Extensive Alternative Splicing Patterns in Systemic Lupus Erythematosus Highlight Sexual Differences

Abstract

Substantial evidence highlights divergences in immune responses between men and women. Women are more susceptible to autoimmunity, whereas men suffer from the more severe presentation of autoimmune disorders. The molecular mechanism of this sexual dimorphism remains elusive. Herein, we conducted a comprehensive analysis of sex differences in whole-blood gene expression focusing on alternative splicing (AS) events in systemic lupus erythematosus (SLE), which is a prototype sex-biased disease. This study included 79 SLE patients with active disease and 58 matched healthy controls who underwent whole-blood RNA sequencing. Sex differences in splicing events were widespread, existent in both SLE and a healthy state. However, we observed distinct gene sets and molecular pathways targeted by sex-dependent AS in SLE patients as compared to healthy subjects, as well as a notable sex dissimilarity in intron retention events. Sexually differential spliced genes specific to SLE patients were enriched for dynamic cellular processes including chromatin remodeling, stress and inflammatory responses. Remarkably, the extent of sexual differences in AS in the SLE patients and healthy individuals exceeded those in gene expression. Overall, this study reveals an unprecedent variation in sex-dependent splicing events in SLE and the healthy state, with potential implications for understanding the molecular basis of sexual dimorphism in autoimmunity.

Keywords: alternative splicing; autoimmunity; genomic variation; intron retention; sex.

Figure 1

(A,B) Female-biased and male-biased alternative splicing events grouped into four major classes (alternative acceptor, alternative donor, exon skipping, intron retention) in healthy individuals (A) and SLE patients (B). The number on top of the bars indicates the actual number of significant alternative splicing events in each group. (C,D) Box plot distribution of female-minus-male delta-PSI values of significant alternative splicing events across the four classes of events in healthy individuals (C) and SLE patients (D).

Figure 2

Pathway enrichment analysis of sexually differential spliced genes in SLE and healthy state. Left column contains the pathways enriched in sex-biased alternatively spliced genes in the whole blood of patients with active SLE. Right column contains the corresponding pathways in healthy subjects.

Figure 3

Pathway analysis in genes affected by sex-biased alternative splicing events specifically in the whole blood of SLE patients. The darkness of the orange color reflects the p-value of the given term. The darker the color, the more significant the p-value is.

Figure 4

The 30 top-prioritized sexually spliced genes (according to delta-PSI value in the female-minus-male comparison) in the whole blood of patients with active SLE. Colors correspond to different classes of AS events. Positive delta-PSI values indicate female-biased whereas negative values indicate male-biased splicing events.

Figure 5

Overlap of genes with sex-dependent differential gene expression and differential alternative splicing in the peripheral blood of active SLE patients (A) and healthy individuals (B).

Figure 6

Pathway enrichment analysis of sexually differentially expressed genes in active SLE patients (left column) and healthy subjects (right column).

Figure 7

Correlation analysis between sex-related intron-retained genes’ delta-PSI scores and expression levels in SLE (A) and healthy (B) individuals. The x-axis denotes the log2-fold change in gene expression between females and males, while the y-axis represents the disparity in the intron retention PSI values for this gene. The shaded areas around the regression line represent the 95% confidence intervals for the regression line.