Core-binding factor β and Runx transcription factors promote adaptive natural killer cell responses

Abstract

Natural killer (NK) cells are innate lymphocytes that have features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin-12 (IL-12) signaling through its downstream transcription factor signal transducer and activator of transcription 4 (STAT4) is required for the generation of memory NK cells after expansion. We identify gene loci that are highly enriched for STAT4 binding using chromatin immunoprecipitation sequencing for STAT4 and the permissive histone mark H3K4me3 in activated NK cells. We found that promoter regions of Runx1 and Runx3 are targets of STAT4 and that STAT4 binding during NK cell activation induces epigenetic modifications of Runx gene loci resulting in increased expression. Furthermore, specific ablation of Runx1, Runx3, or their binding partner Cbfb in NK cells resulted in defective clonal expansion and memory formation during viral infection, with evidence for Runx1-mediated control of a cell cycle program. Thus, our study reveals a mechanism whereby STAT4-mediated epigenetic control of individual Runx transcription factors promotes the adaptive behavior of antiviral NK cells.

Epigenetic control of innate and adaptive immune memory

“…As we recently described, IL-12 + IL-18-induced STAT4 occupancy was primarily located at putative enhancer sites (intronic and intergenic regions; Fig. 3a) 18 . In contrast, STAT1 primarily bound to promoter regions in response to IFN-α (Fig.…”

“…STAT4 chromatin immunoprecipitation (ChIP) was performed as previously described 18 . For STAT1 ChIP, 5−10 × 10 6 NK cells (TCRβ − CD19 − CD3ε − F4/80 − NK1.1 + CD49b + ) were sorted from spleens of pooled C57BL/6 mice and incubated overnight (16–18 h) with 100U/mL IFN- α with or without 10 ng/mL IL-2.…”

“…STAT4 ChIP-seq data was processed as described previously 18 . For STAT1 ChIP-seq data, peak-calling was performed using MACS2 with the arguments “-p 1e-2 -m 2 50 --to-large”.…”

Transcriptional control of natural killer cell differentiation

“…Effector NK cells reach peak numbers at day 7, but most eventually die off in the following weeks, leaving behind a small pool of long‐lived memory cells . The expansion, contraction, and memory phases of the anti‐MCMV NK cell response have distinct transcriptional requirements and current understanding of the specific TFs that regulate these phases is described below …”

“…Functionally, STAT4 acts in part by directing a ‘permissive’ chromatin state, likely through the recruitment of histone remodeling enzymes, around target gene loci. Indeed, H3K4 trimethylation at the Runx , Cbfb , and Irf8 promoters was recently shown to occur in a STAT4‐dependent manner during NK cell activation in vitro . The related TF, STAT1 also contributes to the expansion of MCMV‐specific Ly49H + NK cells, acting downstream of type 1 interferon (IFN‐I) signals that serve to protect NK cells from NKG2D‐dependent fratricide .…”