bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5066: Genome sequence and epigenome map of bladder cancer development from occult field effects
Authors: Czerniak Bogdan A. , Majewski Tadeusz , Bondaruk Jolanta , Zhang Shizhen , Lee Sangkyou , Baggerly Keith , Dinney Colin , Grossman H. Barton , Wu Xifeng , Issa Jean-Pierre , Zhang Wei , Gibbs Richard , Scherer Steven E.
Published: August 2012

We are pursuing a unique strategy to identify early events in bladder cancer development by the genome-wide analysis of somatic changes in tissues from resected bladders and characterized pathologically as urothelial carcinoma. We then extend this analysis into precursor intraurothelial lesions and normal tissue. Here we report on the construction of a high resolution whole-organ histologic and genetic map of bladder cancer development that tracks its progression from in situ precursor conditions to invasive clinically aggressive cancer using total genome and exome sequencing and complemented with HumanOmni 2.5-8 v1 SNP-based Illumina genotyping, combined with CpG island methylation and cDNA microarray platforms derived from 12 whole-organ cystectomy specimens with invasive urothelial carcinoma. This approach provided a high resolution integrated map of structural genome, epigenome, and transcriptome alterations that parallel the development of bladder cancer from early field effects to invasive disease. By analyzing genome-wide patterns of structural genomic, epigenomic, and transcriptome changes, we found three major waves of alterations associated with growth advantage of successive clones reflecting a stepwise conversion of normal urothelial cells into cancer cells. This approach is significant for the identification of specific chromosomal regions as well as epigenetically and transcriptionally modified gene ontologies involved in early clonal expansion of intraurothelial neoplasia and their clonal evolution to carcinoma in situ progressing to invasive cancer. These studies suggest involvement of specific gene networks in early clonal expansion of intraurothelial neoplasia antecedent to microscopically recognizable precursor lesions such as dysplasia and carcinoma in situ. This map represents a prerequisite for specific studies on the mechanisms of incipient phases of bladder cancer development and should have a significant impact on the understanding of human 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 5066. doi:1538-7445.AM2012-5066
Abstract 5070: Paired-end RNA-sequencing reveals novel fusion genes and SNVs in osteosarcoma
Authors: Moon So Young , Bilke Sven , Davis Sean , Walker Robert L. , Pineda Marbin , Zhu Yuelin Jack , Abaan Ogan , Meltzer Paul S.
Published: August 2012

Osteosarcoma is an aggressive cancer of bone, which typically occurs during adolescence. The genetic hallmark of osteosarcoma is the presence of extensive and complex genomic rearrangements. However, few consistent aberrations have been identified, hampering the development of targeted therapy for osteosarcoma. Next generation RNA-sequencing (RNA-seq) is a powerful tool for comprehensive characterization of whole transcriptome, with the unique ability of identifying novel fusion genes. We applied paired-end RNA-seq to explore the transcriptome of 16 human OS cell lines and primary osteoblasts from two healthy individuals. On average, about 21.6 million sequencing reads and 10.6 million aligned reads were obtained for each sample. Several thousand SNVs (single nucleotide variants) that have not been reported in the dbSNP database were identified. Bioinformatic analysis identified several fusion genes (e.g. PAFAH1B2-FOXR1and FAM119B-TSFM), which involved both known cancer related genes as well as genes previously unrelated to cancer. Fusion transcripts were validated using RT-PCR, Western blot and capillary sequencing. These rearrangements tended to occur at copy number transitions on the partner chromosome regions. Our findings have the potential to provide important insights into osteosarcoma biology, and potential translational applications for diagnostic and therapeutic development.

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 5070. doi:1538-7445.AM2012-5070
Abstract 5072: Genome sequencing of metastatic colorectal carcinomas to identify potential targets for therapy in patients
Authors: Shanmugam Viji , Ramanathan Ramesh K. , Sinari Shripad , Chadha Manpreet , Liang Winnie , Kurdoglu Ahmet , Izatt Tyler , Christoforides Alexis , Benson Hollie , Phillips Lori , Baker Angela , Hostetter Galen , Von Hoff Daniel D. , Craig David , Carpten John
Published: August 2012

