Innate lymphoid cell development

Innate lymphoid cells (ILCs) develop from ILC progenitors in the bone marrow. Various ILC precursors (ILCPs) with different ILC subset lineage potentials have been identified based on the expression of cell surface markers and ILC-associated key transcription factor reporter genes. This study characterized an interleukin (IL)-7Rα+IL-18Rα+ ILC progenitor population in the mouse bone marrow with multi-ILC lineage potential on the clonal level. Single-cell gene expression analysis revealed the heterogeneity of this population and identified several subpopulations with specific ILC subset-biased gene expression profiles. The role of IL-18 signaling in the regulation of IL-18Rα+ ILC progenitors and ILC development was further investigated using Il18- and Il18r1-deficient mice, in vitro differentiation assay, and adoptive transfer model. IL-18/IL-18R-mediated signal was found to not be required for early stages of ILC development. While Il18r1-/- lymphoid progenitors were able to generate all ILC subsets in vitro and in vivo like the wild-type counterpart, increased IL-18 level, as often occurred during infection or under stress, suppressed the growth of ILCP/ILC in an IL-18Ra-dependent manner via inhibiting proliferation and inducing apoptosis.

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-1hi) marked a committed ILC progenitor that was essentially identical to an innate lymphoid cell progenitor. Our data defined PD-1hiIL-25Rhi 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-1hi 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.

Early hematopoietic progenitors undergo sophisticated developmental processes to become committed progenitors for innate lymphoid cells (ILC) in hematopoietic tissues, which ultimately become mature ILC subsets in the periphery. Basic leucine zipper ATF-like transcription factor (Batf) plays important roles in lymphocyte biology. We report that Batf regulates the production of bone marrow ILC progenitors and maintenance of peripheral ILCs. Batf is most highly expressed in ILCs among all lymphocytes. Data from in vivo and in vitro ILC differentiation experiments revealed that the expression of Batf is induced in early ILC progenitors at the α-lymphoid progenitor stage in response to the cytokine IL-7. Our Chromatin immunoprecipitation and retroviral gene transfer experiments revealed that up-regulated Batf binds and activates transcription of the Nfil3 gene to promote ILC hematopoiesis. Data from bone marrow chimera and parabiosis experiments support that Batf is intrinsically necessary to maintain normal numbers of early and late ILC progenitors in the bone marrow and mature ILC1, ILC2, ILC3, and NK cells in most peripheral tissues. Batf-deficient mice have ILC3 lymphopenia and fail to control Citrobacter rodentium infection. Moreover, ILC2 responses to cytokines were defective in Batf-deficient mice. Thus, Batf is required for normal ILC responses to inflammatory cytokines and bacterial infection. These data suggest that Batf plays fairly comprehensive roles in supporting bone marrow hematopoiesis, maintenance, and effector functions of ILCs.

Identification and characterization of innate lymphoid cells generated from pluripotent stem cells.

Innate lymphoid cells (ILCs) are immune cells that lack specific antigen receptors but possess similar effector functions as T cells. Interestingly, ILCs and T cells express many of the same transcription factors. One such factor is TOX, a sequence non-specific nuclear transcriptional regulator that is crucial for development of both CD4 T cells and ILCs. TOX-deficient mice have significantly reduced number of early innate lymphoid progenitors (EILP) and ILC progenitors (ILCP). Consequently, the mature NK cells, ILC1, ILC2 and ILC3 subsets are greatly reduced in Tox−/− mice. Interestingly ILC3 numbers in gut are not reduced by the absence of TOX. We have discovered that TOX2, another member of the TOX family of HMG-box proteins, is highly expressed in ILC precursors. We generated Tox2−/− mice and found they have reduced ILC3 in gut; however, ILC3 cells in spleen or lymph node are intact. We also observed ILCP in fetal gut and adult gut were significantly reduced in Tox2−/−mice suggesting TOX2 is required for gut ILC3 development. However, ILCP numbers in adult gut of Tox−/− mice were unaffected. We are currently performing single-cell RNA-sequencing on gut ILC3 from Tox2−/− and Tox−/− mice to transcriptionally characterize these cells and to identify the heterogeneity within the ILC3 population. Taken together, our results indicate the existence of at least two pathways of ILC development: a central pathway in bone marrow and fetal liver that is TOX dependent; and a peripheral pathway of development of ILC3 in gut that requires TOX2.

