Blocking c-met mediated PARP1 phosphorylation enhances anti-tumor effects of PARP inhibitors

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1 CORRECTION NOTICE Nat. Med. 22, (216) Blocking mediated phosphorylation enhances anti-tumor effects of PARP inhibitors Yi Du, Hirohito Yamaguchi, Yongkun Wei, Jennifer L Hsu, Hung-Ling Wang, Yi-Hsin Hsu, Wan-Chi Lin, Wen-Hsuan Yu, Paul G Leonard, Gilbert R Lee IV, Mei-Kuang Chen, Katsuya Nakai, Ming-Chuan Hsu, Chun-Te Chen, Ye Sun, Yun Wu, Wei-Chao Chang, Wen-Chien Huang, Chien-Liang Liu, Yuan-Ching Chang, Chung-Hsuan Chen, Morag Park, Philip Jones, Gabriel N Hortobagyi & Mien-Chie Hung In the version of this article initially published, the concentrations of H 2 O 2 were incorrectly labeled as micromolar (μm) instead of millimolar (mm) in the legends of Supplementary Figures 3, 8f h, 1g,j and 12c,d. The error has been corrected in this file as of 25 August 216.

2 Supplementary Information Journal: Nature Medicine Article Title: Corresponding Author: Blocking -mediated phosphorylation enhances anti-tumor effects of PARP inhibitors Mien-Chie Hung Supplementary Item & Number Supplementary Table 1 Supplementary Table 2 Supplementary Table 3 Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Figure 4 Supplementary Figure 5 Supplementary Figure 6 Supplementary Figure 7 Title or Caption Correlation between 8-OHdG, TNBC, and non-tnbc subtype in human breast cancer tissues -associated receptor tyrosine kinases identified by an antibody array Correlation between py97- and in human triple-negative breast cancer tissues The levels of 8-OHdG (a marker of oxidative DNA damage) and DCF (an ROS marker) are higher in TNBC. TCGA database analysis of ERBB3, MET, and FLT3 associates with Downregulation of sensitizes cells to PARP inhibitors and reduces ROS Overexpression of increases the resistance of cells to PARP inhibitors is important for PARP inhibitor response is involved in DNA damage response Supplementary Figure 8 mediates phosphorylation of at Y97 contributing PARP inhibitor response. Supplementary Figure 9 Clinical correlation of py97 in human breast cancer tumor tissues Supplementary Figure 1 Synergistic effect of combination treatment of PARP and c- Met inhibitors Supplementary Figure 11 Inhibiting tumor growth and evaluating clinical chemistry or body weight of combination treatment of PARP and inhibitors Supplementary Figure 12 Synergistic effect of the combination treatment of PARP and inhibitors in -expressing breast cancer and NSCLC cells Nature Medicine: doi:1.138/nm

3 Supplementary Table 1. Correlation between 8-OHdG, TNBC, and non-tnbc subtype in human breast cancer tissues. 8-OHdG Low High Total Non-TNBC TNBC Total P =.1 Correlation analysis was performed using the Pearson chi-square test. A P value <.5 was considered statistically significant. Supplementary Table 2. -associated receptor tyrosine kinases identified by an antibody array. Density OD/mm 2 Kinases Sodium Arsenite Control Ratio ErbB HGFR () Flt VEGFR EphB EGFR ErbB ALK DDR Mer TrkC EphA VEGFR EphB DDR InR Tie EphB RYK EphA EphA FGFR M-CSFR c-ret ROR MuSK FGFR2a EphA Nature Medicine: doi:1.138/nm

4 FGFR PDGFRb EphA EphA Axl FGFR ROR Tie EphA Dtk IGF-IR Note: the number in the two middle columns is the intensity of the targeted molecules on the antibody array membrane. The ratio indicates the fold change between the sodium arsenite treatment group and non-treatment group. Supplementary Table 3. Correlation between py97- and in human triplenegative breast cancer tissues. py97- Low High Total Low High Total P =.21 Correlation analysis was performed using the Pearson chi-square test. A P value <.5 was considered statistically significant. Nature Medicine: doi:1.138/nm

5 DIC Non-TNBC DCF DIC TNBC DCF 8-OHdG 8-OHdG 8-OHdG Absorbance of DCF (X 1 4 ) a HCC1937 HCC7 BT2 Basal-like -468 SUM149 HCC38 HCC186 c BT549 Hs578T Mesenchymal LAR TNBC Non- TNBC SKBr3 HER2 ER HER2/ ER KPL4 SUM19 MCF-7 T47D ZR751 BT b Basal-like Mesenchymal LAR HCC1937 HCC7 BT2-468 SUM149 HCC38 HCC186 BT549 Hs578T HER2 ER HER2/ ER AU565 SKBr3 KPL4 SUM19 MCF T47D ZR751 BT Supplementary Figure 1. The levels of 8-OHdG (a marker of oxidative DNA damage) and DCF (an ROS marker) are higher in TNBC. (a) Breast cancer cell lines were stained with 8- OHdG antibody, and immunofluorescence signals were screened using a fluorescence microscope. Fluorescence intensity was measured by AxioVision software. Red fluorescent signals represent 8-OHdG. DAPI, blue. Bar, 2 µm. Images are representative of triplicate experiments. (b) DCF signals and differential interference contrast (DIC) images of breast cancer cell lines. Breast cancer cells were incubated with 1 μm 2',7'-dichlorofluorescin diacetate (DCFDA) for 3 min. Fluorescence signals were screened by a fluorescence microscope. Nature Medicine: doi:1.138/nm

6 Fluorescence intensity was measured by AxioVision software. Green fluorescent signals represent DCF. Bar, 1 µm. Images are representative of triplicate experiments. (c) Breast cancer cells (4 x 1 3 ) were seeded onto 96-well plates and treated with 1 μm of DCFDA for 3 min. DCF was measured using a plate reader and analyzed with GraphPad Prism software. Quantitation of triplicate experiments is shown. P <.5, t-test. LAR, luminal androgen receptor. Nature Medicine: doi:1.138/nm

7 HCC1937 HCC7 BT2-468 SUM149 HCC38 HCC186 BT549 Hs578T AU565 SKBr3 KPL4 SUM19 MCF T47D ZR751 BT Breast invasive carcinoma TCGA, n = 15 ERBB3 FLT3 MET ERBB2 ESR1 PGR Log transform median-centered ratio ERBB3 FLT3 MET ERBB2 ESR1 PGR a b TCGA, n = Gene c TNBC Basal-like Mesenchymal LAR Ctrl Non-TNBC HER2 ER HER2/ ER Supplementary Figure 2. TCGA database analysis of ERBB3, MET, and FLT3. (a) Cluster analysis of ERBB3, MET, and FLT3 mrna expression from the TCGA breast invasive carcinoma patient cohort (n = 15). Hierarchical clustering analysis of ERBB3, MET and FLT3 distinguished TNBC from other human breast tumors (n = 15). Breast cancer patients were categorized by mrna subtype as non-tnbc patients (n = 819) and TNBC patients (n = 231) according to expression of ERBB2, ESR1, and PGR (encoding HER2, ER, and PR, respectively). The color scale ranges from saturated green for log ratios of 4. and below to saturated red for log ratios of 4. and above. Red represents high gene expression (> 4), and green represents low Nature Medicine: doi:1.138/nm.432 4

8 gene expression (< 4). (b) Box plot generated from original and log2-transformed mrna expression levels of TNBC-related kinases in TNBC patients and non-tnbc patients by ESR1, PGR, and ERBB2 mrna subtyping. (c) Expression of in a panel of breast cancer cell lines. Cell lysates were subjected to Western blot analysis with indicated antibodies. LAR, luminal androgen receptor. P <.5, t-test. Nature Medicine: doi:1.138/nm

9 a b IP: IgG Flag Input H 2 O 2 Flag- WB V5- IgG WB IP: Input V5 IgG H 2 O 2 Flag- V5- IgG c IP IgG WB H 2 O 2 IgG Input - + H 2 O 2 d IP IgG H 2 O 2 WB IgG Input - + H 2 O 2 e IP IgG Flag H 2 O 2 WB Flag IgG Input - + H 2 O 2 Flag g As H 2 O 2 Control h Nucleus Merge Inset Cytoplasmic Ctrl As H 2 O 2 3 Nuclear 1 2 Ctrl As H 2 O 2 Nuclear (%) Lamin B Calregulin Nuclear (%) i Cyto Nuclear f WB IP IgG Flag H 2 O 2 Flag IgG Control Dyn A Dyn B shrna H 2 O 2 Lamin B Calregulin Dynein IC Lamin B Calregulin j Cyto Nuclear Input - + H 2 O 2 Flag Syn6 pcdna-6a Control Syn6 Syn6 shrna H 2 O 2 Lamin B Calregulin Syn 6 Lamin B Calregulin Supplementary Figure 3. associates with. (a,b) HEK293T cells were transfected with V5- and Flag- and then treated with 1 mm H 2 O 2 for 15 min. The association of and was detected by immunoprecipitation (IP)/Western blot. (c) -231 cells were treated with 2 mm H 2 O 2 for 3 min. The association of and was detected by IP/Western blot. (d) HCC1937 cells were treated with 2 mm H 2 O 2 for 3 min. The association of and was detected by IP/Western blot. (e,f) -436 and MCF-7 cells were transfected with Flag- and then treated with 2 mm H 2 O 2 for 3 min. The association of and was detected by IP/Western blot. (g,h) -231 cells were treated with 2 mm H 2 O 2 for 3 min and 5 µm sodium arsenite (As) for 18 h. Cells were Nature Medicine: doi:1.138/nm

10 subjected to confocal imaging assays and the cellular fractionation assay followed by Western blot analysis of the lysates. The percentage of nuclear (intensity based on confocal images is shown on the right. The percentage of nuclear (normalized to loading control, intensity based on Western blot) is shown below. (i) HeLa cells with or shrnas (Dyn A and Dyn B) of dynein intermediate chains (IC) were treated with H 2 O 2. Cells were subjected to cellular fractionation followed by Western blot with indicated antibodies. (j) HeLa cells expressing syntaxin 6 shrna (3 UTR) and re-expression of syntaxin 6 were treated with H 2 O 2, then subjected to cellular fractionation followed by Western blot with indicated antibodies. Syn 6, syntaxin 6. Nature Medicine: doi:1.138/nm

11 Intensity of DCF shmet-c Absorbance (%) HCC1937 Colony number (%) IC 5 (um, AZD2281) Soft agar cell growth Intensity of DCF -231 Normalized viability (%) Colony numbers (%) IC 5 (um, AG14699) Soft agar cell growth Colony numbers (%) IC 5 (um, ABT-888) Soft agar cell growth Normalized viability (%) IC 5 (um, AZD2281) Normalized viability (%) IC 5 (um, AG14699) Cell viability d e h a 1 IC 5 (um, ABT-888)2 AG14699 (μm) b (μm) Cri Ft shmet-a shmet-b Control AZD2281 (μm) AZD2281 (μm) Cri (.1 μm) Ft (.1 μm) DMSO Cri,.1 μm Ft,.1 μm ABT-888 (mm) g f shmet-a shmet-b shmet-a shmet-b shmet-a shmet-b i ABT-888 (μm) AG14699 (μm) plko control shmet-1 shmet c HCC shmet-a shmet-b AG14699 (μm) shmet-a shmet-b ABT-888 (mm) shmet-a shmet-b AG14699 (µm) j μm 1 μm 4 μm Cri Ft Cri Ft HCC k AG14699 (µm) ABT-888 (mm) shmet-c (Wt) (KD) ABT-888 (mm) shmet-c (Wt) (KD) Supplementary Figure 4. Downregulation of sensitizes cells to PARP inhibitors and reduces ROS. (a) -knockdown cells were treated with PARP inhibitor ABT-888 and Nature Medicine: doi:1.138/nm

12 subjected to cell viability assay. Median inhibitory concentration (IC 5 ) of ABT-888 in MDA- MB-231 cells with knockdown by cell viability assay. (b,c) -knockdown cells were treated with PARP inhibitors AZD2281 and AG14699, and subjected to cell viability assay. IC 5 of AZD2281 is shown on the right. Error bars represent s.d. (d) -231 cells were treated with AG14699 and crizotinib or foretinib and subjected to clonogenic cell survival assay. Representative images of three independent experiments are shown. (e) -231 cells were treated with ABT-888 and crizotinib or foretinib and subjected to cell viability assay. Error bars represent s.d. (f h) -knockdown cells were treated with PARP inhibitors ABT-888, AG14699, or AZD2281, and subjected to soft agar colony formation assay to determine anchorage-independent cell growth. Representative images and IC 5 of inhibitors are shown. (i) -knockdown -231 and HCC1937 cells by plko shrnas were incubated with 1 μm of DCFDA for 3 min. DCF level was then measured using a plate reader with spectra of 495EX nm/529em nm. Error bars represent s.d. (j) -231 and HCC1937 cells were pretreated with inhibitor crizotinib or foretinib for 1 h. Cells were then treated with 1 μm of 2,7 -dichlorofluorescin diacetate (DCFDA) for 3 min. DCF level was measured using a plate reader with spectra of 495EX nm/529em nm. (k) -knockdown (3 UTR) -231 cells re-expressing wild-type (Wt) or kinase dead (KD) were treated with ABT-888 or AG14699 and subjected to clonogenic cell survival assay. Representative images are shown. ABT, ABT-888; Cri, crizotinib; Ft, foretinib. Error bars represent s.d. P <.5, ranova. Nature Medicine: doi:1.138/nm

13 Relative absorbance (%) Colony numbers (%) Colony numbers (%) MCF-7 MCF-7 ABT (mm) MCF-7 MCF-7 Normalized viability (%) Normalized viability (%) Normalized viability (%) a d ABT-888 (mm) b e AG14699 (μm) AG14699 (μm) c f AZD2281 (mm) ABT-888 (mm) ABT-888 (mm) AG14699 (μm) ABT-888 (mm) Supplementary Figure 5. Overexpression of increases the resistance of cells to PARP inhibitors. (a c) -overexpressing MCF-7 cells were treated with PARP inhibitor ABT-888, AG14699, or AZD2281 and subjected to cell viability assay. (d) -overexpressing or control MCF-7 cells were treated with ABT-888 or AG14699 and subjected to clonogenic cell survival assay. Representative images are shown. (e,f) -overexpressing or control MCF-7 cells were treated with ABT-888 or AG14699 and subjected to soft agar colony formation assay to determine anchorage independent cell growth. Representative images are shown. AG, AG Error bars represent s.d. P <.5, ranova. Nature Medicine: doi:1.138/nm

14 Normalized viability (%) Relative absorbance (%) Relative absorbance (%) Normalized viability (%) Normalized viability (%) Normalized viability (%) IC 5 (ABT-888, µm) IC 5 (AG14699, µm) Normalized viability (%) IC 5 (ABT-888, µm) IC 5 (AG14699, µm) a b shmet-a shmet-b ABT -888 (µm) c d (Wt) (KD) ABT -888 (µm) e BRCA1 BRCA2 Actin f BRCA1 BRCA2 Actin g 12 8 shbrca1-a shbrca1-c shbrca2-b shbrca2-c h BRCA1 i 12 8 shbrca1-a shbrca1-c shbrca2-b shbrca2-c 4 4 n.s. j ABT-888 (mm) shbrca1-a shbrca1-c shbrca2-b shbrca2-c n.s. k BRCA2 shbrca1-a shbrca1-c shbrca2-b shbrca2-c n.s. l AG14699 (μm) shbrca1-a shbrca1-c shbrca2-b shbrca2-c n.s ABT-888 (μm) AG14699 (μm) ABT-888 (mm) Supplementary Figure 6. is important for PARP inhibitor response. (a) HCC1937 cells with knockdown were treated with PARP inhibitor AG14699 and subjected to cell viability assay. IC 5 of AG14699 in -knockdown HCC1937 by cell viability assay is shown. (b) HCC1937 cells with knockdown were treated with PARP inhibitor ABT-888 Nature Medicine: doi:1.138/nm

15 and subjected to cell viability assay. IC 5 of ABT-888 in HCC1937 cells is shown on the right. (c) -436 cells expressing wild-type (Wt), kinase dead (KD), or control vector were treated with AG14699 and subjected to cell viability assay. IC 5 of AG14699 in MDA- MB-436 with ectopic expression by cell viability assay is shown. (d) -436 cells expressing wild-type (Wt), kinase dead (KD), or control vector were treated with ABT-888 and subjected to cell viability assay. IC 5 of ABT-888 in -436 is shown on the right. (e,f) -knockdown -231 and -expressing -436 were subjected to Western blot with indicated antibodies. (g) BRCA1- or BRCA2-knockdown MDA- MB-157 cells were treated with ABT-888 and subjected to cell viability assay. (h) BRCA1 and BRCA2 expression in -231 BRCA1- or BRCA2-knockdown cells. (i l) BRCA1- or BRCA2-knockdown cells were treated with ABT-888 and AG114699, then subjected to cell viability assay or clonogenic cell survival assay. Error bars represent s.d. P <.5, ranova. n.s., not significant. Nature Medicine: doi:1.138/nm

16 DNA in the tail (%) DNA in the tail (%) γ-h2ax/ Nuclei DNA in the tail (%) DNA in the tail (%) a H 2 O 2 min 1 min shmet-a shmet-b d c shmet-a shmet-b 1 -Wt 75 -KD min 1 min e 1 75 b Cri shctrl shmet-a shmet-b Untreat H/A min 3 min 6 min only Recovery time after Hu/ Arac and H 2 O 2 treatment f Control ABT Actin Control H 2 O 2 Control H 2 O 2 Supplementary Figure 7. is involved in DNA damage response. (a) knockdown and control -231 cells were treated with H 2 O 2 for the indicated time and incubated with formanidopyrimidine DNA glycosylase (Fpg). DNA damage was assessed by comet assay. Representative images are shown. Quantification of DNA damage is shown on the right. (b) c- Met knockdown and control -231 cells were treated with H 2 O 2 and DNA repair hydroxyurea/cytosine-β-arabinofuranoside (Hu/AraC) to induce and allow DNA damage to accumulate. Hu/Arac and H 2 O 2 were replaced by fresh media, and cells were incubated for the indicated times. Damaged DNA was assessed by comet assay. Cells were incubated with formanidopyrimidine DNA glycosylase (Fpg) prior to a comet assay to evaluate the damaged DNA. Quantification of the levels of DNA damage is shown. (c) Western blot analysis of wild-type (Wt) and kinase dead (KD) mutant expression. (d) -overexpressing and control MCF-7 cells were treated with H 2 O 2 for the indicated times. Cells were incubated with Fpg prior to a comet assay to evaluate the damaged DNA. Quantitation of the damaged DNA is shown. (e) -overexpressing MCF-7 cells were treated with H 2 O 2 or with H 2 O 2 and pretreatment with Nature Medicine: doi:1.138/nm

17 crizotinib for 1h. Cells were incubated with Fpg prior to a comet assay to evaluate the damaged DNA. Quantification of DNA damage from experiments in triplicate is shown. (f) overexpressing and control MCF-7 cells were treated with PARP inhibitor ABT-888 (5 µm) for 18 h. γ-h2ax was detected by immunofluorescence confocal microscopy. Green fluorescence signals indicate γ-h2ax. Bar, 2 µm. Images are representative of triplicate experiments. H/A, Hu/AraC; Cri, crizotinib. Error bars represent s.d. P <.5, t-test. Nature Medicine: doi:1.138/nm.432 5

18 Viability (%) Viability (%) Viability %) Viability (%) ΔH (kj/ mol) ΔH (kj/ mol) ΔH (kj/ mol) Heat Rate (µj/ s) Heat Rate (µj/ s) Heat Rate (µj/ s) sh ABT-888 (µm) Activity (%) % of activity Coomassie blue a Wt 97F 986F b c GST- Wt 97F 986F γ-p32 GST μg py97 hot Y97 cold e sh + + H 2 O 2 py97- py1234- Calregulin f Wt Y97F + + H 2 O 2 py97- py1234- Actin d Dapi py97 Merge py peptide g H 2 O 2 S L py97- py1234- h L o g M B T ) Log μm (ABT-888) Wt Wt F E WtW t - H 2O 2 O 22 Wt W t + H 2O 2 O 2 Y97F Y 9 7 F Y97E Y 9 7 E i l j Time (s) 2, 4, Kd = nm 2 4 [ABT-888]/ [-Wt] Actin Time (s) 2, 4, plko sh-3 UTR -Wt -97F -97E shctrl-pgipz shmet-c 12 Kd = nm [ABT-888]/ [-Y97F] k Wt Y97F Y97E Time (s) H 2 O Y97-1, 3, Kd = nm [ABT-888]/ [-Y97E] ABT-888 (mm) shmet-c shmet-c Wt Y97F Y97E ABT-888 (mm) Wt 97F 97E AG14699 (µm) 4 Wt 97F 97E AG14699 (µm) 51 Nature Medicine: doi:1.138/nm.432

19 Supplementary Figure 8. mediates phosphorylation of at Y97 contributing PARP inhibitor response. (a) Coomassie blue staining of GST fusion wild-type and Y97F and Y986F mutants. (b) GST fusion wild-type and Y97F and Y986F mutants were incubated with [γ- 32 P]-ATP and purified. Radiolabeled ATP in was visualized by autoradiography. Total GST was visualized by Western blot. (c) A dot blot assay was used to evaluate the specific antibody against phosphorylated Y97 (py97) of. (d,e) Characterization of anti-py97- antibody in -knockdown MDA- MB-231 cells by confocal microscopy and Western blot analysis. Bar, 2 µm. (f) - knockdown -231 cells re-expressing wild-type or Y97F were treated with 2 mm H 2 O 2 for 3 min and subjected to Western blot analysis with indicated antibodies. (g) knockdown -231 cells were treated with 2 mm H 2 O 2 for 3 min and subjected to Western blot analysis with indicated antibodies. (h) -knockdown -231 cells reexpressing wild-type, Y97F, or Y97E were treated with 2 mm H 2 O 2 for 3 min. Cell lysates were subjected to PARP enzyme activity assay. IC 5 of wild type and Y97- mutants to ABT-888 by PARP enzyme activity assay. (i) In vitro binding ability of wild type and Y97- mutants to ABT-888 was measured by ITC assay. K d values are shown in the plots. (j) Western blot showing the expression of and in cells re-expressing wild-type or mutant with and without -knockdown. (k,l) Cells described in (j) were treated with PARP inhibitor ABT-888 (k) or AG14699 (l) and subjected to cell viability assay. Wt, wild-type. Error bars represent s.d. P <.5, ranova. Nature Medicine: doi:1.138/nm

20 a No peptide Phosphopeptide Non-phospho- Peptide Non-specific phospho-peptide b py97- c py97 8-OHdG Case 1 High Case 1 High Case 2 Low Case 2 Low py97- Low High Total Low High P < OHdG Low High Total py97 Low py97 High p = Supplementary Figure 9. Clinical correlation of py97 in human breast cancer tumor tissues. (a) A peptide competition assay was carried out to characterize py97- antibody by IHC staining of breast cancer patient tumor tissues. (b) Correlation analysis between and py97- in human non-tnbc tissue microarray. P <.1, Pearson chi-square test. (c) Correlation analysis between 8-OHdG and py97- in human TNBC tissue microarray. P =.19, Pearson chi-square test. Representative images of IHC staining for positive and negative cases are shown for (b) and (c). Nature Medicine: doi:1.138/nm

21 Combination index (CI) Combination index (CI) / 6.25/ /.5 25/ 1 5/ 2 Absorbance (%) CI =.55 CI =.2 CI =.52 CI =.34 Combination index (CI) AG/ Cri Combination Index (CI) Cri AG Ctrl a 2. b AG (μm) c AG (μm) d HCC MDA- 1937MB Cri (μm) Cri (μm) e g MCF-1A AG-Cri MCF-1A ABT-Ft Fraction affected (Fa) ABT (μm) Ft (μm) 6.25/ 12.5/ 25/ 5/ ABT Ft Combination Index (CI) py97- py1234- h / 15/ 3/ 6/ AG/ Cri Combination Index (CI) A134 AG-Cri A134 ABT-Ft ABT (μm) Fraction affected (Fa) i Ft (μm) 3.75/ 7.5/ 15/ 3/ AG/ Cri Combination Index (CI) ABT/ Ft (μm) A1471 ABT-Ft A1471AG-Cri Fraction affected (Fa) f j Fraction affected (Fa) A134 BT549 AG-Cri BT549 ABT-Ft A1471 py97- py1234- Supplementary Figure 1. Synergistic effect of combination treatment of PARP and inhibitors. (a) MCF-1A cells were treated with combinations of PARP inhibitors (AG14699, ABT-888) and inhibitors (crizotinib, foretinib). (b,c) The synergistic effect of inhibitor crizotinib and PARP inhibitor AG14699 was measured by clonogenic cell survival assay following an 8-day treatment in -231 cells (b) and HCC1937 cells (c). Representative images of three independent experiments are shown. (d) The synergistic effect of crizotinib and AG14699 was measured by soft agar assay in -231 cells and HCC1937 cells. Representative images of three independent experiments are shown (e) MDA-B231 cells were treated with foretinib and ABT-888. The synergistic effect of foretinib and ABT-888 was Nature Medicine: doi:1.138/nm

22 measured by the clonogenic cell survival assay. Representative images and quantitation are shown. (f) BT549 cells were treated with PARP and inhibitors, and the synergistic effect of the combination treatment was measured by cell viability assay. (g) BT549 cells were treated with 2 mm H 2 O 2 for 3 min or with H 2 O 2 plus 2 µm crizotinib pre-treatment for 1 h, and cell lysates were subjected to Western blot analysis with the indicated antibodies. (h,i) Mouse breast cancer cells, A134 and A1471, were treated with PARP and inhibitors, and the synergistic effect of the combination treatment was measured by cell viability assay. (j) Mouse breast cancer cells, A134 and A1471, were treated with 2 mm H 2 O 2 for 3 min or with H 2 O 2 plus 2 µm crizotinib pre-treatment for 1 h, and cell lysates were subjected to Western blot analysis with the indicated antibodies. The synergistic effect was determined by calculating the combination index (CI) based on the Chou Talalay method. AG, AG14699; Cri, crizotinib; ABT, ABT-888; Ft, foretinib. Error bars represent s.d. Nature Medicine: doi:1.138/nm

23 Body weight (g) Blood Urea Nitrogen (BUN, mg/ dl) ALT (SGPT, U/ L) Body weight (g) γ-h2ax/ Nuclei Body weight (g) Blood Urea Nitrogen (BUN, mg/ dl) ALT (SGPT, U/ L) Control AG Cri AG/Cri ref Control AG Cri AG/Cri ref Control AG Cri AG/Cri ref Control AG Cri AG/Cri ref Blood Urea Nitrogen (BUN, mg/ dl) Creatinine (mg/ dl) AST (SGOT, U/ L) ALT (SGPT, U/ L) Day 15 Day 5 Tumor size (mm 3 ) Tumor size (mm 3 ) Day 21 Day 21 Day 7 Day 7 a Control AG Cri AG/ Cri 6 b Control ABT Ft ABT/ Ft (X1 4 ) (X1 4 ) e c Control AG Cri AG/ Cri Control AG f (X1 4 ).4 3, 2,4 1,8 1,2 6 Vehicle AG Cri AG-Cri Days after inoculation g 2 d Vehicle AG Cri AG/Cri Days after inoculation 12 Ki67/ Nuclei Tunel/ Nuclei Cri Control Cri Control AG/ Cri AG AG/ Cri AG h Before treatment 21 days after treatment Kidney function i Liver function Cri AG/ Cri j 4 Before treatment 16 days after treatment 3 k Kidney function l Liver function 3 Before treatment 12 days after treatment Kidney function Liver function 56 Nature Medicine: doi:1.138/nm.432

24 Supplementary Figure 11. Inhibiting tumor growth and evaluating clinical chemistry or body weight of combination treatment of PARP and inhibitors. (a,b) Representative IVIS imaging of nude mice bearing -231 tumors after AG14699/crizotinib and ABT- 888/foretinib treatment at the indicated days. (c) A134 cells were injected into the mammary fat pad of FVB mice on day. When the tumor volume reached ~5 mm 3, mice were orally administered crizotinib (5 mg/kg), AG14699 (5 mg/kg), or the combination 5 times per week for 28 days. Representative IVIS imaging of FVB mice bearing A134 tumors on days 7 and 21 after treatment. Tumor volume was measured at the indicated time points. (d) HCC1937 cells were injected into the mammary fat pad of nude mice on day. When the tumor volume reached ~5 mm 3, mice were orally administered crizotinib (5 mg/kg), AG14699 (5 mg/kg), or the combination 5 time per week for 18 days. Tumor volume was measured at the indicated time points. (e) TUNEL, Ki67 and γ-h2ax staining of -231 xenograft tumor tissues treated with crizotinib and AG Representative images of staining results are shown. Bar, 1 μm. (f,g) The effects of AG14699 and/or crizotinib treatment on kidney and liver functions in nude mice with -231 xenografts after treatment for 21 days. (h) The body weight of nude mice before and after 21 days of AG14699 and/or crizotinib treatment. (i) The effects of ABT- 888 and/or foretinib treatment on kidney and liver functions in nude mice with -231 xenografts after treatment for 16 days. (j) The body weight of nude mice before and after 16 days of ABT-888 and/or foretinib treatment. (k) The effects of AG14699 and/or crizotinib treatment on kidney and functions in FVB mice with A134 syngeneic grafts after 12 days treatment. (l) The body weight of FVB mice before and after 12 days of AG14699 and/or crizotinib treatment. AST, aspartate aminotransferase. ALT, alanine transaminase. AG, AG14699; Cri, crizotinib; Nature Medicine: doi:1.138/nm

25 ABT, ABT-888; Ft, foretinib; AST, aspartate aminotransferase; ALT, alanine transaminase. Error bars represent s.d. P <.5, t-test. Nature Medicine: doi:1.138/nm

26 a Combination index (CI) b Combination index (CI) AG-Cri Wt AG-Cri KD AG-Cri Fraction affected (Fa) H1993 ABT-Ft H1993 AG-Cri A549 ABT-Ft A549 AG-Cri Fraction affected (Fa) c d Control Control H1993 H 2 O 2 H 2 O 2 Cri/ H 2 O 2 Cri/ H 2 O 2 Control py97- py1234- A549 H 2 O 2 Cri/ H 2 O 2 e py97- py1234- ROS PARP inhibitor P p- DNA repair Supplementary Figure 12. Synergistic effect of the combination treatment of PARP and inhibitors in -expressing breast cancer and non-small cell lung cancer cells. (a) MCF-7 cells with ectopic expression of vector, wild-type (Wt), or kinase dead (KD) were treated with the combination of AG14699 and crizotinib. The synergistic effect of the combination treatment was measured by cell viability assay. (b) Lung cancer cells H1993 and A549 were treated with PARP inhibitors (AG14699, ABT-888) and inhibitors (crizotinib, foretinib), and the synergistic effect of the combination treatment was measured by cell viability assay. (c) MCF-7/ cells were treated with 2 mm H 2 O 2 for 3 min or H 2 O 2 with 2 µm crizotinib pre-treatment for 1 h, and cell lysates were subjected to Western blot with the indicated antibodies. (d) H1993 and A549 cells were treated with 2 mm H 2 O 2 for 3 min or with H 2 O 2 plus 2 µm crizotinib pre-treatment for 1 h, and cell lysates were subjected to Western Nature Medicine: doi:1.138/nm

27 blot analysis with the indicated antibodies. (e) Proposed model. ROS-activated phosphorylates at Y97. Phosphorylated (p-) enhances DNA repair activity, thereby contributing to PARP inhibitor resistance. The synergistic effect was determined by calculating the combination index (CI) based on the Chou Talalay method. AG, AG14699; Cri, crizotinib; ABT, ABT-888; Ft, foretinib. Nature Medicine: doi:1.138/nm.432 6