Advances in epigenetics link genetics to the environment and disease

Identification of Potential Intervention Targets Involved in Prior Exercise that Attenuates Peripheral Neuropathic Pain by Integrating Transcriptome and Whole-genome Bisulfite Sequencing Analyses

Changes in DNA methylation and subsequent alterations in gene expression have opened a new direction in research related to the pathogenesis of peripheral neuropathic pain (PNP). This study aimed to reveal epigenetic perturbations underlying DNA methylation in the dorsal root ganglion (DRG) of rats with peripheral nerve injury in response to prior exercise and identify potential target genes involved. Male Sprague-Dawley rats were divided into three groups, namely, chronic constriction injury (CCI) of the sciatic nerve, CCI with prior 6-week swimming training (CCI_Ex), and sham operated (Sham). Mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL) were used as the main observation indicators to evaluate behavioral changes associated with pain. In this study, 6-week swimming training before CCI prevented later chronic pain. In particular, CCI rats with prior exercise showed a significant increase in the MWT and TWL of the injured lateral hind paw compared with CCI rats without exercise on days 14, 21, and 28 after CCI. Whole-genome bisulfite sequencing from the injured lumbar (L4-L6) DRGs on the 28th day after surgery was detected. We also generated DNA methylation maps of the two comparisons (sham group vs. CCI and CCI groups vs. CCI_Ex group), and 396 overlapping differentially methylated region-related genes were found between the two comparisons. Moreover, we integrated RNA sequencing to understand the mechanism by which differential DNA methylation after CCI may influence gene expression. Finally, Ryr1 and Xirp2 were identified through association analysis of two omics and quantitative reverse-transcription polymerase chain reaction, respectively. The methylation levels of Ryr1 and Xirp2 were upregulated with a corresponding increase in their mRNA expression in the DRGs of CCI rats, whereas prior exercise downregulated Ryr1 methylation and restore its expression level. Functional enrichment analysis of both omics found that the calcium signaling pathway was significantly enriched. Therefore, the potential intervention targets (Ryr1 and Xirp2) in L4-L6 DRGs may be involved in prior exercise that attenuates PNP induced by CCI. This study provides crucial insights into the epigenetic regulation of PNP responses to prior exercise.

G9a an Epigenetic Therapeutic Strategy for Neurodegenerative Conditions: From Target Discovery to Clinical Trials

This review provides a comprehensive overview of the role of G9a/EHMT2, focusing on its structure and exploring the impact of its pharmacological and/or gene inhibition in various neurological diseases. In addition, we delve into the advancements in the design and synthesis of G9a/EHMT2 inhibitors, which hold promise not only as a treatment for neurodegeneration diseases but also for other conditions, such as cancer and malaria. Besides, we presented the discovery of dual therapeutic approaches based on G9a inhibition and different epigenetic enzymes like histone deacetylases, DNA methyltransferases, and other lysine methyltransferases. Hence, findings offer valuable insights into developing novel and promising therapeutic strategies targeting G9a/EHMT2 for managing these neurological conditions.

Epigenetics is involved in the pleiotropic effects of statins

INTRODUCTION

Statins have significantly reduced mortality from cardiovascular diseases by lowering serum cholesterol levels. Beyond their lipid-lowering effects, statins improve vascular function, reduce inflammation, decrease reactive oxygen species (ROS) formation, and stabilize atherosclerotic plaques. However, the mechanisms underlying these pleiotropic effects remain unclear.

AREA COVERED

This narrative review summarizes and discusses epigenetic mechanisms that may explain part of the pleiotropic effects of statins. This approach allows for a reevaluation of statin use beyond its cholesterol-lowering benefits. A structured search was conducted in the PubMed and Scopus databases using specific search terms, including articles published up to August 2024.

EXPERT OPINION

The pleiotropic effects of statins, including those mediated by the isoprenoid pathway, partially explain their clinical benefits. By inhibiting histone deacetylases (HDACs, the "erasers") and DNA methyltransferases (DNMTs, the "writers"), statins promote increased histone acetylation and reduced DNA methylation at gene promoter regions. These epigenetic modifications enhance chromatin accessibility, facilitating gene transcription and protecting the cardiovascular system. Further investigation into these epigenetic mechanisms could support the repositioning of statins for broader therapeutic applications. Statins may extend beyond their role in managing hypercholesterolemia, potentially becoming a first-line treatment for preventing cardiovascular disease-related mortality.

Coordinated regulation of chromatin modifiers reflects organised epigenetic programming in mouse oocytes

BACKGROUND

Epigenetic modifications provide mechanisms for influencing gene expression, regulating cell differentiation and maintaining long-term memory of cellular identity and function. As oocytes transmit epigenetic information to offspring, correct establishment of the oocyte epigenome is important for normal offspring development. Oocyte epigenetic programming is highly complex, involving a range of epigenetic modifiers which interact to establish a specific distribution of DNA methylation and histone modifications. Disruptions to oocyte epigenetic programming can alter epigenetic memory and prevent normal developmental outcomes in the next generation. Therefore, it is critical that we further our understanding of the interdependent relationships between various epigenetic modifiers and modifications during oogenesis.

RESULTS

In this study we investigated the spatial and temporal distribution of a range of epigenetic modifiers and modifications in growing oocytes of primordial to antral follicles. We provide comprehensive immunofluorescent profiles of SETD2, H3K36me3, KDM6A, RBBP7, H3K27me3, DNMT3A and DNMT3L and compare these profiles to our previously published profiles of the Polycomb Repressive Complex 2 components EED, EZH2 and SUZ12 in growing oocytes of wildtype mice. In addition, we examined the nuclear levels and spatial distribution of these epigenetic modifiers and modifications in oocytes that lacked the essential Polycomb Repressive Complex 2 subunit, EED. Notably, histone remodelling in primary-secondary follicle oocytes preceded upregulation of DNMT3A and DNMT3L in secondary-antral follicle oocytes. Moreover, loss of EED and H3K27me3 led to significantly increased levels of the H3K36me3 methyltransferase SETD2 during early-mid oocyte growth, although the average levels of H3K36me3 were unchanged.

CONCLUSIONS

Overall, these data demonstrate that oocyte epigenetic programming is a highly ordered process, with histone remodelling in early growing oocytes preceding de novo DNA methylation in secondary-antral follicle oocytes. These results indicate that tight temporal and spatial regulation of histone modifiers and modifications is essential to ensure correct establishment of the unique epigenome present in fully grown oocytes. Further understanding of the temporal and spatial relationships between different epigenetic modifications and how they interact is essential for understanding how germline epigenetic programming affects inheritance and offspring development in mammals, including humans.

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.

WTAP-mediated m6A modification of Hmgb2 contributes to spermatogenic damage induced by PM2.5 exposure

N6-methyladenosine (m6A) is extensively involved in complex spermatogenesis while being extremely sensitive to environmental exposure. Numerous studies have revealed the toxicity of fine particulate matter (PM2.5) to the male reproductive system, but the specific epigenetic mechanisms involved have been underexplored. Here, we investigated the effect of m6A modification on PM2.5-induced male reproductive impairment by establishing a real-time PM2.5-exposed mouse model and a GC-2spd cell model. PM2.5 exposure resulted in damage to the spermatogenic epithelium and mitochondrial abnormalities in spermatocytes and significantly reduced sperm motility in mice. Gene enrichment analyses of testicular tissue differential m6A modified genes were significantly enriched to spermatogenesis in the PM2.5-treated mice compared with the control group, and the expression of the methylase WTAP was markedly decreased after PM2.5 exposure. Moreover, PM2.5 exposure resulted in a significant reduction in the expression of the spermatogenesis-related gene Hmgb2, as well as in the level of the Hmgb2 m6A modification. Transcriptome sequencing and verification experiments suggested that Hmgb2 may regulate spermatocyte ATP levels. In addition, we demonstrated that the m6A methylase WTAP affects Hmgb2 mRNA stability via m6A modification. Our study provides new insights into PM2.5-induced damage to spermatogenesis and reduced sperm motility.

