DNA Methylation Analysis Research Articles

Evaluation of Pan-Cancer Immune Heterogeneity Based on DNA Methylation

Abstract: Background/Objectives: The heterogeneity of the tumor immune microenvironment is a key determinant of tumor oncogenesis. This study aims to evaluate the composition of seven immune cells across 5323 samples from 14 cancers using DNA methylation data. Methods: A deconvolution algorithm was proposed to estimate the composition of seven immune cells using 1256 immune cell population-specific methylation genes. Based on the immune infiltration features of seven immune cell fractions, 42 subtypes of 14 tumors (2–5 subtypes per tumor) were identified. Results: Significant differences in immune cells between subtypes were revealed for each cancer. The study found that the methylation values of the selected specific sites correlated with gene expression in most tumor subtypes. Immune infiltration results were integrated with phenotypic data, including survival data and tumor stages, revealing significant correlations between immune infiltration and phenotypes in some tumors. Subtypes with high proportions of CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD14+ monocytes, neutrophils, and eosinophils were identified, with subtype counts of 9, 24, 22, 13, 19, 9, and 11, respectively. Additionally, 2412 differentially expressed genes between these subtypes and normal tissues were identified. Pathway enrichment analysis revealed that these genes were mainly enriched in pathways related to drug response and chemical carcinogens. Differences in ESTIMATE scores for subtypes of seven tumors and TIDE scores for eight tumors were also observed. Conclusions: This study demonstrates the intra-tumor and inter-tumor immune heterogeneity of pan-cancer through DNA methylation analysis, providing assistance for tumor diagnosis.

Retinol-Binding Protein 4 as a Biomarker in Cancer: Insights from a Pan-Cancer Analysis of Expression, Immune Infiltration, and Methylation

Background: Retinol-binding protein 4 (RBP4) is primarily recognized for its role in retinoid transport, but has recently been implicated in cancer progression and prognosis. However, a comprehensive pan-cancer analysis of RBP4’s expression, prognostic significance, and functional associations across various cancers is lacking. Methods: We conducted a pan-cancer analysis of RBP4 using data from public databases. RBP4 expression levels were examined in 33 tumor types, and correlations with clinical outcomes, immune cell infiltration, DNA methylation, and gene mutations were assessed. Enrichment analyses of RBP4 and its co-expressed genes were performed to explore associated biological pathways. Additionally, in vitro experiments were conducted to assess the effects of RBP4 on cell migration and proliferation. Results: RBP4 showed differential expression between tumor and normal tissues, with downregulation in 21 cancer types and upregulation in 6. High expression levels of RBP4 were associated with poor overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in specific cancers, notably in BRCA, HNSC, and STAD, whereas it was a favorable prognostic factor in cancers such as KIRP and MESO. RBP4 expression was also associated with immune cell infiltration, particularly with CD4+ Th2 cells and immune checkpoint genes. DNA methylation analysis suggested that the methylation of RBP4 may play a role in its regulatory mechanisms across cancer types. Enrichment analyses revealed that RBP4 and its co-expressed genes are involved in metabolism-related pathways and immune regulation. Functional assays indicated that RBP4 knockdown promoted tumor cell migration and proliferation. Conclusions: This study provides a comprehensive pan-cancer analysis of RBP4, identifying its prognostic potential and possible involvement in tumor immunity and metabolism. Our findings suggest that RBP4 could serve as a novel biomarker and therapeutic target in cancer, although further experimental studies are required to elucidate its precise mechanisms in specific cancer types.

MethylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.

Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph. Notably, methylGrapher can reconstruct methylation patterns along haplotype paths precisely and efficiently. To demonstrate the utility of methylGrapher, we analyzed the WGBS data derived from five individuals whose genomes were included in the first Human Pangenome draft as well as WGBS data from ENCODE (EN-TEx). Along with standard performance benchmarking, we show that methylGrapher fully recapitulates DNA methylation patterns defined by classic linear genome analysis approaches. Importantly, methylGrapher captures a substantial number of CpG sites that are missed by linear methods, and improves overall genome coverage while reducing alignment reference bias. Thus, methylGrapher is a first step toward unlocking the full potential of Human Pangenome graphs in genomic DNA methylation analysis.

