Search Results (1,219)

Asthma, a chronic respiratory condition characterized by airway inflammation, affects millions of individuals worldwide. Challenges remain in asthma prediction and diagnosis from its complex etiology involving genetic and environmental factors. Here, we investigated the relationship between genome-wide DNA methylation and genetic risk for asthma quantified via polygenic scores in two cohorts from the Netherlands Twin Register; one enriched with asthmatic families measured on the Illumina EPIC array (n = 526) and a general population cohort measured on the Illumina HM450K array (n = 2680). We performed epigenome-wide association studies of asthma polygenic scores in each cohort with results combined through meta-analysis (total samples = 3206). The EWAS meta-analysis identified 63 significantly associated CpGs, (following Bonferroni correction, α = 0.05/358,316). An investigation of previous mQTL associations identified 48 mQTL associations between 24 unique CpGs and 48 SNPs, of which two SNPs have previous associations with asthma. Enrichment analysis using the 63 significant CpGs highlighted previous associations with ancestry, smoking, and air pollution. A dizygotic twin within-pair analysis of the 63 CpGs revealed similar directional effects between the two cohorts in 33 of the 63 CpGs. These findings further characterize the intricate relationship between DNA methylation and genetics relative to asthma. Full article

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. Full article

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 < 0.15) within the PVN, PIT, and AC, respectively. The RNA-Seq analysis revealed 6, 25, and 5 differentially expressed genes (FDR < 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. Full article

Background/Objectives: The purpose of the current study was to compare the methylation of five regions of the CpG island of MLH1 with the presence of microsatellite instability (MSI) in colorectal cancer (CRC) patients. Methods: The study analyzed 138 CRC tumor samples. DNA extraction was performed, followed by bisulfite conversion. MLH1 gene methylation was assessed by methylation-specific PCR (MS-PCR), and the resulting fragments were analyzed using polyacrylamide gels. MSI was evaluated using multiplex PCR, and the fragments were run through capillary electrophoresis. R studio (v4.4.1) and SPSS (v29.0) software were used for the statistical analysis, and values of p < 0.05 were considered statistically significant. Results: The study showed 75.4% unmethylated, 21% partially methylated, and 3.6% fully methylated samples, with region A frequently methylated. MSI was observed in 7.2% of cases (MSI-H: 5.8%, MSI-L: 1.4%). BAT-26 was the most unstable marker. A significant difference between MLH1 methylation and MSI-H (p < 0.01) was identified, but there was no relationship with specific MLH1 regions. Conclusions: No differences were identified when analyzing specific methylation regions in relation to MSI. This study is the first to describe MSI frequency in Mexican patients regardless of age. Full article

Prostate-specific antigen remains a cornerstone biomarker for prostate cancer diagnosis and management. However, the molecular mechanisms regulating its expression, particularly through DNA methylation, are not fully understood. Here, we report a comprehensive analysis of allele-specific CpG and CCWGG methylation in the proximal PSA promoter across aggressive (PC3), indolent (LNCaP), benign (BPH1), and normal (HPrEpiC) prostate cell lines and provide insights into the unique methylation patterns associated with these states. Our findings reveal that PC3 cells, representing an aggressive PCa phenotype, exhibit complete biallelic methylation of the PSA promoter, leading to PSA gene silencing. Conversely, LNCaP cells display a fully unmethylated promoter with biallelic PSA expression. Interestingly, BPH1 cells display a monoallelic CG/CCWGG methylation pattern, yet fail to express PSA, suggesting imprinting defects or RNA decay mechanisms. Notably, acquisition of biallelic PSA promoter methylation status in PC3 was accompanied by upregulation of DNMT1, whereas unmethylated PSA promoter state in LNCaP was associated with downregulation of DNMT1. These findings highlight distinct methylation patterns in the PSA promoter that differentiate between aggressive, indolent, and benign prostate states. Translating this epigenetic insight into clinical diagnostics could enhance the precision of PSA-based diagnostics, addressing limitations such as false negatives in PSA testing for aggressive PCa. Further exploration of CCWGG methylation’s role in imprinting and monoallelic expression is warranted, particularly in patient-derived samples. Full article