Description Innate lymphoid cells (ILCs) arise in the bone marrow from the Common Lymphoid Progenitor (CLP), and are divided in two major groups, cytotoxic ILCs (NKs) and helper ILCs. To test the role of c-Myb in the development of ILCs, we generated c-Mybf/f;IL7Rα-Cre mice. These mice showed major decreases in ILC numbers and percentages in all measured organs (Bone marrow, lung. liver, lamina propria). In contrast, NK cells were less affected, and most of the reduction in this lineage was in mature NKs. Importantly, the effect on ILCs was already complete in c-Mybf/+;IL7Rα-Cre, suggesting that even partial reduction in c-Myb expression is limiting for the development of ILCs. We then analyzed early ILC and NK precursors in the bone marrow. We did not observe any alteration in NK precursors, but there was a major block at the ILCP stage in ILCs. c-Mybº ILCPs fail to upregulate GATA-3, but expression of Id2 or Tcf7 is not affected. However, overexpression of GATA-3 failed to rescue ILC development, suggesting that c-Myb has additional targets in this process. ATAC-Seq analysis of sorted ILC progenitors showed that c-Mybº precursors have decreased chromatin accessibility across a number of loci, enriched for genes involved in lymphoid development. Our results suggest that c-Myb levels in CILPs are rate limiting, and small changes bias the choice between NK and ILC differentiation, probably by regulating chromatin accessibility across genes important for ILC development. Funding Sources Supported by Oklahoma Center for Sdult Stem Cell Research, NIH/GM P30 GM149376 Topic Categories Hematopoiesis and Immune System Development (HEM)

All lymphocytes are thought to develop from common lymphoid progenitors (CLPs) that are found in the Lin−Sca-1locKitloCD127+Flt3hi bone marrow (BM) cell population. However, only small numbers of T cells and innate lymphoid cells (ILCs) are generated from CLPs transplanted into irradiated mice, suggesting that they might mainly develop from alternative progenitors such as lymphoid-primed multipotent progenitors (LMPPs). We now have identified novel progenitors in adult mouse BM that efficiently develop into all lymphocytes including T cells and ILC2s. The novel progenitors are similar to LMPPs and found in the cKithiSca-1+Flt3+ BM cell subset, but unlike LMPPs they express the lymphoid lineage marker CD127, thus resembling early thymic progenitors (ETPs). Upon transplantation into irradiated mice, CD127+ LMPP-like cells robustly engraft and develop into T, B, NK cells and ILC2s. They are more efficient than LMPPs and CLPs in generating T cells and ILC2s. Similar to LMPPs, they also retain myeloid potentials. Flt3L-deficient mice have greatly reduced LMPPs and CLPs but have almost normal numbers of CD127+ LMPP-like progenitors, pre-ILC2 in the BM and mature ILC2 in the lung. While the exact relationship between CD127+ LMPP-like progenitors, CD127- LMPPs and CLPs are yet to be clarified, these results suggest that CD127+ LMPP-like BM cells are important progenitors for T cells and ILC2s independent of CLPs.

Diverse innate lymphoid cell (ILC) subtypes have been defined, based on effector function and transcription factor expression. ILCs derive from common lymphoid progenitors, although the transcriptional pathways leading to ILC lineage specification remain poorly characterized. Here we demonstrate that transcriptional regulator TOX is required for the in vivo differentiation of common lymphoid progenitors to ILC lineage-restricted cells. In vitro modeling demonstrates that TOX deficiency results in early defects in progenitor cell survival or expansion as well as later stage ILC differentiation. In addition, comparative transcriptome analysis of bone marrow progenitors reveals that TOX-deficient cells fail to upregulate many aspects of the ILC gene program, including Notch gene targets, implicating TOX as a key determinant of early ILC lineage specification.

