Role Of Epigenetics Research Articles

Methylation risk score in peripheral blood predictive of conversion from mild cognitive impairment to Alzheimer's Disease

Background Alzheimer’s disease (AD) is a neurodegenerative and heterogeneous disorder with complex etiology. Mild cognitive impairment (MCI) may represent an intermediate stage of AD, and the ability to identify MCI patients at greater risk of conversion to AD could guide personalized treatments. This study sought to develop a methylation risk score predictive of conversion from MCI to AD using publicly available blood DNA methylation (DNAm) data. Methods Using blood DNA methylation data from an epigenome-wide association study of AD that included 111 subjects with MCI, a methylation risk score of MCI conversion was created using an elastic-net framework. The elastic-net model was trained with a high-variance subset of the DNAm data, age and sex as predictors. Results The final model included three CpG sites: SLC6A3 (cg09892121) and TRIM62 (cg25342005), with a third (cg17292662) near the genes ATP6V1H and RGS20. A significant difference (p < 0.0001, t-test) was observed in the scores for MCI stable subjects compared with MCI converters. No statistically significant difference was observed between AD subjects and controls, suggesting specificity of the risk score for susceptibility to conversion. Conclusions The ability to identify MCI patients at greater risk of progression could inform early interventions and is a critical component in mitigation strategies for AD. This study provides insight into a potential role for epigenetics in the development of a multi-omic risk score of conversion.

Recovery of memory decline during aging - role of epigenetics

Aging is a natural phenomenon associated with the accumulation of multiple alterations, including memory loss. Such deterioration of memory is based on the susceptibility of specific brain regions and the disorders that coincide with aging in those areas. Previous findings suggest that the optimal expression of synaptic plasticity-related genes is essential for memory formation and consolidation. Epigenetic modifications are one of the most crucial factors that cause memory deterioration by inducing the differential expression of synaptic plasticity-related genes. Understanding the fundamental cause of cognitive alterations that arise with aging is very essential for the development of therapeutic and/or preventive approaches. Several strategies have been employed to restore or reverse the memory decline caused by age-associated epigenetic alterations. The present article emphasizes the role of epigenetic alterations caused by histone modifications, DNA methylation, and non-coding ribonucleic acids (RNAs) on memory during aging. Also, we highlight the mechanistic switches of brain aging, including physical exercise, nutraceuticals, epigenetic modifiers, modulators of non-coding RNAs, and associated targets for therapeutic interventions. The emerging field of neuropharmacology and pharmacoepigenomics provides evidence that small drug molecules are currently employed to treat memory loss associated with aging, particularly by targeting epigenetic systems like DNA methylation, chromatin remodeling, histone modifications, and small non-coding RNAs. Therefore, targeting epigenetic modifications could be a potential therapeutic approach for the improvement of synaptic plasticity, neuronal activities, memory, and other brain functions during aging.

Identification of lineage-specific epigenetic regulators FOXA1 and GRHL2 through chromatin accessibility profiling in breast cancer cell lines.

Breast cancer is a heterogeneous disease, and breast cancer cell lines are invaluable for studying this heterogeneity. However, the epigenetic diversity across these cell lines remains poorly understood. In this study, we performed genome-wide chromatin accessibility analysis on 23 breast cancer cell lines, including 2 estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative (ER+/HER2-), 3 ER+/HER2+, 3 HER2+, and 15 triple-negative breast cancer (TNBC) lines. These cell lines were classified into three groups based on their chromatin accessibility: the receptor-positive group (Group-P), TNBC basal group (Group-B), and TNBC mesenchymal group (Group-M). Motif enrichment analysis revealed that only Group-P exhibited coenrichment of forkhead box A1 (FOXA1) and grainyhead-like 2 (GRHL2) motifs, whereas Group-B was characterized by the presence of the GRHL2 motif without FOXA1. Notably, Group-M did not show enrichment of either FOXA1 or GRHL2 motifs. Furthermore, gene ontology analysis suggested that group-specific accessible regions were associated with their unique lineage characteristics. To investigate the epigenetic landscape regulatory roles of FOXA1 and GRHL2, we performed knockdown experiments targeting FOXA1 and GRHL2, followed by assay for transposase-accessible chromatin sequencing analysis. The findings revealed that FOXA1 maintains Group-P-specific regions while suppressing Group-B-specific regions in Group-P cells. In contrast, GRHL2 preserves commonly accessible regions shared between Group-P and Group-B in Group-B cells, suggesting that FOXA1 and GRHL2 play a pivotal role in preserving distinct chromatin accessibility patterns for each group. Specifically, FOXA1 distinguishes between receptor-positive and TNBC cell lines, whereas GRHL2 distinguishes between basal-like and mesenchymal subtypes in TNBC lines.