Improving the odds of survival: transgenerational effects of infections

Recent studies argue for a novel concept of the role of chromatin as a carrier of epigenetic memory through cellular and organismal generations, defining and coordinating gene activity states and physiological functions. Environmental insults, such as exposures to unhealthy diets, smoking, toxic compounds, and infections, can epigenetically reprogram germ-line cells and influence offspring phenotypes. This review focuses on intergenerational and transgenerational epigenetic inheritance in different plants, animal species and humans, presenting the up-to-date evidence and arguments for such effects in light of Darwinian and Lamarckian evolutionary theories. An overview of the epigenetic changes induced by infection or other immune challenges is presented, and how these changes, known as epimutations, contribute to shaping offspring phenotypes. The mechanisms that mediate the transmission of epigenetic alterations via the germline are also discussed. Understanding the relationship between environmental fluctuations, epigenetic changes, resistance, and susceptibility to diseases is critical for unraveling disease etiology and adaptive evolution.

DNA methylation of long noncoding RNA cytochrome B in diabetic retinopathy

Diabetic retinopathy, a microvascular complication of diabetes, is the leading cause of blindness in adults, but the molecular mechanism of its development remains unclear. Retinal mitochondrial DNA is damaged and hypermethylated, and mtDNA-encoded genes are downregulated. Expression of a long noncoding RNA (larger than 200 nucleotides, which does not translate into proteins), encoded by mtDNA, cytochrome B (LncCytB), is also downregulated. This study aims to investigate the role of DNA methylation in the downregulation of LncCytB in diabetic retinopathy. Human retinal endothelial cells, incubated in 5 mM (normal) or 20 mM (high) D-glucose, in the presence/absence of Azacytidine (a DNA methyl transferase inhibitor) were analyzed for LncCytB DNA methylation by immunoprecipitation and methylation specific PCR techniques, and LncCytB transcripts by strand-specific PCR and RNA-FISH. Mitochondrial genomic stability was evaluated by quantifying protective mtDNA nucleoids by SYBR green staining and by flow cytometry, and functional stability by oxygen consumption rate using Seahorse analyzer. Results were confirmed in an in vivo model using retina from diabetic rat. While high glucose elevated 5 mC and the ratio of methylated to unmethylated amplicons at LncCytB and downregulated its transcripts, azacytidine prevented LncCytB DNA hypermethylation and decrease in its expression. Azacytidine also ameliorated decrease in nucleoids and oxygen consumption rate. Similarly, azacytidine prevented increase in retinal LncCytB DNA methylation and decrease in its expression in diabetic rats. Thus, DNA hypermethylation plays a major role in the downregulation of retinal LncCytB in diabetes, resulting in impaired mitochondrial homeostasis, and culminating in the development of diabetic retinopathy.

Salt-driven dynamic folding of halophile-origin enzymes: Insights into evolution and protein exploitation

Many years ago, life transitioned from the ocean to land, evolving from halophilic to non-halophilic organisms. Our research indicates that some enzymes from halophiles require salt for soluble expression in E. coli and retain activity within certain salt concentration ranges in the growth medium. The cytoplasmic electrical resistance varies in accordance with the salt concentration in the medium. Further experiments and simulations reveal that the protein structure undergoes dynamic and sophisticated changes under different salt concentrations, affecting soluble expression, surface charge and enzyme activity. This suggests that salt concentrations affect enzyme functionality and potentially influence overall metabolic processes, pointing to a sophisticated adaptive system that operates independently of genetic molecules. Our findings propose insights into a type of environmental cue induced evolution of halophilic microorganisms from the perspective of protein structure. Ultimately, given our extensive marine and other saline resources, our research lays a foundational basis for the development and utilization of halophile-origin enzymes.

Phthalates and uterine disorders

Humans are ubiquitously exposed to environmental endocrine disrupting chemicals such as phthalates. Phthalates can migrate out of products and enter the human body through ingestion, inhalation, or dermal application, can have potential estrogenic/antiestrogenic and/or androgenic/antiandrogenic activity, and are involved in many diseases. As a female reproductive organ that is regulated by hormones such as estrogen, progesterone and androgen, the uterus can develop several disorders such as leiomyoma, endometriosis and abnormal bleeding. In this review, we summarize the hormone-like activities of phthalates, in vitro studies of endometrial cells exposed to phthalates, epigenetic modifications in the uterus induced by phthalate exposure, and associations between phthalate exposure and uterine disorders such as leiomyoma and endometriosis. Moreover, we also discuss the current research gaps in understanding the relationship between phthalate exposure and uterine disorders.

Pre-existing DNA methylation signatures in the prefrontal cortex of alcohol-naïve nonhuman primates define neural vulnerability for future risky ethanol consumption

Alcohol use disorder (AUD) is a highly prevalent, complex, multifactorial and heterogeneous disorder, with 11 % and 30 % of adults meeting criteria for past-year and lifetime AUD, respectively. Identification of the molecular mechanisms underlying risk for AUD would facilitate effective deployment of personalized interventions. Studies using rhesus monkeys and rats, have demonstrated that individuals with low cognitive flexibility and a predisposition towards habitual behaviors show an increased risk for future heavy drinking. Further, low cognitive flexibility is associated with reduced dorsolateral prefrontal cortex (dlPFC) function in rhesus monkeys. To explore the underlying unique molecular signatures that increase risk for chronic heavy drinking, a genome-wide DNA methylation (DNAm) analysis of the alcohol-naïve dlPFC-A46 biopsy prior to chronic alcohol self-administration was conducted. The DNAm profile provides a molecular snapshot of the alcohol-naïve dlPFC, with mapped genes and associated signaling pathways that vary across individuals. The analysis identified 1,463 differentially methylated regions (DMRs) related to unique genes that were strongly associated with average ethanol intake consumed over 6 months of voluntary self-administration. These findings translate behavioral phenotypes into neural markers of risk for AUD, and hold promise for parallel discoveries in risk for other disorders involving impaired cognitive flexibility. SIGNIFICANCE: Alcohol use disorder (AUD) is a highly prevalent and heterogeneous disorder. Prevention strategies to accurately identify individuals with a high risk for AUD, would help reduce the prevalence, and severity of AUD. Our novel epigenomic analysis of the alcohol-naïve nonhuman primate cortex provides a molecular snapshot of the vulnerable brain, pointing to circuitry and molecular mechanisms associated with cortical development, synaptic functions, glutamatergic signaling and coordinated signaling pathways. With a complex disorder like AUD, having the ability to identify the molecular mechanisms underlying AUD risk is critical for better development of personalized effective treatments.

