Supplementary Figure 1. Lkb1-deficient lung ADC progressively transdifferentiates into SCC. (a) A scheme showing the progression pattern of atypical

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Cory George
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1 Supplementary Figure 1. Lkb1-deficient lung ADC progressively transdifferentiates into SCC. (a) A scheme showing the progression pattern of atypical adenomatous hyperplasia/epithelial hyperplasia (AAH/EH), adenoma, ADC and SCC in Kras/Lkb1mice post Ad-Cre treatment. (b) H&E staining and p63 immunohistochemical staining on lung tissues from Kras/Lkb1 1

2 mice at indicated time points post Ad-Cre treatment. Scale bar: 150 μm. (c) Statistic analysis of p63 positive lesions in the lungs from Kras/Lkb1 mice at 2, 4, 6, 8, 10 weeks post Ad-Cre treatment (n=8 each group). Data were shown as mean ± s.e.m. t test, **P < (d) A scheme showing the strategy of serial transplantation of mouse lung ADC with Lkb1 deficiency in nude mice. (e) Representative histology, p63, Ttf1 immunohistochemical staining and collagen staining for tumor xenografts at different passages of serial transplantation in nude mice. Scale bar: 50 μm. (f) Statistic analysis of p63 positive cells on lung tumor sections at passage 1, 2 and 3 from the serial transplatation experiment in nude mice. 10 serial sections were statistically analyzed in each passage. Data were shown as mean ± s.e.m. t test, ***P < (g) Representative histology and immunohistochemical staining of p63 and SP-C on mad-sccs from Kras/Lkb1 mice at 8 and 12 weeks post Ad-Cre treatment. Scale bar: 50 μm. (h) Statistic analysis of SP-C + /p63 + cell ratio in the mad-sccs from Kras/Lkb1 mice at 8 (n=10) and 12 weeks (n=10) post Ad-Cre treatment. 2

3 Supplementary Figure 2. Type II pneumocyte lineage-derived lung ADC with Lkb1 deficiency transdifferentiates into SCC. (a) Representative immunofluorescent photoes for LacZ (Green) and Sox2 (Red) staining in cyro section of SP-C-CreERT2/Rosa26R-LacZ mouse at 2 weeks post tamoxifen administration. Scale bar: 150 μm. (b) Statistic analysis of the percentage of LacZ positive cells in both type II pneumocytes and basal cells. (c) Schematic model (upper panel) and representative histologies (lower panel) for AAH, adenoma, ADC and SCC from SKL mice at a serial of time points post 3

4 tamoxifen administration. Scale bar: 150 μm. (d) Immunohistochemical staining of SP-C on lung tissues containing AAH, adenoma and adenocarcinoma from SKL mice at 4-8 weeks post tamoxifen administration. Scale bar: 150 μm. (e) Statistic analysis of the ADC or SCC incidence in SKL mice at 7 weeks post tamoxifen administration. (f) Representative immunostaining of SP-C, p63 and X-gal staining in ADC and SCC from SRKL mouse at 9 weeks post tamoxifen administration. Scale bar: 150 μm. (g) Representative immunohistochemical staining for p63 and SP-C in lung mad-scc from SKL mice at 9 weeks post tamoxifen administration. Scale bar: 150 μm. (h) Quantification of tumor percentage for mixed mad-scc and typical SCC in SKL mice at indicated time points post tamoxifen administration. n=8 for each time point. (i) Representative histology, p63, SP-C immunohistochemical staining on mad-scc lesions in Kras/Lkb1 mice with 8 and 12 weeks Ad-Cre treatment. Scale bar: 50 μm. (j) Statistic analysis of SP-C+/p63+ cell ratio in the mice with 9-12 (n=8) and (n=10) weeks Ad-Cre treatment.. 4

5 Supplementary Figure 3. Validation of a serial of genes differentially expressed in ADC and SCC from Kras/Lkb1 mouse model. Real-time PCR validation of genes differentially expressed in ADC (n=5) and SCC (n=7) from Kras/Lkb1 mouse model according to microarray data analyses. Data were shown as mean ± s.e.m. t test, *P <0.05, **P < 0.01,***P<

Supplementary Figure 4. Detection of Lox expression and collagen deposition in human lung ADC and SCC samples. (a) Real-time analysis of Lox expression in human lung ADC (n=85) and SCC (n=85) samples.

6 Supplementary Figure 4. Detection of Lox expression and collagen deposition in human lung ADC and SCC samples. (a) Real-time analysis of Lox expression in human lung ADC (n=85) and SCC (n=85) samples. Data were shown as mean ± s.e.m. t test, *P<0.05. (b) Representative photos showing immunohistochemical staining for Lox in human lung ADC and SCC samples. (c) Statistic analysis of Lox expression in human lung ADC and SCC samples. Pearson χ2 test. (d) Representative photos showing Massons Trichrome staining of collagen in human lung ADC and SCC samples. (e) Statistic analysis of collagen deposition in human lung ADC and SCC samples. Pearson χ2 test. 6

7 Supplementary Figure 5. Lentivirus-mediated Gene Expression in Kras/Lkb1 Mice. (a) A scheme of lentivirus-mediated gene expression (Lenti-Cre and Lenti-Cre-MC) in Kras/Lkb1 mouse model. (b) Representative H&E staining, p63 and SP-C immunohistochemical staining of ADC and SCC from Kras/Lkb1 mice virally infected with Lenti-Cre. Scale bar: 150 μm. 7

8 Supplementary Figure 6. Lentivirus-mediated Lox expression in Kras/Lkb1 mice. Representative H&E staining as well as SP-C immunohistochemical staining in lung ADC from Kras/Lkb1 mice virally infected with Lenti-Cre or Lenti-Cre-Lox. Scale bar: 10 μm. 8

9 Supplementary Figure 7. Pharmacological inhibition of LOX enzymatic activity promotes ADC to SCC transdifferentiation. (a) Detection of Lox enzymatic activity in sera from Kras/Lkb1 mice treated with BAPN (n=12), DPA (n=10) or Saline (n=14). Data were shown as mean ± s.e.m. t test ***P < (b) Detection of collagen deposition by Massons Trichrome staining in lung tumors from Kras/Lkb1 9

10 mice treated with BAPN, DPA or saline. Scale bar: 10 μm. (c) Representative histology and immunohistochemical staining of p63 and SP-C on mad-sccs from Kras/Lkb1 mice with or without 4 weeks BAPN treatment after 4 weeks Ad-Cre treatment. Scale bar: 50 μm. (d) Statistic analysis of SP-C + /p63 + cell ratio in the mad-sccs from Kras/Lkb1 mice with or without 4 weeks BAPN treatment after 4 weeks Ad-Cre treatment (n=12 each group). (e) A scheme showing the BAPN treatment strategy in SKL mouse model. (f-g) Quantification of average tumor number per mouse for ADC and SCC (F) and mad-scc (G) from SKL mice treated with BAPN (n=14) or saline (n=18). Data were shown as mean ±s.e.m. t test, *P <0.05, **P < (h-i) Quantification of average tumor size per mouse for ADC and SCC (h) and individual tumor size for SCC (i) from SKL mice post BAPN (n=12) or saline (n=12) treatment. Scale bar: 150 μm. Data were shown as mean ± s.e.m. t test, *P <0.05. (j-k) Quantification of average tumor number per mouse for ADC and SCC (j) and mad-scc (k) from Kras/Lkb1 mice at 4 weeks post DPA (n=14) or saline (n=16) treatment. Data were shown as mean ± s.e.m. t test, *P <0.05, ***P < (l) Quantification of average tumor size per mouse for ADC and SCC from Kras/Lkb1 mice at 4 weeks post DPA (n=14) or saline (n=16) treatment. Data were shown as mean ± s.e.m. (m) Quantification of individual tumor size of SCC in Kras/Lkb1 mice post DPA (n=10) or saline (n=14) treatment. Data were shown as mean ± s.e.m. t test. (n-o) Representative Ki67 immunohistochemical staining (n) and statistical analysis (o) in lung ADC and SCC from Kras/Lkb1 mice post BAPN (n=12), DPA (n=10) or saline (n=14) treatment. More than 200 high-power fields (HPF) were analyzed each mouse. Scale bar: 150 μm. t test, ***P < (p-q) Representative Cleaved caspase 3 immunohistochemical staining (p) and statistical analysis (q) in lung ADC and SCC from Kras/Lkb1 mice post BAPN (n=12), DPA (n=10) or saline (n=14) treatment. More than 200 high-power fields (HPF) were analyzed each mouse. Scale bar: 150 μm. Data were shown as mean ± s.e.m, t test, ***P <

11 Supplementary Figure 8. Activation of DNp63α partially promotes ADC to SCC transdifferentiation. (a) Lung ADC (n=5) and SCC (n=7) dissected from Kras/Lkb1mice at 10 weeks post Ad-Cre treatment were subjected to RNA preparation and real time PCR analyses. Data were shown as mean ± s.e.m.t test. *P <0.05.(b) Western blotting confirmed the ectopic expression of DNp63α in Kras/p53cells. (c) Immunofluorescence staining showed that transient DNp63αexpression partially activates Krt5 and Krt14 expression in Kras/p53cells. Scale bar: 150μm.(d) Distinct morphologies of Kras/p53cells with stablednp63αexpression in contrast to the parental cells. Scale bar: 75μm.

12 Supplementary Figure 9. Full gel scans for mouse Actin, SPC, Lox and p63(dnp63α) blots are shown. 12

13 Supplementary Table 1. The 20 most significantly deregulated signal pathways between ADC and SCC from Kras/Lkb1 mice. Fisher s Exact Test was used to generate the p value. Pathway SCC1 SCC2 SCC3 SCC4 SCC5 ADC1 ADC2 ADC3 ADC4 ADC5 Accuracy Validated transcriptional targets of deltanp E E E E E E E E E E % isoforms Validated transcriptional targets of TAp E E E E E E E E E E % isoforms Tight junction interactions 2.07E E E E E E E E E E % Cell junction organization 2.92E E E E E E E E E E % Direct p53 effectors 3.61E E E E E E E E E E % p53 signaling pathway 1.32E E E E E E E E E E % Apoptosis 1.86E E E E E E E E E E % Muscle cell TarBase 1.11E E E E E E E E E E % Interferon alpha/beta signaling 1.33E E E E E E E E E E % Apoptosis Modulation by HSP E E E E E E E E E E % Nucleotide Metabolism 6.99E E E E E E E E E E % Staphylococcus aureus infection -3.46E E E E E E E E E E % NCAM1 interactions 3.95E E E E E E E E E E % Protein digestion and absorption -1.26E E E E E E E E E E % NCAM signaling for neurite out-growth 1.00E E E E E E E E E E % Adipogenesis -2.87E E E E E E E E E E % Signaling by PDGF 1.00E E E E E E E E E E % Integrin cell surface interactions 7.40E E E E E E E E E E % Initial triggering of complement -1.20E E E E E E E E E E % Beta3 integrin cell surface interactions 1.61E E E E E E E E E E % 13

14 Supplememtary Table 2. Genes significantly deregulated in SCC relative to ADC from Kras/Lkb1 mice. Fisher s Exact Test was used to generate the p value. Description Gene T score P value Lox Lox family Loxl Loxl Loxl Col4a Col4a Col4a Collagen members Col4a Col4a Col14a Col3a Col6a Col6a Timp ECM assembly Timp Timp Vim Snai EMT Fn Cdh Cdh Trp E-06 Sox Squamous markers Krt E-09 Krt6a E-08 Krt ECM degradation Mmp Mmp Perp E-05 Pkp E-05 Pkp Desmosome Jup Dsc E-05 Dsc DSG Dsp Cldn Tight junction Cldn Cldn Cldn

