Disturbances and Correction of Dysbiosis as an Adjunctive Approach to the Treatment of Atopic Dermatitis

Atopic dermatitis (AD) is a chronic inflammatory skin disease with multifactorial and unclear pathogenesis. Its development is characterized by two key elements: epigenetic dysregulation of molecular pathways involved in AD pathogenesis and disrupted skin and gut microbiota (dysbiosis) that jointly trigger and maintain chronic inflammation, a core AD characteristic. Current data suggest that failed inflammation resolution is the main pathogenic mechanism underlying AD development. Inflammation resolution is provided by specialized pro-resolving mediators (SPMs) derived from dietary polyunsaturated fatty acids acting through cognate receptors. SPM levels are reduced in AD patients. Administration of SPMs or their stable, small-molecule mimetics and receptor agonists, as well as supplementation with probiotics/prebiotics, demonstrate beneficial effects in AD animal models. Epidrugs, compounds capable of restoring disrupted epigenetic mechanisms associated with the disease, improve impaired skin barrier function in AD models. Based on these findings, we propose a novel, multilevel AD treatment strategy aimed at resolving chronic inflammation by application of SPM mimetics and receptor agonists, probiotics/prebiotics, and epi-drugs. This approach can be used in conjunction with current AD therapy, resulting in AD alleviation.

AGEs impair osteogenesis in orthodontic force-induced periodontal ligament stem cells through the KDM6B/Wnt self-reinforcing loop

BACKGROUND

Diabetes, occasionally diagnosed in orthodontic patients, can impede orthodontic tooth movement (OTM) by accumulating advanced glycation end products (AGEs) in the periodontium. This accumulation impairs the osteogenic differentiation of periodontal ligament stem cells (PDLSCs) due to alterations in the force-loaded microenvironment, yet the underlying mechanisms remain elusive.

METHODS

Bioinformatics analysis of GSE112122 identified alterations in the mechanical regulation of histone methylation enzyme Lysine Demethylase 6B (KDM6B). OTM models were established in healthy and Nicotinamide/ Streptozotocin-induced type II diabetic rats. The impact of AGEs on mechanically induced osteogenesis and its correlation with KDM6B were evaluated by assessing the therapeutic effects of periodontal ligament injections of the AGEs/RAGE inhibitor FPS-ZM1. To investigate transcriptomic changes, we extracted human PDLSCs, which were subjected to RNA sequencing following the overexpression of KDM6B. Experimental validation further identified potential self-reinforcing loops and their associated antioxidative mechanisms.

RESULTS

Mechanical forces upregulated KDM6B expression and function in PDLSCs, modulating extensive downstream osteogenesis-related transcriptional changes. Experiments with AGEs-treated and FPS-ZM1-treated samples demonstrated that AGEs impaired osteogenesis by compromising KDM6B mechanical responsiveness. A positive feedback loop between KDM6B and Wnt pathways was identified, inhibited by AGEs. This loop regulated superoxide dismutase 2 (SOD2), facilitating antioxidative stress and preventing stem cell ageing.

CONCLUSIONS

This study elucidates a novel mechanism by which AGEs influence the osteogenic process and antioxidative capacity of PDLSCs through the KDM6B/Wnt self-reinforcing loop under orthodontic force. Targeting the AGE/RAGE pathway or enhancing KDM6B may enhance orthodontic treatments for diabetic patients.

Unraveling the genetic basis of epilepsy: Recent advances and implications for diagnosis and treatment

Epilepsy, affecting approximately 1% of the global population, manifests as recurring seizures and is heavily influenced by genetic factors. Recent advancements in genetic technologies have revolutionized our understanding of epilepsy's genetic landscape. Key studies, such as the discovery of mutations in ion channels (e.g., SCN1A and SCN2A), neurotransmitter receptors (e.g., GABRA1), and synaptic proteins (e.g., SYNGAP1, KCNQ2), have illuminated critical pathways underlying epilepsy susceptibility and pathogenesis. Genome-wide association studies (GWAS) have identified specific genetic variations linked to epilepsy risk, such as variants near SCN1A and PCDH7, enhancing diagnostic accuracy and enabling personalized treatment strategies. Moreover, epigenetic mechanisms, including DNA methylation (e.g., MBD5), histone modifications (e.g., HDACs), and non-coding RNAs (e.g., miR-134), play pivotal roles in altering gene expression and synaptic plasticity, contributing to epileptogenesis. These discoveries offer promising avenues for therapeutic interventions aimed at improving outcomes for epilepsy patients. Genetic testing has become essential in clinical practice, facilitating precise diagnosis and tailored management approaches based on individual genetic profiles. Furthermore, insights into epigenetic regulation suggest novel therapeutic targets for developing more effective epilepsy treatments. In summary, this review highlights significant progress in understanding the genetic and epigenetic foundations of epilepsy. By integrating findings from key studies and specifying genes involved in epigenetic modifications, we underscore the potential for advanced therapeutic strategies in this complex neurological disorder, emphasizing the importance of personalized medicine approaches in epilepsy management.

The Role of Epigenetic Switches in Polyphenism Control: Implications from a Nematode Model for the Developmental Regulation of Alternative Phenotypes

Polyphenisms, the capability of organisms to form two or more alternative phenotypes in response to environmental variation, are prevalent in nature. However, associated molecular mechanisms and potential general principles of polyphenisms among major organismal groups remain currently unknown. This review focuses on an emerging model system for developmental plasticity and polyphenism research, the nematode Pristionchus pacificus and explores mechanistic insight obtained through unbiased genetic, experimental and natural variation studies. Resulting findings identify a central role for epigenetic switches in the environmental control of alternative phenotypes and their micro-and macroevolution. Several features observed in P. pacificus are shared with insects and plants and might become general principles for the control of polyphenisms during development.

Mitochondria: the epigenetic regulators of ovarian aging and longevity

Ovarian aging is a major health concern for women. Ovarian aging is associated with reduced health span and longevity. Mitochondrial dysfunction is one of the hallmarks of ovarian aging. In addition to providing oocytes with optimal energy, the mitochondria provide a co-substrate that drives epigenetic processes. Studies show epigenetic alterations, both nuclear and mitochondrial contribute to ovarian aging. Both, nuclear and mitochondrial genomes cross-talk with each other, resulting in two ways orchestrated anterograde and retrograde response that involves epigenetic changes in nuclear and mitochondrial compartments. Epigenetic alterations causing changes in metabolism impact ovarian function. Key mitochondrial co-substrate includes acetyl CoA, NAD+, ATP, and α-KG. Thus, enhancing mitochondrial function in aging ovaries may preserve ovarian function and can lead to ovarian longevity and reproductive and better health outcomes in women. This article describes the role of mitochondria-led epigenetics involved in ovarian aging and discusses strategies to restore epigenetic reprogramming in oocytes by preserving, protecting, or promoting mitochondrial function.

The dual effects of Benzo(a)pyrene/Benzo(a)pyrene-7,8-dihydrodiol-9,10-epoxide on DNA Methylation

Benzo(a)pyrene (BaP) is one of the most thoroughly studied polycyclic aromatic hydrocarbons(PAHs) and a widespread organic pollutant in various areas of human life. Its teratogenic, immunotoxic and carcinogenic effects on organisms are well documented and widely recognized by researchers. In the body, BaP is enzymatically converted to form a more active benzo(a)pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE). BaP/BPDE has the potential to trigger gene mutations, influence epigenetic modifications and cause damage to cellular structures, ultimately contributing to disease onset and progression. However, there are different points of view when studying epigenetics using BaP/BPDE. On the one hand, it is claimed in cancer research that BaP/BPDE contributes to gene hypermethylation and, in particular, induces the hypermethylation of tumor's suppressor gene promoters, leading to gene silencing and subsequent cancer development. Conversely, studies in human and animal populations suggest that exposure to BaP results in genome-wide DNA hypomethylation, potentially leading to adverse outcomes in inflammatory diseases. This apparent contradiction has not been summarized in research for almost four decades. This article presents a comprehensive review of the current literature on the influence of BaP/BPDE on DNA methylation regulation. It demonstrates that BaP/BPDE exerts a dual-phase regulatory effect on methylation, which is influenced by factors such as the concentration and duration of BaP/BPDE exposure, experimental models and detection methods used in various studies. Acute/high concentration exposure to BaP/BPDE often results in global demethylation of DNA, which is associated with inhibition of DNA methyltransferase 1 (DNMT1) after exposure. At certain specific gene loci (e.g., RAR-β), BPDE can form DNA adducts, recruiting DNMT3 and leading to hypermethylation at specific sites. By integrating these different mechanisms, our goal is to unravel the patterns and regulations of BaP/BPDE-induced DNA methylation changes and provide insights into future precision therapies targeting epigenetics.

Normative implications of postgenomic deterministic narratives: the case study of epigenetic harm

What do we mean when we talk about epigenetic harm? This paper presents a multidimensional view of epigenetic harm. It is a plea to take a step back from discussions of epigenetic responsibility distributions prevalent in ELSA literature on epigenetics. Instead, it urges researchers to take a closer look at the normative role played by the concept of epigenetic harm. It starts out by showing that the ways in which the object of epigenetic responsibility has already been conceptualized are all related to 'epigenetic harm': something negative that happens in which epigenetic mechanisms play a role, or rather something that needs to be avoided. Epigenetic harm is then characterized as a bridging concept between relatively neutral findings on epigenetics on the one side, and potential ethical and societal implications of those findings, primarily in terms of responsibility ascriptions and distributions, on the other. The paper proposes that a sufficiently nuanced account of epigenetic harm should include at least three dimensions. The dimension of causation alone leads to an overly narrow understanding of harm, and a wrong understanding of this dimension might prompt researchers to support an excessively simplistic epigenetic determinism. It is argued that a multidimensional analysis of epigenetic harm is less vulnerable to this threat and more reflective of the various kinds of harm that may be experienced by the subjects of epigenetic alterations. The paper applies insights from disability studies and feminist philosophy to draw attention to two other dimensions of epigenetic harm, namely lived experiences and relationality. The paper concludes by exploring what a shift towards a multidimensional approach to epigenetic harm might mean for epigenetic research and responsibility ascriptions by formulating some concrete implications.

Histone Methylation-Mediated Reproductive Toxicity to Consumer Product Chemicals in Caenorhabditis elegans: An Epigenetic Adverse Outcome Pathway (AOP)

The significance of histone methylation in epigenetic inheritance underscores its relevance to disease and the chronic effects of environmental chemicals. However, limited evidence of the causal relationships between chemically induced epigenetic changes and organismal-level effects hinders the application of epigenetic markers in ecotoxicological assessments. This study explored the contribution of repressive histone marks to reproductive toxicity induced by chemicals in consumer products in Caenorhabditis elegans, applying the adverse outcome pathway (AOP) framework. Triclosan (TCS) and tetrabromobisphenol A (TBBPA) exposures caused reproductive toxicity and altered histone methyltransferase (HMT) and histone demethylase (HDM) activities, increasing the level of trimethylation of H3K9 and H3K27. Notably, treatment with an H3K27-specific HMT inhibitor alleviated reproductive defects and the transcriptional response of genes related to vitellogenin, xenobiotic metabolism, and oxidative stress. Comparison of points of departure (PODs) based on calculated benchmark concentrations (BMCs) revealed the sensitivity of histone-modifying enzyme activities to these chemicals. Our findings suggest that the 'disturbance of HMT and HDM' can serve as the molecular initiating event (MIE) leading to reproductive toxicity in the epigenetic AOP for TCS and TBBPA. The study extended the biological applicability of these enzymes by identifying model species with analogous protein sequences and functions. This combined approach enhances the essentiality, empirical support, and taxonomic domain of applicability (tDOA), which are crucial considerations for ecotoxicological AOPs. Given the widespread use and environmental distribution of chemicals in consumer products, this study proposes histone-modifying enzyme activity as an effective screening tool for reproductive toxicants and emphasizes the integration of epigenetic mechanisms into a prospective ERA.

Dysbiosis-epigenetics-immune system interaction and ageing health problems

Background. The growing interest in microbiota-epigenetics-immune system research stems from the understanding that microbiota, a group of micro-organisms colonized in the human body, can influence the gene expression through epigenetic mechanisms and interaction with the immune system. Epigenetics refers to changes in gene activity that are not caused by the alteration in the DNA sequence itself.Discussion. The clinical significance of this research lies in the potential to develop new therapies for diseases linked to the imbalance of these microbial species (dysbiosis), such as cancer and neurodegenerative diseases. The intricate interaction between microbiota and epigenetics involves the production of metabolites and signalling molecules that can impact our health by influencing immune responses, metabolism and inflammation. Understanding these interactions could lead to novel therapeutic strategies targeting microbiota-epigenetic pathways to improve health outcomes.Conclusion. In this context, we aim to review and emphasize the current knowledge and key concepts that link the microbiota to epigenetics and immune system function, exploring their relevance to the development and maintenance of homeostasis and susceptibility to different diseases later in life. We aim to elucidate key concepts concerning the interactions and potential effects among the human gut microbiota, epigenetics, the immune system and ageing diseases linked to dysbiosis.

