Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells

Somatic mutation as an explanation for epigenetic aging

DNA methylation marks have recently been used to build models known as epigenetic clocks, which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In an analysis of multimodal data from 9,331 human individuals, we found that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping allows mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging more rapidly or slowly than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.

Pan-cancer analysis of co-inhibitory molecules revealing their potential prognostic and clinical values in immunotherapy

Background

The widespread use of immune checkpoint inhibitors (anti-CTLA4 or PD-1) has opened a new chapter in tumor immunotherapy by providing long-term remission for patients. Unfortunately, however, these agents are not universally available and only a minority of patients respond to them. Therefore, there is an urgent need to develop novel therapeutic strategies targeting other co-inhibitory molecules. However, comprehensive information on the expression and prognostic value of co-inhibitory molecules, including co-inhibitory receptors and their ligands, in different cancers is not yet available.

Methods

We investigated the expression, correlation, and prognostic value of co-inhibitory molecules in different cancer types based on TCGA, UCSC Xena, TIMER, CellMiner datasets. We also examined the associations between the expression of these molecules and the extent of immune cell infiltration. Besides, we conducted a more in-depth study of VISTA.

Result

The results of differential expression analysis, correlation analysis, and drug sensitivity analysis suggest that CTLA4, PD-1, TIGIT, LAG3, TIM3, NRP1, VISTA, CD80, CD86, PD-L1, PD-L2, PVR, PVRL2, FGL1, LGALS9, HMGB1, SEMA4A, and VEGFA are associated with tumor prognosis and immune cell infiltration. Therefore, we believe that they are hopefully to serve as prognostic biomarkers for certain cancers. In addition, our analysis indicates that VISTA plays a complex role and its expression is related to TMB, MSI, cancer cell stemness, DNA/RNA methylation, and drug sensitivity.

Conclusions

These co-inhibitory molecules have the potential to serve as prognostic biomarkers and therapeutic targets for a broad spectrum of cancers, given their strong associations with key clinical metrics. Furthermore, the analysis results indicate that VISTA may represent a promising target for cancer therapy.

Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta

BACKGROUND

The human placenta is distinct from most organs due to its uniquely low-methylated genome. DNA methylation (DNAme) is particularly depleted in the placenta at partially methylated domains and on the inactive X chromosome (Xi) in XX samples. While Xi DNAme is known to be critical for X-chromosome inactivation (XCI) in other tissues, its role in the placenta remains unclear. Understanding X-linked DNAme variation in the placenta may provide insights into XCI and have implications for prenatal development and phenotypic sex differences.

METHODS

DNAme data were analyzed from over 350 human placental (chorionic villus) samples, along with samples from cord blood, amnion and chorion placental membranes, and fetal somatic tissues. We characterized X chromosome DNAme variation in the placenta relative to sample variables including cell composition, ancestry, maternal age, placental weight, and fetal birth weight, and compared these patterns to other tissues. We also evaluated the relationship between X-linked DNAme and previously reported XCI gene expression status in placenta.

RESULTS

Our findings confirm that the placenta exhibits significant depletion of DNAme on the Xi compared to other tissues. Additionally, we observe that X chromosome DNAme profiles in the placenta are influenced by cell composition, particularly trophoblast proportion, with minimal DNAme variation across gestation. Notably, low promoter DNAme is observed at most genes on the Xi regardless of XCI status, challenging known associations in somatic tissues between low promoter DNAme and escape from XCI.

CONCLUSIONS

This study provides evidence that the human placenta has a distinct Xi DNAme landscape, which may inform our understanding of sex differences during prenatal development. Future research should explore the mechanisms underlying the placenta's unique X-linked DNAme profile, and the factors involved in placental XCI maintenance.

The epigenetic impact of fatty acids as DNA methylation modulators

DNA methylation is a key epigenetic mechanism that regulates gene expression. Fatty acids, the building blocks of many essential lipids, play a crucial role in various biological events. Aberrant acetylation and methylation profiles are linked to a number of non-communicable diseases. Various fatty acids have been identified as potential 'epi-drugs' because of their ability to correct aberrant acetylation and methylation profiles in a number of non-communicable diseases, enhancing the value of their biochemical properties. This review summarizes the effects of selected saturated and unsaturated fatty acids and fatty-acid-rich food items on disease-associated DNA methylation profiles, aiming to justify the classification of fatty acids as DNA methylation modulators.

The spatial zonation of the murine placental vasculature is specified by epigenetic mechanisms

The labyrinthian fetoplacental capillary network is vital for proper nourishment of the developing embryo. Dysfunction of the maternal-fetal circulation is a primary cause of placental insufficiency. Here, we show that the spatial zonation of the murine placental labyrinth vasculature is controlled by flow-regulated epigenetic mechanisms. Spatiotemporal transcriptomic profiling identified a gradual change in the expression of epigenetic enzymes, including the de novo DNA methyltransferase 3a (DNMT3A). Loss of Dnmt3a resulted in DNA hypomethylation and perturbation of zonated placental gene expression. The resulting global DNA hypomethylation impaired the angiogenic capacity of endothelial cells. Global or endothelium-predominant deletion of Dnmt3a resulted in impaired placental vascularization and fetal growth retardation (FGR). Human placental endothelial gene expression profiling associated preeclampsia with reduced DNMT3A expression. Collectively, our study identified DMNT3A as critical methylome-regulator of placental endothelial gene expression and function with clinical implications for placental dysfunction, as it occurs during preeclampsia or FGR.

On correlative and causal links of replicative epimutations

The mitotic inheritability of DNA methylation as an epigenetic marker in higher-order eukaryotes has been established for >40 years. The DNA methylome and mitotic division interplay is now considered bidirectional and highly intertwined. Various epigenetic writers, erasers, and modulators shape the perceived replicative methylation dynamics. This Review surveys the principles and complexity of mitotic transmission of DNA methylation, emphasizing the awareness of mitotic aging in analyzing DNA methylation dynamics in development and disease. We reviewed how DNA methylation changes alter mitotic proliferation capacity, implicating age-related diseases like cancer. We link replicative epimutation to stem cell dysfunction, inflammatory response, cancer risks, and epigenetic clocks, discussing the causative role of DNA methylation in health and disease.

