bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5111: Integrative phospho-proteomic and genomic analyses identify AXL as a potential biomarker and therapeutic target for NRAS-mutated melanoma
Authors: Fedorenko Inna V. , Paraiso Kim H.T. , Joseph Beulah D. , Fang Bin , Koomen John , Eschrich Steven , Nathanson Katherine L. , Wubbenhorst Bradly , Mathew Rahel , Messina Jane , Smalley Keiran S.M. 
Published: June 2012

Abstract
Currently, few therapeutic options exist for the 15-20% of patients whose melanomas harbor activating mutations in NRAS. Here, we have used comprehensive phospho-proteomic and genomic analysis to characterize the patterns of intracellular signaling in a panel of NRAS and BRAF-mutated melanoma cell lines, with the goal of identifying new biomarkers and therapeutic targets for NRAS mutated melanomas. Our preliminary analyses showed BRAF mutated melanomas to have less diverse intracellular signaling than the NRAS group, which tended to have constitutive phosphorylation in a wide-range of receptor tyrosine kinases (RTKs), such as c-MET, EGFR, HER2 and c-Abl. Although these patterns of RTK activity were heterogeneous across the NRAS mutated melanoma cell line panel, all of the NRAS mutated cell lines examined showed constitutive activity in the receptor tyrosine kinase Axl. A role for Axl in the oncogenic behavior of NRAS mutated melanomas was suggested by array CGH studies showing genomic amplification of Axl in a significant fraction of the NRAS mutated melanoma cell lines and by Western Blot experiments demonstrating increased expression of Axl and its ligand Gas6. Mass spectrometry analysis and immunoprecipitation revealed Axl to be constitutively phosphorylated at the Tyr702 autophosphorylation site in NRAS mutated melanoma cell lines only. Functionally, siRNA knockdown and pharmacological inhibition of Axl impaired the survival and invasion of NRAS mutated melanoma cell lines grown under 3D organotypic cell culture conditions. Studies are ongoing to confirm the role of Axl in the initiation and progression of melanomas harboring NRAS mutations and determine whether Axl constitutes a therapeutic target for this melanoma sub-group.
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 5111. doi:10.1158/1538-7445.AM2011-5111
Abstract 5121: A targeted approach to identify activators of class IA phosphoinositide-3-kinase in cancers using tandem mass spectrometry
Authors: Asara John M. , Cantley Lewis C. , Engelman Jeffrey A. 
Published: June 2012

Abstract
A majority of human cancers exhibit aberrant activation of the phosphoinositide 3-Kinase (PI3K) pathway. In many cases this activation is due to mutations or amplifications in upstream activators of PI3K resulting in activation by direct binding of phosphotyrosine proteins (e.g., receptor tyrosine kinases (RTK) or adaptors such as IRS-1/2 or Gab1/2) to the p85 regulatory subunit of PI3K. To date, experiments to identify the mechanisms of PI3K activation in cancer have remained difficult and cumbersome. Since inhibitors of many of these RTKs are either already approved or in clinical trials, identification of the major upstream activators of PI3K in a given tumor could suggest the appropriate therapeutic intervention. Here we present a quantitative mass spectrometry approach (targeted ion MS/MS – TIMM) for identifying the upstream activators of PI3K in cancer cell lines grown on plastic as well as in tumor Xenografts. Importantly, we show that in a series of non small cell lung carcinoma cell lines, it is possible to predict the appropriate drug for treating the cells based on the upstream activator of PI3K as revealed by TIMM. Specifically, we identified how PI3K is activated in MET amplified, EGFR and EML4-ALK driven non-small cell lung cancers (NSCLCs) both in vitro and in vivo, and were successful in identifying the optimal RTK inhibitor treatment for the H1703 NSCLC cell line. Additionally, this technology revealed that TORC1 inhibition leads to activation of PI3K via IRS-2, not IRS-1 in KRAS mutant cell lines.
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 5121. doi:10.1158/1538-7445.AM2011-5121
Abstract 5126: Development of a high throughput quantitative phosphoproteomic method to study trastuzumab resistance
Authors: Boyer Alaina P. , Alvarez Sophie , Boyne Michael , Hicks Leslie , Bose Ron 
Published: June 2012

Abstract
Her2 is a receptor tyrosine kinase that is overexpressed in approximately 20-30% of human breast cancers and affects clinical prognosis and outcome of these cancers. Treatment of Her2-positive breast cancer with the monoclonal antibody, trastuzumab, has improved the outcomes and prognosis for patients with this breast cancer subtype. However, development of resistance to trastuzumab is a major clinical problem in metastatic Her2-positive breast cancer. Many of the known mechanisms of trastuzumab resistance cause changes in protein phosphorylation patterns and therefore we have employed quantitative phosphoproteomics to further study trastuzumab resistance. Quantitative phosphoproteomics is a powerful method to comparatively identify phosphorylated proteins between different samples. Using electrospray tandem-mass spectrometry coupled with immunoaffinity purification and titanium dioxide (TiO2) phosphoenrichment, we wanted to identify differentially phosphorylated proteins in a pair of trastuzumab sensitive and resistant cells. We used stable isotope labeling of amino acids in cell culture (SILAC) to obtain quantitative information on the proteins identified by mass spectrometry. We have obtained quantitative data on two trastuzumab sensitive and resistant pairs of Her2 overexpressing human breast cancer cell lines (BT474 and SKBR3). 275 proteins were identified in the phosphoenriched fraction from the SKBR3 pair with 83 proteins reporting a ratio. 769 proteins were identified in the phosphoenriched fraction from the BT474 pair with 683 proteins reporting a ratio. Treatment of the trastuzumab resistant cells with Her2 siRNA drastically resulted in cell death indicating the sustained dependence of these cells on Her2 despite the resistance to Her2 targeted therapy. RNAi experiments, in combination with trastuzumab exposure, of candidate proteins expressing an increase in phosphorylation will be tested further to determine if trastuzumab resistance can be reversed.
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 5126. doi:10.1158/1538-7445.AM2011-5126
Abstract 5129: Mapping the activity of oncogenic signaling networks with phospho-specific Liquid Tissue® mass spectrometry
Authors: Hembrough Todd A. , Thyparambil Sheeno , Liao Wei-Li , Krizman David , Darfler Marlene , Bengali Kathleen , Abdo Joe , Burrows Jon 
Published: June 2012

Abstract
Many of the current targeted therapies in oncology target the activity of either receptor tyrosine kinases (Her2, EGFR, IGF1R, cMet, FGFR, PGDFR) or cytoplasmic tyrosine kinases (cSrc, AurA, PI3K, MEK, Raf, Akt). The current slate of clinically useful diagnostic tests measure target expression either directly by immunohistochemistry or indirectly by extrapolation from the level of gene or mRNA expression/amplification. These assays are limited by lack of quantitation, and no assay can directly assess the activation state of the signaling pathway components. The lack of information regarding target activation and downstream signal transduction can be overcome using the Liquid Tissue®-SRM technology platform. This approach enables relative and absolute quantification of multiple proteins and their phosphorylation status directly in formalin fixed tissue.
In order to fill this diagnostic ‘gap’ we have used this platform to develop a quantitative multiplexed phospho-target assay format which measures the specific phosphorylation state of many clinically relevant oncogenic kinases (EGFR, cMet, Her3, Erk, cSrc, Mek, Akt, p70S6K) directly in FFPE tumor tissue.
This phosphopeptide multiplex assay was initially preclinically validated on the A431 tumor cell line which harbors an amplification of the EGFR gene. These cells were stimulated with a dose range of EGF (50-200ng/ml) or in a time course study (EGF 50ng/ml for 5-30min). Confluent, EGF stimulated cells were then formalin fixed, subjected to Liquid Tissue® processing, and then phospho-enriched using TiO2 magnetic beads. The resulting enriched phosphopeptides were then analyzed by mass spectrometry. This method demonstrated the feasibility, and reproducibility of this method for quantitating EGFR pY1197, EGFRpT693, AKT pS473, p-p70S6K pS447, ERK pT202/pY204.
We extended this study by performing phosphoenrichment and mass spectrometric analysis of human tumor xenografts, primary human tumor NSCLC explants and clinical trial tissue from EGFR inhibitor treated NSCLC and colorectal cancer patients. In each case we were able to enrich and measure the phosphorylation of a large set of important oncogenic kinases.
Our intention is to develop this diagnostic tool to provide a multiplex assay format in formalin fixed tissue that can be applied from preclinical to clinical studies that will impact both targeted drug development and patient stratification needs in this era of personalized healthcare.
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 5129. doi:10.1158/1538-7445.AM2011-5129
Abstract 5143: The role of VEGFR2 in lung cancer differs between adenocarcinoma and squamous cell carcinoma cell lines
Authors: Larrayoz Marta , Agorreta Jackeline , Pajares Maria J. , Montuenga Luis M. , Pio Ruben 
Published: June 2012

Abstract
Vascular endothelial growth factor A (VEGFA) is a cytokine implicated in proliferation, migration and cell survival that mediates its effects through its major receptor, VEGFR2. VEGFA is highly induced by hypoxia and is a crucial regulator of angiogenesis in both healthy and tumor tissues. For this reason, many efforts have been made to target the VEGFA/VEGFR2 pathway for the treatment of cancer. In lung cancer, an anti-VEGFA therapy (bevacizumab) was approved, in combination with platinum-based chemotherapy, as first line treatment in unresectable advanced non-small cell lung cancer (NSCLC). The expression of VEGFA has been widely reported in NSCLC, supporting the idea that VEGFA is produced by tumor cells and activates its receptors on endothelial cells, leading to vascularization of the tumor. However, it is known that NSCLC cells also express VEGFR2, although its role in tumor progression or response to treatment has not been evaluated.
The aim of the present work was to study the biological role of the autocrine/paracrine VEGFA loop in NSCLC cells, paying special attention to the differences between the two main histological subtypes. To this purpose, we assessed the expression and activation of the VEGFA-VEGFR2 pathway in NSCLC cell lines, analyzing the effect of VEGFR2 inhibition/overexpression in both adenocarcinoma (ADC) and squamous cell carcinoma (SCC) cell lines.
Human NSCLC cell lines were examined for the expression of VEGFA and VEGFR2 by real time PCR and Western blotting. All cell lines expressed VEGFA. Two out of ten ADC cell lines (NCI-H441 and NCI-H358), and two out of eleven SCC cell lines (EPLC-272H and LOU-NH91) showed detectable levels of VEGFR2. Addition of exogenous VEGFA to VEGFR2-positive cells induced phosphorylation of the receptor and activation of its intracellular signaling pathway.
To better understand the role of VEGFR2 in NSCLC, we used lentiviruses to inhibit or retroviruses to overexpress this protein in VEGFR2-positive cell lines. Changes in VEGFR2 levels had no effect in proliferation or migration in the ADC cell lines. However, in the SCC cell lines, the inhibition of the receptor increased proliferation and decreased migration. When the receptor was overexpressed in the SCC cell lines, the opposite effects were observed.
In conclusion, VEGFR2 is expressed by some NSCLC cell lines and its activation may have different effects depending on the histology of the cells. Specifically, in SCC cells the activation of VEGFR2 decreases cell growth. These data illustrate the importance of the different histologies in the study of the VEGFA biology 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 5143. doi:10.1158/1538-7445.AM2011-5143
Abstract 5167: A new panel of tissue markers for the prediction of bone metastatization from primary breast cancer
Authors: Mercatali Laura , Ibrahim Toni , Sacanna Emanuele , Scarpi Emanuela , Fabbri Francesco , Ricci Rossana , Calistri Daniele , Amadori Dino 
Published: June 2012