High-Grade Astrocytoma With Piloid Features.

High-grade astrocytoma with piloid features (HGAP) is a newly recognized glioma defined by its methylation profile. Understanding of its clinical, histologic, and molecular characteristics continues to evolve. To review the HGAP literature, emphasizing updates in our understanding of the entity since its codification in the 2021 World Health Organization (WHO) Blue Book. Additionally, to present a case series illustrating a single institutional experience with HGAP. The English-language HGAP literature from 2018 to 2024 was reviewed. Four cases of HGAP were reviewed, along with relevant medical records. HGAP is an important consideration in the differential diagnosis of isocitrate dehydrogenase-wild-type gliomas and is more frequently encountered in adults. A handful of studies published following the entity's codification in the 2021 WHO Blue Book have refined our understanding of its clinical, histologic, and hallmark molecular characteristics. The most substantial updates include the description of 3 provisional subtypes, further characterization of an association with neurofibromatosis 1 syndrome, identification of new rare molecular alterations, and documentation of a unique case of possible transformation of pilocytic astrocytoma into HGAP. Clues to the diagnosis of HGAP include histologic infiltrating glioma with moderate pleomorphism, posterior fossa location, CDKN2A/B (cyclin dependent kinase inhibitor 2A/B) deletion, MAPK (mitogen-activated protein kinase) pathway alterations, ATRX (alpha thalassemia/mental retardation syndrome X-linked) loss, and association with neurofibromatosis 1 syndrome in some cases; these findings should prompt further molecular testing, including genome-wide DNA methylation analysis, which is currently essential for diagnosis.

Whole Blood DNA Methylation Analysis Reveals Epigenetic Changes Associated with ARSACS.

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare inherited condition described worldwide and characterized by a wide spectrum of heterogeneity in terms of genotype and phenotype. How sacsin loss leads to neurodegeneration is still unclear, and current knowledge indicates that sacsin is involved in multiple functional mechanisms. We hence hypothesized the existence of epigenetic factors, in particular alterations in methylation patterns, that could contribute to ARSACS pathogenesis and explain the pleiotropic effects of SACS further than pathogenic mutations. To investigate this issue, we recruited eight patients affected by ARSACS, four characterized by early onset of the disease and four with late onset. We performed Whole Genome Bisulfite Sequencing using DNA from peripheral blood to define the methylome of patients and compared them with a control group. Our analysis showed that patients with ARSACS exhibit an altered methylation pattern and that the observed differences exist also among affected individuals with different age of onset. Our study provides valuable insights for employing epigenetic biomarkers to assess the severity and progression of this disorder and propels further investigations into the role of epigenetic processes in ARSACS pathogenesis.

Spatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity

BackgroundIntratumoral heterogeneity emerges from accumulating genetic and epigenetic changes during tumorigenesis, which may contribute to therapeutic failure and drug resistance. However, the lack of a quick and convenient approach to determine the intratumoral epigenetic heterogeneity (eITH) limit the application of eITH in clinical settings. Here, we aimed to develop a tool that can evaluate the eITH using the DNA methylation profiles from bulk tumors.MethodsGenomic DNA of three laser micro-dissected tumor regions, including digestive tract surface, central bulk, and invasive front, was extracted from formalin-fixed paraffin-embedded sections of colorectal cancer patients. The genome-wide methylation profiles were generated with methylation array. The most variable methylated probes were selected to construct a DNA methylation-based heterogeneity (MeHEG) estimation tool that can deconvolve the proportion of each reference tumor region with the support vector machine model-based method. A PCR-based assay for quantitative analysis of DNA methylation (QASM) was developed to specifically determine the methylation status of each CpG in MeHEG assay at single-base resolution to realize fast evaluation of epigenetic heterogeneity.ResultsIn the discovery set with 79 patients, the differentially methylated CpGs among the three tumor regions were found. The 7 most representative CpGs were identified and subsequently selected to develop the MeHEG algorithm. We validated its performance of deconvolution of tumor regions in an independent cohort. In addition, we showed the significant association of MeHEG-based epigenetic heterogeneity with the genomic heterogeneity in mutation and copy number variation in our in-house and TCGA cohorts. Besides, we found that the patients with higher MeHEG score had worse disease-free and overall survival outcomes. Finally, we found dynamic change of epigenetic heterogeneity based on MeHEG score in cancer cells under the treatment of therapeutic drugs.ConclusionBy developing a 7-loci panel using a machine learning approach combined with the QASM assay for PCR-based application, we present a valuable method for evaluating intratumoral heterogeneity. The MeHEG algorithm offers novel insights into tumor heterogeneity from an epigenetic perspective, potentially enriching current knowledge of tumor complexity and providing a new tool for clinical and research applications in cancer biology.

