Identification and Validation of ATF3 Serving as a Potential Biomarker and Correlating With Pharmacotherapy Response and Immune Infiltration Characteristics in Rheumatoid Arthritis.
Identification and Validation of ATF3 Serving as a Potential Biomarker and Correlating With Pharmacotherapy Response and Immune Infiltration Characteristics in Rheumatoid Arthritis.
复制标题
DOI：
10.3389/fmolb.2021.761841
复制
发表时间：
2021
影响因子：
5
通讯作者：
Li L
中科院分区：
文献类型：
--
作者：
Hu H;Zhang F;Li L;Liu J;Ao Q;Li P;Zeng J;Li L
背景资料：虽然疾病缓解抗风湿药物（DMARDs）已显着改善类风湿关节炎（RA）患者的预后，约40%的RA患者的反应有限。因此，寻找新的生物标志物对提高RA的治疗效果至关重要。本研究旨在开发一种新的生物标志物，并通过体外研究对其进行验证。 方法：从GEO数据库下载RA患者的RNA-seq和临床病理数据。在GPL 96和GPL 570数据库中筛选差异表达的基因。然后，利用加权基因共表达网络分析（WGCNA），在GPL 96和GPL 570数据库中寻找与正常滑膜和RA滑膜最相关的基因模块。然后将差异表达基因与相关基因模块进行比对，寻找潜在的生物标志物。应用CIBERSORT工具分析活化转录因子3（activated transcription factor 3，ATF 3）表达与免疫细胞浸润的关系，应用基因集富集分析（Gene Set Enrichment Analysis，GSEA）分析高、低ATF 3组差异表达基因的相关信号通路。此外，还在GEO数据库中探索了ATF 3表达与临床参数之间的关系。最后，通过体外细胞实验验证了ATF 3的作用。 结果如下：我们检索了GPL 570和GPL 96数据库中差异表达的基因和最相关的基因模块，并确定ATF 3是一个重要的潜在生物标志物，与一些临床药理学变量相关。免疫浸润分析显示，两个数据库中高ATF 3组活化肥大细胞浸润明显。GSEA显示代谢相关通路属于高ATF 3组，而炎症和免疫调节通路在低ATF 3组中富集。最后，我们验证了ATF 3可以促进RA成纤维细胞样滑膜细胞（FLS）和MH 7A的增殖、迁移和侵袭。流式细胞仪检测显示，ATF 3表达可降低凋亡细胞比例，增加S期和G2/M期细胞比例。 结论：我们成功地鉴定并验证了ATF 3可以作为RA的新生物标志物，其与药物治疗反应和免疫细胞浸润相关。
Background: Although disease-modifying antirheumatic drugs (DMARDs) have significantly improved the prognosis of patients with rheumatoid arthritis (RA), approximately 40% of RA patients have limited response. Therefore, it was essential to explore new biomarkers to improve the therapeutic effects on RA. This study aimed to develop a new biomarker and validate it by an in vitro study. Methods: The RNA-seq and the clinicopathologic data of RA patients were downloaded from Gene Expression Omnibus (GEO) databases. Differentially expressed genes were screened in the GPL96 and GPL570 databases. Then, weighted gene co-expression network analysis (WGCNA) was used to explore the most correlated gene modules to normal and RA synovium in the GPL96 and GPL570 databases. After that, the differentially expressed genes were intersected with the correlated gene modules to find the potential biomarkers. The CIBERSORT tool was applied to investigate the relationship between activated transcription factor 3 (ATF3) expression and the immune cell infiltration, and Gene Set Enrichment Analysis (GSEA) was used to investigate the related signaling pathways of differentially expressed genes in the high and low ATF3 groups. Furthermore, the relationships between ATF3 expression and clinical parameters were also explored in the GEO database. Finally, the role of ATF3 was verified by in vitro cell experiments. Results: We intersected the differentially expressed genes and the most correlated gene modules in the GPL570 and GPL96 databases and identified that ATF3 is a significant potential biomarker and correlates with some clinical–pharmacological variables. Immune infiltration analysis showed that activated mast cells had a significant infiltration in the high ATF3 group in the two databases. GSEA showed that metabolism-associated pathways belonged to the high ATF3 groups and that inflammation and immunoregulation pathways were enriched in the low ATF3 group. Finally, we validated that ATF3 could promote the proliferation, migration, and invasion of RA fibroblast-like synoviocyte (FLS) and MH7A. Flow cytometry showed that ATF3 expression could decrease the proportion of apoptotic cells and increase the proportion of S and G2/M phase cells. Conclusion: We successfully identified and validated that ATF3 could serve as a novel biomarker in RA, which correlated with pharmacotherapy response and immune cell infiltration.