Novel high-resolution targeted sequencing of the cervicovaginal microbiome

BMC Biology

Mengjie Qiu¹  Bernard Pater¹  Thomas H. A. Ederveen¹  Martijn A. Huynen¹  Bas E. Dutilh²  Duaa Elmelik³  Menno Rasing³  William P. J. Leenders⁴  Willem J. G. Melchers⁵  Bram Spruijtenburg⁵  Karolina M. Andralojc⁶  Mariano A. Molina⁷  Ruud L. M. Bekkers⁸  Diede Loopik⁹  Albert G. Siebers^1,10 

[1]Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525, Nijmegen, GA, The Netherlands

[2]Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525, Nijmegen, GA, The Netherlands

[3]Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands

[4]Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525, Nijmegen, GA, The Netherlands

[5]Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525, Nijmegen, GA, The Netherlands

[6]Predica Diagnostics, Toernooiveld 1, 6525, Nijmegen, GA, The Netherlands

[7]Department of Medical Microbiology, Radboud University Medical Center, 6500, Nijmegen, HB, The Netherlands

[8]Department of Medical Microbiology, Radboud University Medical Center, 6500, Nijmegen, HB, The Netherlands

[9]Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525, Nijmegen, GA, The Netherlands

[10]Department of Medical Microbiology, Radboud University Medical Center, 6500, Nijmegen, HB, The Netherlands

[11]Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands

[12]Department of Obstetrics and Gynecology, Catharina Hospital, 5602, Eindhoven, ZA, The Netherlands

[13]GROW, School for Oncology & Developmental Biology, Maastricht University Medical Centre, 6200, Maastricht, MD, The Netherlands

[14]Department of Obstetrics and Gynecology, Radboud University Medical Center, 6500, Nijmegen, HB, The Netherlands

[15]Department of Pathology, Radboud University Medical Center, 6500, Nijmegen, HB, The Netherlands

关键词: Cervicovaginal microbiome;    hrHPV;    Targeted sequencing;    smMIP;    CiRNAseq;    CST;    CIN;   

DOI  :  10.1186/s12915-021-01204-z

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsCiRNAseq 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.

【 授权许可】

CC BY