SLE risk variants shapes IRF5 alternative promoter isoform usage in B cells 2252005

Introduction Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disease driven by a complex interplay of genetic and environmental factors. Emerging evidence highlights the contribution of alternative splicing and isoform dysregulation to SLE pathogenesis, although the underlying mechanisms require further elucidation. Methods We utilised a publicly available RNA-seq dataset to examine isoform usage in B cells from patients with SLE. Our analysis focused on five distinct B cell subsets to identify isoform alterations. We further investigated the role of Interferon Regulatory Factor 5 (IRF5) in double-negative 2 (DN2) B cells through CRISPR-Cas9 knockout and pharmacological inhibition experiments in primary B cells. Additionally, we integrated genome-wide association study fine-mapping, co-localisation analyses and CRISPR base-editing in the GM12878 cell line to identify a putative causal variant in the IRF5 locus. Results Our analysis identified extensive isoform alterations, notably within DN B cells, which displayed significant changes across hundreds of genes. IRF5, a known SLE risk locus, exhibited significant isoform dysregulation. By knocking out IRF5, we observed a substantial reduction in DN2 B cells, plasmablasts, and MKI67+ proliferating cells, accompanied by decreased production of IL-6 and IL-12. Furthermore, we identified a putative causal variant near the IRF5 transcription start site. Conversion of the non-risk allele to the risk allele induced significant upregulation of the E1B isoform. These findings were reproducible in primary B cells homozygous for the risk haplotype, which also displayed enhanced expansion of DN2-differentiating B cells on day 6 in vitro. Conclusion Our findings underscore a critical role for IRF5 in the differentiation of DN2 B cells and demonstrate how a genetic risk variant associated with lupus leads to isoform-specific dysregulation in B cells. Together, these provide new mechanistic insights into the molecular pathways involved in SLE pathogenesis.