EpiAge: a next-generation sequencing-based ELOVL2 epigenetic clock for biological age assessment in saliva and blood across health and disease.

This study introduces EpiAgePublic, a new method to estimate biological age using only three specific sites on the gene ELOVL2, known for its connection to aging. Unlike traditional methods that require complex and extensive data, our model uses a simpler approach that is well-suited for next-generation sequencing technology, which is a more advanced method of analyzing DNA methylation. This new model overcomes some of the common challenges found in older methods, such as errors due to sample quality and processing variations. We tested EpiAgePublic with a large and varied group of over 4,600 people to ensure its accuracy. It performed on par with, and sometimes better than, more complicated models that use much more data for age estimation. We examined its effectiveness in understanding how factors like HIV infection and stress affect aging, confirming its usefulness in real-world clinical settings. Our results prove that our simple yet effective model, EpiAgePublic, can capture the subtle signs of aging with high accuracy. We also used this model in a study involving patients with Alzheimer's Disease, demonstrating the practical benefits of next-generation sequencing in making precise age-related assessments. This study lays the groundwork for future research on aging mechanisms and assessing how different interventions might impact the aging process using this clock.

Integration of CRISPR/dCas9-Based methylation editing with guide positioning sequencing identifies dynamic changes of mrDEGs in breast cancer progression

Dynamic changes in DNA methylation are prevalent during the progression of breast cancer. However, critical alterations in aberrant methylation and gene expression patterns have not been thoroughly characterized. Here, we utilized guide positioning sequencing (GPS) to conduct whole-genome DNA methylation analysis in a unique human breast cancer progression model: MCF10 series of cell lines (representing benign/normal, atypical hyperplasia, and metastatic carcinoma). By integrating with mRNA-seq and matched clinical expression data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), six representative methylation-related differentially expressed genes (mrDEGs) were identified, including CAVIN2, ARL4D, DUSP1, TENT5B, P3H2, and MMP28. To validate our findings, we independently developed and optimized the dCas9-DNMT3L-DNMT3A system, achieving a high efficiency with a 98% increase in methylation at specific sites. DNA methylation levels significantly increased for the six genes, with CAVIN2 at 67.75 ± 1.05%, ARL4D at 53.29 ± 6.32%, DUSP1 at 57.63 ± 8.46%, TENT5B at 44.00 ± 5.09%, P3H2 at 58.50 ± 3.90%, and MMP28 at 49.60 ± 5.84%. RT-qPCR confirmed an inverse correlation between increased DNA methylation and gene expression. Most importantly, we mimicked tumor progression in vitro, demonstrating that transcriptional silencing of the TENT5B promotes cell proliferation in MCF10A cells owing to the crosstalk between hypermethylation and histone deacetylation. This study unveils the practical implications of DNA methylation dynamics of mrDEGs in reshaping epigenomic features during breast cancer malignant progression through integrated data analysis of the methylome and transcriptome. The application of the CRISPR/dCas9-based methylation editing technique elucidates the regulatory mechanisms and functional roles of individual genes within the DNA methylation signature, providing valuable insights for understanding breast cancer pathogenesis and facilitating potential therapeutic approaches in epigenome editing for patients with breast cancer.

Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress.

Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum ('Jitian 3') development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in "phenylpropanoid biosynthesis", "arginine and proline metabolism" and "tyrosine metabolism". Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.

Characterizing biomarkers of ageing in Singaporeans: the ABIOS observational study protocol.

Ageing is the primary driver of age-associated chronic diseases and conditions. Asian populations have traditionally been underrepresented in studies understanding age-related diseases. Thus, the Ageing BIOmarker Study in Singaporeans (ABIOS) aims to characterise biomarkers of ageing in Singaporeans, exploring associations between molecular, physiological, and digital biomarkers of ageing. This is a single-centre, cross-sectional study that recruits healthy community-dwelling adults (≥ 21 years) from three different ethnic groups (Chinese, Malay, and Indian). Molecular biomarkers of ageing include multi-omics approaches, such as DNA methylation analysis and metabolic and inflammatory proteomic profiling in blood, saliva, and stool. Physiological biomarkers of ageing include bone density, body composition, skin autofluorescence, arterial stiffness, physical performance (e.g., muscle strength and flexibility), cognition, and nutritional status. Digital biomarkers of ageing include three-dimensional facial morphology and objectively measured physical activity. Additional measures, such as habitual physical activity, dietary patterns, and medical history, are also examined. The associations between the molecular, physiological, and digital phenotypes will be explored. This study is expected to generate a comprehensive profile of molecular, physiological, and digital biomarkers of ageing in Chinese, Malay, and Indian populations in Singapore. By integrating diverse age-related biomarkers, clinical indicators, and lifestyle factors, ABIOS will offer unique insights into the ageing process specific to Southeast Asian populations. These findings can help identify markers of biological ageing, uncover ethnic-specific patterns, and reveal modifiable lifestyle factors for healthier ageing. The results could inform evidence-based health policies, personalized interventions, and future cross-ethnic comparative studies to enhance understanding of ageing biology across diverse populations.

DNA methylation regulates somatic stress memory and mediates plasticity during acclimation to repeated sulfide stress in Urechis unicinctus.

Stress memory is an adaptive mechanism that enables organisms to develop resilience in response to environmental changes. Among them, somatic stress memory is an important means for organisms to cope with contemporary repeated stress, and is accompanied by transcription memory. Sulfide is a common environmental pollutant; however, some organisms have adapted to survive in sulfur-rich environments. Urechis unicinctus is a sulfur-tolerant organism that enhances sulfide stress tolerance by establishing a somatic sulfide stress memory mechanism. However, the molecular mechanisms that regulate sulfide stress memory remain unclear. To explore whether epigenetics, which plays a role in the response of organisms to environmental stress, is involved in regulating somatic sulfide stress memory, we performed a combined analysis of DNA methylation and transcriptome data. We found that elevated levels of DNA methylation under repetitive sulfide stress regulated gene expression and resulted in enhanced sulfide stress tolerance in U. unicinctus, a phenomenon verified using DNA methylase inhibitors. Transcriptional memory can be induced in genes related to oxidative stress, regulation of autophagy, and maintenance of protein homeostasis by altering the level of DNA methylation to facilitate sulfide stress acclimation. Our results provide new insights into adaptive mechanisms to cope with environmental fluctuations.

Transcriptome and DNA methylation analysis of the goat pineal gland during puberty

Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. To screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, we collected pineal glands from prepubertal and pubertal female goats, then, determined the DNA methylation profile by whole genome bisulfite sequencing and the transcriptome by RNA sequencing on Illumina HiSeqTM2500. We analyzed differentially expressed genes between the Pre group and Pub group using the DESeq2 software (version 1.20.0), and applied the Benjamini and Hochberg method for adjusting P-values. Genes with a P-value less than 0.05 and an absolute log2 fold change greater than 0 were considered differentially expressed genes. Results showed that there was no significant difference in the whole-genome methylation level of the pineal gland between prepubertal and pubertal goats, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland might play a role in regulating the initiation of goat puberty. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes remained unaffected by DNA methylation differences. Genes regulated by DNA methylation regulates genes primarily involved in metabolic processes, oxidative phosphorylation, and signaling pathways related to thermogenesis. Methylation significantly regulated the expression of genes such as ATP5F1D, CACNB2, and PTEN, while genes like LIN28B, GIP, OPN1SW, and DCC showed the most notable fold changes, which may indicate their involvement in the onset of puberty.

