Discovery of functional chimeric mRNA encoded proteins in mammalian immunity 2234

Abstract Description Individual mammalian mRNA and protein are thought to be encoded from single genomic loci. Pre-mRNA derived from a gene can undergo cis-splicing to generate distinct protein isoforms, but whether mRNA from geographically distant genes can undergo trans-splicing to produce divergent chimeric transcripts and functional proteins is unknown. Here we develop a pipeline combining long-read direct RNA-seq paired with targeted mRNA splice-isoform analysis and discover a plethora of chimeric mRNA in macrophages that are dynamically regulated during inflammation. We uncovered a protein-coding chimeric mRNA that represents a fusion between the pore forming protein gasdermin D (GSDMD) and a unique C-terminal domain derived from out-of-frame translation of mRNA from Tmem106a (GSDMD:TMEM106A). GSDMD:TMEM106A is upregulated in myeloid cells in response to viral and bacterial infection, and functional analyses demonstrate that GSDMD:TMEM106A protein promotes inflammasome-mediated release of the cytokine IL-1β during pyroptosis. Using lipid nanoparticle delivery and CRISPR/Cas9 gene-editing, we show that GSDMD:TMEM106A protein is both necessary and sufficient to coordinate bacterial defense in vivo. This discovery unveils a new class of protein-coding mRNA defined by naturally occurring transcript fusion events that are agnostic to chromosomal origin. Identifying and targeting these physiologically relevant chimeric mRNA may reveal new therapeutic intervention strategies for human disease. Funding Sources This work was supported by the NIH Directors New Innovators Program DP2AI169979, the Smith Family Foundation Odyssey Award, the HMS-Moderna Artimis program, the Paul Allen Distinguished Investigator Program, the HMS Blavatnik Biomedical Accelerator Program, and generous HMS lab startup funding. Topic Categories Immune Response Regulation: Molecular Mechanisms (IRM)