Epigenetics and the environment: emerging patterns and implications

Understanding the peroxisome proliferator-activated receptor gamma (PPAR-γ) role in periodontitis and diabetes mellitus: A molecular perspective

Periodontitis and Type 2 Diabetes Mellitus (T2DM) are chronic conditions with dysregulated immune responses. Periodontitis involves immune dysfunction and dysbiotic biofilms, leading to tissue destruction. T2DM is marked by insulin resistance and systemic inflammation, driving metabolic and tissue damage. Both conditions share activation of key pathways, including Nuclear Factor Kappa B (NF-κB), Activator Protein-1 (AP-1), and Signal Transducer and Activator of Transcription (STAT) proteins, reinforcing an inflammatory feedback loop. This review highlights the role of Peroxisome Proliferator-Activated Receptor Gamma (PPAR-γ), a transcription factor central to lipid and glucose metabolism, adipogenesis, and immune regulation. PPAR-γ activation has been shown to suppress inflammatory mediators such as Tumor Necrosis Factor Alpha (TNF-α) and Interleukin 6 (IL-6) through the inhibition of NF-κB, AP-1, and STAT pathways, thereby potentially disrupting the inflammatory-metabolic cycle that drives both diseases. PPAR-γ agonists, including thiazolidinediones (TZDs) and endogenous ligands such as 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2), show promise in reducing inflammation and improving insulin sensitivity, but they are limited by adverse effects. Therapies, including Selective Peroxisome Proliferator-Activated Receptor Modulators (SPPARMs), have been developed to offer a more targeted approach, allowing for selective modulation of PPAR-γ activity to retain its anti-inflammatory benefits while minimizing their side effects. By integrating insights into PPAR-γ's molecular mechanisms, this review underscores its therapeutic potential in mitigating inflammation and enhancing metabolic control.

Genetics of Anorexia Nervosa: Translation to Future Personalized Therapies

Anorexia nervosa (AN) is a debilitating and often refractory eating disorder that is unique among psychiatric disorders insofar as nutrition is key to recovery. Treatment options and efficacy are limited with no approved medications for AN. Genetic studies are clarifying the etiology of AN, with the goal of eventually informing the development of innovative personalized pharmacologic, nutritional, microbial, and behavioral interventions. We present the current state of genome-wide and epigenome-wide association studies, gut microbiome research, and functional genomics investigations and discuss translating this knowledge into clinical practice.

The immune system in Hashimoto's thyroiditis: Updating the current state of knowledge on potential therapies and animal model construction

Hashimoto's thyroiditis (HT) is one of the most prevalent endocrine disorders worldwide, and it can occur in people of all ages, including children. HT has a multifactorial pathogenesis and develops after a combination of gene regulation, environmental modifiers, and infection triggers. Various coamplifying feedback chronic inflammatory systems are involved in immune mechanisms, including oxidative stress, lymphocyte infiltration, and thyroid cell death. Furthermore, there is no effective treatment for HT at their roots. Thus, this review systematically summarizes and updates the existing etiology and pathogenesis, potential malignant transformation, emerging therapeutic drugs and animal model construction, making it more convenient for researchers to obtain effective information about HT and better explore potential strategies for short-term treatment of the disease.

The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms

So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a "fit" between donor and acceptor proteomes and structures. "Fitting" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) "Blending" or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's "gemmules" to "stirps", cytoplasmic and "plasmon" inheritance, "rhizene agency", "communicology", "transdisciplinary membranology" to up to Kirschner's "facilitated variation".

Rapid Neural DNA Methylation Responses to Predation Stress in Trinidadian Guppies

DNA methylation (DNAm) is a well-studied epigenetic mechanism implicated in environmentally induced phenotypes and phenotypic plasticity. However, few studies investigate the timescale of DNAm shifts. Thus, it is uncertain whether DNAm can change on timescales relevant for rapid phenotypic shifts, such as during the expression of short-term behavioural plasticity. DNAm could be especially reactive in the brain, potentially increasing its relevance for behavioural plasticity. Most research investigating neural changes in methylation has been conducted in mammalian systems, on isolated individuals, and using stressors that are less ecologically relevant, reducing their generalisability to other natural systems. We exposed pairs of male and female Trinidadian guppies (Poecilia reticulata) to alarm cue, conspecific skin extract that reliably induces anti-predator behaviour, or a control cue. Whole-genome bisulphite sequencing on whole brains at various time points following cue exposure (0.5, 1, 4, 24, and 72 h) allowed us to uncover the timescale of neural DNAm responses. Males and females both showed rapid shifts in DNAm in as little as 0.5 h. However, males and females differed in the time course of their responses: both sexes showed a peak in the number of loci showing significant responses at 4 h, but males showed an additional peak at 72 h. We suggest that this finding could be due to the differing longer-term plastic responses between the sexes. This study shows that DNAm can be rapidly induced by an ecologically relevant stressor in fish and suggests that DNAm could be involved in short-term behavioural plasticity.

DNA methylation in adipocyte differentiation of porcine mesenchymal stem cells and the impact of the donor metabolic type

The impact of metabolic donor mesenchymal stem cells (MSCs) on DNA methylation, a critical epigenetic mechanism, significantly regulates adipogenesis. In this study, we investigated epigenetic changes during differentiation of synovial MSCs (SMSCs) from two pig breeds differing in metabolic performance (German Landrace (DL) and Angeln Saddleback (AS)). Stimulation of SMSCs to differentiate into adipocytes in vitro revealed several differentially methylated loci and regions, particularly on gene promoter regions, at day 7 and 14. AS breeds, known for higher fat deposition, exhibited more hypermethylation compared to DL. Furthermore, we utilized differentially methylated regions associated with the adipogenic process and breed, especially those in promoter regions, for predicting transcription factor motifs. This study provides insights into the DNA methylation landscape during adipogenesis in pigs of different metabolic types, revealing its role in regulating cell fate and donor memory retention in culture.

Advancing translational exposomics: bridging genome, exposome and personalized medicine

Understanding the interplay between genetic predisposition and environmental and lifestyle exposures is essential for advancing precision medicine and public health. The exposome, defined as the sum of all environmental exposures an individual encounters throughout their lifetime, complements genomic data by elucidating how external and internal exposure factors influence health outcomes. This treatise highlights the emerging discipline of translational exposomics that integrates exposomics and genomics, offering a comprehensive approach to decipher the complex relationships between environmental and lifestyle exposures, genetic variability, and disease phenotypes. We highlight cutting-edge methodologies, including multi-omics technologies, exposome-wide association studies (EWAS), physiology-based biokinetic modeling, and advanced bioinformatics approaches. These tools enable precise characterization of both the external and the internal exposome, facilitating the identification of biomarkers, exposure-response relationships, and disease prediction and mechanisms. We also consider the importance of addressing socio-economic, demographic, and gender disparities in environmental health research. We emphasize how exposome data can contextualize genomic variation and enhance causal inference, especially in studies of vulnerable populations and complex diseases. By showcasing concrete examples and proposing integrative platforms for translational exposomics, this work underscores the critical need to bridge genomics and exposomics to enable precision prevention, risk stratification, and public health decision-making. This integrative approach offers a new paradigm for understanding health and disease beyond genetics alone.

