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Updated: Aug 10, 2025
Author Spotlight: Investigating Liver Cancer Pathogenesis Using Patient-Derived Organoids
Published on: August 18, 2023
Identification of Drug Targets and Agents Associated with Hepatocellular Carcinoma through Integrated Bioinformatics
Md Alim Hossen1, Md Selim Reza1, Md Harun-Or-Roshid1
1Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
Background:
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death globally. The mechanisms underlying the development of HCC are mostly unknown till now.
Objective:
The main goal of this study was to identify potential drug target proteins and agents for the treatment of HCC.
Methods:
The publicly available three independent mRNA expression profile datasets were downloaded from the NCBI-GEO database to explore common differentially expressed genes (cDEGs) between HCC and control samples using the Statistical LIMMA approach. Hub-cDEGs as drug targets highlighting their functions, pathways, and regulators were identified by using integrated bioinformatics tools and databases. Finally, Hub-cDEGs-guided top-ranked drug agents were identified by molecular docking study for HCC.
Results:
We identified 160 common DEGs (cDEGs) from three independent mRNA expression datasets in which ten cDEGs (CDKN3, TK1, NCAPG, CDCA5, RACGAP1, AURKA, PRC1, UBE2T, MELK, and ASPM) were selected as Hub-cDEGs. The GO functional and KEGG pathway enrichment analysis of Hub-cDEGs revealed some crucial cancer-stimulating biological processes, molecular functions, cellular components, and signaling pathways. The interaction network analysis identified three TF proteins and five miRNAs as the key transcriptional and post-transcriptional regulators of HubcDEGs. Then, we detected the proposed Hub-cDEGs guided top-ranked three anti-HCC drug molecules (Dactinomycin, Vincristine, Sirolimus) that were also highly supported by the already published top-ranked HCC-causing Hub-DEGs mediated receptors.
Conclusion:
The findings of this study would be useful resources for diagnosis, prognosis, and therapies of HCC.
Insights
This study identifies key genes and drug targets for hepatocellular carcinoma (HCC), a leading cause of cancer death. Findings highlight potential new therapies for HCC treatment and diagnosis.
Area of Science:
- Oncology
- Bioinformatics
- Genomics
Background:
- Hepatocellular carcinoma (HCC) is a significant global health concern, ranking as the third leading cause of cancer-related mortality worldwide.
- The intricate molecular mechanisms driving HCC development remain largely unelucidated, hindering effective treatment strategies.
Purpose of the Study:
- To pinpoint potential drug target proteins and therapeutic agents for hepatocellular carcinoma (HCC).
- To identify novel therapeutic strategies for HCC by analyzing gene expression profiles and molecular interactions.
Main Methods:
- Utilized three independent mRNA expression datasets from the NCBI-GEO database to identify common differentially expressed genes (cDEGs) in HCC versus control samples.
- Employed bioinformatics tools to identify hub-cDEGs, analyze their functions, pathways, and regulators, and perform molecular docking studies to predict anti-HCC drug agents.
Main Results:
- Identified 160 common DEGs, with ten selected as hub-cDEGs (CDKN3, TK1, NCAPG, CDCA5, RACGAP1, AURKA, PRC1, UBE2T, MELK, ASPM).
- Functional and pathway analyses revealed critical cancer-promoting biological processes and signaling pathways associated with hub-cDEGs.
- Identified Dactinomycin, Vincristine, and Sirolimus as top-ranked drug candidates for HCC treatment, supported by molecular docking and existing literature.
Conclusions:
- The identified hub-cDEGs and drug targets offer valuable insights for HCC diagnosis, prognosis, and therapeutic development.
- This research provides a foundation for further investigation into targeted therapies for hepatocellular carcinoma.
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