Supporting data for “Transcriptomic Features of SLE Patients in Flare and Changes during Acute In-Hospital Treatment”

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease characterized by diverse clinical symptoms. Most patients suffer from varied disease relapse-remission cycles under current treatment regimens, which often leads to acute in-hospital treatment for disease flare. Although the distinct transcriptomic features of SLE have been widely described in comparison to healthy people, how these features could respond to the intensive treatment during disease flare is less discussed.
To better understand the dynamic transcriptomic features during SLE flare and treatment, transcriptome profiles of 65 SLE patients were investigated, before (SLE1) and after (SLE2) patients` acute in-hospital treatment in pairs, via RNA-sequencing profiling of peripheral blood mononuclear cells (PBMCs). Together with 15 healthy donors as controls (HC), SLE-dysregulated transcriptomic features and the corresponding treatment effects on them were identified. 
Generally, differentially expressed genes (DEGs) and differential alternative splicing genes (DSGs) were identified among HC, SLE1, and SLE2. The functional aspects of these genes were described, and key signatures were identified. Together with SLE genetic findings, the interactions between SLE transcriptomic and genetic features were explored and discussed.

系统性红斑狼疮（SLE）是一种异质性的自身免疫性疾病，其临床症状多样。大多数病人在当前治疗方案下经历着不同的疾病复发-缓解周期，这常常导致急性住院治疗以应对疾病发作。尽管与健康人群相比，SLE的特异转录组特征已被广泛描述，但这些特征在疾病发作期间对强化治疗如何作出反应的讨论则相对较少。为了更好地理解SLE发作和治疗过程中的动态转录组特征，我们研究了65名SLE患者的转录组图谱，包括患者急性住院治疗前的（SLE1）和治疗后的（SLE2）情况，通过外周血单个核细胞（PBMCs）的RNA测序分析进行对偶研究。同时，与15名健康捐献者作为对照（HC），确定了SLE失调的转录组特征及其相应的治疗效果。通常，在HC、SLE1和SLE2中发现了差异表达基因（DEGs）和差异选择性剪接基因（DSGs）。描述了这些基因的功能方面，并确定了关键特征。结合SLE的遗传研究结果，探讨了SLE转录组和遗传特征之间的相互作用，并进行了讨论。