Clinical Epigenetics最新文献

Bladder urothelial carcinoma (BLCA) is a common malignant tumor with high invasiveness and recurrence rates, underscoring the need for early diagnosis and effective monitoring. Current diagnostic methods, such as invasive cystoscopy and low-sensitivity urine cytology, have limitations. Oncogene hypermethylation plays a key role in tumorigenesis and progression. However, DNA methylation in BLCA remain underexplored. Identifying and validating new DNA methylation markers in urine samples is crucial to enhance early detection accuracy. In this study, we identified three novel BLCA DNA methylation biomarkers (HIST1H3J, NKX2-4, and YBX3P1 genes), and compared with six known markers (ONECUT2, OTX1, POU4F2, SOX1, TWIST1, VIM). Real-time quantitative methylation-specific PCR (qMSP) was used to detect the methylation levels of biomarkers in 319 urine samples from patients with suspected BLCA. The individual biomarkers of HIST1H3J, NKX2-4, and YBX3P1 achieved Areas Under the Curve (AUCs) of 0.892, 0.914 and 0.871, with accuracies of 84.80%, 85.38% and 81.29%, respectively. In comparison, the six known markers exhibited AUCs ranging from 0.850 to 0.939 and the accuracies of 81.87%-88.30%. These methylation markers can not only identify high-grade BLCA but also low-grade BLCA, highlighting their potential clinical utility. Notably, a four-gene panel (ONECUT2, SOX1, TWIST1 and NKX2-4) significantly improved the detection performance, with an AUC of 0.971 and an accuracy of 92.39%. Our results provide three new DNA methylation markers for BLCA and propose a urine-based DNA methylation detection panel for non-invasive clinical diagnosis.

Laryngeal squamous cell carcinomas (LSCCs) was a frequent malignancy in upper aerodigestive tract. The lack of non-invasive biomarkers for early diagnosis has led to unfavorable prognosis. We firstly identified methylation biomarkers from TCGA and GEO databases. We further validated the diagnostic performance by utilizing blood samples obtained from 43 LSCCs and 50 normal controls (NCs). The HOXD10 cg10364040 was hypermethylated in tumors compared with NCs (P < 0.01), with an area under the curve (AUC) greater than 0.90 in each public database. In clinical validation phase, HOXD10 cg10364040 methylation was able to discriminate LSCCs from NCs with high accuracy (AUC = 0.767, sensitivity: 72.1%, specificity: 82.0%), and exhibited greater sensitivity (85.0%) and specificity (86.0%) in stage I patients than in NCs (AUC = 0.864). In summary, we firstly identified cg10364040 as a novel diagnosis biomarker of LSCC and confirmed it as a noninvasive biomarker in clinical.

Neonatal encephalopathy with suspected hypoxic ischaemic encephalopathy (NESHIE) is a neurological disorder caused by oxygen deprivation and limited blood flow to a neonate's brain. Although various antenatal and perinatal factors have been identified, their precise role in NESHIE pathogenesis remains unclear. The pathophysiology involves multiple molecular pathways that can be explored using a multi-omics approach, including epigenetics. Epigenetics involves heritable changes in gene expression without altering the DNA sequence, encompassing chemical modifications to DNA and histone proteins, as well as changes mediated by non-coding RNAs (ncRNAs). These epigenetic changes regulate gene expression and can be influenced by environmental factors, offering crucial insights into gene regulation and disease mechanisms. This review examines the role of epigenetic mechanisms in NESHIE, focusing on the modulation of hypoxia-inducible factor-1 alpha (HIF-1α) and ncRNA during hypoxic conditions. Additionally, epigenetic-mediated foetal programming may shed light on how maternal and antenatal risk factors contribute to NESHIE susceptibility. Understanding these epigenetic signatures could advance biomarker discovery and the development of novel therapeutic strategies for NESHIE.

