Supplementary Figure 1

Transcription

1 d f a IL7 b IL GATA RORγt h HDM IL IL7 PBS Ilra R7 PBS HDM Ilra R7 HDM Foxp Foxp Ilra R7 HDM HDM Ilra R7 HDM CD + FOXP + T reg cell CD + FOXP T conv cell PBS Ilra R7 PBS HDM Ilra R7 HDM CD + FOXP T conv cell c e g i IL (pg/ml) IL7 (pg/ml) CD + GATA + (%) CD + RORγt + (%) CD + IL + (%) IL (pg/ml) IFNγ (pg/ml) CD + GATA + X CD + RORγt + X CD + IL + X Supplementary Figure IL (pg/ml) Foxp + GATA + (%) Foxp + RORγt + (%) Foxp + IL + (%) p=. PBS Ilra R7 PBS HDM Ilra R7 HDM Foxp + GATA + X Foxp + RORγt + X Foxp + IL + X IFNγ IL CD + Foxp + T reg cell CD + IFNγ + (%) CD + IFNγ + X Foxp + IFNγ + (%) Foxp + IFNγ + X Nature Medicine: doi:./nm.7

2 a Helios PBS Ilra R7 PBS HDM Ilra R7 HDM Foxp Gated on CD + Foxp + T reg cells b CD + Foxp + Helios high (%) Supplementary Figure CD + Foxp + Helios low (%) PBS Ilra R7 PBS HDM Ilra R7 HDM c PBS Ilra R7 PBS HDM Ilra R7 HDM IL7 e CCR PBS Ilra R7 PBS HDM Ilra R7 HDM Gated on CD + Foxp T conv cells Gated on CD + Foxp + T reg cells d CD + CCR + IL7 + (%) CD + Foxp + CCR + IL7 + (%) CCR IL7 IL Gated on CD + Foxp + T reg cells f CD + Foxp + Helios low CCR + (%) CD + Foxp + Helios low IL7 + (%) CD + Foxp + Helios low IL + (%) Helios Nature Medicine: doi:./nm.7

3 a No cytokine TGF β TGF β + IL b No cytokine TGF β Supplementary Figure TGF β + IL RORγt GATA Ilra R7 Foxp Foxp c No cytokine TGF β TGF β + antiil TGF β + antiil TGF β + IL f No cytokine.7.9 TGF β TGF β + IL IL Ilra R7 IL Ilra R7 Foxp + IL + (%) IL d Ilra R7 Foxp + IL + (%) Foxp + IL + IL7 + (%) e Ilra R7 Ilra R7 No cytokine TGF β TGF β + anti IL TGF β + anti IL TGF β + IL CD + Foxp IL9 + (%) g Foxp Ilra R7 CD + Foxp + IL9 + (%) h Ilra R7 No cytokine TGF β TGF β + L Nature Medicine: doi:./nm.7

4 Supplementary Figure a b / / / / / / SSC K K K K K K K K K K Lymphocytes 7. K K K K K MACS presorted CD + cells K K K K K Lymphocytes Lymphocytes K K K K K K K K K K K K K K FSC CDPE.9. GFP. T reg T conv CDPE.9 CDPE.9 GFP. GFP... GFP. Nrp Nrp 97. Count 9. T eff /T reg Cell Trace Violet NO cytokine Ilra R7 T reg c % Of proliferated cells.. / / / / /. IL IL + AntiIL NO cytokine IL IL + AntiIL. T reg Il R7 T reg Il R7 IL d No cytokine IL7 Foxp EGFP+ Nrp + T reg cells IL Ilra R7 e IL + ntreg (%) IL7 + ntreg (%) Il R7 f IL No cytokine CD + CDL + T conv cells. IL7 IL T eff /T reg Foxp + IL + IL7 + (%).7.9 Ilra R7 g CD + IL + (%) CD + IL7 + (%).... No cytokine IL Ilra R7 Ilra R7 NoCytokine cytokine TGF IL β TGF β + anti IL TGF β + anti IL TGF β + IL Nature Medicine: doi:./nm.7

