Identification and characterization of small open reading frames translated during inflammation

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PROJECT SUMMARY Next generation sequencing technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to influence phenotype through sequence and structure and not via translated protein products, despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs also called micropeptides) translated from these transcripts are important contributors to diverse biological processes including inflammation and cell viability. An appropriate inflammatory response is critical for host defense against pathogens, but chronic inflammation is associated with many diseases. Macrophages play a significant role in both initiating and resolving inflammation and understanding their part in this process is scientifically and practically important. One long studied - yet not fully understood - model of macrophage proinflammatory polarization involves lipopolysaccharide (LPS) activation of toll-like receptor 4 (TLR4). Following detection of LPS, a signaling cascade initiates leading to the translocation of transcription factor NFkB to the nucleus. This is followed by increased expression of established inflammatory cytokine and interferon genes. However, this also results in changes in expression of many unstudied lncRNAs. In addition to changes in transcription, changes in translation also follow inflammatory stimulation and these alterations have been observed to increase translation of “noncoding” regions in some cases. Indeed our lab and others have observed dramatic changes in associations between lncRNAs and polysomes following LPS stimulation in mouse macrophages. Therefore, the central hypothesis of this proposal is that translation of lncRNAs produce SEPs that play important roles in the TLR4-NFkB inflammatory response and in macrophage viability. To test this hypothesis, I present a strategy for screening lncRNA sORFs with evidence of coding potential in mouse macrophages. The screen will make use of macrophage cell lines with a NFkB-GFP reporter and CRISPR- Cas9 casssette. Secondly, I propose a biomolecular pipeline for mechanistically characterizing a selection of novel SEPs. This work has the potential to identify many novel SEPs that are important for regulating the inflammatory response. This would further our understanding of a model inflammatory pathway and could help identify novel peptides with therapeutic potential or as therapeutic targets.