Identifying Drug Targets in Pancreatic Ductal Adenocarcinoma Through Machine Learning, Analyzing Biomolecular Networks, and Structural Modeling

• Main Authors: Wenying Yan, Xingyi Liu, Yibo Wang, Shuqing Han, Fan Wang, Xin Liu, Fei Xiao, Guang Hu
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-04-01
• Series: Frontiers in Pharmacology
• Subjects: pancreatic ductal adenocarcinoma; drug targets; support vector machine–recursive feature elimination; protein-protein interactions; structural dynamics; integrins
• Online Access: https://www.frontiersin.org/article/10.3389/fphar.2020.00534/full

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related death and has an extremely poor prognosis. Thus, identifying new disease-associated genes and targets for PDAC diagnosis and therapy is urgently needed. This requires investigations into the underlying molecular mechanisms of PDAC at both the systems and molecular levels. Herein, we developed a computational method of predicting cancer genes and anticancer drug targets that combined three independent expression microarray datasets of PDAC patients and protein-protein interaction data. First, Support Vector Machine–Recursive Feature Elimination was applied to the gene expression data to rank the differentially expressed genes (DEGs) between PDAC patients and controls. Then, protein-protein interaction networks were constructed based on the DEGs, and a new score comprising gene expression and network topological information was proposed to identify cancer genes. Finally, these genes were validated by “druggability” prediction, survival and common network analysis, and functional enrichment analysis. Furthermore, two integrins were screened to investigate their structures and dynamics as potential drug targets for PDAC. Collectively, 17 disease genes and some stroma-related pathways including extracellular matrix-receptor interactions were predicted to be potential drug targets and important pathways for treating PDAC. The protein-drug interactions and hinge sites predication of ITGAV and ITGA2 suggest potential drug binding residues in the Thigh domain. These findings provide new possibilities for targeted therapeutic interventions in PDAC, which may have further applications in other cancer types.