Promoter Methylation Research Articles

Background Among CRC patients with mismatch repair protein deficiency or microsatellite instability (MSI), up to 50% of cases lack germline mutations in MMR genes, BRAF mutations, or MLH1 promoter methylation. Such cases are defined as Lynch-like syndrome (LLS). LLS is a heterogeneous group of diseases that may include all the patients with cancers of the Lynch syndrome spectrum with MSI in which we don’t find a pathogenic variant in MMR genes. Although various methods have been proposed to distinguish Lynch and Lynch-like Syndrome, there is still a lack of consensus on the precise classification of these patients. Methods Four cases of suspected Lynch-like syndrome encountered in daily clinical pathological diagnostic work were reported. The histopathological characteristics and molecular pathological changes of related tumors were analyzed, and the diagnosis and treatment progress of this disease were reviewed via literature. Results Combined with clinical findings and molecular pathological tests, 2 cases were diagnosed as Lynch-like syndrome (LLS), and 2 case was diagnosed as Lynch syndrome with atypical phenotype. Lynch-like syndrome-related tumors can occur in the colorectum and extraintestinal organs. Colorectal tumors show no specific locational or histological features, while extraintestinal tumors often exhibit poor differentiation and abundant interstitial lymphocyte infiltration. Patients with Lynch-like syndrome all exhibit tumoral lesions with loss of MMR protein (MLH1, PMS2, MSH2, MSH6) expression, microsatellite instability (MSI-L/MSI-H), wild-type BRAF , and negative MLH1 promoter methylation. However, heterogeneity exists in MMR protein expression, MSI status, and MLH1 promoter methylation among tumors at different sites in the same patient. No germline pathogenic mutations in MMR genes were detected in any Lynch-like syndrome, but one cases showed variant of uncertain significance in MMR, and two case (Lynch syndrome with atypical phenotype) had likely pathogenic mutation in MLH1. Conclusion Extraintestinal tumors associated with Lynch-like syndrome mostly exhibit histopathological characteristics and MMR/MSI changes similar to classic Lynch syndrome, but without pathogenic germline MMR mutations or MLH1 promoter methylation. Some suspected Lynch-like syndromes with likely germline pathogenic MMR mutations may represent Lynch syndrome with atypical phenotype. Most cases lack germline MMR mutations in normal tissues but harbor somatic MMR mutations in tumor tissues. Germline or somatic mutations in other genes related to MMR function may be observed in some cases.

Constitutional primary monoallelic promoter methylation of hereditary cancer genes, although rare, may explain early-onset cancers without family history. Also, promoter methylation of a hereditary cancer gene secondary to a genetic alteration in a methylation regulatory region can cause a hereditary cancer syndrome. This study investigates constitutional promoter methylation as mechanism of inactivation of cancer predisposition genes in genetically unsolved familial and/or early-onset colorectal cancer (CRC) patients. Bisulfite-treated peripheral blood DNA from 46 early-onset/familial CRC patients was analyzed using the Illumina Infinium MethylationEPIC BeadChip. One early-onset CRC patient exhibited constitutional, likely monoallelic, methylation of CpG island 102 in LTBP4, a gene involved in TGF-β signaling. Somatic methylation of this CpG island is common in CRC, and correlates with LTBP4 downregulation. LTBP4 double knockout mice develop colorectal adenomas and carcinomas, supporting the roleof this gene in CRC predisposition. Noadditional cases with constitutional LTBP4 CpG island 102 methylation or enrichment of deleterious LTBP4 variants in CRC patients compared to controls were found. Another early-onset CRC patient exhibited mosaic BRCA1 promoter methylation, typically associated with increased breast and ovarian cancer risk. No somatic second hit in BRCA1 was detected in the patient's tumor, and homologous recombination deficiency-associated features were inconclusive. Our findings suggest that constitutional methylation of LTBP4 CpG island 102 may be associated with increased CRC risk. Identification of additional cases is needed to confirm the existence of a novel CRC predisposition syndrome driven by epigenetic inactivation of LTBP4, potentially also linked to other clinical phenotypes associated with LTBP4 deficiency, such as pulmonary emphysema. Whether constitutional BRCA1 methylation contributes to CRC risk remains to be determined.

