Figure S1 Time-dependent down-modulation of HER3 by EZN-392 HE ER3 mrna A, %Contr rol 12 No Treatment EZN-392, 2 μm 1 8 6 4 2 2 8 24 Time, h
Figure S2. Specific target down-modulation by HER3 (EZN-392) and β-catenin (EZN-3889 and EZN-3892) LNA-ONs in SW48 cells. A B 16 3 μm 14 1 μm 12 1 8 6 4 14 3 μm 12 1 μm 1 8 6 4 β-catenin mrna, %Control HER3 mrna, %Control 2 2 Untreated EZN-392 EZN-3889 Untreated EZN-3889 EZN-392
Figure S3. In vitro cell uptake of FAM-conjugated EZN-392 2 15 1 15PC3 SK-BR3 A549 2 15 1 2 15 1 min 5 min 1 h 24 h 5 5 5 1e 1e1 1e2 1e3 1e4 1e 1e1 1e2 1e3 1e4 1e 1e1 1e2 1e3 1e4 15 2 HCC827 15 2 LNCap 15 2 22Rv1 5 5 5 1 1 1 1e 1e1 1e2 1e3 1e4 1e 1e1 1e2 1e3 1e4 1e 1e1 1e2 1e3 1e4
Figure S4. Nuclear localization of FAM-EZN-392 in HCC827 but not DLD-1 cells A HCC827 with 5 μm FAM-392 DLD-1 with 5 μm FAM-392 B 12 C 14 HER R3 mrna, %Con ntrol 1 8 6 4 2 HER R3 mrna, %Con ntrol 12 1 8 6 4 2.1.25.5 1 2 EZN-392, μm.25.5 1 2 EZN-392, μm
Figure S5. FAM-EZN-392 was stable in 15PC3 cell culture FAM EZ ZN 392 in culture medium, RLU 2 15 1 5 With cells Without cells %Contro ol 1 8 6 4 2 5 24 Time, hour 1 5 1 [FAM EZN 392], μm FAM EZN 392 With cells Without cells (μm) A B Average ratio A B Average ratio 1 268 249 259 1 172 182 177 1 5 189 119 154 4 786 82 794 4 1 1759 184 1782 7 1351 1555 1453 8
Figure S6. EZN-3889 specifically down-modulated β-catenin in 15PC3 cells β-catenin HER3 β-tubulin
Figure S7. LNA-ASO failed to inhibit synthesis of HER3-Lumio in an in vitro transcription and translation assay A 7 RFU 6 5 Control EZN-415,.1 μm EZN-392,.1 μm HER3-Lumio, 4 3 2 1 C 2 4 6 8 1 12 Time, min HER3-Lumio HER3-Lumio
Figure S8. Down-modulation of mrna in liver and tumors at different time points after one bolus dose HE ER3 mrna, %Control 14 12 1 8 6 4 2 Liver Tumor 1 2 4 7 Time, Day
Table S1. Relative sensitivity of cells to LNA treatment in mrna down-modulation Cell Lines Tumor Type Knockdown Efficiency UMUC-3 Bladder ++++ BT-474 Breast ++ JIMT Breast +++ T47D Breast +++ MDA-MB-361 Breast +++ MDA-MB-453 MB Breast ++++ SKBR3 Breast +++++ HCT-116 Colorectal ++ DLD-1 Colorectal ++ SW48 Colorectal +++ H18 Fibrosarcoma +++++ U87MG Glioma ++++ Huh-7 Hepatoma + A549 Lung ++ H46 Lung ++ H1975 Lung ++ H1581 Lung ++++ A427 Lung ++++ Calu-6 Lung +++++ HCC827 Lung +++++ HCC827R Lung +++++ 518A2 Melanoma +++ BxPC3 Pancreatic +++ 22RV1 Prostate + DU-145 Prostate ++ PC3 Prostate +++ LNCaP Prostate +++ 15PC3 Prostate +++++ % mrna down-modulation at 5 μm within 72 hrs. +++++, 8, < 1; ++++, 6, < 8; +++, 4, < 6; ++, 2, < 4; +,, < 2.
Figure S1. Time-dependent down-modulation of HER3 by EZN-392. 15PC3 (plated at approximately 5,/cm 2 ) were treated with 2 μm of EZN-392 and measured for HER3 mrna levels at different time points as indicated. A corresponding control (Saline) was included for each time point. Data are shown as means ± SE (n = 3). Figure S2. Specific target down-modulation of HER3 (EZN-392) and β-catenin (EZN- 3889) LNA-ONs in SW48 colorectal cancer cells. LNA-ONs were added to tissue culture media at the indicated concentrations and incubated with SW48 cells (plated at approximately 2/cm 2 ). Down-modulation of β-catenin (A) or HER3 (B) mrna after treatment for 6 days was determined by RT-qPCR with TaqMan gene expression assay. Data are shown as mean ± SD of duplicates. Figure S3. In vitro cell uptake of FAM-conjugated EZN-392. Cells cultured (plated at approximately 5,/cm 2 ) in multi-well plates were treated with 4 μm FAM-EZN-392 for designated time. The cultured cells were washed, trypsinized, and re-suspended in medium, and then analyzed using Guava EasyCyte instrument with the Expression Plus module. Figure S4. Nuclear localization of LNA-ONs correlated with mrna down-modulation. (A) HCC827 and DLD-1 cells (plated at approximately 2,/cm 2 )were treated with 5 -FAM-EZN- 392 for 24 h and examined under the microscope for FAM and Hoechst signals (as described in Methods). From left to right: FAM, superimposed FAM and Hoechst, Normarski Differential Interference Contrast (B) HCC827 (left) and DLD-1 (right) were treated with different concentrations of EZN-392 and HER3 mrna levels determined after 24 h. Figure S5. FAM-EZN-392 was stable in 15PC3 cell culture. 15PC3 cells were plated at.1 1 6 /well in 6-well plates and maintained in a 37 C incubator for 24 h. FAM-EZN-392 was added to the 2 ml culture to form final concentrations of 1, 5 and 1 μm. At the indicated time points, medium was collected into Eppendorf tubes and centrifuged. Ten μl of supernatant were injected to an HPLC equipped with a UV detector to determine the relative amount of FAM- EZN-392 (blue line). A parallel experiment also was conducted in 6-well plates without cells to show linearity of the signal in proportion to the input amount of FAM-EZN-392 (red line). The study was performed in duplicate. The relative amount of compound and ratios in one μm input are shown in the table. The insert shows the stability of FAM-EZN-392 in culture medium over 24 h. Figure S6. EZN-3889 specifically down-modulated β-catenin in SW48 cells. SW48 cells (plated at approximately 2,/cm 2 ) were treated with 3 or 5 μm EZN-3889 and analyzed for β- catenin and HER3 protein levels by immunoblotting on day 5. Figure S7. LNA-ON failed to inhibit protein synthesis through steric blocking. The Expressway Lumio Cell-Free Expression System (Invitrogen) was used for in vitro protein synthesis. The gene segment encoding partial human HER3 (amino acid residues 2-814) was cloned from 15PC3 cell by RT-PCR and inserted into the vector pexp3-dest. The resulting expression vector is predicted to direct synthesis of N-terminal lumio tagged HER3 223 amino acid residues in the cell-free expression system (Invitrogen). In vitro transcription and translation was conducted based on the manufacturer-recommended conditions. Briefly, the reaction solution (5 μl) contained the following components: 2 μl Escherichia coli slyd extract, 2.5 μl
reaction mix, 3 μl amino acids solution, 2 μl methionine solution, 1 μl T7 enzyme mix and 1 μg of circular DNA template, 1 μl Lumio green detection reagent, and nuclease-free water with or without.1 μm EZN-392 or EZN-415. The reaction was conducted at 37 C for 1-2 h in a Gemini XS spectrofluorometer (Molecular Devices), where the amount of lumio-tag synthesized was monitored real-time (Ex = 5 nm, Em = 535 nm)(a). The fusion protein product was recovered by cold acetone and analyzed by SDS-PAGE (B). Figure S8. Down-modulation of mrna in liver and tumors at different time points after one bolus dose. Tumor-bearing mice were dosed on day with 1 mg/kg EZN-392. Liver and tumors were harvested on day1, 2, 4, and 7. Total RNA was extract from liver and tumor tissues and HER3 mrna levels determined by real-time PCR. TaqMan gene expression assays specific for mouse and human HER3 were used for liver and tumor samples, respectively.