REDOX Imbalance and Oxidative Stress in the Intervertebral Disc: The Effect of Mechanical Stress and Cigarette Smoking on ER Stress and Mitochondrial Dysfunction

Low back pain is a widespread condition that significantly impacts quality of life, with intervertebral disc degeneration (IDD) being a major contributing factor. However, the underlying mechanisms of IDD remain poorly understood, necessitating further investigation. Environmental risk factors, such as mechanical stress and cigarette smoke, elevate reactive oxygen species levels from both endogenous and exogenous sources, leading to redox imbalance and oxidative stress. The endoplasmic reticulum (ER) and mitochondria, two key organelles responsible for protein folding and energy production, respectively, are particularly vulnerable to oxidative stress. Under oxidative stress conditions, ER stress and mitochondrial dysfunction occur, resulting in unfolded protein response activation, impaired biosynthetic processes, and disruptions in the tricarboxylic acid cycle and electron transport chain, ultimately compromising energy metabolism. Prolonged and excessive ER stress can further trigger apoptosis through ER-mitochondrial crosstalk. Given the unique microenvironment of the intervertebral disc (IVD)-characterized by hypoxia, glucose starvation, and region-specific cellular heterogeneity-the differential effects of environmental stressors on distinct IVD cell populations require further investigation. This review explores the potential mechanisms through which environmental risk factors alter IVD cell activities, contributing to IDD progression, and discusses future therapeutic strategies aimed at mitigating disc degeneration.

Methionine in embryonic development: metabolism, redox homeostasis, epigenetic modification and signaling pathway

Methionine, an essential sulfur-containing amino acid, plays a critical role in methyl metabolism, folate metabolism, polyamine synthesis, redox homeostasis maintenance, epigenetic modification and signaling pathway regulation, particularly during embryonic development. Animal and human studies have increasingly documented that methionine deficiency or excess can negatively impact metabolic processes, translation, epigenetics, and signaling pathways, with ultimate detrimental effects on pregnancy outcomes. However, the underlying mechanisms by which methionine precisely regulates epigenetic modifications and affects signaling pathways remain to be elucidated. In this review, we discuss methionine and the metabolism of its metabolites, the influence of folate-mediated carbon metabolism, redox reactions, DNA and RNA methylation, and histone modifications, as well as the mammalian rapamycin complex and silent information regulator 1-MYC signaling pathway. This review also summarizes our present understanding of the contribution of methionine to these processes, and current nutritional and pharmaceutical strategies for the prevention and treatment of developmental defects in embryos.

Air Pollution and Endurance Exercise: A Systematic Review of the Potential Effects on Cardiopulmonary Health

This systematic review aimed to analyze the implications of endurance exercise in environments with certain levels of air pollution. This study was developed on the basis of the consensus of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The present review is supported by articles containing the main databases PubMed, Elsevier, and Web of Science (WoS), including scientific articles published in the last 20 years. This study highlights that exposure to air pollution during endurance activities, such as cycling and outdoor running, significantly affects cardiopulmonary health. In conclusion, while physical exercise in environments with high air pollution presents significant risks to cardiopulmonary health, implementing preventive measures and adopting public policies are crucial to minimizing these impacts and promoting safe exercise practices. Likewise, on the basis of these results, it is possible to motivate the creation of safe and natural spaces for sports practice.

Effects of Ionizing Radiation on DNA Methylation Patterns and Their Potential as Biomarkers

DNA methylation is a common endogenous chemical modification in eukaryotic DNA, primarily involving the covalent attachment of a methyl group to the fifth carbon of cytosine residues, leading to the formation of 5-methylcytosine (5mC). This epigenetic modification plays a crucial role in gene expression regulation and genomic stability maintenance in eukaryotic systems. Ionizing radiation (IR) has been shown to induce changes in global DNA methylation patterns, which exhibit significant temporal stability. This stability makes DNA methylation profiles promising candidates for radiation-specific biomarkers. This review systematically examines the impact of IR on genome-wide DNA methylation landscapes and evaluates their potential as molecular indicators of radiation exposure. Advancing the knowledge of radiation-induced epigenetic modifications in radiobiology contributes to a deeper understanding of IR-driven epigenetic reprogramming and facilitates the development of novel molecular tools for the early detection and quantitative risk assessment of radiation exposure.

Investigating the epigenetic landscape of symptomatic disk degeneration: a case study

Introduction

This study investigates the epigenetic landscape underlying painful intervertebral disk (IVD) degeneration in a single subject with a history of low back pain (LBP). Intervertebral disk degeneration is associated with LBP in some individuals; however, there is often a discrepancy between degeneration and pain. We hypothesize that DNA methylation, an epigenetic mechanism previously linked to discogenic LBP, is dysregulated in symptomatic vs asymptomatic IVDs.

Objectives

Identify differentially methylated genes and pathways in symptomatic vs asymptomatic IVDs.

Methods

Three lumbar IVDs with similar degeneration severity were tested prior to surgery by discography to identify symptomatic IVDs. Methylation analysis was performed on ∼935,000 cytosine guanine dinucleotide sites on nucleus pulposus DNA. We explored differential methylation and pathway enrichment on cytosine guanine dinucleotide sites located within the promoter regions of genes.

Results

Two IVDs (L3/L4 and L4/L5) evoked pain ratings of 10/10 and 8/10, one IVD (L5/S1) scored 0/10. DNA methylation differed between symptomatic and asymptomatic IVDs. Several identified genes have roles in extracellular matrix remodeling. Other differentially methylated genes were related to immunomodulation and ion channel function. Finally, several long noncoding RNA genes were identified, encouraging further exploration into these regulatory molecules. Enriched pathways were associated with immune response, hormonal regulation, nervous system development, and musculoskeletal development and remodeling.

Conclusion

This case study provides a promising list of candidate genes for therapeutic development for discogenic LBP and suggests a role for DNA methylation in the development of symptomatic vs asymptomatic IVD degeneration, calling for further research to validate and expand these findings.

Impaired angiogenesis in gestational diabetes is linked to succinate/SUCNR1 axis dysregulation in late gestation

Recent research has highlighted the significance of succinate and its receptor in gestational diabetes (GDM) pathogenesis. However, a clear interconnection between placenta metabolism, succinate levels, SUCNR1 signalling and pregnancy pathologies remains elusive. Here, we set out to investigate the potential role of succinate on labour and placental mechanisms by combining clinical and functional experimental data at the same time as exploring the specific SUCNR1-mediated effects of succinate on placenta vascularization, addressing its specific agonist actions. According to our data, succinate levels vary throughout pregnancy and postpartum, with a natural increase during the peripartum period. We also show that SUCNR1 activation in the umbilical cord endothelium promotes angiogenesis under normal conditions. However, in GDM, excessive succinate and impaired SUCNR1 function may weaken this angiogenic response. In conclusion, the present study underlines succinate as an emerging signalling molecule in the placenta, regulating labour and placental processes. The reduced sensitivity of the succinate/SUCNR1 pathway in the GDM environment may serve as a protective physiological mechanism or could have a pathogenic effect. KEY POINTS: Succinate levels increase at delivery in maternal and fetal circulation. Gestational diabetes (GDM) induces succinate accumulation and SUCNR1 downregulation in umbilical cords. GDM compromises angiogenic gene profile modulation by SUCNR1 in umbilical cord endothelium. SUCNR1 activation stimulates sprouting and tube-forming capacity of human umbilical vein endothelial cells from healthy, but not GDM pregnancies.

The relationship between social adversity, micro-RNA expression and post-traumatic stress in a prospective, community-based cohort

Epigenetics influence and are influenced by the impact of social and environmental challenges on biological outcomes. Therefore, pinpointing epigenetic factors associated with social adversity and traumatic stress enables understanding of the mechanisms underlying vulnerability and resilience. We hypothesized that micro-RNAs (miRNAs) expression may be associated with post-traumatic stress disorder symptom severity (i.e., PTSS) following exposure to social adversity. To test this hypothesis, we leveraged blood-derived RNA samples (n=632) and social adversity data from 483 unique participants in the Detroit Neighborhood Health Study, a community-based, prospective cohort of predominantly African Americans. Results identified 86 miRNAs that are associated with social adversities (financial difficulties, perceived discrimination, cumulative trauma) and PTSS. These miRNAs are primarily involved in the immune response, brain and neural function, as well as cell cycle and differentiation, and 22(25%) have previously been associated with conditions related to PTSD, including traumatic brain injury and stress response. Our findings offer a fresh perspective on understanding the epigenetic role of miRNA in the interaction between social adversity and traumatic stress.

