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1 Supplementary Information Title: Role of Cytochrome P450 (CYP)1A in Hyperoxic Lung Injury: Analysis of the Transcriptome and Proteome Authors: Krithika Lingappan a, Suman Maity b, Weiwu Jiang a, Lihua Wang a, Xanthi Couroucli a, Alex Weith a,c, Guodong Zhou d, Cristian Coarfa b and Bhagavatula Moorthy a*

2 Table S1: Up regulated genes across all genotypes (Hyperoxia exposed mice compared to room air controls) WT GDF15 Growth Differentiation Factor NUPR1 Nuclear Protein 1, Transcriptional Regulator MT1 Metallothionein CDKN1A Cyclin Dependent Kinase Inhibitor 1A 8.01 AKAP12 A- Kinase Anchoring Protein ANKRD1 Ankyrin Repeat Domain TNFRSF12A TNF Receptor Superfamily Member 12A 6.36 CTGF Connective Tissue Growth Factor 5.47 GADD45G Growth Arrest And DNA Damage Inducible Gamma 5.47 GDF15 Growth Differentiation Factor NUPR1 Nuclear Protein 1, Transcriptional Regulator ANKRD1 Ankyrin Repeat Domain CDKN1A Cyclin Dependent Kinase Inhibitor 1A 6.53 MT1 Metallothionein TGM2 Transglutaminase TRIB3 Tribbles Pseudokinase TNFRSF12A TNF Receptor Superfamily Member 12A 5.13 Cyp1a2- /-

3 GDF15 Growth Differentiation Factor NUPR1 Nuclear Protein 1, Transcriptional Regulator ANKRD1 Ankyrin Repeat Domain AREG Amphiregulin 7.72 MT1 Metallothionein TNFRSF12A TNF Receptor Superfamily Member 12A 5.92 MTHFD2 Methylenetetrahydrofolate Dehydrogenase (NADP+ Dependent) 2, 5.16 Methenyltetrahydrofolate Cyclohydrolase ASNS Asparagine Synthetase (Glutamine- Hydrolyzing) 5.13 CTGF Connective Tissue Growth Factor 5.04

4 Table S2: Down regulated genes across all genotypes (Hyperoxia exposed mice compared to room air controls) WT ASAH3L N- Acylsphingosine Amidohydrolase 3- Like 0.26 EAR2 V- Erba- Related Protein EDNRB Endothelin Receptor Type B 0.24 FMO1 Flavin- Containing Monooxygenase 0.28 LYZ1 Lysozyme (Renal Amyloidosis) 0.26 MUP2 Methionine Permease 0.24 TMEM100 Transmembrane Protein ASAH3L N- Acylsphingosine Amidohydrolase 3- Like 0.28 CXCL12 C- X- C Motif Chemokine Ligand EAR2 V- Erba- Related Protein LYZ1 Lysozyme (Renal Amyloidosis) 0.22 MUP2 Methionine Permease 0.26 TMEM100 Transmembrane Protein Cyp1a2- /- EAR2 V- Erba- Related Protein EAR3 V- Erba- Related Protein

5 LYZ1 Lysozyme (Renal Amyloidosis) 0.25 SFTPA1 Surfactant Protein A THBD Thrombomodulin 0.28 TMEM100 Transmembrane Protein

6 Table S4: Down regulated genes in Room Air (WT vs. and WT vs. Cyp1a2- /- ) vs. WT CBX1 Chromobox CD200 CD RPL29 Ribosomal protein L NNMT Nicotinamide N- methyltransferase 0.34 EPM2AIP1 EPM2A (laforin) interacting protein MELA Melanoma antigen 0.54 ATG3 Autophagy related CLASRP CLK4- associating serine/arginine rich protein 0.55 WDR82 WD repeat domain containing CD59 CD Cyp1a2- /- vs. WT MUP2 Major urinary protein MUP3 Major urinary protein TTR Transthyretin 0.47 MUP5 Major urinary protein APOA Apolipoprotein A- II 0.51 RHBDL2 Rhomboid, veinlet- like ACTC1 Actin, alpha, cardiac muscle KLF2 Kruppel like factor MT- ND5 NADH dehydrogenase 5, mitochondrial 0.59

7 Table S3: Up regulated genes in Room Air (WT vs. and WT vs. Cyp1a2- /- ) vs. WT ERDR1 Erythroid Differentiation Regulator PGLYRP1 Peptidoglycan recognition protein ADAT2 Adenosine deaminase, trna specific SORL1 Sortilin related receptor Rpl29- ps2 Ribosomal protein L29, pseudogene SLC27A6 Solute carrier family 27 (fatty acid transporter), member HSPA8 Heat shock protein KLF2 Kruppel- like factor IL18 Interleukin Cyp1a2- /- vs. WT MAP3K6 Mitogen- activated protein kinase kinase kinase KLF9 Kruppel- like factor ANGPTL4 Angiopoietin- like FKBP5 FK506 binding protein FAM107A Family with sequence similarity 107, member A 1.93 NPR3 Natriuretic peptide receptor EAR3 Eosinophil- associated, ribonuclease A family, member SPARC Secreted acidic cysteine rich glycoprotein 1.85 LPL Lipoprotein lipase 1.82

8 Figure S1 Room Air Hyperoxia mtor c-met Keap1 PTEN Figure S1. Hyperoxia- exposed WT and Cyp1a1- WT_Room Air WT_Hyperoxia p70s6k E-Cadherin FAK Fibronectin MEK1/2 ps217/221 Src py416 RPS6 IRS1 beta-catenin ps33 Cyclin D1 Stat5 py694 EZH1 Stat5 XRCC1 p53 BRCA1 ATR ps428 Mre11 LCN2 Src py527 p90rsk VEGFR2 BIM cjun ps73 eif4e PTCH CHK2 pt68 ACC1 ps79 GSK-3a/b ps21/9 AMPKa pt172 LKB1 ps428 /- mice are characterized by robust and distinct proteomic changes compared to room air controls. Reverse Phase Protein Analysis (RPPA) was used to generate proteomic profiles of WT and mice exposed to hyperoxia. Differential protein expression was evaluated BM mmh Room Air BM mmm BM mmo BM mhw Hyperoxia BM mh_ BM mh6 using parametric t- test (significance for fdr- Cyp1a1-/- Room Air Cyp1a1-/- Hyperoxia ACC1 ps79 AMPKa pt172 EZH2 LKB1 ps248 Akt ps473 S6 ps235/s236 S6 ps240/s244 ELK-1 ps383 Stat3 py705 GSK-3a/b ps21/9 4EBP1 pt37/t46 Rab25 VEGFR2 Axl py702 PKCa ps657 Caspase7 BRCA1 p38 NFkB p65 PI3K p110a Akt Zeta BIM Src py527 mtor PI3K p85 PTEN FAK Keap1 Stat5 py69 TAZ adjusted q- value<0.25). Proteomic changes of hyperoxia exposed mice compared to room air controls in WT and mice

9 Table S5: RPPA profile of differentially expressed proteins in the lung after exposure to hyperoxia in and Cyp1a2- /- compared to WT mice Antibody Gene Symbol fold change p- value over WT fdr- adjusted q- value Antibody Gene Symbol Cyp1a2- /- fold change Cyp1a2- /- over WT p- value Cyp1a2- /- fdr- adjusted q- value AMPKa pt172 PRKAA c- Raf RAF GSK- 3a/b ps21/9 GSK3A, GSK3B Stat5 STAT CHK2 pt68 CHEK IGF1R IGF1R ELK- 1 ps383 ELK ACC1 ACACA PTCH PTCH mtor FRAP Stat3 py705 STAT VEGFR2 KDR LKB1 ps428 STK Bcl- xl BCL2L eif4e EIF4E p70s6k pt389 RPS6KB Bcl- xl BCL2L Stat3 py705 STAT Stat5 py694 STAT S6 ps240/s244 RPS GSK3B GSK3B PI3K p110a PIK3CA p38 MAPK E- Cadherin CDH PI3K p85 PIK3R Src py527 SRC EBP1 pt37/t46 EIF4EBP p70s6k RPS6KB c- Met MET ACC1 ACACA