Background: Myocardial infarction (MI) is one of the leading causes of death throughout the world. Despite advances in treatment, the molecular mechanisms underlying MI remain poorly understood. Changes in gene expression and DNA methylation, crucial for regulating cellular processes, have received limited exploration. Aims: This study aimed to investigate the role of Fc Gamma Receptor IIa (FCGR2A) and its regulatory mechanism in myocardial infarction, providing potential therapeutic insights. Methods: Our study combined human sample analysis with a rat ischemic model, using RRBS and RNA-Seq to identify and analyze candidate genes via GO and KEGG enrichment. FCGR2A overexpression and knockdown in H9C2 cells were used to assess its role in cell viability and apoptosis under hypoxia and serum deprivation. DNA methylation was analyzed by BSP, while calcium concentration and L-type calcium current density were measured using Fura-2 and patch clamp techniques. Dual-luciferase reporter assays and chromatin immunoprecipitation confirmed ATF3-mediated transcriptional regulation of FCGR2A. In vivo, myocardial infarction was induced by LAD ligation, and AAV9-mediated FCGR2A overexpression or ATF3 knockdown validated its protective effects on the ischemic heart. Results: We combined the analysis of genomic methylation sequencing (RRBS) and RNA-Seq and screened out FCGR2A as a potential target for treatment of myocardial infarction(Fig 2A-G). Hypermethylation in the CpG island of FCGR2A was associated with ischemic heart disease and induces downregulation of FCGR2A (Fig 2H-M). Overexpression of FCGR2A mitigated hypoxia-induced cardiomyocyte apoptosis, reduced L-type calcium channel current density, and alleviated intracellular calcium overload. Additionally, ATF3 was found to regulate FCGR2A transcription by promoting its promoter methylation(Fig 3A-F). In vivo, FCGR2A overexpression or ATF3 knockdown validated its cardioprotective effects and clarified their regulatory relationship in ischemic myocardial injury(Fig 3G-H). Conclusion: FCGR2A plays a critical role in protecting the ischemic heart and is epigenetically regulated by ATF3. Targeting FCGR2A may offer a promising therapeutic strategy for myocardial infarction.

BackgroundLow-grade glioma (LGG) is a diverse group of primary brain tumors, whose molecular heterogeneity hinders classification by traditional pathological methods. Accurate phenotypic subtyping of LGG is essential for capturing tumor characteristics and optimizing clinical management. We intend to identify LGG phenotypic subtypes based on multimodal magnetic resonance imaging (MRI) data, enhancing prognosis evaluation and optimizing treatment strategy.MethodsThis was a retrospective multicenter study, and data were drawn from the First Hospital of Shanxi Medical University (FHSXMU) and Shanxi Provincial People’s Hospital (SPPH) (FHSXMU/SPPH cohort, n = 162), and The Cancer Genome Atlas (TCGA)/The Cancer Imaging Archive (TCIA) (TCGA/TCIA cohort, n = 118). In the FHSXMU/SPPH cohort, LGG phenotypic subtypes were identified using the outcome-weighted integrative clustering method (survClust) based on multimodal MRI data (CE-T1 and T2FLAIR). A multivariate Cox proportional hazards model was applied to evaluate survival differences between subtypes. Statistical comparisons between subtypes were performed, and the statistically significant MRI features were utilized to predict clinically relevant biomarkers – isocitrate dehydrogenase (IDH) mutation combined with O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation. Five models were constructed, including fused kernel partial least squares with the genetic algorithm (GA-fKPLS), logistic regression, random forest, support vector machine, and k-nearest neighbor. In the TCGA/TCIA cohort, we validated the identified phenotypic subtypes and further explored their biological characteristics by analyzing pathway activity and immune infiltration levels using mRNA expression data.ResultsTwo distinct LGG phenotypic subtypes were identified in the FHSXMU/SPPH cohort, and validated in the TCGA/TCIA cohort. In the FHSXMU/SPPH cohort, significant differences in pathological grade, MGMT promoter status, IDH genotype, survival status, tumor volume, and survival outcome (HR: 2.553, 95%CI: [1.226–5.315]) between the two subtypes (P < 0.05). Compared to other four models, the GA-fKPLS model exhibited superior predictive performance (AUC: 0.809). In the TCGA/TCIA cohort, two LGG phenotypic subtypes showed significant differences in pathway activities (JAK-STAT, TNF-α, p53) and immune cell infiltration (M2 macrophages, T cell regulatory, Monocytes) (Padj < 0.05).ConclusionThis study identified two LGG phenotypic subtypes and potential biomarkers, offering supplementary information for clinical evaluation and treatment decision-making.Graphical Supplementary InformationThe online version contains supplementary material available at 10.1186/s12883-025-04420-0.

