bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract C199: Coordinate phosphorylation of multiple residues on single AKT1 and AKT2 molecules.
Authors: Guo Huifang , Gao Meng , Lu Yiling , Liang Jiyong , Lorenzi Philip L. , Bai Shanshan , Hawke David H. , Li Jie , Dogruluk Turgut , Scott Kenneth L. , Jonasch Eric , Mills Gordon B. , Ding Zhiyong 
Published: August 2014

Abstract
Aberrant AKT activation is prevalent across multiple human cancer lineages providing an important new target for therapy. Twenty-two independent phosphorylation sites have been identified on specific AKT isoforms likely contributing to differential isoform regulation. However, the mechanisms regulating phosphorylation of individual AKT isoform molecules have not been elucidated due to the lack of robust approaches able to assess phosphorylation of multiple sites on a single AKT molecule. Using a nanofluidic proteomic immunoassay (NIA), consisting of isoelectric focusing followed by sensitive chemiluminescence detection, we demonstrate that under basal and ligand-induced conditions that the pattern of phosphorylation events is markedly different between AKT1 and AKT2. Indeed, there are at least 12 AKT1 peaks and at least 5 AKT2 peaks consistent with complex combinations of phosphorylation of different sites on individual AKT molecules. Following insulin stimulation, AKT1 was phosphorylated at Thr308 in the T-loop and Ser473 in the hydrophobic domain. In contrast, AKT2 was only phosphorylated at the equivalent sites (Thr309 and Ser474) at low levels. Further, Thr308 and Ser473 phosphorylation occurred predominantly on the same AKT1 molecules, whereas Thr309 and Ser474 were phosphorylated primarily on different AKT2 molecules. While basal AKT2 phosphorylation was sensitive to inhibition of PI3K, basal AKT1 phosphorylation was essentially resistant. PI3K inhibition decreased pThr451 on AKT2 but not pThr450 on AKT1. Thus NIA technology provides an ability to characterize coordinate phosphorylation of individual AKT molecules providing important information about AKT isoform-specific phosphorylation, which is required for optimal development and implementation of drugs targeting aberrant AKT activation.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C199.
Citation Format: Huifang Guo, Meng Gao, Yiling Lu, Jiyong Liang, Philip L. Lorenzi, Shanshan Bai, David H. Hawke, Jie Li, Turgut Dogruluk, Kenneth L. Scott, Eric Jonasch, Gordon B. Mills, Zhiyong Ding. Coordinate phosphorylation of multiple residues on single AKT1 and AKT2 molecules. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C199.
Abstract C201: Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics.
Authors: Chen Li , Dastur Anahita , Benes Cyril 
Published: August 2014

Abstract
The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, and can vary with both the underlying genetic lesion and the origin or type of tumor. For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance. Here we describe a novel gain-of-function forward genetic approach for identifying potential mechanisms of resistance. This system uses a modified piggyBac transposon to generate libraries of mutagenized cells, each containing transposon insertions that randomly activates nearby gene expression. By combining this with high-throughput sequencing, we have performed genome-wide screens for paclitaxel resistance mechanism in a variety of cancer cell lines. Validating this approach, we identified the multidrug transporter ABCB1 as the major contributor to resistance. In addition, we identified several potential novel resistance genes. Therefore we have developed a powerful new pipeline tool to systematically discover common and tumor specific pathways of resistance in human cancers. This cost-effective approach can be readily applied to different cell lines. Moreover, its ability to identify gene interactions and to probe complex genetic context provides a significant advantage over RNAi- or cDNA-based screens.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C201.
Citation Format: Li Chen, Anahita Dastur, Cyril Benes. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C201.
Abstract C202: Probing EGFR, HER2 and c-Met protein-protein interactions using an antibody array.
Authors: Knowles Jacob , Capodilupo Stephen , Noring Richard , Campos-González Roberto , Herrera Julio , Gechtman Zev 
Published: August 2014

Abstract
The receptor tyrosine kinase (RTK) family comprises important disease drivers and validated drug targets. Cooperation between certain RTKs is often achieved through physical interactions and is thought be a contributing factor to some cases of tumor resistance to targeted therapies. Epidermal Growth Factor Receptor (EGFR), HER2/ErbB2, and c-Met are prominent examples of disease driver RTKs that cooperate and form heterodimers. Current methods to detect RTK protein-protein interactions lack proper throughput, are not quantitative, or rely on highly engineered systems and cumbersome workflows. We have developed a planar surface antibody array-based sandwich assay that enables the detection and relative quantification of interactions between EGFR, HER2, and c-Met. The antibody-based assay revealed co-existing combinatorial receptor interactions that were unique to each cell type tested. The assay also pointed to an existence of distinct topological configurations of EGFR-c-Met and EGFR-HER2 heterodimers, unveiling previously not described nuances of these interactions. Lastly, the array-based assay allowed monitoring the disruption of receptor complexes using small molecule inhibitors and revealed differential sensitivity of EGFR-HER2 and EGFR-c-Met complexes to a small molecule EGFR kinase inhibitor, gefitinib. The antibody array sandwich assay described here allows utilizing larger panel of affinity reagents and can be applied to broader range of cases with various topological requirements, thus offering an advantage over technologies that have strict proximity requirement. This novel protein interaction array enables parallel detection of RTK protein-protein interactions, allowing a more systematic monitoring of response to activators or inhibitors.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C202.
Citation Format: Jacob Knowles, Stephen Capodilupo, Richard Noring, Roberto Campos-González, Julio Herrera, Zev Gechtman. Probing EGFR, HER2 and c-Met protein-protein interactions using an antibody array. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C202.
Abstract C213: Protein interaction analysis of mll-aff4 and mll-fel oncogenic fusion proteins using data mining approach.
Authors: Hovhannisyan Grant Henry , Marqaryan Ashot Vardan 
Published: August 2014

Abstract
Mixed-lineage leukemia (MLL) is a transcriptional co-activator that plays an essential role in early development and hematopoiesis. MLL H3K4 methyltransferase activity mediates chromatin remodeling associated with epigenetic regulation of transcription activation. Multiple chromosomal translocations of MLL gene lead to its fusion to numerous partner genes and production of chimeric proteins, which are enrolled in progression of similar phenotypes of leukemia [5]. However, protein interaction models of different MLL fusions are still debated. To assess the pattern of protein interactions of MLL chimeras, we have performed protein-protein interaction (PPI) network analysis for two MLL fusion proteins, MLL-FEL - t(4;11)(q21;q23) and MLL-AFF4 - ins(5;11)(q31;q13q23), which are involved in acute leukemia progression [2]. Protein interaction data was extracted from data mining software GPS-Prot v. 2.0 [4]. PPI network visualization and network parameters evaluation were performed using Cytoscape v. 2.8 [7]. Cluster analysis was made by MCODE plug-in. The statistical significance of cluster extraction was assessed as described [3]. Comparative experimental interaction data taken from previously published papers were manually discarded from our analysis. Our results show that each of the components of studied fusion proteins in native form compose highly interconnected distinct regions. MLL PPI network analysis reveals a clique cluster with cluster density equal to 1, indicating that MLL interacters are united in protein macromolecular complex, which is in a good accordance with previously published experimental data [6]. Worth of mention, that FEL and AFF4 proteins form the same clique clusters, which also is in a good congruence with experimentally obtained data [1]. Therefore, we assume that the MLL-AFF4 and MLL-FEL fusion proteins generate the identical PPI network, which underlie the manifestation of similar malignancy. Further corroboration of this result will confirm the assumption that different fusions can bring to the same disease network, which could possibly has its impact in leukemia therapeutical approaches. To obtain more detailed pattern of protein interactions of MLL-caused leukemias further network analysis is required.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C213.
Citation Format: Grant Henry Hovhannisyan, Ashot Vardan Marqaryan. Protein interaction analysis of mll-aff4 and mll-fel oncogenic fusion proteins using data mining approach. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C213.
Abstract C221: A genome-wide RNA interference screen identifies synthetic lethal interactions with the BRAF oncogene.
Authors: Min Chengyin , Konieczkowski David J. , Kwon Christine , Linja Marika , Vasudevan Krishna , Weir Barbara , Goetz Eva , Garraway Levi 
Published: August 2014

Abstract
Oncogenic mutations in BRAF are found in 50-70% of malignant melanomas and in ∼8% of all cancers. Activating BRAF mutations confer exquisite dependency on RAF/MEK/ERK signaling and RAF and MEK inhibitors achieved striking clinical response in the majority of patients with BRAFV600E-mutant melanoma. However, nearly all patients progress to therapeutic resistance and there are limited treatment options for patients with relapsed tumors. Identification of genes that are essential only in the presence of BRAFV600E mutation may inform alternative as well as combinatorial therapeutic approaches. Here, we used systematic RNA interference to discover synthetic lethal interactions in melanoma cells carrying BRAFV600E mutation. In addition, Project Achilles at the Broad Institute reported systematic loss-of-function studies in more than 100 human cancer cell lines. We intersected the list of genes that are synthetic lethal with BRAFV600E mutation in our melanoma study and that of Project Achilles. As a result, we have identified novel “druggable” targets for cells driven by BRAFV600E mutation. Our extensive in vitro and in vivo validation has confirmed and established key synthetic lethal interactions with BRAFV600E mutation. One major mechanism of acquired resistance to RAF and MEK inhibition is reactivation of MEK/ERK pathway. Importantly, we demonstrated that these synthetic lethal genes are also essential in the context of acquired resistance to RAF and MEK inhibition. Together, our study has identified novel targets for the treatment of oncogenic BRAF-driven melanoma and suggests targeting these genes as novel therapeutic strategies to overcome acquired resistance to RAF and MEK inhibition.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C221.
Citation Format: Chengyin Min, David J. Konieczkowski, Christine Kwon, Marika Linja, Krishna Vasudevan, Barbara Weir, Eva Goetz, Levi Garraway. A genome-wide RNA interference screen identifies synthetic lethal interactions with the BRAF oncogene. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C221.
Abstract C228: A retrospective study of patients with non-small cell lung cancer who have Life Technologies Pervenio™ Lung RS test performed.
Authors: Singh Jaswinder , Hasan Raza , Feeback Jennifer 
Published: August 2014

Abstract
With lung cancer causing the highest mortality in cancer patients, an accurate method to stratify lung cancer patients has been needed. This stratification would allow physicians to tailor their management. Furthermore, even with resection of early-stage NSCLC, there is a 35-50% recurrence, considerably poor when compared to other solid tumors. A new 14-gene PCR assay was created to stratify the risk of patients based on their lung cancer. The Pervenio™ Lung RS Test was established to discriminate the low vs intermediate vs high risk patients in order to provide information regarding mortality rates to guide management. Using this clinically proven PCR assay in a site-specific study, results mirrored the original study. The patients who were stratified as high-risk with the Pervenio™ Lung RS Test, were the same patients who had recurrence and death. Amongst the high-risk group, one patient expired and three remained alive. Furthermore, of the three living patients, two patients had progressive disease with deteriorating conditions and recurrence. This new assay successfully has proven to accurately stratify patients, in regards to survival and recurrence. This stratification will allow physician to alter their management and monitoring. Comprehension of the projected disease course is useful in planning a course of management, whether it may be curative versus palliative.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C228.
Citation Format: Jaswinder Singh, Raza Hasan, Jennifer Feeback. A retrospective study of patients with non-small cell lung cancer who have Life Technologies Pervenio™ Lung RS test performed. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C228.
Abstract C23: Functional characterization of viable circulating tumor cells using nanowells.
Authors: Yao Xiaosai , Choudhury Atish D. , Yamanaka Yvonne J. , Hahn William C. , Wittrup K Dane , Love J Christopher 
Published: August 2014

Abstract
Current characterizations of circulating tumor cells (CTCs) are limited to enumeration, genotyping, and gene expression. Because these assays each require fixation or lysis, it has not been possible to evaluate several important characteristics of live CTCs at the single-cell level. We have interrogated viable, single CTCs using arrays of subnanoliter wells (nanowells), performing functional measurements of viability, migration, and secretion of soluble factors.
We developed a process using nanowells to isolate and characterize viable CTCs from whole blood. Each poly(dimethylsiloxane) (PDMS) array comprises 84,762 cubic wells of 275 pL each. CTCs were enriched from whole blood by negative selection against CD45 and loaded onto the array to settle into the wells by limiting serial dilution. Because CTCs are rare, the loading biased the occupancy of the wells to single CTCs or CTCs in preformed clusters, allowing comparisons among individual CTCs. The defined address of each well allowed spatiotemporal tracking of single CTCs, and subsequent registration of data for functional measures on each CTC. Using this approach, we made three types of measurements on viable CTCs isolated from prostate cancer patients: (1) immediate and short-term viability of CTCs, (2) migration and invasion potential of CTCs, and (3) secretion of soluble factors.
We found a rare subset of CTCs to possess malignant traits indicative of metastatic potential in late-stage, progressing prostate cancer patients. These CTCs were resistant to anoikis after being in the circulation as they stained Calcein AM+/Annexin V−, and remained viable for at least a week in culture. They were invasive in their epithelial state when embedded in Matrigel. They could also secrete proteases capable of cleaving peptide substrates. However, we did not observe such metastatic potential in every CTC, pointing to the presence of heterogeneity within CTCs and suggesting that enumeration of CTCs alone may be insufficient to understand metastasis or stratify patients.
By interrogating the functional behavior of individual CTCs, we identified a rare subset of CTCs with phenotypes consistent with more efficient metastasis. The nanowell technology holds the potential to further investigate the cellular characteristics of rare tumor cells and design therapies to counter metastasis.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C23.
Citation Format: Xiaosai Yao, Atish D. Choudhury, Yvonne J. Yamanaka, William C. Hahn, K Dane Wittrup, J Christopher Love. Functional characterization of viable circulating tumor cells using nanowells. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C23.
Abstract C233: Activation of p53 by the NEDD8 activating enzyme inhibitor MLN4924 is independent of Cdt1 and involves the cullin-RING ligase CRL4-DTL.
Authors: Blank Jonathan L. , Liu Xiaozhen J. , Bernard Hugues , Liao Hua , Cosmopoulos Katherine , Lightcap Eric S. 
Published: August 2014

