Transcription factor-driven regulation of ILC1 and ILC3

ILCs have an important role in mammalian tissues, providing an early immune response and a regulatory function to modify the adaptive and epithelial immune response.Group 1 ILCs (ILC1) are heterogenous depending on the role of either T-bet or Hobit as TFs for maintenance.Group 3 ILC (ILC3) express several TFs that appear to inhibit their plasticity toward ILC1, and these include RORγt, RORα, c-Maf, and HIF1. By contrast, T-bet, in conjunction with Aiolos and Bcl6, promote ILC1.The balance between ILC3 and ILC1 appears to be crucial for the severity outcome of IBD, colorectal cancer, and likely other diseases. Mammalian innate lymphoid cells (ILCs) have functional relevance under both homeostatic and disease settings, such as inflammatory bowel disease (IBD), particularly in the context of maintaining the integrity of mucosal surfaces. Early reports highlighted group 1 and 3 ILC regulatory transcription factors (TFs), T-box expressed in T cells (T-bet; Tbx21) and RAR-related orphan nuclear receptor γt (RORγt; Rorc), as key regulators of ILC biology. Since then, other canonical TFs have been shown to have a role in the development and function of ILC subsets. In this review, we focus on recent insights into the balance between mature ILC1 and ILC3 based on these TFs and how they interact with other key cell-intrinsic molecular pathways. We outline how this TF interplay might be explored to identify novel candidate therapeutic avenues for human diseases. Mammalian innate lymphoid cells (ILCs) have functional relevance under both homeostatic and disease settings, such as inflammatory bowel disease (IBD), particularly in the context of maintaining the integrity of mucosal surfaces. Early reports highlighted group 1 and 3 ILC regulatory transcription factors (TFs), T-box expressed in T cells (T-bet; Tbx21) and RAR-related orphan nuclear receptor γt (RORγt; Rorc), as key regulators of ILC biology. Since then, other canonical TFs have been shown to have a role in the development and function of ILC subsets. In this review, we focus on recent insights into the balance between mature ILC1 and ILC3 based on these TFs and how they interact with other key cell-intrinsic molecular pathways. We outline how this TF interplay might be explored to identify novel candidate therapeutic avenues for human diseases. ILCs are particularly abundant in mammalian mucosal tissues, where they elicit an early immune response and interact with CD4+ T cells and the epithelium [1.Weizman O.E. et al.ILC1 confer early host protection at initial sites of viral infection.Cell. 2017; 171: 795-808Abstract Full Text Full Text PDF PubMed Scopus (234) Google Scholar, 2.Meininger I. et al.Tissue-specific features of innate lymphoid cells.Trends Immunol. 2020; 41: 902-917Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar, 3.Bal S.M. et al.Plasticity of innate lymphoid cell subsets.Nat. Rev. Immunol. 2020; 20: 552-565Crossref PubMed Scopus (113) Google Scholar, 4.Melo-Gonzalez F. et al.Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria.J. Exp. Med. 2019; 216: 728-742Crossref PubMed Scopus (0) Google Scholar, 5.Zhou L. et al.Innate lymphoid cells support regulatory T cells in the intestine through interleukin-2.Nature. 2019; 568: 405-409Crossref PubMed Scopus (113) Google Scholar, 6.Deng T. et al.ILC3-derived OX40L is essential for homeostasis of intestinal Tregs in immunodeficient mice.Cell. Mol. Immunol. 2020; 17: 163-177Crossref PubMed Scopus (13) Google Scholar, 7.Lehmann F.M. et al.Microbiota-induced tissue signals regulate ILC3-mediated antigen presentation.Nat. Commun. 2020; 11: 1794Crossref PubMed Scopus (15) Google Scholar, 8.Goc J. et al.Dysregulation of ILC3s unleashes progression and immunotherapy resistance in colon cancer.Cell. 2021; 184: 5015-5030Abstract Full Text Full Text PDF PubMed Scopus (24) Google Scholar, 9.Jowett G.M. et al.ILC1 drive intestinal epithelial and matrix remodelling.Nat. Mater. 