bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5088: Identification of effective genotype-selective drug combinations in melanoma
Authors: Held Matthew , Langdon Casey , Platt James , Steed Tisheeka , Chakraborty Ashok , Bachiocchi Antonella , Liu Zonghzhi , Bosenberg Marcus , Stern David F.
Published: August 2012

Resistance and partial responses to individual therapeutic agents are major obstacles in cancer treatment. In certain cases, combination therapies are clearly more effective, but systematic approaches to the identification of synergistic combinations of drugs are not well established. Here we present a bioinformatics-guided, high-throughput combinatorial screening platform that tests an array of small molecule drug combinations. A panel of over one hundred fifty agents was curated for compounds that inhibit receptors and signaling pathways active in melanoma, and broader groups of conventional cell cycle-active and genotoxic agents. Sixteen-point dose-effect curves were determined. Forty of the compounds exhibiting activity and representing the major classes tested were further analyzed. Three doses each were chosen, set up in all pair-wise combinations using a hit-picking robot, and analyzed against cell lines with activated BRAF, activated RAS, or neither mutation. Several combinations were selectively effective for melanomas containing activating mutations in BRAF, but were ineffective for mutant RAS melanomas, which were most susceptible to a small group of other drug combinations. Work is underway to validate the effective combinations in animal models, and to mine transcriptome and phosphoproteomic data associated with the cell lines to better predict sensitivity and resistance.

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 5088. doi:1538-7445.AM2012-5088
Abstract 5092: Localized and disseminated histiocytic sarcoma complex: A canine model
Authors: Dervisis Nikolaos , Klahn Shawna L. , Kiupel Matti , Parys Maciej , Gregory-Bryson Emmalena , Yuzbasiyan-Gurkan Vilma
Published: August 2012

Canine histiocytic sarcoma is an aggressive and uniformly-fatal round-cell neoplasm. The localized, peri-articular form of the disease (PAHS) appears to have statistically significant prolonged survival, when compared to the non - peri-articular form of the disease (non-PAHS). Knowledge of the molecular basis for the aggressiveness of the canine histiocytic sarcoma is foundational for developing effective treatments. The aim of this study was to characterize the molecular expression profiles of the different sub-types of the disease. Canine patients, with spontaneously-arising histiocytic sarcoma, were recruited for the study. Tumor tissue samples and peripheral blood were obtained and used for primary cell line development and gene expression analysis. Eight PAHS and 8 non-PAHS tumor samples were selected. RNA extraction, amplification and labeling were performed using standard techniques. Raw gene expression values were obtained using the Affymetrix GeneChip Canine Genome 2.0 Array. Background correction, normalization, PM correction, summarization, and expression analysis were performed using R/affy/limma. Gene set analysis was performed using BRB-ArrayTools, and the Molecular Signatures Database (MSigDB), to investigate gene ontology groups of genes whose expression was differentially regulated. Primary cell lines from tumor biopsies and peripheral blood samples were developed and characterized based on cellular morphology, growth characteristics, and immunophenotyping. In our gene expression array experiments, we identified specific gene transcripts that are more likely to represent true and biologically meaningful differences in expression levels between PAHS and non-PAHS. More specifically, metallopeptidase genes, and homeobox domain gene expression levels were enriched in the PAHS group, while ATP-binding cassette genes, and interleukin 1 receptor signaling gene expression levels were enriched in the non-PAHS group. Our results suggest presence of gene expression signatures that can provide insight in the diverse biologic behavior of the disease and highlight canine spontaneous tumors in understanding tumor biology.

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 5092. doi:1538-7445.AM2012-5092
Abstract 5093: Genome wide DNA copy number analysis of serous type ovarian carcinomas identifies genetic markers predictive of clinical outcome
Authors: Engler David , Gupta Sumeet , Growdan Whitfield , Drapkin Ronny , Nitta Mai , Sergent Petra , Allred Serena , Gross Jenny , Deavers Michael , Kuo Wen-Lin , Karlan Beth , Rueda Bo , Orsulic Sandra , Gershenson David , Birrer Michael , Gray Joe , Mohapatra Gayatry
Published: August 2012

Ovarian cancer is the fifth leading cause of cancer death in women. Ovarian cancers display a high degree of complex genetic alterations involving many oncogenes and tumor suppressor genes. Analysis of the association between genetic alterations and clinical endpoints such as survival will lead to improved patient management via genetic stratification of patients into clinically relevant subgroups. In this study, we aim to define subgroups of high-grade serous ovarian carcinomas that differ with respect to prognosis and overall survival. Genome-wide DNA copy number alterations (CNAs) were measured in 72 clinically annotated, high-grade serous tumors using high-resolution oligonucleotide arrays. Two clinically annotated, independent cohorts were used as validation sets. Unsupervised hierarchical clustering of copy number data resulted in two clusters with significant difference in progression free survival (PFS) and marginal difference in overall survival (OS). GISTIC analysis of the two clusters identified altered regions unique to each cluster. Supervised clustering of two independent large cohorts of high-grade serous tumors using the classification scheme derived from the two initial clusters validated our results and identified 8 genomic regions that are distinctly different among the subgroups. These 8 regions map to 8p21.3, 8p23.2, 12p12.1, 17p11.2, 17p12, 19q12, 20q11.21 and 20q13.12; and harbor potential oncogenes and tumor suppressor genes that are likely to be involved in the pathogenesis of ovarian carcinoma. We have identified a set of genetic alterations that could be used for stratification of high-grade serous tumors into clinically relevant treatment subgroups.

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 5093. doi:1538-7445.AM2012-5093
Abstract 51: Stromal AKT2 controls epithelial invasions
Authors: Cichon Ann-Christin , Pickard Adam , Patel Daksha , McCance Dennis
Published: August 2012

The tumor microenvironment is gaining importance in the regulation of tumorigenesis, invasion and metastasis. Loss of PTEN, a negative regulator of AKT, in stromal fibroblasts results in an increased tumor occurrence in ErbB2 expressing murine mammary tumors. Furthermore, we have shown that activation of AKT in stromal fibroblasts, following loss of the Retinoblastoma Protein (Rb), induces epithelial invasions in organotypic raft cultures, via an increase in Keratinocyte Growth Factor (KGF) expression. In addition, we have shown that loss of the PTEN tumor suppressor in stromal fibroblasts and subsequent activation of AKT, increases invasive potential of Human Papilloma Virus Type 16 E6 and E7 expressing keratinocytes. This is mediated by an increase in KGF expression. There are three isoforms of AKT expressed in human fibroblasts, AKT1, AKT2 and AKT3. By depleting each individual AKT isoform in stromal fibroblasts we have been able to establish that AKT2 is essential in regulating the cross talk between epithelium and stroma, and depletion of stromal AKT2 inhibits invasions. However, loss of stromal AKT2 does not function exclusively through regulation of KGF levels as it activates a second, protective pathway, which is able to counteract the effects of KGF. This protective pathway is mediated by increased Interleukin1 beta levels produced by the fibroblasts. Preliminary data from head and neck cancer specimens show that AKT is activated in stroma of cells associated with tumor but not normal tissue. Future work will determine the AKT dependent pathways that lead to increased KGF and Interleukin1 beta expression as well as how these factors mediate invasions.

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 51. doi:1538-7445.AM2012-51
Abstract 5102: Identifying targets for melanoma therapy: Biological and clinical implications of BRAF L597 mutants
Authors: Dahlman Kimberly Brown , Xia Junfeng , Hutchinson Katherine , Hucks Donald , Jia Peilin , Su Zengliu , Hicks Donna J. , Netterville James L. , Vnencak-Jones Cindy L. , Sosman Jeffrey , Zhao Zhongming , Pao William
Published: August 2012

Recurrent driver mutations in BRAF (V600), NRAS (G12/13, Q61), KIT (W557, V559, L576, K642, D816), GNAQ (Q209) and GNA11 (Q209) have previously been identified in malignant melanomas, but over one-third of cases have no known potentially actionable targets. To identify novel drivers, we performed whole-genome sequencing of a tumor-normal pair from a patient with an aggressive, chemotherapy-naïve metastatic melanoma which was pan-negative for the mutations listed above. Our data analysis pipeline revealed the landscape of somatic single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variations, and structural variants. A subset of the nonsynonymous SNPs was validated by direct sequencing, resulting in the identification of a somatic BRAF L597R mutation. Surrogate kinase assays suggest that this mutant is sensitive to both BRAF and MEK inhibitors. Subsequent mutational analyses showed that BRAF L597 mutations were in 2 of 34 (6%) ‘pan-negative’ tumors. Collectively, these data demonstrate the frequency and potential therapeutic implications of BRAF L597 mutations in melanoma.

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 5102. doi:1538-7445.AM2012-5102
Abstract 5104: Identification of key tumorigenic pathways in pancreatic adenocarcinoma patients using massively parallel DNA and RNA sequencing
Authors: Liang Winnie S. , Craig David W. , Carpten John , Borad Mitesh J. , Demeure Michael J. , Weiss Glen J. , Kiefer Jeffrey A. , Posner Richard , Hostetter Galen H. , Izatt Tyler , Sinari Shripad , Christoforides Alexis , Aldrich Jessica , Kurdoglu Ahmet , Phillips Lori , Benson Hollie , Baker Angela , Han Haiyong , Lake Douglas , Stites Edward C. , Ramanathan Ramesh K. , Fonseca Rafael , Stewart A. Keith , Hoff Daniel Von
Published: August 2012

Purpose: Pancreatic adenocarcinoma is among the most lethal forms of all malignancies. While significant research has implicated multiple genes in disease pathogenesis, identification of therapeutic leads has been difficult. The majority of currently available therapies provide only marginal benefit. To address this issue, our goal was to assess global somatic events across multiple pancreatic tumors by using next-generation sequencing technologies (NGS). Experimental Design: We performed whole genome sequencing (WGS) on paired tumor and normal samples from 3 pancreatic adenocarcinoma patients. Additionally, we performed whole transcriptome sequencing (WTS) on 2 of these patients’ tumors for which tumor RNA was available. Results: We generated on average 132 billion mappable bases across all patients using WGS, and identified 140 somatic coding events including point mutations, insertion/deletions, and chromosomal copy number variants. Data from WGS and WTS were integrated and analyzed to identify the most heavily affected pancreatic cancer pathways across all patients. The KRAS signaling pathway was identified as the most significant map. Unbiased global pathway analysis was also performed to identify processes that may be impacted. Consistent with the previous analysis, the most significant pathway from this analysis is also KRAS signaling. This integrated analysis specifically identifies heavily affected pathways in pancreatic cancer and pinpoints genes and processes that may be considered as targets for more effective therapies. Conclusions: While sequencing of additional patients is necessary to strengthen selection of key pathways, we demonstrate the utility of using NGS to understand the processes driving pancreatic adenocarcinoma so that standardized treatments for patients may be improved.

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 5104. doi:1538-7445.AM2012-5104
Abstract 5106: A HHIP derived gene expression signature for the prediction of patient survival after adjuvant chemotherapy of pancreatic cancer
Authors: Pilarsky Christian , Gorille Tobias , Rückert Felix , Grützmann Robert , Saeger Hans Detlev
Published: August 2012

Prognosis for patients with pancreatic carcinoma (PDAC) remains poor. Despite of increasing knowledge about the molecular basis of PDAC neither a specific marker for early diagnosis nor target proteins for a new therapeutic approach have been identified so far. However, reliable prediction of survival might help to improve the therapeutic outcome for patients with PDAC. In recent years it has become evident, that the Hedgehog (Hh) signal transduction pathway is a key regulator of pancreatic cancer development. Hedgehog interacting protein (HHIP) is a key modulator of Hh action and is overexpressed in the tumor stroma of PDACs. Reasoning that HHIP could serve as an indicator of Hh signaling activation we identified HHIP associated genes (HAG) using guilt by association (GBA) analysis in a set of PDAC gene expression profiles from microdissected tissue. Using the Affymetrix GeneChip U133 2.0 array and TNASAS we analyzed the gene expression profile of 59 PDAC samples and identified prognostic marker from HAG for survival of PDAC patients with adjuvant therapy. GBA analysis of gene expression profiles from microdissected PDAC tissue yielded 276 HAGs. TNASAS analysis using these genes revealed a prognostic gene expression signature of 50 genes, which was able to identify patients receiving adjuvant therapy with gemcitabine surviving more than 24 month with a total error of 0.087. TNASAS analysis of samples from patients treated without adjuvant therapy failed to identify a gene set with prognostic significance. Gene expression analysis is able to identify genes with prognostic significance in patients with adjuvant chemotherapy. These genes seem to be correlated with the efficacy of adjuvant gemcitabine therapy. Further analysis of those genes can reveal more insights in the signal transduction mechanisms associated with those genes.

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 5106. doi:1538-7445.AM2012-5106
Abstract 5109: Identical cancer cell lines from Sanger & Broad CCLE programs sometimes differ
Authors: Doman Thompson N.
Published: August 2012

The Sanger Institute in the UK has an ongoing initiative termed the “Cancer Genome Project” to systematically characterize the genetics and genomics of 770 cancer cell lines. Similarly, the Broad Institute in the US collaborates on the “Cancer Cell Line Encyclopedia” or CCLE project, entailing the eventual characterization of approximately 1000 cancer cell lines. At present, there are over 400 cell lines shared by these two initiatives. As part of a number of computational efforts in cancer biology we have used data from these two programs and have observed some unexpected differences in cell lines at the DNA and/or transcript level as well as some phenotypic differences, and we present here an analysis of these results including implications to the use of cancer cell lines in drug discovery and the larger question of genomic stability 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 5109. doi:1538-7445.AM2012-5109
Abstract 5111: Selection vs modification in cancer
Authors: Gorlov Ivan P. , Byun Jinyoung , Gorlova Olga , Logothetis Christopher , Zhao Hongya
Published: August 2012

Tumors differ from normal tissues by a distinct pattern of up- and down-regulated genes. A difference in gene expression profiles between normal and tumorous tissues can be (1) a result of the selection of preexisting variation in gene expression or (2) a modification of expression. In the simplest scenario, for genes fitting the selection model (SM genes), one can expect to find bimodal distribution of the expression values in normal tissue with only 1 peak in the tumor tissue. For genes fitting the modification model (MM genes), one can expect significant differences in mean gene expression values, with a similar expected variance in normal and tumorous tissues. Using these criteria and Gene Expression Omnibus (GEO) data, we have identified 200 SM genes and 200 MM genes. To identify SM and MM genes, we analyzed the distribution of gene expression values in normal prostate tissue derived from prostate free of any pathologic alterations (NP), normal-appearing prostate tissue adjacent to tumor (NA), primary prostate tumor (PT), and prostate tumor metastasis (MPT). We identified 3 sets of SM genes: (1) bimodal distribution in NP and unimodal in PT, (2) bimodal distribution in NA and unimodal in PT, and (3) bimodal distribution in PT and unimodal in MPT. Similarly, we identified 3 sets of MM genes. We found that SM genes are enriched by actin cytoskeleton genes for all 3 sets of genes: for set 1, P<10E-13; for set 2, P<10E-11; and for set 3, P<10E-2. MM genes were enriched by the genes from cancer-related pathways (P<10E-6) in set 1 and regulation of cell proliferation (P<10E-1) in set 2; no specific enrichment was found in set 3. We have also estimated an overlap between candidate genes for prostate cancer identified in genome-wide association studies (GWAS) and SM genes. GWAS candidates were overrepresented among the first set selection genes (10 vs expected 0.003 ± 0.002) and in the second set of genes (4 vs expected 0.003 ± 0.003), but for the third set of the genes, there was no indication of the enrichment (0 vs expected 0.003±0.002). For the MM genes, there was no indication of GWAS candidate enrichment. Taken together, our results suggest that selection of the preexisting variation in gene expression is important for early stages of carcinogenesis, whereas modification of gene expression is more important for 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 5111. doi:1538-7445.AM2012-5111
Abstract 5112: Foxa1 and Foxa2 are essential for gender dimorphism in liver cancer
Authors: Li Zhaoyu , Tuteja Geetu , Schug Jonathan , Kaestner Klaus H.
Published: August 2012

Hepatocellular carcinoma (HCC) is sexually dimorphic in both rodents and humans, with significantly higher incidence in males, an effect that is dependent on sex hormones. The molecular mechanisms by which estrogens prevent and androgens promote liver cancer remain unclear. Here, we discover that sexually-dimorphic HCC is completely reversed in Foxa1- and Foxa2-deficient mice after diethylnitrosamine-induced hepatocarcinogenesis. Co-regulation of target genes by Foxa1/a2 and either the estrogen receptor (ERalpha) or the androgen receptor (AR) was increased during hepatocarcinogenesis in normal female or male mice, respectively, but was lost in Foxa1/2-deficient mice. Thus, both estrogen-dependent resistance to and androgen-mediated facilitation of HCC depend on Foxa1/2. Strikingly, single nucleotide polymorphisms at FOXA2 binding sites reduce binding of both FOXA2 and ERalpha to their targets in human liver, and correlate with HCC development in women. Thus, Foxa factors and their targets are central for the sexual dimorphism of HCC. (Cell, accepted in press)

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 5112. doi:1538-7445.AM2012-5112
Abstract 5116: Identification and rapid in vivo validation of a novel drug combination for treating melanoma
Authors: Berndt Jason D. , Frazier Jason , Grenley Marc , Bahrami Bahram , Moon Randall T. , Olson Jim , Klinghoffer Richard
Published: August 2012

The well-established capability of tumors to resist single agent chemotherapies underscores the need to identify novel synergistic drug combinations to treat patients with cancer. Here we use an innovative arrayed needle technology to provide rapid in vivo validation of findings from a genome scale RNAi screen and reveal the potential of an unexpected drug combination to treat patients with melanoma. Our efforts focused on the β-catenin pathway. The β-catenin pathway impacts cancer progression in a context dependent manner. In some malignancies such as colon cancer, increased β-catenin activity drives oncogenesis. In contrast activation of β-catenin has been associated with decreased tumor proliferation and improved prognosis in patients with melanoma. A screen with an arrayed library of 14,000 lentiviral shRNA vectors revealed that silencing of dihydrofolate reductase, the target of the classic chemotherapeutic methotrexate, led to synergistic activation of the β-catenin pathway when combined with an inhibitor of GSK3. We therefore explored whether combination therapy, consisting of a GSK3 inhibitor and methotrexate could represent a potential treatment for melanoma patients. Two distinct small molecule inhibitors of GSK3, 6-bromoindirubin-3αoxime (BIO) and Chiron 99021, demonstrated synergy with methotrexate to activate β-catenin signaling in the melanoma cell line A375. To rapidly assess whether the observed synergy translates to the context of a living tumor, precision multiplexed microinjection using Presage technology was performed on mice harboring flank melanoma tumors. Discreet positions on each tumor were injected with either vehicle control, methotexate as a single agent, Chiron 99021 as a single agent, or the combination of the two agents. Analysis of the activation of beta-catenin and histology for markers of cellular proliferation, death, and differentiation allowed us to rapidly evaluate the efficacy of this drug combination. This rapid in vivo validation approach sets the stage for full preclinical evaluation of combined methotrexate and GSK3 inhibitor therapy using advanced co-clinical models of melanoma.

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 5116. doi:1538-7445.AM2012-5116
Abstract 5132: Pooled shRNA screens conducted in vitro and in vivo identify genes that are essential for the growth and/or survival of human tumor cells
Authors: Young Tara M. , Pasnikowski Elizabeth , Sahoo Padmini , Thurston Gavin , Daly Christopher
Published: August 2012

Identification of novel drug targets is a major challenge in cancer research. While numerous studies have identified genes that are mutated and/or amplified in cancers, the functional significance of most of these genetic alterations remains unknown. To directly identify genes that are required for the growth of human tumor cells, and that could potentially be targets for therapeutic monoclonal antibodies, we employed a custom shRNA library containing ∼13,000 shRNAs targeting 3,210 genes (∼4 shRNAs per gene) that encode cell surface or secreted proteins. Cultured tumor cells were infected with the virally-packaged shRNA library such that each shRNA (and an associated molecular barcode) was integrated into ∼200 cells. Cells that expressed shRNAs that target essential genes were progressively depleted from the population upon in vitro passage or following implantation into mice, resulting in decreased representation of those shRNAs/barcodes versus reference samples. In vitro screens were conducted in 3 colorectal cancer cell lines (HCT116, DLD1 and Colo320DM) and in NCI-H1975 lung cancer cells. About 1-3% of the genes in the library were identified as essential for tumor cell growth and/or survival in vitro. Importantly, these genes included positive controls such as PCNA that were included in the library to validate the screening procedure, as well as components of pathways that are known to control cell growth such as IGF-1R, Wnt9a, sonic hedgehog and RON. In vivo screens were performed with HCT116 and NCI-H1975 cells by implanting cells into mice immediately following shRNA integration. Representation of shRNAs versus the reference sample was assessed in small tumors (∼100 mm3) and in large tumors (1000 mm3). While we observed very few hits in small tumors, the number of hits in large tumors was greater than that observed in vitro (e.g., ∼3-fold higher for HCT116), suggesting that tumor growth in vivo is dependent on a larger set of genes than is cell growth in vitro. Interestingly, the genes that were uniquely essential in tumors versus in vitro included several that are involved in cell/cell adhesion (e.g., cadherin 24, claudin 3) and cell signaling (epidermal growth factor receptor). In summary, our shRNA screens focusing on secreted and cell surface targets have identified genes that may be essential for tumor growth, including many genes that have not previously been implicated in this process. Upon further validation, these genes could potentially serve as novel targets for therapeutic antibodies 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 5132. doi:1538-7445.AM2012-5132
Abstract 5134: The identification and characterization of genetic variations in lung adenocarcinomas in a Japanese population
Authors: Mimaki Sachiyo , Suzuki Ayako , Matsushima Koutatsu , Suzuki Makito , Ogasawara Naomi , Suzuki Yutaka , Tsuchihara Katsuya , Esumi Hiroyasu
Published: August 2012

Lung adenocarcinoma is a major histological subtype of non-small cell lung cancer. Previous studies have revealed substantial clinical and molecular differences between the Asian and Caucasian populations. Kinase inhibitor-sensitive EGFR mutations are frequently detected in Asian, female and non-smoker population. These findings suggest unique genetic and/or environmental background of carcinogenesis of this tumor. In the present study, we generated and analyzed a dataset of single-nucleotide variants (SNVs) and small insertions and deletions (indels) in the entire exon regions (exomes) in Japanese lung adenocarcinomas. We chose consecutive 97 of surgically resected T2 cases registered to the database containing clinicopathological and lifestyle information established at National Cancer Center Hospital East. High integrity genomic DNA was extracted from archived methanol fixed paraffin embedded tissue samples. Whole exons were captured using Agilent SureSelect system and we generated 76-base paired-end sequences with an Illumina GAIIx platform. Approximately 30 million mapped sequences were obtained for each sample, providing 75x coverage of the target regions and 93% of the target regions also had 5x coverage. Using the sequence data, we identified SNVs and indels by BWA, SAMtools and GATK. EGFR mutations were observed among 55 cases and Sanger sequencing validated them. As well, known lung cancer-related gene mutations such as KRAS and TP53 were detected in exome data. Detailed profiling of somatic mutations provided wide variety of heterogeneity of known and novel gene mutations with both EGFR-mutant and -wildtype background. These heterogenity might define the unique signature of an individual tumor and be waited for further classification suitable for understanding genetic mechanism of carcinogenesis.

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 5134. doi:1538-7445.AM2012-5134
Abstract 5137: A genome wide RNAi screen identify STAT3 activation as essential for ErbB2 mediated transforamtion of breast cancer cells
Authors: Barrueco Ruth Rodriguez
Published: August 2012

The generation of multidimensional datasets characterizing genetic, epigenetic, and functional properties of large normal and tumor-related samples is creating unique opportunities for the systems-level dissection of mechanisms associated with malignant phenotypes. Integrated data sets may lead to more efficient and specific approaches for the elucidation of therapeutic targets and biomarkers and for the identification of specific small molecule inhibitors. However, the power of these computational methods to study human cancer from an unbiased global perspective is severely compromised by the low through-put approaches necessary to functionally validate the in silico predictions. During the last years, RNA interference (RNAi) emerged as a very powerful genetic strategy to functionally interrogate the entire genome by loss-of-function studies. This cellular process can be experimentally controlled to knock down the expression of any specific gene. Our group has pioneered the development of RNAi-based genetic tools to translate RNAi studies to mammalian systems generating a shRNA-mir pooled lentiviral library that allows performing functional studies at genome-wide level. ErbB2 is a receptor tyrosine kinase found overexpressed in 20-40% of breast tumors correlating with a malignant phenotype and worse prognosis. Different targeted therapies have been developed to specifically inhibit its activity such the monoclonal antibody Herceptin, or the small tyrosine kinase inhibitor Lapatinib. Despite of the success of these inhibitors in the treatment of tumors that overexpress ErbB2, about 30% of them become resistant making necessary to look for alternative targets in these cases. The combination of the state-of-the-art computational analysis and RNAi-based technology toward system biology studies must represent a powerful tool to dissect the regulatory networks that govern the homeostasis of breast tumors. Applying this combined approach to an overexpressing ErbB2 breast cancer model we have identified the genes that are critical in those 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 5137. doi:1538-7445.AM2012-5137
Abstract 5139: Therapeutic targets for neuroblastoma by genome scale siRNA screens
Authors: Howie Heather , Toyoshima Masafumi , Annis James E. , Richard Lauren , Park Julie R. , Grandori Carla
Published: August 2012

∼ 30 % of Neuroblastoma harbor amplifications of the MYCN oncogene, which is the strongest molecular marker of poor prognosis. However, a subset of high-risk neuroblastoma does not carry alterations of the MYCN gene and the molecular pathways underlying their aggressive behavior remains to be elucidated. We have utilized a functional genomics approach with both genetically defined cell systems, as well as molecularly defined neuroblastoma cell lines, to identify critical survival pathways that distinguish MYCN-amplified versus non-amplified neuroblastoma. The results of high throughput siRNA screens targeting the druggable genome will be presented and discussed in light of public microarray data and validation experiments carried out in our laboratory. These findings revealed that different chromatin-remodeling genes, DNA-repair and developmental pathways differentiate MYCN amplified neuroblastoma versus non-amplified, thus highlighting specific new therapeutic targets associated with MYCN status as well as other molecular markers. In addition to pinpointing novel therapeutic targets for high-risk neuroblastoma, our study also functional defines signaling pathways activated in high-risk neruoblastoma and could be utilized to guide rational therapeutic choices.

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 5139. doi:1538-7445.AM2012-5139
Abstract 514: Relationship between loss of heterozygosity of HLA-A gene and HLA class I expression in gastric cancer
Authors: Yoshii Mami , Tanaka Hiroaki , Sakurai Katsunobu , Nagahara Hisashi , Kimura Kenjiro , Amano Ryosuke , Noda Eiji , Kubo Naoshi , Muguruma Kazuya , Yamada Nobuya , Yashiro Masakazu , Maeda Kiyoshi , Sawada Tetsuji , Ohira Masaichi , Ishikawa Tetsuro , Hirakawa Kosei
Published: August 2012

[Introduction]Human leukocyte antigen (HLA), located on 6p21.3, encodes for genes involved in antigen processing and presentation. Loss of heterozygosity (LOH) at 6p21.3 may cause downregulation of HLA class I, and may provide tumor cells with an immune-escape tumor phenotype. The aim of this study is to examine HLA class I expression in gastric cancer tissues and cell lines, to clarify the clinical impact of HLA-A dawnregulation on progression of gastric cancer. [Materials and methods]We examined HLA class I expression in clinical samples from 206 patients by immunohistochemical staining. By flow cytometric analysis, we analyzed the expression of HLA class I antigen in gastric cancer cell lines. Furthermore, we performed HLA-A typing in gastric cancer cell lines by PCR-SBT method. [Results]We observed that HLA class I expression was downregulated in metastatic lymph node compared with in primary lesion. HLA class I expression in primary lesion was associated with ly factors and histological types. Furthermore, patients with negative expression of HLA class I showed significantly poorer prognosis. In vitro, we observed the downregulation of HLA class I antigen in OCUM-2MLN cells which have a high potential for lymph node metastasis. By PCR-SBT method, we detected loss of heterozigosity of HLA-A gene in OCUM-2MLN. [Conclusion]We observed that HLA class I expression was associated with poor prognosis of gastric cancer and LOH of HLA-A was recognized in cancer cell line which has potential to develop lymph node metastasis. Our findings suggested that LOH of HLA-A gene would result in provide cancer cells with capacity to metastasize into lymph nodes.

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 514. doi:1538-7445.AM2012-514
Abstract 5150: Oncogene amplification in glioblastomas associates specifically with the increased expression of multiple glycolytic mediators
Authors: Beckner Marie E. , Kant Jeffrey A. , Pollack Ian F. , Nordberg Mary L. , Hamilton Ronald L.
Published: August 2012

Although aberrant enhancement of glycolytic potential is a defining attribute of malignancy, the underlying mechanisms are complex and difficult to ascertain. A network of contributing factors is suspected to permit multiple inputs and redundancy. In this study, 79 oncogenes in glioblastomas were examined by multiplex ligation-dependent amplification (MLPA) for copy number changes to test for associations with real-time quantitative PCR expression levels of genes encoding lactate dehydrogenases (LDHA, LDHC), ATP citrate lyase (ACLY), glycogen synthase (GYS1), carbonic anhydrases (CA3, CA12), a monocarboxylate transporter (SLC16A3), hypoxia inducible factor-1A (HIF1A), and growth factors (VEGFA, PDGFA, & EGF). All were normalized to housekeeping genes and then adjusted to the level of glycolysis by division with concurrent expression of (ENO1) that encodes enolase, a key glycolytic enzyme. Tumors were separated into two groups by a cut-off of 1.10 times ENO1 to define increased and non-increased gene expression relative to glycolysis. Except for CA12 (increased in almost all tumors), expression levels yielded two groups to quantify differences in regard to the percent of tumors with amplified oncogenes. Copy numbers of oncogenes determined by MLPA to be at least 3-fold greater than normal brain DNA (tested concurrently) defined increased levels of amplification for each gene. Of the 17 amplified oncogenes (0-6 per tumor), EGFR was most frequent (11/22 tumors). The greatest difference (52%, p = 0.01) occurred between increased versus non-increased LDHC groups for tumors with amplified oncogenes. The table lists differences for each gene. Thus, amplified oncogenes associate specifically with enhanced expression levels of genes for glycolytic mediators in glioblastomas. Identification of the amplified oncogenes (EGFR &/or others) in individual tumors provides potential targets for down-regulating aberrant glycolysis in brain tumors.

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 5150. doi:1538-7445.AM2012-5150
Abstract 5161: Role of glutamine in cancer growth, invasion and progression: Therapeutic modulation of glutamine pathway
Authors: Yang Lifeng , Nagrath Deepak
Published: August 2012

Glutamine, an alternative carbon source to glucose, has recently been shown to be important for the cancer cell survival, growth and progression. The link between glycolysis, glutaminolysis and fatty acid oxidation is not known. Thus, there is a strong motivation to study metabolic alternations caused by glutamine and uncover links between various fuel sources for highly and less invasive cancer cells. Here, we postulate that glutamine will increase glutamine uptake through up-regulating ASCT2 expression, while decreasing the glucose uptake by down-regulating GLUT1 expression for aggressive cancer cells. However, for non-aggressive cancer cells, glutamine will have no effect on glutamine and glucose uptake. Our findings indicate that NAD+/NADH ratio regulates the glutamine's direct effect on the lactate production irrespective of the bioenergetic substrate requirement for different kinds of cancer cells. Our findings using quantification of metabolites pertaining to central carbon and nitrogen metabolism provided clues as to which pathways relevant to glycolysis, the pentose phosphate pathway, the TCA and urea cycles, lipid cycle, and amino acid and nucleotide metabolisms, may be altered by glutamine in cancer cells, resulting in identification of dominant factors which control cancer metabolism. Through this study, we clearly demonstrate the exact of glutamine's effect on cancer metabolism. Our results set the stage for the development of glutaminolysis inhibitors based therapeutics for reprogramming of cancer metabolism. We believe that development of our oncosecretomics based metabolic strategy provides an unprecedented opportunity for the development of nutritional supplementation that can deregulate the adaptations and alterations induced by various nutrients in cancer metabolism.

