The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy

Abstract Background Viral infections are prevalent in human cancers and they have great diagnostic and theranostic values in clinical practice. Recently, their potential of shaping the tumor immune microenvironment (TIME) has been related to the immunotherapy of human cancers. However, the landscape...

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Autores principales:	Siyuan Chen, Hongyan Lai, Jingjing Zhao, Bing Chen, Yan Li, Yuchen Li, Qin Li, Qiupeng Zheng, Shenglin Huang, Xiaodong Zhu
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Viral infections Tumor immune microenvironment (TIME) Immunotherapy Machine learning pan-cancer analysis Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
Acceso en línea:	https://doaj.org/article/d86aa981a6a34c0ab70c878dcbc2150d
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spelling	oai:doaj.org-article:d86aa981a6a34c0ab70c878dcbc2150d2021-11-08T11:02:13ZThe viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy10.1186/s12885-021-08871-91471-2407https://doaj.org/article/d86aa981a6a34c0ab70c878dcbc2150d2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12885-021-08871-9https://doaj.org/toc/1471-2407Abstract Background Viral infections are prevalent in human cancers and they have great diagnostic and theranostic values in clinical practice. Recently, their potential of shaping the tumor immune microenvironment (TIME) has been related to the immunotherapy of human cancers. However, the landscape of viral expressions and immune status in human cancers remains incompletely understood. Methods We developed a next-generation sequencing (NGS)-based pipeline to detect viral sequences from the whole transcriptome and used machine learning algorithms to classify different TIME subtypes. Results We revealed a pan-cancer landscape of viral expressions in human cancers where 9 types of viruses were detected in 744 tumors of 25 cancer types. Viral infections showed different tissue tendencies and expression levels. Multi-omics analyses further revealed their distinct impacts on genomic, transcriptomic and immune responses. Epstein-Barr virus (EBV)-infected stomach adenocarcinoma (STAD) and Human Papillomavirus (HPV)-infected head and neck squamous cell carcinoma (HNSC) showed decreased genomic variations, significantly altered gene expressions, and effectively triggered anti-viral immune responses. We identified three TIME subtypes, in which the “Immune-Stimulation” subtype might be the promising candidate for immunotherapy. EBV-infected STAD and HPV-infected HNSC showed a higher frequency of the “Immune-Stimulation” subtype. Finally, we constructed the eVIIS pipeline to simultaneously evaluate viral infection and immune status in external datasets. Conclusions Viral infections are prevalent in human cancers and have distinct influences on hosts. EBV and HPV infections combined with the TIME subtype could be promising biomarkers of immunotherapy in STAD and HNSC, respectively. The eVIIS pipeline could be a practical tool to facilitate clinical practice and relevant studies.Siyuan ChenHongyan LaiJingjing ZhaoBing ChenYan LiYuchen LiQin LiQiupeng ZhengShenglin HuangXiaodong ZhuBMCarticleViral infectionsTumor immune microenvironment (TIME)ImmunotherapyMachine learningpan-cancer analysisNeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENBMC Cancer, Vol 21, Iss 1, Pp 1-22 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Viral infections Tumor immune microenvironment (TIME) Immunotherapy Machine learning pan-cancer analysis Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
spellingShingle	Viral infections Tumor immune microenvironment (TIME) Immunotherapy Machine learning pan-cancer analysis Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Siyuan Chen Hongyan Lai Jingjing Zhao Bing Chen Yan Li Yuchen Li Qin Li Qiupeng Zheng Shenglin Huang Xiaodong Zhu The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
description	Abstract Background Viral infections are prevalent in human cancers and they have great diagnostic and theranostic values in clinical practice. Recently, their potential of shaping the tumor immune microenvironment (TIME) has been related to the immunotherapy of human cancers. However, the landscape of viral expressions and immune status in human cancers remains incompletely understood. Methods We developed a next-generation sequencing (NGS)-based pipeline to detect viral sequences from the whole transcriptome and used machine learning algorithms to classify different TIME subtypes. Results We revealed a pan-cancer landscape of viral expressions in human cancers where 9 types of viruses were detected in 744 tumors of 25 cancer types. Viral infections showed different tissue tendencies and expression levels. Multi-omics analyses further revealed their distinct impacts on genomic, transcriptomic and immune responses. Epstein-Barr virus (EBV)-infected stomach adenocarcinoma (STAD) and Human Papillomavirus (HPV)-infected head and neck squamous cell carcinoma (HNSC) showed decreased genomic variations, significantly altered gene expressions, and effectively triggered anti-viral immune responses. We identified three TIME subtypes, in which the “Immune-Stimulation” subtype might be the promising candidate for immunotherapy. EBV-infected STAD and HPV-infected HNSC showed a higher frequency of the “Immune-Stimulation” subtype. Finally, we constructed the eVIIS pipeline to simultaneously evaluate viral infection and immune status in external datasets. Conclusions Viral infections are prevalent in human cancers and have distinct influences on hosts. EBV and HPV infections combined with the TIME subtype could be promising biomarkers of immunotherapy in STAD and HNSC, respectively. The eVIIS pipeline could be a practical tool to facilitate clinical practice and relevant studies.
format	article
author	Siyuan Chen Hongyan Lai Jingjing Zhao Bing Chen Yan Li Yuchen Li Qin Li Qiupeng Zheng Shenglin Huang Xiaodong Zhu
author_facet	Siyuan Chen Hongyan Lai Jingjing Zhao Bing Chen Yan Li Yuchen Li Qin Li Qiupeng Zheng Shenglin Huang Xiaodong Zhu
author_sort	Siyuan Chen
title	The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
title_short	The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
title_full	The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
title_fullStr	The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
title_full_unstemmed	The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
title_sort	viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy
publisher	BMC
publishDate	2021
url	https://doaj.org/article/d86aa981a6a34c0ab70c878dcbc2150d
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The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy

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