bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4905: Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers
Authors: Benz Stephen C. , Vaske Charles , Ng Sam , Sanborn John Zachary , Zhu Jing , Haussler David , Stuart Joshua
Published: June 2012

Cancer is a disease of genomic perturbations that lead to dysregulation of multiple pathways within the cellular system. While common pathways are believed to be shared within specific cancer types, the mechanisms of why particular patients respond differently to treatment is not fully understood. Current -omics studies such as The Cancer Genome Atlas (TCGA) and Stand Up To Cancer (SU2C) have attempted to address this issue by using large-scale whole-genome measurements of mRNA expression, DNA copy number, and epigenetic features. Typical analysis of these measurements relies on integrating data from multiple samples to distinguish signal from noise. However, few analytical methods allow for sample-specific differences to identify features and pathways that are significant for prognosis and clinical treatment classifications.

We developed a pathway inference method called PARADIGM (PAthway Recognition Algorithm using Data Integration on Genomic Models) (Bioinformatics (2010) vol. 26 (12) pp. i237) to identify patient- and sample-specific pathway activities. Previously we have shown that PARADIGM is capable of stratifying patients into clinically relevant subgroups in both TCGA ovarian serous carcinoma and glioblastoma multiforme using gene expression and copy number alteration values. We have since enhanced PARADIGM in multiple ways allowing more in-depth analysis and discovery across multiple cancer types.

We have expanded the underlying pathway database previously consisting of NCI's Pathway Interaction Database to include pathways from BioCarta and Reactome, increasing the number of pathways by ten-fold and increasing the total number of features to approximately 22,000. We have refined the central dogma framework underlying all features in each pathway to support a more accurate regulatory model, allowing us to efficiently learn the strength of each interaction. Finally, PARADIGM now supports additional input data sources in the form of methylation and mutational interventions. By adding gene-level mutational information on the new regulatory model we show it is possible to distinguish between gain-of-function and loss-of-function mutations in each patient. In addition, through these enhancements we show increased ability to identify key pathway activities that effectively stratify patient cohorts.

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 4905. doi:10.1158/1538-7445.AM2011-4905
Abstract 4913: Systematic analysis of LY30-induced sensitization of cancer cells to TRAIL
Authors: Shi Yuan , Tucker-Kellogg Lisa , White Jakob , Pervaiz Shazib
Published: June 2012

TRAIL (Tumor necrosis factor-Related Apoptosis Inducing Ligand) can selectively induce apoptosis in cancer cells expressing the TRAIL receptors. However, the problem of TRAIL resistance poses a significant therapeutic challenge. We recently demonstrated that the small molecule compound, LY30, sensitizes human cancer cells to TRAIL induced apoptosis via mechanisms that involve upregulation and/or oligomerization of the death receptors. However, the underlying biology of this phenomenon remains less well defined. Here we describe a mathematical modeling approach to tease out the molecular circuitry in the synergistic response of human cervical cancer cells (HeLa) to LY30 and TRAIL mediated apoptosis. We made use of ODE (Ordinary Differential Equation) to build two distinct pathway models for Hela cells to represent TRAIL-induced apoptosis (TRAIL Model) or LY30-induced cellular modification (LY30 Model) using the existing models and previous data sets. Moreover, in accordance with the experimental settings we integrated the LY30 Model and TRAIL Model as the CTM (Combination Treatment Model). The CTM showed that the level of simulated death correlated well with experimental observations, including the synergistic level of death from the combination treatment. However, simulation and experimental data exhibited numerous mismatches for some molecules in the pathway, such as differences in the slope and onset of the synergistic activation of caspase-8 and caspase-3. Such mismatch implies some flaw in the model and thus led us to additional measurement on the early dynamics of the species involved upstream of the apoptotic pathway. In specific, assessment of cFLIP, an inhibitor of caspase-8 activation, showed slight up-regulation very early after LY30 treatment (1 hour), followed by a significant down-regulation over prolonged exposure. By including such biological phenomenon into the CTM, we are able to improve the agreement between data and simulation while maintaining the consistency in synergistic cell death. Further model analysis revealed the fluctuation of FLIP is regulated by LY30 through a complicated ratio change between two main ROS (Reactive Oxygen Species), superoxide and hydrogen peroxide. These data provide a novel means for assessment of mechanisms for small molecule-induced sensitization of human cancer cells to TRAIL mediated apoptosis, with broader clinical implications.

