Identification and functional annotation of alternative splicing events using RNA sequencing in systemic lupus erythematosus

Abstract

Characterised by a wide variety of clinical manifestation and laboratory findings, the heterogeneity of systemic lupus erythematosus (SLE) is prominent and formidable. The transcriptome profile of SLE is a critical bridge between genetic information and disease phenotypes, the research on which has been enabled and promoted by the advancement of high-throughput sequencing technologies such as RNA sequencing in the past decade. However, the feature of alternative mRNA splicing, which is the crucial step for the maturation of mRNA that contributes to the diversity of transcriptome and proteome, has been overlooked in SLE. In this study, the alternative splicing (AS) profiles in SLE were identified and characterised, providing additional insights into the underlying mechanisms of SLE pathogenesis.

The alternatively spliced mRNAs were examined through the comparison between 15 healthy controls and 111 SLE patients in our cohort based on paired-end RNA sequencing data, which was further validated in combination with a publicly available single-end RNA-seq dataset consisting of 18 controls and 99 SLE patients from Europe. Leveraging both exon- and isoform-level AS analysis protocols, 90 alternatively spliced isoforms were identified in SLE patients, which exhibited strong enrichment to antigen presentation, interferon-alpha/beta pathways, as well as lupus and other autoimmune disorders. Furthermore, these AS events were classified into three categories based on their impact on open reading frame and functional protein domains, from which the isoforms of PEPD, MARCHF8, and LRR1 exhibited distinct patterns of alternative splicing with potential functional impact on the autoimmune-related pathways and components. Besides, exon-intron splicing analysis facilitated the demonstration of post-transcriptional activity, where several immunoglobulin genes and alternatively spliced isoforms were observed to be up-regulated in SLE patients.

In conclusion, alternative mRNA splicing is a pivotal mechanism responsible for the diversity of transcriptome and proteome, which has been indicated to participate in the pathophysiology of various autoimmune disorders. This study shed light on the signature of alternative mRNA splicing in SLE together with more functional annotations on its impact, which contributed to the explication of the pathogenesis of SLE.

(332 words)