2021; 20: 250-259Crossref PubMed Scopus (29) Google Scholar]. ILC subsets are distinct from natural killer (NK) cells and have been categorized into four groups, depending on the characteristic expression of TFs defining T-bet+ (see Glossary) type 1 ILC (ILC1), GATA-binding protein 3 (GATA3)+ type 2 ILC (ILC2), RORγt+ type 3 ILC (ILC3), and RORγt+ lymphoid tissue inducer cells (LTi) ILC3 in mice and humans [2.Meininger I. et al.Tissue-specific features of innate lymphoid cells.Trends Immunol. 2020; 41: 902-917Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar,3.Bal S.M. et al.Plasticity of innate lymphoid cell subsets.Nat. Rev. Immunol. 2020; 20: 552-565Crossref PubMed Scopus (113) Google Scholar] (Box 1). This review focuses on the roles of ILC1 and ILC3 because the balance between these has been associated with inflammatory bowel disease (IBD) and colorectal carcinoma (CRC) [2.Meininger I. et al.Tissue-specific features of innate lymphoid cells.Trends Immunol. 2020; 41: 902-917Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar,3.Bal S.M. et al.Plasticity of innate lymphoid cell subsets.Nat. Rev. Immunol. 2020; 20: 552-565Crossref PubMed Scopus (113) Google Scholar,8.Goc J. et al.Dysregulation of ILC3s unleashes progression and immunotherapy resistance in colon cancer.Cell. 2021; 184: 5015-5030Abstract Full Text Full Text PDF PubMed Scopus (24) Google Scholar].Box 1Identification of ILCsLiterature on ILCs is often compounded by the lack of ILC-specific markers, a non-uniform use of lineage markers to define non-ILC leukocytes in the gating strategy, or by diverse gating strategies to analyze ILC1 and ILC3 subsets. In terms of lineage markers, the use of CD3 and a B cell marker, such as CD19, is the minimal requirement for detecting ILCs in mouse and human, but it is recommended and practiced in most studies reviewed here to use additional lineage markers targeting macrophages, neutrophils, granulocytes, and platelets. Some studies also use CD5 in the lineage cocktail [10.Cuff A.O. Male V. Conventional NK cells and ILC1 are partially ablated in the livers of Ncr1 iCreTbx21 fl/fl mice.Wellcome Open Res. 2017; 2: 39Crossref PubMed Scopus (0) Google Scholar, 11.Ducimetière L. et al.Conventional NK cells and tissue-resident ILC1s join forces to control liver metastasis.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2026271118Crossref PubMed Scopus (10) Google Scholar, 12.Fachi J.L. et al.Hypoxia enhances ILC3 responses through HIF-1alpha-dependent mechanism.Mucosal Immunol. 2021; 14: 828-841Crossref PubMed Scopus (6) Google Scholar, 13.Fiancette R. et al.Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity.Nat. Immunol. 2021; 10: 1231-1244Google Scholar, 14.Friedrich C. et al.Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues.Nat. Immunol. 2021; 22: 1256-1267Crossref PubMed Scopus (7) Google Scholar, 15.Li S. et al.Aryl hydrocarbon receptor signaling cell intrinsically inhibits intestinal group 2 innate lymphoid cell function.Immunity. 2018; 49: 915-928Abstract Full Text Full Text PDF PubMed Scopus (81) Google Scholar, 16.McFarland A.P. et al.Multi-tissue single-cell analysis deconstructs the complex programs of mouse natural killer and type 1 innate lymphoid cells in tissues and circulation.Immunity. 2021; 54: 1320-1337Abstract Full Text Full Text PDF PubMed Google Scholar, 17.Pokrovskii M. et al.Characterization of transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells.Immunity. 2019; 51: 185-197Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar, 18.Schroeder J.H. et al.Innate lymphoid cells lacking surface expression of CD90 are functional.BioRxiv. 2021; (Published online December 11, 2021)http://dx,doi.org/10.1101/2021.12.11.472210Google Scholar, 19.Schroeder J.H. et al.Sustained post-developmental T-bet expression is critical for the maintenance of type one innate lymphoid cells in vivo.Front. Immunol. 2021; 12760198Crossref Scopus (2) Google Scholar, 20.Schroeder J.H. et al.T-bet controls cellularity of intestinal group 3 innate lymphoid cells.Front. Immunol. 2021; 11623324Crossref PubMed Scopus (2) Google Scholar, 21.Stehle C. et al.T-bet and RORα control lymph node formation by regulating embryonic innate lymphoid cell differentiation.Nat. Immunol. 