Candidate Marker Genes for Diagnosis of Osteoarthritis and Prediction of Their Regulatory Mechanisms

Zhang, Zuyang; Liu, Wei; Xiong, Jiepeng; Chen, Tianhua; Jiang, Liangdong; Liu, Mingjiang

doi:10.14712/fb2023069010022

Folia Biologica > Archive > 2023, Vol. 69 > Issue 1 > Candidate Marker Genes for Diagnosis of…

Fol. Biol. 2023, 69, 22-33

https://doi.org/10.14712/fb2023069010022

Candidate Marker Genes for Diagnosis of Osteoarthritis and Prediction of Their Regulatory Mechanisms

Zuyang Zhang, Wei Liu, Jiepeng Xiong, Tianhua Chen, Liangdong Jiang, Mingjiang Liu

Department of Orthopedics, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan 410004, China

Received February 2023
Accepted July 2023

We have screened candidate marker genes for the diagnosis of osteoarthritis and predicted their regulatory mechanisms. Six expression chips of tissue samples and one expression chip of peripheral blood mononuclear cell (PMBC) samples were obtained from the GEO database. Differential analysis, GSEA, and WGCNA were performed on the integrated tissue sample data with batch correction. Candidate genes were obtained from the intersection of the genes significantly related to osteoarthritis in the WGCNA and the differentially expressed genes. ROC analysis was performed on the candidate genes in the tissue and PMBC samples. Genes with AUC values greater than 0.6 were retained as final candidates, and their upstream regulatory miRNAs were predicted. A total of 106 genes with differential expression were found in osteoarthritis tissue samples, which were mainly enriched in cell cycle and p53 signalling pathways. WGCNA selected a gene module significantly correlated with the occurrence of osteoarthritis. Fourteen candidate genes were obtained from the intersection of the genes in the module and the differentially expressed genes. ROC analysis showed that among these 14 candidate genes, only ADM, CX3CR1 and GADD45A had AUC values greater than 0.6 in both tissue and PMBC samples. The AUC values of the gene set of these three genes were greater than 0.7. Multiple miRNAs were predicted to be regulators of these three genes. ADM, CX3CR1 and GADD45A have potential as diagnostic marker genes for osteoarthritis and may be regulated by multiple miRNAs.

Keywords

gene expression omnibus, weighted gene co-expression network analysis, gene set enrichment analysis, adrenomedullin, C-X3-C motif chemokine receptor 1, growth arrest and DNA damage inducible alpha, receiver operating characteristic curve.

Funding

The study was supported by the Scientific Research Project of Education Department Hunan Province (No. 21C0282), the Research Project of Health Commission of Hunan Province (No. 202104070138), Scientific Research Project of Changsha Central Hospital (No. YNKY202107), Clinical Medical Innovation Guidance Program (No. 2020sk53304) and Hunan Province Graduate Research Innovation Project (CX20231009).