May 8th, 2014 Dear Dr. Blagosklonny We plan to submit the revised version of the manuscript entitled “Novel peptides suppress VEGFR-3 activity and antagonize VEGFR-3-mediated oncogenic effects” by Chang et al be considered for publication in Oncotarget. We have answered every point of comments raised by reviewers. Your kind consideration of our replies is greatly appreciated. Based on reviewer’s suggestions, we have performed new experiments and made substantial changes in this revised version (Figure 3E-3H, Figure 4, Figure 5A and B, Supplemental Figure S1-S6) and these newly added description are marked by red color in this manuscript. The suggestions and questions raised by reviewers were addressed specifically as below. Sincerely yours, Jen-Liang Su, Ph. D National Institute of Cancer Research, National Health Research Institutes Graduate Institute of Cancer Biology, College of Medicine, China Medical University Center for Molecular Medicine, China Medical University Hospital 1 No. 35, Keyan Road, Zhunan, Miaoli Country 35053, Taiwan. Tel: +886-37-246-166 Fax: +886-37-586-401 E-mail: jlsu@nhri.org.tw 2 Response to Reviewer D: Point 1: Q: Figure 1. There is a discrepancy regarding peptide 7. It had a low binding affinity to VEGFR-3, but a strong inhibitory effect on VEGFR-3. This needs to be explained. Ans: The discrepancy regarding P7 peptide in Figure 1A (low binding affinity) and Figure 1B (high inhibitory effects on VEGFR-3) may results from non-specific inhibition and sensitivity of performed experiments. The reason we thought the effect may due to non-specific function because we can’t detect significant inhibitory effects of P7 peptide on VEGFR-3 activity by other VEGFR-3 activity related experiments, for example, both KIRA-ELISA assay (Figure 1C), western blot assay (Figure 2A and 2B) shows VEGF-C-induced VEGFR-3 activation did not significantly inhibit by P7 peptide. Point 2: Q: Figure 3A-D. It is unclear whether the authors presented net migration and net invasiveness rates independent of cell survival. Normalization against proliferation rates is needed. Ans: Thanks for reviewer’s comments. All migration and invasion assays in this study were normalized to the proliferation rate. We have added the description in 3 the Material and Methods section on page 14, line 31 and changed Y-axis labeling to migration/proliferation (% of control) and invasion/proliferation (% of control) in corresponding figures. Point 3: Q: Fig. 4. MCF-7 cells were not tested for peptide 6. Ans: We have tested peptide 6 (P6) in MCF-7 cells for the sphere-forming assay and we found that P6 blocked VEGF-C-induced tumor initiating cells (TICs) formation in A549 cells but not in MCF-7 cells (Supplemental Figure S5B). The different effects of P6 on TICs in A549 and MCF-7 cells is an interesting issue and detailed mechanism and cell specificity need further studies. Point 4: Q: English editing will improve the manuscript. Ans: Thanks for reviewer’s suggestion, we have sent our manuscript to English editing by Nature Publishing Group Language Editing to improve our manuscript and enclosed with the editing certificate. Response to Reviewer 2: 4 Point 1: Q: The paper is written with mistakes in every sentence and with using phrases that make little sense in the context In the Abstract. “has been documented as a gatekeeper signal molecule to trigger” “The above-mentioned results from bench and bedside, and its widespread and specific expression in cancers strongly suggest that VEGFR-3 is a crucial RTK and its therapeutic potential strongly merits further investigation.” This sentence has no meaning with completely incorrect grammar: I rewrote Abstract, all text must be edited. Ans: Thanks for reviewer’s comments and appreciated reviewer rewrote the abstract for us. We have sent our manuscript to English editing by Nature Publishing Group Language Editing to improve our manuscript and enclosed with the editing certificate. Point 2: Q: taxol should be paclitaxel or Taxol Ans: We corrected “taxol” to ‘Taxol” on page 8, lines 2 and 15, page 10 line 21, and page 12 line 6. Point 3: 5 Q: Fig. 3 E, F – effect on drug resistance. These drugs cause cell cycle arrest and inhibit proliferation in A549 and MDA cells. These cells do not die after 48 hrs of treatment. MTT inhibition is just 50% (whereas cells proliferate in control). MTT test cannot be used here. Use cell count, trypan blue, flow cytometry. VEGF cannot possibly decrease effect of Taxol on proliferation. This is simply impossible to believe. The data may be falsified. Ans: According to reviewer’s suggestion, we used trypan blue exclusion assay and DNA flow cytometric assay to detect the effects of VEGF-C on drug resistance in A549 cells (Figure 3E-3H). As shown in Figure 3E and 3F, VEGF-C significantly decreased Taxol and cisplatin-mediated cell death by flow cytometric analysis. By trypan blue exclusion assay, we also found that VEGF-C treatment increases the cell viability in the present of Taxol and cisplatin (Figure 3G and 3H). In addition, P5 and P6 peptides significantly abolished VEGF-C-induced drug resistance was also verified by both flow cytometry and trypan blue