5 a OVA i.p. Thy. + Ilra R7 mouse recipients Thy. + EGFP + % OVA it reg (i.v.) Nebulized Analysis b Supplementary Figure PBS OVA(No T reg )OVA OVA( T reg )OVA OVA(Ilra R7 T reg )OVA Inflammation Score Thy. + CD + IL7 + (%) c f D 7 9 EGFP g PAS Score Thy. + CD + IL7 + X ( ) OVA(iT reg ) OVA CD OVA(Ilra R7 it reg )OVA EGFP h Gated on Thy. + cells it reg ext reg Gated on Thy. + cells it reg ext reg DO. d Eosinophils x Thy. + CD + Foxp + IL7 + (%) it reg Ilra R7 it reg CD + EGFP + X DO. + EGFP X i Neutrophils x Thy. + CD + Foxp + IL7 + X ( ) IL j IL7 Thy. + CD + IL + (%) PBSOVA OVAOVA OVAOVA OVA(T OVA(T reg )OVA OVA(Ilra R7 T reg )OVA it reg Ilra R7 it reg Thy. + CD + IL + X ( ) ext reg Ilra R7 ext reg e Resistance (over baseline) IL7 + (it reg ) X IL + (it reg ) X PBS Methacholine (mg/ml) Thy. + CD + Foxp + IL + (%) IL7 + (exit reg ) X IL + (exit reg ) X PBSOVA OVAOVA OVA(T reg )OVA OVA(Ilra R7 T reg ) OVA Thy. + CD + Foxp + IL + X ( ) OVA(T reg )OVA OVA(Ilra R7 T reg ) OVA Nature Medicine: doi:./nm.7

6 a GRB IP. Peptide Lys b c d Supplementary Figure STAT YQ pyq pyr % of Lys YQ pyq pyr YQ pyq pyr e Il (Fold induction) GRB STAT IL PInh (µm) Ilra R f g IL pp P Ilra R7 MEKInh Ilra R h IL (pg/ml) TGFβ IL PInh MEKInh AntiIL Ilra R i Isotype Ab PInh ERKInh AntiIL AntiIL j Isotype Ab PInh ERKInh AntiIL AntiIL Foxp IL Ilra R7 CD IL7 Nature Medicine: doi:./nm.7

7 Supplementary Figure 7 a % of Max pstat Isotype ( h) IL + IgG ( h) IL + antiil ( h) Ilra R7 pstat (MFI) (IL) Ilra R7 (IL) (IL + AntiIL) Ilra R7 (IL + AntiIL) Min b pstat (MFI) Purified CD + cells (IL) Ilra R7 Min c pstat (MFI) Purified CD + cells (IL) Ilra R7 Min d % of Max Isotype ( h) IL + IgG ( h) IL + antiil ( h) Ilra R7 pstat (MFI) (IL) Ilra R7 (IL) (IL + AntiIL) Ilra R7 (IL + AntiIL) e pstat (MFI) (IL) Ilra R7 (IL) (IL + AntiIL) Ilra R7 (IL + AntiIL) pstat Min Hr Min Hr f Ccl (Fold induction) 9 Ilra R7 MED IL IL g Ccl Promoter (% Input) Mock(IgG) UnStim (STAT) IL (STAT) IL (STAT) IL + AntiIL (STAT) Ilra R7 h Ccl (Fold induction) 7 ILRa R7 (IL) ILRa R7 (IL) SCR RNA STAT sirna i SCR RNA STAT sirna Nature Medicine: doi:./nm.7

8 Supplementary Figure Gated on CD + Foxp + cells....9 Q7/Q R7/R7 Foxp CCR..7 CCR CD Helios IL7 Nature Medicine: doi:./nm.7

9 Supplementary Figure 9 CD + Foxp + X c a Foxp + IL7 + X d FOXP YFPCre LoxP RORc LoxP CD + IL7 + X b Rorc (Fold changes).... e IL7 (pg/ml) CD + CD + Foxp Foxp + Foxp YFPCre Foxp YFPCre Rorc / Foxp YFPCre (PBS) Ilra R7 Rorc fl/fl (PBS) Foxp YFPCre Rorc / (PBS) Ilra R7 Foxp YFPCre Rorc / (PBS) Foxp YFPCre (OVA) Ilra R7 Rorc fl/fl (OVA) Foxp YFPCre Rorc / (OVA) Ilra R7 Foxp YFPCre Rorc / (OVA) Foxp + CCR + X f CD + CCR + X Foxp + IL + X g CD + IL + X IL (pg/ml) h Nature Medicine: doi:./nm.7

10 a b f Ilra (Fold change) FOXP Total IgE (µg/ml) YFPCre LoxP Ilra LoxP.... CD + CD + Foxp Foxp + Foxp YFPCre Foxp YFPCre Ilra / OVAIgE (µg/ml)..... c Foxp YFPCre Ilra R7 Foxp YFPCre Ilra / g Neutrophils X Ilra R7 Ilra fl/fl Foxp YFPCre (PBS) Ilra R7 Ilra fl/fl (PBS) Ilra R7 Foxp YFPCre Ilra / (PBS) Foxp YFPCre (OVA) Ilra R7 Ilra fl/fl (OVA) Ilra R7 Foxp YFPCre Ilra / (OVA) d Eosinophils X Inflammation Score Supplementary Figure e Resistance (over baseline) PAS Score Methacholine (mg/ml) Lymphocytes X h CD + Foxp + (%) i Foxp + IL7 + (%) CD + IL7 + (%) j Foxp + IL + (%) CD + IL + (%) CD + Foxp + X Foxp + IL7 + X CD + IL7 + X Foxp + IL + X CD + IL + X Nature Medicine: doi:./nm.7

11 Supplementary Figure Resistance (Over baseline) a b c (IsoAb HDM) (AntiIL HDM) Il R7 PBS Il R7 (IsoAb HDM) Il R7 (AntiIL HDM) PBS Methacholine (mg/ml) (IsoAb HDM) Ilra R7 (IsoAb HDM) (antiil HDM) Ilra R7 (antiil HDM) Inflammaion Score PAS Score Il R7 Il R7 d IgE(µg/ml) Il R7 e Eosinophils X Il R7 Neutrophils X Il R7 f CD + Foxp + (%) Il R7 Foxp + IL7 + (%) Il R7 Foxp + IL + (%) Il R7 g CD + IL7 + (%) Il R7 CD + IL + (%) Il R7 h IL7 (pg/ml) Ilra R7 IL (pg/ml) Ilra R7 CCL(pg/ml) Il R7 PBS HDM AntiIL HDM PBS HDM AntiIL HDM Nature Medicine: doi:./nm.7

12 a (IsoAb HDM) (AntiIL7 HDM) Il R7 PBS Il R7 (IsoAb HDM) Il R7 (AntiIL7 HDM) b (IsoAb HDM) (antiil7 HDM) Supplementary Figure Resistance (Over baseline) Ilra R7 (IsoAb HDM) Ilra R7 (antiil7 HDM) Inflammaion Score CD + Foxp + (%) c f Il R7 Il R7 g CD + IL7 + (%) PAS Score PBS Methacholine (mg/ml) Il R7 CD + IL + (%) Il R7 IgE(µg/ml) Il R7 d IL7 (pg/ml) h Il R7 e Il R7 Eosinophils X IL (pg/ml) Il R7 Neutrophols X Il R7 PBS PBS HDM HDM AntiIL7 AntiIL7 HDM HDM CCL(pg/ml) Il R7 Il R7 Nature Medicine: doi:./nm.7

13 Supplementary Figure a (IsoAb HDM) (AntiCCL HDM) Il R7 PBS Il R7 (IsoAb HDM) Il R7 (AntiCCL HDM) b IsoAb HDM AntiCCL HDM Resistance (Over baseline) IsoAb HDM AntiCCL HDM PBS Methacholine (mg/ml) Ilra R7 c Inflammaion Score Il R7 PAS Score d Il R7 IgE(µg/ml) Il R7 PBS HDM AntiCCL HDM e Eosinophils X Il R7 Neutrophils X Il R7 f CD + Foxp + (%) Il R7 g IL7 (pg/ml) Ilra R7 IL (pg/ml) Ilra R7 h CCL(pg/ml) Il R7 Nature Medicine: doi:./nm.7

