Figure S1. Innate Lymphoid Cell Precursors (Ilcps)

Figure S1. Innate lymphoid cell precursors (ILCPs) decrease with age and are depleted in patients hospitalized with COVID-19 (A) Representative gating for ILCP identification in PBMCs. Cells were first gated on lymphoid cells, singlets, live/dead, and CD45+. Lineage (Lin) markers included antibodies against: CD3, CD4, TCRαβ, TCRγδ, CD19, CD20, CD22, CD34, FcεRIα, CD11c, CD303, CD123, CD1a, and CD14. (B) Effect of age (X-axis) on log2 ILCP abundance per million total lymphocytes (Y-axis). Each dot represents an individual blood donor, with yellow for female and blue for male. Shading represents the 95%CI. P-values are from the regression analysis for comparisons to the control group. (C) Lymphoid cell abundance by group, shown as estimated marginal means with 95%CI, generated from the multiple linear regressions in (B), and averaged across age and sex. P-values represent pairwise comparisons on the estimated marginal means, adjusted for multiple comparisons with the Tukey method.

Figure S2. Association of blood ILC depletion with COVID-19 severity in an independent cohort of adults. (A) Effect of age (X-axis) on log2 ILC abundance per million total lymphocytes (Y-axis) in adult controls from this paper and patients with COVID-19 from Kuri-Cervantes et al., 2020. Patients were stratified into two groups by disease severity. The first group included patients maintained on room air or treated with O2 by nasal cannula. The second group included those with ARDS. Each dot represents an individual blood donor, with yellow for female and blue for male. Shading represents the 95%CI. P-values are from the regression analysis for comparisons to the control group. (C) Table of regression coefficients for log2 fold difference in ILC abundance for patients with COVID-19, in comparison to the adult healthy control cohort, adjusted for effects of age and sex.

Figure S3. Effects of pediatric COVID-19 and MIS-C on blood lymphoid cell subsets in comparison to full combined adult and pediatric control group

Effect of age (X-axis) on log2 abundance per million total lymphocytes of the indicated lymphoid cell populations (Y-axis). Each dot represents an individual blood donor, with yellow for female and blue for male. Shading represents the 95%CI. P-values are from the regression analysis for comparisons to the control group.

Figure S4. T cells increase during follow-up from MIS-C

Log2 ILC abundance per million lymphocytes in longitudinal pairs of samples collected during acute presentation and during follow-up, from individual children with COVID-19 or MIS-C. P-values are for change in ILC abundance at follow-up, as determined with a linear mixed model, adjusting for age, sex, and group, and with patient as a random effect. Differences in sample size among cell types was due to limited sample availability.

Figure S5. Males have lower percent AREG+ ILCs, and lower AREG MFI in ILCs, than do females, and there is no effect of age on these parameters (A) Effect of age (X-axis) on % AREG+ ILCs or MFI in ILCs (Y- axis as indicated). Each dot represents an individual blood donor, with yellow for female and blue for male. Shading represents the 95%CI. (B) Table of results for regression analyses plotted in (A)

Figure S6. Representative gating strategy (A) All cell subsets were first gated on lymphoid cells, singlets, live/dead, and CD45+. Lineage (Lin) markers included antibodies against: CD3, CD4, TCRαβ, TCRγδ, CD19, CD20, CD22, CD34, FcεRIα, CD11c, CD303, CD123, CD1a, and CD14. (B) ILCs were identified as Lin-CD56-CD16-CD127+ using 14 lineage markers (C) CD16+ NK cells were identified as Lin-TBX21+CD16+ (E) CD4+ T cells were identified as Lin+CD4+ (D), and CD8+ T cells were identified as Lin+CD8+

Table S1: Race and Ethnicity of Adult Cohorts Healthy Control Hospitalized Outpatient Characteristic N=86 N=40 N=51 Race or ethnic group – number (%) White 25 (29.1) 17 (42.5) 46 (90.2) Black or African American 0 (0) 6 (15) 2 (3.9) Asian 1 (1.2) 1 (2.5) 1 (2) Unknown or not reported 60 (69.8) 16 (40) 2 (3.9) Hispanic or latinx 1 (1.2) 11 (27.5) 3 (5.9) Percentages may not equal 100 because of rounding

Table S2: Demographic and Clinical Characteristics of Pediatric Blood Donor Groups Control COVID-19 COVID follow-up MIS-C MISC-C follow-up Characteristic N=17 N=19 N=14 N=11 N=7 Mean age (range) - 10.6 (2-19) 13 (0.7-21.4) 13.8 (1-22) 10.1 (1.2-22) 6.3 (2.2-13.1) years Sex – number (%) Male 8 (47.1) 13 (68.4) 7 (50) 7 (63.6) 5 (71.4) 9 (52.9) 6 (31.6) 7 (50) 4 (36.4) 2 (28.6) Female Hospital admission 11 (57.9) 4 (28.6) 0 0 for COVID-19 – number (%) Hospital admission 11 (100) 7 (100) for MIS-C – number (%) Intubation with mechanical 1 (5.3) 0 1 (9.1) 1 (14.3) ventilation or ECMO – number (%) Deaths – number (%) 0 0 0 0 Mean time 8 (2-17) 7.5 (1-16) hospitalized (range) – days Max lab value – mean (range) CRP – mg/L 119 (0.2-385) 161 (9-300)

Table S3: Change in Lymphocyte

Abundance Due to Age, Sex, and COVID-19 Severity in Adult cohorts

Fold difference (log2) [±95%CI]

Lymphocytesa

Age -0.008*** [-0.012, -0.004] Male -0.267*** [-0.400, -0.135]

Hospitalized -0.411*** [-0.572, -0.250] Outpatient 0.129 [-0.030, 0.289]

R2 0.416

* p < 0.05, ** p < 0.01, *** p < 0.001 a 6 per 10 PBMCs ‘

Table S4: Change in Cell Abundance Due to Age, Sex, and COVID-19 Severity Fold difference (log2) [±95%CI] CD4+ Ta ILCa CD8+ Ta CD16+ NKa Age -0.020*** -0.051*** -0.017*** 0.014* [-0.029, -0.010] [-0.063, -0.040] [-0.025, -0.008] [0.002, 0.026] Male -0.678*** -0.609** -0.411** -0.049 [-0.980, -0.375] [-0.983, -0.235] [-0.688, -0.134] [-0.435, 0.336] Hospitalized -0.241 -1.280*** -0.034 -1.466*** [-0.608, 0.126] [-1.734, -0.826] [-0.369, 0.301] [-1.932, -0.999] Outpatient 0.461* 0.009 0.224 -0.276 [0.099, 0.824] [-0.441, 0.458] [-0.110, 0.558] [-0.741, 0.189] R2 0.364 0.552 0.224 0.194 * p < 0.05, ** p < 0.01, *** p < 0.001 aper 106 PBMCs

Table S5: Odds of Hospitalization in Pediatric Cohorta Cell countb Odds Ratioc 95% Confidence Interval P-Value

CD4+ T 1.75 0.0593 – 43.3 0.724

ILC 0.712 0.26– 1.73 0.463

CD8+ T 0.217 0.00509 – 5.9 0.366

CD16+ NK 0.386 0.0554 – 1.23 0.194 aAdjusted for age and sex bper 106 lymphocytes cper 2-fold increase in cell population abundance

Table S6: Change in Pediatric Cohort Cell Abundance due to Group; Adjusted for Effects of Age and Sex with Combined Pediatric and Adult Control Data Fold difference (log2) [±95%CI] CD4+ Ta ILCa CD8+ Ta CD16+ NKa COVID -0.085 -0.924** -0.078 0.400 [-0.421, 0.251] [-1.474, -0.373] [-0.424, 0.269] [-0.161, 0.961] MIS-C -0.814*** -1.183*** -0.538* -0.493 [-1.224, -0.404] [-1.856, -0.511] [-0.969, -0.106] [-1.190, 0.205] R2 0.292 0.541 0.165 0.261 * p < 0.05, ** p < 0.01, *** p < 0.001 aper 106 lymphocytes

Table S7: Gene ontology analysis results ID Description GeneRatio BgRatio pvalue p.adjust qvalue geneID Count interleukin- IL17RA/NLRP3/IL GO:00 13 4.47E- 0.001120 0.00100 18/TNFSF4/ARG2 32616 production 7/294 17/9263 07 26 638 /GATA3/RARA 7 NLRP3/CD81/IL1 type 2 8/BCL3/TNFSF4/ GO:00 immune 6.33E- 0.001120 0.00100 ARG2/GATA3/RA 42092 response 8/294 25/9263 07 26 638 RA 8 positive NLRP3/CD81/IL1 regulation of 8/HLA- T cell B/IL23R/HSPD1/T GO:00 mediated 1.28E- 0.001223 0.00109 NFSF4/HLA- 02711 immunity 9/294 36/9263 06 25 89 A/GATA3 9 T-helper 2 cell NLRP3/IL18/BCL3 GO:00 differentiatio 1.38E- 0.001223 0.00109 /TNFSF4/GATA3/ 45064 n 6/294 13/9263 06 25 89 RARA 6 positive regulation of type 2 NLRP3/CD81/IL1 GO:00 immune 2.35E- 0.001235 0.00110 8/TNFSF4/GATA3 02830 response 6/294 14/9263 06 26 969 /RARA 6 regulation of type 2 NLRP3/CD81/IL1 GO:00 immune 2.40E- 0.001235 0.00110 8/TNFSF4/ARG2/ 02828 response 7/294 21/9263 06 26 969 GATA3/RARA 7 NLRP3/CD81/IL1 regulation of 8/HLA- T cell B/IL23R/HSPD1/T GO:00 mediated 2.44E- 0.001235 0.00110 NFSF4/HLA- 02709 immunity 10/294 49/9263 06 26 969 A/GATA3/WAS 10 regulation of interleukin- IL17RA/NLRP3/T GO:00 13 3.82E- 0.001690 0.00151 NFSF4/ARG2/GA 32656 production 6/294 15/9263 06 36 854 TA3/RARA 6 NLRP3/CD81/IL1 8/HLA- positive B/CD28/LAMP1/IL regulation of 23R/HSPD1/TNF lymphocyte SF4/HLA- GO:00 mediated 6.38E- 0.002126 0.00190 A/GATA3/EXOSC 02708 immunity 12/294 79/9263 06 09 997 6 12 NLRP3/CD81/IL1 8/HLA- B/CD28/LAMP1/IL regulation of 23R/HSPD1/TNF lymphocyte SF4/HLA- GO:00 mediated 107/926 6.60E- 0.002126 0.00190 A/ARRB2/GATA3/ 02706 immunity 14/294 3 06 09 997 EXOSC6/WAS 14 RASAL3/FOXP1/ NLRP3/CD81/IL1 8/RC3H1/CD28/B alpha-beta T CL3/IL23R/TCF7/ GO:00 cell 107/926 6.60E- 0.002126 0.00190 TNFSF4/ARG2/G 46631 activation 14/294 3 06 09 997 ATA3/RARA 14 CD4- FOXP1/NLRP3/C GO:00 positive, 9.66E- 0.002741 0.00246 D81/IL18/RC3H1/ 35710 alpha-beta T 11/294 69/9263 06 22 257 BCL3/IL23R/TNF 11