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 5161. doi:1538-7445.AM2012-5161
Abstract 517: Anti-glycan IgM and IgG antibodies as new biomarkers for serous ovarian cancers
Authors: Tse Brian WC , Jacob Francis , Pochechueva Tatiana , Nixdorf Sheri , Fedier Andre , Huflejt Margaret , Bovin Nicolai , Fink Daniel A. , Hacker Neville F. , Heinzelmann-Schwarz Viola A.
Published: August 2012

Introduction: Patients with advanced-stage serous cancers (ovarian, peritoneal and tubal) often develop ascites, a protein-rich fluid within the peritoneal cavity which causes significant morbidity and is associated with a poor prognosis. Aberrant glycosylation is a common feature of these cancers and this may impact on the humoral immune response. We hypothesized that serous cancer patients and healthy women have different profiles of anti-glycan antibodies in plasma and ascites. Method: Matched pairs of plasma and ascites were collected from 11 patients with advanced stage disease. A custom-made printed glycan array (PGA) allowed the simultaneous detection of anti-glycan antibodies (AGAs) to 203 chemically synthesised glycans, including some tumour-associated carbohydrate antigens. Identified candidate AGAs were additionally detected using a suspension array in an independent patient cohort of 230 patients. Candidates were selected by their discriminatory power between cancer and healthy controls. One top candidate was further analyzed for its biological behavior using ovarian cancer cell lines. Results: Using PGA, we detected a multitude of AGAs in both plasma and ascites. Levels of AGAs in serum and ascites correlated independent of ascites volume. Serous cancer patients had significantly different levels of plasma IgM to 31 glycans when compared to plasma of 14 healthy control patients, with IgM levels being lower in the cancer group. Significant differences in IgG plasma levels were found for 4 glycans. The trisaccharide P1, part of the P blood group system, was selected for further analyses. Plasma expression of P1 was found independent of cohort and method used. The human serous ovarian cancer cell line, IGROV1, was shown to express P1 and was subsequently sorted into P1-high, P1-low, and P1-negative subpopulations. We found that IGROV1/P1-expressing cells correlated with faster tumor cell migration and invasion. Treatment with a human anti-P1 IgM (clone P3NIL100) inhibited the proliferation of these tumour cells in vitro. Conclusion: P1 expression can be detected in ovarian cancer patients in independent of cohorts. P1 seems to be involved in cancer migration and invasion, and is therefore a potential target for ovarian cancer diagnosis and therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 517. doi:1538-7445.AM2012-517
Abstract 518: Immunogenicity of cancer/testis antigen XAGE-1d in patients with non-small cell lung cancer (NSCLC)
Authors: Matsumoto Hirofumi , Ohue Yoshihiro , Eikawa Shingo , Mizote Yu , Kurose Koji , Isobe Midori , Uenaka Akiko , Nagayasu Takeshi , Oka Mikio , Nakayama Eiichi
Published: August 2012

BACKGROUND: Cancer/testis (CT) antigens expresses in various cancers and normal testis. Because of no expression of HLA class-I antigen in normal testis, CT antigens are promising molecular target for specific cancer immunotherapy. XAGE-1 gene has been identified as a CT-like antigen, and XAGE-1 gene has four alternative splice variants: XAGE-1a, XAGE-1b, XAGE-1c, and XAGE-1d. We previously reported that the transcript of XAGE-1a and XAGE-1b coded the same protein (GAGED2, isoform a, 81 amino acids) and the transcript of XAGE-1d coded another protein (GAGED2, isoform b, 69 amino acids). The first half of XAGE-1b and 1d protein (1-32 amino acids) is same sequence. On the other hand, XAGE-1c transcript codes some peptides but not a protein. Previously, immunogenic analyses of XAGE-1b have been performed because of its dominant expression, however, few analysis of XAGE-1d was performed. In this study, we investigated the immunogenicity of XAGE-1d in patients with non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: Tumor tissue samples for extracting mRNA were obtained from NSCLC patients treated surgical resection at Nagasaki University Hospital during the period from 2005 to 2010. Sera and PBMCs were obtained from NSCLC patients who visited Kawasaki Medical School Hospital during the period from 2005 to 2010. Splising variants of XAGE-1 gene were analyzed by quantitative real-time PCR with specific TaqMan probe-primer sets. Antibody responses to XAGE-1d were analyzed by ELISA using synthesized XAGE-1b protein. In antibody-positive patients, CD4+ T-cell responses against XAGE-1d were examined by IFN-γ ELISA. Epitope-peptides recognized by XAGE-1d specific T-cells were determined by ELISA using XAGE-1d-overlapping peptides (OLPs). RESULTS: In quantitative real-time PCR, expression of XAGE-1d mRNA was observed in 16/38 specimens (42.1%) that were also positive with XAGE-1b mRNA. The correlation coefficiency of the expression was 0.8047. Protein expression of XAGE-1d was observed in cytoplasm, being different from that of XAGE-1b in the nucleus in lung cancer cell lines by immunohistochemical staining. Antibody against XAGE-1d was detected in lung cancer patients who were also positive with XAGE-1b antibody. By a limiting dilution, a CD4+ T-cell clone was obtained from PBMCs in a seropositive patient. HLA class II restricted recognition of XAGE-1d was confirmed using various allogeneic EBV-B cells as APC. 14-mer minimal epitope peptide was determined. CONCLUSION: The findings indicate that XAGE-1d co-expresses with XAGE-1b and is immunogenic in NSCLC 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 518. doi:1538-7445.AM2012-518