The Role of Epigenetics in the Formation of Serial Killers: Nature vs. Nurture

The Role of Epigenetics in the Formation of Serial Killers: Nature vs. Nurture

Sex and Gender in Ageing and Longevity: Highlights From an International Course.

Gender medicine is a multidisciplinary science and represents an important perspective for pathophysiological and clinical studies in the third millennium. Here, it is provided an overview of the topics discussed in a recent course on the Role of Sex and Gender in Ageing and Longevity. The paper highlights three themes discussed in the course, i.e., the interaction of gender/sex with, i) the pathophysiology of age-related diseases; ii), the role of genetics and epigenetics in ageing and longevity and, iii) the immune responses of older people to pathogens, vaccines, autoantigens, and allergens. Although largely unexplored, it is clear that sex and gender are modulators of disease biology and treatment outcomes. It is becoming evident that men and women should no longer be considered as subgroups, but as biologically distinct groups of patients deserving consideration for specific therapeutic approaches.

Emerging Roles of Epigenetics in Grapevine and Winegrowing.

Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype-environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.

Epigenetic role of LINE-1 methylation and key genes in pregnancy maintenance

Spontaneous abortion is a pregnancy complication characterized by complex and multifactorial etiology. About 5% of childbearing women are globally affected by early pregnancy loss (EPL) and most of them experience recurrence (RPL). Epigenetic mechanisms and controlled inflammation are crucial for pregnancy maintenance and genetic predispositions may increase the risk affecting the maternal–fetal crosstalk. Combined analyses of global methylation, inflammation and inherited predispositions may contribute to define pregnancy loss etiopathogenesis. LINE-1 epigenetic regulation plays crucial roles during embryo implantation, and its hypomethylation has been associated with senescence and several complex diseases. By analysing a group of 230 women who have gone through pregnancy interruption and comparing those experiencing spontaneous EPL (n = 123; RPL, 54.5%) with a group of normal pregnant who underwent to voluntary interruption (VPI, n = 107), the single statistical analysis revealed significant lower (P < 0.00001) LINE-1 methylation and higher (P < 0.0001) mean cytokine levels (CKs: IL6, IL10, IL17A, IL23) in EPL. Genotyping of the following SNPs accounted for different EPL/RPL risk odds ratio: F13A1 rs5985 (OR = 0.24; 0.06–0.90); F13B rs6003 (OR = 0.23; 0.047–1.1); FGA rs6050 (OR = 0.58; 0.33–1.0); CRP rs2808635/rs876538 (OR = 0.15; 0.014–0.81); ABO rs657152 (OR = 0.48; 0.22–1.08); TP53 rs1042522 (OR = 0.54; 0.32–0.92); MTHFR rs1801133/rs1801131 (OR = 2.03; 1.2–3.47) and FGB rs1800790 (OR = 1.97; 1.01–3.87), although Bonferroni correction did not reach significant outputs. Principal Component Analysis (PCA) and logistic regression disclosed further SNPs positive/negative associations (e.g. APOE rs7412/rs429358; FGB rs1800790; CFH rs1061170) differently arranged and sorted in four significant PCs: PC1 (F13A, methylation, CKs); PC3 (CRP, MTHFR, age, methylation); PC4 (F13B, FGA, FGB, APOE, TP53, age, methylation); PC6 (F13A, CFH, ABO, MTHFR, TP53, age), yielding further statistical power to the association models. In detail, positive EPL risk association was with PC1 (OR = 1.81; 1.33–2.45; P < 0.0001) and negative associations with PC3 (OR = 0.489; 0.37–0.66; P < 0.0001); PC4 (OR = 0.72; 0.55–0.94; P = 0.018) and PC6 (OR = 0.61; 0.46–0.81; P = 0.001). Moreover, significant inverse associations were detected between methylation and CKs levels in the whole group (rIL10 = − 0.22; rIL17A = − 0.25; rIL23 = − 0.19; rIL6 = − 0.22), and methylation with age in the whole group, EPL and RPL subgroups (r2TOT = 0.147; r2EPL = 0.136; r2RPL = 0.248), while VPI controls lost significance (r2VPI = 0.011). This study provides a valuable multilayer approach for investigating epigenetic abnormalities in pregnancy loss suggesting genetic-driven dysregulations and anomalous epigenetic mechanisms potentially mediated by LINE-1 hypomethylation. Women with unexplained EPL might benefit of such investigations, providing new insights for predicting the pregnancy outcome and for treating at risk women with novel targeted epidrugs.

