Clinical Epigenetics最新文献

Background: Trimethylamine N-oxide (TMAO) and its related metabolites have been linked to cardiovascular disease (CVD), but their impact on DNA methylation remains unclear. Investigating these relationships may clarify the role of epigenetic mechanisms in diseases.

Methods: This study analyzed data from 1,356 adults from the Cardiovascular Health Study (CHS) and the Multi-Ethnic Study of Atherosclerosis (MESA). Using stable-isotope dilution liquid chromatography with on-line electrospray ionization tandem mass spectrometry (LC-MS), we quantified TMAO and five related metabolites. DNA methylation levels were measured using Illumina BeadChip arrays. Epigenome-wide association analyses and meta-analyses were conducted across approximately 430,000 CpG sites. To explore the functional significance of the identified CpGs, we performed gene set enrichment analysis and Mendelian randomization (MR) analyses.

Results: We identified 143 metabolite-CpG pairs at FDR < 0.05, including four CpGs for TMAO (P ≤ 4.03e-7), 12 for betaine (P ≤ 1.19e-6), 53 for γ-butyrobetaine (P ≤ 6.11e-6), five for carnitine (P ≤ 5.42e-7), six for choline (P ≤ 2.81e-7), and 63 for crotonobetaine (P ≤ 7.25e-6). CpGs associated with γ-butyrobetaine showed moderate correlation with crotonobetaine-associated CpGs. In total, these metabolite-linked CpGs were mapped to 108 genes. Gene set enrichment analysis revealed 145 significantly enriched gene sets, including nine highly relevant to CVD risk. Furthermore, CpGs were enriched in 80 immunologic signature gene sets (FDR < 0.05). MR analysis identified three CpGs associated with coronary artery disease (CAD), including hypermethylation at cg18705301 (NDUFAF1), which was inversely associated with betaine levels and linked to a lower risk of CAD (P = 1.8e-5).

Conclusion: This study identified specific DNA methylation sites associated with TMAO and related metabolites. These epigenetic changes may contribute to CVD risk through multiple pathways. Future research should validate these findings and explore their clinical implications.

Background: Epigenetic clocks assess DNA aging based on DNA methylation. We aimed to study the utility of methylation clocks in understanding the distinct characteristics of sporadic and hereditary neuroendocrine neoplasms (NEN).

Methods: Epigenetic age and acceleration were calculated based on Horvath multi-tissue, Levine, and Hannum clocks, and compared by genetic predisposition and NEN grading (WHO-defined G1, G2 and G3).

Results: Following quality assessment and filtering of the data, 93/96 samples were analyzed. Of them, 41/93, 42/93, and 10/93 were sporadic, multiple endocrine neoplasia 1 (MEN1) and von Hippel-Lindau (VHL)-related NEN, respectively. Forty-eight (48/93) were pancreatic NEN (PanNEN). mDNA age positively correlated with chronological age based on three different clock algorithms, but stronger correlations were found in the hereditary NEN subgroups (Horvath clock, r = 0.65, p < 0.001 for MEN1-relatd NEN, and r = 0.86, p = 0.002 in VHL-related NEN). Epigenetic age acceleration was higher in sporadic NEN compared to hereditary NEN, both based on chronological age-adjusted epigenetic age (Hannum clock, sporadic vs. MEN, p = 0.03; sporadic vs. VHL, p = 0.0002), and based on the difference between epigenetic age and chronological age (Hannum clock, sporadic vs. MEN1, p = 0.009; sporadic vs. VHL, p = 0.0005). Finally, epigenetic age (p = 0.04) and age acceleration (p = 0.03) were higher among adult patients with NEN (G2/3 vs. G1).

Conclusions: Epigenetic age and age acceleration analysis demonstrate distinct patterns in sporadic and hereditary NEN, suggesting lower impact of epigenetic alteration or DNA aging in the pathogenesis of hereditary NEN.

Esophageal cancer is a highly aggressive malignant tumor of the digestive tract, with significant heterogeneity in its pathogenesis and clinical manifestations. Despite advances in treatment strategies such as surgery, chemotherapy, and radiotherapy, the prognosis of esophageal cancer remains poor. In recent years, increasing evidence has shown that epigenetic regulation plays a critical role in the occurrence and development of esophageal cancer. Epigenetic mechanisms, including DNA methylation, histone modification, and non-coding RNA, can regulate gene expression without changing the DNA sequence and are involved in a variety of biological processes, including cell proliferation, apoptosis, and invasion. Abnormal epigenetic alterations are not only key drivers of tumorigenesis but also promising biomarkers and therapeutic targets. This review focuses on the epigenetic mechanisms involved in esophageal cancer and summarizes the latest progress in epigenetic-based therapeutic strategies, including the development and application of DNA methyltransferase inhibitors, histone deacetylase inhibitors, and drugs targeting non-coding RNAs. Moreover, it discusses the challenges and future prospects of epigenetic therapy in the clinical management of esophageal cancer.

Background: Animal models suggest a role of epigenetic mechanisms, including DNA methylation, in neural tube closure; however, studies characterizing DNA methylation profiles in nervous system tissue from humans with spina bifida are limited. In this study, we assessed DNA methylation profiles in dural tissue of infants with spina bifida, collected at the time of surgical closure of the defect, and examined whether whole blood or buccal swab are appropriate surrogate tissues, as they are more practical to collect in large-scale epidemiological studies. DNA methylation was measured in dural tissue, buccal swab, and whole blood samples collected from 27 unique infants using the Illumina Infinium MethylationEPIC BeadChip array.

Results: Correlation analysis for each CpG site comparing DNA methylation from all participants in dural tissue to DNA methylation in whole blood DNA or buccal swab DNA yielded 1555 statistically significant associations for the whole blood analysis and 920 significant associations for the buccal swab analysis at the Bonferroni threshold of significance. We also performed paired analysis, calculating differences between tissues within each individual and then averaging differences across individuals. After accounting for multiple hypothesis testing using the FDR adjustment, 33% of CpG sites assessed were not significantly differentially methylated between dural tissue and whole blood samples, compared to the 27% of sites not differentially methylated between dural tissue and buccal swab samples.

Conclusions: These results suggest that in the absence of dural tissue, both whole blood and buccal swab samples may be considered as surrogates for dural tissue. The study warrants replication in larger groups to validate findings and may assist researchers restricted to more accessible biospecimens (i.e., blood) to further characterize epigenetic contributors to neural tube defect etiology.

Background: Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder with characteristic clinical features such as overgrowth and macroglossia. Hypermethylation of the H19/IGF2:IG-differentially methylated region (H19-DMR) is identified in 5% of BWS patients. Although defects in the OCT4/SOX2 binding sites (OBS) on the maternal allele have been reported in patients with hypermethylated H19-DMR, the precise methylation patterns in patients with OBS abnormalities remain elusive. Nanopore long-read sequencing (LRS) obtains sequence reads 10-100 kb long together with single-molecule DNA modifications, such as 5-methylcytosines. Furthermore, LRS can separate reads into haplotypes 1 and 2 based on information from single-nucleotide variants and indels on reads. Here, we conducted LRS to elucidate the abnormal hypermethylation patterns of the H19-DMR in BWS patients with and without OBS abnormalities and evaluate the differences between mothers and their offspring in familial cases with OBS abnormalities.

Results: We included 14 sporadic patients and four familial patients from two families with BWS showing hypermethylation of the H19-DMR. Amplicon sequencing for the H19-DMR detected OBS abnormalities in four (28.6%) sporadic cases (three point mutations, one 21-bp microdeletion overlapping OBS), an OBS point mutation in family A, and a 2.6 kb deletion involving OBS in family B. Subsequently, we conducted targeted LRS and examined methylation indexes for 247 CpGs in the H19-DMR in three sporadic patients with OBS abnormalities, two sporadic patients without OBS abnormalities, and all familial patients with OBS abnormalities. In patients with point mutations and a 21-bp microdeletion affecting a single base in OBS, CpGs in the H19-DMR had obvious hypermethylation in the vicinity of OBS and mild-to-moderate hypermethylation with increased distance from OBS; however, in patients with deletions including OBS, CpGs had moderate hypermethylation in the entire H19-DMR. In families A and B, methylation levels were higher in offspring than in their mothers.

Conclusion: Because 28.6% of sporadic patients had OBS abnormalities, genetic examination for OBS should be considered in BWS patients with hypermethylated H19-DMR. LRS analysis for the H19-DMR revealed differences in methylation patterns between patients with and without OBS abnormalities and the methylation levels of each CpG between mothers and their offspring in families with OBS abnormalities.

Background: Protein EpiScores are a novel class of DNA methylation (DNAm)-based metrics proposed to measure peripheral immune system characteristics. Although Protein EpiScores have been associated with chronic disease risk, their relationship with colorectal cancer (CRC) survival has not been investigated.

Methods: We generated new genome-wide DNAm data on pre-treatment whole blood samples from a case-control sample of 136 newly diagnosed CRC patients nested in the ColoCare Study and calculated 107 Protein EpiScores using the developer's algorithm. Over a median follow-up of 7.3 years (range: 0.3-13.8 years), 35 (26%) patients experienced disease recurrence, and 47 (35%) died. Protein EpiScore associations with disease-free and overall survival were tested using Cox regression models, adjusted for patient and clinical characteristics, and prognostic discrimination was assessed using Harrell's C-index.

Results: In fully-adjusted models, HCII, VEGFA, CCL17, and LGALS3BP Protein EpiScores were associated with worse disease-free survival (HRs between 1.62 and 1.71, all FDR < 0.05). Adding these Protein EpiScores to traditional clinical prognosis risk factors significantly improved disease-free survival prediction (C-index: 0.64 vs 0.70, P-diff= 0.03). The LGALS3BP Protein EpiScore was associated with worse overall survival (HR: 1.80, 95% CI 1.29, 2.51,P = 0.0005, FDR= 0.056), and improved prediction (C-index: 0.70 vs 0.75, P-diff= 0.02). Protein EpiScores for HCII, LGALS3BP, MMP12, and VEGFA showed positive association with both disease-free and overall survival (HRs > 1.5).

Conclusions: Protein EpiScores are significantly associated with CRC survival. These findings highlight biological pathways underlying CRC prognosis and support the utility of Protein EpiScores for modeling survivorship.

Background: Epigenetic factors underlying telomere length (TL) may provide insight into telomeric homeostasis, with direct links to cigarette smoking and lung cancer susceptibility. It is unclear, nevertheless, to what extent effects of TL and its related DNA methylation on the smoking-induced lung tumorigenesis.

Methods: A case-cohort study is performed within the Dongfeng-Tongji (DFTJ) cohort, including a randomly selected subcohort of 1399 subjects and 359 incident lung cancer cases. We use a linear regression model to conduct EWAS of TL, while the associations of TL and candidate CpGs with lung cancer risk are evaluated using weighted Cox proportional hazard regression models. Furthermore, the causal inference test (CIT) and mediation analysis are used to elucidate the causality of TL and its relevant CpGs in the smoking-induced lung tumorigenesis. The methylation-expression associations are assessed in SY panel (n = 144), adjacent normal lung tissues (n = 32) and solid normal tissues in TCGA (n = 375).

Results: We identified 31 CpGs with significant associations with TL at FDR < 0.05, and their annotated genes are mainly enriched in oxidative stress, energy metabolism and immunity regulation pathways. Among the 31 TL-related CpGs, 3 CpGs showed substantial associations with both lung cancer risk and smoking status (all FDR < 0.1), including cg26563141 in RGPD1/RGPD2, cg03964851in MIR1974/KIAA0825, and cg08976633 in ZNF74. The further mediation analyses suggest that these three CpGs could mediate 2.89%~8.83% effect on lung cancer risk induced by smoking (all FDR < 0.1). The further CIT and multiple mediation analysis reveal that the effect of smoking on lung cancer risk is primarily mediated by TL (> 10%) while being mildly mediated via DNA methylation pathway (< 1%). Also, hypermethylation of cg26563141 is related to low expression of RGPD1 and RGPD2 across blood and tissue samples.

Conclusions: Both TL attrition and the three candidate CpGs showed significant mediation effects on lung cancer risk induced by smoking. These findings provide novel insight into the epigenetic control of telomere homeostasis mechanisms and clues for methylation alteration and TL in smoking-induced lung tumorigenesis.

Background: Drug resistance, characterized by high heterogeneity and complex mechanisms, poses a significant challenge in cancer treatment. Stratifying resistant tumors into biologically and clinically meaningful subgroups can improve prognostic evaluation and help guide treatment decisions. However, the DNA methylation-based subtypes of resistant tumors have not yet been comprehensively characterized.

Results: DNA methylation profiles from resistant tumors were retrieved from public database including TCGA and GEO. For each tumor type resistant to a specific treatment drug, consensus clustering based on the most variable methylated probes was conducted to identify the DNA methylation subtypes of resistant tumors. For low-grade glioma (LGG) resistant to Temozolomide, consensus clustering of highly variable CpGs identified two subtypes: cancer resistance CpG island methylator phenotype-positive (CR_CIMP+) and -negative (CR_CIMP-). The CR_CIMP- subtype associates with poorer prognosis, reduced drug response, and more advanced histology, exhibiting higher tumor mutation burden and greater activity in drug resistance-related pathways, such as PI3K/AKT/mTOR signaling. CR_CIMP subtypes with distinct clinical or molecular features were also identified in pancreatic adenocarcinoma and bladder urothelial carcinoma resistant to Gemcitabine, as well as in non-small cell lung cancer resistant to anti-PD1/PD-L1 immunotherapy. Based on predicted drug responses, the study screens candidate drugs for each CR_CIMP subtype. Finally, a random forest model is proposed to predict CR_CIMP subtypes in LGG patients resistant to Temozolomide.

Conclusions: This study uncovers DNA methylation subtypes within resistant tumors, enabling more precise stratification to inform prognosis and therapy selection.

Immune infiltration is now recognised as an important prognostic factor in triple negative breast cancer (TNBC). DNA methylation, due to its cell-type specificity, offers a promising approach for quantifying immune cell abundance as a biomarker for risk stratification. Here, we used EpiDISH, a DNA methylation-based cellular deconvolution method, to estimate immune cell proportions from genome-wide methylation data across four independent breast cancer datasets. We show that increased methylation-estimated immune cell percentage in TNBC patients is associated with improved outcomes. This highlights the potential of DNA methylation-based estimates of cell composition for prognosis in TNBC.