Characterization of an Enhancer RNA Signature Reveals Treatment Strategies for Improving Immunotherapy Efficacy in Cancer

Abstract Non-coding RNA transcribed from active enhancers, known as enhancer RNA (eRNA), is a critical element in gene regulation with a highly specific expression pattern in the regulatory networks of tumor-infiltrating cells. Therefore, eRNA signatures could potentially be applied to represent antitumor immune cells and to improve cancer immunotherapy. In this study, we identified thousands of eRNAs that were significantly correlated with infiltrating immune cell abundance in more than 10,000 patient samples across a variety of cancer types. The expression of these eRNAs was mediated by transcription factors with high expression in antitumor immune cells, as identified through single-cell assays. An eRNA immunotherapy signature (eRIS) developed using the antitumor eRNAs was highly associated with the objective response rate of immunotherapy and was elevated in patients who benefited from immune checkpoint blockade treatment. In comparison with a signature based on protein-coding genes, the eRIS was more effective in predicting the response to immunotherapy. Integration of the eRIS with pharmacogenomic data revealed hundreds of anticancer drugs that have the potential to enhance immunotherapy efficacy. Finally, treatment of a mouse model of IDH-mutant glioma with the histone deacetylase inhibitor vorinostat improved the effects of anti–PD-1 immunotherapy through increased abundance of infiltrating immune cells. Taken together, this study developed an eRIS with demonstrated efficacy in predicting immunotherapy response and used the eRIS to identify a series of effective combination drugs, thus highlighting the clinical utility of the eRIS in immunotherapy enhancement. Significance: An eRNA immunotherapy signature developed using antitumor eRNAs in tumor-infiltrating immune cells improves the prediction of response to immunotherapy and identifies a series of effective drug combinations to enhance immunotherapy efficacy.