14 a BAC b Il (Fold change) f FOXP.... Total IgE (µg/ml) EGFPCre LoxP Il/Il LoxP CD + CD + Foxp Foxp + Foxp EGFPCre Foxp EGFPCre Il/ / OVAIgE (µg/ml) c Foxp EGFPCre Foxp EGFPCre Il/ / g Ilra R7 Il/ fl/fl Ilra R7 Foxp EGFPCre Il/ / Eosinophils X d Inflammation Score PAS Score Neutrophils X Supplementary Figure e Lymphocytes X Resistance (Over baseline) PBS Methacholine (mg/ml) Foxp EGFPCre (PBS) Ilra R7 Foxp EGFPCre (PBS) Ilra R7 Foxp EGFPCre Il/ / (PBS) Foxp EGFPCre (OVA) Ilra R7 Foxp EGFPCre (OVA) Foxp EGFPCre Il/ / (OVA) Ilra R7 Foxp EGFPCre Il/ / (OVA) h i j CD + Foxp + (%) Foxp + IL + (%) CD + IL + (%) Foxp + IL7 + (%) CD + IL7 + (%) CD + Foxp + X Foxp + IL + X CD + IL + X Foxp + IL7 + X CD + IL7 + X Nature Medicine: doi:./nm.7

15 a Foxp EGFPCre Ilra R7 Foxp EGFPCre Il/ / Ilra F79 Foxp EGFPCre (PBS) Ilra F79 (PBS) Ilra F79 Foxp EGFPCre Il/ / (PBS) Foxp EGFPCre (OVA) Ilra F79 OVAOVA Ilra F79 Foxp EGFPCre Il/ / (OVA) b Inflammation Score PAS Score c Resistance (Over baseline) Supplementary Figure PBS Methacholine (mg/ml) d Total IgE (µg/ml) OVAIgE (µg/ml) e Eosinophils x Neutrophils X Lymphocytes X f CD + Foxp + (%) g Foxp + IL + (%) CD + IL + (%) h Foxp + IL7 + (%) CD + IL7 + (%) CD + Foxp + X Foxp + IL7 + X CD + IL7 + X Foxp + IL + X CD + IL + X Nature Medicine: doi:./nm.7

16 Supplementary Figure Legends Supplementary Figure Ilra R7 polymorphism promotes the acquisition by lung tissue T reg cells of T H and T H 7 celllike phenotypes. (a,b) Flow cytometric analysis of IL7 vs. IL (a) and IL vs. IL7 (b) cytokine expression in and Ilra R7 Foxp + T reg cells within lung tissues of the HDMtreated mouse groups. (c) IL, IL, IL, IL 7 and IFNγ cytokine levels in BAL fluids of the respective mouse groups (n = mice for PBS and mice for HDMtreated groups). (d g) Flow cytometric analysis, cell frequencies and absolute numbers of GATA (d,e) and RORγt (f,g) expression in CD + Foxp T conv and CD + Foxp + T reg cells within lung tissue of the same mouse groups shown in c (n = mice per group). (h,i) Flow cytometric analysis (h), cell frequencies and absolute numbers (i) of IL and IFNγ expression in CD + T conv and CD + Foxp + T reg cells in lung tissues of the same mouse groups shown in c (n = mice per group). Each dot represents one mouse. Data represent means ± s.e.m. from one experiment. P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. Supplementary Figure Characterization of cytokine production by CD + Foxp + it reg and nt reg cells in HDM treated Ilra R7 mice. (a,b) Flow cytometric analysis (a) and frequencies (b) Helios high Foxp + and Helios low Foxp + T reg cell populations in lung tissues of the respective mouse groups (n = mice per group). (c,d) Flow cytometric analysis (c) and frequencies (d) of CCR and IL7 coexpression in CD + Foxp T conv and CD + Foxp + T reg cells in lung tissues of the same mouse groups shown in b (n = mice per group). (e,f) Flow cytometric analysis (e) and frequencies (f) of CCR, IL7 or IL vs. Helios coexpression in CD + Foxp + T reg cell populations in lung tissues of the Nature Medicine: doi:./nm.7