2021; 22: 1231-1244Crossref PubMed Scopus (2) Google Scholar, 22.Yagi R. et al.The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells.Immunity. 2014; 40: 378-388Abstract Full Text Full Text PDF PubMed Scopus (267) Google Scholar, 23.Zhong C. et al.Differential expression of the transcription factor GATA3 specifies lineage and functions of innate lymphoid cells.Immunity. 2020; 52: 83-95Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar]. However, the use of CD5 as a lineage marker is controversial because ILCs have been reported to express CD5, while CD5+ ILCs have also been shown to express αβTCR and have been related to nonfunctional T cells [2.Meininger I. et al.Tissue-specific features of innate lymphoid cells.Trends Immunol. 2020; 41: 902-917Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar,24.Burkhard S.H. et al.T cell contamination in flow cytometry gating approaches for analysis of innate lymphoid cells.PLoS ONE. 2014; 9e94196Crossref Scopus (12) Google Scholar,25.Alisjahbana A. et al.CD5 surface expression marks intravascular human innate lymphoid cells that have a distinct ontogeny and migrate to the lung.Front. Immunol. 2021; 12752104Crossref Scopus (3) Google Scholar]. Furthermore, CD127 is often used as a mouse and human ILC marker; however, CD127 expression in murine ILCs can be lost upon stimulation with IL7 [18.Schroeder J.H. et al.Innate lymphoid cells lacking surface expression of CD90 are functional.BioRxiv. 2021; (Published online December 11, 2021)http://dx,doi.org/10.1101/2021.12.11.472210Google Scholar, 19.Schroeder J.H. et al.Sustained post-developmental T-bet expression is critical for the maintenance of type one innate lymphoid cells in vivo.Front. Immunol. 2021; 12760198Crossref Scopus (2) Google Scholar, 20.Schroeder J.H. et al.T-bet controls cellularity of intestinal group 3 innate lymphoid cells.Front. Immunol. 2021; 11623324Crossref PubMed Scopus (2) Google Scholar,26.Cavagnero K.J. et al.Unconventional ST2- and CD127-negative lung ILC2 populations are induced by the fungal allergen Alternaria alternata.J. Allergy Clin. Immunol. 2019; 144: 1432-1435Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar, 27.Martin C.E. et al.Interleukin-7 Availability is maintained by a hematopoietic cytokine sink comprising innate lymphoid cells and T cells.Immunity. 2017; 47: 171-182Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar, 28.Bernink J.H. et al.Human type 1 innate lymphoid cells accumulate in inflamed mucosal tissues.Nat. Immunol. 2013; 14: 221-229Crossref PubMed Scopus (689) Google Scholar, 29.Bernink J.H. et al.Interleukin-12 and -23 control plasticity of CD127(+) group 1 and group 3 innate lymphoid cells in the intestinal lamina propria.Immunity. 2015; 43: 146-160Abstract Full Text Full Text PDF PubMed Scopus (398) Google Scholar, 30.Robinette M.L. et al.Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets.Nat. Immunol. 2015; 16: 306-317Crossref PubMed Scopus (448) Google Scholar, 31.Mazzurana L. et al.Suppression of Aiolos and Ikaros expression by lenalidomide reduces human ILC3-ILC1/NK cell transdifferentiation.Eur. J. Immunol. 2019; 49: 1344-1355Crossref PubMed Scopus (37) Google Scholar, 32.Mazzurana L. et al.Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.Cell Res. 2021; 31: 554-568Crossref PubMed Scopus (46) Google Scholar, 33.Miyamoto C. et al.Runx/Cbfbeta complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation.Nat. Commun. 2019; 10: 447Crossref PubMed Scopus (32) Google Scholar, 34.Parker M.E. et al.c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program.J. Exp. Med. 2020; 217e20191030Crossref PubMed Scopus (18) Google Scholar, 35.Walker J.A. et al.Polychromic reporter mice reveal unappreciated innate lymphoid cell progenitor heterogeneity and elusive ILC3 progenitors in bone marrow.Immunity. 2019; 51: 104-118Abstract Full Text Full Text PDF PubMed Scopus (55) Google Scholar]. Similarly, CD90 expression, in particular its high expression, has been used in a few studies to detect ILC3 [12.Fachi J.L. et al.Hypoxia enhances ILC3 responses through HIF-1alpha-dependent mechanism.Mucosal Immunol. 