bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB-217: A universal cancer detection platform which measures telomerase activity from live circulating tumor cells captured on microfilter
Authors: Xu Tong , Lu Bo , Tai Yu-Chong , Goldkorn Amir 
Published: February 2011

Abstract
Objective. · Circulating tumor cells (CTCs) quantified in cancer patients’ blood can predict disease outcome and response to therapy. However, the CTC analysis platforms currently used are expensive, labor-intense, operator-dependent, and only applicable to tumors of epithelial origin. To address these limitations, we engineered a universal cancer detection platform which measures telomerase activity from live circulating tumor cells captured on microfilter.
Methodology: Microfilters were fabricated from parylene-C by a multi-step Reactive Ion Etching (RIE) technique and then connected to a constant low-pressure fluid delivery system. To optimize slot size and filtration pressure, PC3 prostate cancer cells were stained with live-cell dye (Calcein-AM) and spiked into whole blood. After filtration, the captured cells were counter-stained with dead-cell stain (propidium iodide, PI) and counted to determine capture efficiency, viability, and enrichment. Telomerase activity measurement was accomplished using blood spiked with cancer cell lines as well as actual patient samples. Briefly, 7.5 ml blood samples were depleted of red blood cells by ficoll gradient centrifugation, and the PBMC fraction was resuspended in PBS, captured on microfilter and lysed. Telomerase activity was assayed from the cell lysates using a modified quantitative PCR telomere repeat amplification protocol (qPCR-TRAP).
Results: The optimized microfilter platform was capable of cell capture from 7.5 ml of whole blood in under 15 minutes, achieving 80% capture efficiency, 90% cell viability and 1500-fold sample enrichment. Importantly, the captured cells retained normal morphology by scanning electron microscopy and could be readily manipulated, further analyzed, or expanded on- or off-filter. Remarkably, telomerase activity was reliably detected by qPCR-TRAP from as few as 25 cancer cells spiked into 7.5 ml whole blood, as well as from actual CTCs in patient blood samples and even from single cancer cells captured on microfilter.
Conclusions: We present a novel cancer biomarker platform capable of assaying telomerase activity in live CTCs captured on microfilter from human blood. This new technology can be used to elucidate the basic biology of cancer dissemination and also applied clinically to improve prognostication, treatment, or even early detection of common malignancies. It is fast and simple yet fully quantitative and applicable to nearly all solid tumor types, making microfilter telomerase analysis a truly universal and highly promising cancer biomarker platform.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-217.
Abstract LB-222: Identification of rare KRAS codons 12 and 13 mutations by shifted termination assay
Authors: Doong Howard , Li Xiaofei , Chen Caifu , Walker Julian 
Published: February 2011

Abstract
We have developed a sensitive and specific method for research studies, using Shifted Termination Assay (STA) to detect 12 possible KRAS mutations in codons 12 and 13. In this study, we analyzed 118 samples collected from formalin-fixed and paraffin-embedded (FFPE) metastatic colorectal cancer tumors.
The detection method includes carrying out a primer extension reaction in the presence of a wild-type DNA sequence. The primer extension reaction is stopped when encountered by a mutated base. If no mutation is detected the reaction terminates at the next nucleotide resulting in a large wild-type fragment. This creates a shift in the amount of labeled nucleotides incorporated on the primer extended product, and is then differentiated by fragment analysis using Applied Biosystems capillary electrophoresis systems.
Among the 118 samples tested, 32 were found to carry a mutation with 9 different variants. The most common mutations found in codon 12 were GGT&gt;TGT (G12C, 9/32) and GGT&gt;GTT (G12V, 8/32). Two rare variants in codon 12, GGT&gt;GCT (G12A, 1/32) and GGT&gt;CGT (G12A, 1/32), were also observed. For codon 13, the most common mutation found in the samples was GGC &gt;GAC (G13D). In this study, we found 4 variants with 3 different types - 2 samples of GGC&gt;AGC (G13S), 1 sample of GGC&gt;GAC (G13D) and 1 sample of GGC&gt;CGC (G13R). In summary, our data suggest that more KRAS mutations were observed in codon 13 relative to codon 12 in research samples, and the STA assay is an easy to use, robust method to detect possible KRAS mutations in codons 12 & 13. STA is currently for research use only, not for use in diagnostic procedures.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-222.
Abstract LB-228: YAP-dependent induction of amphiregulin identifies a non-cell-autonomous component of the Hippo pathway
Authors: Zhang Jianmin , Ji Jun-Yuan , Yi Min , Overholtzer Michael , Smolen Gromoslaw A. , Wang Rececca , Brugge Joan S. , Dyson Nicholas J. , Haber Daniel A. 
Published: February 2011

