Clinical Epigenetics最新文献

Background: Cancers can be hematological or solid, sharing many hallmarks, although their clinical behaviors are distinct. Identifying biomarkers that differentiate hematological from non-hematological malignancies could aid differential diagnosis by providing the basis for developing point-of-care diagnostic devices. In this respect, complex histone populations are secreted and detectable in biological fluids in various disease settings. To our knowledge, studies analyzing the circulating histone profile complexity by comparing healthy individuals, patients with hematological malignancies, and solid cancer patients are currently lacking.

Results: We assessed the plasma histone signature of healthy subjects (n = 30), and of patients with myelodysplastic syndrome (MDS, n = 43), colorectal cancer (CRC, n = 39), lung cancer (non-small cell lung cancer [NSCLC, n = 15]), small cell lung cancer [SCLC, n = 4]), or breast cancer [BC, n = 16]). Principal component analysis (PCA) demonstrated the segregation of circulating histones and histone complexes between oncological and healthy patients. Individual histones (H2A, H2B, H3, H4, macroH2A1.1, and macroH2A1.2), histone dimers and nucleosomes were assayed by ImageStream(X)-advanced flow cytometry. We found general increases in circulating histone abundance in the blood of cancer patients versus healthy controls. MDS and solid cancers could be discriminated among themselves for an increased abundance of histones H2A and macroH2A1.2 (p < 0.01), and a decreased abundance of H2A/H2B/H3/H4 and H3/H4 histone complexes (p < 0.01). Moreover, macroH2A1.2 and H2A/H2B/H3/H4 levels negatively or positively correlated with age in healthy subjects versus MDS patients, respectively.

Conclusions: Overall, we identified circulating histone signatures able to discriminate between solid and MDS, using a rapid and non-invasive imaging technology, which may improve patient diagnosis.

Background: Preeclampsia (PE) is a pregnancy-specific hypertensive disorder associated with placental dysfunction and oxidative stress. This study explored whether WTAP regulates ferroptosis in trophoblasts through m⁶A-dependent control of NCOA4 and YTHDF2.

Methods: WTAP expression and global m⁶A levels in PE placentas were examined by qRT-PCR, western blot, and immunohistochemistry, along with histopathological analysis. WTAP, NCOA4, and YTHDF2 expression were manipulated in HTR-8/SVneo trophoblasts using siRNAs or overexpression plasmids. Cell proliferation, migration, cell-cycle distribution, oxidative stress, and ferroptosis markers were evaluated. MeRIP-qPCR and RIP-qPCR were used to assess NCOA4 m⁶A methylation and YTHDF2 binding. A PE mouse model was established to assess in vivo effects and the potential rescue by Ferrostatin-1 (Fer-1).

Results: WTAP expression and global m⁶A levels were reduced in PE placentas, accompanied by villous structural damage. Functionally, WTAP knockdown suppressed trophoblast proliferation and migration, induced G1 arrest, and enhanced oxidative stress, while WTAP overexpression had opposite effects. Mechanistically, WTAP promoted m⁶A methylation of NCOA4 mRNA and its YTHDF2-dependent degradation. In PE placentas, YTHDF2 was downregulated and NCOA4 upregulated, consistent with in vitro findings. NCOA4 overexpression impaired trophoblast function and increased ferroptosis, whereas silencing had protective effects. YTHDF2 knockdown and NCOA4 overexpression acted synergistically to exacerbate ferroptosis, both in trophoblasts and in a PE mouse model, leading to aggravated hypertension, proteinuria, and fetal growth restriction, which were partially reversed by Fer-1.

Conclusion: WTAP suppresses ferroptosis in PE by enhancing YTHDF2-dependent m⁶A methylation and degradation of NCOA4. Disruption of this pathway exacerbates oxidative stress, trophoblast dysfunction, and adverse pregnancy outcomes.

Background: Obstructive sleep apnea (OSA) is a highly prevalent sleep disorder characterized by recurrent episodes of intermittent hypoxia (IH) and sleep fragmentation. OSA is strongly associated with cardiometabolic morbidities, many of which correlate with the severity of IH. While the genetic basis of OSA remains unclear, epigenetic modifications, particularly DNA methylation, have emerged as key contributors to its pathophysiology.

Methods: In this pooled analysis, we systematically examined publicly available DNA methylation datasets from OSA patients and murine IH models to identify common methylation signatures at both the single-gene and pathway levels.

Results: We found 720 differentially methylated genes in human OSA, suggesting a regulatory role of DNA methylation in OSA-associated cardiometabolic dysfunction. While the specific differentially methylated genes differed between human OSA and murine IH models, there were notable similarities. In contrast, there was substantial overlap between the human and animal data at the pathway level. Most notably, differential methylation affected oxidative stress, inflammation, lipid metabolism, and PI3-AKT signaling pathways.

