# The development of innate lymphoid cells

Arundhoti Das, Yi Ding, Christelle Harly, Avinash Bhandoola

► To cite this version:

Arundhoti Das, Yi Ding, Christelle Harly, Avinash Bhandoola. The development of innate lymphoid cells. Nature Immunology, 2026, 10.1038/s41590-025-02414-1. hal-05522214

HAL Id: hal-05522214

https://hal.science/hal-05522214v1

Submitted on 21 Feb 2026

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons CC BY 4.0 - Attribution - International License
# Title: The development of innate lymphoid cells

Arundhoti Das<fnref n="1" />,<fnref n="2" />, Yi Ding<fnref n="1" />, Christelle Harly<fnref n="3" /> and Avinash Bhandoola<fnref n="1" />*

## Abstract

Innate lymphoid cells are a diverse group of immune cells that possess many effector functions of T cells but lack somatically generated receptors. They play crucial roles in early immune responses and in maintaining tissue integrity. We review ILC developmental pathways and progenitors in mice, with a particular focus on adult bone marrow but also addressing fetal liver. We present recent insights into the earliest steps of ILC specification, as well as new evidence for developmental pathways that generate two functionally distinct types of natural killer cells. The anatomical locations where ILC progenitors are identified are outlined and evidence supporting ILC development in tissues examined. In addition, key transcriptional regulators that support ILC development are discussed. Although ILC and T-lineage cells use many of the same transcriptional controllers during development, we present new evidence indicating ILC transcriptional programs diverge from T-lineage programs at the earliest known steps of ILC lineage specification.

## Introduction

Innate lymphoid cells (ILC) are immune cells that lack somatically rearranged antigen receptors, distinguishing them from adaptive T and B lymphocytes. They share a developmental origin with adaptive lymphocytes, and they possess the “small, rounded cell” morphology of most lymphocytes when in circulation<fnref n="1" />,<fnref n="2" />. Their small size may enhance motility into and within tissues, and they are capable of extensive proliferation on demand, which can approach levels exhibited by T cells<fnref n="3" />,⁴. ILC are well characterized in mice and humans. They are present in other species although studied in less detail. Natural Killer (NK) cell-like and ILC2-like cells are present in jawless vertebrates, with key ILC-associated genes including *Id2*, *Gata3*, *Nfil3*, *Tcf7* (gene for TCF-1) and *Zbtb16* (gene for PLZF) conserved across both jawless and jawed vertebrates⁵,⁶. However, *RAG* genes, essential for V(D)J recombination in adaptive lymphocytes, are only identified in jawed vertebrates⁷, indicating that ILC likely existed prior to the evolution of adaptive immunity⁵.

The properties and functions of ILC have been reviewed extensively elsewhere⁸⁻¹⁰, and are only briefly mentioned here. ILC share many of the effector functions of T cells, and are capable of rapid cytokine production in response to tissue damage and local environmental cues¹¹. Although their function is often redundant with T cells, ILC can act independently, especially in early life when adaptive immunity is not fully developed¹⁰,¹²,¹³. ILC are equipped with a diverse array of surface receptors by which they sense and respond to a wide range of signals including cytokines,

<footnote n="1">¹ Laboratory of Genomic Integrity, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA</footnote>

<footnote n="2">² Department of Biological Sciences, BITS Pilani, K K Birla Goa Campus, Goa, India 403726</footnote>

<footnote n="3">³ Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, 44007, Nantes, France</footnote>

<footnote>* Corresponding author</footnote>
neurotransmitters and neuropeptides, microbial products, and metabolic cues, allowing them to act
as first responders and modulators of local immune responses<sup>14-17</sup>. Their functions extend beyond
classical immunity, as they contribute to the regulation of tissue repair, metabolism and
thermogenesis<sup>18,19</sup>. Consistent with these roles, many ILC are tissue-resident, demonstrated by
studies using parabiotic mice and photoconvertible reporter “Kaede” mice. These studies revealed
that in mice, ILC at barrier sites are maintained locally at steady state with minimal contribution
from circulating cells<sup>20,21</sup>. Indeed, ILC residing in different tissues display a transcriptional imprint
of their tissue of residence, that presumably reflects their tissue-specific adaptation<sup>22,23</sup>. Although
innate lymphocytes were previously suggested to lack the capacity to form memory, it is becoming
clear that NK cells, ILC2, and ILC3 exhibit some features of memory, sometimes referred to as
trained immunity<sup>24-28</sup>. An important long-term goal is to understand how transcriptional and
epigenetic programming during development befits ILC for their subsequent function.

ILC were initially classified into three major groups based on their effector functions and key
transcription factors expressed at mature stage<sup>29</sup>: T-bet<sup>+</sup> group 1 ILC, which were NK cells and
ILC1 (ref. <sup>30</sup>); GATA-3<sup>+</sup> group 2 ILC, ILC2 (refs. <sup>31-35</sup>); and RORγt<sup>+</sup> group 3 ILC, that were
NKp46-expressing ILC3 (ILC3 in this review) and CCR6-expressing lymphoid tissue inducer
(LTi) cells<sup>36-38</sup>. Group 1 ILC defend against intracellular pathogens<sup>39,40</sup>, ILC2 protect against
multicellular parasites<sup>41,42</sup>, and ILC3 provide protection against extracellular pathogens<sup>43-46</sup>. NK
cells differ from ILC1 as they express and require transcription factor EOMES (ref. <sup>47</sup>) in addition
to T-bet, and have been intensively studied for their ability to kill tumors<sup>3,18,48,49</sup>. LTi cells play a
critical role in the organogenesis of secondary lymphoid structures, including lymph nodes,
Peyer's patches, cryptopatches, and isolated lymphoid follicles<sup>50-54</sup>. This earlier classification was
modified because of newer knowledge of developmental pathways, initially of LTi and more
recently of NK cells<sup>3,10,55</sup>. We thus consider LTi cells, NK cells, ILC1, ILC2, and ILC3 separately
in this review<sup>10</sup>.

ILC can acquire intermediate phenotypes that exhibit characteristics of more than one group<sup>22,30,56-58</sup>, especially under inflammatory conditions<sup>59-62</sup>. In addition, newly described RORγt<sup>+</sup> antigen presenting cells (APC) are tolerogenic antigen-presenting populations expressing RORγt<sup>63-70</sup>. Although distinct from ILC3<sup>66,68,70</sup> (but see refs.<sup>14,65,71</sup>), some RORγt<sup>+</sup> APC populations can be shown to derive from lymphoid progenitors<sup>66,72</sup>. At this time, their developmental pathways remain incompletely understood and they are not further discussed here. Additionally, there is a RORγt<sup>+</sup> population termed double negative ILC3, which lack both NKp46 and CCR6 expression but can secrete IL-17 and IL-22 (refs.<sup>22,73,74</sup>). Their provenance remains to be determined, and they may be heterogeneous, likely including ILC3 and also some RORγt<sup>+</sup> APC.

In this review, we highlight recent advances in understanding early developmental stages of ILC
originating from lymphoid progenitors in mice. We place particular emphasis on central ILC
development within the adult bone marrow (BM) in mice, while also providing a concise overview
of current understanding of ILC development in fetal liver and peripheral tissues.

**Multipotent ILC precursor populations**

ILC differentiation begins in the fetal liver and continues in adult BM<sup>75,76</sup> (Figure 1). All ILC originate from hematopoietic stem cells (HSC) via All-Lymphoid Progenitors (ALP) (Figure 1,
see **Table 1** for progenitor definitions) that possess efficient lymphoid potential but also possess dendritic cell as well as a degree of myeloid lineage potential<sup>77-82</sup>. ALP include the fraction of Common Lymphoid Progenitors (CLP) that possess multipotent lymphoid potential (Flt3<sup>hi</sup> Ly6D<sup>lo</sup> fraction), together with the IL-7Rα<sup>+</sup> fraction of lymphoid-primed multipotent progenitors (LMPP) (ref. 78) that have a similar developmental potential<sup>83</sup>. ALP efficiently generate T cells, B cells and ILC *in vivo*<sup>78,83-85</sup>. *In vitro*, they generate T cells or B cells at single cell level when in appropriate culture conditions. However, only minimal ILC potential can be evidenced *in vitro*<sup>85</sup>, suggesting that this ILC potential most likely derives from a rare subset of precursors within ALP that have initiated ILC specification.

The earliest ILC-committed progenitors are suggested to be common innate lymphoid progenitors (CILP) with the ability to generate all innate lymphocytes<sup>86,87</sup>. Historically, an α<sub>4</sub>β<sub>7</sub>-expressing lymphoid progenitor population (αLP) defined as Lineage-marker<sup>-</sup>IL-7Rα<sup>+</sup>α<sub>4</sub>β<sub>7</sub><sup>+</sup>Kit<sup>low</sup>Flt3<sup>-</sup> was considered to contain early precursors of innate lymphocytes<sup>88-90</sup>. Reporter mice for Id2 (inhibitor of DNA binding 2) and PLZF transcription factors helped refine this population. The multilineage ILC potential of αLP was shown to be restricted to its Id2<sup>+</sup> fraction, termed Common Helper ILC Precursors (CHILP)<sup>30</sup>. CHILP were suggested to represent dedicated precursors for helper ILC lineages that were thought to be LTi cells, ILC1, ILC2, and ILC3 (ref. <sup>10</sup>). Within the CHILP population, multilineage ILC potential was subsequently shown to be restricted to the PLZF<sup>+</sup> fraction, termed ILC Precursors (ILCP). However, it is now evident from the work of several groups that the ILCP population efficiently generates NK cells in addition to ILC1, ILC2, and ILC3, but not LTi cells<sup>3,55,91,92</sup>. Thus, whether a dedicated precursor of helper ILC exists requires reassessment.

Upstream ILC progenitors were initially difficult to identify, partly due to their low IL-7Rα expression. Using TCF-1 reporter mice, Early ILC Progenitors (EILP) were identified in adult BM<sup>93</sup>. ALP can give rise to EILP *in vivo*, and EILP are lineage-traced by IL-7Rα although expressing low levels of IL7Rα, together indicate that EILP develop from IL-7Rα-expressing ALP<sup>85</sup>. EILP can generate NK/ILC1, ILC2, and ILC3 in clonal assays<sup>85,93,94</sup>. Furthermore, short-term culture of EILP resulted in their differentiation into IL-7Rα-expressing PLZF<sup>+</sup> ILCP<sup>85</sup>, suggesting that ILCP are downstream of EILP. Heterogeneity for lineage potential existed within the originally described EILP population<sup>94,95</sup>, with one subset possessing dendritic cell lineage potential in addition to ILC lineage potential; and one subset committed to ILC lineages, similar to ILCP. Thus, we now use the term EILP to describe specified ILC progenitors that possess dendritic and ILC lineage potential and express TCF-1, but not PLZF; whereas ILCP refer to committed ILC progenitors downstream of EILP, expressing both TCF-1 and PLZF<sup>3,55,85,92,94,95</sup>.

The identification of IL-7Rα<sup>lo/-</sup> EILP (ref. 93) raised the possibility that IL-7Rα was downregulated early during ILC specification from ALP, and therefore, that developmental intermediates between ALP and EILP might lack IL-7Rα. To identify such precursors, an *Il7r*-lineage tracing mouse was used to characterize all early lymphoid precursors that had an history of expression of IL-7Rα, called *Il7r*<sup>LT+</sup> population<sup>96</sup>. This strategy identified ALP, EILP, and presumably all developmental intermediates in between. In particular, it identified an α<sub>4</sub>β<sub>7</sub><sup>+</sup>Tcf7<sup>-</sup> population that efficiently generated ILC *in vitro*, and thus likely included ILC-specified precursors upstream of EILP. scRNAseq of the *Il7r*<sup>LT+</sup> population confirmed the inclusion of developmental intermediates between ALP and EILP, and captured progressive transcriptional changes from ALP to EILP,
indicating that it likely includes nearly all developmental intermediates between these two
precursor populations⁹⁶. These rare intermediates included precursors expressing NFIL3 but not
TCF-1 that have been identified by scRNAseq, but remain to be phenotypically defined. We refer
to these NFIL3⁺TCF-1⁻ precursors as NLP (NFIL3⁺ Lymphoid Precursors) in this review.

Thus, a BM ILC developmental pathway proceeds through the successive stages of multipotent precursors ALP, NLP, EILP, and ILCP (Figure 1). Stage specific requirements for transcription factors support the distinction of these populations: RUNX factors are required for ALP development onward⁸⁵, NFIL3 is required for the specification of ALP into NLP⁹⁶, TOX is required for progression of NLP into EILP⁹⁶, TCF-1 is required at the commitment checkpoint between EILP and ILCP⁹⁵. Id2 and GATA-3 additionally play important functions at EILP stage⁸⁵,⁹³, although their precise points of requirement remain to be clarified.

## Shared pathway to ILC1, ILC2 and ILC3 differentiation

Gene-targeted mice that abrogate ILC development at specific developmental transitions are useful to investigate the origin of individual ILC lineages. Mice deficient for NFIL3 or TOX, which are required for NLP and EILP development respectively⁸⁵,⁹⁵,⁹⁶, lack most ILC lineages⁹⁷⁻¹⁰³. This result implied that these lineages develop through the shared developmental pathway characterized in the adult mouse BM, or through very similar pathways, up to the EILP stage. However, some tissue-resident ILC lineages were reported to still be present in NFIL3-deficient mice⁹⁷,¹⁰⁰,¹⁰⁴⁻¹⁰⁶, and in TOX-deficient mice¹⁰⁷. Because compensatory mechanisms such as proliferation at mature stage might mask developmental defects, competitive BM chimeras can be necessary to provide evidence of clear developmental defects. The development of salivary gland tissue-resident NK cells from NFIL3-deficient hematopoietic precursors has been confirmed in a competitive setting¹⁰⁸, clearly indicating that this lineage develops independently of the main BM developmental pathway.

