DNA Methylation Research Articles

DNA methylation and immune evasion in triple-negative breast cancer: challenges and therapeutic opportunities

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Chemotherapy remains the primary treatment option, yet TNBC frequently develops resistance, leading to relapse and metastasis. Emerging evidence highlights the potential of combining DNA methylation inhibitors with immune checkpoint inhibitors (ICIs). DNA methylation contributes to immune escape by silencing immune-regulatory genes, thereby reducing the tumor’s visibility to immune cells. Reversing this epigenetic modification can reinvigorate immune surveillance and enhance the efficacy of immunotherapies. This review discusses the role of DNA methylation in TNBC progression and immune evasion, focusing on recent advances in combination therapies involving DNA methylation inhibitors and ICIs. We discuss the underlying mechanisms that enable these therapeutic synergies, preclinical and clinical evidence supporting the approach, and the challenges posed by tumor heterogeneity, drug resistance, and toxicity. Finally, we explore the potential for personalized treatment strategies incorporating multi-omics data to optimize therapeutic outcomes. The integration of epigenetic therapies and immunotherapy offers a promising avenue for improving survival in TNBC patients.

A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits

Background DNA methylation (DNAm) provides a window to characterize the impacts of environmental exposures and the biological aging process. Epigenetic clocks are often trained on DNAm using penalized regression of CpG sites, but recent evidence suggests potential benefits of training epigenetic predictors on principal components. Methodology/findings We developed a pipeline to simultaneously train three epigenetic predictors; a traditional CpG Clock, a PCA Clock, and a SuperLearner PCA Clock (SL PCA). We gathered publicly available DNAm datasets to generate i) a novel childhood epigenetic clock, ii) a reconstructed Hannum adult blood clock, and iii) as a proof of concept, a predictor of polybrominated biphenyl exposure using the three developmental methodologies. We used correlation coefficients and median absolute error to assess fit between predicted and observed measures, as well as agreement between duplicates. The SL PCA clocks improved fit with observed phenotypes relative to the PCA clocks or CpG clocks across several datasets. We found evidence for higher agreement between duplicate samples run on alternate DNAm arrays when using SL PCA clocks relative to traditional methods. Analyses examining associations between relevant exposures and epigenetic age acceleration (EAA) produced more precise effect estimates when using predictions derived from SL PCA clocks. Conclusions We introduce a novel method for the development of DNAm-based predictors that combines the improved reliability conferred by training on principal components with advanced ensemble-based machine learning. Coupling SuperLearner with PCA in the predictor development process may be especially relevant for studies with longitudinal designs utilizing multiple array types, as well as for the development of predictors of more complex phenotypic traits.

Epigenetic Modulation Directs Recovery Post LASIK and SMILE Surgery: An Experimental Study

Purpose: refractive surgery, such as LASIK and SMILE, induces a wound healing response that leads to significant corneal stromal remodeling. We have shown that the protein profile in the stroma changes dramatically immediately post-surgery. However, the methylation status of the DNA post-refractive surgery remains unknown. Design/Participants: DNA methylation study. Refractive surgery (SMILE/LASIK) performed on donor eye globes. Method: we investigated the epigenetic changes post-surgery in relation to long term ECM remodeling in an experimental ex vivo study design. Donor globes (n = 19) were obtained from the eye bank. Three globes served as non-surgical controls while SMILE (-6DS) and LASIK surgery (-6DS) were performed on eight globes each and incubated for 3 days and 2 weeks (n = 4 per group per time point). Here, we compared the DNA methylation landscapes of LASIK and SMILE stroma using the Illumina Infinium Human Methylation 850 EPIC array (HM850). Results: significant changes in DNA methylation patterns were observed post-operatively in both LASIK and SMILE groups. Specific genes involved in the activation of actin cytoskeleton and inflammation (smad3, prkca and ssh2) showed hypomethylation in LASIK after 2 weeks and LASIK SMILE after 3 days, respectively, suggesting their active role in corneal repair. The genes (gaa, gstm1, mgat1, galnt9 and galnt5) involved in sphingolipid metabolism and mucin biosynthesis showed hypomethylation in SMILE after 3 days. Conclusions: our results suggest that altered DNA methylation patterns may have relevance to the development of complications of haze post-refractive surgery. It also presents the opportunity to utilize drugs that regulate chromatin remodeling for optimal outcomes.