Helper innate lymphoid cells (ILCs) combat pathogen infection by rapid secretion of cytokines whereas killer ILCs (NK cells) eliminate virus-infected cells or tumor cells during early defense. However, the early development of NK cells and lineage relationships between NK cells and helper ILCs remain elusive. In PLZF lineage tracing model, normal NK cells are traced at a much lower ratio than helper ILCs, which indicates most NK cells develop from progenitors that do not express PLZF. However, it is also possible that most NK cells develop from PLZF-expressing ILC progenitors (ILCPs), but PLZF-labelled NK cells may proliferate less than unlabeled NK cells. To address these possibilities, we transferred ILCPs and its upstream progenitors early innate lymphoid progenitors (EILPs) and all lymphoid progenitors (ALPs), and then assessed PLZF labelling in NK cells derived from these progenitors. We found that ILCP-derived NK cells were traced at a ratio as high as in helper ILCs whereas EILP and ALP-derived NK cells were labelled at a much lower ratio, which is similar to the ratio in normal NK cells. These results indicate that NK cells develop from both ILCP-dependent and ILCP-independent pathways. Our findings establish novel lineage relationships between NK cells and helper ILCs. We are currently assessing whether different developmental pathways of NK cells lead to functionally distinct subsets of NK cells.

The discovery of innate lymphoid cells (ILCs) has revolutionized our understanding of innate immunity and immune cell interactions at epithelial barrier sites. Their presence and maintenance are critical for modulating immune homeostasis, responding to injury or infection, and repairing damaged tissues. To date, ILCs have been defined by a set of transcription factors, surface antigens and cytokines, and their functions resemble those of three major classes of helper T cell subsets, Th1, Th2 and Th17. Despite this, the lack of antigen-specific surface receptors and the notion that ILCs can develop in the absence of the thymic niche have clearly set them apart from the T-cell lineage and promulgated a dogma that ILCs develop directly from progenitors in the bone marrow. Interestingly however, emerging studies have challenged the BM-centric view of adult ILC development and suggest that ILCs could arise neonatally from developing T cell progenitors. In this review, we discuss ILC development in parallel to T-cell development and summarize key findings that support a T-cell-centric view of ILC ontogeny.

Cell lineages derived from common lymphoid progenitors (CLPs) play a critical role in antigen recognition, acute and long term protection against pathogens, and maintenance of immune homeostasis. CLPs give rise to adaptive immune cells that bear unique antigen receptors and to innate immune cells that perform non-redundant roles, particularly during early effector responses, by facilitating local immunity and shaping the ensuing adaptive response. Recent discoveries indicate that innate lymphoid cells (ILCs) exert essential modulatory effects in normal and pathological responses. Because adaptive and innate lymphoid cells share transcription factors, cytokines, and molecular surface markers, it is essential to dissect the contribution of innate lymphoid cell subsets to immune tolerance, maintenance of tissue homeostasis and during the development of inflammatory responses. In this research topic we will focus on the functional diversity and individual roles that the variety of innate lymphoid cell subsets perform in steady state as well as in different pathological conditions including infection and autoimmunity. This will contribute to the generation of a more comprehensive and integrated view of how these cells interact with the environment, collaborate with other cells and regulate tissue homeostasis and immunity in a context-dependent manner. We welcome Original Research, Review, and Mini-review articles related to, but not limited to the following topics: 1. Innate lymphoid cell development and migration 2. Characterization and identification of signals controlling innate lymphoid differentiation and function 3. Molecular interactions between innate lymphoid cells and other immune and non-immune subsets 4. Role of ILCs in tissue homeostasis 5. Role of ILCs in pathology We acknowledge the initiation and support of this Research Topic by the International Union of Immunological Societies (IUIS). We hereby state publicly that the IUIS has had no editorial input in articles included in this Research Topic, thus ensuring that all aspects of this Research Topic are evaluated objectively, unbiased by any specific policy or opinion of the IUIS.