One lineage-tracing mouse model based on Cre expression driven by Zbtb16 locus control elements has further been instrumental in discriminating between ILC lineages that originate from Zbtb16-expressing precursors, or independently of such precursors⁵⁵. However, because some HSC were labelled by Zbtb16, reliable lineage-tracing could only be obtained in hematopoietic chimeras reconstituted with non-lineage traced HSC⁵⁵. This caveat entails that Zbtb16-lineage tracing cannot be investigated during fetal life, and that ILC development in these chimeras may not be fully representative of physiological ILC development, which is layered throughout embryonic and adult life⁷⁵,¹⁰⁹⁻¹¹². Nonetheless, this model suggested that during adult life, so-called “helper” ILC lineages originate from ILCP or other putative Zbtb16-expressing precursor. On the other hand, LTi cells and most NK cells appeared to diverge from the main path of ILC development prior to the Zbtb16-expressing stage³,⁵⁵. It thus initially implied the existence of a developmental split between helper ILC and NK cells. However, the recent identification of a functionally distinct subset of EOMES-dependent splenic NK cells called NK2 that is highly lineage traced, as opposed to non-lineage-traced NK1 (ref. ³), may challenge this helper ILC versus cytotoxic NK cell developmental model (Figure 1).

Lineage-restricted progenitors have also been identified in adult BM in mice: ILC2-restricted progenitors also referred to as mature ILC2 (refs. 23,32,92,113); putative ILC1 progenitors³⁰; and rare ILC3 progenitors¹¹⁴. In humans, the developmental pathway of ILC is less well defined than in
mice<sup>115,116</sup>. Human ILC originate from CD34<sup>+</sup> progenitors found in the BM, cord blood and peripheral blood<sup>117,118</sup>. Several ILC progenitors are found in peripheral tissues in mouse and human, and are discussed in detail later.

Thus, available results together indicate that development of adult ILC in the BM proceeds through ALP, NLP, EILP and ILCP stages. NK1 cells and adult LTi diverge from the main BM ILC developmental pathway prior to the ILCP stage, whereas ILC1, ILC2, ILC3 and NK2 cells diverge after this stage (Figure 1).

## NK cell development

Early steps of NK cell development occur in the BM in adult mice<sup>119</sup>, and several populations of BM cells have been proposed to represent dedicated NK precursor populations. Refined NK cell progenitors (rNKP), identified as Lineage-marker CD27<sup>+</sup>2B4<sup>+</sup>Flt3<sup>-</sup>CD122<sup>+</sup>, can give rise to NK cells<sup>120</sup>. However, their ability to differentiate into other ILC subsets was not evaluated. Notably, a subset of rNKP expresses PLZF and α4β7, and about 40% are lineage-traced by PLZF, suggesting that rNKP are a heterogeneous population that may include some ILCP<sup>121</sup>.

Only ~20% of NK cells are lineage-traced by Zbtb16 versus ~70-80% of ILC1 and ILC2, suggesting that most NK cells could develop independently of PLZF<sup>+</sup> ILCP<sup>55</sup>. Consistent with this, recent work identified Early NK Progenitors (ENKP) in adult BM that are biased toward the NK lineage and likely represent the main source of NK cells<sup>3</sup>. ENKP are minimally traced by PLZF, and ENKP-derived NK cells (termed NK1) also show low levels of PLZF tracing (~10%). Thus, they are distinct from ILCP-derived NK cells (termed NK2), which are highly traced by PLZF (~70%), similar to ILC. This supports the idea that NK cells develop through at least two distinct pathways: an ILCP-independent pathway via ENKP that generates most NK cells which are NK1, and an ILCP-dependent pathway that generates a smaller subset of cells within the NK population which are NK2<sup>3</sup> (Figure 1). Tissue-resident NK cells are lowly traced by PLZF, suggesting they may be developmentally related to splenic NK1 cells<sup>3,122,123</sup>. Transcriptional differences observed between splenic NK1 and NK2 cells are also evident when human blood CD56<sup>dim</sup> and CD56<sup>bright</sup> NK cells are compared, suggesting these developmental pathways may be conserved between mice and humans<sup>3,124</sup>. Unlike in mice, where high levels of PLZF lineage-tracing can identify NK2, and Ly49H and Ly49D expression can reliably identify NK1 (ref. <sup>3</sup>), available markers used to define human NK lineages including CD56 are likely to be plastic<sup>125</sup>, and reliable markers that can distinguish human NK1 from NK2 lineages by flow cytometry are not yet described.

Together with differences in Ly49H and Ly49D expression, NK1 and NK2 cells are functionally distinct<sup>3,92</sup>. Greater frequencies of NK2 cells produce IFN-γ in some disease models<sup>3</sup>. Compared to NK1, NK2 also express higher level of XCL-1, a chemokine that attracts dendritic cells to tissues including tumors, suggesting possible anti-tumor roles of NK2 cells<sup>3,126</sup>. Treating mice with Ibiglustat, a glucosylceramide synthase inhibitor, particularly affected Ly49H<sup>+</sup> (NK1) cells<sup>127</sup>. Thus, NK1 and NK2 may have different requirements for glycosphingolipid synthesis for their development. In human, the transcription factor MEF2C is preferentially required for the development of CD56<sup>dim</sup> NK cell over CD56<sup>bright</sup> NK cells<sup>128</sup>. These data indicate mechanistic differences in the development of NK1 and NK2 cells.
Another progenitor population called aceNKP was described in the BM<sup>129</sup>. It gives rise to ILC1 and NK cells but not other ILC subsets, both *in vivo*, and at the clonal level *in vitro*<sup>129</sup>. AceNKP express NKG2A/C/E<sup>129</sup>, and are thus phenotypically distinct from ENKP<sup>3</sup>. Furthermore, aceNKP generate NK cells that lack Ly49H or Ly49D<sup>129</sup>, consistent with the NK2 phenotype<sup>3</sup>. Therefore, aceNKP could be an NK/ILC1 progenitor downstream of ILCP. Recently, EOMES<sup>hi</sup>NK<sup>neg</sup> progenitors, defined as Lineage-marker<sup>-</sup>NK1.1<sup>-</sup>*Eomes*-GFP<sup>+</sup>*Tcf7*-mCherry<sup>+</sup>, were also identified in the BM with NK lineage-biased potential<sup>130</sup>. As ENKP expressed low levels of EOMES, they are likely developmentally earlier progenitors than EOMES<sup>hi</sup>NK<sup>neg</sup> progenitors.

Expression of CD27, CD11b, and KLRG1 on the cell surface has been used to track NK cell maturation<sup>131,132</sup>. However, their expression also differs between NK1 and NK2 mature subsets<sup>3</sup>, suggesting they may in fact also reflect NK lineage heterogeneity. Hence, studies of NK maturation using these markers should also differentiate NK1 and NK2 cell lineages.

Together, these findings suggest NK cell development follows at least two distinct trajectories (Figure 1): an ILCP-independent pathway via ENKP and likely downstream EOMES<sup>hi</sup>NK<sup>neg</sup> progenitors, which give rise to the majority of NK cells (NK1); and an ILCP-dependent pathway via ILCP that may generate aceNKP, contributing to a smaller NK2 subset. Although the precise developmental relationships among these NK-committed progenitors remain unclear, their existence highlights the diverse origins of functionally distinct NK cells.

LTi cell development

Lymphoid tissue inducer (LTi) cells were the first identified members of the ILC family. They emerge during embryogenesis, and are important in initiating the formation of secondary lymphoid structures including lymph nodes, Peyer's patches, and intestinal lymphoid follicles<sup>38,133,134</sup>.

The fetal liver is the dominant source of LTi progenitors and mature LTi cells<sup>57,89,110,135,136</sup>. LTi cells arise from CLP in the fetal liver around embryonic day 12.5 via αLP (ref. <sup>89</sup>) redefined in later studies to include Flt3-expressing cells<sup>94,137</sup>. Fate-mapping studies using *iCdh5<sup>tdT</sup>* and *iCxcr4<sup>tdT</sup>* mouse models indicated that embryonic LTi cells derive from hematopoietic cells in the aorta-gonad-mesonephros region rather than the yolk sac<sup>135</sup>. These embryonic LTi progenitors colonize developing lymphoid structures during gestation but are gradually replaced after birth by BM-derived counterparts as the half-life of LTi cells is around three weeks<sup>57</sup>.

Commitment to the LTi lineage is marked by the induction of *Rorc* in αLP, distinguishing these cells from ILCP within the same αLP population that express PLZF<sup>94</sup>. *Rorc*<sup>+</sup> αLP are the earliest identified stage in LTi cell development (Figure 1). These *Rorc*<sup>+</sup> αLP are abundant in the fetal liver but are rare in adult BM<sup>94</sup>. *Rorc*<sup>+</sup> αLP do not express TCF-1 but express RORγt whereas EILP express TCF-1 but lack RORγt expression<sup>94</sup>. Short-term culture of *Rorc*<sup>+</sup> αLP led to upregulation of TCF-1 expression and generation of downstream LTi progenitors (LTiP)<sup>94</sup>. LTiP have been identified in fetal liver and adult BM<sup>94,138,139</sup>. These LTiP express high levels of RORγt and Id2 but lower levels of GATA-3 compared to ILCP<sup>94,138</sup>. They efficiently give rise to LTi cells, but not ILC1, ILC2, ILC3 and NK cells in small intestinal lamina propria (siLP) *in vivo*<sup>138</sup>. *Rorc*<sup>+</sup> αLP were proposed to arise directly downstream of CLP<sup>94</sup>. Consistently, fetal LTi were reported in NFIL3-deficient mice, albeit in two-fold diminished numbers<sup>88,96,98,101,102</sup>, implying that LTi may
diverge from other ILC very early during development, possibly prior to the NLP stage (Figure 1).

**Other distinct aspects of fetal ILC development**

In addition to LTi progenitors, other early ILC progenitors, EILP and ILCP, were identified in fetal liver and fetal gut⁵⁵,⁹⁴,¹³⁶,¹⁴⁰,¹⁴¹. Arginase-1-expressing ILCP (Arg-1⁺ ILCP) were detected in both fetal gut and fetal liver; however, these Arg-1⁺ ILCP have not been detected in adult BM¹⁴⁰. It remains unclear whether Arg-1⁺ ILCP represent a distinct fetal population with limited similarity to adult BM ILCP. Because PLZF lineage tracing experiment to assess contribution of ILCP can only be performed in BM chimeras, our knowledge of fetal ILC is necessarily more limited.

During fetal development, several lineage-committed ILC progenitors have been identified, revealing added complexity in the early establishment of ILC lineages. A Lineage-marker Sca1⁺Mac1⁺ hematopoietic progenitor population can preferentially give rise to ILC1 over NK cells and undergoes local expansion via IFN-γ-mediated feedback from ILC1 (ref. ¹⁴²). In addition, bipotent CD94-expressing ILC1-ILC3 precursors (ILC1/ILC3P) capable of generating both ILC1 and ILC3, as well as unipotent ILC2P, were detected at higher frequencies in the fetal liver, lung and intestine compared to adult tissues⁷⁵. Short-term *in vitro* culture and *in vivo* transfer of ILCP resulted in their differentiation into ILC1/3P, indicating that ILC1/3P are downstream of ILCP⁷⁵. This study also used *Fgd5* fate-mapping mice, which specifically labels HSC from both fetal liver and BM, but does not directly label downstream progenitors such as ALP or ILCP in the fetal liver, adult BM or peripheral tissues. The *Fgd5* fate-mapping analysis revealed that fetal liver hematopoiesis continued to contribute to ILC progenitors in tissues. The contribution of BM hematopoiesis to tissue-resident ILC progenitors and mature ILC was lower but detectable, both at steady state and during infection. BM hematopoiesis primarily contributed to BM ILC2 and NK cell pools⁷⁵. A study in humans reported that yolk sac contained hematopoietic progenitors with ILC potential¹⁴³, however in mice such progenitors with ILC potential were not identified⁷⁵,¹³⁵, suggesting potential differences in ILC developmental pathways between mice and humans.

These findings together indicate how progenitors from distinct sources, fetal liver and adult BM, contribute to shape the adult ILC pool. This layered developmental input adds to the potential complexity of ILC populations. Whether these distinct precursor origins during fetal and adult life lead to functional heterogeneity among adult ILC is an important question for future investigation.

**ILC progenitors in tissues**

At steady state and also during infection that induces ILC population expansion, the contribution of BM hematopoiesis is relatively low⁷⁵. This suggests that ILCP residing in peripheral tissues may contribute to the local ILC pool¹⁴⁴, with the tissue microenvironment influencing their developmental fate¹⁴⁵. In a process termed ILC-poiesis, ILCP circulate, and are thought to enter tissues where local signals trigger their differentiation into mature ILC subsets on demand¹⁴⁴,¹⁴⁶,¹⁴⁷. Alternatively, ILCP (see Table 2 for ILC progenitors in tissues) found in tissues may originate partly or entirely from upstream progenitors that are themselves tissue-resident⁷⁵,¹⁴⁸. This requires further investigation in each individual tissue containing ILC.
In the lung, ILCP are present in both neonatal and adult mice<sup>109,111,149-151</sup>. Lung ILCP share transcriptional similarity with BM ILCP and possess the capacity to differentiate into ILC1, ILC2, ILC3, and NK cells<sup>111,149</sup>. A recent study identified tissue-resident ILCP in the adult siLP using Id2 and RORγt transcription factor reporter mice. These siLP ILCP were transcriptionally similar to BM ILCP. Although siLP ILCP retained the potential to generate all ILC subsets, they showed a bias toward the ILC3 fate within the siLP. Interestingly, when siLP ILCP settled in other peripheral tissues, their lineage potential was heavily skewed towards group 1 ILC, distinct from BM ILCP<sup>145</sup>. These, together with other findings<sup>150,152,153</sup>, highlight the critical role of the local tissue microenvironment in directing ILC lineage specification and maturation.