Background: Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase that catalyzes the trimethylation of histone H3 at lysine 27 (H3K27me3), has been implicated in promoting renal fibrogenesis. Nevertheless, its precise role and underlying mechanisms remain incompletely defined.

Methods: To investigate the role of EZH2 in partial epithelial-mesenchymal transition (pEMT) and renal fibrosis, we utilized a mouse model with renal tubular cell-specific EZH2 deletion and administered gambogic acid (GA), a selective EZH2 degrader, following unilateral ureteral obstruction (UUO). In vitro, mouse renal epithelial cells were stimulated with TGF-β1 and treated with either EZH2-specific siRNA or GA to assess the effects on EMT and Notch1/3 signaling. In addition, chromatin immunoprecipitation (ChIP) assays were conducted to evaluate the binding of EZH2 and H3K27me3 to the promoters of Notch1 and Notch3.

Results: Compared with wild-type controls, mice with tubular cell-specific EZH2 deletion exhibited significantly reduced renal fibrosis, characterized by decreased expression of fibronectin, collagen III, vimentin, and Snail, while preserving E-cadherin levels in injured kidneys. Pharmacological degradation of EZH2 with GA produced comparable antifibrotic effects. UUO injury markedly upregulated Notch1, Notch3, the Notch intracellular domain, Hes1, Hey2, and Jagged-1; these increases were significantly suppressed by either EZH2 deletion or GA treatment. Similarly, in vitro, GA or EZH2-specific siRNA inhibited the expression of Notch signaling molecules in TGF-β1-treated renal epithelial cells. Chromatin immunoprecipitation analyses revealed direct binding of EZH2 and H3K27me3 to the Notch1 and Notch3 promoters. UUO injury enhanced EZH2 binding while reducing H3K27me3 enrichment at these sites, effects reversed by GA treatment.

Conclusions: These findings demonstrate that epithelial EZH2 contributes to pEMT in renal tubular cells and promotes renal fibrosis, at least in part through activation of Notch signaling. Targeting EZH2 may hold potential as a therapeutic approach for chronic kidney disease.

Colorectal cancer (CRC) is commonly associated with epigenetic modifications, including altered DNA methylation. Recent studies suggest that tumour-resident bacteria may influence CRC development, yet the impact of bacteria on epigenetic regulation is not understood. This study investigates the effect of lipopolysaccharide (LPS) from Fusobacterium periodonticum and Bacteroides fragilis, bacteria that are abundant in CRC tumours with high CpG island methylator phenotype (CIMP), on DNA methylation in HT29 colorectal cancer cells. HT29 cells were treated with LPS from F. periodonticum, B. fragilis, or a combination of both. DNA methylation was assessed using reduced representation bisulfite sequencing (RRBS), followed by bioinformatic analysis to identify differentially methylated CpG sites. RT-qPCR was used to analyse the expression of selected genes with altered CpG promoter methylation. F. periodonticum LPS treatment induced both hypermethylation and hypomethylation in HT29 cells, with significant hypermethylation observed near specific promoter regions, including PEPD and VAV3, with associated decrease in gene expression of these genes. B. fragilis LPS treatment predominantly induced hypomethylation. Co-treatment with both LPS molecules resulted in distinct methylation patterns, with B. fragilis LPS attenuating F. periodonticum LPS-induced hypermethylation. Bacterial LPS can induce dynamic alterations in DNA methylation profiles in HT29 colorectal cancer cells, leading to changes in gene expression. These findings suggest a novel link between tumour-resident bacteria and DNA methylation in colorectal cancer, highlighting, for the first time, a potential mechanism by which bacteria may influence colorectal carcinogenesis.

Background: Lung disease is variable among patients with cystic fibrosis (CF) and depends on genetic and environmental factors. To better understand the molecular determinants of lung disease variability, we carried out an epigenome-wide association study (EWAS) in sputum samples from patients with CF.

Methods: We profiled 64 sputum samples using Human Methylation EPIC BeadChips and assessed the correlation between DNA methylation levels and four clinical traits: lung function (FEV1_pp), lung function variation (FEV1_pp slope), presence and number of pulmonary exacerbations. Sputum samples were collected at four time points over an 18-month follow-up period. Selected CpG sites were reassessed in independent sputum samples from the same cohort by pyrosequencing.

Results: In the EWAS, we identified two differentially methylated CpG sites (cg11047325/SOCS3, p = 4 × 10^-6; cg18608055/SBNO2, p = 6 × 10^-7) that correlated with lung function. They were validated in independent sputum samples from the same cohort using pyrosequencing. Additionally, three CpG sites (cg23107754, cg03209812 and cg09600088) split patients with declining lung function from those whose lung function either improved or remained stable (accuracy = 0.80). Of interest for CF-related diabetes, one of these CpG sites (cg09600088) maps to the BRSK2 gene, which plays a role in pancreatic beta cell function. Finally, a DNA methylation signature of 23 CpG sites predicted patients with pulmonary exacerbation (accuracy = 0.84).

Conclusions: We provide the first longitudinal assessment of genome-wide DNA methylation in a cohort of patient with CF and identify CpG sites that predict clinical traits of key importance for lung disease. The associated genes play a critical role in inflammation or pancreatic endocrine activity. Overall, our results underscore the emerging role of DNA methylation as a key modulator of disease severity in CF.

Aberrant activity of histone deacetylases (HDACs) is a pathological phenomenon in several diseases, including Duchenne muscular dystrophy (DMD). In DMD, the upregulation of HDACs is driven by the disassembly of the dystrophin-associated protein complex (DAPC), which, under normal physiological conditions, provides mechanical stability to muscle fibres and acts as a signalling hub anchoring signalling proteins and molecules to their functional sites. In dystrophic muscle, DAPC disassembly causes delocalisation of signalling proteins and, therefore, disrupts signalling pathways. Displacement of epigenetic signalling molecules leads to the uncontrolled activity of HDACs and excessive removal of acetyl groups from histone proteins. Consequently, chromatin becomes tightly bound, preventing the expression of genes involved in muscle homeostasis. The pathological consequences of increased HDAC activity extend beyond muscle fibres, affecting several cell types, translating into a chronically activated immune system, promoting fibrotic and adipose tissue formation and impairing muscle regeneration. Here, we review the current evidence implicating HDACs as a key driver in DMD disease development and progression. We describe the mechanism of HDAC overactivity and the downstream consequences that contribute to the pathogenesis of the disease by disrupting muscle repair and regeneration. Finally, we highlight HDACs as targets for inhibition, offering a novel therapeutic strategy to counteract the multiple pathological events in DMD.

Background: Lung cancer (LC) remains the leading cause of cancer-related mortality worldwide. Its poor prognosis is largely attributed to late-stage diagnosis, highlighting the need for sensitive, minimally invasive biomarkers for early detection. In this study, we aimed to identify circulating cell-free DNA (cfDNA) methylation-based biomarkers for LC through genome-wide profiling of plasma-derived cfDNA from patients with LC (stages I-IV) using the Infinium DNA MethylationEPIC array (> 850,000 CpGs). A relaxed elastic net penalized logistic regression model was applied to identify differentially methylated CpGs between LC patients and non-neoplastic controls, and selected candidates were validated in an independent cohort.

Results: A 21-CpG episignature was identified, predominantly hypomethylated in LC, which distinguished cases (n = 25) from controls (n = 8) with a cross-validated area under the curve (AUC) of 0.70. Two CpGs with the largest effect sizes (associated with EMP2 and IKZF2) were selected for validation. Digital droplet PCR (ddPCR) analysis in an independent cohort of 47 individuals (23 LC patients and 24 controls) confirmed significant hypomethylation at the EMP2 locus (median % methylation: 73.60% in tumors vs. 86.83% in controls; p = 0.0034), achieving an AUC of 0.75.