17 respective mouse groups (n = mice per group). Each dot represents one mouse. Data represent means ± s.e.m. from one experiment. P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. Supplementary Figure Acquisition by in vitro derived Ilra R7 it reg cells of T H 7 and T H celllike attributes. (a,b) Flow cytometric analysis of RORγt (a) and GATA (b) in naïve and Ilra R7 cells treated with anti CD + anti CD mabs in the absence or presence of TGF β and TGF β + IL. (ce) Flow cytometric analysis (c) and frequencies (d,e) of IL (d) and IL (e) expression in naïve T cells activated with anti CD + anticd mabs in the absence or presence of TGF β, TGF β + anti IL mab, TGF β + anti IL mab and TGF β + IL (n = replicates). (f h) Flow cytometric analysis (f) and frequencies (g,h) of IL9 expression in CD + Foxp T conv (g) and CD + Foxp + T reg cell populations (h) within naïve T cells activated with anti CD + anti CD mabs in the absence or presence of TGF β or TGF β + IL (n = replicates). Data represent means ± s.e.m. from two independent experiments. P <. by oneway ANOVA with Bonferroni posttest analysis. Supplementary Figure Il R7 nt reg cells exhibit comparable phenotypic and functional characterization to the counterparts. (a) Flow cytometric analysis of CD + GFP T conv and or Il R7 CD + GFP + Nrp + T reg cells purity after purification by MACS bead and FACS. (b,c) Representative flow cytometric analysis (b) and frequencies (c) of proliferating CD + T (T eff ) cells cocultured with or Ilra R7 Nrp + CD + Foxp + nt reg cells added at the indicated ratios. Cultured cells were stimulated with anti CD + anti CD mabs in the absence or presence of recombinant IL or IL and antiil mab and assessed for their proliferation by the dilution of a Nature Medicine: doi:./nm.7

18 proliferative dye (n = replicates). (d,e) Flow cytometric analysis (d) and frequencies (e) of IL and IL7 production by Nrp + CD + Foxp + nt reg cells that were isolated from spleens of naïve or Ilra R7 mice and stimulated in culture with anti CD + anti CD mabs in the absence or presence of recombinant IL (n = replicates). (e,f) flow cytometric analyses (f) and quantification (g) of IL and IL7 production by naïve CD + CDL + CD T conv isolated from spleen of naïve or Ilra R7 mice after culture with anti CD + anti CD mab in the absence or presence of recombinant IL (n = replicates). Data represent means ± s.e.m. from two independent experiments. P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For suppression analyses by repeated measures twoway ANOVA. Supplementary Figure Antigen specific Ilra R7 it reg cells fail to protect against allergic airway inflammation. (a) Schema of the experimental design. In vitro derived or Ilra R7 Thy. + DO. + Rag / Foxp EGFP+ it reg cells were adoptively transferred to OVA sensitized Thy. + Ilra R7 mice prior to challenge with nebulized OVA. (b) PAS staining of lung sections isolated from the respective recipient mice (, scale bar µm). (c) Inflammation and PAS scores (n = counts per fieldofview) (d) absolute numbers of lung tissue eosinophils and neutrophils and (e) Methacholine induced AHR in the respective mouse groups. (f) Frequencies and absolute numbers of endogenous (Thy. + ) IL and IL7 producing CD + Foxp T eff and CD + Foxp + T reg cells in the lung tissues of the mouse groups shown in d. (g,h) Flow cytometric analysis of transferred CD + EGFP + it reg cells (g), DO. + EGFP + (it reg ) and DO. + EGFP (ext reg ) cells gated on Thy. + population (h), all recovered from lung tissues of recipients of the mouse groups shown in d. (i) Absolute numbers of transferred it reg and Nature Medicine: doi:./nm.7

19 ext reg cells in lung tissues of the recipients. (j) Flow cytometric analysis and absolute numbers of IL and IL7 producing it reg and ext reg cells within Thy. + population (n = mice per group for c j). Data represent means ± s.e.m. from independent experiments. P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analysis, P <. and P <. by repeated measures twoway ANOVA. Supplementary Figure ILRαR7 activates GRBcoupled MAPK cascades. (a) Binding of GRB and STAT in human PBMC lysates to the indicated biotinylated human ILRα peptides as revealed by immunoblotting and quantified by densitometry (n = replicates). (b,c) Time course of MAPK activation in Ilra R7 and splenocytes stimulated with IL for the indicated times and probed for pcraf, perk/ (b), p MKK/MKK, pp (c) and their corresponding nonphosphorylated proteins. (d) IL RαR7mediated activation of ERK/ but not p MAPK is crafdependent. Cell lysates of IL treated, Ilra R7 or craf inhibitor (crafinh)treated Ilra R7 splenocytes were immunoblotted for the respective unmodified and phosphorylated proteins. (e) RTPCR analysis of Il transcripts in and Ilra R7 splenocytes either untreated or treated with IL in the presence of graded concentrations of pinh (n = replicates). (f,g) ILRαR7 mediates sustained NFκB p phosphorylation in an ERK/dependent manner. Splenocytes were stimulated with IL in the absence (f) or presence (g) of MEKInh and immunoblotted for NFκB pp and p. (h) IL production in the cultures of differentiated it reg cells for the indicated treated groups (n = replicates). (i) Flow cytometric analysis of and Ilra R7 it reg cells differentiated from naïve CD + T conv cells in the presence of MEKInh ( µm) or pinh ( µm), Nature Medicine: doi:./nm.7