In humans, committed ILC progenitors are identified in many tissues<sup>154</sup>. Common innate lymphoid cell progenitors (CILCP), defined as Lineage-marker<sup>-</sup>CD34<sup>+</sup>CD45RA<sup>+</sup>Kit<sup>+</sup>IL-1R1<sup>+</sup>RORγt<sup>+</sup>, are described in secondary tissues such as tonsils, spleen, and lymph nodes but are absent in the BM, cord blood or peripheral blood. CILCP are suggested to generate all ILC subsets, but not T cells or dendritic cells *in vitro*, although clonal assays have not been performed<sup>155</sup>. CD34<sup>-</sup>Kit<sup>+</sup> ILC progenitors were identified in peripheral blood and tissues that generated ILC *in vivo* and *in vitro*<sup>146,156</sup>. Another study identified Lineage-marker<sup>-</sup>CD34<sup>+</sup>CD127<sup>+</sup>IL3RA<sup>+</sup> progenitors using single-cell RNA sequencing in human fetal liver and intestine from 8-12 post-conception weeks. These progenitors generated NK cells, ILC1 and ILC2 as well as T cells, B cells and myeloid cells but not ILC3 (ref. <sup>157</sup>). Several additional lineage-restricted progenitor populations are described in humans<sup>118,144,155,156,158</sup>.

Together, these studies indicate the presence of ILC progenitors across various tissues in both mice and humans (Table 2), revealing that ILC development can occur at extramedullary sites. Peripheral tissues harbor ILCP whose lineage potential is shaped by local microenvironment. The contribution of these tissue-resident progenitors adds substantial complexity to our understanding of ILC development, highlighting that ILC diversity arises not only from central progenitors but also from locally maintained precursor pools. However, the relative contribution of tissue-resident versus BM-derived ILC progenitors to the functional and phenotypic diversity of ILC remains to be better defined.

Transcriptional control of early ILC specification

Comparison between ILC development and T cell development has provided important insights
into the mechanisms underlying early ILC development<sup>159-161</sup>. Indeed, ILC and T cells develop
from a common progenitor, ALP (refs. <sup>162-164</sup>) and share expression of several transcriptional
controllers, including transcription factors TOX, TCF-1, GATA-3, and Bcl11B during
development<sup>29,85,93,95,107,165</sup>. Furthermore, at mature stages, T cell subsets and corresponding ILC
lineages express the shared factors T-bet, GATA-3, and RORγt, which control shared functions
including cytokine production<sup>2,161,166,167</sup>. The striking similarities between T cells and ILC extend
to Tcr expression in early ILC precursors, although these genes do not have known functions in
ILC<sup>85,91</sup>. However, differences between ILC and T cells are also evident early during development,
including expression of ILC-specific factors NFIL3 and Id2; and some of the mechanisms
controlling expression of the shared transcription factors T-bet, GATA-3, and RORγt also differ
between these two lineages<sup>168</sup>. Studies investigating the functions and mechanisms of action of
shared and ILC-specific transcription factors in T cells and ILC in mice have started unveiling
possible mechanisms that underlie the acquisition of similarities and differences between the two lineages.

TCF-1 and GATA-3 are each required early during T cell and ILC development, at ETP (for T cells) and EILP (for ILC) stages (Figure 1) respectively⁸⁵,⁹⁵,¹⁶⁵,¹⁶⁹⁻¹⁷³. This suggests they may play similar functions in both lineages, and may underlie the acquisition of some of the functional similarities evident at mature stages. This speculation is supported by the available data for TCF-1. Indeed, forced expression of TCF-1 in lymphoid precursors *in vitro* is sufficient to drive the expression of shared genes such as *Gata3*, *Bcl11b*, and *Tcr* genes, and TCF-1 binds to shared regions in T cells and ILC, including an enhancer important for the regulation of *Gata3* expression in T cell and ILC precursors¹⁷⁴,¹⁷⁵. TCF-1 may also repress myeloid and dendritic cell fate by directly repressing myeloid genes such as *Gata2*⁹⁵,¹⁷¹,¹⁷⁶. Nonetheless, TCF-1 additionally plays lineage-specific functions. In ILCP, it may contribute to the induction of PLZF, which is required for ILC2 (ref. ⁵⁵), but is not required for early T cell development¹⁷⁷. It also contributes to the expression of *Tox2* at the ILCP stage, which is required for the maintenance of gut-resident ILC3 and LTi cells²². Similar to what is known for early T-lineage development¹⁷⁸, GATA-3 levels are critical for gene regulation in ILC subsets, as low levels of GATA-3 expression restored by a transgene in *Gata3*fl/fl *Vav*Cre mice were sufficient to rescue the number and function of LTi cells, whereas they failed to promote the development of ILCP and mature ILC1, ILC2 and ILC3 in peripheral tissues¹³⁸. TCF-1 and GATA3 can co-bind to lineage-defining sites in EILP, indicating these factors may work together to mediate ILC lineage commitment¹⁷¹.

In contrast to TCF-1 and GATA-3, the requirement for TOX and Bcl11B is distinct between T cells and ILC. TOX is required from the EILP stage, where it contributes to the regulation of *Tcf7* and *Zbtb16* induction⁸⁵,⁹⁶. It is further necessary for the generation of all ILC except gut-resident ILC3⁸⁵,⁹⁵,¹⁰⁷. In T cells, TOX is required at relatively late stages of development, for CD4⁺ and CD8⁺ mature T cell development¹⁷⁹,¹⁸⁰. Bcl11B plays critical functions at the T cell commitment checkpoint, and it is required for the generation of most T cells¹⁸¹⁻¹⁸³. In the ILC lineage, it is required for the development of ILCP into ILC2⁸⁵,¹⁸⁴⁻¹⁸⁶. Comparison of Bcl11B function between a T cell precursor cell line and an ILC2 cell line indicated that this factor regulates almost completely distinct sets of genes in these two cell lineages¹⁸⁷.

The distinct functions of shared transcription factors thus appear to be driven, at least in part, by ILC lineage-specific controllers that act early during development. Among candidate ILC lineage specific factors, Id2 is required for all ILC development. Id2 inhibits the activity of E-proteins, thereby contributing to the loss of T and B cell potential in both mice and humans¹⁸⁸⁻¹⁹⁰. Id2-deficiency leads to a reduction in the number of ILCP and mature ILC subsets including LTi cells, ILC2 and ILC3 (refs. ⁹³,¹³³,¹⁹¹⁻¹⁹³), and Id2 is also essential for the maturation and function of NK cells¹³³. However, Id2 deficiency only has modest impact on EILP⁹³. Thus, the requirement for Id2 is only evident at later stages of ILC development, and may not reflect a requirement in a shared precursor cell.

Like Id2, NFIL3 is required by adult ILC developing in BM; and it is likely to be required very early in ILC development⁸⁸,⁹⁶,⁹⁸⁻¹⁰²,¹⁹⁴ (Figure 1). The recent analysis of NLP identified several transcription factors expressed at this early stage including NFIL3⁹⁶, which is critical for the development of all ILC subsets in adult mice including adult LTi, yet is not required for T cell differentiation in the thymus⁸⁸,⁹³,⁹⁶,⁹⁸⁻¹⁰⁰,¹⁰². Forced expression of NFIL3 in ALP drove ILC
development *in vitro*, recapitulating stages of development normally observed in mouse BM. Mechanistically, NFIL3 induced expression of the known key controllers of ILC development, including the ILC-specific controllers *Id2*, *Zbtb16* and *Tox2* and the controllers shared with T cells, *Tox*, *Gata3*, *Tcf7* and *Bcl11b*⁹⁶. The mechanisms by which NFIL3 regulates its gene targets remain to be fully elucidated. However, analysis of NFIL3 binding and chromatin accessibility in ILC precursors indicates that NFIL3 may act in part through chromatin remodeling, in cooperation with other factors⁹⁶. The enrichment of a motif bound by NFIL3 in the vicinity of ILC2-specific regions bound by Bcl11B¹⁸⁷ raises the possibility that NFIL3 might contribute to ILC-specific functions of some of the controllers shared with T cells. Importantly, NFIL3 upregulated *Tcf7* independently of Notch signaling⁹⁶, as predicted by earlier work¹³⁷,¹⁹⁵, whereas TCF-1 is initially upregulated by Notch signals in ETP¹⁶⁹,¹⁷².

Thus, although T cell and ILC specification can each initiate in lymphoid progenitors, the earliest events of ILC specification and T cell specification are distinct, imposing lineage-specific chromatin landscapes, and providing an explanation for differences in how shared transcription factors are deployed across the genome.

## Conclusion

There has been significant progress in delineating the developmental pathways of ILC, from identification of early ILC progenitors in the adult BM and tissues, to characterizing lineage-restricted ILC subset progenitors in peripheral tissues. Key progenitor stages such as NLP, EILP, ILCP, and subset-specific intermediates have been defined, and advances in fate mapping and single-cell transcriptomics have significantly refined our understanding of ILC ontogeny. The discovery of distinct developmental routes for LTi cells and dual pathways for NK cell generation highlights the complexity and diversity within the ILC compartment.

Several gaps remain in the field. The local signals that shape ILC differentiation in tissues and elicit tissue-specific ILC population abundances are poorly understood. How is tissue specificity encoded? What signals govern the development of tissue-resident ILC populations, such as salivary gland NK cells that develop in the absence of NFIL3, or gut ILC3 that are present in the absence of TOX? How do ILC in different tissues acquire distinct transcriptional programs and functions? Molecular mechanisms governing the development of newly-described precursors for cytotoxic NK cell lineages are not yet known. Fate-mapping studies have revealed a distinct developmental pathway for adult LTi cells, separate from ILCP-dependent ILC3, but the extent to which adult LTi cells share developmental origins and functional roles with fetal LTi cells remains poorly understood, and the requirement for NFIL3 in adult LTi cells but not fetal liver LTi cells is an unresolved puzzle. A more comprehensive understanding of developmental stages and transcriptional programs in LTi development during fetal and adult life is needed. Compared to mice, the developmental pathways of ILC in humans are not well-characterized and warrant further investigation. Bridging these gaps will be instrumental in advancing our understanding of ILC development and function.

Another major gap in the ILC development field is the limited mechanistic understanding of roles played by key transcription factors. This is in part due to the rarity of ILC precursor populations and a lack of appropriate *in vitro* model systems. The most commonly used *in vitro* system relies on stromal cells to support the differentiation of purified progenitor populations, EILP and ILCP,
from both mice and humans into mature ILC<sup>85,146,196</sup>. However, this system requires isolation of rare progenitor populations. Recent work addressed this limitation by developing an *in vitro* system in which NFIL3 is forcibly expressed in ALP. This system should enable the characterization of mechanisms acting downstream of ALP as it allows generation of progenitor populations in sufficient numbers to enable mechanistic studies<sup>96</sup>. Continued improvements in approaches to assess transcription factor binding and function in very small numbers of cells or single cells will allow a better understanding of mechanisms acting in progenitors *in vivo*<sup>95,171,197</sup>. Because of the essential role of ILC in the response to pathogens and tissue homeostasis, improved insight into how these cells develop is an important goal, and will allow us to understand and manipulate ILC function.
Figure Legend