Conclusions: These findings provide further evidence that epigenetic mechanisms, particularly DNA methylation, mediate the systemic effects of OSA and IH. Our study underscores the need for targeted research to elucidate the causal role of these epigenetic changes and their potential reversibility through therapeutic interventions.

Background: Trisomy 18 (T18, Edwards syndrome) is a lethal chromosomal disorder characterized by multiple congenital anomalies and high perinatal mortality. Although epigenetic alterations have been described in aneuploidy conditions, their causal role in the pathogenesis of T18 remains unclear. This study aimed to characterize genome-wide DNA methylation changes associated with T18 during early development.

Material and methods: Genomic DNA was extracted from chorionic villi of five T18 and five euploid fetuses, as well as from normal maternal blood, at 11-13 weeks of gestation. High-resolution methyl-capture sequencing (MC-seq) was performed to profile DNA methylation at approximately 3.2 million CpG sites. Differentially methylated CpG sites (DMCs) and regions (DMRs) were identified. Functional and disease-association enrichment analyses were conducted using multiple bioinformatics tools.

Results: A global trend of DNA hypermethylation was observed in the chorionic villi of T18 fetuses. A total of 6,510 DMCs were identified, including 4,022 hypermethylated and 2,488 hypomethylated CpG sites. Additionally, 301 DMRs were identified, comprising 233 hypermethylated and 68 hypomethylated regions. Notably, chromosome 18, the disease-causing chromosome, contained the highest number of hypermethylated DMRs. Functional enrichment analysis of the 283 genes, including 301 DMRs, revealed significant involvement in biological processes and disease phenotypes relevant to T18, including nervous system development, anatomical structure morphogenesis, and embryonic morphogenesis (adjusted P < 0.001 for all). Among them, 76 DMRs exhibited completely inverse methylation patterns in maternal blood and were identified as potential epigenetic biomarkers for non-invasive prenatal testing of T18.

Conclusions: To our knowledge, this is the first comprehensive MC-seq-based analysis of T18-specific DNA methylation patterns in first-trimester chorionic villi. These findings suggest that DNA methylation changes may represent downstream consequences of chromosomal imbalance in T18 and provide a foundation for future investigations into its pathophysiology and the development of epigenetic biomarkers for early non-invasive detection.

Background: Post-transplant obliterative bronchiolitis (OB) is a major cause of lung graft dysfunction and failure, with the epithelial-mesenchymal transition (EMT) process playing a pivotal role in driving extracellular matrix (ECM) deposition and fibrosis.

Methods: A mouse heterotopic tracheal allograft model was established to replicate the clinical manifestations of post-transplant OB. Histopathological alterations of tracheal grafts were assessed using Hematoxylin and Eosin (HE) staining. Gene expression was quantified through enzyme-linked immunosorbent assay (ELISA), immunofluorescence (IF), immunohistochemistry (IHC), reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and Western blot assays. Differentially expressed genes (DEGs) in heterotopic tracheal grafts were identified by RNA sequencing (RNA-Seq). Chromatin accessibility was evaluated using assay for transposase-accessible chromatin with sequencing (ATAC-Seq).

Results: Histological analysis revealed progressive luminal occlusion (7-14 days), with significant inflammatory infiltration at day 7 and ECM deposition at day 14. Elevated IL-1β/IL-6 levels and reduced IL-10 confirmed immune activation. High mobility group at-hook 1 (HMGA1) was upregulated in allografts and mediated TGF-β1-driven EMT in vitro. Integration of ATAC-seq and RT-qPCR in pulmonary epithelial cells demonstrated that HMGA1 orchestrates extensive chromatin remodeling during OB pathogenesis. HMGA1 directly enhanced chromatin accessibility at EMT-promoting loci, including specificity protein 1 (SP1), dedicator of cytokinesis 4 (DOCK4), serum response factor (SRF), and anillin (ANLN). Epigenetic reprogramming of these regulatory regions induced TGF-β1-mediated EMT.

Conclusions: HMGA1 promotes EMT in OB by facilitating chromatin accessibility at EMT-associated loci, highlighting its potential as a therapeutic target for post-transplant intervention.

Background: Ubiquitin-specific proteases (USPs) play a critical role in the development of various cancers. The study aimed to elucidated the pathogenic molecular mechanisms and analyze its clinical significance in esophageal squamous cell carcinoma (ESCC).

Methods: Pyrosequencing, RT-qPCR and Western blot were used to detect the promoter DNA methylation level and expression of USP44 in ESCC tissues and cell lines, and the significance of USP44/SENP2 in the progression of ESCC was evaluated by in vitro and in vivo experiments. The regulatory mechanism of USP44 on SENP2 was explored by liquid chromatography-mass spectrometry, co-immunoprecipitation (Co-IP) combined with cycloheximide (CHX) tracking assay and ubiquitination analysis. Finally, 182 ESCC tissues were stained with immunohistochemistry (IHC), and the correlation between USP44 and prognosis was evaluated by Kaplan-Meier survival analysis, Cox regression and Nomogram model.

Results: In ESCC tumor tissues and cell lines, USP44 is frequently hypermethylated and downregulated. Overexpression of USP44 significantly inhibits ESCC cell invasion and metastasis both in vitro and in vivo. Mechanistically, USP44 interacts with and stabilizes ubiquitin-like modifier (SUMO)-specific peptidase 2 (SENP2) through deubiquitination, thereby inhibiting the progression of ESCC. Knockdown of SENP2 reduced the inhibitory effect of USP44 on ESCC cell migration and invasion. Clinically, low expression of USP44 indicates poor prognosis and is an independent prognostic factor in ESCC patients, as evidenced by Kaplan-Meier curve and cox regression analysis (HR = 0.345, 95% CI 0.227-0.524, p < 0.001). We established a nomogram model with robust predictive power for the 1-, 3-, and 5-year survival of ESCC patients (AUC = 0.849).

Conclusion: USP44-SENP2 axis is a pivotal factor in the progression of ESCC, and provides potential therapeutic targets for ESCC patients.

Objective: The epigenetic clock is recognized as a highly accurate predictor of biological aging, but the relationship between epigenetic age acceleration and oral diseases remains poorly understood. This study aimed to investigate the causal associations between epigenetic age acceleration and oral diseases and identify the shared gene expressions.

Methods: A two-phase study design was used: in phase 1, we conducted MR analysis to investigate the association between epigenetic age acceleration and common oral diseases. In phase 2, we conducted transcriptome-wide association studies (TWAS) to identify gene expressions linked to phenotypes with positive outcomes. Subsequently, we performed summary-based MR (SMR) analyses integrating expression quantitative trait loci (eQTL) datasets to ascertain whether these gene expressions could affect the phenotypes. Finally, we performed biological pathway enrichment analysis to investigate the potential mechanisms.

Results: MR analysis revealed significant causal relationships between epigenetic age acceleration and oral diseases. Specifically, GrimAge was associated with an increased risk of periodontitis (OR = 1.160, 95% CI 1.010-1.333, p = 0.036 in FinnGen cohort; OR = 1.120, 95% CI 1.000-1.255, p = 0.049 in GLIDE consortium). PhenoAge showed a significant association with stomatitis (OR = 1.062, 95% CI 1.007-1.120, p = 0.026). Intrinsic epigenetic age acceleration (IEAA) was linked to a higher risk of oral lichen ruber planus (OR = 1.128, 95% CI 1.036-1.230, p = 0.006). Reverse MR analysis identified a bidirectional causal relationship between oral lichen ruber planus and IEAA (OR = 1.127, 95% CI 1.006-1.263, p = 0.039). No significant associations were observed between epigenetic age acceleration and dental caries, recurrent aphthous ulcers, or oral leukoplakia (all p > 0.05). Sensitivity analyses confirmed the robustness of these findings. TWAS and SMR identified eight genes associated with the effect of GrimAge on periodontitis, six genes associated with the effect of PhenoAge on stomatitis, four genes associated with the effect of IEAA on oral lichen ruber planus and seven genes associated with the effect of lichen ruber planus on IEAA.

Conclusions: This study revealed causal relationships between epigenetic age acceleration and common oral diseases, and explored the relevant mechanisms, highlighting the potential novel strategies for prevention.

Objective: To investigate the expression profile, clinical significance, and underlying molecular mechanisms of C1orf112 in endometrial cancer (EC).

Methods: We performed bioinformatics analyses using data from The Cancer Genome Atlas to evaluate C1orf112 expression and its association with clinicopathological parameters in EC. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, as well as protein-protein interaction network analysis, were conducted to explore the functional roles and regulatory pathways of C1orf112. A multi-omics integrative approach was used to elucidate the regulatory mechanisms underlying C1orf112 expression. Furthermore, we constructed and validated a prognostic scoring model incorporating C1orf112 expression.