A sequence-specific RNA acetylation catalyst

N4-acetylcytidine (ac4C) is a ubiquitous RNA modification incorporated by cytidine acetyltransferase enzymes. Here, we report the biochemical characterization of Thermococcus kodakarensis Nat10 (TkNat10), an RNA acetyltransferase involved in archaeal thermotolerance. We demonstrate that TkNat10's catalytic activity is critical for T. kodakarensis fitness at elevated temperatures. Unlike eukaryotic homologs, TkNat10 exhibits robust stand-alone activity, modifying diverse RNA substrates in a temperature, ATP, and acetyl-CoA-dependent manner. Transcriptome-wide analysis reveals TkNat10 preferentially modifies unstructured RNAs containing a 5'-CCG-3' consensus sequence. Using a high-throughput mutagenesis approach, we define sequence and structural determinants of TkNat10 substrate recognition. We find TkNat10 can be engineered to facilitate use of propionyl-CoA, providing insight into its cofactor specificity. Finally, we demonstrate TkNat10's utility for site-specific acetylation of RNA oligonucleotides, enabling analysis of ac4C-dependent RNA-protein interactions. Our findings establish a framework for understanding archaeal RNA acetylation and a new tool for studying the functional consequences of ac4C in diverse RNA contexts.

Engineered S. cerevisiae construction for high-gravity ethanol production and targeted metabolomics

Strong sugar tolerance and high bioethanol yield of yeast under high-gravity fermentation have caused great attention in the bioethanol industry. In this study, Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR-Cas9) technology was used to knock out S. cerevisiae GPD2, FPS1, ADH2, DLD3, ERG5, NTH1, and AMS1 to construct engineering strain S. cerevisiae GFADENA. Under high-gravity fermentation with 400 g/L of sucrose, S. cerevisiae GFADENA produced 135 g/L ethanol, which increased 17% compared with the wild-type strain. In addition, S. cerevisiae GFADENA produced 145 g/L of ethanol by simultaneous saccharification and fermentation (SSF) using 400 g/L of corn syrup with a sugar-ethanol conversion rate of 41.1%. Further, the targeted metabolomics involving energy, amino acid, and free fatty acid metabolisms were performed to unravel its molecular mechanisms. The deletion of seven genes in S. cerevisiae GFADENA caused a more significant effect on energy metabolism compared with amino acid and free fatty acid metabolisms based on the significantly different metabolites. Two metabolites α-ketoglutaric acid and fructose-1,6-bisphosphate were the most significantly different upregulation and downregulation metabolites, respectively (p < 0.05). Functions of metabolism, environmental information processing, and genetic information processing were related to sucrose tolerance enhancement and ethanol production increase in S. cerevisiae GFADENA by the regulation of significantly different metabolites. This study provided an effective pathway to increase ethanol yield and enhance sucrose tolerance in S. cerevisiae through bioengineering modification. KEY POINTS: • S. cerevisiae GFADENA with gene deletion was constructed by the CRISPR-Cas9 approach • S. cerevisiae GFADENA could produce ethanol using high-gravity fermentation condition • The ethanol yield of 145 g/L was produced using 400 g/L corn syrup by the SSF method.

A Model of Epigenetic Inheritance Accounts for Unexpected Adaptation to Unforeseen Challenges

Accumulated evidence of transgenerational inheritance of epigenetic and symbiotic changes raises fundamental questions about the possible types, significance and duration of impacts on the population, as well as whether, and under which conditions, the inheritance of non-genetic changes confers long-term advantage to the population. To address these questions, a population epigenetics model of individuals undergoing stochastic changes and/or induced responses that are transmitted to the offspringis introduced. Potentially adaptive and maladaptive responses are represented, respectively, by environmentally driven changes that reduce and increase the selective pressure. Analytic solutions in a simplified case of populations that are exposed to either periodic or progressively deteriorating environments shows that acquisition and transmission of non-genetic changes that alleviate the selective pressure confer long-term advantage and may facilitate escape from extinction. Systematic analysis of outcomes as a function of population properties further identifies a non-traditional regime of adaptation mediated by stochastic changes that are rapidly acquired within a lifetime. Contrasting model predictions with experimental findings shows that inheritance of dynamically acquired changes enables rapid adaptation to unforeseen challenges and can account for population dynamics that is either unexpected or beyond the scope of traditional models.

Design and Synthesis of Novel Deazapurine DNMT 1 Inhibitors with In Vivo Efficacy in DLBCL

The application of drugs to regulate abnormal epigenetic changes has become an important means of tumor treatment. In this study, we employed computer-aided design methods to develop a novel deazapurine compound targeting DNA methyltransferase 1 (DNMT1). Through screening for enzyme activity, selectivity, and cellular efficacy, we optimized three structural skeletons, ultimately yielding compound 55, exhibiting an IC50 of 2.42 μM for DNMT1. Compound 55 displayed excellent in vitro inhibitory effects on various hematological tumor and solid tumor cell lines, especially lymphoma cells, with IC50 values in the nanomolar range. In vitro studies confirmed compound 55 selectively inhibited DNMT1 and exhibited demethylation ability. In vivo mouse model validated the DNA methylation inhibition of compound 55. Compound 55 demonstrated good antitumor activity in vivo. Specifically, compound 55 combined with chidamide demonstrated a superior therapeutic effect over the first-line therapy RTX-CHOP in both the DEL and TP53 mutant DLBCL PDX tumor models.

Neurodegenerative diseases: Epigenetic regulatory mechanisms and therapeutic potential

Neurodegenerative diseases (NDDs) are a class of diseases in which the progressive loss of subtype-specific neurons leads to dysfunction. NDDs include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), among others. Previous studies have demonstrated that the pathogenesis of NDDs involves various mechanisms, including genetic factors, oxidative stress, apoptosis, and the immune response. Recent studies have shown that epigenetic regulation mediates the interactions between DNA methylation, chromatin remodeling, histone modification, and non-coding RNAs, thus affecting gene transcription. A growing body of research links epigenetic modifications to crucial pathways involved in the occurrence and development of NDDs. Epigenetics has also been found to regulate and maintain nervous system function, and its imbalance is closely related to the occurrence and development of NDDs. The present review summarizes focuses on the role of epigenetic modifications in the pathogenesis of NDDs and provides an overview of the key genes regulated by DNA methylation, histone modification, and non-coding RNAs in NDDs. Further, the current research status of epigenetics in NDDs is summarized and the potential application of epigenetics in the clinical diagnosis and treatment of NDDs is discussed.

EXO1's pan-cancer roles: diagnostic, prognostic, and immunological analyses through bioinformatics

Cancer remains a leading cause of mortality worldwide, with human exonuclease 1 (EXO1) emerging as a key player in DNA repair and damage response pathways, critical for genomic stability and tumor evolution. The aim of this study was to conduct a comprehensive pan-cancer analysis to elucidate the multifaceted roles of EXO1 in various malignancies. Leveraging public databases including TCGA, GTEx, HPA, cBioPortal, UALCAN, STRING, CancerSEA and TISIDB database, we examined EXO1's expression, diagnostic potential, prognostic significance, mutational characteristics, functional roles, and immunological effects across different cancer types. EXO1 was found to be upregulated in multiple cancers, with significant diagnostic potential as indicated by high AUC values in ROC analyses. Elevated EXO1 expression correlated with adverse prognosis in several cancer types, including breast, lung, and pancreatic cancers. Epigenetic alterations, including DNA methylation and mRNA modifications, were also associated with EXO1 expression. Enrichment analyses identified EXO1-related genes involved in DNA recombination, replication, and repair, with GSEA implicating EXO1 in cell cycle regulation and DNA processing pathways. Importantly, immunogenomic analyses revealed EXO1's significant role in modulating the tumor microenvironment, as it is associated with immune cell infiltration and cytokine expression, suggesting its involvement in tumor immunology and immune response regulation. These results implied that EXO1 as a significant biomarker with prognostic and diagnostic potential across various malignancies, suggesting its potential as a therapeutic target and its involvement in immunomodulatory processes within the tumor microenvironment.

