Single-Cell Gene Expression Analyses Reveal Heterogeneous Responsiveness of Fetal Innate Lymphoid Progenitors to Notch Signaling

T and innate lymphoid cells (ILCs) share some aspects of their developmental programs. However, although Notch signaling is strictly required for T cell development, it is dispensable for fetal ILC development. Constitutive activation of Notch signaling, at the common lymphoid progenitor stage, drives T cell development and abrogates ILC development by preventing Id2 expression. By combining single-cell transcriptomics and clonal culture strategies, we characterize two heterogeneous α4β7-expressing lymphoid progenitor compartments. αLP1 (Flt3+) still retains T cell potential and comprises the global ILC progenitor, while αLP2 (Flt3−) consists of ILC precursors that are primed toward the different ILC lineages. Only a subset of αLP2 precursors is sensitive to Notch signaling required for their proliferation. Our study identifies, in a refined manner, the diversity of transitional stages of ILC development, their transcriptional signatures, and their differential dependence on Notch signaling. [Display omitted] •Global ILC progenitor and T precursors are found in the αLP1 compartment•αLP2 compartment is heterogeneously composed of primed ILC precursors•Notch signaling specifically acts on proliferation of an αLP2 ILC2 primed subset•Constitutive NICD expression drives T cell development and restrains Id2 expression Molecular pathways and transcription factors involved in innate lymphoid cell (ILC) development are currently under intense investigation. Chea et al. now characterize different stages of ILC progenitors, from a global ILC progenitor (GILP) to committed ILC precursors, that are differentially sensitive to Notch signaling.