Inflammatory ILC2s migrate to distal tissues during infection using stage-specific S1P receptors
Data files
Mar 13, 2026 version files 4.38 GB
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1-IgG_DupMarked_BowT_CPM.bw
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ATAC_Migratory_iILC2_merged.bw
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ATAC_Resident_gILC2_merged.bw
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Fig_2A_IL-25_MLN.tif
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Fig_2A_PBS_MLN.tif
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Fig_2D_Lta_KO_IL-25.tif
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Fig_2D_Lta_KO_PBS.tif
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Fig_2D_Map3k14_KO_IL-25_.tif
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Fig_2D_Map3K14_KO_PBS.tif
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Fig_2D_Rorc_KO_IL-25.tif
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Fig_2D_Rorc_KO_PBS.tif
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Fig_2D_WT_IL-25.tif
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Fig_2D_WT_PBS.tif
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Fig_6A_S1pr5_KO_IL-25.tif
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Fig_6A_S1pr5_KO_PBS.tif
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Fig_6A_S1pr5_WT_IL-25.tif
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Fig_6A_S1pr5_WT_PBS.tif
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Fig_6I_S1pr1_fl_fl_IL-25.tif
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Fig_6I_S1pr1_fl_fl_PBS.tif
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Fig_6I_S1pr1_KO_IL-25.tif
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Fig_6I_S1pr1_KO_PBS.tif
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Fig_8A_NB_S1P5_KO_200um.tif
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Fig_8A_NB_WT_200um.tif
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Fig_8A_PBS_WT_200um.tif
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Fig_8F_S1PR5_KO_Adoptive_trasnfer_Nb.jpg
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Fig_8F_S1PR5_KO_Nb.jpg
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Fig_8F_WT_Nb.jpg
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Fig_8H_NB_S1pr1_fl_fl_200um.tif
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Fig_8H_NB_S1pr1_KO_200um.tif
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Fig_8H_PBS_S1pr1_fl_fl_200um.tif
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Fig_S3D_IL-25.tif
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Fig_S3D_PBS.tif
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GSE268826_genomon_fpkm_table.csv.gz
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GSE270373_Gut_ILC2_merged.bw
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GSE270373_iILC2_merged.bw
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Ito_et_al_Suppl._Excel_seq1_v1.xlsx
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KLF2_DupMarked_BowT_CPM.bw
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README.md
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ZEB2_DupMarked_BowT_CPM.bw
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Abstract
Tissue-resident lymphocytes can recirculate, but the underlying molecular mechanism is poorly understood. Here, we show that helminth infection–induced redistribution of group 2 innate lymphoid cells (ILC2s) requires access to lymphatic vessels. Interleukin (IL)-25 signal induces a dramatic change in the epigenetic landscape of intestinal ILC2s, and transcription factors KLF2 and ZEB2 upregulate the expression of sphingosine-1-phosphate receptor 1 (S1PR1) and S1PR5, respectively. S1PR5 regulates ILC2 exit from the intestine to the lymph, whereas S1PR1 is critical for ILC2 egress from the mesenteric lymph nodes to the blood and then to distal tissues including the lung, where redistributed ILC2s contribute to tissue repair. The requirement of two S1PRs is largely due to the dynamic expression of CD69, which mediates S1PR1 internalization. These findings demonstrate that S1PRs modulate ILC2 emigration from nonlymphoid and lymphoid organs in a stage-specific manner, providing a framework for understanding the multistep migration of tissue-resident immune cells.
Dataset DOI: 10.5061/dryad.76hdr7t8z
Description of the data and file structure
Files and variables
File: GSE268826_genomon_fpkm_table.csv.gz
Description: Fragments Per Kilobase Million (FPKM) data of bulk RNA sequencing (RNA-seq) performed on steady-state gut-resident ILC2s (gILC2s) of untreated mice and inflammatory ILC2s (iILC2s) from the gut, mesenteric lymph nodes (mLNs), and lung of interleukin-25 (IL-25)–treated mice.
File: GSE270373_Gut_ILC2_merged.bw
Description: Bigwig (.bw) file of Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) performed on gILC2s and IL-25–elicited mLN iILC2s.
File: GSE270373_iILC2_merged.bw
Description: .bw file for ATAC-seq performed on gILC2s and IL-25–elicited mLN iILC2s.
File: ATAC_Resident_gILC2_merged.bw
Description: .bw file for ATAC-seq performed on gILC2s and IL-25–elicited mLN iILC2s.
File: ATAC_Migratory_iILC2_merged.bw
Description: .bw file for ATAC-seq performed on gILC2s and IL-25–elicited mLN iILC2s.
File: Fig_2A_IL-25_MLN.tif
Description: .tif file of a confocal image of the mLNs of C57BL/6 mice treated with IL-25. Green = CD3, magenta = KLRG1, blue = B220.
File: Fig_2A_PBS_MLN.tif
Description: .tif file of a confocal image of the mLNs of C57BL/6 mice treated with PBS. Green = CD3, magenta = KLRG1, blue = B220.
File: Fig_2D_Lta_KO_PBS.tif
Description: .tif file of a confocal image of the small intestine of lymphotoxin-a knock-out (Lta-/-) mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_Lta_KO_IL-25.tif
Description: .tif file of a confocal image of the small intestine of Lta-/- mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_Map3K14_KO_PBS.tif
Description: .tif file of a confocal image of the small intestine of mitogen-activated protein kinase kinase kinase 14 knock-out (Map3k14-/-) mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_Rorc_KO_IL-25.tif
Description: .tif file of a confocal image of the small intestine of RAR-Related Orphan Receptor C knock-out (Rorc-/-) mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_Map3k14_KO_IL-25_.tif
Description: .tif file of a confocal image of the small intestine of Map3k14-/- mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_Rorc_KO_PBS.tif
Description: .tif file of a confocal image of the small intestine of Rorc-/- mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_WT_PBS.tif
Description: .tif file of a confocal image of the small intestine of C57BL/6 wild-type mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_2D_WT_IL-25.tif
Description: .tif file of a confocal image of the small intestine of C57BL/6 wild-type mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6A_S1pr5_KO_IL-25.tif
Description: .tif file of a confocal image of the small intestine of sphingosine-1-phosphate receptor 5 knock-out (S1pr5-/-) mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6I_S1pr1_fl_fl_IL-25.tif
Description: .tif file of a confocal image of the small intestine of sphingosine-1-phosphate receptor 1 floxed (S1pr1fl/fl) mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6A_S1pr5_KO_PBS.tif
Description: .tif file of a confocal image of the small intestine of S1pr5-/- mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6A_S1pr5_WT_IL-25.tif
Description: .tif file of a confocal image of the small intestine of C57BL/6 wild-type mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6I_S1pr1_fl_fl_PBS.tif
Description: .tif file of a confocal image of the small intestine of S1pr1fl/fl mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6A_S1pr5_WT_PBS.tif
Description: .tif file of a confocal image of the small intestine of C57BL/6 wild-type mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6I_S1pr1_KO_IL-25.tif
Description: .tif file of a confocal image of the small intestine of Klrg1-Cre S1pr1^fl/fl ^mice treated with IL-25. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_6I_S1pr1_KO_PBS.tif
Description: .tif file of a confocal image of the small intestine of Klrg1-Cre S1pr1^fl/fl ^mice treated with PBS. White = CD3, red = KLRG1, yellow = Lyve-1, blue = EPCAM.
File: Fig_S3D_IL-25.tif
Description: .tif file of a confocal image of the mLNs of C57BL/6 mice treated with IL-25. Green = CD3, magenta = KLRG1, blue = B220.
File: Fig_S3D_PBS.tif
Description: .tif file of a confocal image of the mLNs of C57BL/6 mice treated with PBS. Green = CD3, magenta = KLRG1, blue = B220.
File: Fig_8A_NB_S1P5_KO_200um.tif
Description: .tif file of hematoxylin & eosin (H&E) staining performed on a lung section from S1pr5-/- mice infected with Nippostrongylus brasiliensis (Nb) stage L3 for eight days.
File: Fig_8F_S1PR5_KO_Adoptive_trasnfer_Nb.jpg
Description: .jpg file of H&E staining performed on a lung section from S1pr5-/- mice infected with Nb L3 for eight days that received an adoptive transfer of iILC2s from IL-25–treated recombination activating gene 1 (Rag1)−/− mice on day four of Nb stage L3 infection.
File: Fig_8A_NB_WT_200um.tif
Description: .tif file of H&E staining performed on a lung section from C57BL/6 wild-type mice infected with Nb stage L3 for eight days.
File: Fig_8F_S1PR5_KO_Nb.jpg
Description: .jpg file of H&E staining performed on a lung section from S1pr5-/- mice infected with Nb stage L3 for eight days.
File: Fig_8A_PBS_WT_200um.tif
Description: .tif file of H&E staining performed on a lung section from C57BL/6 wild-type mice treated with PBS.