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 4913. doi:10.1158/1538-7445.AM2011-4913
Abstract 4916: Systems biology analysis of subpopulation-based heterogeneity for cellular radiosensitivity modeling
Authors: Kam Yoonseok , Rejniak Katarzyna A. , Zhao Haiyan , Torres-Roca Javier F.
Published: June 2012

Intrinsic cellular radiosensitivity is a key parameter used in radiotherapy modeling. Our previous studies showed that a cellular model based on the in vitro clonogenic assay measuring survival fraction at 2Gy (SF2) accurately predicts tumor response in patients treated with radiotherapy. However, SF2 as determined from a heterogeneous cell population represents its averaged sensitivity, whilst we have shown, using live cell imaging, that cultured tumor cell populations include colonies of varying sizes, cell numbers and growth rates. In order to link this subpopulation-based heterogeneity to the parental cell line radiosensitivity, and to build an integrative predicting model, we designed a novel systems biology approach that combines SF2 clonogenic assay experimentation, high-content screening and image analysis together with a quantitative bio-mathematical study. We integrated a 96-well plate-based SF2 assay with a semi-automated image analysis using CellProfilerTM, and measured morphological parameters including SF2, colony tightness index (colony density), and colony growth rate. We have also developed new algorithms to complement those implemented in CellProfilerTM to identify some highly dispersed colonies. As a preliminary trial, we analyzed five non-small cell lung cancer (NSCLC) cell lines characterized by different levels of radiosensitivity in vitro. We observed several common phenotypic shifts after irradiation, such as reduction in growth rate and cell density. However, the response patterns for each subpopulation was highly heterogenous across cell lines. Interestingly, the variability in morphological response was better correlated to radiosensitivity than the average colony density. In order to further assess subpopulation heterogeneity, we isolated 15 random sub-clones from H460 cells and found significant intrinsic SF2 heterogeneity. In addition to morphology, we examined the intrinsic variability in the expression level of several molecular biomarkers including STAT1, a molecular maker in our prediction model, and CD44, a cancer stem cell marker proposed to be related with radioresistance. Both markers showed significant variability, which was negatively correlated with the colony density. In conclusion, we propose a novel systems-based approach that integrates high content phenotypic information at a single cell level to study tumor-intrinsic heterogeneity and its contribution to clinically-relevant radioresistance.

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 4916. doi:10.1158/1538-7445.AM2011-4916
Abstract 4918: Predicting the effect of drug combination schedules on xenograft growth using the Virtual Tumor
Authors: Orrell David , Fernandez Eric , Cronier Damien , Gelbert Lawrence M. , Fell David A. , De Alwis Dinesh , Chassagnole Christophe
Published: June 2012

Since the early 1960s, drug combination therapy has been used to treat cancer, because of the limited number of malignancies that could respond to single-agent chemotherapy. Combination chemotherapy regimens have been designed on the basis of mechanism of action of the drugs, tumor cell specificity, balance between effectiveness and toxicity, and synergy between drugs. But when multiple drugs, combination schedules, sequences and doses are considered, the number of possibilities increases combinatorically, and can not be realistically tested either clinically or in animal models.

We have developed a “Virtual Tumor” model to aid with the design of optimal drug schedules. The model combines disparate data, at the cell and tumor level, into a consistent picture, and leverages them to make testable predictions about tumor response. Thousands of simulations can be performed if necessary to find the best treatment regime.

We present here a validation study of our Virtual Tumor. We predicted xenograft growth of two anti-cancer drug combinations using experimental data collected from single drug exposure uniquely. We accurately predicted the xenograft course for two different regimens – one simultaneous and one sequential – of the two drugs, which were compared with experimental results in a single-blind test. We show how a computational approach helps explain how multiple drug exposure and correct sequence leads to synergy, and how it can be used to subsequently design optimal schedule and combination treatments.

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 4918. doi:10.1158/1538-7445.AM2011-4918
Abstract 4919: Multiplexed EGFR signaling pathway analysis in FFPE tissue using quantitative mass spectrometry
Authors: Hembrough Todd , Thyparambil Sheeno , Krizman David , Darfler Marlene , Wei Yuhong , Taylor Paul , Tong Jiefei , Pham Nhu-An , Jasani Bharat , Adams Richard , Tsao Ming-Sound , Moran Michael , Burrows Jon
Published: June 2012

The epidermal growth factor receptor (EGFR) is a drug target for both small molecule and antibody therapeutics and has been approved in non small-cell lung carcinoma (NSCLC) and colorectal carcinoma (CRC) among other indications. These drugs block receptor signaling though blockade of the tyrosine kinase domain, or through inhibition of ligand binding. Current genomic tests measure receptor amplification, RNA levels, the mutation status of receptor or pathway molecules (EGFR or kRAS mutations) but no current assay can directly assess the activation state of the EGFR or its downstream signaling pathway components. Indeed, the EGFR mutation positive NSCLC tumors (thought to be constitutively active) show a high response rate to TKI therapy, but the many non responders (50% or more) demonstrate the limitation of genomic analysis.

Since activation of EGFR is necessary for the response to these targeted agents, it is critical to measure what levels of receptor activation and downstream signaling determines tumor responsiveness to EGFR targeted therapies in these patients. For this reason, we have developed a panel of new diagnostic assays which measure the activation of the EGFR and key downstream signaling proteins through quantitation of the phosphorylation state of these proteins. These assays are based on the Liquid Tissue®-SRM technology platform. This approach enables relative and absolute quantification of proteins and their phosphorylation status directly in formalin fixed paraffin embedded (FFPE) tissue.

We preclinically validated the multiplexed Liquid Tissue® phospho-SRM assay on formalin fixed EGF stimulated A431 cells. We followed up these in vitro studies with phospho-SRM analysis of FFPE NSCLC xenograft explants where extensive independent histopathologic and molecular characterization had been performed, allowing us to benchmark our phospho-SRM analysis with standard diagnostic analyses.

We have now extended these quantitation studies by measuring the expression of EGFR and phospho-EGFR in FFPE tissues obtained from relevant human clinical trial cohorts – Gefitinib treated NSCLC and Cetuximab treated CRC. It is hoped that we will be able to correlate EGFR expression, activation and signaling in these tumors with responsiveness to EGFR targeted therapy, and to validate this assay for use as a companion diagnostic to guide therapy in both NSCLC and CRC.

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 4919. doi:10.1158/1538-7445.AM2011-4919
Abstract 4935: microRNA profiling of esophageal squamous cell carcinoma patients from formalin-fixed paraffin-embedded (FFPE) specimens
Authors: Shimada Yutaka , Okumura Tomoyuki , Sekine Shin-ichi , Osawa Soshi , Fukuoka Junya , Tsukada Kazuhiro
Published: June 2012

Introduction: microRNA (miRNA) are small non-coding RNAs which target specific mRNA. Recent progression of RNA extraction technology from formalin-fixed paraffin-embedded (FFPE) tissues enables us to access miRNA profiling using world wide stored specimens. Here, we present miRNA profiling of esophageal squamous cell carcinoma (ESCC) patients from FFPE specimens.

Method: First, we examined and contrasted the levels of cross-linking caused by formalin and degradation of mRNA and miRNA from daily to yearly time frames. Then, we established the criteria of evaluable RNA from FFPE specimens. The miRNA profiling was obtained from 44 ESCC patients who received operations from 1991 to 2009 using 3D-Gene human miRNA chip (Toray) which contains 904 has-miRNAs. The approval number from Toyama University institutional review board was #19-67.

Results: Out of 44 paired samples, 24 pairs (54.5%) were determined evaluable with our criteria. We found that 39 miRNAs (including miR-21, and miR-25) were significantly up-regulated and that 24 miRNAs (including miR-145) were down-regulated in ESCC in comparison to normal esophageal tissue. Of these, miR-15b, miR-200c and miR761 were identified as prognostic factors of ESCC patients. Furthermore, we found 22 miRNAs that have association with the hematogenic recurrence and 9 miRNAs (including miR-103) have association with lymph node metastasis.

Conclusion: We have discovered miRNAs that are associated with prognosis, hematogenic recurrence and lymph node metastasis in ESCC patients. miRNA profiling using FFPE specimens is a useful and promising method of evaluation of world wide stored specimens that accompany many valuable clinical 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 4935. doi:10.1158/1538-7445.AM2011-4935
Abstract 4936: MicroRNAs located on 13q and 20q are differentially expressed between normal mucosa, adenomas and carcinomas of the large intestine
Authors: Timmer Lisette M. , Bolijn Anne S. , Carvalho Beatriz , Mulder Chris J.J. , Cuppen Edwin , Meijer Gerrit A. , Diosdado Begoña
Published: June 2012

Background: In colorectal cancer (CRC) miRNA expression profiling studies have reported differences in expression between colorectal carcinomas and controls, microsatellite stable, microsatellite instable and chromosomal instable tumors, and demonstrated prognostic value for some miRNAs. However, the role of miRNAs in CRC pathogenesis has been only partially investigated. CRC results from the gradual accumulation of multiple genetic and epigenetic changes in the colorectal epithelial cells. The majority of CRCs (85%) shows an accumulation of chromosomal abnormalities. In CRC, up to 15% of the annotated miRNAs are located at regions of chromosomal instability implicated in colorectal adenoma to carcinoma progression. Two of the most frequent chromosomal aberrations in CRC are gain of 13q (>50%) and gain of 20q (>65%). A total of 36 miRNAs are located on these chromosomal arms. However, the leading cause of the miRNA's aberrant expression and the pathways through which they contribute to CRC have not been elucidated.

Aim: To investigate the expression of miRNAs located on 13q and 20q in normal colon mucosa, adenomas and CRC.

Materials & Methods: DNA and total RNA was isolated from 48 colorectal adenomas, 51 CRCs and 10 normal mucosa samples. Multiplex Ligation-dependent Probe Amplification (MLPA) was used to determine DNA copy number gain of 13q and/or 20q. Expression levels of 17 miRNAs located on 13q and 19 miRNAs on 20q (miRBase release 15) were measured by TaqMan miRNA assays.

Results: 11 Of the miRNAs located on 13q and 8 of the miRNAs located on 20q were detected in colon tissue. 15 Of these miRNAs were significantly differentially expressed between colorectal tumors compared to controls and 13 were differentially expressed between carcinomas and adenomas (p<0.05). In addition, 11 miRNAs were significantly differentially expressed between tumors with or without a 13q and/or 20q gain (p<0.05).