Epigenetic Clock: DNA Methylation as a Marker of Biological Age and Age-Associated Diseases

Age is one of the key criteria of human health used in practical medicine to predict the risk of common chronic diseases. However, biological age, which reflects the state of an individual organism, functional capabilities, social well-being, and risk of premature death from various causes, often does not coincide with chronological age. To determine biological age of a particular individuals and the rate of their aging, specific panels of DNA methylation markers called "epigenetic clock" (EC) were proposed. This review summarizes the data about the main types of ECs developed to date and their key characteristics. We described the results of works studying individual aging rates in common age-associated diseases and outlined main directions, development of which could expand application of ECs in fundamental and practical medicine. There is no doubt that revealing complex mechanisms underlying interaction between the rate of epigenetic aging and the risk of age-associated diseases could play a key role for prediction and early diagnosis, as well as for the development of preventive measures that could delay onset of the disease.

Epigenetic modifications and emerging therapeutic targets in cardiovascular aging and diseases

The complex mechanisms underlying the development of cardiovascular diseases remain not fully elucidated. Epigenetics, which modulates gene expression without DNA sequence changes, is shedding light on these mechanisms and their heritable effects. This review focus on epigenetic regulation in cardiovascular aging and diseases, detailing specific epigenetic enzymes such as DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), and histone deacetylases (HDACs), which serve as writers or erasers that modify the epigenetic landscape. We also discuss the readers of these modifications, such as the 5-methylcytosine binding domain proteins, and the erasers ten-eleven translocation (TET) proteins. The emerging role of RNA methylation, particularly N6-methyladenosine (m6A), in cardiovascular pathogenesis is also discussed. We summarize potential therapeutic targets, such as key enzymes and their inhibitors, including DNMT inhibitors like 5-azacytidine and decitabine, HDAC inhibitors like belinostat and givinotide, some of which have been approved by the FDA for various malignancies, suggesting their potential in treating cardiovascular diseases. Furthermore, we highlight the role of novel histone modifications and their associated enzymes, which are emerging as potential therapeutic targets in cardiovascular diseases. Thus, by incorporating the recent studies involving patients with cardiovascular aging and diseases, we aim to provide a more detailed and updated review that reflects the advancements in the field of epigenetic modification in cardiovascular diseases.

Unravelling 2-oxoglutarate turnover and substrate oxidation dynamics in 5-methylcytosine-oxidising TET enzymes

Fe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenases use 2OG and O2 cofactors to catalyse substrate oxidation and yield oxidised product, succinate, and CO2. Simultaneous detection of substrate and cofactors is difficult, contributing to a poor understanding of the dynamics between substrate oxidation and 2OG decarboxylation activities. Here, we profile 5-methylcytosine (5mC)-oxidising Ten-Eleven Translocation (TET) enzymes using MS and 1H NMR spectroscopy methods and reveal a high degree of substrate oxidation-independent 2OG turnover under a range of conditions. 2OG decarboxylase activity is substantial (>20% 2OG turned over after 1 h) in the absence of substrate, while, under substrate-saturating conditions, half of total 2OG consumption is uncoupled from substrate oxidation. 2OG kinetics are affected by substrate and non-substrate DNA oligomers, and the sequence-agnostic effects are observed in amoeboflagellate Naegleria gruberi NgTet1 and human TET2. TET inhibitors also alter uncoupled 2OG kinetics, highlighting the potential effect of 2OG dioxygenase inhibitors on the intracellular balance of 2OG/succinate.

Metabolites and metabolism in vascular calcification: links between adenosine signaling and the methionine cycle

The global population of individuals with cardiovascular disease is expanding, and a key risk factor for major adverse cardiovascular events is vascular calcification. The pathogenesis of cardiovascular calcification is complex and multifaceted, with external cues driving epigenetic, transcriptional, and metabolic changes that promote vascular calcification. This review provides an overview of some of the lesser understood molecular processes involved in vascular calcification and discusses the links between calcification pathogenesis and aspects of adenosine signaling and the methionine pathway; the latter of which salvages the essential amino acid methionine, but also provides the substrate critical for methylation, a modification that regulates the function and activity of DNA and proteins. We explore the complex and dynamic nature of osteogenic reprogramming underlying intimal atherosclerotic calcification and medial arterial calcification (MAC). Atherosclerotic calcification is more widely studied; however, emerging studies now show that MAC is a significant pathology independent from atherosclerosis. Furthermore, we emphasize metabolite and metabolic-modulating factors that influence vascular calcification pathogenesis. Although the contributions of these mechanisms are more well-define in relation to atherosclerotic intimal calcification, understanding these pathways may provide crucial mechanistic insights into MAC and inform future therapeutic approaches. Herein, we highlight the significance of adenosine and methyltransferase pathways as key regulators of vascular calcification pathogenesis.

Train and Reprogram Your Brain: Effects of Physical Exercise at Different Stages of Life on Brain Functions Saved in Epigenetic Modifications

Multiple studies have demonstrated the significant effects of physical exercise on brain plasticity, the enhancement of memory and cognition, and mood improvement. Although the beneficial impact of exercise on brain functions and mental health is well established, the exact mechanisms underlying this phenomenon are currently under thorough investigation. Several hypotheses have emerged suggesting various possible mechanisms, including the effects of hormones, neurotrophins, neurotransmitters, and more recently also other compounds such as lactate or irisin, which are released under the exercise circumstances and act both locally or/and on distant tissues, triggering systemic body reactions. Nevertheless, none of these actually explain the long-lasting effect of exercise, which can persist for years or even be passed on to subsequent generations. It is believed that these long-lasting effects are mediated through epigenetic modifications, influencing the expression of particular genes and the translation and modification of specific proteins. This review explores the impact of regular physical exercise on brain function and brain plasticity and the associated occurrence of epigenetic modifications. It examines how these changes contribute to the prevention and treatment of neuropsychiatric and neurological disorders, as well as their influence on the natural aging process and mental health.