Implications of petrochemical exposure and epigenetic alterations on human health

The petrochemical industry and automobiles contribute significantly to hazardous waste, which contains a broad array of organic and inorganic compounds posing serious health risks. Identifying biomarkers of exposure and creating predictive models for toxicity characterization necessitate a thorough understanding of the underlying epigenetic mechanisms. The development of disease is intricately linked to epigenetic processes, such as DNA methylation, histone modifications, and microRNA (mi-RNA) regulation, which mediate gene-environment interactions. While previous studies have investigated these alterations as markers for petrochemical-induced changes, there is still a need for deeper exploration in this area, with particular emphasis on advanced gene-editing technologies. This review highlights the specific epigenetic processes, especially gene-specific DNA methylation changes, associated with prolonged petrochemical exposure. Notably, the demethylation of long interspersed nuclear element 1 (LINE-1), Alu elements, and forkhead box P3 (FOXP3), as well as hypermethylation of interferon gamma (IFN-γ) and hypomethylation of interleukin-4 (IL-4) promoter regions, are discussed. These alterations in DNA methylation patterns serve as valuable biomarkers, potentially offering insights into early detection and personalized treatment options for diseases caused by long-term exposure to petrochemicals. Furthermore, CRISPR-based gene editing techniques, while underexplored, present a promising approach for correcting petrochemical-induced mutations. In addition, AI-driven radiomics holds promise for early disease detection, though it is currently limited by its lack of integration with multi-omics data. In conclusion, it is crucial to refine disease modelling, develop comprehensive risk assessment models, and innovate targeted therapeutic strategies. Future research should focus on enhancing exposure evaluation, incorporating computational tools to analyze molecular changes, and improving our understanding of how these modifications influence disease prevention and treatment.

Rationale and design of the Dog Aging Project precision cohort: a multi-omic resource for longitudinal research in geroscience

A significant challenge in multi-omic geroscience research is the collection of high quality, fit-for-purpose biospecimens from a diverse and well-characterized study population with sufficient sample size to detect age-related changes in physiological biomarkers. The Dog Aging Project designed the precision cohort to study the mechanisms underlying age-related change in the metabolome, microbiome, and epigenome in companion dogs, an emerging model system for translational geroscience research. One thousand dog-owner pairs were recruited into cohort strata based on life stage, sex, size, and geography. We designed and built a novel implementation of the REDCap electronic data capture system to manage study participants, logistics, and biospecimen and survey data collection in a secure online platform. In collaboration with primary care veterinarians, we collected and processed blood, urine, fecal, and hair samples from 976 dogs. The resulting data include complete blood count, chemistry profile, immunophenotyping by flow cytometry, metabolite quantification, fecal microbiome characterization, epigenomic profile, urinalysis, and associated metadata characterizing sample conditions at collection and during lab processing. The project, which has already begun collecting second- and third-year samples from precision cohort dogs, demonstrates that scientifically useful biospecimens can be collected from a geographically dispersed population through collaboration with private veterinary clinics and downstream labs. The data collection infrastructure developed for the precision cohort can be leveraged for future studies. Most important, the Dog Aging Project is an open data project. We encourage researchers around the world to apply for data access and utilize this rich, constantly growing dataset in their own work.

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.

Can nutraceuticals counteract the detrimental effects of the environment on male fertility? A parallel systematic review and expert opinion

INTRODUCTION

Male fertility relies on a complex physiology that may be negatively influenced by lifestyle, diet, and environment. The beneficial effect of nutraceuticals on male fertility is a debated claim. The aim of this study was to assess if the positive effect of nutraceuticals can counteract the negative effects of the environment on male fertility.

EVIDENCE ACQUISITION

PubMed®/MEDLINE®, Embase and Cochrane Database were searched (September-October 2023), along with crosschecking of references and search for ongoing studies of the effects of the environment and nutraceuticals on male fertility, in accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA).

EVIDENCE SYNTHESIS

Several environmental factors such as microplastic and other endocrine-disrupting chemicals and climate changes may affect the sperm quality in terms of reduction of sperm count number, mobility and altered morphology and thereby reduce male fertility. On the other hand, new evidence demonstrates that a balanced diet rich in antioxidants and essential nutrients, together with minimized exposure to environmental toxins, may improve male fertility and reproductive health. Several nutraceutical compounds proved a protective role against negative environmental effects on male fertility.

CONCLUSIONS

Available evidence confirms that the environment may negatively impact male fertility, and this impact is estimated to rise in the forthcoming years. On the other hand, new data indicate that nutraceuticals may have a protective role against the negative impact of environmental factors on male fertility. The need for future studies to monitor and explore these aspects of men's health cannot be underestimated.

Sex-Specific Methylomic and Transcriptomic Responses of the Avian Pineal Gland to Unpredictable Illumination Patterns

In the production environment of chickens, exposure to unpredictable light patterns is a common painless stressor, widely used to influence growth rate and egg production efficiency. The pineal gland, a key regulator of circadian rhythms through melatonin secretion, responds to environmental light cues, and its function is modulated by epigenetic mechanisms. In this study, we investigated how the pineal gland methylome and transcriptome (including micro-RNAs) interact to respond to a rearing exposure to unpredictable illumination patterns, with a particular focus on sex differences. We conducted an integrative multi-omic analysis-including methylomic (MeDIP-seq), transcriptomic (RNA-seq), and miRNA expression profiling-on the pineal gland of Hy-Line White chickens (n = 34, 18 females, 16 males) exposed to either a standard 12:12 light-dark cycle (control) or a randomized, unpredictable light schedule from Days 3 to 24 post-hatch. Our findings reveal that unpredictable light exposure alters the pineal gland methylome and transcriptome in a sex-specific manner. However, while transcriptomic differences between sexes increased due to the stress, methylomic differences decreased, particularly on the Z chromosome. These changes were driven by females (the heterogametic sex in birds), which became more male-like in their pineal methylome after exposure to the illumination stress, leading to reduced epigenetic sexual dimorphism while maintaining differences at the gene expression level. Further, we implemented a fixed sex effect model as a biological proof of concept, identifying a network of 12 key core genes interacting with 102 other genes, all linked to circadian regulation and stress adaptation. This network of genes comprises a core regulatory framework for circadian response. Additionally, tissue-specific expression analysis and cell-type specific expression analysis revealed enrichment in brain regions critical for circadian function, including neuronal populations involved in circadian regulation and the hypothalamic-pituitary-thyroid axis. Together, these findings provide strong evidence of sex-specific epigenetic transcriptomic responses of the pineal gland upon illumination stress and offer valuable insights into the interplay of different omic levels in relation to circadian response.

Systematic review on the DNA methylation role in endometriosis: current evidence and perspectives

BACKGROUND

Endometriosis appears to have a multilayered etiology, with genetic and epigenetic factors each contributing half of the pathogenesis. The molecular processes that underlie the onset of endometriosis are yet unclear, but it is assumed that an important contributor in the etiopathology of the disease is DNA methylation.

METHODS

We conducted a systematic review of the literature regarding DNA methylation in endometriosis following PRISMA guidelines. Records were obtained from PubMed and Web of Science on May 31, 2024. Original research articles analyzing regional or genome-wide DNA methylation in patients with confirmed endometriosis (by surgery and/or histological examination) were given consideration for inclusion. Only human studies were included, and there were no restrictions on the types of tissue that was analyzed (i.e., endometrium, blood, or fetal tissue). The study selection process was run by two manual reviewers. In parallel, an adapted virtual artificial intelligence-powered reviewer operated study selection and results were compared with the manual reviewers' selection. Studies were divided into targeted (e.g., single gene or region level) and epigenome-wide association studies. For each, we extracted a list of genes studied with precise location of CpGs analyzed and the DNA methylation status according to the groups compared. Quality assessment of studies was performed following the Newcastle-Ottawa scale. Quality of evidence was graded following the Grading of Recommendations Assessment, Development and Evaluation.