Conclusion: Gene dosage effects of miRNAs located on chromosomes 13q and 20q play an important role in CRC progression, and taking this into account is essential to achieve a comprehensive understanding of the pathogenesis 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 4936. doi:10.1158/1538-7445.AM2011-4936
Abstract 4940: Microrna expression profiling in adrenocortical neoplasia: Implications on tumor size and functionality
Authors: Velázquez-Fernández David , Caramuta Stefano , Özata Deniz M , Akcakaya Pinar , Höög Anders , Hamberger Bertil , Bäckdahl Martin , Larsson Catharina , Zedenius Jan , Lui Weng-Onn
Published: June 2012

Background: Tumors arising from the adrenal cortex (ACT) can be hormonally hyperfunctioning or silent. This functional phenotype, as well as their size, is of clinical importance. MicroRNAs are a class of small non-coding RNAs that negatively regulates gene expression. There is increasing evidence for their significant role in tumorigenesis. Their relevance on the functional phenotype and size of these tumors has not been previously documented.

Aim: To characterize differential expression patterns of microRNAs regarding the increasing size and the functional phenotypes of ACT.

Methods: Seventy frozen tissue samples were included: 16 aldosterone-producing adenomas (APA), 14 cortisol producing adenomas (CPA), 14 non-hyperfunctioning adenomas (NhFA), 19 adrenocortical carcinomas (ACC) and 7 normal adrenal cortices as controls. Global microRNA expression profiles were determined using the Agilent Human microRNA microarray, and the results were verified by quantitative real-time PCR.

Results: We observed distinct microRNA expression patterns among different ACT phenotypes: majority of the APA was clustered separately from NhFA and CPA, and the ACC was independently clustered apart from all benign tumors. A larger number of miRNAs were differentially expressed between APA and CPA, while a smaller subset of differently expressed microRNAs was found between functional and non-hyperfunctional adenomas. Among the benign tumors, we found miR-21 expression was significantly correlated with increasing tumor size.

Conclusion: Deregulation of microRNA expression is associated with the functional phenotype and size in ACT, and these microRNAs may have implication related to the development of adrenocortical tumors.

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 4940. doi:10.1158/1538-7445.AM2011-4940
Abstract 4943: microRNAs as clinical biomarkers for lung cancer classification
Authors: Edmonston Tina , Kushnir Michal , Yanai Gila Lithwick , Benjamin Hila , Bibbo Marluce , Thurm Craig , Horowitz Laurie , Huang Yajue , Feinmesser Meora , Barshack Iris , Gilad Shlomit , Chajut Ayelet
Published: June 2012

Background: Lung cancers have traditionally been subdivided into two main groups: Small Cell Lung Cancer (SCLC) and Non Small Cell Lung Cancer (NSCLC). Due to limited tumor sample amounts and an abundance of poor quality samples, accurate subclassification of primary lung cancer using small pre-operative biopsies presents a diagnostic challenge using current tools (H&E and immunohistochemical stains). For patients with primary lung cancer, accurate determination of the tumor type significantly influences treatment decisions. Our previous studies have shown that microRNAs are differentially expressed in different subtypes of lung cancer; hence microRNA expression profiling holds a promising new strategy for the precise subclassification of lung cancers. Based on these findings, we present here the development of a microRNA-based qRT-PCR diagnostic assay that uses pathology and cytology samples in order to classify primary lung cancers into four subtypes: squamous, non-squamous, SCLC and carcinoid.

Methods: FFPE tissue blocks and cell blocks from different histological subtypes of lung cancer, taken from primary lung cancer resection or pre-operative diagnostic procedures, were collected. High-quality RNA, including the well-preserved microRNA fraction, was extracted from the samples using proprietary protocols. Expression levels of potential microRNA biomarkers were profiled using a sensitive and specific qRT-PCR platform.

Results: We find that combinations of a few microRNAs can successfully differentiate between different histological types of lung tumors. A classification algorithm was developed that reached high accuracy in the identification of the four main subtypes of lung tumors.

Conclusion:

We developed a highly accurate microRNA-based diagnostic assay that classifies primary lung cancer types with very high sensitivity and specificity. This assay is a simple and reliable diagnostic assay which will offer an accurate and standardized tool for primary lung cancer cytological samples, including those that presently fail pathological evaluation.

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 4943. doi:10.1158/1538-7445.AM2011-4943
Abstract 495: Overexpression of the cold-inducible RNA binding protein RBM3 attenuates the stem cell-like features of PC-3 cells
Authors: Zeng Yu , Kim John , Li Youqiang , Mooney Steven , Shiraishi Takumi , Kulkarni Prakash , Getzenberg Robert
Published: June 2012

Introduction: It has long been thought that the stem cell-like features of cancer cells contribute to their evolutionary capability to escape therapeutic strategies, such as chemotherapy, radiotherapy, or hormone deprivation in prostate cancer (PCa). At the same time, temperature is perhaps one of the most important elements of the environment. One of the most clinically relevant examples of the effect of temperature on stem-like cells is cryptorchidism, in which germ cells maintained at body temperature that is several degrees higher than in the scrotum do not function to form sperm. In contrast, these pluripotential cells have a high likelihood to develop cancer if they are not rescued by relocating them to the scrotum and therefore a lower environmental temperature, in very early childhood. RNA binding motif 3 (RBM3) belongs to a cold-inducible RNA binding protein family and has been shown to be highly expressed in normal testis tissue but is decreased in cryptorchid mouse. We previously reported that RBM3 was decreased by heat treatment in PCa cell lines. The goal of this study is to investigate the effect of RBM3 over-expression on stem cell-like features of PC-3 cells. Methods: RBM3 mRNA expression was detected by RT-PCR in fetal and adult human tissues, as well as in PCa samples. The normal prostate cell line, PrEc, was sorted with the stem cell surface marker CD133 using flow cytometry. PC-3 cells were transfected with pCMV6-RBM3-GFP vector. The soft agar clonogenic assay was performed with RBM3- or control vector-transfected cells. The expression of stem cell-related genes and miRNAs was determined using PCR array. Results: The RBM3 mRNA level is decreased in fetal tissues and CD133 (+) PrEc cells in comparison to adult tissues and CD133 (−) cells, respectively. Metastatic PCa expresses lower RBM3 mRNA than primary tumors. Moreover, RBM3 expression was decreased upon treatment of chemotherapy and maintained at a low level in the surviving clones after intensive chemo- or heat treatment in both PC-3 and DU-145 cells. PC-3 cells that over-express RBM3 demonstrated less heterogenic morphology than those with a control vector. Importantly, RBM3 over-expression greatly attenuates the anchorage-independent clonogenic ability of PC-3 cells. Additionally, a panel of genes and miRNAs that are involved in neural cell differentiation and self-renew are altered upon RBM3 expression. Conclusion: Taken together, these data suggest that lowering RBM3 may play an important role in maintaining the stem cell-like features of cancer cells during development and progression under environmental stress.

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 495. doi:10.1158/1538-7445.AM2011-495
Abstract 4951: 2-Methoxyestradiol (2-ME2) induces microRNA alterations in prostate cancer cells: Role for miRs in 2-ME2-induced biological effects
Authors: Xie Jianping , Ghosh Rita , Kumar Addanki P.
Published: June 2012

Prostate cancer is the second most common cause of death related to cancer in Western societies. 2-Methoxyestradiol (2-ME2), an endogenous metabolite of 17-β estradiol inhibits tumor cell proliferation in various cancer cells, including the prostate. Previous studies from our laboratory showed that 2-ME2 (i) inhibits proliferation of both androgen responsive and independent cells through induction of apoptosis involving G2/M check point block; (ii) prevents the development of prostate tumors in transgenic adenocarcinoma of mouse prostate (TRAMP) model. Although various molecular targets have been proposed, the mechanism of action behind its antiproliferative activity is still uncertain. Here we investigated the possible role for 2-ME2 induced antiproliferative activity by examining the altered regulation of microRNA (miRNAs). MicroRNAs are small non-coding RNAs that down regulate gene expression during cellular processes including proliferation and apoptosis. We compared the microRNA profile in non-tumorigenic (RWPE-1), androgen responsive (LNCaP) and androgen independent (PC-3) cells in response to 2-ME2 treatment in the presence and absence of androgen-stimulation (only in LNCaP cells) using the stem-loop RT-PCR based Taqman® Array Human MicroRNA Cards (Array A and B) representing 754 unique assays specific to human mature miRNAs (Applied Biosystems, Foster City, CA). Analysis of these data identified expression of only 50% of miRs in prostate cancer cells. About 26% and 12% of these are upregulated; 20.5% and 26% were down regulated in LNCaP and PC-3 cells respectively. However androgen stimulation of LNCaP cells resulted in upregulation of 34.2% and 15% down regulation of miRs whereas 2-ME2 treatment down regulated 28.7% of miRs. Target transcripts for these miRs have been identified. To the best of our knowledge this is the first study to report in-depth investigation of global miR changes in response to 2-ME2 induced biological effects. These data demonstrate that 2-ME2 suppresses proliferation and induces apoptosis in prostate cancer cells through modulation of microRNA signature. Supported by NIH CA 135451 (APK).

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 4951. doi:10.1158/1538-7445.AM2011-4951
Abstract 4956: Identification of microRNAs differentially expressed between lung squamous cell carcinoma and lung adenocarcinoma
Authors: Hamamoto Junko , Yoda Satoshi , Naoki Katsuhiko , Nakayama Sohei , Satomi Ryosuke , Terai Hideki , Ikemura Shinnosuke , Sato Takashi , Hayashi Yuichiro , Soejima Kenzo
Published: June 2012

Introduction: Recent advances in the treatment of non-small-cell lung cancer (NSCLC) with new agents require accurate histological subtyping at diagnosis in order to avoid the higher risk of an adverse response and obtain a maximum therapeutic response. However, interobserver variability, tumor heterogeneity and the degree of differentiation may influence the decision concerning a pathological diagnosis of NSCLC. We therefore in this study attempted to identify specific microRNAs as standardized biomarkers with high sensitivity and specificity for distinguishing between squamous cell carcinoma (SCC) and adenocarcinoma (AC).

Methods: Quantitative real time polymerase chain reaction (qRT-PCR) based microRNA array was performed to identify microRNAs differentially expressed between SCC and AC using 86 resected NSCLC samples as well as adjacent normal tissues. The results were confirmed by independent qRT-PCR assays with the same test samples and an additional 88 validation samples and the usefulness of the identified microRNAs as biomarkers to distinguish between SCC and AC was evaluated.