Perfluorooctanesulfonic acid (PFOS) induced cancer related DNA methylation alterations in human breast cells: A whole genome methylome study

DNA methylation plays a pivotal role in cancer. The ubiquitous contaminant perfluorooctanesulfonic acid (PFOS) has been epidemiologically associated with breast cancer, and can induce proliferation and malignant transformation of normal human breast epithelial cells (MCF-10A), but the information about its effect on DNA methylation is sparse. The aim of this study was to characterize the whole-genome methylome effects of PFOS in our breast cell model and compare the findings with previously demonstrated DNA methylation alterations in breast tumor tissues. The DNA methylation profile was assessed at single CpG resolution in MCF-10A cells treated with 1 μM PFOS for 72 h by using Enzymatic Methyl sequencing (EM-seq). We found 12,591 differentially methylated CpG-sites and 13,360 differentially methylated 100 bp tiles in the PFOS exposed breast cells. These differentially methylated regions (DMRs) overlapped with 2406 genes of which 494 were long non-coding RNA and 1841 protein coding genes. We identified 339 affected genes that have been shown to display altered DNA methylation in breast cancer tissue and several other genes related to cancer development. This includes hypermethylation of GACAT3, DELEC1, CASC2, LCIIAR, MUC16, SYNE1 and hypomethylation of TTN and KMT2C. DMRs were also found in estrogen receptor genes (ESR1, ESR2, ESRRG, ESRRB, GREB1) and estrogen responsive genes (GPER1, EEIG1, RERG). The gene ontology analysis revealed pathways related to cancer phenotypes such as cell adhesion and growth. These findings improve the understanding of PFOS's potential role in breast cancer and illustrate the value of whole-genome methylome analysis in uncovering mechanisms of chemical effects, identifying biomarker candidates, and strengthening epidemiological associations, potentially impacting risk assessment.

DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor

The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. How HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains largely unknown. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding, and simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.

Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response

Environmental stress significantly affects plant growth, development, and survival. Plants respond to stressors such as temperature fluctuations, water scarcity, nutrient deficiencies, and pathogen attacks through intricate molecular and physiological adaptations. Epigenetic mechanisms are crucial in regulating gene expression in response to environmental stress. This review explores the current understanding of epigenetic modifications, including DNA methylation, and their roles in modulating gene expression patterns under environmental stress conditions. The dynamic nature of epigenetic modifications, their crosstalk with stress-responsive pathways, and their potential implications for plant adaptation and crop improvement are highlighted in the face of changing environmental conditions.

Metformin exposure during pregnancy and lactation affects offspring's long-term body weight and adipose tissue mass independent of the maternal metabolic state

The increasing prevalence of obesity, type 2 diabetes mellitus (T2DM), and gestational diabetes (GDM) among pregnant women has risen dramatically worldwide. The antihyperglycemic drug metformin is the most common drug for T2DM treatment in non-pregnant individuals; nevertheless, it is increasingly being used for diabetes-complicated pregnancies. Studies on the long-term metabolic effects of this drug in offspring remain scarce. This work aimed to determine the effect of metformin exposure during pregnancy and lactation on the offspring of a model of diet-induced maternal hyperglycemia. Cohorts of pregnant mice were fed a 46% fat diet (HFD) or a control standard diet (SD). A group of dams were exposed to metformin during pregnancy and lactation. After weaning, the offspring were fed SD for 8 weeks and then challenged with a 46% HFD after puberty for 12 weeks. Irrespective of the maternal diet, offspring of metformin-exposed mothers had a lower body weight and reduced inguinal white adipose tissue (iWAT) mass after HFD challenge. This was associated with increased expression of Pparg, Fabp4, Glut4, Srebp1, and Fasn in the iWAT during adulthood in the metabolically impaired dams exposed to metformin, suggesting increased adipogenesis and de novo lipogenesis. Increased expression of Fasn associated with decreased methylation levels at its promoter and proximal coding region in the iWAT was found. These results suggest that metformin modulates gene expression levels by epigenetic mechanisms in maternal metabolic-impaired conditions.

Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation

The phenotype of human placental extravillous trophoblast (EVT) at the end of pregnancy reflects both first trimester differentiation from villous cytotrophoblast (CTB) and later gestational changes, including loss of proliferative and invasive capacity. Invasion abnormalities are central to two major placental pathologies, preeclampsia and placenta accreta spectrum, so characterization of the corresponding normal processes is crucial. In this report, our gene expression analysis, using purified human CTB and EVT cells, highlights an epithelial-mesenchymal transition (EMT) mechanism underlying CTB-EVT differentiation and provides a trophoblast-specific EMT signature. In parallel, DNA methylation profiling shows that CTB cells, already hypomethylated relative to non-trophoblast cell lineages, show further genome-wide hypomethylation in the transition to EVT. However, a small subgroup of genes undergoes gains of methylation (GOM) in their regulatory regions or gene bodies, associated with differential mRNA expression (DE). Prominent in this GOM-DE group are genes involved in the EMT, including multiple canonical EMT markers and the EMT-linked transcription factor RUNX1, for which we demonstrate a functional role in modulating the migratory and invasive capacities of JEG3 trophoblast cells. This analysis of DE associated with locus-specific GOM, together with functional studies of an important GOM-DE gene, highlights epigenetically regulated genes and pathways acting in human EVT differentiation and invasion, with implications for obstetric disorders in which these processes are dysregulated.

