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Table S1. Top 50 Genes Upregulated by POU2AF1 in Human Airway Basal Cells1

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Table S1. Top 50 Genes Upregulated by POU2AF1 in Human Airway Basal Cells1 Table S1. Top 50 Genes Upregulated by POU2AF1 in Human Airway Basal Cells1 Average expression l1evel Fold-change (RPKM) (lenti- Gene Un- Lenti- Lenti- POU2AF1 vs symbol Full name infected RFP POU2AF1 lenti-RFP)2 Intracellular pathogen response MX2 myxovirus (influenza virus) resistance 2 0.1 0.2 143.0 708.9 (mouse) CMPK2 cytidine monophosphate (UMP-CMP) kinase 0 0.1 30.8 435.4 2, mitochondrial IFI44L interferon-induced protein 44-like 0.1 0.1 46.6 419.8 RSAD2 radical S-adenosyl methionine domain contain- 0.2 0.3 89.1 326.3 ing 2 IFIT1 interferon-induced protein with tetratricopep- 1.9 2.0 328.0 163.1 tide repeats 1 MX1 myxovirus (influenza virus) resistance 1, inter- 1.9 2.2 318.2 144.0 feron-inducible protein p78 (mouse) IFI6 interferon, alpha-inducible protein 6 10.9 9.2 940.6 102.6 ISG15 ISG15 ubiquitin-like modifier 9.5 11.7 1055.9 90.4 IFI27 interferon, alpha-inducible protein 27 9.5 8.5 717.7 84.7 XAF1 XIAP associated factor 1 0.4 0.5 39.4 81.8 IFIT3 interferon-induced protein with tetratricopep- 1.7 2.3 185.5 79.3 tide repeats 3 IFIT2 interferon-induced protein with tetratricopep- 0.3 0.5 27.8 55.7 tide repeats 2 HERC5 HECT and RLD domain containing E3 ubiqui- 0.1 0.2 9.8 51.4 tin protein ligase 5 IFI44 interferon-induced protein 44 1.7 2.5 118.2 46.7 BST2 bone marrow stromal cell antigen 2 1.7 1.7 68.9 41.5 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 1.3 1.8 61.1 33.3 OASL 2'-5'-oligoadenylate synthetase-like 1.1 1.3 40.9 32.4 IFITM1 interferon induced transmembrane protein 1 28.3 23.5 745.9 31.8 UBD Ubiquitin D 0 0 0.2 27.8 OAS1 2'-5'-oligoadenylate synthetase 1, 40/46kDa 3.5 3.9 106.6 27.3 OAS2 2'-5'-oligoadenylate synthetase 2, 69/71kDa 4.5 4.8 128.9 26.7 IRF7 interferon regulatory factor 7 1.8 1.5 39.6 26.1 BATF2 basic leucine zipper transcription factor, ATF- 0.5 0.4 9.6 22.2 like 2 GBP5 guanylate binding protein 5 0.1 0.1 3.1 22.1 ZBP1 Z-DNA Binding Protein 1 0 0 1 N/A Extracelluar/surface host defense MMP13 matrix metallopeptidase 13 (collagenase 3) 0.1 0.1 5.5 44.2 CD53 CD53 molecule 0 0 0.1 30 DEFB4A Defensin, beta 4A 0 0 0.1 N/A Cytokines, chemokines IL19 interleukin 19 0 0 0.2 41.3 Table S1. Top 50 Genes Upregulated by POU2AF1 in Human Airway Basal Cells1 (page 2) Average expression l1evel Fold-change (RPKM) (lenti- Gene Un- Lenti- Lenti- POU2AF1 vs symbol Full name infected RFP POU2AF1 lenti-RFP)2 CXCL10 chemokine (C-X-C motif) ligand 10 0.8 1.0 31.5 30.9 CXCL11 chemokine (C-X-C motif) ligand 11 0.2 0.5 14.2 29.4 IFNB1 interferon, beta 1, fibroblast 0 0 0.7 28.7 IFNL1 Interferon, Lambda 1 0 0 0.5 22.4 IFNL2 Interferon, Lambda 2 0 0 0.1 N/A Complement C1R complement component 1, r subcomponent 3.2 3.0 70.1 23.0 Antigen presentation HLA-DRA major histocompatibility complex, class II, DR 0 0 0.7 21.9 alpha Negative regulator of host defence response USP18 ubiquitin specific peptidase 18 1.5 1.5 30.8 21.2 Unclear role in host defense SLC16A10 solute carrier family 16, member 10 (aromatic 0 0 0.3 93.9 amino acid transporter) COMP cartilage oligomeric matrix protein 0 0 0.4 55.9 COL2A1 collagen, type II, alpha 1 0 0 0.3 53.2 ST18 suppression of tumorigenicity 18 (breast carci- 0 0 0.2 51.6 noma) (zinc finger protein) CH25H cholesterol 25-hydroxylase 0 0 0.9 35.6 LAMP3 lysosomal-associated membrane protein 3 0.8 0.8 25.8 31.6 EPSTI1 epithelial stromal interaction 1 (breast) 1.0 1.0 28.7 29.4 C12orf74 chromosome 12 open reading frame 74 0 0 0.3 28.7 FMOD fibromodulin 0.1 0.1 3.8 28.2 KIF6 kinesin family member 6 0 0 0.1 26.1 ETV7 ets variant 7 0.1 0.1 2.9 22.6 PLEKHG7 Pleckstrin Homology Domain Containing, 0 0 0.4 22.2 Family G (With RhoGef Domain) Member 7 S100A7A S100 Calcium Binding Protein A7A 0 0 0.1 N/A 1 The table is the summary of RNAseq data assessing genes induced by POU2AF1 in the human airway basal cells. The TOP 50 genes were selected based on the fold-changes between the average gene expression in lenti-POU2AF1 group vs lenti-RFP group. 2 N/A, not applicable, unable to calculate because denominator is 0. Table S2. Antibodies Working Concentration1 Protein name Company Catalog number IHC2 IF3 Western4 POU2AF1 Santa Cruz Biotechnology sc-955 1/800 1/50 N/A TP63 Santa Cruz Biotechnology sc-8431 1/200 N/A N/A DNAI1 Sigma-Aldrich HPA021649 N/A N/A 1/2000 SCGB1A1 BioVendor RD181022220 N/A 1/200 1/2000 KRT5 Thermo Scientific PA1-37974 N/A N/A 1/2000 CD20 Abcam ab9475 1/50 N/A N/A CD79B Abcam ab134147 1/250 N/A N/A Beta-tubulin IV BioGenex MU178-UC N/A 1/100 N/A MX1 GeneTex GTX110256 N/A N/A 1/1000 HLA-DR Santa Cruz Biotechnology sc-53319 N/A N/A 1/1000 IFIT3 GeneTex GTX112442 N/A N/A 1/2000 IFITM1 GeneTex GTX101728 N/A 1/500 1/1000 GFP OriGene Technologies TA150041 N/A N/A 1/5000 B-Actin Sigma-Aldrich A2228 N/A N/A 1/10000 OCT-1 Santa Cruz Biotechnology sc-8024 N/A 1/50 1/100 OCT-2 Santa Cruz Biotechnology sc-377475 N/A 1/50 1/100 1 N/A - not applicable. 2 IHC – immunohistochemistry. 3 IF - immunofluorescence staining. 4 Western - western analysis. Figure S1 A. POU2AF1 mRNA expression B. Relative POU2AF1 mRNA expression NM_006235 (POU2AF1 mRNA structure) 100 75 30 Nonsmokers 0 Subject 1 POU2AF1 30 50 6.0 RPKM requency (%) requency 0 Subject 2 30 25 0 Subject 3 30 Relative f Relative 0 Subject 4 0 30 0.1 1 10 100 1000 Read coverage depth coverage Read 0 Subject 5 Gene expression of airway epithelial transcription factors (RPKM) C. POU2AF1 protein, human airway Spleen, positive control Trachea, IgG control Tracheal, POU2AF1 Bronchus, POU2AF1 Figure S1. POU2AF1 expression in the human airway epithelium. A, B. RNA-Seq assessment of POU2AF1 expression in small airway epithelium brushed from 5 healthy nonsmokers. A. POU2AF1 sequence alignments with the read coverage depth. B. POU2AF1 expression relative to other airway epithelial transcription factors. POU2AF1 expression is >50% of all transcription factors. C. POU2AF1 protein expression in human airway epithelium. Blue - hematoxylin, Red - anti POU2AF1. Shown are: positive control (spleen germinal center), tracheal IgG control, tracheal POU2AF1, and bronchus POU2AF1. Bar = 20 µm. Figure S2 Un-infected Lenti-RFP Lenti-POU2AF1 BCL2 SPP1 TRAF3 PLCG1 CDC37 PRDM1 IL6 Row Z- BCL6 score ID2 HLA-DRA -1.98 SORD CCND3 ID3 ownstream genes d MYL4 0 CXCR5 RBP1 PTPRS CD36 1.98 CREG1 S100A10 KCNN4 Known POU2AF1 B4GALT1 PCDHGA1 CTNNA1 IDH2 SOC1 LCK Figure S2. RNA-Seq data, from airway basal cells modified with lentivirus-mediated RFP and POU2AF1, assessed using unsupervised hierarchical clustering of known POU2AF1 downstream genes known to be expressed in B cells. The downstream genes were summarized from the literature. Only the genes with expression > detection limit (0.04 FPKM) in either group were plotted. Shown in red are the host defense genes. .
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