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Novel high-resolution targeted sequencing of the cervicovaginal microbiome
BACKGROUND: The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) i...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8680041/ https://www.ncbi.nlm.nih.gov/pubmed/34915863 http://dx.doi.org/10.1186/s12915-021-01204-z |
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author | Andralojc, Karolina M. Molina, Mariano A. Qiu, Mengjie Spruijtenburg, Bram Rasing, Menno Pater, Bernard Huynen, Martijn A. Dutilh, Bas E. Ederveen, Thomas H. A. Elmelik, Duaa Siebers, Albert G. Loopik, Diede Bekkers, Ruud L. M. Leenders, William P. J. Melchers, Willem J. G. |
author_facet | Andralojc, Karolina M. Molina, Mariano A. Qiu, Mengjie Spruijtenburg, Bram Rasing, Menno Pater, Bernard Huynen, Martijn A. Dutilh, Bas E. Ederveen, Thomas H. A. Elmelik, Duaa Siebers, Albert G. Loopik, Diede Bekkers, Ruud L. M. Leenders, William P. J. Melchers, Willem J. G. |
author_sort | Andralojc, Karolina M. |
collection | PubMed |
description | BACKGROUND: The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. RESULTS: We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes’ abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. CONCLUSIONS: CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01204-z. |
format | Online Article Text |
id | pubmed-8680041 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-86800412021-12-20 Novel high-resolution targeted sequencing of the cervicovaginal microbiome Andralojc, Karolina M. Molina, Mariano A. Qiu, Mengjie Spruijtenburg, Bram Rasing, Menno Pater, Bernard Huynen, Martijn A. Dutilh, Bas E. Ederveen, Thomas H. A. Elmelik, Duaa Siebers, Albert G. Loopik, Diede Bekkers, Ruud L. M. Leenders, William P. J. Melchers, Willem J. G. BMC Biol Research Article BACKGROUND: The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. RESULTS: We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes’ abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. CONCLUSIONS: CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01204-z. BioMed Central 2021-12-16 /pmc/articles/PMC8680041/ /pubmed/34915863 http://dx.doi.org/10.1186/s12915-021-01204-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Andralojc, Karolina M. Molina, Mariano A. Qiu, Mengjie Spruijtenburg, Bram Rasing, Menno Pater, Bernard Huynen, Martijn A. Dutilh, Bas E. Ederveen, Thomas H. A. Elmelik, Duaa Siebers, Albert G. Loopik, Diede Bekkers, Ruud L. M. Leenders, William P. J. Melchers, Willem J. G. Novel high-resolution targeted sequencing of the cervicovaginal microbiome |
title | Novel high-resolution targeted sequencing of the cervicovaginal microbiome |
title_full | Novel high-resolution targeted sequencing of the cervicovaginal microbiome |
title_fullStr | Novel high-resolution targeted sequencing of the cervicovaginal microbiome |
title_full_unstemmed | Novel high-resolution targeted sequencing of the cervicovaginal microbiome |
title_short | Novel high-resolution targeted sequencing of the cervicovaginal microbiome |
title_sort | novel high-resolution targeted sequencing of the cervicovaginal microbiome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8680041/ https://www.ncbi.nlm.nih.gov/pubmed/34915863 http://dx.doi.org/10.1186/s12915-021-01204-z |
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