20 antiil or anti IL mab, as indicated. (j) IL7 and IL expression in and Ilra R7 it reg cells treated as in (j). Data represent means ± s.e.m. from independent experiments. P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. Supplementary Figure 7 ILRαR7 mediates sustained STAT activation in T cells and BMDM in an IL dependent manner. (a) Flow cytometric analysis and MFI (right panel) of pstat expression in and Ilra R7 naïve CD + T cells stimulated with IL in the absence or presence of non specific IgG or anti IL mab for h or indicated times. (b,c) MFI of pstat (b) and pstat (c) in and Ilra R7 naïve CD + T cells stimulate with IL or IL respectively. (d) Flow cytometric analysis and MFI (right panel) of pstat in and Ilra R7 BMDM stimulated with IL in the presence of non specific IgG or anti IL mab, for h or indicated times. (e) MFI of pstat in and Ilra R7 BMDM treated with IL for the indicated times (n = replicates for a e). (f) RTPCR analysis of Ccl transcripts in and Ilra R7 BMDM with indicated treatment. (g) ChIP analysis of STAT and STAT occupancy on Ccl promoter in or Ilra R7 BMDM either untreated or treated for hr with IL or IL + anti IL. (h) RTPCR analysis of Ccl transcripts in scrambled or Stat sirna treated BMDM either untreated or treated with IL ( min) (n = replicates for h j). (i) Representative STAT protein expression in scrambled or Stat sirna treated BMDM, determined by immunoblotting. Results represent means ± s.e.m. from independent experiments. P <. by oneway ANOVA with Bonferroni posttest analysis. Supplementary Figure Gating strategy of identification of T reg cell subpopulations in peripheral blood mononuclear cells (PBMC) of asthmatic human subjects. PBMCs of Nature Medicine: doi:./nm.7

21 asthmatic Q7/Q7 and R7/R7 subjects were analyzed by flow cytometry. Gated CD + Foxp + T cells were further analyzed for Helios v.s. CCR and CCR v.s. IL7 expression, as shown. Supplementary Figure 9 Characterization of allergic airway inflammation in and Ilra R7 mice with T reg cell lineagespecific deletion of Rorc. (a) Scheme for the generation of Foxp YFPCre Rorc Δ/Δ mice. (b) RTPCR analysis of Rorc mrna transcripts in CD + Foxp T conv and CD + Foxp + T reg cells of Foxp YFPCre and Foxp YFPCre Rorc Δ/Δ mice (n = mice). (c) Absolute numbers of CD + Foxp + T reg cells in lung tissues of the respective mouse groups (d) Absolute numbers of IL7 producing CD + Foxp + T reg and CD + Foxp T conv cells. (e) IL7 concentrations in BAL fluids of the respective mouse groups. (f) Absolute numbers of CCRexpressing CD + Foxp + T reg and CD + Foxp T conv cells. (g) Absolute numbers of IL producing CD + Foxp + T reg and CD + Foxp T conv cells. (h) IL concentrations in BAL fluids of the respective mouse groups within lung tissues of the respective mouse groups (n = mice for PBS and mice for OVA treated groups for c h). Each dot represents one mouse. Results represent means ± s.e.m. from one to two experiments. P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. Supplementary Figure Specific deletion of Ilra in Foxp + T reg cells of Ilra R7 mice reduces induced airway inflammation to those of counterparts. (a) Scheme for the generation of Foxp YFPCre Ilra Δ/Δ mice. (b) RTPCR analysis of Ilra mrna transcripts in sorted CD + Foxp T conv and CD + Foxp + T reg cells of Foxp YFPCre and Foxp YFPCre Ilra Δ/Δ mice (n = mice). (c) PAS staining of lung sections of Foxp YFPCre, Ilra R7 Ilra fl/fl, Ilra R7 Foxp EGFPCre Ilra / mice immunized and challenged with OVA Nature Medicine: doi:./nm.7

