Impact of transposable elements on cis-regulatory variation in T cell activation

PROJECT SUMMARY The immune system is a rapidly evolving defense mechanism against threats both internal: cancer, and external: viruses, bacteria, and other pathogens. Intraspecific sequence variation in both mice and humans can dramatically change infection responses, raising the question: What is driving these regulatory changes in immune responsiveness between individuals? Transposable elements (TEs) are mobile genetic elements that comprise nearly half of the human and mouse genomes, represent a potent source of inter- and intra-species genetic diversity, and can act as cis-regulatory elements by regulating nearby genes. However, the full regulatory contribution of TEs in intraspecific variation within the immune system is understudied. Preliminary analyses in naïve and activated mouse CD8+ T cells, an immune cell responsible for killing infected or cancerous cells, highlight TEs as key sources of cis-regulatory activity. In particular, I have predicted regulatory links between TEs and 1668 genes, of which 178 are differentially expressed across genetically distinct mice strains. Although these results suggest that TEs contribute a sizable number of intraspecific regulatory interactions in mouse CD8+ T cells, it remains unclear whether TEs provide a similar regulatory contribution in human intraspecific variation of CD8+ T cell activation. I propose an interdisciplinary project that will characterize the intraspecific cis-regulatory impact of TEs in both human and mouse CD8+ T cells. Specific aim 1 will use scATAC-seq, scRNA-seq, long-read Nanopore sequencing, and in vitro phenotypic assays on CD8+ T cells from genetically distinct mice lines to validate the intraspecific regulatory activity of candidate TEs from preliminary analyses. The results of aim 1 will – for the first time – identify the phenotypic impact of candidate TE enhancers on CD8+ T cell activation in mouse. Specific aim 2 will utilize publicly available and in-house anonymized human CD8+ T cell genomic data to quantify and compare the gene targets of TE-derived intraspecific variation to those identified from preliminary data in mouse. The results of aim 2 will provide – for the first time – a direct characterization of the cis-regulatory activities of TEs and their contribution to intraspecific variation between human and mouse CD8+ T cell activation. I will utilize prior bioinformatics experience in complex single-cell analyses alongside extensive training in molecular biology to perform the proposed experiments. Further refinement of critical thinking and scientific communication skills will ensure my development into a well-rounded scientist and facilitate a smooth transition into a postdoctoral position post-graduation. The Feschotte and Grimson labs, alongside collaborators in the Rudd lab and Genomics Innovation Hub at Cornell University, have access to considerable experience and resources that will ensure mastery of these skills. Together, this proposal will further our understanding of how TEs facilitate the rapid evolution of the immune system within and between human and mouse.