ZBTB46 defines and regulates ILC3s that protect the intestine

ROR gamma t is a lineage-specifying transcription factor that is expressed by immune cells that are enriched in the gastrointestinal tract and promote immunity, inflammation and tissue homeostasis(1-15). However, fundamental questions remain with regard to the cellular heterogeneity among these cell types, the mechanisms that control protective versus inflammatory properties and their functional redundancy. Here we define all ROR gamma t(+) immune cells in the intestine at single-cell resolution and identify a subset of group 3 innate lymphoid cells (ILC3s) that expresses ZBTB46, a transcription factor specifying conventional dendritic cells(16-20). ZBTB46 is robustly expressed by CCR6(+) lymphoid-tissue-inducer-like ILC3s that are developmentally and phenotypically distinct from conventional dendritic cells, and its expression is imprinted by ROR gamma t, fine-tuned by microbiota-derived signals and increased by pro-inflammatory cytokines. ZBTB46 restrains the inflammatory properties of ILC3s, including the OX40L-dependent expansion of T helper 17 cells and the exacerbated intestinal inflammation that occurs after enteric infection. Finally, ZBTB46(+) ILC3s are a major source of IL-22, and selective depletion of this population renders mice susceptible to enteric infection and associated intestinal inflammation. These results show that ZBTB46 is a transcription factor that is shared between conventional dendritic cells and ILC3s, and identify a cell-intrinsic function for ZBTB46 in restraining the pro-inflammatory properties of ILC3s and a non-redundant role for ZBTB46(+) ILC3s in orchestrating intestinal health.

Automated summary

This study defines ROR gamma t(+) immune cells in the intestine at single-cell resolution and identifies a subset of ILC3s that expresses ZBTB46, a transcription factor shared with conventional dendritic cells. ZBTB46 restrains the inflammatory properties of ILC3s and plays a non-redundant role in orchestrating intestinal health.