Background/Objectives: Breast cancer is a heterogeneous disease, and the role of the transcription factor SPDEF remains controversial. We aimed to clarify the prognostic value of SPDEF, explore demographic and molecular correlates of its expression, and investigate potential regulatory mechanisms underlying its dysregulation. Methods: Genomic and clinical data for 1218 breast cancer tumors were obtained from The Cancer Genome Atlas (TCGA). SPDEF mRNA expression was compared across intrinsic subtypes, age, and race, and prognostic significance was evaluated by Kaplan–Meier analysis. Promoter methylation patterns and DNA methyltransferase (DNMT) expression were examined as potential regulatory drivers. Co-expression analysis was performed using gene panels representing luminal differentiation, basal identity, EMT, proliferation, DNA repair, and immune signaling. Results: Low SPDEF expression was significantly associated with worse overall, relapse-free, and metastasis-free survival across all breast cancers. Expression was lowest in Basal tumors, as well as among younger and Black or African American patients. Promoter methylation at six CpG islands correlated with both reduced SPDEF expression and inferior survival, and DNMT1, DNMT3A, and DNMT3B overexpression also aligned with poor prognosis and Basal enrichment. Co-expression analysis revealed that SPDEF downregulation coincided with loss of luminal markers and increased EMT, proliferation, DNA repair, and immune pathways. Conclusions: SPDEF functions as a tumor suppressor in breast cancer, with reduced expression linked to poor outcomes, aggressive molecular features, and epigenetic regulation. These findings highlight SPDEF and DNMT-driven methylation as potential prognostic biomarkers for enhanced risk stratification and targets for novel therapies, particularly in Basal breast cancers.

Chronic hepatitis B (CHB) is a major risk factor for liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Genes involved in the JAK/STAT signalling pathway play a critical role in the pathogenesis of HBV-related liver diseases, especially HCC. Although SOCS1 and SOCS3 have been extensively studied, the role of SOCS6 in HBV infection and disease progression remains unclear. This study aimed to investigate the association between SOCS6 gene polymorphisms and promoter methylation with HBV-related liver diseases. This study examined SOCS6 gene polymorphisms in a cohort of 335 patients with HBV-related liver diseases (120 with CHB, 100 with LC and 115 with HCC) and 120 healthy controls (HCs). In addition, SOCS6 promoter methylation was analysed in tumour and adjacent tissues from 41 HCC patients. We found that the rs2062345GA genotype and the dominant genetic model were associated with an increased risk of HBV infection and HCC. The rs7228049GA genotype increased the risk of LC and HCC. Conversely, the rs7228049AA genotype and the recessive model were associated with a reduced risk of CHB, LC and HCC. The SNPs rs2062345, rs7228049 and rs11151580 were related to several clinical parameters such as AST, albumin and prothrombin levels, platelet counts in LC and HCC patients. Promoter hypermethylation of SOCS6 was more prevalent in tumour tissues, especially in larger tumours with poorer histological differentiation (p<0.01 and p<0.05, respectively). SOCS6 gene variants and promoter methylation are associated with susceptibility and progression of HBV-related liver diseases. These findings suggest their potential utility as useful prognostic biomarkers for HCC.

Melatonin inhibits adipogenesis and enhances osteogenesis of BMSCs through increasing KLF5 expression.

DNA methylation-regulated DDX27 promotes colorectal cancer progression through EZH2.