DNA Methylation in the Adaptive Response to Exercise

Emerging evidence published over the past decade has highlighted the role of DNA methylation in skeletal muscle function and health, including as an epigenetic transducer of the adaptive response to exercise. In this review, we aim to synthesize the latest findings in this field to highlight: (1) the shifting understanding of the genomic localization of altered DNA methylation in response to acute and chronic aerobic and resistance exercise in skeletal muscle (e.g., promoter, gene bodies, enhancers, intergenic regions, un-annotated regions, and genome-wide methylation); (2) how these global/regional methylation changes relate to transcriptional activity following exercise; and (3) the factors (e.g., individual demographic or genetic features, dietary, training history, exercise parameters, local epigenetic characteristics, circulating hormones) demonstrated to alter both the pattern of DNA methylation after exercise, and the relationship between DNA methylation and gene expression. Finally, we discuss the changes in non-CpG methylation and 5-hydroxymethylation after exercise, as well as the importance of emerging single-cell analyses to future studies-areas of increasing focus in the field of epigenetics. We anticipate that this review will help generate a framework for clinicians and researchers to begin developing and testing exercise interventions designed to generate targeted changes in DNA methylation as part of a personalized exercise regimen.

Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome

Transcription factors (TFs) intricately navigate the vast genomic landscape to locate and bind specific DNA sequences for the regulation of gene expression programs. These interactions occur within a dynamic cellular environment, where both DNA and TF proteins experience continual chemical and structural perturbations, including epigenetic modifications, DNA damage, mechanical stress, and post-translational modifications (PTMs). While many of these factors impact TF-DNA binding interactions, understanding their effects remains challenging and incomplete. This review explores the existing literature on these dynamic changes and their potential impact on TF-DNA interactions.

Functional significance of DNA methylation: epigenetic insights into Sjögren's syndrome

Sjögren's syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.

Can methylated purine bases act as photoionization hotspots?

The direct photoionization of DNA canonical bases under ultraviolet radiation is difficult due to the high ionization potentials. According to previous quantum chemical calculations, methylation can have great influence on the ionization potential. Are methylated nucleobases prone to photoionization and cause DNA damage? As an important epigenetic modification in transcription, expression, and regulation of genes, it is of great biological significance to explore the effect of methylation on base photoionization from the experimental perspective. Herein, we study the photoionization behavior of methylated purines 6 mA and 6mG at 266 nm using a nanosecond transient UV-Vis spectroscopy. The hydrated electron and methylated base radicals are observed, indicating the occurrence of photoionization for both 6mG and 6 mA. We measured one-photon ionization yields to be (5.0 ± 0.2) × 10-3 and (1.4 ± 0.2) × 10-3 for 6mG and 6 mA, respectively. These are higher than those of (dA)20 and (dA20 )·(dT20 ) previously reported, indicating that methylation significantly promotes base photoionization with a stronger effect than base stacking, consistent with calculations in literature. Given that the hydrated electrons and methylated base radicals from photoionization can trigger a cascade of deleterious reactions, the methylated purine bases may act as hotspots of DNA photoionization damage of living organisms.

Unraveling the epigenetic fabric of type 2 diabetes mellitus: pathogenic mechanisms and therapeutic implications

Type 2 diabetes mellitus (T2DM) is a rapidly escalating global health concern, with its prevalence projected to increase significantly in the near future. This review delves into the intricate role of epigenetic modifications - including DNA methylation, histone acetylation, and micro-ribonucleic acid (miRNA) expression - in the pathogenesis and progression of T2DM. We critically examine how these epigenetic changes contribute to the onset and exacerbation of T2DM by influencing key pathogenic processes such as obesity, insulin resistance, β-cell dysfunction, cellular senescence, and mitochondrial dysfunction. Furthermore, we explore the involvement of epigenetic dysregulation in T2DM-associated complications, including diabetic retinopathy, atherosclerosis, neuropathy, and cardiomyopathy. This review highlights recent studies that underscore the diagnostic and therapeutic potential of targeting epigenetic modifications in T2DM. We also provide an overview of the impact of lifestyle factors such as exercise and diet on the epigenetic landscape of T2DM, underscoring their relevance in disease management. Our synthesis of the current literature aims to illuminate the complex epigenetic underpinnings of T2DM, offering insights into novel preventative and therapeutic strategies that could revolutionize its management.

Drug addiction and treatment: An epigenetic perspective

Drug addiction is a complex disease affected by numerous genetic and environmental factors. Brain regions in reward pathway, neuronal adaptations, genetic and epigenetic interactions causing transcriptional enhancement or repression of multiple genes induce different addiction phenotypes for varying duration. Addictive drug use causes epigenetic alterations and similarly epigenetic changes induced by environment can promote addiction. Epigenetic mechanisms include DNA methylation and post-translational modifications like methylation, acetylation, phosphorylation, ubiquitylation, sumoylation, dopaminylation and crotonylation of histones, and ADP-ribosylation. Non-coding RNAs also induce epigenetic changes. This review discusses these above areas and stresses the need for exploring epidrugs as a treatment alternative and adjunct, considering the limited success of current addiction treatment strategies. Epigenome editing complexes have lately been effective in eukaryotic systems. Targeted DNA cleavage techniques such as CRISPR-Cas9 system, CRISPR-dCas9 complexes, transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs) have been exploited as targeted DNA recognition or anchoring platforms, fused with epigenetic writer or eraser proteins and delivered by transfection or transduction methods. Efficacy of epidrugs is seen in various neuropsychiatric conditions and initial results in addiction treatment involving model organisms are remarkable. Epidrugs present a promising alternative treatment for addiction.

Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts

Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.

Somatic mutation as an explanation for epigenetic aging

DNA methylation marks have recently been used to build models known as "epigenetic clocks" which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In analysis of multimodal data from 9,331 human individuals, we find that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but also with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping enables mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging faster or slower than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.

Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis

DNA methylation (DNAme) alterations are known to initiate from the precancerous stage of tumorigenesis. Herein, we investigated the global and local patterns of DNAme perturbations in tumorigenesis by analysing the genome-wide DNAme profiles of the cervix, colorectum, stomach, prostate, and liver at precancerous and cancer stages. We observed global hypomethylation in tissues of both two stages, except for the cervix, whose global DNAme level in normal tissue was lower than that of the other four tumour types. For alterations shared by both stages, there were common hyper-methylation (sHyperMethyl) and hypo-methylation (sHypoMethyl) changes, of which the latter type was more frequently identified in all tissues. Biological pathways interrupted by sHyperMethyl and sHypoMethyl alterations demonstrated significant tissue specificity. DNAme bidirectional chaos indicated by the enrichment of both sHyperMethyl and sHypoMethyl changes in the same pathway was observed in most tissues and was a common phenomenon, particularly in liver lesions. Moreover, for the same enriched pathways, different tissues may be affected by distinct DNAme types. For the PI3K-Akt signalling pathway, sHyperMethyl enrichment was observed in the prostate dataset, but sHypoMethyl enrichment was observed in the colorectum and liver datasets. Nevertheless, they did not show an increased possibility in survival prediction of patients in comparison with other DNAme types. Additionally, our study demonstrated that gene-body DNAme changes of tumour suppressor genes and oncogenes may persist from precancerous lesions to the tumour. Overall, we demonstrate the tissue specificity and commonality of cross-stage alterations in DNA methylation profiles in multi-tissue tumorigenesis.

Potential therapies targeting nuclear metabolic regulation in cancer

The interplay between genetic alterations and metabolic dysregulation is increasingly recognized as a pivotal axis in cancer pathogenesis. Both elements are mutually reinforcing, thereby expediting the ontogeny and progression of malignant neoplasms. Intriguingly, recent findings have highlighted the translocation of metabolites and metabolic enzymes from the cytoplasm into the nuclear compartment, where they appear to be intimately associated with tumor cell proliferation. Despite these advancements, significant gaps persist in our understanding of their specific roles within the nuclear milieu, their modulatory effects on gene transcription and cellular proliferation, and the intricacies of their coordination with the genomic landscape. In this comprehensive review, we endeavor to elucidate the regulatory landscape of metabolic signaling within the nuclear domain, namely nuclear metabolic signaling involving metabolites and metabolic enzymes. We explore the roles and molecular mechanisms through which metabolic flux and enzymatic activity impact critical nuclear processes, including epigenetic modulation, DNA damage repair, and gene expression regulation. In conclusion, we underscore the paramount significance of nuclear metabolic signaling in cancer biology and enumerate potential therapeutic targets, associated pharmacological interventions, and implications for clinical applications. Importantly, these emergent findings not only augment our conceptual understanding of tumoral metabolism but also herald the potential for innovative therapeutic paradigms targeting the metabolism-genome transcriptional axis.

Elucidating distinct molecular signatures of Lewy body dementias

Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.

DNA methylation and the opposing NMDAR dysfunction in schizophrenia and major depression disorders: a converging model for the therapeutic effects of psychedelic compounds in the treatment of psychiatric illness

Psychedelic compounds are being increasingly explored as a potential therapeutic option for treating several psychiatric conditions, despite relatively little being known about their mechanism of action. One such possible mechanism, DNA methylation, is a process of epigenetic regulation that changes gene expression via chemical modification of nitrogenous bases. DNA methylation has been implicated in the pathophysiology of several psychiatric conditions, including schizophrenia (SZ) and major depressive disorder (MDD). In this review, we propose alterations to DNA methylation as a converging model for the therapeutic effects of psychedelic compounds, highlighting the N-methyl D-aspartate receptor (NMDAR), a crucial mediator of synaptic plasticity with known dysfunction in both diseases, as an example and anchoring point. We review the established evidence relating aberrant DNA methylation to NMDAR dysfunction in SZ and MDD and provide a model asserting that psychedelic substances may act through an epigenetic mechanism to provide therapeutic effects in the context of these disorders.

Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications

BACKGROUND

DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals.

OBJECTIVE

This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application.

METHODS

The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics.

CONCLUSION

The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.

Cellular specificity is key to deciphering epigenetic changes underlying Alzheimer's disease

Different cell types in the brain play distinct roles in Alzheimer's disease (AD) progression. Late onset AD (LOAD) is a complex disease, with a large genetic component, but many risk loci fall in non-coding genome regions. Epigenetics implicates the non-coding genome with control of gene expression. The epigenome is highly cell-type specific and dynamically responds to the environment. Therefore, epigenetic mechanisms are well placed to explain genetic and environmental factors that are associated with AD. However, given this cellular specificity, purified cell populations or single cells need to be profiled to avoid effect masking. Here we review the current state of cell-type specific genome-wide profiling in LOAD, covering DNA methylation (CpG, CpH, and hydroxymethylation), histone modifications, and chromatin changes. To date, these data reveal that distinct cell types contribute and react differently to AD progression through epigenetic alterations. This review addresses the current gap in prior bulk-tissue derived work by spotlighting cell-specific changes that govern the complex interplay of cells throughout disease progression and are critical in understanding and developing effective treatments for AD.

Quantitative investigation of the effects of DNA modifications and protein mutations on MeCP2-MBD-DNA interactions

DNA methylation as an important epigenetic marker, has gained attention for the significance of three oxidative modifications (hydroxymethyl-C (hmC), formyl-C (fC), and carboxyl-C (caC)). Mutations occurring in the methyl-CpG-binding domain (MBD) of MeCP2 result in Rett. However, uncertainties persist regarding DNA modification and MBD mutation-induced interaction changes. Here, molecular dynamics simulations were used to investigate the underlying mechanisms behind changes due to different modifications of DNA and MBD mutations. Alanine scanning combined with the interaction entropy method was employed to accurately evaluate the binding free energy. The results show that MBD has the strongest binding ability for mCDNA, followed by caC, hmC, and fCDNA, with the weakest binding ability observed for CDNA. Further analysis revealed that mC modification induces DNA bending, causing residues R91 and R162 closer to the DNA. This proximity enhances van der Waals and electrostatic interactions. Conversely, the caC/hmC and fC modifications lead to two loop regions (near K112 and K130) closer to DNA, respectively. Furthermore, DNA modifications promote the formation of stable hydrogen bond networks, however mutations in the MBD significantly reduce the binding free energy. This study provides detailed insight into the effects of DNA modifications and MBD mutations on binding ability. It emphasizes the necessity for research and development of targeted Rett compounds that induce conformational compatibility between MBD and DNA, enhancing the stability and strength of their interactions.

Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA

BACKGROUND

DNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a significant role in various biological processes. Nonetheless, the presence of 5-methylcytosine (5mC) in mitochondrial DNA remains controversial, as data ranging from the lack of 5mC to very extensive 5mC have been reported.

RESULTS

By conducting comprehensive bioinformatic analyses of both published and our own data, we reveal that previous observations of extensive and strand-biased mtDNA-5mC are likely artifacts due to a combination of factors including inefficient bisulfite conversion, extremely low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). To reduce false positive mtDNA-5mC signals, we establish an optimized procedure for library preparation and data analysis of bisulfite sequencing. Leveraging our modified workflow, we demonstrate an even distribution of 5mC signals across the mtDNA and an average methylation level ranging from 0.19% to 0.67% in both cell lines and primary cells, which is indistinguishable from the background noise.

CONCLUSIONS

We have developed a framework for analyzing mtDNA-5mC through bisulfite sequencing, which enables us to present multiple lines of evidence for the lack of extensive 5mC in mammalian mtDNA. We assert that the data available to date do not support the reported presence of mtDNA-5mC.

The role of epigenetic modification in postoperative cognitive dysfunction

With the ageing of the population, the health problems of elderly individuals have become particularly important. Through a large number of clinical studies and trials, it has been confirmed that elderly patients can experience postoperative cognitive dysfunction after general anesthesia/surgery. However, the mechanism of postoperative cognitive dysfunction is still unknown. In recent years, the role of epigenetics in postoperative cognitive dysfunction has been widely studied and reported. Epigenetics includes the genetic structure and biochemical changes of chromatin not involving changes in the DNA sequence. This article summarizes the epigenetic mechanism of cognitive impairment after general anesthesia/surgery and analyses the broad prospects of epigenetics as a therapeutic target for postoperative cognitive dysfunction.

The human placenta exhibits a unique transcriptomic void

The human placenta exhibits a unique genomic architecture with an unexpectedly high mutation burden and many uniquely expressed genes. The aim of this study is to identify transcripts that are uniquely absent or depleted in the placenta. Here, we show that 40 of 46 of the other organs have no selectively depleted transcripts and that, of the remaining six, the liver has the largest number, with 26. In contrast, the term placenta has 762 depleted transcripts. Gene Ontology analysis of this depleted set highlighted multiple pathways reflecting known unique elements of placental physiology. For example, transcripts associated with neuronal function are in the depleted set-as expected given the lack of placental innervation. However, this demonstrated overrepresentation of genes involved in mitochondrial function (p = 5.8 × 10-10), including PGC-1α, the master regulator of mitochondrial biogenesis, and genes involved in polyamine metabolism (p = 2.1 × 10-4).

Immunotherapeutic Approaches for the Treatment of Glioblastoma Multiforme: Mechanism and Clinical Applications

Glioma is one of the most aggressive types of primary brain tumor with a high-grade glioma known as glioblastoma multiforme (GBM). Patients diagnosed with GBM usually have an overall survival rate of less than 18 months after conventional therapy. This bleak prognosis underlines the need to consider new therapeutic interventions for GBM treatment to overcome current treatment limitations. By highlighting different immunotherapeutic approaches currently in preclinical and clinical trials, including immune checkpoint inhibitors, chimeric antigen receptors T cells, natural killer cells, vaccines, and combination therapy, this review aims to discuss the mechanisms, benefits, and limitations of immunotherapy in treating GBM patients.

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.

Prediction of chronological age and its applications in forensic casework: methods, current practices, and future perspectives

Estimating an individual's age can be relevant in several areas primarily related to the clinical and forensic fields. In the latter, estimation of an individual's chronological age from biological material left by the perpetrator at a crime scene may provide helpful information for police investigation. Estimation of age is also beneficial in immigration cases, where age can affect the person's protection status under the law, or in disaster victim identification to narrow the list of potential missing persons. In the last decade, research has focused on establishing new approaches for age prediction in the forensic field. From the first forensic age estimations based on morphological inspections of macroscopic changes in bone and teeth, the focus has shifted to molecular methods for age estimation. These methods allow the use of samples from human biological material that does not contain morphological age features and can, in theory, be investigated in traces containing only small amounts of biological material. Molecular methods involving DNA analyses are the primary choice and estimation of DNA methylation levels at specific sites in the genome is the most promising tool. This review aims to provide an overview of the status of forensic age prediction using molecular methods, with particular focus in DNA methylation. The frequent challenges that impact forensic age prediction model development will be addressed, together with the importance of validation efforts within the forensic community.

Microbiota and epigenetics: Health impact

Epigenetic changes associated with disease development and progressions are of increasing importance because of their potential diagnostic and therapeutic applications. Several epigenetic changes associated with chronic metabolic disorders have been studied in various diseases. Epigenetic changes are mostly modulated by environmental factors, including the human microbiota living in different parts of our bodies. The microbial structural components and the microbially derived metabolites directly interact with host cells, thereby maintaining homeostasis. Microbiome dysbiosis, on the other hand, is known to produce elevated levels of disease-linked metabolites, which may directly affect a host metabolic pathway or induce epigenetic changes that can lead to disease development. Despite their important role in host physiology and signal transduction, there has been little research into the mechanics and pathways associated with epigenetic modifications. This chapter focuses on the relationship between microbes and their epigenetic effects in diseased pathology, as well as on the regulation and metabolism of the dietary options available to the microbes. Furthermore, this chapter also provides a prospective link between these two important phenomena, termed "Microbiome and Epigenetics."

