bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2960: Factor dependent chromatin structure and nucleosome dynamics
Authors: He Housheng H. , Meyer Clifford A. , Liu Shirley X. , Brown Myles
Published: August 2012

Transcription factor cistromes are highly cell-type specific. Chromatin accessibility, histone modifications and nucleosome occupancy have all been found to play a role in defining these binding locations. Here, we show that hormone-induced DNase I hypersensitivity changes (≥DHS) are highly predictive of androgen receptor (AR) and estrogen receptor (ER) binding in prostate cancer and breast cancer cells, respectively. The chromatin structure prior to binding and the nucleosome occupancy after binding are strikingly different for ER and AR. AR binding is associated with changes in both the local nucleosome occupancy and the DNase I hypersensitivity. In contrast, while globally ER binding is unrelated to changes in nucleosome occupancy, DNase I hypersensitivity dynamics predict the ER cistrome. These findings suggest that AR and ER have distinct modes of interaction with chromatin and that DNase I hypersensitivity dynamics provides a general approach for predicting cell-type specific cistromes.

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 2960. doi:1538-7445.AM2012-2960
Abstract 2962: FOXM1 mediates Dox resistance in breast cancer by enhancing DNA repair
Authors: Park Yun-Yong , Jung Sung Yun , Rodriguez-Aguayo4 Cristian , Peng Guang , Lee Se-Ra , Kim Sang Bae , Kim Kyounghyun , Leem Sunhee , Lin Shiaw-Yih , Lopez-Berestein Gabriel , Sood Anil K. , Lee Ju-Seog
Published: August 2012

Transcription factors (TFs) are direct effectors of altered signaling pathways in cancer. To uncover new TFs that would determine clinical outcomes in breast cancer patients, we systematically analyzed gene expression data from breast cancer patients. Our results revealed that forkhead box protein M1 (FOXM1) is the top-ranked survival-associated TF with triple-negative breast cancer. Surprisingly, silencing FOXM1 expression led breast cancer cells to become more sensitive to doxorubicin (Dox). We found that FOXM1-dependent resistance to Dox is mediated by regulating DNA repair genes. We further demonstrated that NF-κB1 interacts with FOXM1 in the presence of Dox to protect breast cancer cells from DNA damage. Finally, silencing FOXM1 expression in a mouse xenograft model significantly sensitized the cells to Dox. Our systematic approaches identified an unexpected role of FOXM1 in Dox resistance by regulating DNA repair genes and FOXM1 may be a promising therapeutic target for sensitizing breast cancer cells to Dox.

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 2962. doi:1538-7445.AM2012-2962
Abstract 2974: Combating breast cancer brain metastasis by targeting Src family kinases
Authors: Zhang Siyuan , Zhang Chenyu , Huang Wen-Chien , Lowery Frank J. , Huang Suyun , Aldape Kenneth D. , Steeg Patricia S. , Yu Dihua
Published: August 2012

Background: Among 1.3 million women diagnosed with breast cancer every year, 10-16% will develop brain metastases. The median survival of patients with brain metastases is less than one year. A most challenging problem is no effective treatment for patients with refractory metastatic breast cancer to the brain. Therefore, novel and effective therapeutic approaches are urgently needed for this population. Recently, our retrospective analyses revealed a significant up-regulation of Src family kinase (SFK) in breast cancer brain metastasis lesions compared with primary tumors. Additionally, HER2-overexpressing breast cancers with Src activation have a higher incidence of brain metastasis. Thus, we hypothesize that activation of SFK plays a critical role in promoting breast cancer brain metastasis. Aims and Methodology: The major aims of this project are: 1) study the role of Src activation in breast cancer brain metastasis; 2) investigate the pre-clinical efficacy of combination Src inhibitor and HER2-targeting therapy Lapatinib in treatment of brain metastasis. We used HER2-overexpressing breast cancer cell line models, in vitro assays of metastasis-properties, and in vivo brain metastasis mouse model (intracarotid artery injection) to test our hypothesis. Results and Conclusions: Src activity is up-regulated in both brain-seek cells lines and human brain metastasis tumors when compared to either parental cells lines or primary breast cancers respectively. To test the role of Src activation in brain metastasis, we established stable cells lines with constitutive-activation of Src. The Src activation enhanced the tumor cell trans-blood brain barrier migration in vitro. Src activation in cells led to a higher brain metastasis incidence in vivo after intracarotid artery injection. We treated Src-activated brain metastasis in vivo with a Src inhibitor saracatinib, a drug under Phase II clinical trial. This Src-targeting treatment decreased the overall incidence of brain metastasis. Combining sarcatinib with EGFR-HER2 dual-targeting agent lapatinib further prolonged the overall survival of tumor bearing mice and significantly inhibited both micro- and macro-metastasis. In summary, novel SFK targeting regimens may be developed as promising therapies for breast cancer patients with brain metastasis.

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 2974. doi:1538-7445.AM2012-2974
Abstract 298: Tumor-associated lymphatic vessels: Hijacking mechanisms of peripheral tolerance
Authors: Swartz Melody A. , Lund Amanda W. , Shields Jacqueline D. , Kourtis Iraklis C. , Hirosue Sachiko
Published: August 2012

Lymphatic vessels drain fluid, antigens, and immune cells from the periphery to the lymph nodes (LNs). In addition to transporting activated dendritic cells to mount adaptive immune responses in the LN, lymphatic drainage is brings soluble antigens from the periphery to LN-resident immature dendritic cells and B cells. It is also the most common site for cancer metastasis. Despite its importance, the role of tumor-associated lymphatic vessels and their drainage to the LN in regulating host immune responses to the tumor is poorly understood. We show that tumor expression of VEGF-C, the most potent lymphatic growth factor, promotes pro-tumor immune tolerance by several mechanisms. For one, it enhances drainage to the draining LN, where tumor antigens along with suppressive cytokines bathe the LN and could affect B and T cell education there. Second, tumor VEGF-C upregulates CCL21 in the tumor stroma and surrounding lymphatic vessels, which itself promotes T cell infiltration and suppression. Third, VEGF-C drives peritumoral and LN lymphangiogenesis, which can modulate the myeloid cell repertoire towards more suppressive phenotypes. These changes resulted in increased infiltrations of regulatory T cells and myeloid-derived suppressor cells, and increased levels of regulatory cytokines. Interestingly, VEGF-C-expressing tumors were impervious to prior immunization against tumor antigen, unlike control-transfected tumors, which were hindered by the vaccine-induced immune response. Together, these findings suggest that lymphatic drainage serves to maintain peripheral tolerance and that tumors may hijack such mechanisms to escape host immunity.

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 298. doi:1538-7445.AM2012-298
Abstract 2980: An integrated cross-species transcriptional network analysis of metastatic susceptibility
Authors: Hu Ying , Wu Gang , Rusch Michael , Lukes Luanne , Buetow Kenneth H. , Zhang Jinghui , Hunter Kent W.
Published: August 2012

Metastatic disease is the proximal cause of mortality for most cancers and remains a significant problem for the clinical management of neoplastic disease. Recent advances in global transcriptional analysis have enabled better prediction of individuals likely to progress to metastatic disease. However, minimal overlap between predictive signatures has precluded easy identification of key biological processes contributing to the pro-metastatic transcriptional state. To overcome this limitation, we have applied network analysis to two independent human breast cancer data sets and three different mouse populations developed for quantitative analysis of metastasis. Analysis of these data sets revealed that the gene membership of the networks is highly conserved within and between species, and that these networks predicted distant metastasis free survival. Furthermore these results suggest that inherited susceptibility to metastatic disease is cell autonomous in ER+ tumors and associated with the mitotic spindle checkpoint. In contrast, susceptibility to metastasis is tumor non-autonomous in ER- patients and associated with an inherited difference in immune infiltration of the primary tumor. These results suggest that the application of network analysis across species may provide a robust method to identify key biological programs associated with human 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 2980. doi:1538-7445.AM2012-2980
Abstract 2987: Regulatory network discovery using 3-way integration of high-dimensional mRNA, miRNA and lncRNA expression data from the entire NCI60 cancer cell line panel
Authors: Mestdagh Pieter , Hellemans Jan , D'haene Barbara , Derveaux Stefaan , Wong Kee , Kotturi Paul , Ginzinger David , Vandesompele Jo
Published: August 2012

With the discovery of different non-coding RNA species, the complexity of the transcriptome and its regulation has increased dramatically. Next to the well-studied small non-coding miRNAs, several thousands of long non-coding RNAs (lncRNAs) have recently been described. Like miRNAs, lncRNAs appear to predominantly function as regulators of gene expression and are implicated in various regulatory networks involving both miRNAs and protein-coding genes. In order to facilitate the search for miRNA-lncRNA-mRNA regulatory networks in cancer we have profiled the expression of each of these RNA information layers using the high-throughput SmartChip RT-qPCR technology on the entire NCI60 cancer cell line panel. In total, three SmartChip Panels with 1050 miRNAs, 1250 cancer-focused mRNAs, and 1718 lncRNAs, respectively, were quantified with a minimum of 3 technical replicates against each cell line. Here, we present the results of an unprecedented integrated analysis aimed at identifying networks of highly co-regulated miRNA-lncRNA-mRNA clusters. In brief, individual clusters are annotated using a pathway enrichment approach whereby network edges are evaluated using miRNA target, lncRNA target, and transcription factor target predictions. MiRNA-lncRNA-mRNA clusters centered around key cancer genes are annotated and the complex interplay is described. This unique and extensive high quality dataset, comprised of three major information layers of the NCI60 cell line transcriptome offers numerous opportunities towards a better understanding of complex regulatory networks 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 2987. doi:1538-7445.AM2012-2987
Abstract 2988: Exploring the association between immune-related genetic variations and virally mediated head and neck cancer
Authors: Levovitz Chaya , Posner Marshall , McKay James , Boffetta Paolo , Sikora Andrew
Published: August 2012

OBJECTIVES: Human papilloma virus (HPV)-related cancer of the oropharynx (tonsil and tongue base) makes up an increasing proportion of head and neck cancers. This raises the possibility that the host immune response may modulate susceptibility to HPV-related head and neck cancer. The overall goal of this project is to identify candidate immune-related genes associated with an increased risk of developing virally-mediated head and neck squamous cell carcinoma (HNSCC). STUDY DESIGN: Data from a two-phased Genome Wide Association Study (GWAS) performed by the International Head and Neck Cancer Epidemiology Consortium (INHANCE) was evaluated for associations between genetic variants in candidate immune related genes and the risk of developing HNSCC. METHODS: We analyzed the GWAS dataset using a hypothesis-driven multi-candidate gene approach which incorporates improved methods for data quality control and candidate gene prioritization. This involved performing an association analysis using multi-variate logistic regression with over 300,000 SNPs. The candidate gene list, including over 900 immune-related genes, was developed using the Gene Ontology (GO) database and prioritized by both the GO priority score and a novel literature based ranking schema. Separate association analyses were performed on all samples and then on samples from patients with oropharyngeal cancer only. RESULTS: After adjusting for multiple testing, 15 of the immune related candidate genes had p values that reached significance in the association study performed on oropharyngeal samples including CBFA2T3, MAPKAPK2, ZAP70, CRTAM, PBX1, MAPK10, CD80, IL10, SOCS5, TGFBR1, EBF1, IGF1R, LYN, ITGAV. Mutations in many of these genes have previously been implicated in cancer risk, viral host-response, or epithelial immunity. CONCLUSIONS: Our analysis suggests that the immune system may modulate risk of developing virally-mediated HNSCC. Genes identified in this study may provide biomarkers for patient or population risk assessments that can potentially be used in implementing behavioral interventions, HPV vaccination, and other preventative strategies. Validation of immune-related genes associated with HNSCC susceptibility may provide clues to pathogenic mechanisms driving the acquisition of virally-related HNSCC. This abstract has been submitted on behalf of ARCAGE and the CE UADT.

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 2988. doi:1538-7445.AM2012-2988
Abstract 2993: Comparison of copy number variation using exome sequencing and affymetrix SNP6.0 genotype array in human cancer cell lines
Authors: Wang Jian , Doman Thompson N. , Ma Xiwen , Li Dan S. , Aggarwal Amit , Yue Yong G. , Higgs Richard E. , Barber Thomas D.
Published: August 2012

Whole exome sequencing has been used successfully as a cost effective and unbiased method in the detection of single nucleotide variants (SNVs) in the coding regions of the human genome. Its application in identifying another class of genetic variability - copy number variation (CNV) - has been hindered by numerous factors including inconsistent exome capture probe specificity and efficiency for the target regions, discontinuous targets, and variable exon lengths etc. In the current work, we applied ExomeCNV, a depth-of-coverage based statistical analysis method developed by Sathirapongsauti et. al., to exome NGS data from a larger collection of cancer cell lines. The exomes were captured using Agilent SureSelect Human All Exon Kit and sequenced on the average depth of 70x using the Illumina HiSeq platform. To control for sequence coverage biases introduced by the capture technology, CNVs for each cancer cell line are presented as a ratio to a baseline control constructed using pooled samples processed in the same manner. Genotyping arrays are standard methods of choice for CNV discovery in cancer cell lines from the Cancer Genome Project by the Sanger Institute and the Cancer Cell Line Encyclopedia project by the Broad Institute. We obtained Affymetrix SNP6.0 genotype data for the cancer cell lines from these two sources. CNVs detected from exome sequencing were compared with those discovered from genotyping arrays in the same set of cancer cell lines. We present here a comprehensive comparison of the cancer cell line gene copy number determination from exome sequencing and genotyping methods. Our results indicate that, with sufficient exome coverage and properly constructed controls, copy number detection using exome data is a valuable alternative to genotype based approach.

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 2993. doi:1538-7445.AM2012-2993
Abstract 2998: BRG1 (SMARCA4) protein loss has profound effects on the transcriptome of non-small cell lung cancer (NSCLC) cell lines
Authors: Zhang Wei , Yao Yibing , Yan Jingsheng , Zhang Yu-An , Rios Jonathan , Girard Luc , Pertsemlidis Alexander , Wakeland Ward , Xie Yang , Solis Luisa M. , Wistuba Ignacio I. , Hanash Samir M. , Minna John D. , Gazdar Adi F.
Published: August 2012

Purpose: To study the gene expression profile of NSCLC cell lines with BRG1 protein loss. Background: BRG1 is the major catalytic subunit of the SWI/SNF chromatin remodeling complex and provides ATPase activity necessary for transcriptional regulation of multiple cellular pathways. BRG1 is frequently inactivated in lung cancers and loss of BRG1 is correlated with poor prognosis. Methods: Sixty eight NSCLC cell lines were analyzed. BRG1 protein was detected by western blotting using nuclear extracts. SMARCA4 deletions or mutations were identified by NextGen sequencing and/or Sanger sequencing using genomic DNA or cDNA. Published reports and SNP analysis were also used to verify our results. Gene expression profiles were determined by Illumina human WG-6 V3 beadchip. Microarray expression data was analyzed by Significance Analysis of Microarray (SAM) and Hierarchical clustering analysis. Results: Twenty five NSCLC cell lines had lost BRG1 protein expression. Sequencing analysis found homozygous mutations (deletions, nonsense, splicing site) in twenty two of the lines. Among forty three NSCLC cell lines with BRG1 protein expression, five had homozygous missense mutations, four had heterozygous mutations. Gene expression profiling demonstrated that nearly 1500 transcripts were differentially up or down regulated (false discovery rate <5%) among the cell lines without BRG1 protein compared to the ones with WT BRG1. These transcripts are involved in many important cellular functions including proliferation, adhesion, epithelial-mesenchymal transition, signaling pathway, steroid receptor and oncogene expression. Hierarchical clustering analysis using these transcripts distinguished NSCLC cell lines without BRG1 protein as a group, different from other NSCLC cells as well as immortalized respiratory epithelial cells, while NSCLC cell lines with BRG1 missense mutations showed heterogeneity of expression patterns. Conclusions: BRG1 protein loss is frequent in lung cancer cells and has a distinct signature and profound effects on the transcriptome of NSCLC cell lines. Our findings support the concept that BRG1 functions as a “master regulator of master regulators.”

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 2998. doi:1538-7445.AM2012-2998
Abstract 3: HER2 gene-amplified human breast cancer cells harboring a gatekeeper T768M mutation in HER2 overexpress EGFR ligands and are sensitive to dual therapeutic blockade of EGFR and HER2
Authors: Ghosh Ritwik , Narasanna Archana , Chakrabarty Anindita , Engelman Jeffrey A. , Arteaga Carlos L.
Published: August 2012

Intrinsic or acquired mutations in receptor tyrosine kinases (RTKs) can confer resistance to RTK-targeted therapies. A previous study reported that a ‘gatekeeper’ T768M mutation in HER2 confers resistance to the tyrosine kinase inhibitor (TKI) lapatinib. We generated BT474 cells stably expressing either T768M HER2 or GFP. Treatment with lapatinib disrupted HER3-p85 complex and blocked phosphorylation of HER2, HER3, AKT and Erk1/2 in BT474-GFP but not in BT474-T768M cells. BT474-T768M cells were also resistant to other anti-HER2 therapies such as trastuzumab. BT474-T768M cells were sensitive to the PI3K inhibitor BKM120 but not the MEK inhibitor CI1040, suggesting they still depend on the PI3K pathway for survival. Treatment with the irreversible HER2/EGFR inhibitor BIBW2992 (afatinib) eliminated P-HER2 and inhibited growth of cells expressing the mutant, suggesting they still depend on the ErbB receptor network to activate PI3K. Indeed, like in BT474-GFP (control) cells, BIBW2992 disrupted the association of p85 (PI3K) with HER3 and blocked phosphorylation of AKT. A co-culture experiment with varying proportions of BT474-GFP and BT474-T768M cells revealed that lapatinib-resistant acini emerge when as low as 5% of the population has T768M HER2. Moreover, we found that only 3.2% of the HER2 alleles had the T768M mutation in the BT474-T768M cells. This result suggests that allelic dilution will render it difficult to identify this drug resistant mutation with conventional sequencing techniques (i.e., Sanger) in patients with HER2 gene-amplified breast cancer. Next, we stably expressed either wild-type or T768M HER2 in MCF10A cells. Both WT and T768M HER2 resulted in increased phosphorylation of HER3 and AKT. MCF10A-HER2 but not MCF10A-T768M cells were sensitive to growth inhibition by lapatinib. Lapatinib blocked HER2, HER3 and tyrosine phoshorylation in MCF10A-HER2 but not in MCF10A-T768M cells. Quantitative PCR indicated that the BT474-T768M cells produce more EGFR ligands (EGF, TGFα, amphiregulin and HB-EGF) compared to BT474-GFP cells. Treatment with cetuximab, an EGFR antibody that blocks ligand binding, restored sensitivity of BT474-T768M cells to trastuzumab. Further, the BT474-T768M cells were sensitive to a combination of trastuzumab and lapatinib both in vitro and in vivo. Hence, dual blockade of HER2 and EGFR might be effective at trumping the development of HER2-overexpressing cancers bearing a gatekeeper mutation in T768M.

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 3. doi:1538-7445.AM2012-3
Abstract 300: Blockage of OPN induction via HGF/cMET signaling in multiple myeloma cells suppresses both MMP9 expression and RUNX2 expression of BMSCs associating with bone erosion of MM patients
Authors: Jung Woo June , Ahn Kwang-Sung , Ryu JIyeon , Park Soyoung , Park Juwon , Lee Chansu , Bae Eunkyung , Yoon Sung-Soo
Published: August 2012

Dynamic interaction between multiple myeloma cells (MM) and bone marrow stromal cells plays critical roles in progression of MM. Hepatocyte growth factor (HGF), one of these factors, as a c-Met ligand, activates mitogenic activation protein kinase (MAPK). OPN binds with integrins and CD44 variants and activates cell signaling involved in invasiveness, angiogenesis and bone remodeling. Increasing lines of evidence provide that HGF and OPN, respectively, associate with the progression of MM. However, the role of HGF in MM largely remains unknown. In bone marrow serum of MM patients, HGF expression correlated with OPN expression (p=0,0095), suggesting that HGF derived from bone marrow stromal cells stimulates OPN expression in MM cells. Firstly, we found that expression levels of OPN in HFG-treated MM cells (fraction of CD138+ cells) obtained from MM patients was higher than either HFG-treated bone marrow stromal cells or HFG-treated MM cells (fraction of CD138- cells). Also, induction of DKK1 by HGF, suggesting the inhibition of osteogenesis, was found in U266 cells and RPMI8226, Both HGF-mediated MAPK and PI3K/AKT results in activating NF-kB and increasing OPN expression and DKK1. Those expressions were effectively down-regulated in U266 cells transfected with shRNA c-MET. RUNX2 mRNA and MMP-9 mRNA was increased in bone marrow stromal cells (BMSCs) treated with OPN. In addition, combined cMET inhibitor and PI3K inhibitor effectively inhibited the RUNX2 and the MMP9 mRNA expression in both OPN alone treatment and co-treatment with OPN and HGF in BMSCs. Taken together, since Induction of OPN and DKK1 by HGF in MM cells could be one of the major factors for the progression of MM through interaction of MM cells and BMSCs, blockage of HGF/cMET signaling leading to increasing levels of OPN and DKK1 may help to prevent from progressing bone erosion of MM patients.

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 300. doi:1538-7445.AM2012-300
Abstract 3002: Identification of frequently altered protein networks in ependymomas
Authors: Bischof Jared M. , Scholtens Denise , Arndt Kelly , Wang Min , Wang Deli , Huang Chiang-Ching , Bonaldo Maria de Fatima , Gilbertson Richard J. , Soares Marcelo Bento
Published: August 2012

Ependymomas are glial tumors that originate from the walls of the cerebral ventricles or from the spinal canal. The five-year survival for intracranial ependymomas in children is approximately 65%. Ependymomas exhibit a wide range of DNA copy number alterations that vary greatly in size and location. We hypothesize that an underlying protein network exists that is consistently compromised by such DNA copy number alterations in ependymomas. In this study, we analyzed an array-comparative genomic hybridization dataset generated by Johnson and colleagues [Nature 466(7306):632-6, 2010] to determine whether a protein interaction network could be identified that might be consistently functionally compromised in pediatric ependymomas. This cohort of 203 primary ependymomas consisted of 106 posterior fossa, 56 supratentorial, and 41 spinal ependymomas. The genes within each altered region were used to perform network analyses with GeneGo and Ingenuity to uncover protein networks that were altered in a significant number of tumors. For calculation of statistical significance, 100,000 samplings of randomly selected regions - equal in gene number to the regions of gain or loss - were performed. Indeed, some protein networks were found to be over-represented in the structural alterations exhibited by this cohort (p<0.05). These results warrant future investigations to demonstrate the role of the identified networks in the development and progression of ependymomas.

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 3002. doi:1538-7445.AM2012-3002
Abstract 3006: A systematical view on key genetic factors affecting somatic copy number alternations in different cancers
Authors: Li Yudong , Yuan Yuan , Liang Han
Published: August 2012

Along with somatic mutations and translocations, somatic copy number alternations (SCNAs) play essential roles in the development of cancers. However, it remains poorly understood what mutagenic features driving cancer SCNAs are encoded in the genome sequence and how their effects vary across different cancer types. Taking advantage of recently available the Cancer Genome Atlas (TCGA) data, we performed a systematic analysis on the effects of various genetic sequence features on cancer SCNAs. We first assessed the correlations of breakpoint density across different cancer types and found that they overall showed very strong positive correlations, but in some cases, the correlations varied from chromosome to chromosome. Next, we investigated the dependence of SCNAs on 16 sequence features and found that compared to copy number variations in human populations, SCNAs showed much weaker correlations, suggesting a stronger effect of functional selection on their observed patterns. Finally, we built integrative models to identify key features affecting different cancer SCNAs. Our study provides a systematic view how genome-wide sequence features affect cancer SCNAs and lays a foundation for identifying key SCNAs driving cancer pathogenesis.

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 3006. doi:1538-7445.AM2012-3006
Abstract 3066: Effect of stable knockdown of NOX1 gene expression with siRNA in human colon cancer cells
Authors: Juhasz Agnes , Antony Smitha , Wu Yongzhong , Lu Jiamo , Jiang Guojian , Liu Han , Roy Krishnendu , Doroshow James H.
Published: August 2012

NADPH oxidase (Nox)-dependent reactive oxygen species (ROS) play a critical role in cell signaling, cell proliferation, and mitogenesis. We have previously shown that silencing NOX1 gene expression with siRNA decreases cell growth and angiogenesis in human HT-29 colon cancer xenografts. To investigate the mechanism of growth inhibition, we studied cell cycle and signaling pathways. We found using RT-PCR and Western analysis that the expression of the INK4 inhibitors (p15, p18, p19), as well as CDK6, phospho-Cyclin E, Cyclin E, and Cyclin D1 were all decreased when NOX1 was decreased by >80%. We detected important changes in the Raf-MEK-ERK pathway that were associated with NOX1 knockdown. Our stable knock-out cells (clone 6A) showed lower phosphorylation of Rac1, c-Raf, MEK1/2, ERK1/2, p90RSK and CREB. To understand this observation, we studied the activity of Tyr and Ser/Threonine protein phosphatases (PP) in our stable siRNA containing cells (6A) compared to stable scrambled siRNA containing cells (SA) and parental HT-29 cells. PTP1B activity was elevated (100.4+4.4 pmol of phosphate/min/µg) in 6A cells compared to both SA (69.2+3.8) and parental (47.8+2.1) cell controls, P<0.05. Serine/Threonine protein phosphatases demonstrated a similar pattern; elevated in 6A cells (127.3+3.8 pmol of phosphate/min/µg) versus both SA cells (91.7+2.1) and the parental line (88.9+1.9), P<0.05. To demonstrate that protein phosphatases play a key role in the regulation of ERK-CREB signaling, we used a c-Raf antibody to immunoprecipitate the c-Raf-PPs complex, and detected PTP1B and PP2C proteins by Western analysis. These data indicate that siRNA-mediated gene silencing of Nox1 deactivated ERK-CREB signaling, and that increased activity of protein phosphatases, that occur as a consequence of decreased Nox-mediated ROS formation, might play role in modifying the growth enhancing effects of the MAP kinase pathway in HT-29 colon cancer cells.

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 3066. doi:1538-7445.AM2012-3066
Abstract 3068: Hedgehog signaling regulates drug sensitivity by targeting ABC transporters in epithelial ovarian cancer (EOC)
Authors: Chen Yi , Bieber Marcia , Bhat Neelima , Teng Nelson N.H.
Published: August 2012

A major challenge of successful chemotherapy in treatment of ovarian cancer is overcoming intrinsic or acquired multi-drug resistance caused mostly by the active efflux mediated by ATP-binding cassette (ABC) transporters. The regulation of these transporters in ovarian cancer is poorly understood. Our research shows that in ovarian cancer, abnormal regulation of the hedgehog (Hh) signaling pathway is involved in regulation of ABC transporters. Hh is a known regulator of cancer cell proliferation and differentiation in several other types of invasive and metastatic malignancies. Our work on Gli1, a key Hh downstream signaling gene, has shown frequent activation of the Hh pathway in ovarian cancer. Inhibition of the Hh signaling pathway by inhibitors or Gli1 siRNA increases ABC gene expression levels and the response of ovarian cancer cells to certain chemotherapeutic drugs. The mechanism underlying is a direct association of Gli1 with a specific consensus sequence located in the promoter region of ABC genes. This study provides new information in the knowledge of ABC gene regulation and will contribute to generating new targets/markers to detect and anticipate ovarian cancer patient chemotherapy drug sensitivity which could lead to more effective treatments and improved survival.

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 3068. doi:1538-7445.AM2012-3068
Abstract 307: Acquisition of the invasive phenotype and EMT profile by CXCL7 transfection
Authors: Kosir Mary A. , Ju Donghong
Published: August 2012

Introduction: The expression of CXCL7 is associated with the invasive phenotype through interaction with the CXCL7/CXCR2 axis and heparan sulfate. A component of the epithelial to mesenchymal transition (EMT) is degradation of extracellular matrix and acquisition of migration, both of which support invasiveness. The purpose of this study is to quantify the expression of genes associated with EMT by CXCL7-expressing cells with the invasive phenotype. Methods: Total RNA from CXCL7-transfected breast cells (MCF10AT) was tested for relative gene expression using RT2 ProfilerTM PCR array for EMT (SABiosciences). Vector transfected cells were compared. Each result was verified by real time PCR assay. Results: The expression of GNG11 and TCF4 was upregulated and SPP1 downregulated as expected for the EMT profile. Specifically, GNG11 (Guanine nucleotide binding protein (G protein), gamma 11) expression was increased 2.94 fold and TCF4 (Transcription factor 4) increased 1.89 fold. The expression of SPP1 (Secreted phosphoprotein 1) was decreased by 6.8 fold. The expression of ZEB2 (Zinc finger E-box binding homeobox 2) was decreased by 1.96 as a transcription factor. Summary: The CXCL7-transfected cells with invasive phenotype express genes associated with the EMT expression profile including G-protein signaling pathway.

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 307. doi:1538-7445.AM2012-307
Abstract 3073: EphrinA1 inhibits non small cell lung cancer (NSCLC) tumor growth via induction of miRNA-122
Authors: Sukka-Ganesh BhagyaLaxmi , Mohammed Kamal A. , Goldberg Eugene P. , Nasreen Najmunnisa
Published: August 2012

Introduction: Ephrin-A1 ligand exerts anti-oncogeneic effect in NSCLC tumor cells through activation and down regulation of the EphA2 receptor. Alteration in their expression levels is associated with aggressive tumor growth. The underlying mechanisms for altered expression of Ephrin-A1 and EphA2 receptor are yet to be defined. MicroRNAs (miR) are small non-coding RNAs play a key role in tumorogenesis. MiR-122 directly targets Bcl-w which harbours a putative miR-122 binding site in its 3′-UTR. However, if EphrinA1 induces miR-122 expression in NSCLC is not known. Here we demonstrate a novel mechanism of EphrinA1 mediated miR-122 signalling in the inhibition of NSCLC growth. Methods: NSCLC cell lines (A-549 and H-23) were activated with Ephrin-A1 over time (3 hr, 6hr, 12hr and 24 hr) and miR-122 expression was measured by Real-time PCR and In situ hybridization. Furthermore, in order to understand the underlying mechanisms EphrinA-1 mediated signalling, Bach-1 and Bcl-w protein expression were studied through Western blotting analysis. In addition, Tumor growth and Cell migration studies were performed in Ephrin-A1 activated and premiR-122 transfected NSCLC cells. Results: The data from this study demonstrates that Ephrin-A1 activation of NSCLC enhanced Bach-1 and miR-122 expression over time. When NSCLC transfected with pre-miR-122, we noticed a significant down-regulation of Bcl-w gene and protein expression, suggesting miR-122 specifically targets to anti-apoptotic gene Bcl-w and induced apoptosis in NSCLC. In situ hybridization demonstrated strong signals for miR-122 in EphrinA1 activated NSCLC cells as compared to control cells. Furthermore, knock down of Bach-1 gene expression using siRNA, showed significant down-regulation of miR-122, suggesting Ephrin-A1 mediated signalling is regulated by the transcription factor Bach-1 via miR-122 in NSCLC. In addition, this was confirmed by transfection of NSCLC by premiR-122 that inhibited tumor growth and migration of NSCLC cells. Conclusions: Our study suggests that Ephrin-A1 mediated signalling is regulated by the transcription factor Bach-1 via miR-122 expression. MiR-122 targets the anti-apoptotic gene Bcl-w and triggers apoptosis in NSCLC cells. The present study provides a new insight into the complex regulating pathways of Ephrin-A1/Eph receptor, and also understanding the direct role of miRNA-122 in Ephrin-A1 mediated signalling pathway that may lead to new therapeutic strategies for lung adenocarcinoma. Funding Source: RC1 form Florida Department of Health; VA Merit Review

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 3073. doi:1538-7445.AM2012-3073
Abstract 3075: NOTCH1 dimerization directly activates Rag1 and Rag2 in murine T-cell leukemia
Authors: Liu Hudan , Yashiro-Ohtani Yumi , Chi Anthony W.S. , Pear Warren S.
Published: August 2012

The NOTCH transcriptional complex forms dimer in the nucleus on some target gene promoters/enhancers bearing sequence-paired sites (SPS) that are properly spaced and orientated. We previously reported that NOTCH1 dimerization is required for the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL). Although NOTCH1 dimers are suggested to regulate only a subset of target genes, identification of these targets and analysis of their function to mediate NOTCH1-induced T-ALL are very limited. Based on a genome-wide microarray gene profiling to screen dimer-dependent targets in a murine T-ALL cell line T6E, we report here that both Rag1 and Rag2 are direct dimeric NOTCH1 transcriptional targets. We also defined a SPS in the upstream enhancer region of Rag2 locus, which bears a canonical strong binding site and a consensus-deviated weak binding site. Chromatin precipitation assay (Chip) suggests that intracellular NOTCH1 occupies the SPS-containing region in T6E. Mutagenesis of either binding site abrogates NOTCH1-mediated transcriptional activation using the luciferase reporter. In addition, only the expression of dimerization competent NOTCH1 in the HSC derived from RAG1 or RAG2 GFP-reporter mice is able to induce GFP level. Taken together, we have identified two novel NOTCH1 dimer-dependent targets Rag1 and Rag2. These results provide additional examples showing that one conventional and one cryptic CSL binding site can constitute a functional SPS. Together with the observation of gain-of-function NOTCH1 truncations identified in murine T-ALL, our data suggest an important role of NOTCH1-RAG1/2 axis to amplify oncogenic signal strength in murine T-ALL.

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 3075. doi:1538-7445.AM2012-3075
Abstract 3077: Nek3/Vav2 modulation of the expression of genes involved in breast cancer pathogenesis
Authors: Ratajczak Christine , Clevenger Charles
Published: August 2012

The pituitary hormone prolactin (PRL) is generally recognized for its role in breast growth and differentiation; however, a role for PRL in the pathogenesis of breast cancer has emerged from epidemiological studies and basic science research using both human breast cancer cells and animal models. Activation of the prolactin receptor (PRLr) by PRL contributes to the growth, survival, and motility of human breast cancer cells. PRLr stimulation by PRL results in the activation of multiple signaling complexes including serine/threonine kinase Nek3 and guanine nucleotide exchange factor Vav2. Nek3 is necessary for the activation of Vav2, and Nek3 knockdown results in decreased cytoskeletal re-organization, cell motility, and cell invasion in PRL-stimulated human breast cancer cells. The overexpression of a kinase inactive form of Nek3 in human breast cancer cells results in increased apoptosis, indicating a pro-survival function for Nek3. Furthermore, Nek3 expression is increased in malignant vs. normal human breast tissue. These data make the Nek3/Vav2 complex an interesting target for novel breast cancer therapeutics. To this end, a greater understanding of the role of Nek3/Vav2 in breast cancer pathogenesis is necessary. We hypothesized that the Nek3/Vav2 complex modulates PRL-driven expression of genes involved in the pathogenesis of breast cancer. In these studies, luciferase assays and quantitative PCR were used to evaluate the effects of gain- or loss-of-function of Nek3/Vav2 on the expression of CISH (cytokine-inducible SH2-containing protein). Gain- or loss-of-function of Nek3/Vav2 was found to alter the expression of CISH in response to PRL in both MCF7 and T47D human breast cancer cell lines. The CISH promoter has 4 binding sites for the transcription factor Stat5, which is known to contribute to malignant transformation and tumor growth in breast cancer. Luciferase assay showed that gain- or loss-of-function of Nek3 was also found to alter the activation of a reporter construct containing the lactogenic hormone response element which consists of six tandem Stat5 DNA-binding elements. This suggests that Nek3/Vav2 modulates the PRL-driven expression of CISH by regulating activity of the transcription factor Stat5. Gain- or loss-of-function of Nek3/Vav2 was not found to alter the subcellular localization of Stat5 in response to PRL. Ongoing studies are examining the mechanism of Nek3/Vav2 modulation of PRL-responsive gene expression in breast cancer cells.

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 3077. doi:1538-7445.AM2012-3077
Abstract 3078: Effects of neuregulins in the regulation of EGFR in breast cancer cell lines
Authors: Kuilan-Torres Laurimer , Perez-Torres Marianela
Published: August 2012

The epidermal growth factor receptor (EGFR) is a member of the ERBB family of oncoproteins which consist of four related receptors: EGFR/ErbB1, ErbB2, ErbB3 and ErbB4. Overexpression of EGFR and other members of ERBB family were found to induce erroneous development and unrestricted proliferation in human malignancies including breast cancer. Neuregulins (NRG) are signaling proteins that produce cell-cell interactions and can bind to the extracellular domain of ErbB3 or ErbB4, activating signaling pathways leading to cellular responses that include stimulation or inhibition of proliferation, apoptosis, and gene regulation. Previous studies showed that constitutive expression of neuregulin 1-beta (NRG-1α) in MCF-7 cells decreased the levels of estrogen receptor (ER) and progesterone receptor (PR), which may contribute to the transformation from estrogen-responsive into a hormone-independent phenotype. An inverse correlation between expression of ER and EGFR has been demonstrated. Our hypothesis is that EGFR levels are regulated by neuregulins in breast cancer cell lines. We treated the breast cancer cell lines ZR-75-1 and MDA-MB-231 with NRG-1α or NRG-1α at different concentrations for 4 hours. In addition, both cells lines were treated with selected concentrations of NRG-1α or NRG-1α at different time points. Isolated mRNA was used to measure EGFR expression using reverse-transcriptase real-time PCR and levels of protein were determined by western blot analysis. Our results show that EGFR mRNA levels increased when ZR-75-1 cells were treated with increasing concentrations of neuregulins. In this regard, treatment with 100 ng/mL of NRG-1α increased EGFR expression by 10-fold in ZR-75-1 cells. However, when MDA-MB-231 cells were treated with NRG-1α or NRG-1α, the expression of EGFR mRNA levels did not change. Western blots analysis of ZR-75-1 cells treated with NRG-1α shows activated ErbB3, confirming that this activation is related to the increase in EGFR mRNA levels. Our data suggest a role for neuregulins in the EGFR up-regulation. One of the mechanisms related to ErbB3 activation is the activation of phosphatidylinositol 3-kinases (PI3K) and mitogen-activated protein kinase (MAPK), thus current efforts are directed towards elucidating the role of these pathways in the NRG-upregulation of EGFR. Supported by NIH/NIGMS Grant #SC2GM084789, NIH-RCMI Grant #G12 RR 03051.

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 3078. doi:1538-7445.AM2012-3078