Magnetic resonance imaging fractal analysis of O(6)-methylguanine-DNA methyltransferase promoter methylation status in isocitrate dehydrogenase wild-type glioblastoma

Both absolute and presumably active rDNA (with a hypomethylated promoter region) copy number (CN) in the haploid human sperm genome are highly variable among individuals. Using a combination of droplet digital PCR and deep bisulfite sequencing, we have quantified absolute and presumably active rDNA CN in sperm samples (N = 190) with normal (NSPs) vs. abnormal semen parameters (ASPs), as well as in samples leading or not leading to a clinical pregnancy. ASP samples had a significantly lower presumably active CN (104 ± 31) than normozoospermic samples (115 ± 31). The loss of presumably active rDNA copies is explained by an increased promoter methylation (13.9% in ASP vs. 12.1% in NSP). When correcting for confounding factors, most importantly semen quality, samples not leading to a clinical pregnancy after IVF/ICSI displayed a significantly lower absolute (225 ± 51) and presumably active CN (103 ± 30) than samples with pregnancy (249 ± 62 and 115 ± 31, respectively). This between-group difference was most noticeable in normozoospermic males: absolute CN 220 ± 54; presumably active CN 107 ± 32 in samples without pregnancy and absolute CN 246 ± 63; presumably active CN 120 ± 28 in samples with pregnancy. We propose that absolute/active rDNA CN in sperm is a modulating factor contributing to idiopathic male infertility. In NSP samples, presumably active CN increases with absolute CN, which may have a positive impact on fertility and ART outcome. Our results suggest that approximately 60 active sperm rDNA copies are sufficient to establish a pregnancy.

Epigenetic regulation of sex: the role of DNA methylation and zbtb38 in zebrafish sex differentiation and heat-induced masculinization.

Metastatic colorectal cancer is commonly treated with oxaliplatin. However, patients may develop resistance to treatment over time, and currently, there are no validated predictive biomarkers for this resistance. A differential analysis of the transcriptome and DNA methylome of colorectal cancer cell lines, classified by their varying IC50 values for oxaliplatin, revealed that genes associated with resistance were enriched for interferon regulatory factor pathways. In contrast, sensitive genes showed enrichment for transcription, amino acid metabolism, development, and binding motifs of c-MyC:Max, AP1 and others. In univariate Cox’s proportional hazard model analysis, it was found that UBE2H expression is linked to shorter survival time in the TCGA dataset and was further validated across five GEO datasets of colorectal cancer. The transcription of UBE2H, along with its gene body methylation, and copy number variation was found to be higher in resistant cell lines compared to sensitive ones. Additionally, UBE2H levels were higher in cancer samples than in control samples, while the promoter methylation is lower in cancer samples than in control samples. In groups with high UBE2H, there was an increased infiltration of eight cell types, including CD8+ T cells and type 2 T helper cells. Conversely, only T helper 17 cells showed reduced infiltration. Moreover, UBE2H expression was positively correlated with checkpoint inhibitors, CTLA4 and PDCD1, along with immune regulatory genes, such as FOXP3, IL10, IGFB1, CD274, and LAG3, etc. Analysis of single cell RNA-sequencing data revealed that UBE2H expression is elevated in undifferentiated and proliferative cells located at the base of intestinal crypts in normal colon tissue. Our findings suggest that UBE2H could serve as a resistance marker to oxaliplatin, as it is associated with methylation, the presence of proliferative and undifferentiated cancer cells, and immune exhaustion. The proposed analytical pipeline may also be applicable to other cancers and diseases.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12935-025-03996-4.

Cyclin-Dependent Kinase Subunit 1B (CKS1B) is significantly upregulated in lung adenocarcinoma (LUAD) tissues and is associated with poor clinical outcomes, such as shorter overall survival (OS) and progression-free survival (PFS). High CKS1B expression correlates with advanced tumor stage, aggressive pathology, and increased immune cell infiltration, indicating its role in modulating the tumor microenvironment and promoting immune evasion. We confirmed the elevated expression of CKS1B in LUAD cell lines through quantitative real-time polymerase chain reaction and Western blot analysis. Knockdown of CKS1B using small interfering RNA (siRNA) reduced cell proliferation, increased apoptosis, and impaired invasion. Additionally, CKS1B knockdown upregulated E-cadherin and downregulated N-cadherin, indicating suppression of epithelial-mesenchymal transition (EMT). We further demonstrated that CKS1B knockdown decreased the phosphorylation of MEK and ERK, suggesting inhibition of MAPK/ERK signaling. Bioinformatic analysis revealed that higher levels of hsa-miR-140-3p negatively correlate with CKS1B expression and are associated with improved survival outcomes, pointing to a potential tumor-suppressive axis. Decreased promoter methylation of CKS1B in LUAD tissues, along with its association with tumor mutation burden (TMB) and immune checkpoint expression, highlights its role in tumor progression and resistance to immunotherapy. A nomogram integrating CKS1B expression with clinical parameters effectively predicted 3- and 5-year survival probabilities, offering a tool for personalized risk assessment. In conclusion, our findings position CKS1B as a key factor in LUAD progression and suggest that targeting MAPK/ERK signaling could enhance the efficacy of immunotherapy and overcome chemoresistance.Graphical

BackgroundOral squamous cell carcinoma (OSCC) remains a major global health burden, often diagnosed at advanced stages, with limited survival improvement. Epigenetic dysregulation, particularly promoter hypermethylation, plays a significant role in OSCC pathogenesis. Previous study by Demokan et al. identified Gamma-Aminobutyric Acid Receptor Beta-2 (GABRB2) as a candidate gene subject to methylation-dependent transcriptional silencing. This study aimed to evaluate the methylation and expression profiles of GABRB2 in OSCC and to explore its potential as a diagnostic biomarker.MethodsTissue and serum samples from 48 OSCC patients and 15 healthy controls were analyzed for GABRB2 promoter methylation via quantitative methylation-specific PCR and for gene expression levels via quantitative real-time PCR. Relationships between methylation, expression levels, clinicopathological parameters, and patient outcomes were statistically assessed.ResultsGABRB2 promoter hypermethylation was detected in 14.6% of tumor samples, predominantly in floor of the mouth and buccal tumors. Decreased GABRB2 expression was observed in 52.1% of tumor tissues compared to matched-normal tissues, while 22.9% of tumors exhibited increased expression. Methylation-dependent expression loss was confirmed in 71.4% of methylated tumors. Notably, decreased expression and hypermethylation of GABRB2 were correlated with poor prognosis parameters (p < 0.05). ROC analysis showed moderate discrimination for GABRB2 expression in distinguishing tumor from normal tissues (AUC = 0.635, p = 0.022), while serum-based analysis demonstrated poor diagnostic performance. Survival analysis revealed no statistically significant prognostic impact of GABRB2 expression levels (p > 0.05). However, alcohol consumption (p = 0.006) and recurrence developed (p = 0.030) as independent predictors of poor prognosis in multivariate analysis.ConclusionOur study suggests that there was association between methylation-based expression loss of GABRB2 with OSCC’ subgroups. To our knowledge, this is the first study to investigate GABRB2 gene methylation and expression profiling in both invasive/non-invasive samples from OSCC patients. Hypermethylation in the newly identified candidate GABRB2 gene may play a role in the development of tumors originating from the mouth floor and buccal anatomical regions of the oral cavity. However, since the loss of expression seen in the majority of our patients, we thought that only methylation may not the inhibition mechanism for GABRB2 gene decreased expression. The new identified candidate gene may be specific for the OSCC’s subgroups.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12903-025-06899-y.

Preeclampsia (PE) is a pregnancy-specific disease that seriously endangers the health of the pregnant woman and the fetus. DNA hydroxymethylation, an epigenetic modification, plays crucial roles in the development of PE. However, the molecular mechanism remains to be elucidated. TET1 is a DNA demethylase that regulates placental trophoblast function. Herein, we investigated the role of TET1 in PE occurrence. Firstly, we confirmed that the 5-methylcytosine (5-mC) levels were reduced in placental tissues from human PE patients and a mouse PE model, while TET1 expression was upregulated. In an oxidative stress model of HTR8/SVneo cells, knockdown of TET1 partially restored the impaired cell invasion and migration caused by H2O2. To elucidate the mechanism, bioinformatics analysis of TET1-knockdown RNA sequencing and ChIP-seq data identified ornithine decarboxylase (ODC1), a rate-limiting enzyme in the polyamine biosynthesis, as a potential target. Similarly, knockdown of ODC1 alleviated the H2O2-induced dysfunction in HTR8/SVneo cells. Moreover, the CUT&RUN and dual-luciferase assays revealed that TET1 regulates the expression of ODC1 by affecting the methylation level of its promoter. Collectively, these results demonstrate that TET1-mediated DNA hydroxymethylation is associated with the occurrence of PE. This is partially attributed to the regulation of ODC1 through altered promoter methylation, which leads to trophoblast dysfunction and contributes to the development of PE.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-22116-w.

