Clinical Epigenetics最新文献

Background: Clear cell renal cell carcinoma (ccRCC), with rising incidence globally, shows heterogeneous responses to immune checkpoint blockade (ICB). DNA methylation dysregulation impacts tumor immunity, necessitating predictive CpG methylation biomarkers for ICB efficacy.

Methods: Genome-wide methylation profiling (TCGA/GEO) identified prognostic promoter CpG islands linked to CD8⁺ T cell infiltration. Single-CpG resolution analysis guided TaqMan probe design, validated in two independent cohorts: non-ICB (n = 335) for prognosis and ICB-treated (n = 45) for immunotherapy prediction.

Results: High-throughput methylation analysis identified hypermethylation at the FBLN2 promoter (chr3:13590414-13591008), which correlated with advanced tumor stage, higher grade, and poorer overall survival (OS) and progression-free survival (PFS). This locus exhibited significant associations with CD8⁺ T cell infiltration and IFNγ pathway activation. In the non-ICB cohort, validation using a 5-CpG TaqMan assay confirmed FBLN2 hypermethylation as an independent prognostic marker for both OS (HR = 3.45, P < 0.001) and PFS (HR = 2.43, P = 0.023). Subsequent IHC analysis of 74 tumor specimens demonstrated strong concordance between FBLN2 percent methylation ratio (PMR) and CD8⁺ T cell density (r = 0.62, P < 0.0001). In the anti-PD-1-treated cohort, high FBLN2 methylation was associated with a favorable immunotherapy response (Cohen's weighted Kappa = 0.607, P < 0.001) and predicted superior PFS (median 11.2 vs 3.4 months, HR = 0.35, P = 0.006), suggesting its potential as a novel predictive biomarker for ICB efficacy.

Conclusions: FBLN2 promoter hypermethylation is a promising prognostic biomarker in ccRCC and a potential predictor of immunotherapy response. These findings warrant further investigation to validate its potential for enhancing personalized patient management.

Background: The prevalence of insomnia and mental illness varies by sex. The mRNA expression level of the CRY gene in patients with insomnia is significantly decreased, and the expression level of the CRY2 gene is closely related to depression. However, sex differences in the link between insomnia and symptoms of anxiety, depression, and stress, as well as whether CRY2 gene DNA methylation can regulate this association, are not yet fully understood.

Objective: Investigate sex-specific differences in the associations between insomnia symptoms and symptoms of anxiety, depression, and stress among young adults. Furthermore, we explored whether the CRY2 clock DNA methylation moderates these relationships.

Methods: A total of 1100 participants from two Chinese universities provided baseline data on insomnia symptoms and follow-up symptoms of anxiety, depression, and stress assessments 1 year later. Among them, 605 participants contributed DNA methylation data for the CRY2 gene. Binary logistic regression and restricted cubic spline models were employed to analyze both linear and nonlinear relationships. Moderation analyses examined the effect of CRY2 gene DNA methylation, complemented by stratified analyses for sex-specific differences.

Results: Significant sex-specific differences emerged in recognizing symptoms of anxiety, depression, and stress, with insomnia symptoms notably increasing the risk of symptoms of anxiety, depression, and stress. Logistic regression revealed a significant association between insomnia symptoms and symptoms of anxiety, depression, and stress exclusively in females. Furthermore, restricted cubic spline analyses demonstrated a consistent nonlinear relationship in both males and females. Notably, CRY2 gene DNA methylation negatively moderated the relationship between insomnia symptoms and symptoms of anxiety, depression, and stress, and had sex-specific difference.

Conclusion: Elevated insomnia symptoms at baseline correlated with an increased risk of symptoms of anxiety, depression, and stress after 1 year, with significant sex differences observed. Logistic regression revealed that this association was significant only in females, although a consistent nonlinear pattern was seen in both sexes. Furthermore, CRY2 gene DNA methylation acted as a negative moderator of this relationship. These results highlight the necessity of an early monitoring strategy for females incorporating epigenetic factors.