<figure><img src="image_2.png" /></figure>

**Figure 1.** Steps of early ILC development in BM of adult mice. Transcription factors noted above cells are first expressed at that stage, whereas transcription factors noted above arrows denoting developmental transitions are required for that step. Solid arrows represent validated steps; dashed arrows indicate hypothetical transitions. All lymphoid progenitors (ALP) require NFIL3 to generate NLP (NFIL3<sup>+</sup> Lymphoid Precursors) that subsequently express TOX to give rise to Early ILC progenitors (EILP) expressing *Tcf7*. EILP retain dendritic cell potential and generate Innate Lymphoid Cell Precursor (ILCP) that lack this potential. ILCP are marked by PLZF and differentiate into ILC1, ILC2, ILC3, and one type of NK cell (ILCP-derived NK, NK2 cells). Majority of NK cells derive from Early NK progenitors (ENKP) and are ENKP-derived NK cells or NK1 cells. Other recently-described precursors are EOMES<sup>hi</sup>NK<sup>-</sup> cells<sup>130</sup>, that are likely downstream of ENKP (ref. 198) and appear restricted to the NK1-lineage; aceNKP<sup>129</sup>, which are downstream of ILCP, and possess ILC1 and NK2 lineage potential; and ILC1/3P, that are downstream of ILCP and possess ILC1 and ILC3 lineage potential<sup>75</sup>. The earliest LTi precursors, *Rorc<sup>+</sup>*αLP, express RORγt but not TCF-1. These give rise to LTi progenitors (LTiP), defined by TCF-1, Id2, and RORγt, which develop into mature LTi cells. * Transcription factors required for both NK1 and NK2 cells. Lineage-defining transcription factors are indicated within each mature ILC subset.
<table><caption>**Table 1.** Early ILC progenitor definitions in mice. “Lin” refers to a cocktail of antibodies to appropriate lineage markers described in the associated references. Lin<sup>-</sup> (Lineage negative) populations lack expression of these markers and are enriched for progenitor cells.</caption><thead><tr><th>Name of the progenitor</th><th>Abbreviation</th><th>Definition</th><th>Ref.</th></tr></thead><tbody><tr><td>All-Lymphoid Progenitors</td><td>ALP</td><td>Lin<sup>-</sup> Ly6D<sup>-</sup> Kit<sup>+</sup> Flt3<sup>+</sup> IL-7Rα<sup>+</sup> α<sub>4</sub>β<sub>7</sub><sup>-</sup></td><td>78,83,85</td></tr><tr><td>Early ILC Progenitors</td><td>EILP</td><td>Lin<sup>-</sup> Kit<sup>+</sup> Flt3<sup>+</sup> TCF-1<sup>+</sup> Thy1<sup>-</sup> IL-7Rα<sup>lo/-</sup> α<sub>4</sub>β<sub>7</sub><sup>+</sup> PLZF<sup>-</sup></td><td>93</td></tr><tr><td>Early NK Progenitors</td><td>ENKP</td><td>Lin<sup>-</sup> NK1.1<sup>-</sup> CD5<sup>-</sup> CD3ε<sup>-</sup> CD27<sup>+</sup> 2B4<sup>+</sup> Flt3<sup>+</sup> CD122<sup>+</sup></td><td>3</td></tr><tr><td>aceNKP</td><td></td><td>Lin<sup>-</sup> Id2<sup>+</sup> IL-7Rα<sup>+</sup> CD25<sup>-</sup> α<sub>4</sub>β<sub>7</sub><sup>-</sup> NKG2A/C/E<sup>+</sup> Bcl11B<sup>-</sup></td><td>129</td></tr><tr><td>Common helper ILC Precursors</td><td>CHILP</td><td>Lin<sup>-</sup> Flt3<sup>-</sup> Id2<sup>+</sup> Thy1<sup>+</sup> IL-7Rα<sup>+</sup> α<sub>4</sub>β<sub>7</sub><sup>+</sup></td><td>30</td></tr><tr><td>Innate Lymphoid Cell Precursors</td><td>ILCP</td><td>Lin<sup>-</sup> Kit<sup>+</sup> Thy1<sup>+</sup> IL-7Rα<sup>+</sup> α<sub>4</sub>β<sub>7</sub><sup>+</sup> Flt3<sup>-</sup> (TCF-1<sup>+</sup> or PD1<sup>+</sup> or PLZF<sup>+</sup>)*<br/>*This definition excludes a transitional population functionally similar to ILCP and residing between EILP and ILCP, that express Zbtb16 (encoding PLZF) and are IL-7Rα<sup>low</sup>, Thy1<sup>low</sup>, PD1<sup>low</sup> (refs. 94,95)</td><td>55,91,145</td></tr><tr><td>Fetal gut ILCP</td><td></td><td>Lin<sup>-</sup> Id2<sup>+</sup> IL-7Rα<sup>+</sup> α<sub>4</sub>β<sub>7</sub><sup>+</sup> Flt3<sup>-</sup> Arg1<sup>+</sup></td><td>140</td></tr><tr><td>Rorc<sup>-</sup> expressing α<sub>4</sub>β<sub>7</sub><sup>+</sup> Lymphoid Precursors</td><td>Rorc<sup>+</sup>αLP</td><td>Lin<sup>-</sup> IL-7Rα<sup>+</sup> Flt3<sup>lo/-</sup> α<sub>4</sub>β<sub>7</sub><sup>+</sup> Thy1<sup>-</sup> TCF-1<sup>-</sup> PLZF<sup>-</sup> RORγt<sup>+</sup></td><td>94</td></tr><tr><td>Lymphoid Tissue inducer Precursors</td><td>LTiP</td><td>Lin<sup>-</sup> Kit<sup>+</sup> Flt3<sup>-</sup> IL-7Rα<sup>+</sup> α<sub>4</sub>β<sub>7</sub><sup>+</sup> CCR6<sup>+</sup> RORγt<sup>+</sup></td><td>94,136,138</td></tr></tbody></table>
<table><caption>**Table 2.** Tissue-Resident ILC Progenitors and its presence in Mice and Humans</caption><thead><tr><th>Source</th><th>Name of ILC progenitor</th><th>Human (h) or Mouse (m)</th><th>Reference</th></tr></thead><tbody><tr><td rowspan="2">Lung</td><td>HSC</td><td>(m)</td><td>148</td></tr><tr><td>ILCP</td><td>(m), (h)</td><td>111,145,146,149-151</td></tr><tr><td rowspan="10">Liver (Fetal or Adult)</td><td>HSC</td><td>(m), (h)</td><td>199,200</td></tr><tr><td>ALP/CLP</td><td>(m)</td><td>89,94,135-137</td></tr><tr><td>αLP</td><td>(m)</td><td>94,136,137</td></tr><tr><td>EILP</td><td>(m)</td><td>94</td></tr><tr><td>ILCP</td><td>(m), (h)</td><td>55,94,136,137,140,145,146</td></tr><tr><td>Rorc<sup>+</sup>αLP</td><td>(m)</td><td>94</td></tr><tr><td>LTiP</td><td>(m)</td><td>94,135,136</td></tr><tr><td>NKP</td><td>(h)</td><td>201,202</td></tr><tr><td>LSM</td><td>(h)</td><td>142</td></tr><tr><td>IL-3R<sup>+</sup>LP</td><td>(h)</td><td>157</td></tr><tr><td>ILC1/3P</td><td>(m)</td><td>75</td></tr><tr><td rowspan="5">Spleen</td><td>CLP</td><td>(m)</td><td>89</td></tr><tr><td>αLP</td><td>(m)</td><td>137</td></tr><tr><td>ILCP</td><td>(m)</td><td>145</td></tr><tr><td>CILCP</td><td>(h)</td><td>155</td></tr><tr><td>CILCP</td><td>(h)</td><td>155</td></tr><tr><td rowspan="4">Tonsil</td><td>NKP</td><td>(h)</td><td>201,202</td></tr><tr><td>ILC3P</td><td>(h)</td><td>118,155</td></tr><tr><td>ILCP</td><td>(h)</td><td>146,156</td></tr><tr><td>CILCP</td><td>(h)</td><td>155</td></tr><tr><td rowspan="5">Small intestinal lamina propria</td><td>ILC3P</td><td>(h)</td><td>118</td></tr><tr><td>ILCP</td><td>(m)</td><td>140,145</td></tr><tr><td>IL-3R+ LP</td><td>(h)</td><td>157</td></tr><tr><td>ILC1/3P</td><td>(m)</td><td>75</td></tr><tr><td>NKP</td><td>(m)</td><td>203</td></tr><tr><td rowspan="3">Thymus</td><td>ETP</td><td>(m)</td><td>204</td></tr><tr><td>NKP</td><td>(h)</td><td>201,202</td></tr><tr><td>ILCP</td><td>(h)</td><td>146</td></tr><tr><td rowspan="2">Blood</td><td>CLP</td><td>(m)</td><td>89</td></tr><tr><td>CILCP</td><td>(h)</td><td>155</td></tr><tr><td>Lymph node</td><td>αLP</td><td>(m)</td><td>137</td></tr></tbody></table>
References

1. Brink, R. Immunology and Immunopathology – B Lymphocytes. Encyclopedia of Life Support Systems (EOLSS)

2. Robinette, M.L., and Colonna, M. (2016). Immune modules shared by innate lymphoid cells and T cells. J Allergy Clin Immunol 138, 1243-1251. 10.1016/j.jaci.2016.09.006.

3. Ding, Y., Lavaert, M., Grassmann, S., Band, V.I., Chi, L., Das, A., Das, S., Harly, C., Shissler, S.C., Malin, J., et al. (2024). Distinct developmental pathways generate functionally distinct populations of natural killer cells. Nat Immunol. 10.1038/s41590-024-01865-2.

4. Sun, J.C., and Lanier, L.L. (2011). NK cell development, homeostasis and function: parallels with CD8(+) T cells. Nat Rev Immunol 11, 645-657. 10.1038/nri3044.

5. Vivier, E., van de Pavert, S.A., Cooper, M.D., and Belz, G.T. (2016). The evolution of innate lymphoid cells. Nat Immunol 17, 790-794. 10.1038/ni.3459.

6. Hirano, M., Guo, P., McCurley, N., Schorpp, M., Das, S., Boehm, T., and Cooper, M.D. (2013). Evolutionary implications of a third lymphocyte lineage in lampreys. Nature 501, 435-438. 10.1038/nature12467.

7. Fugmann, S.D. (2010). The origins of the Rag genes--from transposition to V(D)J recombination. Semin Immunol 22, 10-16. 10.1016/j.smim.2009.11.004.

8. Eberl, G., Colonna, M., Di Santo, J.P., and McKenzie, A.N. (2015). Innate lymphoid cells. Innate lymphoid cells: a new paradigm in immunology. Science 348, aaa6566. 10.1126/science.aaa6566.

9. Ebbo, M., Crinier, A., Vely, F., and Vivier, E. (2017). Innate lymphoid cells: major players in inflammatory diseases. Nat Rev Immunol 17, 665-678. 10.1038/nri.2017.86.

10. Vivier, E., Artis, D., Colonna, M., Diefenbach, A., Di Santo, J.P., Eberl, G., Koyasu, S., Locksley, R.M., McKenzie, A.N.J., Mebius, R.E., et al. (2018). Innate Lymphoid Cells: 10 Years On. Cell 17, 1054-1066. 10.1016/j.cell.2018.07.017.

11. Artis, D., and Spits, H. (2015). The biology of innate lymphoid cells. Nature 517, 293-301. 10.1038/nature14189.

12. Vely, F., Barlogis, V., Vallentin, B., Neven, B., Piperoglou, C., Ebbo, M., Perchet, T., Petit, M., Yessaad, N., Touzot, F., et al. (2016). Evidence of innate lymphoid cell redundancy in humans. Nat Immunol 17, 1291-1299. 10.1038/ni.3553.

13. Sonnenberg, G.F., Monticelli, L.A., Elloso, M.M., Fouser, L.A., and Artis, D. (2011). CD4(+) lymphoid tissue-inducer cells promote innate immunity in the gut. Immunity 34, 122-134. 10.1016/j.immuni.2010.12.009.

14. Hepworth, M.R., Fung, T.C., Masur, S.H., Kelsen, J.R., McConnell, F.M., Dubrot, J., Withers, D.R., Hugues, S., Farrar, M.A., Reith, W., et al. (2015). Immune tolerance. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4(+) T cells. Science 348, 1031-1035. 10.1126/science.aaa4812.

15. Sonnenberg, G.F., and Hepworth, M.R. (2019). Functional interactions between innate lymphoid cells and adaptive immunity. Nat Rev Immunol 19, 599-613. 10.1038/s41577-019-0194-8.

16. Nagasawa, M., Spits, H., and Ros, X.R. (2018). Innate Lymphoid Cells (ILCs): Cytokine Hubs Regulating Immunity and Tissue Homeostasis. Cold Spring Harb Perspect Biol 10. 10.1101/cshperspect.a030304.
17. Yano, H., and Artis, D. (2022). Neuronal regulation of innate lymphoid cell responses. Curr Opin Immunol 76, 102205. 10.1016/j.coi.2022.102205.

18. Ryu, S., Lim, M., Kim, J., and Kim, H.Y. (2023). Versatile roles of innate lymphoid cells at the mucosal barrier: from homeostasis to pathological inflammation. Exp Mol Med 55, 1845-1857. 10.1038/s12276-023-01022-z.

19. Xiong, L., Nutt, S.L., and Seillet, C. (2022). Innate lymphoid cells: More than just immune cells. Front Immunol 13, 1033904. 10.3389/fimmu.2022.1033904.

20. Gasteiger, G., Fan, X., Dikiy, S., Lee, S.Y., and Rudensky, A.Y. (2015). Tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs. Science 350, 981-985. 10.1126/science.aac9593.

21. Mackley, E.C., Houston, S., Marriott, C.L., Halford, E.E., Lucas, B., Cerovic, V., Filbey, K.J., Maizels, R.M., Hepworth, M.R., Sonnenberg, G.F., et al. (2015). CCR7-dependent trafficking of RORgamma(+) ILCs creates a unique microenvironment within mucosal draining lymph nodes. Nat Commun 6, 5862. 10.1038/ncomms6862.

22. Das, A., Martinez-Ruiz, G.U., Bouladoux, N., Stacy, A., Moraly, J., Vega-Sendino, M., Zhao, Y., Lavaert, M., Ding, Y., Morales-Sanchez, A., et al. (2024). Transcription factor Tox2 is required for metabolic adaptation and tissue residency of ILC3 in the gut. Immunity 57, 1019-1036 e1019. 10.1016/j.immuni.2024.04.001.

23. Ricardo-Gonzalez, R.R., Van Dyken, S.J., Schneider, C., Lee, J., Nussbaum, J.C., Liang, H.E., Vaka, D., Eckalbar, W.L., Molofsky, A.B., Erle, D.J., and Locksley, R.M. (2018). Tissue signals imprint ILC2 identity with anticipatory function. Nat Immunol 19, 1093-1109. 10.1038/s41590-018-0201-4.

24. Martinez-Gonzalez, I., Matha, L., Steer, C.A., Ghaedi, M., Poon, G.F., and Takei, F. (2016). Allergen-Experienced Group 2 Innate Lymphoid Cells Acquire Memory-like Properties and Enhance Allergic Lung Inflammation. Immunity 45, 198-208. 10.1016/j.immuni.2016.06.017.

25. Serafini, N., Jarade, A., Surace, L., Goncalves, P., Sismeiro, O., Varet, H., Legendre, R., Coppee, J.Y., Disson, O., Durum, S.K., et al. (2022). Trained ILC3 responses promote intestinal defense. Science 375, 859-863. 10.1126/science.aaz8777.

26. Trabanelli, S., Ercolano, G., Wyss, T., Gomez-Cadena, A., Falquet, M., Cropp, D., Imbratta, C., Leblond, M.M., Salvestrini, V., Curti, A., et al. (2022). c-Maf enforces cytokine production and promotes memory-like responses in mouse and human type 2 innate lymphoid cells. EMBO J 41, e109300. 10.15252/embj.2021109300.

27. Verma, M., Michalec, L., Sripada, A., McKay, J., Sirohi, K., Verma, D., Sheth, D., Martin, R., Dyjack, N., Seibold, M.A., et al. (2021). The molecular and epigenetic mechanisms of innate lymphoid cell (ILC) memory and its relevance for asthma. J Exp Med 218. 10.1084/jem.20201354.

28. Sun, J.C., Beilke, J.N., and Lanier, L.L. (2009). Adaptive immune features of natural killer cells. Nature 457, 557-561. 10.1038/nature07665.

29. Zook, E.C., and Kee, B.L. (2016). Development of innate lymphoid cells. Nature Immunology 17, 775-782. 10.1038/ni.3481.

30. Klose, C.S.N., Flach, M., Mohle, L., Rogell, L., Hoyler, T., Ebert, K., Fabiunke, C., Pfeifer, D., Sexl, V., Fonseca-Pereira, D., et al. (2014). Differentiation of type 1 ILCs from a common progenitor to all helper-like innate lymphoid cell lineages. Cell 157, 340-356. 10.1016/j.cell.2014.03.030.
mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22. *J Exp Med* 211, 1571-1583. 10.1084/jem.20140678.