Colorectal carcinoma is one of the most common cancers in the western world, being the third most common cause of cancer-related morbidity and mortality. The outcome of patients with metastatic colorectal carcinoma (mCRC) following first line therapy, especially with a Kras mutation is poor with median survival of less than one year. The purpose of this study was to identify therapeutically actionable somatic events in mCRC patient samples, so as to obtain select targeted treatment strategies for individual patients. Fresh frozen needle biopsies of liver metastases were collected from three mCRC patients along with whole blood for the extraction of constitutional DNA. All patients had greater than 2 prior regimens and had known K-ras mutations. Whole genome sequencing was performed using Illumina paired-end chemistry on HiSeq2000 sequencing system, which yielded coverage of greater than 30X for both the normal and tumor samples. Somatic genomic alterations (point mutations and indels, copy number alterations, translocations and rearrangements) were analyzed using our custom pipeline for paired analysis. We found that all 3 tumor samples had KRAS mutations, while 2 samples had mutations in the APC gene and the PIK3CA gene. Other genes with therapeutic implications in single tumor samples were INPPL1, INPP4B and SMAD4. No EGFR amplifications were detected in our sample set. Pathway analysis revealed K-RAS regulation and apoptosis and survival pathways in these tumor samples. Analysis of paired-end data from these three tumors did not reveal the presence of translocations at the recently discovered TCF7L2 locus (Bass et al, Nature Genetics, 2011). The concomitant mutations in MAPK (KRAS) and PI3K (PIK3CA, INPPL1, INPP4B) pathways suggest that combination therapies might be required for effective treatment of these tumors. By harnessing the power of Next-Gen Sequencing, our study has revealed a series of therapeutically actionable events in mCRC that might provide insights into treating these difficult to treat advanced 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 5072. doi:1538-7445.AM2012-5072
Abstract 5077: Array CGH genomic profile of hereditary breast cancer tumors: Identification of tumor suppressor genes in deleted regions, determination of promoter hypermethylation and their protein expression in tumor biopsies
Authors: Alvarez Carolina , Tapia Teresa , Cornejo Valeria , Aravena Andres , Fernandez Wanda , Alvarez Manuel , Camus Mauricio , Maass Alejandro , Carvallo Pilar
Published: August 2012

Breast cancer, as other cancer types, is a genetic disease caused by sequential accumulation of mutations and genomic alterations involving tumor suppressor genes and oncogenes. In this matter, inactivation of tumor suppressor genes may occur by deletion, promoter hypermethylation or point mutations. We analyzed by array-CGH tumor DNA from 52 patients with hereditary breast cancer: 3 BRCA1, 4 BRCA2 and 45 from patients with no identified mutations (BRCAX). Our analysis revealed that BRCA1 mutated tumors have different genomic alterations compared to BRCA2 tumors. BRCAX tumors showed frequent deletions at: 1q21.3 (20%), 1p31.1 and 9q33.1 (18%); and frequent amplifications at 1q23.1 (20%), followed by 1q21.1 and several gains in chromosome 19 (18%). All genes involved in the deleted or amplified regions were compared with gene expression data in the ONCOMINE database finding correspondence among genomic alterations and gene expression. Based on these results, we selected 3 tumor suppressor genes for promoter methylation and protein expression analyses: RASSF1A, SLIT2 and WIF1. Methylation analysis through MS-PCR revealed that RASSF1A promoter was hypermethylated in 67% of hereditary tumors, and significantly associated to loss of expression (p=0.007, OR 9.6, CI 1.77-52.19). WIF1 promoter was hypermethylated in 68% of tumors with a significant association to loss of expression (p=0.042, OR 6.4, CI 1.155-35.45). Finally, SLIT2 was found as the most frequently hypermethylated promoter among tumors (80%) showing loss of expression in 90% of these tumors. Our results indicate that silencing of RASSF1A, SLIT2 and WIF1 through promoter hypermethylation may have an important role in hereditary breast tumor development. Fondecyt 1040779 y 1080595.

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 5077. doi:1538-7445.AM2012-5077
Abstract 5098: Identification of copy number alterations associated with the progression and clinical outcomes of oral cavity squamous cell carcinoma
Authors: Chien Huei-Tzu , Huang Shiang-Fu , Cheng Sou-De , Chen I-How , Liao Chun-Ta , Wang Hung-Ming , Hsieh Ling-Ling
Published: August 2012

The molecular mechanisms contributing to the progression of oral cavity squamous cell carcinoma (OSCC) remain poorly understood. The primary treatment for advanced-stage OSCC is radical surgery with post-operative chemoradiation. However, the prognoses are usually discouraging. If we can better understand the characteristics of OSCCs, this may ultimately help clinicians to provide OSCC patients with more appropriate treatment. The advent of genome-wide profiling methods has opened up new possibility to catalogue chromosomal abnormal regions at high resolution. In the present study, 72 advanced-stage OSCCs were analyzed using two microarray platforms (26 cases with Affymetrix SNP 500K and 46 cases with Affymetrix SNP 6.0). Genomic copy number was determined by calculating the intensity ratio between the OSCC and a set of 270 normal DNAs from HapMap project. Segmented copy numbers for each tumor were inferred with the hidden markov model (HMM) using the Partek GS software. To identify regions for copy-number alterations (CNAs), GISTIC (genomic identification of significant targets in cancer) was applied to determine the significance. With this approach, 46 (14 gain and 32 loss) and 208 (48 gain and 160 loss) significant regions (FDR q-value < 0.25) were identified from SNP 500K and SNP 6.0 platform, respectively. Among them, 15 focal CNAs (8 gains (3q26.1, 7p11.2, 11q13.3, 13q22.1, 15q11.2, 17p13.3, 18p11.23-18p11.31, and 20p11.22) and 7 losses (1q21.1, 6p21.33, 7q31.3, 12q14.1, 2 focal regions in 14q11.2, 15q11.2)) are identical in these 2 platforms. Amplification of 11q13.3 containing a known oncogene CCND1 was confirmed by fluorescence in situ hybridization (FISH) with Vysis CCND1/CEP11 FISH probe kit. The clinicopathologic significances of these 15 CNAs were examined. Gain of 3q26.1 and 18p11.23-18p11.31, and loss of 15q11.2 were correlated significantly with lymph node metastasis. Furthermore, loss of two focal regions in 14q11.2 was significantly associated with disease-free and overall survival. In conclusion, CNAs associated with the progression and clinical outcomes of Taiwanese OSCC were identified by genomic approach using high-density SNP array. These results provide useful clues for future characterization of important oncogenes or tumor suppressor genes associated with the behaviors of the disease.