Results: C1orf112 was found to be significantly highexpressed in EC tissues and its expression was closely associated with clinical stage, histological grade, and patient prognosis. Functional enrichment analyses indicated that C1orf112 and its co-expressed genes are primarily involved in cell cycle regulation, DNA replication, and the p53 signaling pathway. Notably, our bioinformatics predictions suggest that C1orf112 may be subject to bidirectional regulation by RNA-binding proteins, including LIN28B and SRRM4, potentially establishing a regulatory balance between oncogenic and tumor-suppressive pathways. Multi-omics analysis demonstrated that C1orf112 expression is co-regulated by genetic alterations and epigenetic modifications, with promoter DNA methylation levels showing a strong inverse correlation with transcriptional activity. However, further molecular and phenotypic validation is required to confirm these interactions. The prognostic scoring model incorporating C1orf112 expression exhibited robust predictive performance.

Conclusion: Our findings highlight the potential clinical utility of C1orf112 as a diagnostic and prognostic biomarker in EC, and provide new insights into its regulatory molecular network. This study proposes a conceptual framework for understanding EC pathogenesis and guiding the development of targeted therapies. Nonetheless, further prospective clinical studies and mechanistic investigations are warranted to validate these findings.

Background: Polypharmacy, defined as taking ≥ 5 different daily medications, is common in older adults and has been linked with neuropsychiatric/neurological and other health conditions. To clarify the potential molecular implications, we tested the hypothesis that polypharmacy may influence DNA methylation (DNAm) patterns in aging, in a longitudinal Italian cohort (N = 1,098; mean (SD) age at recruitment: 58.8 (5.6) years, 51.3% women; median (IQR) follow-up 12.6 (1.1) years).

Results: We tested associations of polypharmacy with several DNAm aging clocks (Hannum, Horvath, GrimAge, DNAmPhenoAge, DunedinPACE), through linear mixed models incrementally adjusted for age, sex, education, prevalent health conditions and lifestyles, leukocyte counts and residual batch effects. This revealed significant positive associations of GrimAge acceleration and DunedinPACE with the switch to polypharmacy status during follow-up (Beta (SE): 0.024 (0.008) and0.0012 (0.0004)). While the association of GrimAge was driven by a DNAm-based surrogate of tissue inhibitor metalloproteinase 1 (TIMP-1), no significant association was detected for component CpGs of DunedinPACE. When we tested associations of polypharmacy with 668,413 CpGs epigenome-wide, we observed no statistically significant findings (top hit: cg07675998; chr11q13.1; Beta (SE) = 0.009 (0.002); p = 1.5 × 10^-6). However, these showed significant enrichments of several biological functions and pathways related to renal tissue, lipoproteins, inflammatory and immune response.

Conclusions: These findings suggest an influence of polypharmacy on accelerated epigenetic aging and on altered methylation patterns in the genome, suggesting a potential implication of pathways related to renal tissue development, lipoproteins and cholesterol homeostasis, inflammatory and immune response, in line with previous proteomic analyses of polypharmacy mouse models. These observations also suggest potential targets for mitigating disruptive effects of polypharmacy on elderly health.

Background: DNA methylation profiling has emerged as a promising tool for improving pathological diagnosis. This study investigates the diagnostic efficacy and subgroup heterogeneity of SHOX2, RASSF1A, Septin9, and HOXA9 methylation in pleural effusion lymphoma, aiming to enhance diagnostic accuracy and identify high-risk molecular subgroups.

Methods: A cohort of 109 patients (73 lymphoma, 36 benign pleural effusions) was analyzed using quantitative methylation-specific PCR for the four biomarkers. Receiver operating characteristic (ROC) curves were constructed to determine optimal cutoff values for each marker, and their diagnostic performance was evaluated in different lymphoma subgroups.

Results: The cycle threshold values for the internal control β-actin predominantly ranged from 18 to 23, suggesting consistent DNA input for methylation analysis. ROC curve revealed that the area under the curve (AUC) values were 0.871 (SHOX2), 0.779 (HOXA9), 0.611 (Septin9), and 0.548 (RASSF1A). When combined, the four markers achieved an AUC of 0.896, with an overall diagnostic sensitivity of 83.6% and a specificity of 94.4%. SHOX2 and HOXA9 demonstrated higher sensitivity within diffuse large B-cell lymphoma (DLBCL) subgroups, with SHOX2 achieving 100% sensitivity in the non-GCB subgroup and HOXA9 achieving 90.9% sensitivity in the GCB subgroup. Septin9 methylation was significantly associated with the presence of B symptoms (P = 0.041). Importantly, RASSF1A methylation was more strongly associated with TP53 deletion rather than with Bcl-2/IGH, Bcl-6, or c-MYC rearrangements.

Conclusion: Integrating methylation markers SHOX2, HOXA9, Septin9, and RASSF1A exhibits significant diagnostic potential in pleural effusion lymphoma, especially within DLBCL subgroups. These markers could prove valuable in identifying high-risk subgroups and guiding clinical decision-making.