bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4177: Copy number variations of FGFR1 and 2 in NSCLC; implications for targeted drug development
Authors: Otte Marcus , Ivan Kanchev , Stacher Elvira , Sharp Michael , Alvarez John D. , Popper Helmut , Winkler Hans , Platero Suso 
Published: July 2012

Abstract
NSCLC is the cancer with highest death rate; it is typically diagnosed at a late stage and has limited therapeutic options. FGFR signaling is a potential oncogenic driver in many cancers, including NSCLC. In this study we evaluated the copy number variations (CNVs) of FGFR1 and FGFR2 by dual color FISH in specimens from 139 NSCLC patients (78 SCC, 46 ADC, 15 other).
CNVs were observed for both FGF receptors. However, FGFR1 was more frequently affected by CNV than FGFR2 (45% vs. 17%). Only a small fraction of patients exhibited CNV of both receptors. In general, the level of gene amplification was higher for FGFR1 as compared with FGFR2. Interestingly, FGFR2 CNV exhibited a high degree of intra-tumor heterogeneity.
FGFR1 gene dose elevations were observed due to gene locus amplification (27%) as well as polysomy of chromosome 8 (17%). The degree of gene locus amplification was classified from low (gene ratio 1.5 – 2.5) to high (&gt;4.5). An analysis of the two most common histologies (i.e. Squamous Cell Carcinoma (SCC) and Adenocarcinoma (ADC)) indicated that gene locus amplifications were more frequent in SCC (38%) as compared with ADC (7%), while polysomy of chromosome 8 was observed at similar rates (18-19%). Lack of FGFR1 rearrangements was confirmed using a break-apart FISH probe.
FGFR2 gene dose elevations show gene locus amplifications and polysomy of chromosome 10. Locus amplifications of FGFR2 were observed in 11% of SCC, but were not found in ADC. Similar rates for polysomy of FGFR1were observed in SCC (7%) and ADC (5%).
Overall, gene dose elevation of FGFR1 and FGFR2 were found more frequently in SCC. Of higher relevance is the fraction of patients with gene dose elevation due to gene locus amplification. Approximately 40% of the SCC patients possess gene locus amplification of at least one of the two probed FGF-receptors. However, only ∼9% of the SCC patients have both loci amplified. In conclusion here we present for the first time evidence for a potential genetic addiction of NSCLC, specifically on FGFR1 gene locus amplification. Therefore targeting FGFR in combination with proper patient stratification, may be an attractive opportunity to develop improved clinical options for treatment of NSCLC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4177. doi:10.1158/1538-7445.AM2011-4177
Abstract 4178: Circulating cell-free DNA in plasma of never smokers with advanced lung adenocarcinoma receiving gefitinib or standard chemotherapy as a first-line therapy
Authors: Lee Young Joo , Yoon Kyong-Ah , Lee Jin Soo 
Published: July 2012

Abstract
Background: Circulating cell-free DNA (CFDNA) has been investigated as a potential screening or prognostic marker in a variety of cancers, including lung cancers. This study aimed to investigate prospectively its clinical significance in never smokers with advanced lung adenocarcinoma (ALAC) undergoing chemotherapy.
Methods: We analyzed blood samples of 134 patients among 309 never smokers with ALAC who were enrolled to a prospective randomized phase III study comparing gefitinib with gemcitabine plus cisplatin (GP) as first-line therapy from April 2005 to November 2007 (the First-SIGNAL). An amount of plasma CFDNA was measured by real-time quantitative polymerase chain reaction targeting human β-actin genomic sequence.
Results: Median baseline CFDNA value was 122.3 ng/ml (range, 11.5 to 2487.9 ng/ml). Patients with &gt; 2 of metastatic sites had higher plasma CFDNA compared those with ≤ 2 metastatic sites (P = 0.015). Baseline plasma CFDNA was positively associated with peak standardized uptake value of primary tumor on 18F-FDG PET (coefficient = 0.316; P = 0.056). In GP arm, high CFDNA group showed higher response rate (RR) than low CFDNA group (60.7% vs. 37.8%; P = 0.047). However, in gefitinib arm, no difference was observed in RR between the two groups (47.2% vs. 58.1%; P = 0.376). The risk of death was elevated with increasing baseline plasma CFDNA [hazard ratio (HR) = 1.23; 95% CI, 1.01-1.50; P = 0.045)]. The low tertile group of baseline CFDNA showed longer overall survival (OS) than the high tertile group [HR of low vs. high groups = 0.52 (95% CI, 0.31-0.87); median OS, 28.6 vs. 16.0 months; P = 0.041].
Conclusion: High plasma CFDNA at diagnosis predicts an aggressive behavior and poor survival outcomes in these patients.
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 4178. doi:10.1158/1538-7445.AM2011-4178
Abstract 418: Cellular mechanisms underlying the evasion of detachment-induced cell death in inflammatory breast cancer cells
Authors: Angarola Brittany L. , Schafer Zachary T. 
Published: July 2012

Abstract
Inflammatory Breast Cancer (IBC) is a rare and aggressive form of breast cancer that results from cancerous epithelial cells that invade and block the lymphatic vessels. Because the cancerous cells have already migrated from the epithelium into the lymphatic system, these cells are inherently metastatic and have the ability to survive in the absence of attachment to the extracellular matrix (ECM). Non-cancerous epithelial cells require ECM attachment for normal cell signaling and survival, however IBC cells are able to persist without ECM attachment in the lymphatic vessels. Here we demonstrate that both the SUM149 and the ErbB2-overexpressing SUM190 cell lines derived from primary IBC tumors have acquired mechanisms to aid in their survival in detached environments. Using an in vitro model of ECM detachment, we reveal that detached IBC cells exhibit a dramatic evasion of anoikis (detachment-induced apoptosis). In the SUM149 cells, this evasion of anoikis seems to be mediated by the MAPK pathway as inhibition of this pathway with UO126 abrogates the inhibition of detachment-induced caspase activation. However, the evasion of anoikis in SUM190 cells is unaffected by U0126 treatment and is instead mediated by the PI(3)K pathway. Furthermore, when compared to the SUM149 cells, the SUM190 cells are much more effective at inhibiting anoikis. Interestingly, SUM190 cells exhibit a complete inhibition of the ECM-detachment-induced increase in pro-caspase-3, a mechanism that may explain the more efficient anoikis inhibition in these cells. Additionally, both the SUM149 cells and the SUM190 cells are able to overcome detachment-induced metabolic stress. This is demonstrated through the ability of both the SUM149 and SUM190 cells to maintain ATP levels upon detachment. However, while western blotting clearly demonstrates detachment-induced PI(3)K activation in both cell lines, we have discovered that this upregulation is necessary for metabolic rescue only in the SUM149 cell line. Neither the MAPK nor PI(3)K pathway is involved in the maintenance of ATP following ECM detachment, suggesting that these cells may utilize an alternative signaling pathway to maintain ATP levels. These results show that IBC cells have the capacity to alter both apoptotic and metabolic pathways to survive in detached environments. Further elucidation of these mechanisms may reveal new chemotherapeutic targets that permit the specific elimination of detached IBC cells within the lymphatic system.
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 418. doi:10.1158/1538-7445.AM2011-418
Abstract 4181: Retrospective tissue microarray analysis finds potential predictors of nodal metastasis in early tongue cancer
Authors: Khwaja Fatima W. , Faiz Sabeen , Azhar Rafay , Ahmad Qasim , Jamshed Arif 
Published: July 2012

Abstract
Introduction: Pakistan has one of the highest incidences of oral cancer in the world. In Shaukat Khanum Memorial Cancer Hospital and Research Center (SKMCH&RC), Squamous Cell Carcinoma of Tongue (SCCOT) is the second most common head and neck malignancy. To date only neck dissection, a highly invasive and costly procedure, can predict regional and distant recurrence of disease. However, only 20-30% of patients with early tongue carcinoma will actually have metastatic disease. Therefore, there is a pressing need to find low cost, and sensitive methods to identify patients requiring this invasive procedure. In this study we aim to examine a subset of proteins through tissue microarray (TMA) that could potentially serve as prognostic markers of nodal metastasis in early SCCOT in order to minimize unnecessary neck dissection in patients with early disease.
Method: Retrospective analysis was performed in a double-blind manner on 2 tissue microarrays (5 cores/patient) created from paraffin-embedded specimens from 67 patients with well documented clinical history of the disease. The training set included 30 of the patients and was used to identify potential markers. The top two markers were then validated using the remaining 37 patients as the test set. Twenty five different proteins were tested as potential biomarkers of metastasis based on published literature on SCCOT and analyzed through IHC.
Results: The partial protein profiles from TMA analyses recovered differential protein expression pattern in patients with recurrence versus those who remain disease free upto 36 months post treatment. Among these a glycoprotein, podoplanin (p&lt;0.0001) and two cytokines, β-2 microglobulin (p&lt;0.0001) and interleukin-8 (p = 0.004) were found up regulated and E-cadherin (p = 0.007) was down regulated in samples that metastasized following surgery. The expression of these three proteins combined in a potential biomarker panel could reliably predict outcome in 100% of the cases using k-nearest neighbor algorithm. These results were further confirmed using a verification set of 46 patients. In this new set, the potential biomarker panel was sufficient in predicting metastasis in 97.2% of SCCOT patients coming in with early disease.
Conclusion: This study provides proof of principle data to show that individual proteins can be found through statistical analyses to compile a biomarker panel that can distinguish between patients with node positive versus node negative disease. These markers can be used either individually or in the form of a panel to optimize staging and treatment of SCCOT patients.
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 4181. doi:10.1158/1538-7445.AM2011-4181
Abstract 4183: Ribonucleotide reductase small subunit M2B associates with better survival of colorectal cancers through inhibiting tumor invasion and metastasis
Authors: Liu Xiyong , Wang Xiaochen , Loera Sofia , Wu Jun , Hu Shuya , Zhang Keqiang , Kuo Mei-ling , Xue Lijun , Zhou Lun , Zhang Hang , Wang Yan , Zhou Bingshen , Chu Peiguo , Nelson Rebecca , Chen Lirong , Zheng Shu , Zhang Suzhan , Lai Lily , Yen Yun 
Published: July 2012

Abstract
Previous studies have demonstrated that RRM2B suppresses the invasion and metastasis of cancer cells. Here, we examined the hypothesis that RRM2B may be related to better survivability and serve as a prognostic biomarker for colorectal cancer (CRC). The RRM2B-overexpressing transfectant HCT-116/RRM2B or the corresponding vector control transfectant was implanted into NSG mouse to generate orthotopic xenograft mouse models. The lung and liver metastasis occurred in 60% of the HCT-116/vector mice (3 of 5 cases) but in none of the HCT-116/RRM2B mice (0 of 6 cases). The outcome studies were conducted on a training set with 103 CRC cases and were validated on a set with 220 consecutive CRC cases. All participants underwent surgery and periodically followed-up to determine survivability. Immunohistochemistry (IHC) was conducted on tissue arrays to determine the expression level of RRM2B. In the training set, the Kaplan-Meier and multivariate COX analysis revealed that the RRM2B is associated with better overall survival (OS) of CRC patients, especially in stage IV CRCs (Hazard ratio, HR=0.40; 95% CI 0.18-0.86). This result has been validated as HRs of RRM2B were 1.02 (95% CI 0.31-4.58) and 0.53(95% CI 0.29-1.01) for stage 0-II and stage III-IV, respectively. Multivariate analysis indicated that the adjusted HR of RRM2B was 0.48 (95% CI 0.26-0.91). Further analysis suggested that RRM2B significantly reduces the relative risk of death due to colon cancer (HR = 0.38; 95% CI 0.16-0.87) but not rectal cancer. Therefore, we conclude that RRM2B plays a critical role in suppressing invasiveness ability of cancer cells and it associates with a better prognosis for CRC patients.
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 4183. doi:10.1158/1538-7445.AM2011-4183
Abstract 4184: Expression analysis of iPS inductive gene in gastrointestinal cancer by tissue microarray
Authors: Sekine Shinichi , Shimada Yutaka , Okumura Tomoyuki , Osawa Soshi , Moriyama Makoto , Matsui Koshi , Sawada Shigeaki , Nagata Takuya , Fukuoka Junya , Tsukada Kazuhiro 
Published: July 2012