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 5098. doi:1538-7445.AM2012-5098
Abstract 5108: A combined processing and assessment workflow for SNV and indel calling on exome sequencing of tumor samples
Authors: Wong Swee Seong , Calley John N. , Wang Jian , Ting Jason C. , Wulur Isabella H. , Li Shuyu Dan , Yue Yong Gang , Barber Thomas D. , Aggarwal Amit , Donoho Gregory P.
Published: August 2012

A workflow for exome sequencing is established using multiple callers for SNV and indel. A spectrum of measures is looked at to understand the diversity and characteristics of the samples. Two common workflows for variant calling are used, namely GATK unified genotyper and Samtools mpileup. Illumina paired end 90 base reads are mapped to the human genome using BWA. Variants called by GATK and Samtools are compared and merged to give a unified set of calling in VCF format. This approach gives additional confidence in calls supported by both callers as there are technical differences in the two workflows. dbSNP rate and TI/TV ratio are used to assess the general quality (sensitivity and specificity) of the calls. It is observed that tumor samples with very low and high TI/TV novel ratio are largely lung and melanoma samples respectively. They are likely to be UV and smoking induced DNA mutation. This affects the overall TI/TV ratio. A handful of samples also exhibit high variant count that is uniquely found (private) in the sample alone. This correlates with lower than expected dbSNP rate.

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 5108. doi:1538-7445.AM2012-5108
Abstract 511: Characterization of humoral response profiles of ovarian cancer patients as diagnostic biomarkers
Authors: Roberson Carolyn D. , Gercel-Taylor Cicek , Taylor Douglas D.
Published: August 2012

Ovarian cancer is the 5th leading cause of cancer death among women and is the leading cause of death among gynecologic malignancies as a result of limitations in early diagnosis. It is associated with the induction of humoral immunity, characterized by the generation of IgG against a wide range of tumor-associated antigens. Although the role of circulating tumor-reactive IgG is unclear, it has been demonstrated to correlate with poor prognosis and survival. The use of tumor-reactive IgG as a potential diagnostic and/or prognostic tool has been limited since most studies have identified components with shared expression in non-neoplastic tissue and failed to define targets exhibiting ubiquitous expression in ovarian cancers. A number of these limitations result from the use of recombinant proteins (translated in non-mammalian cells) as targets to define immunoreactivity. The power in utilizing the autologous humoral response is its ability to define alterations which might lead to the altered appearance or aberrant association of antigen with other cellular components, thereby resulting in the induction of humoral responses. We therefore hypothesize that the ovarian patient humoral response to specific tumor antigens can serve as diagnostic biomarkers of ovarian cancer. To investigate patients’ humoral response to “natural” tumor antigens, ovarian tumor cell lysates and tumor-derived exosomes were separated into antigenic proteins by first dimension isoelectric focusing via an immobilized pH gradient and/or rotofor fractionation. Reactive proteins were further separated by second dimension SDS-PAGE, followed by western immunoblotting using autologous or heterologous patient sera. Circulating tumor-reactive IgG was found to recognize shared (MW 37-75 kD, pI 3.0-5.5) and distinct (MWexo ∼50 kD, pI 9.0-10.5; MWlys∼15 kD, pI 4.3-6.5) ovarian tumor cell proteins. Recognition of these antigenic proteins was not observed using antibodies derived from normal control patients. Collectively, our data supports that the circulating IgG produced in the ovarian cancer humoral response recognizes specific tumor antigens (many of which are shared among cancer patients) and will thus have utility in diagnosing these patients. Further identification of these antigenic proteins by mass spectrometry will produce specific diagnostic targets and may provide insights on common driver mechanisms in ovarian 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 511. doi:1538-7445.AM2012-511
Abstract 5110: Divergent gene expression profiles in HPV-positive and HPV-negative head and neck squamous cell carcinomas
Authors: Tomar Swati , Kowli Sangeeta , Altomare Diego , Sutkowski Natalie , Gillespie Marion Boyd , Glover Saundra H. , Creek Kim E. , Pirisi-Creek Lucia A.
Published: August 2012

Up to 60% of oropharyngeal cancers and 25% of head and neck squamous cell carcinomas (HNSCC) are due to high-risk Human Papillomavirus (HPV), primarily HPV16. Differences in risk factors, age of presentation and clinical behavior of these tumors indicate that HPV+ and HPV- tumors develop with different molecular mechanisms and are biologically distinct. To further investigate the molecular characteristics of these tumors, we compared the gene expression profiles of three HPV- and four HPV+ HNSCC specimens, obtained from the Medical University of South Carolina ENT/Head and Neck Surgery clinic. All HPV+ tumors were positive for HPV16 and expressed E7, as documented by real-time RT/PCR using tumor-derived RNA. Gene expression profiles were determined on Agilent 4x44K human oligonucleotide microarrays. Identification of differentially expressed genes (>2-fold change, p<0.05) and pathway analysis were performed using GeneSifter Software (Geospiza). Overall, 125 genes were up-regulated and 223 were down-regulated in HPV+ in comparison with HPV- tumors. Gene Ontology analysis of the dataset revealed that pathways related to cell cycle control, mitotic checkpoint, regulation of cell proliferation, programmed cell death and DNA metabolism were heavily affected in HPV+ tumors, while pathways affected in HPV- tumors included regulation of cell motility and migration, angiogenesis and integrin-mediated signaling. We confirmed by Real-Time RT/PCR the differential expression of a panel of genes of interest on these samples and several additional HNSCC specimens, and then we extended our follow-up analysis to specimens from over 30 new cases of HNSCC. Among the genes we targeted for follow-up is the MET oncogene, which encodes the hepatocyte growth factor/scatter factor receptor. MET is overexpressed about 5-fold in HPV- tumors, in comparison with HPV+ tumors actively expressing E7. The MET product, which controls growth, invasion and metastasis in cancer cells, has been recently proposed as a new therapeutic target for HNSCC. Supported by grant #P20MD001770 from the NIH/NIMHD.

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 5110. doi:1538-7445.AM2012-5110
Abstract 5121: Acquired inactivating ARID2 mutations in lung non small cell carcinoma
Authors: Didelot Audrey , Letouzé Eric , Manceau Gilles , pallier Karine , Guichard Cecile , Cazes Aurélie , Fabre Elizabeth , Zucman-rossi Jessica , Laurent-Puig Pierre , blons Helene F.
Published: August 2012

The genetic alterations involved in the development lung adenocarcinoma (ADC) have been widely characterized allowing the identification of the most frequent oncogenes or tumor suppressor genes linked to this malignancy. Most studies have focus on proliferation pathway, anti-apoptotic factors or cell cycle alterations. Here we show that alterations in chromatin remodeling complexes are frequent in lung ADC. Chromatin structure plays a key role in the regulation of tissue-specific gene expression during development and differentiation therefore it is not surprising that proteins implicated in remodeling complexes play a role in cancer development. For example, mutations have been found in genes belonging to the SWI/SNF complex in different tumors. In lung cancer BRG1 knockout was shown to potentiate tumor development and mutations were recently identified in tumors by the use of a very sensitive method: massive parallel DNA pyrosequencing that suggests the presence of the alteration in cell subclones. In the course of identifying novel chromatin remodeling complex genes implicated in lung ADC development we analyzed a series of 82 lung adenocarcinomas by SNP array and looked for the presence of homozygous deletions on the entire genome. Three regions of homozygous deletions in known tumor suppressor genes CDKN2A, FHIT and PTEN and in JARID2, which is involved in chromatin remodeling, were found in more than 2 samples. Another ARID-domain containing gene; ARID2 was found deleted in one sample and we therefore decided to screen both ARID-domain genes for mutations by direct sequencing on cryopreserved tumor tissues. One missense somatic mutation was found in JARID2 and 6/82 tumors had ARID2 alterations predicted to inactivate the protein in at least 4 out of 6 samples. Indeed 3 mutations were frameshift or non-sense, one specimen had a homozygous deletion and 4 tumors demonstrated loss of heterozygosity associated to the mutation. Our results indicate that ARID2 inactivation is a common feature of lung cancer development and provide new insight on the impact of chromatin remodeling alteration in lung ADC.

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 5121. doi:1538-7445.AM2012-5121
Abstract 5130: Integrative approaches for the identification of therapeutic targets in basal like breast cancer from multi-level molecular data
Authors: Tesson Bruno M. , Rigaill Guillem , Vincent-Salomon Anne , Gentien David , Roman-Roman Sergio , Pierré Alain , Cruzalegui Francisco , Depil Stéphane , Tucker Gordon , Dubois Thierry , Barillot Emmanuel
Published: August 2012

Basal-like breast cancer is a molecular subtype of breast carcinoma accounting for up to 15% of cases and associated with a poor prognosis. There is no targeted therapy for this disease; since most basal-like breast cancers do not over-express HER2 and are negative for hormone receptors, they cannot be treated with trastuzumab antibody (anti-HER2) or anti-hormonal therapies. Finding therapeutic targets for the treatment of basal-like tumors is therefore a priority in breast cancer research. In this project, biopsies for the different subclasses of breast cancer (46 basal-like, 33 HER2+/ER-, 35 luminal A and 40 luminal B) were obtained from the Biological Center of Institut Curie and characterized by immuno-histochemistry. Using different microarray platforms, genome-wide profiles were obtained at the DNA, messenger RNA, and microRNA levels. Additionally, data were collected for a selection of 150 proteins using Reverse Phase Protein Arrays. We present the results of separate analyses of each of these molecular levels, and we introduce methods that integrate information across multiple layers of data to pinpoint potential drivers of the disease. In particular, we propose an approach to identify genome regions where copy number alterations correlate with transcriptome-wide perturbation of gene expression. Such correlation suggests that these regions may harbor genes playing an important role in carcinogenesis. Using criterions based on co-expression and on prior biological knowledge, the method determines the genes in these regions that are most likely to be cancer drivers and may therefore be relevant as therapeutic targets. Using HER2+ tumors to illustrate the approach, we show that the method is indeed able to designate the HER2 oncogene as a likely driver. With the addition of miRNA and protein data to these integrated studies, we hope that such approaches will suggest putative cancer driving genes as novel potential therapeutic targets.

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 5130. doi:1538-7445.AM2012-5130
Abstract 5140: The functional c-Myc dependent polymorphisms of telomerase promoter control hTERT expression and are associated with telomere length
Authors: Woong Son Ji , Choi Yi Young , Park Jae Yong , Jeon Hyo-Sung
Published: August 2012

Telomere shorting occurs after repeated cell division and has a key role in cell senescence, differentiation, and immortalization. Thus, telomere maintenance is critical for cancer progression. Telomere length is mainly regulated by telomerase activity associated with transcriptional activity of human telomerase reverse transcriptase (hTERT), a subunit of telomerase. The dysregulation and reactivation of hTERT gene expression may play an important role in facilitating tumor development. The hTERT promoter region was well identified and is rich in transcription factor binding sites including c-myc, SP1, and esterogen. In our previous study, hTERT polymorphisms, rs2753940 (-1327C>T), rs2853669(-244 T>C), rs2736100 and MNS16A, were examined for lung cancer association study. To identity effect of the hTERT polymorphisms on telomere length and transcriptional activity, we determined telomere length according to hTERT polymorphisms. The two hTERT polymorphisms, rs2753940 (-1327C>T), rs2853669 (-244 T>C), have a significant association with telomere length (P = 0.04, P = 0.013, respectively). This telomere length may be determined by hTERT expression which was regulated promoter polymorphism (rs2853669) by changing of c-MYC binding. We evaluated that rs2853669 is significantly associated with lung cancer prognosis in NSCLCs. Two promoter SNPs have a role in expression of hTERT, which may affect telomere length. These two polymorphisms may be used for risk and prognostic marker of lung 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 5140. doi:1538-7445.AM2012-5140
Abstract 5154: Fatty acids mediated regulation of cancer metabolism
Authors: Rizi Bahar Salimian , Nagrath Deepak
Published: August 2012

Although fatty acids have been shown to modulate progression, growth and invasiveness of cancer cells, it remains unclear how saturated and unsaturated fatty acids affect metabolic reprogramming of aggressive and nonaggressive cancer metabolism. In this study, we tested the hypothesis that fatty acids induce differential competitive effects on glucose oxidation in aggressive and nonaggressive ovarian cancer cells. Normal cells rely mainly on mitochondrial oxidative phosphorylation for their required energy supply, however, cancer cells utilize aerobic glycolysis pathway for their energetic need. We hypothesized that high fat diet could deregulate this metabolic alteration in cancer cells. Such as glucose, fatty acids are an influential source of ATP, energy currency, within a cell. In our study, using metabolic footprinting we studied the affect of both saturated (stearic and palmitic acid) and unsaturated fatty acids (linoleic and oleic) on glycolysis, pentose phosphate pathway and TCA cycle. Moreover, we also studied the effect of glucose on fatty acid oxidation, uptake and endogenous fatty acid synthesis. Metabolic flux analysis was done for comparative metabolic profiling under various nutritional conditions. We observed that fatty acids differentially regulate highly invasive ovarian cancer (SKOV3 and SKOV3ip) cells than less invasive ovarian cancer (OVCAR3) cells. Interestingly, we found strong effect of fatty acids on glycolysis in less invasive cancer cells. In contrast, our study showed that glucose has dominant effect on aggressive cells compared to less aggressive cells. Our studies emphasize the role of fatty acids in ovarian cancer growth, invasion and migration and underlie the need to develop therapy based on high fat diet synergistically with existing chemotherapeutics and cancer drugs.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5154. doi:1538-7445.AM2012-5154
Abstract 5174: Novel signaling interactions of type XV collagen: Implications for tumor suppression
Authors: Clementz Anthony G. , Mutolo Michael J. , Harris Ann
Published: August 2012

