Splicing Factors Uniquely Regulate Macrophage Immune Responses

Abstract

The innate immune response is primarily carried out by phagocytic macrophage cells, which are designed to remove infected and dying cells to protect the host. Macrophages receive thousands of different signals, activating specific responses by the cell. Gene transcription and regulation are therefore very important in order to respond specifically and quickly. Macrophages have evolved to produce a diversified proteome of defense genes through post-transcriptional processing, but how this is regulated by the cell is less clear. One major diversification processing point is pre-mRNA splicing, carried out by both core and auxillary splicing factors. Here, we performed a knockdown screen of the major regulatory splicing protein families in RAW 264.7 macrophage like cell lines: hnRNPs (heterogeneous nuclear ribonucleoproteins) and SRSFs (serine arginine-rich splicing factors). Following RNA-seq and bioinformatics analysis to measure alternative splicing and transcript abundance before and after infection with the bacterial pathogen Salmonella enterica serovar Typhimurium, we identified the gene expression profile of Srsf6 knockdown cells as unique amongst splicing factors queried. Notably, loss of SRSF6 caused upregulation of a subset of innate immune genes called interferon stimulated genes in resting macrophages. We further assessed the potential targets of SRSF6 in macrophages and found that a novel Bax isoform called Bax-k, induces mitochondria stress leading to type I interferon activation via cytosolic DNA sensing and promotes of a pre-apoptotic cell state. Finally, we show that SRSF6 impacts replication of intercellular pathogens Vesicular stomatitis virus and Mycobacterium tuberculosis, illustrating the importance of splicing regulation in regulating infection outcomes.