Abstract
The Hippo signaling pathway was initially identified in Drosophila and components in this pathway are highly conserved in mammals. We and others have recently shown that the Hippo pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. The pivotal effector of this pathway is YAP, a transcriptional co-activator amplified in mouse and human cancers, where it promotes epithelial to mesenchymal transition (EMT) and malignant transformation. To date, studies of YAP target genes have focused on cell-autonomous mediators. Here, we show that YAP-expressing MCF10A breast epithelial cells secrete growth factors that enhance the proliferation of neighboring untransfected cells, implicating a non-cell autonomous mechanism. Using cytokine and growth factor array analysis, we identified the epidermal growth factor receptor (EGFR) ligand, amphiregulin (AREG), as a transcriptional target of YAP, whose induction contributes to YAP-mediated cell proliferation and migration. Knockdown of AREG or addition of an EGFR kinase inhibitor abrogates the proliferative effects of YAP expression. Suppression of the negative YAP regulators LATS1/2 is sufficient to induce AREG expression, consistent with a physiological regulation of AREG by the Hippo pathway. Furthermore, genetic interactions between the Drosophila YAP orthologue Yki and Egfr signaling components support the link between these two highly conserved signaling pathways. In conclusion, YAP-dependent secretion of AREG implicates activation of EGFR signaling as an important non-cell autonomous effector of the Hippo pathway, with relevance for the regulation of both physiological and malignant cell proliferation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-228.
Abstract LB-239: The Rho GEF, GEF-H1, is regulated by and activates Rho in response to 3-D collagen matrix density in breast epithelial cells
Authors: Jessica Heck N. , Ponik Suzanne M. , Provenzano Paolo P. , Keely Patricia J. 
Published: February 2011

Abstract
Cell interactions with the extracellular matrix (ECM) have a profound influence on carcinoma progression, invasion, and metastasis. We and others have established that breast epithelial cells sense and respond to the stiffness of their ECM environment using the small GTPase Rho, however the exact signaling mechanism has not been identified. In addition to Rho, focal adhesion kinase (FAK) has been linked to mechanosensing, and studies from our lab have revealed FAK as a key mediator of breast tumor progression. We have found that mammary specific deletion of FAK results in tumors that are neither locally invasive nor metastatic. Expression analysis from FAK−/− tumors demonstrated that a number of Rho regulatory molecules were regulated by FAK. Of particular interest, mRNA for the Rho GEF, GEF-H1, was significantly decreased in FAK−/− mammary tumors. While relatively little is known about GEF-H1, it has been implicated in the crosstalk between microtubules and the actin cytoskeleton, positioning it as a potential regulator of Rho-mediated contractility. While it is established that Rho activity is regulated by matrix stiffness, Rho regulatory molecules that modulate signaling in 3D matrices, and specifically in response to changes in matrix stiffness, have yet to be identified. Here we demonstrate that the Rho specific exchange factor, GEF-H1, is activated by and in turn regulates Rho activation as well as Rho-mediated contractility in breast epithelial cells in response to 3D matrix density. Because we have demonstrated that extracellular signal-regulated kinase (ERK) is activated in response to increased 3D collagen matrix density, and others have shown that ERK signaling modulates GEF-H1 exchange activity for RhoA, we are investigating whether ERK mediates mechanosignaling to GEF-H1. Additional studies are underway to determine the role of GEF-H1 in 3D breast cell invasion.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-239.
Abstract LB-241: Cancer-associated fibroblasts modulate growth- and metastasis-promoting pathways in human pancreatic cancer cells and augment orthotopic tumor growth in mice
Authors: Walters Dustin M. , Adair Sara J. , Stokes Jayme B. , Lowrey Bryce , Parsons J. Thomas , Bauer Todd W. 
Published: February 2011

Abstract
Background: The role of cancer-associated fibroblasts (CAFs) in the development, progression, and metastasis of pancreatic ductal adenocarcinoma (PDAC) is not completely understood. We sought to better characterize the role of CAFs by evaluating the effect of co-culturing CAFs and pancreatic cancer cells on growth and metastasis pathways.
Methods: Resected human PDACs were grown orthotopically in mice. From these tumors, human pancreatic cancer cells and mouse CAFs were isolated and grown in culture. Three cell culture environments were created: 1) pure (&gt;99%) human pancreatic cancer cells, 2) pure (97%) mouse CAFs, and 3) co-culture of both cell types. IHC and FACS were used to confirm cell type and species of origin. Phospho-receptor tyrosine kinase (pRTK) and cytokine arrays were performed on the three groups. Additionally, the effect of CAFs on PDAC growth was evaluated in nude mice by orthotopically injecting cancer cells (1 × 106 cells) with and without CAFs (1 × 106 cells).
Results: CAFs stained positively for -smooth muscle actin (-SMA) but were negative for E-cadherin, while cancer cells stained positively for E-cadherin, but not -SMA. FACS for MHC-I confirmed mouse origin of the CAFs (negative) and human origin of the cancer cells (positive). Co-culture of mouse fibroblasts and human tumor cells led to significant upregulation of cell proliferation pathways (evidenced by increased human pRTKs and cytokines, including EGFR1, EGFR2, c-Met, Ron, IGF-1R, and thrombospondin-2), angiogenic pathways (evidenced by increased secretion of VEGF, IL-8, and angiogenin) and matrix degradation and remodeling pathways (increased secretion of MMPs 8 and 9, TIMPs 1 and 4, and uPA). Orthotopic mouse injection of human pancreatic cancer cells in combination with mouse CAFs (1:1 ratio) led to larger tumors at 3 weeks as compared to injection with cancer cells alone (1129 mm3 vs. 443 mm3, p &lt; 0.005).
Conclusions: Using co-culture of CAFs and pancreatic cancer cells we have recapitulated the modulation of pathways responsible for cell proliferation, angiogenesis, and matrix remodeling thought to occur in vivo during tumor progression. Further, we show that co-injection of CAFs and pancreatic cancer cells significantly augments orthotopic tumor growth in mice. These studies lay the groundwork for future studies to define the critical factors produced by stromal fibroblasts and the role of such factors in PDAC progression, allowing new insights into improving patient therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-241.
Abstract LB-247: Regulation signatures consistently detect activity of EGFR pathway in different cell lines
Authors: Dezso Zoltan , Webb Craig , Miller Jeremy , Cherba David , Bugrim Andrej 
Published: February 2011

Abstract
In this work we introduce a concept of “regulation signatures” which aims to overcome shortcomings of existing methods of molecular diagnostics. In this approach we utilize our recently developed methodology for identifying key regulatory proteins in biological networks. The procedure works by combining high-throughput molecular data from individual biological samples with the knowledge-base on the global network of protein interactions. The algorithm performs scoring of signaling proteins in the global network to identify those that most likely represent key regulators responsible for observed downstream changes in gene and protein expression. Using these scores we construct “regulation signatures” - sets of proteins that characterize core cell signaling activity associated with a condition of interest. In the present study we illustrate this approach by building a signature for the EGFR pathway activation using gene-expression profiles from different cell lines stimulated with EGF. We demonstrate that our algorithm consistently predicts activity of the EGFR pathway despite significant variation in gene expression profiles across different samples. We also illustrate that this signature can detect signaling patterns associated with constitutive RAS activity. We discuss how regulation signatures could be applied to develop more accurate, robust and mechanistically relevant methods for predicting drug sensitivity, disease progression, and other clinical end-points.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-247.
Abstract LB-248: Towards a global picture of breast cancer: transcriptional networks, pathways, regulators, and validation
Authors: Zhang Bin , Tran Linh , Jonathan Derry , Zhu Jun , Friend Stephen 
Published: February 2011

Abstract
The unprecedented volumes of large-scale genomic and genetic data being generated today, combined with the poor understanding of the genetics underlying complex biological systems, demand a systems biology approach to identify a global landscape of interactomes that contribute to a variety of clinical endpoints such as tumor progression. Along this direction, two kinds of gene network analyses, association (gene coexpression network) and causality inference (Bayesian network), have been almost independently developed in the past decade. In spite of the significant success of the methods, it is still far away from generating a clear picture for even a single pathway involved in complex human disease like cancer due to insufficient information and various limitations of the methods. Here we present a framework to combine the two types of network analyses with an aim of integrating many high-throughput gene expression datasets on multiple platforms. By applying the integrative network approach to four large scale microarray datasets in breast cancer, we first systematically uncover gene modules/pathways involved in breast cancer progression through a weighted gene coexpression network analysis, then use these gene modules to partition a complex Bayesian network constructed from the same datasets, and finally identify key regulators of the modules predictive of outcomes. A significant portion of the predicted novel gene targets are validated through a large number of siRNA experiments in breast cancer cell lines. This allows us to globally validate breast cancer gene networks. The integrative approach and the findings will have a significant impact on breast cancer research and drug development.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-248.
Abstract LB-253: Mesenchymal stem cells of fallopian tube cancers are specifically attracted by mature ovulating follicles: implication of fallopian tube origin of serous ovarian carcinoma
Authors: Yeh Ching-Hua , Lin Shih-Rung , Chu Tang-Yuan 
Published: February 2011

Abstract
Background: Recent studies of surgical specimens resected from carriers of breast ovarian cancer syndrome have suggested a fallopian tube origin of serous carcinoma of the ovary. We tested the following hypothesis: Cancer initiating cells arising from fallopian tube home to ovulation wound via chemotaxis of follicular fluid.
Materials and Methods: Mesenchymal stem cells from fallopian tube cancers (FTC-MSC) and normal fallopian tubes (FT-MSC) were respectively culture-isolated from two patients with FIGO stage 3C serous adenocarcinoma of fallopian tube and three patients with uterine myoma. Tissues were digested with collagenase type I and dispase and cells were grown in anti-oxidant DMEM medium containing 5% fetal bovine serum. Characteristics of stem cells including cell surface markers, colony formation, trans-differentiation and hTERT expression were analyzed. Follicular fluids and cells were procured and cultured from ovulating women receiving in-vitro fertilization program. Chemotaxis and cell migration activities were studied by trans-well migration assay and wound healing assay.
Results: The isolated FTC-MSC had a doubling time of around 25h and gave a typical mesenchymal stem cell phenotypes with anchorage independent growth, lack of gap junction communication, positive for CD24, CD44, CD133, CD29, CD90, CD56, CD117 and CD146, negative for CD 34 and CD45, and had high hTERT expression. Capabilities of osteogenic and adipogenic differentiation and chemo-resistence paclitaxol and cisplatin were evident. FTC-MSC but not FT-MSC highly responded to mature, ovulating follicular fluid, and to condition media of cultured follicular cells or ovarian stromas, and much less to those derived from immature follicles, and to conditional media of endometrial, cervical and peritoneal cells in culture.
Conclusions: The highly specific chmotaxic effect of mature, ovulating follicles to FTC-MSC supports the hypothesis of fallopian tube origin of serous ovarian carcinoma.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-253.
Abstract LB-254: Efficiently targeting cancer stem cells requires tactical activation from their dormant state and subsequent exhaustion
Authors: Lin Edward H. , He Xi C. , Yan Xiaowei , Deng Yanhong , Yeung Raymond , Gu Jian , Curley Stephen , Haug Jeff , Blau Anthony , Wu Xifeng , Tian Qiang , Li Linheng 
Published: February 2011

Abstract
Akin to normal tissue stem cells (NTSCs), cancer stem cells (CSCs) may have adopted dual active-dormant mechanisms to respectively sustain growth while eluding exhaustion from conventional chemotherapy such as 5-fluorouracil (5-FU). How to effectively target dual active-dormant CSCs while preserving NTSCs is essential to curing cancers. We compared the kinetic states of NTSCs in gut and bone marrow as well as leukemia stem cells following 5-FU treatment and found a narrow window of opportunity when forcibly activated dormant NTSC/CSCs can be targeted following depletion of proliferating progeny. Given that stemness factors predict poor overall survival (OS) in many cancers, we proposed a novel two-step ADAPT strategy_activate from dormancy and potentiate subsequent targeting_ in an attempt to synchronize cytotoxic effects of 5-FU on proliferating cells with stemness inhibitors targeting activated CSCs respectively. We applied the two-step protocol using capecitabine, an oral 5-FU prodrug, and celecoxib, a selective COX-2 inhibitor that is also a stemness inhibitor (it down-regulates LGR5/6, CD133, Oct4/Sox effectors, ALDH, CD24, Wnt, Sonic Hedghog) in patients with unresectable metastatic colorectal cancer. We found that the ADAPT strategy resulted in complete or near complete response rate in 27 patients with surgically unresectable metastatic colorectal cancer, especially if coupled with radiation. The median survival for this group of patients reached 92.7 months (95% CI, 53.5 months - not reached). Paradoxically, patients who had confirmed complete response without surgery but with long-term ADAPT therapy enjoyed 100% 5-year relapse free survival compared to 42% of patients who had undergone surgical resection of metastasis (p=0.04 log rank). Intriguingly, Celecoxib exerted many opposite biologic effects compared to 5-FU on cell cycle, apoptosis, DNA repair/synthesis, particularly stemness genes/pathways, and thus produced conflicting effect in short-term colon cancer cultures when combined with 5-FU. This observation potentially explains the 6 months gain in OS in the responding patients and the lack of OS for all patients in reported phase III BICC-C study that randomized Celecoxib vs placebo with 5FU based chemotherapy.. Thus, optimal ADAPT strategy to target CSCs requires initial cytoreduction of proliferating progeny and activation of dormant/drug-resistant CSCs, and subsequent cyclical exhaustion via long-term exposure to stemness inhibitors along with intermittent cytotoxic agents such as 5-FU.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-254.