The efficiency of helical locomotion in snake-like robots along high-voltage transmission lines is often hindered by low motion efficiency, high joint signal noise, and challenges in traversing obstacles. This study aims to address these issues by proposing a gait generation method that leverages a standardized Central Pattern Generator (CPG). We modify the traditional Hopf-CPG model by incorporating constraint functions and a frequency-tuning mechanism to regulate the oscillator, which allows for the generation of asymmetric waveform signals for deflection joints and facilitates rapid convergence. The method begins by determining initial and obstacle-crossing state parameters, such as deflection angles and helical radii of the snake-like robot, using the backbone curve method and the Frenet–Serret framework. Subsequently, a CPG neural network is constructed based on Hopf oscillators, with a limit cycle convergent speed adjustment factor and amplitude bias signals to establish a fully connected matrix model for calculating multi-joint output signals. Simulation analysis using Simulink–CoppeliaSim evaluates the robot’s obstacle-crossing ability and the optimization of deflection joint signal noise. The results indicate a 55.70% increase in the robot’s average speed during cable traversal, a 57.53% reduction in deflection joint noise disturbance, and successful crossing of the vibration damper. This gait generation method significantly enhances locomotion efficiency and noise suppression in snake-like robots, offering substantial advantages over traditional approaches. Full article

Background: The methylation of cytosine residues at CpG sites within the O6-methylguanine-DNA methyltransferase (MGMT) promoter is a key biomarker in glioblastoma therapy. The MGMT promoter (MGMTp) contains multiple guanine-rich sequences capable of folding into G-quadruplexes (G4s), but their relevance for MGMTp methylation is poorly understood. Objectives: Our study explores the impact of potential G-quadruplex-forming sequences (PQS) in the MGMT promoter CpG island on the activity of de novo DNA methyltransferase Dnmt3a. Additionally, we investigate their influence on the accuracy of methylation pattern detection using nanopore sequencing. Methods: Nanopore sequencing was employed to analyze the methylation of 94 clinically significant CpG sites in the human MGMTp using an in vitro de novo methylation system. Circular dichroism spectroscopy was used to identify G4 structures within the MGMTp CpG island. Interactions between the catalytic domain of Dnmt3a and the PQS from the MGMTp were examined by biolayer interferometry. Results: Guanine-rich DNA strands of the PQSs in the MGMTp were hypomethylated, while the complementary cytosine-rich strands were methylated by DNA methyltransferase Dnmt3a with higher efficiency. The accuracy of detecting modified bases in the PQS was significantly lower compared to surrounding sequences. Single-stranded guanine-rich DNA sequences from the MGMTp exhibited strong binding to Dnmt3a-CD, with an affinity approximately 10 times higher than their cytosine-rich complements (K_d = 3 × 10⁻⁸ M and 3 × 10⁻⁷ M, respectively). By binding to Dnmt3a, G4-forming oligonucleotides from MGMTp effectively inhibited the methylation reaction (IC₅₀ 6 × 10⁻⁷ M). Conclusions: The obtained data indicate the role of PQSs in establishing de novo methylation of the MGMT promoter. They also highlight the challenges of sequencing guanine-rich regions and the impact of specific de novo methylation patterns on clinical data interpretation. Full article

Hidradenitis suppurativa (HS) is a chronic skin condition that primarily affects areas with dense hair follicles and apocrine sweat glands, such as the underarms, groin, buttocks, and lower breasts. Intense pain and discomfort in HS have been commonly noted, primarily due to the lesions’ effects on nearby tissues. Pain is a factor that can influence DNA methylation patterns, though its exact role in HS is not fully understood. We aim to identify molecular markers of chronic pain in HS patients. We performed DNA methylome of peripheral blood DNA derived from a group of 24 patients with HS and 24 healthy controls, using Illumina methylation array chips. We identified 253 significantly differentially methylated CpG sites across 253 distinct genes regulating pain sensitization in HS, including 224 hypomethylated and 29 hypermethylated sites. Several genes with pleiotropic roles include transporters (ABCC2, SLC39A8, SLC39A9), wound healing (MIR132, FGF2, PDGFC), ion channel regulators (CACNA1C, SCN1A), oxidative stress mediators (SCN8A, DRD2, DNMT1), cytochromes (CYP19A, CYP1A2), cytokines (TGFB1, IL4), telomere regulators (CSNK1D, SMAD3, MTA1), circadian rhythm (IL1R2, ABCG1, RORA), ultradian rhythms (PHACTR1, TSC2, ULK1), hormonal regulation (PPARA, NR3C1, ESR2), and the serotonin system (HTR1D, HTR1E, HTR3C, HTR4, TPH2). They also play roles in glucose metabolism (POMC, IRS1, GNAS) and obesity (DRD2, FAAH, MMP2). Gene ontology and pathway enrichment analysis identified 43 pathways, including calcium signaling, cocaine addiction, and nicotine addiction. This study identified multiple differentially methylated genes involved in chronic pain in HS, which may serve as biomarkers and therapeutic targets. Understanding their epigenetic regulation is crucial for personalized pain management and could enhance the identification of high-risk patients, leading to better preventative therapies and improved maternal and neonatal outcomes. Full article

