Analysis of hub genes associated with inflammation injury in non-alcoholic fatty liver disease based on gene expression omnibus database

doi:10.3877/cma.j.issn.1673-9450.2025.02.003

Abstract

Abstract:

Objective

To explore the hub genes related to inflammation injury that changed significantly during the development of non-alcoholic fatty liver disease （NAFLD）.

Methods

A total of 98 patients with NAFLD were selected from the GSE167523 dataset in the Gene Expression Omnibus （GEO）database to calculate the inflammatory indices by performing the gene set variation analysis （GSVA）.Two separate groups of high-inflammatory indices and low-inflammatory indices were set up for comparison purposes.Using the limma software package in R language to identify differentially expressed genes （DEGs）between the groups.ClusterProfile software package in R language was used for gene ontology （GO）enrichment analysis and Kyoto encyclopedia of genes and genomes （KEGG） enrichment analysis on DEGs.Hub genes were screened by protein-protein interaction （PPI） network analysis using STRING database.Additionally， gene expression levels were validated in the GSE89632 and GSE130970 datasets.Used the ROC curves to evaluate the diagnostic ability of them and performed the miRNA and transcription factor regulatory network analysis.

Results

A total of 308 DEGs were identified， including 243 upregulated genes and 65 downregulated genes.The enrichment analysis results showed that these DEGs were mainly enriched in chemokine signaling pathways， interactions between viral proteins and cytokines， as well as cytokine receptor interactions.PPI network analysis showed that the key modules containing 16 genes， including TOP2A， MKI67，CDC20，DLGAP5，and MCM10.ROC curves analysis implied that these 16 hub genes were potential biomarkers of NAFLD.Among them， the expression of 11 hub genes showed statistically significant differences between control group and NAFLD group in the GSE89632 dataset， and between high inflammation indices group and low inflammation indices group in the GSE130970 dataset （P ＜0.05）.

Conclusion

Inflammation-related hub genes， such as TOP2A， CDC20， and HJURP， show promise as potential diagnostic and therapeutic targets for NAFLD.

Key words: Gene Expression Omnibus datasets, Non-alcoholic fatty liver disease, Inflammatory damage, Hub genes

Cheng Cheng, Shuai Lu, Rong Chen, Xinping Li, Ruifeng Bai, Gengli Cui, Shuo Chen, Jiawei Yin, Jianpeng Hu, Yaozhuo Wang, Xieyuan Jiang, Hailing Chen. Analysis of hub genes associated with inflammation injury in non-alcoholic fatty liver disease based on gene expression omnibus database[J]. Chinese Journal of Injury Repair and Wound Healing(Electronic Edition), 2025, 20(02): 99-106.

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References 42

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