Zhao Chengmao
Zibo Municipal Hospital, Zibo, 255400, Shandong, China.
Clin Rheumatol. 2021 Mar;40(3):1027-1037. doi: 10.1007/s10067-020-05311-0. Epub 2020 Aug 12.
Nowadays, there are more and more people who have been diagnosed osteoarthritis (OA). However, due to the complex changes of OA, the treatment outcome is not very well. In order to improve this situation, I decided to aggregate a series of data and use complex bioinformatical methods to analyze them, hoping to explore new therapeutic targets.
After downloading and processing the data from Gene Expression Omnibus (GEO) database, I analyzed the relationship between genes and OA formation by the weighted correlation network analysis (WGCNA)and selected the turquoise module which owned the closest relationship with clinical traits. Then, via online database and CIBERSORT algorithm method, I analyzed the function of this key module and the situation of immune infiltration in OA tissues.
With the help of WGCNA and functional enrichment analysis, I found out that most of genes in the turquoise module took part in the inflammation development, immune responses, and cell proliferation, especially the hub gene PRKACB. At the same time, my results of immune infiltration and expression level analysis also showed that PRKACB has a close relationship with immune cells, especially M2 macrophage.
In a word, my results suggested that PRKACB played an essential role in osteoarthritis development. Key Points • Used the "sva" R package to combine the data of 59 samples from four studies to do the bioinformatical analysis. • Identifying the hub gene PRKACB as potential marker for OA and using validation sets to confirm it. • Detecting the situation of immune infiltration in synovium by CIBERSORT algorithm method.
如今，被诊断为骨关节炎（OA）的人越来越多。然而，由于OA的变化复杂，治疗效果并不理想。为了改善这种情况，我决定汇总一系列数据并使用复杂的生物信息学方法进行分析，希望探索新的治疗靶点。
从基因表达综合数据库（GEO）下载并处理数据后，我通过加权基因共表达网络分析（WGCNA）分析基因与OA形成之间的关系，并选择了与临床特征关系最密切的绿松石模块。然后，通过在线数据库和CIBERSORT算法方法，我分析了这个关键模块的功能以及OA组织中的免疫浸润情况。
借助WGCNA和功能富集分析，我发现绿松石模块中的大多数基因参与了炎症发展、免疫反应和细胞增殖，尤其是枢纽基因PRKACB。同时，我的免疫浸润和表达水平分析结果也表明PRKACB与免疫细胞，尤其是M2巨噬细胞密切相关。
总之，我的结果表明PRKACB在骨关节炎发展中起重要作用。要点 • 使用“sva”R包合并来自四项研究的59个样本的数据进行生物信息学分析。 • 将枢纽基因PRKACB鉴定为OA的潜在标志物并使用验证集进行确认。 • 通过CIBERSORT算法方法检测滑膜中的免疫浸润情况。