RESULTS

A total of 955 studies were screened, and 70 were identified as relevant for systematic review. Our analyses displayed that endometriosis could be polyepigenetic and with alterations in specific genes implicated in major signaling pathways contributing to the disease etiopathology (cell proliferation, differentiation, and division [PI3K-Akt and Wnt-signaling pathway], cell division [MAPK pathway], cell adhesion, cell communication, developmental processes, response to hormone, apoptosis, immunity, neurogenesis, and cancer).

CONCLUSION

Our systematic review indicates that endometriosis is associated with DNA methylation modifications at specific genes involved in key endometrial biological processes, particularly in the ectopic endometrium. As DNA methylation appears to be an integral component of the pathogenesis of endometriosis, the identification of DNA methylation biomarkers would likely help better understand its causes and aggravating factors as well as potentially facilitate its diagnosis and support the development of new therapeutic approaches.

iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation

Understanding the interaction between genetic and epigenetic variation remains a challenge due to confounding environmental factors. We propose that human induced Pluripotent Stem Cells (iPSCs) are an excellent model to study the relationship between genetic and epigenetic variation while controlling for environmental factors. In this study, we have created a comprehensive resource of high-quality genomic, epigenomic, and transcriptomic data from iPSC lines and three iPSC-derived cell types (neural stem cell (NSC), motor neuron, monocyte) from three healthy donors. We find that epigenetic variation is most strongly associated with genetic variation at the iPSC stage, and that relationship weakens as epigenetic variation increases in differentiated cells. Additionally, cell type is a stronger source of epigenetic variation than genetic variation. Further, we elucidate a utility of studying epigenetic variation in iPSCs and their derivatives for identifying important loci for GWAS studies and the cell types in which they may be acting.

Epitranscriptomics in the Glioma Context: A Brief Overview

Epitranscriptomics, the study of chemical modifications in RNA, has emerged as a crucial field in cellular regulation, adding another layer to the established landscape of DNA- and histone-based epigenetics. A wide range of RNA modifications, including N6-methyladenosine, pseudouridine, and inosine, have been identified across nearly all RNA species, influencing essential processes such as transcription, splicing, RNA stability, and translation. In the context of brain tumors, particularly gliomas, specific epitranscriptomic signatures have been reported to play a role in tumorigenesis. Despite growing evidence, the biological implications of various RNA modifications remain poorly understood. This review offers an examination of the main RNA modifications, the interplay between modified and unmodified molecules, how they could contribute to glioma-like phenotypes, and the therapeutic impact of targeting these mechanisms.

Prenatal choline supplementation enhances metabolic outcomes with differential impact on DNA methylation in Wistar rat offspring and dams

Choline is an essential nutrient required for proper functioning of organs and serves as a methyl donor. In liver where choline metabolism primarily occurs, glucose homeostasis is regulated through insulin receptor substrates (IRS) 1 and 2. The objective of this research was to determine the role of prenatal choline as a modulator of metabolic health and DNA methylation in liver of offspring and dams. Pregnant Wistar rat dams were fed an AIN-93G diet and received drinking water either with supplemented 0.25% choline (w/w) as choline bitartrate or untreated control. All offspring were weaned to a high-fat diet for 12 weeks. Prenatal choline supplementation led to higher insulin sensitivity in female offspring at weaning as well as lower body weight and food intake and higher insulin sensitivity in female and male adult offspring compared to offspring from untreated dams. Higher hepatic betaine concentrations were observed in dams and female offspring of choline-supplemented dams at weaning and higher glycerophosphocholine in female and male offspring at postweaning compared to the untreated control, suggestive of sustaining different choline pathways. Hepatic gene expression of Irs2 was higher in dams at weaning and female offspring at weaning and postweaning, whereas Irs1 was lower in male offspring at postweaning. Gene-specific DNA methylation of Irs2 was lower in female offspring at postweaning and Irs1 methylation was higher in male offspring at postweaning that exhibited an inverse relationship between methylation and gene expression. In conclusion, prenatal choline supplementation contributes to improved parameters of insulin signaling but these effects varied across time and offspring sex.

Seasonal Adaptation of Mammalian Development: Effect of Early-Life Photoperiod on Reproduction, Somatic Growth, and Neurobehavioral Systems

For the survival and efficient breeding of wild-living animals, it is crucial to predict seasonal changes and prepare appropriate physiological functions and neurobehavioral mechanisms. In mammals, photoperiod serves as a reliable cue for seasonal changes in the environment, primarily transmitted by melatonin. This review focuses on the seasonal adaptation of mammalian development, specifically the effect of early-life photoperiod on reproductive, somatic, and neurobehavioral development in small- and large-sized mammals. Prediction of seasons through early-life photoperiod is particularly important for small mammals, which have relatively short longevity, to adjust their maximum growth and breeding ability in appropriate seasons during the birth year or the following round. Brain plasticity, as well as cognitive and emotional behaviors, are also highly modulated by early-life photoperiods for successful mating and spatial memory for foraging. This review first summarizes the basic knowledge and recent progress in the programming and epigenetic regulatory mechanisms of reproductive and neurobehavioral development in small mammals, including C57BL/6J mice, which cannot produce detectable amounts of melatonin. The review then focuses on the influence of perinatal environmental conditions or birth season on adult phenotypes in large livestock and humans. Studies have advanced on the concept of the developmental origins of health and disease (DOHaD). Evidence from large mammals suggests that the prediction of seasons is crucial for high-fitness functions over several years. Finally, this review discusses the association of the season of birth with life course physiology and diseases in humans, and the possible mechanisms.

Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues

Non-communicable diseases (NCDs) such as cardiovascular diseases, chronic respiratory diseases, cancers, diabetes, and mental health disorders pose a significant global health challenge, accounting for the majority of fatalities and disability-adjusted life years worldwide. These diseases arise from the complex interactions between genetic, behavioral, and environmental factors, necessitating a thorough understanding of these dynamics to identify effective diagnostic strategies and interventions. Although recent advances in multi-omics technologies have greatly enhanced our ability to explore these interactions, several challenges remain. These challenges include the inherent complexity and heterogeneity of multi-omic datasets, limitations in analytical approaches, and severe underrepresentation of non-European genetic ancestries in most omics datasets, which restricts the generalizability of findings and exacerbates health disparities. This scoping review evaluates the global landscape of multi-omics data related to NCDs from 2000 to 2024, focusing on recent advancements in multi-omics data integration, translational applications, and equity considerations. We highlight the need for standardized protocols, harmonized data-sharing policies, and advanced approaches such as artificial intelligence/machine learning to integrate multi-omics data and study gene-environment interactions. We also explore challenges and opportunities in translating insights from gene-environment (GxE) research into precision medicine strategies. We underscore the potential of global multi-omics research in advancing our understanding of NCDs and enhancing patient outcomes across diverse and underserved populations, emphasizing the need for equity and fairness-centered research and strategic investments to build local capacities in underrepresented populations and regions.

Inter- and Transgenerational Effects of In Ovo Stimulation with Bioactive Compounds on Cecal Tonsils and Cecal Mucosa Transcriptomes in a Chicken Model

Exploring how early-life nutritional interventions may impact future generations, this study examines the inter- and transgenerational effects of in ovo injection of bioactive compounds on gene expression in the cecal tonsils and cecal mucosa using a chicken model. Synbiotic PoultryStar® (Biomin) and choline were injected in ovo on the 12th day of egg incubation. Three experimental groups were established in the generation F1: (1) a control group (C) receiving 0.9% physiological saline (NaCl), (2) a synbiotic group (SYN) receiving 2 mg/embryo, and (3) a combined synbiotic and choline group (SYNCH) receiving 2 mg synbiotic and 0.25 mg choline per embryo. For the generations F2 and F3, the SYN and SYNCH groups were each divided into two subgroups: (A) those injected solely in F1 (SYNs and SYNCHs) and (B) those injected in each generation (SYNr and SYNCHr). At 21 weeks posthatching, cecal tonsil and cecal mucosa samples were collected from F1, F2, and F3 birds for transcriptomic analysis. Gene expression profiling revealed distinct intergenerational and transgenerational patterns in both tissues. In cecal tonsils, a significant transgenerational impact on gene expression was noted in the generation F3, following a drop in F2. In contrast, cecal mucosa showed more gene expression changes in F2, indicating intergenerational effects. While some effects carried into F3, they were less pronounced, except in the SYNs group, which experienced an increase compared to F2. The study highlights that transgenerational effects of epigenetic modifications are dynamic and unpredictable, with effects potentially re-emerging in later generations under certain conditions or fading or intensifying over time. This study provides valuable insights into how epigenetic nutritional stimulation during embryonic development may regulate processes in the cecal tonsils and cecal mucosa across multiple generations. Our findings provide evidence supporting the phenomenon of epigenetic dynamics in a chicken model.

Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer

Oncogenes are typically overexpressed in tumor tissues and often linked to poor prognosis. However, recent advancements in bioinformatics have revealed that many highly expressed genes in tumors are associated with better patient outcomes. These genes, which act as tumor suppressors, are referred to as "paradoxical genes." Analyzing The Cancer Genome Atlas (TCGA) confirmed the widespread presence of paradoxical genes, and KEGG analysis revealed their role in regulating tumor metabolism. Mechanistically, discrepancies between gene and protein expression-affected by pre- and post-transcriptional modifications-may drive this phenomenon. Mechanisms like upstream open reading frames and alternative splicing contribute to these inconsistencies. Many paradoxical genes modulate the tumor immune microenvironment, exerting tumor-suppressive effects. Further analysis shows that the stage- and tumor-specific expression of these genes, along with their environmental sensitivity, influence their dual roles in various signaling pathways. These findings highlight the importance of paradoxical genes in resisting tumor progression and maintaining cellular homeostasis, offering new avenues for targeted cancer therapy.

Genetics and Epigenetics of Human Pubertal Timing: The Contribution of Genes Associated With Central Precocious Puberty

Human puberty is a dynamic biological process determined by the increase in the pulsatile secretion of GnRH triggered by distinct factors not fully understood. Current knowledge reveals fine tuning between an increase in stimulatory factors and a decrease in inhibitory factors, where genetic and epigenetic factors have been indicated as key players in the regulation of puberty onset by distinct lines of evidence. Central precocious puberty (CPP) results from the premature reactivation of pulsatile secretion of GnRH. In the past decade, the identification of genetic causes of CPP has largely expanded, revealing hypothalamic regulatory factors of pubertal timing. Among them, 3 genes associated with CPP are linked to mechanisms involving DNA methylation, reinforcing the strong role of epigenetics underlying this disorder. Loss-of-function mutations in Makorin Ring-Finger Protein 3 (MKRN3) and Delta-Like Non-Canonical Notch Ligand 1 (DLK1), 2 autosomal maternally imprinted genes, have been described as relevant monogenic causes of CPP with the phenotype exclusively associated with paternal transmission. MKRN3 has proven to be a key component of the hypothalamic inhibitory input on GnRH neurons through different mechanisms. Additionally, rare heterozygous variants in the Methyl-CpG-Binding Protein 2 (MECP2), an X-linked gene that is a key factor of DNA methylation machinery, were identified in girls with sporadic CPP with or without neurodevelopmental disorders. In this mini-review, we focus on how the identification of genetic causes of CPP has revealed epigenetic regulators of human pubertal timing, summarizing the latest knowledge on the associations of puberty with MKRN3, DLK1, and MECP2.

Epigenetics in Neurodegenerative Diseases

Healthy brain functioning requires a continuous fine-tuning of gene expression, involving changes in the epigenetic landscape and 3D chromatin organization. Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD) are three multifactorial neurodegenerative diseases (NDDs) that are partially explained by genetics (gene mutations and genetic risk factors) and influenced by non-genetic factors (i.e., aging, lifestyle, and environmental conditions). Examining comprehensive studies of global and locus-specific (epi)genomic and transcriptomic alterations in human and mouse brain samples at the cell-type resolution has uncovered important phenomena associated with AD. First, DNA methylation and histone marks at promoters contribute to transcriptional dysregulation of genes that are directly implicated in AD pathogenesis (i.e., APP), neuroplasticity and cognition (i.e., PSD95), and microglial activation (i.e., TREM2). Second, the presence of AD genetic risk variants in cell-type-specific distal enhancers (i.e., BIN1 in microglia) alters transcription, presumably by disrupting associated enhancer-promoter interactions and chromatin looping. Third, epigenomic erosion is associated with widespread transcriptional disruption and cell identity loss. And fourth, aging, high cholesterol, air pollution, and pesticides have emerged as potential drivers of AD by inducing locus-specific and global epigenetic modifications that impact key AD-related pathways. Epigenetic studies in ALS/FTD also provide evidence that genetic and non-genetic factors alter gene expression profiles in neurons and astrocytes through aberrant epigenetic mechanisms. We additionally overview the recent development of potential new therapeutic strategies involving (epi)genetic editing and the use of small chromatin-modifying molecules (epidrugs).

Control of Mycobacterium tuberculosis infection in the elderly: Is there a role for epigenetic reprogramming reversal?

With the increase in the elderly population worldwide, the number of subjects suffering from tuberculosis (TB) has shown an increased prevalence in this group. Immunosenescence is essential in this phenomenon because it may reactivate the lesions and render their adaptive immunity dysfunctional. In addition, inflammation in the lungs of the elderly subjects is also dysfunctional. Although effective drugs are available, they are often tolerated inadequately, reducing adherence to the therapy and leading to therapeutic failure. Comorbidities, poor general health status, and other medications may lead to increased drug adverse reactions and reduced adherence to treatment in the elderly. Hence, older adults require an individualized approach for better outcomes. Trained immunity, which involves epigenetic reprogramming, may contribute to balancing the dysfunction of innate and adaptive immunity in older people. This review analyzes the relationship between inflammation, age, and Mycobacterium tuberculosis. Moreover, we hypothesize that immunomodulation using trained immunity activators will help reduce inflammation while enhancing antimicrobial responses in the elderly. Understanding immunomodulation's molecular and physiological effects will lead to informed decisions about TB prevention and treatment strategies uniquely designed for the elderly.

Impact of Wood Smoke Exposure on Aortic Valve Mineralization: Microvesicles as Mineral Conveyors in Patients with Coronary Stenosis

Background: Aortic valve calcification results from degenerative processes associated with several pathologies. These processes are influenced by age, chronic inflammation, and high concentrations of phosphate ions in the plasma, which contribute to induce mineralization in the aortic valve and deterioration of cardiovascular health. Environmental factors, such as wood smoke that emits harmful and carcinogenic pollutants, carbon monoxide (CO), and nitrogen oxide (NOx), as well as other reactive compounds may also be implicated. The purpose of this research was to study the impact of wood smoke on specific aortic valve characteristics, including lesion size and percentage of mineralization, in patients with aortic valve stenosis (AS). Methods: This observational study included 65 patients who underwent primary valve replacement surgery at the National Institute of Cardiology, 11 of whom were exposed to wood smoke. For each patient, approximately 0.5 cm of aortic valve tissue was collected along with a blood sample anticoagulated with sodium citrate. The valves were analyzed using scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS). Since extracellular microvesicles (MVs) may induce epigenetic changes in target cells by transferring their cargo, we also analyzed their mineral content. Results: Individuals exposed to wood smoke exhibit more extensive lesion (835 µm2) characteristics compared to those with no exposure (407.5 µm2). Interestingly, FESEM images of MVs showed the presence of minerals on their surface, thus providing evidence on their possible role in the pathophysiology of mineralization. Conclusions: Our study uniquely demonstrates imaging-based evidence of structural damage and mineralization in aortic valve tissue, with chronic wood smoke exposure emerging as a significant causative factor.

