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Enteric GABAergic neuron-derived γ-aminobutyric acid initiates expression of Igfbp7 to sustain ILC3 homeostasis

Abstract

Neuronal signals have emerged as critical factors that regulate group 3 innate lymphoid cell (ILC3) response and tissue homeostasis, but the molecular mechanisms underlying this regulation remain largely elusive. Here, we identified that the enteric GABAergic neuron-derived neurotransmitter γ-aminobutyric acid (GABA) inhibited proliferation and IL-17A production in ILC3s in a manner dependent on the GABA receptors Gabbr1 and Gabbr2. Conditional deletion of Gabbr1 or ablation of GABAergic neurons caused increased IL-17A production and aggravated colitis. Mechanistically, GABA suppressed the expression of the LIP isoform of the transcription factor C/EBP-β in ILC3s, which repressed the transcription of Igfbp7, which encodes the secreted factor Igfbp7. Autocrine Igfbp7 signaling through the receptor Igf1R inhibited ILC3 proliferation and IL-17A production. Suppression of signaling through the GABA-C/EBP-β-IGFBP7 pathway highly correlated with severity of intestinal inflammation in patients with inflammatory bowel disease (IBD). Collectively, our findings describe an important molecular mechanism underlying the maintenance of gut immune homeostasis.

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Fig. 1: GABA inhibits ILC3 activation and alleviates DSS-induced colitis.
Fig. 2: Gabbr1 conditional knockout causes ILC3 hyperactivation and spontaneous colitis.
Fig. 3: GABA ablation exacerbates DSS-induced colitis.
Fig. 4: GABA signaling suppresses C/EBP-β expression.
Fig. 5: LIP recruits PRC2 complex onto Igfbp7 promoter to inhibit its transcription.
Fig. 6: Igfbp7 engagement with Igf1R suppresses ILC3 expansion and IL-17A production.
Fig. 7: The GABA-CEBPB-IGFBP7 axis correlates with IBD.

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Data availability

The source data for Figs. 17 and Extended Data Figs. 110 are provided as a Source Data file. The RNA sequencing data generated in this study have been deposited in the Gene Expression Omnibus database under accession code GSE (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE250452). All other data are included in the supplemental information or available from the authors upon reasonable requests. Source data are provided with this paper.

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Acknowledgements

We thank J. Hou, J. Pan, Z. Liu, Y. Xu and J. Jia for technical support. We thank Y. Wang for technical support in high-throughput confocal imaging and analysis. We also thank J. Li (Cnkingbio Company, Beijing, China) for technical assistance. This work was supported by National Key R&D Program of China (2020YFA0803501, 2021YFA1302000, 2019YFA0508501), Joint Funding of Henan Provincial Science and Technology R&D Plan (222301420015), National Natural Science Foundation of China (82371826, 32400745, 32170874, 31930036, 82130088, 81921003) and National Science Fund for Excellent Young Scholars (82122057), Strategic Priority Research Programs of the Chinese Academy of Sciences (XDB0570000), and Natural Science Foundation of Beijing (Z231100007223013).

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Authors and Affiliations

Authors

Contributions

N.L., J.H., Y.Y., Y.W. and L.Z. performed experiments; N.L. designed the project, analyzed the data and wrote the paper. N.L., J.H., Y.Y., Y.W., L.Z., Z. Xiao, Z. Xiong, S.Z., Y.L., Y.X., J.W., Y.G., Y.D., P.Z. and Z.Z. analyzed data; Z.F., B.L. and X.F. initiated the study and organized, designed and wrote the paper.

Corresponding authors

Correspondence to Xinjuan Fan, Benyu Liu or Zusen Fan.

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The authors declare no competing interests.

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Nature Immunology thanks Matthew Hepworth and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Ioana Staicu was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 GABA-B type receptors are highly expressed in ILC3s.

a, 3D-immunofluorescent microscopy of ILC3s and enteric neurons in intestine tissues. Scale bar, 100μm. n = 3 times of experiments were repeated independently with similar results. b, Information of neurotransmitter chemical library targeting different neural receptor families. c, d, Time dependent assay of IL-17A production in ILC3s treated with IL-23 and indicated chemicals for 6 hours using flow cytometry assay (c; n = 5 per group) and ELISA analysis (d; n = 4 per group). e, ELISA analysis of the production of IL-17A in small intestinal LPLs from wild-type mice, stimulated with IL-23 and different concentration of indicated chemicals. n = 3 per group. f, g, Time dependent assay of IL-17A production in ILC3s treated with IL-23 and indicated chemicals for 6 hours using flow cytometry assay (f; n = 5 per group) and ELISA analysis (g; n = 4 per group). h, GEO dataset analysis of the expression of GABA receptor family genes in indicated immune cells under accession number GSE85154, GSE229887 and GSE145857. i, j, RT-qPCR analysis of Gabbr1 and Gabbr2 expression in ILC3 subsets isolated from RorcEGFP/+ mice (i), and gene knockdown efficiency of GABA receptor genes in small intestinal LPLs isolated from wild-type mice (j). n = 3 biological independent experiments. k, Diagram of DSS-induced colitis and chemicals administration strategy. l-p, Bacterial loads (CFUs) in feces (l; left) and indicated tissues (l; middle), intestinal permeability assay (l; right), H&E staining assay (m), histopathological damage evaluation (n), FACS analysis of IL-17A (o) and IL-22 (p) production of wild-type mice infected with 5 × 109 CFU C.rodentium and treated with indicated chemicals as described in k. Scale bar, 100μm. n = 5 per group. q, r, H&E staining assay (q) or histopathological damage evaluation (r) of mice infected with 5 × 109 CFU C.rodentium and treated with indicated chemicals and IL-22 neutralization antibody or isotype control. Scale bar, 100 μm. n = 5 per group. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data are representative of at least three independent experiments.

Source data

Extended Data Fig. 2 Gabbr1ΔRorc mice display increased intestinal ILC3s.

a, Diagram of loxP sequence insertion sites in Gabbr1flox/flox mice and validation by DNA sequencing. b–d, FACS analysis of ILC3 Gabbr1 expression (b; CD3CD19CD127+CD45+RORγt+gated), ILC1s (c; CD3CD19CD45+CD127+gated) and ILC2s (d; CD3CD19CD127+CD90+gated) in small intestines isolated from Rorc-CreGabbr1fl/fl (hereafter Gabbr1WT) and Rorc-Cre+Gabbr1fl/fl (hereafter Gabbr1ΔRorc) mice. n = 5 per group. e, Calculation of ILC numbers as in c, d. n = 5 per group. f, g, Immunofluorescent microscopy of ILC3s in the isolated lymphoid follicles (f) and cryptopatches (g) in small intestines from Gabbr1WT and Gabbr1ΔRorc mice. Scale bar, 100μm. n = 3 times of experiments were repeated independently with similar results. h, i, H&E staining assay (h) and number statistical analysis (i) of small intestinal lymphoid tissues (SILTs) from Gabbr1WT and Gabbr1ΔRorc mice. n = 5 per group. j, k, Flow cytometry assay of the number of ILC3 subsets (CD3CD19CD45lo gated) in small intestine (j) and colon (k) from Gabbr1WTRag1−/−and Gabbr1ΔRorcRag1−/−mice. n = 5 per group. l-n, FACS analysis of CLPs (l), CHILPs (m) and ILCPs (n) in bone marrow cells from Gabbr1WT and Gabbr1ΔRorc mice. n = 5 per group. o, Cell number statistical analysis of progenitor cells as indicated in l-n. n = 5 per group. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data are representative of at least independent experiments.

Source data

Extended Data Fig. 3 Gabbr1ΔRorc mice show increased production of IL-17A and spontaneous colitis.

a, FACS assay of the proliferation of ILC3 subsets in the colon from Gabbr1WT and Gabbr1ΔRorc mice. n = 5 per group. b, Calculation of the percentage of Ki-67+ ILC3 subsets as in a. n = 5 per group. c, FACS assay of the percentage of Ki-67+ ILC3 subsets in the small intestine (left) and colon tissue (right) from Gabbr1WTRag1−/−and Gabbr1ΔRorcRag1−/−mice. n = 5 per group. d, FACS analysis of the apoptosis of ILC3 apoptosis in the small intestine from Gabbr1WT and Gabbr1ΔRorc mice. n = 5 per group. e, FACS analysis of IL-22 production in ILC3s in the small intestine from Gabbr1WT and Gabbr1ΔRorc mice infected with 5 × 109 CFU C.rodentium. n = 5 per group. f, g, H&E staining assay (f) and histopathological damage evaluation (g) in the colon from Gabbr1WT and Gabbr1ΔRorc mice infected with 5 × 109 CFU C. rodentium and intraperitoneally administrated with IL-22 neutralization antibody or isotype control. Scale bar, 100μm. n = 5 per group. h, FACS analysis of IL-17A production in ILC3 (CD3CD19CD45lo gated) subsets in the small intestine from wild-type mice (h; n = 3 per group). n = 3 biological independent experiments. i-k, FACS analysis of the production of IL-17A in ILC3 subsets in the small intestine from wild-type mice, treated with indicated chemicals and IL-23 (i), in the colon from Gabbr1WT and Gabbr1ΔRorc mice (j), in the small intestine (k; left) and colon (k; right) from Gabbr1WTRag1−/−; and Gabbr1ΔRorcRag1−/−mice. n = 5 per group. l-q, H&E staining assay and histopathological damage evaluation of colon tissues from Gabbr1WT and Gabbr1ΔRorc mice intraperitoneally administrated with anti-IL17A antibody or isotype during TNBS-induced colitis (l, m), from Gabbr1WTRag1−/−and Gabbr1ΔRorcRag1−/−mice during DSS-induced colitis (n, o), and from Gabbr1WT and Gabbr1ΔRorc mice collected at steady state or 7 days after DSS-induction (p, q). Scale bar, 100μm. n = 5 per group. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data are representative of at least independent experiments.

