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. 2024 Feb 23:17:639-650.
doi: 10.2147/IJGM.S444847. eCollection 2024.

Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis

Kuihan Tang  1 , Li Sun  2 , Long Chen  2 , Xiaobo Feng  1 , Jiarui Wu  2 , Hao Guo  2 , Yong Zheng  1
Affiliations

Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis

Kuihan Tang et al. Int J Gen Med. .

Abstract

Background: Mitochondrial autophagy is closely related to the pathogenesis of osteoarthritis, In order to explore the role of mitochondrial autophagy related genes in knee osteoarthritis (KOA) and its molecular mechanism.

Methods: KOA-related transcriptome data were extracted from the Gene Expression Omnibus (GEO) database. Differentially expressed mitochondrial autophagy gene (DEMGs) were screened in patients with KOA by differential expression analysis. The STRING website was used to construct a protein-protein interaction (PPI) network among DEMGs. Molecular complex detection (MCODE) method in Cytoscape software was performed to identify hub DEMGs. Support vector machine recursive feature elimination (SVM-RFE) method was used to construct the hub DEMG diagnosis model. Genes with diagnostic value were identified as biomarkers by plotting receiver operating characteristic (ROC) curves and Expression validation. CIBERSORT algorithm was used to calculate the proportion of 22 immune cells in each sample in the GSE114007 dataset. Finally, biomarker expression was verified by qPCR.

Results: A total of 15 DEMGs were obtained and enrichment analyses showed that these DEMG strains were mainly enriched in the mitophagy-animal, shigellosis, autophagy-animal and FoxO signal pathways. The PPI network unveiled 13 DEMGs with interactions. In addition, 8 hub DEMGs (ULK1, CALCOCO2, MAP1LC3B, BNIP3L, GABARAPL1, BNIP3, FKBP8 and FOXO3) were obtained for KOA. And 5 model DEMGs (BNIP3L, BNIP3, MAP1LC3B, ULK1 and FOXO3) were screened. The ROC curves revealed that BNIP3 and FOXO3 has strong diagnostic value in these models of DEMG. Immune-infiltration and correlation analysis showed that BNIP3 and FOXO3 were significantly correlated with three different immune cells, including primary B cells, M0 macrophage and M2 macrophage. The cartilage tissue samples qPCR verification results show that FOXO3 and BNIP3 were all down-regulated in KOA (p < 0.01), and the validation results are consistent with the above analysis.

Conclusion: BNIP3 and FOXO3 have been identified as biomarkers for the diagnosis of KOA, which might supply a new insight for the pathogenesis and treatment of KOA.

Keywords: Gene Expression Omnibus; bioinformatics analysis; biomarkers; diagnostic; immune infiltration.

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Conflict of interest statement

The authors have no relevant financial or non-financial interests to disclose for this work.

Figures

Figure 1
Figure 1
Differential expression analysis. (a) Differentially expressed gene expression volcano plot between KOA and normal controls. (b) Differentially expressed gene expression heatmap between KOA and normal controls (adjusted p<0.05 and a |log2FC|>0.5). (c) Venn diagram shows the intersection of DEGs and MGs.
Figure 2
Figure 2
Functional enrichment analysis. (a) GO enrichment analysis based on differentially expressed genes was performed in the GSE114007 databases. (b) KEGG enrichment analysis was performed to explore the associated pathways in the GSE114007 databases.
Figure 3
Figure 3
The PPI network of DEMGs. (a) The PPI network shows the DEMGs with a minimum required interaction score >0.4. (b) The most significant module was obtained from PPI network with 8 hub genes.
Figure 4
Figure 4
Identification of model DEMGs. (a) The SVM-RFE algorithm was performed to identify 5 model DEMGs (BNIP3L, BNIP3, MAP1LC3B, ULK1, and FOXO3). (b) ROC analysis of 5 model DEMGs on the training set. (c) ROC analysis of 5 model DEMGs on the validation set.
Figure 5
Figure 5
Immune infiltration analysis. (a) Violin diagram of the proportion of 22 different immune cell types and functional states between KOA and normal samples. (b) Correlation between BNIP3 and immune cells. (c) Correlation between FOXO3 and immune cells. *p < 0.05.
Figure 6
Figure 6
qPCR validation of the BNIP3 and FOXO3 between KOA (Case) and normal controls. **p < 0.01, ***p < 0.001.
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