exclusion assays. We have carefully searched references and found that previous studies also detect the effects of Taxol and cisplatin on cell viability by MTT assay [1-6]. In fact, it has been reported that VEGF-C helps cancer cells to survive Taxol treatment via downregulation of mTORC1 function in prostate and pancreatic cancers [7]; additionally, VEGF-C was shown to enhance cisplatin-resistance through NF-κB activation in gastric 6 cancer [8]. Moreover, VEGF-C-induced Akt activation has been suggested to promote prostate cancer cell survival [9]. Depletion of VEGF-C has further been shown to inhibit cell proliferation and cell invasion in non-small cell lung cancer (NSCLC) [10]. VEGFR-3 overexpression or activation also confers chemo-resistance to treatment in leukemia cancer by enhancing Bcl-2 expression [11]. According to above studies and our experimental data, VEGF-C increased cancer cell survival, proliferation and resistant to Taxol and cisplatin treatment is reasonable and believable. We have added above data into Results section (page 8 lines 1-9), the description of these two assays (trypan blue exclusion assay and DNA flow cytometric assay) were included in Material and Methods section on page 14 lines 32-34 to page 15 lines 1-7 and we moved MTT results into Supplemental Figure S3. Figure 3 7 Point 4: Q: Labeling and especially labeling on Y-axis is too small to be visible in print. Ans: We have refined the Y-axis labeling of our figures to make it more clearly. Point 5: Q: Figure 4. the effect is small. I suggest to move it to supplement and not to emphasize Ans: According to reviewer’s suggestion, we have moved these data to Supplemental Figure S5. Major points: Major Point 1: Q: Structures of the peptides must be provided. Ans: We have provided the structures of peptides in Supplemental Figure S1 and added description on page 6 line 12. Major Point 2: Q: Endothelial cells, including lymphatic endothelial cells, should be tested 8 Ans: According to reviewer’s suggestion, we invegestigated the effects of VEGFR-3-inhibitroy peptides on VEGF-C-induced VEGFR-3 phosphorylation, migration and proliferation in lymphatic endothelial cells (LECs) in Figure 4A. Our data indicated that VEGF-C-induced VEGFR-3 phosphorylation, cell migration and proliferation of LECs were abolished by the P5 and P6 peptides. We have added the description of above data into Results section on page 8 lines 28-35. Figure 4 Major Point 3: Q: A wide panel of cancer and normal cells must be tested Ans: As suggested by the reviewer, we have examined the effects of P5 and P6 peptides on VEGFR-3 phosphorylation and cell migration and invasion in various cancer cells lines (breast cancer cell lines: MDA-MB-231, BT474, HS578T, HBL100, MDA-MB-361, and MCF-7; lung cancer cell lines: CL1-5, H460 and H322) ( Figure 9 4B-4E and Supplemental Figure S4). Our results indicated that P5 and P6 peptides significantly inhibit VEGF-C-induced VEGFR-3 phosphorylation, cell migration and invasion ability in all tested cancer cell lines. We also examined the effect of VEGFR-3-inhibitory peptides on cell proliferation and migration of LECs. As shown in Figure 4A, our data indicated that P5 and P6 peptides inhibit VEGF-C-induced VEGFR-3 phosphorylation, cell migration and proliferation in LECs. We have added above description in Results section on page 8 lines 28-36 to page 9 lines 1-5 and cell line information in Material and Methods section on page 12 lines 14-26. Figure 4 10 Major Point 4: Q: The effect on tumor model must be shown in animal model, in mice Ans: According to reviewer’s suggestion, we performed the expermental metastasis animal model to confirm our in vitro findings. Briefly, we stably transfected VEGF-C-expressing vector (MDA-MB-231/VEGF-C) or control vector (MDA-MB-231/vector) into MDA-MB-231 cells for experimental metastasis assay by tail-vein injection. Control (P4), P5 and P6 peptides were i.v. injected into mice one day before the cancer cell injection. After injected with indicated cancer cells into mice, peptides were administered twice weekly for 8 weeks and detect the lung metastatic nodules by bioluminescent imaging system. Our data demonstrated that VEGF-C-induced metastasis was significantly inhibit by P5 and P6 peptides in animal model (Figure 5A and 5B). These data was described on page 9 lines 24-33 and experimental procedures was incorporated into Material and Methods section on page 15 lines 33-34 to page 16 lines 1-11. Figure 5 11 REFERENCES 1. Holleman A, Chung I, Olsen RR, Kwak B, Mizokami A, Saijo N, Parissenti A, Duan Z, Voest EE and Zetter BR. miR-135a contributes to paclitaxel resistance in tumor cells both in vitro and in vivo. Oncogene. 2011; 30(43):4386-4398. 2. Zhang D, Qiu L, Jin X, Guo Z and Guo C. Nuclear factor-kappaB inhibition by parthenolide potentiates the efficacy of Taxol in non-small cell lung cancer in vitro and in vivo. Molecular cancer research : MCR. 2009; 7(7):1139-1149. 3. Sui M, Huang Y, Park BH, Davidson NE and Fan W. Estrogen receptor alpha mediates breast cancer cell resistance to paclitaxel through inhibition of apoptotic cell death. 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