Proximity ligation-based sequencing for the identification of human papillomavirus genomic integration sites in formalin-fixed paraffin embedded oropharyngeal squamous cell carcinomas.

Autor: Demers I; Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands., Balaji H; Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany.; Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany., Feitsma H; Cergentis B.V., Utrecht, The Netherlands., Stelloo E; Cergentis B.V., Utrecht, The Netherlands., Swennenhuis J; Cergentis B.V., Utrecht, The Netherlands., Sergeeva I; Cergentis B.V., Utrecht, The Netherlands., Wuerdemann N; Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany., van den Hout MFCM; Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands., Wagner S; Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Giessen, Giessen, Germany., Kremer B; Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., Klussmann JP; Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany.; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany., Huebbers CU; Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany.; Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany., Speel EM; Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands.; Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands.
Jazyk: angličtina
Zdroj: Journal of medical virology [J Med Virol] 2024 Aug; Vol. 96 (8), pp. e29837.
DOI: 10.1002/jmv.29837
Abstrakt: Human papillomavirus (HPV) infections are an increasing cause of oropharyngeal squamous cell carcinomas (OPSCC). Integration of the viral genome into the host genome is suggested to affect carcinogenesis, however, the correlation with OPSCC patient prognosis is still unclear. Research on HPV integration is hampered by current integration detection technologies and their unsuitability for formalin-fixed paraffin-embedded (FFPE) tissues. This study aims to develop and validate a novel targeted proximity-ligation based sequencing method (targeted locus amplification/capture [TLA/TLC]) for HPV integration detection in cell lines and FFPE OPSCCs. For the identification of HPV integrations, TLA/TLC was applied to 7 cell lines and 27 FFPE OPSCCs. Following preprocessing steps, a polymerase chain reaction (PCR)-based HPV enrichment was performed on the cell lines and a capture-based HPV enrichment was performed on the FFPE tissues before paired-end sequencing. TLA was able to sequence up to hundreds of kb around the target, detecting exact HPV integration loci, structural variants, and chromosomal rearrangements. In all cell lines, one or more integration sites were identified, in accordance with detection of integrated papillomavirus sequences PCR data and the literature. TLC detected integrated HPV in 15/27 FFPE OPSCCs and identified simple and complex integration patterns. In general, TLA/TLC confirmed PCR data and detected additional integration sites. In conclusion TLA/TLC reliably and robustly detects HPV integration in cell lines and FFPE OPSCCs, enabling large, population-based studies on the clinical relevance of HPV integration. Furthermore, this approach might be valuable for clonality assessment of HPV-related tumors in clinical diagnostics.
(© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)
Databáze: MEDLINE
Externí odkaz: