Transcription factor ID2 prevents E proteins from enforcing a naïve T lymphocyte gene program during NK cell development

Abstract

All innate lymphoid cells (ILCs) require the small helix-loop-helix transcription factor ID2, but the functions of ID2 are not well understood in these cells. We show that mature natural killer (NK) cells, the prototypic ILCs, developed in mice lacking ID2 but remained as precursor CD27CD11b cells that failed to differentiate into CD27CD11b cytotoxic effectors. We show that ID2 limited chromatin accessibility at E protein binding sites near naïve T lymphocyte-associated genes including multiple chemokine receptors, cytokine receptors, and signaling molecules and altered the NK cell response to inflammatory cytokines. In the absence of ID2, CD27CD11b NK cells expressed ID3, a helix-loop-helix protein associated with naïve T cells, and they transitioned from a CD8 memory precursor-like to a naïve-like chromatin accessibility state. We demonstrate that ID3 was required for the development of ID2-deficient NK cells, indicating that completely unfettered E protein function is incompatible with NK cell development. These data solidify the roles of ID2 and ID3 as mediators of effector and naïve gene programs, respectively, and revealed a critical role for ID2 in promoting a chromatin state and transcriptional program in CD27CD11b NK cells that supports cytotoxic effector differentiation and cytokine responses.

Helix–loop–helix proteins and the advent of cellular diversity: 30 years of discovery

“…The Id proteins contain an HLH domain but lack a basic region and, upon heterodimerization, neutralize the DNA-binding activities of bHLH proteins. That Id proteins are involved primarily in targeting E proteins was revealed in studies showing that a decline in E-protein activity overcomes the need for Id expression to promote developmental progression (Yan et al 1997;Rivera et al 2000;Boos et al 2007;Miyazaki et al 2011Miyazaki et al , 2017Zook et al 2018).…”

Transcriptional control of natural killer cell differentiation

“…ID2 is expressed throughout early NK cell development and peaks in mNK cells . While Id2 −/− mice have normal numbers of NKPs and iNK cells, the most mature CD27 − CD11b + subset of mNK cells is significantly reduced . Consistent with a role for ID2 in inhibiting E protein activity, mNK cell development in the BM (although not spleen) was normalized in mice lacking both ID2 and the E protein, E2A .…”

“…10,64,65 While Id2 À/À mice have normal numbers of NKPs and iNK cells, the most mature CD27 À CD11b + subset of mNK cells is significantly reduced. 64,66,67 Consistent with a role for ID2 in inhibiting E protein activity, mNK cell development in the BM (although not spleen) was normalized in mice lacking both ID2 and the E protein, E2A. 64 At a transcriptional level, Id2 À/À NK cells ectopically express many T cellrelated genes and have aberrantly open chromatin at T cell-related gene loci, but express lower levels of NK cellrelated genes.…”

“…At a transcriptional level, Id2 −/− NK cells ectopically express many T cell‐related genes and have aberrantly open chromatin at T cell‐related gene loci, but express lower levels of NK cell‐related genes. These findings suggest that ID2 acts to suppress a T cell and promote an NK cell gene signature . In addition, ID2 may also act to tune IL‐15 responsiveness, as treatment of Id2 −/− NK cells with high doses of IL‐15, or deletion of the negative regulator of IL‐15 signaling, suppressor of cytokine signaling 3 (SOCS3), was sufficient to overcome the requirement for ID2 in NK cell development .…”

“…These findings suggest that ID2 acts to suppress a T cell and promote an NK cell gene signature. 65,67 In addition, ID2 may also act to tune IL-15 responsiveness, as treatment of Id2 À/À NK cells with high doses of IL-15, or deletion of the negative regulator of IL-15 signaling, suppressor of cytokine signaling 3 (SOCS3), was sufficient to overcome the requirement for ID2 in NK cell development. 65 ID2 expression and activity are subject to multiple levels of regulation.…”