Juvenile myelomonocytic leukemia (JMML) is a rare pediatric myelodysplastic/myeloproliferative neoplasm characterized by distinct epigenetic signatures that facilitate molecular classification. This study aimed to evaluate the diagnostic utility of locus-specific DNA methylation in the bone morphogenetic protein 4 (BMP4) gene as a single predictor of disease outcomes in a cohort of 111 children diagnosed with JMML, alongside 9 healthy controls. Methylation levels of BMP4, assessed through targeted bisulfite next-generation sequencing (bs-NGS), were heterogeneous within the JMML cohort and were significantly associated with clinical risk factors, such as patient age, and fetal hemoglobin (HbF) levels. A comparative analysis of BMP4 bs-NGS and genome-wide methylation array data revealed a strong positive correlation (p < 0.001). The sensitivity and specificity of BMP4 bs-NGS for classifying high-methylation cases were 0.612 and 0.887, respectively. For PTPN11-mutant patients (N = 40), the sensitivity was 0.667 and the specificity was 0.842. Survival analysis indicated that patients with high BMP4 methylation (BMP4h) had lower 5-year disease-free survival (DFS) rates than those with normal BMP4 methylation (BMP4n). Specifically, the 20% of patients with highest BMP4 methylation had a 5-year DFS of 0.38, in contrast to 0.62 for the lowest 20% (p = 0.007). These findings highlight the potential of BMP4 methylation analysis as a complementary biomarker for JMML risk stratification, mirroring genome-wide methylation profiles known to associate with prognostic subgroups.

DNA methylation (DNAm) has been touted as a potential unified marker of the contributions of both inherited and environmental factors on an individual's health. Changes in DNAm have been associated with several chronic diseases and mortality, and DNAm risk scores, or epigenetic clocks, have been proposed as metrics to quantify the process of 'biological ageing'. Unfortunately, research involving epigenetic clocks is not free from the issues faced in other fields of genomic research. Namely, individuals of European ancestry make up the vast majority of epigenetic study participants and it is unclear whether epigenetic clocks will provide equitable benefits when applied in diverse populations. Although some studies have reported variation in DNAm between populations, it can be difficult to identify the mechanisms underlying these differences. This has implications for clinical application of epigenetic clocks. In this review, we discuss epigenetic clocks, missing diversity in epigenetic research and the potential consequences of the latter on the equitable translation of epigenetic clocks to diverse populations.

Background: We previously reported improved respiratory outcomes in babies born to pregnant smokers supplemented with vitamin C (500 mg/day) versus placebo in a randomized clinical trial. Improved respiratory outcomes persisted to 5 years of age and were associated with buccal DNA methylation (DNAm) measured using the InfiniumMethylationEPIC array. The objective of this study was to examine associations of vitamin C treatment and lung function with buccal DNAm using a custom-content Asthma&Allergy array enriched for asthma and allergy loci likely to have a functional impact on gene expression.

Results: We profiled DNAm at 36,999 CpGs in loci previously associated with asthma or allergic diseases using custom-content Asthma&Allergy arrays in 137 subjects (65 placebo; 72 vitamin C) with pulmonary function testing (PFT) at the 5-year visit in the "Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function" (VCSIP) double-blind, placebo-controlled randomized clinical trial. We examined the association of buccal DNAm with (1) vitamin C treatment vs placebo, (2) forced expiratory flow between 25 and 75% of expired volume (FEF_25-75) and (3) wheeze at 4-6 years of age. We identified 9 genome-wide differentially methylated CpGs (DMCs; FDR < 0.05) and 2 differentially methylated regions (DMRs) between vitamin C and placebo subjects and one CpG associated with FEF_25-75 at FDR significance. DNAm at 5 CpGs mediated a significant proportion of the vitamin C treatment effect on lung function, including 2 CpGs annotated to the SLC25A37 gene involved in mitochondrial iron transport.

Conclusions: Our study revealed association of in utero vitamin C supplementation and childhood lung function with DNAm at novel loci, providing additional insight toward potential mechanisms for the persistent effects of vitamin C supplementation to pregnant smokers.

Clinical trial registration: ClinicalTrials.gov, NCT01723696 (Registered on November 6, 2011) and NCT03203603 (Registered on March 28, 2017).

Background: Alzheimer's disease (AD) is identified by a distinct progression of aging-associated cognitive and functional impairment. Recent advances recognize the DNA methylation-based epigenetic clock as a precise predictor of aging processes and their related health outcomes. However, observational studies exploring this link are often compromised by confounding factors and reverse causality bias. To address the question, our study employs a bidirectional Mendelian randomization (MR) analysis to explore the causal relationship between epigenetic age acceleration (EAA) and AD.

Methods: Genome-wide association study (GWAS) statistics for epigenetic clocks (GrimAge, PhenoAge, HorvathAge, and HannumAge) were sourced from Edinburgh DataShare and the Alzheimer Disease Genetics Consortium (ADGC). The dataset comprised 63,926 participants, and among them, 21,982 cases were AD patients and 41,944 were controls. The primary analytical method for the MR was the inverse variance weighted (IVW). The potential pleiotropy and heterogeneity among the instrumental variables were evaluated by additional sensitivity analyses.

Results: Employing the random-effects IVW approach, we found that, as indicated by GrimAge, EAA was associated with an increased risk of AD (Odds Ratio [OR] = 1.025, 95% Confidence Interval [CI]: 1.006-1.044, p = 0.009). Quality control assessments confirmed the reliability and robustness of our findings. However, the evidence did not support a causal relationship between AD and epigenetic aging in the reverse direction.

Conclusions: Our MR study indicates a positive causal relationship between EAA and AD. Further research is necessary to explore the underlying physiological mechanisms.

ABCA1 methylation and N⁶-methyladenine DNA have been identified as epigenetic markers in coronary artery disease. We performed a cross-sectional exploratory study to analyze whether global DNA methylation and ABCA1 promoter methylation in monocytes are associated with coronary atherosclerosis in asymptomatic HIV individuals without cardiovascular disease. Coronary atherosclerosis was defined as a coronary plaque in at least one coronary segment. We included 27 individuals, 15 of whom had coronary atherosclerosis. ABCA1 DNA methylation was higher in participants with coronary atherosclerosis, with statistically significant differences at specific loci related to the activator protein-2 (AP-2) binding site. There were no differences in global levels of 5-methylcytosine and N⁶-methyladenine DNA between individuals with or without coronary atherosclerosis. ABCA1 methylation showed moderate correlations with both the Leaman score and coronary plaque volume, whereas global DNA N⁶-methyladenine had a negative moderate correlation with the segment severity score and LDL cholesterol. Among participants with coronary atherosclerosis, we found a strong negative correlation between ABCA1 methylation and total atheroma plaque volume, with certain loci (CpG 9 and 12) exhibiting very strong associations.

Backgrounds: Consensus molecular subtype 4 (CMS4) of colorectal cancer (CRC) is characterized by TGF-β activation, and generally accompanied with metastasis and recurrence. Nevertheless, molecular biomarkers and regulatory mechanisms underlying CMS4 CRC remain elusive. This study investigated methylation sites in CMS4 CRC and explored the mechanistic role of SLAMF6 in CRC.

Methods: Random forest and LASSO regression identified significant methylation sites, and Kaplan Meier analysis pinpointed prognosis-related sites. The mRNA and protein expression levels of SLAMF6 were identified by qPCR, western blot, immunohistochemistry and public database. Bisulfite sequencing PCR and methylation specific PCR were employed to validate SLAMF6 promoter methylation. Western blot was applied to study the specific mechanism underlying TGF-β regulating SLAMF6 methylation. Chromatin immunoprecipitation and electrophoretic mobility shift assay were conducted to evaluate the relationship between SMAD3 and DNMT1. The anti-tumor effect of methyltransferase inhibitor (5-Aza) and PD-L1 antibody was assessed in tumor bearing mice.

Results: We detected 726 differentially methylated sites between CMS4 and CMS1-3 subtypes (p < 0.05), with CMS4 showing prominently elevated methylation. Machine learning approaches refined to 43 methylation sites and 8 methylation sites were involved with significant prognostic value. The methylation level of SLAMF6 in CMS4 was much higher than other subtypes. Diminished SLAMF6 expression was firstly authenticated in CRC compared with normal colon tissues. It was more emphatic in CRC with metastasis and related with worse prognosis. Mechanically, p-SMAD2/3 and DNMT1 were acknowledged as the downstream effector of TGF-β activation. Next, p-SMAD3 was demonstrated to bound to DNMT1 promoter inducing SLAMF6 hypermethylation. Most interestingly, SLAMF6 was positively correlated with multiple immune cells and the combination of 5-Aza and PD-L1 antibody impeded tumor growth and upregulated CD8⁺ T cells and CD4⁺ T cells.

Conclusions: Together, our study illustrated a novel epigenetic mechanism mediated by TGF-β/SMAD3/DNMT1, and suggested a potential target for CRC prognosis and immunotherapy.

Background & aims: Patients with residual liver fibrosis after hepatitis C virus infection clearance represent an important challenge. The primary objective of this study was to evaluate epigenetic marks in DAA-responders HCV, Hispanic patients with remaining fibrosis who were treated with prolonged-release pirfenidone (PR-PFD).

Methods: Forty-four DAA-responders HCV patients presenting remaining fibrosis received PR-PFD (1200 mg/day) for 12 months. Liver biopsies and serum samples were analyzed. Patients were classified as regressive fibrotic profile (RFP), stable fibrosis profile (SFP), or progressive fibrotic profile (PFP) based on liver stiffness (Fibroscan) (± 30% variation). A control cohort of 20 DAA-responders HCV patients received only standard of care treatment. Additionally, six non-fibrotic controls were included to compare epigenetic marks.

Results: Thirty-eight patients completed the 12-month treatment; 28.94% showed a reduction in at least one fibrosis stage based on liver biopsies. Fibroscan revealed that 44.73% of patients in the PR-PFD group exhibited RFP. Bilirubin, alkaline phosphatase, AST, INR and APRI values significantly decreased in this group. Noteworthy, 85% of 20 control patients had SFP. Profibrogenic miRNAs displayed a significant increase in expression in advanced fibrosis versus controls without fibrosis. PR-PFD treatment restored the expression of miR-34a, miR-16, miR-192, miR-200a, and miR-122. PDGFA CpGs hypermethylation in both cell-free DNA and liver biopsies has been found in advanced fibrosis. Interestingly, four CpGs in PPARD were hypomethylated compared to controls. PR-PFD treatment resulted in hypermethylation of three TGFB1-CpGs.

Conclusion: These findings indicate for the first time that PR-PFD might exert therapeutic effects in Hispanic patients with residual fibrosis by modulating the expression of miRNAs and methylation of specific CpG sites.

Clinical trial number: NCT05542615. Registration Date 09/13/2022.

Background: Bisulfite conversion is considered the gold standard for DNA methylation analysis, but it damages DNA and performs sub-optimally with clinical samples (e.g., formalin-fixed paraffin-embedded and circulating free plasma DNA (cfDNA)). Here we describe a comprehensive comparison of bisulfite and enzymatic methylation sequencing, using commercially available assays in clinically relevant patient samples and cell lines. We also report the first clinical enzymatic whole genome methylation sequencing (WGMS) in a cohort of patients with chronic lymphocytic leukemia (CLL). We report data from a multi-arm experiment comprising controlled reference material and clinically relevant samples to assess technical differences between enzymatic and chemical methylation conversion technologies.

Results: Enzymatic methylation sequencing was highly concordant to bisulfite data but outperformed bisulfite conversion in key sequencing metrics; the enzymatic method demonstrated significantly higher estimated counts of unique reads, reduced DNA fragmentation, and higher library yields than bisulfite conversion. Enzymatic conversion produced inferior methylation array data. Although bisulfite and enzymatic methods were highly concordant, the increased quality of multiple sequencing metrics seen in the enzymatic method enabled the development of robust clinical sample pipelines including targeted sequencing in cfDNA.

Conclusions: Using the enzymatic methylation sequencing methods described, we report a putative link of interleukin (IL)-15 methylation changes to acalabrutinib treatment response in a CLL clinical trial cohort (ACE-CL-001 trial, NCT02029443).