45. Song, C., Lee, J.S., Gilfillan, S., Robinette, M.L., Newberry, R.D., Stappenbeck, T.S., Mack, M., Cella, M., and Colonna, M. (2015). Unique and redundant functions of NKp46+ ILC3s in models of intestinal inflammation. *J Exp Med* 212, 1869-1882. 10.1084/jem.20151403.

46. Pearson, C., Thornton, E.E., McKenzie, B., Schaupp, A.L., Huskens, N., Griseri, T., West, N., Tung, S., Seddon, B.P., Uhlig, H.H., and Powrie, F. (2016). ILC3 GM-CSF production and mobilisation orchestrate acute intestinal inflammation. *Elife* 5, e10066. 10.7554/eLife.10066.

47. Gordon, S.M., Chaix, J., Rupp, L.J., Wu, J., Madera, S., Sun, J.C., Lindsten, T., and Reiner, S.L. (2012). The transcription factors T-bet and Eomes control key checkpoints of natural killer cell maturation. *Immunity* 36, 55-67. 10.1016/j.immuni.2011.11.016.

48. Kupz, A., Scott, T.A., Belz, G.T., Andrews, D.M., Greyer, M., Lew, A.M., Brooks, A.G., Smyth, M.J., Curtiss, R., 3rd, Bedoui, S., and Strugnell, R.A. (2013). Contribution of Thyl+ NK cells to protective IFN-gamma production during Salmonella typhimurium infections. *Proc Natl Acad Sci U S A* 110, 2252-2257. 10.1073/pnas.1222047110.

49. Chiossone, L., and Vivier, E. (2022). Bringing natural killer cells to the clinic. *J Exp Med* 219. 10.1084/jem.20220830.

50. van de Pavert, S.A. (2021). Lymphoid Tissue inducer (LTi) cell ontogeny and functioning in embryo and adult. *Biomed J* 44, 123-132. 10.1016/j.bj.2020.12.003.

51. Colonna, M. (2009). Interleukin-22-producing natural killer cells and lymphoid tissue inducer-like cells in mucosal immunity. *Immunity* 31, 15-23. 10.1016/j.immuni.2009.06.008.

52. Cupedo, T., Crellin, N.K., Papazian, N., Rombouts, E.J., Weijer, K., Grogan, J.L., Fibbe, W.E., Cornelissen, J.J., and Spits, H. (2009). Human fetal lymphoid tissue-inducer cells are interleukin 17-producing precursors to RORC+ CD127+ natural killer-like cells. *Nat Immunol* 10, 66-74. 10.1038/ni.1668.

53. Sun, Z., Unutmaz, D., Zou, Y.R., Sunshine, M.J., Pierani, A., Brenner-Morton, S., Mebius, R.E., and Littman, D.R. (2000). Requirement for RORgamma in thymocyte survival and lymphoid organ development. *Science* 288, 2369-2373. 10.1126/science.288.5475.2369.

54. Bouskra, D., Brezillon, C., Berard, M., Werts, C., Varona, R., Boneca, I.G., and Eberl, G. (2008). Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. *Nature* 456, 507-510. 10.1038/nature07450.

55. Constantinides, M.G., McDonald, B.D., Verhoef, P.A., and Bendelac, A. (2014). A committed precursor to innate lymphoid cells. *Nature* 508, 397-401. 10.1038/nature13047.

56. Ren, G., Zhang, Y., Liu, J., Cheng, W., Wu, D., Han, M., Zeng, Y., Zhao, X., Hu, L., Zeng, M., et al. (2024). Decreased GATA3 levels cause changed mouse cutaneous innate lymphoid cell fate, facilitating hair follicle recycling. *Dev Cell* 59, 1809-1823 e1806. 10.1016/j.devcel.2024.04.015.

57. Sawa, S., Cherrier, M., Lochner, M., Satoh-Takayama, N., Fehling, H.J., Langa, F., Di Santo, J.P., and Eberl, G. (2010). Lineage relationship analysis of RORgammat+ innate lymphoid cells. *Science* 330, 665-669. 10.1126/science.1194597.
58. Krabbendam, L., Bernink, J.H., and Spits, H. (2021). Innate lymphoid cells: from helper to killer. Curr Opin Immunol 68, 28-33. 10.1016/j.coi.2020.08.007.

59. Bal, S.M., Golebski, K., and Spits, H. (2020). Plasticity of innate lymphoid cell subsets. Nat Rev Immunol 20, 552-565. 10.1038/s41577-020-0282-9.

60. Colonna, M. (2018). Innate Lymphoid Cells: Diversity, Plasticity, and Unique Functions in Immunity. Immunity 48, 1104-1117. 10.1016/j.immuni.2018.05.013.

61. Bernink, J.H., Krabbendam, L., Germar, K., de Jong, E., Gronke, K., Kofoed-Nielsen, M., Munneke, J.M., Hazenberg, M.D., Villaudy, J., Buskens, C.J., et al. (2015). Interleukin-12 and -23 Control Plasticity of CD127(+) Group 1 and Group 3 Innate Lymphoid Cells in the Intestinal Lamina Propria. Immunity 43, 146-160. 10.1016/j.immuni.2015.06.019.

62. Cella, M., Gamini, R., Secca, C., Collins, P.L., Zhao, S., Peng, V., Robinette, M.L., Schettini, J., Zaitsev, K., Gordon, W., et al. (2019). Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues. Nat Immunol 20, 980-991. 10.1038/s41590-019-0425-y.

63. Akagbosu, B., Tayyebi, Z., Shibu, G., Paucar Iza, Y.A., Deep, D., Parisotto, Y.F., Fisher, L., Pasolli, H.A., Thevin, V., Elmentaite, R., et al. (2022). Novel antigen-presenting cell imparts T(reg)-dependent tolerance to gut microbiota. Nature 610, 752-760. 10.1038/s41586-022-05309-5.

64. Kedmi, R., Najar, T.A., Mesa, K.R., Grayson, A., Kroehling, L., Hao, Y., Hao, S., Pokrovskii, M., Xu, M., Talbot, J., et al. (2022). A RORgammat(+) cell instructs gut microbiota-specific T(reg) cell differentiation. Nature 610, 737-743. 10.1038/s41586-022-05089-y.

65. Lyu, M., Suzuki, H., Kang, L., Gaspal, F., Zhou, W., Goc, J., Zhou, L., Zhou, J., Zhang, W., Bank, J.R.I.L.C., et al. (2022). ILC3s select microbiota-specific regulatory T cells to establish tolerance in the gut. Nature 610, 744-751. 10.1038/s41586-022-05141-x.

66. Rodrigues, P.F., Wu, S., Trsan, T., Panda, S.K., Fachi, J.L., Liu, Y., Du, S., de Oliveira, S., Antonova, A.U., Khantakova, D., et al. (2025). Rorgammat-positive dendritic cells are required for the induction of peripheral regulatory T cells in response to oral antigens. Cell 188, 2720-2737 e2722. 10.1016/j.cell.2025.03.020.

67. Wang, J., Lareau, C.A., Bautista, J.L., Gupta, A.R., Sandor, K., Germino, J., Yin, Y., Arvedson, M.P., Reeder, G.C., Cramer, N.T., et al. (2021). Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. Sci Immunol 6, eabl5053. 10.1126/sciimmunol.abl5053.

68. Fu, L., Upadhyay, R., Pokrovskii, M., Chen, F.M., Romero-Meza, G., Griesemer, A., and Littman, D.R. (2025). PRDM16-dependent antigen-presenting cells induce tolerance to gut antigens. Nature 642, 756-765. 10.1038/s41586-025-08982-4.

69. Narasimhan, H., Richter, M.L., Shakiba, R., Papaioannou, N.E., Stehle, C., Ravi Rengarajan, K., Ulmert, I., Kendirli, A., de la Rosa, C., Kuo, P.Y., et al. (2025). RORgammat-expressing dendritic cells are functionally versatile and evolutionarily conserved antigen-presenting cells. Proc Natl Acad Sci U S A 122, e2417308122. 10.1073/pnas.2417308122.

70. Sun, I.H., Qualls, A.E., Yin, H.S., Wang, J., Arvedson, M.P., Germino, J., Horner, N.K., Zhong, S., Du, J., Valdearcos, M., et al. (2025). RORgammat eTACs mediate oral tolerance and Treg induction. J Exp Med 222. 10.1084/jem.20250573.
71. Hepworth, M.R., Monticelli, L.A., Fung, T.C., Ziegler, C.G., Grunberg, S., Sinha, R., Mantegazza, A.R., Ma, H.L., Crawford, A., Angelosanto, J.M., et al. (2013). Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. *Nature* **498**, 113-117. 10.1038/nature12240.

72. Hoelting, T.L.B., Park, T., and Brown, C.C. (2025). Antigen-presenting cells as arbiters of mucosal tolerance and immunity. *Nat Immunol* **26**, 1890-1902. 10.1038/s41590-025-02320-6.

73. Klose, C.S., Kiss, E.A., Schwierzeck, V., Ebert, K., Hoyler, T., d'Hargues, Y., Goppert, N., Croxford, A.L., Waisman, A., Tanriver, Y., and Diefenbach, A. (2013). A T-bet gradient controls the fate and function of CCR6-RORgammat+ innate lymphoid cells. *Nature* **494**, 261-265. 10.1038/nature11813.

74. Vonarbourg, C., Mortha, A., Bui, V.L., Hernandez, P.P., Kiss, E.A., Hoyler, T., Flach, M., Bengsch, B., Thimme, R., Holscher, C., et al. (2010). Regulated expression of nuclear receptor RORgammat confers distinct functional fates to NK cell receptor-expressing RORgammat(+) innate lymphocytes. *Immunity* **33**, 736-751. 10.1016/j.immuni.2010.10.017.

75. Wang, X., Li, J., Rebuffet, L., Cheng, M., Bao, B., Chen, Y., Zheng, X., Chen, Y., Sun, H., Sun, R., et al. (2025). Innate lymphoid cells originate from fetal liver-derived tissue-resident progenitors. *Sci Immunol* **10**, eadu7962. 10.1126/sciimmunol.adu7962.

76. Yang, Q., and Bhandoola, A. (2016). The development of adult innate lymphoid cells. *Curr Opin Immunol* **39**, 114-120. 10.1016/j.coi.2016.01.006.

77. Kondo, M., Weissman, I.L., and Akashi, K. (1997). Identification of clonogenic common lymphoid progenitors in mouse bone marrow. *Cell* **91**, 661-672. 10.1016/s0092-8674(00)80453-5.

78. Inlay, M.A., Bhattacharya, D., Sahoo, D., Serwold, T., Seita, J., Karsunky, H., Plevritis, S.K., Dill, D.L., and Weissman, I.L. (2009). Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development. *Genes & Development* **23**, 2376-2381. 10.1101/gad.1836009.

79. Adolfsson, J., Mansson, R., Buza-Vidas, N., Hultquist, A., Liuba, K., Jensen, C.T., Bryder, D., Yang, L., Borge, O.J., Thoren, L.A., et al. (2005). Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential a revised road map for adult blood lineage commitment. *Cell* **121**, 295-306. 10.1016/j.cell.2005.02.013.

80. Welner, R.S., Pelayo, R., Nagai, Y., Garrett, K.P., Wuest, T.R., Carr, D.J., Borghesi, L.A., Farrar, M.A., and Kincade, P.W. (2008). Lymphoid precursors are directed to produce dendritic cells as a result of TLR9 ligation during herpes infection. *Blood* **112**, 3753-3761. 10.1182/blood-2008-04-151506.

81. Bell, J.J., and Bhandoola, A. (2008). The earliest thymic progenitors for T cells possess myeloid lineage potential. *Nature* **452**, 764-767. 10.1038/nature06840.

82. Das, A., Harly, C., Ding, Y., and Bhandoola, A. (2022). ILC Differentiation from Progenitors in the Bone Marrow. *Adv Exp Med Biol* **1365**, 7-24. 10.1007/978-981-16-8387-9_2.

83. Ghaedi, M., Steer, C.A., Martinez-Gonzalez, I., Halim, T.Y.F., Abraham, N., and Takei, F. (2016). Common-Lymphoid-Progenitor-Independent Pathways of Innate and T Lymphocyte Development. *Cell Rep* **15**, 471-480. 10.1016/j.celrep.2016.03.039.

84. Adolfsson, J., Borge, O.J., Bryder, D., Theilgaard-Monch, K., Astrand-Grundstrom, I., Sitnicka, E., Sasaki, Y., and Jacobsen, S.E. (2001). Upregulation of Flt3 expression
within the bone marrow Lin(-)Sca1(+)c-kit(+) stem cell compartment is accompanied by
loss of self-renewal capacity. Immunity 15, 659-669. 10.1016/s1074-7613(01)00220-5.

85. Harly, C., Cam, M., Kaye, J., and Bhandoola, A. (2018). Development and differentiation of early innate lymphoid progenitors. Journal of Experimental Medicine 215, 249-262. 10.1084/jem.20170832.

86. Diefenbach, A., Colonna, M., and Koyasu, S. (2014). Development, differentiation, and diversity of innate lymphoid cells. Immunity 41, 354-365. 10.1016/j.immuni.2014.09.005.

87. Tufa, D.M., Yingst, A.M., Trahan, G.D., Shank, T., Jones, D., Shim, S., Lake, J., Winkler, K., Cobb, L., Woods, R., et al. (2020). Human innate lymphoid cell precursors express CD48 that modulates ILC differentiation through 2B4 signaling. Sci Immunol 5. 10.1126/sciimmunol.aay4218.

88. Yu, X., Wang, Y., Deng, M., Li, Y., Ruhn, K.A., Zhang, C.C., and Hooper, L.V. (2014). The basic leucine zipper transcription factor NFIL3 directs the development of a common innate lymphoid cell precursor. Elife 3. 10.7554/eLife.04406.

