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Identification of Key lncRNAs, circRNAs, and mRNAs in Osteoarthritis via Bioinformatics Analysis

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Abstract

Osteoarthritis (OA) is a common degenerative joint disorder that adversely affects the quality of life of patients. Identification of novel diagnostic biomarkers is pivotal for the early detection and prevention of OA. Dataset GSE185059 was selected from Gene Expression Omnibus database to obtain differentially expressed lncRNAs (DE-lncRNAs), mRNAs (DE-mRNAs), and circRNAs (DE-circRNAs) between OA and normal samples. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as protein–protein interaction (PPI) network construction of DE-mRNAs were conducted. Hub genes were identified from PPI networks and validated by RT-qPCR. starBase database was utilized for predicting miRNAs binding with hub genes, selected DE-lncRNAs and DE-circRNAs, respectively. The competing endogenous RNA (ceRNA) networks were constructed. A total of 818 DE-mRNAs, 191 DE-lncRNAs, and 2053 DE-circRNAs were identified. The DE-mRNAs were significantly enriched in several inflammation-related GO terms and KEGG pathways such as positive regulation of cell–cell adhesion, TNF-alpha signaling pathway and NF-kappa B signaling pathway. Thirteen hub genes were identified, which were CFTR, GART, SMAD2, NCK1, TJP1, UBE2D1, EFTUD2, PRKACB, IL10, SNRPG, CHD4, RPS24, and SRSF6. OA-related DE-lncRNA/circRNA-miRNA-hub gene networks were constructed. We identified 13 hub genes and constructed the ceRNA networks related to OA, providing a theoretical basis for further research.

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Authors and Affiliations

  1. Department of Rheumatic Immunity, Changzhi People’s Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China

    Wen**g Zhang, Chun Wei & Ling Wang

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  1. Wen**g Zhang
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Correspondence to Ling Wang.

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This study was approved by the medical Ethics Committee of Changzhi People’s Hospital (approval number: IEC202302003). Written informed consent was obtained from each participant.

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Zhang, W., Wei, C. & Wang, L. Identification of Key lncRNAs, circRNAs, and mRNAs in Osteoarthritis via Bioinformatics Analysis. Mol Biotechnol 66, 1660–1672 (2024). https://doi.org/10.1007/s12033-023-00790-3

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