Epigenetic modifications in bladder cancer: crosstalk between DNA methylation and miRNAs

Bladder cancer (BC) is a malignant tumor characterized by a high incidence of urinary system diseases. The complex pathogenesis of BC has long been a focal point in medical research. With the robust development of epigenetics, the crucial role of epigenetic modifications in the occurrence and progression of BC has been elucidated. These modifications not only affect gene expression but also impact critical biological behaviors of tumor cells, including proliferation, differentiation, apoptosis, invasion, and metastasis. Notably, DNA methylation, an important epigenetic regulatory mechanism, often manifests as global hypomethylation or hypermethylation of specific gene promoter regions in BC. Alterations in this methylation pattern can lead to increased genomic instability, which profoundly influences the expression of proto-oncogenes and tumor suppressor genes. MiRNAs, as noncoding small RNAs, participate in various biological processes of BC by regulating target genes. Consequently, this work aims to explore the interaction mechanisms between DNA methylation and miRNAs in the occurrence and development of BC. Research has demonstrated that DNA methylation not only directly influences the expression of miRNA genes but also indirectly affects the maturation and functionality of miRNAs by modulating the methylation status of miRNA promoter regions. Simultaneously, miRNAs can regulate DNA methylation levels by targeting key enzymes such as DNA methyltransferases (DNMTs), thereby establishing a complex feedback regulatory network. A deeper understanding of the crosstalk mechanisms between DNA methylation and miRNAs in BC will contribute to elucidating the complexity and dynamics of epigenetic modifications in this disease, and may provide new molecular targets and strategies for the early diagnosis, treatment, and prognostic evaluation of BC.

Epigenome-Wide Association Study of Asthma Exacerbations in Europeans.

Asthma exacerbations (AEs) represent the major contributor to the global asthma burden. Although genetic and environmental factors have been associated with AEs, the role of epigenetics remains uncovered. This study aimed to identify whole blood DNA methylation (DNAm) markers associated with AEs in Europeans. DNAm was assessed in 406 blood samples from Spanish individuals using the Infinium MethylationEPIC microarray (Illumina). An epigenome-wide association study was conducted to test the association of DNAm with AEs at differentially methylated positions, regions, and epigenetic modules. CpGs suggestively associated with AEs(false discovery rate [FDR] < 0.1) were followed up for replication in 222 European individuals, and the genome-wide significance (p < 9 × 10-8) was declared after meta-analyzing the discovery and replication samples. Additional assessment was performed using nasal tissue DNAm data from 155 Spanish individuals. The effects of genetic variation on DNAm were assessed through cis-methylation quantitative trait loci (meQTL) analysis. Enrichment analyses of previous EWAS signals were conducted. Four CpGs were associated with AEs, and two were replicated and reached genomic significance in the meta-analysis (annotated to ZBTB16 and BAIAP2). Of those, CpG cg25345365 (ZBTB16) was cross-tissue validated in nasal epithelium (p= 0.003) and associated with five independent meQTLs (FDR < 0.05). Additionally, four differentially methylated regions and one module were significantly associated with AEs. Enrichment analyses revealed an overrepresentation of prior epigenetic associations with prenatal and environmental exposures, immune-mediated diseases, and mortality. DNAm in whole blood and nasal samples may contribute to AEs in Europeans, capturing genetic and environmental risk factors.