2021; 14: 828-841Crossref PubMed Scopus (6) Google Scholar,14.Friedrich C. et al.Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues.Nat. Immunol. 2021; 22: 1256-1267Crossref PubMed Scopus (7) Google Scholar,22.Yagi R. et al.The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells.Immunity. 2014; 40: 378-388Abstract Full Text Full Text PDF PubMed Scopus (267) Google Scholar,36.Klose C.S. et al.A T-bet gradient controls the fate and function of CCR6-RORγt+ innate lymphoid cells.Nature. 2013; 494: 261-265Crossref PubMed Scopus (500) Google Scholar, 37.Krzywinska E. et al.Loss of HIF-1α in natural killer cells inhibits tumour growth by stimulating non-productive angiogenesis.Nat. Commun. 2017; 8: 1597Crossref PubMed Scopus (97) Google Scholar, 38.Song C. et al.Unique and redundant functions of NKp46+ ILC3s in models of intestinal inflammation.J. Exp. Med. 2015; 212: 1869-1882Crossref PubMed Google Scholar, 39.Wagage S. et al.The group 3 innate lymphoid cell defect in aryl hydrocarbon receptor deficient mice is associated with T cell hyperactivation during intestinal infection.PLoS ONE. 2015; 10e0128335Crossref PubMed Scopus (26) Google Scholar, 40.Yu H.B. et al.Vasoactive intestinal peptide promotes host defense against enteric pathogens by modulating the recruitment of group 3 innate lymphoid cells.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2106634118Crossref Scopus (5) Google Scholar]. However, preliminary data suggest that CD90 expression in ILCs is also lost in vitro and in vivo, and that ILC1 and ILC2 might have high expression of CD90 [18.Schroeder J.H. et al.Innate lymphoid cells lacking surface expression of CD90 are functional.BioRxiv. 2021; (Published online December 11, 2021)http://dx,doi.org/10.1101/2021.12.11.472210Google Scholar] (pers. commun. from J.H.S. and G.M.L.), although this remains to be robustly validated. CD49a is sometimes used as a murine ILC1 marker in studies investigating ILC1 from non-intestinal tissues [11.Ducimetière L. et al.Conventional NK cells and tissue-resident ILC1s join forces to control liver metastasis.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2026271118Crossref PubMed Scopus (10) Google Scholar,14.Friedrich C. et al.Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues.Nat. Immunol. 2021; 22: 1256-1267Crossref PubMed Scopus (7) Google Scholar,16.McFarland A.P. et al.Multi-tissue single-cell analysis deconstructs the complex programs of mouse natural killer and type 1 innate lymphoid cells in tissues and circulation.Immunity. 2021; 54: 1320-1337Abstract Full Text Full Text PDF PubMed Google Scholar,41.Cortez V.S. et al.SMAD4 impedes the conversion of NK cells into ILC1-like cells by curtailing non-canonical TGF-β signaling.Nat. Immunol. 2017; 18: 995-1003Crossref PubMed Scopus (185) Google Scholar, 42.Ebihara T. et al.Runx3 specifies lineage commitment of innate lymphoid cells.Nat. Immunol. 2015; 16: 1124-1133Crossref PubMed Google Scholar, 43.Mackay L.K. et al.Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes.Science. 2016; 3524594-63Crossref PubMed Scopus (469) Google Scholar, 44.Yomogida K. et al.Hobit confers tissue-dependent programs to type 1 innate lymphoid cells.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2117965118Crossref PubMed Scopus (1) Google Scholar, 45.Zhang L.H. et al.The aryl hydrocarbon receptor is required for the maintenance of liver-resident natural killer cells.J. Exp. Med. 2016; 213: 2249-2257Crossref PubMed Google Scholar, 46.Nixon B.G. et al.Cytotoxic granzyme C-expressing ILC1s contribute to antitumor immunity and neonatal autoimmunity.Sci Immunol. 2022; 7eabi8642Crossref PubMed Scopus (1) Google Scholar]. The detection strategies in other mouse studies reviewed here consider the fact that ILC1 do not express RORγt, while it is a key marker of ILC3. Literature on ILCs is often compounded by the lack of ILC-specific markers, a non-uniform use of lineage markers to define non-ILC leukocytes in the gating strategy, or by diverse gating strategies to analyze ILC1 and ILC3 subsets. In terms of lineage markers, the use of CD3 and a B cell marker, such as CD19, is the minimal requirement for detecting ILCs in mouse and human, but it is recommended and practiced in most studies reviewed here to use additional lineage markers targeting macrophages, neutrophils, granulocytes, and platelets. Some studies also use CD5 in the lineage cocktail [10.Cuff A.O. Male V. Conventional NK cells and ILC1 are partially ablated in the livers of Ncr1 iCreTbx21 fl/fl mice.Wellcome Open Res. 2017; 2: 39Crossref PubMed Scopus (0) Google Scholar, 11.Ducimetière L. et al.Conventional NK cells and tissue-resident ILC1s join forces to control liver metastasis.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2026271118Crossref PubMed Scopus (10) Google Scholar, 12.Fachi J.L. et al.Hypoxia enhances ILC3 responses through HIF-1alpha-dependent mechanism.Mucosal Immunol. 2021; 14: 828-841Crossref PubMed Scopus (6) Google Scholar, 13.Fiancette R. et al.Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity.Nat. Immunol. 2021; 10: 1231-1244Google Scholar, 14.Friedrich C. et al.Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues.Nat. Immunol. 2021; 22: 1256-1267Crossref PubMed Scopus (7) Google Scholar, 15.Li S. et al.Aryl hydrocarbon receptor signaling cell intrinsically inhibits intestinal group 2 innate lymphoid cell function.Immunity. 2018; 49: 915-928Abstract Full Text Full Text PDF PubMed Scopus (81) Google Scholar, 16.McFarland A.P. et al.Multi-tissue single-cell analysis deconstructs the complex programs of mouse natural killer and type 1 innate lymphoid cells in tissues and circulation.Immunity. 2021; 54: 1320-1337Abstract Full Text Full Text PDF PubMed Google Scholar, 17.Pokrovskii M. et al.Characterization of transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells.Immunity. 2019; 51: 185-197Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar, 18.Schroeder J.H. et al.Innate lymphoid cells lacking surface expression of CD90 are functional.BioRxiv. 2021; (Published online December 11, 2021)http://dx,doi.org/10.1101/2021.12.11.472210Google Scholar, 19.Schroeder J.H. et al.Sustained post-developmental T-bet expression is critical for the maintenance of type one innate lymphoid cells in vivo.Front. Immunol. 2021; 12760198Crossref Scopus (2) Google Scholar, 20.Schroeder J.H. et al.T-bet controls cellularity of intestinal group 3 innate lymphoid cells.Front. Immunol. 2021; 11623324Crossref PubMed Scopus (2) Google Scholar, 21.Stehle C. et al.T-bet and RORα control lymph node formation by regulating embryonic innate lymphoid cell differentiation.Nat. Immunol. 2021; 22: 1231-1244Crossref PubMed Scopus (2) Google Scholar, 22.Yagi R. et al.The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells.Immunity. 2014; 40: 378-388Abstract Full Text Full Text PDF PubMed Scopus (267) Google Scholar, 23.Zhong C. et al.Differential expression of the transcription factor GATA3 specifies lineage and functions of innate lymphoid cells.Immunity. 2020; 52: 83-95Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar]. However, the use of CD5 as a lineage marker is controversial because ILCs have been reported to express CD5, while CD5+ ILCs have also been shown to express αβTCR and have been related to nonfunctional T cells [2.Meininger I. et al.Tissue-specific features of innate lymphoid cells.Trends Immunol. 2020; 41: 902-917Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar,24.Burkhard S.H. et al.T cell contamination in flow cytometry gating approaches for analysis of innate lymphoid cells.PLoS ONE. 2014; 9e94196Crossref Scopus (12) Google Scholar,25.Alisjahbana A. et al.CD5 surface expression marks intravascular human innate lymphoid cells that have a distinct ontogeny and migrate to the lung.Front. Immunol. 2021; 12752104Crossref Scopus (3) Google Scholar]. Furthermore, CD127 is often used as a mouse and human ILC marker; however, CD127 expression in murine ILCs can be lost upon stimulation with IL7 [18.Schroeder J.H. et al.Innate lymphoid cells lacking surface expression of CD90 are functional.BioRxiv. 2021; (Published online December 11, 2021)http://dx,doi.org/10.1101/2021.12.11.472210Google Scholar, 19.Schroeder J.H. et al.Sustained post-developmental T-bet expression is critical for the maintenance of type one innate lymphoid cells in vivo.Front. Immunol. 2021; 12760198Crossref Scopus (2) Google Scholar, 20.Schroeder J.H. et al.T-bet controls cellularity of intestinal group 3 innate lymphoid cells.Front. Immunol. 2021; 11623324Crossref PubMed Scopus (2) Google Scholar,26.Cavagnero K.J. et al.Unconventional ST2- and CD127-negative lung ILC2 populations are induced by the fungal allergen Alternaria alternata.J. Allergy Clin. Immunol. 2019; 144: 1432-1435Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar, 27.Martin C.E. et al.Interleukin-7 Availability is maintained by a hematopoietic cytokine sink comprising innate lymphoid cells and T cells.Immunity. 2017; 47: 171-182Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar, 28.Bernink J.H. et al.Human type 1 innate lymphoid cells accumulate in inflamed mucosal tissues.Nat. Immunol. 2013; 14: 221-229Crossref PubMed Scopus (689) Google Scholar, 29.Bernink J.H. et al.Interleukin-12 and -23 control plasticity of CD127(+) group 1 and group 3 innate lymphoid cells in the intestinal lamina propria.Immunity. 2015; 43: 146-160Abstract Full Text Full Text PDF PubMed Scopus (398) Google Scholar, 30.Robinette M.L. et al.Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets.Nat. Immunol. 2015; 16: 306-317Crossref PubMed Scopus (448) Google Scholar, 31.Mazzurana L. et al.Suppression of Aiolos and Ikaros expression by lenalidomide reduces human ILC3-ILC1/NK cell transdifferentiation.Eur. J. Immunol. 2019; 49: 1344-1355Crossref PubMed Scopus (37) Google Scholar, 32.Mazzurana L. et al.Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.Cell Res. 2021; 31: 554-568Crossref PubMed Scopus (46) Google Scholar, 33.Miyamoto C. et al.Runx/Cbfbeta complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation.Nat. Commun. 2019; 10: 447Crossref PubMed Scopus (32) Google Scholar, 34.Parker M.E. et al.c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program.J. Exp. Med. 2020; 217e20191030Crossref PubMed Scopus (18) Google Scholar, 35.Walker J.A. et al.Polychromic reporter mice reveal unappreciated innate lymphoid cell progenitor heterogeneity and elusive ILC3 progenitors in bone marrow.Immunity. 2019; 51: 104-118Abstract Full Text Full Text PDF PubMed Scopus (55) Google Scholar]. Similarly, CD90 expression, in particular its high expression, has been used in a few studies to detect ILC3 [12.Fachi J.L. et al.Hypoxia enhances ILC3 responses through HIF-1alpha-dependent mechanism.Mucosal Immunol. 2021; 14: 828-841Crossref PubMed Scopus (6) Google Scholar,14.Friedrich C. et al.Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues.Nat. Immunol. 2021; 22: 1256-1267Crossref PubMed Scopus (7) Google Scholar,22.Yagi R. et al.The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells.Immunity. 2014; 40: 378-388Abstract Full Text Full Text PDF PubMed Scopus (267) Google Scholar,36.Klose C.S. et al.A T-bet gradient controls the fate and function of CCR6-RORγt+ innate lymphoid cells.Nature. 2013; 494: 261-265Crossref PubMed Scopus (500) Google Scholar, 37.Krzywinska E. et al.Loss of HIF-1α in natural killer cells inhibits tumour growth by stimulating non-productive angiogenesis.Nat. Commun. 2017; 8: 1597Crossref PubMed Scopus (97) Google Scholar, 38.Song C. et al.Unique and redundant functions of NKp46+ ILC3s in models of intestinal inflammation.J. Exp. Med. 2015; 212: 1869-1882Crossref PubMed Google Scholar, 39.Wagage S. et al.The group 3 innate lymphoid cell defect in aryl hydrocarbon receptor deficient mice is associated with T cell hyperactivation during intestinal infection.PLoS ONE. 2015; 10e0128335Crossref PubMed Scopus (26) Google Scholar, 40.Yu H.B. et al.Vasoactive intestinal peptide promotes host defense against enteric pathogens by modulating the recruitment of group 3 innate lymphoid cells.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2106634118Crossref Scopus (5) Google Scholar]. However, preliminary data suggest that CD90 expression in ILCs is also lost in vitro and in vivo, and that ILC1 and ILC2 might have high expression of CD90 [18.Schroeder J.H. et al.Innate lymphoid cells lacking surface expression of CD90 are functional.BioRxiv. 2021; (Published online December 11, 2021)http://dx,doi.org/10.1101/2021.12.11.472210Google Scholar] (pers. commun. from J.H.S. and G.M.L.), although this remains to be robustly validated. CD49a is sometimes used as a murine ILC1 marker in studies investigating ILC1 from non-intestinal tissues [11.Ducimetière L. et al.Conventional NK cells and tissue-resident ILC1s join forces to control liver metastasis.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2026271118Crossref PubMed Scopus (10) Google Scholar,14.Friedrich C. et al.Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues.Nat. Immunol. 2021; 22: 1256-1267Crossref PubMed Scopus (7) Google Scholar,16.McFarland A.P. et al.Multi-tissue single-cell analysis deconstructs the complex programs of mouse natural killer and type 1 innate lymphoid cells in tissues and circulation.Immunity. 2021; 54: 1320-1337Abstract Full Text Full Text PDF PubMed Google Scholar,41.Cortez V.S. et al.SMAD4 impedes the conversion of NK cells into ILC1-like cells by curtailing non-canonical TGF-β signaling.Nat. Immunol. 2017; 18: 995-1003Crossref PubMed Scopus (185) Google Scholar, 42.Ebihara T. et al.Runx3 specifies lineage commitment of innate lymphoid cells.Nat. Immunol. 2015; 16: 1124-1133Crossref PubMed Google Scholar, 43.Mackay L.K. et al.Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes.Science. 2016; 3524594-63Crossref PubMed Scopus (469) Google Scholar, 44.Yomogida K. et al.Hobit confers tissue-dependent programs to type 1 innate lymphoid cells.Proc. Natl. Acad. Sci. U. S. A. 2021; 118e2117965118Crossref PubMed Scopus (1) Google Scholar, 45.Zhang L.H. et al.The aryl hydrocarbon receptor is required for the maintenance of liver-resident natural killer cells.J. Exp. Med. 2016; 213: 2249-2257Crossref PubMed Google Scholar, 46.Nixon B.G. et al.Cytotoxic granzyme C-expressing ILC1s contribute to antitumor immunity and neonatal autoimmunity.Sci Immunol. 2022; 7eabi8642Crossref PubMed Scopus (1) Google Scholar]. The detection strategies in other mouse studies reviewed here consider the fact that ILC1 do not express RORγt, while it is a key marker of ILC3. ILC1 have a beneficial role during the early immune response in mice to Mouse Cytomegalovirus (MCMV) in the liver, to Toxoplasma gondii in the brain, and to epithelial infection with Cryptosporidium parvum, but can also be pathogenic in association with colitis in mouse models, and during IBD in humans [1.Weizman O.E. et al.ILC1 confer early host protection at initial sites of viral infection.Cell. 2017; 171: 795-808Abstract Full Text Full Text PDF PubMed Scopus (234) Google Scholar,19.Schroeder J.H. et al.Sustained post-developmental T-bet expression is critical for the maintenance of type one innate lymphoid cells in vivo.Front. Immunol. 2021; 12760198Crossref Scopus (2) Google Scholar,28.Bernink J.H. et al.Human type 1 innate lymphoid cells accumulate in inflamed mucosal tissues.Nat. Immunol. 2013; 14: 221-229Crossref PubMed Scopus (689) Google Scholar,29.Bernink J.H. et al.Interleukin-12 and -23 control plasticity of CD127(+) group 1 and group 3 innate lymphoid cells in the intestinal lamina propria.Immunity. 2015; 43: 146-160Abstract Full Text Full Text PDF PubMed Scopus (398) Google Scholar,47.Gullicksrud J.A. et al.Enterocyte-innate lymphoid cell crosstalk drives early IFN-γ-mediated control of Cryptosporidium.Mucosal Immunol. 2022; 15: 362-372Crossref PubMed Scopus (2) Google Scholar,48.Steffen J. et al.Type 1 innate lymphoid cells regulate the onset of Toxoplasma gondii-induced neuroinflammation.Cell Rep. 2022; 38110564Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar]. The detrimental effect of ILC1 appears to be mediated by the production of IFNγ and TNFα, both of which induce apoptosis of epithelial cells in vi