Differential regulation of lineage-determining transcription factor expression in innate lymphoid cell and adaptive T helper cell subsets

Abstract

CD4 T helper (Th) cell subsets, including Th1, Th2 and Th17 cells, and their innate counterparts innate lymphoid cell (ILC) subsets consisting of ILC1s, ILC2s and ILC3s, display similar effector cytokine-producing capabilities during pro-inflammatory immune responses. These lymphoid cell subsets utilize the same set of lineage-determining transcription factors (LDTFs) for their differentiation, development and functions. The distinct ontogeny and developmental niches between Th cells and ILCs indicate that they may adopt different external signals for the induction of LDTF during lineage commitment. Increasing evidence demonstrates that many conserved cis-regulatory elements at the gene loci of LDTFs are often preferentially utilized for the induction of LDTF expression during Th cell differentiation and ILC development at different stages. In this review, we discuss the functions of lineage-related cis-regulatory elements in inducing T-bet, GATA3 or RORγt expression based on the genetic evidence provided in recent publications. We also review and compare the upstream signals involved in LDTF induction in Th cells and ILCs both in vitro and in vivo. Finally, we discuss the possible mechanisms and physiological importance of regulating LDTF dynamic expression during ILC development and activation.

Keywords: CD4 T helper cells; ILC development; Th cell differentiation; epigenetic modification; innate lymphoid cells; lineage-determining transcription factor.

Figure 1

Cis-regulatory elements at the murine Tbx21, Gata3 and Rorc gene loci. (A) The chromatin accessibility of the Tbx21 gene locus in Th1 cells, NK cells and ILC1s. Tbx21 promoter region is partially accessible in Th1 cells, NK cells and ILC1s. Tbx21-CNS-12 is the major highly accessible site at the Tbx21 gene locus in Th1 cells, and it contains STAT binding motifs and is essential for IL-12/STAT4- and IFN-γ/STAT1-mediated T-bet expression during Th1 cell differentiation. Tbx21-CNS-12 is also a responsive element for T-bet expression during NK cell and ILC1 activation, but it is dispensable for T-bet induction during NK cell and ILC1 development. Tbx21-CNS-3 is an NK-specific DHS, and it is critical for T-bet induction during NK cell development. Tbx21-CNS-8.5 is an NK cell- and ILC1-specific DHS, but this region is dispensable for T-bet induction in NK cells and ILC1s. (B) The chromatin accessibility of the Gata3 gene locus in Th2 cells and ILC2s. Long-range elements and promoter region are critical for the Gata3 transcriptional activity. Gata3-CNS+280 is highly accessible and important for GATA3 expression during thymic T cell and ILCP development, but it is only partially accessible and dispensable for the high levels of GATA3 expression in Th2 cells and ILC2s. The chromatin accessibility around Gata3-CNS+700 increases as cells developing from ILCPs into ILC2Ps and ILC2s. The accessibility of Gata3-CNS+700 is much higher in ILC2s than in Th2 cells, and this region is important for GATA3 expression in ILC2s and has a minimal effect on GATA3 expression in Th2 cells. Gata3-CNS+761/762 has the Gata3 enhancer activity in Th2 cells and ILC2s. Gata3-CNS+740 is a Th2- and ILC2-specific DHS. Gata3-CNS+300 and Gata3-CNS+520 are Th2-specific DHSs. Gata3-CNS+510 is an ILC2-specific DHS. (C) Chromatin accessibility of the Rorc gene locus in Th17 cells, CCR6⁺ ILCs and NKp46⁺ ILC3s. Overall chromatin accessibility at the Rorc gene locus in ILC3s is much higher than that in Th17 cells. Rorc-CNS-1.5 and Rorc-CNS+6 are important for epigenetic modifications of the whole Rorc gene locus associated with active chromatin and the induction of RORγt during Th17 cell differentiation. These two elements are accessible in CCR6⁺ ILC3s and NKp46⁺ ILC3s, but they have limited effect on ILC3 population in steady state. Whether they are responsive elements for RORγt expression upon ILC3 activation is unknown. Rorc-CNS-11 is highly accessible in Th17 cells and ILC3s, and it is important for RORγt maintenance in Th17 cells. Rorc-CNS-7 is an ILC3-specific element. The color from light to dark corresponds to chromatin accessibility from low to high. The width of elements stands for the width of peaks according to DHS-Seq or ATAC-Seq results. The approximate distance of the middle of peaks from TSS is labeled, and the “-” is for upstream and “+” is for downstream of TSS.

Figure 2

T-bet induction in Th1 cells, NK cells and ILC1s (A) IL-12/STAT4, IFN-γ/STAT1, IL-21/STAT1 and IL-27/STAT1 signaling induce T-bet expression through Tbx21-CNS-12 during Th1 cell differentiation and maintenance. IFN-γ and IL-27 also upregulate IL-12R expression in T cells. (B) IL-18/NF-κB signaling induces RUNX3 expression and plays a role in the initial T-bet induction through Tbx21-CNS-3 during NK cell development. ETS1 is critical for the T-bet expression in NKPs, pro-NK cells and mature NK cells. Whether ETS1 directly regulates T-bet induction or indirectly regulates T-bet induction through RUNX3 is not clear. T-bet may self-regulate its expression during NK cell development. IL-18/NF-κB/RUNX3 regulates T-bet expression through Tbx21-CNS-3, and IL-12/STAT4, IFN-γ/STAT1, IL-21/STAT1 and IL-27/STAT1 regulate T-bet expression through Tbx21-CNS-12 during NK cell activation. (C) The mechanism of T-bet induction during ILC1 development is not clear. IL-12/STAT4 and IFN-γ/STAT1 may regulate T-bet expression during ILC1 activation. Only a small proportion of ILC1s express IL-18R.

Figure 3

GATA3 induction in Th2 cells and ILC2s. (A) The Gata3 promoters are critical for the GATA3 induction during Th2 cell differentiation. IL-4/STAT6 directly and vigorously induces GATA3 expression. Notch signal regulates Gata3 promoter activity in CD4 T cells. TCR/NFAT/NF-κB signal is involved in GATA3 induction. GATA3 may self-regulate its expression in Th2 cells under certain circumstances. BCL11B works as a repressive regulator of GATA3 expression in already differentiated Th2 cells. (B) The booster of GATA3 induction during ILC2 lineage determination is unclear. IL-7 signaling may play a role in GATA3 expression in ILC2s. The release of repressive factor BCL11B may be important for the high levels of GATA3 expression. TSLP/STAT5 regulates GATA3 expression in the mature ILC2s, but it is dispensable for GATA3^hi ILC2 development.

Figure 4

RORγt induction in Th17 cells and ILC3s. (A) IL-6/STAT3 and TGF-β/SMAD signaling induce RORγt expression through Rorc-CNS-1.5 and Rorc-CNS+6 during Th17 cell differentiation. IL-23/STAT3 plays a role in RORγt expression when IL-23R is upregulated upon naïve CD4 T cell activation. IL-21 synergizes with TGF-β to upregulate RORγt. RORα and RORγt bind to Rorc-CNS-11 and play important roles in maintaining RORγt levels in Th17 cells. NFIL3 represses RORγt expression in CD4 T cells. (B, C) IL-23 upregulates RORγt expression during CCR6⁺ ILC3 development in vitro, but STAT3 is dispensable for RORγt expression during ILC3 development in vivo. IL-23/STAT3 signaling regulates RORγt expression in mature ILC3s. Hypoxia induced HIF-1α regulates RORγt expression in ILC3s. RA receptor RAR binds to the Rorc gene locus and regulates RORγt expression during CCR6⁺ ILC3 development and ILC3 activation. RUNX3 is critical for the RORγt expression in NKp46⁺ ILC3s. The role of RORα and RORγt in regulating RORγt expression in ILC3s is unclear. c-Maf benefits RORγt levels, but whether this is a direct effect is unknown. RANKL represses RORγt expression in CCR6⁺ ILC3s.