The Mitochondrial Blueprint: Unlocking Secondary Metabolite Production

Mitochondrial metabolism plays a pivotal role in regulating the synthesis of secondary metabolites, which are crucial for the survival and adaptation of organisms. These metabolites are synthesized during specific growth stages or in response to environmental stress, reflecting the organism's ability to adapt to changing conditions. Mitochondria, while primarily known for their role in energy production, directly regulate secondary metabolite biosynthesis by providing essential precursor molecules, energy, and reducing equivalents necessary for metabolic reactions. Furthermore, they indirectly influence secondary metabolism through intricate signaling pathways, including reactive oxygen species (ROS), metabolites, and redox signaling, which modulate various metabolic processes. This review explores recent advances in understanding the molecular mechanisms governing mitochondrial metabolism and their regulatory roles in secondary metabolite biosynthesis, which highlights the involvement of transcription factors, small RNAs, and post-translational mitochondrial modifications in shaping these processes. By integrating current insights, it aims to inspire future research into mitochondrial regulatory mechanisms in Arabidopsis thaliana, Solanum tuberosum, Nicotiana tabacum, and others that may enhance their secondary metabolite production. A deeper understanding of the roles of mitochondria in secondary metabolism could contribute to the development of new approaches in biotechnology applications.

DNA Imprinting and Differentially Expressed Genes in Longissimus thoracis Muscle of Bos indicus Submitted to Early Weaning Management

Background/Objectives: Early weaning management followed by energy supplementation can lead to metabolic alterations in the calf that exert long-term effects on the animal's health and performance. It is believed that the main molecular basis underlying these metabolic adaptations are epigenetic mechanisms that regulate, activate, or silence genes at different stages of development and/or in response to different environmental stimuli. However, little is known about postnatal metabolic programming in Bos indicus. Therefore, this study aimed to compare the DNA methylation profile of Nellore animals submitted to conventional and early weaning and to correlate the findings with genes differentially expressed in the Longissimus thoracis skeletal muscle of Bos indicus cattle. Methods: For this, we used Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Sequencing techniques to prospect differentially methylated genes (DMGs). Results: A total of 481 differentially methylated regions were identified, with 52% (250) being hypermethylated and 48% (231) hypomethylated. Functional enrichment analysis of 53 differentially methylated and differentially expressed genes was performed. The main enriched terms and pathways were associated with 3'-5'-cyclic adenosine monophosphate (cAMP) signaling, which presents the upregulated adenylate cyclase 3 (ADCY3) gene and significatively hypomethylated in the promoter region. Alterations in cAMP signaling are involved in numerous processes, many of them related to lipid metabolism. The relative differential expression of key genes of this pathway demonstrates the relationship between cAMP signaling and de novo lipogenesis. Conclusions: These findings suggest an important role of postnatal metabolic programming through DNA methylation mechanisms in determining fat deposition in beef.

Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat

BACKGROUND

Plants respond to environmental stimuli by altering gene transcription that is highly related with chromatin status, including histone modification, chromatin accessibility, and three-dimensional chromatin interaction. Vernalization is essential for the transition to reproductive growth for winter wheat. How wheat reshapes its chromatin features, especially chromatin interaction during vernalization, remains unknown.

RESULTS

Combinatory analysis of gene transcription and histone modifications in winter wheat under different vernalization conditions identifies 17,669 differential expressed genes and thousands of differentially enriched peaks of H3K4me3, H3K27me3, and H3K9ac. We find dynamic gene expression across the vernalization process is highly associated with H3K4me3. More importantly, the dynamic H3K4me3- and H3K9ac-associated chromatin-chromatin interactions demonstrate that vernalization leads to increased chromatin interactions and gene activation. Remarkably, spatially distant targets of master regulators like VRN1 and VRT2 are gathered together by chromatin loops to achieve efficient transcription regulation, which is designated as a "shepherd" model. Furthermore, by integrating gene regulatory network for vernalization and natural variation of flowering time, TaZNF10 is identified as a negative regulator for vernalization-related flowering time in wheat.

CONCLUSIONS

We reveal dynamic gene transcription network during vernalization and find that the spatially distant genes can be recruited together via chromatin loops associated with active histone mark thus to be more efficiently found and bound by upstream regulator. It provides new insights into understanding vernalization and response to environmental stimuli in wheat and other plants.

Application of biomechanics in tumor epigenetic research

The field of cancer research is increasingly recognizing the complex interplay between biomechanics and tumor epigenetics. Biomechanics plays a significant role in the occurrence, development, and metastasis of cancer and may exert influence by impacting the epigenetic modifications of tumors. In this review, we investigate a spectrum of biomechanical tools, including computational models, measurement instruments, and in vitro simulations. These tools not only assist in deciphering the mechanisms behind these epigenetic changes but also provide novel methods for characterizing tumors, which are significant for diagnosis and treatment. Finally, we discuss the potential of new therapies that target the biomechanical properties of the tumor microenvironment. There is hope that by altering factors such as the stiffness of the extracellular matrix or interfering with mechano-sensing pathways, we can halt tumor progression through epigenetic mechanisms. We emphasize the necessity for multidisciplinary efforts to integrate biomechanics with tumor epigenetics more comprehensively. Such collaboration is anticipated to advance therapeutic strategies and enhance our understanding of cancer biology, signaling the dawn of a new era in cancer treatment and research.

Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental villous tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated new and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n = 36) with robust partial correlation based on the top 30 hyper- and hypomethylated sites identified per cell type. To test deconvolution performance, we evaluated root mean square error in predicting principal components of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n = 368,435 sites) from 12 cell types: cytotrophoblasts (n = 18), endothelial cells (n = 19), Hofbauer cells (n = 26), stromal cells (n = 21), syncytiotrophoblasts (n = 4), six lymphocyte types (n = 36), and nucleated red blood cells (n = 11). Median cell composition was consistent with placental biology: 60.9% syncytiotrophoblast, 17.3% stromal, 8.8% endothelial, 3.7% cytotrophoblast, 3.7% Hofbauer, 1.7% nucleated red blood cells, and 1.2% neutrophils. Our expanded reference outperformed an existing reference in predicting DNAm variation (PC1, 15.4% variance explained, IQR = 21.61) with cell composition estimates (mean square error of prediction: 8.62 vs. 10.79, p-value < 0.001). This cell type reference can robustly estimate cell composition from whole placental DNAm data to detect important cell types, reveal biological mechanisms, and improve causal inference.

