scholarly journals Registered report: Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
David Blum ◽  
Samuel LaBarge ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered Report describes the proposed replication plan of key experiments from ‘Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion’ by Straussman and colleagues, published in Nature in 2012 (<xref ref-type="bibr" rid="bib10">Straussman et al., 2012</xref>). The key experiments being replicated in this study are from Figure 2A, C, and D (and Supplemental Figure 11) and Figure 4C (and Supplemental Figure 19) (<xref ref-type="bibr" rid="bib10">Straussman et al., 2012</xref>). Figure 2 demonstrates resistance to drug sensitivity conferred by co-culture with some stromal cell lines and identifies the secreted factor responsible as HGF. In Figure 4, Straussman and colleagues show that blocking the HGF receptor MET abrogates HGF’s rescue of drug sensitivity. The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
David Blum ◽  
Haiping Hao ◽  
Michael McCarthy ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Transcriptional amplification in tumor cells with elevated c-Myc’ by <xref ref-type="bibr" rid="bib5">Lin et al. (2012)</xref>, published in Cell in 2012. The experiments that will be replicated are those reported in Figures 3E and 3F. In these experiments, elevated levels of c-Myc in the P493-6 cell model of Burkitt's lymphoma results in an increase of the total level of RNA using UV/VIS spectrophotometry (Figure 3E; <xref ref-type="bibr" rid="bib5">Lin et al., 2012</xref>) and on the mRNA levels/cell for a large set of genes using digital gene expression technology (Figure 3F; <xref ref-type="bibr" rid="bib5">Lin et al., 2012</xref>). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published in eLife.


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Brad Evans ◽  
Erin Griner ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (<xref ref-type="bibr" rid="bib3">Errington et al., 2014</xref>). This Registered report describes the proposed replication plan of key experiments from ‘Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases’ by Xu and colleagues, published in Cancer Cell in 2011 (<xref ref-type="bibr" rid="bib15">Xu et al., 2011</xref>). The key experiments being replicated include Supplemental Figure 3I, which demonstrates that transfection with mutant forms of IDH1 increases levels of 2-hydroxyglutarate (2-HG), Figures 3A and 8A, which demonstrate changes in histone methylation after treatment with 2-HG, and Figures 3D and 7B, which show that mutant IDH1 can effect the same changes as treatment with excess 2-HG. The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ajay Bhargava ◽  
Madan Anant ◽  
Hildegard Mack ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (<xref ref-type="bibr" rid="bib4">Errington et al., 2014</xref>). This Registered Report describes the proposed replication plan of key experiments from "Kinase-dead BRAF and oncogenic RAS cooperate to drive tumor progression through CRAF" by Heidorn and colleagues, published in Cell in 2010 (<xref ref-type="bibr" rid="bib9">Heidorn et al., 2010</xref>). The experiments to be replicated are those reported in Figures 1A, 1B, 3A, 3B, and 4D. Heidorn and colleagues report that paradoxical activation of the RAF-RAS-MEK-ERK pathway by BRAF inhibitors when applied to BRAFWT cells is a result of BRAF/CRAF heterodimer formation upon inactivation of BRAF kinase activity, and occurs only in the context of active RAS. The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Mitch Phelps ◽  
Chris Coss ◽  
Hongyan Wang ◽  
Matthew Cook ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (<xref ref-type="bibr" rid="bib8">Errington et al., 2014</xref>). This Registered Report describes the proposed replication plan of key experiments from “Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous 'mRNAs' by Tay and colleagues, published in Cell in 2011 (<xref ref-type="bibr" rid="bib23">Tay et al., 2011</xref>). The experiments to be replicated are those reported in Figures 3C, 3D, 3G, 3H, 5A and 5B, and in Supplemental Figures 3A and B. Tay and colleagues proposed a new regulatory mechanism based on competing endogenous RNAs (ceRNAs), which regulate target genes by competitive binding of shared microRNAs. They test their model by identifying and confirming ceRNAs that target PTEN. In Figure 3A and B, they report that perturbing expression of putative PTEN ceRNAs affects expression of PTEN. This effect is dependent on functional microRNA machinery (Figure 3G and H), and affects the pathway downstream of PTEN itself (Figures 5A and B). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
John P Vanden Heuvel ◽  
Jessica Bullenkamp ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about the reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (<xref ref-type="bibr" rid="bib7">Errington et al., 2014</xref>). This Registered Report describes the proposed replication plan of key experiments from “Systematic identification of genomic markers of drug sensitivity in cancer cells” by Garnett and colleagues, published in Nature in 2012 (<xref ref-type="bibr" rid="bib9">Garnett et al., 2012</xref>). The experiments to be replicated are those reported in Figures 4C, 4E, 4F, and Supplemental Figures 16 and 20. Garnett and colleagues performed a high throughput screen assessing the effect of 130 drugs on 639 cancer-derived cell lines in order to identify novel interactions for possible therapeutic approaches. They then tested this approach by exploring in more detail a novel interaction they identified in which Ewing’s sarcoma cell lines showed an increased sensitivity to PARP inhibitors (Figure 4C). Mesenchymal progenitor cells (MPCs) transformed with the signature EWS-FLI1 translocation, the hallmark of Ewing’s sarcoma family tumors, exhibited increased sensitivity to the PARP inhibitor olaparib as compared to MPCs transformed with a different translocation (Figure 4E). Knockdown mediated by siRNA of EWS-FLI1 abrogated this sensitivity to olaparib (Figure 4F). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Irawati Kandela ◽  
James Chou ◽  
Kartoa Chow ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Coadministration of a tumor-penetrating peptide enhances the efficacy of cancer drugs’ by Sugahara and colleagues, published in Science in 2010 (<xref ref-type="bibr" rid="bib10">Sugahara et al., 2010</xref>). The key experiments being replicated include Figure 2 and Supplemental Figure 9A. In Figure 2, Sugahara and colleagues presented data on the tumor penetrance of doxorubicin (DOX) when co-administered with the peptide iRGD, as well as the effect of co-treatment of DOX and iRGD on tumor weight and cell death. In Supplemental Figure 9A, they tracked body weight of mice treated with DOX and iRGD to provide evidence that iRGD does not increase known DOX toxicity. The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Samrrah Raouf ◽  
Claire Weston ◽  
Nora Yucel ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Senescence surveillance of pre-malignant hepatocytes limits liver cancer development’ by <xref ref-type="bibr" rid="bib9">Kang et al. (2011)</xref>, published in Nature in 2011. The experiments that will be replicated are those reported in Figures 3B, 3C, 3E, and 4A. In these experiments, <xref ref-type="bibr" rid="bib9">Kang et al. (2011)</xref> demonstrate the phenomenon of oncogene-induced cellular senescence and immune-mediated clearance of senescent cells after intrahepatic injection of NRAS (Figures 2I, 3B, 3C, and 3E). Additionally, <xref ref-type="bibr" rid="bib9">Kang et al. (2011)</xref> show the specific necessity of CD4+ T cells for immunoclearance of senescent cells (Figure 4A). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Kate Eaton ◽  
Wanwan Yang ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota’ by <xref ref-type="bibr" rid="bib2">Arthur et al. (2012)</xref>, published in Science in 2012. Arthur and colleagues identified a genotoxic island in Escherichia coli NC101 that appeared to be responsible for causing neoplastic lesions in inflammation-induced IL10−/− mice treated with azoxymethane. The experiments that will be replicated are those reported in Figure 4 (<xref ref-type="bibr" rid="bib2">Arthur et al., 2012)</xref>. Arthur and colleagues inoculated IL10−/− mice with a mutated strain of E. coli NC101 lacking the genotoxic island, and showed that those mice suffered from fewer neoplastic lesions than mice inoculated with the wild type form of E. coli NC101 (Figure 4). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Denise Chroscinski ◽  
Darryl Sampey ◽  
Nimet Maherali ◽  

