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（Systemic lupus erythematosus, SLE）是一类异质性自身免疫性疾病，以多样的临床症状为核心特征。当前多数患者在现有治疗方案下仍会经历不同程度的疾病复发-缓解周期，常因疾病发作需接受住院急症治疗。尽管相较于健康个体，SLE的特征性转录组改变已被广泛报道，但此类特征在疾病发作期接受强化治疗后的响应机制却鲜有探讨。 为更深入解析SLE发作期及治疗过程中的动态转录组特征，本研究对65名SLE患者的配对样本进行了分析：分别采集其住院急症治疗前（SLE1组）与治疗后（SLE2组）的外周血单个核细胞（PBMCs），并通过RNA测序（RNA-sequencing）开展转录组分析。同时纳入15名健康对照者（HC）作为对照组，以此鉴定SLE相关转录组失调特征及其对应的治疗调控效应。 总体而言，本研究在HC、SLE1及SLE2三组样本中分别鉴定出差异表达基因（DEGs）与差异可变剪接基因（DSGs），对上述基因的功能特征进行了系统阐释，并挖掘得到关键分子特征。结合已报道的SLE遗传学研究成果，本研究还对SLE转录组与遗传学特征之间的相互作用进行了探讨与分析。