89. Possot, C., Schmutz, S., Chea, S., Boucontet, L., Louise, A., Cumano, A., and Golub, R. (2011). Notch signaling is necessary for adult, but not fetal, development of RORgammat(+) innate lymphoid cells. Nat Immunol 12, 949-958. 10.1038/ni.2105.

90. Yoshida, H., Kawamoto, H., Santee, S.M., Hashi, H., Honda, K., Nishikawa, S., Ware, C.F., Katsura, Y., and Nishikawa, S.I. (2001). Expression of alpha(4)beta(7) integrin defines a distinct pathway of lymphoid progenitors committed to T cells, fetal intestinal lymphotoxin producer, NK, and dendritic cells. J Immunol 167, 2511-2521. 10.4049/jimmunol.167.5.2511.

91. Yu, Y., Tsang, J.C., Wang, C., Clare, S., Wang, J., Chen, X., Brandt, C., Kane, L., Campos, L.S., Lu, L., et al. (2016). Single-cell RNA-seq identifies a PD-1(hi) ILC progenitor and defines its development pathway. Nature 539, 102-106. 10.1038/nature20105.

92. Xu, W., Cherrier, D.E., Chea, S., Vosshenrich, C., Serafini, N., Petit, M., Liu, P., Golub, R., and Di Santo, J.P. (2019). An Id2RFP-Reporter Mouse Redefines Innate Lymphoid Cell Precursor Potentials. Immunity 50, 1054-1068.e1053. 10.1016/j.immuni.2019.02.022.

93. Yang, Q., Li, F., Harly, C., Xing, S., Ye, L., Xia, X., Wang, H., Wang, X., Yu, S., Zhou, X., et al. (2015). TCF-1 upregulation identifies early innate lymphoid progenitors in the bone marrow. Nat Immunol 16, 1044-1050. 10.1038/ni.3248.

94. Kasal, D.N., and Bendelac, A. (2021). Multi-transcription factor reporter mice delineate early precursors to the ILC and LTi lineages. Journal of Experimental Medicine 218. 10.1084/jem.20200487.

95. Harly, C., Kenney, D., Ren, G., Lai, B., Raabe, T., Yang, Q., Cam, M.C., Xue, H.H., Zhao, K., and Bhandoola, A. (2019). The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage. Nat Immunol 20, 1150-1160. 10.1038/s41590-019-0445-7.

96. Leger, J., Artano, E., Coulais, D., Belletoise, N., Fadhloun, R., Kenney, D., Bhandoola, A., and Harly, C. (2025). The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors. Immunity 58, 2685-2703 e2686. 10.1016/j.immuni.2025.10.005.
97. Cortez, V.S., Fuchs, A., Cella, M., Gilfillan, S., and Colonna, M. (2014). Cutting edge: Salivary gland NK cells develop independently of Nfil3 in steady-state. J Immunol 192, 4487-4491. 10.4049/jimmunol.1303469.

98. Geiger, T.L., Abt, M.C., Gasteiger, G., Firth, M.A., O'Connor, M.H., Geary, C.D., O'Sullivan, T.E., van den Brink, M.R., Pamer, E.G., Hanash, A.M., and Sun, J.C. (2014). Nfil3 is crucial for development of innate lymphoid cells and host protection against intestinal pathogens. J Exp Med 211, 1723-1731. 10.1084/jem.20140212.

99. Male, V., Nisoli, I., Kostrzewski, T., Allan, D.S.J., Carlyle, J.R., Lord, G.M., Wack, A., and Brady, H.J.M. (2014). The transcription factor E4bp4/Nfil3 controls commitment to the NK lineage and directly regulates Eomes and Id2 expression. Journal of Experimental Medicine 211, 635-642. 10.1084/jem.20132398.

100. Seillet, C., Huntington, N.D., Gangatirkar, P., Axelsson, E., Minnich, M., Brady, H.J.M., Busslinger, M., Smyth, M.J., Belz, G.T., and Carotta, S. (2014). Differential Requirement for Nfil3 during NK Cell Development. The Journal of Immunology 192, 2667-2676. 10.4049/jimmunol.1302605.

101. Seillet, C., Rankin, L.C., Groom, J.R., Mielke, L.A., Tellier, J., Chopin, M., Huntington, N.D., Belz, G.T., and Carotta, S. (2014). Nfil3 is required for the development of all innate lymphoid cell subsets. Journal of Experimental Medicine 211, 1733-1740. 10.1084/jem.20140145.

102. Xu, W., Domingues, Rita G., Fonseca-Pereira, D., Ferreira, M., Ribeiro, H., Lopez-Lastra, S., Motomura, Y., Moreira-Santos, L., Bihl, F., Braud, V., et al. (2015). NFIL3 Orchestrates the Emergence of Common Helper Innate Lymphoid Cell Precursors. Cell Reports 10, 2043-2054. 10.1016/j.celrep.2015.02.057.

103. Gascoyne, D.M., Long, E., Veiga-Fernandes, H., de Boer, J., Williams, O., Seddon, B., Coles, M., Kioussis, D., and Brady, H.J. (2009). The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development. Nat Immunol 10, 1118-1124. 10.1038/ni.1787.

104. Dadi, S., Chhangawala, S., Whitlock, B.M., Franklin, R.A., Luo, C.T., Oh, S.A., Toure, A., Pritykin, Y., Huse, M., Leslie, C.S., and Li, M.O. (2016). Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells. Cell 164, 365-377. 10.1016/j.cell.2016.01.002.

105. Doisne, J.M., Balmas, E., Boulenouar, S., Gaynor, L.M., Kieckbusch, J., Gardner, L., Hawkes, D.A., Barbara, C.F., Sharkey, A.M., Brady, H.J., et al. (2015). Composition, Development, and Function of Uterine Innate Lymphoid Cells. J Immunol 195, 3937-3945. 10.4049/jimmunol.1500689.

106. Sojka, D.K., Plougastel-Douglas, B., Yang, L., Pak-Wittel, M.A., Artyomov, M.N., Ivanova, Y., Zhong, C., Chase, J.M., Rothman, P.B., Yu, J., et al. (2014). Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells. Elife 3, e01659. 10.7554/eLife.01659.

107. Seehus, C.R., Aliahmad, P., de la Torre, B., Iliev, I.D., Spurka, L., Funari, V.A., and Kaye, J. (2015). The development of innate lymphoid cells requires TOX-dependent generation of a common innate lymphoid cell progenitor. Nat Immunol 16, 599-608. 10.1038/ni.3168.

108. Erick, T.K., Anderson, C.K., Reilly, E.C., Wands, J.R., and Brossay, L. (2016). NFIL3 Expression Distinguishes Tissue-Resident NK Cells and Conventional NK-like Cells in
the Mouse Submandibular Glands. J Immunol 197, 2485-2491.
10.4049/jimmunol.1601099.

109. Schneider, C., Lee, J., Koga, S., Ricardo-Gonzalez, R.R., Nussbaum, J.C., Smith, L.K., Villeda, S.A., Liang, H.E., and Locksley, R.M. (2019). Tissue-Resident Group 2 Innate Lymphoid Cells Differentiate by Layered Ontogeny and In Situ Perinatal Priming. Immunity 50, 1425-1438 e1425. 10.1016/j.immuni.2019.04.019.

110. van de Pavert, S.A. (2023). Layered origins of lymphoid tissue inducer cells. Immunological Reviews 315, 71-78. 10.1111/imr.13189.

111. Zeis, P., Lian, M., Fan, X., Herman, J.S., Hernandez, D.C., Gentek, R., Elias, S., Symowski, C., Knopper, K., Peltokangas, N., et al. (2020). In Situ Maturation and Tissue Adaptation of Type 2 Innate Lymphoid Cell Progenitors. Immunity 53, 775-792 e779.
10.1016/j.immuni.2020.09.002.

112. Das, A., Harly, C., Yang, Q., and Bhandoola, A. (2018). Lineage specification in innate lymphocytes. Cytokine Growth Factor Rev 42, 20-26. 10.1016/j.cytogfr.2018.01.005.

113. Halim, T.Y., MacLaren, A., Romanish, M.T., Gold, M.J., McNagny, K.M., and Takei, F. (2012). Retinoic-acid-receptor-related orphan nuclear receptor alpha is required for natural helper cell development and allergic inflammation. Immunity 37, 463-474.
10.1016/j.immuni.2012.06.012.

114. Walker, J.A., Clark, P.A., Crisp, A., Barlow, J.L., Szeto, A., Ferreira, A.C.F., Rana, B.M.J., Jolin, H.E., Rodriguez-Rodriguez, N., Sivasubramaniam, M., et al. (2019). Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow. Immunity 51, 104-118.e107. 10.1016/j.immuni.2019.05.002.

115. Juelke, K., and Romagnani, C. (2016). Differentiation of human innate lymphoid cells (ILCs). Curr Opin Immunol 38, 75-85. 10.1016/j.coi.2015.11.005.

116. Su, X., Deng, Z., Lan, Y., Liu, B., and Liu, C. (2025). Helper ILCs in the human hematopoietic system. Trends Immunol 46, 244-257. 10.1016/j.it.2025.01.009.

117. Hernández, D.C., Juelke, K., Müller, N.C., Durek, P., Ugursu, B., Mashreghi, M.-F., Rückert, T., and Romagnani, C. (2021). An in vitro platform supports generation of human innate lymphoid cells from CD34+ hematopoietic progenitors that recapitulate ex vivo identity. Immunity 54, 2417-2432.e2415. 10.1016/j.immuni.2021.07.019.

118. Montaldo, E., Teixeira-Alves, Luiz G., Glatzer, T., Durek, P., Stervbo, U., Hamann, W., Babic, M., Paclik, D., Stölzel, K., Gröne, J., et al. (2014). Human RORγt+CD34+ Cells Are Lineage-Specified Progenitors of Group 3 RORγt+ Innate Lymphoid Cells. Immunity 41, 988-1000. 10.1016/j.immuni.2014.11.010.

119. Goh, W., and Huntington, N.D. (2017). Regulation of Murine Natural Killer Cell Development. Front Immunol 8, 130. 10.3389/fimmu.2017.00130.

120. Fathman, J.W., Bhattacharya, D., Inlay, M.A., Seita, J., Karsunky, H., and Weissman, I.L. (2011). Identification of the earliest natural killer cell-committed progenitor in murine bone marrow. Blood 118, 5439-5447. 10.1182/blood-2011-04-348912.

121. Constantinides, M.G., Gudjonson, H., McDonald, B.D., Ishizuka, I.E., Verhoef, P.A., Dinner, A.R., and Bendelac, A. (2015). PLZF expression maps the early stages of ILC1 lineage development. Proceedings of the National Academy of Sciences 112, 5123-5128.
10.1073/pnas.1423244112.

122. Flommersfeld, S., Bottcher, J.P., Ersching, J., Flossdorf, M., Meiser, P., Pachmayr, L.O., Leube, J., Hensel, I., Jarosch, S., Zhang, Q., et al. (2021). Fate mapping of single NK
cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive
recognition of viral infection. Immunity 54, 2288-2304 e2287.
10.1016/j.immuni.2021.08.002.

123. Sparano, C., Solis-Sayago, D., Zangger, N.S., Rindlisbacher, L., Van Hove, H., Vermeer, M., Westermann, F., Mussak, C., Rallo, E., Dergun, S., et al. (2025). Autocrine TGF-beta1 drives tissue-specific differentiation and function of resident NK cells. J Exp Med 222. 10.1084/jem.20240930.

124. Rebuffet, L., Melsen, J.E., Escaliere, B., Basurto-Lozada, D., Bhandoola, A., Bjorkstrom, N.K., Bryceson, Y.T., Castriconi, R., Cichocki, F., Colonna, M., et al. (2024). High-dimensional single-cell analysis of human natural killer cell heterogeneity. Nat Immunol 25, 1474-1488. 10.1038/s41590-024-01883-0.

125. Du, X., Zhu, H., Jiao, D., Nian, Z., Zhang, J., Zhou, Y., Zheng, X., Tong, X., Wei, H., and Fu, B. (2022). Human-Induced CD49a(+) NK Cells Promote Fetal Growth. Front Immunol 13, 821542. 10.3389/fimmu.2022.821542.

126. Bottcher, J.P., Bonavita, E., Chakravarty, P., Blees, H., Cabeza-Cabrerizo, M., Sammicheli, S., Rogers, N.C., Sahai, E., Zelenay, S., and Reis e Sousa, C. (2018). NK Cells Stimulate Recruitment of cDC1 into the Tumor Microenvironment Promoting Cancer Immune Control. Cell 172, 1022-1037 e1014. 10.1016/j.cell.2018.01.004.

127. Morrison, T.A., Vigee, J., Tovar, K.A., Talley, T.A., Mujal, A.M., Kono, M., Philips, R., Nagashima, H., Brooks, S.R., Dada, H., et al. (2025). Selective requirement of glycosphingolipid synthesis for natural killer and cytotoxic T cells. Cell. 10.1016/j.cell.2025.04.007.

128. Li, J.H., Zhou, A., Lee, C.D., Shah, S.N., Ji, J.H., Senthilkumar, V., Padilla, E.T., Ball, A.B., Feng, Q., Bustillos, C.G., et al. (2024). MEF2C regulates NK cell effector functions through control of lipid metabolism. Nat Immunol 25, 778-789. 10.1038/s41590-024-01811-2.

129. Rodriguez-Rodriguez, N., Clark, P.A., Gogoi, M., Ferreira, A.C.F., Kerscher, B., Crisp, A., Jolin, H.E., Murphy, J.E., Sivasubramaniam, M., Pedro, L., et al. (2022). Identification of aceNKPs, a committed common progenitor population of the ILC1 and NK cell continuum. Proc Natl Acad Sci U S A 119, e2203454119. 10.1073/pnas.2203454119.

130. Liang, Z., Anderson, H.D., Locher, V., O'Leary, C., Riesenfeld, S.J., Jabri, B., McDonald, B.D., and Bendelac, A. (2024). Eomes expression identifies the early bone marrow precursor to classical NK cells. Nat Immunol 25, 1172-1182. 10.1038/s41590-024-01861-6.