Harnessing Nanomaterials for Next-Generation DNA Methylation Biosensors.

DNA methylation is an epigenetic mechanism that regulates gene expression and is implicated in diseases such as cancer and atherosclerosis. However, traditional clinical methods for detecting DNA methylation often lack sensitivity and specificity, making early diagnosis challenging. Nanomaterials offer a solution with their unique properties, enabling highly sensitive photochemical and electrochemical detection techniques. These advanced methods enhance the accuracy and efficiency of identifying DNA methylation patterns, providing a powerful tool for early diagnosis and treatment of methylation-related diseases. This review summarizes nanomaterial-based techniques, categorized into electrochemical and photochemical methods for developing next-generation biosensors for DNA methylation. Electrochemical approaches based on nanostructured or nanomaterial-modified electrodes can detect methylation through electrical signals and can directly identify methylation sites via ionic current changes based on nanopore sequencing. Photochemical methods based on nanoparticles allow for optical detection through colorimetry, fluorescence, surface plasmon resonance, and Raman spectroscopy. Nanotechnology-implemented methodologies enable ultrasensitive and selective biosensors as point-of-care platforms for DNA methylation analysis, thereby advancing epigenetic research and clinical diagnostics.

Accelerated epigenetic ageing after burn injury.

Individuals who suffer a major burn injury are at higher risk of developing a range of age-associated diseases prematurely leading to an increase in mortality in adult and juvenile burn injury survivors. One possible explanation is that injury is accelerating the biological ageing process. To test this hypothesis, we analysed DNA methylation in peripheral blood mononuclear cells from adult burn-injured patients (> 5%TBSA) upon admission to hospital and 6 months later, to calculate an epigenetic clock value which can be used to determine biological age. Fifty-three burn-injured participants (mean age 45.43 years, 49 male, mean TBSA 37.65%) were recruited at admission and 34 again 6 months post injury (mean age 40.4 years, 34 male, mean TBSA 30.91%). Twenty-nine healthy controls (mean age 43.69 years, 24 male) were also recruited. Epigenetic age acceleration at admission by PhenoAge was + 7.2 years (P = 8.31e-5) but by month 6 was not significantly different from healthy controls. PCGrimAge acceleration was + 9.23 years at admission (P = 5.79e-11) and remained 4.18 years higher than in controls by month 6 (P = 2.64e-6). At admission, the burn-injured participants had a Dunedin PACE of ageing score 31.65% higher than the control group (P = 2.14e-12), the equivalent of + 115 days per year of biological ageing. Six months post injury the Dunedin PACE of ageing remained significantly higher (+ 11.36%, 41 days/year) than in the control group (P = 3.99e-5). No differences were seen using the Horvath and Hannum clocks. Enrichment analysis revealed that key pathways enriched with burn injury related to immune function, activation, and inflammation. The results reveal that epigenetic age, specifically the PACE of ageing and PCGrimAge, was accelerated in burn-injured adults at admission, with some return towards control values by 6 months. That these two clocks are built upon morbidity outcomes suggests that the injury is invoking a biological response that increases the risk of disease. Burn injury in adults induces epigenetic changes suggestive of an acceleration of the ageing process, which may contribute to the increased morbidity and mortality in these patients.

DNA methylation patterns are influenced by Pax3::Foxo1 expression and developmental lineage in rhabdomyosarcoma tumours forming in genetically engineered mouse models.