Results: Three microRNAs (hsa-miR-196b, hsa-miR-205 and hsa-miR-375) were identified. Discriminant analysis combining all 3 microRNAs appeared to distinguish SCC from AC accurately in the test samples and the validation samples, showing sensitivity and specificity of 76% and 80%, and 85% and 83%, respectively.

Conclusions: Hsa-miR-196b, hsa-miR-205 and hsa-miR-375 were identified as biomarkers capable of distinguishing between lung SCC and lung AC. These newly identified microRNAs may prove to be highly valuable molecular markers for the classification of NSCLC histologic subtypes, and could potentially contribute to the pathogenesis of each subtype of 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 4956. doi:10.1158/1538-7445.AM2011-4956
Abstract 4959: Deregulation of microRNA expression patterns during cervical carcinogenesis
Authors: Wilting Saskia M. , Snijders Peter JF , van de Wiel Mark A. , van Wieringen Wessel N. , Meijer Chris JLM , Steenbergen Renske DM
Published: June 2012

At present little is known about the involvement of alterations in microRNA (miRNA) expression patterns during the development of cervical cancer. In this study we investigated genome-wide miRNA expression profiles in normal cervical squamous epithelium, high-grade precancerous lesions (CIN2/3), squamous cell carcinomas (SCC) and adenocarcinomas (AdCAs), all of which were high-risk HPV positive. In addition, miRNA expression profiles were integrated with previously generated genome-wide chromosomal profiles of the same samples.

Unsupervised hierarchical clustering showed that miRNA expression profiling enables the distinction of normal cervical squamous epithelium, CIN2/3 lesions, SCCs and AdCAs. Differential miRNA expression analysis comparing normals, CIN2/3 lesions and SCCs identified early (temporal), late, and continuously differentially expressed miRNAs in cervical carcinogenesis (n=106). Differential expression of selected miRNAs could be validated by qRT-PCR in the same samples as well as in cervical scrapes of women with abnormal cytology and underlying high-grade CIN disease compared to control scrapes. In general, miRNAs located in the same cluster showed similar expression profiles, suggesting common regulatory mechanisms. For 5 of the 106 differentially expressed miRNAs, altered expression could be directly linked to underlying chromosomal alterations. Finally, cell viability assays indicated that ectopic expression of 2 selected miRNAs influenced cell proliferation in vitro, indicating functional relevance of differential miRNA expression during cervical carcinogenesis.

In conclusion, deregulation of miRNA expression patterns occurs during cervical carcinogenesis and has functional relevance for cervical cancer development. Since deregulated miRNA expression in cervical (pre)malignant disease is reflected and detectable in cervical scrapes, miRNAs represent a highly promising class of disease markers for further improvement of the triage of high-risk HPV positive women.

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 4959. doi:10.1158/1538-7445.AM2011-4959
Abstract 4961: MicroRNA profile predicts recurrence after resection in patients with hepatocellular carcinoma within the Milan criteria
Authors: Sato Fumiaki , Hatano Etsuro , Kitamura Koji , Myomoto Akira , Fujiwara Takeshi , Takizawa Satoko , Tsuchiya Soken , Uemoto Shinji , Shimizu Kazuharu
Published: June 2012

Objective: Hepatocellular carcinoma (HCC) is difficult to manage due to the high frequency of post-surgical recurrence. Early detection of the HCC recurrence after liver resection is important in making further therapeutic options, such as salvage liver transplantation. In this study, we utilized microRNA expression profiling to assess the risk of HCC recurrence after liver resection.

Methods: We examined microRNA expression profiling in paired tumor and non-tumor liver tissues from 73 HCC patients who satisfied the Milan Criteria. We constructed prediction models of recurrence-free survival using the Cox proportional hazard model and principal component analysis. The prediction efficiency was assessed by the leave-one-out cross-validation method, and the time-averaged area under the ROC curve (ta-AUROC).

Results: The univariate Cox analysis identified 13 and 56 recurrence-related microRNAs in the tumor and non-tumor tissues, such as miR-96. The number of recurrence-related microRNAs was significantly larger in the non-tumor-derived microRNAs (N-miRs) than in the tumor-derived microRNAs (T-miRs, P<0.0001). The best ta-AUROC using the whole dataset, T-miRs, N-miRs, and clinicopathological dataset were 0.8281, 0.7530, 0.7152, and 0.6835, respectively. The recurrence-free survival curve of the low-risk group stratified by the best model was significantly better than that of the high-risk group (Log-rank: P=0.00029). The T-miRs tend to predict early recurrence better than late recurrence, whereas N-miRs tend to predict late recurrence better (P<0.0001). This finding supports the concept of early recurrence by the dissemination of primary tumor cells. and multicentric late recurrence by the ‘field effect’.

Conclusion: microRNA profiling can predict HCC recurrence in Milan criteria cases.

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 4961. doi:10.1158/1538-7445.AM2011-4961
Abstract 4970: Mutational and functional analysis reveals ADAMTS18 metalloproteinase as a novel driver in melanoma
Authors: Prickett Todd D. , Wei Xiaomu , Viloria Cristina G. , Molinolo Alfredo , Lin Jimmy C. , Cruz Pedro , Rosenberg Steven A. , Davies Michael A. , Gershenwald Jeffrey E. , López-Otin Carlos , Samuels Yardena
Published: June 2012

An important feature of cellular signaling and migration involves the proteolytic cleavage of extracellular matrix and/or pro-ligands involved in signal transduction. Proteins called proteases are responsible for this action and include the matrix-metalloproteinase family and the A Disintegrin and Metalloproteinases family to name a few. The A Disintegrin and Metalloproteinases with Thrombospondin domains (ADAMTS) have been suggested to function as tumor suppressors as several have been found to be epigenetically silenced in various cancers. Thus further analysis is warranted in determining if ADAMTS genes/proteins play a role in melanoma genesis.

In the present study we performed a mutational analysis of 19 ADAMTS gene family members in human melanoma and identified a large fraction of melanomas to harbor somatic mutations. To evaluate the functional consequences of the most commonly mutated gene, ADAMTS18, six of its mutations were biologically examined. ADAMTS18 mutations had little effect on melanoma cell growth under standard conditions, but reduced cell dependence on growth factors. ADAMTS18 mutations also reduced adhesion to Laminin-I and increased migration in vitro and metastasis in vivo. Melanoma cells expressing mutant ADAMTS18 had reduced cell migration after shRNA-mediated knockdown of ADAMTS18, suggesting that ADAMTS18 mutations are growth-, migration- and metastasis- promoting in melanoma. These results demonstrate that the ADAMTS18 is a major target for mutational activation in melanoma and may be a useful diagnostic and/or therapeutic target.

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 4970. doi:10.1158/1538-7445.AM2011-4970
Abstract 4973: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep-sequencing
Authors: Kannan Kalpana , Wang Liguo , Wang Jianghua , Ittmann Michael , Li Wei , Yen Laising
Published: June 2012

Chimeric transcripts unrelated to chromosomal rearrangement are primarily generated by two transcription-induced mechanisms: read-through/splicing and trans-splicing. Both mechanisms result in fused transcripts that possess sequences from both genes. Although the exact cause and regulation of chimeric transcripts are unknown, chimeric RNAs, like fusion genes, are expected to increase the proteomic diversity in cells through chimeric proteins or altered regulation of participating mRNAs. Despite its importance, few studies have reported on chimeric RNAs, especially regarding their presence and roles in human cancers. In this study, we took advantage of the analytical power of paired-end high throughput sequencing to characterize chimeric transcripts enriched in human prostate cancer. By deep-sequencing the transcribed mRNA (transcriptome) of 20 clinical prostate cancer tissues, in addition to 10 matched benign prostate tissues from the same patients, we obtained greater than 500 million useful sequence reads. This strategy combined with stringent bioinformatic criteria enabled the identification of 27 novel and highly recurrent chimeric RNAs that have never been described before. The novel chimeric transcripts were experimentally validated to be present in human prostate cancer samples in a recurrent manner. Further experimental analysis identify several chimeric transcripts are present in the human prostate cancer cell lines, but not in primary human prostate epithelium cells, implying their associations with cancer mechanisms. Importantly, one of these chimeras appeared to be highly cancer-enriched, as it is confirmed to be expressed at significantly higher levels in human prostate cancers but present at very low levels in non-cancer prostates. Our results suggest that chimeric RNAs are more abundant than previously estimated. The RNA fusion junctions of these novel recurrent chimeras, as determined experimentally, suggest that many of them would generate altered or aberrant protein sequences, potentially leading to abnormal functions in 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 4973. doi:10.1158/1538-7445.AM2011-4973
Abstract 498: MicroRNA200c attenuated metastatic abilities in head and neck squamous cell carcinoma-derived cancer cells
Authors: Chiou Shih-Hwa , Chen Kuan-Hsuan , Lo Wen-Liang , Chen Yi-Wei , Chen Yu-Chih
Published: June 2012

MicroRNA-200c (miR200c) is emerging as an important regulator of epithelial-mesenchymal transition (EMT), tumorigenicity and cancer metastasis. Recent investigation showed miR200c can regulate the stemness in breast cancer stem cell through directly binding the 3’UTR of Bmi1. However, the role of miR200c in head and neck squamous cell carcinoma (HNSCC) and HNSCC-associated CSC has never been determined. In this study, we first demonstrated that miR200c expression was significantly decreased but Bmi1 expression was increased in HNSCC tissues as compared to adjacent normal cells. Secondly, HNSCC-ALDH1+CD44+ cells presented tumor initiating and radioresistant properties with high EMT. Consistently, the Bmi1 expression was significantly up-regulated and miR200c was down-regulated in HNSCC-ALDH1+CD44+ compared to other isolated subsets of HNSCC cells. Furthermore, miR-200c overexpression or Bmi1 knockdown through lentiviral infection could significantly inhibit the clonogenic and invasive abilities of HNSCC-ALDH1+CD44+ cells. Moreover, overexpression of Bmi-1 promoted HNSCC-ALDH1−CD44− to acquire CSC properties which are similar to HNSCC-ALDH1+CD44+. In contrast, overexpressing of miR200c shifted transcriptomes profiles of ALDH1+CD44+ similar to those of ALDH1-/CD44- populations and abolished self-renewal as well as EMT properties in ALDH1+CD44+. Most importantly, overexpression of miR-200c in ALDH1+CD44+ or ALDH1−CD44−Bmi-1over cells effectively blocked tumor growth and lung metastasis, and significantly prolonged survival time in neck orthotropic-transplanted immunocompromised mice. Lastly, miR200c is significantly reduced in high grade, metastatic HNSCC tissues compared to low-grade HNSCC tissues. In sum, these results show that miR200c negatively modulates Bmi1 expression and plays a role as a tumor suppressor in HNSCC through eliminating HNSCC-CSC population. Restoration of miR200c in HNSCC and CSC may pave a new approach for therapeutic treatment in the future.

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 498. doi:10.1158/1538-7445.AM2011-498
Abstract 4983: Integrative analysis of DNA copy number and gene expression identifies G3BP1 and HIRA as potential therapeutic targets against metastatic oral squamous cell carcinoma
Authors: Xu Chang , Liu Yan , Wang Pei , Fan Wenhong , Upton Melissa P. , Houck John R. , Lohavanichbutr Pawadee , Doody David R. , Futran Neal D. , Zhao Lue Ping , Schwartz Stephen M. , Chen Chu , Méndez Eduardo
Published: June 2012

The presence of lymph node metastasis is associated with a 50% reduction of 5-year survival in patients with oral squamous cell carcinoma (OSCC). We set out to combine DNA copy number aberrations (CNAs) with gene expression profiles, to identify CNAs-associated genes dysregulated in metastatic OSCC, and determine whether these genes can be targeted to selectively kill metastatic OSCC tumor cells. Toward this end, we interrogated DNA and RNA of the same OSCC cell populations laser micro-dissected from non-metastatic primary tumors (n=17) and metastatic lymph nodes (n=20) using Affymetrix 250K Nsp single-nucleotide polymorphism (SNP) arrays and U133 Plus 2.0 arrays, respectively. With a false discovery rate (FDR) < 5%, 1988 transcripts were found to be differentially expressed between primary and metastatic OSCC. Out of these, 114 transcripts showed significant correlation between their DNA copy number alternations (estimated using SNPs within 250 kb upstream and downstream of the transcript) and gene expression (FDR < 0.01). Among these CNA-correlated transcripts, 95 had significantly different DNA copy numbers between metastatic and non-metastatic OSCC (FDR <0.01 by Wilcoxon rank test). These 95 transcripts (representing 87 genes) mainly clustered around three genomic locations: 3p25.3-22.1, 9p24.1- 22.3 and 18q21.1-22.3. Among these 87 genes, we selected 28 of the 58 genes that were over-amplified and over-expressed in metastatic OSCC and conducted a high-throughput siRNA-mediated gene knockdown screen in five cell lines derived from primary and lymph node metastatic OSCC. The expression-knockdown of 18 genes showed 30% or more growth suppression in at least one cell line as compared to mock controls in which the cells were treated with transfection reagent only without the siRNA (P < 0.01). In particular, knocking-down G3BP1 and HIRA selectively suppressed the growth of all OSCC cell lines derived from lymph node metastases when compared to non-metastatic lines. Further investigation is warranted to confirm these findings and to examine the biological role of G3BP1 and HIRA in OSCC metastasis and their potential as therapeutic targets.

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 4983. doi:10.1158/1538-7445.AM2011-4983
Abstract 4991: Upregulation and the role of IKBKE in non-small cell lung cancer
Authors: Kim Donghwa , Guo Jianping , Gao Jingchun , Shu Shaokun , Haura Eric B. , Cheng Jin Q.
Published: June 2012

IKBKE is a serine/threonine protein kinase that belongs to the IKK kinase family. Recent studies have shown IKBKE as a breast and ovary cancer oncogene. Here we evaluated IKBKE expression and kinase activity in 30 NSCLC cell lines and 176 primary NSCLC specimens including 38 tumor/normal lung tissue pairs. Elevated protein levels of IKBKE were detected in 16 (52.6%) cell lines and 91 (51.7%) primary tumors. The mRNA levels and kinase activity of IKBKE are consistent with its protein status, suggesting that post-transcriptional regulation is not involved in increase IKBKE protein expression and that the IKBKE activation largely depends on its protein levels in NSCLCs. In addition, ectopic expression of IKBKE decreases and depletion of IKBKE increases the apoptosis induced by chemotherapeutic agents. Moreover, IKBKE is considerably induced by tobacco-derived carcinogens NNK and nicotine through Stat3 pathway. These findings demonstrated for the first time that deregulation of IKBKE is a recurrent event in NSCLC and could play a pivotal role in NSCLC development, and thus IKBKE is a critical therapeutic target in 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 4991. doi:10.1158/1538-7445.AM2011-4991