BackgroundADAM12, a member of the disintegrin and metalloproteinase family, has been involved in multiple cancers, yet its precise role in pan-cancer progression still remains elusive.MethodsIn our current study, we conducted a comprehensive analysis of ADAM12 expression, diagnosis, prognosis, genomic variations, DNA methylation, functional enrichment, immune infiltration as well as immunotherapy in pan-cancer utilizing public datasets. Additionally, a series of biological functional experiments of ADAM12 were performed in gastric cancer cells including cell counting kit-8 (CCK-8), colony formation, wound healing analysis, and Transwell analyses.ResultsADAM12 expression was prominently elevated and correlated with unfavorable prognosis in most cancer types. It exhibited elevated mutation frequency and a negative correlation with DNA methylation promoters across various tumors. ADAM12 expression strongly linked to ESTIMATE, immune/stromal scores, immune checkpoint genes, tumor mutation burden (TMB), and microsatellite instability (MSI) in specific cancer types. Single-cell and bulk RNA sequencing analysis revealed heightened ADAM12 levels in fibroblasts, highlighting its importance in tumor immunity. Furthermore, the predictive value of immunotherapy surpassed that of tumor mutational burden based on TIDE. Functional enrichment analysis associated ADAM12 with focal adhesion, PI3K-Akt signaling, and ECM-receptor interactions. In vitro experiments confirmed that ADAM12 downregulation significantly impeded proliferation, migration, and invasion of gastric cancer cells.ConclusionsADAM12 might be a valuable prognostic biomarker and a promising candidate for tumor immunotherapy.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12672-025-03837-w.

Background/ObjectivesEpstein-Barr Virus (EBV) is a ubiquitous virus associated with a variety of diseases including cancers. Evidence has emerged that the C promoter is methylated in many EBV-associated malignancies, whereas in free virion DNA it is unmethylated. We have developed and evaluated a methylation-specific PCR assay for the EBV C Promoter (MSPCP) that can be applied to human biological specimens to quantify EBV methylation.MethodsTwo sets of methylation-specific primers were designed to anneal to bisulfite-converted DNA sequences with 3 CpGs in the forward primer binding site, and 2 CpGs in the reverse primer binding site. We evaluated this method in synthetic oligonucleotides, DNA extracted from cell lines, virion supernatants, and a variety of clinical specimens. EBV methylation of Cp, as measured by MSPCP, was validated with two orthogonal methods in select samples.ResultsIn contrived samples, this method had a linear range between 0–100% methylation. Application of this assay to DNA extracted from 11 formalin-fixed paraffin-embedded biopsy specimens showed high-level C promoter methylation in EBV-associated tumors (94–100%) but not in EBV-associated lymphoid hyperplasia. High-level EBV methylation was also detected in cell-free DNA extracted from the plasma of 13 patients with EBV-associated Hodgkin lymphoma. In contrast, EBV methylation was either not-detected, or detected at very low levels, in saliva from 25 adults in a general university population consistent with the presence of virion DNA.ConclusionsMSPCP is a simple, rapid and accurate method that characterizes the methylation status of the EBV C promoter, which may be useful in a variety of research and clinical settings.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13027-025-00702-x.

The nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) inflammasome is a multiprotein complex fundamental for the secretion of pro-inflammatory cytokines during the innate immune response. NLRP3 dysregulation is implicated in the pathogenesis of several diseases, such as inflammatory bowel disease, arthritis, cancer, Alzheimer's disease, and type 2 diabetes. The pharmacological modulation of NLRP3 by several compounds, which are fully described in this review, represents an important strategy to regulate inflammatory processes. Moreover, NLRP3 is also involved in drug-related adverse reactions, and its pharmacological modulation represents a rapid strategy to mitigate such adverse effects, as reported in this study. NLRP3 inflammasome activation is tightly regulated by post-transcriptional modifications and epigenetic factors, such as long non-coding RNAs (lncRNAs) and DNA methylation, as well as other interacting regulators. Recently, different studies have revealed the importance of NLRP3 levels in predicting drug response. In particular, the methylation of the NLRP3 promoter, which is associated with the inflammasome expression level, emerged as a new promising pharmacoepigenetic biomarker for the glucocorticoid therapy response in several inflammatory disease conditions.

Cholangiocarcinoma (CC) is a highly lethal malignancy that urgently requires reliable prognostic biomarkers. Although MUC1 expression and promoter methylation have been implicated in CC, the clinical significance of promoter methylation pattern composition, beyond average methylation levels, remains unclear. Here, we investigated the relationship between MUC1 promoter methylation heterogeneity, MUC1 mRNA expression, and prognosis in CC. We analyzed bisulfite amplicon sequencing data and mRNA expression of MUC1, DNA methylation-related enzymes (TET1, TET2, TET3, Dnmt1, and Dnmt3a), and tumor microenvironment stress markers in 131 CC tissues. In the neoplastic region, high MUC1 mRNA expression was associated with poor overall survival (HR = 0.131, 95% CI: 0.02to0.95, p = 0.042) and correlated with the abundance of completely unmethylated promoter patterns (r = 0.386, p < 0.001). Among the enzymes analyzed, only TET3 expression significantly correlated with the abundance of completely unmethylated patterns in the neoplastic region (Cohen's f2 = 0.108, p = 0.009), suggesting a potential region-specific regulatory association. We visualized beta-diversity in methylation pattern composition using t-SNE and classified samples into two groups based on a linear decision boundary in the t-SNE space. This classification stratified prognosis independently of clinical factors (HR = 0.291, 95% CI: 0.06to0.94, p = 0.037; multivariate p = 0.021). These findings propose a novel, composition-based epigenetic stratification framework in CC, revealing that MUC1 promoter methylation pattern structure-rather than average methylation level-has prognostic relevance. Our results highlight the potential of pattern-resolved methylation profiling in the development of clinically applicable epigenetic biomarkers.

Glioblastoma (GBM) remains incurable, largely due to inherent radiotherapy resistance driven by synergistic crosstalk between spatial heterogeneity and epigenetic dysregulation. Distinct tumor microenvironments—hypoxic cores, invasive edges, and perivascular regions—harbor glioblastoma-initiating cells (GICs) with unique epigenetic traits that promote radiation evasion: hypoxic cores activate the HIF–SIRT axis to maintain quiescence; invasive edges employ EZH2-mediated H3K27me3 to drive proneural–mesenchymal transition (PMT); and perivascular niches utilize HDAC–DNA repair and BRD4–super-enhancer mechanisms to sustain stemness. Concurrent epigenetic alterations—such as MGMT promoter methylation, aberrant histone modifications, and chromatin remodeling—further enhance adaptive plasticity. This review synthesizes recent preclinical and clinical evidence (2019–2024) to delineate how spatial and epigenetic mechanisms form a “resistance loop” that subverts radiotherapy. We argue that effective radiosensitization requires niche-specific strategies: HDAC inhibitors in hypoxic regions to impair DNA repair, EZH2 inhibitors at invasive margins to suppress PMT, and BET inhibitors in perivascular zones to target stemness programs. We propose a “spatial-epigenetic precision pipeline” involving: (1) mapping niche-specific epigenetic signatures via spatial multi-omics; (2) developing ligand-functionalized nanocarriers for targeted delivery; and (3) designing adaptive combinatory regimens (epigenetic agents with radiotherapy and immunotherapy) based on dynamic response monitoring. This framework aims to disrupt spatial–epigenetic crosstalk, potentially transforming GBM into a chronically manageable disease.