The Role of Epigenetics and Contributing Impact of Stress, Multigenerational, and Developmental Factors in Opiate Addiction.

Drug addiction is characterized by maladaptive neural plasticity, particularly in vulnerable individuals exposed to drugs of abuse. Epigenetic factors include environmental influences, events during development, and stress adaptations, which seem to play an important role in the neuropathogenesis of drug addiction. This critical review hypothesizes that epigenetic modulation increases an individual's susceptibility to opiate addiction in three key areas of epigenetic study: developmental, stress-related, and transgenerational effects. The widespread use of opioids for clinical and recreational purposes raises significant societal and scientific concerns. Despite the increasing prevalence of opioid abuse, there is limited comprehensive knowledge about the impact of epigenetic factors on opiate addiction manifestation. This review hypothesizes that epigenetic modulation increases susceptibility to opiate addiction, exploring three key areas of epigenetic study: developmental, stress-related, and transgenerational effects. Current literature reveals a correlation between epigenetic influences and vulnerability to drug addiction, specifically in the context of opioid use. Epigenetics, the modulation of genetic expression beyond genotypic predisposition, plays a crucial role in an individual's susceptibility to drug addiction. Studies suggest that epigenetic mechanisms, once considered static in the adult brain, continue to influence synaptic plasticity and long-term memory, particularly in the endogenous opioid system. This review examines the effects of opioids and stress on epigenetic modifications, providing evidence of increased vulnerability to opiate addiction. Animal studies demonstrate how developmental adversities and adolescent exposure to substances can induce persistent epigenetic changes, predisposing individuals to opiate addiction in adulthood. Moreover, the review explores the transgenerational effects of opioid exposure during adolescence, suggesting that functional epigenetic neuroadaptations within the nucleus accumbens can persist for multiple generations. The examination of DNA methylation patterns in opioid addicts reveals potential markers for identifying susceptibility to opiate vulnerability. A critical analysis of research reports supports the hypothesis that developmental, transgenerational, and stress-related epigenetic mechanisms have a profound role in increasing the risk of opioid addiction susceptibility. Each study confirmed that developmental, stress-related, or transgenerational epigenetic regulations have a correlation to increased opiate sensitization and vulnerability. Unfortunately, every study reviewed was unable to elucidate an epigenetic mechanism to explain a specific neuropathogenesis of opiate drug addiction vulnerability, emphasizing our lack of knowledge in the complex pathology of epigenetics.

Modifications to gene body methylation do not alter gene expression plasticity in a reef-building coral.

As coral reefs continue to decline due to climate change, the role of coral epigenetics (specifically, gene body methylation, GBM) in coral acclimatization warrants investigation. The evidence is currently conflicting. In diverse animal phyla, the baseline GBM level is associated with gene function: continuously expressed "housekeeping" genes are typically highly methylated, while inducible context-dependent genes have low or no methylation at all. Some authors report an association between GBM and the environment and interpret this observation as evidence of the GBM's role in acclimatization. Yet, others argue that the correlation between GBM change and gene expression change is typically absent or negligible. Here, we used the reef-building coral, Acropora millepora, to test whether environmentally driven changes in GBM are associated with a gene's ability to respond to environmental changes (plasticity) rather than expression level. We analyzed two cases of modified gene expression plasticity observed in a 3-week-long heat acclimatization experiment. The first one was a group of heat-induced genes that failed to revert their expression after the coral was translocated back to the control tank. The second case involved genes that changed the magnitude of their response to the daily temperature fluctuations over the course of the experiment. In both cases, we found negligible or no association with GBM change. We conclude that although both gene expression plasticity and GBM can change during acclimatization, there is no direct association between the two. This adds to the increasing volume of evidence that the function of GBM in invertebrates is unrelated to acclimatization on physiological timescales.

Single-cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines in L. major infection.

The hallmark characteristic of macrophages lies in their inherent plasticity, allowing them to adapt to dynamic microenvironments. Leishmania strategically modulates the phenotypic plasticity of macrophages, creating a favorable environment for intracellular survival and persistent infection through regulatory cytokine such as interleukin (IL)-10. Nevertheless, these effector cells can counteract infection by modulating crucial cytokines like IL-12 and key components involved in its production. Using sophisticated tool of single-cell assay for transposase accessible chromatin (ATAC) sequencing, we systematically examined the regulatory axis of IL-10 and IL-12 in a time-dependent manner during Leishmania major infection in macrophages Our analysis revealed the cellular heterogeneity post-infection with the regulators of IL-10 and IL-12, unveiling a reciprocal relationship between these cytokines. Notably, our significant findings highlighted the presence of sleepy macrophages and their pivotal role in mediating reciprocity between IL-10 and IL-12. To summarize, the roles of cytokine expression, transcription factors, cell cycle, and epigenetics of host cell machinery were vital in identification of sleepy macrophages, which is a transient state where transcription factors controlled the epigenetic remodeling and expression of genes involved in pro-inflammatory cytokine expression and recruitment of immune cells.IMPORTANCELeishmaniasis is an endemic affecting 99 countries and territories globally, as outlined in the 2022 World Health Organization report. The disease's severity is compounded by compromised host immune systems, emphasizing the pivotal role of the interplay between parasite and host immune factors in disease regulation. In instances of cutaneous leishmaniasis induced by L. major, macrophages function as sentinel cells. Our findings indicate that the plasticity and phenotype of macrophages can be modulated to express a cytokine profile involving IL-10 and IL-12, mediated by the regulation of transcription factors and their target genes post-L. major infection in macrophages. Employing sophisticated methodologies such as single-cell ATAC sequencing and computational genomics, we have identified a distinctive subset of macrophages termed "sleepy macrophages." These macrophages exhibit downregulated housekeeping genes while expressing a unique set of variable features. This data set constitutes a valuable resource for comprehending the intricate host-parasite interplay during L. major infection.

Updates on the Role of Periodontitis-Related Epigenetics, Inflammation, Oral Microbiome, and Treatment in Cardiovascular Risk.

