bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2914: Creation of a novel biochemical and biophysical assay suite to enable the identification of inhibitors targeting inactive kinases
Authors: France Dennis S. , Chen Chang-Rung , Volckova Erika , Eathiraj Sudharshan , Cornell-Kennon Susan , Huang Li , McSweeney Denise , Szwaya Jeffrey , Palma Rocio , Ashwell Mark A. , Chan Thomas C.k. 
Published: August 2012

Abstract
We have recently reported the implementation of a structural biology-based drug design platform for the identification of protein kinase inhibitors which utilize hydrophobic clusters to stabilize the inactive state of a kinase. These clusters are not formed in active kinases and result in the conversion of the ATP binding cleft into a non-polar environment which is sterically and electrostatically incompatible with ATP binding. We have industrialized this approach, designated the ArQule Kinase Inhibitor Platform (AKIPTM), and synthesized a library of more than 15,000 small molecules through the application of an in silico guided process. This has allowed us to rapidly generate leads to a variety of kinases, including receptor tyrosine kinases, non-receptor tyrosine kinases, and serine-threonine kinases. By virtue of their unique binding modes, many of these inhibitors would not be identified in standard assays using highly activated kinases. We have therefore deliberately re-engineered standard biochemical kinase assays using unphosphorylated inactive kinases to aid in the optimization of these inhibitors. In addition to these biochemical assays, we have also implemented a variety of well-established technologies not commonly used early in the hit generation process, including a thermal shift assay (TSA), affinity mass spectrometry, endogenous tryptophan fluorescence detection, an ATP-exclusion assay using a non-hydrolyzable ATP analogue, classical kinetic analysis to assess ATP-dependence and mechanism-of-inhibition, X-ray crystallography, and finally, cross-competition experiments with known inhibitors. Using the cumulative knowledge gained from these technologies throughout the hit generation, hit-to-lead, and lead optimization stages has enabled us to make informed decisions and resulted in identification of many potent ATP-independent inhibitors. The AKIP technology to date has produced at least one clinical candidate, ARQ 092, which potently inhibits AKT with a high degree of selectivity amongst the human kinome. Further examples of the application of these various technologies will be provided for a diverse range of kinases, including c-Met, FGFR, Ack, and TNIK.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2914. doi:1538-7445.AM2012-2914
Abstract 2916: Discovery of pyrazolimidazopyridine compounds as potent in vitro and in vivo anaplastic lymphoma kinase inhibitors
Authors: Saeh Jamal C. , Yang Bin , Peng Bo , Kamhi Victor , Harrison Rane , Rivard Caroline , Wu Allan , Drew Lisa , Russell Daniel J. 
Published: August 2012

Abstract
Translocations linking anaplastic lymphoma kinase (ALK) to multiple fusion partners were identified in anaplastic large cell lymphoma (ALCL), inflammatory myofibroblastic tumors, esophageal squamous cell carcinomas, neuroblastoma, and in non small cell lung cancer (NSCLC). This fusion leads to constitutive activation of ALK and has potent transforming activity. The recent approval of Crizotinib validated clinically the usefulness of treating EML4-ALK +ve patients with an Alk inhibitor. We report two novel series of compounds that potently inhibit ALK both in vitro and in vivo. Two series of pyrazolimidazolpyridine compounds, with good physical properties, were identified as part of our screening effort as potent ALK inhibitors in ALK enzyme assays. Subsequent testing of the mode of action of these compounds in Del cell lines containing NPM-ALK fusions demonstrated strong inhibition of phospho-ALK. In vivo, oral administration of 10 mg/kg of a pyrazolimidazopyridine compound in a Del xenograft model in SCID mice resulted in greater than 90% inhibition of phospho-ALK over 6 hours. In conclusion, we have identified two series of pyrazolimidazopyridine compounds as potent ALK inhibitors both in vitro and in vivo.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2916. doi:1538-7445.AM2012-2916
Abstract 2918: Estrogen receptor coactivator MED1 in mammary progenitor/stem cell determination and tamoxifen resistance of breast cancer
Authors: Zhang Xiaoting 
Published: August 2012

Abstract
Mediator has recently emerged as the central player to directly transduce signals from transcription factors to the transcription machinery. MED1 (also named TRAP220, DRIP205 and MED220) subunit of the Mediator complex has been shown to directly interact and mediate the transcription of nuclear receptors, in a ligand-dependent fashion, through two classical LxxLL motifs. We have recently generated MED1 LxxLL motifs mutant knockin mice and interestingly, found these mutations do not affect the overall survival and the development of most tissues. However, we did observe severe defects in pubertal mammary gland development of MED1-mutant mice. Consistent with this phenotype, expression of a number of known ERα-regulated genes was downregulated in MED1-mutant mammary epithelial cells and these genes could no longer respond to estrogen stimulation. Interestingly, along with the restricted expression of MED1 in luminal but not basal mammary epithelial cells, we observed a very significant increase in the luminal stem/progenitor cell population in the mammary glands of MED1 mutant mice. We have further crossed this MED1 mutant knockin mice with a MMTV-PyVT mouse model that produce mainly luminal type of mammary tumors. Our date indicate that, although MED1 mutations did not affect the time and number of tumors formed, it significantly impacted the tumor progression and cancer stem cell formation in this model. To further study the role of MED1 in human breast cancer, we examined MED1 protein expression by using human breast cancer tissue microarrays. Consistent with previously reports that MED1 coamplifies with HER2, we found MED1 protein expression level is correlated most strongly with HER2 status. Further study supports HER2 as a major upstream regulator responsible for MED1 phosphorylation at sites known to be critical for MED1 activation. Interestingly, we found an increased recruitment of phosphorylated MED1 but not corepressors SMRT or NcoR to endogenous ER target genes’ promoter by tamoxifen in HER2-overexpressing cells. Importantly, knockdown of MED1 significantly sensitized the otherwise resistant HER2 overexpressing cells to the tamoxifen treatment. These results support MED1 as a key convergence point between ER and HER2 signaling pathways in mediating endocrine resistance. In summary, our studies revealed new roles of MED1 in mediating ER functions in both mammary stem/progenitor cell determination and tamoxifen resistance of breast cancer, and support potential use of MED1 as a tissue-specific therapeutic target for the treatment of human breast cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2918. doi:1538-7445.AM2012-2918
Abstract 2922: Androgen receptor driven transcription in a subtype of estrogen receptor negative breast cancer is controlled by FoxA1
Authors: Robinson Jessica L. , Brown Gordon D. , Neal David E. , Tilley Wayne D. , Carroll Jason S. 
Published: August 2012

Abstract
Breast cancer is a heterogeneous disease and several distinct subtypes exist based on differential gene expression patterns. Molecular apocrine tumors were recently identified as an additional subgroup, characterised as ERα- AR+, but with an expression profile that resembles ERα+ luminal breast cancer. Previously, we mapped global AR binding events in a cell line model of molecular apocrine breast cancer (termed MDA-MB-453 cells) using ChIP-seq. Our results suggested that these tumours are driven by AR through its interaction with critical ER cis-regulatory elements, resulting in a transcriptional programme reminiscent of ER-mediated transcription in luminal breast cancers. Additionally, we found that AR binding is a near-perfect subset of FoxA1 binding regions, a level of concordance never previously seen with a Nuclear Receptor. By silencing FoxA1 using specific siRNA, we observe dramatic changes in the gene expression profile of the cells (730 genes are differentially expressed) including many of the signature molecular apocrine genes. Furthermore, silencing of FoxA1 in these breast cancer cells results in altered AR binding to the chromatin (lost, conserved and de novo binding events are found) as has been previously seen in the prostate cancer cell line, LNCaP. We are investigating this phenomenon further using proteomics to discover new AR interacting proteins and histone mark ChIP-seq to understand the proteins and epigenetic events that may mediate the reprogrammed AR binding in the absence of FoxA1.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2922. doi:1538-7445.AM2012-2922
Abstract 2923: Androgen receptor activation changes chromatin structure and transcriptional activation
Authors: Tewari Alok K. , Yardimci Galip G. , Crawford Gregory E. , Febbo Phillip G. 
Published: August 2012

Abstract
Epigenetic mechanisms such as chromatin accessibility and histone modifications impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of prostate cancer initiation and progression, acts primarily through ligand-activated transcription of target genes. By combining deep sequencing with DNase I hypersensitivity analysis (DNase-seq) and RNA analysis (RNA-seq) we assessed genome-wide chromatin structure and transcription and combined this data with publicly available AR chromatin immunoprecipitation data (AR Chip-seq). We find that 64% of DNase I hypersensitive sites (DHS) overlap each other before and after androgen in LNCaP cells. Interestingly, in regions with increased chromatin accessibility following androgen induction, the canonical AR DNA recognition motif is enriched. Comparing identified DHS to AR binding sites from three different data sets consistently reveals that 50% of AR binding overlaps a DHS in induced cells. Of those sites with both DHS and AR binding, approximately half are available prior to androgen induction (i.e. “primed”) and half open in response to androgen stimulation. This contrasts with the glucocorticoid receptor (GR), which was recently reported to bind to DNA primarily in regions that are accessible to nuclease cleavage prior to ligand activation. Our RNA-seq analysis discovered 367 genes regulated by AR activation (FDR &lt; 0.05), including 16 of the 19 most commonly identified AR-mediated genes in several other studies. Importantly, we find that regions of increased chromatin accessibility are significantly associated with genes identified as AR-regulated by RNA-seq. Finally, base pair resolution of the DNase-seq signal reveals distinct footprinting patterns associated with the AR-DNA interaction. Analysis of chromatin structure, AR binding, and transcription prior to and following androgen induction demonstrates that AR activation by ligand induces genome-wide changes in chromatin accessibility, these changes correspond to AR binding to the genome, and they impact AR-mediated transcriptional response. These findings suggest that interaction between the AR and DNA alters chromatin structure and transcriptional specificity.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2923. doi:1538-7445.AM2012-2923
Abstract 2929: Predictors of survival in never-smokers with non-small cell lung cancer: A large-scale, two-phase genetic study
Authors: Pu Xia , Ye Yuanqing , Spitz Margaret R. , Wang Liang , Gu Jian , Lippman Scott M. , Hildebrandt Michelle AT , Hong Waun K. , Minna John D. , Roth Jack A. , Yang Ping , Wu Xifeng 
Published: August 2012