NKp46+ innate lymphoid cells (ILC) modulate tissue homeostasis and anti-microbial immune responses. ILC development and function are regulated by cytokines such as Interleukin (IL)−7 and IL-15. However, the ILC-intrinsic pathways translating cytokine signals into developmental programs are largely unknown. Here we show that the anti-apoptotic molecule cellular FLICE-like inhibitory protein (c-FLIP) is crucial for the generation of IL-7/IL-15-dependent NKp46+ ILC1, including conventional natural killer (cNK) cells, and ILC3. Cytokine-induced phosphorylation of signal transducer and activator of transcription 5 (STAT5) precedes up-regulation of c-FLIP, which protects developing NKp46+ ILC from TNF-induced apoptosis. NKp46+ ILC-specific inactivation of c-FLIP leads to the loss of all IL-7/IL-15-dependent NKp46+ ILC, thereby inducing early-onset chronic colitis and subsequently microbial dysbiosis; meanwhile, the depletion of cNK, but not NKp46+ ILC1/3, aggravates experimental colitis. In summary, our data demonstrate a non-redundant function of c-FLIP for the generation of NKp46+ ILC, which protect T/B lymphocyte-sufficient mice from intestinal inflammation.

Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells

Innate lymphoid cells (ILCs) are tissue resident cells that are triggered through a relatively broad spectrum of alarmins, inflammatory cues, neuropeptides, and hormones. Functionally, ILCs are akin to subsets of helper T cells and are characterized by a similar effector cytokine profile. They also share a dependency on many of the same essential transcription factors identified for the maintenance and survival of T cells. The key distinguishing factor between the ILC family and T cells is the lack of antigen-specific T cell receptor (TCR) on ILCs and, thus, they can be considered the "ultimate invariant T cells". ILCs, like T cells, orchestrate downstream effector inflammatory responses by adjusting the cytokine microenvironment in a fashion that promotes protection, health, and homeostasis at mucosal barrier sites. But also, like T cells, ILCs have recently been implicated in several pathological inflammatory disease states. This review focuses on the selective role of ILCs in the development of allergic airway inflammation (AAI) and fibrosis in the gut where a complex ILC interplay has been shown to either attenuate or worsen disease. Finally, we discuss new data on TCR gene rearrangements in subsets of ILCs that challenge the current dogma linking their origin to committed bone marrow progenitors and instead propose a thymic origin for at least some ILCs. In addition, we highlight how naturally occurring TCR rearrangements and the expression of major histocompatibility (MHC) molecules in ILCs provide a useful natural barcode for these cells and may prove instrumental in studying their origins and plasticity.

ABSTRACTResearch on innate lymphoid cells (ILC) has recently been a fast paced topic of immunological research. As ILCs are able to produce signature Th cytokine, ILCs have garnered considerable attention and have been described to represent the innate counterpart of the CD4+ T helper (Th) cells. The development and function of ILCs are precisely regulated by a network of crucial transcription factors, which are also involved in the development or differentiation of conventional natural killer (cNK) cells and T cells. In this review, we will summarize the key transcriptional regulators and their functions through each phases of ILC development. With the phase of ILC lineage commitment, we will focus in particular on the roles of the transcription regulators Id2 and GATA-3, which in collaboration with other transcriptional factors, are critically involved in the generation of ILC fate determined progenitors. Once an ILC lineage has been established, several other transcription factors are required for the specification and functional regulation of distinct mature ILC subsets. Thus, a comprehensive understanding of the interactions and regulatory mechanisms mediated by these transcription factors will help us to further understand how ILCs exert their helper-like functions and bridge the innate and adaptive immunity.