The TET3 inflammasome senses unique long HSV-1 proteins for virus particle budding from the nucleus

Inflammasomes play important roles in resisting infections caused by various pathogens. HSV-1 is a highly contagious virus among humans. The process by which HSV-1 particles bud from the nucleus is unique to herpes viruses, but the specific mechanism is still unclear. Here, we screened genes involved in HSV-1 replication. We found that TET3 plays an essential role in HSV-1 infection. TET3 recognizes the UL proteins of HSV-1 and, upon activation, can directly bind to caspase-1 to activate an ASC-independent inflammasome in the nucleus. The subsequent cleavage of GSDMD in the nucleus is crucial for the budding of HSV-1 particles from the nucleus. Inhibiting the perforation ability of GSDMD on the nuclear membrane can significantly reduce the maturation and spread of HSV-1. Our results may provide a new approach for the treatment of HSV-1 in the future.

Comprehensive multi-omics analysis identifies chromatin regulator-related signatures and TFF1 as a therapeutic target in lung adenocarcinoma through a 429-combination machine learning approach

Introduction

Lung cancer is a leading cause of cancer-related deaths, with its incidence continuing to rise. Chromatin remodeling, a crucial process in gene expression regulation, plays a significant role in the development and progression of malignant tumors. However, the role of chromatin regulators (CRs) in lung adenocarcinoma (LUAD) remains underexplored.

Methods

This study developed a chromatin regulator-related signature (CRRS) using a 429-combination machine learning approach to predict survival outcomes in LUAD patients. The CRRS model was validated across multiple independent datasets. We also investigated the impact of CRRS on the immune microenvironment, focusing on immune cell infiltration. To identify potential therapeutic targets, TFF1, a chromatin regulator, was knocked down using siRNA in LUAD cells. We assessed its impact through apoptosis analysis, proliferation assays, and in vivo tumor growth studies. Additional validation was performed using Ki67 expression and TUNEL assays.

Results

The CRRS accurately predicted survival outcomes and was shown to modulate immune cell infiltration in the tumor microenvironment. High-risk patients demonstrated increased activity in cell cycle regulation and DNA repair pathways, along with distinct mutation profiles and immune responses compared to low-risk patients. TFF1 emerged as a key therapeutic target. Knockdown of TFF1 significantly inhibited LUAD cell proliferation, induced apoptosis, and suppressed in vivo tumor growth. Ki67 and TUNEL assays confirmed the role of TFF1 in regulating tumor growth and cell death.

Discussion

These findings highlight the potential of chromatin regulators in prognostic modeling and immune modulation in LUAD. TFF1 was identified as a promising therapeutic target, suggesting that targeting TFF1 could provide new treatment strategies. Further research is warranted to explore its full potential and therapeutic applicability.

Rectifying METTL4-Mediated N6-Methyladenine Excess in Mitochondrial DNA Alleviates Heart Failure

BACKGROUND

Myocardial mitochondrial dysfunction underpins the pathogenesis of heart failure (HF), yet therapeutic options to restore myocardial mitochondrial function are scarce. Epigenetic modifications of mitochondrial DNA (mtDNA), such as methylation, play a pivotal role in modulating mitochondrial homeostasis. However, their involvement in HF remains unclear.

METHODS

Experimental HF models were established through continuous angiotensin II and phenylephrine (AngII/PE) infusion or prolonged myocardial ischemia/reperfusion injury. The landscape of N6-methyladenine (6mA) methylation within failing cardiomyocyte mtDNA was characterized using high-resolution mass spectrometry and methylated DNA immunoprecipitation sequencing. A tamoxifen-inducible cardiomyocyte-specific Mettl4 knockout mouse model and adeno-associated virus vectors designed for cardiomyocyte-targeted manipulation of METTL4 (methyltransferase-like protein 4) expression were used to ascertain the role of mtDNA 6mA and its methyltransferase METTL4 in HF.