An update: epigenetic mechanisms underlying methamphetamine addiction

Methamphetamine (METH) is one of the most widely abused illicit drugs globally. Despite its widespread abuse, the effects of methamphetamine on the brain and the precise mechanisms underlying addiction remain poorly understood. Elucidating these biological mechanisms and developing effective treatments is of utmost importance. Researchers have adopted a multi-faceted approach, combining studies at the genetic, molecular, organ, and individual levels, to explore the epigenetic changes that methamphetamine use brings to an organism from both micro and macro perspectives. They utilize a comparative analysis of experimental animal data and clinical cases to ascertain differences and identify potential targets for translating METH addiction research from the experimental to the clinical setting. Recent studies have demonstrated that epigenetic regulation plays a pivotal role in neural mechanisms, encompassing DNA methylation, histone modifications (such as acetylation and methylation), ubiquitination, phosphorylation, and the regulation of non-coding RNA. These epigenetic factors influence an individual's susceptibility and response to methamphetamine addiction by regulating the expression of specific genes. Specifically, methamphetamine use has been observed to cause alterations in DNA methylation status, which in turn affects the expression of genes associated with neuroreward pathways, leading to alterations in brain function and structure. Furthermore, histone modifications have significant implications for the neurotoxicity associated with methamphetamine addiction. For instance, the methylation and acetylation of histone H3 modify chromatin structure, consequently influencing the transcriptional activity of genes. Non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), also play a pivotal role in methamphetamine addiction by interacting with messenger RNAs (mRNAs) and regulating gene expression. To further advance our understanding, researchers employ advanced technologies such as high-throughput sequencing, chromatin immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) to comprehensively analyze epigenetic changes in both animal models and human subjects. These technologies enable researchers to identify specific epigenetic markers associated with methamphetamine addiction and to explore their functional consequences. This article reviews the role of these epigenetic mechanisms in methamphetamine addiction and discusses their potential implications for future clinical treatment strategies, particularly in the development of drugs targeting methamphetamine addiction. By deepening our comprehension of these epigenetic regulatory mechanisms, it is anticipated that targeted therapeutic strategies may be devised to reverse the gene expression alterations associated with methamphetamine addiction, thus enhancing the efficacy of addiction treatment and paving the way for future research in this domain.

Epigenetic Study of Cohort of Monozygotic Twins With Hypertrophic Cardiomyopathy Due to MYBPC3 (Cardiac Myosin-Binding Protein C)

BACKGROUND

Hypertrophic cardiomyopathy is an autosomal dominant cardiac disease. The mechanisms that determine its variable expressivity are poorly understood. Epigenetics could play a crucial role in bridging the gap between genotype and phenotype by orchestrating the interplay between the environment and the genome regulation. In this study we aimed to establish a possible correlation between the peripheral blood DNA methylation patterns and left ventricular hypertrophy severity in patients with hypertrophic cardiomyopathy, evaluating the potential impact of lifestyle variables and providing a biological context to the observed changes.

METHODS AND RESULTS

Methylation data were obtained from peripheral blood samples (Infinium MethylationEPIC BeadChip arrays). We employed multiple pair-matched models to extract genomic positions whose methylation correlates with the degree of left ventricular hypertrophy in 3 monozygotic twin pairs carrying the same founder pathogenic variant (MYBPC3 p.Gly263Ter). This model enables the isolation of the environmental influence, beyond age, on DNA methylation changes by removing the genetic background. Our results revealed a more anxious personality among more severely affected individuals. We identified 56 differentially methylated positions that exhibited moderate, proportional changes in methylation associated with left ventricular hypertrophy. These differentially methylated positions were enriched in regions regulated by repressor histone marks and tended to cluster at genes involved in left ventricular hypertrophy development, such as HOXA5, TRPC3, UCN3, or PLSCR2, suggesting that changes in peripheral blood may reflect myocardial alterations.

CONCLUSIONS

We present a unique pair-matched model, based on 3 monozygotic twin pairs carrying the same founder pathogenic variant and different phenotypes. This study provides further evidence of the pivotal role of epigenetics in hypertrophic cardiomyopathy variable expressivity.

Induction of insulin resistance in female mice due to prolonged phenanthrene exposure: Unveiling the low-dose effect and potential mechanisms

Phenanthrene (Phe) is a commonly occurring polycyclic aromatic hydrocarbon (PAH) found in various food sources and drinking water. Previous studies have shown that long-term exposure to Phe in male mice leads to insulin resistance in a dose-dependent manner. However, the effect of Phe on glucose homeostasis in female mice remains unknown. To address this knowledge gap, female Kunming mice were exposed to Phe through their drinking water at concentrations of 0.05, 0.5, and 5 ng/mL. After 270 d of exposure, we surprisingly discovered a low-dose effect of Phe on insulin resistance in female mice, which differed from the effect observed in male mice and showed sexual dimorphism. Specifically, insulin resistance was only observed in the 0.05 ng/mL treatment, and this low-dose effect was also reflected in the concentration of Phe in white adipose tissue (WAT). Differences in metabolic enzyme activities in the liver may potentially explain this effect. The observed sexual dimorphism in Phe exposure could be attributed to variations in estrogen (E2) level and estrogen receptor beta (ERβ) expression in WAT. These findings highlight the association between environmental factors and the development of insulin resistance, emphasizing the pathogenic effect of even low doses of Phe. Moreover, sex dependent-effect should be given more attention when studying the toxic effects of environmental pollutants.

Changes in global methylation patterns of Mytilus galloprovincialis exposed to microplastics

Microplastics (MPs) disturb the normal activity of aquatic organisms at different levels, causing physiological stress and altering feeding, growth, and reproduction. Alterations of epigenetic patterns due to exposure to MPs have scarcely been studied in invertebrates. In this study, Mytilus galloprovincialis mussels (N = 61) were intermittently exposed to different concentrations of pure polystyrene microbeads for three weeks. The concentrations used in this research were similar to those currently found in certain polluted environments (E1), as well as higher doses to which mussels could be further exposed (E2 and E3). After exposure period, the global methylation patterns were investigated using Amplified Fragment Length Polymorphism (AFLPs). Significantly lower methylation was found in exposed groups compared to the control group. The level of hypomethylation increased with the concentration of microbeads. Similar results were found from field samples inhabiting two sites differentially MPs-polluted. The implications of this discovery were analysed and discussed, noting the already known effects of MPs on metabolism and cell division. Further studies on this and other sentinel organisms are recommended to understand the response of the aquatic species to the currently increasing MPs pollution.

DNA Methylation and Non-Coding RNAs in Metabolic Disorders: Epigenetic Role of Nutrients, Dietary Patterns, and Weight Loss Interventions for Precision Nutrition

BACKGROUND

Dysregulation of epigenetic processes and abnormal epigenetic profiles are associated with various metabolic disorders. Nutrition, as an environmental factor, can induce epigenetic changes through both direct exposure and transgenerational inheritance, continuously altering gene expression and shaping the phenotype. Nutrients consumed through food or supplementation, such as vitamin B12, folate, vitamin B6, and choline, play a pivotal role in DNA methylation, a critical process for gene regulation. Additionally, there is mounting evidence that the expression of non-coding RNAs (ncRNAs) can be modulated by the intake of specific nutrients and natural compounds, thereby influencing processes involved in the onset and progression of metabolic diseases.

SUMMARY

Evidence suggests that dietary patterns, weight loss interventions, nutrients and nutritional bioactive compounds can modulate the expression of various microRNA (miRNAs) and DNA methylation levels, contributing to the development of metabolic disorders such as obesity and type 2 diabetes. Furthermore, several studies have proposed that DNA methylation and miRNA expression could serve as biomarkers for the effects of weight loss programs.

KEY MESSAGE

Despite ongoing debate regarding the effects of nutrient supplementation on DNA methylation levels and the expression of ncRNAs, certain DNA methylation marks and ncRNA expressions might predict the risk of metabolic disorders and act as biomarkers for forecasting the success of therapies within the framework of precision medicine and nutrition. The role of DNA methylation and miRNA expression as potential mediators of the effects of weight loss underscores their potential as biomarkers for the outcomes of weight loss programs. This highlights the influence of dietary patterns and weight loss interventions on the regulation of miRNA expression and DNA methylation levels, suggesting an interaction between these epigenetic factors and the body's response to weight loss.