22 (, scale bar µm). (d) Inflammation and PAS scores (n = counts per fieldofview). (e) Methacholine induced AHR. (f) Total and OVA specific serum IgE concentrations. (g) Frequencies of lung tissue eosinophils, neutrophils and lymphocytes. (h j) Frequencies and absolute numbers of Foxp + T reg cells (h), IL (i) and IL7 (j) producing Foxp + T reg and CD + T conv cells in lung tissues of respective mouse groups. Results represent means ± s.e.m. from one experiment (n = for PBSand for OVA treated groups for e j). P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analyses, P <. by repeated measures twoway ANOVA. Supplementary Figure Treatment with a neutralizing anti IL mab abrogated the aggravated HDMinduced airway inflammation and AHR in Ilra R7 mice. (a) Methacholineinduced AHR in PBS and HDMtreated and Ilra R7 mice that received either anti IL or isotype control mab prior to antigenchallenge. (b) PAS staining of lung sections (, scale bar µm). (c) Inflammation and PAS scores (n = counts per fieldofview). (d) Total serum IgE concentration. (e) Absolute numbers of lung tissue eosinophils and neutrophils. (f) Frequencies of CD + Foxp +, Foxp + IL7 + and Foxp + IL + T reg cells in lung tissue of the respective groups. (g) Frequencies of lung tissue CD + IL7 + and CD + IL + T conv cells. (h) IL7, IL and CCL cytokines levels in BAL fluids of respective treated groups (n = for PBS and for HDMtreated groups). Data represent means ± s.e.m. from two independent experiments. P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analyses, P <. and P <. by repeated measures twoway ANOVA. Nature Medicine: doi:./nm.7

23 Supplementary Figure Treatment with a neutralizing anti IL7 mab partially reverses the augmentation in HDMinduced airway inflammation and AHR in Ilra R7 mice. Methacholineinduced AHR in PBS and HDMtreated and Ilra R7 mice that received either anti IL7 or isotype control mab prior to antigenchallenge. (b) PAS staining of lung sections (, scale bar µm). (c) Inflammation and PAS scores (n = counts per fieldofview). (d) Total serum IgE concentration. (e) Absolute numbers of lung tissue eosinophils and neutrophils. (f) Frequencies of lung tissue Foxp + T reg cells. (g) Frequencies of lung tissue CD + IL7 + and CD + IL + T conv cells. (h) IL7, IL and CCL cytokines levels in BAL fluids of respective treated groups (n = for PBSand for HDMtreated groups). Data represent means ± s.e.m. from two independent experiments. P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analyses, P <. by repeated measures twoway ANOVA. Supplementary Figure AntiCCL partially inhibited HDMinduced airway inflammation in and Ilra R7 mice. (a) Methacholineinduced AHR in PBS or HDMtreated and Ilra R7 mice that received anticcl or isotype antibody prior to antigenchallenge. (b) PAS staining of lung sections (, scale bar µm). (c) Inflammation and PAS scores (n = counts per fieldofview). (d) Frequencies of lung tissue eosinophils and neutrophils and total serum IgE concentration. (e) Frequencies of Foxp + T reg cells. (f) IL7 and IL cytokine levels in BAL fluids in the respective groups. (g) CCL levels in BAL fluids of respective groups. (n = mice for PBS and mice for HDMtreated groups). Data represent means ± s.e.m. from one experiment. P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analyses, P <. by repeated measures twoway ANOVA. Nature Medicine: doi:./nm.7

24 Supplementary Figure Specific deletion of Il/Il in Foxp + T reg cells was not sufficient to ameliorate aggravated airway inflammation in Ilra R7 mice. (a) Scheme for the generation of Foxp EGFPCre Il/ Δ/Δ mice. (b) RTPCR analysis of Il mrna transcripts in sorted CD + Foxp T conv and CD + Foxp + T reg cells of Foxp EGFPCre and Foxp EGFPCre Il/ Δ/Δ mice (n = mice). (c) PAS staining of lung sections of Foxp EGFPCre, Ilra R7 Il/l fl/fl, Foxp EGFPCre Il/l / and Ilra R7 Foxp EGFPCre Il/l / mice immunized and challenged with OVA (, scale bar µm). (d) Inflammation and PAS scores (n = counts per fieldofview). (e) Methacholine induced AHR. (f) Total and OVA specific serum IgE concentrations. (g) Frequencies of lung tissue eosinophils, neutrophils and lymphocytes. (h j) Frequencies and absolute numbers of CD + Foxp + T reg cells (h), IL (i) and IL7 (j) producing CD + Foxp + T reg and CD + Foxp T conv cells in lung tissues of the respective mouse groups. Data represent means ± s.e.m. from two independent experiments (n = 7 mice for PBS and mice for OVAtreated groups). P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analyses, P <. and P <. by repeated measures oneway ANOVA. Supplementary Figure Specific deletion of Il/Il in Foxp + T reg cells rescued aggravated airway inflammation in Ilra F79 mice. (a) PAS staining of lung sections of Foxp EGFPCre, Ilra F79 Il/l fl/fl, Foxp EGFPCre Il/l / and Ilra F79 Foxp EGFPCre Il/l / mice immunized and challenged with OVA (, scale bar µm). (b) Inflammation and PAS scores (n = counts per fieldofview). (c) Methacholineinduced AHR. (d) Total and OVAspecific serum IgE concentrations. (e) Frequencies of lung tissue eosinophils, neutrophils and lymphocytes. (f h) Frequencies Nature Medicine: doi:./nm.7

