Molecular basis for contrasting programs of fetal and adult T cell development

California Institute Of Technology, Pasadena CA

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Abstract

Project Summary T cells are generated in the thymus from gestation through much of the lifespan in mice and humans, and in some ways the products of fetal and postnatal T cell development are highly similar. However, there are several distinct waves of precursors that enter the T-cell program from mid-gestation to puberty, and successive waves make T cells with distinctive, specific differences in their developmental kinetics and qualitative lineage outputs. First-wave fetal thymocytes, for example, generate unique innate lymphoid cell subsets (ILCs) as well as T cells, give rise to unique gd T cell subsets, limit their diversity of T-cell receptor (TCR) gene rearrangements, and differentiate quickly, reaching early maturation milestones in a fraction of the time of postnatal thymocytes. In all these ways they differ from postnatal thymocytes. Importantly, these differences in T-cell development are not only observed in vivo, where the thymic structure itself is undergoing changes, but also, when they differentiate in a common microenvironment, as distinct waves of precursors maintain most of their unique developmental features in vitro in cocultures with Notch ligand-presenting stromal cells (e.g. OP9-DLL1). Thus, fetal and adult precursors are intrinsically programmed to differentiate with strikingly different kinetics and some differences in pathway, despite many similar outputs. Our goal is to determine the regulatory mechanisms that endow the cells with these different versions of the T-cell program. This proposal is for a renewal of a systems biology grant that focused on identifying T-cell developmental speed controllers. Our goal now is to determine how these and other mechanisms may be responsible for ontogenic control of T cell program differences. It is based on new results from our recent single-cell transcriptome analyses, ATAC-seq analyses, in vitro differentiation studies, and novel views of the cells’ regulatory states using specialized transgenic reporter mouse strains. We focus on three proposed mechanisms to explain the difference between first-wave fetal and postnatal precursors: the potential role of genome-wide chromatin states and accessibility; the role of transcription factor Meis1; and the potential modulation of differentiation by a select group of other regulatory factors. We will exploit novel knock-in fluorescent reporter mouse strains to identify previously unidentified developmental branchpoints unique to the first-wave fetal T-cell precursors. In addition, we will use lineage tracing to track whether the cells that give rise to the most fetal-unique descendants also give rise to conventional postnatal-type T cells or whether the fetal thymus is populated by a mosaic of precursors with different lineage biases. Our aims will be: (1) To determine the chromatin states across the genome that distinguish fetal and postnatal T cell precursors (2) To define the impact of Meis1 and select additional trans-acting factors on fetal T cell development (3) To determine whether common or distinct lineage precursors give rise to conventional vs. fetal-restricted cell fates, and to determine the developmental branchpoints when lineage-biasing mechanisms are deployed.