The evolution of ACEs: From coping behaviors to epigenetics as explanatory frameworks for the biology of adverse childhood experiences

Adverse childhood experiences (ACEs) have become a topic of public and scientific attention. ACEs denote a range of negative experiences in early life, from sexual abuse to emotional neglect, that are thought to impact health over the life course. The term was coined in the CDC-Kaiser ACE Study, an epidemiological study that surveyed 17,421 adults about ACEs and correlated the responses with participants' current health records. Shortly after the study was published in 1998, the US CDC deemed ACEs an important public health target; however, it is only recently that ACEs feature prominently in scientific and public discourses. We contend that this rise in popularity is linked to the adoption of epigenetic explanations for how ACEs affect health. Based on a literature analysis, we trace the evolution of explanatory frameworks for ACEs-from coping behaviors to allostatic load to epigenetics-and analyze how each of these explanations not only reconsiders the mechanisms by which ACEs affect health, but also who should be held responsible for addressing ACEs and how. Epigenetics provides distinctly different discursive possibilities than previous frameworks: firstly, it offers one distinct molecular mechanism for how ACEs work, lending "molecular credibility" to epidemiological findings; secondly, it raises the possibility of reversing the negative effects of ACEs on the biological level. This epigenetic articulation makes ACEs attractive for new actors in science and society. Particularly, it facilitates novel interdisciplinary collaborations and attracts actors in health advocacy who are interested in non-deterministic readings of ACEs that counteract stigma and support positive health interventions and healing.

Environmental exposures influence multigenerational epigenetic transmission

Epigenetic modifications control gene expression and are essential for turning genes on and off to regulate and maintain differentiated cell types. Epigenetics are also modified by a multitude of environmental exposures, including diet and pollutants, allowing an individual's environment to influence gene expression and resultant phenotypes and clinical outcomes. These epigenetic modifications due to gene-environment interactions can also be transmitted across generations, raising the possibility that environmental influences that occurred in one generation may be transmitted beyond the second generation, exerting a long-lasting effect. In this review, we cover the known mechanisms of epigenetic modification acquisition, reprogramming and persistence, animal models and human studies used to understand multigenerational epigenetic transmission, and examples of environmentally induced epigenetic change and its transmission across generations. We highlight the importance of environmental health not only on the current population but also on future generations that will experience health outcomes transmitted through epigenetic inheritance.

Impacts of Hyperglycemia on Epigenetic Modifications in Human Gingival Fibroblasts and Gingiva in Diabetic Rats

Periodontal disease is considered one of the diabetic complications with high morbidity and severity. Recent studies demonstrated the involvement of the epigenome on diabetic complications. Histone modifications change chromatin architecture and gene activation. Histone modifications have been reported to alter chromatin structure and regulate gene transcription. In this study, we investigated the impacts of H3 lysine 4 trimethylation (H3K4me3) and specific histone methyltransferases of H3K4 methylation, su(var)3-9, enhancer-of-zeste, and trithorax domain 1A (SETD1A) on periodontal tissue affected by the diabetic condition. We observed the increase in H3K4me3 and SETD1A in gingival tissue of diabetic rats compared with the normal rats. Cultured human fibroblasts (hGFs) confirmed a high glucose-induced increase in H3K4me3 and SETD1A. We further demonstrated that high glucose increased the gene expression of matrix metalloproteinase (MMP) 1 and MMP13, which were canceled by sinefungin, an SETD1A inhibitor. Our investigation suggests that diabetes triggers histone modifications in the gingival tissue, resulting in gingival inflammation. Histone modifications may play crucial roles in the development of periodontal disease in diabetes.

Mitochondrial DNA content and methylation in sperm of patients with asthenozoospermia

PURPOSE

The aim of the current study was to investigate the mtDNA methylation levels and mtDNA copy numbers in the sperm of patients with asthenozoospermia and compare them to those observed in controls with normozoospermia.

METHODS

Pyrosequencing analysis of the methylation levels of the mitochondrial D-loop and MT-CO1/chr1:631,907-632083/chrX:26,471,887-126,472,063 (hereinafter referred to as "MT-CO1-AVG") region and quantitative PCR analysis of the mtDNA copy number were performed on sperm from 30 patients with asthenozoospermia and 30 controls with normozoospermia.

RESULTS

Compared with those of controls with normozoospermia, the methylation levels of D-loop and MT-CO1-AVG regions and mtDNA copy number were significantly higher in patients with asthenozoospermia. The methylation level of the D-loop region in patients with asthenozoospermia and controls with normozoospermia and that of MT-CO1-AVG region in patients with asthenozoospermia showed a decreasing tendency with increasing total sperm motility. A significant inverse correlation between the mtDNA copy number and total sperm motility was observed in patients with asthenozoospermia but not in controls with normozoospermia. In patients with asthenozoospermia, but not in controls with normozoospermia, we observed a significant inverse correlation between D-loop methylation levels and mtDNA copy number, while no significant correlation was observed between MT-CO1-AVG methylation levels and mtDNA copy number.

CONCLUSION

These results reveal the occurrence of mtDNA methylation in human sperm and altered D-loop and MT-CO1-AVG methylation levels in patients with asthenozoospermia. Additional research is needed to determine the function of these features in the etiology and course of asthenozoospermia.

Agricultural insect pests as models for studying stress-induced evolutionary processes

Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.

Skin Rejuvenation by Modulation of DNA Methylation

Skin aging is driven by a complex set of cellular pathways. Among these, epigenetic mechanisms have garnered particular attention, because of their sensitivity to environmental and lifestyle factors. DNA methylation represents the longest known and best understood epigenetic mechanism. We explain how DNA methylation might function as an interface between the environment and the genome of human skin. Exposures to different environmental factors and lifestyles are known to modulate age-related methylation patterns, as illustrated by their effect on DNA methylation clocks. Human skin provides a particularly well-suited tissue for understanding age-related methylation changes and it has been shown recently that modulation of DNA methylation can induce skin rejuvenation. We explain how the use of mildly demethylating agents can be safeguarded to ensure the specific removal of age-related DNA methylation changes. We also identify important areas of future research, leading to a deeper understanding of the mechanisms that drive epigenetic aging and to the development of further refined intervention strategies.

DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)

Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2827 ppm), whole-genome bisulfite sequencing (WGBS) and RNA-seq data were generated from adult female gonad tissue and male sperm samples. Although differentially methylated loci (DMLs) were identified in females (89) and males (2916), there were no differentially expressed genes and only one differentially expressed transcript in females. However, gene body methylation impacted other forms of gene activity in sperm, such as the maximum number of transcripts expressed per gene and changes in the predominant transcript expressed. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DMLs revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates.

Cell-type specific methylation changes in the newborn child associated to obstetric pain relief

Although it is widely known that various pharmaceuticals affect the methylome, the knowledge of the effects from anesthesia is limited, and nearly nonexistent regarding the effects of obstetric anesthesia on the newborn child. Using sequencing based-methylation data and a reference-based statistical deconvolution approach we performed methylome-wide association studies (MWAS) of neonatal whole blood, and for each cell-type specifically, to detect methylation variations that are associated with the pain relief administered to the mother during delivery. Significant findings were replicated in a different dataset and followed-up with gene ontology analysis to pinpoint biological functions of potential relevance to these neonatal methylation alterations. The MWAS analyses detected methylome-wide significant (q<0.1) alterations in the newborn for laughing gas in granulocytes (two CpGs, p<5.50x10-9, q = 0.067), and for pudendal block in monocytes (five CpGs across three loci, p<1.51 x10-8, q = 0.073). Suggestively significant findings (p<1.00x10-6) were detected for both treatments for bulk and all cell-types, and replication analyses showed consistent significant enrichment (odds ratios ranging 3.47-39.02; p<4.00×10-4) for each treatment, suggesting our results are robust. In contrast, we did not observe any overlap across treatments, suggesting that the treatments are associated with different alterations of the neonatal blood methylome. Gene ontology analyses of the replicating suggestively significant results indicated functions related to, for example, cell differentiation, intracellular membrane-bound organelles and calcium transport. In conclusion, for the first time, we investigated and detected effect of obstetric pain-relief on the blood methylome in the newborn child. The observed differences suggest that anesthetic treatment, such as laughing gas or pudendal block, may alter the neonatal methylome in a cell-type specific manner. Some of the observed alterations are part of gene ontology terms that previously have been suggested in relation to anesthetic treatment, supporting its potential role also in obstetric anesthesia.

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.