Clinical Epigenetics最新文献

Background: Pediatric critical illness can disrupt circadian rhythms, potentially leading to long-term deficits in growth, neurocognition, and behavior. Disturbances in circadian rhythms have been associated with altered gene expression and DNA methylation. We investigated long-term DNA methylation alterations in circadian entrainment and clock genes in children previously admitted to the pediatric intensive care unit (PICU), the influence of parenteral nutrition (PN) timing hereon and their associations with long-term health outcomes.

Methods: This study is a secondary analysis of the PEPaNIC randomized controlled trial (RCT) and its two-year follow-up. The PEPaNIC-RCT randomized critically ill children to early initiation of supplemental PN within the first 24 h or its omission in the first week of PICU admission. DNA methylation of 127 circadian entrainment and clock genes was studied in buccal mucosa DNA of former PICU patients (n = 818) and matched healthy children (n = 392) at the two-year follow-up using Infinium® HumanMethylation EPIC BeadChips. Multivariable linear models were used to identify differential methylation between former patients and controls and their association with randomization group and outcomes at two-year follow-up.

Results: Former PICU patients showed 61 differentially methylated CpG sites (DMPs) within 34 of the genes, with 60 (98.4%) showing hypomethylation as compared with healthy children. Omitting early PN during PICU stay did not affect CpG site methylation. 702 associations (34.9%) were observed between abnormal DNA methylation and adverse long-term health and developmental outcomes, most notably visual-motor integration (47 DMPs, 77%), height (46 DMPs, 75%) and total IQ (46 DMPs, 75%).

Conclusion: Former PICU patients exhibited altered DNA methylation in circadian entrainment and clock genes compared to healthy children, and this was associated with impaired growth, neurocognition and behavioral problems at two-year follow-up. Disruptions in circadian entrainment and clock gene methylation may contribute to the adverse long-term health consequences that children experience after critical illness.

Background: The use of vaginal self-sampling for cervical cancer screening is promising and increasing. However, triage cytology cannot be performed on vaginal self-sampling material after a high-risk human papilloma virus (hrHPV)-positive result. In our recent discovery study, we identified a three-marker panel with high sensitivity (82%) and specificity (74%) for CIN3 or worse (CIN3+). In the present study, we performed the clinical validation of this three-marker panel using real-world hrHPV-positive vaginal self-samples obtained through the Dutch screening programme.

Methods: The markers LHX8, EPB41L3 and ANKRD18CP were analysed using quantitative methylation-specific PCR (QMSP) on a consecutive cohort of hrHPV-positive vaginal self-samples (n = 2482: 408 CIN3+ and 2074 

Results: The three-marker panel showed 73% (298/408) sensitivity and 79% (1640/2071) specificity to detect CIN3+, and identified 96% (21/22) of cervical cancer cases. A scenario analysis was performed on a virtual population of 100 000 hrHPV-positive women using vaginal self-sampling, comparing our methylation triage test with current cytology triage testing. This analysis revealed that more cancers (864 vs. 684 or 770 for 80 or 90% uptake) would be detected with our methylation panel, while referral rates (29% vs. 31% for both 80 and 90% uptake) and detection of CIN3 (72% vs. 68 or 77% for 80 or 90% uptake) would be similar for methylation and cytology.

Conclusion: Compared to cytology triage testing, DNA methylation triage analysis using our three-marker panel offers an appropriate alternative to detect CIN3+ in hrHPV-positive vaginal self-samples. Implementation of the DNA methylation triage test would not only increase cancer detection, but would also eliminate the need for physician visits for cytological triage testing. In addition, it would accelerate referral decisions, ultimately reducing uncertainty and ensuring timely screening completion for all women.

Background: Tfh cells play a crucial role in the pathogenesis of SLE. Our previous research confirmed that SETD3, which is upregulated in CD4⁺ T cells of SLE patients, mediates the overexpression of CXCR5 by upregulating the CXCR5 promoter histones H3K4me3 and H3K36me3. However, the recent study demonstrates that SETD3, in contrast to other protein lysine methyltransferases, does not methylate histones; its sole verified substrate is H73 of actin. Consequently, the molecular mechanism by which SETD3 influences histone methylation requires further investigation. The most important transcription factor in the development and differentiation of Tfh cells is Bcl-6. Whether SETD3 can directly participate in the regulation of Tfh cell differentiation by regulating the expression of Bcl-6 remains to be further studied.

Results: Our results demonstrated that SETD3 maintained a high level of expression throughout the differentiation process of Tfh cells. Moreover, following the interference with SETD3 expression, the expression of Bcl-6 and the differentiation of Tfh cells were notably impeded. SETD3 mediates the H3K4me3/K36me3 and H3K9ac/K14ac modifications of Bcl-6 promoter by interacting with NSD3, SMYD2, p300 and CBP, thereby upregulating Bcl-6 expression in Tfh differentiation. In addition, we also confirmed that the levels of H3K4me3/K36me3 and H3K9ac/K14ac in Bcl-6 promoter of SLE CD4⁺ T cells were significantly higher than those of healthy controls, which was related to SETD3 mediated upregulation of NSD3, SMYD2, p300 and CBP binding to Bcl-6 promoter. Inhibiting SETD3 expression in CD4⁺ T cells from SLE patients effectively reduces the levels of H3K4me3/K36me3, and H3K9ac/K14ac at the Bcl-6 promoter, thereby downregulating Bcl-6 expression.

Conclusions: Elevated SETD3 expression in SLE CD4⁺ T cells recruits NSD3, SMYD2, p300, and CBP to the Bcl-6 promoter, thus upregulating histone H3K4/K36 methylation and H3K9/K14 acetylation at this locus, which mediates the upregulation of Bcl-6 expression.

Air pollution exposure during pregnancy increases the risk of allergic and respiratory diseases, yet its epigenetic effects across the maternal-fetal interface remain poorly understood. We conducted a pilot study of 10 mother-infant dyads near Fresno, California, to investigate whether prenatal air pollution exposure is associated with differential DNA methylation (DNAm) in maternal peripheral blood mononuclear cells (PBMCs) and infant cord blood mononuclear cells (CBMCs). Using a custom DNAm array targeting high-value allergy- and asthma-associated loci, we identified 24 CpG sites in maternal PBMCs and 18 in infant CBMCs associated with PM2.5 exposure. Only one CpG site was shared between PBMCs and CBMCs, suggesting largely distinct DNAm responses to PM2.5 in maternal and fetal circulations. Further research is needed to validate these associations and determine their functional implications for immune development and disease risk.

Histone 3 lysine 27 (H3K27) demethylation is a key post-translational modification of chromatin and plays a fundamental role in gene activation. Demethylation of H3K27 is mediated by Jumonji C domain-containing lysine demethylase 6 A (KDM6A) and its paralog, KDM6B, both of which are responsible for homeostasis, autoimmune response, infectious diseases, and cancers. To date, mounting studies dedicate the roles of KDM6A/B on tumor promotion or suppression, and there are many reviews systematically summarize the relevant mechanisms of KDM6A/B in tumor development and therapy. KDM6A and KDM6B also contribute to the regulation of therapeutic insensitivity to chemotherapy, targeted response, radiotherapy and immunotherapy. Herein, we outline the current knowledge of KDM6A/B in regulation of therapeutic resistance, and suggest that KDM6A/B holds immense potential in recovering therapeutic resistance.

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.