Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, China.
BMC Genomics. 2023 Sep 12;24(1):539. doi: 10.1186/s12864-023-09651-4.
5-methylcytosine (m5C) modification is widely associated with many biological and pathological processes. However, knowledge of m5C modification in osteoarthritis (OA) remains lacking. Thus, our study aimed to identify common m5C features in OA.
In the present study, we identified 1395 differentially methylated genes (DMGs) and 1673 differentially expressed genes (DEGs) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) and RNA-sequencing. A co-expression analysis of DMGs and DEGs showed that the expression of 133 genes was significantly affected by m5C methylation. A protein-protein interaction network of the 133 genes was constructed using the STRING database, and the cytoHubba plug-in of Cytoscape was used to hub genes were screen out 11 hub genes, including MMP14, VTN, COL15A1, COL6A2, SPARC, COL5A1, COL6A3, COL6A1, COL8A2, ADAMTS2 and COL7A1. The Pathway enrichment analysis by the ClueGO and CluePedia plugins in Cytoscape showed that the hub genes were significantly enriched in collagen degradation and extracellular matrix degradation.
Our study indicated that m5C modification might play an important role in OA pathogenesis, and the present study provides worthwhile insight into identifying m5C-related therapeutic targets in OA.
5- 甲基胞嘧啶（m5C）修饰广泛与许多生物学和病理学过程相关。然而，骨关节炎（OA）中 m5C 修饰的知识仍然缺乏。因此，我们的研究旨在确定 OA 中的常见 m5C 特征。
在本研究中，我们使用甲基化 RNA 免疫沉淀测序（MeRIP-seq）和 RNA-seq 鉴定了 1395 个差异甲基化基因（DMGs）和 1673 个差异表达基因（DEGs）。DMGs 和 DEGs 的共表达分析表明，133 个基因的表达受到 m5C 甲基化的显著影响。使用 STRING 数据库构建了 133 个基因的蛋白质-蛋白质相互作用网络，并使用 Cytoscape 的 cytoHubba 插件筛选出 11 个枢纽基因，包括 MMP14、VTN、COL15A1、COL6A2、SPARC、COL5A1、COL6A3、COL6A1、COL8A2、ADAMTS2 和 COL7A1。Cytoscape 中的 ClueGO 和 CluePedia 插件进行的通路富集分析表明，枢纽基因显著富集在胶原蛋白降解和细胞外基质降解中。
我们的研究表明，m5C 修饰可能在 OA 发病机制中发挥重要作用，本研究为鉴定 OA 中与 m5C 相关的治疗靶点提供了有价值的见解。