10 EGFR py1173 EGFR mtor FRAP Keap1 KEAP PKCa PRKCA Zeta YWHAZ beta- Catenin ps33 CTNNB PKCa ps657 PRKCA VEGFR2 KDR BRCA1 BRCA PTEN PTEN LCN2 LCN Mre11 MRE11A

11 Table S6: RPPA profile of differentially expressed proteins in the lung after exposure in WT and mice after exposure to hyperoxia compared to room air (RA) controls. Antibody Gene Symbol WT O 2 RA fold change WT O 2 RA p- value WT O 2 RA fdr- adjusted q- value Antibody Gene Symbol O 2 over RA fold change O 2 over RA p- value O 2 over RA fdr- adjusted q- value LCN2 LCN Caspase7 CASP Mre11 MRE11A BIM BCL2L VEGFR2 KDR BRCA1 BRCA PTEN PTEN PKCa ps657 PRKCA BRCA1 BRCA Stat5 py694 STAT c- Met MET PTEN PTEN Src py416 SRC Keap1 KEAP p70s6k RPS6KB VEGFR2 KDR E- Cadherin CDH p38 MAPK AKT1 AKT2 beta- Catenin ps33 CTNNB Akt AKT p53 TP Zeta YWHAZ Src py527 SRC EBP1 pt37/t46 EIF4EBP BIM BCL2L Src py527 SRC Stat5 STAT Axl py702 AXL Keap1 KEAP PI3K p85 PIK3R mtor FRAP FAK PTK RPS6 RPS mtor FRAP XRCC1 XRCC PI3K p110a PIK3CA

12 p90rsk RPS6KA NFkB p65 NFKB IRS1 IRS TAZ WWTR ATR ps428 ATR Rab25 RAB Fibronectin FN EZH2 EZH Cyclin D1 CCND ELK- 1 ps383 ELK FAK PTK ACC1 ps79 ACACA ACACB Stat5 py694 STAT GSK- 3a/b ps21/9 GSK3A, GSK3B EZH2 EZH LKB1 ps428 STK MEK1/2 ps217/221 MAP2K Stat3 py705 STAT AKT1 AKT2 LKB1 ps428 STK Akt.pS473 AKT eif4e EIF4E AMPKa pt172 PRKAA cjun ps73 JUN S6 ps235/s236 RPS PTCH PTCH S6 ps240/s244 RPS CHK2 pt68 CHEK GSK- 3a/b ps21/9 GSK3A, GSK3B AMPKa pt172 PRKAA ACC1 ps79 ACACA ACACB

13 Table S7: Primer List Gene Symbol Gene name Identifier 1 Ankrd1 Ankyrin repeat domain 1 Mm _m1 2 Gdf15 Growth differentiation factor 15 Mm _m1 3 Nupr1 Nuclear protein transcription regulator 1 Mm _m1 4 Areg Amphiegulin Mm m1 5 P21(Trp63) Transformation protein63 Mm m1 6 CTGF Connective tissue growth factor Mm g1 7 Hmox1 Heme oxygenase1 Mm m1 8 Dusp1 daul specificity phosph Mm g1 9 Slc2a3 solutate carrier family2 member3 Mm m1 10 Nme1 Nucleoside diphosphate kines1 Mm m1 11 PCNA Proliferating cell nuclear antigen Mm g1 12 XPC Xeroderma pigmentosum complementation groupc Mm m1 13 CD63 CD63 antigen Mm g1 14 Abca1 ATP- binding casette sub- family A (ABC1),member1 Mm m1