RESULTS

METTL4 was predominantly localized within adult cardiomyocyte mitochondria. 6mA modifications were significantly more abundant in mtDNA than in nuclear DNA. Postnatal cardiomyocyte maturation presented with a reduction in 6mA levels within mtDNA, coinciding with a decrease in METTL4 expression. However, an increase in both mtDNA 6mA level and METTL4 expression was observed in failing adult cardiomyocytes, suggesting a shift toward a neonatal-like state. METTL4 preferentially targeted mtDNA promoter regions, which resulted in interference with transcription initiation complex assembly, mtDNA transcriptional stalling, and ultimately mitochondrial dysfunction. Amplifying cardiomyocyte mtDNA 6mA through METTL4 overexpression led to spontaneous mitochondrial dysfunction and HF phenotypes. The transcription factor p53 was identified as a direct regulator of METTL4 transcription in response to HF-provoking stress, thereby revealing a stress-responsive mechanism that controls METTL4 expression and mtDNA 6mA. Cardiomyocyte-specific deletion of the Mettl4 gene eliminated mtDNA 6mA excess, preserved mitochondrial function, and mitigated the development of HF upon continuous infusion of AngII/PE. In addition, specific silencing of METTL4 in cardiomyocytes restored mitochondrial function and offered therapeutic relief in mice with preexisting HF, irrespective of whether the condition was induced by AngII/PE infusion or myocardial ischemia/reperfusion injury.

CONCLUSIONS

Our findings identify a pivotal role of cardiomyocyte mtDNA 6mA and the corresponding methyltransferase, METTL4, in the pathogenesis of mitochondrial dysfunction and HF. Targeted suppression of METTL4 to rectify mtDNA 6mA excess emerges as a promising strategy for developing mitochondria-focused HF interventions.

Epigenetic DNA Methylation and Protein Homocysteinylation: Key Players in Hypertensive Renovascular Damage

Hypertension has been a threat to the health of people, the mechanism of which, however, remains poorly understood. It is clinically related to loss of nephron function, glomerular sclerosis, or necrosis, resulting in renal functional declines. The mechanisms underlying hypertension's development and progression to organ damage, including hypertensive renal damage, remain to be fully elucidated. As a developing approach, epigenetics has been postulated to elucidate the phenomena that otherwise cannot be explained by genetic studies. The main epigenetic hallmarks, such as DNA methylation, histone acetylation, deacetylation, noncoding RNAs, and protein N-homocysteinylation have been linked with hypertension. In addition to contributing to endothelial dysfunction and oxidative stress, biologically active gases, including NO, CO, and H2S, are crucial regulators contributing to vascular remodeling since their complex interplay conducts homeostatic functions in the renovascular system. Importantly, epigenetic modifications also directly contribute to the pathogenesis of kidney damage via protein N-homocysteinylation. Hence, epigenetic modulation to intervene in renovascular damage is a potential therapeutic approach to treat renal disease and dysfunction. This review illustrates some of the epigenetic hallmarks and their mediators, which have the ability to diminish the injury triggered by hypertension and renal disease. In the end, we provide potential therapeutic possibilities to treat renovascular diseases in hypertension.

The Effect of the Oral Contraceptive Pill on Acute Glycaemic Response to an Oral Glucose Bolus in Healthy Young Women: A Randomised Crossover Study

Background/Objective: The oral contraceptive pill (OCP) is widely used by women worldwide, yet the influence of the OCP on carbohydrate metabolism remains under-investigated, with existing studies being few and largely cross-sectional. The study objective was to assess, for the first time, the effect of the combined OCP on postprandial glycaemic response to an oral glucose bolus, using a randomised crossover design. Methods: The effect of a combined monophasic OCP phase on glucose homeostasis and metabolic profile was investigated in 21 healthy young women, who were regular users of either androgenic or anti-androgenic OCP formulations. Plasma glycaemic markers (glucose, insulin and C-peptide) were assessed prior to a 60 g glucose drink (fasting) and for a further 4 h postprandially; once during the "active" (hormone-containing) pill phase and once during the "inactive" (hormone-free) pill phase of the OCP usage cycle. Results: Despite no change in fasting values, in androgenic pill users, postprandial glucose and insulin responses to an oral glucose bolus were ~100% and ~50% greater, respectively, during the active versus inactive phase. In contrast, in anti-androgenic pill users there was no significant change in response between the two OCP usage cycle phases. Conclusions: These findings highlight an acute, but potentially detrimental, influence of the combined OCP on glucose homeostasis, particularly in users of formulations containing androgenic progestogens. Given the high global prevalence of OCP use and increasingly common prolonged active pill regimens, which may continue for months, years or even decades, potential cumulative effects of such changes on metabolic risk demand further investigation.