Rhabdomyosarcoma (RMS) is a family of phenotypically myogenic paediatric cancers consisting of two major subtypes: fusion-positive (FP) RMS, most commonly involving the PAX3::FOXO1 fusion gene, formed by the fusion of paired box 3 (PAX3) and forkhead box O1 (FOXO1) genes, and fusion-negative (FN) RMS, lacking these gene fusions. In humans, DNA methylation patterns distinguish these two subtypes as well as mutation-associated subsets within these subtypes. To investigate the biological factors responsible for these methylation differences, we profiled DNA methylation in RMS tumours derived from genetically engineered mouse models (GEMMs) in which various driver mutations were introduced into different myogenic lineages. Our unsupervised analyses of DNA methylation patterns in these GEMM tumours yielded two major clusters, corresponding to high and no/low expression of Pax3::Foxo1, which mirrored the results for human FP and FN RMS tumours. Two distinct methylation-defined subsets were found for GEMM RMS tumours with no/low Pax3::Foxo1 expression: one subset enriched in Pax7 lineage tumours and a second subset enriched in myogenic factor 5 (Myf5) lineage tumours. Integrative analysis of DNA methylation and transcriptomic data in mouse and human RMS revealed a common group of differentially methylated and differentially expressed genes, highlighting a conserved set of genes functioning in both human RMS models and GEMMs of RMS. In conclusion, these studies provide insight into the roles of oncogenic fusion proteins and developmental lineages in establishing DNA methylation patterns in FP and FN RMS respectively. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Discovery of a DNA methylation profile in individuals with Sifrim-Hitz-Weiss syndrome.

Pathogenic heterozygous variants in CHD4 cause Sifrim-Hitz-Weiss syndrome, a neurodevelopmental disorder associated with brain anomalies, heart defects, macrocephaly, hypogonadism, and additional features with variable expressivity. Most individuals have non-recurrent missense variants, complicating variant interpretation. A few were reported with truncating variants, and their role in disease is unclear. DNA methylation episignatures have emerged as highly accurate diagnostic biomarkers in a growing number of rare diseases. We aimed to study evidence for the existence of a CHD4-related DNA methylation episignature. We collected blood DNA samples and/or clinical information from 39 individuals with CHD4 variants, including missense and truncating variants. Genomic DNA methylation analysis was performed on 28 samples. We identified a sensitive and specific DNA methylation episignature in samples with pathogenic missense variants within the ATPase/helicase domain. The same episignature was observed in a family with variable expressivity, a de novo variant near the PHD domain, variants of uncertain significance within the ATPase/helicase domain, and a sample with compound heterozygous variants. DNA methylation data revealed higher percentages of shared probes with BAFopathies, CHD8, and the terminal ADNP variants encoding a protein known to form the ChAHP complex with CHD4. Truncating variants, as well as a sample with a recurrent pathogenic missense variant, exhibited DNA methylation profiles distinct from the ATPase/helicase domain episignature. These DNA methylation differences, together with the distinct clinical features observed in those individuals, provide preliminary evidence for clinical and molecular sub-types in the CHD4-related disorder.

Glyphosate-Based Herbicide Stress During Pregnancy Impairs Intestinal Development in Newborn Piglets by Modifying DNA Methylation.

Glyphosate-based herbicide (GBH), a feed contaminant, has been proven to impair the growth and development of humans and animals. Previous research has revealed that maternal toxin exposure during pregnancy could cause permanent fetal changes by epigenetic modulation. However, there was insufficient evidence of the involvement of DNA methylation in maternal GBH exposure-induced intestinal health of offspring. Here, we established pregnant sow exposure models to investigate the effects of GBH on the intestinal DNA methylation of newborn piglets. The results showed gestational exposure to GBH compromises the intestinal function of newborn piglets as well as decreases the mRNA expression of Dnmt1 and Dnmt3b jejunum. Further RRBS DNA methylation analysis revealed genomic hypomethylation in jejunum, and the differentially methylated regions were enriched in the pathways of intestinal development and food digestion and the related GO terms. Additionally, integrative analysis of methylome and transcriptome identified 23 genes showing inverse correlations and indicated the underlying injury mechanisms upon maternal GBH. These findings provide new insights and fundamental knowledge into the possible involvement of DNA methylation in the intestinal injury of offspring induced by maternal GBH exposure during pregnancy, which drives manufacturers to develop low-toxicity herbicide to ensure food safety and human health.

Comprehensive analysis of DNA methylation and gene expression to identify tumor suppressor genes reactivated by MLN4924 in acute myeloid leukemia.

This study investigated whether the neddylation inhibitor MLN4924 induces aberrant DNA methylation patterns in acute myeloid leukemia and contributes to the reactivation of tumor suppressor genes. DNA methylation profiles of Kasumi-1 and KU812 acute myeloid leukemia cell lines before and after MLN4924 treatment were generated using the 850K Methylation BeadChip. RNA sequencing was used to obtain transcriptomic profiles of Kasumi-1 cells. Target genes were identified through a combined analysis of methylation and transcriptome data. Methylation-specific PCR and quantitative PCR validated the changes in methylation and expression. Prognostic analysis of target genes was performed using databases, and Pearson correlation was used to examine the relationship between methylation and expression levels. In Kasumi-1 and KU812 cells, 301 and 469 differentially methylated sites, respectively, were identified. A total of 4310 differential expression genes were detected in Kasumi-1. Combined analysis revealed that TRIM58 exhibited significant demethylation and upregulation after MLN4924 treatment, as confirmed by quantitative and methylation-specific PCR. Furthermore, database analysis revealed that both down-expression and promoter hypermethylation of TRIM58 were correlated with poor prognosis in acute myeloid leukemia. A negative correlation was observed between TRIM58 methylation and expression levels. This study suggests that MLN4924 alters DNA methylation patterns in acute myeloid leukemia and reactivates TRIM58, a potential tumor suppressor gene, through demethylation.

Selective adsorption of unmethylated DNA on ZnO nanowires for separation of methylated DNA.

DNA methylation is a crucial epigenetic modification used as a biomarker for early cancer progression. However, existing methods for DNA methylation analysis are complex, time-consuming, and prone to DNA degradation. This work demonstrates selective capture of unmethylated DNAs using ZnO nanowires without chemical or biological modifications, thereby concentrating methylated DNA, particularly those with high methylation levels that can predict cancer risk. We observe varying affinities between methylated and unmethylated DNA on ZnO nanowires, which may be influenced by differences in hydrogen bonding strength, potentially related to the effects of methylation on DNA strand behavior, including self-aggregation and stretching inhibition. As a result, the nanowire-based microfluidic device effectively collects unmethylated DNA, leading to a significantly increased ratio of methylated to unmethylated DNA, particularly for collecting low-concentration methylated DNA. This simplified microfluidic device, composed of ZnO nanowires, enables direct separation of specific methylated DNA, offering a potential approach for DNA methylation mapping in clinical disease diagnostics.

DNA Methylation in Pituitary Adenomas: A Scoping Review.

Pituitary adenomas are a diverse group of neoplasms with variable clinical behavior. Despite advances in genetic analysis, understanding the role of epigenetic modifications, particularly DNA methylation, remains an area under investigation. This scoping review aimed to update and synthesize the current body of literature on DNA methylation in pituitary adenomas, focusing on methodological advancements and clinical correlations. A systematic search conducted across multiple databases, including Embase, Scopus, MEDLINE, and CENTRAL, identified 107 eligible studies. Early methods, such as methylation-restricted digestion and methylation-specific PCR (MSP), have evolved into more comprehensive approaches, such as chip-based DNA methylation analysis. Key findings suggest that genes like POMC, SOCS-1, and RASSF1A show a significant association between methylation and clinical behavior. However, methylation patterns alone are insufficient to fully explain tumorigenesis. Emerging data suggest that DNA methylation might serve as a prognostic marker for invasive growth and recurrence, but further longitudinal studies are needed. This review highlights the need for future research to explore the methylome more thoroughly and to better define the clinical impact of epigenetic modifications in pituitary adenomas.