Regulation of immune response by ATP-dependent chromatin remodeling complexes

Abstract

Cells require several epigenetic programs for development and differentiation, maintenance of homeostasis, and response to environmental stimuli. Dysregulation of these processes can result in developmental disorders, cancers, immunodeficiencies, and other conditions. Immune response to a given stimulus requires a series of tightly controlled epigenetic and gene regulatory events. CD8+ T lymphocyte activation is essential to mediating the immune response to intracellular pathogens and cancer cells. Previous studies have shown that CD8+ T cell activation from a naïve state to an effector state is associated with a net increase in chromatin accessibility, however, the mechanisms by which distinct genomic regions become accessible following stimulation are incompletely defined. The focus of this dissertation is to define the role of the mammalian SWI/SNF (mSWI/SNF or BAF) chromatin remodeling complex, an ATP-dependent multi-subunit protein complex that mediates chromatin accessibility, in CD8+ T lymphocyte activation. Here, we mapped the genome-wide occupancy of mSWI/SNF complexes following activation in primary murine CD8+ T cells and found enhanced chromatin occupancy over regions containing motifs for NFAT and AP-1, transcription factors involved in T cell activation. These changes correlated with increased DNA accessibility and nearest gene expression, activating critical T cell gene regulatory networks critical for T cell response. Importantly, inhibition of mSWI/SNF catalytic activity using a small molecule inhibitor of BRG1/BRM ATPases prior to CD8+ T cell activation resulted in significantly decreased chromatin accessibility at regions occupied by mSWI/SNF complexes and altered expression of genes central to CD8+ T cell activation pathways. In parallel studies, upon deletion of non-canonical mSWI/SNF (ncBAF) complex subunits in a T lymphocyte cell line, we were able to assay the functional role of this complex in responding to stimulus, defining how the ncBAF complex regulates the transcriptional response to activation and upregulation of cell surface markers, including PD-1. Taken together, these studies demonstrate that mSWI/SNF complex activities play critical roles in T cell activation. This knowledge at the level of chromatin accessibility and gene regulatory control furthers our understanding of T cell-mediated responses against viral infections and cancers, and will inform efforts to advance T cell immunotherapies using epigenetic engineering strategies.