Transcriptional Landscapes In Lymphocyte Development And Differentiation: Tcf-1 Enforces Epigenetic Identity In Developing T Cells And T-Bet Resolves Functionally Distinct Memory B Cells

An important role of cellular differentiation is to establish distinct and durable cell subsets that serve different functions over the course of an immune response. Here, I investigate the problem of cellular differentiation by considering 1) how epigenetic repression is overcome to establish unique preimmune lymphocyte identity and 2) the durability of intraclonal and interclonal diversification resulting from an immune response. The epigenetic states of hematopoietic cells contain cell-type specific accessible chromatin structures which are developmentally constructed from repressive, compacted chromatin. However, these structures feature binding sites for lineage-specific transcription factors, suggesting these factors play a role in their generation. I used measurements of chromatin accessibility in sequential stages of T cell development from bone-marrow derived progenitors alongside alternative lymphocyte lineages to identify the central role that TCF-1 plays in creating T-cell specific chromatin during differentiation. Genetic deficiency of TCF-1 reduced the accessible T cell chromatin state and the T cell gene program, whereas the ectopic expression of TCF-1 in fibroblasts caused T cell chromatin to become accessible and T cell genes to be expressed. These findings demonstrate that TCF-1 can overcome repressive chromatin to establish a naïve T cell identity distinct from other lymphocyte lineages. Despite our improved understanding of preimmune lymphocyte differentiation, much less is known about the course of lymphocyte differentiation beyond the naïve stage. During immune responses, some activated B lymphocytes express the transcription factor T-bet, but the clonal relationship to their T-bet- counterparts and the durability of the T-bet+ phenotype is unclear. I found that T-bet+ B cells are generated early after influenza infection and develop into a persistent memory pool. Immune repertoire profiling of influenza hemagglutinin-specific T-bet+ and T-bet- memory B cells demonstrates that most clones are unique to their respective subset, but lineage tree analysis of the remaining shared clones shows that T-bet+ clones can stably bifurcate from T-bet- cells. Further, genetic fate-mapping indicates that T-bet expression in B cells is stable. Together, these and other findings suggest that T-bet+ B cells are a distinct and durable memory subset and uniquely contribute to the anti-viral humoral response.