Epigenetic Regulation of T cell differentiation

National Heart, Lung, And Blood Institute

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Abstract

Previously we analysed the epigenomic differences between various T helper cells. The mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNA). These transcripts play essential roles in regulating gene expression and affect various biological processes during development and in pathological conditions. The study of lincRNA function in the immune system is an emerging field. T helper (TH) cells are critical for orchestrating adaptive immune responses to a variety of pathogens; they are also involved in the pathogenesis of different types of immunological diseases including allergy, asthma and autoimmunity. In our recent studies, we have investigated histone modification enzymes in the differentiation of T helper cells. MLL4 is an essential subunit of the H3K4 methylation complexes. We report that MLL4 deficiency compromised regulatory T (Treg) cell development and resulted in substantial decreases in H3K4me1 and chromatin interaction at putative enhancers, a remarkable portion of which were not direct targets of MLL4 but were enhancers that interact with MLL4-bound sites. The decrease in H3K4me1 and chromatin interaction at the MLL4-unbound enhancers correlated with MLL4 binding at distant-interacting regions. Deletion of an upstream MLL4 binding site reduced H3K4me1 at the Foxp3 regulatory elements looped to the MLL4 binding site and compromised both thymic Treg and inducible Treg cell differentiation. We show that MLL4 catalyzed H3K4 methylation at distant unbound enhancers via chromatin looping, thus providing a new mechanism of regulating T cell enhancer landscape and impacting Treg cell differentiation. Even though T-cell receptor (TCR) stimulation together with co-stimulation is sufficient for the activation of both nave and memory T cells, the memory cells are capable of producing lineage specific cytokines much more rapidly than the nave cells. The mechanisms behind this rapid recall response of the memory cells are still not completely understood. Here, we performed epigenetic profiling of human resting nave, central and effector memory T cells using ChIP-Seq and found that unlike the nave cells, the regulatory elements of the cytokine genes in the memory T cells are marked by activating histone modifications even in the resting state. Therefore, the ability to induce expression of rapid recall genes upon activation is associated with the deposition of positive histone modifications during memory T cell differentiation. We propose a model of T cell memory, in which immunological memory state is encoded epigenetically, through poising and transcriptional memory. How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4+CD8+ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment. The transcription factor BCL11B, a critical regulator of T cell commitment, is associated with increased chromatin interaction, and Bcl11b deletion compromised chromatin interaction at its target genes. We propose that these large-scale and concerted changes in chromatin organization present an energy barrier to prevent the cell from reversing its fate to earlier stages or redirecting to alternatives and thus lock the cell fate into the T lineages. More recently, in collaboration with the Zhu and Bhandoola labs, we found the precise timing of transcription factors, T-bet and TCF1, plays critical roles in cell fate decision (JEM, 2018; Nature Immunology 2019). In addition, the nucleosome structure established in naive CD4 T cells can predict the potential of T cell differentiation (Nature, 2018). Using the TrAC-looping technique, we identified thousands of promoter-enhancer interactions during T cell activation, which may be regulated by the AP1 family of transcription factors (Nature Methods, 2018). In collaboration with Drs. Avinash Bhandoola and Jeff Zhu's labs, we have investigated the critical roles of transcription factors TCF1 and GATA3 during ILC development. We found that conditional deletion of these genes critically compromised the generation of these cell in vivo and in vitro. In collaboration with Dr. Jeff Zhu'a lab, we demonstrated that the generation of IgA-producing plasma cells from B cells in the gut occurred efficiently in the absence of both T cells and helper-like ILCs and without engaging TGF- signaling. Nevertheless, B cell recruitment and/or retention in the gut required functional NKp46-CCR6+ LTis. Therefore, while CCR6+ LTis contribute to the accumulation of B cells in the gut through inducing lymphoid structure formation, helper-like ILCs are not essential for the T cell-independent generation of IgA-producing plasma cells. Differentiation of Innate lymphoid cells (ILCs) from hematopoietic stem cells needs go through several multipotent progenitor stages. However, it remains unclear whether the fates of multipotent progenitors are predefined by epigenetic states. Here we report the identification of distinct accessible chromatin regions in all lymphoid progenitors (ALPs), EILPs, and ILC precursors (ILCPs). Single-cell MNase-seq analyses revealed that EILPs contained distinct sub-populations epigenetically primed toward either dendritic cell lineages or ILC lineages. We found that TCF-1 and GATA3 co-bound to the lineage-defining sites for ILCs (LDS-Is), while PU.1 binding was enriched in the LDSs for alternative dendritic cells (LDS-As). TCF-1 and GATA3 were indispensable for the epigenetic priming of LDSs at the EILP stage. Our results suggest that the multipotency of progenitor cells is defined by the existence of heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors.