scholarly journals Registered report: Transcriptional amplification in tumor cells with elevated c-Myc

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 ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
L Michelle Lewis ◽  
Meredith C Edwards ◽  
Zachary R Meyers ◽  
C Conover Talbot ◽  
Haiping Hao ◽  
...  

As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Blum et al., 2015), that described how we intended to replicate selected experiments from the paper ‘Transcriptional amplification in tumor cells with elevated c-Myc’ (Lin et al., 2012). Here we report the results. We found overexpression of c-Myc increased total levels of RNA in P493-6 Burkitt’s lymphoma cells; however, while the effect was in the same direction as the original study (Figure 3E; Lin et al., 2012), statistical significance and the size of the effect varied between the original study and the two different lots of serum tested in this replication. Digital gene expression analysis for a set of genes was also performed on P493-6 cells before and after c-Myc overexpression. Transcripts from genes that were active before c-Myc induction increased in expression following c-Myc overexpression, similar to the original study (Figure 3F; Lin et al., 2012). Transcripts from genes that were silent before c-Myc induction also increased in expression following c-Myc overexpression, while the original study concluded elevated c-Myc had no effect on silent genes (Figure 3F; Lin et al., 2012). Treating the data as paired, we found a statistically significant increase in gene expression for both active and silent genes upon c-Myc induction, with the change in gene expression greater for active genes compared to silent genes. Finally, we report meta-analyses for each result.


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.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2048-2048
Author(s):  
Adrian Wiestner ◽  
Elinor Lee ◽  
Berengere Vire ◽  
Federica Gibellini ◽  
Ndegwa Njuguna ◽  
...  

Abstract Proposed mechanisms on how the monoclonal anti-CD20 antibody rituximab (R) depletes B-cells include antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. In vitro studies have suggested that R induced pro-apoptotic signals contribute to clinical efficacy and may sensitize cells to chemotherapy. To investigate the effect of R on tumor biology in vivo, we analyzed the molecular changes in leukemic cells of 12 previously untreated CLL patients during the first R (375mg/m2) infusion. The median reduction of circulating tumor cells within 24h was 50% (range 0–67%). We first determined whether R affects gene expression in CLL cells obtained before and at 6h and 24h after the start of R. Cells were purified by CD19+ selection and gene expression was measured on Affymetrix HU133A 2.0 arrays. A one-way ANOVA test with a stringent cutoff (false discovery rate of &lt;20%) identified 69 genes whose expression increased &gt;50% at 6h compared to pre treatment, and 31 genes whose expression decreased by &gt;30%. Most of the up-regulated genes are known to be regulated by interferon (IFN) and include the pro-apoptotic genes IRF1, STAT1, FAS and OAS2. Of 12 cytokines assayed in the serum, we found that only IFNy, IL–6, IL–8, IL–10, and TNFa were induced by R with a peak at 2h. Consistent with a dominant role of IFNy on gene expression in the CLL cells, STAT1, a direct and essential mediator of IFNy signaling, was activated in circulating leukemic cells in vivo. In addition, when comparing the response between patients, IFNy serum protein levels correlated strongly with the intensity of the gene expression changes in the tumor cells (r=0.83, p=0.008). We could not detect any IFNy mRNA in CLL cells and conclude that the IFNy is most likely released by NK cells activated through FcyRIII signaling. Considering the long half-life of R, we were surprised to see that both cytokine serum levels and gene expression changes almost completely subsided by 24h. Intriguingly, among the few genes that were down-regulated by treatment, the gene encoding CD20 was the most strongly and consistently affected showing a 50% decrease in expression at 24h. We also assessed CD20 protein levels by Western blotting. Total CD20 levels were markedly decreased already at 6h and by 24h almost all CD20 had been lost. The more rapid and more pronounced decrease of CD20 protein as opposed to mRNA levels is consistent with a process previously described as shaving, during which R bound CD20 is pulled of the cell surface (Kennedy AD, J Immunol. 2004). Despite the absence of a clinical cytokine release syndrome, we observed basically identical changes in serum cytokines and gene expression with subsequent infusions in 2 patients analyzed. In summary, R induced a characteristic gene expression signature in CLL cells that is dominated by IFN response genes, many of which have well characterized pro-apoptotic functions. Thus, our data suggest that signaling for apoptosis is not so much a direct effect of R, but due to a complex immune response to the R coated CLL cells. Modified treatment schedules capable of delivering sustained pro-apoptotic signals hold promise for improved efficacy of R and should be explored.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2830-2830
Author(s):  
Bani M Azari ◽  
Marc J. Braunstein ◽  
H. Uwe Kluppelberg ◽  
Sadeaqua S Scott ◽  
Eric LP Smith ◽  
...  

Abstract Abstract 2830 Poster Board II-806 Background: Multiple myeloma (MM) is an incurable disease of clonal plasma cells that accumulate in the bone marrow (BM), causing monoclonal IG production, bone marrow failure, osteolytic lesions and kidney disease. Although initially treatable, MM ultimately becomes refractory to treatment, and is invariably fatal, when tumor cells that harbor genetic mutations expand without regulation. Therefore novel treatment targets need to be identified. A key mechanism in MM pathogenesis is regulation of tumor growth by the bone marrow (BM) microenvironment, particularly by bone marrow neo-vascularization and adhesion of tumor cells to the marrow stroma. Aberrantly expressed genes that regulate angiogenesis by MM cells enhance MM progression and constitute targets in its treatment. JAM-A/F11R is an endothelial cell (EC) adhesion molecule of the immunoglobulin superfamily which is a multifunctional cell membrane protein that mediates intracellular signaling events that alter EC migration and paracellular permeability. For example, in breast cancer, attenuation of JAM-A increases tumor invasion and metastasis through a decrease in tumor adhesion (Ulas Naik Cell Adh Migr. 2008 Oct;2(4):249-51.). In this study we explored the JAM-A/F11R expression in MM tumor cells and in patients to determine the potential role of this molecule in the pathogenesis and progression of MM. Methods: The MM cell lines examined were RPMI-8266, U266, and NCI-H929. Human umbilical vein endothelial cells (HUVECs) served as controls. Informed consent was obtained from patients and control subjects. Primary BM tumor cells were enriched to > 95% CD138+ cells by positive selection using anti-CD138 MACS MicroBeads. The CD138-negative fraction was used for outgrowth of confluent EPCs (> 98% vWF/CD133/KDR+). JAM-A mRNA expression was assessed using an microarray gene expression profile, JAM-A probe based real-time PCR, and JAM-A levels in each sample were measure using a standard curve and normalized to GADPH. JAM-A protein levels in MM cell lines and primary tumor cells were measured by flow cytometry and immunofluorescence. For serum studies, peripheral blood was obtained from 25 newly diagnosed MM patients and 8 healthy, age- and sex-matched controls, and JAM-A levels were measured using an ELISA. Statistical analysis was performed using Student's t-test, two-tailed, with P ' .05 considered significant. Results: JAM-A mRNA levels were significantly increased in MM cell lines RPMI-8266, U266, and NCI-H929 compared to HUVECs (U266, P = 3×10-5; RPM1-8266, P = 1×10-6; NC1-H929, P= 5×10-4). The JAM-A mRNA levels were significantly greater in RPMI-8226; P < .04 compared to TNFα-activated HUVECs for 24 hours which is a proangiogenic switch for HUVEC gene expression. The elevated mRNA expression of the JAM-A in MM cell lines was confirmed by immunofluorescence and flow cytometry which showed the presence of both membrane and cytoplasmic JAM-A protein. Microarray analysis of gene expression profiles from 20 patients' corresponding tumor cells and microenvironmental EPCs showed that JAM-A had a higher level of expression in tumor cells versus MM EPC by 12.62 fold, (P=.0000642). Furthermore, JAM-A had a higher level of expression in MM EPC versus normal control EPC by 2.41 fold, (P=.00113) reflecting a complex regulatory role of F11 signaling in MM, similar to breast cancer (Naik, U. et al 2008). JAM-A was also found to be 12.6 fold greater in tumor cells compared to EPCS (P=.0000642). In addition, circulating levels of soluble JAM-A were found to be significantly greater in the serum of MM patients compared to controls (P < .005), with an average 2-fold increase. Serum levels of JAM-A in MM patients also decreased 71% with treatment n=5, P<.05. Conclusion: We show for the first time that JAM-A expression is highly elevated in MM tumor cells and its levels respond to treatment. In addition, MM patients have higher circulating JAM-A levels compared to healthy individuals and circulating JAM-A levels were reduced following treatment, suggesting that JAM-A may serve as a novel biomarker in MM. Current studies in the lab are aimed at correlating these levels with clinical parameters to determine whether JAM-A levels reflect disease severity and response to treatment. Results of these analyses, as well as results of ongoing experiments using JAM-A siRNA and antibody-inhibition approaches to target JAM-A in myeloma tumor and ECs will be presented. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1837-1837
Author(s):  
Vendela C Parrow ◽  
Anna Eriksson ◽  
Hanna Göransson ◽  
Linda Rickardson ◽  
Fredrik Lehmann ◽  
...  