Substantial evidence has recently been gathered to substantiate the epidemiological correlation between this oral inflammatory ailment and several systemic health disorders, such as cardiovascular diseases (CVDs). It is worth noting that certain shared factors exist among individuals with periodontal disease (PD) and CVDs, like obesity or overweight, minimal physical activities, smoking habits, male gender, low socioeconomic position, advanced age, and limited educational attainment. Moreover, recent research suggests a distinct and separate relationship between PD and CVDs. This literature review discusses the association between CVDs and PD and their underlying mechanisms and connections. Current literature strongly confirms a correlation between cardiovascular risk and PD. The underlying mechanisms involve inflammation, epigenetics, epithelial dysfunction, oral microbiome dysbiosis, and the efficacy of periodontitis treatment. Future investigations are required to comprehend these complex interactions and develop targeted interventions for oral health improvement and reduction in cardiovascular risk.

The role of epigenetics in male and female infertility

Introduction. Today, infertility is a global problem that affects about 48.5 million married couples worldwide. It has been suggested that epigenetic aberrations are of great importance for reproductive health, as they account for an interactive relationship between genomic landscape, interplay with gene environment and disease phenotype. A new understanding on etiology of complex non-Mendelian disease traits has aroused a growing interest in reproductive epigenetics.Aim: to analyze available publications on epigenetic aspects of male and female infertility as well as nutrition-related risk factors.Materials and Methods. There was conducted a search for publications in the electronic databases PubMed, Google Scholar and Library to be selected in accordance with PRISMA recommendations. All relevant articles published before November 2023 were included in this review. As a result of the search, there were extracted 530 publications from PubMed, 57 publications – from eLibrary and 23 publications – from Google Scholar. Duplicates and non-full-text article versions were excluded.Results. Environmental factors play an important role in generation and maintenance of epigenetic marks. DNA methylation abnormalities can lower human fertility. Altered protamine level may affect epigenetic paternally transmitted DNA information. Long-term infertility is associated with a modified methylome in euploid blastocysts primarily affecting regulation of genomic imprinting. Both excess and deficiency of trace elements are associated with adverse pregnancy outcomes, similarly applied infertility.Conclusion. Despite that epigenetic mechanisms, genes, nutrition and dietary supplements discussed here affect infertility, while a relevant recommended dose has not yet been determined, it was noted that such parameters may positively influence fertility. However, more comprehensive and longitudinal human studies are required to examine their relationship to male and female reproductive functions.

Hypomethylation of Wnt signaling regulator genes in developmental language disorder.

Background: Developmental language disorder (DLD) is a neurodevelopmental disorder. Considering the pivotal role of epigenetics in neurodevelopment, we examined any altered DNA methylation between DLD and control subjects. Materials & methods: We looked into genome-wide methylation differences between DLD and control groups. The findings were validated by quantitative PCR (qPCR). Results: In the DLD group, differential methylation of CpG sites was observed in the Wnt signaling regulator genes APCDD1, AMOTL1, LRP5, MARK2, TMEM64, TRABD2B, VEPH1 and WNT2B. Hypomethylation of APCDD1, LRP5 and WNT2B was confirmed by qPCR. Conclusion: This is the first report associating Wnt signaling with DLD. The findings are relevant in the light of the essential role of Wnt in myelination, and of the altered myelination in DLD.

Serotonin Transporter-dependent Histone Serotonylation in Placenta Contributes to the Neurodevelopmental Transcriptome

Brain development requires appropriate regulation of serotonin (5-HT) signaling from distinct tissue sources across embryogenesis. At the maternal-fetal interface, the placenta is thought to be an important contributor of offspring brain 5-HT and is critical to overall fetal health. Yet, how placental 5-HT is acquired, and the mechanisms through which 5-HT influences placental functions, are not well understood. Recently, our group identified a novel epigenetic role for 5-HT, in which 5-HT can be added to histone proteins to regulate transcription, a process called H3 serotonylation. Here, we show that H3 serotonylation undergoes dynamic regulation during placental development, corresponding to gene expression changes that are known to influence key metabolic processes. Using transgenic mice, we demonstrate that placental H3 serotonylation is dependent on 5-HT uptake by the serotonin transporter (SERT/SLC6A4). SERT deletion robustly reduces enrichment of H3 serotonylation across the placental genome, and disrupts neurodevelopmental gene networks in early embryonic brain tissues. Thus, these findings suggest a novel role for H3 serotonylation in coordinating placental transcription at the intersection of maternal physiology and offspring brain development.

Integrative analysis identifies gene signatures mediating the effect of DNA methylation on asthma severity and lung function

DNA methylation (DNAm) changes play a key role in regulating gene expression in asthma. To investigate the role of epigenetics and transcriptomics change in asthma, we used publicly available DNAm (asthmatics, n = 96 and controls, n = 46) and gene expression (asthmatics, n = 79 and controls, n = 39) data derived from bronchial epithelial cells (BECs). We performed differential methylation/expression and weighted co-methylation/co-expression network analyses to identify co-methylated and co-expressed modules associated with asthma severity and lung function. For subjects with both DNAm and gene expression data (asthmatics, n = 79 and controls, n = 39), machine-learning technique was used to prioritize CpGs and differentially expressed genes (DEGs) for asthma risk prediction, and mediation analysis was used to uncover DEGs that mediate the effect of DNAm on asthma severity and lung function in BECs. Finally, we validated CpGs and their associated DEGs and the asthma risk prediction model in airway epithelial cells (AECs) dataset. The asthma risk prediction model based on 18 CpGs and 28 DEGs showed high accuracy in both the discovery BEC dataset with area under the receiver operating characteristic curve (AUC) = 0.99 and the validation AEC dataset (AUC = 0.82). Genes in the three co-methylated and six co-expressed modules were enriched in multiple pathways including WNT/beta-catenin signaling and notch signaling. Moreover, we identified 35 CpGs correlated with DEGs in BECs, of which 17 CpGs including cg01975495 (SERPINE1), cg10528482 (SLC9A3), cg25477769 (HNF1A) and cg26639146 (CD9), cg17945560 (TINAGL1) and cg10290200 (FLNC) were replicated in AECs. These DEGs mediate the association between DNAm and asthma severity and lung function. Overall, our study investigated the role of DNAm and gene expression change in asthma and provided an insight into the mechanisms underlying the effects of DNA methylation on asthma, asthma severity and lung function.

Role of Epigenetics for the Efficacy of Cisplatin.

The clinical utility of the chemotherapeutic agent cisplatin is restricted by cancer drug resistance, which is either intrinsic to the tumor or acquired during therapy. Epigenetics is increasingly recognized as a factor contributing to cisplatin resistance and hence influences drug efficacy and clinical outcomes. In particular, epigenetics regulates gene expression without changing the DNA sequence. Common types of epigenetic modifications linked to chemoresistance are DNA methylation, histone modification, and non-coding RNAs. This review provides an overview of the current findings of various epigenetic modifications related to cisplatin efficacy in cell lines in vitro and in clinical tumor samples. Furthermore, it discusses whether epigenetic alterations might be used as predictors of the platinum agent response in order to prevent avoidable side effects in patients with resistant malignancies. In addition, epigenetic targeting therapies are described as a possible strategy to render cancer cells more susceptible to platinum drugs.

Epigenetics and the improvement of crop plants

Epigenetics is a term that refers to the changes in gene expression that are heritable and induced by DNA methylation, histones post-translational modifications, or sncRNA, not resulting from the DNA sequence rearrangements. Epigenetic modifications influence gene expression, and thus, the plasticity of plants' development and phenotype in response to external and internal factors. Until recently, the only known epigenetic modification of the DNA in eukaryotic organisms was 5-methylcytosine. The growing interest in epigenetics and the development of sensitive detection methods enabled the discovery of other modifications of the DNA nitrogenous bases, i.e., 4-methylcytosine and 6-methyladenine. However, whilst research on the 5mC distribution and role in eukaryotic organisms is widespread, analyses regarding 6mA are scarced. Nevertheless, there are indications of a potential epigenetic role of 6-methyladenine in eukaryotic genomes. Understanding epigenetic mechanisms, which are triggered in response to environmental changes, is crucial for agriculture. This review shows epigenetic mechanisms, with particular emphasis on adenine methylation in plants, as well as the role of epigenetic variation in epibreeding, affecting the improvement of agronomic traits.