Source data

Extended Data Fig. 4 Gabbr1ΔCd4 mice display similar colitis symptoms compared with littermate Gabbr1WT mice.

a, FACS analysis of TH17 (CD3+CD45+TCRγδ-RORγt+) and γδT (CD3+CD45+TCRγδ+RORγt+/-) cells in the small intestine from Gabbr1WT and Gabbr1ΔRorc mice small. n = 5 per group. b, Cell number calculation of TH17 and γδT cells as in a. n = 5 per group. c-e, FACS analysis of ILC1s (c; CD3CD19CD45+CD127+NKp46+NK1.1+), ILC2s (d; CD3CD19CD127+CD90+Sca-1+KLRG1+) and ILC3s (e; CD3CD19CD45loCD127+RORγt+) in the small intestine from Cd4-Cre-Gabbr1fl/fl (hereafter Gabbr1WT) and Cd4-Cre+Gabbr1fl/fl (hereafter Gabbr1ΔCd4) mice. n = 5 per group. f, Cell number calculation of ILC subsets as in c-e. g-i, Weight change(g), H&E staining assay (h) and histopathological damage evaluation (i) of colon tissues from Gabbr1WT and Gabbr1ΔCd4 mice during DSS-induced colitis. Scale bar, 100μm. n = 5 per group. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data are representative of five independent experiments.

Source data

Extended Data Fig. 5 Enteric GABAergic neurons are major source of GABA.

a, b, Fecal bacterial load calculation (a) and ELISA assay of small intestinal GABA (b) in wild-type mice fed with vehicle or antibiotics in drinking water for 14 days. n = 3 per group. c, Diagram of GABA biosynthesis. d, QPCR analysis of Gad2 gene expression in dorsal root ganglions (DRG) and enteric neurons isolated from wild-type mice. n = 3 biological independent experiments. e, Immunofluorescent microscopy of Gad2 in small intestine (up) and colon (down) from wild-type mice, and nNOS (f) and CGRP (g) in colon tissues collected from Gad2-Cre+Rosa26LSL-tdTomato mice. Scale bar, 100μm. n = 3 times of experiments were repeated independently with similar results. h, QPCR analysis of knockdown efficiency (left) and ELISA analysis of GABA production in supernatants (right) of in vitro cultured enteric neurons infected with AAVs carrying shRNAs or a control sequence. n = 3 per group. i, Scheme of Gad2 knockout mice construction and validation by DNA sequencing. j, k, Immunoblotting assay of Gad2 expression in small intestine tissues (j) and ELISA analysis of GABA production in enteric neurons (k) from Gad2+/+ and Gad2-/- mice. n = 3 per group. l, m, FACS analysis of ILC1s (l; CD3CD19CD45+CD127+NKp46+NK1.1+) and ILC2s (m; CD3CD19CD127+CD90+Sca-1+KLRG1+) in the small intestine from Gad2+/+ and Gad2-/- mice. n = 5 per group. n, Calculation of indicated ILC numbers as in l, m. n = 5 per group. o, FACS analysis of Ki-67 the proliferation (left) and IL-17A production of (right) of ILC3 subsets in the colon from Gad2+/+ and Gad2-/- mice. n = 5 per group. p, q, H&E staining assay (p) and histopathological damage evaluation (q) of colon tissues from Gad2+/+ and Gad2-/- mice intraperitoneally administrated with IL17A neutralization antibody or isotype during TNBS-induced colitis. Scale bar, 100μm. n = 5 per group. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data were representative of at least three independent experiments.