Abstract
Background: It is known that numerous molecular markers associated with proliferation, invasion and adhesion processes, growth factors, chemokines and their receptors, and molecules with bone-like phenotype are involved in metastasization to bone. Only cancer cells with specific molecular profiles are capable of reaching and colonizing bone tissue. The early prediction of relapse in this site could be used to select candidates for tailored therapy with bone-specific drugs such as bisphosphonates or RANK-L inhibitors. In the present study we aimed to identify primary tumor markers capable of predicting relapse to bone.
Material and methods: The expression of different markers was retrospectively analyzed in frozen breast cancer tissue samples from 40 patients comprising 15 cases with no evidence of disease (NEDP), 15 with bone metastases (BMP), and 10 with visceral metastases (VMP). Twelve transcripts were analyzed by Quantitative Real time PCR: trefoil factor 1(TFF1), DKK1, bone sialoprotein (IBSP), heparanase (HPSE), osteopontin (SPP1), Agr2, SPARC, CTGF, COMP, follistatin (FST), osteoprotegerin and RANK. The predictive accuracy of each marker was calculated using receiver operating characteristic (ROC) curves.
Results: The analysis of marker expression in the 3 different subgroups showed twofold higher median values of COMP and HPSE in BMP with respect to either NEDP or VMP (no significant difference). Furthermore, TFF1 median value was about sevenfold higher in BMP than in the other 2 subgroups (p=0.05). The area under the curve (AUC) was 0.73 for TFF1 and 0.62 for COMP and HPSE. In the dichotomous variable analysis, the most important result was observed for TFF1; in particular, TFF1 positivity was observed in 67% of cases in the BMP subgroup compared to only 21% and 20 % in NEDP and VMP, respectively. The combination analysis of TFF1 and other markers showed that positivity to at least one of the three markers, TFF1, DKK1, or IBSP, was observed in 80% of cases for the BMP group, and in only in 21% and 20% of cases in NEDP and VMP subgroups, respectively (p=0.041).
Conclusions: The results from this preliminary study suggest that Real-Time PCR analysis of gene expression and, in particular, the coexpression of some markers in primary breast cancer could identify patients destined to bone relapse who could benefit from adjuvant treatment with bone-specific drugs.
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 5167. doi:10.1158/1538-7445.AM2011-5167
Abstract 5171: Expression and function of Snail2 in osteosarcoma
Authors: Sharili Amir Shaya S. , Allen Steve , Smith Ken , Price Joanna , McGonnell Imelda M. 
Published: June 2012

Abstract
Purpose: Snail2 is a well established regulator of EMT in malignant epithelial tumors, however in sarcomas it is not known if this protein is present and contributes to tumor progression. Here we examine the expression of Snail2 in clinical cases of one type of sarcoma; osteosarcoma. We hypothesize that Snail2 is expressed in osteosarcomas and that this expression correlates with tumor grade. In addition, we also hypothesized that Snail2 promotes metastasis in osteosarcomas.
Experimental design: Snail2 localization was determined in clinical biopsies of different grades of canine osteosarcomas using immunohistochemistry. The function of Snail2 in OS was evaluated using stable human and canine OS cell lines in which loss of function was achieved using small interfering RNA (siRNA) and gain of function using over-expression vectors. These lines were used to assess changes in cell motility and invasion using in vitro assays.
Results: Nuclear Snail2 staining was observed in all cases of osteosarcoma examined. Ordinal logistic regression analysis revealed that elevated Snail2 expression was significantly (P=0.014) correlated with tumor grade. Cell lines of canine (D-17) and human (Saos-2) osteosarcoma stably transfected with Snail2 siRNA showed a loss of osteoblastic morphology becoming flattened whereas those overexpressing Snail2 appeared more spindle shaped. Scratch assays showed that motility of osteosarcoma cells was correlated with levels of Snail2 expression.
Conclusion: This is the first time Snail2 has been associated with any sarcoma and this study shows that Snail2 may be a useful prognostic marker for osteosarcoma. In addition, it indicates that Snail2 may play a role in osteosarcoma metastasis. Thus it may be a potential target for clinical intervention in this disease.
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 5171. doi:10.1158/1538-7445.AM2011-5171
Abstract 5209: The roles of Notch signaling in the development of non-small cell lung cancer
Authors: Osanyingbemi-Obidi Joyce O. , Rudin Charles M. 
Published: June 2012