Abstract
Background: Recent progress is enabling us to induce iPS cells using somatic differentiated cells. We are now establishing iPS cells from normal gastrointestinal epithelial cells. However, the risks associated with transfection of iPS inductive genes (Sox2, Oct 3/4, klf4 and c-Myc) to somatic differentiated cells has not been well examined. Thus, in order to understand the role of iPS inductive genes in gastrointestinal cancer, we examined the expression of Sox2, Oct3/4, klf4, c-Myc and Nanog by cancer tissue microarray.
Methods: We examined gene expression in 86 esophageal cancers, 50 gastric cancers, 80 colorectal cancers, 37 biliary tract cancers and 34 pancreatic cancers. Immunohistochemical expression levels of 5 genes were evaluated by the combination of their intensity and distribution. The expression level was compared to the clinico-pathological data of the patients.
Results: Klf4 reduction was associated with lymph node metastasis of colorectal cancer which resulted in a poor prognosis for the patients (p=0.02). Klf4 reduction also tended to indicate a poor prognosis in esophageal cancer (P=0.06). Furthermore, Sox2 reduction was an independent prognostic factor in gastric cancer (p=0.03) and a high expression of OCT3/4 tended to indicate a poor prognosis in esophageal cancer (p=0.07). Nanog reduction was associated with poor prognosis in biliary tract and pancreatic cancer(p=0.02). On the other hand, c-Myc did not have any association with clinico-pathological factors of gastrointestinal cancer. Clustering analysis revealed that prognosis of the subgroup of simultaneous positive expressions of iPS inductive genes was better than that of other subgroups in colon cancer, however there was no difference among subtypes in esophageal cancer.
Conclusions: The role of iPS inductive genes may differ in various gastroenterological cancer patients. However, further large-scale analysis is needed to elucidate this issue.
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 4184. doi:10.1158/1538-7445.AM2011-4184
Abstract 4185: Serum concentrations of angiogenesis-related molecules in patients with pancreatic cancer
Authors: Kimura Hideharu , Sakamoto Hiroki , Nagai Tomoyuki , Kudo Kanae , Furuta Kazuyuki , Arao Tokuzo , Kitano Masayuki , Kudo Masatoshi , Nishio Kazuto 
Published: July 2012

Abstract
Objectives: A number of antiangiogenic inhibitors have been studied in clinical settings, some of which are now under clinical evaluation in pancreas cancers (PC), therefore, prognostic marker of angiogenesis-related molecules in PC is needed. The aim of this study is to evaluate the serum levels of angiogenesis-related factors in patients with pancreas cancer.
Methods: The plasma samples obtained from 45 pancreas cancers (PC) were analyzed compared with 9 pancreatitis (P), 16 benign hepatobiliary diseases (HD) and 58 colorectal cancers (CC). Serum angiogenesis-related factors including Angiopoietin-2, Follistatin, G-CSF, HGF, IL-8, Leptin, PDGF-BB, PECAM-1 and VEGF were determined by antibody suspension bead arrays system.
Results: All of the serum angiogenesis-related factors were not increased in PC compared with P and HD, while those of CC were markedly increased. Although IL-8 levels were not increased in most samples of PC, it was significantly increased in patients with distant metastases and there was a trend toward to a shorter survival. Conclusions: Serum levels of angiogenesis-related factors were basically not increased in patients with PC, however, serum IL-8 levels may reflect PC progression and shorter survival.
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 4185. doi:10.1158/1538-7445.AM2011-4185
Abstract 4188: Association of HOX gene expression with osteopontin in ovarian cancer: Implications for biomarker development
Authors: Tait David L. , Thompson Kevin J. , Haloi Rimki , Bahrani-Mostafavi Zahra , Richardson Christine , Mostafavi M. Taghi 
Published: July 2012

Abstract
Ovarian cancer is characterized by poor early detection and serves as an excellent model system to develop potential markers for early diagnosis. Osteopontin is a glycophosphoprotein known to demonstrate multiple functions including mediation of cellular adhesion, suppression of macrophage interleukin production, prevention of angiogenesis, apoptosis, and inhibition of anchorage-dependent growth. Studies of Osteopontin in ovarian cancer have described increased expression and a role as a candidate biomarker. Secretion of Osteopontin into the extra cellular matrix is reported to facilitate metastasis and has been reported to be inhibited by the presence of cytoplasmic Homeobox proteins (HOX). The HOX family of genes encodes transcription factors involved in basic developmental processes and has been linked to oncogenesis. Dysregulation of HOX genes may be an early event in malignant transformation making the HOX gene family appealing for biomarker investigation. In this study we characterize HOX gene expression in malignant tumors of the ovary compared to Osteopontin, a known biomarker for ovarian cancer.
Methods: Microarray analysis of mRNA from human ovarian tissues was performed on samples of normal, benign, and malignant ovarian tissues. These samples were analyzed using the Affymetrix Human Genome Focus GeneChip (HG-Focus) microarray to distinguish the differential pattern of mRNA expression between the three types of samples. Immunohistochemistry staining of ovarian tissue samples was utilized to analyze confirmatory protein expression of the microarray findings.
Results: Microarray analysis demonstrated up-regulation of HOXB2, HOXB7, and Osteopontin genes in malignant ovarian tumor samples compared to normal ovarian tissue controls. Conversely, HOXC6 was down-regulated in malignant tissue samples. Immunohistochemistry was performed for HOXB2, HOXC6 and Osteopontin on OCT embedded tissues samples. Similarly, increased protein expression was shown for HOXB2 and Osteopontin in malignant samples and increased HOXC6 in non-cancerous samples.
Conclusion: Our results demonstrate multiple HOX genes to be up-regulated in ovarian cancer. Increased expression of HOXB2 and HOXB7, correlated with increased Osteopontin expression found in malignant ovarian tissue samples. HOXC6 demonstrated an inverse relationship with Osteopontin in non-cancerous ovarian tissue samples. The association of these HOX genes with Osteopontin expression warrants further investigation into the role of HOX genes as candidate biomarkers for ovarian 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 4188. doi:10.1158/1538-7445.AM2011-4188
Abstract 4189: Utilization of Champions Tumorgraft™ models to identify putative biomarkers and signatures of response
Authors: Friedman Jay A. , Hewit Theodore H. , Hidalgo Manuel , Rowinsky Eric K. , Sidransky David , Bruckheimer Elizabeth M. 
Published: July 2012

Abstract
Champions Biotechnology has developed an innovative platform for oncology research that utilizes the implantation of primary human tumors in immune-deficient mice in a manner that preserves the biological properties of the original human tumor. Given the unique features and extensive characterization of the Champions Tumorgraft™ platform, it can be utilized for the identification and validation of putative biomarkers and signatures of response which predict resistance or sensitivity to anti cancer agents in specific patient populations. Models of colorectal cancer, NSCLC, and pancreatic cancer were subjected to cetuximab or irinotecan, cisplatin or paclitaxel, and gemcitabine, respectively. Tumor growth inhibition of 50% was utilized as the criteria to delineate sensitive versus resistant models. Baseline whole genome-transcriptome profiles were compared in sensitive and resistant models, and the top 100 genes differentially expressed between these phenotypes were selected by signal-to-noise metric. Pathways up regulated in sensitive and resistant Tumorgraft™ models were determined by an unbiased gene set enrichment analysis. Colon Tumorgraft™ models treated with either cetuximab or irinotecan showed sensitivity in 6/14 models and 8/11 models, respectively. NSCLC Tumorgraft™ models treated with either cisplatin or paclitaxel showed sensitivity in 4/12 models and 10/13 models, respectively. Lastly, pancreatic Tumorgraft™ models treated with gemcitabine showed sensitivity in 15/17 models. Bioinformatic analysis revealed, for example, that a number of signaling pathways involved in survival, proliferation, angiogenesis, adhesion, cell cycle control, metabolism, and apoptosis are significantly modulated in these sensitive and resistant cancer models. Validation of key genes and pathways is onging. Together, these results demonstrate that Champions TumorgraftTM models can be utilized to identify potential biomarkers of response and represent a novel in vivo platform capable of predicting the clinical effectiveness of anti cancer drugs. Furthermore, the combined framework of Champions Tumorgrafts™ and bioinformatic analyses, as described here, can not only be applied to clinically approved agents, but also to agents in development, hereby increasing the efficiency of oncology drug development by identifying those patients most likely to respond to a given 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 4189. doi:10.1158/1538-7445.AM2011-4189