bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4835: Genetic determinants of mTOR inhibitor response in breast and endometrial cancer
Authors: Weigelt Britta , Warne Patricia H. , Lambros Maryou , Reis-Filho Jorge S. , Downward Julian
Published: August 2012

Background: Breast and endometrial cancers frequently harbour genetic aberrations that result in increased activation of the PI3K-AKT-mTOR signalling pathway including amplification and overexpression of receptor tyrosine kinases, activating PIK3CA mutations, and inactivating PTEN mutations or loss of PTEN function. Given the pivotal role of the PI3K-AKT-mTOR pathway in cancer cell growth and survival, inhibitors of several of its components are currently being tested in clinical trials. The aim of this study was to define the genetic determinants of mTOR inhibitor response in breast and endometrial cancer cells. Methods: A panel of 31 breast and 26 endometrial cancer cell lines was treated with serial dilutions of ‘rapalogs’ (i.e. allosteric inhibitors of mTOR complex 1 (mTORC1)) and mTOR kinase inhibitors targeting mTORC1 and mTORC2. Cell viability was determined using CellTiter Blue. PTEN protein levels and mutations in PTEN transcripts were assessed in all cell lines using western blotting and Sanger sequencing, respectively. PIK3CA mutations were assessed using Sanger sequencing in the breast cancer cells, and hot-spot mutations in PIK3CA and 18 additional oncogenes using the Sequenom OncoCarta Panel v1.0 in the endometrial cancer cells. Results: Response of breast cancer cells to both the rapalog everolimus and the mTOR kinase inhibitor PP242 was determined by the presence of activating PIK3CA mutations but not PTEN loss of function. In addition, PP242 treatment induced a more efficient response in HER2-amplified breast cancer cell lines, irrespective of the PIK3CA mutation status. By contrast, endometrial cancer cell lines not only harbouring mutations in PIK3CA but also in PTEN were sensitive to treatment with the rapalog temsirolimus. The mTOR kinase inhibitor AZD8055 induced a strong reduction in cell viability in all endometrial cancer cell lines tested. Conclusions: Our results suggest that response to mTOR inhibitors in breast and endometrial cancer cells may be determined by the presence of alterations affecting PIK3CA and PTEN. Our data further indicate, however, that the epistatic interactions between different components of the PI3K-AKT-mTOR pathway are distinct in cancers of the breast and endometrium.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4835. doi:1538-7445.AM2012-4835
Abstract 4840: Blockade of IL-10 production in effector B cells significantly increases their therapeutic efficacy in cancer adoptive immunotherapy
Authors: Zheng Fang , Pan Qin , Egenti Martin , Chang Alfred E. , Li Qiao
Published: August 2012

We have previously reported the antitumor reactivity of adoptively transferred effector B cells and the mechanisms by which they mediate tumor regression in a spontaneous metastasis model. 4T1 breast cancer cells were inoculated into syngeneic Balb/c mice to prime tumor-draining lymph node (TDLN). TDLNs were subsequently harvested and B cells activated ex vivo. When adoptively transferred into mice inoculated with 4T1 tumor in the mammary fat pad, these activated B cells alone mediated the inhibition of spontaneous metastases to the lung. In this study, we used IL-10−/− Balb/c mice to generate IL-10−/− TDLN, and evaluated the antitumor immunity of IL-10−/− TDLN B cells. Adoptively transferred IL-10−/− TDLN B cells mediated significantly more effective antitumor immunity than equal numbers of WT TDLN B cells (p<0.05). Activated IL-10−/− effector 4T1 TDLN B cells were capable of killing 4T1 tumor cells in a tumor antigen specific manner in in vitro cytotoxicity assays independent of antibody and complement. Adoptive transfer of IL-10−/− TDLN B cells resulted in the induction of host T and B cell antitumor immunity significantly more than adoptive transfer of WT TDLN B cells (p<0.05). This was evident by significantly modulated cytokine production (e.g. up-regulated IFN-gamma and IL-2 production by host T cells, but down-regulated IL-10 production by host B cells). In addition, adoptively transferred IL-10−/− TDLN B cells increased the production of IgG which bound to 4T1 tumor cells. Furthermore, IL-10−/− TDLN B cell infusion significantly increased tumor cell lysis (CTL) activity mediated by host B cells as well as T cells in an immunologically specific fashion. The molecular and cellular pathways involved in the direct killing of 4T1 tumor cells by IL-10−/- 4T1 TDLN effector B cells and by host B cells subjected to IL-10−/- 4T1 TDLN effector B cell adoptive transfer is under active investigation in our lab. While the role played by B cells in the host immune response to cancer is complex and controversial, our results indicate that removal of IL-10-producing B cell subsets may represent an effective strategy to augment the therapeutic efficacy of TDLN B cells used in adoptive immunotherapy. Mechanistically, adoptive transfer of B cells depleted of IL-10-producing subsets destroys tumor cells directly and confers greater host cellular and humoral antitumor immunity by shifting cytokine production to a Type 1 profile and by producing tumor-reactive antibodies respectively.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4840. doi:1538-7445.AM2012-4840
Abstract 4841: Lysis of cancer cells by highly purified T regulatory cells engaged via an EpCAM/CD3-bispecific BiTE antibody
Authors: Münz Markus , Murr Alexander , Hoffmann Petra , Edinger Matthias , Baeuerle Patrick A. , Kufer Peter , Raum Tobias
Published: August 2012

BiTE antibodies are single-chain bispecific antibody constructs with dual specificity for CD3 on T cells and a surface antigen on target cells. By bridging cytotoxic T cells and cancer cells, BiTE antibodies are capable to temporarily mount a polyclonal T cell response that is not restricted by T cell receptor specificity, presence of MHC class I, generation and presentation of peptide antigen, or the need for T cell co-stimulation. Examples are the CD19/CD3-bispecific BiTE antibody blinatumomab, which has shown high response rates and durable remissions in leukemia and lymphoma patients, and EpCAM/CD3-bispecific BiTE antibody solitomab (MT110), which is in a dose-escalating phase 1 study in patients with solid tumors. CD8+ and CD4+ effector memory T cells were found to be the most potent effector cells for BiTE antibodies. Here, we have assessed whether highly purified T regulatory cells (T regs) can also serve as effector cells for BiTE antibody MT110, despite multiple reports suggesting that T regs rather suppress the anti-tumor activity of cytotoxic T cells. T regs were purified from human peripheral blood mononuclear cells (PBMC) using anti-CD25 magnetic beads and fluorescence-activated cell sorting (FACS) for expression of CD4 and CD45RA markers, followed by expansion in the presence of IL-2 (Hoffmann P. et al., Methods Mol. Biol. 677:15-30, 2011). Purified naïve CD4+/CD25high/CD45RA+/FOXP3+ T regs had a purity of 96-99.6%, and contained no detectable CD8+ T cells. In co-culture experiments, a small fraction of purified T regs up-regulated the expression of granzyme B and perforin when stimulated with MT110 in the presence of EpCAM+ target cells. As shown by chromium release assay and phase contrast microscopy, T regs caused a MT110 dose-dependent, redirected lysis of target cells. No target cell lysis was observed with a BiTE antibody solely binding to CD3 on T cells, and by T regs alone. We then tested the activity of T regs against spheroids formed in vitro from colorectal cancer stem cells. Only in the presence of MT110, T regs could significantly reduce the size and integrity of spheroids. In that respect, T regs had a similar activity as PBMC. Our study suggests that T regs, which often are associated with immune escape of tumors, can be effectively engaged for redirected cancer cell lysis by a BiTE antibody.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4841. doi:1538-7445.AM2012-4841
Abstract 4907: Effect of arsenic trioxide on cholangiocarcinoma: Use of an in vitro test and an in vivo xenograft model
Authors: Kim Eun Young , Roh Seon Ae
Published: August 2012

Objective: Arsenic trioxide (As2O3), an ingredient of many traditional Chinese medicines, has been shown to be active against many types of tumors. To assess whether local application of As2O3 inhibited cholangiocarcinoma development, we assayed the in vitro and in vivo effects of the chemical on human cholangiocarcinoma cancer cells of the CC-t6 line. Materials and methods: The effect of As2O3 on CC-t6 cell survival was determined using MTT assays and the mechanism of action was evaluated by flow cytometry following Annexin V-PI staining. The in vivo effect of As2O3 on tumor volume was explored using a nude mouse xenograft model. Results: In the MTT assay, As2O3 inhibited CC-t6 cells more strongly than did than cisplatin or adriamycin. As2O3 reduced CC-t6 cell proliferation via G0/G1 phase arrest and caused dose-dependent induction of apoptosis. Injection of As2O3 into CC-t6-induced tumors in nude mice inhibited the growth of subcutaneous tumor xenografts. Conclusions: As2O3 treatment dose-dependently inhibited the proliferation of CC-t6 cells via G0/G1 phase arrest and retarded tumor growth in nude mice, suggesting that As2O3 may be effective in the treatment of cholangiocarcinoma. Keywords: arsenic trioxide (As2O3), cholangiocarcinoma, intratumoral injection, tumor xenografts

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4907. doi:1538-7445.AM2012-4907
Abstract 4908: The apoptotic response of the triple negative breast cancer cell line HCC1806 to chemotherapeutics
Authors: Rorie Checo J. , King Jamie , Bryant Relena , Gurley Kashenya
Published: August 2012

Triple negative breast cancer is characterized by the loss or low expression of estrogen receptor, progesterone receptor, and HER2 proteins which have been targeted and established as somewhat effective therapy regiments in other breast cancer subtypes including luminal breast cancer. Since triple negative tumors are missing these established drug targets, there has been little advancement in the establishment of drug therapies to specifically target this breast cancer subtype. Triple negative breast cancer is described as aggressive due to its invasiveness and metastatic properties. One potential mediator of triple negative breast cancer aggressive behavior may be due to the fact that this breast cancer subtype may have as high as an 80% p53 tumor suppressor gene mutation rate. While the p53 gene may be mutated at high rates, it may be possible to design drugs to target some of the downstream genes that p53 transactivates, including the cyclin dependent kinase inhibitor p21 and the pro-apoptotic gene PUMA, in order to inhibit the further growth of the triple negative breast cancer cells. We previously reported that classic chemotherapeutics including actinomycin-D, staurosporine, and doxorubicin, were effective in eliciting apoptosis in breast cancer cell lines. We initially stressed breast cancer cell lines with all three chemotherapeutics listed above. We showed that all of the cell lines underwent significant apoptosis by 24hrs. Interestingly, the “normal” breast cancer cell line AG11132 had a delayed apoptosis response to doxorubicin treatment as compared to the breast cancer cell lines HCC1806, HCC70 and HCC1500. Therefore, we treated the breast cancer cell lines with a titration of various doxorubicin concentrations. Here we show that even at lower doxorubicin concentrations, a significant amount of apoptosis was measured at 24hrs in all of the cell lines including the triple negative breast cancer cell line HCC1806. We measured apoptosis by the physical characteristics as observed under light microscopy and by using the cell viability assay. We are currently monitoring the p53 tumor suppressor pathway network in all of these cells to determine the network's integrity and whether there is a direct or indirect involvement of p53 on the apoptosis responses. We are also further analyzing the chemotherapeutic agents to determine their effectiveness in killing breast cancer cells with limited cytotoxic effects to normal breast cells at various time-points.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4908. doi:1538-7445.AM2012-4908
Abstract 4913: A quantitative integrated systems biology approach for modeling cell cycle pathways in normal and tumor cells
Authors: Tummala Hemanth , Khalil Hilal S. , Goszcz Katarzyna , Tupone Maria Grazia , Stoyanova Vili , Nikolova Ekaterina , Mitev Vanio , Zhelev Nikolai
Published: August 2012

We have developed a novel biological system for quantitative analysis of biochemical pathways in normal and tumour human cells. The system is based on cells growing in tissue culture media where the concentrations of growth factors, hormones and other components of the media are precisely defined and continuously monitored. Quantitative immunoblotting and luminescence-based reporter assays are then used to measure the cellular concentration of key cell cycle regulatory proteins and their activity in real time in live cells. This technology resulted in accurate measurement of cellular concentration of a number of key cell cycle regulatory proteins such as Cyclins, CDKs and CDK inhibitors during the cell cycle. The data are being utilized in the development of a quantitative integrated systems biology approach to the cell cycle. The approach consists of a comprehensive network of the molecular interaction pathways regulating cell cycle in normal and tumor cells and a model which incorporates the activity of key molecular species in a single dynamical system which can be solved using genetic algorithms designed to match experimental data, both qualitative and quantitative, to the model kinetics. The model could be utilized for the development of new drug targets and would be capable of consistently measuring the effects of existing drugs (either single or in combination) and opens up a methodology for establishing the effectiveness of these drugs with clear implications for cost/benefit assessment. Major impact is expected on clinical research where the model can be a tool in determining intervention strategies in the molecular pathways concerned. Apart from the development of new drug targets the model will be capable of consistently measuring the effects of existing drugs (either single or in combination) and opens up a methodology for establishing the effectiveness of anti-cancer drugs.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4913. doi:1538-7445.AM2012-4913
Abstract 4926: Modeling the transcriptome landscape of HER2+ breast cancer
Authors: Kalari Krishna R. , Chai High-Seng , Asmann Yan W. , Tang Xiaojia , Rossell David , Baheti Saurabh , Nair Asha , Baker Tiffany R. , Necela Brian M. , Carr Jennifer M. , Hart Steve N. , Sun Zhifu , Kachergus Jennifer M. , Younkin Curtis S. , Kocher Jean-Pierre A. , Thompson Aubrey E. , Perez Edith A.
Published: August 2012

Motivation: Overexpression of HER2 (the product of the ERBB2 gene) occurs in about 15% of all breast tumors. We have undertaken to use next generation transcriptome sequencing technology to identify genomic features that are unique to HER2+ tumors. Interactome mapping was then used to integrate the genes associated with these features into a transcriptome landscape model, with a view towards identifying nodes of interaction that might be targeted in HER2+ tumors. Methods: We performed 50nt paired-end RNA-sequencing for 24 breast tumors: 8 each HER2+, ER+, triple negatives (TN). In addition to breast adenocarcinomas, we also sequenced 8 early passage non-transformed HMEC cell lines as normal controls. Reads from RNA sequencing were aligned to the genome and exon junctions using TopHat software. Gene counts were summarized and annotations were performed using our in-house programs. Tukey's test was used to obtain genes or transcripts that are specific to HER2 tumor group compared to other tumors/normal. A combination of bioinformatics softwares and algorithms were used to identify SNVs. Results: Only 13527 genes with median gene count greater than 16 reads in at least one of the 4 groups were considered for differential gene expression and splicing analysis. Some 696 genes were differentially expressed in HER2+ tumors compared to ER+, TN tumors and HMECs. We identified 272 alternately spliced transcripts for which the HER2+ tumors exhibited a mean transcript expression ratio significantly different from the means of other tumor groups. We also identified 4735 expressed single nucleotide variants that are uniquely associated with HER2+ tumors compared to other tumors/normal groups. Among these 3579/4735 sequence polymorphisms were not present in the 1000 genome germline sequence database or in the dbSNP132 database of naturally occurring germline polymorphisms. Integration of all the genes obtained from genomic feature analyses (differential expression, alternative splicing, single nucleotide variance) has been carried out to indentify biological processes that are specific to the HER2+ tumor subtype. Key nodes and pathways that are specific to HER2+ tumors will be evaluated for association with clinical outcome in a large series of patients who have received HER2-targeted therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4926. doi:1538-7445.AM2012-4926
Abstract 4931: Biomarker discovery in a large panel of cell lines shows different sample size requirement for prediction of response across a set of compounds
Authors: Nebozhyn Michael , Cristescu Razvan , Liu Yaping , Feldman Igor , Lezhnin Sergey , Zhang Theresa , Zawel Leigh , Fawell Stephen , Dai Hongyue , Li Jing , Loboda Andrey
Published: August 2012

A panel of more than 600 cell lines from 17 tumor types has been profiled and sensitivity to a set of FDA approved compounds with different mechanisms of action has been tested. Comparison of gene expression profiles with overlapping set of publicly available profiles showed 100% accuracy of cell line identity prediction using nearest neighbor classifier. Similar analysis of CNV data had 80% accuracy due to relatively little CNV perturbation in some of the cell lines. Significant gene expression signatures have been detected for 80% of compounds. De-novo agnostic classification based on 50% train/test split and a linear classifier resulted in significant prediction on the test set for about 40% of the compounds, such as dasatinib, 5FU, paclitaxel, but failed to produce a significant prediction for others, such as doxorubicine, irinotecan, and vinblastine. For most of the compounds, the prediction of response is complex, with multiple distinct molecular features contributing to a classification algorithm. This inherent complexity requires integration of gene expression, CNV and mutation data as well as a large cell line sets for development of accurate classification algorithms. We defined functional CNV and SNV events using gene expression based modules as a functional readout. Predictive models that incorporate prior knowledge of mechanism of action of the compounds and rely on functional SNV and CNV events out perform completely agnostic methods of prediction.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4931. doi:1538-7445.AM2012-4931
Abstract 4932: Exploration of EMT-related microRNAs using function-based screening with expression analysis of E-cadherin in Panc1 line
Authors: Harazono Yosuke , Kozaki Ken-ichi , Muramatsu Tomoki , Kurasawa Yasuhiro , Uzawa Narikazu , Amagasa Teruo , Inazawa Johji
Published: August 2012

Recently, epithelial-mesenchymal transition (EMT) has been demonstrated to contribute to malignant transformation during cancer progression. To perform the function-based screening of EMT-related microRNAs (miRNAs), we first generated an in vitro model using a pancreatic cancer cell line, Panc1, in which a transcriptional reporter construct containing E-cadherin promoter region and a reporter gene, GFP, was transfected. After the selection of independent clones by the limiting dilution and the examination of GFP-upregulation in response to overexpression of ectopic miR-200b/a, we successfully established a stable transfectant clone, Panc1-EPG8. Then, we performed function-based screening with expression analysis of GFP in Panc1-EPG8 cells 4 days after ectopic transfection of 470 synthetic miRNAs. We further reexamined the expression level of E-cadherin after ectopic transfection with selected candidate miRNAs in Panc1-EPG8 cells by Western blotting and qRT-PCR, resulting in the identification of a novel miRNA as a candidate EMT-related miRNA. Our findings strongly suggest that this miRNA may play a crucial role during EMT in cancer progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4932. doi:1538-7445.AM2012-4932
Abstract 4936: Network signatures of survival in glioblastoma multiforme
Authors: Patel Vishal , Gokulrangan Giridharan , Chowdhury Salim , Chen Yanwen , Sloan Andrew , Koyuturk Mehmet , Barnholtz-Sloan Jill , Chance Mark
Published: August 2012

Glioblastoma multiforme (GBM) is the most common primary malignant brain tumor in adults and also the most aggressive, with a median survival time of approximately 1 year. Differences in age and pathology have long been recognized as key factors in determining prognosis, and, more recently, comprehensive mRNA profiling has been undertaken to establish the molecular basis underlying prognosis. Though early mRNA expression-based gene sets represented unbiased queries into molecular differences in gliomas, they only uncovered differences in survival ex post facto1, 2. Newer gene sets capitalize upon advances in technology, yet they suffer for their unwieldy size and ambiguous biological meaning3. Though the myriad gene sets proposed share little overlap with each other, recent work has demonstrated that the use of interaction networks can consolidate these differences. To determine the molecular basis of prognostic differences in GBM directly, we employed an existing computational framework, CRANE, to exhaustively search protein interaction networks and identify molecular signatures distinguishing short-term (<225 days) and long-term (>635 days) survivors of GBM in The Cancer Genome Atlas gene expression microarray dataset. Using CRANE, we identified a 50 gene subnetwork signature of survival in GBM, which we validated in an independent dataset of 91 patients (80% classification accuracy). We further hypothesized that the use of interaction networks consolidates variation in mRNA expression into more stable features at higher phenotypic levels. To test this hypothesis, we examined protein expression levels of the 50 network targets in an independent cohort of 16 patients (10 patients: survival<9 months; 6 patients: survival>18 months) using label-free proteomics. Of the 17 network targets identified in common with our 50 subnetwork signature genes, 8 were significantly differentially expressed between short-term and long-term survivors, and expression levels of 3 of the proteins (STAT3, Calnexin, and HSPA9) predicted phenotype (LTS vs. STS) with 75% or more accuracy (12 or 13 correct out of 16). Our conclusion is that data integration using interaction networks can drive discovery of a stable subnetwork signature exhibiting clear differences in protein expression. This manageable subset of proteomic targets will prove invaluable in the design of cost-effective clinical assays (e.g. IHC) suitable for retrospective analysis from FFPE tumor tissue in existing biobanks, as well as for prospective studies predicting patient survival - a much desired endpoint for clinicians and patients alike.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4936. doi:1538-7445.AM2012-4936
Abstract 494: Proteolysis of pseudokinase PTK7 controls cancer cell invasion
Authors: Golubkov Vladislav , Strongin Alex
Published: August 2012

Deregulated cell motility promotes cancer progression and metastasis, a major cause of cancer patient death. Understanding the molecular mechanisms regulating cell motility in malignancy will facilitate an identification of novel anti-metastatic therapies. Recently, we identified a new mechanism, the proteolytic control of directional cell motility and invasion. The membrane protein tyrosine kinase 7 (PTK7) controls the orientation of cells in a tissue plane (planar cell polarity, PCP) and inhibits cancer cell invasion. The pro-invasive membrane type-1 matrix metalloprotease (MT1-MMP/MMP-14) directly cleaves PTK7 at the cell surface and reverses the inhibitory anti-invasive signal of the full-length PTK7. Thus, PTK7 proteolysis by MT1-MMP turns on cell motility and invasion. This ubiquitous mechanism is conserved in processes as diverse as embryo development and cancer cell invasion. Because both the pro-invasive MT1-MMP and the polarity regulating PTK7 are linked to cancer, the precise understanding of the role of PTK7 proteolysis in cancer progression is important to discover novel therapies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 494. doi:1538-7445.AM2012-494
Abstract 4940: Activated signaling mechanism of glioblastoma recurrence derived from genetics, epigenetics, and genomics abnormalities
Authors: Jin Guangxu , Gao Junfeng , Wong Stephen T.C.
Published: August 2012

Recurrence or progession happens to certain glioblastoma (GBM) patients after given surgeries and complex treatment regimens. This implies that the pathways related to cell growth or apoptosis resistance have been activated. However, it lacks an efficient model to identify the activated pathways from a variety of data generated by the platforms on genetics, epigenetics, and genomics. Here, we develop a new computational model, called as CSB-MOO (Cancer Signaling Bridges - Multiple Objective Optimization), to address signaling mechanism associated with the recurrence or progression of GBM. We used a pathway-driven method to address the activated pathways. In the model of CSB-MOO, a new type of network elements, Cancer Signaling Bridge (CSB), was used to expand the known signaling pathways to the cancer genes (with genetic disorders) of GBM. Facilitated by CSBs, more than 60 known signaling pathways are found to be connected with the cancer genes for GBM. Then, a well-established mathematical method, Multi-Objective Optimization (MOO), was applied to identify activated pathways from multiple-type data. We used Pareto optimal to solve this MOO problem. We applied the CSB-MOO to the multiple-type data of GBM in TCGA (n=595). 15 proteins are activated in the 7 common pathways for both of the patients with and without recurrence/progression. These proteins include EGFR and JAK proteins. The patients without recurrence or progression activate another 11 activated proteins related to metabolic of amino acids (Tryptophan and Phenylalanine). Specifically, the patients with recurrence or progression activate another seventeen proteins, e.g., PIK3R1, and 2 protein complexes, i.e., [PLCG2/PLCG1] and [ITPR3/ITPR2/ITPR1], in which the SH2 domain of PIK3R1 acts an adaptor between the kinases [PLCG2/PLCG1] and the targeted proteins. In addition, these proteins facilitate the signal transduction from EGFR to downstream proteins through mediating phosphorylation. This is consistent with the fact that the recurrence/progression patients can activate the progession of GMB. The identified activated pathways classify the GBM patients with and without recurrence/progression in an accuracy of 80.89% (P < 10−4, Fisher exact test). Survival analysis indicates that the activated pathways with genetics, epigenetics, and genomics patterns accurately predict the patients’ lifespan (P = 0.0007, Chi-squared test). Acknowledgements: This work was supported by NIH grant U54CA149196 to STCW.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4940. doi:1538-7445.AM2012-4940
Abstract 495: Overexpression of TIS21/BTG2/PC3 inhibits formation of invadopodia in the highly metastatic breast cancer cells MDA-MB-231
Authors: Choi Jung A , Lim In Kyoung
Published: August 2012

Invasion of cancer cells depends on the proteolytic degradation of extracellular matrix and it is initiated by the actin-driven membrane protrusions, called invadopodia. However, the mechanisms underlying invadopodia formation remain largely unknown. In this study, we report that TIS21/BTG2/PC3, tumor suppressor gene, suppress invadopodia formation in the highly invasive breast cancer cells, MDA-MB-231. To understand downstream mechanisms regulating invadopodia formation by TIS21, generation of ROS (reactive oxygen species) by NADPH oxidase (Nox) was examined and observed that adenoviral transduction of TIS21 markedly attenuated generation of ROS. The transduction of TIS21 significantly inhibited mRNA expression of Nox1 and Nox4, but not p22phox. In contrast, formation of invadopodia was much higher in the TIS21KO-mouse embryo fibroblasts (TIS21−/- MEF) along with elevated expression of Nox1 and Nox4, compared with those of the wild type MEF. The data strongly suggest that TIS21 contributes inhibition of invadopodia formation through the regulation of Nox expression. Noticeably, transduction of TIS21 regulated reorganization of actin-assoicated protein and cytockelectal proteins such as F-actin and vimentin. Similarly, inhibition of Nox-derived ROS by using DPI reversed reorganization of the proteins. The above data clearly indicate that generation of Nox-derived ROS play a critical role in the distribution of actin-assoicated protein and cytockelectal proteins. Taken together, present report demonstrates, for the first time, that the TIS21/BTG2-ROS-linked cascades is required for formation of invadopodia in the highly invasive breast cancer cells and may provide insight into mechanisms of metastatic signaling in breast cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 495. doi:1538-7445.AM2012-495
Abstract 4950: Discovery of the pro-apoptotic genes induced by tumor suppressor p53
Authors: DASHZEVEG Nurmaa , TAIRA Naoe , MIKI Yoshio , YOSHIDA Kiyotsugu
Published: August 2012

The tumor suppressor p53 regulates apoptosis in response to DNA damage. Promoter selectivity of p53 depends mainly on its phosphorylation. Notably, the phosphorylation at serine-46 (Ser46) of p53 is indispensable to promote pro-apoptotic genes. However, little is known about the pro-apoptotic genes induced by Ser46 phosphorylation of p53. In our study, we aimed to investigate pro-apoptotic genes induced by p53 using microarray analysis and ChIP sequencing assay. Although microarray analysis became common tool in molecular biology, novelty of our research is combining microarray analysis with ChIP sequencing assay to discover direct target of p53 in Ser46 specific manner. Analyze of microarray showed specific up-regulation of 2723 genes in wild type p53 (wt-p53). Alternatively, 1338 genes were interacted directly with only wt-p53 but not with mutant p53 (Ser46 is substituted with alanine, p53S46A) in ChIP sequencing assay. The comparison of two assays, microarray analysis and ChIP sequencing assay, investigated thirty genes in relation with Ser46 phosphorylation of tumor suppressor p53. Those thirty genes were clarified by real time RT-PCR and the genes strongly elicited were chosen further study. The research will be continued with more clarification and apoptotic function of candidate genes in response to DNA damage will be investigated. We hope that the discovery of pro-apoptotic genes induced by p53 will convey the important role in cancer research and therapy. Acknowledgement: This project is partly supported by Global Center of Excellence (GCOE) program at TMDU.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4950. doi:1538-7445.AM2012-4950
Abstract 4952: Persistent expression of Nqo1 by p62-mediated Nrf2 activation facilitates p53-dependent mitotic catastrophe
Authors: Bui Chi Bao
Published: August 2012

Prolonged mitosis due to aberrant chromosome segregation permits cells to enter the G1 phase without cytokinesis and subsequently triggers the p53-dependent cell death program, known as mitotic catastrophe. Cells which fail to go through mitotic catastrophe create aneuploidy, posing a risk of oncogenesis. In the present report, we show that p62-mediated non-canonical activation of Nrf2 leads to the persistent expression of Nqo1, which plays a critical role for p53 stabilization during mitotic catastrophe. With prolonged exposure to nocodazole, a microtubule-depolymerizing agent, p62-deficient HCT116 cells exhibited an accumulation of a polyploid population with a limited appearance of apoptoic cells, which was attributable to the attenuated stabilization of p53. Combinatorial gene manipulation analysis verified that the regulatory cascade with a hierarchy of p62-Keap1-Nrf2-Nqo1 is required for p53 stabilization for mitotic catastrophe. This is consistent with the role of Nqo1 as a gatekeeper for proteasomal degradation of p53. Thus, we demonstrate for the first time the functional connection between the non-canonical Nrf2 pathway and p53-dependent cell death program upon prolonged mitosis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4952. doi:1538-7445.AM2012-4952
Abstract 4957: Mixed Lineage Kinase 3 mediates vanadium-induced cell death in cancer cells
Authors: Rangasamy Velusamy , Sondarva Gautam , Tuladhar Sushan , Rana Basabi , Rana Ajay
Published: August 2012

Vanadium is a transition metal and occurs naturally in a variety of minerals. In mammals, vanadium has been shown to promote cancer cell death and can also mimic insulin action, most probably through the inhibition of cellular tyrosine phosphatase and subsequent activation of signaling pathways. The mechanism by which vanadium causes cancer cell death is still not known. Interestingly, it has been shown that various mitogen activated protein kinase (MAPK) members are activated upon vanadium treatment. However, the contribution of any specific MAPK member that mediates vanadium-induced cell death has not been clearly delineated. It has been reported that JNK is activated by vanadium and therefore we investigated the role of Mixed Lineage Kinase 3 (MLK3) on vanadium-induced cell death. MLK3 is a MAP3K member that is known to specifically activate JNK pathway. We have earlier reported that MLK3 activation promotes cell death in cancer and neuronal cells. Our results demonstrated that endogenous MLK3 was activated by vanadium and MLK3 was highly phosphorylated on tyrosine residues. We also identified Src as a tyrosine kinase that phosphorylated MLK3 on specific tyrosine residues and phosphorylation of these tyrosine residues by Src was essential for MLK3 activation. Vanadium-induced cancer cell death was mediated by MLK3 or MLKs, because CEP-1347, a pan MLK inhibitor, prevented this cell death. Furthermore, the tyrosine phospho-deficient mutants of MLK3 also prevented vanadium-induced cell death. Interestingly, the activity of Src was seen to be in parallel with MLK3 kinase activity in human primary breast tumors. Taken together, our data demonstrate that tyrosine phosphorylation of MLK3 by oncogenic Src leads to MLK3 activation, which subsequently promotes vanadium-induced cell death in cancer cells. Our results also implicate a paradoxical pro-apoptotic role of Src in cancer cells, and thus it is conceivable that in tumors where both Src and MLK3/MLKs activities are higher, targeting of this axis might promote cell death.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4957. doi:1538-7445.AM2012-4957
Abstract 5044: Radiation modulates expression of microRNAs in breast cancer cell lines grown under adherent and stem cell promoting culture conditions
Authors: Debeb Bisrat G. , Xu Wei , Lacerda Lara , Li Li , Caimiao Wei , Reuben James M. , Ueno Naoto T. , Buchholz Thomas A. , Woodward Wendy A.
Published: August 2012

Although mounting evidence demonstrates that cancer stem/progenitor cells are radioresistant, explicit mechanisms of resistance have not been fully explored. MicroRNAs (miRNAs) are small noncoding RNAs that are involved in regulating cancer stem cell self-renewal and play an important role in response to cellular stress. Few studies have been conducted to investigate the role of specific miRNAs in cellular radiation response. Knowledge of how radiation therapy modulates miRNA expression in cancer stem cells vs. non-stem cells is critical to developing cancer stem cell sensitizers. We isolated total RNA from adherent (2D) and non-adherent mammosphere (3D) cultures of six breast cancer cell lines (MCF12F, MCF7, SUM190, SUM149, MDA-IBC-3, and SUM159) subjected to 0Gy or 4Gy radiation and examined differentially expressed miRNAs using Exiqon's miRCURY microarray. Analysis of the data showed 62 differentially expressed miRNAs between 2D and 3D independent of radiation treatment (fold change of at least 1.5, FDR <0.1; P<0.05). While no radiation based signature was observed when comparing all irradiated samples to unirradiated samples, assessment of each cell line indicated that the levels of specific microRNAs were altered in response to radiation treatment in 2D and 3D cells. Further studies to validate the functions of top candidate miRNAs using inhibitors or mimics to alter the self renewal and radiosensitivity of cancer stem cells are underway.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5044. doi:1538-7445.AM2012-5044
Abstract 5045: miR-10b mediates melanoma progression induced by BRAFV600E
Authors: Datar Ila J.
Published: August 2012

The protein kinase BRaf plays an important role in the mitogen-activated protein kinase (MAPK) pathway initiated by Ras. Raf, after activated by Ras activates Erk and its downstream effectors to carry out normal cellular functions, which include differentiation, proliferation, survival and senescence. BRafV600E mutation has been implicated in 50-60% of all melanoma cases. It is a constitutively active mutation that has been linked to the progression of melanoma. Many microRNAs have been implicated in cancer proliferation and metastasis. Of special interest is the miR-10b, which is known to play a crucial role in tumor invasion and metastasis as previously observed in a mouse mammary tumor model. Our preliminary data show that miR-10b was upregulated in melanoma cell-lines that carried either N-Ras gain-of-function mutation or BRafV600E. BRafV600E knockdown in melanoma cell lines reduces the expression of TWIST, a transcriptional activator of miR-10b, as well as the expression of miR-10b. Further, BrafV600E is known to mediate senescence through several factors including the transcriptional regulator DMTF1. Concordantly, we detected an increase in the expression of DMTF1 on BRafV600E knockdown. Thus, we hypothesize that in melanoma, BRafV600E activates the expression of TWIST which then activates miR-10b, leading to inhibition of DMTF1 and ultimately a failure to bring about cell-cycle arrest.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5045. doi:1538-7445.AM2012-5045
Abstract 5051: microRNA based classification of non-BRCA1/2 hereditary breast cancer tumors
Authors: Tanic Miljana , Marquez-Rodas Ivan , Fernandez Victoria , Benitez Javier , Martinez-Delgado Beatriz
Published: August 2012

Familial breast cancer comprises 5-10% of all breast cancer cases. Germline mutations in the currently known BRCA1 or 2 high risk-breast cancer genes are common in familial breast cancer, but they can explain, 20-25% of the overall familial risk. Still, the large majority of breast cancer cases that arise in families with strong familial aggregation are not explained by mutations in any know breast cancer susceptibility gene, and are designated as BRCAX tumors. MicroRNA (miRNA) deregulation has been extensively implicated in cancer pathogenesis. Specifically, in breast cancer, there are miRNA expression profiles associated to specific subtypes or biological features such as hormone receptor, HER2 status, metastasis, progression or proliferation. However, there are no publications describing miRNA expression profiles in hereditary breast tumors. We established the miRNA expression profiles associated to familial breast tumors from different genetic subtypes, BRCA1, BRCA2 and BRCAX. The discovery of differentially expressed miRNAs may improve the diagnosis of these tumors and will provide new insight into the molecular biology of the tumors. We selected tumor areas from 80 FFPE samples (66 hereditary breast tumors, 10 sporadic and 4 normal breast samples). The samples were analyzed by miRNA microarray expression profiling using LNA-based Exiqon platform and interesting miRNAs were validated by QT-PCR. Hierarchical clustering of BRCAX tumors revealed clear heterogeneity, with 4 apparent groups. For class discovery we have used Consensus clustering algorithm that confirmed the existence of 4 different subgroups among BRCAX tumors (A, B, C and D). Interestingly, Group C clusters with BRCA1/2 mutated tumors, while Group A clusters along with normal breast tissue. Group B appears as a homogenous group of tumors, while group D represents a very heterogeneous group, lacking a specific miRNA signature. Next, we identified miRNA signatures for each of the well defined groups (A, B, C) and we performed pathway enrichment analysis using IPA and identified associated biological processes for each of the miRNA clusters. We found that miRNAs contributed to a better definition of BRCAX group of tumors, which could potentially be subclassified into distinct groups. The identification of key target genes and pathways regulated by significant miRNAs would give as a better understanding of the mechanisms of tumorigenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5051. doi:1538-7445.AM2012-5051
Abstract 5060: Identification of somatic retrotransposon insertions across cancer types using RetroSeq
Authors: Helman Elena , Lawrence Mike , Stewart Chip , Getz Gad , Meyerson Matthew
Published: August 2012

Retrotransposons comprise over 40% of the human genome and represent an important class of genetic variation. Though most elements are stationary ancient relics, it has recently been shown that some 100 elements remain highly active, copying and pasting themselves throughout the genome with each generation. Retrotransposon insertions can disrupt gene function, modulate gene expression, and lead to genomic rearrangement. These events have previously been implicated in cancer, including an account of insertional mutagenesis in APC as an early event in colon cancer progression. Due to the inherent difficulty in localizing repeat elements, however, an extensive investigation of retrotransposons’ role in cancer has not yet been performed. We developed RetroSeq, a computational framework to identify novel insertions of retrotransposons from paired-end sequencing data. In simulated data, RetroSeq identifies retrotransposon insertions with 99% sensitivity and 99% specificity. We ran RetroSeq on whole-genome sequencing data from a panel of tumors (including 9 colorectal, 20 non-small cell lung, 24 prostate and 22 breast tumors) and matched normal samples to determine the extent of somatic retrotransposon activity. We find a broad range of novel retrotransposon insertion events specific to each tumor, with some insertions falling in exonic as well as intronic and intergenic regions. These events were validated experimentally and integrated with expression and methylation data to provide a global view of retrotransposon activity in these samples. In sum, using RetroSeq we are able to localize novel retrotransposon insertions in paired-end sequencing data and provide evidence for the reactivation of retrotransposons in cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5060. doi:1538-7445.AM2012-5060