Roberto Cherchi, Roberto Cusano, Sandro Orrù, Paolo A Ferrari, Matteo Massidda, Giorgio Fotia, Sara De Matteis, Pierluigi Cocco
{"title":"呼气凝析液中miRNA检测的新一代测序:一项初步研究。","authors":"Roberto Cherchi, Roberto Cusano, Sandro Orrù, Paolo A Ferrari, Matteo Massidda, Giorgio Fotia, Sara De Matteis, Pierluigi Cocco","doi":"10.1177/25168657231160985","DOIUrl":null,"url":null,"abstract":"<p><strong>Introduction: </strong>Exhaled breath condensate (EBC) sampling has been suggested as a less-invasive and cost-effective method to detect biological macromolecules, including miRNA. To explore the feasibility of its use as a biomarker of early effects of asbestos exposure, we conducted a preliminary test on male volunteers by comparing the miRNA profile in the EBC and the plasma using 2 different sequencing platforms.</p><p><strong>Methods: </strong>Six male volunteers, all retired and unexposed to dust or fumes, participated in the test. RNA was extracted from 200 μL EBC samples and same-size plasma samples. Sample aliquots were processed in 2 laboratories using 2 different sequencing platforms: a MiSeq Illumina<sup>®</sup> platform and a more performing HiSeq Illumina<sup>®</sup> platform.</p><p><strong>Results: </strong>The HiSeq3000<sup>®</sup> sequencing platform identified twice as many unique molecular indexes (UMI)-validated miRNA as the MiSeq<sup>®</sup> platform. The Spearman's correlation coefficient between EBC counts and plasma counts was significant in 5/6 subjects with either platform (MiSeq<sup>®</sup> = 0.128-0.508, <i>P</i> = .026-<.001; HiSeq<sup>®</sup> = 0.156-0.412, <i>P</i> = .001-<.001). The intraclass correlation coefficient confirmed the consistency of the miRNA profile over the 6 participants with both biospecimens. Exploring the agreement between the EBC and plasma samples with Bland-Altman plots showed that using the HiSeq3000<sup>®</sup> platform substantially improved the EBC miRNA detection rate.</p><p><strong>Conclusion: </strong>Our preliminary study confirms that, when using the HiSeq<sup>®</sup> sequencing platform, EBC sampling is a suitable, non-invasive method to detect the miRNA profile in healthy subjects.</p>","PeriodicalId":41996,"journal":{"name":"Epigenetics Insights","volume":null,"pages":null},"PeriodicalIF":3.2000,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9d/23/10.1177_25168657231160985.PMC10070752.pdf","citationCount":"0","resultStr":"{\"title\":\"Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study.\",\"authors\":\"Roberto Cherchi, Roberto Cusano, Sandro Orrù, Paolo A Ferrari, Matteo Massidda, Giorgio Fotia, Sara De Matteis, Pierluigi Cocco\",\"doi\":\"10.1177/25168657231160985\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Introduction: </strong>Exhaled breath condensate (EBC) sampling has been suggested as a less-invasive and cost-effective method to detect biological macromolecules, including miRNA. To explore the feasibility of its use as a biomarker of early effects of asbestos exposure, we conducted a preliminary test on male volunteers by comparing the miRNA profile in the EBC and the plasma using 2 different sequencing platforms.</p><p><strong>Methods: </strong>Six male volunteers, all retired and unexposed to dust or fumes, participated in the test. RNA was extracted from 200 μL EBC samples and same-size plasma samples. Sample aliquots were processed in 2 laboratories using 2 different sequencing platforms: a MiSeq Illumina<sup>®</sup> platform and a more performing HiSeq Illumina<sup>®</sup> platform.</p><p><strong>Results: </strong>The HiSeq3000<sup>®</sup> sequencing platform identified twice as many unique molecular indexes (UMI)-validated miRNA as the MiSeq<sup>®</sup> platform. The Spearman's correlation coefficient between EBC counts and plasma counts was significant in 5/6 subjects with either platform (MiSeq<sup>®</sup> = 0.128-0.508, <i>P</i> = .026-<.001; HiSeq<sup>®</sup> = 0.156-0.412, <i>P</i> = .001-<.001). The intraclass correlation coefficient confirmed the consistency of the miRNA profile over the 6 participants with both biospecimens. Exploring the agreement between the EBC and plasma samples with Bland-Altman plots showed that using the HiSeq3000<sup>®</sup> platform substantially improved the EBC miRNA detection rate.</p><p><strong>Conclusion: </strong>Our preliminary study confirms that, when using the HiSeq<sup>®</sup> sequencing platform, EBC sampling is a suitable, non-invasive method to detect the miRNA profile in healthy subjects.</p>\",\"PeriodicalId\":41996,\"journal\":{\"name\":\"Epigenetics Insights\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.2000,\"publicationDate\":\"2023-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9d/23/10.1177_25168657231160985.PMC10070752.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Epigenetics Insights\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1177/25168657231160985\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Epigenetics Insights","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1177/25168657231160985","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study.
Introduction: Exhaled breath condensate (EBC) sampling has been suggested as a less-invasive and cost-effective method to detect biological macromolecules, including miRNA. To explore the feasibility of its use as a biomarker of early effects of asbestos exposure, we conducted a preliminary test on male volunteers by comparing the miRNA profile in the EBC and the plasma using 2 different sequencing platforms.
Methods: Six male volunteers, all retired and unexposed to dust or fumes, participated in the test. RNA was extracted from 200 μL EBC samples and same-size plasma samples. Sample aliquots were processed in 2 laboratories using 2 different sequencing platforms: a MiSeq Illumina® platform and a more performing HiSeq Illumina® platform.
Results: The HiSeq3000® sequencing platform identified twice as many unique molecular indexes (UMI)-validated miRNA as the MiSeq® platform. The Spearman's correlation coefficient between EBC counts and plasma counts was significant in 5/6 subjects with either platform (MiSeq® = 0.128-0.508, P = .026-<.001; HiSeq® = 0.156-0.412, P = .001-<.001). The intraclass correlation coefficient confirmed the consistency of the miRNA profile over the 6 participants with both biospecimens. Exploring the agreement between the EBC and plasma samples with Bland-Altman plots showed that using the HiSeq3000® platform substantially improved the EBC miRNA detection rate.
Conclusion: Our preliminary study confirms that, when using the HiSeq® sequencing platform, EBC sampling is a suitable, non-invasive method to detect the miRNA profile in healthy subjects.