Redox regulation: mechanisms, biology and therapeutic targets in diseases

Redox signaling acts as a critical mediator in the dynamic interactions between organisms and their external environment, profoundly influencing both the onset and progression of various diseases. Under physiological conditions, oxidative free radicals generated by the mitochondrial oxidative respiratory chain, endoplasmic reticulum, and NADPH oxidases can be effectively neutralized by NRF2-mediated antioxidant responses. These responses elevate the synthesis of superoxide dismutase (SOD), catalase, as well as key molecules like nicotinamide adenine dinucleotide phosphate (NADPH) and glutathione (GSH), thereby maintaining cellular redox homeostasis. Disruption of this finely tuned equilibrium is closely linked to the pathogenesis of a wide range of diseases. Recent advances have broadened our understanding of the molecular mechanisms underpinning this dysregulation, highlighting the pivotal roles of genomic instability, epigenetic modifications, protein degradation, and metabolic reprogramming. These findings provide a foundation for exploring redox regulation as a mechanistic basis for improving therapeutic strategies. While antioxidant-based therapies have shown early promise in conditions where oxidative stress plays a primary pathological role, their efficacy in diseases characterized by complex, multifactorial etiologies remains controversial. A deeper, context-specific understanding of redox signaling, particularly the roles of redox-sensitive proteins, is critical for designing targeted therapies aimed at re-establishing redox balance. Emerging small molecule inhibitors that target specific cysteine residues in redox-sensitive proteins have demonstrated promising preclinical outcomes, setting the stage for forthcoming clinical trials. In this review, we summarize our current understanding of the intricate relationship between oxidative stress and disease pathogenesis and also discuss how these insights can be leveraged to optimize therapeutic strategies in clinical practice.

Intracellular HIV-1 Tat regulator induces epigenetic changes in the DNA methylation landscape

Introduction

The HIV regulatory protein Tat enhances viral transcription and also modifies host gene expression, affecting cell functions like cell cycle and apoptosis. Residual expression of Tat protein is detected in blood and other tissues even under antiretroviral treatment. Cohort studies have indicated that, despite virologic suppression, people with HIV (PWH) are at increased risk of comorbidities linked to chronic inflammation, accelerated immune ageing, and cellular senescence, sometimes associated with abnormal genomic methylation patterns. We analysed whether Tat influences DNA methylation and subsequently impacts the transcriptional signature, contributing to inflammation and accelerated ageing.

Methods

We transfected Jurkat cells with full-length Tat (Tat101), Tat's first exon (Tat72), or an empty vector (TetOFF). We assessed DNA methylation modifications via the Infinium MethylationEPIC array, and we evaluated transcriptomic alterations through RNA-Seq. Methylation levels in gene promoters or body regions were correlated to their expression data, and subsequently, we performed an overrepresentation analysis to identify the biological terms containing differentially methylated and expressed genes.

Results

Tat101 expression caused significant hyper- and hypomethylation changes at individual CpG sites, resulting in slightly global DNA hypermethylation. Methylation changes at gene promoters and bodies resulted in altered gene expression, specifically regulating gene transcription in 5.1% of differentially expressed genes (DEGs) in Tat101- expressing cells. In contrast, Tat72 had a minimal impact on this epigenetic process. The observed differentially methylated and expressed genes were involved in inflammatory responses, lipid antigen presentation, and apoptosis.

Discussion

Tat expression in HIV infection may constitute a key epigenetic modelling actor that contributes to HIV pathogenesis and chronic inflammation. Clinical interventions targeting Tat blockade may reduce chronic inflammation and cellular senescence related to HIV infection comorbidities.

Epigenetic ALYREF/UHRF1/RHOB Axis in Corneal Wound Healing and Implications for Epithelial Tumorigenesis

Purpose

Corneal epithelial wound healing (CEWH) is a complex process influenced by epigenetic regulation. Ubiquitin-like with plant homeodomain (PHD) and ring finger domains 1 (UHRF1), it plays a key role in integrating epigenetic signals. However, its precise function in modulating CEWH remains poorly understood. We describe here the functional mechanisms of UHRF1 in modulating CEWH.

Methods

Quantitative Reverse Transcription PCR (RT-qPCR), immunofluorescence, and gene manipulation were used to investigate UHRF1 expression patterns and functions during CEWH. Integrated multi-omics and targeted bisulfite sequencing (TBS) were performed to reveal the downstream target of UHRF1. Mutation assay was used to examine whether Aly/REF export factor (ALYREF) can recognize and bind RNA m5C-UHRF1. Gene expression profiling interactive analysis (GEPIA) was utilized to validate the correlation of UHRF1 with its upstream and downstream targets.

Results

In this study, we demonstrate that UHRF1 enhances CEWH and sustains DNA methylation during CEWH, which is essential for this effect. A multi-omics analysis identified Ras homolog family member B (RHOB) as a downstream target of UHRF1. Our findings further revealed that UHRF1 epigenetically downregulates RHOB, thereby facilitating CEWH. Moreover, we showed that ALYREF binds to m5C sites on UHRF1 mRNA and enhances its translation. Finally, our analysis of molecular alterations and the clinical significance of ALYREF, UHRF1, and RHOB expression suggests that this epigenetic axis is also relevant in epithelial-derived tumors, which represent approximately 90% of all tumors.

Conclusions

Our study identifies a novel epigenetic ALYREF/UHRF1/RHOB axis that enhances CEWH. Importantly, this axis appears to be conserved across various epithelial-derived tumors, suggesting its broader biological significance.

Mechanistic insights into microwave radiation induced cognitive impairments: The role of m6A epigenetic modifications and HNRNPA2B1 in TrkB regulation

Microwave radiation, a prevalent environmental stressor, significantly impacts human health. Based on previous studies, we hypothesize that microwave-induced cognitive impairments and vulnerability in the hippocampal dentate gyrus (DG) region are due to abnormal synaptic plasticity regulated by both newborn and mature neurons derived from neural stem cells (NSCs). Epigenetics links external factors to organisms, offers insights into the health effects of environmental influences. To explore the molecular mechanisms underlying the effects of microwave radiation on neuronal synaptic plasticity from the perspective of mRNA N6-methyladenosine (m6A) modification. We first assessed the impact of microwave radiation on cognitive memory abilities in rats through behavioral tests. Immunofluorescence staining were applied to clarify the influence of microwave radiation on both neurons and NSCs. Molecular mechanisms were investigated by ELISA, q-PCR, Western blot, MeRIP-seq, and RNA pull-down experiments. The microwave radiated rat model exhibiting learning and memory deficits. Impaired synaptic plasticity in mature hippocampal neurons alongside hindered NSCs proliferation and development were observed. Using our established non-contact co-culture model, we replicated the in vivo adverse effects of microwave radiation. Down-regulated HNRNPA2B1 leads to reduced binding of TrkB m6A and promoted TrkB degradation. This feedback loop results in low BDNF expression, ultimately causing cognitive impairments. Our study emphasizes the neurotoxicity of microwave radiation and identifies TrkB m6A modification as a potential target for protecting against cognitive damage induced by electromagnetic radiation.

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.

Adverse Childhood Experiences and Accelerated Epigenetic Aging in the Hispanic Community Health Study/Study of Latinos: Nativity as an Effect Modifier

BACKGROUND

Whether adverse childhood experiences (ACEs) are associated with accelerated epigenetic aging over time among the Hispanic/Latino population remains unknown. This study examined the longitudinal association between ACEs and epigenetic age acceleration (EAA), as well as potential effect modifiers, among a sample of Hispanic/Latino adults.

METHODS

We analyzed 960 Hispanic/Latino adults with DNA methylation (DNAm) profile data from two visits (approximately six years apart) sampled from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We used PhenoAge, GrimAge, and DunedinPace, a biomarker for the pace of biological aging, to calculate epigenetic aging deviations. Linear mixed models were fit to estimate the association between ACEs and EAA measured by each epigenetic aging measure, adjusting for sex, age, and parental highest education level. Sex and nativity were also assessed as potential effect modifiers.

RESULTS

A one-unit increase in ACE score was associated with a 0.16-year (95 %CI: 0.06, 0.26, p = 0.002) higher GrimAge acceleration (AgeAccelGrim) at Visit 1. Among US-born individuals, a one-unit increase in ACE score was associated with a 0.35-year (95 %CI: 0.12, 0.58, p = 0.003) higher AgeAccelGrim and 0.01-biological year/calendar year (95 %CI: 0.01, 0.02, p = 0.0003) higher DunedinPACE at Visit 1, but statistically significantly weaker associations were found among foreign/US-territory born individuals (p for interaction=0.039 in AgeAccelGrim and 0.001 in DuendinPACE). No association was found between ACEs and the rate of change in EAA between two visits.

CONCLUSION

ACEs are associated with a higher EAA over time among Hispanic/Latino adults at a constant rate. Hispanic/Latino born in the US are more susceptible to the increased EAA related to ACEs compared with those born in a foreign country or US territory.

Paternal fenvalerate exposure causes depressive-like behaviour by altering Grb10 gene DNA methylation in adolescent offspring

Fenvalerate, a typical pyrethroid pesticide, is a neurological toxicant. This study aimed to evaluate the effect of paternal exposure to fenvalerate on depressive-like behaviours in adolescent offspring. Depression-like behavior was determined by Sucrose Preference Test (SPT), Tail Suspension Test (TST) and Forced Swimming Test (FST) in adolescent offspring. The level of dopamine was reduced in the midbrain of fenvalerate-exposed adolescent offspring. Tyrosine hydroxylase (Th), a rate limiting enzyme for dopamine synthesis, was significantly reduced in the midbrain of adolescent offspring exposed to fenvalerate. And Th was decreased in the midbrain and hindbrain of fetuses exposed to fenvalerate. Transcriptome analysis revealed growth factor receptor-bound protein 10 (Grb10) was decreased in the fetal hindbrain exposed to fenvalerate. Grb10 mRNA and protein were reduced in the fetal hindbrain exposed to fenvalerate. Interestingly, in vitro experiments, Th was reduced by si-Grb10. Conversely, Th was increased by oe-Grb10. Mechanistically, the 5mC content of Grb10 gene at one CpG fragment was reduced in the fetal hindbrain exposed to fenvalerate. And the 5mC content of Grb10 gene at eighteen CpG sites was decreased in paternal sperm exposed to fenvalerate. In summary, paternal fenvalerate exposure causes depressive-like behavior by altering DNA methylation of Grb10 gene in the sperm.

[Physiological and pathophysiological changes of the ageing lung]

BACKGROUND

Due to age-related changes the lung function decreases. At the same time there is an increase in pulmonary diseases that lead to restrictions in mobility and autonomy.

RESEARCH QUESTION

What are the underlying changes in lung ageing? To what extent do they affect lung function and are there factors that can be influenced?

METHOD

Literature search.

RESULTS

Ageing of the lungs is associated with a loss of elasticity and distensibility. Senescence-associated factors play an important role at the molecular level. Accumulation of damaged DNA and proteins, oxidative stress and chronic inflammation are major factors. Avoidance of harmful environmental factors can reduce the disease burden.

CONCLUSION

Age-related pathophysiological changes lead to increased work of breathing with decreasing muscle strength. Patients should be encouraged to avoid inhaling noxious agents as these are associated with a diminution of lung function loss even in older age.

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 kidney 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% to 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 noncoding 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.

Cell type-specific 3D-genome organization and transcription regulation in the brain

3D organization of the genome plays a critical role in regulating gene expression. How 3D-genome organization differs among different cell types and relates to cell type-dependent transcriptional regulation remains unclear. Here, we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the mouse cerebral cortex. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the size of the cell nucleus to higher-order chromosome structures and radial positioning of chromatin loci within the nucleus. These cell type-dependent variations in nuclear architecture and chromatin organization exhibit strong correlations with both the total transcriptional activity of the cell and transcriptional regulation of cell type-specific marker genes. Moreover, we found that the methylated DNA binding protein MeCP2 promotes active-inactive chromatin segregation and regulates transcription in a nuclear radial position-dependent manner that is highly correlated with its function in modulating active-inactive chromatin compartmentalization.

Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees

Maternal trauma influences infant and adult health outcomes and may impact future generations through epigenetic modifications such as DNA methylation (DNAm). Research in humans on the intergenerational epigenetic transmission of trauma effects is limited. In this study, we assessed DNAm signatures of war-related violence by comparing germline, prenatal, and direct exposures to violence across three generations of Syrian refugees. We compared families in which a pregnant grandmother versus a pregnant mother was exposed to violence and included a control group with no exposure to war. We collected buccal swab samples and survey data from mothers and 1-2 children in each of 48 families (n = 131 participants). Based on an epigenome-wide association study (EWAS), we identified differentially methylated regions (DMPs): 14 were associated with germline and 21 with direct exposure to violence. Most DMPs showed the same directionality in DNAm change across germline, prenatal, and direct exposures, suggesting a common epigenetic response to violence. Additionally, we identified epigenetic age acceleration in association with prenatal exposure to violence in children, highlighting the critical period of in utero development. This is the first report of an intergenerational epigenetic signature of violence, which has important implications for understanding the inheritance of trauma.

MTHFR variant links homocysteine metabolism and endothelial cell dysfunction by targeting mitophagy in human thoracic aortic dissection patient induced pluripotent stem cell (iPSC) models

AIMS

Genetics and environmental cues boost the development of human diseases. Methylenetetrahydrofolate reductase (MTHFR) is involved in the metabolism of homocysteine, and a common variant rs1801133 of MTHFR has been reported in human cardiovascular diseases. This study aims to providing a novel strategy for patient stratification with specific genetic and metabolic screening, finally for personalized healthcare for patients with thoracic aortic dissection.

METHODS AND RESULTS

We corrected the MTHFR variant to generate an isogenic control iPSC line (Isogenic-iPSC) with CRISPR/Cas9 method, and this isogenic-iPSC shared the same other genetic information with our previously established MTHFR-iPSC line, providing a promising approach for analysis the phenotype and mechanism of rs1801133. During the direct differentiation of endothelial cells from both iPSC lines, rs1801133 variant did not affect the endothelial cell fate determination. Without homocysteine, this variant has little effect on endothelial cell function. While administration of homocysteine, the MTHFR-iPSC derived endothelial cells exhibited disrupted mitophagy, increased cell apoptosis and decreased cell viability. Bulk RNA-seq data indicated LAMP3 is a target of homocysteine, activation of LAMP3 might contribute to homocysteine induced the disruption of mitochondrial structure and cell apoptosis. With chemical compounds screening, kaempferol ameliorated the homocysteine-induced cell toxicity by restoring the mitochondrial structure. The direct relationship between homocysteine metabolism and MTHFR rs1801133 variant was investigated, and the molecular target for homocysteine and translational perspective has also been demonstrated.

CONCLUSIONS

Collectively, this study provided the direct evidence of a specific genetic variant in MTHFR and homocysteine metabolism. Investigating the molecular mechanism of homocysteine activated LAMP3 on endothelial cell dysfunction and mitophagy could provide novel insights for targeted disease prevention and improving individual outcomes.

TRANSLATIONAL PERSPECTIVE

Thoracic aortic dissection (TAD) is a life-threatening cardiovascular disease with a high mortality, lacking effective medical treatment and early diagnosis. Endothelial cells dysfunction has been considered into the development of TAD. Here, we show that MTHFR variant is responsible for the elevated homocysteine in iPSC-ECs, and disrupted mitochondrial structures by homocysteine significantly impaired endothelial function. Understanding the mechanism and translational medicine of homocysteine-induced endothelial toxicity in human with MTHFR variant could benefit the novel strategy for prevention and vessel protection against metabolism injury. Meanwhile, targeting mitophagy and application of small molecule, such as kaempferol, also provide an insight for endothelial protection.

A possible role for epigenetics in cancer initiation

Cancer is one of the leading causes of mortality worldwide. Known since antiquity, its understanding has evolved over time and has significantly advanced with new technologies over the past four decades. Cancer initiation is currently admitted to be explainable by the somatic mutation theory, which postulates that DNA mutations altering the function of oncogenes and tumor suppressor genes initiate cancer. In addition to these mutations, epigenetic alterations, which heritably change gene expression without altering the DNA sequence, also play a key role. Recent data suggests that epigenetic components regulate all aspects of tumor progression, including cancer initiation. These discoveries prompt a reevaluation of the somatic mutation theory, of cancer prevention and treatment strategies.

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.

Environmental pollutants and atherosclerosis: Epigenetic mechanisms linking genetic risk and disease

Over the past half-century, significant strides have been made to identify key risk factors, genetic mechanisms, and treatments for atherosclerosis. Yet, coronary artery disease (CAD) remains a leading global public health challenge. While the heritability of CAD is well-documented, there is increasing focus on the role of environmental exposures, such as smoking, air pollution, and heavy metals, on global CAD risk. Recent research has shed light on the interplay between genetic variation and environmental factors, offering insights into gene-environment (GxE) interactions. Moreover, emerging evidence suggests that environmental toxicants can profoundly impact the epigenome, altering gene regulation beyond the genetic sequence itself, revealing novel mechanisms underlying disease. Epigenetic changes - such as modifications in DNA methylation, chromatin structure, and non-coding RNA function - are now recognized as key molecular determinants of atherosclerosis. These observations have created a foundational paradigm that environment, genetics, and epigenetic mechanisms influence risk through a highly complex interaction regulating cellular phenotype, pathology, and disease progression. In this review, we explore the mechanisms by which environmental exposures influence the epigenome and contribute to the regulation of atherosclerotic disease. Additionally, we examine the transgenerational epigenetic effects of these exposures on disease risk. Advancing our understanding of these mechanisms is essential for informing public health strategies aimed at mitigating harmful environmental exposures and reducing the global burden of cardiovascular disease.

The Fetal Effect of Maternal Caffeine Consumption During Pregnancy-A Review

Caffeine is commonly used to excess by the general public, and most pregnant women drink caffeine on a daily basis, which can become a habit. Maternal caffeine intake during pregnancy is associated with severe gestational outcomes. Due to its lipophilic nature, caffeine can cross the blood-brain barrier, placental barrier, and even amniotic fluid. It can be found in substantive amounts in breast milk and semen. There has been a reported drop in neonatal anthropometric measurements with increased caffeine consumption in some cohort studies. This narrative review using literature titles and abstracts from the electronic databases of PubMed, Embase, and Scopus investigates the data linking maternal caffeine use to unfavorable pregnancy outcomes. It also evaluates the validity of the recommendations made by health professionals on caffeine consumption by mothers from the available literature. The results of our comprehensive literature search of case-control studies, cohort studies, randomized control trials, and meta-analyses, imply that caffeine use during pregnancy is linked to miscarriage, stillbirth, low birth weight, and babies that are small for gestational age. It was also found that there may be effects on the neurodevelopment of the child and links to obesity and acute leukemia. These effects can even be seen at doses well below the daily advised limit of 200 mg. The genetic variations in caffeine metabolism and epigenetic changes may play a role in the differential response to caffeine doses. It is crucial that women obtain solid, evidence-based guidance regarding the possible risks associated with caffeine.

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.

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.

Parkinson's disease-associated alterations in DNA methylation and hydroxymethylation in human brain

Epigenetic mechanisms are mediators of interactions between aging, genetics, and environmental factors in sporadic Parkinson's disease (PD). Multiple studies have explored the DNA modifications in PD, but few focus on 5-hydroxymethylcytosine (5-hmC), which is important in the central nervous system and sensitive to environmental exposures. To date, studies have not differentiated between 5-methylcytosine (5-mC) and 5-hmC or have analyzed them separately. In this study, we modeled paired 5-mC and 5-hmC data simultaneously. We identified 108 cytosines with significant PD-associated shifts between these marks in an enriched neuronal population from PD postmortem parietal cortex, within 83 genes and 34 enhancers associated with 67 genes. These data potentially link epigenetic regulation of genes related to LRRK2 and endolysosomal sort (RAB32 and AGAP1), and genes involved in neuroinflammation, the inflammasome, and neurodevelopment with early changes in PD and suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes not captured by standard methods.

Integrated analysis of methylome and transcriptome responses to exercise training in children with overweight/obesity

We examined the effects of a 20-wk exercise intervention on whole blood genome-wide DNA methylation signature and its association with the exercise-induced changes in gene expression profiles in boys and girls with overweight/obesity (OW/OB). Twenty-three children (10.05 ± 1.39 yr, 56% girls) with OW/OB were randomized to either a 20-wk exercise intervention [exercise group (EG); n = 10; 4 boys/6 girls] or to usual lifestyle [control group (CG); n = 13; 6 boys/7 girls]. Whole blood genome-wide methylome (CpG sites) analysis using Infinium Methylation EPIC array and transcriptome analysis using RNA-seq (STRT2 protocol) were performed. Exercise-induced modifications in DNA methylation at 485 and 386 CpGs sites in boys and girls, respectively. These CpG sites are mapped to loci enriched in distinct gene pathways related to metabolic diseases, fatty acid metabolism, and immune function. In boys, changes in the DNA methylation of 87 CpG sites (18% of the 485 CpGs sites altered by exercise) were associated with changes in the gene expression levels of 51 genes also regulated by exercise. Among girls, changes in DNA methylation at 46 CpG sites (12% of the initial 386 significant CpGs) were associated with changes in the expression levels of 30 exercise-affected genes. Genes affected by exercise that were associated with DNA methylation are related to obesity, metabolic syndrome, and inflammation. Multiomics analysis of whole blood samples from children with OW/OB suggests that gene expression response to exercise may be modulated by DNA methylation and involve gene pathways related to metabolism and immune functions.NEW & NOTEWORTHY This study pioneers the exploration into the effects of exercise on whole blood genome-wide DNA methylation patterns and its association with changes in transcriptome profiles in children with overweight/obesity. Exercise potentially impacts molecular pathways involved in metabolism and immune functions in children with overweight/obesity (sex-specific responses) through the modification of epigenetic and transcriptomic profiles. Our preliminary results provide initial steps to understand better the molecular mechanisms underlying cardiometabolic benefits of exercise in children with overweight/obesity.

Embryonic temperature influences transcriptomic and methylation profiles in the liver of juvenile largemouth bass

Understanding the impacts of environmental conditions at early life stages on phenotypes and physiological responses to thermal variability at later stages is crucial for elucidating adaptive strategies in fish species. This study investigated the lasting effects of embryonic temperature on the growth performance, transcriptomic profiles, and CpG methylation status of juvenile largemouth bass (Micropterus salmoides) under normal and heat stress (HS) conditions. Embryos were incubated at three temperatures (22 °C, 25 °C, and 28 °C), reared at a constant 25 °C for three months, and subjected to acute HS at 37 °C. Liver samples were collected before and after HS for mRNA sequencing and reduced representation bisulfite sequencing. Significant differences in body size, body weight, condition factor, and hepatosomatic index were observed among groups. Fish hatched at 28 °C displayed a significantly higher standard length and body weight and lower hepatosomatic index than those hatched at lower temperatures. PCA analysis and Venn diagrams based on transcriptomes revealed transcriptomic response to HS differed at 28 °C while 22 and 25 °C were similar. Heat shock protein genes followed a similar trend. Epigenetic analyses revealed distinct CpG methylation patterns across incubation groups, while DNA methylation barely contributes to transcriptional differences. Under HS, different incubation groups exhibit various DNA methylation alterations. The "Neuroactive ligand-receptor interaction" pathway appeared to play an important role in the response to HS, suggesting a potential involvement of epigenetic regulation. Additionally, the atrnl1 gene may be involved in a DNA methylation-mediated regulatory mechanism in response to HS.

Epigenetic regulation in coronary artery disease: from mechanisms to emerging therapies

Atherosclerosis, the primary cause of coronary artery disease (CAD), remains a leading global cause of mortality. It is characterized by the accumulation of cholesterol-rich plaques and inflammation, which narrow the coronary arteries and increase the risk of rupture. To elucidate this complex biological process and improve therapeutic strategies, CAD has been extensively explored from an epigenetic perspective over the past two decades. Epigenetics is a field investigating heritable alterations in gene expression without DNA sequence changes, such as DNA methylation, histone modifications, and non-coding RNAs. Increasing evidence has indicated that the development of CAD is significantly influenced by epigenetic changes. Meanwhile, the impact of epigenetics in CAD is now transitioning from pathophysiology to therapeutics. Focusing on the key epigenetic enzymes and their target genes will help to facilitate the diagnosis and treatment of CAD. This review synthesizes novel epigenetic insights into CAD, addressing the pathological processes, key molecular mechanisms, and potential biomarkers. Furthermore, we discuss emerging therapeutic strategies targeting epigenetic pathways. By focusing on pivotal enzymes and their associated genes, this work aims to advance CAD diagnostics and interventions.

Histone Modifications and DNA Methylation in Psoriasis: A Cellular Perspective

In recent years, epigenetic modifications have attracted significant attention due to their unique regulatory mechanisms and profound biological implications. Acting as a bridge between environmental stimuli and changes in gene activity, they reshape gene expression patterns, providing organisms with regulatory mechanisms to respond to environmental changes. A growing body of evidence indicates that epigenetic regulation plays a crucial role in the pathogenesis and progression of psoriasis. A deeper understanding of these epigenetic mechanisms not only helps unveil the molecular mechanisms underlying the initiation and progression of psoriasis but may also provide new insights into diagnostic and therapeutic strategies. Given the unique roles and significant contributions of various cell types involved in the process of psoriasis, a thorough analysis of specific epigenetic patterns in different cell types becomes a key entry point for elucidating the mechanisms of disease development. Although epigenetic modifications encompass multiple complex layers, this review will focus on histone modifications and DNA methylation, describing how they function in different cell types and subsequently impact the pathophysiological processes of psoriasis. Finally, we will summarize the current problems in research concerning histone modifications and DNA methylation in psoriasis and discuss the clinical application prospects and challenges of targeting epigenetic modifications as therapeutic strategies for psoriasis.

Acquired sperm hypomethylation by gestational arsenic exposure is re-established in both the paternal and maternal genomes of post-epigenetic reprogramming embryos

BACKGROUND

DNA methylation plays a crucial role in mammalian development. While methylome changes acquired in the parental genomes are believed to be erased by epigenetic reprogramming, accumulating evidence suggests that methylome changes in sperm caused by environmental factors are involved in the disease phenotypes of the offspring. These findings imply that acquired sperm methylome changes are transferred to the embryo after epigenetic reprogramming. However, our understanding of this process remains incomplete. Our previous study showed that arsenic exposure of F0 pregnant mice paternally increased tumor incidence in F2 offspring. The sperm methylome of arsenic-exposed F1 males exhibited characteristic features, including enrichment of hypomethylated cytosines at the promoters of retrotransposons LINEs and LTRs. Hypomethylation of retrotransposons is potentially detrimental. Determining whether these hypomethylation changes in sperm are transferred to the embryo is important in confirming the molecular pathway of intergenerational transmission of paternal effects of arsenic exposure.

RESULTS

We investigated the methylome of F2 male embryos after epigenetic reprogramming by reduced representation bisulfite sequencing (RRBS) and allele-specific analysis. To do so, embryos were obtained by crossing control or gestationally arsenic-exposed F1 males (C3H/HeN strain) with control females (C57BL/6 strain). The results revealed that the methylome of F2 embryos in the arsenic group was globally hypomethylated and enriched for hypomethylated cytosines in certain genomic regions, including LTR and LINE, as observed in F1 sperm of the arsenic group. Unexpectedly, the characteristic methylome features were detected not only in the paternal genome but also in the maternal genome of embryos. Furthermore, these methylation changes were found to rarely occur at the same positions between F1 sperm and F2 embryos.

CONCLUSIONS

The results of this study revealed that the characteristics of arsenic-induced methylome changes in F1 sperm are reproduced in both the paternal and maternal genomes of post-epigenetic reprogramming embryos. Furthermore, the results suggest that this re-establishment is achieved in collaboration with other factors that mediate region-specific methylation changes. These results also highlight the possibility that arsenic-induced sperm methylome changes could contribute to the development of disease predisposition in offspring.

