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. 2023 Apr 2:16:25168657231160985.
doi: 10.1177/25168657231160985. eCollection 2023.

Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study

Roberto Cherchi  1 , Roberto Cusano  2 , Sandro Orrù  3   4 , Paolo A Ferrari  1 , Matteo Massidda  2 , Giorgio Fotia  2 , Sara De Matteis  4 , Pierluigi Cocco  5
Affiliations

Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study

Roberto Cherchi et al. Epigenet Insights. .

Abstract

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.

Keywords: biomarkers; exhaled breath condensate; miRNA; next generation sequencing.

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Conflict of interest statement

The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Figures

Figure 1.
Figure 1.
Frequency distribution of the miRNA counts in the EBC and the plasma (white: undetected; increasing shade of grey from the left: below the median; third quartile; fourth quartile; above the 90th percentile) of the 6 participants: A EBC, MiSeq® platform; B plasma, MiSeq® platform; C EBC, HiSeq3000® platform; D plasma, HiSeq platform®.
Figure 2.
Figure 2.
Bland-Altman plots of agreement between miRNA counts in the EBC and plasma using the MiSeq® (a) and the HiSeq3000® (b) platforms. In the y axis is the difference between the log plasma count and the log EBC count; in the x axis is the mean between the log plasma count and the log EBC count; the thick line represents the average difference between the 2 instruments; the upper and lower dashed lines represent the 95% confidence interval of such difference; the thin 0 line is the line of perfect agreement.
See this image and copyright information in PMC

References

    1. Pal M, Muinao T, Boruah HPD, Mahindroo N. Current advances in prognostic and diagnostic biomarkers for solid cancers: detection techniques and future challenges. Biomed Pharmacother. 2022;146:112488. - PubMed
    1. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75:843-854. - PubMed
    1. Apostoli P, Boffetta P, Bovenzi M, et al.. Position paper on asbestos of the Italian society of occupational medicine. Med Lav. 2019;110:459-485. - PMC - PubMed
    1. Aberle DR, Adams AM, Berg CD, et al.. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med. 2011;365:395-409. - PMC - PubMed
    1. Singh DK, Bose S, Kumar S. Role of microRNA in regulating cell signaling pathways, cell cycle, and apoptosis in non-small cell lung cancer. Curr Mol Med. 2016;16:474-486. - PubMed