Most clinical therapeutics used to date depend on specific targeting of cellular components to treat cancers. However, the environment outside the tumor cell is also critical since it may provide new targets to treat malignant and resistant cancers, independent of the tumor. We aim to advance the understanding of the early stages of cancer, prior to metastasis by determining the role of a non-fibrillar collagen (Type XV) and its interactions with the tumor stroma and extracellular environment. Type XV collagen (COLXV) is found in basement membrane zones where it assumes a pretzel-like structure but unlike the majority of fibrillar collagens does not form tight lattice networks surrounding the cell. Loss of COLXV during progression of aggressive cancers (including breast, pancreas, and ovarian carcinomas and melanomas) precedes basement membrane invasion and metastasis. Moreover, the loss of COLXV from the distal side of basement membrane zones and the resulting deficit in its interactions with other proteins may determine its specific function in tumor progression and eventual metastasis. In this context we have identified critical collagen-binding cell surface receptors on the tumor cell, which interact with COLXV and appear to mediate its functions. These receptors have also been reported to show altered signaling in cancer. We previously showed that over-expression of COLXV in cervical cancer cells alters the growth properties of these cells both in vitro and in vivo, and showed that type XV collagen is a dose-dependent suppressor of tumorigenicity in vivo. We now show that over-expression of COLXV inhibits epithelial to mesenchymal transition (EMT) in vitro and has a dramatic effect on the associated signaling events. We are now further investigating the mechanisms of tumor/stroma crosstalk that are impacted by COLXV and subsequently by its depletion.

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 5174. doi:1538-7445.AM2012-5174
Abstract 5268: Standardized and validated ATCC breast cancer panels: A tool for the rapid validation of biological hypotheses.
Authors: Zhang Chengkang (CK) , Elias-Bachrach Michal , Challberg Sherry , Bettoun David
Published: August 2012

Advances in personalized medicine rely on knowledge of validated markers that predict response to treatment. The availability of such information could significantly impact preclinical drug optimization and reduce the cost of clinical trials. Conversely, improving drug efficacy based on clinical data requires performing studies in defined biological systems. These defined systems typically are clonal cell lines, which have been key in advancing our understanding of numerous disease states, including cancer. A number of recent comprehensive studies have demonstrated that individual cell lines are restricted along discreet lineages and therefore do not recapitulate tumor heterogeneity observed in patients However, the use of a combination of such cell lines reflected the clinical diversity observed in patient. (Neve et al, 2006; Kao J et al, 2006; Keller PJ et al 2010). We postulated that the use of carefully characterized cell lines combined into biologically relevant panels might provide valuable insights into studies on target validation, lead optimization, mechanisms of action and evaluation of efficacy in various patient subgroups. The lack of uniform culture conditions among various tumor cell lines hampers the design and conduct of experiments using such cell line panels and complicates the interpretation of the results obtained from them. We therefore undertook to combine panels of breast cancer cell lines that represented major clinical manifestations of the disease and culture them under standardized conditions. We were able to establish culture conditions that maintained the expression of mRNA and cell surface proteins for validated therapeutic and clinical markers. Using a small collection of clinically validated and investigational compounds we provide several example about how carefully selected and characterized cell panels can be used to carry out pharmacology studies and address questions pertinent to tumor biology and anti-cancer drug development.

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 5268. doi:1538-7445.AM2012-5268
Abstract 5277: MMP-2 suppression abrogates irradiation-induced microtubule formation in endothelial cells by inhibiting αvβ3-mediated SDF-1/CXCR4 signaling
Authors: Maddirela Dilip , Kesanakurti Divya , Chetty Chandramu , Dinh Dzung H. , Rao Jasti S.
Published: August 2012

The majority of glioblastoma multiforme (GBM) tumors recur after the radiation (IR) treatment by increasing angiogenesis and IR-induced signaling events in endothelial cells that are involved in tumor neovascularization; these signaling events have yet to be well characterized. We observed that IR (8 Gy) significantly elevated MMP-2 expression and gelatinolytic activity in 4910 and 5310 human GBM xenograft cells. In addition, endothelial cells treated with tumor conditioned media (CM) obtained from IR-treated 4910 and 5310 cells showed increased microtubule formation. Thus, we investigated the possible anti-angiogenic effects of MMP-2 downregulation using siRNA (pMMP-2.si) in IR-treated cells and further determined the effect of CM obtained from mock, pSV (scrambled vector) and pMMP-2.si on endothelial cell growth and vessel formation. pMMP-2.si-CM-treated endothelial cells showed inhibited IR-CM-induced αvβ3, SDF-1, CXCR4, phospho-PI3K and phospho-AKT expression levels. In vitro angiogenesis assay showed that the pMMP-2.si+IR decreased the IR-induced vessel formation in endothelial cells. Immunofluorescence and immunoprecipitation experiments indicated the abrogation of αvβ3-SDF1 interaction in pMMP-2.si-CM-treated endothelial cells when compared to mock or pSV treatments. External supplementation of either rhMMP-2 or rhSDF-1 counteracted and noticeably reversed the pMMP-2.si-inhibited SDF-1, CXCR4, phospho-PI3K and phospho-AKT expression levels and angiogenesis, thereby confirming the role of MMP-2 in the regulation of αvβ3-mediated SDF-1/CXCR4 signaling. In corroboration with the in vitro results, the in vivo mouse dorsal air sac model also showed reduced angiogenesis with the injection of pMMP-2.si-treated xenograft cells whereas injection of mock or pSV-treated cells resulted in robust formation of characteristic neovascularization. Collectively, our data indicate the role of MMP-2 in the regulation of SDF-1/CXCR4 signaling-mediated angiogenesis in endothelial cells and demonstrates the anti-angiogenic efficacy of combining MMP-2 downregulation and IR when treating GBM in the future.