Alterations in the methylation of genetic material can influence carcinogenesis by the downregulation or overexpression of ADAMTS (a disintegrin-like and metalloprotease with thrombospondin motifs) protease genes. Through their proteolytic activity, these enzymes are also capable of promoting angiogenesis. Consequently, ADAMTS proteases can either facilitate or inhibit cancer progression. This study aimed to evaluate the methylation levels of the ADAMTS6, ADAMTS9, and ADAMTS12 genes in non-small-cell lung cancer (NSCLC) using data from bioinformatics databases. The focus was on differences between lung adenocarcinoma (LUAD) and lung squamous-cell carcinoma (LUSC) subtypes and their impact on patient overall survival (OS). ADAMTS6 gene expression is significantly reduced in LUSC, and analysis of ADAMTS9 gene expression showed a significantly reduced gene transcript level in LUAD and LUSC, while both NSCLC subtypes demonstrated ADAMTS12 upregulation. In LUSC, significantly elevated promoter methylation was found in all of the aforementioned genes, while in LUAD, higher promoter methylation was observed only for ADAMTS9 and ADAMTS12. The differential methylation region (DMR) pattern demonstrated by ADAMTS6, ADAMTS9, and ADAMTS12 is a useful tool for distinguishing normal from cancer cells. The areas under the curve (AUCs) ranged from 0.86 to 0.99 for both LUAD and LUSC subtypes. The methylation level of different CpG sites among selected ADAMTS members is related to patient survival, suggesting it may have value as a prognostic marker. The methylation degree of promoter regions in genes encoding ADAMTS family proteins could significantly influence LUSC and LUAD. Increased promoter methylation could also reduce certain gene expression, contributing to cancer progression. The expression levels and specific DMRs of ADAMTS genes may serve as prognostic markers correlating with patient OS. Assessing ADAMTS gene methylation could become a diagnostic tool for differentiating NSCLC subtypes and potentially guide therapeutic strategies. Further research is needed to fully understand the activity and mechanisms of ADAMTS family proteins. Full article

DNA methylation has been widely studied with the goal of correlating the genome profiles of various diseases with epigenetic mechanisms. Multiple approaches have been developed that employ extensive steps, such as bisulfite treatments, polymerase chain reactions (PCR), restriction digestion, sequencing, mass analysis, etc., to identify DNA methylation. In this article, we report a facile label-free surface-enhanced Raman scattering (SERS) spectroscopy system that utilizes gold nanoparticles (AuNPs) for signal enhancement of methylated DNA. The key innovation of this work is to use anionic nanoparticles at a high ionic strength to introduce the aggregation of AuNPs with anionic DNA. When target methylated DNA is present, the presence of a methyl group in the cytosine C5 position of CpG sites induces a Raman peak at 1350 cm⁻¹. Our amplification-free system has a limit of detection (LOD) of 5% and a limit of quantification (LOQ) of 16% with good specificity. The method was applied to determine the hypermethylated levels of the germline of colorectal cancer cell lines SW48 and SW480. Our simple label-free method holds the potential to read the disease-associated methylation of genomic DNA. Full article

Recoding strategies have emerged as a promising approach for developing safer and more effective vaccines by altering the genetic structure of microorganisms, such as viruses, without changing their proteins. This method enhances vaccine safety and efficacy while minimizing the risk of reversion to virulence. Recoding enhances the frequency of CpG dinucleotides, which in turn activates immune responses and ensures a strong attenuation of the pathogens. Recent advancements highlight synonymous recoding’s potential, offering improved genetic stability and immunogenicity compared to traditional methods. Live vaccines attenuated using classical methods pose a risk of reversion to virulence and can be time-consuming to produce. Synonymous recoding, involving numerous codon alterations, boosts safety and vaccine stability. One challenge is balancing attenuation with yield; however, innovations like Zinc-finger antiviral protein (ZAP) knockout cell lines can enhance vaccine production. Beyond viral vaccines, recoding can apply to bacterial vaccines, as exemplified by modified Escherichia coli and Streptococcus pneumoniae strains, which show reduced virulence. Despite promising results, challenges like ensuring genetic stability, high yield, and regulatory approval remain. Briefly, ongoing research aims to harness these innovations for comprehensive improvements in vaccine design and deployment. In this commentary, we sought to further engage the community’s interest in this elegant approach by briefly highlighting its main advantages, disadvantages, and future prospects. Full article

