Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow

Abstract

Summary Innate lymphoid cells (ILCs) play strategic roles in tissue homeostasis and immunity. ILCs arise from lymphoid progenitors undergoing lineage restriction and the development of specialized ILC subsets. We generated “5x polychromILC” transcription factor reporter mice to delineate ILC precursor states by revealing the multifaceted expression of key ILC-associated transcription factors (Id2, Bcl11b, Gata3, RORγt, and RORα) during ILC development in the bone marrow. This approach allowed previously unattained enrichment of rare progenitor subsets and revealed hitherto unappreciated ILC precursor heterogeneity. In vivo and in vitro assays identified precursors with potential to generate all ILC subsets and natural killer (NK) cells, and also permitted discrimination of elusive ILC3 bone marrow antecedents. Single-cell gene expression analysis identified a discrete ILC2-committed population and delineated transition states between early progenitors and a highly heterogeneous ILC1, ILC3, and NK precursor cell cluster. This diversity might facilitate greater lineage potential upon progenitor recruitment to peripheral tissues.

Single-cell analysis of RORα tracer mouse lung reveals ILC progenitors and effector ILC2 subsets

“…Cytokine-producing ILCs are divided into three groups: group 1 (ILC1s), group 2 (ILC2s), and group 3 (ILC3s). ILCs develop from ILC progenitors (ILCPs) in the bone marrow (BM; Yang et al, 2015; Klose et al, 2014; Constantinides et al, 2014; Xu et al, 2019; Walker et al, 2019). These BM progenitors differentiate along the ILC lineage as they gradually up-regulate the transcription factors TCF-1 (encoded by Tcf7 ), TOX ( Tox ), ID2 ( Id2 ), and PLZF ( Zbtb16 ; Yu et al, 2016; Ishizuka et al, 2016; Harly et al, 2018).…”

The Transcription Factor Promyelocytic Leukemia Zinc Finger Protein Is Associated With Expression of Liver‐Homing Receptors on Human Blood CD56bright Natural Killer Cells

“…(20) PLZF is furthermore highly expressed in murine innate lymphoid cell (ILC) precursors, which give rise to several ILC classes and NK cells. (21)(22)(23)(24) These PLZF hi ILC precursors were able to generate high numbers of lrNK cells, (21)(22)(23) which are considered to be ILC1s in mice. (25) In human NK cells, PLZF expression has also been detected (26,27) but varies between different NK cell subsets.…”

Novel, Non–Gene-Destructive Knock-In Reporter Mice Refute the Concept of Monoallelic Gata3 Expression

“…Whereas traditional methods of cytometric identification require at least five distinct parameters (Lin 2 , CD90 high , Sca-1 high , CD25 + , and CD127 + ) (10), in GATIR mice, two parameters suffice (Lin 2 , vYFP/Gata3 high ). In a recent study, comprehensive characterization of BM-resident ILC progenitors using polychrome knock-in reporter mice and single-cell transcriptome analysis neatly confirms high Gata3 expression as a key marker for ILC2Ps (13). The usefulness of GATIR mice for the identification and quantification of Th2 and ILC2 cell populations has also been highlighted in a recent collaborative study investigating the heterogeneity of ILC2 subsets in mouse models of allergic airway inflammation (63).…”

“…In mature CD4 + T cells, Gata3 expression is essential for the generation of Th2 cells (4)(5)(6). Gata3 is also required for the development and function of several innate lymphoid cell (ILC) subsets (7)(8)(9), including ILC2 progenitors (ILC2Ps), which express particularly high levels of Gata3 transcripts (10)(11)(12)(13). Elevated levels of Gata3 expression have also been noted in a distinct subset of thymus-derived NK cells, termed thymic NK (tNK) cells (14,15).…”