Chromatin architecture regulating trained immunity in antiviral NK cells

Project Summary Trained immunity is the process by which cells of the innate immune system gain a “memory” of previous infections. Natural killer (NK) cells, innate lymphoid cells, macrophages are among the components of innate immunity where such training has been documented. This R01 will attempt to better understand the molecular mechanisms that underlie trained immunity in NK cells. NK cells protect us against viral infection, and because these cytotoxic lymphocytes are lacking in newborns and immunocompromised people (including cancer and transplant patients), these individuals are highly susceptible to viral infections, most prominently cytomegalovirus. Trained immunity in NK cells can be studied using mouse cytomegalovirus (MCMV) infection, an accurate model of human disease, where we first demonstrated NK cells possess features of adaptive immunity, including antigen specificity, clonal expansion, and long- lived memory. Over the years, my lab has uncovered many transcriptional and epigenetic mechanisms that control the adaptive NK cell response to MCMV infection. This current R01 A1 resubmission will attempt to understand how the genomic 3D architecture impacts trained immunity in antiviral NK cells. In exciting preliminary Hi-C and CUT&RUN data, we observe distinct patterns in the 3D genomic landscape, CTCF binding, and histone modifications as NK cells differentiate in response to MCMV. To investigate how the 3D chromatin architecture controls trained immunity in NK cells during viral infection, we have generated new transgenic and knockout mice, along with novel sequencing techniques (for low numbers of primary lymphocytes) to be used in all 3 aims. In Aim 1, we will test how chromatin organizers regulate 3D genomic landscape dynamics in NK cells during viral infection. Aim 2 will identify transcription factors that control the genomic 3D architecture in MCMV-specific NK cells. In Aim 3, we will determine the importance of putative enhancers and specific chromatin loops that regulate trained immunity in NK cells. This R01 will enhance our understanding of the epigenetic mechanisms underlying NK cell responses, with the hopes of establishing innovative methods by which this potent cytotoxic lymphocyte can be targeted for treatment against infectious diseases and cancer.