Background/Purpose: T cells from systemic lupus erythematosus (SLE) patients exhibit a hyperactive phenotype with defects in homeostasis, signaling and cytokine production. By discovery approaches, we previously identified the serine arginine-rich splicing factor 1 (SRSF1) in human T cells and showed that it controls genes involved in signaling and cytokine production. We further showed that SRSF1 expression is decreased in SLE T cells, and associates with worse disease. We recently found that mice with conditional knockout of Srsf1 in T cells (Srsf1-T cell ko) exhibit T cell hyperactivity, systemic autoimmunity and lupus nephritis. However, little is known about the molecular targets controlled by SRSF1. Our goal is to identify the genes and pathways controlled by SRSF1 in mice and by comparative analysis evaluate if these are implicated in SLE.

Methods: Effector CD4 T (Teff) cells were generated by stimulating naïve CD4 T cells from spleens of Srsf1-T cell-ko or control WT (n=3) mice for 72h with CD3/CD28 antibodies. RNA from CD4 Teffs was subjected to RNA-sequencing (R-seq). Data was analyzed for differentially expressed (DE) genes, gene set enrichment, Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) pathways. Gene expression omnibus (GEO)2R was used to identify a publicly available dataset (GDS4888) from CD4 T cells in patients with active SLE (n=6, SLEDAI range 6-22, ANA and dsDNA positive) and 4 healthy controls. Comparative analysis of mouse (Srsf1-T cell ko) and human (SLE) gene array data was performed using Metascape to identify overlapping gene signatures in SLE patients controlled by SRSF1.

Results: R-seq analysis from CD4 Teff cells of Srsf1-T cell ko mice revealed 608 significant DE genes compared to WT mice at the 2-fold cutoff with p< 0.05. In the human SLE CD4 T cells transcriptomics analysis, SRSF1 was confirmed to be significantly downregulated in active SLE patients compared to healthy controls. 290 genes were significantly (p< 0.05) changed between patients with active SLE and healthy controls. The top pathways represented in the DE genes in ko mice were cell cycle, Th1 and Th2 differentiation, Th17 differentiation and cytokine-cytokine receptor interaction. Overall the CD4 Teffs showed an elevated T cell activation gene signature. Pathway analysis of the 290 DE genes in SLE patients identified interferon signaling, cytokine production, cytokine receptor interaction, cell migration and lysosomal clearance pathways. Overlapping genes between human and mouse transcriptomics data were analyzed. Specifically, we found 11 genes (CCR1, RHOG, ELL2, IFI16, IFIT3, OAS2, ZER1, PRKD2, RGS3, SAT1, SOCS1) to be significantly altered in active SLE patients, which were regulated by SRSF1 as confirmed by our mouse R-seq analysis.

Conclusion: SRSF1 controls genes involved in T cell homeostasis, activation, cytokine regulation/signaling and differentiation, which are altered in patients with active SLE. Therefore SRSF1 is an important regulator of T cell function and its deficiency may lead to the hyperactive T cell phenotype in active SLE patients. Targeting SRSF1 to correct the aberrant T cell phenotype may lead to novel therapeutics particularly in SLE patients with decreased SRSF1.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/bioinformatics-analysis-of-transcriptomics-data-reveals-that-srsf1-is-a-novel-molecular-brake-for-the-t-cell-activation-program-and-controls-key-cytokine-signaling-genes-implicated-in-systemic-lupus-e/