Extended Data Fig. 4: Pulmonary ILCs are tissue-resident cells and express markers of migration.

a, CD69, CD103, CD62L and NK-p44 expression on the circulating ILCs in human peripheral blood and lung tissue were measured by flow cytometry. Percentage of total human ILCs expressing these markers in paired samples of participants with tuberculosis shown (paired samples n = 5; NK-p44 expression unpaired samples, lung n = 26; blood n = 34). Significance of CD69, CD103 and CD62L expression was calculated using a one-way Wilcoxon matched-pairs test. Significance of NK-p44 expression was analysed using an unpaired Mann–Whitney U-test. b, c, NK-p44 and CD56 expression were measured in tuberculosis-infected lung tissues in comparison to control samples. Significance is analysed using a unpaired Mann–Whitney U-test (b) and a Kruskal–Wallis test with adjustments for multiple comparisons (c). d, Percentages of ILC1, ILC2, ILC3, CD56^low NK cells, and CD56^high NK cells in human lung tissue were measured by flow cytometry TB⁻HIV⁻ control subjects (n = 4–6), participants with tuberculosis without HIV (TB⁺HIV⁻, n = 7–13) and with tuberculosis with HIV coinfection (TB⁺HIV⁺, n = 7–22). e, CXCL13 protein levels were measured in the plasma of participants with tuberculosis without (n = 18–20) and with HIV coinfection(n = 9). Significance is calculated by Mann–Whitney U-test (no significance after Bonferonni correction). f, Frequencies of CD103⁺ ILCs were measured by flow cytometry in the blood of TB⁻HIV⁻ control subjects (n = 24), participants with tuberculosis without (n = 10) and with HIV coinfection (n = 5). Significance is analysed using a Mann–Whitney U-test with Bonferroni corrections (only values that were significant after correction are shown). g, Representative FACS plots showing two distinct subpopulations of CD103- and CXCR5-expressing ILCs measured in lung tissues from three subjects with tuberculosis; in these populations most CXCR5-expressing cells are CD117⁺ ILC3s and CD103⁺ lung ILCs are a combination of CD117⁺ ILC3s, CRTH2⁺ ILCs and CD117⁻CRTH2⁻ cells. Green, CD117⁺; red, CRTH2⁺. h, C57BL/6 mice were aerosol-infected with approximately 100 CFU Mtb and lungs were collected at 14 d.p.i. Lung ILCs were sorted from single-cell suspensions (ILCs: CD45⁺CD127⁺Lin^–NK1.1⁻).The ability of sorted ILCs to migrate towards medium alone or a gradient of mouse CXCL13 was quantified in a transwell migration assay. n = 3–5 biological replicates. Significance is calculated by one-way ANOVA, *P < 0.05, **P < 0.01. i, Human ILC3s sorted from lungs migrated in response to recombinant human CXCL13 in transwell migration assays. Significance is calculated by one-tailed Wilcoxon signed-rank test. Data are paired values (a, left three graphs and i, right) or mean ± s.d. and individual values (b–f, h).

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