{"title":"利用纳米孔测序技术检测口腔拭子中的 DNA 甲基化,以研究发育迟缓问题。","authors":"Alim El-Hakim, Inswasti Cahyani, Muhammad Zulfikar Arief, Gilang Akbariani, Asep Muhamad Ridwanuloh, Syam Budi Iryanto, Ratih Rahayu, Daeng Deni Mardaeni, Vincentius Budhyanto, Yusnita, Wening Sari, Anggi Pn Hidayati, Intan Razari, Silviatun Nihayah, Kinasih Prayuni, Chandra Utomo, Ratih Asmana Ningrum, Susanti Susanti, Ahmad Utomo","doi":"10.1080/15592294.2024.2418717","DOIUrl":null,"url":null,"abstract":"<p><p>Stunting is the result of chronic malnutrition due to the lack of micronutrient-based methyl donors required for epigenetic programming during the first 1000 days of life. Methylation studies using bisulfite conversion from blood DNA are invasive and may not be practical for large-scale epidemiological investigation or nutrition intervention programs. Buccal epithelial methylation may reflect early germline methylation. Therefore, buccal cells can serve as convenient sample sources to collect biomarkers associated with the risk of stunting. This study aims to describe the feasibility of nanopore adaptive sampling in detecting DNA methylation from children's buccal DNA. We used adaptive sampling of Oxford Nanopore Technology on barcoded samples to describe differential methylation associated with malnutrition. Overall, the level of 5-methylcytosine (5mC) was lower in stunted children than in normal children. We also found differentially methylated regions at the MIR6724 and RNA45SN1 gene loci on chromosome 21, which was higher in stunted children than in normal children. We described and detected differential DNA methylation in the locus previously not known to be associated with stunting. Interestingly, this locus on chromosome 21 has been implicated in the stunted phenotype of Down syndrome.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2418717"},"PeriodicalIF":2.9000,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540103/pdf/","citationCount":"0","resultStr":"{\"title\":\"Detection of DNA methylation from buccal swabs using nanopore sequencing to study stunting.\",\"authors\":\"Alim El-Hakim, Inswasti Cahyani, Muhammad Zulfikar Arief, Gilang Akbariani, Asep Muhamad Ridwanuloh, Syam Budi Iryanto, Ratih Rahayu, Daeng Deni Mardaeni, Vincentius Budhyanto, Yusnita, Wening Sari, Anggi Pn Hidayati, Intan Razari, Silviatun Nihayah, Kinasih Prayuni, Chandra Utomo, Ratih Asmana Ningrum, Susanti Susanti, Ahmad Utomo\",\"doi\":\"10.1080/15592294.2024.2418717\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Stunting is the result of chronic malnutrition due to the lack of micronutrient-based methyl donors required for epigenetic programming during the first 1000 days of life. Methylation studies using bisulfite conversion from blood DNA are invasive and may not be practical for large-scale epidemiological investigation or nutrition intervention programs. Buccal epithelial methylation may reflect early germline methylation. Therefore, buccal cells can serve as convenient sample sources to collect biomarkers associated with the risk of stunting. This study aims to describe the feasibility of nanopore adaptive sampling in detecting DNA methylation from children's buccal DNA. We used adaptive sampling of Oxford Nanopore Technology on barcoded samples to describe differential methylation associated with malnutrition. Overall, the level of 5-methylcytosine (5mC) was lower in stunted children than in normal children. We also found differentially methylated regions at the MIR6724 and RNA45SN1 gene loci on chromosome 21, which was higher in stunted children than in normal children. We described and detected differential DNA methylation in the locus previously not known to be associated with stunting. Interestingly, this locus on chromosome 21 has been implicated in the stunted phenotype of Down syndrome.</p>\",\"PeriodicalId\":11767,\"journal\":{\"name\":\"Epigenetics\",\"volume\":\"19 1\",\"pages\":\"2418717\"},\"PeriodicalIF\":2.9000,\"publicationDate\":\"2024-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540103/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Epigenetics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1080/15592294.2024.2418717\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/11/3 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q3\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Epigenetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1080/15592294.2024.2418717","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/11/3 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
发育迟缓是慢性营养不良的结果,原因是在生命的最初 1000 天内缺乏表观遗传编程所需的微量元素甲基供体。利用血液 DNA 进行亚硫酸氢盐转化的甲基化研究具有侵入性,可能不适合大规模流行病学调查或营养干预计划。颊上皮甲基化可能反映了早期种系甲基化。因此,颊细胞可以作为方便的样本来源,收集与发育迟缓风险相关的生物标志物。本研究旨在描述纳米孔自适应采样检测儿童颊细胞DNA甲基化的可行性。我们利用牛津纳米孔技术对条形码样本进行自适应采样,以描述与营养不良相关的不同甲基化情况。总体而言,发育迟缓儿童的 5-甲基胞嘧啶(5mC)含量低于正常儿童。我们还在 21 号染色体上的 MIR6724 和 RNA45SN1 基因位点发现了不同的甲基化区域,发育迟缓儿童的甲基化水平高于正常儿童。我们描述并检测了以前不知道与发育迟缓有关的基因位点的不同 DNA 甲基化。有趣的是,21 号染色体上的这个基因座与唐氏综合征的发育迟缓表型有关。
Detection of DNA methylation from buccal swabs using nanopore sequencing to study stunting.
Stunting is the result of chronic malnutrition due to the lack of micronutrient-based methyl donors required for epigenetic programming during the first 1000 days of life. Methylation studies using bisulfite conversion from blood DNA are invasive and may not be practical for large-scale epidemiological investigation or nutrition intervention programs. Buccal epithelial methylation may reflect early germline methylation. Therefore, buccal cells can serve as convenient sample sources to collect biomarkers associated with the risk of stunting. This study aims to describe the feasibility of nanopore adaptive sampling in detecting DNA methylation from children's buccal DNA. We used adaptive sampling of Oxford Nanopore Technology on barcoded samples to describe differential methylation associated with malnutrition. Overall, the level of 5-methylcytosine (5mC) was lower in stunted children than in normal children. We also found differentially methylated regions at the MIR6724 and RNA45SN1 gene loci on chromosome 21, which was higher in stunted children than in normal children. We described and detected differential DNA methylation in the locus previously not known to be associated with stunting. Interestingly, this locus on chromosome 21 has been implicated in the stunted phenotype of Down syndrome.
期刊介绍:
Epigenetics publishes peer-reviewed original research and review articles that provide an unprecedented forum where epigenetic mechanisms and their role in diverse biological processes can be revealed, shared, and discussed.
Epigenetics research studies heritable changes in gene expression caused by mechanisms others than the modification of the DNA sequence. Epigenetics therefore plays critical roles in a variety of biological systems, diseases, and disciplines. Topics of interest include (but are not limited to):
DNA methylation
Nucleosome positioning and modification
Gene silencing
Imprinting
Nuclear reprogramming
Chromatin remodeling
Non-coding RNA
Non-histone chromosomal elements
Dosage compensation
Nuclear organization
Epigenetic therapy and diagnostics
Nutrition and environmental epigenetics
Cancer epigenetics
Neuroepigenetics