TY - JOUR TI - A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer AU - Yang, Chen AU - Zhang, Hailin AU - Chen, Mengnuo AU - Wang, Siying AU - Qian, Ruolan AU - Zhang, Linmeng AU - Huang, Xiaowen AU - Wang, Jun AU - Liu, Zhicheng AU - Qin, Wenxin AU - Wang, Cun AU - Hang, Hualian AU - Wang, Hui A2 - Mangoni, Arduino A A2 - Franco, Eduardo VL - 11 PY - 2022 DA - 2022/02/22 SP - e71880 C1 - eLife 2022;11:e71880 DO - 10.7554/eLife.71880 UR - https://doi.org/10.7554/eLife.71880 AB - Pharmacologic perturbation projects, such as Connectivity Map (CMap) and Library of Integrated Network-based Cellular Signatures (LINCS), have produced many perturbed expression data, providing enormous opportunities for computational therapeutic discovery. However, there is no consensus on which methodologies and parameters are the most optimal to conduct such analysis. Aiming to fill this gap, new benchmarking standards were developed to quantitatively evaluate drug retrieval performance. Investigations of potential factors influencing drug retrieval were conducted based on these standards. As a result, we determined an optimal approach for LINCS data-based therapeutic discovery. With this approach, homoharringtonine (HHT) was identified to be a candidate agent with potential therapeutic and preventive effects on liver cancer. The antitumor and antifibrotic activity of HHT was validated experimentally using subcutaneous xenograft tumor model and carbon tetrachloride (CCL4)-induced liver fibrosis model, demonstrating the reliability of the prediction results. In summary, our findings will not only impact the future applications of LINCS data but also offer new opportunities for therapeutic intervention of liver cancer. KW - drug prediction KW - connectivity map KW - LINCS KW - liver cancer KW - homoharringtonine JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -