Pluto Bioinformatics

GSE135118: CD28 regulation of global alternative splicing changes in activated human CD4+ T cells

Bulk RNA sequencing

Alternative splicing consists of exons that are selectively either included or excluded from the mature mRNA transcript. Previous studies have demonstrated that ~10-15% of alternatively spliced genes undergo signal-induced changes in isoform abundance in activated primary human CD4+ T cells. In the past, signal-induced alternative splicing changes in T cells have been characterized in the context of CD3 and CD28 activation. CD3 is a component of the T Cell Receptor (TCR) which is responsible for recognizing foreign peptides presented on antigen presenting cells. CD28 enhances various signaling events downstream of the TCR to boost the survival of T cells and is required for full T cell stimulation. The contribution of CD28 signaling to transcriptional changes has been well documented, but the impact on splicing has not been investigated.; Here we test the hypothesis that CD28 exerts some of its functional impact through the enhancement of splicing changes in stimulated T cells. We utilized poly(A) RNA-seq and the MAJIQ alternative splicing algorithm to analyze splicing events of human CD4+ T cells stimulated with through CD3 in the presence and absence of co-stimulation with CD28. Consistent with previous studies, we identified approximately 400 and 1,000 significant splicing events induced by CD3/CD28 stimulation at 8 and 48 hours of culture, respectively. Alternative splicing changes induced by CD3 and CD3/CD28 stimuli are highly correlative, however, approximately 23% of alternative splicing changes are further enhanced with additional CD28 costimulation at 8 hours of culture. This enhancement drops to 8% of alternative splicing events by 48 hours. Therefore, we conclude that CD28 costimulation increases the magnitude of splicing during T cell activation, in a manner that is eventually compensated for over time with CD3 stimulation alone. SOURCE: Kristen Lynch (klync@pennmedicine.upenn.edu) - Kristen Lynch University of Pennsylvania