Study of DNA methylation of hsd17β, er and reproductive endocrine disrupting effects in female Chlamys farreri under benzo[a]pyrene stress

Benzo[a]pyrene (B[a]P) is one kind of persistent organic pollutants (POPs) in the marine environment which has multiple toxic effects. However, epigenetic studies correlated with reproductive endocrine disruption in invertebrates have not been explored. In our study, Chlamys farreri in the mature stage were exposed to B[a]P (0, 0.4, 2 and 10 μg/L) for 5 and 10 d to explore the effects on reproductive endocrine and DNA methylation. The results proved that B[a]P stress significantly restrained the growth of mature oocytes, reduced the content of sex hormones, and affected the expression of genes related to ovarian development. Histological observation showed that the ovarian microstructure was damaged. The detection of SAM/SAH, dnmts, GNMT in the ovary showed that the level of global DNA methylation fluctuated. Significant hypermethylation of the hsd17β promoter region in the ovary was associated with a significant downregulation of its gene expression. In summary, our results suggested that exposure to B[a]P might affect DNA methylation to regulate key reproductive genes, interfere with the synthesis of sex hormones, and inhibit ovarian development. These findings provide a basis for a better understanding of how epigenetic mechanisms are involved in the response of marine invertebrates to POPs stress, opening up new avenues for incorporating environmental epigenetic approaches into marine invertebrate management and conservation plans.

Aging Hallmarks and the Role of Oxidative Stress

Aging is a complex biological process accompanied by a progressive decline in the physical function of the organism and an increased risk of age-related chronic diseases such as cardiovascular diseases, cancer, and neurodegenerative diseases. Studies have established that there exist nine hallmarks of the aging process, including (i) telomere shortening, (ii) genomic instability, (iii) epigenetic modifications, (iv) mitochondrial dysfunction, (v) loss of proteostasis, (vi) dysregulated nutrient sensing, (vii) stem cell exhaustion, (viii) cellular senescence, and (ix) altered cellular communication. All these alterations have been linked to sustained systemic inflammation, and these mechanisms contribute to the aging process in timing not clearly determined yet. Nevertheless, mitochondrial dysfunction is one of the most important mechanisms contributing to the aging process. Mitochondria is the primary endogenous source of reactive oxygen species (ROS). During the aging process, there is a decline in ATP production and elevated ROS production together with a decline in the antioxidant defense. Elevated ROS levels can cause oxidative stress and severe damage to the cell, organelle membranes, DNA, lipids, and proteins. This damage contributes to the aging phenotype. In this review, we summarize recent advances in the mechanisms of aging with an emphasis on mitochondrial dysfunction and ROS production.

Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation

Enhancers are cis-regulatory elements that control the establishment of cell identities during development. In mammals, enhancer activation is tightly coupled with DNA demethylation. However, whether this epigenetic remodeling is necessary for enhancer activation is unknown. Here, we adapted single-molecule footprinting to measure chromatin accessibility and transcription factor binding as a function of the presence of methylation on the same DNA molecules. We leveraged natural epigenetic heterogeneity at active enhancers to test the impact of DNA methylation on their chromatin accessibility in multiple cell lineages. Although reduction of DNA methylation appears dispensable for the activity of most enhancers, we identify a class of cell-type-specific enhancers where DNA methylation antagonizes the binding of transcription factors. Genetic perturbations reveal that chromatin accessibility and transcription factor binding require active demethylation at these loci. Thus, in addition to safeguarding the genome from spurious activation, DNA methylation directly controls transcription factor occupancy at active enhancers.

Tet Enzyme-Mediated Response in Environmental Stress and Stress-Related Psychiatric Diseases

Mental disorders caused by stress have become a worldwide public health problem. These mental disorders are often the results of a combination of genes and environment, in which epigenetic modifications play a crucial role. At present, the genetic and epigenetic mechanisms of mental disorders such as posttraumatic stress disorder or depression caused by environmental stress are not entirely clear. Although many epigenetic modifications affect gene regulation, the most well-known modification in eukaryotic cells is the DNA methylation of CpG islands. Stress causes changes in DNA methylation in the brain to participate in the neuronal function or mood-modulating behaviors, and these epigenetic modifications can be passed on to offspring. Ten-eleven translocation (Tet) enzymes are the 5-methylcytosine (5mC) hydroxylases of DNA, which recognize 5mC on the DNA sequence and oxidize it to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Tet regulates gene expression at the transcriptional level through the demethylation of DNA. This review will elaborate on the molecular mechanism and the functions of Tet enzymes in environmental stress-related disorders and discuss future research directions.

Epigenetic markers in the embryonal germ cell development and spermatogenesis

Spermatogenesis is the process of generation of male reproductive cells from spermatogonial stem cells in the seminiferous epithelium of the testis. During spermatogenesis, key spermatogenic events such as stem cell self-renewal and commitment to meiosis, meiotic recombination, meiotic sex chromosome inactivation, followed by cellular and chromatin remodeling of elongating spermatids occur, leading to sperm cell production. All the mentioned events are at least partially controlled by the epigenetic modifications of DNA and histones. Additionally, during embryonal development in primordial germ cells, global epigenetic reprogramming of DNA occurs. In this review, we summarized the most important epigenetic modifications in the particular stages of germ cell development, in DNA and histone proteins, starting from primordial germ cells, during embryonal development, and ending with histone-to-protamine transition during spermiogenesis.

M, K M, Dey T, Zargar MI, Singh J. Recent advance of herbal medicines in cancer- a molecular approach

Bioactive compounds are crucial for an extensive range of therapeutic uses, and some exhibit anticancer activity. Scientists advocate that phytochemicals modulate autophagy and apoptosis, involved in the underlying pathobiology of cancer development and regulation. The pharmacological aiming of the autophagy-apoptosis signaling pathway using phytocompounds hence offers an auspicious method that is complementary to conventional cancer chemotherapy. The current review aims to explore the molecular level of the autophagic-apoptotic pathway to know its implication in the pathobiology of cancer and explore the essential cellular process as a druggable anticancer target and therapeutic emergence of naturally derived phytocompound-based anticancer agents. The data in the review were collected from scientific databases such as Google search, Web of Science, PubMed, Scopus, Medline, and Clinical Trials. With a broad outlook, we investigated their cutting-edge scientifically revealed and/or searched pharmacologic effects, a novel mechanism of action, and molecular signaling pathway of phytochemicals in cancer therapy. In this review, the evidence is focused on molecular pharmacology, specifically caspase, Nrf2, NF-kB, autophagic-apoptotic pathway, and several mechanisms to understand their role in cancer biology.

The epigenetic players and the chromatin marks involved in the articular cartilage during osteoarthritis

Epigenetics defines the modifications of the genome that do not involve a change in the nucleotide sequence of DNA. These modifications constitute a mechanism of gene regulation poorly explored in the context of cartilage physiology. They are now intensively studied by the scientific community working on articular cartilage and its related pathology such as osteoarthritis. Indeed, epigenetic regulations can control the expression of crucial gene in the chondrocytes, the only resident cells of cartilage. Some epigenetic changes are considered as a possible cause of the abnormal gene expression and the subsequent alteration of the chondrocyte phenotype (hypertrophy, proliferation, senescence…) as observed in osteoarthritic cartilage. Osteoarthritis is a joint pathology, which results in impaired extracellular matrix homeostasis and leads ultimately to the progressive destruction of cartilage. To date, there is no pharmacological treatment and the exact causes have yet to be defined. Given that the epigenetic modifying enzymes can be controlled by pharmacological inhibitors, it is thus crucial to describe the epigenetic marks that enable the normal expression of extracellular matrix encoding genes, and those associated with the abnormal gene expression such as degradative enzyme or inflammatory cytokines encoding genes. In this review, only the DNA methylation and histone modifications will be detailed with regard to normal and osteoarthritic cartilage. Although frequently referred as epigenetic mechanisms, the regulatory mechanisms involving microRNAs will not be discussed. Altogether, this review will show how this nascent field influences our understanding of the pathogenesis of OA in terms of diagnosis and how controlling the epigenetic marks can help defining epigenetic therapies.

Epigenetic biomarkers for animal welfare monitoring

Biomarkers for holistic animal welfare monitoring represent a considerable unmet need in veterinary medicine. Epigenetic modifications, like DNA methylation, provide important information about cellular states and environments, which makes them highly attractive for biomarker development. Up until now, much of the corresponding research has been focused on human cancers. However, the increasing availability of animal genomes and epigenomes has greatly improved our capacity for epigenetic biomarker development. In this review, we provide an overview about animal DNA methylation patterns and the technologies that enable the analysis of these patterns. We also describe the key frameworks for compound DNA methylation biomarkers, DNA methylation clocks and environment-specific DNA methylation signatures, that allow complex, context-dependent readouts about animal health and disease. Finally, we provide practical examples for how these biomarkers could be applied for health and environmental exposure monitoring, two key aspects of animal welfare assessments. Taken together, our article provides an overview about the molecular and biological foundations for the development of epigenetic biomarkers in veterinary science and their application potential in animal welfare monitoring.

Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation

DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. By combining the RNA inherent capabilities of inhibiting DNMT1 with an aptamer platform, we generated a first-in-class DNMT1-targeted approach - aptaDiR. Molecular modelling of RNA-DNMT1 complexes coupled with biochemical and cellular assays enabled the identification and characterization of aptaDiR. This RNA bio-drug is able to block DNA methylation, impair cancer cell viability and inhibit tumour growth in vivo. Collectively, we present an innovative RNA-based approach to modulate DNMT1 activity in cancer or diseases characterized by aberrant DNA methylation and suggest the first alternative strategy to overcome the limitations of currently approved non-specific hypomethylating protocols, which will greatly improve clinical intervention on DNA methylation.

DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease

Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.

Role of primary aging hallmarks in Alzheimer´s disease

Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.

Deciphering transcription factors and their corresponding regulatory elements during inhibitory interneuron differentiation using deep neural networks

During neurogenesis, the generation and differentiation of neuronal progenitors into inhibitory gamma-aminobutyric acid-containing interneurons is dependent on the combinatorial activity of transcription factors (TFs) and their corresponding regulatory elements (REs). However, the roles of neuronal TFs and their target REs in inhibitory interneuron progenitors are not fully elucidated. Here, we developed a deep-learning-based framework to identify enriched TF motifs in gene REs (eMotif-RE), such as poised/repressed enhancers and putative silencers. Using epigenetic datasets (e.g., ATAC-seq and H3K27ac/me3 ChIP-seq) from cultured interneuron-like progenitors, we distinguished between active enhancer sequences (open chromatin with H3K27ac) and non-active enhancer sequences (open chromatin without H3K27ac). Using our eMotif-RE framework, we discovered enriched motifs of TFs such as ASCL1, SOX4, and SOX11 in the active enhancer set suggesting a cooperativity function for ASCL1 and SOX4/11 in active enhancers of neuronal progenitors. In addition, we found enriched ZEB1 and CTCF motifs in the non-active set. Using an in vivo enhancer assay, we showed that most of the tested putative REs from the non-active enhancer set have no enhancer activity. Two of the eight REs (25%) showed function as poised enhancers in the neuronal system. Moreover, mutated REs for ZEB1 and CTCF motifs increased their in vivo activity as enhancers indicating a repressive effect of ZEB1 and CTCF on these REs that likely function as repressed enhancers or silencers. Overall, our work integrates a novel framework based on deep learning together with a functional assay that elucidated novel functions of TFs and their corresponding REs. Our approach can be applied to better understand gene regulation not only in inhibitory interneuron differentiation but in other tissue and cell types.