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Tumour vascularization via endothelial differentiation of glioblastoma stem-like cells’ by Ricci-Vitiani and colleagues, published in Nature in 2010 (<xref ref-type="bibr" rid="bib13">Ricci-Vitiani et al., 2010</xref>). The experiments that will be replicated are those reported in Figure 4B and Supplementary Figure 10B (<xref ref-type="bibr" rid="bib13">Ricci-Vitiani et al., 2010</xref>), which demonstrate that glioblastoma stem-like cells can derive into endothelial cells, and can be selectively ablated to reduce tumor progression in vivo, and Supplementary Figures S10C and S10D (<xref ref-type="bibr" rid="bib13">Ricci-Vitiani et al., 2010</xref>), which demonstrate that fully differentiated glioblastoma cells cannot form functionally relevant endothelium. The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1373-1373
Author(s):  
Kristine Misund ◽  
Katarzyna Anna Baranowska ◽  
Toril Holien ◽  
Christoph Rampa ◽  
Dionne Klein ◽  
...  

Abstract Abstract 1373 The aim of this work was to establish a robust and simple method for the measurement of drug sensitivity in myeloma cells under conditions mimicking aspects of the bone marrow microenvironment. In particular we wanted to measure drug sensitivity in myeloma cells cultivated in the presence of stromal cells. The tumor microenvironment can profoundly affect tumor cell survival as well as alter antitumor drug activity, and it is generally believed that growth and survival of myeloma cells is critically dependent on the bone marrow microenvironment. Bone marrow stromal cells (BMSC) have been shown to protect myeloma cells from common cytostatic or cytotoxic drugs in vitro. Common in vitro assays used for high-throughput drug screening cannot easily discriminate between stromal and tumor cell responses in co-cultures. Although a few recent studies have overcome this problem (Ramasamy K. et al., 157(5):564–79,2012, McMillin D. et al., 16(4):483–9, 2010), the application of stable transfection for labeling of cells limits the practical application of these co-culture studies to cell lines, excluding primary myeloma cells that inherently may be hard to transduce even by retroviral vectors. Here, we analyzed survival of myeloma cells co-cultured with BMSC using an automated fluorescence microscope, ScanR. ScanR is a microscope based screening station. By staining the cell nuclei with DRAQ5, we were able to discriminate between BMSC and myeloma cells, based on their staining intensity and nuclear shape. Using the apoptotic marker YO-PRO-1, the effects of drug treatment on the viability of the myeloma cells in the presence of stromal cells could be measured. The main advantages of this method are the non-necessity of cell manipulation before co-culture and the low number of myeloma cells (5000 primary cells) that are needed per measurement, which makes the method ideal for experiments with primary myeloma cells. In fact, the analysis was easier and more robust when using slowly growing cells, i.e. by using primary myeloma cells compared to more rapidly proliferating myeloma cell lines. This method should be well-suited for high throughput analysis, as the cells are stained in situ with no washing, centrifugation, or fixation steps before analysis. The method was compared to a conventional method for detecting cell viability; flow cytometry where annexin V labeling was used to detect apoptotic cells. As shown in figure 1, the dose-response curves obtained for ANBL-6 cells treated with different doses of melphalan were similar and showed the same trends for both methods. However, the effects of melphalan treatment were more evident analyzed by the ScanR system than by flow cytometry (EC50 YO-PRO-1 = 11μM versus EC50Annexin V= 15μM). The stromal cell population applied in this study was able to support IL-6 dependent myeloma cell lines without addition of IL-6. This as IL-6 dependent INA-6 cells cultivated in the presence of BMSC survived in the absence of added IL-6. This study shows the importance of stromal cell support for primary myeloma cell survival in vitro, as half of the cell samples had a marked increase in their viability when cultured in the presence of BMSC. Stromal cell-induced protection against common myeloma drugs was also observed with this method. For instance, experiments with primary myeloma cells from patient MM7, showed that in the presence of BMSC, the EC50 for the common myeloma drug cyclophosphamide was increased from 5 μM to approximately 10 μM (figure 2). Figure 1 Figure 1. Figure 2 Figure 2. Disclosures: No relevant conflicts of interest to declare.


Sign in / Sign up

Export Citation Format

Share Document