File: Fig_8F_WT_Nb.jpg
Description: .tif file of H&E staining performed on a lung section from C57BL/6 wild-type mice infected with Nb stage L3 for eight days.
File: Fig_8H_NB_S1pr1_fl_fl_200um.tif
Description: .tif file of H&E staining performed on a lung section from S1pr1^fl/fl ^mice infected with Nb stage L3 for eight days.
File: Fig_8H_NB_S1pr1_KO_200um.tif
Description: .tif file of H&E staining performed on a lung section from Klrg1-Cre S1pr1^fl/fl ^mice infected with Nb stage L3 for eight days.
File: Fig_8H_PBS_S1pr1_fl_fl_200um.tif
Description: .tif file of H&E staining performed on a lung section from S1pr1^fl/fl ^mice treated with PBS.
File: 1-IgG_DupMarked_BowT_CPM.bw
Description: .bw file of Cleavage Under Targets & Release Using Nuclease (CUT&RUN) data of isotype control genomic binding sites (IgG) in mLN iILC2s from IL-25–treated mice.
File: KLF2_DupMarked_BowT_CPM.bw
Description: .bw file of CUT&RUN data of KLF2 genomic binding sites in mLN iILC2s from IL-25–treated mice.
File: ZEB2_DupMarked_BowT_CPM.bw
Description: .bw file of CUT&RUN data of ZEB2 genomic binding sites in mLN iILC2s from IL-25–treated mice.
File: Ito_et_al_Suppl._Excel_seq1_v1.xlsx
Description: Excel file of raw data corresponding to figures.
Figure 1: Intestinal ILC2 redistribution requires access to the tissue-draining lymphatic system.
1C: Lung iILC2s of CD45+ (%) (left) and Lung iILC2s (x105) (right)
1D: Blood iILC2s of CD45+ (%) (left) and Blood iILC2s / 100 μl (x103) (right)
1F: iILC2s of CD45+ (‰)
1H: iILC2s of CD45+ (‰)
1J: Bone marrow (BM) ILC2 progenitors (ILC2Ps) of live cells (10-2) (%)
1K: BM ILC2Ps (x103)
1L: iILC2s of CD45+ (%)
1M: Ratio of Kikume-Red+ (KikR+)/Kikume-Green+ (KikG+) lung iILC2s
1N: Ratio of KikR+/KikG+ natural ILC2s (nILC2s)
Figure 2: Secondary lymphoid organs are not required for intestinal ILC2 migration.
2B: iILC2s (x103/mm2). Quantified from Fig_2A_PBS_MLN.tif and Fig_2A_IL-25_MLN.tif.
2C: Subcapsular sinus iILC2s (x103/mm2). Quantified from Fig_2A_PBS_MLN.tif and Fig_2A_IL-25_MLN.tif.
2E: Lung iILC2s (x104)
2F: Lung iILC2s (x103)
2G: mRNA level (relative to Gapdh)
2I: Normalized donor/recipient ratio (%)
2J: CD45.1+ iILC2s (x104)
Figure 4: KLF2 and ZEB2 regulate the expression of S1PR1 and S1PR5, respectively.
4E: mRNA level (relative to Gapdh)
4F: mRNA level (relative to Gapdh)
4G: mRNA level (relative to Gapdh)
4H: mRNA level (relative to Gapdh)
Figure 5: S1PR1 and S1PR5 regulate ILC2 migration both in vivo and in vitro.
5B: Lung iILC2s (x104) (left) and Lung CD4 T cells (x105) (right)
5C: Lung iILC2s of CD45+ cells (%) (left) and Blood iILC2s of CD45+ cells (%) (right)
5D: Lung iILC2s of CD45+ cells (%) (left) and Blood iILC2s of CD45+ cells (%) (right)
5E: Lung iILC2s of CD45+ cells (%) (left) and Blood iILC2s of CD45+ cells (%) (right)
5F: iILC2 transmigration (Relative % to control)
5G: iILC2 transmigration (Relative % to control)
5H: iILC2 transmigration (Relative % to control)
5I: iILC2 transmigration (Relative % to control)
Figure 6: S1PR5 and S1PR1 regulate ILC2 migration in a stage-specific manner.
6B: ILC2s / Villus. Quantified from Fig_6A_S1pr5_WT_PBS.tif; Fig_6A_S1pr5_WT_IL-25.tif; Fig_6A_S1pr5_KO_PBS.tif; Fig_6A_S1pr5_KO_IL-25.tif.
