Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay
Abstract Background Cervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection is a pre-requisite for the development of most precan...
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BMC
2025-05-01
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| Series: | Molecular Medicine |
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| Online Access: | https://doi.org/10.1186/s10020-025-01238-x |
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| author | Julia Faillace Thiesen Elise Jacquemet Pascal Campagne Denis Chatelain Etienne Brochot Yves-Edouard Herpe Nolwenn M. Dheilly Fabrice Bouilloux Bénédicte Rognon Alexandre Douablin Guillaume Leboucher Florent Percher Marc Eloit Philippe Pérot |
| author_facet | Julia Faillace Thiesen Elise Jacquemet Pascal Campagne Denis Chatelain Etienne Brochot Yves-Edouard Herpe Nolwenn M. Dheilly Fabrice Bouilloux Bénédicte Rognon Alexandre Douablin Guillaume Leboucher Florent Percher Marc Eloit Philippe Pérot |
| author_sort | Julia Faillace Thiesen |
| collection | DOAJ |
| description | Abstract Background Cervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection is a pre-requisite for the development of most precancerous lesions, the mere detection of viral nucleic acids, also present in transient infections, is not specific of the underlying cellular state, resulting in poor positive predictive values (PPV) regarding lesional states. There is a need to increase the specificity of molecular tests for better stratifying individuals at risk of cancer and to adapt follow-up strategies. Methods HPV-RNA-SEQ, a targeted RNA next generation sequencing assay allowing the detection of up to 16 hrHPV splice events and key human transcripts, has previously shown encouraging PPV for the detection of precancerous lesions. Herein, on 302 patients with normal cytology (NILM, n = 118), low-grade (LSIL, n = 104) or high-grade squamous intraepithelial lesions (HSIL, n = 80), machine learning-based model improvement was applied to reach 2-classes (NILM vs HSIL) or 3-classes (NILM, LSIL, HSIL) predictive models. Results Linear (elastic net) and nonlinear (random forest) approaches resulted in five 2-class models that detect HSIL vs NILM in a validation set with specificity up to 0.87, well within the range of PPV of other competing RNA-based tests in a screening population. Conclusions HPV-RNA-SEQ improves the detection of HSIL lesions and has the potential to complete and eventually replace current molecular approaches as a first-line test. Further performance evaluation remains to be done on larger and prospective cohorts. |
| format | Article |
| id | doaj-art-ce100239c9684096b7c283130d3b9ca6 |
| institution | OA Journals |
| issn | 1528-3658 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
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| series | Molecular Medicine |
| spelling | doaj-art-ce100239c9684096b7c283130d3b9ca62025-08-20T02:00:03ZengBMCMolecular Medicine1528-36582025-05-0131111610.1186/s10020-025-01238-xMolecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assayJulia Faillace Thiesen0Elise Jacquemet1Pascal Campagne2Denis Chatelain3Etienne Brochot4Yves-Edouard Herpe5Nolwenn M. Dheilly6Fabrice Bouilloux7Bénédicte Rognon8Alexandre Douablin9Guillaume Leboucher10Florent Percher11Marc Eloit12Philippe Pérot13Institut Pasteur, Université Paris Cité, Pathogen Discovery LaboratoryInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubAmiens Picardie University Hospital, Service d’anatomie Et Cytologie PathologiquesAmiens Picardie University Hospital, Research Department, Biobanque de Picardie (BRIF N BB-0033-00017)Amiens Picardie University Hospital, Research Department, Biobanque de Picardie (BRIF N BB-0033-00017)Institut Pasteur, Université Paris Cité, Pathogen Discovery LaboratoryBiomnigene SABiomnigene SABiomnigene SALabtooLabtooInstitut Pasteur, Université Paris Cité, Pathogen Discovery LaboratoryInstitut Pasteur, Université Paris Cité, Pathogen Discovery LaboratoryAbstract Background Cervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection is a pre-requisite for the development of most precancerous lesions, the mere detection of viral nucleic acids, also present in transient infections, is not specific of the underlying cellular state, resulting in poor positive predictive values (PPV) regarding lesional states. There is a need to increase the specificity of molecular tests for better stratifying individuals at risk of cancer and to adapt follow-up strategies. Methods HPV-RNA-SEQ, a targeted RNA next generation sequencing assay allowing the detection of up to 16 hrHPV splice events and key human transcripts, has previously shown encouraging PPV for the detection of precancerous lesions. Herein, on 302 patients with normal cytology (NILM, n = 118), low-grade (LSIL, n = 104) or high-grade squamous intraepithelial lesions (HSIL, n = 80), machine learning-based model improvement was applied to reach 2-classes (NILM vs HSIL) or 3-classes (NILM, LSIL, HSIL) predictive models. Results Linear (elastic net) and nonlinear (random forest) approaches resulted in five 2-class models that detect HSIL vs NILM in a validation set with specificity up to 0.87, well within the range of PPV of other competing RNA-based tests in a screening population. Conclusions HPV-RNA-SEQ improves the detection of HSIL lesions and has the potential to complete and eventually replace current molecular approaches as a first-line test. Further performance evaluation remains to be done on larger and prospective cohorts.https://doi.org/10.1186/s10020-025-01238-xHuman Papillomavirus (HPV)Molecular testScreeningPrecancerous lesionsTranscriptomeNext-Generation Sequencing (NGS) |
| spellingShingle | Julia Faillace Thiesen Elise Jacquemet Pascal Campagne Denis Chatelain Etienne Brochot Yves-Edouard Herpe Nolwenn M. Dheilly Fabrice Bouilloux Bénédicte Rognon Alexandre Douablin Guillaume Leboucher Florent Percher Marc Eloit Philippe Pérot Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay Molecular Medicine Human Papillomavirus (HPV) Molecular test Screening Precancerous lesions Transcriptome Next-Generation Sequencing (NGS) |
| title | Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay |
| title_full | Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay |
| title_fullStr | Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay |
| title_full_unstemmed | Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay |
| title_short | Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay |
| title_sort | molecular detection of hrhpv induced high grade squamous intraepithelial lesions of the cervix through a targeted rna next generation sequencing assay |
| topic | Human Papillomavirus (HPV) Molecular test Screening Precancerous lesions Transcriptome Next-Generation Sequencing (NGS) |
| url | https://doi.org/10.1186/s10020-025-01238-x |
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