Exploring the hub genes and mechanisms of Daphne altaica treating esophageal squamous cell carcinoma based on network pharmacology and bioinformatics analysis

Sendaer Hailati; Ziruo Talihati; Kayisaier Abudurousuli; Meng Yuan Han; Muhadaisi Nuer; Nawaz Khan; Nulibiya Maihemuti; Jimilihan Simayi; Dilihuma Dilimulati; Nuerbiye Nueraihemaiti; Wenting Zhou

doi:10.1007/s00432-023-04797-w

Exploring the hub genes and mechanisms of Daphne altaica treating esophageal squamous cell carcinoma based on network pharmacology and bioinformatics analysis

J Cancer Res Clin Oncol. 2023 Sep;149(11):8467-8481. doi: 10.1007/s00432-023-04797-w. Epub 2023 Apr 23.

Affiliations

¹ Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
² Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China. zwt@xjmu.edu.cn.

^# Contributed equally.

PMID: 37087696
DOI: 10.1007/s00432-023-04797-w

Abstract

Purpose: Esophageal squamous cell carcinoma (ESCC), is a frequent digestive tract malignant carcinoma with a high fatality rate. Daphne altaica (D. altaica), a medicinal plant that is frequently employed in Kazakh traditional medicine, and which has traditionally been used to cure cancer and respiratory conditions, but research on the mechanism is lacking. Therefore, we examined and verified the hub genes and mechanism of D. altaica treating ESCC.

Methods: Active compounds and targets of D. altaica were screened by databases such as TCMSP, and ESCC targets were screened by databases such as GeneCards and constructed the compound-target network and PPI network. Meantime, data sets between tissues and adjacent non-cancerous tissues from GEO database (GSE100942, GPL570) were analyzed to obtain DEGs using the limma package in R. Hub genes were validated using data from the Kaplan-Meier plotter database, TIMER2.0 and GEPIA2 databases. Finally, AutoDock software was used to predict the binding sites through molecular docking.

Results: In total, 830 compound targets were obtained from TCMSP and other databases. In addition, 17,710 disease targets were acquired based on GeneCards and other databases. In addition, we constructed the compound-target network and PPI network. Then, 127 DEGs were observed (82 up-regulated and 45 down-regulated genes). Hub genes were screened including TOP2A, NUF2, CDKN2A, BCHE, and NEK2, and had been validated with the help of several publicly available databases. Finally, molecular docking results showed more stable binding between five hub genes and active compounds.

Conclusions: In the present study, five hub genes were screened and validated, and potential mechanisms of action were predicted, which could provide a theoretical understanding of the treatment of ESCC with D. altaica.

Keywords: Bioinformatics analysis; Daphne altaica; Esophageal squamous cell carcinoma; Hub genes; Network pharmacology.

MeSH terms

Carcinoma*
Computational Biology
Daphne* / genetics
Esophageal Neoplasms* / drug therapy
Esophageal Neoplasms* / genetics
Esophageal Squamous Cell Carcinoma* / drug therapy
Esophageal Squamous Cell Carcinoma* / genetics
Humans
Molecular Docking Simulation
NIMA-Related Kinases
Network Pharmacology

Substances

NEK2 protein, human
NIMA-Related Kinases