Background/Objectives: Oral cancers in patients with proliferative verrucous leukoplakia (PVL-OSCC) exhibit different clinical and prognostic outcomes from those seen in conventional oral squamous cell carcinomas (cOSSCs). The aim of the present study is to compare the genome-wide DNA methylation signatures in fresh frozen tissues between oral squamous cell carcinomas in patients with PVL and cOSCC using the Illumina Infinium MethylationEPIC BeadChip. Methods: This case–control study was carried out at the Stomatology and Maxillofacial Surgery Department of the General University Hospital of Valencia. For the epigenomic study, unsupervised exploratory bioinformatic analyses were performed using principal component and heatmap analysis. Supervised differential methylation analyses were conducted using a rank-based regression model and a penalized logistic regression model to identify potential prognostic biomarkers. Results: The unsupervised analyses of the global methylation profiles did not allow us to differentiate between the distinct oral cancer groups. However, the two supervised analyses confirmed the existence of two oral carcinoma phenotypes. We identified 21 differentially methylated CpGs corresponding to 14 genes. Among them, three CpGs had not been previously assigned to any known gene, and the remaining were associated with genes unrelated to oral cancer. The AGL, WRB, and ARL15 genes were identified as potential prognostic biomarkers. Conclusions: This study emphasizes the significant role of epigenetic dysregulation in OSCC, particularly in cases preceded by PVL. We have provided data on differential methylation genes that could be involved in the molecular carcinogenesis of PVL-OSCC. Full article

The DNA methylation of CYP24A1 can regulate its gene expression and may play a role in the occurrence and progression of colorectal cancer (CRC). However, the association between CYP24A1 DNA methylation and the prognosis of CRC patients has not yet been reported. In this study, differential methylation analysis was conducted in both blood and tissue cohorts, and differential expression analysis was performed in the tissue cohort with in vitro validation. GO and KEGG enrichment analyses were performed on CYP24A1-related genes. A correlation between CYP24A1 promoter methylation and its gene expression was explored. Kaplan–Meier survival and Cox regression analyses were performed to investigate the impact of CYP24A1 DNA methylation on the prognosis of CRC patients. Prognostic risk scores were constructed for survival prediction. Immune infiltration analysis was also conducted. Our results showed that the hypermethylation of cg02712555 in tumor tissues (hazard ratio, 0.48; 95% confidence interval, 0.24–0.94; p = 0.032) and CpG site 41 in peripheral leukocytes (HR, 0.35; 95%CI, 0.14–0.84; p = 0.019) were both associated with decreased overall mortality in CRC patients. Prognostic risk scores showed robust predictive capabilities of these two CpG loci for the prognosis of CRC patients. CYP24A1 hypermethylation was positively correlated with infiltration levels of activated CD4 + T cells, activated CD8 + T cells, activated B cells, activated dendritic cells, and macrophages. Taken together, our findings indicate that the methylation levels of specific CpG sites within the CYP24A1 promoter region in blood leukocytes and tumors are potential prognostic and predictive markers for overall survival in CRC patients. Full article

Synthetic cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs) are promising candidates for vaccine adjuvants, because they activate immune responses through the Toll-like receptor 9 (TLR9) pathway. However, unmodified CpG ODNs are quickly degraded by serum nucleases, and their negative charge hinders cellular uptake, limiting their clinical application. Our group previously reported that guanine-quadruplex (G4)-forming CpG ODNs exhibit enhanced stability and cellular uptake. G4 structures can form in parallel, anti-parallel, or hybrid topologies, depending on strand orientation, but the effects of these topologies on CpG ODNs have not yet been explored. In this study, we designed three distinct G4 topologies as scaffolds for CpG ODNs. Among the three topology, the parallel G4 CpG ODN demonstrated the highest serum stability and cellular uptake, resulting in the strongest immune response from macrophage cells. Additionally, we investigated the binding affinities of the different G4 topologies to macrophage scavenger receptor-1 and TLR9, both of which are key to immune activation. These findings provide valuable insights into the development of CpG ODN-based vaccine adjuvants. Full article

The tissue specificity of DNA methylation refers to the significant differences in DNA methylation patterns in different tissues. This specificity regulates gene expression, thereby supporting the specific functions of each tissue and the maintenance of normal physiological activities. Abnormal tissue-specific patterns of DNA methylation are closely related to age-related diseases. This abnormal methylation pattern affects the regulation of gene expression, which may lead to changes in cell function and promote the occurrence of pathological conditions. By analyzing the differences in these methylation patterns, key CpG sites for disease diagnosis can be effectively screened. The main goal of this paper is to use the characteristics associated with tissue-specific abnormal expression and disease to construct an age-related disease diagnosis model. First, we combined chi-square tests and logistic regression to identify tissue-specific and disease-specific CpG sites, laying the foundation for accurate medical diagnosis, and verified the biological relevance of these CpG sites through enrichment analysis. Then we used the Transformer model to fit these CpG sites and realized the automatic diagnosis of age-related diseases. Our work proves that the tissue specificity of DNA methylation has the potential to diagnose age-related diseases, and proves the scientific nature of our proposed diagnostic method from a biological perspective. Full article