Advancing Efficacy Prediction for EHR-based Emulated Trials in Repurposing Heart Failure Therapies
Authors: Zong Nansu , Chowdhury Shaika , Zhou Shibo , Rajaganapathy Sivaraman , Yu Yue , Wang Liewei , Dai Qiying , Li Pengyang , Liu Xiaoke , Bielinski Suzette J. , Chen Jun , Chen Yongbin , Cerhan James R. 
Published: June 2023

AbstractIntroductionThe High mortality rates associated with heart failure (HF) have propelled the strategy of drug repurposing, which seeks new therapeutic uses for existing, approved drugs to enhance the management of HF symptoms effectively. An emerging trend focuses on utilizing real-world data, like EHR, to mimic randomized controlled trials (RCTs) for evaluating treatment outcomes through what are known as emulated trials (ET). Nonetheless, the intricacies inherent in EHR data—comprising detailed patient histories in databases, the omission of certain biomarkers or specific diagnostic tests, and partial records of symptoms— introduce notable discrepancies between EHR data and the stringent standards of RCTs. This gap poses a substantial challenge in conducting an ET to accurately predict treatment efficacy.ObjectiveThe objective of this research is to predict the efficacy of drugs repurposed for HF in randomized trials by leveraging EHR in ET.MethodsWe proposed an ET framework to predict drug efficacy, integrating target prediction based on biomedical databases with statistical analysis using EHR data. Specifically, we developed a novel target prediction model that learns low-dimensional representations of drug molecules, protein sequences, and diverse biomedical associations from a knowledge graph. Additionally, we crafted strategies to improve the prediction by considering the interactions between HF drugs and biological factors in the context of HF prognostic markers.ResultsOur validation of the drug-target prediction model against the BETA benchmark demonstrated superior performance, with an average AUCROC of 97.7%, PRAUC of 97.4%, F1 score of 93.1%, and a General Score of 96.1%, surpassing existing baseline algorithms. Further analysis of our ET framework on identifying 17 repurposed drugs—derived from 266 phase 3 HF RCTs—using data from 59,000 patients at the Mayo Clinic highlighted the framework’s remarkable predictive accuracy. This analysis took into account various factors such as biological variables (e.g., gender, age, ethnicity), HF medications (e.g., ACE inhibitors, Beta-blockers, ARBs, Loop Diuretics), types of HF (HFpEF and HFrEF), confounders, and prognostic markers (e.g., NT-proBNP, BUN, creatinine, and hemoglobin). The ET framework significantly improved the accuracy compared to the baseline efficacy analysis that utilized EHR data. Notably, the best results were improved in AUC-ROC from 75.71% to 93.57% and in PRAUC from 78.66% to 90.34%, compared to the baseline models.ConclusionOur study presents an ET framework that significantly enhances drug efficacy emulation by integrating EHR-based analysis with target prediction. We demonstrated substantial success in predicting the efficacy of 17 HF drugs repurposed for phase 3 RCTs, showcasing the framework’s potential in advancing HF treatment strategies.