Abstract Abstract 1837 AKN-028 (formerly BVT-II, abstract presented at EHA 2008, Eriksson A et al) is a tyrosine kinase inhibitor originally identified in a screen targeting FLT-3. In vitro testing by fluorometric microculture cytotoxicity assay (FMCA, Lindhagen E. et al, Nat Protoc 2008; 3:1364-9) on primary tumor cells from 29 patients with different haematological malignancies showed that the cytotoxic activity was most pronounced in acute myeloic leukaemia (AML). In vivo, efficacy was demonstrated in a hollow fiber mouse model using MV4-11 cells and primary tumor cells from AML patients. Kinase inhibitors interacting with the ATP-binding pocket usually targets more than one kinase. PKC-412, presently in phase III trials in AML, is a staurosporine analogue targeting many kinases. In this study we show the kinase inhibition profile of AKN-028 when characterised on a broad panel of 320 different kinases. AKN-028 is relatively specific compared to the staurosporine analogues. To further analyse the difference in mechanism of action between the multi-targeting inhibitor PKC-412 and the more selective AKN-028, we have performed global gene expression analysis by Affymetrix arrays using two different leukaemia cell-lines, HL-60 and MV4-11 (expressing FLT3-ITD), and tumour cells from a patient with FLT3-ITDpos AML. The cells were treated with 10 μM of either compound or vehicle control for 6 h. Principal component (PC) analysis was used to visualise the global gene expression pattern, see fig 1. Searching for differential expression of mRNA levels showed that treatment with AKN-028 resulted in significantly altered gene expression in all three cell types tested, compared to vehicle control treated cells. 430 mRNAs were down-regulated, and 280 were up-regulated. By contrast, treatment with PKC-412 caused very few significant alterations of mRNA levels when compared to vehicle treated cells. Further analysis of gene expression patterns to elucidate the mechanism of action of AKN-028 is ongoing. In conclusion, even though AKN-028 is a relatively selective kinase inhibitor targeting FLT-3, it has more profound effects altering gene expression both in cultured AML cell-lines and a primary AML tumor sample than the multikinase inhibitor PKC-412. Disclosures: Parrow: Akinion Pharmaceuticals: Employment, Equity Ownership. Lehmann:Akinion Pharmaceuticals: Consultancy. Larsson:Akinion Pharmaceuticals: Consultancy.


Endocrinology ◽  
2005 ◽  
Vol 146 (9) ◽  
pp. 3821-3835 ◽  
Author(s):  
Longfei Huo ◽  
Guodong Fu ◽  
Xinyan Wang ◽  
Wendy K. W. Ko ◽  
Anderson O. L. Wong

Abstract Calmodulin (CaM), the Ca2+ sensor in living cells, is essential for biological functions mediated by Ca2+-dependent mechanisms. However, modulation of CaM gene expression at the pituitary level as a means to regulate pituitary hormone synthesis has not been characterized. In this study we examined the functional role of CaM in the feedback control of GH by IGF using grass carp pituitary cells as a cell model. To establish the structural identity of CaM expressed in the grass carp, a CaM cDNA, CaM-L, was isolated from the carp pituitary using 3′/5′ rapid amplification of cDNA ends. The open reading frame of this cDNA encodes a 149-amino acid protein sharing the same primary structure with CaMs reported in mammals, birds, and amphibians. This CaM cDNA is phylogenetically related to the CaM I gene family, and its transcripts are ubiquitously expressed in the grass carp. In carp pituitary cells, IGF-I and IGF-II induced CaM mRNA expression with a concurrent drop in GH transcript levels. These stimulatory effects on CaM mRNA levels were not mimicked by insulin and appeared to be a direct consequence of IGF activation of CaM gene transcription without altering CaM transcript stability. CaM antagonism and inactivation of calcineurin blocked the inhibitory effects of IGF-I and IGF-II on GH gene expression, and CaM overexpression also suppressed the 5′ promoter activity of the grass carp GH gene. These results, as a whole, provide evidence for the first time that IGF feedback on GH gene expression is mediated by activation of CaM gene expression at the pituitary level.


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.


2018 ◽  
Author(s):  
Roberto Ferrari ◽  
Lara Isabel de Llobet Cucalon ◽  
Chiara Di Vona ◽  
François Le Dilly ◽  
Enrique Vidal ◽  
...  

Summary paragraphThe mammalian genome is shaped by the expansion of repetitive elements that provide new regulatory networks for coordinated control of gene expression1 and genome folding2–4. Alu elements (AEs) are selectively retained close to the transcription start site of genes5, show protoenhancer functions6, correlate with the level of chromatin interactions7 and are recognized by transcription factor III (TFIIIC)8, but the relevance of all this is not clear. Here we report regulatory mechanisms that unveil a central role of AEs and TFIIIC in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of pre-marked AEs near cell cycle genes recruit TFIIIC to alter their chromatin accessibility via TFIIIC-mediated acetylation of histone H3 Lysine-18 (H3K18). This facilitates AEs contact with distant CTCF sites near other cell cycle genes promoters, which also become hyperacetylated at H3K18. These changes ensure basal transcription of crucial cell cycle genes, and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor adjusts 3D genome folding and gene expression. We anticipate that expansion of several families of repetitive elements during evolution might have served to generate new genomic cis-regulatory circuits enabling the coordinated regulation of a large set of genes relevant for cellular stress survival. As growth factor withdrawal is a situation relevant in cancer biology, our study identifies TFIIIC as a new potential target for clinical intervention.


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.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 450-450
Author(s):  
Bani M Azari ◽  
Danielle F Joseph ◽  
Marc J Braunstein ◽  
H. Uwe Klueppelberg ◽  
Eric LP Smith ◽  
...  

Abstract Abstract 450 Background: Multiple myeloma (MM) is a disease of clonal plasma cells that accumulate in the bone marrow (BM), causing monoclonal immunoglobulin (IG) production, BM failure, osteolytic lesions, and kidney disease. Although initially treatable, tumor cells ultimately become resistant to drug-treatment, and the disease is invariably fatal. Therefore, novel treatment targets need to be identified. The tumor microenvironment, and vascular endothelial cells in particular, play a key role in the adhesion and migration of MM cells and thus govern tumor survival and growth, as well as the acquisition of drug-resistance. Hence, the adhesion/migration systems of MM cells are key potential therapeutic targets. The cell membrane protein JAM-A/F11R is an endothelial cell (EC) adhesion molecule of the IG superfamily, and its expression is upregulated by TNF-a through NF-κB signaling. F11R also alters EC migration and paracellular permeability via stabilization of β1 integrin. We have previously shown that F11R gene expression and serum levels are upregulated in patients with MM compared to healthy controls. In this study, we further explored the functions of F11R within MM cells in order to gain insight into the potential role of this molecule in the progression and treatment of MM. Methods: The MM cell line RPMI-8266 (RPMI) was examined for functional studies in vitro. Informed consent was obtained from all subjects. Primary BM tumor cells were enriched to > 95% CD138+ cells by positive selection using anti-CD138 MACS MicroBeads. The CD138– fraction was used for outgrowth of confluent EPCs (> 98% vWF/CD133/KDR+). Human umbilical vein endothelial cells (HUVECs) served as controls. F11R mRNA levels were assessed by Affymetrix GeneChip analysis and by F11R probe-based real-time PCR compared to a standard curve normalized to GAPDH mRNA levels. F11R protein levels were measured by immunofluorescence (IF) and flow cytometry. The role of F11R in MM cell migration and survival was quantified by examining these functions in RPMI cells in which F11R was knocked down by siRNA silencing and comparing them with control untransfected RPMI cells or cells transfected with a non-targeting siRNA or lipofectamine. Tumor migration and survival were determined by the Millipore QCM Chemotaxis assay (using a 5 micron pore size) and an Promega Cell Proliferation Assay, respectively. Each assay was performed in triplicate and replicated at least twice. Statistical analyses were performed using Student's t-test, two-tailed; P≤.05 was considered significant. Results: Inhibition of F11R gene expression by siRNA resulted in 70% cell death compared to control untransfected (P<.001), non-targeting siRNA (P=.04), or lipofectamine-treated (P=.003) MM cells (RPMI). Moreover, migration of MM cells was also inhibited by 23% after silencing of F11R expression compared to cells transfected with control siRNA (P=.008). Elevated F11R mRNA levels in MM cell lines and patient-derived tumor endothelial progenitor cells (EPCs) was confirmed by IF and flow cytometry using a specific monoclonal antibody, and showed increased expression of both membrane and cytoplasmic F11R compared to controls. Gene expression profiles from 20 patients' corresponding BM tumor cells and EPCs showed that F11R mRNA levels in tumor cells were higher than MM in EPCs by 12.62 fold, (P=1×10-4). However, F11R had a higher level of expression in MM EPCs compared to healthy control EPCs by 2.41 fold (P=.001), reflecting a complex regulatory role of F11 signaling in MM, similar to breast cancer cells (Naik et al., 2008). Conclusion: We show, for the first time, that targeted inhibition of F11R/JAM-A expression bears key anti-myeloma consequences, defined by inhibition of tumor migration and survival. Taken together with elevated gene and protein expression of F11R/JAM-A expression, these results underscore the importance of this receptor as a tumor biomarker and a potential MM treatment target that warrants further validation. Future studies: Under investigation are the in vivo effect of F11R silencing in combination with other anti-myeloma strategies in a murine myeloma model; and also, whether F11R effects on MM cell migration involve stabilization of β1 integrin, as recently described in cardiovascular disease by Azari BM et al. 2010. Disclosures: No relevant conflicts of interest to declare.


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