Integrated in Silico and in Vitro Analysis of Peroxisome-Related Genes PEX16 and DHRS4 in Hepatocellular Carcinoma

Abstract

Objective: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide, characterized by profound metabolic reprogramming and limited therapeutic options. Peroxisomes are essential metabolic organelles involved in lipid metabolism, redox homeostasis, and detoxification, and increasing evidence suggests that peroxisomal dysfunction contributes to tumor progression. However, the role of peroxisome biogenesis–related genes in HCC remains insufficiently characterized. This study aimed to investigate the potential involvement of the peroxisome-related genes PEX16 and DHRS4 in HCC by integrating bioinformatics analyses with experimental validation.
Methods: Differential gene expression analyses were performed using the GEO datasets GSE183349 and GSE14945 to identify peroxisome-associated genes altered in HCC. The expression levels of PEX16 and DHRS4 were subsequently validated in vitro using quantitative real-time PCR (qPCR) in the HepG2 hepatocellular carcinoma cell line and HUVEC cells as controls.
Results: Bioinformatics analyses revealed that PEX16 and DHRS4 were significantly upregulated in HCC datasets. Consistent with the in silico findings, qPCR analysis demonstrated significantly increased expression of both genes in HepG2 cells compared with HUVEC cells (PEX16: p=0.0021; DHRS4: p=0.038). The integrated in silico and in vitro analyses demonstrate that PEX16 and DHRS4 are consistently upregulated in hepatocellular carcinoma.
Conclusions: These findings suggest that both genes may serve as peroxisome-associated molecular biomarkers reflecting metabolic reprogramming in HCC. Further validation in patient-derived samples and functional studies are warranted to evaluate their diagnostic and prognostic potential.
 

Keywords

• Hepatocellular carcinoma
• Gene expression
• Peroxisome
• PEX16
• DHRS4

Supporting Institution

This study was supported by the Istanbul University–Cerrahpasa Scientific Research Projects Coordination Unit (Project No. 37431).

Project Number

37431

Thanks

The authors sincerely thank the Istanbul University–Cerrahpasa Scientific Research Projects Coordination Unit (Project No. 37431).

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