Age-related changes in DNA methylation in a sample of elderly Brazilians

BackgroundAge-related changes in DNA methylation (DNAm) play a critical role in regulating gene expression. However, most epigenome-wide association studies have predominantly focused on individuals of European descent. This study aims to characterize longitudinal changes in DNAm patterns in a cohort of elderly Brazilian participants.MethodsDNAm profiles were collected approximately nine years apart from 23 elderly Brazilian individuals using the Illumina Infinium MethyationEPIC BeadChip. Using mixed-effects models, we examined changes in DNAm patterns using both quantitative age and binary timepoint (e.g., baseline vs. follow-up) as predictors of interest to identify differentially methylated positions (DMPs). Significant DMPs were compared with a list of previously identified age-related DMPs. Differentially methylated regions (DMRs) were also identified using DMRcate. Gene ontology (GO) pathway enrichment analyses were performed to explore the functional significance of identified DMPs and DMRs.ResultsOf the 586,229 autosomal probes included in the differential methylation analyses, 2768 significant (FDR < 0.05) age-associated DMPs (aDMPs) and 2757 significant (FDR < 0.05) timepoint-associated DMPs (tpDMPs) were identified. Of the 2768 aDMPs, 1471 were replicated from previous studies. Of the 1297 non-replicated CpGs, 77.4% were exclusive to the EPIC array. The DMR analyses identified 305 age-associated DMRs (aDMRs) and 372 timepoint-associated DMRs (tpDMRs). Both aDMPs and aDMRs exhibited age-related hypermethylation within CpG islands and promoter regions of the genome, whereas hypomethylation predominantly occurred in interCGI and intergenic regions and introns. The GO enrichment analyses identified several neurological and cognition-related pathways enriched for hypermethylated CpG islands, many of which were mapped near transcription start sites and first exon regions.ConclusionsThis longitudinal study identified age-associated and timepoint-associated DMPs and DMRs in a sample of elderly Brazilians. Most of the non-replicated CpGs were found to be on the new EPIC array, suggesting that more age-related studies using the EPIC array are required to validate these CpGs. The GO pathway enrichment analyses identified age-related enrichment of several gene sets related to cognitive and physical decline in elderly populations. The enrichment of these sites could provide evidence for age-related neurodegeneration and cognitive decline in elderly populations.

DNA Methylation in Long-term Memory.

Understanding neural mechanisms of memory has been one of the key questions in biology. Long-term memory specifically, allows one to travel mentally without constraints of time and space (1). A long-term memory must have gone through a series of temporal processes: encoding, consolidation, storage, and retrieval. Decades of studies have revealed cellular and molecular mechanisms underlying each process. In this paper, we will first review the emerging concept of memory engrams and technologies of engram labeling, as these methods provide a new avenue to study the molecular mechanisms for memory. Then, we will focus on DNA methylation and its role in long-term memory. Lastly, we will discuss some key remaining questions in this field and their implications in memory-related disease.

The Role of the DNA Methyltransferase Family and the Therapeutic Potential of DNMT Inhibitors in Tumor Treatment

Members of the DNA methyltransferase (DNMT) family have been recognized as major epigenetic regulators of altered gene expression during tumor development. They establish and maintain DNA methylation of the CpG island of promoter and non-CpG region of the genome. The abnormal methylation status of tumor suppressor genes (TSGs) has been associated with tumorigenesis, leading to genomic instability, improper gene silence, and immune evasion. DNMT1 helps preserve methylation patterns during DNA replication, whereas the DNMT3 family is responsible for de novo methylation, creating new methylation patterns. Altered DNA methylation significantly supports tumor growth by changing gene expression patterns. FDA-approved DNMT inhibitors reverse hypermethylation-induced gene repression and improve therapeutic outcomes for cancer. Recent studies indicate that combining DNMT inhibitors with chemotherapies and immunotherapies can have synergistic effects, especially in aggressive metastatic tumors. Improving the treatment schedules, increasing isoform specificity, reducing toxicity, and utilizing genome-wide analyses of CRISPR-based editing to create personalized epigenetic therapies tailored to individual patient needs are promising strategies for enhancing therapeutic outcomes. This review discusses the interaction between DNMT regulators and DNMT1, its binding partners, the connection between DNA methylation and tumors, how these processes contribute to tumor development, and DNMT inhibitors’ advancements and pharmacological properties.

Epigenome-wide association study, meta-analysis, and multiscore profiling of whole blood in Parkinson's disease.

An increasing body of evidence indicates altered DNA methylation in Parkinson's disease, yet the reproducibility and utility of such methylation changes are largely unexplored. We aimed to further elucidate the role of dysregulated DNA methylation in Parkinson's disease and to evaluate the biomarker potential of methylation-based profiling. We conducted an epigenome-wide association study (EWAS) in whole blood, including 280 Parkinson's disease and 279 control participants from Oslo, Norway. Next, we took advantage of data from the Parkinson's Progression Markers Initiative (PPMI) and a previously published EWAS to conduct a whole blood EWAS meta-analysis in Parkinson's disease, incorporating results from a total of 3068 participants. Finally, we generated multiple methylation-based scores for each Oslo and PPMI participant and tested their association with disease status, individually and in a joint multiscore model. In EWAS meta-analysis, we confirm SLC7A11 hypermethylation and nominate a novel differentially methylated CpG near LPIN1. A joint multiscore model incorporating polygenic risk and methylation-based estimates of epigenetic Parkinson's disease risk, smoking, and leukocyte proportions differentiated patients from control participants with an area under the receiver-operator curve of 0.82 in the Oslo cohort and 0.65 in PPMI. Our results highlight the power of DNA methylation profiling to capture multiple aspects of disease risk, indicating a biomarker potential for precision medicine in neurodegenerative disorders. The reproducibility of specific differentially methylated CpGs across data sets was limited but may improve if future studies are designed to account for disease stage and incorporate environmental exposure data.

Associations between lifestyle factors, physiological conditions, and epigenetic age acceleration in an Asian population

Epigenetic clocks use DNA methylation (DNAm) levels to predict an individual’s biological age. However, relationships between lifestyle/biomarkers and epigenetic age acceleration (EAA) in Asian populations remain unknown. We here explored associations between lifestyle factors, physiological conditions, and epigenetic markers, including HannumEAA, IEAA, PhenoEAA, GrimEAA, DunedinPACE, DNAm-based smoking pack-years (DNAmPACKYRS), and DNAm plasminogen activator inhibitor 1 level (DNAmPAI1). A total of 2474 Taiwan Biobank (TWB) individuals aged between 30 and 70 provided physical health examinations, lifestyle questionnaire surveys, and blood and urine samples. Partial correlation analysis (while adjusting for chronological age, smoking, and drinking status) demonstrated that 29 factors were significantly correlated with at least one epigenetic marker (Pearson’s correlation coefficient |r|> 0.15). Subsequently, by exploring the model with the smallest Akaike information criterion (AIC), we identified the best model for each epigenetic marker. As a DNAm-based marker demonstrated to predict healthspan and lifespan with greater accuracy, GrimEAA was also found to be better explained by lifestyle factors and physiological conditions. Totally 15 factors explained 44.7% variability in GrimEAA, including sex, body mass index (BMI), waist-hip ratio (WHR), smoking, hemoglobin A1c (HbA1c), high-density lipoprotein cholesterol (HDL-C), creatinine, uric acid, gamma-glutamyl transferase (GGT), hemoglobin, and five cell-type proportions. In summary, smoking, elevated HbA1c, BMI, WHR, GGT, and uric acid were associated with more than one kind of EAA. At the same time, higher HDL-C and hemoglobin were related to epigenetic age deceleration (EAD). These findings offer valuable insights into biological aging.

Epigenomic Echoes—Decoding Genomic and Epigenetic Instability to Distinguish Lung Cancer Types and Predict Relapse

Genomic and epigenomic instability are defining features of cancer, driving tumor progression, heterogeneity, and therapeutic resistance. Central to this process are epigenetic echoes, persistent and dynamic modifications in DNA methylation, histone modifications, non-coding RNA regulation, and chromatin remodeling that mirror underlying genomic chaos and actively influence cancer cell behavior. This review delves into the complex relationship between genomic instability and these epigenetic echoes, illustrating how they collectively shape the cancer genome, affect DNA repair mechanisms, and contribute to tumor evolution. However, the dynamic, context-dependent nature of epigenetic changes presents scientific and ethical challenges, particularly concerning privacy and clinical applicability. Focusing on lung cancer, we examine how specific epigenetic patterns function as biomarkers for distinguishing cancer subtypes and monitoring disease progression and relapse.

