Only about 2% of the mammalian genome contains genes that are translated into proteins. Yet, the vast majority of the genome is transcribed as RNA and lncRNAs account for most of these transcripts. Emerging evidence from our lab and others has defined long non-coding RNAs (lncRNAs) as important regulators of immunity providing a new perspective on gene regulation in the immune system. To date, our studies have focused on murine macrophages and studies in animals. This R21 proposal will advance our understanding of lncRNAs with immunomodulatory functions in human cells, specifically dendritic cells. We will focus on an intergenic lincRNA- Lucat-1; which we identified as a dynamically regulated gene in human monocyte derived dendritic cells exposed to Influenza virus, Herpes Simplex virus and lipopolysaccharide. Using loss and gain of function CRISPr/Cas9-based genome editing approaches we have found that lucat-1 acts as a negative feedback regulator of type I interferon and interferon stimulated gene expression in human dendritic cells.
Aim 1 will advance our understanding of this lincRNA by exploring its role in controlling immune gene expression, defining its genomic targets and identifying its protein binding partners.
Aim 2 will characterize the role of lucat-1 in controlling Influenza virus infection using newly generated lucat-1 KO mice. The underlying hypothesis to be explored in this proposal is that lucat1 represents a conserved regulatory component of the anti-viral response that acts to shut down the type I IFN response in infected cells. We propose that nuclear localized chromatin associated lncRNAs such as Lucat-1 bind the genome to regulate the expression of anti-viral genes. The versatility of these molecules and their ability to engage protein complexes with gene regulatory capacity endows these lncRNAs with the capacity to alter the immune response. Detailed mechanistic studies of how Lucat-1 impact ISG expression in human cells and animals could unveil novel drug targets that could potentially lead to the development of improved therapeutics for diseases associated with excessive production of type I IFNs such as lupus.
The inflammatory response protects us against infection but can also have destructive effects resulting in diseases such as lupus. It is essential that we fully understand how inflammation is controlled. It has been over 10 years since the human genome was sequenced. Since then there has been huge improvements in our ability to carry out sequencing. The classical understanding of the genome was that DNA is transcribed into RNA, which makes proteins that carry out various biological functions. However sequencing studies have shown that only a small portion (2%) of the genome results in protein, yet there are very large amounts of RNA being produced (85% of the genome). The major class of RNA molecules produced from the genome are called long noncoding RNA (lncRNA), which appear to regulate the expression of other protein coding genes. The studies proposed in this application focus on how lncRNAs control immune responses. Our lab has identified important lncRNAs that regulate the immune response in murine cells and animals. Here we propose to study a lncRNA that we have identified which regulates the immune response in human cells. We propose to study the regulation and function of this lncRNA in human dendritic cells and the role of this gene in protecting animals from viral infection. Understanding how lncRNAs function could lead to improved drugs for autoimmune diseases.