{"title":"Tackling somatic DNA contamination in sperm epigenetic studies.","authors":"Anamika Kumari, Rajender Singh","doi":"10.3389/frph.2025.1506117","DOIUrl":null,"url":null,"abstract":"<p><strong>Introduction: </strong>Recent interest in sperm epigenetics has stemmed from its implication in sperm DNA quality, sperm fertility, environmental toxicity, and transgenerational inheritance. Sperm epigenetic data may be significantly affected by somatic DNA contamination, resulting in misleading conclusions. However, detecting and dealing with somatic DNA contamination in semen samples can be a challenging task.</p><p><strong>Methods: </strong>In the present study, we worked out a detailed and robust plan to deal with somatic cell DNA contamination in sperm epigenetic studies in order to draw error-free scientific conclusions. Apart from incorporating simple quality checks, such as microscopic examination and somatic cell lysis buffer (SCLB) treatment, we compared the Infinium Human Methylation 450K BeadChip data for sperm and blood samples to identify the CpG sites that were highly methylated in blood samples in comparison to sperm, but were unrelated to infertility.</p><p><strong>Results and discussion: </strong>The comparison of Infinium Human Methylation 450K BeadChip data for sperm and blood samples identified 9564 CpG sites that can be used as markers for analyzing somatic DNA contamination. We have put together a comprehensive plan including evaluation under a microscope, SCLB treatment, inclusion of CpG biomarkers for sample quality evaluation, and applying a 15% cut off at the time of data analysis to completely eliminate the influence of somatic DNA contamination in sperm epigenetic studies. We conclude that if this comprehensive plan is followed, the influence of somatic DNA contamination in sperm epigenetic studies can be completely eliminated.</p>","PeriodicalId":73103,"journal":{"name":"Frontiers in reproductive health","volume":"7 ","pages":"1506117"},"PeriodicalIF":2.3000,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835817/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in reproductive health","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3389/frph.2025.1506117","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH","Score":null,"Total":0}
引用次数: 0
Abstract
Introduction: Recent interest in sperm epigenetics has stemmed from its implication in sperm DNA quality, sperm fertility, environmental toxicity, and transgenerational inheritance. Sperm epigenetic data may be significantly affected by somatic DNA contamination, resulting in misleading conclusions. However, detecting and dealing with somatic DNA contamination in semen samples can be a challenging task.
Methods: In the present study, we worked out a detailed and robust plan to deal with somatic cell DNA contamination in sperm epigenetic studies in order to draw error-free scientific conclusions. Apart from incorporating simple quality checks, such as microscopic examination and somatic cell lysis buffer (SCLB) treatment, we compared the Infinium Human Methylation 450K BeadChip data for sperm and blood samples to identify the CpG sites that were highly methylated in blood samples in comparison to sperm, but were unrelated to infertility.
Results and discussion: The comparison of Infinium Human Methylation 450K BeadChip data for sperm and blood samples identified 9564 CpG sites that can be used as markers for analyzing somatic DNA contamination. We have put together a comprehensive plan including evaluation under a microscope, SCLB treatment, inclusion of CpG biomarkers for sample quality evaluation, and applying a 15% cut off at the time of data analysis to completely eliminate the influence of somatic DNA contamination in sperm epigenetic studies. We conclude that if this comprehensive plan is followed, the influence of somatic DNA contamination in sperm epigenetic studies can be completely eliminated.
近年来人们对精子表观遗传学的兴趣源于精子DNA质量、精子生育能力、环境毒性和跨代遗传的影响。精子表观遗传数据可能受到体细胞DNA污染的显著影响，从而导致误导性结论。然而，检测和处理精液样本中的体细胞DNA污染可能是一项具有挑战性的任务。方法：在本研究中，我们制定了一个详细而稳健的方案来处理精子表观遗传学研究中的体细胞DNA污染，以便得出无差错的科学结论。除了结合简单的质量检查，如显微镜检查和体细胞溶解缓冲液（SCLB）处理，我们比较了精子和血液样本的Infinium Human Methylation 450K BeadChip数据，以确定血液样本中与精子相比高度甲基化的CpG位点，但与不育无关。结果与讨论：将Infinium Human Methylation 450K BeadChip数据与精子和血液样本进行比较，鉴定出9564个CpG位点，可作为分析体细胞DNA污染的标记。我们制定了一个全面的计划，包括显微镜下评价，SCLB处理，纳入CpG生物标志物进行样品质量评价，并在数据分析时采用15%的切断，以完全消除体细胞DNA污染对精子表观遗传学研究的影响。我们的结论是，如果遵循这一综合计划，可以完全消除精子表观遗传学研究中体细胞DNA污染的影响。
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