25 and absolute numbers of CD + Foxp + T reg cells (f), IL (g) and IL7 (h) producing CD + Foxp + T reg and CD + Foxp T conv cells in lung tissues of the respective mouse groups. Data represent means ± s.e.m. from two independent experiments (n = 7 mice for PBS and mice for OVAtreated groups). P <., P <., P <. and P <. by oneway ANOVA with Bonferroni posttest analysis. For AHR analysis, P <. by repeated measures twoway ANOVA. Nature Medicine: doi:./nm.7

26 Supplemental Table Demographic Characteristics and genotype of enrolled nonasthmatic study participants. Subject Genotype Age (Y) Sex Q7/Q7 M Q7/Q7 M Q7/Q7 M Q7/Q7 M Q7/Q7 F Q7/Q7 F 7Q7/Q7 F Q7/Q7 7 F 9Q7/Q7 9 M Q7/Q7 M Q7/Q7 M Q7/Q7 M Q7/Q7 M Q7/R7 M Q7/R7 7 M Q7/R7 F 7Q7/R7 M Q7/R7 M 9R7/R7 7 M R7/R7 M R7/R7 M Nature Medicine: doi:./nm.7

27 Supplemental Table Demographics, genotype and clinical characteristics of enrolled asthmatic study participants. Subject Genotype Age (Y) Sex Asthma Severity Q7/Q7 M Intermittent Q7/Q7 M Persistent Mild Q7/Q7 F Persistent Mild Q7/Q7 F Persistent Mild Q7/Q7 F Intermittent Q7/Q7 M Persistent Severe 7Q7/Q7 7 M Persistent Moderate Q7/Q7 M Persistent Mild 9Q7/Q7 M Intermittent Q7/Q7 F Persistent Moderate Q7/Q7 M Intermittent Q7/Q7 F Persistent Mild Q7/Q7 M Persistent Moderate Q7/Q7 F Persistent Moderate Q7/Q7 F Persistent Mild Q7/Q7 F Persistent Mild 7Q7/Q7 7 F Persistent Mild Nature Medicine: doi:./nm.7

28 Q7/Q7 F Persistent Moderate 9Q7/Q7 F Persistent Mild Q7/R7 F Persistent Moderate Q7/R7 F Persistent Mild Q7/R7 F Persistent Moderate Q7/R7 M Persistent Moderate R7/R7 9 F Persistent Moderate R7/R7 F Persistent Moderate R7/R7 F Persistent Moderate 7R7/R7 M Persistent Severe R7/R7 M Persistent Severe 9R7/R7 M Persistent Severe R7/R7 M Persistent Severe Asthma severity was classified as follows: Intermittent (symptoms < days/week), Mild (symptoms> days/week but not daily), Moderate (daily symptoms), and Severe (symptoms throughout the day). An average asthma severity score was calculated for each group by assigning intermittent asthma a score of, mild persistent asthma a score of, moderate persistent asthma a score of and severe asthma a score of. The average severity score for asthmatics homozygous for the Q7 residue (n = 9) was. ±.9 and those heterozygous or homozygous for the R7 reside (n=) was.7 ±.9 (p=.7 by Student s unpaired two tailed t test). The two groups were otherwise not significantly different by age (p =. by Student s unpaired two tailed t test) or sex (.9 by Fisher s exact test). Nature Medicine: doi:./nm.7