Inferences of individual drug responses across diverse cancer types using a novel competing endogenous RNA network

Differences in individual drug responses are an obstacle to progression in cancer treatment, and predicting responses would help to plan treatment. The accumulation of cancer molecular profiling and drug response data provides opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs. This study evaluated drug responses with a competing endogenous RNA (ce RNA ) system that depended on competition between diverse RNA species. We identified drug response‐related ce RNA ( DRCE s) by combining the sequence and expression data of long noncoding RNA (lnc RNA ), micro RNA (mi RNA ), and messenger RNA ( mRNA ), and the survival data of cancer patients treated with drugs. We constructed a patient–drug two‐layer integrated network and used a linear weighting method to predict individual drug responses. DRCE s were found to be significantly enriched in known cancer and drug‐associated data resources, involved in biological processes known to mediate drug responses, and correlated to drug activity in cancer cell lines. The dysregulation of DRCE expression influenced drug response‐associated functions and pathways, suggesting DRCE s as potential therapeutic targets affecting drug responses. A further case study in breast invasive carcinoma ( BRCA ) found that DRCE expression was consistent with the drug response pattern and the aberrant expression of the two NEAT 1‐related DRCE s may lead to poor response to tamoxifen therapy for patients with TP 53 mutations. In summary, this study provides a framework for ce RNA ‐based evaluation of clinical drug responses across multiple cancer types. Understanding the underlying molecular mechanisms of drug responses will allow improved response to chemotherapy and outcomes of cancer treatment.