Abstract
Lung cancer is the most common cause of cancer related deaths in the United States, accounting for 29% of all cancer deaths. Approximately 85% of all lung cancers are of non-small cell histology. Although current therapies have marginally improved survival and quality of life for patients with Non-Small Cell Lung Carcinoma (NSCLC), this remains a nearly universally fatal disease. New approaches to drug development and further studies of the biology of this disease are critically needed. We hypothesized that high level Notch signaling would define a subpopulation of NSCLC cells with markedly elevated clonogenic potential, and that inhibition of Notch signaling could inhibit NSCLC tumorigenesis. To test these hypotheses and to define the potential utility of Notch inhibitors in NSCLC, we have evaluated the temporal and spatial activation of Notch signaling in a murine model of NSCLC tumorigenesis, evaluated a dominant negative transgenic mouse model, and are assessing whether Notch activation correlates with clonogenic and tumorigenic potential in human NSCLC lines. Down regulation of Notch signaling using a selective γ-secretase inhibitor (Mrk 003; Merck) was evaluated in three NSCLC cell lines (NCI-H1299, and -H1435). Cells were incubated for 96 hours with Mrk 003 at concentrations ranging from 0.1uM to 10.0μM. After 96 hours, a 60% suppression of Hes 1 expression was observed. In conjunction with these studies we have created a double transgenic model, LSL-K-rasG12D × DNMAML (dominant negative mastermind) mice. Expression of the DN-MAML gene results in inhibition of the Notch pathway. We administered adenoviral CRE intranasally to these mice and generated intraparenchymal lung tumors in both KRAS and KRAS/DN-MAML mice. Surprisingly, and in contrast to our hypothesis, tumor burden was not decreased in the double transgenic model relative to the Kras control group. Mastermind-1 may have effects other than regulation of Notch signaling, including a possible interaction with p53 that is being currently explored, and which may explain these surprising findings. Characterization of highly clonogenic progenitor populations in NSCLC, and definition of the roles of Notch pathway regulators in tumorigenesis, may aid in the development of more effective therapeutics.
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 5209. doi:10.1158/1538-7445.AM2011-5209
Abstract 5212: Loss of G-protein coupled calcium sensing receptor augments malignancy and bestows cancer stem cell-like properties in human colon carcinoma cells
Authors: Singh Navneet , Liu Guangming , Chakrabarty Subhas 
Published: June 2012

Abstract
The G-protein coupled calcium sensing receptor (CaSR) is a robust promoter of differentiation in colonic epithelial cells. Loss of CaSR expression allows cancer cells to escape from CaSR control. Loss of CaSR expression augments the malignant phenotype in vitro and is associated with undifferentiated and invasive colon carcinomas in vivo (Cancer Res. 63: 67, 2003; 65: 493, 2005; Int. J. Cancer 121: 1455, 2007;126: 631, 2010; Mol. Carcinogenesis 48: 202, 2009). Interestingly, human colon carcinoma cell lines contain small subpopulations (10-20%) that do not express CaSR (termed CaSR null cells). Here, we report the isolation and characterization of CaSR null cells from the CBS and HCT116 human colon carcinoma cell lines.
We isolated CaSR null cells by magnetic cell sorting using monoclonal anti-CaSR antibody. CaSR null cells were cultured and maintained in stem cell culture medium. Biologic characterization of CaSR null cells showed that these cells were non-adherent and grew as three-dimensional spherical clusters with an increase in propensity for anchorage independent growth. CaSR null cells were highly invasive in matrigel invasion assays and resistant to treatment with cytotoxic drugs. Western analysis showed that CaSR null cells expressed a high level of thymidylate synthase and survivin which have been reported to be an underlying basis of drug resistance in colon cancer. Western analysis also showed that CaSR null cells expressed a high level of the previously reported cancer stem cell markers CD133, CD44 and Nanog. Molecular profiling by quantitative RT-PCR revealed a significant increase in the expression of epithelial-mesenchymal transition associated mRNAs in CaSR null cells. These mRNAs were N-cadherin, β-catenin, vimentin, fibronectin, FSP1, Snail1, Snail2, Twist, FOXC2 and SIP1. Interestingly, CaSR null cells re-expressed CaSR, over time, when placed in culture medium used to propagate the parental CBS and HCT116 cells. Re-expression of CaSR in CaSR null cells attenuated the expression of markers associated with the malignant phenotype.
We conclude that CaSR null cells represent a highly malignant subpopulation of colon cancer cells and that these cells may possess cancer stem cell-like properties.
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 5212. doi:10.1158/1538-7445.AM2011-5212