Sungwan Prin, Lert-Itthiporn Worachart, Silsirivanit Atit, Klinhom-On Nathakan, Okada Seiji, Wongkham Sopit, Seubwai Wunchana
Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand.
Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.
PeerJ. 2021 Mar 17;9:e11067. doi: 10.7717/peerj.11067. eCollection 2021.
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.
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.
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.
Using integrated bioinformatics analysis, CDC20 was identified as a novel candidate therapeutic target for CCA.
胆管癌（CCA）是一种起源于胆管细胞的恶性肿瘤。CCA的发病率和死亡率非常高，尤其是在东南亚国家。此外，大多数CCA患者的预后很差。目前，CCA仍然没有有效的治疗方案。对几种标准化疗药物的耐药性经常出现；因此，迫切需要寻找一种新的有效的CCA治疗方法。
在本研究中，基于来自基因表达综合数据库（GEO）的三个微阵列基因表达谱（GSE26566、GSE32225和GSE76297）进行了全面的生物信息学分析，以鉴定CCA治疗的新靶基因。基于差异表达基因（DEG）进行基因本体和通路富集分析。使用STRING和Cytoscape软件分析蛋白质-蛋白质相互作用（PPI）和枢纽基因鉴定。然后，使用实时PCR在CCA细胞系中检测生物信息学分析中候选基因的表达。最后，在二维和三维细胞培养模型下培养的CCA细胞系中研究针对候选基因的特异性抑制剂的抗肿瘤活性。
这三个微阵列数据集显示在CCA中有一个由226个DEG组成的交集（124个上调基因和102个下调基因）。根据Reactome通路分析，DEG在细胞周期、止血和代谢通路中显著富集。此外，使用蛋白质-蛋白质相互作用（PPI）网络和子PPI网络分析鉴定了CCA中的20个潜在枢纽基因。随后，基于药物优先级程序，CDC20被鉴定为CCA的一种潜在新靶向药物。此外，在CCA细胞系中研究了一种潜在的CDC20抑制剂即dinaciclib的抗肿瘤活性。Dinaciclib表现出巨大的抗肿瘤活性，优于CCA的标准化疗药物吉西他滨。
通过综合生物信息学分析，CDC20被鉴定为CCA的一种新的候选治疗靶点。
