Identification of biomarkers related to autophagy in osteoarthritis via bioinformatics analysis and experimental validation (Preprint)

Abstract

BACKGROUND Osteoarthritis(OA) is a degenerative disease with few effective early interventions and therapeutic options, autophagy is thought to play a significant role in progression of OA. OBJECTIVE We used bioinformatics analysis and experimental validation to identify biomarkers related to autophagy in OA with the aim of therapeutic targets. METHODS The series matrix file GSE82107 was downloaded from Gene Expression Omnibus (GEO) public databases. The data were processed and differentially expressed genes (DEGs) were identified via R 4.2.2 software. The autophagy related-DEGs were subsequently defined as DEGs from GSE82107 that overlapped with autophagy-related genes and were subsequently selected on the basis of a Venn diagram. The autophagy related-DEGs were screened via Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, protein-protein interaction (PPI) analysis and immune cell infiltration analysis. Based on the constructed PPI network, the hub genes were identified via the CytoHubba plugin. Moreover, the hub genes were confirmed via the receiver operating characteristic (ROC) curve analysis of the GSE129147 and GSE169077 datasets. In addition, we collected synovial tissue from the knees of ten patients: five OA patients who underwent total knee arthroplasty and five young patients who underwent arthroscopic surgery for anterior cruciate ligament rupture. The collected synovial samples were subjected to RNA extraction followed by real-time quantitative RT-PCR.Finally, we verified the expression of the HUB gene by calculating the corresponding mRNA expression levels. RESULTS Five genes namely, BCL2L1, CTSD, ATG3, GABARAPL2 and CTSB were identified as hub autophagy related-DEGs. ROC analysis revealed that almost all the hub genes had good diagnostic value, but by the Q-PCR results of the clinical samples revealed that BCL2L1, GABARAPL2, and CTSB were all upregulated in OA (p < 0.05). The relative expressions of CTSD and ATG3 were not significantly different between the OA group and the control group (p > 0.05). CONCLUSIONS This study identified hub genes related to autophagy in OA, including BCL2L1, GABARAPL2, and CTSB. These genes are promising targets for OA treatment.