Protocol to identify novel immunotherapy biomarkers based on transcriptomic data in human cancers

Immune checkpoint inhibitors have transformed the management of advanced cancers, but biomarkers for the prediction of therapeutic responses have not been fully uncovered. Here, we provide a step-by-step approach for the identification of novel biomarkers from public transcriptomic datasets. We comp...

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Bibliographic Details
Published in:STAR protocols 2023-06, Vol.4 (2), p.102258, Article 102258
Main Authors: Mei, Jie, Cai, Yun, Xu, Rui, Zhu, Yichao, Zhao, Xinyuan, Zhang, Yan, Mao, Wenjun, Xu, Junying, Yin, Yongmei
Format: Article
Language:English
Subjects:
Bioinformatics
Cancer
Clinical Protocol
Gene Expression
Immunology
Protocol
RNAseq
Sequence Analysis
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Summary:Immune checkpoint inhibitors have transformed the management of advanced cancers, but biomarkers for the prediction of therapeutic responses have not been fully uncovered. Here, we provide a step-by-step approach for the identification of novel biomarkers from public transcriptomic datasets. We comprehensively summarize the available transcriptomic datasets containing immunotherapy information and describe the necessary procedures to evaluate the effectiveness of a novel immunotherapy biomarker, which may accelerate the identification of novel immunotherapy biomarkers. For complete details on the use and execution of this protocol, please refer to Mei et al.1 [Display omitted] •Detailed steps to identify novel immunotherapy biomarkers in human cancers•Step-by-step approach to select candidate biomarkers, public and in-house cohorts•Necessary parameters to evaluate the feasibility of immunotherapy biomarkers Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Immune checkpoint inhibitors have transformed the management of advanced cancers, but biomarkers for the prediction of therapeutic responses have not been fully uncovered. Here, we provide a step-by-step approach for the identification of novel biomarkers from public transcriptomic datasets. We comprehensively summarize the available transcriptomic datasets containing immunotherapy information and describe the necessary procedures to evaluate the effectiveness of a novel immunotherapy biomarker, which may accelerate the identification of novel immunotherapy biomarkers.
ISSN:2666-1667
2666-1667
DOI:10.1016/j.xpro.2023.102258