Fang Yuxuan, Xu Nan, Shen Jiacheng, Chen Hongyi, Li Guoqing
Department of Rheumatology and Immunology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China.
Biochem Genet. 2024 Dec 10. doi: 10.1007/s10528-024-10989-x.
Programmed cell death (PCD) and circular RNA (circRNA) have been found to involve in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to explore PCD mechanisms and gene regulatory networks in RA. RA related to circRNA, mRNA and single-cell data sets were obtained from the GEO database. The limma package was used to screen differentially expressed circRNA and differentially expressed genes (DEGs) of RA. The PCD gene set from literature was intersected with the DEGs of RA to obtain PCD-related DEGs of RA. The ENCORI database was used to predict and construct a competing endogenous RNAs (ceRNA) regulatory network to obtain key circRNAs and PCD-related DEGs. Hub genes were identified from the key PCD-related DEGs in the ceRNA regulatory network through LASSO regression, and a diagnostic model was constructed based on these hub genes. The expression of hub genes in various cells and stages was analyzed using single-cell datasets. Finally, the expression of key circRNAs and hub genes in peripheral blood of RA patients and healthy individuals was verified by PCR. In this study, a total of 71 differential circRNAs and 221 DEGs in RA were obtained, and 23 PCD-related DEGs were identified. Through ceRNA regulatory network, three key circRNAs (hsa_circ_0001241, hsa_circ_0089761, and hsa_circ_0001654) and four hub PCD-related DEGs. Among them, TXN and RRAGD were highly expressed, and PARP1 and TXNIP were lowly expressed in RA. Single-cell analysis revealed that these genes were significantly differentially expressed in myeloid cell subpopulation. PCR results indicated that among the 7 key factors, the expression of hsa_circ_0001241, hsa_circ_0089761, TXN, and RRAGD in RA was consistent with the results of bioinformatics analysis. Hsa_circ_0001241, hsa_circ_0089761, TXN and RRAGD may be potential biomarkers for RA, and their interactions may have significant implications for the pathology of RA.
程序性细胞死亡（PCD）和环状RNA（circRNA）已被发现参与类风湿关节炎（RA）的发病机制。本研究的目的是探索RA中的PCD机制和基因调控网络。从GEO数据库中获取与RA相关的circRNA、mRNA和单细胞数据集。使用limma软件包筛选RA的差异表达circRNA和差异表达基因（DEG）。将文献中的PCD基因集与RA的DEG进行交集分析，以获得RA中与PCD相关的DEG。利用ENCORI数据库预测并构建竞争性内源RNA（ceRNA）调控网络，以获得关键circRNA和与PCD相关的DEG。通过LASSO回归从ceRNA调控网络中与PCD相关的关键DEG中鉴定出枢纽基因，并基于这些枢纽基因构建诊断模型。使用单细胞数据集分析枢纽基因在各种细胞和阶段的表达。最后，通过PCR验证RA患者和健康个体外周血中关键circRNA和枢纽基因的表达。在本研究中，共获得RA中的71个差异circRNA和221个DEG，并鉴定出23个与PCD相关的DEG。通过ceRNA调控网络，确定了三个关键circRNA（hsa_circ_0001241、hsa_circ_0089761和hsa_circ_0001654）和四个与PCD相关的枢纽DEG。其中，TXN和RRAGD在RA中高表达，PARP1和TXNIP在RA中低表达。单细胞分析显示这些基因在髓样细胞亚群中显著差异表达。PCR结果表明，在7个关键因子中，hsa_circ_0001241、hsa_circ_0089761、TXN和RRAGD在RA中的表达与生物信息学分析结果一致。Hsa_circ_0001241、hsa_circ_0089761、TXN和RRAGD可能是RA的潜在生物标志物，它们之间的相互作用可能对RA的病理学具有重要意义。