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 5277. doi:1538-7445.AM2012-5277
Abstract 5278: Suppression of angiogenic potential of breast cancer by the inhibition of SAF-1 transcription factor activity
Authors: Ray Alpana , Dhar Srijita , Ray Bimal K.
Published: August 2012

Angiogenesis plays an important role in the tumor growth and metastasis by facilitating increased blood supply and thus fueling unwanted growth factors and nutrients to the growing tumor. Vascular endothelial growth factor (VEGF) is recognized as a multifunctional angiogenic stimulator that stimulates blood vessel formation and endothelial cell survival. Recent therapeutic trials with anti-VEGF antibody bevacizumab (Avastin), although produced beneficial effects on some cancers including colorectal and lung cancers, had very limited beneficial outcome in breast cancer. The diverse response of avastin raised questions about the efficacy of anti-VEGF antibody approach for breast cancer therapy. Despite the disappointing outcome, it cannot be ignored that regulation of angiogenesis plays a critical role in breast cancer. We hypothesized that angiogenesis may be better controlled by blocking the synthesis of VEGF protein as opposed to the present approach that attempts to block the functions of VEGF by using antibodies. Induction of VEGF by a plethora of physiological and environmental stimuli strongly suggests the presence of multiple routes of VEGF synthesis, which are incompletely understood. We present evidence for a novel mode of transcriptional induction of VEGF, regulated by an inflammation-responsive transcription factor, SAF-1. Incidentally, inflammatory breast cancer exhibits increased angiogenesis and has a higher metastatic potential than noninflammatory breast cancer, supporting the notion that chronic inflammation plays a strong role in angiogenesis and in the progression of cancer. SAF-1 is present in high abundance in human breast cancer tissues. We show that inhibition of endogenous SAF-1 by antisense shRNA can markedly inhibit VEGF expression and block cancer cell-supported vascular endothelial cell function and angiogenesis. Furthermore, SAF-1 inhibition by shRNA reduces tumor growth in mouse tumor model. We provide evidence that SAF-1-mediated induction of VEGF remains suppressed by KLF-4 transcription factor which is abundantly present in normal breast epithelial cells but absent in breast cancer cells. Mutually exclusive interaction of KLF-4 and SAF-1 at the VEGF promoter provides a mechanism for regulation of low-expression of VEGF in normal breast tissues. In correlation, lack of KLF-4 in breast cancer cells appears to be linked to un-restricted interaction of SAF-1 leading to the induction of VEGF expression. Together, our studies provide a new insight into the molecular mechanisms of VEGF expression regulated by SAF-1 and its impact in angiogenesis.

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 5278. doi:1538-7445.AM2012-5278
Abstract 5284: EMMPRIN mediates VEGF activation of VEGFR-2 in melanoma cells
Authors: Khayati Farah , Mourah Samia
Published: August 2012

EMMPRIN's expression in melanoma tissue was reported to be predictive of poor prognosis. Here we demonstrate that EMMPRIN up-regulated VEGF receptor-2 (VEGFR-2) in two different primary melanoma cell lines and consequently increased migration and proliferation of these cells while inhibiting their apoptosis. SiRNA inhibition of VEGFR-2 expression abrogated these EMMPRIN effects. EMMPRIN regulation of VEGFR-2 was mediated through the over-expression of HIF-2α and its translocation to the nucleus where it forms heterodimers with HIF-1β. These results were supported by an in vivo correlation between the expression of EMMPRIN with that of VEGFR-2 in human melanoma tissues as well as with the extent of HIF-2α localization in the nucleus. They demonstrate a novel mechanism by which EMMPRIN promotes tumor progression through HIF-2α/VEGFR-2 mediated mechanism, with an autocrine role in melanoma cell malignancy. As VEGF/VEGFR2 system has been implicated in regulation of melanoma cells migration, proliferation and apoptosis, the role of EMMPRIN in the regulation of these cellular properties was investigated. Blocking EMMPRIN by siRNA have shown that VEGF enhancement of melanoma cell migration requires EMMPRIN. The inhibition of EMMPRIN in cancer may thus simultaneously target both the VEGFR-2/VEGF system and the matrix degrading proteases to block tumor cell growth and invasion.