Abstract
NEDD8-activating enzyme (NAE) is an E1 involved in the activation of a large family of E3 ubiquitin ligases termed the cullin-RING ligases (CRLs) through conjugation of cullin proteins with the ubiquitin-like modifier NEDD8. Polyubiquitination of CRL substrates targets them for degradation by the 26S proteasome. NAE thereby regulates the stability of many proteins including those required for cancer cell growth and survival. MLN4924 is an investigational small molecule inhibitor of NAE with 2-3 orders of magnitude selectivity over the related E1’s ubiquitin-activating enzyme (UAE) and sumo-activating enzymes (SAE; Ref. 1). Recently, a genome-wide siRNA screen in the A375 melanoma cell line identified key DNA damage response genes affecting sensitivity of cells to MLN4924, many of which were associated with the p53 pathway which activates a p21-dependent intra-S-phase checkpoint (2). A comparison of the effects of TP53 RNAi in A375 cells to genetic deletion of TP53 in HCT116 cells (HD 104-001 cells, Horizon Discovery Ltd) suggests that p21 induces a cell cycle arrest within 24 h, whereas analysis of the p53-regulated transcriptional signature indicates that proapoptotic proteins are up-regulated at later times. Surprisingly, stabilization of p53 by MLN4924 appears independent of the replication licensing factor Cdt1, ATR activation, or p53 neddylation, but rather involves the E3 ligase complex Cul4A/B-Ddb1-DTL. Furthermore, Nutlin-3induced ubiquitination of p53 could be blocked by MLN4924, suggesting that Mdm2 and DTL may cooperate in the ubiquitination of p53.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C233.
Citation Format: Jonathan L. Blank, Xiaozhen J. Liu, Hugues Bernard, Hua Liao, Katherine Cosmopoulos, Eric S. Lightcap. Activation of p53 by the NEDD8 activating enzyme inhibitor MLN4924 is independent of Cdt1 and involves the cullin-RING ligase CRL4-DTL. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C233.
Abstract C235: An investigation of the p53 ubiquitin-proteasome system using a novel non-steady-state enzyme kinetic model.
Authors: Talwai Prem M. 
Published: August 2014

Abstract
Overzealous MDM2-mediated ubiquitination of p53 characterizes and sustains over 50% of all human cancers. Successful targeted cancer therapy hinges on a thorough understanding of the ubiquitination process. Unfortunately, current steady-state enzyme kinetic models fail to accurately describe the ubiquitin-proteasome system, due to the assumption that the enzyme (E3 ligase) is expressed at infinitesimally smaller concentrations than the substrates (ubiquitin-conjugated E2 and target protein). This limitation of the quasi-steady state assumption prohibits the use of steady-state models when analyzing the cancerous consequences of extreme ubiquitin-ligase overexpression. This paper derives a novel non-steady-state mathematical model of reversible ordered ternary complex enzyme kinetics, which can be used to simulate the behavioral response of the ubiquitin-proteasome system to specific variations in the cellular concentrations of p53, MDM2, and ubiquitin-conjugated E2D3. Computer simulations of the model were used to study the effects of E2D3-Ub and MDM2 concentrations on the rates of p53 ubiquitination at different temperatures. In each process, it was observed that the ubiquitin-ligase MDM2 accelerates the carcinogenic ubiquitination process, while ubiquitin-conjugated E2 inhibits it. It was also discovered that E2D3-Ub is more effective inhibitor of overzealous p53 ubiquitination when present at higher concentrations. However, it was also observed that high concentrations of p53 hinder the ability of E2D3-Ub to decelerate the reaction. The mathematical model successfully reproduced the experimentally observed p53-MDM2 interaction. The derived model therefore suggests MDM2 as a prospective target for cancer therapy. In addition, the findings of this project propose recombinant E2D3-Ub as a new promising protein-based anticancer drug for targeting overzealous p53 ubiquitination. The derived model can suggest new therapeutic solutions for decreasing the harmful effects of many human cancers, bacterial infections, and inflammatory diseases (such as rheumatoid arthritis) characterized by an overzealous ubiquitin-proteasome system. Finally, computational simulation of this novel model provides a safe, fast, and cost-effective preliminary alternative to expensive in vitro experimentation.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C235.
Citation Format: Prem M. Talwai. An investigation of the p53 ubiquitin-proteasome system using a novel non-steady-state enzyme kinetic model. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C235.