15 Gap junction Gjb Gjd Pcdhb E-06 Cadm Pvrl Others Mpzl Efs Pcdh Csf3r E-05 Thbs

16 Supplementary Table 3. The primers used for regular PCR and genomic sequencing Gene Primers for PCR (5'-3') Primers for sequencing (5'-3') Pi3k-ca (E542) Pi3k-ca (E545) Pi3k-ca(H1047) p53 (CDS) NRF2 (CDS) Keap1 (CDS) Cul3 (CDS) p16 (CDS) p19 (CDS) AAGGAGGAGCACTGTCCGTT AAGGAGGAGCACTGTCCGTT TGGGCCACTTCGTCTCTGGA TGGGCCACTTCGTCTCTGGA AAGGAGGAGCACTGTCCGTT AAGGAGGAGCACTGTCCGTT TGGGCCACTTCGTCTCTGGA TGGGCCACTTCGTCTCTGGA GATGTGTTACAAGGCTTACCT GATGTGTTACAAGGCTTACCT CTTGCTCAAGTCCTAATGTT CTTGCTCAAGTCCTAATGTT GGTAGCGACTACAGTTAGGGGGCA GGTAGCGACTACAGTTAGGGGGCA CAGCAGAAGGGACCGGGAGGA CAGCAGAAGGGACCGGGAGGA GCCTCACCTCTGCTGCAAGT GCCTCACCTCTGCTGCAAGT TTTCACATCACAGTAGGAAG TTTCACATCACAGTAGGAAG CTGTGCTTAGTCACCGTGA GCTAGCAGAGGAACTGTGTCT CTTTAGTACAGAGAAGCAGT TGTTCCACGCGTGCATCGAC CCTCCGAGTGCGAGCCGCA CCTCCGAGTGCGAGCCGCA CCTCCGAGTGCGAGCCGCA CCTCCGAGTGCGAGCCGCA GTAGACAGAGGAGCAATAAGA CACTGAATCTCCGCGAGGAA CACTGAATCTCCGCGAGGAA AGCCACATGCTAGACACGCT AGCCACATGCTAGACACGCT TGGGGGCGGCGCTTCTCACCT TGGGGGCGGCGCTTCTCACCT GGCTGAGGCCGGATTTAGCT GGCTGAGGCCGGATTTAGCT 16

17 Supplementary Table 4. Description and frequency of LKB1 genetic alterations Exonic deletion n(%) Deletion of whole exon 2(1.98) Deletion of exon 1 5(4.95) Deletion of exon10 2(1.98) Deletion of exon 1-4 1(0.99) Deletion of exon 1-6 1(0.99) Deletion of exon 5-8 1(0.99) Deletion of exon 7-8 1(0.99) 17

18 Supplementary Table 5. The primers used for real-time PCR Gene Forward primer Reverse primer β-actin TGAGCGCAAGTACTCTGTGTGGAT ACTCATCGTACTCCTGCTTGCTGA Brf2 CCTTCCTGGCATGGCAGTCTCT CACCACCGACCGCTTGTTAAGTT Cldn8 GCAACCTACGCTCTTCAAATGG TTCCCAGCGGTTCTCAAACAC cmyc CAACGACAGCAGCTCGCCCA AGCCCGACTCCGACCTCTTGG Col1a1 GCTCCTCTTAGGGGCCACT CCACGTCTCACCATTGGGG Col4a1 CTGGCACAAAAGGGACGAG ACGTGGCCGAGAATTTCACC Col4a5 GGAGAACGGGGGTTTCCAG CTCCCTTGGTTCCATTGCATC Col4a6 GAACTGGCAGAATCGGGACAG TCCAATGGGACCCTTATCTCC Col6a1 CTGCTGCTACAAGCCTGCT CCCCATAAGGTTTCAGCCTCA Col6a2 GCTCCTGATTGGGGGACTCT CCAACACGAAATACACGTTGAC Dcn GTCATCTTCGAGTGGTGCAGT CGGGTGGAAAATCCCAGGG Dlx5 TCTCTAGGACTGACGCAAACA GTTACACGCCATAGGGTCGC DLX5 AAGCGCCACCAACCAGCCAG CGTTCCGGCAAGGCGAGGTA Dsc2 ATGGCGGCTGTGGGATCTAT GCAAGGATCGCAAGGGTCAA Dsg2 CGTGGTTGAAGGCATTCATTTC TAGCTGCTTGACCAGTGTCTT Gjb2 ATCCTCGGGGGTGTCAACAA AGACAAAATCGGCTTGCTCATC Hif1a ACCTTCATCGGAAACTCCAAAG CTGTTAGGCTGGGAAAAGTTAGG Itga6 GCAGAAGCACTCCCGCTGCA TTGCCCCCTGGACCTTGGCT Jup TGGCAACAGACATACACCTACG GGTGGTAGTCTTCTTGAGTGTG Klf5 CCTCCGTCCTATGCCGCTACAA GCTTCTCGCCCGTATGAGTCCT KLF5 TCGGATGAGCTGACCCGCCA TCAGAGCGCGAGAAGCTGCG Krt14 CAGCGGCCCACTGAGATCAAAG CTTGGTCCGGAAGTCATCGGCA Krt15 TTTGGAGGCAGCTCTACCCGAGG CTGCCCCCGAGGAGACAAACC Krt17 CGGGGCCAGCCAGAGACTAC TCGGCTCTGGCCAGGGTCAG Krt5 GGCCCACAGAGACTGCTTCTTT AACATTTTGGGGTCTGGGTCAC Krt6a TCCCAGATGTCATGGCTGCAGAA AGATGAGCAGTGGGGACCCATG Lox TCTTCTGCTGCGTGACAACC GAGAAACCAGCTTGGAACCAG Mmp14 CAGTATGGCTACCTACCTCCAG GCCTTGCCTGTCACTTGTAAA Mmp9 TGTCTGGAGATTCGACTTGAAGTC TGGTGTGCCCTGGAACTCA Oct1 AGCTCTTGCTTCTAGTGGCTC CTGGCTGTAGGTGCAGAGTTC p63 GTGTTGGTGTGGCACAGGGG TCTTCCCCACAGCTCTGGCT Perp ATCGCCTTCGACATCATCGC CCCCATGCGTACTCCATGAG Sccro AGAGTGTAAAAGGATCGTTGGAC CTGGATCGAGGGCCAGATCA 18

19 Sox2 TGCTGCCTCTTTAAGACTAGGGCT CGGGCGAAGTGCAATTGGGA Spc ATGGACATGAGTAGCAAAGAGGT CACGATGAGAAGGCGTTTGAG Timp1 GCAACTCGGACCTGGTCATAA CGGCCCGTGATGAGAAACT Timp2 TCAGAGCCAAAGCAGTGAGC GCCGTGTAGATAAACTCGATGTC Timp3 CTTCTGCAACTCCGACATCGT GGGGCATCTTACTGAAGCCTC Trim29 AGAATGGCACTAAAGCAGACAG AAATAGGCCACTCTTCCCCTC TRIM29 GGGGTGAGTGGAGTGCACCG GAGCTGCCTTGGACGACGGG 19

Supplementary Figures

Supplementary Figures Supplementary Figure 1 Correlation between LKB1 and YAP expression in human lung cancer samples. (a) Representative photos showing LKB1 and YAP immunohistochemical staining in human