bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3061: Somatic mutation profiling to tumor samples using OncoCarta Panel
Authors: Furuta Kazuyuki , Arao Tokuzo , Yanagihara Kazuyoshi , Sekijima Masaru , Nishio Kazuto
Published: June 2012

Clinical decision-making based on tumor genetic information have emerged as a key approach for targeted-based drugs in cancer therapy. New diagnostic approach is needed to profile for pivotal genetic mutations in multiple oncogenes simultaneously. In this study, we evaluated the validity and sensitivity of high-throughput mutation profiling approach, ‘OncoCarta Panel’, in cancer marker evaluation research. It enables us to simultaneously detect 238 mutations across 19 key oncogenes including ABL1, AKT1, AKT2, BRAF, CDK, EGFR, ERBB2, FGFR1, FGFR3, FLT3, HRAS, JAK2, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA and RET. We analyzed the somatic mutations using the OncoCarta Panel on 44 cancer cell lines and 41 clinical tumor samples. The 57% (n=25) of cancer cell lines contained one or more mutations among 44 cancer cell lines; EGFR (5/44), KRAS (13/44), BRAF (4/44), PIK3CA (3/44) and NRAS (3/44) mutations in lung, colorectal, gastric, liver and pancreatic cancer cell lines. Some samples exhibited co-occurring oncogene mutations which might modify the clinical response. In addition, this analysis was also able to perform for DNA isolated from formalin-fixed, paraffin-embedded samples. The obtained data were in concordance with the data from Sanger sequencing and Scorpions-ARMS PCR methods. The mutation was detectable even when the mutated DNA represented only 10% of the total DNA, and this was approximately 2.5-fold more sensitive than Sanger Sequencing. We conclude that the OncoCarta Panel is more rapid, sensitive and cost-effective method for mutation profiling than the commonly used Sanger sequencing.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3061. doi:10.1158/1538-7445.AM2011-3061
Abstract 3073: Isothermal whole genome amplification of FFPE samples to detect copy number changes in the progression from colonic adenoma to carcinoma
Authors: Hirsch Daniela , Stapleton Mark , Ried Thomas , Camps Jordi , Gaiser Timo
Published: June 2012

Screening tumor genomes for somatic aberrations by aCGH is a commonly used high-resolution tool used both in research and clinical diagnostics. Unfortunately, the full utility of this technique is compromised with formalin fixed paraffin embedded (FFPE) tissue samples due to their inherently high degree of DNA degradation and the presence of DNA adducts acquired during the fixation and storage process. DNA degradation tends to worsen with storage time, making the analysis of archived samples even more challenging. We have developed a highly sensitive and robust whole genome amplification system for FFPE tumor samples that takes advantage of the proprietary Single Primer Isothermal Amplification (SPIA®) technology. The system uses 100 ng of routinely isolated FFPE DNA and produces 3-5 µg of DNA suitable for multiple downstream applications such as aCGH, enrichment strategies, and next generation sequencing (NGS). We evaluated the performance of the amplification system in the context of identifying aberrations by aCGH. Data will be presented that highlights the performance of the SPIA amplified material benchmarked against its unamplified counterpart along with the system's effectiveness on an array of sample qualities ranging from highly degraded FFPE DNA to highly intact FFPE DNA samples. Lastly, we employed the amplification system to examine the progression from adenoma to carcinoma using FFPE samples from human colon carcinomas within high-grade adenomas. Colonic epithelia gains numerous genetic alterations when degraded to dysplastic adenoma and then to cancer. While genetic alterations for each entity are well known, little data are available for combined lesions. Our results indicate that the SPIA amplified DNA performs equivalently to unamplified FFPE DNA in detecting copy number variations by aCGH, the system is suitable for a broad range of FFPE sample qualities, and is a flexible solution that allows for higher resolution analyses with NGS platforms.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3073. doi:10.1158/1538-7445.AM2011-3073
Abstract 3088: Regulation of tight junction protein claudin 1 mRNA expression by AU-rich element-binding (ELAV) proteins in colon cancer
Authors: Sharma Ashok , Singh Amar B. , Dhawan Punita
Published: June 2012

Tight junction associated proteins are key molecular components governing cellular adhesion, polarity and play critical roles in cellular proliferation via their functions as couplers of the extracellular milieu to intracellular signaling pathways. Claudin-1, a tight junction protein, expression is dysregulated in the majority of human colorectal carcinomas. We have previously reported that claudin-1 is regulated at post-transcriptional levels on treatment with HDAC inhibitor, TSA and its mRNA stability is modulated by 3’-UTR as the major mechanism underlying HDAC-dependent claudin-1 expression. It has putative AU-rich (ARE) cis-elements in its long 3’UTR (∼ 2.3Kb). Presence of a long 3’UTR is frequently indicative of post-translational regulation of gene expression via modulation of mRNA stability.

ELAV like RNA-binding proteins Hu antigen R (HuR) and tristetraprolin (TTP) associate with labile mRNAs bearing AU-rich elements located in the 3’ untranslated regions (3′-UTRs) and modulate their stability. We have identified putative AU rich elements in the proximal region of the claudin 1 3’-UTR and demonstrate that HuR interacts with these AU-rich elements. We further show a role of HuR and TTP during colon tumorigenesis and their ability to regulate Claudin-1 mRNA expression in presence TSA. We found that Claudin-1 mRNA was stabilized by HUR in both SW480 and SW620 cells, whereas its overexpression decreased the expression of TTP; We used a ribonomic approach to test the binding of HuR and TTP to claudin 1 3’UTR and their role in stabilization/destabilization of claudin-1 mRNA in the presence of TSA. On treatment with TSA the binding of HuR to claudin-1 3’UTR decreases while the binding of TTP increases correlating well with the rapid decay of claudin-1 mRNA in presence of TSA. Thus, our data suggest that claudin 1 is regulated via mRNA stability and a novel regulatory feedback loop between HuR and TTP in colon tumorigenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3088. doi:10.1158/1538-7445.AM2011-3088
Abstract 3118: Regulation of SDF-1 (CXCL12) production by mesenchymal stromal cells
Authors: Amiri Sohrab
Published: June 2012

The tumor microenvironment is made up of a number of cell types including neoplastic epithelial cells, myofibroblasts, smooth muscle cells, pericytes, adipocytes, endothelial cells and their precursors, fibroblasts and immune cells. The interaction between cellular components of the microenvironment is critical for processes such as tumor progression, growth, angiogenesis, and metastasis. Mesenchymal stromal cells (MSCs) are an important component of the tumor microenvironment with roles in key aspects of tumor development such as cell growth and metastasis. Stromal-derived factor -1 (SDF-1) has been identified as a key-signaling molecule in the interaction between MSCs and neoplastic cells. SDF-1 acting through its cognate receptors CXCR4 and CXCR7 is known to mediate diverse processes such as chemotaxis, angiogenesis, hematopoiesis, metastasis, and tumor growth. In this study, we investigated the regulation of SDF-1 production by MSCs.

We show that the tumor suppressor p53 is an important regulator of SDF-1 signaling in MSCs within the tumor stroma. A decrease in p53 function leads to increased SDF-1 production by MSCs and increased migration of MSCs in response to tumor cells. An improved understanding of the molecular mechanisms controlling SDF-1 production by MSCs may identify novel ways to therapeutically target tumor – stromal interactions.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3118. doi:10.1158/1538-7445.AM2011-3118
Abstract 3136: c-Kit / CD117 is a predictive prognostic marker for patients with basal-like breast cancer
Authors: Kashiwagi Shinichiro , Yashiro Masakazu , Takashima Tsutomu , Aomatsu Naoki , Kawajiri Hidemi , Tanaka Hiroaki , Onoda Naoyoshi , Nakata Bunzo , Ishikawa Tetsuro , Hirakawa Kosei
Published: June 2012

Purpose: The mortality of breast carcinoma is decreasing because of recent developments in diagnostic techniques and therapies; however, the mortality of the basal-like breast cancer (BLBC) remains poor. BLBC a poorly characterized subtype of tumor with no validated clinical assay to identify them. In breast cancer, although there were some reports of survival analysis regarding c-Kit expression, the significance of c-Kit expression is controversial. In addition, little is known about the c-Kit expression levels of BLBC. The aim of this study is to clarify the correlation between c-Kit and BLBC.

Experimental Design: A total of 667 patients who had undergone resection of a primary breast cancer at our institute were enrolled. ER, PR, HER2, EGFR, CK5/6 and c-Kit expression were assessed by immunohistochemistry. We examined the association between BLBC and other clinicopathologic variables, and evaluated the significance of c-Kit expression.

Results: Of informative 667 breast cancer cases, basal-like phonotype was 149 (78.4%) of 190 cases of triple-negative phenotype. c-Kit expression was found in 111 patients (16.6%), and it was significantly many results in BLBC (42/149, 28.2%) (p<0.001). The c-Kit positive patients experienced significantly poorer outcomes in terms of overall survival (p<0.001). In 149 patients with BLBC, a statistically significant difference was observed between c-Kit positive and negative in regard to the degree of high age (p=0.037), lymph node metastasis (p=0.008) and lymphatic invasion (p=0.017). In BLBC, cases with c-Kit expression showed a poor overall survival time (p<0.001), and disease-free interval period (p<0.001), and it was an independent indicator of a poor prognosis by multivariate analyses (p=0.024, OR=2.291).

Conclusions: c-Kit is one of predictive prognostic marker and molecular targets in BLBC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3136. doi:10.1158/1538-7445.AM2011-3136
Abstract 315: Human metabotropic glutamate receptor 1 (GRM1) may be essential for melanoma cell survival and activation of angiogenic signaling
Authors: Wen Yu , Li Jiadong , Shin Seung-Shick , Chen Suzie , Goydos James
Published: June 2012

Our group has demonstrated that ectopic expression of murine GRM1 results in transformation of mouse melanocyte cells, and we have found that human GRM1 is ectopically expressed in more than 60% human melanomas. We recently reported on the results of a Phase 0 preclinical trial targeting GRM1 signaling using a glutamate release-inhibitor, Riluzole. We demonstrated inhibition of signaling through the PI3K/AKT and MAPK pathways and a reduction in tumor size in 40% of patients treated. To better examine the mechanisms of Riluzole treatment effect and to begin to understand the function of GRM1 signal transduction in melanoma, cell lines that over-express GRM1 (UACC903 G2 and UACC903G4) were constructed using the native, low GRM1-expressing, UACC903 human melanoma cell line. We found that UACC903G2 and G4 cells produce elevated levels of GRM1 and were much more sensitive to treatment with 25uM Riluzole than the vector transfected control cell line UACC903V1. We also found that UACC903G2 and G4 cells produced much larger tumors in nude mice than the vector control cells. Tumors formed by UACC903G2 and G4 xenografts also do not demonstrate areas of hemorrhage necrosis as is found in UACC903V1 xenografts, and there are significantly more tumor blood vessels in the GRM1-overexpressing xenograft tumors. To confirm the angiogenic effect of GRM1 over-expression in UACC903 cells, an endothelial cell migration assay was performed. We found that culturing UACC903G2 and G4 cells in serum-free basic medium stimulated HMVECnd endothelial cell migration, an effect not seen with the vector control UACC903V1 cells. We next examined whether increased GRM1 expression in UACC903 cells resulted in the release of angiogenesis factor(s) from these cells. An angiogenesis antibody array (from Affymetrix) experiment was performed and we found that the conditioned medium from UACC903G2 and G4 cells had significantly higher levels of IL8 and VEGF (angiogenesis promoters), but decreased level of TIMP-2 and TIMP-1 (angiogenesis inhibitors) as compared to the conditioned medium from the UACC903V1 vector control cells. We conclude that over-expression of human GRM1 promotes proliferation, activates angiogenesis signaling, and renders cells more susceptible to the inhibitory effects of the glutamate-release inhibitor Riluzole. Further experiments examining the molecular mechanism of GRM1 in cell survival and angiogenesis are need to better understand the mechanisms at work.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 315. doi:10.1158/1538-7445.AM2011-315
Abstract 3166: Lung cancer bio-signatures in plasma based on the analysis of mouse models
Authors: Taguchi Ayumu , Politi Katerina , Pitteri Sharon J. , Lockwood William W. , Faça Vitor M. , Sage Julien , Kemp Christopher J. , Varmus Harold E. , Hanash Samir M.
Published: June 2012

Genetically engineered mouse models of cancer have been shown to recapitulate many of the molecular and biological features of human cancer. To identify plasma proteins that show altered abundance during lung cancer development, we applied in-depth quantitative proteomic analysis to plasma from three mouse models of lung adenocarcinoma driven by mutant EGFR, Kras or induced by urethane exposure; a mouse model of small cell lung cancer (SCLC); models of pancreatic, ovarian, colon, prostate and breast cancer; and two mouse models of inflammatory disease as confounders. Plasma proteins from mice with disease and age-matched littermate controls were analyzed by mass spectrometry (MS). Whole cell lysates and conditioned media from 12 lung adenocarcinoma cell lines were also analyzed by MS to identify enriched proteins in conditioned media in common with proteins with increased levels in plasmas from lung tumor bearing mice.

Proteins corresponding to 3744 non-redundant IPIs (International Protein Index) that represented protein products from 2260 unique genes were quantified in one or more experiments. Unsupervised hierarchical clustering of plasma proteins revealed clustering of the four lung cancer models and the two breast cancer models, suggesting that protein signatures in the blood are organ-type specific. Fifty-eight percent of the elevated proteins in plasmas from mice with lung adenocarcinoma were identified in conditioned media of one or more human lung cell lines. A biosignature based on plasma proteins regulated by the Titf1/Nkx2-1 transcription factor was identified in plasmas from mouse models of lung adenocarcinoma. In addition, protein network analysis showed that many proteins whose abundance is altered in the plasma of the lung cancer mouse model engineered to express mutant human EGFR are associated with EGFR. A plasma protein signature that is enriched in proteins associated with neuroendocrine development was also identified in a SCLC model. Exploratory studies in human lung cancer and control plasmas of candidate markers identified in mouse models yielded altered levels in lung cancer plasmas concordant with findings in mouse models.

Our studies of mouse models have identified plasma based signature for lung cancer that reflect developmental and signaling pathways applicable to human lung cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3166. doi:10.1158/1538-7445.AM2011-3166
Abstract 317: 1q32.1 and 16q21 genomic alterations implicate KIF14/MDM4/PIK3C2ß and CDH11 as independent prognostic markers of relapse in localized Ewing Family of Tumors
Authors: Ayala Fernanda R.R , da Cunha Isabela Werneck , Yoshimoto Maisa , Zielenska Maria , Squire Jeremy Andrew , Soares Fernando Augusto
Published: June 2012

EWS-ETS genetic fusion appears to be the initiating mechanism behind Ewing Family of Tumors (EFT) pathogenesis; however, progression of the disease is dependent on additional genetic alterations. Using the Progenetix database, we identified mainly alterations at 1q, and at 16q, as the most recurrent genetic alterations in EFT without consistency as markers of relapse. Clinic features of a large genotype cohort of 135 patients with EFT were retrospectively reviewed from A.C. Camargo hospital records. Tissue microarrays (TMA) were built for multi-color interphase fluorescent in situ hybridization (iFISH) analysis of aberrations at 1q32.1 (KIF14/MDM4/PIK3C2ß) and 16q21 (CDH11) using in-house probes. Gains were defined by the presence of more than three hybridization signals per interphase nucleus with simultaneous intact centrosome signal occurring in more than 5% of tumor nuclei. Losses were indicated by one target signal with the intact centrosome signals in more than 30% of nuclei. The frequencies of gene copy number alterations (CNA) were compared with clinical parameters and follow-ups. Statistical analyses were performed by SPSS program. A p-value of less than 0.05 was considered significant.

CNA analysis showed gains at 1q32.1 in 15/128 (11.7%) cases, while abnormalities at 16q21 were seen in 24/118 (20.3%) patients, split into two groups. One group of patients, 11/118 (9.3%), showed only hemizygous deletion, whereas, the other group with 13/118 (11%) patients showed gain. A significant association between 1q32.1 gains and 16q21 losses (p=0.029) was detected, but not a significant clinical synergism when interacting at the same patient. Univariate analyses showed gains at 16q21 (p=0.029) or at 1q32.1 (p=0.005) associated with tumor relapse in the localized disease subgroup. Disease-free survival curves represented these gained regions as unfavorable outcome parameters (p<0.05) for EFT patients. The multivariate model confirmed 1q32.1 or 16q21 gains as independent prognostic markers for relapse. Hence, copy number gains at 1q32.1 and 16q21 constitute valuable markers of relapse in localized EFT. Genomic alterations of the critical genes in these chromosomal regions probably activate key downstream target genes of distinct pathways, which thus lead to an intricate molecular mechanism for EFT growth and aggressiveness.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 317. doi:10.1158/1538-7445.AM2011-317
Abstract 3171: Stromal palladin is a poor prognostic marker in renal cell carcinoma
Authors: Gupta Vivekanand , Simons Jeffrey , Bassi Daniel , Al-Saleem Tahseen I. , Uzzo Robert G. , Cukierman Edna
Published: June 2012

Renal cell carcinoma (RCC) is a fatal disease in urgent need of novel diagnostic and treatment tools. Metastasis to the secondary site is the main cause of death in RCC. Although renal tumor cells are intercalated within a mesenchymal stromal microenvironment during RCC tumorigenesis, not much is known about this specific stroma. Therefore, questioning the specific importance of RCC's stroma is of noteworthy interest. In this study we questioned whether stromal and tumor components progress at similar rates and whether assessing rates of stromal progression are of clinical importance. Our experimental system uses fibroblasts harvested from patient matched normal kidney, as well as primary and secondary RCC surgical samples. We tested several stromal markers such as actin binding protein palladin, alpha-smooth muscle actin and fibronectin spliced form EDA, all known to be upregulated in tumor associated stroma, and uncovered that their expression levels depend on the production of stromal extracellular matrices (ECMs) using an in vitro 3-D stromal system derived from the harvested fibroblasts. In addition, using a well annotated tumor micro array, we specifically demonstrate that stromal palladin and α-SMA expression levels correlate to each other. Moreover, we observed that stromal palladin expression levels are indicative of poor outcomes in early non-metastatic RCCs. Here we not only introduce an in vitro 3-D stroma system which accurately mimics the in vivo features of human RCC-associated stroma, but we demonstrate a clinical relevance to assessing stromal activation in human pathological RCC samples. Results from this study underscore a distinctive clinical relevance to assessing stromal progression in renal cell carcinomas.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3171. doi:10.1158/1538-7445.AM2011-3171
Abstract 3172: Methylation portraits discriminate between hepatocellular carcinoma cases and controls
Authors: Guerrero-Preston Rafael , Soudry Ethan , Jaffe Andrew , Ili-Gangas Carmen , Brebi-Mieville Priscilla , Pérez Jimena , Zhong Xiaoli , Yang Quiang , Meltzer Stephen J. , Esteller Manel , Sidransky David
Published: June 2012

Background: Most genome-wide methylation studies have focused on technology to profile and identify therapeutic biomarkers in HCC. However, attempts to integrate these technologies to clinical and population based studies are still lacking.

Objective: Our aim was to identify existing methylation profiling technologies that can be used in translational epigenomic efforts.

Methods: We examined Quantitative Methylation specific PCR, oligonucleotide methylation tiling arrays (MeDIP-chip), and Methylation BeadChip arrays and their ability to distinguish between HHC cases and controls, a key goal in Phase I biomarker development trials. Scatterplots, histograms and heat maps of genome-wide DNA methylation array data were used to provide a snapshot of the differences in methylation patterns between tumor and normal samples.

Results: The representative tumor sample had a lower methylation score median and less significant genome-wide methylated probes (1,503) than either normal liver tissue samples (2,585 and 2,2887 respectively). RASSF1A and B4GALT1 had a sensitivity of 52%, a specificity of 100% and an AUC of 0.73 (RASSF1A) and 0.75 (B4GALT1). SSBP2 had a sensitivity of 38%, a specificity of 100% and an AUC of 0.58. A panel combining these genes with HCC risk factors had a sensitivity of 87%, a specificity of 100% and an AUC of 0.91.

Conclusions: We have shown that genome-wide and gene-specific methylation platforms, which interrogate gene promoter regions, can be used to examine novel biomarkers and differentiate HCC from normal liver tissue. Additional studies will confirm the value of using methylation-profiling technologies to evaluate these new markers as we move forward.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3172. doi:10.1158/1538-7445.AM2011-3172
Abstract 3194: Thymidine Kinase 1 staining aids in lung cancer prognosis
Authors: Alegre Melissa M. , Abegg-Lawrence Taylor , Alegre Ballantines F. , LaPorte Wesley D. , Yu Jessica , Weyant Michael , Robison Richard A. , O'Neill Kim L.
Published: June 2012

Lung cancer kills more patients than breast, colon, prostate, melanoma, and kidney cancers combined. One way to improve the high lung cancer mortality rate is through early detection and better prognosis. There have been attempts to establish spiral CT scan imaging protocols or early detection assays to improve the diagnosis of lung cancer. Although these detection methods show merit, they are often costly, and are only useful for a subset of the potential lung cancer population such as high-risk smokers. One biomarker that shows promise is Thymidine Kinase 1 (TK1). Recently, it has been demonstrated that TK1 has diagnostic potential in both small cell and non-small cell lung cancer. Therefore, the present study was conducted to elucidate whether TK1 could be used in early detection and lung cancer prognosis. Five tissue microarrays (TMA) including a lung carcinoma screen, lung adenocarcinoma grade III, large cell carcinoma, small cell carcinoma, and one normal lung TMA consisting of 376 lung cancer tissue cores from 172 patients and 63 control lung tissue cores from 22 normal individuals, were stained with a TK1 monoclonal antibody produced by our lab. Mesothelioma and some of the lung cancers including squamous cell, small cell, adenosquamous cell, undifferentiated, adenocarcinoma, and bronchioloalveolar carcinoma stained positive for TK1. Papillary carcinoma, sarcoma, neuroendrocrine carcinoma, and undifferentiated large cell carcinoma showed considerably less TK1 staining. Normal and inflammatory lung tissue showed zero to minimal staining which was significantly different from positively stained lung cancer tissue. There are various increasing grades of squamous cell carcinoma patients from grade I, I-II, II, II-III and III. There was a definitive increase in TK1 staining as the grade of the lung tumor increase. A similar pattern was found with adenocarcinoma tissue grade II, II-III, and III; the more progressive the tumor, the more intense the TK1 staining. This preliminary data supports further investigation of TK1 as a marker for early detection and prognosis of numerous lung cancer subtypes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3194. doi:10.1158/1538-7445.AM2011-3194
Abstract 3195: HMGA1 and HMGA2 over-expression in human lung carcinoma
Authors: Piscuoglio Salvatore , Pallante Pierlorenzo , Cappuzzo Federico , Zlobec Inti , Lugli Alessandro , Fusco Alfredo , Terracciano Luigi M.
Published: June 2012

Background: Lung cancer is the leading cause of cancer death worldwide with an overall 5-year survival rate of only 15%. Therefore, research focusing on lung carcinogenesis is strongly needed. High mobility group A (HMGA) proteins play an important role in the regulation of transcription, differentiation, and neoplastic transformation. The HMGA gene family includes HMGA1, which encodes the HMGA1a and HMGA1b protein isoforms, and HMGA2, which encodes HMGA2. These chromatin-binding proteins function in transcriptional regulation and recent studies also suggest a role in cellular senescence. HMGA1 proteins also appear to participate in cell cycle regulation and malignant transformation, whereas HMGA2 has been implicated primarily in the pathogenesis of benign mesenchymal tumors.

Aims: The aim of this study was to investigate on the potential role of HMGA 1 and 2 in lung carcinogenesis.

Materials and methods: A tissue microarray (TMA) including normal and neoplastic non-small cell lung cancer (NSCLC; n=454) tissues was constructed and HMGA1 and 2 analyzed by immunohistochemistry. HMGA1 was detectable in a 454 patients and HMGA2 in 409 patients, respectively. Immunoreactivity was scored semi-quantitatively by evaluating the number of positive tumor cells over the total number of tumor cells. Scores were assigned using 5% intervals and ranged from 0% to 100%. Median protein expression levels were used as cut-off scores to define protein marker positivity and the findings were associated with clinical-pathological parameters.

Results: HMGA1 and A2 are over-expressed in NSCLC tissues compared to normal lung (p<0,001), and more specifically, the HMGA2 expression is significant higher in non-adenocarcinomas than in adenocarcinomas (p<0,001. A significant relationship between HMGA2 over-expression and tumor grade (p<0,013), cN stage (p<0,037), cM stage (p<0,002), pT stage (p<0,003), pM stage (p<0,002), and recurrence (p<0,002). Additionally, HMGA1 over-expression showed a significant relationship with gender (p<0,003), tumor grade (p<0,028), pT stage (p<0,006) and recurrence (p<0,002).

Conclusion: HMGA1 and A2 over-expression seems to play an important role in lung carcinogenesis and additional studies are needed to demonstrate a potential prognostic impact of HMGA1 and HMGA2 expression in NSCLC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3195. doi:10.1158/1538-7445.AM2011-3195
Abstract 3208: Impact of targeted therapy on circulating tumor cells in metastatic breast cancer treated by first-line chemotherapy: IC 2006-04 study
Authors: Pierga Jean-Yves , Hajage David , Bachelot Thomas , Delaloge Suzette , Brain Etienne , Campone Mario , Asselain Bernard , Mathiot Claire , Bidard François-Clément
Published: June 2012

Circulating tumor cells (CTC) have been reported to be a prognostic marker in metastatic breast cancer. This study was designed to test whether changes in CTC counts during treatment are associated with outcome of first-line chemotherapy with/without targeted therapy.

Methods: CTC were counted (CellSearch®) at baseline, before cycle 2 (C2) and C3/4 in 267 metastatic breast cancer patients. Usual prognostic variables, serum tumor markers, tumor response according to RECIST criteria and events were prospectively registered and compared with CTC status and outcome over time.

Results: Median follow-up was 16 months, 45 patients (17%) had HER2 positive tumor and received trastuzumab, 55 (21%) had triple negative tumor, 125 received bevacizumab associated with CT. Baseline CTC positivity (65%; ≥1CTC/7.5ml threshold, 45% ≥5CTC/7.5ml threshold) was correlated with tumour markers, bone/liver involvement and number of metastatic sites, as well as performance status but was not statistically different according to breast cancer subtypes (hormone-positive, HER2-positive or triple-negative). At multivariate analysis, CTC ≥5CTC/7.5ml was an independent prognostic factor for progression-free survival (PFS), RR=1.9 (CI95% 1.26-2.88), p=0.002, with triple negative status, poor performance status and elevated CEA. For overall survival, CTC ≥5CTC/7.5ml was an independent prognostic factor with triple negative status and poor performance status (RR=2.41, p=0.02). Changes with a threshold ≥5CTC/7.5ml, between baseline and Cycle 2 were highly correlated with both PFS (p=5e-07) and OS (p=3e-07). Persistent CTC positivity at C2 was associated with lower tumor response (p=4e-03). Among CTC-positive patients at baseline treated by chemotherapy only, chemotherapy/bevacizumab and chemotherapy/anti-HER2, CTC counts decreased respectively below the ≥5CTC/7.5ml positivity threshold before cycle 2 in 53%, 64% and 83% of patients, and before cycle 3 or 4, in 62%, 77% and 100% of patients (p=0.04). Prognostic value of CTC count at baseline and C2 remained in all subgroups.

Conclusions: CTC count appeared to decrease more markedly in the patients who received also bevacizumab or trastuzumab. However, CTC remain a reliable independent prognostic marker in metastatic breast cancer treated by first-line chemotherapy with/without targeted therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3208. doi:10.1158/1538-7445.AM2011-3208
Abstract 3210: Profiling of DNA methylation signature for different phases of prostate cancer development
Authors: Chang Michelle , Liem Natalia , Goh Liang Kee , Kalaw Emarene , Lim Pei Li , Geronimo Carla , Sim Allen , Huang Hong Hong , Chong Tsung Wen , Tan Puay Hoon , Soong Richie , Cheng Christopher , Sim Hong Gee
Published: June 2012

Prostate cancer is the third most common cancer in Singaporean men. Compared to Western countries, the prostate cancer incidence is lower in Asian countries but recent data suggest that incidence is increasing, especially in rapidly urbanized countries. Recent studies provide evidence that methylated genes can be useful and promising molecular biomarkers for detection of prostate cancers. The aim of our study is to identify a panel of global gene methylation signatures that are unique and specific for different phases of prostate cancer development and different prostate cancer phenotypes. This may thus differentiate cancers from non-cancers, and aggressive cancers from indolent ones. We have profiled methylation of genes using the Illumina's GoldenGate Methylation System. The Standard GoldenGate Methylation Cancer Panel I (Illumina Inc, San Diego, CA) spans 1,505 CpG loci selected from 807 genes that have been shown in literature to play important roles in cancer. Methylation levels of candidate genes were quantified in 28 benign tissues without prostate cancer, 52 tissues of Gleason score 3+3, 66 tissues of Gleason score 4+x and 37 tissues of Gleason score 5+x. DNA used for the assays were obtained from laser capture microdissected paraffin embedded archival tissues. Interestingly, our results showed that 28 different CpG loci were methylated in Gleason 3+3 prostate cancer tissues compared to benign prostatic hyperplasia tissues that were used as controls. In addition, methylation levels in prostate cancer samples of high Gleason index (4+x and 5+x) were significantly higher than the paired prostate cancer samples of low Gleason index (3+3) in at least 10 candidate genes. These genes include VIM (p-value 3.59E-08), ASCL2 (p-value 1.71E-09), DAB2IP (p-value 6.55E-08) and FRZB (p-value 6.44E-08). Together with bioinformatics and quantitative methylation-specific PCR, we identified a set of potentially phenotype-specific gene methylation signatures in Asian men. Our studies contributed to the improvement of diagnostic capability for prostate cancer beyond available tumour markers such as PSA as it is a more sensitive molecular correlate.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3210. doi:10.1158/1538-7445.AM2011-3210
Abstract 3211: FGFR1 and FGFR2 gene copy number variations in prostate cancer
Authors: Otte Marcus , Kanchev Ivan , Sharp Michael C. , Alvarez John , Winkler Hans , Platero Suso
Published: June 2012

Patients with hormone refractory prostate cancer (HRPC) have very few clinical options. A bottle neck in development of new therapies is the poor understanding of the molecular basis of hormone independency. A pathway thought to be important in this progression is FGFR. Amplification of FGFR1 has been observed in breast cancer and has led to the hypothesis that it is involved in Tamoxifen resistance (Turner et al., 2010). Here we evaluated the copy number variations (CNV) of the gene loci of FGFR1 (8p12) and FGFR2 (10q26) by dual color FISH in FFPE tissue of recurrent PC patients (n=28), non-recurrent PC patients (n=15), PC patients undergoing palliative RPE (n=15), patients with benign prostate hyperplasia (n=17) and tumor free tissue samples (n=12). We analyzed CNV between different clinical patient subgroups. Two types of CNV for the gene loci of FGFR1 and FGFR2 were observed. Either the gene dose of the target gene locus occurred to be amplified or the gene dose was elevated due to polysomy of the respective chromosome. Furthermore patients with CNV of FGFR1 or FGFR2 exhibited in 40-50% intra tumor heterogeneity by presenting normal cells and cells with CNV. FGFR1 gene dose elevations (either due to gene locus amplification or polysomy of chromosome 8) were observed in 7% (1/15) of patients without recurrence but in 49% (17/35) of the patients with recurrence. Also, in patients undergoing palliative RPE 75% (12/16) of the patients exhibited FGFR1 gene dose elevation. In the case of FGFR2, gene dose elevations (gene locus amplification or polysomy of chromosome 10) were observed in none of the patients without recurrence but in 13% of the patients with recurrence and in 20% of patients undergoing palliative RPE. In the control groups such variations were not found. Interestingly, the gene dose variations differed in the prostate cancer patients depending on their hormone sensitivity. 47% (7/15) of hormone refractory patients and 30% (6/20) of the hormone sensitive patients showed elevated FGFR1 gene dose, for FGFR2, 30% and 20% of the respective subgroups were affected. In summary we conclude that this is first evidence that CNV of FGFR1 and FGFR2 might have implications for hormone resistance in PC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3211. doi:10.1158/1538-7445.AM2011-3211
Abstract 3227: Bioactivity and metabolic stability of indirubins
Authors: Merz Karl-Heinz , Cheng Xinlai , Eisenbrand Gerhard
Published: June 2012

Indirubins are known to induce cell cycle arrest in G1/S and/or G2/M followed by apoptosis and potently inhibit proliferation of human tumor cells. In general, they have unfavorable pharmacokinetic properties as a consequence of poor solubility, resulting in low bioavailability. They are CYP450 substrates, undergoing deactivating metabolic transformations by formation of hydroxylated metabolites, especially in 6- and 7’-positions. The antiproliferative activity of these metabolites was decreased or nearly completely abrogated.

To improve metabolic stability and solubility, novel indirubins were synthesized: hydrophilic N-methylpiperazinoethyl (E748) or N,N-dimethylaminophenyl groups were attached to the indirubin core by a 5-carboxamide anchor (E748 and E 744, respectively) or by a 3’-oxime ether link (E857). Moreover, to block 7’-hydroxylation, 7’-aza-5-methylindirubin (E844) was synthesized. Compounds were incubated in vitro with liver microsomes and metabolites were analyzed. E844 yielded as main metabolites 7’-aza-5-methyl-6-hydroxy-indirubin and 7’-aza-5-hydroxymethyl-indirubin. E748 yielded the 7’-hydroxy derivative as main metabolite. In contrast to E748, E744 did not appear to undergo detectable metabolic transformation. In addition, E857 and its water soluble hydrochloride (E857a) were not found to be hydroxylated at the respective bisindole positions. Main biotransformation of E857 rather occurred in the side chain, resulting in the formation of N- methylpiperazinoethyl-N-oxide. In contrast to E 857, the hydrochloride E857a was found hydroxylated at the methylpiperazino group.

The results demonstrate that deactivating metabolic transformation of indirubins can be mitigated by introducing N-atoms into the bisindole core, and/or by directing metabolic attack into the 3’ side chain, through attachment of hydrophilic substituents. In summary, the metabolic stability of the bisindole pharmacophore can be increased by appropriate molecular modifications that also improve pharmacokinetics.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3227. doi:10.1158/1538-7445.AM2011-3227
Abstract 3236: Role of mouse and human CYP2A enzymes in the bioactivation of the tobacco-specific lung procarcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)
Authors: Ding Xinxin , Zhou Xin
Published: June 2012

NNK is a potent lung procarcinogen. Previously, we have demonstrated that NNK-induced lung tumorigenesis depends on target-tissue metabolic activation by pulmonary P450 enzymes. The aim of this study is to test the hypotheses that 1) mouse CYP2A5 plays an essential role in NNK bioactivation in the lung, and 2) transgenic expression of human CYP2A13, known to be selectively expressed in the respiratory tract, and be the most efficient enzyme for NNK metabolic activation in vitro, can increase the rates of NNK metabolic activation in the mouse lung. We determined the rates of in vitro formation of 4-oxo-4-(3-pyridyl)-butanal (OPB), representing the reactive intermediate that can lead to the further formation of O6-mehtylguanine (O6-mG) DNA adduct, in liver and lung microsomes of wild-type, Cyp2a5-null, and CYP2A13-humanized (CYP2A13-transgenic/Cyp2a5-null) mice. We found that, in both liver and lung microsomes, the loss of CYP2A5 resulted in significant decreases in the rates of formation of OPB; whereas, the gain of CYP2A13 led to recovery of the microsomal activity in the lung, but not in the liver. Furthermore, we observed that the levels of O6-mG, the DNA adduct known to be most highly correlated with incidences of lung tumor formation, were significantly higher in the lungs of the CYP2A13-humanized mice, than in the Cyp2a5-null mice. In control experiments, rates of systemic clearance of NNK and its major circulating metabolite, NNAL, were confirmed to be not different among the three mouse strains. These results indicate that CYP2A13 can catalyze NNK bioactivation in vivo, and they support the idea that CYP2A13 genetic polymorphisms can influence the risks of tobacco-induced lung tumorigenesis in humans. (Supported in part by NIH grant CA092596)

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3236. doi:10.1158/1538-7445.AM2011-3236
Abstract 3244: Design, synthesis and biological evaluation of substituted furo[2,3-d]pyrimidines as potent microtubule targeting antitumor agents that circumvent Pgp and βIII-tubulin mediated resistance
Authors: Gangjee Aleem , Zhang Xin , Namjoshi Ojas , Devambatla Ravi Kumar Vyas , Hamel Ernest , Mooberry Susan L.
Published: June 2012

Despite the unprecedented success of microtubule targeting agents such as paclitaxel in cancer chemotherapy, overexpression of P-glycoprotein (Pgp) and/or βIII-tubulin can cause clinical resistance to these agents. This limits their utility as cancer chemotherapeutic agents. In addition, several antitubulin agents, particularly the taxoids, have poor water solubility, so that their administration requires formulations that generate hypersensitivity reactions. Recently, we reported two analogs based on 2,6-dimethylcyclopenta[d]pyrimidine and pyrrolo[2,3-d]pyrimidine scaffolds that circumvent both these drawbacks. To study the structure-activity relationship of these new antimitotic agents, we have designed furo[2,3-d]pyrimidines as isosteres of pyrrolo[2,3-d]pyrimidines. We synthesized 2-methyl- and 2-desmethylfuro[2,3-d]pyrimidines AG1 and AG16 from the corresponding 4-chloro and 4-amino analogs, respectively, by treatment with N-methyl-4-methoxyaniline or with 4-methoxyiodobenzene followed by N4-methylation. The synthesis of the 4-chloro analog involved the reaction between acetamidine chloride and diethyl 2-(prop-2-ynyl)malonate in the presence of sodium metal, followed by base-catalyzed cyclization and chlorination. The 4-amino analog was synthesized by treating 1-hydroxypropan-2-one with malononitrile followed by cyclization using formamidine. The compounds AG1 and AG16 inhibit the growth of all the tumor cells in the NCI 60-cell panel with two-digit nanomolar GI50 values and also depolymerize cellular microtubules at low nanomolar concentrations. These compounds inhibit the assembly of purified tubulin (AG1, IC50 = 1.9 ± 0.1 µM; AG16, IC50 = 3.3 ± 0.5 µM) and the binding of colchicine to tubulin (AG1, 63% inhibition at 1 µM, 86% at 5 µM; AG16, 71% at 1 µM, 96% at 5 µM). These compounds are fully active in tumor cells overexpressing either Pgp or βIII-tubulin, thus overcoming two important mechanisms associated with tumor resistance to paclitaxel. We have thus identified a potentially important new scaffold, the furo[2,3-d]pyrimidine, for antitubulin agents.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3244. doi:10.1158/1538-7445.AM2011-3244
Abstract 3249: Design and synthesis of imidazopyridine derivatives as novel HSP90 inhibitors for the treatment of cancer
Authors: Cai Xiong , Zhai Hai-Xiao , Wang Jing , Samson Maria , Atoyan Ruzanna , Forrester Jeffrey , Qu Hui , Yin Ling , Wang Dagong , Zifcak Brian , DellaRocca Steven , Xu Guang-Xin , Lai Cheng-Jung , Bao Rudi , Simonin Marie-Paule , Keegan Mitchell , Pepicelli Carmen V. , Qian Changgeng
Published: June 2012

The molecular chaperone heat shock protein 90 (HSP90) is involved in folding and stabilization of a wide range of client proteins, including key proteins involved in cancer. Through structure-based design, we synthesized a novel imidazopyridine class of potent HSP90 inhibitors. The synthesis and SAR surrounding this class of compounds will be discussed. The extensive SAR study and lead optimization resulted in the identification of the development candidate CUDC-305, later renamed Debio 0932. Debio 0932 displays high oral bioavailability (96% in mouse), high drug concentrations and a prolonged half-life (20 hr) in tumor tissues. In vitro, Debio 0932 displays potent HSP90 inhibitory activity (IC50, 100 nM) as well as anti-proliferation and apoptosis-inducing activities against a broad range of cancer cell lines (IC50, 40 – 900 nM). In vivo, Debio 0932 is highly effective against various cancer models including NSCLC, AML, breast and colorectal cancers, as well as brain cancers, benefited by its ability to cross the blood-brain barrier to reach therapeutic levels in brain tissue. Debio 0932 also exhibits high selectivity and a favorable safety profile. It was therefore selected as a drug candidate and is currently in Phase 1 clinical trials.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3249. doi:10.1158/1538-7445.AM2011-3249