Expanding Role of Epigenetics in Human Health and Disease

Expanding Role of Epigenetics in Human Health and Disease

Transcriptomic analysis identifies B-lymphocyte kinase as a therapeutic target for desmoplastic small round cell tumor cancer stem cell-like cells

Desmoplastic small round cell tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The tumor is refractory to treatment with a 5-year survival rate of only 15–25%, necessitating the development of novel therapeutics, especially those able to target chemoresistant subpopulations. Novel in vitro cancer stem cell-like (CSC-like) culture conditions increase the expression of stemness markers (SOX2, NANOG) and reduce DSRCT cell line susceptibility to chemotherapy while maintaining the ability of DSRCT cells to form xenografts. To gain insights into this chemoresistant model, RNA-seq was performed to elucidate transcriptional alterations between DSRCT cells grown in CSC-like spheres and normal 2-dimensional adherent state. Commonly upregulated and downregulated genes were identified and utilized in pathway analysis revealing upregulation of pathways related to chromatin assembly and disassembly and downregulation of pathways including cell junction assembly and extracellular matrix organization. Alterations in chromatin assembly suggest a role for epigenetics in the DSRCT CSC-like state, which was further investigated with ATAC-seq, identifying over 10,000 differentially accessible peaks, including 4444 sphere accessible peaks and 6,120 adherent accessible peaks. Accessible regions were associated with higher gene expression, including increased accessibility of the CSC marker SOX2 in CSC-like culture conditions. These analyses were further utilized to identify potential CSC therapeutic targets, leading to the identification of B-lymphocyte kinase (BLK) as a CSC-enriched, EWSR1-WT1-regulated, druggable target. BLK inhibition and knockdown reduced CSC-like properties, including abrogation of tumorsphere formation and stemness marker expression. Importantly, BLK knockdown reduced DSRCT CSC-like cell chemoresistance, making its inhibition a promising target for future combination therapy.

Alterations in leukocyte DNA methylome are associated to immunosuppression in severe clinical phenotypes of septic patients.

Sepsis patients experience a complex interplay of host pro- and anti-inflammatory processes which compromise the clinical outcome. Despite considering the latest clinical and scientific research, our comprehension of the immunosuppressive events in septic episodes remains incomplete. Additionally, a lack of data exists regarding the role of epigenetics in modulating immunosuppression, subsequently impacting patient survival. To advance the current understanding of the mechanisms underlying immunosuppression, in this study we explored the dynamics of DNA methylation using the Infinium Methylation EPIC v1.0 BeadChip Kit in leukocytes from patients suffering from sepsis, septic shock, and critically ill patients as controls, within the first 24 h after admission in the Intensive Care Unit of a tertiary hospital. Employing two distinct analysis approaches (DMRcate and mCSEA) in comparing septic shock and critically ill patients, we identified 1,256 differentially methylated regions (DMRs) intricately linked to critical immune system pathways. The examination of the top 100 differentially methylated positions (DMPs) between septic shock and critically ill patients facilitated a clear demarcation among the three patient groups. Notably, the top 6,657 DMPs exhibited associations with organ dysfunction and lactate levels. Among the individual genes displaying significant differential methylation, IL10, TREM1, IL1B, and TNFAIP8 emerged with the most pronounced methylation alterations across the diverse patient groups when subjected to DNA bisulfite pyrosequencing analysis. These findings underscore the dynamic nature of DNA methylation profiles, highlighting the most pronounced alterations in patients with septic shock, and revealing their close association with the disease.