Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma

Prin Sungwan; Worachart Lert-Itthiporn; Atit Silsirivanit; Nathakan Klinhom-On; Seiji Okada; Sopit Wongkham; Wunchana Seubwai

doi:10.7717/peerj.11067

Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma

PeerJ. 2021 Mar 17:9:e11067. doi: 10.7717/peerj.11067. eCollection 2021.

Authors

Prin Sungwan^{1

2}, Worachart Lert-Itthiporn³, Atit Silsirivanit³, Nathakan Klinhom-On^{2

3}, Seiji Okada⁴, Sopit Wongkham^{2

3}, Wunchana Seubwai^{2

5}

Affiliations

¹ Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand.
² Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.
³ Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
⁴ Division of Hematopoeisis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
⁵ Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.

Abstract

Background: Cholangiocarcinoma (CCA) is a malignancy that originates from bile duct cells. The incidence and mortality of CCA are very high especially in Southeast Asian countries. Moreover, most CCA patients have a very poor outcome. Presently, there are still no effective treatment regimens for CCA. The resistance to several standard chemotherapy drugs occurs frequently; thus, searching for a novel effective treatment for CCA is urgently needed.

Methods: In this study, comprehensive bioinformatics analyses for identification of novel target genes for CCA therapy based on three microarray gene expression profiles (GSE26566, GSE32225 and GSE76297) from the Gene Expression Omnibus (GEO) database were performed. Based on differentially expressed genes (DEGs), gene ontology and pathway enrichment analyses were performed. Protein-protein interactions (PPI) and hub gene identifications were analyzed using STRING and Cytoscape software. Then, the expression of candidate genes from bioinformatics analysis was measured in CCA cell lines using real time PCR. Finally, the anti-tumor activity of specific inhibitor against candidate genes were investigated in CCA cell lines cultured under 2-dimensional and 3-dimensional cell culture models.

Results: The three microarray datasets exhibited an intersection consisting of 226 DEGs (124 up-regulated and 102 down-regulated genes) in CCA. DEGs were significantly enriched in cell cycle, hemostasis and metabolism pathways according to Reactome pathway analysis. In addition, 20 potential hub genes in CCA were identified using the protein-protein interaction (PPI) network and sub-PPI network analysis. Subsequently, CDC20 was identified as a potential novel targeted drug for CCA based on a drug prioritizing program. In addition, the anti-tumor activity of a potential CDC20 inhibitor, namely dinaciclib, was investigated in CCA cell lines. Dinaciclib demonstrated huge anti-tumor activity better than gemcitabine, the standard chemotherapeutic drug for CCA.

Conclusion: Using integrated bioinformatics analysis, CDC20 was identified as a novel candidate therapeutic target for CCA.

Keywords: Bioinformatic analysis; CDC20; Cholangiocarcinoma; Dinaciclib; GEO; In silico; Spheroid; TCGA.

Grants and funding

This research was supported by the Program Management Unit for Human Resources & Institutional Development, Research and Innovation [630000050061-4] and Mekong Health Science Research Institute (MeHSRI), Khon Kaen University for Wunchana Seubwai. P. Sungwan and W. Seubwai are scholars of Research Fund for Supporting Lecturer to Admit High Potential Student to Study and Research on His Expert Program (601H109) from Graduate School, Khon Kaen University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.