Epigenetic insights into fertility: involvement of immune cell methylation in dairy cows reproduction.

Infertility and post-partum reproductive diseases are significant challenges in cattle farming, with the maternal immune system's ability to recognize and tolerate the embryo being crucial for successful gestation. DNA methylation in hematopoietic cells may influence susceptibility to post-partum fertility issues, making the identification of epigenetic changes vital for sustainable animal production. This study aimed to characterize the methylome of immune cells in relation to fertility, potentially enabling early detection of subfertility. Using whole epigenome sequencing and enzymatic methyl-seq, we analyzed DNA methylation patterns in blood from twelve Holstein cows before the onset of any disease. Our findings revealed 216,990 differentially methylated cytosines (DMCs) between fertile and subfertile cows. Notably, three genes-Interferon tau-3 (IFNT3), KIAA0825, and RAS-Related Protein 2A-showed high significance in their differential methylation between fertile and subfertile cows. IFNT3, crucial for early embryonic development, had seven DMCs in its TSS shores in subfertile cows. Additionally, the KLRA1 gene (Ly49), was identified as containing DMCs across all five genomic regions analyzed (TSS shores, exons, introns, downstream, and distal intergenic). Its widespread differential methylation highlights its potential impact on fertility. Key interleukin genes, including IL6, IL15, IL22, and IL36G, also showed multiple DMCs, reinforcing the role of the immune system in bovine fertility. These findings illustrate the potential control that immune cell epigenetics exert on cattle post-partum fertility. Additionally, this study suggests that the risk of developing subfertility could potentially be estimated with as few as 220 biomarkers, paving the way for enhanced animal health management and improved fertility treatments.

Melampsora larici-populina homologous effectors Mlp72983 and Mlp52166 display cell-type specific accumulation in Arabidopsis and Populus

Plants interact with microorganisms that can cause diseases and reduce crop productivity. The fungal pathogen Melampsora larici-populina (Mlp) causes the leaf rust disease of poplar trees by secreting proteins, termed effectors, into host tissues to promote pathogenesis. In this study, we functionally characterized two homologous Mlp candidate secreted effector proteins (CSEPs), Mlp72983 and Mlp52166. Confocal microscopy experiments revealed that Mlp72983 has cell type-specific differential localization. It accumulates in the guard cells’ chloroplast of the epidermis and in the nucleus of the spongy mesophyll of Arabidopsis thaliana and Populus alba x Populus tremula. Mlp52166 has a nucleocytosolic accumulation in the epidermal layer and has nuclear localization in the mesophyll layer of the two species. Transcriptomic experiments showed that Mlp72983 and Mlp52166 deregulate plant genes, when constitutively expressed in either Arabidopsis or poplar. The two CSEPs deregulate genes that encode histones, hydroxysteroid dehydrogenases and multidrug and toxic compound extrusion proteins, with roles in DNA repair, methylation, and xenobiotic detoxification. Inoculation assays showed that CSEPs overexpression in poplar transgenics did not enhance susceptibility to rust infection. Despite being closely related in sequence identity, Mlp72983 and Mlp52166 have cell-type specific subcellular localization and deregulate mostly unique sets of plant genes.

S-Adenosylmethionine: A Multifaceted Regulator in Cancer Pathogenesis and Therapy

S-adenosylmethionine (SAMe) is a key methyl donor that plays a critical role in a variety of cellular processes, such as DNA, RNA and protein methylation, essential for maintaining genomic stability, regulating gene expression and maintaining cellular homeostasis. The involvement of SAMe in cancer pathogenesis is multifaceted, as through its multiple cellular functions, it can influence tumor initiation, progression and therapeutic resistance. In addition, the connection of SAMe with polyamine synthesis and oxidative stress management further underscores its importance in cancer biology. Recent studies have highlighted the potential of SAMe as a biomarker for cancer diagnosis and prognosis. Furthermore, the therapeutic implications of SAMe are promising, with evidence suggesting that SAMe supplementation or modulation could improve the efficacy of existing cancer treatments by restoring proper methylation patterns and mitigating oxidative damage and protect against damage induced by chemotherapeutic drugs. Moreover, targeting methionine cycle enzymes to both regulate SAMe availability and SAMe-independent regulatory effects, particularly in methionine-dependent cancers such as colorectal and lung cancer, presents a promising therapeutic approach. Additionally, exploring epitranscriptomic regulations, such as m6A modifications, and their interaction with non-coding RNAs could enhance our understanding of tumor progression and resistance mechanisms. Precision medicine approaches integrating patient subtyping and combination therapies with chemotherapeutics, such as decitabine or doxorubicin, together with SAMe, can enhance chemosensitivity and modulate epigenomics, showing promising results that may improve treatment outcomes. This review comprehensively examines the various roles of SAMe in cancer pathogenesis, its potential as a diagnostic and prognostic marker, and its emerging therapeutic applications. While SAMe modulation holds significant promise, challenges such as bioavailability, patient stratification and context-dependent effects must be addressed before clinical implementation. In addition, better validation of the obtained results into specific cancer animal models would also help to bridge the gap between research and clinical practice.

Identifying common pathways for doxorubicin and carfilzomib-induced cardiotoxicities: transcriptomic and epigenetic profiling

Cancer therapy-related cardiovascular toxicity (CTR-CVT) is now recognised as one of the leading causes of long-term morbidity and mortality in cancer patients. To date, potential overlapping cardiotoxicity mechanism(s) across different chemotherapeutic classes have not been elucidated. Doxorubicin, an anthracycline, and Carfilzomib, a proteasome inhibitor, are both known to cause heart failure in some patients. Given this common cardiotoxic effect of these chemotherapies, we aimed to investigate differential and common mechanism(s) associated with Doxorubicin and Carfilzomib-induced cardiac dysfunction. Primary human cardiomyocyte-like cells (HCM-ls) were treated with 1 µM of either Doxorubicin or Carfilzomib for 72 h. Both Doxorubicin and Carfilzomib induced a significant reduction in HCM cell viability and cell damage. DNA methylation analysis performed using MethylationEPIC array showed distinct and common changes induced by Doxorubicin and Carfilzomib (10,270 or approximately 12.9% of the DMPs for either treatment overlapped). RNA-seq analyses identified 5,643 differentially expressed genes (DEGs) that were commonly dysregulated for both treatments. Pathway analysis revealed that the PI3K-Akt signalling pathway was the most significantly enriched pathway with common DEGs, shared between Doxorubicin and Carfilzomib. We identified that there are shared cardiotoxicity mechanisms for Doxorubicin and Carfilzomib pathways that can be potential therapeutic targets for treatments across 2 classes of anti-cancer agents.

Dimethyl sulfoxide-induced DNA demethylation during vitrification of early cleavage-stage embryos and possible countermeasures.

Dimethyl sulfoxide (DMSO) alters DNA methylation in vitrified-warmed embryos and potentially affects subsequent development. This study aimed to examine possible countermeasures against DMSO-induced demethylation. In vitro-produced bovine embryos (8-cell stage) were vitrified using a combination of DMSO and ethylene glycol (EG) or propylene glycol (PG) + EG. After warming, the lipid content and expression levels of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), DNMTs, and TETs were examined. In addition, RNA-sequencing was performed on blastocysts derived from the vitrified embryos. Furthermore, the effect of supplementation with a vitrification medium containing DMSO and N-acetyl-L-cysteine (NAC, 5mM) on the levels of 5mC in embryos was examined. Vitrification decreased the levels of 5mC and increased the levels of 5hmC in 8-cell stage embryos. Low levels of 5mC persisted until the blastocyst stage in the DMSO group but increased in the PG group. The expression level of TET3A was higher in the DMSO group than in the fresh group, but not in the PG group. Both cryoprotectants reduced the lipid levels in post-warmed 8-cell stage embryos. The addition of NAC ameliorated DMSO-induced demethylation at both the 8-cell and blastocyst stages. RNA-seq analysis revealed that PG-specific pathways included ribosomes and mitochondria and that both DMSO and PG affected cGMP-PGK, MAPK, Wnt, and insulin secretion-related signaling. The K-medoids method predicted that DMSO affected cell adhesion molecules and that MAPK signaling was affected the most. PG and NAC may antagonize DMSO-induced demethylation; however, PG exerts adverse effects on embryos.

The important roles of ERAP1, ERAP2 genes polymorphisms and their DNA methylation levels in pulmonary tuberculosis

BackgroundGenetic variations in endoplasmic reticulum aminopeptidase (ERAP1, ERAP2) genes are associated with the pathogenesis of multiple diseases, including infectious diseases. The objective of our study was to assess whether ERAP1, ERAP2 genes polymorphisms and methylation levels affect the risk of pulmonary tuberculosis (PTB).MethodsWe genotyped ten single nucleotide polymorphisms (SNPs) in ERAP1, ERAP2 genes among 497 PTB patients and 502 controls by SNPscan technique. Additionally, we detected the ERAP1, ERAP2 genes methylation levels in 98 PTB patients and 97 controls through Illumina Hiseq platform.ResultsOur results showed that the GG genotype, G allele frequencies of ERAP2 gene rs2549782 were significantly increased in PTB patients compared to controls, and rs2549782 polymorphism was related to the increased risk of PTB under recessive model. In addition, no significant relationship was found between ERAP1 gene rs13167972, rs17086651, rs469783, rs26618, rs3734016, ERAP2 gene rs17524572, rs1230358, rs2549794, rs117041256 and PTB susceptibility. Among PTB patients, the frequencies of rs17524572 TT genotype, T allele were significantly associated with drug-induced liver injury, and rs1230358, rs2549782, rs2549794 polymorphisms were linked to the occurrence of fever. Haplotype analysis of ERAP2 gene suggested that the frequency of CTGGT haplotype was higher, while the frequency of CTGTT haplotype was lower in PTB patients. When compared with controls, the ERAP1 methylation level was lower in PTB patients, while the ERAP2 methylation level was significantly increased. Moreover, rs1230358 polymorphism was found to affect the ERAP2 methylation level.ConclusionThe ERAP2 rs2549782 variant and altered methylation levels of ERAP1, ERAP2 genes were related to susceptibility to PTB.

Evaluation of Prenatal Transportation Stress on DNA Methylation (DNAm) and Gene Expression in the Hypothalamic–Pituitary–Adrenal (HPA) Axis Tissues of Mature Brahman Cows

Background/Objectives: The experience of prenatal stress results in various physiological disorders due to an alteration of an offspring’s methylome and transcriptome. The objective of this study was to determine whether PNS affects DNA methylation (DNAm) and gene expression in the stress axis tissues of mature Brahman cows. Methods: Samples were collected from the paraventricular nucleus (PVN), anterior pituitary (PIT), and adrenal cortex (AC) of 5-year-old Brahman cows that were prenatally exposed to either transportation stress (PNS, n = 6) or were not transported (Control, n = 8). The isolated DNA and RNA samples were, respectively, used for methylation and RNA-Seq analyses. A gene ontology and KEGG pathway enrichment analysis of each data set within each sample tissue was conducted with the DAVID Functional Annotation Tool. Results: The DNAm analysis revealed 3, 64, and 99 hypomethylated and 2, 93, and 90 hypermethylated CpG sites (FDR &lt; 0.15) within the PVN, PIT, and AC, respectively. The RNA-Seq analysis revealed 6, 25, and 5 differentially expressed genes (FDR &lt; 0.15) in the PVN, PIT, and AC, respectively, that were up-regulated in the PNS group relative to the Control group, as well as 24 genes in the PIT that were down-regulated. Based on the enrichment analysis, several developmental and cellular processes, such as maintenance of the actin cytoskeleton, cell motility, signal transduction, neurodevelopment, and synaptic function, were potentially modulated. Conclusions: The methylome and transcriptome were altered in the stress axis tissues of mature cows that had been exposed to prenatal transportation stress. These findings are relevant to understanding how prenatal experiences may affect postnatal neurological functions.

Exploring DNA methylation, telomere length, mitochondrial DNA, and immune function in patients with Long-COVID

BackgroundLong-COVID is defined as the persistency or development of new symptoms 3 months after the initial SARS-CoV-2 infection, with these symptoms lasting for at least 2 months with no other explanation. Common persistent symptoms are fatigue, sleep disturbances, post-exertional malaise (PEM), pain, and cognitive problems. Long-COVID is estimated to be present in about 65 million people. We aimed to explore clinical and biological factors that might contribute to Long-COVID.MethodsProspective longitudinal cohort study including patients infected with SARS-CoV-2 between March 2020 and March 2022. Patients were assessed between 4 and 12 months after infection at the COVID follow-up clinic at UZ Leuven. We performed a comprehensive clinical assessment (including questionnaires and the 6-min walking test) and biological measures (global DNA methylation, telomere length, mitochondrial DNA copy number, inflammatory cytokines, and serological markers such as C-reactive protein, D-dimer, troponin T).ResultsOf the 358 participants, 328 were hospitalised, of which 130 had severe symptoms requiring intensive care admission; 30 patients were ambulatory referrals. Based on their clinical presentation, we could identify 6 main clusters. One-hundred and twenty-seven patients (35.4%) belonged to at least one cluster. The bigger cluster included PEM, fatigue, sleep disturbances, and pain (n = 57). Troponin T and telomere shortening were the two main markers predicting Long-COVID and PEM-fatigue symptoms.ConclusionsLong-COVID is not just one entity. Different clinical presentations can be identified. Cardiac involvement (as measured by troponin T levels) and telomere shortening might be a relevant risk factor for developing PEM-fatigue symptoms and deserve further exploring.

PI3K-mediated Kif1a DNA methylation contributes to neuropathic pain: an in vivo study.

Neuropathic pain (NP) is a chronic condition caused by nerve injuries, such as nerve compression. Understanding its underlying neurobiological mechanisms is critical for developing effective treatments. Previous studies have shown that Kinesin family member 1A (Kif1a) heterozygous deficient mice display sensory deficits in response to nociceptive stimuli. PI3K has been found to mitigate these sensory deficits by enhancing Kif1a transcription, highlighting KIF1A's key role in sensory pain. However, the exact mechanism through which PI3K regulates KIF1A expression in relation to pain remains unclear. In this study, we observed a significant increase in PI3K/AKT/CREB (cyclic AMP response element-binding protein) protein levels in the dorsal root ganglia and spinal cord after chronic constriction injury in both male and female C57BL/6 mice. Notably, elevated levels of TET1, as well as Kif1a mRNA and protein, were detected in both male and female mice. Activated (phosphorylated-CREB) p-CREB recruited the DNA demethylase TET1, which interacted with the Kif1a promoter, reducing methylation and increasing Kif1a mRNA and protein expression. PI3K inhibition using wortmannin reversed the demethylation of Kif1a and decreased its expression in male mice. Furthermore, TET1 knockdown or overexpression significantly affected pain-related behaviors, as well as Kif1a methylation and transcription. Female mice given intrathecal injections of PI3K inhibitors exhibited similar molecular and behavioral outcomes as male mice. These findings offer new insights into NP mechanisms, suggesting that targeting the PI3K/KIF1A axis could be a promising therapeutic approach for NP treatment.