cell SF4/ARG2/GATA activation 3/RARA CD6/RASAL3/NL RP3/GRAP2/CD8 1/IL18/CD28/FLT3 LG/CD5/LAMP1/I L23R/HSPD1/TNF positive SF4/RAC1/CDC4 regulation of 2/ADAM8/CSK/G GO:00 lymphocyte 209/926 1.02E- 0.002741 0.00246 ATA3/RARA/EXO 51251 activation 20/294 3 05 22 257 SC6 20 CD6/RASAL3/NL RP3/GRAP2/CD8 1/IL18/CD28/CD5/ positive IL23R/HSPD1/TN regulation of FSF4/RAC1/CDC GO:00 T cell 159/926 1.11E- 0.002741 0.00246 42/ADAM8/CSK/G 50870 activation 17/294 3 05 22 257 ATA3/RARA 17 positive regulation of interleukin- IL17RA/NLRP3/T GO:00 13 1.23E- 0.002741 0.00246 NFSF4/GATA3/R 32736 production 5/294 23316 05 22 257 ARA 5 FOXP1/NLRP3/IL T-helper cell 18/RC3H1/BCL3/I GO:00 differentiatio 1.36E- 0.002741 0.00246 L23R/TNFSF4/GA 42093 n 9/294 47/9263 05 22 257 TA3/RARA 9 regulation of CD4- positive, NLRP3/CD81/IL1 alpha-beta T 8/RC3H1/IL23R/T GO:20 cell 1.36E- 0.002741 0.00246 NFSF4/ARG2/GA 00514 activation 9/294 47/9263 05 22 257 TA3/RARA 9 CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/CD5/IL 23R/HSPD1/LAT/ TNFSF4/RAC1/A regulation of RG2/CDC42/ADA GO:00 T cell 232/926 1.44E- 0.002741 0.00246 M8/CSK/GATA3/ 50863 activation 21/294 3 05 22 257 RARA 21 RASAL3/NLRP3/ regulation of CD81/IL18/RC3H alpha-beta T 1/CD28/IL23R/TN GO:00 cell 1.47E- 0.002741 0.00246 FSF4/ARG2/GAT 46634 activation 11/294 72/9263 05 22 257 A3/RARA 11 CD6/RASAL3/FO XP1/CASP3/NLR P3/GRAP2/CD81/ IL18/RC3H1/IRF2 BP2/CD28/FLT3L G/CD5/HDAC9/LA MP1/BCL3/PLCG 2/IL23R/AKAP17A /TCF7/HSPD1/LA T/TNFSF4/RAC1/ ARG2/ZBTB7A/C DC42/ADAM8/CS K/GATA3/RARA/E GO:00 lymphocyte 498/926 1.83E- 0.003024 0.00271 XOSC6/STK11/W 46649 activation 34/294 3 05 12 671 AS 34

positive regulation of adaptive immune response based on somatic recombinatio n of immune NLRP3/CD81/IL1 receptors 8/HLA- built from B/CD28/IL23R/HS immunoglob PD1/TNFSF4/HLA ulin - GO:00 superfamily 1.92E- 0.003024 0.00271 A/GATA3/EXOSC 02824 domains 11/294 74/9263 05 12 671 6 11 CD4- positive, alpha-beta T cell differentiatio FOXP1/NLRP3/IL n involved in 18/RC3H1/BCL3/I GO:00 immune 1.94E- 0.003024 0.00271 L23R/TNFSF4/GA 02294 response 9/294 49/9263 05 12 671 TA3/RARA 9 regulation of adaptive immune response based on somatic recombinatio n of immune NLRP3/CD81/IL1 receptors 8/RC3H1/HLA- built from B/CD28/IL23R/HS immunoglob PD1/TNFSF4/HLA ulin - GO:00 superfamily 103/926 2.10E- 0.003024 0.00271 A/GATA3/EXOSC 02822 domains 13/294 3 05 12 671 6/WAS 13 CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/CD5/T NR/IL23R/ADAM1 9/HSPD1/TNFSF4 /RAC1/ARG2/CD regulation of C42/ADAM8/CSK/ GO:00 cell-cell 276/926 2.16E- 0.003024 0.00271 GATA3/RGCC/RA 22407 adhesion 23/294 3 05 12 671 RA 23 CD6/RASAL3/NL RP3/GRAP2/CD8 1/IL18/CD28/CD5/ IL23R/ADAM19/H positive SPD1/TNFSF4/R regulation of AC1/CDC42/ADA GO:00 cell-cell 185/926 2.27E- 0.003024 0.00271 M8/CSK/GATA3/ 22409 adhesion 18/294 3 05 12 671 RARA 18 alpha-beta T cell activation FOXP1/NLRP3/IL involved in 18/RC3H1/BCL3/I GO:00 immune 2.31E- 0.003024 0.00271 L23R/TNFSF4/GA 02287 response 9/294 50/9263 05 12 671 TA3/RARA 9

alpha-beta T cell differentiatio FOXP1/NLRP3/IL n involved in 18/RC3H1/BCL3/I GO:00 immune 2.31E- 0.003024 0.00271 L23R/TNFSF4/GA 02293 response 9/294 50/9263 05 12 671 TA3/RARA 9 FOXP1/NLRP3/C D81/IL18/RC3H1/ lymphocyte CD28/LAMP1/BC activation L3/PLCG2/IL23R/ involved in HSPD1/TNFSF4/ GO:00 immune 136/926 2.54E- 0.003212 0.00288 GATA3/RARA/EX 02285 response 15/294 3 05 86 626 OSC6 15 CD6/RASAL3/NL RP3/GRAP2/CD8 positive 1/IL18/CD28/CD5/ regulation of IL23R/HSPD1/TN leukocyte FSF4/RAC1/CDC GO:19 cell-cell 171/926 2.90E- 0.003542 0.00318 42/ADAM8/CSK/G 03039 adhesion 17/294 3 05 28 22 ATA3/RARA 17 CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/CD5/IL regulation of 23R/HSPD1/TNF leukocyte SF4/RAC1/ARG2/ GO:19 cell-cell 225/926 3.01E- 0.003547 0.00318 CDC42/ADAM8/C 03037 adhesion 20/294 3 05 23 665 SK/GATA3/RARA 20 CD6/RASAL3/FO XP1/CASP3/NLR P3/GRAP2/CD81/ IL18/RC3H1/CD2 8/CD5/BCL3/IL23 R/TCF7/HSPD1/L AT/TNFSF4/RAC 1/ARG2/CDC42/A DAM8/CSK/GATA GO:00 T cell 344/926 3.46E- 0.003843 0.00345 3/RARA/STK11/W 42110 activation 26/294 3 05 09 243 AS 26 CD6/RASAL3/NL RP3/GRAP2/CD8 1/IL18/DOCK5/CD 28/CD5/SPOCK2/ IL23R/ADAM19/H SPD1/RSU1/TNF positive SF4/RAC1/CDC4 regulation of 2/ADAM8/CSK/G GO:00 cell 265/926 3.47E- 0.003843 0.00345 ATA3/RARA/ITGB 45785 adhesion 22/294 3 05 09 243 1BP1 22 NLRP3/CD81/IL1 8/HLA- positive B/CD28/IL23R/HS regulation of PD1/TNFSF4/HLA adaptive - GO:00 immune 3.61E- 0.003873 0.00348 A/GATA3/EXOSC 02821 response 11/294 79/9263 05 96 017 6 11 regulation of alpha-beta T RASAL3/CD81/IL GO:00 cell 4.72E- 0.004820 0.00433 18/CD28/TNFSF4 46640 proliferation 6/294 22/9263 05 39 039 /ARG2 6

CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/FLT3L G/CD5/LAMP1/IL 23R/HSPD1/LAT/ TNFSF4/RAC1/A regulation of RG2/CDC42/ADA GO:00 lymphocyte 310/926 4.76E- 0.004820 0.00433 M8/CSK/GATA3/ 51249 activation 24/294 3 05 39 039 RARA/EXOSC6 24 CD6/RASAL3/NL RP3/GRAP2/CD8 1/IL18/CD28/FLT3 LG/CD5/LAMP1/I L23R/HSPD1/TNF positive SF4/RAC1/CDC4 regulation of 2/ADAM8/CSK/G GO:00 leukocyte 235/926 5.59E- 0.005498 0.00493 ATA3/RARA/EXO 02696 activation 20/294 3 05 79 983 SC6 20 T cell differentiatio FOXP1/NLRP3/IL n involved in 18/RC3H1/BCL3/I GO:00 immune 5.90E- 0.005646 0.00507 L23R/TNFSF4/GA 02292 response 9/294 56/9263 05 57 259 TA3/RARA 9 CD4- positive, alpha-beta T FOXP1/NLRP3/IL cell 18/RC3H1/BCL3/I GO:00 differentiatio 6.81E- 0.006349 0.00570 L23R/TNFSF4/GA 43367 n 9/294 57/9263 05 78 432 TA3/RARA 9 CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/FLT3L G/CD5/LAMP1/L MO4/IL23R/HSPD 1/TSPAN32/LAT/ TNFSF4/RAC1/A RG2/CDC42/ADA regulation of M8/CSK/GATA3/ GO:00 cell 381/926 7.46E- 0.006772 0.00608 RARA/EXOSC6/T 50865 activation 27/294 3 05 55 411 EC 27 PCBP2/HSF1/CD 6/FOXP1/HSPA1 B/IL17RA/NLRP3/ CD81/IL18/IRAK3/ DDX3X/LTB/CD2 8/HDAC9/HSPA1 A/BCL3/TXK/PLC G2/IFNGR1/IL23R /HSPD1/TMSB4X/ TNFSF4/RAC1/A regulation of RG2/ADAM8/CSK GO:00 cytokine 468/926 7.76E- 0.006867 0.00616 /ARRB2/GATA3/R 01817 production 31/294 3 05 07 902 GCC/RARA 31 CD6/RASAL3/NL RP3/GRAP2/CD8 1/IL18/CD28/FLT3 positive LG/CD5/LAMP1/I regulation of L23R/HSPD1/TNF GO:00 cell 241/926 7.96E- 0.006874 0.00617 SF4/RAC1/CDC4 50867 activation 20/294 3 05 11 535 2/ADAM8/CSK/G 20

ATA3/RARA/EXO SC6 GRAP2/CD81/CD T cell 28/CD5/TNFSF4/ GO:00 costimulatio 8.54E- 0.007011 0.00629 RAC1/CDC42/CS 31295 n 8/294 46/9263 05 77 902 K 8 CD6/RASAL3/CA SP3/CD164/NLRP 3/GRAP2/CD81/IL 18/RC3H1/DOCK 5/CD28/CD5/SPO CK2/TNR/IL23R/A DAM19/HSPD1/R SU1/TNFSF4/RA C1/ARG2/CDC42/ ADAM8/CSK/ARH regulation of GDIA/GATA3/RG GO:00 cell 427/926 8.60E- 0.007011 0.00629 CC/RARA/ITGB1 30155 adhesion 29/294 3 05 77 902 BP1 29 NLRP3/CD81/IL1 8/HLA- positive B/CD28/LAMP1/IL regulation of 23R/HSPD1/TNF leukocyte SF4/HLA- GO:00 mediated 102/926 8.78E- 0.007011 0.00629 A/GATA3/EXOSC 02705 immunity 12/294 3 05 77 902 6 12 NLRP3/CD81/IL1 8/RC3H1/HLA- B/CD28/IL23R/HS regulation of PD1/TNFSF4/HLA adaptive - GO:00 immune 118/926 8.91E- 0.007011 0.00629 A/GATA3/EXOSC 02819 response 13/294 3 05 77 902 6/WAS 13 GRAP2/CD81/CD lymphocyte 28/CD5/TNFSF4/ GO:00 costimulatio 0.0001 0.007710 0.00692 RAC1/CDC42/CS 31294 n 8/294 47/9263 0016 21 646 K 8 alpha-beta T RASAL3/CD81/IL GO:00 cell 0.0001 0.007783 0.00699 18/CD28/TNFSF4 46633 proliferation 6/294 25/9263 0332 96 271 /ARG2 6 CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/CD5/IL 23R/HSPD1/TNF leukocyte SF4/RAC1/ARG2/ GO:00 cell-cell 247/926 0.0001 0.008248 0.00740 CDC42/ADAM8/C 07159 adhesion 20/294 3 1181 1 967 SK/GATA3/RARA 20 regulation of T-helper cell NLRP3/IL18/RC3 GO:00 differentiatio 0.0001 0.009226 0.00828 H1/IL23R/TNFSF 45622 n 6/294 26/9263 3077 61 871 4/RARA 6 T cell FOXP1/NLRP3/C activation D81/IL18/RC3H1/ involved in BCL3/IL23R/TNF GO:00 immune 0.0001 0.009226 0.00828 SF4/GATA3/RAR 02286 response 10/294 76/9263 3302 61 871 A 10 regulation of CD4- positive, NLRP3/IL18/RC3 GO:00 alpha-beta T 0.0001 0.009226 0.00828 H1/IL23R/TNFSF 43370 cell 7/294 37/9263 3713 61 871 4/GATA3/RARA 7

