Neuropilin-1 Is Expressed on Lymphoid Tissue Residing LTi-like Group 3 Innate Lymphoid Cells and Associated with Ectopic Lymphoid Aggregates

Abstract

Here, we characterize a subset of ILC3s that express Neuropilin1 (NRP1) and are present in lymphoid tissues, but not in the peripheral blood or skin. NRP1⁺ group 3 innate lymphoid cells (ILC3s) display in vitro lymphoid tissue inducer (LTi) activity. In agreement with this, NRP1⁺ ILC3s are mainly located in proximity to high endothelial venules (HEVs) and express cell surface molecules involved in lymphocyte migration in secondary lymphoid tissues via HEVs. NRP1 was also expressed on mouse fetal LTi cells, indicating that NRP1 is a conserved marker for LTi cells. Human NRP1⁺ ILC3s are primed cells because they express CD45RO and produce higher amounts of cytokines than NRP1^- cells, which express CD45RA. The NRP1 ligand vascular endothelial growth factor A (VEGF-A) served as a chemotactic factor for NRP1⁺ ILC3s. NRP1⁺ ILC3s are present in lung tissues from smokers and patients with chronic obstructive pulmonary disease, suggesting a role in angiogenesis and/or the initiation of ectopic pulmonary lymphoid aggregates.

Keywords: HEVs; ILC3; LA; LTi; NRP1; VEGF-A; chemotaxis; high endothelial venues; human innate lymphoid cells 3; lymphoid tissue inducer cells; neuropilin-1; smoke-induced pulmonary lymphoid aggregates; vascular endothelial growth factor A.

Graphical abstract

Figure 1

NRP1⁺ ILC3s Are Present in Lymphoid Tissues but Not in the Peripheral Blood or Skin (A) Flow cytometry analysis of human tonsil cell suspension; representative dot plots of gating strategy lineage CD3⁻CD45⁺CD127⁺CD161⁺CD117⁺ ILC3s. Lineage mixture of antibodies added to exclude leukocytes includes CD3, TCRα/β, TCRγ/δ (T cells), CD14 (monocytes), CD16 (monocytes, NK cells), CD19 (B cells), CD94 (NK cells), FcεR1α (mast cell) and CD123, and BDCA2 (pDCs). (B) Pie diagram showing mean frequency of ILC2s, ILC1s, and ILC3^{NKp44+/−NRP1+/−} in human tonsil. (C) Transcriptional analysis using qRT-PCR showing the relative expression of RORγt in tonsillar NRP1⁺ ILC3s, NRP1⁻ ILC3s, NRP1⁻ NKp44⁻ ILC3, and ILC1. Samples were normalized to mRNA encoding β-actin (ACTB). Data are representative of three independent experiments and donors. (D) Expression of NRP1 analyzed by flow cytometry, on ILC from adult lymphoid and non-lymphoid tissue, including peripheral blood, skin, gut, mLN, spleen, and post-natal thymus. Filled histogram shows isotype control. (E) Dot plot representing the expression of NRP1 and CD117 on ILCs from fetal gut, analyzed by flow cytometry. (F) Expression of NRP1 (open histogram) analyzed by flow cytometry, on ILC3s from fetal mLN and fetal spleen. Filled histogram shows isotype control. (G) Percentage of NRP1⁺ (black bar) and NRP1⁻ (white bar) ILC3s in fetal and adult lymphoid tissue. Data are mean of three to four donors.

Figure 2

Violin Plots Showing the Gene Expression Distribution in NRP1⁺ and NRP1⁻ ILC3s (A) Group 3 ILC3s signature genes. Violin plots show gene expression distribution in NRP1⁺ and NRP1⁻ ILC3s with color according to mean expression value. (B and C) Bar plots with the top five enriched GO terms (B) and MSigDB curated gene sets (C) with bar height according to adjusted p value. (D) Violin plots with genes in GO term “Cell chemotaxis, immune response.” (E) Violin plots with genes in Reactome pathway “Immunoregulatory interaction between a lymphoid and non-lymphoid cell.”

Figure 3

NRP1⁺ ILC3s Express CD45RO and Produce Higher Amounts of Cytokines Than NRP1⁻ ILC3s (A) Freshly isolated ILC3s were in vitro stimulated with PMA plus ionomycin and analyzed for intracellular IL-22 (n = 4, ^∗p < 0.05, Mann-Whitney two-tailed t test). (B) Luminex bead-based assay was used to measure multiple cytokine secretion. Soluble GM-CSF (ng/mL) and TNF-α, IL-8, and IFN-γ from cultured and IL-2-, IL-1β-, and IL-23-stimulated ILC3s. Data are representative of three individual tonsil samples analyzed in different experiments; horizontal bars represent the median value for each group. (C) Freshly isolated ILC3s from fetal mLN in vitro stimulated with PMA plus ionomycin and intracellular cytokine stain for IL-22 and IL-17A on NRP1⁺ (black bar) and NRP1⁻ (white bar) ILC3s, analyzed by flow cytometry (n = 4, ^∗p < 0.05, Mann-Whitney two-tailed t test). (D) CD45RA and CD45RO expression on NRP1⁺ (red) and NRP1⁻ (blue) ILC3s in tonsil. (E and F) Histogram showing the expression of NRP1 on NRP1⁻ ILC3s in tonsil (E) and NRP1, HLA-DR, and NKp44 on peripheral blood NRP1⁻ ILC3s (F) after stimulation with IL-2 alone (blue lines) or with IL-2 and IL-1β (red lines). Filled histogram shows isotype control.

