Frontiers in Epigenetics and Epigenomics最新文献

筛选

英文中文

Benchmark of the Oxford Nanopore, EM-seq, and HumanMethylationEPIC BeadChip for the detection of the 5mC sites in cancer and normal samples 牛津纳米孔、EM-seq 和 HumanMethylationEPIC BeadChip 检测癌症和正常样本中 5mC 位点的基准测试

Frontiers in Epigenetics and Epigenomics Pub Date : 2024-07-25 DOI: 10.3389/freae.2024.1362926

Kseniia A. Deinichenko, Valentina G. Vynogradskaya, P. A. Grebnev, V. M. Mikova, Dmitriy O. Bobylev, Abusaid M Shaymardanov, A. A. Ivashechkin, M. V. Erokhina, A. Akinshina, Anna V. Semyanihina, S. I. Mitrofanov, Konstantin S. Grammatikati, V. Yudin, Sergey M. Yudin, A. Makhotenko, A. A. Keskinov, S. Kraevoy, Anna S Makarova, E. A. Snigir, Dmitry V Svetlichnyy, V. I. Skvortsova

{"title":"Benchmark of the Oxford Nanopore, EM-seq, and HumanMethylationEPIC BeadChip for the detection of the 5mC sites in cancer and normal samples","authors":"Kseniia A. Deinichenko, Valentina G. Vynogradskaya, P. A. Grebnev, V. M. Mikova, Dmitriy O. Bobylev, Abusaid M Shaymardanov, A. A. Ivashechkin, M. V. Erokhina, A. Akinshina, Anna V. Semyanihina, S. I. Mitrofanov, Konstantin S. Grammatikati, V. Yudin, Sergey M. Yudin, A. Makhotenko, A. A. Keskinov, S. Kraevoy, Anna S Makarova, E. A. Snigir, Dmitry V Svetlichnyy, V. I. Skvortsova","doi":"10.3389/freae.2024.1362926","DOIUrl":"https://doi.org/10.3389/freae.2024.1362926","url":null,"abstract":"Introduction: Whole-genome DNA methylation identification is crucial for profiling physiologically and clinically relevant epigenetic changes. Although there are multiple experimental methods, their accuracy, advantages, and disadvantages need to be investigated in their application to complex tissue objects. In this study, we performed a benchmark of 5mC detection with Oxford Nanopore and enzymatic methyl-sequencing (EM-seq) methods.Material and Methods: To this end, we profiled in a genome-wide manner 5mC sites in colorectal tumors and normal tissues for three patients and applied the HumanMethylationEPIC BeadChip as an additional control approach. We estimated the whole-genome scale of the methylation detection that each method yields.Results: Our investigation describes the sensitivity and specificity of each platform and the impact that sequencing coverage brings. Our analysis revealed the higher sensitivity and specificity of Nanopore sequencing over the EM-seq method. Moreover, Oxford Nanopore Technology (ONT) sequencing, followed by Megalodon methylation detection, demonstrates better quantitative agreement of the epigenetic signals between biological replicates. Furthermore, our analysis highlights that with 40× and above coverage, EM-seq slightly outperforms ONT and yields highly accurate detection of the 5mC signals (AuPR = 0.99178 and AuROC = 0.98161).Conclusion: The study was performed on colon cancer and adjacent normal tissue samples, placing our investigation close to the real application of methylation studies in oncology.","PeriodicalId":484006,"journal":{"name":"Frontiers in Epigenetics and Epigenomics","volume":"48 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141803734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advancements in the clinical application of gene methylation for early cancer detection 基因甲基化在早期癌症检测中的临床应用进展

Frontiers in Epigenetics and Epigenomics Pub Date : 2024-07-19 DOI: 10.3389/freae.2024.1430294

Xin Xu, Yanru Guo, Mulin Liu, Yunxiang Hu, Shijun Li

{"title":"Advancements in the clinical application of gene methylation for early cancer detection","authors":"Xin Xu, Yanru Guo, Mulin Liu, Yunxiang Hu, Shijun Li","doi":"10.3389/freae.2024.1430294","DOIUrl":"https://doi.org/10.3389/freae.2024.1430294","url":null,"abstract":"This review provides an overview of common assays used to screen for gene methylation and early biomarkers of methylation in various cancers. DNA methylation, one of the most well-studied epigenetic modifications, plays a crucial role in normal cell and tissue development. It is increasingly utilized as a biomarker for early cancer and precancerous lesion detection. In this review, we describe common methods associated with gene methylation, including bisulfite sequencing PCR (BSP), pyrosequencing technology (PYR), methylation-specific polymerase chain reaction (MS-PCR/MSP), methylation-sensitive high-resolution melting (MS-HRM), methylation sensitive single nucleotide primer extension (MS-SnuPE), Epityper, Droplet digital PCR (ddPCR), methylation-sensitive restriction enzyme (MSRE) analysis, COBRA and PacBio SMRT sequencing. Additionally, we summarize methylation markers and their sample types for early cancer screening, focusing on colorectal cancer, hepatocellular carcinoma, gastric cancer, pancreatic cancer, esophageal cancer (digestive system), lung cancer (respiratory system), breast cancer, ovarian cancer, cervical cancer (female reproductive system), bladder cancer, and prostate cancer (urinary system). Furthermore, we discuss the recent detection of methylation biomarkers in clinical samples such as blood, urine, sputum, feces, and tissues. The aim of this review is to summarize early methylation biomarkers that are expected or have already been clinically applied. For future large-scale studies or the integration of available methylome level data, the discovery of sufficiently sensitive clinical biomarkers is essential.","PeriodicalId":484006,"journal":{"name":"Frontiers in Epigenetics and Epigenomics","volume":" 619","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141823823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protein arginine methylation in transcription and epigenetic regulation 蛋白精氨酸甲基化在转录和表观遗传调控中的作用

Frontiers in Epigenetics and Epigenomics Pub Date : 2023-08-04 DOI: 10.3389/freae.2023.1245832

Hoang Quoc Hai Pham, Xiaoqun Tao, Yanzhong Yang

{"title":"Protein arginine methylation in transcription and epigenetic regulation","authors":"Hoang Quoc Hai Pham, Xiaoqun Tao, Yanzhong Yang","doi":"10.3389/freae.2023.1245832","DOIUrl":"https://doi.org/10.3389/freae.2023.1245832","url":null,"abstract":"Arginine methylation is a prevalent post-translational modification found in all eukaryotic systems. It involves the addition of a methyl group to the guanidino nitrogen atoms of arginine residues within proteins, and this process is catalyzed by a family of enzymes called protein arginine methyltransferases (PRMTs). In mammals, there exist nine PRMTs (PRMT1–9) that catalyze three distinct types of arginine methylation: monomethylarginine, asymmetric dimethylarginine, and symmetric dimethylarginine. These modifications play critical roles in numerous fundamental cellular processes, including transcription, RNA metabolism, genome maintenance, and signaling transduction. Aberrations in protein arginine methylation have been implicated in various human diseases, such as neurodevelopmental disorders and cancer. This review offers a general overview of arginine methylation, covering its deposition, its impact on protein function, and the diverse regulatory mechanisms involved. We specifically focus on an in-depth view of the role of arginine methylation in transcription and the epigenetic regulation of gene expression. Readers are directed towards additional reviews that encompass other aspects of arginine methylation biology.","PeriodicalId":484006,"journal":{"name":"Frontiers in Epigenetics and Epigenomics","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136144120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0