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 5284. doi:1538-7445.AM2012-5284
Abstract 529: Impaired NF-κB signaling in myeloid cells enhances urethane-induced lung carcinogenesis
Authors: McLoed Allyson G. , Zaynagetdinov Rinat , Sherrill Taylor , Yull Fiona E. , Blackwell Timothy S.
Published: August 2012

Nuclear Factor κB (NF-κB) regulates airway inflammation and has been implicated in lung tumorigenesis. We and others have previously described a pro-tumorigenic role for NF-κB activity in airway epithelial cells. However, the role of NF-κB signaling in other cell types, including myeloid cells, in modulation of lung tumorigenesis is unknown. The goal of these studies is to determine the role of myeloid cell-specific NF-κB in lung tumorigenesis. In mice with myeloid cell-targeted IKKβ deletion (IKKβΔmye mice), we observed increased inflammatory mediator expression at 1 week after intraperitoneal injection of urethane (1 μg/g). At 6 weeks post-urethane injection, lungs of IKKβΔmye mice exhibited an increased atypical adenomatous hyperplastic lesion burden, which was accompanied by an increased inflammatory cell influx into the lungs of IKKβΔmye mice compared to wild-type (WT) controls. No difference in total macrophages or the proportion of M2 polarized macrophages in whole lungs was observed by flow cytometry at 6 weeks post-urethane; however, the proportion of CD11b+Gr1hi cells was increased in IKKβΔmye mice. At 4 months after urethane injection, we found an increase in lung tumor numbers (5.6±0.6 in WT, 10.0±1.5 in IKKβΔmye) and a trend towards decreased tumor size in IKKβΔmye mice compared to WT controls. IKKβΔmye mice contained significantly higher numbers of neutrophils in bronchoalveolar lavage at this time point compared to WT controls. In addition, lungs of IKKβΔmye mice exhibited more CD11b+Gr1hi cells in whole lungs as measured by flow cytometry. Our data indicate that inhibition of NF-κB signaling in myeloid cells results in a paradoxical increase in lung inflammation accompanied by enhanced urethane-induced lung tumorigenesis. We conclude that the impact of NF-κB signaling on lung tumorigenesis is cell type specific and that NF-κB activation in myeloid cells functions to limit urethane-induced inflammation and reduce tumor formation in the lungs.

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 529. doi:1538-7445.AM2012-529
Abstract 5294: Increased angiogenesis resulting from TIMP-1 inhibition of TSP-1 is mediated by PI3kinase and FAK interactions
Authors: Ohja Juhi , Gayatri Sitaram , Nalluri Srilatha , Rojiani Amyn M. , Rojiani Mumtaz V.
Published: August 2012

Tissue Inhibitor of Matrix Metalloprotease -1 (TIMP-1), one of the four natural inhibitors of matrix metalloproteinases was initially identified for its Erythroid Potentiating Activity. Since then, it has been shown to independently induce cell proliferation and inhibit apoptosis in a number of cell types. TIMP-1 has also been shown to promote, but also more often to inhibit angiogenesis. Previously, we have shown that TIMP-1 overexpression in a lung adenocarcinoma cell line (H2009) resulted in more aggressive and vascular tumors in nude mice and increased capillary network formation and tumorigenicity in vitro. An angiogenesis pathway-specific gene array had identified a 3-fold reduction in thrombospondin 1 (TSP-1) levels in the TIMP-1 overexpressing clone HB-1. TSP-1 siRNA clone exhibited a similar increase in in vitro angiogenesis assays. In the present study, we have sought to identify the signaling pathway involved whereby TIMP-1 inhibits TSP-1. To this end, we have used specific inhibitors to inhibit TIMP1 initiated signaling pathways. MAP kinase, PI3/Akt inhibitors were used, either singly or in combination with Focal Adhesion kinase (FAK) inhibitor. Our results indicate a synergistic interaction between PI3/Akt pathway and FAK signaling, which restores TSP-1 levels by approximately 3-fold relative to control. Gelatin zymography of serum-free conditioned media (SFCM) revealed a reduction in proMMP-9 level in the HB-1 clone versus H2009. Additionally MMP9 specific ELISA reveals a two-fold reduction in MMP9 levels. This is in tune with the role of TSP-1 as an inhibitor of MMP-9 activation such that decreased TSP-1 level results in increased activation of MMP-9 with a concomitant reduction in the extracellular level of proMMP-9. Thus our findings define interaction of TIMP-1 via PI3kinase and FAK signaling. resulting in TSP-1 decrease and subsequent downstream promotion of angiogenesis with increased tumor kinetics.

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 5294. doi:1538-7445.AM2012-5294