131. Chiossone, L., Chaix, J., Fuseri, N., Roth, C., Vivier, E., and Walzer, T. (2009). Maturation of mouse NK cells is a 4-stage developmental program. Blood 113, 5488-5496. 10.1182/blood-2008-10-187179.

132. Huntington, N.D., Tabarias, H., Fairfax, K., Brady, J., Hayakawa, Y., Degli-Esposti, M.A., Smyth, M.J., Tarlinton, D.M., and Nutt, S.L. (2007). NK cell maturation and peripheral homeostasis is associated with KLRG1 up-regulation. J Immunol 178, 4764-4770. 10.4049/jimmunol.178.8.4764.

133. Boos, M.D., Yokota, Y., Eberl, G., and Kee, B.L. (2007). Mature natural killer cell and lymphoid tissue-inducing cell development requires Id2-mediated suppression of E protein activity. J Exp Med 204, 1119-1130. 10.1084/jem.20061959.
134. Cherrier, M., Sawa, S., and Eberl, G. (2012). Notch, Id2, and RORgammat sequentially orchestrate the fetal development of lymphoid tissue inducer cells. J Exp Med 209, 729-740. 10.1084/jem.20111594.

135. Simic, M., Manosalva, I., Spinelli, L., Gentek, R., Shayan, R.R., Siret, C., Girard-Madoux, M., Wang, S., de Fabritus, L., Verschoor, J., et al. (2020). Distinct Waves from the Hemogenic Endothelium Give Rise to Layered Lymphoid Tissue Inducer Cell Ontogeny. Cell Rep 32, 108004. 10.1016/j.celrep.2020.108004.

136. Ishizuka, I.E., Chea, S., Gudjonson, H., Constantinides, M.G., Dinner, A.R., Bendelac, A., and Golub, R. (2016). Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue-inducer cell lineage. Nat Immunol 17, 269-276. 10.1038/ni.3344.

137. Chea, S., Schmutz, S., Berthault, C., Perchet, T., Petit, M., Burlen-Defranoux, O., Goldrath, A.W., Rodewald, H.R., Cumano, A., and Golub, R. (2016). Single-Cell Gene Expression Analyses Reveal Heterogeneous Responsiveness of Fetal Innate Lymphoid Progenitors to Notch Signaling. Cell Rep 14, 1500-1516. 10.1016/j.celrep.2016.01.015.

138. Zhong, C., Zheng, M., Cui, K., Martins, A.J., Hu, G., Li, D., Tessarollo, L., Kozlov, S., Keller, J.R., Tsang, J.S., et al. (2020). Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells. Immunity 52, 83-95 e84. 10.1016/j.immuni.2019.12.001.

139. Zheng, M., Yao, C., Ren, G., Mao, K., Chung, H., Chen, X., Hu, G., Wang, L., Luan, X., Fang, D., et al. (2023). Transcription factor TCF-1 regulates the functions, but not the development, of lymphoid tissue inducer subsets in different tissues. Cell Rep 42, 112924. 10.1016/j.celrep.2023.112924.

140. Bando, J.K., Liang, H.-E., and Locksley, R.M. (2014). Identification and distribution of developing innate lymphoid cells in the fetal mouse intestine. Nature Immunology 16, 153-160. 10.1038/ni.3057.

141. Stehle, C., Ruckert, T., Fiancette, R., Gajdasik, D.W., Willis, C., Ulbricht, C., Durek, P., Mashreghi, M.F., Finke, D., Hauser, A.E., et al. (2021). T-bet and RORalpha control lymph node formation by regulating embryonic innate lymphoid cell differentiation. Nat Immunol 22, 1231-1244. 10.1038/s41590-021-01029-6.

142. Bai, L., Vienne, M., Tang, L., Kerdiles, Y., Etiennot, M., Escaliere, B., Galluso, J., Wei, H., Sun, R., Vivier, E., et al. (2021). Liver type 1 innate lymphoid cells develop locally via an interferon-gamma-dependent loop. Science 371. 10.1126/science.aba4177.

143. Ni, Y., You, G., Gong, Y., Su, X., Du, Y., Wang, X., Ding, X., Fu, Q., Zhang, M., Cheng, T., et al. (2024). Human yolk sac-derived innate lymphoid-biased multipotent progenitors emerge prior to hematopoietic stem cell formation. Dev Cell 59, 2626-2642 e2626. 10.1016/j.devcel.2024.06.010.

144. Lim, A.I., and Di Santo, J.P. (2019). ILC-poiesis: Ensuring tissue ILC differentiation at the right place and time. Eur J Immunol 49, 11-18. 10.1002/eji.201747294.

145. Clark, P.A., Gogoi, M., Rodriguez-Rodriguez, N., Ferreira, A.C.F., Murphy, J.E., Walker, J.A., Crisp, A., Jolin, H.E., Shields, J.D., and McKenzie, A.N.J. (2024). Recipient tissue microenvironment determines developmental path of intestinal innate lymphoid progenitors. Nat Commun 15, 7809. 10.1038/s41467-024-52155-2.

146. Lim, A.I., Li, Y., Lopez-Lastra, S., Stadhouders, R., Paul, F., Casrouge, A., Serafini, N., Puel, A., Bustamante, J., Surace, L., et al. (2017). Systemic Human ILC Precursors
Provide a Substrate for Tissue ILC Differentiation. Cell 168, 1086-1100.e1010.
10.1016/j.cell.2017.02.021.

147. Di Santo, J.P., Lim, A.I., and Yssel, H. (2017). 'ILC-poiesis': generating tissue ILCs from naive precursors. Oncotarget 8, 81729-81730. 10.18632/oncotarget.21046.

148. Lefrançais, E., Ortiz-Muñoz, G., Caudrillier, A., Mallavia, B., Liu, F., Sayah, D.M., Thornton, E.E., Headley, M.B., David, T., Coughlin, S.R., et al. (2017). The lung is a site of platelet biogenesis and a reservoir for haematopoietic progenitors. Nature 544, 105-109. 10.1038/nature21706.

149. Ghaedi, M., Shen, Z.Y., Orangi, M., Martinez-Gonzalez, I., Wei, L., Lu, X., Das, A., Heravi-Moussavi, A., Marra, M.A., Bhandoola, A., and Takei, F. (2020). Single-cell analysis of RORalpha tracer mouse lung reveals ILC progenitors and effector ILC2 subsets. J Exp Med 217. 10.1084/jem.20182293.

150. Oherle, K., Acker, E., Bonfield, M., Wang, T., Gray, J., Lang, I., Bridges, J., Lewkowich, I., Xu, Y., Ahlfeld, S., et al. (2020). Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Immunity 52, 275-294.e279. 10.1016/j.immuni.2020.01.005.

151. Huang, Q., W. H.J.C., Curio, S., Yu, H., Denman, R., Chen, E., Schreuder, J., Dight, J., Chaudhry, M., Jacquelot, N., et al. (2024). GFI1B specifies developmental potential of innate lymphoid cell progenitors in the lungs. Sci Immunol 9, eadj2654.
10.1126/sciimmunol.

152. Koga, S., Hozumi, K., Hirano, K.-i., Yazawa, M., Terooatea, T., Minoda, A., Nagasawa, T., Koyasu, S., and Moro, K. (2018). Peripheral PDGFRα+gp38+ mesenchymal cells support the differentiation of fetal liver-derived ILC2. Journal of Experimental Medicine 215, 1609-1626. 10.1084/jem.20172310.

153. Spencer, S.P., Wilhelm, C., Yang, Q., Hall, J.A., Bouladoux, N., Boyd, A., Nutman, T.B., Urban, J.F., Jr., Wang, J., Ramalingam, T.R., et al. (2014). Adaptation of innate lymphoid cells to a micronutrient deficiency promotes type 2 barrier immunity. Science 343, 432-437. 10.1126/science.1247606.

154. Scoville, S.D., Freud, A.G., and Caligiuri, M.A. (2019). Cellular pathways in the development of human and murine innate lymphoid cells. Current Opinion in Immunology 56, 100-106. 10.1016/j.coi.2018.11.003.

155. Scoville, S.D., Mundy-Bosse, B.L., Zhang, M.H., Chen, L., Zhang, X., Keller, K.A., Hughes, T., Chen, L., Cheng, S., Bergin, S.M., et al. (2016). A Progenitor Cell Expressing Transcription Factor RORgammat Generates All Human Innate Lymphoid Cell Subsets. Immunity 44, 1140-1150. 10.1016/j.immuni.2016.04.007.

156. Chen, L., Youssef, Y., Robinson, C., Ernst, G.F., Carson, M.Y., Young, K.A., Scoville, S.D., Zhang, X., Harris, R., Sekhri, P., et al. (2018). CD56 Expression Marks Human Group 2 Innate Lymphoid Cell Divergence from a Shared NK Cell and Group 3 Innate Lymphoid Cell Developmental Pathway. Immunity 49, 464-476 e464.
10.1016/j.immuni.2018.08.010.

157. Liu, C., Gong, Y., Zhang, H., Yang, H., Zeng, Y., Bian, Z., Xin, Q., Bai, Z., Zhang, M., He, J., et al. (2021). Delineating spatiotemporal and hierarchical development of human fetal innate lymphoid cells. Cell Research 31, 1106-1122. 10.1038/s41422-021-00529-2.

158. Nagasawa, M., Heesters, B.A., Kradolfer, C.M.A., Krabbendam, L., Martinez-Gonzalez, I., de Bruijn, M.J.W., Golebski, K., Hendriks, R.W., Stadhouders, R., Spits, H., and Bal, S.M. (2019). KLRG1 and NKp46 discriminate subpopulations of human
CD117(+)CRTH2(-) ILCs biased toward ILC2 or ILC3. J Exp Med 216, 1762-1776.
10.1084/jem.20190490.

159. De Obaldia, M.E., and Bhandoola, A. (2015). Transcriptional Regulation of Innate and Adaptive Lymphocyte Lineages. Annual Review of Immunology 33, 607-642.
10.1146/annurev-immunol-032414-112032.

160. Spinner, C.A., and Lazarevic, V. (2021). Transcriptional regulation of adaptive and innate lymphoid lineage specification. Immunol Rev 300, 65-81. 10.1111/imr.12935.

161. Cherrier, M., Ramachandran, G., and Golub, R. (2020). The interplay between innate lymphoid cells and T cells. Mucosal Immunol 13, 732-742. 10.1038/s41385-020-0320-8.

162. Ding, Y., Harly, C., Das, A., and Bhandoola, A. (2023). Early Development of Innate Lymphoid Cells. Methods Mol Biol 2580, 51-69. 10.1007/978-1-0716-2740-2_3.

163. Seillet, C., Mielke, L.A., Amann-Zalcenstein, D.B., Su, S., Gao, J., Almeida, F.F., Shi, W., Ritchie, M.E., Naik, S.H., Huntington, N.D., et al. (2016). Deciphering the Innate Lymphoid Cell Transcriptional Program. Cell Rep 17, 436-447.
10.1016/j.celrep.2016.09.025.

164. Serafini, N., Vosshenrich, C.A., and Di Santo, J.P. (2015). Transcriptional regulation of innate lymphoid cell fate. Nat Rev Immunol 15, 415-428. 10.1038/nri3855.

165. Yagi, R., Zhong, C., Northrup, D.L., Yu, F., Bouladoux, N., Spencer, S., Hu, G., Barron, L., Sharma, S., Nakayama, T., et al. (2014). The transcription factor GATA3 is critical for the development of all IL-7Ralpha-expressing innate lymphoid cells. Immunity 40, 378-388. 10.1016/j.immuni.2014.01.012.

166. Shih, H.Y., Sciume, G., Mikami, Y., Guo, L., Sun, H.W., Brooks, S.R., Urban, J.F., Jr., Davis, F.P., Kanno, Y., and O'Shea, J.J. (2016). Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell 165, 1120-1133.
10.1016/j.cell.2016.04.029.

167. Shih, H.Y., Sciume, G., Poholek, A.C., Vahedi, G., Hirahara, K., Villarino, A.V., Bonelli, M., Bosselut, R., Kanno, Y., Muljo, S.A., and O'Shea, J.J. (2014). Transcriptional and epigenetic networks of helper T and innate lymphoid cells. Immunol Rev 261, 23-49.
10.1111/imr.12208.

168. Fang, D., Healy, A., and Zhu, J. (2022). Differential regulation of lineage-determining transcription factor expression in innate lymphoid cell and adaptive T helper cell subsets. Front Immunol 13, 1081153. 10.3389/fimmu.2022.1081153.

169. Germar, K., Dose, M., Konstantinou, T., Zhang, J., Wang, H., Lobry, C., Arnett, K.L., Blacklow, S.C., Aifantis, I., Aster, J.C., and Gounari, F. (2011). T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling. Proc Natl Acad Sci U S A 108, 20060-20065. 10.1073/pnas.1110230108.

170. Pai, S.Y., Truitt, M.L., Ting, C.N., Leiden, J.M., Glimcher, L.H., and Ho, I.C. (2003). Critical roles for transcription factor GATA-3 in thymocyte development. Immunity 19, 863-875. 10.1016/s1074-7613(03)00328-5.

171. Ren, G., Lai, B., Harly, C., Baek, S., Ding, Y., Zheng, M., Cao, Y., Cui, K., Yang, Y., Zhu, J., et al. (2022). Transcription factors TCF-1 and GATA3 are key factors for the epigenetic priming of early innate lymphoid progenitors toward distinct cell fates. Immunity 55, 1402-1413.e1404. 10.1016/j.immuni.2022.06.019.

172. Weber, B.N., Chi, A.W., Chavez, A., Yashiro-Ohtani, Y., Yang, Q., Shestova, O., and Bhandoola, A. (2011). A critical role for TCF-1 in T-lineage specification and differentiation. Nature 476, 63-68. 10.1038/nature10279.
173. Hosoya, T., Kuroha, T., Moriguchi, T., Cummings, D., Maillard, I., Lim, K.C., and Engel, J.D. (2009). GATA-3 is required for early T lineage progenitor development. *J Exp Med* **206**, 2987-3000. 10.1084/jem.20090934.

174. Kasal, D.N., Liang, Z., Hollinger, M.K., O'Leary, C.Y., Lisicka, W., Sperling, A.I., and Bendelac, A. (2021). A Gata3 enhancer necessary for ILC2 development and function. *Proc Natl Acad Sci U S A* **118**. 10.1073/pnas.2106311118.

175. Ohmura, S., Mizuno, S., Oishi, H., Ku, C.J., Hermann, M., Hosoya, T., Takahashi, S., and Engel, J.D. (2016). Lineage-affiliated transcription factors bind the Gata3 Tcel enhancer to mediate lineage-specific programs. *J Clin Invest* **126**, 865-878. 10.1172/JCI83894.

176. Goldman, N., Chandra, A., Johnson, I., Sullivan, M.A., Patil, A.R., Vanderbeck, A., Jay, A., Zhou, Y., Ferrari, E.K., Mayne, L., et al. (2023). Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. *Nat Immunol* **24**, 1698-1710. 10.1038/s41590-023-01599-7.

177. Savage, A.K., Constantinides, M.G., Han, J., Picard, D., Martin, E., Li, B., Lantz, O., and Bendelac, A. (2008). The transcription factor PLZF directs the effector program of the NKT cell lineage. *Immunity* **29**, 391-403. 10.1016/j.immuni.2008.07.011.

178. Taghon, T., Yui, M.A., and Rothenberg, E.V. (2007). Mast cell lineage diversion of T lineage precursors by the essential T cell transcription factor GATA-3. *Nat Immunol* **8**, 845-855. 10.1038/ni1486.

179. Aliahmad, P., O'Flaherty, E., Han, P., Goularte, O.D., Wilkinson, B., Satake, M., Molkentin, J.D., and Kaye, J. (2004). TOX provides a link between calcineurin activation and CD8 lineage commitment. *J Exp Med* **199**, 1089-1099. 10.1084/jem.20040051.

180. Aliahmad, P., Kadavallore, A., de la Torre, B., Kappes, D., and Kaye, J. (2011). TOX is required for development of the CD4 T cell lineage gene program. *J Immunol* **187**, 5931-5940. 10.4049/jimmunol.1101474.

181. Ikawa, T., Hirose, S., Masuda, K., Kakugawa, K., Satoh, R., Shibano-Satoh, A., Kominami, R., Katsura, Y., and Kawamoto, H. (2010). An essential developmental checkpoint for production of the T cell lineage. *Science* **329**, 93-96. 10.1126/science.1188995.

182. Li, L., Leid, M., and Rothenberg, E.V. (2010). An early T cell lineage commitment checkpoint dependent on the transcription factor Bcl11b. *Science* **329**, 89-93. 10.1126/science.1188989.

183. Li, P., Burke, S., Wang, J., Chen, X., Ortiz, M., Lee, S.C., Lu, D., Campos, L., Goulding, D., Ng, B.L., et al. (2010). Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion. *Science* **329**, 85-89. 10.1126/science.1188063.

184. Califano, D., Cho, Jonathan J., Uddin, Mohammad N., Lorentsen, Kyle J., Yang, Q., Bhandoola, A., Li, H., and Avram, D. (2015). Transcription Factor Bcl11b Controls Identity and Function of Mature Type 2 Innate Lymphoid Cells. *Immunity* **43**, 354-368. 10.1016/j.immuni.2015.07.005.

185. Walker, J.A., Oliphant, C.J., Englezakis, A., Yu, Y., Clare, S., Rodewald, H.R., Belz, G., Liu, P., Fallon, P.G., and McKenzie, A.N. (2015). Bcl11b is essential for group 2 innate lymphoid cell development. *J Exp Med* **212**, 875-882. 10.1084/jem.20142224.

186. Yu, Y., Wang, C., Clare, S., Wang, J., Lee, S.-C., Brandt, C., Burke, S., Lu, L., He, D., Jenkins, N.A., et al. (2015). The transcription factor Bcl11b is specifically expressed in
group 2 innate lymphoid cells and is essential for their development. Journal of Experimental Medicine 212, 865-874. 10.1084/jem.20142318.

187. Hosokawa, H., Romero-Wolf, M., Yang, Q., Motomura, Y., Levanon, D., Groner, Y., Moro, K., Tanaka, T., and Rothenberg, E.V. (2020). Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells. J Exp Med 217. 10.1084/jem.20190972.

188. Miyazaki, M., Miyazaki, K., Chen, K., Jin, Y., Turner, J., Moore, A.J., Saito, R., Yoshida, K., Ogawa, S., Rodewald, H.R., et al. (2017). The E-Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development. Immunity 46, 818-834 e814. 10.1016/j.immuni.2017.04.022.

189. Wang, H.C., Qian, L., Zhao, Y., Mengarelli, J., Adrianto, I., Montgomery, C.G., Urban, J.F., Jr., Fung, K.M., and Sun, X.H. (2017). Downregulation of E Protein Activity Augments an ILC2 Differentiation Program in the Thymus. J Immunol 198, 3149-3156. 10.4049/jimmunol.1602009.

190. Nagasawa, M., Germar, K., Blom, B., and Spits, H. (2017). Human CD5+ Innate Lymphoid Cells Are Functionally Immature and Their Development from CD34+ Progenitor Cells Is Regulated by Id2. Frontiers in Immunology 8. 10.3389/fimmu.2017.01047.

191. Monticelli, L.A., Sonnenberg, G.F., Abt, M.C., Alenghat, T., Ziegler, C.G., Doering, T.A., Angelosanto, J.M., Laidlaw, B.J., Yang, C.Y., Sathaliyawala, T., et al. (2011). Innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus. Nat Immunol 12, 1045-1054. 10.1031/ni.2131.

192. Satoh-Takayama, N., Lesjean-Pottier, S., Vieira, P., Sawa, S., Eberl, G., Vosshenrich, C.A., and Di Santo, J.P. (2010). IL-7 and IL-15 independently program the differentiation of intestinal CD3-NKp46+ cell subsets from Id2-dependent precursors. J Exp Med 207, 273-280. 10.1084/jem.20092029.

193. Yokota, Y. (1999). Development of peripheral lymphoid organs and natural killer cells depends on the helix-loop-helix inhibitor Id2. Nature.

194. Kamizono, S., Duncan, G.S., Seidel, M.G., Morimoto, A., Hamada, K., Grosveld, G., Akashi, K., Lind, E.F., Haight, J.P., Ohashi, P.S., et al. (2009). Nfil3/E4bp4 is required for the development and maturation of NK cells in vivo. Journal of Experimental Medicine 206, 2977-2986. 10.1084/jem.20092176.

195. Golub, R. (2021). The Notch signaling pathway involvement in innate lymphoid cell biology. Biomed J 44, 133-143. 10.1016/j.bj.2020.12.004.

196. Schmitt, T.M., and Zuniga-Pflucker, J.C. (2002). Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17, 749-756. 10.1016/s1074-7613(02)00474-0.

197. Skene, P.J., and Henikoff, S. (2017). An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6. 10.7554/eLife.21856.

198. Patey, E., and Bjorkstrom, N.K. (2024). Elusive early NK cell progenitor identified. Nat Immunol 25, 1126-1128. 10.1038/s41590-024-01871-4.

199. Taniguchi, H., Toyoshima, T., Fukao, K., and Nakauchi, H. (1996). Presence of hematopoietic stem cells in the adult liver. Nat Med 2, 198-203. 10.1038/nm0296-198.

200. Wang, X.Q., Lo, C.M., Chen, L., Cheung, C.K., Yang, Z.F., Chen, Y.X., Ng, M.N., Yu, W.C., Ming, X., Zhang, W., et al. (2012). Hematopoietic chimerism in liver
transplantation patients and hematopoietic stem/progenitor cells in adult human liver.
Hepatology 56, 1557-1566. 10.1002/hep.25820.

201. Freud, A.G., Becknell, B., Roychowdhury, S., Mao, H.C., Ferketich, A.K., Nuovo, G.J., Hughes, T.L., Marburger, T.B., Sung, J., Baiocchi, R.A., et al. (2005). A human CD34(+) subset resides in lymph nodes and differentiates into CD56bright natural killer cells. Immunity 22, 295-304. 10.1016/j.immuni.2005.01.013.

202. Renoux, V.M., Zriwil, A., Peitzsch, C., Michaelsson, J., Friberg, D., Soneji, S., and Sitnicka, E. (2015). Identification of a Human Natural Killer Cell Lineage-Restricted Progenitor in Fetal and Adult Tissues. Immunity 43, 394-407. 10.1016/j.immuni.2015.07.011.

203. Ferreira, A.C.F., Szeto, A.C.H., Heycock, M.W.D., Clark, P.A., Walker, J.A., Crisp, A., Barlow, J.L., Kitching, S., Lim, A., Gogoi, M., et al. (2021). RORalpha is a critical checkpoint for T cell and ILC2 commitment in the embryonic thymus. Nat Immunol 22, 166-178. 10.1038/s41590-020-00833-w.

204. Carlyle, J.R., Michie, A.M., Furlonger, C., Nakano, T., Lenardo, M.J., Paige, C.J., and Zuniga-Pflucker, J.C. (1997). Identification of a novel developmental stage marking lineage commitment of progenitor thymocytes. J Exp Med 186, 173-182. 10.1084/jem.186.2.173.

**Acknowledgements**

We thank Chrysothemis Brown (Memorial Sloan Kettering Cancer Center), Marco Colonna (Washington University School of Medicine), Han-Yu Shih (National Eye Institute), Hergen Spits (University of Amsterdam), Eric Vivier (Marseille Medical School and Assistance Publique des Hôpitaux de Marseille) and Jinfang Zhu (National Institute of Allergy and Infectious Diseases) for criticism and comments.

**Author Contributions**

A.D., Y.D., C.H., and A.B. wrote this review. All authors edited and approved the final version of the manuscript.

**Funding**

A.D., Y.D. and A.B. were supported by the Intramural Research Program of the Center for Cancer Research, National Cancer Institute. C.H. was supported by *INSERM*, CNRS, Université de Nantes, Fondation pour la Recherche Médicale, (DEQ20170839118), Conseil Région Pays de la Loire (Etoiles Montantes), ANR (LabEX IGO, ANR-11-LABX-0016; HémaNext, ANR-16-IDEX-0007; JCJC-AAPG2022, ANR-22-CE15-0040-01).

**Ethics Declarations**

Competing interests: C.H. has submitted a patent on the use of NFIL3 to generate ILC precursors *in vitro* (application number PCT/EP2025/072604). The other authors declare no competing interests.
**Selected References (# S.No of the reference in superscript):**

1. Klose et al., 2014³⁰: This study identified Id2-expressing Common Helper ILC progenitors (CHILP), which predominantly generated helper ILC and only a small fraction of NK cells.

2. Constantinides et al., 2014⁵⁵: This study identified PLZF-expressing committed ILC Precursors (ILCP) that give rise to all ILC. PLZF lineage tracing established that all ILC1, ILC2 and ILC3 were highly labelled by PLZF expression, whereas LTi cells and NK cells had lower levels or were minimally labelled by PLZF. This work therefore indicated that most NK cells and LTi cells have distinct developmental pathways from ILC1, ILC2 and ILC3.

3. Yang et al., 2015⁹³: This work identified a population of Early ILC progenitors (EILP) marked by high TCF-1 expression, that efficiently differentiated into NK cells, ILC1, ILC2 and ILC3.

4. Harly et al., 2018⁸⁵: The authors established EILP as developmental intermediates between ALP and ILCP, and characterized key transcriptional requirements at successive stages of ILC development.

5. Liang et al., 2024¹³⁰: This study identified and characterized an EOMES-expressing NK progenitor population which was heterogenous, and included committed NK progenitors but also some PLZF-expressing cells that generated both ILC1 and NK cells.

6. Ding et al., 2024³: This study identified and characterized the earliest known NK-biased progenitors, termed early NK progenitors (ENKP). The authors demonstrated that NK cells arise by at least two developmental pathways, with another pathway of NK development mediated by ILCP. They further established these NK cell subsets are functionally distinct.

7. Seehus et al., 2015¹⁰⁷: This study showed that the transcription factor TOX is essential for development of all known ILC subsets and early ILC progenitors, but not ILC3 in the gut.

8. Yu et al., 2014⁸⁸: This work, together with other papers¹⁰¹,¹⁰², showed that NFIL3 is essential for generating nearly all ILC. The authors characterized a CXCR6⁺ αLP population that differentiated into ILC but not T cells and B cells.

9. Leger et al., 2025⁹⁶: This study established that forced expression of NFIL3 in ALP led to upregulated expression of many ILC transcription factors including TOX, TCF-1, and PLZF; and resulted in differentiation of ILC *in vitro*. Studies of genome-wide NFIL3 binding indicated NFIL3 provided direct regulatory inputs to many ILC genes.

10. Lim et al., 2017¹⁴⁶: This study identified ILCP in human peripheral blood that gave rise to ILC1, ILC2 and ILC3. These observations suggested distinct ILC populations in different tissues might be generated from colonizing multipotential ILC precursors responding to tissue-specific signals, which the authors termed "ILC-poiesis".

11. Wang et al., 2025⁷⁵: This study demonstrated that extramedullary and intramedullary ILC in mice have separate developmental origins during ontogeny. It further showed local microenvironment instructs ILCP fate, directing them towards bipotent ILC1/3P in liver and intestine, and towards ILC2P in lung.

12. Kasal et al., 2020⁹⁴: This study identified the earliest specified precursor for LTi cells, termed *Rorc*⁺ αLP, which expressed RORγt but lacked TCF-1.

13. Simic et al., 2020¹³⁵: This study identified the origin of embryonic LTi cells as hematopoietic cells derived from the aorta-gonad-mesonephros region, rather than the yolk sac.