Establishing of 3D-FISH on frozen section and its applying in chromosome territories analysis in Populus trichocarpa

KEY MESSAGE

Fluorescence in situ hybridization with frozen sections of root tips showed difference of chromosome territories distribution between autosome and sex-chromosome homologous pairs in Populus trichocarpa. The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biologic processes. Three-dimensional fluorescence in situ hybridization (3D-FISH) is a powerful tool for analyzing CTs, but its application in plants is limited. In this study, we established a 3D-FISH technique using frozen sections of Populus trichocarpa root tips, which was an improvement over the use of paraffin sections and enabled us to acquire good FISH signals. Using chromosome-specific oligo probes, we were able to analyze CTs in interphase nuclei in three dimensions. The distribution of chromosome pairs 17 and 19 in the 3D-preserved nuclei of P. trichocarpa root tip cells were analyzed and showed that the autosome pair 17 associated more often than sex chromosome 19. This research lays a foundation for further study of the spatial position of chromosomes in the nucleus and the relationship between gene expression and spatial localization of chromosomes in poplar.

Beyond simple tails: poly(A) tail-mediated RNA epigenetic regulation

The poly(A) tail is an essential structural component of mRNA required for the latter's stability and translation. Recent technologies have enabled transcriptome-wide profiling of the length and composition of poly(A) tails, shedding light on their overlooked regulatory capacities. Notably, poly(A) tails contain not only adenine but also uracil, cytosine, and guanine residues. These findings strongly suggest that poly(A) tails could encode a wealth of regulatory information, similar to known reversible RNA chemical modifications. This review aims to succinctly summarize our current knowledge on the composition, dynamics, and regulatory functions of RNA poly(A) tails. Given their capacity to carry rich regulatory information beyond the genetic code, we propose the concept of 'poly(A) tail epigenetic information' as a new layer of RNA epigenetic regulation.

Neonatal Nucleus Accumbens Microstructure Modulates Individual Susceptibility to Preconception Maternal Stress in Relation to Externalizing Behaviors

OBJECTIVE

Maternal stress influences in utero brain development and is a modifiable risk factor for offspring psychopathologies. Reward circuitry dysfunction underlies various internalizing and externalizing psychopathologies. This study examined (1) the association between maternal stress and microstructural characteristics of the neonatal nucleus accumbens (NAcc), a major node of the reward circuitry, and (2) whether neonatal NAcc microstructure modulates individual susceptibility to maternal stress in relation to childhood behavioral problems.

METHOD

K-means longitudinal cluster analysis was performed to determine trajectories of maternal stress measures (Perceived Stress Scale [PSS], hair cortisol) from preconception to the third trimester. Neonatal NAcc microstructural measures (orientation density index [ODI] and intracellular volume fraction [ICVF]) were compared across trajectories. We then examined the interaction between maternal stress and neonatal NAcc microstructure on child internalizing and externalizing behaviors, assessed between ages 3 and 4 years.

RESULTS

Two trajectories of maternal stress magnitude ("low"/"high") were identified for both PSS (n = 287) and hair cortisol (n = 336). Right neonatal NAcc ODI (rNAcc-ODI) was significantly lower in "low" relative to "high" PSS trajectories (n = 77, p = .04). PSS at preconception had the strongest association with rNAcc-ODI (r = 0.293, p = .029). No differences in NAcc microstructure were found between hair cortisol trajectories. A significant interaction between preconception PSS and rNAcc-ODI on externalizing behavior was observed (n = 47, p = .047).

CONCLUSION

Our study showed that the preconception period contributes to in utero NAcc development, and that NAcc microstructure modulates individual susceptibility to preconception maternal stress in relation to externalizing problems.

PLAIN LANGUAGE SUMMARY

In the S-PRESTO population-based cohort study conducted in Singapore with 351 women and their children, higher levels of maternal perceived stress within the year before pregnancy were associated with increased dendritic complexity within offsprings' nucleus accumbens, indicative of a more advanced developmental profile. Variations in right nucleus accumbens microstructure significantly modulated the association between maternal perceived stress at preconception and externalizing behaviors in early childhood. Study findings suggest that maternal stress in the preconception period accelerates in-utero nucleus accumbens development, leading to differential risk to externalizing problems in later childhood.

Implication of microRNAs as messengers of exercise adaptation in junior female triathlonists

While expression profile of muscle-specific miRNAs following endurance training is well-characterized, information about exercise-induced changes of metabolism-regulating miRNAs is limited, especially in female and junior athletes. Major aim of this study was to examine a set of miRNAs related to mitochondrial function and metabolism in highly professional junior female athletes. The Hungarian National Junior Triathlon Team (n = 4), completed standardized running and cycling sessions. Expression levels of miR-133a, miR-210, miR-494 and miR-127-3p were determined by RT-qPCR in whole blood and serum samples, withdrawn directly before, and after the exercise, and 24 and 48 h later. The expression of miR-494, miR-127-3p and miR-210 showed strong correlation with each other. In serum, nearly significant increment of miR-127-3p levels was detected, that may be a novel biomarker of exercise adaptation. Its expression was significantly higher than that of miR-210. In whole blood, significantly higher miR-210 than miR-494 and miR-127-3p levels were observed. MiRNA expression profile of the youngest athlete was markedly different compared to others. Our results suggest that miRNAs related to mitochondrial function and metabolism are involved in exercise adaptation. The present study may facilitate further research with larger potential participant pools, contributing to improved prevention and treatment of chronic diseases of civilization.

Pharmacological and molecular mechanisms of miRNA-based therapies for targeting cardiovascular dysfunction

Advances in understanding gene expression regulation through epigenetic mechanisms have contributed to elucidating the regulatory mechanisms of noncoding RNAs as pharmacological targets in several diseases. MicroRNAs (miRs) are a class of evolutionarily conserved, short, noncoding RNAs regulating in a concerted manner gene expression at the post-transcriptional level by targeting specific sequences of the 3'-untranslated region of mRNA. Conversely, mechanisms of cardiovascular disease (CVD) remain largely elusive due to their life-course origins, multifactorial pathophysiology, and co-morbidities. In this regard, CVD treatment with conventional medications results in therapeutic failure due to progressive resistance to monotherapy, which overlooks the multiple factors involved, and reduced adherence to poly-pharmacology approaches. Consequently, considering its role in regulating complete gene pathways, miR-based drugs have appreciably progressed into preclinical and clinical testing. This review summarizes the current knowledge about the mechanisms of miRs in cardiovascular disease, focusing specifically on describing how clinical chemistry and physics have improved the stability of the miR molecule. In addition, a comprehensive review of the main miRs involved in cardiovascular disease and the clinical trials in which these molecules are used as active pharmacological molecules is provided.

Epigenetic Modifications and Neuroplasticity in the Pathogenesis of Depression: A Focus on Early Life Stress

Major depressive disorder (MDD) is a debilitating mental illness, and it is considered to be one of the leading causes of disability globally. The etiology of MDD is multifactorial, involving an interplay between biological, psychological, and social factors. Early life represents a critical period for development. Exposure to adverse childhood experiences is a major contributor to the global burden of disease and disability, doubling the risk of developing MDD later in life. Evidence suggests that stressful events experienced during that timeframe play a major role in the emergence of MDD, leading to epigenetic modifications, which might, in turn, influence brain structure, function, and behavior. Neuroplasticity seems to be a primary pathogenetic mechanism of MDD, and, similarly to epigenetic mechanisms, it is particularly sensitive to stress in the early postnatal period. In this review, we will collect and discuss recent studies supporting the role of epigenetics and neuroplasticity in the pathogenesis of MDD, with a focus on early life stress (ELS). We believe that understanding the epigenetic mechanisms by which ELS affects neuroplasticity offers potential pathways for identifying novel therapeutic targets for MDD, ultimately aiming to improve treatment outcomes for this debilitating disorder.