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Bioinformatics analysis and experimental validation of differentially expressed genes in mouse articular chondrocytes treated with IL‑1β using microarray data

  • Authors:
    • Fan Liang
    • Le Peng
    • Yong-Gang Ma
    • Wei Hu
    • Wei-Bing Zhang
    • Ming Deng
    • Ya-Ming Li

  • View Affiliations

  • Published online on: October 27, 2021     https://doi.org/10.3892/etm.2021.10928
  • Article Number: 6

  • Copyright: © Liang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Osteoarthritis (OA) is the most prevalent chronic degenerative disease that affects the health of the elderly. The present study aimed to identify significant genes involved in OA via bioinformatics analysis. A gene expression dataset (GSE104793) was downloaded from the Gene Expression Omnibus. Bioinformatics analysis was then performed in order to identify differentially expressed genes (DEGs) between untreated chondrocytes and chondrocytes cultured with interleukin‑1β (IL‑1β) for 24 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using Metascape. A protein‑protein interaction network of DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes. Gene set enrichment analysis (GSEA) was performed using GSEA software. Furthermore, chondrocytes were extracted and treated with IL‑1β (10 ng/ml) for 24 h, and reverse‑transcription quantitative PCR was used to confirm differential expression of hub genes. Patient samples were also collected to verify the bioinformatic analysis results. Based on the cut‑off criteria used for determination of the DEGs, a total of 844 DEGs, including 498 upregulated and 346 downregulated DEGs, were identified. The DEGs were mainly enriched in the GO terms and KEGG pathways ‘inflammatory response’, ‘negative regulation of cell proliferation’, ‘ossification’, ‘taxis’, ‘blood vessel morphogenesis’, ‘extracellular structure organization’, ‘mitotic cell cycle process’ and ‘TNF signaling pathway’. The majority of the PCR results, namely the differential expression of kininogen 2, complement C3, cyclin B1, cell division cycle 20, cyclin A2, 1‑phosphatidylinositol 4‑kinase, BUB1 mitotic checkpoint serine/threonine kinase, kinesin family member 11, cyclin B2 and BUB1 mitotic checkpoint serine/threonine kinase B were consistent with the bioinformatics results. Collectively, the present observations provided a regulation network of IL‑1β‑stimulated chondrocytes, which may provide potential targets of OA therapy.
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January-2022
Volume 23 Issue 1

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Spandidos Publications style
Liang F, Peng L, Ma Y, Hu W, Zhang W, Deng M and Li Y: Bioinformatics analysis and experimental validation of differentially expressed genes in mouse articular chondrocytes treated with IL‑1β using microarray data. Exp Ther Med 23: 6, 2022.
APA
Liang, F., Peng, L., Ma, Y., Hu, W., Zhang, W., Deng, M., & Li, Y. (2022). Bioinformatics analysis and experimental validation of differentially expressed genes in mouse articular chondrocytes treated with IL‑1β using microarray data. Experimental and Therapeutic Medicine, 23, 6. https://doi.org/10.3892/etm.2021.10928
MLA
Liang, F., Peng, L., Ma, Y., Hu, W., Zhang, W., Deng, M., Li, Y."Bioinformatics analysis and experimental validation of differentially expressed genes in mouse articular chondrocytes treated with IL‑1β using microarray data". Experimental and Therapeutic Medicine 23.1 (2022): 6.
Chicago
Liang, F., Peng, L., Ma, Y., Hu, W., Zhang, W., Deng, M., Li, Y."Bioinformatics analysis and experimental validation of differentially expressed genes in mouse articular chondrocytes treated with IL‑1β using microarray data". Experimental and Therapeutic Medicine 23, no. 1 (2022): 6. https://doi.org/10.3892/etm.2021.10928