Conclusions: Our findings support the utility of methylome-wide cfDNA profiling for LC biomarker discovery. EMP2 promoter methylation represents a promising candidate for the minimally invasive detection of LC across heterogeneous clinical presentations.

Background: Childhood obesity is a pressing public health and pediatric issue. Recently, epigenome-wide association study (EWAS) has received increasing research attention and revealed the association between cord blood methylation and pediatric health problems. However, the relationship between cord blood DNA methylation and childhood obesity remains incompletely understood. This study aimed to assess cord blood DNA methylation and its association with childhood obesity using an EWAS.

Results: The present study included 12-year-old children with obesity and control participants from the Hokkaido Study on Environment and Children's Health (the Hokkaido cohort), a prospective birth cohort study. The Hokkaido cohort study collected participants' cord blood samples at birth, which were evaluated using an EWAS. We conducted robust linear regression analysis for the differentially methylated positions (DMPs). Thereafter, we also conducted differentially methylated region (DMR) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. As a result, our analysis involved 500 children, comprising 218 individuals with obesity and 282 controls with no obesity. After quality control, 428 high-quality samples remained (192 children with obesity and 236 controls). Although our DMP analysis did not produce statistically significant results with adjusted p-values with Bonferroni correction and local false discovery rate (FDR) correction, our DMP analysis identified potential candidate genes with a global FDR correction of < 0.05. Three differentially methylated cytosine-phosphate-guanine candidate sites (cg27093962 in dynein regulatory complex 1 [DRC1], cg25187049 in Potassium Voltage-Gated Channel Subfamily B Member 2 [KCNB2], and cg07817806 in Uromodulin [UMOD]) were found to be potentially associated with childhood obesity. Among them, KCNB2 and UMOD are implicated in metabolic and inflammatory pathways relevant to obesity. While DMR analysis did not produce statistically significant results, KEGG analysis revealed potential pathways associated with childhood obesity.

Conclusion: The present study suggests three candidate DMPs and pathways that may explain the association between DNA methylation at birth and obesity at 12 years of age.

Background: DNA methylation (DNAm) provides a plausible mechanism by which adverse exposures become embodied and contribute to health inequities, due to its role in genome regulation and responsiveness to social and biophysical exposures tied to societal context. However, scant epigenome-wide association studies (EWAS) have included structural and lifecourse measures of exposure, especially in relation to structural discrimination. Our study tested the hypothesis that DNAm is a mechanism by which racial discrimination, economic adversity, and air pollution become biologically embodied, via a series of cross-sectional EWAS, conducted in two population-based samples of US-born Black non-Hispanic (Black NH), white non-Hispanic (white NH), and Hispanic individuals (My Body My Story:: n = 224 Black NH and 69 white NH;; and the Multi-Ethnic Study of Atherosclerosis:: n = 229 Black NH, n = 555 white NH and n = 191 Hispanic). Genome-wide changes in DNAm were measured using the Illumina EPIC BeadChip (MBMS; using frozen blood spots) and Illumina 450 k BeadChip (MESA; using purified monocytes).

Results: We observed the strongest associations with traffic-related air pollution (between 0 and 22 DNAm sites associated at p < 2.4e-07, measured via black carbon and nitrogen oxides exposure), with evidence from both studies suggesting that air pollution exposure may induce epigenetic changes related to inflammatory processes. However, we did not replicate previous air pollution EWAS findings. We also found suggestive associations of DNAm variation with measures of structural racial discrimination (e.g. for Black NH participants, in MBMS born in a Jim Crow state associates with a DNAm site in ZNF286B at p = 8.43E-08; and in MESA adult exposure to racialized economic residential segregation associates with a DNAm site in FUT6 at p = 4.05E-08) situated in genes with plausible links to effects on health.

Conclusions: Overall, this work suggests that DNAm is a biological mechanism through which structural racism and air pollution (of which distribution of exposure is inequitable) become embodied and may lead to health inequities. Due to the extensive range of exposures we tested, further replication in additional studies and other tissues is warranted.