Epigenetic Control of Redox Pathways in Cancer Progression

Significance: Growing evidence indicates the importance of redox reactions homeostasis, mediated predominantly by reactive oxygen species (ROS) in influencing the development, differentiation, progression, metastasis, programmed cell death, tumor microenvironment, and therapeutic resistance of cancer. Therefore, reviewing the ROS-linked epigenetic changes in cancer is fundamental to understanding the progression and prevention of cancer. Recent Advances: We review in depth the molecular mechanisms involved in ROS-mediated epigenetic changes that lead to alteration of gene expression by altering DNA, modifying histones, and remodeling chromatin and noncoding RNA. Critical Issues: In cancerous cells, alterations of the gene-expression regulatory elements could be generated by the virtue of imbalance in tumor microenvironment. Various oxidizing agents and mitochondrial electron transport chain are the major pathways that generate ROS. ROS plays a key role in carcinogenesis by activating pro-inflammatory signaling pathways and DNA damage. This loss of ROS-mediated epigenetic regulation of the signaling pathways may promote tumorigenesis. We address all such aspects in this review. Future Directions: Developments in this growing field of epigenetics are expected to contribute to further our understanding of human health and diseases such as cancer and to test the clinical applications of redox-based therapy. Recent studies of the cancer-epigenetic landscape have revealed pervasive deregulation of the epigenetic factors in cancer. Thus, the study of interaction between ROS and epigenetic factors in cancer holds a great promise in the development of effective and targeted treatment modalities. Antioxid. Redox Signal. 00, 000-000.

A tale of two strands: Decoding chromatin replication through strand-specific sequencing

DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells.

Prostate cancer epigenetics - from pathophysiology to clinical application

Prostate cancer is a multifactorial disease influenced by various molecular features. Over the past decades, epigenetics, which is the study of changes in gene expression without altering the DNA sequence, has been recognized as a major driver of this disease. In the past 50 years, advancements in technological tools to characterize the epigenome have highlighted crucial roles of epigenetic mechanisms throughout the entire spectrum of prostate cancer, from initiation to progression, including localized disease, metastatic dissemination, castration resistance and neuroendocrine transdifferentiation. Substantial advances in the understanding of epigenetic mechanisms in the pathophysiology of prostate cancer have been carried out, but translating preclinical achievements into clinical practice remains challenging. Ongoing research and biomarker-oriented clinical trials are expected to increase the likelihood of successfully integrating epigenetics into prostate cancer clinical management.

Epigenetic drug screening identifies enzyme inhibitors A-196 and TMP-269 as novel regulators of sprouting angiogenesis

Epigenetic therapy has gained interest in treating cardiovascular diseases, but preclinical studies often encounter challenges with cell-type-specific effects or batch-to-batch variation, which have limited identification of novel drug candidates targeting angiogenesis. To address these limitations and improve the reproducibility of epigenetic drug screening, we redesigned a 3D in vitro fibrin bead assay to utilize immortalized human aortic endothelial cells (TeloHAECs) and screened a focused compound library with 105 agents. Compared to the established model using primary human umbilical vein endothelial cells, TeloHAECs needed a higher-density fibrin gel for optimal sprouting, successfully forming sprouts under both normoxic and hypoxic cell culture conditions. We identified two epigenetic enzyme inhibitors as novel regulators of sprouting angiogenesis: A196, a selective SUV4-20H1/H2 inhibitor, demonstrated pro-angiogenic effects through increased H4K20me1 levels and upregulation of cell cycle associated genes, including MCM2 and CDK4. In contrast TMP-269, a selective class IIa HDAC inhibitor, exhibited anti-angiogenic effects by downregulating angiogenesis-related proteins and upregulating pro-inflammatory signaling. These findings highlight the suitability of the modified TeloHAEC fibrin bead assay for drug screening purposes and reveal both pro-angiogenic and anti-angiogenic drug candidates with therapeutic potential.

Epigenetics in Skin Homeostasis and Ageing

The skin, the largest organ of the human body, plays numerous essential roles, including protection against environmental hazards and the regulation of body temperature. The processes of skin homeostasis and ageing are complex and influenced by many factors, with epigenetic mechanisms being particularly significant. Epigenetics refers to the regulation of gene expression without altering the underlying DNA sequence. The dynamic nature of the skin, characterized by constant cellular turnover and responsiveness to environmental stimuli, requires precise gene activity control. This control is largely mediated by epigenetic modifications such as DNA methylation, histone modification, and regulation by non-coding RNAs. The present review endeavours to provide a comprehensive exploration and elucidation of the role of epigenetic mechanisms in regulating skin homeostasis and ageing. By integrating our current knowledge of epigenetic modifications with the latest advancements in dermatological research, we can gain a deeper comprehension of the complex regulatory networks that govern skin biology. Understanding these mechanisms also presents promising avenues for therapeutic interventions aimed at improving skin health and mitigating age-related skin conditions.

Investigating the origins of the mutational signatures in cancer

Most of the risk factors associated with chronic and complex diseases, such as cancer, stem from exogenous and endogenous exposures experienced throughout an individual's life, collectively known as the exposome. These exposures can modify DNA, which can subsequently lead to the somatic mutations found in all normal and tumor tissues. Understanding the precise origins of specific somatic mutations has been challenging due to multitude of DNA adducts (i.e. the DNA adductome) and their diverse positions within the genome. Thus far, this limitation has prevented researchers from precisely linking exposures to DNA adducts and DNA adducts to subsequent mutational outcomes. Indeed, many common mutations observed in human cancers appear to originate from error-prone endogenous processes. Consequently, it remains unclear whether these mutations result from exposure-induced DNA adducts, or arise indirectly from endogenous processes or are a combination of both. In this review, we summarize approaches that aim to bridge our understanding of the mechanism by which exposure leads to DNA damage and then to mutation and highlight some of the remaining challenges and shortcomings to fully supporting this paradigm. We emphasize the need to integrate cellular DNA adductomics, long read-based mapping, single-molecule duplex sequencing of native DNA molecules and advanced computational analysis. This proposed holistic approach aims to unveil the causal connections between key DNA modifications and the mutational landscape, whether they originate from external exposures, internal processes or a combination of both, thereby addressing key questions in cancer biology.

The comprehensive assessment of epigenetics changes during skin development

Epigenetic regulation is critical to multiple physiological and pathological processes. However, little is known regarding the epigenetic changes during neonatal skin development and skin aging, and in response to ultraviolet (UV) exposure. The transcriptomes of human skin samples from different ages or irradiated with different types and doses of UV light were analyzed using R (version 4.0.3) software. The epigenetic landscape of the skin, including histone modifications, genetic imprinting and m6A modification, which are mainly involved in collagen formation, extracellular matrix organization, immune function and keratinization, underwent significant changes during neonatal to adult development. Epigenetic effectors such as IGF2BP2, GATA2, GATA3, CPA4 and CDK1 were significantly correlated with extracellular matrix organization, and VEGFA, CDK1 and PRKCB with skin immune function. The m6A readers such as IGF2BP2, IGF2BP3, HNRNPA2B1 and EIF3G showed significant correlation with extracellular matrix organization, metabolism, or antigen processing and presentation. Small doses of UV exposure only induced changes in the expression levels of some epigenetic effectors, without any significant effect on the overall epigenetic landscape. However, the minimal erythema dose of UV exposure altered multiple epigenetic effectors regulating extracellular matrix organization, cell-matrix adhesion, innate immune response, mitochondrial function and mRNA processing. In addition, epigenetic changes following UV exposure were more pronounced in the elderly skin compared to the younger skin. In conclusion, histone modifications, genetic imprinting and m6A modification play critical roles during skin development, and a large dose of UV exposure can significantly change the expression of multiple epigenetic effectors.

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.

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.