bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4912: A network model of circulating tumor cell dynamics: Uncovering the mechanism of metastasis
Authors: Scott Jacob G. , Kuhn Peter , Anderson Alexander R A , Newton Paul
Published: June 2012

Background: Hematogenous metastasis is a poorly understood process that accounts for the lion's share of cancer death. We hypothesize that this process can be explained by circulating tumor cells (CTCs). We endeavor to deconvolute this complex process by means of a mathematical model of CTC population dynamics within the human vascular system.

Methods: We have represented the human vasculature as a network with organs represented as nodes and vascular connections as directed edges and written a system of Ordinary Differential Equations to model the dynamics of circulating tumor cells (CTCs) as they populate the body from a source tumor. We have introduced several novel concepts such as a ‘filtration fraction’ which represents the fraction of CTCs that arrest in a given organ, the ‘shedding rate’ which represents the rate at which a primary tumor sheds CTCs into the vasculature and a ‘clearance rate’ which represents the combined effects of CTC apoptosis and immune clearance.

Experimental parametrization of this model is accomplished through a clinical trial at The Scripps Institute during which we measure CTC concentrations at each of the most highly connected nodes at several time points before and after definitive surgery for – to include the portal vein, the superior vena cava, peripheral venous and peripheral arterial blood.

Results: Initial exploration of the model using clinical data for validation has shown that certain tumor types follow flow driven patterns of metastasis while others seem to ignore the logical spread (e.g. prostate cancer spreading to the bone does not follow the flow directed network while sarcoma to the lungs does). Reasons for this dichotomy are as of yet unknown, though we suspect that both CTC heterogeneity and some form of biological signaling response are at play. We will utilize our theoretical model to investigate this dichotomy by explicitly incorporating CTC heterogeneity and by making specific biological, phenotypic observations of CTCs from different points in the network.

Conclusion: We present the first network based, filter and flow model of CTC dynamics. The act of building the theoretical model and comparing it to clinical data alone has inspired several biological hypotheses and we look forward to testing more specific questions through clinical studies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4912. doi:10.1158/1538-7445.AM2011-4912
Abstract 4914: A novel integrative network study identifies key genes and pathways in the progression of Hepatitis C virus induced hepatocellular carcinoma
Authors: Zhao Zhongming , Zheng Siyuan
Published: June 2012

Hepatocellular carcinoma (HCC) is the third most common cause of cancer mortality in the world. Incidence of hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) has been increasing in the United States and Europe during recent years. Although HCV-associated HCC shares many pathological characteristics with other types of HCC, the molecular mechanisms underlying its progression remain elusive. To investigate the underlying pathology, we developed a systematic approach to identify deregulated biological networks in HCC by integrating gene expression profiles with high-throughput protein-protein interaction data. This integrative approach to searching for deregulated networks during each pathological stage is different from typical search of common pathway resources like Gene Ontology or KEGG biochemical pathways. It has at least two advantages: 1) a high throughput protein interaction network covers more genes; and 2) the resulting network gives gene interaction information, which provides a simpler framework to explore the functional associations between genes and generate new biological hypotheses. By comparing sets of consecutive pathological stages, we identified four networks in five groups of samples corresponding to normal, cirrhosis, dysplasia, early HCC and advanced HCC. The functional annotation of each network demonstrates a high degree of consistency with current knowledge of HCC. By assembling these functions into a modular map, we were able to depict the stepwise pathways that are dysregulated in HCV-induced hepatocarcinogenesis. Additionally, these networks enable us to identify important genes and pathways by developmental stage, such as LCK signaling pathways in cirrhosis, MMP genes and TIMP genes in dysplastic liver, and CDC2-mediated cell cycle signaling in early and advanced HCC. CDC2 (alternative symbol CDK1), a regulatory gene in cell cycle control, is particularly interesting due to its topological position in temporally deregulated networks. Our study uncovers a temporal spectrum of functional deregulation, and prioritizes key genes and pathways in the progression of HCV induced HCC. These findings present a wealth of information for further investigation.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4914. doi:10.1158/1538-7445.AM2011-4914
Abstract 4920: Integrative identification of stochastically activated signaling sub-networks in individual cancer cells
Authors: Sergio Iadevaia , Ram Prahlad
Published: June 2012

Traditional studies on signal transduction are focused on measuring the average levels of proteins in populations of isogenic cells to determine the regulatory properties of cell signaling networks and design effective intervention strategies for cancer therapy. However, the average protein levels measured in populations of cells may be quite different from the protein levels measured in individual cells. Signaling differentiation in individual cells is often associated with stochastic events that may activate different cellular sub-networks at different times to generate diverse responses. It is therefore critical to elucidate these stochastic events to design therapeutic interventions that may effectively inhibit abnormal signaling sub-networks in individual cells. In this work, we analyzed the epidermal growth factor (EGF) signaling network in the MDA-MB468 breast cancer cell line and the insulin-like growth factor (IGF-1) signaling network in the MBA-MB231 breast cancer cell line. We measured the average changes in the phosphorylation of proteins after EGF or IGF-1 stimulation using reverse-phase protein arrays (RPPA). We developed a detailed mathematical model to predict the deterministic and stochastic dynamics of EGF and IGF-1 signaling networks. We used particle swarm optimization to train the deterministic model to predict the average transient changes in the phosphorylation of proteins measured by RPPA and infer the unknown model parameters. Using the estimated model parameters, we implemented the stochastic model to predict the transient changes in the phosphorylation of proteins in individual cells. The modeling results showed that protein phosphorylation in individual cells could attain levels that were several fold higher or lower that those attained by the average cell in the population. We used a multicolor fluorescence-activated cell sorter (FACS) to measure the distribution in the phosphorylation of protein after EGF or IGF-1 stimulation and experimentally validate the modeling predictions. We finally compared the overall signal transduction of individual cells whose protein phosphorylation attained higher and lower levels to computationally identify cellular sub-networks that were differentially activated. The integrative approach described here is therefore a useful tool for computationally predicting the stochastic events responsible for signaling differentiation in individual cells and optimizing experimental intervention strategies for cancer therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4920. doi:10.1158/1538-7445.AM2011-4920
Abstract 4923: Myofibroblasts induce specific epithelial-to-mesenchymal transition (EMT) patterns in colorectal cancer cells by enhanced secretion of bone morphogenic protein (BMP) inhibitors
Authors: Karagiannis George S. , Musrap Natasha , Diamandis Eleftherios P.
Published: June 2012

Epithelial-to-mesenchymal transition (EMT) is dictated by both cell-autonomous and stromal oncogenic signals. We hypothesized that colon cancer desmoplasia provides multiple signals, inducing EMT in cancer cells. To address this issue, we first developed cell-contact cocultures of SW480 and SW620 cell lines with normal fibroblasts. Cocultured fibroblasts (myofibroblasts) acquired the myofibroblastic phenotype with increased alpha-SMA and MMP2 expression, which was reversed by TGF-beta disruption. We identified oncogenic signals from myofibroblasts, after subjecting mono- and cocultures to secretome analysis with mass spectrometry (LC-MS/MS). In a total of 1551 identified proteins (>2 peptides), a) secretome algorithms based on prediction of secretion, were deployed, allowing the removal of intracellular contaminants from the generated coculture lists and b) monoculture datasets were used as exclusion datasets to denote the non-specific-to-desmoplasia proteins. Subsequent bioinformatic analysis in this “desmoplastic” dataset (124 proteins) was used for protein clustering and recovery of a potential EMT cluster. We deployed: a) Ingenuity pathway analysis, b) Gene ontology, c) Smooth muscle enrichment analysis with Genevestigator d) Protein-protein interaction network analysis with STRING. Interestingly, this integration revealed GREM1, FST and FSTL3, three Bone Morphogenic Protein (BMP) inhibitors, as potent MET disruptors in colorectal cancer. We thus hypothesized that cancer cells recruit stromal fibroblasts to disrupt unfavorable BMP signaling (through generation of multiple BMP inhibitors), which supports a cancer cell undifferentiated state. To test this, a colon cancer cell line (HT29; active BMP signaling), was treated with human BMP7 and decreased cell migration (p<0.05) and proliferation (p<0.05) were shown. These lysates were further used for proteomic analysis (LC-MS/MS) with label-free quantitation to investigate differential protein expression. Using gene expression meta-analysis from fetal tissues, a significant (p<0.01) shift from mesenchymal to epithelial protein dominance was noticed, after 200 ng/mL BMP7 treatment. Differentially expressed proteins remain to be validated, to better characterize the “BMP-7-disrpuption” EMT signatures in colon cancer. In conclusion, integrative “systems biology” approaches may support the identification and validation of EMT signatures with important causative links to cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4923. doi:10.1158/1538-7445.AM2011-4923
Abstract 4929: Dissection of protein-protein interaction-mediated cross-talk pathways in hepatocellular carcinoma
Authors: Chen Tzu-Chi , Liu Chia-Hung , Lee Pei-Ying Lee , Lin Kuan-Ting , Liu Yu-Wen , Huang Chi-Ying
Published: June 2012

Multiple dys-regulated cell signaling pathways and extensive cross-talks, which can be depicted via protein-protein interactions (PPIs), among individual signaling pathways, characterize cancer development and progression. However, systematic analysis of the cross-talk events from distinct pathways via PPIs remains fragmentary, and the reliability of PPI datasets, particularly at the cellular level, remains to be vigorously examined. Here, we first build the cross-talk pathway map of heptocellular carcinoma (HCC) through overexpression patterns in HCC among 23 pathways. By detecting endogenous PPIs in two HCC cell lines, Huh7 (low invasive cells) and Mahlavu (high invasive cells), we validate 50 PPI events within pathway and 19 PPI-mediated cross-talk events among 23 pathways in HCC. Not surprisingly, many distinct PPIs are present between Huh7 and Mahlavu, providing the opportunity to characterize tumor invasion. By analyzing topology of cross-talk PPI network, CRKL has a pivotal role in cross-talk pathway. This initial attempt to map the cross-talk pathways in HCC may represent the first step in deciphering hepatocarcinogenesis at the systems level and might reveal a novel strategy for HCC treatment.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4929. doi:10.1158/1538-7445.AM2011-4929
Abstract 4931: Cancer stem cells in solid tumors: Symmetric division, niche size, and invasive tumor morphology
Authors: Enderling Heiko , Hlatky Lynn , Hahnfeldt Philip
Published: June 2012

In recent years cancer stem cells have been identified as a minor subpopulation in numerous solid tumors that drives tumor initiation, development and metastasis. Although cancer stem cells have yet to be reliably isolated, populations enriched for tumor-initiating cells give an indication of the order of magnitude of the stem cells niche within primary tumors. Here we develop and discuss the predictions of a simple theoretical model of cancer stem cells and tumor growth dynamics. We evaluate the impact of cancer stem cell symmetric/asymmetric division and progeny cancer cell proliferation capacity on tumor progression and morphology. The model predicts that the frequency of symmetric cancer stem cell division determines the resulting stem cell pool size, and that the symmetric division frequency and the stem cell fraction are both typically small, consistent with the cancer stem cell hypothesis. At the same time, we show that intrinsic competition for space and environmental confinement can lead to an increasing stem cell fraction over time despite a fixed, low symmetric division probability. These findings offer a novel explanation for the apparent differences in reported stem cell numbers for different tumors as well as tumors of the same organ, and thus challenging the hypothesis of a fixed stem cell ratio for different tumors. The pivotal role of stem cell division strategies and stem cell ratio on spatio-temporal morphology evolution and self-organizing tumor patterning is discussed.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4931. doi:10.1158/1538-7445.AM2011-4931
Abstract 4933: Modeling the sequence-sensitive gemcitabine/docetaxel combination using the Virtual Tumor
Authors: Fernandez Eric , Orrell David , Mignard Caroline , Koob Zina , France Damien , Hoffman Nicolas , Bichat Francis , Fell David , Chassagnole Christophe
Published: June 2012

In recent years there has been great interest in determining synergistic drug combinations. A difficulty, however, is that the number of different possible schedules increases combinatorically when more than one drug is considered, so it is very hard to know what schedules should be tested. Physiomics, a computational biology company based in Oxford UK, has therefore developed a predictive PK-PD “Virtual Tumor” model that allows us to rationally design schedules for drug combination. This poster presents simulations of xenograft experiments, performed in collaboration with Oncodesign, for the sequence-sensitive gemcitabine/docetaxel combination regimen, which is widely used to treat various types of cancer. By producing xenograft and biomarker data of each drug in isolation, we have built a Virtual Tumor capable of simulating the outcome of various regimens using this combination, and proposed new optimal administration schemas. This technology can be used to design new regimens with proprietary compounds as well as standard of care, small molecules or biotherapeutical agents; help test possible schedules for combinations of different drugs that would be effectively impossible to investigate experimentally; and allow prioritisation of the most effective drug combinations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4933. doi:10.1158/1538-7445.AM2011-4933
Abstract 4934: Up-regulation of microRNA-21 correlates with lower survival of kidney cancer
Authors: Zaman Mohd Saif , Deng Guoren , Shahryari Varahram , Singh Kamaldeep , Sandhu Herman , Dahiya Rajvir
Published: June 2012

MicroRNA-21 is up-regulated in a variety of cancers, such as breast, colorectal, lung, head and neck, etc. However, the regulation of miR-21 in kidney cancer has not yet been studied systematically. We measured miR-21 levels in 40 pairs of kidney cancers and their normal matched tissues by real-time PCR. In 36 cases (90%), miR-21 was increased (ratios of miR-21 levels in tumors to normal tissues T/N were greater than 1.5). The expression level of miR-21 was correlated with 5 year survival and the stage of the patients. For patients with low miR-21 expression, all survived 5 years after the operation, while in case of high miR-21 expression, only 59% survived. In groups of patients having low expression (T/N <1.5), moderate high expression (T/N 1.5-10) and very high expression (T/N >10), the percent of early stage (Stage I) decreased: 100%, 76% and 43%, respectively. To study the biological effect of miR-21 up-regulation, a kidney cancer cell line A498 was transfected with miR-21 anti-miRNA inhibitor. The miR-21 level was reduced by more than 99%, as compared to the negative control. Flow cytometry analysis of the cell cycle showed a significant increase in G0/G1 phase (9.1%), with a concomitant reduction in the G2/M phase (6.8%), indicating that the forced reduction of miR-21 expression in A498 cells could inhibit the cell growth and cause G0/G1 arrest. Apoptosis assay using flow cytometry showed a significant increase in the number of total apoptotic cells in the miR-21 anti-miRNA inhibitor transfected cells as compared to the negative control. MiR-21 gene was mapped to chromosome 17q23, and increased copy numbers of this section, which includes oncogenes like erb-B2/HER-2, RPS6KB1, etc., were frequently present in cancers. We compared the miR-21 expression levels with the amplification of this section in 30 cancer cell lines, including 5 kidney cancer, 6 breast cancer, 15 colorectal cancer, 3 prostate cancer, and 1 bladder cancer. We observed a significant correlation between the amplification of 17q and high miR-21 expression. In conclusion, the up-regulated miR-21 in kidney cancer could be used as a tumor marker for diagnosis. The inhibition of miR-21 and/or its adjacent oncogenic genes may prove to be useful in controlling cancers with up-regulated miR-21.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4934. doi:10.1158/1538-7445.AM2011-4934
Abstract 4945: Androgen-mediated phenotypic change produces a miRNA fingerprint in prostate carcinoma cells
Authors: Segal Corrinne V. , Powell Christopher J. , Gooderham Nigel J.
Published: June 2012

Activation of the androgen receptor (AR) results in phenotypic change in androgen-responsive cells; for example, in the human prostate carcinoma cell line (LNCaP) androgens mediate cell proliferation. Factors controlling the range of phenotypic responses mediated by androgens are only partially understood, but include both transcriptional and post-transcriptional mechanisms. One such mechanism that appears to offer wide ranging, yet highly selective control, is microRNA-mediated post-transcriptional regulation. In the present study, we assessed the influence of endocrine-active compounds that act via the AR pathway on the microRNA (miRNA) profile. As negative regulators of gene expression, miRNA are short non-coding RNA that are able to suppress translation or induce degradation of their target mRNA transcripts leading to decreased protein expression.

The effect of exposure of LNCaP cells to a model synthetic AR agonist, a physiological androgen and a therapeutic AR antagonist was determined at various time points up to 120 hours. Phenotypic response to exposure was assessed as an alteration of proliferative ability, expression of prostate-specific antigen (PSA) and alteration of the miRNA-ome. As expected, the agonists significantly induced proliferation and PSA expression, compared to vehicle control, whilst the antagonist itself had no effect on proliferation and PSA expression except when cultured in the presence of the natural ligand resulting in potentiation of the ligand's effects.

The temporal effects of the compounds on the expression profile of 866 miRNAs were assessed using Agilent's miRNA microarray version 3. A number of miRNAs were found to be altered in a compound-specific and temporal manner, including some implicated in cell cycle control. qRT-PCR of select miRNAs proceeded to validate the fold changes observed by microarray. Targets for altered miRNAs were deduced using bio-informatic approaches and immunoblotting of target proteins has confirmed that protein levels are inversely correlated. These data describe an androgen-mediated miRNA ‘fingerprint’ that is compound and temporally dependent and provides mechanistic insights into the biological responses of cells to such compounds.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4945. doi:10.1158/1538-7445.AM2011-4945
Abstract 4947: microRNA expression in soft tissue sarcomas is associated with prognosis
Authors: Greither Thomas , Würl Peter , Grochola Lukasz , Bond Gareth , Bache Matthias , Kappler Matthias , Lautenschläger Christine , Holzhausen Hans-Jürgen , Eckert Alexander , Taubert Helge W.
Published: June 2012

The levels of miR-210 known as hypoxia regulated microRNA were analyzed by quantitative RT-PCR in a cohort of 78 soft tissue sarcomas (STS). The microRNA levels were separated according to the tercentile in low, intermediate and high expression and possible association of microRNA expression and patients’ survival was examined using multivariate Cox's regression hazard analyses. A significant correlation between intermediate miR-210 expression and disease specific death of female STS patients was observed compared to patients with a high expression level in their tumors (RR=11.28; P=0.010). Furthermore, expression of miR-210 was significantly associated with age of tumor onset in a gender-specific manner. Male patients with an intermediate expression of miR-210 showed a 9.6 years later age of tumor onset compared to males with a low expression of miR-210 in their tumors. However, this was not the case for female patients. This study provides the first evidence for a correlation of expression levels of a single microRNA (miR-210) with prognosis and a gender specific association with age of tumor onset for soft tissue sarcoma patients.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4947. doi:10.1158/1538-7445.AM2011-4947
Abstract 4962: Assessing serum miRNA as putative biomarkers for serous epithelial ovarian cancer
Authors: Kan Casina W. , Hahn Michael A. , Marsh Deborah J. , Howell Viive M.
Published: June 2012

Serous epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy; due in part to vague and non-specific symptoms resulting in delayed diagnosis. The biomarker in routine clinical use for EOC is CA-125, with the OVA1 test (Quest Diagnostics) recently available to aid in predicting the likelihood that an ovarian mass is malignant. Current diagnostic tests have limitations which may be improved by expansion of biomarker panels. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that regulate important cellular processes. They exhibit distinct expression profiles in cancers and have recently been discovered in serum and other body fluids. Tumor miRNAs may be shed into the circulation, raising the possibility of their use as serum biomarkers for the detection of EOC.

Exiqon LNA miRNA microarrays were performed using RNA from cell line models of serous EOC. Over-expressed miRNAs were selected as candidates for assessment in serum. These were measured in RNA extracted from serum of patients with serous EOC (n=30) and healthy age-matched volunteers (n=30) by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). As there are currently no routine methods for the normalization of miRNA in serum, a group of highly and uniformly expressed miRNAs with no reported involvement in cancer was selected for assessment as endogenous controls.

Five miRNAs, miR-182, miR-96 and miR-200a, miR-200b and miR-200c were identified as highly expressed in a panel of serous EOC cell lines consistent with previous reports, and therefore selected for investigation as putative serous EOC biomarkers. In addition, miR-92a, miR-103, miR-638 and RNU48 were selected as candidate endogenous controls given that they were consistently expressed at high levels in the cell line panel. qRT-PCR data will be presented on the expression of these 8 candidate miRNAs and RNU48 either with or without pre-amplification of target sequence.

In conclusion, miR-92a, miR-103 and miR-638 were observed to show little variation between patients and healthy volunteer serum. These results identify the potential for these miRNAs to be used as endogenous controls for the expression of miRNA in serum. Reliable detection of specific miRNAs in serum from women with serous EOC may improve the detection of this malignancy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4962. doi:10.1158/1538-7445.AM2011-4962
Abstract 4968: TNF-alpha promotes genome-wide replacement of TAp73 chromatin occupancy by cREL and DeltaNp63
Authors: Lu Hai , Si Han , Yang Xinping , Burnett Jeffery , Davis Sean , Sun Hongwei , Xiao Wenming , Wei Lai , Meltzer Paul , Van Waes Carter , Chen Zhong
Published: June 2012

cREL, DeltaNp63, and TAp73, members of NFkappaB and TP53 transcription factor (TF) families, together regulate broad biological processes critical for inflammation and cancer survival. However, the underlying mechanisms explaining their cross-regulation of transcriptome and interactive signal network have not been revealed. Here, we demonstrate that inflammatory cytokine TNF-alpha induces a dynamic, genome-wide increase in cREL and DeltaNp63 chromatin occupancy after replacing TAp73 binding activity, using ChIP-seq and fitting the data into a negative binomial distribution model integrated in CisGenome. Globally, most of the binding peaks were localized in intergenic and intronic areas, with 4.2% and 5.6% peaks significantly enriched into promoter regions (3000 bp upstream of transcription starting sites) of cREL and DeltaNp63 bound DNAs in response to TNF-alpha respectively, and co-localized peaks for any of the two TFs are prevalent within a distance of ∼200 bp. De novo motif search using Gibbs Sampler identified TP53 and novel binding motifs. A total of 188 differentially expressed genes are associated with the TNF-alpha-induced chromatin occupancy shift by the three TFs. These genes are enriched in cancer-related transcription factors and TP53 signaling pathways. Our data reveal a novel mechanism of genome-wide replacement of TAp73 by cREL and DeltaNp63, supporting cross-regulation and an interactive network between NFkappaB and TP53 families.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4968. doi:10.1158/1538-7445.AM2011-4968
Abstract 497: Loss of Notch-1 expression in human prostate epithelial cells results in reduced PTEN expression and altered differentiative capacity
Authors: Angus C. William , Willis David F. , Salvador Wenimar D. , Bertrand Fred E.
Published: June 2012

Notch-1 is part of an evolutionarily ancient cell surface receptor signaling pathway that functions in the determination of stem/progenitor cell fate. The human genome encodes four Notch-receptors (Notch-1, -2, -3, and -4) and at least five Notch-ligands (Delta-1, -3, -4, Jagged-1, and-2). Signaling is initiated upon ligand binding to the Notch receptor, which results in a series of proteolytic cleavages that release constitutively active intracytoplamsic Notch (ICN). Nuclear translocation of ICN results in activation of the CBF-1 transcription factor which in turn increases expression of developmentally regulated transcription factors such as Hes-1 and Hey-1. The PTEN tumor suppressor gene is a recently identified Notch-1 target. We have reported that Notch-1 signaling increases expression of the PTEN tumor suppresser gene in prostate tumor cell lines and that Notch-1 signaling is lost in the tumor foci of prostate adenocarcinoma patients. To test the hypothesis that loss of Notch-1 will result in deregulation of normal prostate epithelial cell differentiation and promote tumorigenesis, a lentiviral vector bearing a Notch-1 shRNA (shN1) was used to stably knockdown Notch-1 expression in the benign human prostate epithelial cell line, RWPE-1. Western blotting revealed that RWPE-1/shN1 cells lacked Notch-1 expression, and exhibited reduced expression of Hes-1, confirming that loss of Notch-1 expression resulted in loss of Notch signaling. PTEN protein expression was also reduced, consistent with our previous studies demonstrating that Notch-1 signaling regulated PTEN expression. RT-PCR experiments verified that loss of PTEN expression was mediated at the level of transcription. RWPE-1/shN1 cells lacking Notch-1 expression exhibited a more rounded morphology, as compared with the parental cell line. Rhodamine-phalloidin staining revealed that RWPE-1/shN1 cells had less numerous and shorter cell surface actin projections. RWPE-1/shN1 cells lacking Notch-1 expression exhibited a 2-fold increase in acinar differentiation upon 3-D culture in matrigel as compared with the parental cell line. Flow cytometric analysis revealed that RWPE-1 cells without Notch-1 expression had reduced surface expression of TROP2 and CD149f. Preliminary RT-PCR results indicate that expression of the basal cell marker keratin-5 is reduced in RWPE-1/shN1 cells as compared with parental RWPE-1 cells. Our data suggest that loss Notch-1 expression, and hence loss of signaling, may promote developmental plasticity in prostate epithelial cells.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 497. doi:10.1158/1538-7445.AM2011-497
Abstract 4972: High-throughput functional profiling of dedifferentiated liposarcoma cell lines
Authors: Banerji Shantanu , Barretina Jordi , Crago Aimee , Frederick Abbie , Okamoto Michael , Weir Barbara , Cowley Glenn , Root David , Ladanyi Marc , Singer Sam , Meyerson Matthew L.
Published: June 2012

We previously profiled several adult soft-tissue sarcoma subtypes using sequencing, copy number analysis, and gene expression arrays. This high-throughput genetic profiling revealed dozens of candidate genes deserving of further functional validation.

To prioritize genes, we performed a pooled shRNA screen to identify essential genes in liposarcoma. Dedifferentiated liposarcoma (DDLS) served as a model for this approach as multiple robust cell lines are available. Five DDLS cell lines (DDLS8817, LPS141, FU-DDLS-1, RDD8107, and LP6) were infected with a pool of 54,020 lentiviral shRNAs targeting ∼11,000 genes (median 5 shRNAs per gene) and passaged for 16 doublings. DNA was extracted and hairpin sequences were PCR amplified and hybridized to a custom microarray that interrogates all shRNAs in the pool. shRNAs were ranked according to their differential abundance between early and late passages. Genes corresponding to the most significantly depleted shRNAs are presumed to affect cell proliferation and are candidate oncogenes.

We compared the pattern of hairpin depletion in the DDLS cell lines to a panel of over 60 cell lines representing other common cancers screened with the same pooled shRNA library. The 5 DDLS cell lines clustered into 3 distinct groups. Only one gene appeared to be essential in all 3 groups: WWTR1 (TAZ1), a master-regulator of adipocyte differentiation. Twenty-eight genes appeared essential in at least two DDLS groups including MDM2 and ZBTB2, both reported to negatively regulate the tumor suppressor gene TP53. Low-throughput in vitro experiments have confirmed that WWTR1 knockdown using two shRNA clones inhibits LPS141 proliferation by 78 and 75% after 4 days as compared to scramble (p=0.004 and 0.06 respectively).

Our complementary genome-scaled functional screen has confirmed a known oncogene in DDLS and revealed additional candidate genes that appear to have a role in proliferation. Further integration of existing datasets may nominate additional genes essential for liposarcoma pathogenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4972. doi:10.1158/1538-7445.AM2011-4972
Abstract 4974: Allele-specific mRNA and protein expression on genetic variants of CCNE1 associated with risk of bladder cancer
Authors: Kohaar Indu , Fu Yi-Ping , Tang Wei , Tarway McAnthony , Muchmore Brian , Porter-Gill Patricia , Prokunina-Olsson Ludmila
Published: June 2012

A single nucleotide polymorphism (SNP), rs8102137, located 6 Kb upstream from the cyclin E1 gene (CCNE1) on chromosome 19q12, has recently been identified as a risk factor for bladder cancer (OR, p=1.7×10-11, Rothman et al, Nat Gen, 2010). We found a higher expression of CCNE1 mRNA in cDNA samples from bladder tumors (n=42) compared to adjacent normal bladder tissue (n=41, 3.7 fold, p=2.7×10-12). However, the expression did not correlate with genotypes of rs8102137. We also performed allelic expression imbalance (AEI) using a coding synonymous variation in the last exon (rs7257694, Ser390Ser) that is in high LD with the GWAS rs8102137 (normal bladder tissue samples, n = 41, D’=1.0, r2=0.815 and in HapMap CEU samples, n=60, D’=0.95, r2=0.68). In normal and tumor tissue samples heterozygous for both SNPs, the risk variant of rs8102137 was associated with lower expression of allele T of rs7257694 (p=2.2×10-4 in normal samples and 1.11×10-10 in tumor samples).

Western blot protein analysis with bladder tissue and prostate cell lines lysates showed that this allele-specific difference in mRNA expression is likely to be related to two protein isoforms that showed a differential pattern of expression dependent on rs8102137 and rs7257694 genotypes. CCNE1 regulates cell cycle G1/S transition, and alternative protein forms may have differential functions in cell cycle regulation, thereby affecting the risk of cancer. Alternative splicing forms of CCNE1 have been cloned and their functional analysis is ongoing.

In conclusion, our results suggest that bladder cancer associated genetic variants within the CCNE1 gene may affect mRNA splicing and protein structure of the gene, contributing to altered regulation of cell cycle and risk of bladder and other cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4974. doi:10.1158/1538-7445.AM2011-4974
Abstract 4984: Association of PTEN and p16 mutational status with MITF expression may provide a novel context for a phenotype switch in melanoma
Authors: Brooks Bradford R. , Yin Holly , Chow Donald , Sereduk Chris , Koeman Julie , Qian Chaonan , MacKeigan Jeffrey P. , Jung Sungwon , Kim Seungchan , Xu Mai , Weeraratna Ashani , Brown Kevin M. , Trent Jeffrey
Published: June 2012

For the last decade, array-based genomic screening has significantly advanced our understanding of genes involved in cancer development and progression. Moreover, genes identified in those screenings have subsequently been the focus of drug development efforts, ultimately leading to clinical trials. However, the efficient translation of cancer genomics results into the development of more effective therapeutics has been limited in part by the need for robust, high-throughput, functional validation of genes and pathways of interest in well-defined model systems. In order to identify new therapeutic targets in melanoma genomes, we have applied high-throughput RNA interference (RNAi) screening to well-characterized melanoma cell lines. We characterized a panel of 65 melanoma cell lines for genome-wide copy number changes and gene expression, as well as the mutation status of known melanoma genes (BRAF, HRAS, NRAS, KRAS, PTEN, CDKN2A, and TP53). From this panel, 18 cell lines were screened against some 1,250 genes (696 kinases, 550 supplemental; 4 siRNAs per gene) to identify modifiers of melanoma cell survival. A striking finding from our data is that MITF expression appears to be a determinant of invasive context and, furthermore, is associated with changes in both p16 and PTEN status. In the cell lines we examined, high MITF expression correlated with wild-type PTEN status, whereas PTEN was deleted or mutated in 30-35% of cell lines having low MITF expression. Similarly, p16 was unaltered in 40-45% of the cell lines that had high MITF expression but remained unaltered in only 20-25% of low MITF-expressing cell lines. The loss of p16 and PTEN are correlated with an aggressive phenotype in melanoma, and we confirmed by Western analysis that in cell lines with high MITF, p16 is present, but in cell lines with low MITF, p16 expression is absent. In agreement with the current literature, no association could be found with BRAF mutational status. Moreover, these data confirm that MITF is associated with the switch in phenotype from a proliferative to an invasive state in melanoma in a BRAF-independent manner, which in turn is associated with an increase in WNT5A expression, a change we previously have suggested is a critical determinant of melanoma metastasis. Results to be presented, aligned with new studies of sequence variants of MITF (Brown et al., unpublished), may help define a novel context for invasive potential of the important disease.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4984. doi:10.1158/1538-7445.AM2011-4984
Abstract 4985: The UCSC Cancer Genomics Browser
Authors: Zhu Jingchun , Sanborn J. Zachary , Benz Stephen C. , Craft Brian , Szeto Christopher , Kober Kord M. , Goldman Mary , Meyer Laurence , Vaske Charles , Collisson Eric , Stuart Joshua , Haussler David
Published: June 2012

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple datasets can be viewed simultaneously as coordinated “heatmap tracks” to compare across studies or different data modalities. Users can order, filter, aggregate, classify, and display data interactively based on any given feature set including clinical features, annotated biological pathways, and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available datasets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and PARADIGM pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4985. doi:10.1158/1538-7445.AM2011-4985
Abstract 4992: A Sox2-EGFR positive feedback loop contributes to oncogenesis of lung cancer
Authors: Chou Yu-Ting , Lee Chih-Chan , Lin Sheng-Chieh , Wu Cheng-Wen
Published: June 2012

Sox2, a core transcription factor regulating self-renewal of stem cells, is highly expressed in a subset of lung cancer. Nonetheless, how Sox2 contributes to lung tumorigenesis is still elusive. In this study, we report the discovery and mechanistic characterization of the Sox2 as an oncogene in lung cancer cells and its role as a key mediator of EGFR expression. Ectopic expression of Sox2 promoted cell proliferation and anchorage-independent cell growth. Knockdown of Sox2 induced autophagic death and attenuated oncogenic properties of lung cancer. A cDNA microarray analysis and immunoblotting revealed that Sox2 induced expression of EGFR, which contributed to tumorigenesis of lung cancer. In support of this notion, Sox2 bound to the EGFR promoter and enhanced its activity. In addition, EGFR activation or ectopic expression of c-Myc induced Sox2 expression in lung cancer, suggesting that Sox2-EGFR positive feedback loop promotes oncogenesis of lung cancer via a c-Myc dependent pathway. Indeed, c-Myc bond to Sox2 promoter and enhanced its expression under EGFR stimulation. Overexpression of Sox2 promoted tumor growth with increased EGFR expression in xenograft mouse model, and knockdown of Sox2 inhibited tumor growth with attenuated EGFR expression. Our findings suggest that Sox2 could induce EGFR mediated oncogene addiction in lung cancer, with potential applications as a novel therapeutic target for lung cancer treatment.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4992. doi:10.1158/1538-7445.AM2011-4992
Abstract 4993: Nicotine induced EMT and metastasis of human NSCLC : Role of beta-arrestin-1
Authors: Pillai Smitha , Trevino Jose , Rawal Bhupendra , Singh Sandeep , Li Xueli , Schell Michael , Haura Eric , Bepler Gerold , Chellappan Srikumar
Published: June 2012

Cigarette smoking is a major risk factor in the development of non-small cell lung cancer (NSCLC), which accounts for 80% of all lung cancers. Nicotine, an active component of tobacco smoke has been found to induce proliferation, invasion and epithelial-mesenchymal transition in NSCLC cell lines and promote the metastasis of NSCLC in mice. Nicotine induces cell proliferation utilizing a scaffolding protein, β-arrestin-1, which translocates to nucleus and associates with E2F1 transcription factor in response to nicotine stimulation. Here we demonstrate that mesenchymal markers such as vimentin and fibronectin are E2F1 regulated and β-arrestin-1 is involved in regulating nicotine induced expression of these genes. Vimentin and fibronectin promoters were E2F responsive and E2F1 could be detected on these promoters by chromatin immunoprecipitation (ChIP) assays. Depletion of β-arrestin-1 resulted in down-regulation of vimentin and fibronectin expression as well as inhibition of nicotine induced invasion of cells. Quantitative RT-PCR conducted on patient samples revealed a significant correlation between the levels of β-arrestin-1 and the expression of these genes. A microarray analysis conducted on nicotine stimulated parental A549 cells and those lacking β-arrestin-1 showed that about 290 genes were upregulated in the absence of β-arrestin-1, while 787 genes were downregulated. These included genes for transcription factors, growth factor receptors and signaling molecules. We further analyzed the global association of β-arrestin-1 in the genomic region upon nicotine stimulation by ChIP-sequencing and found that β-arrestin-1 is recruited on the promoters of many genes that regulate EMT such as ZEB2 (Zinc Finger E-box Binding Homeobox-2) as well as other regulatory pathways. ChIP assays conducted on NSCLC cell lines revealed the association of β-arrestin-1 on ZEB1 (Zinc Finger E-box Binding Homeobox-1) and ZEB2 promoters. Depletion of β-arrestin-1 in A549 cells resulted in the downregulation of ZEB1 and ZEB2. Additionally, in an orthotopic lung cancer model in SCID-beige mice, implantation of A549-luciferase stable cells lacking β-arrestin-1 showed a decrease in primary tumor growth and also resulted in significantly lower levels of nicotine-induced metastasis when compared to controls. Taken together, these data suggest that β-arrestin-1 contributes to nicotine induced progression and metastasis of NSCLC, especially in patients exposed to tobacco smoke. Further, β-arrestin-1 and its associated molecules might be targeted for the development of novel agents to combat NSCLC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4993. doi:10.1158/1538-7445.AM2011-4993