Clinical Epigenetics最新文献

{"title":"Epigenetic silencing and CRISPR-mediated reactivation of tight junction protein claudin10b (CLDN10B) in renal cancer.","authors":"Sarah Arroyo Villora, Yufen Zhao, Paula Castellanos Silva, Alba A Hahn, Vivien Olanin, David Groll, Sandra Maurer, Vera Roetzer, Witold Szymanski, Tara Procida-Kowalski, Niklas Philipp, Aline Koch, Marek Bartkuhn, Johannes Graumann, Richard Volckmann, Jan Koster, Oliver Rossbach, Denise Salzig, Reinhard Dammann, Cornelia Sigges, Jan Halbritter, Silke Haerteis, Antje Maria Richter","doi":"10.1186/s13148-025-01911-2","DOIUrl":"10.1186/s13148-025-01911-2","url":null,"abstract":"<p><strong>Background: </strong>The kidney's tubular system relies on cell polarity and tight junctions to maintain structure and function and disruptions contribute to diseases like cancer. Loss of tight junction proteins such as Claudins can actively contribute to tumorigenesis.</p><p><strong>Results: </strong>We aimed to identify biomarkers for renal carcinoma, after kidney transplantation and conventional kidney tumors. We identified the epigenetic silencing of the Claudin 10 gene isoform B (CLDN10B) through DNA hypermethylation in renal cancers, including clear cell (ccRCC), papillary (pRCC) and post-transplantation renal carcinoma (PT-ccRCC). In contrast, CLDN10A was hypomethylated in ccRCC and pRCC. Differential methylation of the isoforms discriminates RCC from other malignancies. The epigenetic alteration of CLDN10B significantly correlated with reduced patient survival and advanced tumor staging. CLDN10B overexpression or induction significantly inhibited migration, cell cycle progression, and cellular growth. Using a CRISPR-based epigenetic editing tool reactivated CLDN10B to its endogenous level using VP160 and TET1 by promoter demethylation and significantly demonstrated its tumor-suppressive effects in 2D and 3D cell models.</p><p><strong>Conclusion: </strong>Our findings suggest that CLDN10B acts as a tumor suppressor, and its epigenetic regulation may represent a therapeutic target for RCC. Ultimately, understanding CLDN10B's regulation and function could provide new insights into renal cancer treatment.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"102"},"PeriodicalIF":4.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-omics and mediation-based genetic screening approach identifies STX4 as a key link between epigenetic regulation, immune cells, and childhood asthma.","authors":"Yuan Zhang, Xiaochen Du, Yujuan Yang, Yaqiong Ren, Lijun Zhou, Jun Hua, Hongying Wang","doi":"10.1186/s13148-025-01908-x","DOIUrl":"10.1186/s13148-025-01908-x","url":null,"abstract":"<p><strong>Background: </strong>Childhood asthma presents a multifaceted immune-driven pathology shaped by genetic, epigenetic, and immune regulatory interactions. Despite extensive genome-wide analyses pinpointing multiple susceptibility loci, the precise functional contributors to asthma pathogenesis remain elusive. This study employs a comprehensive multi-omics framework and Mendelian randomization (MR) analysis to systematically identify and validate key genetic determinants implicated in childhood asthma.</p><p><strong>Methods: </strong>A genome-wide screening of over 19,000 human genes was performed to identify cis-eQTL-regulated genes associated with childhood asthma. Two-sample MR was conducted to assess causality, followed by Summary-based Mendelian Randomization (SMR) to validate findings in independent datasets. Colocalization analysis determined whether gene expression and asthma GWAS signals share a common causal variant. Protein quantitative trait loci (pQTL) analysis further validated gene associations at the protein level. DNA methylation quantitative trait loci (mQTL) MR and mediation analysis explored epigenetic regulatory mechanisms, while linkage disequilibrium score regression (LDSC) quantified genome-wide genetic correlations. Immune cell mediation analysis examined potential immune-driven effects, and Phenome-Wide Association Study (PheWAS) evaluated pleiotropy and therapeutic safety.</p><p><strong>Results: </strong>Following systematic screening, STX4 emerged as a strong candidate gene for childhood asthma. MR and SMR analyses confirmed its causal role, while colocalization analysis provided robust genetic evidence supporting STX4's regulatory influence on childhood asthma susceptibility. pQTL validation confirmed that STX4's effects extend to the protein level, strengthening its biological relevance. DNA methylation analysis revealed key CpG (Cytosine-phosphate-Guanine) sites regulating STX4 expression, with higher methylation levels reducing childhood asthma risk. Immune cell mediation analysis demonstrated that STX4 influences childhood asthma risk via CD4+ and CD8+ T cell subsets. LDSC analysis reinforced a significant genetic correlation between STX4 and childhood asthma, while PheWAS detected no major pleiotropy, suggesting that STX4 is a specific and promising therapeutic target.</p><p><strong>Conclusions: </strong>This study systematically identifies and validates STX4 as a key genetic regulator in childhood asthma by integrating large-scale genetic, epigenetic, and immune regulatory data. These findings provide strong evidence for STX4's role in childhood asthma pathogenesis, highlighting STX4 as a potential target for future precision therapies in childhood asthma.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"101"},"PeriodicalIF":4.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12164099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Restoring endogenous Dlg4/PSD95 expression by an artificial transcription factor ameliorates cognitive and motor learning deficits in the R6/2 mouse model of Huntington's disease.","authors":"Germán Fernández, Kevin Leiva, Fernando J Bustos, Brigitte van Zundert","doi":"10.1186/s13148-025-01903-2","DOIUrl":"10.1186/s13148-025-01903-2","url":null,"abstract":"<p><strong>Background: </strong>Huntington's disease (HD) is an incurable hereditary disorder caused by an expansion of CAG repeats in exon 1 of the Huntingtin gene (HTT). HD is characterized by motor dysfunction and cognitive decline. The pathophysiology of HD begins in cortico-striatal circuits and later spreads to other brain regions, notably the hippocampus. At the cellular level, structural changes in synapses have been observed prior to neuronal degeneration, significantly disrupting the formation and maintenance of neuronal circuits. The postsynaptic density protein 95 (PSD-95, hereafter Dlg4/PSD95) is a key synaptic plasticity protein reduced in HD and other neurodegenerative diseases such as Alzheimer's disease (AD). Epigenetic silencing of plasticity and memory genes contributes to AD pathology and cognitive impairment. To restore endogenous Dlg4/PSD95 expression in AD, we previously developed an epigenetic editing strategy where a zinc finger DNA-binding domain targeting the Dlg4/PSD95 gene promoter was fused to the transactivation domain VP64 and driven under a CMV promoter. AAV-PhP.B-mediated delivery of this artificial transcription factor (ATF) CMV-PSD95-6ZF-VP64 improved cognition in an AD mouse model. Here, we assessed the therapeutic potential of AAV9-mediated delivery of the synapsin-driven ATF PSD95-6ZF-VP64 in the R6/2 HD mouse model.</p><p><strong>Results: </strong>Consistent with the previous studies, R6/2 mice exhibited reduced hippocampal Dlg4/PSD95 mRNA and protein levels in young adulthood (7 weeks), which persisted into early adulthood (14 weeks). Starting at adolescents (4 weeks), the R6/2 mice also displayed motor (i.e., accelerated rotarod) and cognitive (i.e., Barnes maze and object location memory) impairments. In wild-type primary hippocampal cultures, AAV9-PSD95-6ZF-VP64 led to an increase in synaptic PSD-95 clusters and spine size. Intracerebroventricular injections of neonatal R6/2 mice with AAV9-PSD95-6ZF-VP64 elevated hippocampal Dlg4/PSD95 expression levels to those observed in control non-transgenic mice. Importantly, AAV9-PSD95-6ZF-VP64 effectively improved hippocampal-dependent deficits in spatial learning and memory in young adult HD mice, as well as impairments in motor coordination and motor skill learning, with these benefits persisting into adulthood.</p><p><strong>Conclusion: </strong>This work validates Dlg4/PSD95 as a key player in the prodromal phase of HD pathology and establishes the ATF PSD95-6ZF-VP64 as an attractive therapeutic tool for treating the disease's early phase.