Figure 4

Tonsillar NRP1⁺ ILC3s Are Detected in Proximity to HEVs and the NRP1 Ligand VEGF-A Serves as a Chemotactic Factor for NRP1⁺ ILC3s (A) Cell surface expression of CCR7, CCR6, LFA-1, CD62L, CXCR5, and NRP1 on freshly isolated ILC3s from tonsil, NRP1⁺ ILC3s (black line), and NRP1⁻ ILC3s (dark blue dashed line) assessed by flow cytometry. Filled histogram shows isotype control. (B and C) Photomicrographs showing immunohistochemically (IHC) stained paraffin-embedded sections from two different donor tonsils. Tissue sections were double stained for NRP1⁺ (brown stain) CD3⁻BDCA2⁻ (black stain). White arrowheads indicate NRP1⁺BDCA2⁻ cells, and black arrowheads indicate NRP1⁺CD3⁺BDCA2⁺ pDCs. Dotted red lines show HEV-like structures. Black scale bar, 100 μm; white scale bar, 50 μm. (D) VEGFR2 expression on NRP1⁺ ILC3 (black line) and NRP1⁻ ILC3s (dark blue dashed line) and positive control endothelial cells (red dashed line). (E) Five-micrometer Transwell chemotaxis assay migratory/chemotaxis properties measured by fluorometric detection. Chemoattractants used were VEGFR2-NRP1 ligand VEGF-165 (VEGF-A), VEGFR2 ligand VEGF-C, and CXCR5 ligand CXCL13. NRP1⁺ ILC3s chemotaxis toward VEGF-A (n = 5, SD 66 ± 12) and NRP1⁻ ILC3s chemotaxis toward VEGF-A (n = 8, SD 20 ± 4.5), ^∗p < 0.01. Baseline represents medium without chemoattractant.

Figure 5

NRP1⁺ ILC3s Exhibit In Vitro LTi Activity (A) qRT-PCR of mRNAs for LTA (LT-α), LTB (LT-β), and RANKL in fetal mLN NRP1⁺ and NRP1⁻ ILC3s, normalized to mRNA encoding β-actin (ACTB). Data are represented as mean of four donors ± SD, ^∗p < 0.05 (B-E). The functional lymphoid tissue inducing ability of lymphoid (fetal mLN, tonsil) and peripheral blood ILC3s was tested by induced expression of ICAM1 and VCAM1 on MSCs cultured alone or with ILC3s for 5 days. (B) Tonsillar ILC3s co-cultured with MSCs, showing ICAM1 and VCAM1 expression on MSCs. MSCs co-cultured NRP1⁺ ILC3s (black line), MSCs co-cultured NRP1⁻ ILC3s (dark blue dashed line), and MSCs cultured alone (filled gray bar) are shown. (C) NRP1 and CCR6 expression tonsillar ILC3s after co-cultured with MSC. Gray filled histogram shows isotype control and NRP1⁺ (black line) and NRP1⁻ (dark blue dashed line) ILC3s. (D) ILC3s co-cultured with MSCs, showing ICAM1 and VCAM1 expression on MSCs. MSCs co-cultured freshly isolated peripheral blood ILC3s (red line), MSC co-cultured with tonsillar ILC3s (dark line), and MSCs cultured alone (filled gray bar) are shown. (E) NRP1 expression on peripheral blood ILC3s after co-cultured with MSCs. Gray filled histogram shows isotype control, freshly isolated ILC3s (gray line), and in vitro expanded ILC3s (blue line).

Figure 6

Primed NRP1⁺ ILC3s Detected in the Lung Tissue of Smokers without COPD and COPD Patients (A) NRP1 and NKp44 expression on ILC3s from peripheral blood of COPD patients. (B) NRP1 and NKp44 expression on ILC3s from the lung tissue of COPD patients. (C) Quantification of NRP1⁺ ILC3s in never-smoking control patients (without COPD, n = 4, SD 1% ± 1% of total ILC3s) compared with smokers and COPD GOLD stage I–II patients (n = 4, SD 11% ± 5% of total ILC3, ^∗p < 0.05). (D) NKp44 and NRP1 on NRP1⁻ and NRP1⁺ lung tissue ILC3s. (E) CD45RA and CD45RO expression on NRP1⁻ and NRP1⁺ COPD lung tissue ILC3s. Quantification of CD45RO⁺ ILC3s (n = 4, ^∗p = 0.03) is shown. (F) In vitro expanded lung ILC3s co-cultured with MSCs, showing ICAM1 and VCAM1 expression on MSCs. MSCs co-cultured with ILC3s (blue line) or cultured alone (filled gray bar) are shown.

Figure 7

RORγt⁺NRP1⁺ Cells Located in Proximity to Pulmonary Blood Vessels and Ectopic Lymphoid Aggregates (A) Bright-field micrograph of peripheral lung tissue showing NRP1 staining in alveolar (Alv) lumen and pulmonary lymphoid aggregate (LA). Black endogenous pigments are visible. (B) Bright-field micrograph showing RORγt staining in alveolar lumen and LA. (C) Double IHC staining for NRP1 (brown stain) and lymphatic vessel stained with podoplanin (blue-green stain) in alveolar lumen. White arrowheads indicate NRP1⁺ cells in proximity to blood vessels (Bv). (D–F) Double IHC staining for RORγt (brown stain) and NRP1 (blue-green stain) in (D) alveolar lumen and (E and F) in the surroundings of LAs. White arrowheads indicate RORγt⁺NRP1⁺ cells. (G) Percentage of NRP1 immunostaining in the peripheral lung of never-smoking (n = 6) and smoking (n = 7) subjects with suspected bronchial tumor, quantified using image analysis program (^∗∗p < 0.01). Black scale bars, 100 μm; white scale bars, 50 μm.