Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway

Abstract

Innate lymphoid cells (ILCs) functionally resemble T lymphocytes in cytotoxicity and cytokine production but lack antigen-specific receptors, and they are important regulators of immune responses and tissue homeostasis. ILCs are generated from common lymphoid progenitors, which are subsequently committed to innate lymphoid lineages in the α-lymphoid progenitor, early innate lymphoid progenitor, common helper innate lymphoid progenitor and innate lymphoid cell progenitor compartments. ILCs consist of conventional natural killer cells and helper-like cells (ILC1, ILC2 and ILC3). Despite recent advances, the cellular heterogeneity, developmental trajectory and signalling dependence of ILC progenitors are not fully understood. Here, using single-cell RNA-sequencing (scRNA-seq) of mouse bone marrow progenitors, we reveal ILC precursor subsets, delineate distinct ILC development stages and pathways, and report that high expression of programmed death 1 (PD-1) marked a committed ILC progenitor that was essentially identical to an innate lymphoid cell progenitor. Our data defined PD-1IL-25R as an early checkpoint in ILC2 development, which was abolished by deficiency in the zinc-finger protein Bcl11b but restored by IL-25R overexpression. Similar to T lymphocytes, PD-1 was upregulated on activated ILCs. Administration of a PD-1 antibody depleted PD-1 ILCs and reduced cytokine levels in an influenza infection model in mice, and blocked papain-induced acute lung inflammation. These results provide a perspective for exploring PD-1 and its ligand (PD-L1) in immunotherapy, and allow effective manipulation of the immune system for disease prevention and therapy.

Functional and phenotypic heterogeneity of group 3 innate lymphoid cells

“…1). 11, 23 Whereas ID2 + CHILP give rise to all major ILC subsets, PLZF‐expressing progenitors (ILCP) gave rise to ILC1, ILC2 and NKp46 + ILC3 – but not LTi‐like ILC3 – suggesting that PLZF + ILCP have lost the capacity to generate LTi‐like ILC3 progeny 11. In line with this finding, a bifurcation of ILC progenitor programming occurs before acquisition of PLZF expression that generates a distinct LTi precursor that is Id2 + PLZF − and characterized by the expression of CXCR5, α 4 β 7 and CCR6 (Fig.…”

A Major Population of Functional KLRG1– ILC2s in Female Lungs Contributes to a Sex Bias in ILC2 Numbers

“…The transcription factors Gata3 , Rora , Tcf1 , Ets1 , and Bcl11b guide ILC2 differentiation, and a subset of these are maintained at high levels in mature ILC2s and are required for survival or function in tissues (40). BM ILC precursors (ILCPs) expressing the transcription factor PLZF and surface PD-1 differentiate into the ILC subsets but not NK cells (41, 42). However, parabiosis experiments with adult mice showed that most tissue ILC2s are not circulating or replenished via blood in homeostasis, suggesting the existence of a tissue-resident precursor (43).…”

Re(de)fining Innate Lymphocyte Lineages in the Face of Cancer

“…A fraction of CHILP highly expresses PLZF and PD1 and retains potential for all CD127 hi ILCs, but not LTis. These cells can also give rise to liver-resident innate lymphocytes at a much higher frequency than giving rise to conventional NK cells in both adoptive transfer settings and during the steady state (18,20). Although by this criteria, the vast majority of liver CD49a þ innate lymphocytes are ILC1s, whether circulating NK cells can also upregulate CD49a, downregulate Eomes, and acquire a tissue-resident program is still unknown.…”

“…7). A common progenitor for all ILCs has been identified as expressing both the transcription factor PLZF and the surface marker PD1 (18,20). This population has lost LTi potential, suggesting that, although expressing RORgt, LTis are a distinct lineage of ILCs from ILC3s.…”

“…Of the three classes of ILCs, ILC2s are the most homogeneous and have an identified committed progenitor in the bone marrow (17)(18)(19). ILC3s, although more heterogeneous than ILC2s, share a core signature gene expression program driven by RORgt (encoded by Rorc; ref.…”