Huang Gangyong, Zhao Guanglei, Xia Jun, Wei Yibing, Chen Feiyan, Chen Jie, Shi Jingsheng
Department of Orthopaedics, Huashan Hospital, Fudan University, Shanghai 200040, China.
Department of Orthopaedics, Huashan Hospital, Fudan University, Shanghai 200040, China.
Gene. 2018 Apr 30;652:39-47. doi: 10.1016/j.gene.2018.01.090. Epub 2018 Jan 31.
Osteonecrosis of the femoral head (ONFH) is a common orthopedic disease associated with high disability, and femoral neck fracture (FNF) is one of the most common reasons for traumatic ONFH. This study was designed to reveal the mechanisms underlying ONFH. Using fastx_toolkit and prinseq-lite tools, quality control was conducted for the sequencing data. The differentially expressed genes (DEGs, including both mRNAs and lncRNAs) between ONFH and FNF samples were identified using the edgeR package in R, and were then subjected to enrichment analysis using the BioCloud platform. Subsequently, protein-protein interaction (PPI) networks were constructed using Cytoscape software. After the target genes of DE-lncRNAs were predicted based on Spearman's rank correlation coefficient, lncRNA-gene coexpression network was visualized using the Cytoscape software. Furthermore, functional enrichment analysis was carried out for the target genes using the clusterprofiler package in R. Additionally, the key genes were detected by quantitative real-time polymerase chain reaction (qRT-PCR). A total of 2965 DEGs were identified from the ONFH samples, including 602 DE-lncRNAs (such as downregulated FAM201A). In the PPI networks, eight upregulated genes (including FGF2, IGF1, SOX9, and COL2A1) and 11 downregulated genes were among the top 20 genes according to all of the scores, such as degree centrality, closeness centrality, and betweenness centrality scores. Functional enrichment analysis showed that IGF1, SOX9, and COL2A1 were significantly enriched during skeletal system development. Moreover, qRT-PCR experiments detected the upregulation of FGF2 and downregulation of FAM201A in ONFH samples. FGF2 and FAM201A were correlated with the development of ONFH. Besides, IGF1, SOX9, and COL2A1 might also affect the pathogenesis of ONFH.
股骨头坏死（ONFH）是一种常见的致残率较高的骨科疾病，而股骨颈骨折（FNF）是创伤性ONFH最常见的原因之一。本研究旨在揭示ONFH的潜在机制。使用fastx_toolkit和prinseq-lite工具对测序数据进行质量控制。使用R语言中的edgeR软件包鉴定ONFH和FNF样本之间的差异表达基因（DEG，包括mRNA和lncRNA），然后使用BioCloud平台进行富集分析。随后，使用Cytoscape软件构建蛋白质-蛋白质相互作用（PPI）网络。基于Spearman等级相关系数预测DE-lncRNA的靶基因后，使用Cytoscape软件可视化lncRNA-基因共表达网络。此外，使用R语言中的clusterprofiler软件包对靶基因进行功能富集分析。另外，通过定量实时聚合酶链反应（qRT-PCR）检测关键基因。从ONFH样本中总共鉴定出2965个DEG，包括602个DE-lncRNA（如下调的FAM201A）。在PPI网络中，根据度中心性、接近中心性和中介中心性得分等所有得分，前20个基因中有8个上调基因（包括FGF2、IGF1、SOX9和COL2A1）和11个下调基因。功能富集分析表明，IGF1、SOX9和COL2A1在骨骼系统发育过程中显著富集。此外，qRT-PCR实验检测到ONFH样本中FGF2上调和FAM201A下调。FGF2和FAM201A与ONFH的发生发展相关。此外，IGF1、SOX9和COL2A1也可能影响ONFH的发病机制。
