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.