Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling
Summary: The role of oncoviral genotype and co-infection driving oncogenesis remains unclear. We have developed a scalable, high throughput tool for sensitive and precise oncoviral genotype deconvolution. Using tumor RNA sequencing data, we applied it to 537 virally infected liver, cervical, and hea...
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doaj-fe79134d736e460da35b53867cbd18862021-04-26T05:58:03ZengElsevieriScience2589-00422021-04-01244102368Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profilingAdrian Bubie0Fabien Zoulim1Barbara Testoni2Brett Miles3Marshall Posner4Augusto Villanueva5Bojan Losic6Departments of Genetics and Genomic Sciences, New York, NY 10029, USAINSERM, U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, FranceINSERM, U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, FranceDepartment of Otolaryngology Head and Neck Surgery, New York, NY 10029, USADivision of Hematology Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USADepartments of Genetics and Genomic Sciences, New York, NY 10029, USA; Division of Liver Diseases, Division of Hematology/Oncology, Department of Medicine, Graduate School of Biomedical Sciences, Tisch Cancer Institute, Diabetes, Obesity, and Metabolism Institute, New York, NY 10029, USADepartments of Genetics and Genomic Sciences, New York, NY 10029, USA; Division of Liver Diseases, Division of Hematology/Oncology, Department of Medicine, Graduate School of Biomedical Sciences, Tisch Cancer Institute, Diabetes, Obesity, and Metabolism Institute, New York, NY 10029, USA; Corresponding authorSummary: The role of oncoviral genotype and co-infection driving oncogenesis remains unclear. We have developed a scalable, high throughput tool for sensitive and precise oncoviral genotype deconvolution. Using tumor RNA sequencing data, we applied it to 537 virally infected liver, cervical, and head and neck tumors, providing the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor oncoviral genotype. We find that HBV and HPV genotype and co-infection serve as significant predictors of patient survival and immune activation. Finally, we demonstrate that HPV genotype is more associated with viral oncogene expression than cancer type, implying that expression may be similar across episomal and stochastic integration-based infections. While oncoviral infections are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections.http://www.sciencedirect.com/science/article/pii/S2589004221003369GenomicsVirologyCancer |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Adrian Bubie Fabien Zoulim Barbara Testoni Brett Miles Marshall Posner Augusto Villanueva Bojan Losic |
spellingShingle |
Adrian Bubie Fabien Zoulim Barbara Testoni Brett Miles Marshall Posner Augusto Villanueva Bojan Losic Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling iScience Genomics Virology Cancer |
author_facet |
Adrian Bubie Fabien Zoulim Barbara Testoni Brett Miles Marshall Posner Augusto Villanueva Bojan Losic |
author_sort |
Adrian Bubie |
title |
Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling |
title_short |
Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling |
title_full |
Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling |
title_fullStr |
Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling |
title_full_unstemmed |
Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling |
title_sort |
landscape of oncoviral genotype and co-infection via human papilloma and hepatitis b viral tumor in situ profiling |
publisher |
Elsevier |
series |
iScience |
issn |
2589-0042 |
publishDate |
2021-04-01 |
description |
Summary: The role of oncoviral genotype and co-infection driving oncogenesis remains unclear. We have developed a scalable, high throughput tool for sensitive and precise oncoviral genotype deconvolution. Using tumor RNA sequencing data, we applied it to 537 virally infected liver, cervical, and head and neck tumors, providing the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor oncoviral genotype. We find that HBV and HPV genotype and co-infection serve as significant predictors of patient survival and immune activation. Finally, we demonstrate that HPV genotype is more associated with viral oncogene expression than cancer type, implying that expression may be similar across episomal and stochastic integration-based infections. While oncoviral infections are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections. |
topic |
Genomics Virology Cancer |
url |
http://www.sciencedirect.com/science/article/pii/S2589004221003369 |
work_keys_str_mv |
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