Table S1
Relation of participant characteristics to FEV1/FVC ratio at enrollment, exacerbation and convalescent visits
FEV1/FVC RatioEnrollment (n=40) / Exacerbation (n=36) / Convalescent (n=36)
n / mean (SD) / n / mean (SD) / n / mean (SD)
Ethnicity / Non-Hispanic / 10 / 84.4 (4.3) / 10 / 85.2 (7.3) / 9 / 85.4 (4.6)
Hispanic / 30 / 84.9 (6.2) / 26 / 83.3 (5.4) / 27 / 84.7 (6.5)
p-valueA / 0.8 / 0.4 / 0.8
Gender / Female / 22 / 85.0 (5.8) / 19 / 86.1 (6.3) / 20 / 85.2 (5.6)
Male / 18 / 84.6 (5.7) / 17 / 81.3 (4.5) / 16 / 84.4 (6.7)
p-valueA / 0.8 / 0.01 / 0.7
Ever Hospitalized
for Asthma / No / 34 / 84.7 (5.9) / 30 / 83.7 (6.3) / 31 / 84.4 (5.9)
Yes / 6 / 85.8 (4.5) / 6 / 84.3 (3.7) / 5 / 87.8 (6.2)
p-valueA / 0.7 / 0.8 / 0.2
Aeroallergen skin
test positive / No / 10 / 84.4 (7.6) / 9 / 83.1 (5.2) / 9 / 83.9 (6.0)
Yes / 27 / 84.9 (5.0) / 24 / 84.4 (6.5) / 24 / 84.9 (5.9)
p-valueA / 0.8 / 0.6 / 0.7
Picornavirus positive
at exacerbation / No / 19 / 83.7 (5.0) / 18 / 82.6 (4.1) / 17 / 84.2 (5.7)
Yes / 17 / 85.9 (6.6) / 14 / 84.0 (6.4) / 16 / 85.8 (6.6)
p-valueA / 0.3 / 0.5 / 0.5
Concurrent Medication
Use / Combo - / ICS - / 15 / 85.7 (5.7) / 9 / 84.9 (7.9) / 9 / 87.3 (5.0)
Combo - / ICS + / 12 / 82.3 (6.3) / 13 / 81.6 (6.3) / 14 / 81.5 (6.1)
Combo + / ICS - / 13 / 86.2 (4.8) / 14 / 85.1 (3.6) / 13 / 86.8 (5.3)
p-valueA / 0.2 / 0.3 / 0.02
A The p-values were calculated with t.test or Anova. Abbreviations: Combo, combination therapy; ICS, inhaled corticosteroids. High quality lung function data was available for all subjects at enrollment, but was either missing or did not meet ATS guidelines for some subjects during the exacerbation or at convalescence.
Table S2
Complete set of genes identified in module III from Figure 1 - the “Th1-like/cytotoxic pathway”.
Probe ID / Gene Symbol / Gene name / Chromosome8140782 / ABCB1 / ATP-binding cassette, sub-family B (MDR/TAP), member 1 / 7q21.1
8115490 / ADAM19 / ADAM metallopeptidase domain 19 (meltrin beta) / 5q32-q33
8150375 / ADAM3A / ADAM metallopeptidase domain 3A (cyritestin 1) / 8p21-p12
7918533 / ADORA3 / adenosine A3 receptor / 1p13.2
7934898 / ANKRD22 / ankyrin repeat domain 22 / 10q23.31
8075695 / APOL3 / apolipoprotein L, 3 / 22q13.1
7985285 / ARNT2 / aryl-hydrocarbon receptor nuclear translocator 2 / 15q24
8030557 / ATF5 / activating transcription factor 5 / 19q13.3
7949340 / BATF2 / basic leucine zipper transcription factor, ATF-like 2 / 11q13.1
8023646 / BCL2 / B-cell CLL/lymphoma 2 / 18q21.3
7953993 / BCL2L14 / BCL2-like 14 (apoptosis facilitator) / 12p13-p12
7979721 / C14orf83 / chromosome 14 open reading frame 83 / 14q24.1
8111925 / C5orf39 / chromosome 5 open reading frame 39 / 5p12
7982757 / CASC5 / cancer susceptibility candidate 5 / 15q14
8006440 / CCL7 / chemokine (C-C motif) ligand 7 / 17q11.2-q12
8006453 / CCL8 / chemokine (C-C motif) ligand 8 / 17q11.2
8079401 / CCR5 / chemokine (C-C motif) receptor 5 / 3p21.31
7960771 / CD163L1 / CD163 molecule-like 1 / 12p13.3
8047677 / CD28 / CD28 molecule / 2q33
8018189 / CD300E / CD300e molecule / 17q25.1
8094240 / CD38 / CD38 molecule / 4p15
7940409 / CD5 / CD5 molecule / 11q13
7902913 / CDC7 / cell division cycle 7 homolog (S. cerevisiae) / 1p22
8140955 / CDK6 / cyclin-dependent kinase 6 / 7q21-q22
7934916 / CH25H / cholesterol 25-hydroxylase / 10q23
7966089 / CMKLR1 / chemokine-like receptor 1 / 12q24.1
8050102 / CMPK2 / cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial / 2p25.2
7985159 / CRABP1 / cellular retinoic acid binding protein 1 / 15q24
8047692 / CTLA4 / cytotoxic T-lymphocyte-associated protein 4 / 2q33
8101126 / CXCL10 / chemokine (C-X-C motif) ligand 10 / 4q21
8101131 / CXCL11 / chemokine (C-X-C motif) ligand 11 / 4q21.2
8101118 / CXCL9 / chemokine (C-X-C motif) ligand 9 / 4q21
7934026 / DNA2 / DNA replication helicase 2 homolog (yeast) / 10q21.3-q22.1
8152522 / ENPP2 / ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) / 8q24.1
8123744 / F13A1 / coagulation factor XIII, A1 polypeptide / 6p25.3-p24.3
8106393 / F2R / coagulation factor II (thrombin) receptor / 5q13
8017867 / FAM20A / family with sequence similarity 20, member A / 17q24.2
8121596 / FAM26F / family with sequence similarity 26, member F / 6q22.1
8136115 / FAM40B / family with sequence similarity 40, member B / 7q32.1
8004195 / FBXO39 / F-box protein 39 / 17p13.2
7906777 / FCGR2B / Fc fragment of IgG, low affinity IIb, receptor (CD32) / 1q23
8027856 / FFAR3 / free fatty acid receptor 3 / 19q13.1
8030094 / FUT2 / fucosyltransferase 2 (secretor status included) / 19q13.3
7970329 / GAS6 / growth arrest-specific 6 / 13q34
7902850 / GBP6 / guanylate binding protein family, member 6 / 1p22.2
8137244 / GIMAP4 / GTPase, IMAP family member 4 / 7q36.1
8137257 / GIMAP5 / GTPase, IMAP family member 5 / 7q36.1
8137240 / GIMAP7 / GTPase, IMAP family member 7 / 7q36.1
8137232 / GIMAP8 / GTPase, IMAP family member 8 / 7q36.1
8043236 / GNLY / granulysin / 2p11.2
8091503 / GPR171 / G protein-coupled receptor 171 / 3q25.1
7978366 / GZMB / granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) / 14q11.2
8105331 / GZMK / granzyme K (granzyme 3; tryptase II) / 5q11-q12
8027819 / HAMP / hepcidin antimicrobial peptide / 19q13.1
7991224 / HAPLN3 / hyaluronan and proteoglycan link protein 3 / 15q26.1
8096335 / HERC6 / hect domain and RLD 6 / 4q22.1
8088285 / HESX1 / HESX homeobox 1 / 3p14.3
8005097 / HS3ST3B1 / heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 / 17p12-p11.2
8160360 / IFNB1 / interferon, beta 1, fibroblast / 9p21
7964787 / IFNG / interferon, gamma / 12q14
7923907 / IL10 / interleukin 10 / 1q31-q32
7902205 / IL12RB2 / interleukin 12 receptor, beta 2 / 1p31.3-p31.2
8097553 / IL15 / interleukin 15 / 4q31
7931899 / IL15RA / interleukin 15 receptor, alpha / 10p15-p14
8102707 / IL21 / interleukin 21 / 4q26-q27
7931914 / IL2RA / interleukin 2 receptor, alpha / 10p15-p14
8038487 / IL4I1 / interleukin 4 induced 1 / 19q13.3-q13.4
8146092 / INDO / indoleamine-pyrrole 2,3 dioxygenase / 8p12-p11
8116559 / IRF4 / interferon regulatory factor 4 / 6p25-p23
7969482 / IRG1 / Immunoresponsive 1 homolog / 13q22.3
7896817 / ISG15 / ISG15 ubiquitin-like modifier / 1p36.33
8078619 / ITGA9 / integrin, alpha 9 / 3p21.3
7985317 / KIAA1199 / KIAA1199 / 15q24
7974214 / KLHDC1 / kelch domain containing 1 / 14q22.1
7953949 / KLRD1 / killer cell lectin-like receptor subfamily D, member 1 / 12p13
8025382 / LASS4 / LAG1 homolog, ceramide synthase 4 / 19p13.2
8039180 / LILRB5 / leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5 / 19q13.4
8044391 / MERTK / c-mer proto-oncogene tyrosine kinase / 2q14.1
7937020 / MKI67 / antigen identified by monoclonal antibody Ki-67 / 10q25-qter
7940253 / MS4A6E / membrane-spanning 4-domains, subfamily A, member 6E / 11q12.2
8151101 / MYBL1 / v-myb myeloblastosis viral oncogene homolog (avian)-like 1 / 8q22
8038809 / NKG7 / natural killer cell group 7 sequence / 19q13.33
8136967 / OR2A5 / olfactory receptor, family 2, subfamily A, member 5 / 7q35
7939942 / OR5D14 / olfactory receptor, family 5, subfamily D, member 14 / 11q11
7906374 / OR6K6 / olfactory receptor, family 6, subfamily K, member 6 / 1q23.1
8011415 / P2RX5 / purinergic receptor P2X, ligand-gated ion channel, 5 / 17p13.3
7905116 / PLEKHO1 / pleckstrin homology domain containing, family O member 1 / 1q21.2
7934161 / PRF1 / perforin 1 (pore forming protein) / 10q22
8009301 / PRKCA / protein kinase C, alpha / 17q22-q23.2
7931930 / PRKCQ / protein kinase C, theta / 10p15
7974366 / PTGER2 / prostaglandin E receptor 2 (subtype EP2), 53kDa / 14q22
7908125 / RGL1 / ral guanine nucleotide dissociation stimulator-like 1 / 1q25.3
8018731 / RHBDF2 / rhomboid 5 homolog 2 (Drosophila) / 17q25.1
7973110 / RNASE2 / ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin) / 14q24-q31
7929976 / RP11-529I10.4 / deleted in a mouse model of primary ciliary dyskinesia / 10q24.32
8040223 / RRM2 / ribonucleotide reductase M2 polypeptide / 2p25-p24
8084732 / RTP4 / receptor (chemosensory) transporter protein 4 / 3q27.3
7913805 / RUNX3 / runt-related transcription factor 3 / 1p36
8129482 / SAMD3 / sterile alpha motif domain containing 3 / 6q23.1
7966621 / SDS / serine dehydratase / 12q24.13
8169792 / SH2D1A / SH2 domain protein 1A, Duncan's disease (lymphoproliferative syndrome) / Xq25-q26
8066038 / SLA2 / Src-like-adaptor 2 / 20q11.23
7921652 / SLAMF1 / signaling lymphocytic activation molecule family member 1 / 1q22-q23
8060745 / SMOX / spermine oxidase / 20p13
7999423 / SOCS1 / suppressor of cytokine signaling 1 / 16p13.13
8009526 / SSTR2 / somatostatin receptor 2 / 17q24
8080344 / STAB1 / stabilin 1 / 3p21.1
8057771 / STAT4 / signal transducer and activator of transcription 4 / 2q32.2-q32.3
7922337 / TNFSF18 / tumor necrosis factor (ligand) superfamily, member 18 / 1q23
8081537 / TRAT1 / T cell receptor associated transmembrane adaptor 1 / 3q13
8035896 / TSHZ3 / teashirt zinc finger homeobox 3 / 19q12
8100210 / TXK / TXK tyrosine kinase / 4p12
8019842 / TYMS / thymidylate synthetase / 18p11.32
8074606 / USP18 / ubiquitin specific peptidase 41 / 22q11.21
8071155 / USP18 / ubiquitin specific peptidase 18 / 22q11.21
Table S3
Complete set of genes identified in module IV from Figure 1 - the “interferon signalling pathway”.
Probe ID / Gene Symbol / Gene name / Chromosome8073088 / APOBEC3G / apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G / 22q13.1-q13.2
8072735 / APOL1 / apolipoprotein L, 1 / 22q13.1
8072710 / APOL6 / apolipoprotein L, 6 / 22q12.3
8170794 / AVPR2 / arginine vasopressin receptor 2 (nephrogenic diabetes insipidus) / Xq28
8127534 / C6orf150A / chromosome 6 open reading frame 150 / 6q13
8006433 / CCL2 / chemokine (C-C motif) ligand 2 / 17q11.2-q12
8154233 / CD274B / CD274 molecule / 9p24
8063156 / CD40B / CD40 molecule, TNF receptor superfamily member 5 / 20q12-q13.2
8089771 / CD80 / CD80 molecule / 3q13.3-q21
7927710 / CDC2 / cell division cycle 2, G1 to S and G2 to M / 10q21.1
8099760 / CENTD1 / centaurin, delta 1 / 4p14
8067140 / CYP24A1B / cytochrome P450, family 24, subfamily A, polypeptide 1 / 20q13
8103563 / DDX60A / DEAD (Asp-Glu-Ala-Asp) box polypeptide 60 / 4q32.3
8015511 / DHX58B / DEXH (Asp-Glu-X-His) box polypeptide 58 / 17q21.2
8051501 / EIF2AK2(PKR)A / eukaryotic translation initiation factor 2-alpha kinase 2 / 2p22-p21
7971296 / EPSTI1A / epithelial stromal interaction 1 (breast) / 13q13.3
8006836 / FLJ43826 / FLJ43826 protein / 17q12
8119198 / FTSJD2 / FtsJ methyltransferase domain containing 2 / 6p21.2
7917561 / GBP4 / guanylate binding protein 4 / 1p22.2
7917548 / GBP7 / guanylate binding protein 7 / 1p22.2
7979269 / GCH1 / GTP cyclohydrolase 1 (dopa-responsive dystonia) / 14q22.1-q22.2
8078569 / GOLGA4 / golgi autoantigen, golgin subfamily a, 4 / 3p22-p21.3
8096361 / HERC5A / hect domain and RLD 5 / 4q22.1
8007446 / IFI35 / interferon-induced protein 35 / 17q21
7902553 / IFI44A / interferon-induced protein 44 / 1p31.1
7902541 / IFI44LA / interferon-induced protein 44-like / 1p31.1
7914127 / IFI6B / interferon, alpha-inducible protein 6 / 1p35
8056285 / IFIH1B / interferon induced with helicase C domain 1 / 2q24
7929065 / IFIT1A / interferon-induced protein with tetratricopeptide repeats 1 / 10q25-q26
7929052 / IFIT3A / interferon-induced protein with tetratricopeptide repeats 3 / 10q24
7929072 / IFIT5A / interferon-induced protein with tetratricopeptide repeats 5 / 10q23.31
7945371 / IFITM3 / interferon induced transmembrane protein 3 (1-8U) / 11p15.5
7945462 / IRF7 / interferon regulatory factor 7 / 11p15.5
8046695 / ITGA4 / integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) / 2q31.3
8037898 / KPTN / kaptin (actin binding protein) / 19q13.32
8092348 / LAMP3 / lysosomal-associated membrane protein 3 / 3q26.3-q27
7994541 / LAT / linker for activation of T cells / 16p11.2
8031223 / LILRB1A / leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1 / 19q13.4
7896759 / LOC643837 / hypothetical LOC643837 / 1p36.33
8111922 / LOC648987B / hypothetical LOC648987 / 5p12
7909898 / MIA3 / melanoma inhibitory activity family, member 3 / 1q41
7904050 / MOV10A / Mov10, Moloney leukemia virus 10, homolog (mouse) / 1p13.2
7948455 / MS4A6AA / membrane-spanning 4-domains, subfamily A, member 6A / 11q12.1
8068713 / MX1A / myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) / 21q22.3
8139433 / MYO1G / myosin IG / 7p13-p11.2
8121861 / NCOA7 / nuclear receptor coactivator 7 / 6q22.31-q22.32
8138842 / NOD1 / nucleotide-binding oligomerization domain containing 1 / 7p15-p14
8137414 / NUB1B / negative regulator of ubiquitin-like proteins 1 / 7q36
7958913 / OAS2B / 2'-5'-oligoadenylate synthetase 2, 69/71kDa / 12q24.2
7958895 / OAS3A / 2'-5'-oligoadenylate synthetase 3, 100kDa / 12q24.2
7967117 / OASL / 2'-5'-oligoadenylate synthetase-like / 12q24.2
8091511 / P2RY14 / purinergic receptor P2Y, G-protein coupled, 14 / 3q24-q25.1
8060722 / PANK2 / pantothenate kinase 2 (Hallervorden-Spatz syndrome) / 20p13
8143327 / PARP12 / poly (ADP-ribose) polymerase family, member 12 / 7q34
7984779 / PMLA / promyelocytic leukemia / 15q22
8052331 / PNPT1A / polyribonucleotide nucleotidyltransferase 1 / 2p15
8172531 / PRAF2 / PRA1 domain family, member 2 / Xp11.23
8022393 / PTPN2 / protein tyrosine phosphatase, non-receptor type 2 / 18p11.3-p11.2
8061247 / RIN2A / Ras and Rab interactor 2 / 20p11.22
8040080 / RSAD2B / radical S-adenosyl methionine domain containing 2 / 2p25.2
8140971 / SAMD9LA / sterile alpha motif domain containing 9-like / 7q21.2-q21.3
7914282 / SDC3 / syndecan 3 / 1pter-p22.3
7906613 / SLAMF7 / SLAM family member 7 / 1q23.1-q24.1
7935639 / SLC25A28B / solute carrier family 25, member 28 / 10q23-q24
8101992 / SLC39A8 / solute carrier family 39 (zinc transporter), member 8 / 4q22-q24
8053484 / ST3GAL5 / ST3 beta-galactoside alpha-2,3-sialyltransferase 5 / 2p11.2
7964119 / STAT2A / signal transducer and activator of transcription 2, 113kDa / 12q13.2
8156688 / TDRD7 / tudor domain containing 7 / 9q22.33
8007483 / TMEM106A / transmembrane protein 106A / 17q21.31
8137264 / TMEM176AA / transmembrane protein 176A / 7q36.1
8092169 / TNFSF10B / tumor necrosis factor (ligand) superfamily, member 10 / 3q26
8102594 / TNIP3A / TNFAIP3 interacting protein 3 / 4q27
7958828 / TRAFD1B / TRAF-type zinc finger domain containing 1 / 12q
7938035 / TRIM22A / tripartite motif-containing 22 / 11p15
8009568 / TTYH2 / tweety homolog 2 (Drosophila) / 17q25.1
8008139 / UBE2Z / ubiquitin-conjugating enzyme E2Z / 17q21.32
8004184 / XAF1A / XIAP associated factor 1 / 17p13.2
8067221 / ZBP1 / Z-DNA binding protein 1 / 20q13.31
The stability of this module was tested using a leave-one-out procedure as detailed in Methods.
A These genes were detected in the same cluster in every iteration of the leave-one-out validation procedure.
B These genes were detected in the same cluster in four out of five iterations of the leave-one-out validation procedure.
Table S4
Complete set of genes identified in module II from Figure 1 - the “epithelial differentiation pathway”.
Probe ID / Gene Symbol / Gene name / Chromosome7953775 / A2ML1 / alpha-2-macroglobulin-like 1 / 12p13.31
7905283 / ANXA9 / annexin A9 / 1q21
8029086 / CEACAM5 / carcinoembryonic antigen-related cell adhesion molecule 5 / 19q13.1-q13.2
8029098 / CEACAM6 / carcinoembryonic antigen-related cell adhesion molecule 6 / 19q13.2
8037053 / CEACAM7 / carcinoembryonic antigen-related cell adhesion molecule 7 / 19q13.2
7902738 / CLCA4 / chloride channel, calcium activated, family member 4 / 1p31-p22
8012126 / CLDN7 / claudin 7 / 17p13
7918768 / DENND2C / DENN/MADD domain containing 2C / 1p13.2
7988350 / DUOX2 / dual oxidase 2 / 15q15.3
7905220 / ECM1 / extracellular matrix protein 1 / 1q21
7908793 / ELF3 / E74-like factor 3 (ets domain transcription factor, epithelial-specific ) / 1q32.2
7999387 / EMP2 / epithelial membrane protein 2 / 16p13.2
7917875 / F3 / coagulation factor III (thromboplastin, tissue factor) / 1p22-p21
8088425 / FAM3D / family with sequence similarity 3, member D / 3p14.2
8005483 / FBXW10 / F-box and WD repeat domain containing 10 / 17p12
8109926 / GABRP / gamma-aminobutyric acid (GABA) A receptor, pi / 5q33-q34
8126820 / GPR110 / G protein-coupled receptor 110 / 6p12.3
7954065 / GPRC5A / G protein-coupled receptor, family C, group 5, member A / 12p13-p12.3
7945680 / H19 / H19, imprinted maternally expressed transcript / 11p15.5
7959102 / HSPB8 / heat shock 22kDa protein 8 / 12q24.23
7981722 / IGHA1 / immunoglobulin heavy constant alpha 1 / 14q32.33
7981601 / IGHD / immunoglobulin heavy constant delta / 14q32.33
7981718 / IGHM / immunoglobulin heavy constant mu / 14q32.33
8053690 / IGKC / immunoglobulin kappa constant / 2p12
7981730 / IGLJ3 / immunoglobulin lambda joining 3 / 22q11.1-q11.2
8044548 / IL1F6 / interleukin 1 family, member 6 (epsilon) / 2q12-q14.1
8015323 / KRT13 / keratin 13 / 17q12-q21.2
8013465 / KRT16 / hypothetical gene supported by BC039169; NM_005557 / 17p11.2
8015387 / KRT17 / keratin 17 / 17q12-q21
7955637 / KRT18 / keratin 18 / 12q13
7963523 / KRT3 / keratin 3 / 12q12-q13
7963534 / KRT4 / keratin 4 / 12q12-q13
7963555 / KRT78 / keratin 78 / 12q13.13
8158167 / LCN2 / lipocalin 2 / 9q34
7969438 / LMO7 / LIM domain 7 / 13q22.2
8043480 / LOC100132426 / 9q21.11
8028600 / LOC342897 / similar to F-box only protein 2 / 19q13.2
8043459 / LOC647506
8043504 / MAL / mal, T-cell differentiation protein / 2cen-q13
7920642 / MUC1 / mucin 1, cell surface associated / 1q21
8033674 / MUC16 / mucin 16, cell surface associated / 19p13.2
8179224 / MUC21 / chromosome 6 open reading frame 205 / 6p21.32
8092978 / MUC4 / mucin 4, cell surface associated / 3q29
7977621 / NDRG2 / NDRG family member 2 / 14q11.2
8063410 / PARD6B / par-6 partitioning defective 6 homolog beta (C. elegans) / 20q13.13
7999253 / PPL / periplakin / 16p13.3
8148548 / PSCA / prostate stem cell antigen / 8q24.2
8163149 / PTPN3 / protein tyrosine phosphatase, non-receptor type 3 / 9q31
8146921 / RDH10 / retinol dehydrogenase 10 (all-trans) / 8q21.11
7991283 / RHCG / Rh family, C glycoprotein / 15q25
7969493 / SCEL / sciellin / 13q22
8021635 / SERPINB2 / serpin peptidase inhibitor, clade B (ovalbumin), member 2 / 18q21.3
8169504 / SLC6A14 / solute carrier family 6 (amino acid transporter), member 14 / Xq23-q24
8109001 / SPINK5 / serine peptidase inhibitor, Kazal type 5 / 5q32
8003875 / SPNS2 / spinster homolog 2 (Drosophila) / 17p13.2
7905544 / SPRR1A / small proline-rich protein 1A / 1q21-q22
7905553 / SPRR1B / small proline-rich protein 1B (cornifin) / 1q21-q22
7920205 / SPRR2A / small proline-rich protein 2A / 1q21-q22
7905548 / SPRR3 / small proline-rich protein 3 / 1q21-q22
7916584 / TACSTD2 / tumor-associated calcium signal transducer 2 / 1p32-p31
8060432 / TGM3 / transglutaminase 3 / 20q11.2
8091411 / TM4SF1 / transmembrane 4 L six family member 1 / 3q21-q25
8100675 / TMPRSS11A / transmembrane protease, serine 11A / 4q13.2
8100701 / TMPRSS11B / transmembrane protease, serine 11B / 4q13.2
8100664 / TMPRSS11D / transmembrane protease, serine 11D / 4q13.2
8095364 / TMPRSS11E / transmembrane protease, serine 11E / 4q13.2
8070467 / TMPRSS2 / transmembrane protease, serine 2 / 21q22.3
7944164 / TMPRSS4 / transmembrane protease, serine 4 / 11q23.3
8012953 / TRIM16 / tripartite motif-containing 16 / 17p11.2
8005475 / TRIM16L / tripartite motif-containing 16-like / 17p11.2
8173941 / TSPAN6 / tetraspanin 6 / Xq22
Table S5
Biological functions of representative genes from the Th1-like/cytotoxic pathway, the interferon signaling pathway, the epithelial differentiation pathway, and Th2-related pathways.
Gene symbol / Biological functionTh1-like/cytotoxic pathway
CXCL10 (IP-10) / Highly expressed during rhinovirus-induced asthma exacerbations. Attracts CD4 T cells, CD8 T cells, and iNKT cells via CXCR3.1
IFN- / IFN-/ induce a robust antiviral state, are essential for immunity to most viruses, and are potent inducers of cytotoxic responses.2, 3
IFN- / Principal Th1 cytokine and macrophage activating factor. Essential for immunity to mycobacterium and some viruses.2
IL-2R / IL-2 signaling regulates immune responses via the maintenance of Treg and induction of activation-induced cell death, promotes the proliferation and differentiation of NK and T cells, and programs antiviral CD8 T cell memory responses.4, 5
IL-15 / Role in development, growth, homeostasis, and cytotoxic function of CD8 T cells, NK and iNKT cells.6
IL-21 / Enhances cytotoxic function of CD8 T cells, NK and iNKT cells 6. Essential for control of chronic viral infections 7. Regulates IgE responses.8, 9
GZMB (granzyme B) / Principal mediator of CD8 T cell and NK cytotoxic responses. Role in antiviral defence.10
PRF1 (perforin-1) / Delivers cytotoxic granules containing granzyme B to induce apoptosis of target cells. Essential for immunity to some viruses.10
Interferon signaling pathway
Mx1 / Induced by IFN-, -, -.11 Traps viral components and inhibits viral replication.12
PKR / Induced by IFN-, -, -.13 Inhibits protein translation via phosphorylation of EIF2α.12
PML / Induced by IFN-/ and IFN-, forms nuclear bodies and inhibits viral replication.14
CCL2 (MCP-1) / Induced by IFN-/.15 Essential for recruitment of macrophages and protection of the alveolar epithelium during respiratory viral infections.16
Epithelial differentiation pathway
ECM1 / Loss-of-function mutations in ECM1 cause Urbach-Wiethe disease, a rare, autosomal recessive disorder characterized by abnormalities in skin and mucous membranes.17
KRT4 / Structural protein expressed in differentiated layers of mucosal and esophageal epithelia [source Entrez Gene].
SPRR3 / Marker of squamous epithelium.18
TMPRSS11D / Trypsin-like protease expressed in bronchial epithelial cells. May play a role in airway remodelling.19
Th2-related pathways
FCER1A / High affinity receptor subunit for IgE which is upregulated on Mo/DC during viral-driven exacerbations in children20 and on DC in viral-driven lung disease in mice.21
IL-5 / Role in the pathogenesis of exacerbations in eosinophilic, refractory form of asthma.22
IL-13 / Mediates cardinal features of asthma and viral-driven lung diseases in mice.23, 24 Role in the pathogenesis of allergen-driven late phase response in humans.25
References
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Table S6
Among those with low sputum squamous cells (less than 30 % of total cells), correlation of gene expression levels in induced sputum during an acute exacerbation with FEV1/FVC ratio at enrollment, exacerbation and convalescent visits.
FEV1/FVC ratioEnrollment (n=21) / Exacerbation (n=17) / Convalescent (n=20)
Gene symbol / Rho / p-valueA / Rho / p-valueA / Rho / p-valueA
Th1-like/cytotoxic pathway
CXCL10 (IP-10) / 0.50 / 0.02 / 0.06 / 0.8 / 0.44 / 0.05
IFN-1 / 0.36 / 0.1 / 0.21 / 0.4 / 0.26 / 0.3
IFN- / 0.72 / 0.0002 / 0.18 / 0.5 / 0.67 / 0.001
IL-2R / 0.54 / 0.01 / 0.03 / 0.9 / 0.53 / 0.02
IL-15 / 0.58 / 0.006 / -0.12 / 0.7 / 0.55 / 0.01
IL-21 / 0.60 / 0.004 / 0.13 / 0.6 / 0.69 / 0.001
GZMB / 0.66 / 0.001 / -0.02 / 0.9 / 0.58 / 0.007
PRF-1 / 0.70 / 0.0005 / 0.22 / 0.4 / 0.65 / 0.002
Interferon signaling pathway
Mx1 / 0.57 / 0.007 / -0.06 / 0.8 / 0.49 / 0.03
PKR / 0.56 / 0.008 / -0.02 / 0.9 / 0.47 / 0.04
PML / 0.49 / 0.03 / -0.11 / 0.7 / 0.36 / 0.1
CCL2 (MCP-1) / 0.62 / 0.003 / 0.14 / 0.6 / 0.53 / 0.02
Epithelial differentiation pathway
ECM1 / 0.17 / 0.5 / -0.10 / 0.7 / 0.21 / 0.4
KRT4 / -0.023 / 0.9 / -0.35 / 0.2 / -0.01 / 0.9
SPPR3 / 0.026 / 0.9 / -0.21 / 0.4 / 0.12 / 0.6
TMPRS11D / 0.034 / 0.9 / -0.14 / 0.6 / 0.13 / 0.6
Th2-related pathways
FCER1A / -0.00 / 0.9 / -0.11 / 0.7 / 0.03 / 0.9
IL-5 / 0.031 / 0.9 / -0.23 / 0.4 / 0.05 / 0.8
IL-13 / 0.15 / 0.5 / 0.11 / 0.7 / 0.13 / 0.6
Reference gene
HMBS / -0.16 / 0.5 / 0.17 / 0.5 / -0.10 / 0.7
A Gene expression levels were measured by qRT-PCR in sputum cells obtained from asthmatic children during an exacerbation. Statistical analysis by Spearman Rank correlation, unadjusted.High quality lung function data was available for all subjects at enrollment, but was either missing or did not meet ATS guidelines for some subjects during the exacerbation or at convalescence.
Table S7
Association of gene expression levels in induced sputum during an acute exacerbation with skin test reactivity to aeroallergens, concurrent picornovirus infection, and variations in the use of medications at the time of the exacerbation, adjusted for percent squamous cells in sputum.
Skin test positive (n=36)A / Picornavirus Positive (n=36)A / MedicationCInhaled corticosteroids (n=14) / Combination
Therapy (n=15)
Gene symbol / Coeff / p-valueB / Coeff / p-valueB / Coeff / p-valueB / Coeff / p-valueB
Th1-like/cytotoxic pathway
CXCL10 (IP-10) / 0.73 / 0.02 / 0.70 / 0.03 / -0.49 / 0.1 / 0.27 / 0.4
IFN-1 / 0.55 / 0.1 / 0.45 / 0.2 / -0.51 / 0.2 / 0.19 / 0.6
IFN- / 0.59 / 0.06 / 0.06 / 0.9 / -0.17 / 0.6 / 0.31 / 0.4
IL-2R / 0.38 / 0.1 / 0.15 / 0.6 / -0.23 / 0.4 / 0.32 / 0.3
IL-15 / 0.17 / 0.2 / 0.11 / 0.5 / -0.21 / 0.2 / 0.14 / 0.4
IL-21 / 0.28 / 0.2 / 0.03 / 0.9 / -0.10 / 0.7 / 0.26 / 0.3
GZMB / 0.55 / 0.03 / 0.21 / 0.5 / -0.28 / 0.3 / 0.10 / 0.7
PRF-1 / 0.53 / 0.5 / 0.25 / 0.4 / -0.33 / 0.3 / 0.05 / 0.9
Interferon signaling pathway
Mx1 / 0.28 / 0.2 / 0.33 / 0.1 / -0.38 / 0.06 / 0.11 / 0.6
PKR / 0.23 / 0.1 / 0.18 / 0.3 / -0.24 / 0.1 / 0.15 / 0.4
PML / 0.13 / 0.5 / 0.32 / 0.08 / -0.30 / 0.1 / -0.17 / 0.4
CCL2 (MCP-1) / 0.41 / 0.1 / 0.34 / 0.2 / -0.43 / 0.1 / 0.25 / 0.4
Epithelial differentiation pathway
ECM1 / 0.39 / 0.08 / -0.11 / 0.6 / 0.17 / 0.5 / 0.44 / 0.08
KRT4 / 0.16 / 0.3 / -0.04 / 0.8 / 0.02 / 0.9 / 0.15 / 0.5
SPPR3 / 0.17 / 0.3 / -0.08 / 0.7 / -0.03 / 0.9 / 0.31 / 0.2
TMPRS11D / 0.23 / 0.1 / -0.11 / 0.6 / 0.11 / 0.6 / 0.31 / 0.1
Th2-related pathways
FCER1A / 0.25 / 0.1 / 0.01 / 0.9 / 0.01 / 0.9 / 0.27 / 0.2
IL-5 / 0.17 / 0.3 / 1.02 / 0.05 / -0.17 / 0.8 / 0.03 / 0.9
IL-13 / 0.25 / 0.6 / 0.58 / 0.1 / 0.18 / 0.7 / 0.12 / 0.8
Reference gene
HMBS / -0.15 / 0.4 / -0.08 / 0.7 / 0.36 / 0.07 / 0.13 / 0.5
Gene expression levels were measured by qRT-PCR in sputum cells obtained from asthmatic children during an acute exacerbation.
ASkin test reactivity and viral data was missing for four subjects.
B Statistical analysis by parametric Tobit regression, adjusted for percent squamous cells as a continuous variable
C The medication variable is included in the model as three categories: Inhaled corticosteroids only, combination therapy only and the reference group, neither inhaled corticosteroids nor combination therapy
Table S8
Linear regression of exacerbation gene expression with enrollment, exacerbation and convalescent FEV1/FVC ratio, adjusted for medicationsA at exacerbation
FEV1/FVC Ratio (%)Enrollment(n=40) / Exacerbation (n=36) / Convalescent (n=36)
Gene symbol / Coeff / p-value / Coeff / p-value / Coeff / p-value
Th1-like/cytotoxic pathway
CXCL10 (IP-10) / 2.73 / 0.02 / -0.02 / 0.9 / 3.90 / 0.001
IFN-1 / 2.03 / 0.05 / 1.23 / 0.3 / 2.61 / 0.02
IFN- / 2.08 / 0.07 / 0.45 / 0.7 / 4.24 / 0.001
IL-2R / 3.27 / 0.01 / 0.04 / 0.9 / 3.86 / 0.005
IL-15 / 5.60 / 0.03 / -2.10 / 0.4 / 7.54 / 0.004
IL-21 / 3.57 / 0.02 / 0.45 / 0.8 / 5.40 / 0.001
GZMB / 3.24 / 0.007 / -0.17 / 0.9 / 4.10 / 0.001
PRF-1 / 3.70 / 0.005 / 1.16 / 0.4 / 4.65 / 0.001
Interferon signaling pathway
Mx1 / 4.81 / 0.007 / -1.15 / 0.6 / 6.68 / <0.001
PKR / 5.37 / 0.02 / -2.48 / 0.3 / 6.16 / 0.01
PML / 4.77 / 0.012 / -0.93 / 0.7 / 6.15 / 0.002
CCL2 (MCP-1) / 3.47 / 0.009 / -0.02 / 0.9 / 4.43 / 0.001
Epithelial differentiation pathway
ECM1 / -0.14 / 0.9 / 0.86 / 0.6 / -0.46 / 0.8
KRT4 / -1.00 / 0.6 / -0.73 / 0.7 / -1.19 / 0.5
SPPR3 / 0.42 / 0.8 / 0.28 / 0.9 / -0.74 / 0.7
TMPRS11D / 0.41 / 0.8 / -0.01 / 0.9 / 0.35 / 0.9
Th2-related pathways
FCER1A / -0.68 / 0.7 / -2.38 / 0.2 / 1.41 / 0.5
IL-5 / 0.62 / 0.4 / -0.35 / 0.6 / 1.00 / 0.2
IL-13 / 1.58 / 0.1 / 0.53 / 0.6 / 1.78 / 0.1
Reference gene
HMBS / -1.85 / 0.3 / 1.15 / 0.5 / -0.73 / 0.7
Gene expression levels were measured by qRT-PCR in sputum cells obtained from asthmatic children during an acute exacerbation.High quality lung function data was available for all subjects at enrollment, but was either missing or did not meet ATS guidelines for some subjects during the exacerbation or at convalescence.