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"100"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12164150/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144282689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-omics prognostic model of cuproptosis affects the prognosis of stomach adenocarcinoma.","authors":"Yinying Wu, Yangwei Fan, Xuyuan Dong, Danfeng Dong, Yu Shi, Meichen Wang, Jia Wang, Yuqian Yang, Nan Yang, Fengyun Ou, Enxiao Li","doi":"10.1186/s13148-025-01894-0","DOIUrl":"10.1186/s13148-025-01894-0","url":null,"abstract":"<p><strong>Background: </strong>Cuproptosis, a form of cell death associated with copper ions, has been linked to the pathogenesis of various cancers, including gastric cancer. Investigating the role of cuproptosis-related genes through multi-omics analysis can enhance our understanding of disease mechanisms and improve prognosis prediction.</p><p><strong>Objective: </strong>This study aims to elucidate the role of cuproptosis-related genes in gastric cancer from a multi-omics perspective.</p><p><strong>Materials and methods: </strong>We utilized multi-omics sequencing data from TCGA and GEO databases to explore the relationships between cuproptosis genes and gastric carcinogenesis, clinical phenotypes, and prognosis. This analysis encompassed mutation, copy number variation, methylation, mRNA expression, alternative splicing, and APA alterations. Additionally, we examined the regulatory roles of cuproptosis genes in gastric cancer through ceRNA interactions, gene mutations, and DNA methylation. A multi-omics prognostic model for gastric cancer was subsequently constructed.</p><p><strong>Results: </strong>Our findings revealed that CDKN2A was the most frequently mutated gene in gastric cancer. Overall mutations in cuproptosis genes and copy number alterations of PDHB significantly impacted gastric cancer prognosis. Methylation, alternative splicing, and APA alterations of CDKN2A also influenced patient outcomes. Notably, MTF1, a key gene in cuproptosis, was found to affect apoptosis and invasion in gastric cancer cell lines.</p><p><strong>Conclusion: </strong>We successfully developed a multi-omics prognostic model for gastric cancer that offers significant predictive value for patient outcomes.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"99"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144282688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling.","authors":"Jialing Sun, Xinfeng Sun, Weihuang He, Bingding Huang, Wenxing Feng, Zhiyi Han, Ruyun Ruan, Yuanke Pan, Jinxin Zhu, Jing Li, Xin Zhong, Mengqing Ma, Rui Hu, Minling Lv, Qi Huang, Wei Zhang, Mingji Feng, Jinyu Yi, Pin Cui, Xiaozhou Zhou","doi":"10.1186/s13148-025-01909-w","DOIUrl":"10.1186/s13148-025-01909-w","url":null,"abstract":"<p><strong>Background: </strong>Early detection of hepatocellular carcinoma (HCC) can greatly improve the survival rate of patients. Plasma cfDNA methylation has been shown to have the potential to be a non-invasive method for diagnosing HCC. However, the identified HCC plasma cfDNA methylation sites were less sensitive to early HCC diagnosis. Therefore, we aimed to develop a highly sensitive marker panel based on cell-free DNA (cfDNA) methylation for the detection of HCC.</p><p><strong>Methods: </strong>The study included 374 participants, including 102 healthy individuals, 51 HBV patients, 50 cirrhosis patients, and 171 HCC patients (56 at stage 0 or A according to BCLC staging). Two cfDNA methylation sequencing assays (whole genome bisulfite sequencing (WGBS) and targeted bisulfite sequencing (TBS)) were used along with machine learning modeling to detect HBV-related HCC based on differentially methylated regions (DMR) among the four participant groups.</p><p><strong>Results: </strong>TBS analysis achieved an overall sensitivity of 96.67% at a specificity of 93.7% than alpha-fetoprotein (AFP) of 18%-60%, to discriminate all stages of HCC patients from healthy people, and sensitivity of 90.0% at a specificity of 93.75% to discriminate early-stage HCC patients from healthy people. A number of significant DMRs between HCC and non-cancer groups were identified, providing candidate biomarkers for HCC detection. Among these DMRs, one that locates in the promoter region of GJA4, was found to be consistently present in the whole process of HBV-related HCC carcinogenesis. Using data from TCGA, comparison of expression profile of GJA4 between 160 healthy people and 369 HCC patients further supported this scenario.</p><p><strong>Conclusions: </strong>This study provides biomarkers for detecting, staging and early detection of HCC using plasma cfDNA methylome profiling. Additionally, the dynamic alteration of GJA4 promoter methylation may serve as a molecular clue for studying HBV-related HCC carcinogenesis and prognosis.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"98"},"PeriodicalIF":4.8,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144274319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EZH1 deficiency promotes ferroptosis resistance by activating NRF2 in sepsis-associated liver injury.","authors":"Meihua Mei, Ying You, Ningxin Tan, Xiaoshun He, Junqi Huang","doi":"10.1186/s13148-025-01892-2","DOIUrl":"10.1186/s13148-025-01892-2","url":null,"abstract":"<p><p>Sepsis-associated acute liver injury (SALI) is a major clinical complication of sepsis due to excessive, unfettered inflammation. In recent years, the role of epigenetic regulatory mechanisms in SALI has been gradually emphasized. Here, we investigated the effects of a Histone-lysine N-methyltransferase EZH1 (Enhancer of zeste homolog 1) inhibition on promoting ferroptosis resistance to activate nuclear factor, erythroid derived 2, like 2 (NRF2) in SALI. We found that EZH1 deficiency improved animal survival in lethal sepsis. EZH1 deficiency mice exhibited alleviated SALI with decreased hepatocellular ferroptosis. EZH1 deficiency attenuated the H3K27me3 modification in the Nfe2l2 promoter, lending to the increased expression and nuclear translocation of NRF2. In the in vitro, LPS-induced ferroptosis model, EZH1 inhibitor DS3201 exhibited an anti-ferroptosis effect, which was reversed NRF2 inhibitor ML385. These findings indicate that EZH1 deficiency or inhibition with DS3201 alleviates ferroptosis in the liver by activating the NRF2, and it is suggested that targeting EZH1 may be a new therapeutic strategy in SALI.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"96"},"PeriodicalIF":4.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12147250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-locus methylation analyses reveal GNAS methylation defects in three patients with the Beckwith-Wiedemann syndrome phenotype and no molecular defects in the 11p15.5 imprinted region.","authors":"Tatsuki Urakawa, Yuri Kanamaru, Naoko Amano, Akira Uchida, Maki Fukami, Masayo Kagami","doi":"10.1186/s13148-025-01907-y","DOIUrl":"10.1186/s13148-025-01907-y","url":null,"abstract":"<p><strong>Background: </strong>Beckwith-Wiedemann syndrome (BWS) is a congenital imprinting disorder (ID) caused by molecular defects in the 11p15.5 imprinted region, such as hypomethylation of the KCNQ1OT1:TSS-differentially methylated region (KCNQ1OT1-DMR) and hypermethylation of the H19/IGF2:IG-DMR, and maternal CDKN1C pathogenic variants, with various clinical characteristics, including overgrowth and macroglossia. Recently, the concept of Beckwith-Wiedemann spectrum (BWSp) and a clinical scoring system for BWS have been proposed, and cases with four or more points are diagnosed with classic BWS, and 20% of cases with BWS have no molecular defects in the 11p15.5 imprinted region. Pseudohypoparathyroidism type 1B (PHP1B, alias inactivating parathyroid hormone (PTH)/PTH-related protein signaling disorder 3) has characteristics of hormone resistance, particularly PTH, caused by methylation defects in DMRs at the GNAS locus (GNAS-DMRs). Some cases with PHP1B show postnatal overgrowth, which overlaps the BWS-phenotype. However, no studies have conducted a multi-locus methylation analysis for the ID-responsible DMRs other than the DMRs in 11p15.5 in cases with the BWS-phenotype and without molecular defects in the 11p15.5 imprinted region.</p><p><strong>Results: </strong>We conducted methylation analysis using pyrosequencing in 77 patients showing the BWS-phenotype without molecular defects in the 11p15.5 imprinted region. Consequently, we identified three patients with methylation defects in the GNAS-DMRs. Patients 1, 2, and 3 had 9, 5, and 4 points in a BWSp score, respectively. All three patients had macroglossia and postnatal overgrowth. Further analyses, methylation-specific multiple ligation-dependent probe amplification for multiple DMRs, array-based methylation analysis, exome sequencing, array comparative genome hybridization analysis, and microsatellite marker analysis showed 9p deletion in Patient 1 and paternal uniparental isodisomy of chromosome 20 in Patient 2 together with multiple methylation defects in DMRs other than the GNAS-DMRs. Patient 3 had methylation defects in only the GNAS-DMRs.</p><p><strong>Conclusion: </strong>Methylation defects in the GNAS-DMRs can cause the BWS-phenotype. For cases with the BWS-phenotype but no molecular defects in the 11p15.5 imprinted region, methylation analysis for the DMRs at the GNAS locus should be considered.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"97"},"PeriodicalIF":4.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12150451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mutational landscape and DNA methylation-based classification of squamous cell carcinoma and urothelial carcinoma.","authors":"Min Ren, Midie Xu, Chen Chen, Ran Wei, Qianlan Yao, Liqing Jia, Peng Qi, Qifeng Wang, Qianming Bai, Xiaoli Zhu, Sheng Wu, Qinghua Xu, Xiaoyan Zhou","doi":"10.1186/s13148-025-01902-3","DOIUrl":"10.1186/s13148-025-01902-3","url":null,"abstract":"<p><strong>Background: </strong>Identification of the tissue of origin is fundamental for cancer treatment. However, squamous cell carcinomas from different sites lack representative histological and immunohistochemical features. This study aimed to identify mutational profiles and further establish a DNA methylation-based classification for squamous cell carcinoma and urothelial carcinoma. Samples of unambiguous squamous cell carcinomas and urothelial carcinomas were collected for targeted next-generation sequencing and mutational landscape analysis. Moreover, using Illumina methylation BeadChip data from public datasets and a local cohort, we developed a DNA methylation-based classifier utilizing the CatBoost algorithm to identify four common types of squamous cell carcinoma (lung, head and neck, esophagus, and cervix) as well as urothelial carcinoma.</p><p><strong>Results: </strong>The DNA mutational profiles of squamous cell carcinomas from different sites overlapped greatly, and there was no significant difference in tumor mutation burden or microsatellite status. On the basis of public datasets and analyses via various machine learning algorithms, a DNA methylation-based classification containing 106 features by the CatBoost algorithm was constructed and reached an accuracy of 98.79% (490/496) in the training set from PanCanAtlas datasets. The predictive accuracies of the methylation classification in the public validation set and local FUSCC validation set 1 with known primary were 86.96% (340/391) and 84.87% (101/119), respectively. The predictive accuracy for the primary samples (89.66%, 78/87) was obviously greater than that for the metastatic samples (71.88%, 23/32). FUSCC validation set 2 included ten complicated cancer of unknown primary (CUP) samples with squamous cell differentiation. When a well-established 90-gene expression assay was compared with the present classification, our methylation-based classification successfully classified two samples with no eligible RNA expression; the results for four sample were consistent with higher methylation prediction scores in three, and those for two samples were inconsistent. The methylation-based classification results of the remaining two samples were more compatible with the results of the clinical evaluation.</p><p><strong>Conclusion: </strong>We successfully established a DNA methylation-based classification for squamous cell carcinomas (lung, head and neck, esophagus, and cervix) and urothelial carcinomas with outstanding diagnostic performance for the first time. This classification has high potential for clinical translation to address the dilemma of identifying the origin of squamous cell carcinoma of unknown primary.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"95"},"PeriodicalIF":4.8,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12147257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation in monozygotic twins discordant for acute lymphoblastic leukemia: a case report and systematic review.","authors":"Mao-Ling Sun, Yang Li, Rong-Xi Man, Si-Wen Wang, Rong Guo, Ying Yang, Yu-Qing Pan","doi":"10.1186/s13148-025-01906-z","DOIUrl":"10.1186/s13148-025-01906-z","url":null,"abstract":"<p><p>Acute lymphoblastic leukemia (ALL) is a prevalent malignant hematologic disease characterized by the abnormal proliferation and accumulation of immature lymphocytes in bone marrow and lymphoid tissues. In our study, Oxford Nanopore Technologies (ONT) sequencing was performed to investigate four types of methylation modifications-6 mA, CHG, CHH, and CpG-in a pair of monozygotic twins, where one twin has ALL and the other is healthy. The results showed the significant global hypomethylation of CpG sites and an increase in 6 mA, CHG, and CHH methylation in the twin diagnosed with ALL. Notably, the hypomethylation of CpG was particularly increased in the open sea, gene body, and 3'UTR regions, while 6 mA and CHG modifications exhibited high methylation levels in the gene body, TSS1500, TSS200, and 3'UTR regions. Additionally, CHH modifications showed high methylation across all genomic regions. Within the differential methylation loci (DML), we identified several genes related to tumorigenesis and progression (such as ZDHHC11, NBPF1, and TPTE). Furthermore, we systemically reviewed the literatures on leukemia and DNA methylation modifications, providing a comprehensive description of their correlation. In summary, these findings indicate that DNA methylation plays a crucial role in the onset and progression of ALL, offering valuable insights for future research into its impact on leukemia development.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"94"},"PeriodicalIF":4.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12144706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of enzymatic and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses.","authors":"Stine H Kresse, Evy Marie Thorkildsen, Sara Brandt-Winge, Heidi Pharo, Hege Marie Vedeld, Guro E Lind","doi":"10.1186/s13148-025-01901-4","DOIUrl":"10.1186/s13148-025-01901-4","url":null,"abstract":"<p><strong>Background: </strong>Detection of DNA methylation biomarkers in circulating cell-free DNA (cfDNA) has great clinical potential for cancer management, but there is a high need for method optimization and standardization. Bisulfite conversion of DNA is the gold-standard pre-treatment method for DNA methylation analyses, but causes also DNA fragmentation and loss. Enzymatic conversion of DNA represents a promising alternative due to the more gentle treatment minimizing damage to DNA. The aim of this study was to evaluate and compare enzymatic and bisulfite conversion to identify the best pre-treatment method for detecting DNA methylation biomarkers in cfDNA from plasma using droplet digital PCR (ddPCR).</p><p><strong>Results: </strong>The performance of the NEBNext Enzymatic Methyl-seq Kit (both the full kit intended for sequencing and the sub-component NEBNext Enzymatic Methyl-seq Conversion Module) and the EpiTect Plus DNA Bisulfite Kit was evaluated and compared using normal cfDNA and tumor cfDNA samples from colorectal cancer patients. The cytosine conversion efficiency was 99-100% for both enzymatic and bisulfite conversion. Enzymatic conversion resulted in longer DNA fragments with higher peak fragment sizes compared to bisulfite conversion, but the DNA recovery was considerably lower after enzymatic conversion (34-47%) compared to bisulfite conversion (61-81%). For enzymatic conversion, the full kit gave slightly better DNA recovery than the conversion module. A comparison of five magnetic bead brands, as well as several different magnetic bead-to-sample ratios revealed no major improvements in DNA recovery for the enzymatic conversion. DNA methylation of the biomarker BCAT1 was detected at similar rates in parallel tumor cfDNA samples pre-treated with either enzymatic or bisulfite conversion. However, enzymatic conversion resulted in lower number of positive droplets for both target and control ddPCR assays, in line with the lower DNA recovery after conversion.</p><p><strong>Conclusions: </strong>Based on a thorough evaluation of enzymatic and bisulfite conversion of cfDNA using ddPCR, bisulfite conversion emerges as the best pre-treatment method due to higher DNA recovery after conversion and higher number of positive droplets in the ddPCR reactions.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":"17 1","pages":"93"},"PeriodicalIF":4.8,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}