6C: Lung iILC2s (x105) (left), mLN iILC2s (x105) (middle), and Blood iILC2s (x103) (right)
6D: Lung iILC2s (x103) (left) and mLN iILC2s (x103) (right)
6E: Normalized gut iILC2 (% of total)
6F: Ki-67+ gut iILC2s (%)
6G: Fold increase (gut iILC2s/steady state gILC2)
6H: Normalized ratio (WT/S1pr5-/-)
6J: ILC2s / Villus. Quantified from Fig_6I_S1pr1_fl_fl_PBS.tif; Fig_6I_S1pr1_fl_fl_IL-25.tif; Fig_6I_S1pr1_KO_PBS.tif; Fig_6I_S1pr1_KO_IL-25.tif.
6K: Lung iILC2s (x105) (left), mLN iILC2s (x105) (middle), and Blood iILC2s (x102) (right)
6L: Lung iILC2s (x103) (left) and mLN iILC2s (x103) (right)
Figure 7: CD69 inhibits the presence of S1PR1 on iILC2 cell surface.
7B: mRNA level (relative to Gapdh)
7D: Mean fluorescence intensity (MFI) of S1PR1
7F: MFI of CD69
7H: MFI of S1PR1
7I: mLN iILC2s of CD45+ cells (%)
Figure 8: S1PR5/S1PR1–mediated ILC2 redistribution is essential for lung tissue repair.
8B: Lacunarity score. Quantified from Fig_8A_PBS_WT_200um.tif; Fig_8A_NB_WT_200um.tif; Fig_8A_NB_S1P5_KO_200um.tif.
8C: Lung iILC2s (x103)
8D: ST2+ T helper 2 cells (TH2) of CD4 T cells (%)
8E: mRNA level (relative to Gapdh)
8G: Lacunarity score. Quantified from Fig_8F_WT_Nb.jpg; Fig_8F_S1PR5_KO_Nb.jpg; Fig_8F_S1PR5_KO_Adoptive_trasnfer_Nb.jpg.
8I: Lacunarity score. Quantified from Fig_8H_PBS_S1pr1_fl_fl_200um.tif; Fig_8H_NB_S1pr1_fl_fl_200um.tif; Fig_8H_NB_S1pr1_KO_200um.tif.
8J: Lung iILC2s (x103)
8K: ST2+ TH2 of CD4 T cells (%)
8L: mRNA level (relative to Gapdh)
Supplementary Figure 2: iILC2s migrate from the gut to the lung via the mLNs.
S2B: Ratio of KikR+/KikG+ mLN iILC2s
S2C: Ratio of KikR+/KikG+ spleen iILC2s
Supplementary Figure 3: A fraction of iILC2s can be retained in the mLNs for a long term.
S3C: mLN iILC2s (x105)
S3E: iILC2s (x103/mm2). Quantified from Fig_S3D_PBS.tif and Fig_S3D_IL-25.tif.
S3F: Subcapsular sinus iILC2s (x103/mm2)
Supplementary Figure 4: Secondary lymphoid organ deficiency does not affect ILC2 development and homeostasis.
S4B: Gut ILC2s (x104)
S4D: Gut ILC2s (x104)
S4F: Gut ILC2s (x104)
S4G: ILC2s / Villi. Quantified from Fig_2D_WT_PBS.tif; Fig_2D_WT_IL-25.tif; Fig_2D_Map3K14_KO_PBS.tif; Fig_2D_Map3k14_KO_IL-25_.tif; Fig_2D_Rorc_KO_PBS.tif; Fig_2D_Rorc_KO_IL-25.tif; Fig_2D_Lta_KO_PBS.tif; Fig_2D_Lta_KO_IL-25.tif.
Supplementary Figure 5: Lta deficiency does not affect the cytokine-producing capabilities of iILC2s.
S5A: RORγt MFI
S5B: IL-4+ ILC2s (%) (left), IL-13+ ILC2s (%) (middle), and IL-17+ ILC2s (%) (right)
Supplementary Figure 7: ILC2 transcriptome profiles correlate with its migration stages.
S7E: mRNA level (relative to Gapdh)
Access information
Other publicly accessible locations of the data:
- GEO Accession for CUT&Run, ATAC-seq, and RNA-seq: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE314963
Data was derived from the following sources:
- Fig. S6: 1) GSE117567, related to DOI:10.1038/s41590-018-0201-4 2) GSE124880, related to DOI:10.1016/j.immuni.2019.09.004 3) GSE132273, related to DOI:10.1038/s41590-019-0567-y
Data accessible via the following available softwares:
- Confocal images and H&E staining images can be opened using ImageJ. .bw files can be opened using Integrated Genome Viewer (IGV).
