Analysis of sex-specific DNA methylation differences in saliva by multiplex SNaPshot assay

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-05-26 DOI:10.1016/j.genrep.2025.102268

Priyanka Govender , Meenu Ghai , Farzeen Kader , Moses Okpeku , Marvellous Zhou

{"title":"Analysis of sex-specific DNA methylation differences in saliva by multiplex SNaPshot assay","authors":"Priyanka Govender , Meenu Ghai , Farzeen Kader , Moses Okpeku , Marvellous Zhou","doi":"10.1016/j.genrep.2025.102268","DOIUrl":null,"url":null,"abstract":"<div><div>DNA methylation (DNAm) analysis is emerging as a sensitive method for studying sex-specific differences in humans. Methylation SNaPshot (mSNaPshot) is a robust technique which allows rapid quantification of site-specific DNAm levels and can multiplex several markers in a single reaction. Sex-specific DNAm differences have been observed in blood, placental and brain tissue, but it is not well studied in saliva and African populations. Therefore, this study was undertaken to multiplex three saliva-specific CpG sites in a mSNaPshot assay to analyze sex-specific differences in DNAm patterns of 100 healthy Sub-Saharan Africans. Three saliva-specific CpG sites located in genes, <em>FAM43A</em> (cg09652652-55d), <em>BCA</em>S<em>4</em> (Chr20: 4844305) and <em>FNDC1</em> (cg09107912) were selected for the multiplex assay. These markers were referred to as SAL-1 (<em>FAM43A</em>), SAL-2 (<em>BCAS4</em>) and SAL-3 (<em>FNDC1</em>). SAL-1 and SAL-3 displayed hypermethylation and hypomethylation, respectively in saliva. However, SAL-2 showed an unmethylation signal. Overall, males displayed higher average methylation (50.07 %) than females (42.39 %) for all three markers. Significant sex-specific DNAm differences were observed for SAL-1 and SAL-3 (<em>p</em> < 0.0001). Age did not affect DNAm at the three target sites. Our results indicated that sex-specific DNAm differences exist in body fluids, and SAL-1 and SAL-3 could assist in sex identification of a saliva sample by mSNaPshot assay. DNAm varies in different populations; hence, future studies should target diverse populations from different geographical locations to ascertain the specificity of the findings. We also highlight that sex-specific differential methylation holds great potential for identifying sex-specific biomarkers, improving diagnostics, early disease detection and monitoring, and development of target therapeutics.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102268"},"PeriodicalIF":0.9000,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Gene Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2452014425001414","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

Abstract

DNA methylation (DNAm) analysis is emerging as a sensitive method for studying sex-specific differences in humans. Methylation SNaPshot (mSNaPshot) is a robust technique which allows rapid quantification of site-specific DNAm levels and can multiplex several markers in a single reaction. Sex-specific DNAm differences have been observed in blood, placental and brain tissue, but it is not well studied in saliva and African populations. Therefore, this study was undertaken to multiplex three saliva-specific CpG sites in a mSNaPshot assay to analyze sex-specific differences in DNAm patterns of 100 healthy Sub-Saharan Africans. Three saliva-specific CpG sites located in genes, FAM43A (cg09652652-55d), BCAS4 (Chr20: 4844305) and FNDC1 (cg09107912) were selected for the multiplex assay. These markers were referred to as SAL-1 (FAM43A), SAL-2 (BCAS4) and SAL-3 (FNDC1). SAL-1 and SAL-3 displayed hypermethylation and hypomethylation, respectively in saliva. However, SAL-2 showed an unmethylation signal. Overall, males displayed higher average methylation (50.07 %) than females (42.39 %) for all three markers. Significant sex-specific DNAm differences were observed for SAL-1 and SAL-3 (p < 0.0001). Age did not affect DNAm at the three target sites. Our results indicated that sex-specific DNAm differences exist in body fluids, and SAL-1 and SAL-3 could assist in sex identification of a saliva sample by mSNaPshot assay. DNAm varies in different populations; hence, future studies should target diverse populations from different geographical locations to ascertain the specificity of the findings. We also highlight that sex-specific differential methylation holds great potential for identifying sex-specific biomarkers, improving diagnostics, early disease detection and monitoring, and development of target therapeutics.

查看原文本刊更多论文

多重SNaPshot法分析唾液中性别特异性DNA甲基化差异

DNA甲基化（DNAm）分析正在成为研究人类性别特异性差异的一种敏感方法。甲基化快照（mSNaPshot）是一种强大的技术，可以快速定量位点特异性DNAm水平，并且可以在单个反应中多重使用多个标记。在血液、胎盘和脑组织中已观察到性别特异性dna差异，但在唾液和非洲人群中尚未得到很好的研究。因此，本研究在mSNaPshot检测中对三个唾液特异性CpG位点进行多重定位，以分析100名健康的撒哈拉以南非洲人dna模式的性别特异性差异。三个唾液特异性CpG位点位于FAM43A (cg09652652-55d), BCAS4 （Chr20: 4844305）和FNDC1 （cg09107912）基因中进行多重检测。这些标记物被称为SAL-1 （FAM43A）、SAL-2 （BCAS4）和SAL-3 （FNDC1）。唾液中SAL-1和SAL-3分别表现出高甲基化和低甲基化。然而，SAL-2显示出非甲基化信号。总体而言，男性在所有三个标记上的平均甲基化率（50.07%）高于女性（42.39%）。sal1和sal3的DNAm存在显著的性别差异(p <；0.0001)。年龄对三个靶点的dna没有影响。我们的研究结果表明，体液中存在性别特异性的dna差异，并且通过mSNaPshot检测，SAL-1和SAL-3可以帮助唾液样本的性别鉴定。脱氧核糖核酸在不同人群中有所不同；因此，未来的研究应该针对不同地理位置的不同人群，以确定研究结果的特异性。我们还强调，性别特异性差异甲基化在识别性别特异性生物标志物、改善诊断、早期疾病检测和监测以及开发靶向治疗方面具有巨大潜力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.