Abstract
PurposeSteroid-induced osteonecrosis of the femoral head (SONFH) is a refractory orthopaedic hip joint disease that occurs in young- and middle-aged people. Previous experimental studies have shown that autophagy might be involved in the pathological process of SONFH, but the pathogenesis of autophagy in SONFH remains unclear. We aimed to identify and validate the key potential autophagy-related genes involved in SONFH to further illustrate the mechanism of autophagy in SONFH through bioinformatics analysis.MethodsThe GSE123568 mRNA expression profile dataset, including 10 non-SONFH (following steroid administration) samples and 30 SONFH samples, was downloaded from the Gene Expression Omnibus (GEO) database. Autophagy-related genes were obtained from the Human Autophagy Database (HADb). The autophagy-related genes involved in SONFH were screened by intersecting the GSE123568 dataset with the set of autophagy genes. The differentially expressed autophagy-related genes involved in SONFH were identified with R software. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the differentially expressed autophagy-related genes involved in SONFH were conducted by using R software. Then, the correlations between the expression levels of the differentially expressed autophagy-related genes involved in SONFH were confirmed with R software. Moreover, the protein–protein interaction (PPI) network was analysed by using the Search Tool for the Retrieval of Interacting Genes (STRING), significant gene cluster modules were identified with the MCODE Cytoscape plugin, and hub genes among the differentially expressed autophagy-related genes involved in SONFH were screened by using the CytoHubba Cytoscape plugin. Finally, the expression levels of the hub genes of the differentially expressed autophagy-related genes involved in SONFH were validated in hip articular cartilage specimens from necrotic femur heads (NFHs) by using the GSE74089 dataset and further verification by qRT-PCR.ResultsA total of 34 differentially expressed autophagy-related genes were identified between the peripheral blood samples of SONFH patients and non-SONFH patients based on the defined criteria, including 25 upregulated genes and 9 downregulated genes. The GO and KEGG pathway enrichment analyses revealed that these 34 differentially expressed autophagy-related genes involved in SONFH were particularly enriched in death domain receptors, the FOXO signalling pathway and apoptosis. Correlation analysis revealed significant correlations among the 34 differentially expressed autophagy-related genes involved in SONFH. The PPI results demonstrated that the 34 differentially expressed autophagy-related genes interacted with each other. Ten hub genes were identified by using the MCC algorithms of CytoHubba. The GSE74089 dataset showed that TNFSF10, PTEN and CFLAR were significantly upregulated while BCL2L1 was significantly downregulated in the hip cartilage specimens, which was consistent with the GSE123568 dataset. TNFSF10, PTEN and BCL2L1 were detected with consistent expression by qRT-PCR.ConclusionsThirty-four potential autophagy-related genes involved in SONFH were identified via bioinformatics analysis. TNFSF10, PTEN and BCL2L1 might serve as potential drug targets and biomarkers because they regulate autophagy. These results expand the autophagy-related understanding of SONFH and might be useful in the diagnosis and prognosis of SONFH.
Highlights
Steroid-induced osteonecrosis of the femoral head (SONFH) is a chronic refractory orthopaedic disease characterized by accumulation of microfractures without continuous remodelling or the collapse of the femoral head, with high mortality, disability and dysfunction [1, 2]
Thirty-four potential autophagy-related genes involved in SONFH were identified via bioinformatics analysis
The GSE123568 mRNA expression profile dataset was obtained from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/) database according to the following inclusion criteria: (1) “Steroid-induced Osteonecrosis of the Femoral Head” or “SONFH”; (2) Homo sapiens; and (3) “Expression Profiling by array” or “Expression profiling by high throughput sequencing”
Summary
Steroid-induced osteonecrosis of the femoral head (SONFH) is a chronic refractory orthopaedic disease characterized by accumulation of microfractures without continuous remodelling or the collapse of the femoral head, with high mortality, disability and dysfunction [1, 2]. As the SONFH study deepened, accumulating highly recognized mechanistic hypotheses of pathogenicity have been proposed to explain their developmental mechanisms, including uncoupled bone remodelling or unbalanced osteogenic and adipogenic differentiation of BMSCs, cell proliferation and programmed cell death [4]. Among these biological processes, programmed cell death plays a critical role in the development of SONFH. A programmed cell death-like process, has been identified after SONFH, but the mechanism of autophagy in bone repair and bone homeostasis remains unclear
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