differentiatio n positive regulation of T cell GO:00 cytokine 0.0001 0.009226 0.00828 NLRP3/CD81/IL1 02726 production 5/294 17/9263 4071 61 871 8/TNFSF4/GATA3 5 positive regulation of T-helper cell GO:00 differentiatio 0.0001 0.009226 0.00828 NLRP3/IL18/IL23 45624 n 5/294 17/9263 4071 61 871 R/TNFSF4/RARA 5 positive regulation of alpha-beta T GO:00 cell 0.0001 0.009226 0.00828 RASAL3/CD81/IL 46641 proliferation 5/294 17/9263 4071 61 871 18/CD28/TNFSF4 5 YWHAZ/TRADD/ BCL2L12/CASP3/ HSPA1B/GNAI2/X PA/HINT1/DDX3X /MPV17L/MAL/TN FSF12/CD28/RR M2B/CD5/CHCHD 10/LAMP1/HSPA1 A/SLC9A3R1/BCL 3/TMC8/YWHAB/ apoptotic SKIL/ARRB2/JUN GO:00 signaling 440/926 0.0001 0.009364 0.00841 /PPP3CC/STK11/ 97190 pathway 29/294 3 4545 48 257 CDKN2D/IFI6 29 NLRP3/CD81/IL1 8/HLA- T cell B/IL23R/HSPD1/T GO:00 mediated 0.0001 0.009399 0.00844 NFSF4/HLA- 02456 immunity 10/294 77/9263 4866 95 443 A/GATA3/WAS 10 positive regulation of RASAL3/NLRP3/ alpha-beta T CD81/IL18/CD28/I GO:00 cell 0.0001 0.009781 0.00878 L23R/TNFSF4/RA 46635 activation 8/294 50/9263 5745 49 719 RA 8 positive regulation of GO:00 interleukin-5 0.0001 0.010772 0.00967 IL17RA/NLRP3/G 32754 production 4/294 10/9263 7948 11 711 ATA3/RARA 4 regulation of T-helper 2 cell GO:00 differentiatio 0.0001 0.010772 0.00967 NLRP3/IL18/TNF 45628 n 4/294 10/9263 7948 11 711 SF4/RARA 4 positive regulation of NLRP3/CD28/TN GO:00 interleukin-4 0.0001 0.011201 0.01006 FSF4/GATA3/RA 32753 production 5/294 18/9263 898 17 255 RA 5 CD6/RASAL3/CA SP3/NLRP3/GRA P2/CD81/IL18/RC 3H1/CD28/FLT3L G/CD5/LAMP1/IL 23R/HSPD1/TSP regulation of AN32/LAT/TNFSF GO:00 leukocyte 361/926 0.0001 0.011536 0.01036 4/RAC1/ARG2/CD 02694 activation 25/294 3 9874 73 401 C42/ADAM8/CSK/ 25

GATA3/RARA/EX OSC6 alpha-beta T FOXP1/NLRP3/IL cell 18/RC3H1/BCL3/I GO:00 differentiatio 0.0002 0.011611 0.01043 L23R/TCF7/TNFS 46632 n 10/294 80/9263 0518 93 156 F4/GATA3/RARA 10 CD6/NLRP3/CD8 1/IL18/RC3H1/LI ME1/HLA- B/TAP2/CD28/BC L3/TXK/IL23R/HS PD1/LAT/TNFSF4 adaptive /ARG2/CSK/HLA- GO:00 immune 299/926 0.0002 0.011611 0.01043 A/GATA3/EXOSC 02250 response 22/294 3 066 93 156 6/TEC/WAS 22 PCBP2/HSF1/NL RP3/IRAK3/HDAC 9/BCL3/IL23R/TM negative SB4X/TNFSF4/R regulation of AC1/ARG2/CSK/A GO:00 cytokine 182/926 0.0002 0.011847 0.01064 RRB2/GATA3/RG 01818 production 16/294 3 1414 82 347 CC/RARA 16 positive regulation of CD4- positive, alpha-beta T NLRP3/CD81/IL1 GO:20 cell 0.0002 0.013483 0.01211 8/IL23R/TNFSF4/ 00516 activation 6/294 29/9263 4901 73 309 RARA 6 CD6/RASAL3/CA SP3/CD164/NLRP 3/GRAP2/CD81/IL 18/RC3H1/CD28/ CD5/TNR/IL23R/A DAM19/HSPD1/T SPAN32/PCDH9/ TNFSF4/RAC1/A RG2/CDC42/ADA M8/CSK/GATA3/ GO:00 cell-cell 410/926 0.0002 0.013483 0.01211 RGCC/RARA/BL 98609 adhesion 27/294 3 5132 73 309 OC1S4 27 YWHAZ/HSF1/NU P98/HNRNPA0/R C3H1/YBX1/ELAV L1/HSPA1A/SFS WAP/SNRNP70/R BM17/SF3B4/AN regulation of P32A/U2AF2/CPS mRNA F7/YWHAB/KHSR GO:19 metabolic 266/926 0.0003 0.015981 0.01435 P/ZBTB7A/PTBP1 03311 process 20/294 3 0239 28 676 /EXOSC6 20 TNK2/RASAL3/G RAP2/SH3BP1/M APKAP1/ABCA1/ DOCK5/CFL1/SP RY1/STMN3/PSD 4/DNMT1/GDI1/R small AB11B/RAB2A/LA GTPase T/PLEKHG3/RAC mediated 1/TAGAP/CDC42/ GO:00 signal 350/926 0.0003 0.016087 0.01445 ARHGEF18/ARH 07264 transduction 24/294 3 0894 76 242 GDIA/JUN/WAS 24

establishme nt or maintenance of epithelial cell ANK1/SH3BP1/SL GO:00 apical/basal 0.0003 0.016597 0.01491 C9A3R1/MARK2/ 45197 polarity 5/294 20/9263 2597 48 032 CDC42 5 NLRP3/CD81/IL1 8/HLA- B/CD28/LAMP1/IL regulation of 23R/HSPD1/TNF leukocyte SF4/HLA- GO:00 mediated 152/926 0.0003 0.016597 0.01491 A/ARRB2/GATA3/ 02703 immunity 14/294 3 2811 48 032 EXOSC6/WAS 14 GO:00 Golgi 0.0004 0.019664 0.01766 YWHAZ/SLC9A3 51645 localization 4/294 12/9263 0227 57 564 R1/CDC42/STK11 4 regulation of T cell GO:00 cytokine 0.0004 0.019664 0.01766 NLRP3/CD81/IL1 02724 production 5/294 21/9263 1682 57 564 8/TNFSF4/GATA3 5 regulation of NLRP3/CD28/TN GO:00 interleukin-4 0.0004 0.019664 0.01766 FSF4/GATA3/RA 32673 production 5/294 21/9263 1682 57 564 RA 5 establishme nt or maintenance of ANK1/SH3BP1/SL GO:00 apical/basal 0.0004 0.019664 0.01766 C9A3R1/MARK2/ 35088 cell polarity 5/294 21/9263 1682 57 564 CDC42 5 establishme nt or maintenance ANK1/SH3BP1/SL GO:00 of bipolar 0.0004 0.019664 0.01766 C9A3R1/MARK2/ 61245 cell polarity 5/294 21/9263 1682 57 564 CDC42 5 regulation of interleukin- FOXP1/IRAK3/LT GO:00 12 0.0004 0.019664 0.01766 B/IL23R/HSPD1/T 32655 production 7/294 44/9263 2206 57 564 NFSF4/ARRB2 7 interleukin- FOXP1/IRAK3/LT GO:00 12 0.0004 0.022370 0.02009 B/IL23R/HSPD1/T 32615 production 7/294 45/9263 8644 01 606 NFSF4/ARRB2 7 BCL2L12/RASAL 3/GNAI2/SESN1/ NLRP3/IRAK3/DD X3X/SH3BP1/MA PKAP1/RRM2B/C RTC3/SPRY1/TA OK3/HSPA1A/ST negative MN3/SLC9A3R1/ regulation of TMSB4X/CSK/AR intracellular RB2/STK11/ITGB GO:19 signal 340/926 0.0004 0.022651 0.02034 1BP1/CDKN2D/C 02532 transduction 23/294 3 9896 49 894 ALM3 23 HSF1/MXD4/CAS P3/HSPA1B/CD1 64/RC3H1/SPRY1 /HSPA1A/SLC9A3 negative R1/KLF13/TSPAN regulation of 32/HPGDS/ARG2/ cell CSK/DACH1/JUN/ GO:00 population 384/926 0.0005 0.022683 0.02037 GATA3/SKI/RGC 08285 proliferation 25/294 3 0608 84 8 C/RARA/SF1/STK 25

11/ITGB1BP1/CD KN2D/PTGDR2 FOXP1/NLRP3/G RAP2/CD81/IL18/ RC3H1/LIME1/HL A- B/KRT1/CD28/LA MP1/TXK/PLCG2/ IL23R/HSPD1/LA T/TNFSF4/RAC1/ CDC42/ADAM8/C positive SK/HLA- regulation of A/GATA3/RGCC/ GO:00 immune 475/926 0.0005 0.023239 0.02087 RARA/EXOSC6/T 50778 response 29/294 3 2503 12 683 EC/STK11/WAS 29 RASAL3/GRAP2/ MAPKAP1/ABCA 1/CFL1/SPRY1/S TMN3/PSD4/DNM T1/GDI1/RAB11B/ RAB2A/LAT/PLEK Ras protein HG3/RAC1/CDC4 GO:00 signal 278/926 0.0005 0.023393 0.02101 2/ARHGEF18/AR 07265 transduction 20/294 3 3512 29 533 HGDIA/JUN/WAS 20 GO:00 interleukin-5 0.0005 0.024173 0.02171 IL17RA/NLRP3/G 32634 production 4/294 13/9263 6661 19 595 ATA3/RARA 4 regulation of GO:00 interleukin-5 0.0005 0.024173 0.02171 IL17RA/NLRP3/G 32674 production 4/294 13/9263 6661 19 595 ATA3/RARA 4 EMC10/PFN1/FO XP1/SH3BP1/TNF SF12/DOCK5/HD AC9/TMSB4X/JU N/GATA3/RGCC/I GO:00 epithelial cell 161/926 0.0005 0.024547 0.02205 TGB1BP1/GIPC1/ 10631 migration 14/294 3 8925 25 199 CORO1B 14 EMC10/PFN1/FO XP1/SH3BP1/TNF SF12/DOCK5/HD AC9/TMSB4X/JU N/GATA3/RGCC/I GO:00 epithelium 161/926 0.0005 0.024547 0.02205 TGB1BP1/GIPC1/ 90132 migration 14/294 3 8925 25 199 CORO1B 14 regulation of mitochondria l outer membrane permeabiliza tion involved YWHAZ/MPV17L/ in apoptotic CHCHD10/HSPA GO:19 signaling 0.0006 0.025403 0.02282 1A/YWHAB/PPP3 01028 pathway 6/294 34/9263 1697 24 097 CC 6 EMC10/PFN1/FO XP1/SH3BP1/TNF SF12/DOCK5/HD AC9/TMSB4X/JU N/GATA3/RGCC/I GO:00 tissue 162/926 0.0006 0.025517 0.02292 TGB1BP1/GIPC1/ 90130 migration 14/294 3 2695 7 379 CORO1B 14 GO:00 tube 0.0006 0.025637 0.02303 PFN1/CASP3/CF 35148 formation 9/294 76/9263 3713 15 11 L1/LMO4/SEMA4 9

C/GATA3/SKI/RA RA/ITGB1BP1 positive regulation of CD4- positive, alpha-beta T cell GO:00 differentiatio 0.0006 0.026031 0.02338 NLRP3/IL18/IL23 43372 n 5/294 23/9263 5427 14 504 R/TNFSF4/RARA 5 NLRP3/CD81/IL1 8/HLA- B/CD28/LAMP1/B CL3/IL23R/HSPD lymphocyte 1/TNFSF4/HLA- GO:00 mediated 182/926 0.0006 0.026243 0.02357 A/ARRB2/GATA3/ 02449 immunity 15/294 3 6703 82 61 EXOSC6/WAS 15 YWHAZ/MPV17L/ CHCHD10/HSPA apoptotic 1A/HSPD1/YWHA GO:00 mitochondria 0.0007 0.027261 0.02449 B/ARRB2/JUN/PP 08637 l changes 10/294 93/9263 006 77 058 P3CC/IFI6 10 CD4- positive, alpha-beta T GO:00 cell cytokine 0.0007 0.029453 0.02645 NLRP3/CD81/IL1 35743 production 4/294 14/9263 7356 54 955 8/GATA3 4 semaphorin- plexin SH3BP1/RAC1/A GO:00 signaling 0.0007 0.029453 0.02645 RHGDIA/SEMA4 71526 pathway 4/294 14/9263 7356 54 955 C 4 EMC10/PFN1/FO XP1/SH3BP1/TNF SF12/DOCK5/CF L1/HDAC9/TMSB 4X/JUN/SEMA4C/ ameboidal- GATA3/RGCC/IT GO:00 type cell 205/926 0.0008 0.030393 0.02730 GB1BP1/GIPC1/C 01667 migration 16/294 3 0684 83 426 ORO1B 16 SH3BP1/CFL1/SP RY1/SLC9A3R1/ establishme MARK2/CDC42/G GO:00 nt of cell 0.0008 0.031576 0.02836 ATA3/STK11/FAM 30010 polarity 9/294 79/9263 4717 99 715 89B 9 JUNB/HSF1/CD6/ FOXP1/CASP3/N FKBIB/NLRP3/HN RNPA0/IL18/IRAK response to 3/ABCA1/PLCG2/I GO:00 lipopolysacc 228/926 0.0009 0.034139 0.03066 L23R/TNFSF4/JU 32496 haride 17/294 3 3407 06 878 N/PLSCR3/RARA 17 regulation of alpha-beta T cell NLRP3/IL18/RC3 GO:00 differentiatio 0.0009 0.034139 0.03066 H1/IL23R/TNFSF 46637 n 7/294 50/9263 3519 06 878 4/GATA3/RARA 7 YWHAZ/TRADD/ BCL2L12/HSPA1 regulation of B/GNAI2/DDX3X/ apoptotic MPV17L/MAL/TN GO:20 signaling 291/926 0.0009 0.034309 0.03082 FSF12/RRM2B/C 01233 pathway 20/294 3 4953 13 156 HCHD10/HSPA1A 20

/SLC9A3R1/TMC 8/YWHAB/SKIL/A RRB2/PPP3CC/C DKN2D/IFI6 EMC10/FOXP1/S H3BP1/TNFSF12/ HDAC9/TMSB4X/ endothelial GATA3/RGCC/IT GO:00 cell 114/926 0.0009 0.034404 0.03090 GB1BP1/GIPC1/C 43542 migration 11/294 3 6189 49 723 ORO1B 11 positive regulation of actin filament PFN1/SORBS3/R GO:00 bundle 0.0009 0.034520 0.03101 AC1/CDC42/RGC 32233 assembly 6/294 37/9263 8464 97 187 C/ITGB1BP1 6 negative regulation of tumor necrosis HSF1/IRAK3/BCL GO:00 factor 0.0009 0.034520 0.03101 3/ARG2/ARRB2/R 32720 production 6/294 37/9263 8464 97 187 ARA 6 PFN1/SORBS3/R regulation of AC1/CDC42/RGC GO:00 stress fiber 0.0010 0.036627 0.03290 C/ITGB1BP1/WA 51492 assembly 7/294 51/9263 5506 13 393 S 7 embryonic PFN1/CASP3/CF epithelial L1/LMO4/SEMA4 GO:00 tube 0.0010 0.037337 0.03354 C/GATA3/SKI/RA 01838 formation 8/294 66/9263 8608 8 236 RA 8 CASP3/MORF4L2 /CD81/FLT3LG/H DAC9/DNMT1/G6 muscle cell PD/PTBP1/CDC4 GO:00 differentiatio 153/926 0.0011 0.038480 0.03456 2/ARRB2/SEMA4 42692 n 13/294 3 388 69 908 C/SKI/RARA 13 PCBP2/NLRP3/C D81/IL18/RC3H1/I RAK3/HLA- B/CD28/LAMP1/IL 23R/HSPD1/TSP AN32/TNFSF4/HL regulation of A- immune A/ARRB2/GATA3/ GO:00 effector 274/926 0.0011 0.038480 0.03456 RARA/EXOSC6/ 02697 process 19/294 3 4105 69 908 WAS 19 NLRP3/CD28/TN GO:00 interleukin-4 0.0011 0.039197 0.03521 FSF4/GATA3/RA 32633 production 5/294 26/9263 8306 58 309 RA 5 CD6/HSPA1B/IL1 7RA/NLRP3/CD8 1/IL18/DDX3X/LT B/CD28/HSPA1A/ BCL3/TXK/PLCG positive 2/IFNGR1/IL23R/ regulation of HSPD1/TNFSF4/ GO:00 cytokine 318/926 0.0011 0.039197 0.03521 ADAM8/GATA3/R 01819 production 21/294 3 8445 58 309 GCC/RARA 21 PFN1/CASP3/CF epithelial L1/LMO4/SEMA4 GO:00 tube 0.0012 0.039346 0.03534 C/GATA3/SKI/RA 72175 formation 8/294 67/9263 0007 86 72 RA 8

negative regulation of tumor necrosis factor superfamily HSF1/IRAK3/BCL GO:19 cytokine 0.0013 0.042218 0.03792 3/ARG2/ARRB2/R 03556 production 6/294 39/9263 1033 06 654 ARA 6 morphogene PFN1/CASP3/CF sis of L1/LMO4/SEMA4 GO:00 embryonic 0.0013 0.042218 0.03792 C/GATA3/SKI/RA 16331 epithelium 8/294 68/9263 2341 06 654 RA 8 regulation of IL18/BCL3/TXK/IL interferon- 23R/HSPD1/TNF GO:00 gamma 0.0013 0.042218 0.03792 SF4/GATA3/RAR 32649 production 8/294 68/9263 2341 06 654 A 8 JUNB/HSF1/CD6/ FOXP1/CASP3/N FKBIB/NLRP3/HN response to RNPA0/IL18/IRAK molecule of 3/ABCA1/PLCG2/I GO:00 bacterial 236/926 0.0013 0.043155 0.03876 L23R/TNFSF4/JU 02237 origin 17/294 3 6499 73 889 N/PLSCR3/RARA 17 GADD45A/GADD 45G/CD81/IL18/U BE2S/DDX3X/MA PKAP1/TAOK3/D GKZ/JTB/MARK2/ RPS2/LMO4/PFK FB2/IL23R/LAT/T MSB4X/AXIN1/SE positive RINC5/ADAM8/C regulation of SK/RGCC/STK11/ GO:00 transferase 412/926 0.0013 0.043531 0.03910 ITGB1BP1/CALM 51347 activity 25/294 3 8916 04 605 3 25 T cell GO:00 cytokine 0.0014 0.043561 0.03913 NLRP3/CD81/IL1 02369 production 5/294 27/9263 1474 7 359 8/TNFSF4/GATA3 5 positive NUP98/HSPA1A/ GO:00 regulation of 0.0014 0.043561 0.03913 SNRNP70/SF3B4/ 33120 RNA splicing 5/294 27/9263 1474 7 359 U2AF2 5 FOXP1/NLRP3/IL 18/RC3H1/IRF2B P2/CD28/FLT3LG /HDAC9/BCL3/PL CG2/IL23R/TCF7/ lymphocyte TNFSF4/ZBTB7A/ GO:00 differentiatio 258/926 0.0014 0.043639 0.03920 ADAM8/GATA3/R 30098 n 18/294 3 296 67 364 ARA/STK11 18 CD6/RASAL3/CA regulation of SP3/CD81/IL18/R GO:00 T cell 103/926 0.0015 0.046823 0.04206 C3H1/CD28/IL23 42129 proliferation 10/294 3 4901 46 379 R/TNFSF4/ARG2 10 EMC10/PFN1/FO positive XP1/DOCK5/HDA regulation of C9/TMSB4X/JUN/ GO:00 epithelial cell 0.0015 0.046823 0.04206 GATA3/ITGB1BP 10634 migration 9/294 86/9263 6034 46 379 1 9 NLRP3/CD81/IL1 positive 8/HLA- GO:00 regulation of 159/926 0.0016 0.048142 0.04324 B/CD28/LAMP1/IL 02699 immune 13/294 3 179 73 895 23R/HSPD1/TNF 13

effector SF4/HLA- process A/GATA3/RARA/E XOSC6 regulation of PFN1/SORBS3/R actomyosin AC1/CDC42/RGC GO:01 structure 0.0016 0.048983 0.04400 C/ITGB1BP1/WA 10020 organization 7/294 55/9263 6 89 461 S 7 ANK1/SH3BP1/M establishme APKAP1/CFL1/SP nt or RY1/SLC9A3R1/ maintenance MARK2/CDC42/G GO:00 of cell 122/926 0.0016 0.049083 0.04409 ATA3/STK11/FAM 07163 polarity 11/294 3 7725 93 448 89B 11 positive regulation of natural killer GO:00 cell 0.0017 0.049512 0.04447 IL18/FLT3LG/LAM 32816 activation 4/294 17/9263 0588 51 949 P1/IL23R 4

Table S8: Primers for bulk RNA-Seq Barcoded primers for reverse transcription and final library amplification in bulk RNA- Seq Reverse transcription primers for 5 ILC sorted from blood (raw reads deposited in GSM5134071) donor 1 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNGTTGCATTTTTTTTTTTTTTTTTTTTTTTTV donor 2 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNACCATGTTTTTTTTTTTTTTTTTTTTTTTTV donor 3 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNACTCGATTTTTTTTTTTTTTTTTTTTTTTTV donor 4 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNACGTACTTTTTTTTTTTTTTTTTTTTTTTTV donor 5 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNCTGTGATTTTTTTTTTTTTTTTTTTTTTTTV Reverse transcription primers for 4 ILC samples sorted from blood (raw reads deposited in GSM5134072) donor1 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNTCACCATTTTTTTTTTTTTTTTTTTTTTTTV donor2 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNTCTGTCTTTTTTTTTTTTTTTTTTTTTTTTV donor3 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNGTTGAGTTTTTTTTTTTTTTTTTTTTTTTTV donor4 ILCs: GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNACAGACTTTTTTTTTTTTTTTTTTTTTTTTV Final library amplification primers for all libraries: RP1: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GA RPI1: CAA GCA GAA GAC GGC ATA CGA GAT CGT GAT GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA