Epigenome signature as an immunophenotype indicator prompts durable clinical immunotherapy benefits in lung adenocarcinoma

Abstract

Abstract Intertumoral immune heterogeneity is a critical reason for distinct clinical benefits of immunotherapy in lung adenocarcinoma (LUAD). Tumor immunophenotype (immune ‘Hot’ or ‘Cold’) suggests immunological individual differences and potential clinical treatment guidelines. However, employing epigenome signatures to determine tumor immunophenotypes and responsive treatment is not well understood. To delineate the tumor immunophenotype and immune heterogeneity, we first distinguished the immune ‘Hot’ and ‘Cold’ tumors of LUAD based on five immune expression signatures. In terms of clinical presentation, the immune ‘Hot’ tumors usually had higher immunoactivity, lower disease stages and better survival outcomes than ‘Cold’ tumors. At the epigenome levels, we observed that distinct DNA methylation patterns between immunophenotypes were closely associated with LUAD development. Hence, we identified a set of five CpG sites as the immunophenotype-related methylation signature (iPMS) for tumor immunophenotyping and further confirmed its efficiency based on a machine learning framework. Furthermore, we found iPMS and immunophenotype-related immune checkpoints (IPCPs) could contribute to the risk of tumor progression, implying IPCP has the potential to be a novel immunotherapy blockade target. After further parsing of the role of iPMS-predicted immunophenotypes, we found immune ‘Hot’ was a protective factor leading to better survival outcomes when patients received the anti-PD-1/PD-L1 immunotherapy. And iPMS was also a well-performed signature (AUC = 0.752) for predicting the durable/nondurable clinical benefits. In summary, our study explored the role of epigenome signature in clinical tumor immunophenotyping. Utilizing iPMS to characterize tumor immunophenotypes will facilitate developing personalized epigenetic anticancer approaches.