Source data

Extended Data Fig. 6 Gad2 deficiency in enteric GABAergic neurons results in elevated IL-17A production and exacerbates DSS-induced colitis.

a, Immunofluorescent microscopy of small intestinal organoids from Gad2-Cre+Rosa26LSL-tdTomato mice. Scale bar, 100μm. b, c, Co-culture of ILC3s and organoids derived of small intestine from Gad2+/+ and Gad2-/- mice (b) and FACS analysis of IL-17A production in ILC3s 6 hours after co-culture. SIO, small intestine organoid. n = 5 per group. d, e, Immunoblotting assay of Gad2 expression in intestinal epithelial cells (d; n = 3 per group) and FACS analysis of ILC3s (e; n = 5 per group) in the small intestine from Vil1-Cre+Rosa26LSL-Cas9 mice intravenously injected with AAVs carrying gRNAs against Gad2 (hereafter sgGad2) or a control sequence (hereafter sgCtrl). f, g, HE staining assay (f) and histopathological damage evaluation (g) of colon tissues from sgCtrl and sgGad2 mice during DSS-induced colitis. Scale bar, 100μm. n = 5 per group. h, i, FACS analysis of ILC3 subsets (CD3CD19CD45lo gated) in small intestines (h) or colons (i) fromVil1-CreGad2fl/fl (Gad2WT) and Vil1-Cre+Gad2fl/fl (Gad2ΔVil1) mice. n = 5 per group. j-l, Immunoblotting assay of Gad2 expression in enteric neurons (j; n = 3 per group) and FACS analysis of ILC3 subsets (CD3CD19CD45lo gated) in the small intestine (k) or colon (l) from Wnt1-CreGad2fl/fl (hereafter Gad2WT) and Wnt1-Cre+Gad2fl/fl (hereafter Gad2ΔWnt1) mice. n = 5 per group. m, FACS analysis of IL-17A production of ILC3 subsets in the small intestine (left) and colon (right) from Gad2WT and Gad2ΔWnt1 mice. n = 5 per group. n, o, H&E staining assay (n) and histopathological damage evaluation (o) of colon tissues from Gad2WT and Gad2ΔWnt1 mice during DSS-induction. Scale bar, 100μm. n = 5 per group. p, 3D-immunofluorescent microscopy of GABAergic neurons in the small intestine from Gad2-Cre+Rosa26LSL-tdTomato and Gad2-Cre+Rosa26LSL-tdTomatoRosa26LSL-DTA mice. n = 3 times of experiments were repeated independently with similar results as in a, d, j, p. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data were representative of at least three independent experiments.

Source data

Extended Data Fig. 7 Single-cell atlas of intestinal CD127+ immune cells and EpCAM+ epithelial cells.

a, FACS sorting strategy for single-cell RNA sequencing. CD45-EpCAM+ epithelial cells and CD45+CD127+ immune cells were mixed at 1:1 ratio of Gabbr1WT and Gabbr1ΔRorc mice small intestine in the context of 2.5% DSS-induced colitis. b, UMAP plot showing cell clusters annotation of scRNA-seq data as in a. c, Violin plot displaying the mean expression of indicated genes in annotated cell types. d, Heatmap showing scaled marker genes expression of annotated cell types. e, f, Dot plots showing mean expression of indicated genes in annotated cell types grouped by immune cells (e) and epithelial cells (f). g, Gene ontology (GO) functional enrichment analysis of genes downregulated in Gabbr1ΔRorc enterocytes compared to Gabbr1WT enterocytes. h, Volcano plot showing differential expressed genes in Gabbr1ΔRorc DN ILC3s (left) or NKp46+ILC3s (right) versus Gabbr1WT ILC3s of scRNA-seq dataset. Red dots indicate upregulated genes and blue dots represent downregulated genes. FC, fold change. i, Dot plot displaying the expression of Cebpb in Gabbr1WT and Gabbr1ΔRorc ILC subsets. j, Motif analysis of calcium-responsive motifs in the Cebpb promoter via JASPAR database (https://jaspar.genereg.net/).

