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26 March 2020 : Clinical Research  

RNA-Sequencing, Connectivity Mapping, and Molecular Docking to Investigate Ligand-Protein Binding for Potential Drug Candidates for the Treatment of Wilms Tumor

Jia-Yuan Luo1CDE, Shi-Bai Yan2BF, Gang Chen1ACDEF, Peng Chen3BCD, Song-Wu Liang3BF, Qiong-Qian Xu3DE, Jin-Han Gu3BF, Zhi-Guang Huang1ACE, Li-Ting Qin1DE, Hui-Ping Lu1CD, Wei-Jia Mo1ABCDEF, Yi-Ge Luo3AE, Jia-Bo Chen3AEG*

DOI: 10.12659/MSM.920725

Med Sci Monit 2020; 26:e920725

Abstract

BACKGROUND: Wilms tumor, or nephroblastoma, is a malignant pediatric embryonal renal tumor that has a poor prognosis. This study aimed to use bioinformatics data, RNA-sequencing, connectivity mapping, molecular docking, and ligand-protein binding to identify potential targets for drug therapy in Wilms tumor.

MATERIAL AND METHODS: Wilms tumor and non-tumor samples were obtained from high throughput gene expression databases, and differentially expressed genes (DEGs) were analyzed using the voom method in the limma package. The overlapping DEGs were obtained from the intersecting drug target genes using the Connectivity Map (CMap) database, and systemsDock was used for molecular docking. Gene databases were searched for gene expression profiles for complementary analysis, analysis of clinical significance, and prognosis analysis to refine the study.

RESULTS: From 177 cases of Wilms tumor, there were 648 upregulated genes and 342 down-regulated genes. Gene Ontology (GO) enrichment analysis showed that the identified DEGs that affected the cell cycle. After obtaining 21 candidate drugs, there were seven overlapping genes with 75 drug target genes and DEGs. Molecular docking results showed that relatively high scores were obtained when retinoic acid and the cyclin-dependent kinase inhibitor, alsterpaullone, were docked to the overlapping genes. There were significant standardized mean differences for three overlapping genes, CDK2, MAP4K4, and CRABP2. However, four upregulated overlapping genes, CDK2, MAP4K4, CRABP2, and SIRT1 had no prognostic significance.

CONCLUSIONS: RNA-sequencing, connectivity mapping, and molecular docking to investigate ligand-protein binding identified retinoic acid and alsterpaullone as potential drug candidates for the treatment of Wilms tumor.

Keywords: Genes, Wilms Tumor, Molecular Docking Simulation, Receptors, Retinoic Acid, Drug Evaluation, Preclinical, Gene Expression Regulation, Neoplastic, gene ontology, Kaplan-Meier Estimate, Ligands, Prognosis, Protein Binding, ROC Curve, Sequence Analysis, RNA, Wilms Tumor

Editorial

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Editorial: Current Status of Two Adjuvanted Malaria Vaccines and the World Health Organization (WHO) Strategy to Eradicate Malaria by 2030

Dinah V. Parums
Science Editor, Medical Science Monitor, International Scientific Information, Inc., Melville, NY, USA

DOI: 10.12659/MSM.939357

Med Sci Monit 2023; 29:e939357

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Medical Science Monitor eISSN: 1643-3750
Medical Science Monitor eISSN: 1643-3750