siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers.

XiuLiang Cui, Lu Han, Yang Liu, Ying Li, Wen Sun, Bin Song, Wenxia Zhou, Yongxiang Zhang, Hongyang Wang

Journal: Briefings in bioinformatics 2021;22(5):bbab058

PMID: 33822887

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Abstract

It is pivotal and remains challenge for cancer precision treatment to identify the survival outcome interactions between genes, cells and drugs. Here, we present siGCD, a web-based tool for analysis and visualization of the survival interaction of Genes, Cells and Drugs in human cancers. siGCD utilizes the cancer heterogeneity to simulate the manipulated gene expression, cell infiltration and drug treatment, which overcomes the data and experimental limitations. To illustrate the performance of siGCD, we identified the survival interaction partners of EGFR (gene level), T cells (cell level) and sorafenib (drug level), and our prediction was consistent with previous reports. Moreover, we validate the synergistic effect of regorafenib and glyburide, and found that glyburide could significantly improve the regorafenib response. These results demonstrate that siGCD could benefit cancer precision medicine in a wide range of advantageous application scenarios including gene regulatory network construction, immune cell regulatory gene identification, drug (especially multiple target drugs) response biomarker screening and combination therapeutic design.

Address: National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China.; Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.; State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China.; Institute for Hepatology, The Second Affiliated Hospital, South University of Science and Technology, 29 Bulan Road, Longgang District, Shenzhen 518112, China.; Department of Pharmacy, Eastern Hepatobiliary Surgery Hospital, the Second Military Medical University, Shanghai 200438, China.; Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200438, China.; National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China.; International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, 200438, Shanghai, China.

DOI: 10.1093/bib/bbab058