Extended Data Fig. 8 CebpbΔRorc mice show alleviated ILC3 proinflammatory activation.

a, Time course imaging of calcium signaling in MNK-3 cells using Fluo-4, AM calcium probe and stimulated with PMA or PMA + GABA. b, Calcium reporter luciferase assay of MNK-3 cells using pGL4.29 plasmid and treated with indicated chemicals. n = 3 per group. c, d, H&E staining assay (c) and histopathological damage evaluation (d) of colon tissues from CebpbWT and CebpbΔRorc mice during TNBS-induced colitis. Scale bar, 100μm. n = 5 per group. e, Immunoblotting assay of C/EBP-β expression in ILC3s from Rorc-Cre+Rosa26LSL-Cas9Rag1-/- mice infected with AAVs carrying gRNAs against Cebpb (hereafter sgCebpbRag1-/-) or control sequence (hereafter sgCtrlRag1-/-). f-i, FACS analysis of the cell number (f, h), proliferation (g, i; left) and IL-17A production (g, i; right) of ILC3 subsets in the small intestine and colon from sgCtrlRag1-/-and sgCebpbRag1-/- mice. j, k, H&E staining assay (j) and histopathological damage evaluation (k) of colon from sgCtrlRag1-/-and sgCebpbRag1-/- mice. Scale bar, 100μm. n = 5 per group. l, m, H&E staining assay (l) and histopathological damage evaluation (m) of colon tissues from Gabbr1WT, Gabbr1ΔRorc and Gabbr1ΔRorcCebpbΔRorc mice at age of eight weeks under steady state. Scale bar, 100μm. n = 5 per group. n, Luciferase reporter assay of C/EBP-β LIP isoform function on transcription of indicated genes. o, Luciferase reporter assay of C/EBP-β LIP isoform function on Igfbp7 transcription. p, Mass spectrometry analysis of C/EBP-β interacting proteins. Peptide information of Rbbp4 (up) and CEBP/β (down) were displayed. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data were representative of at least three independent experiments.

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Extended Data Fig. 9 Igfbp7ΔRorc mice show increased proliferation and production in ILC3s.

a, Diagram of colitis induction and Igfbp7 administration strategy. b, c, H&E staining assay (b) and histopathological damage evaluation (c) of colon tissues from indicated mice. Scale bar, 100μm. n = 5 per group. d, FACS analysis of TH17 (CD3+CD45+TCRγδ-RORγt+) and γδT (CD3+CD45+TCRγδ+RORγt+/-) cells in the small intestine from Igfbp7WT and Igfbp7ΔRorc mice. n = 5 per group. e, Cell number statistical analysis of TH17 and γδT cells as in d. n = 5 per group. f-i, FACS analysis of the cell number ILC3 subsets (f, h; CD3CD19CD45lo gated), proliferation (g, i; left) and IL-17A production (g, i; right) in ILC3s in the small intestine (f, g) and colon (h, i) from Igfbp7WTRag1−/−and Igfbp7ΔRorcRag1−/−mice. n = 5 per group. j, k, H&E staining assay of small intestine (j) and analysis of small intestinal lymphoid tissues (SILTs) numbers (k) from Igfbp7WT and Igfbp7ΔRorc mice. n = 5 per group. ns, not significant. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data are representative of five independent experiments.

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Extended Data Fig. 10 The GABA-CEBPB-IGFBP7 axis correlates with IBD.

a, b, H&E staining assay (a) and histopathological damage evaluation (b) of colon tissues fromIgfbp7WTRag1−/−andIgfbp7ΔRorcRag1−/−mice 7 days during DSS-induction. Scale bar, 100μm. n = 5 per group. c, Flow cytometry analysis of Igf1R expression in thymic T cells (CD3+CD45+), splenic B cells (NK1.1CD19+CD45+) and NK cells (NK1.1+CD19CD45+) and intestinal ILC1s (CD3CD19CD45+CD127+NK1.1+NKp46+), ILC2s (CD3CD19CD127+CD90+KLRG1+Sca1+) and ILC3s (CD3CD19CD127+CD45loRORγtEGFP/+). d, QPCR analysis of the expression of indicated genes expression in Gabbr1WT or Gabbr1ΔRorc ILC3s co-cultured with wild-type enteric neurons, and treated with IL-23 or IL-23+Igfbp7. e-g, IHC staining of GABA (e), QPCR analysis of CEBPB (f; left) or IGFBP7 (f; right) and immunofluorescent microscopy of IGFBP7+ ILC3s (g). in colon tissues collected from ulcerative colitis patients. Scale bar, 100μm. n = 15 pair of noninflamed or inflamed tissues were analyzed in f. n = 3 times of experiments were repeated with similar results as in f, g. * P < 0.05. ** P < 0.01. *** P < 0.001. Data were analyzed by an unpaired two-side Student’s t-test and shown as means ± SD. Data are representative of at least three independent experiments.

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Liu, N., He, J., Yang, Y. et al. Enteric GABAergic neuron-derived γ-aminobutyric acid initiates expression of Igfbp7 to sustain ILC3 homeostasis. Nat Immunol 26, 404–415 (2025). https://doi.org/10.1038/s41590-025-02081-2

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