Genome-Wide Analysis of Immune Activation in Human T and B Cells Reveals Distinct Classes of Alternatively Spliced Genes

Abstract

Alternative splicing of pre-mRNA is a mechanism that increases the protein diversity of a single gene by differential exon inclusion/exclusion during post-transcriptional processing. While alternative splicing is established to occur during lymphocyte activation, little is known about the role it plays during the immune response. Our study is among the first reports of a systematic genome-wide analysis of activated human T and B lymphocytes using whole exon DNA microarrays integrating alternative splicing and differential gene expression. Purified human CD2+ T or CD19+ B cells were activated using protocols to model the early events in post-transplant allograft immunity and sampled as a function of time during the process of immune activation. Here we show that 3 distinct classes of alternatively spliced and/or differentially expressed genes change in an ordered manner as a function of immune activation. We mapped our results to function-based canonical pathways and demonstrated that some are populated by only one class of genes, like integrin signaling, while other pathways, such as purine metabolism and T cell receptor signaling, are populated by all three classes of genes. Our studies augment the current view of T and B cell activation in immunity that has been based exclusively upon differential gene expression by providing evidence for a large number of molecular networks populated as a function of time and activation by alternatively spliced genes, many of which are constitutively expressed.

Identification of CD3ɛ, CD4, CD8β splice variants of Atlantic salmon

“…Because alternative splicing is increasingly known as a regulator of immune function [56,57], we also examined the effect of pathogen encounter on the expression of CD3 3, CD4 and CD8b variants. Interestingly, when fish were infected with IPNV CD3 3 and CD8b variants were not detected in head kidney of salmon suggesting that the gene expression might be shut down in helper and cytotoxic T cells.…”

Interleukin 7 Up-regulates CD95 Protein on CD4+ T Cells by Affecting mRNA Alternative Splicing

“…As transmembrane domain-encoded exon 6 inclusion of CD95 mRNA is reported to be increased during T cell activation ( Fig. 1D) (45), it is possible that alternative splicing could also be involved in the induction of CD95 by IL-7. To validate this hypothesis, RT-PCR was then performed to identify possible changes in CD95 splicing pattern.…”

Allogeneic T cell responses are regulated by a specific miRNA-mRNA network

“…We next determined whether the mRNA landscape of the T cells that respond to alloantigens, syngeneic stimulus, or CD3/28 stimulation is different and linked those to the changes in miRNA enrichment after CLIP, because miRNAs functionally guide miRNPs to target mRNAs (13). T cell activation is dominated by widespread differential gene upregulation (22), which is due at least in part to the alleviation of the miRNA-associated repression of genes. We focused on the group 3 miRNAs, which was the group in which they were decreased in the Allo T cells but increased or unchanged in the CD3/28 T cells when compared with Syn T cells (see above and Supplemental Figure 2).…”

“…Thus, the potential targets in the distinct gene set that is differentially reg- Table 3). The formation of miRNA/AGO/mRNA ternary complexes (11) after CLIP preserves the coexistence of miRNAs and their target transcripts in RISCs and thus permits the identification of more stringent and direct miRNA-mRNA interactions and enhances the true target prediction rate (11,22,23). We therefore used TargetScan (version 6) and miRanda to determine the target frequencies of the group 3 miRNAs (decreased in Allo T cells but increased or unchanged in the CD3/28 T cells when compared with Syn T cells) and their potential targets (Table 1).…”