Abstract
Lung cancer in never-smokers is increasingly recognized as distinct from that in ever-smokers owing to substantial differences in etiology, clinical characteristics, and prognosis. Therefore, we aimed to identify prognostic markers specific for lung cancer in never-smokers in a two-stage study. First, 11,930 single-nucleotide polymorphisms (SNPs) in 904 inflammation-related genes were genotyped, and their associations with overall survival in 411 never-smokers with lung cancer at The University of Texas MD Anderson Cancer Center were analyzed. Next, fast-track validation of the top 37 SNPs in 311 never-smokers with lung cancer at Mayo Clinic was performed. Three SNPs (interleukin 17 receptor A:rs879576, bone morphogenetic protein 8A:rs698141, and spleen tyrosine kinase:rs290229) were validated (p&lt;0.05), and two more SNPs (CD74:rs1056400 and CD38:rs10805347) were borderline significant (p=0.08) in the Mayo Clinic population. In combined analysis of the MD Anderson and Mayo Clinic patients, IL17RA:rs879576 resulted in a 40% reduction in the risk of death (p=4.1 × 10−5 [p=0.61, heterogeneity test]). We successfully validated a survival tree created in MD Anderson population based on gene-gene interactions in the Mayo Clinic population. This survival tree stratified patients into subsets with significantly different risks of death: patients at MD Anderson with the rs1056400_GG/rs698141_GA+AA genotype had a 2.32-fold higher risk of death (p=1.72 × 10−5) and 9-month shorter median survival time (MST) (p=4.5 × 10−4, log-rank test) than did those with the rs1056400_GG/rs698141_GG or rs1056400_GA+AA genotype in the discovery phase. Also, the patients at Mayo Clinic with the former genotype had an approximately twofold higher risk of death (p=0.02) and a strikingly shorter (by 26 months) MST (p=0.029, log-rank test) than did those with the latter genotype in the validation phase. We evaluated these five SNPs in 996 ever-smokers and found no significant associations. To our knowledge, this is the first study to systematically evaluate the associations of genetic variations in major inflammation-related genes with outcome of lung cancer in never-smokers. It provides strong evidence that inflammation-related genetic variations can affect clinical outcomes in these patients, which may lead to significant biological insight into these outcomes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2929. doi:1538-7445.AM2012-2929
Abstract 293: Tumor cell cross-talk with tumor-associated leukocytes leads to induction of tumor exosomal fibronectin and promotes tumor progression
Authors: Zhang Huang-Ge , Deng ZhongBin 
Published: August 2012

Abstract
Exosomes play an important role in intercellular communication. However, most data published are based on exosomes released from in vitro cultured cells that do not exhibit communication with neighboring cells located in the same microenvironment as the exosomal producing cells, and therefore in vitro culture experiments do not represent what occurs in vivo. In this study, our data show that co-culture of leukocytes isolated from breast tumor tissue leads to uptake of fibronectin on/in the tumor exosomes (Exofib+). The induction of fibronectin and exosomal uptake is tumor tissue derived, leukocyte specific, as leukocytes isolated from peripheral blood of naïve mice failed to induce fibronectin uptaken by tumor exosomes. Furthermore, depletion of both CD25+ cells and Gr-1+ cells from tumor-associated leukocytes causes a reduction of Exofib+ suggesting that tumor-associated CD25+ cells and Gr-1+ cells play a role in fibronectin production and uptake by tumor exosomes resulting in Exofib+. As a result of tumor cells taking up Exofib+ two major events are induced: FAK/Src-dependent signaling pathways are activated, and the production of proinflammatory cytokines and metalloproteinase 9 is enhanced in response to taking up exosomes and this in turn enhances tumor cell invasion in vitro as well as in vivo. Collectively, our findings provide evidence that exosomes released from freshly excised tumor tissue cells that have communicated/interacted with immune cells gain new immune evasion capacity.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 293. doi:1538-7445.AM2012-293
Abstract 2932: Knockdown of polypyrimidine tract-binding protein (PTB) sensitizes ovarian cancer cells to chemotherapeutic agents in vitro
Authors: Arslan Ahmet D. , Maggio Matthew , El-Shennawy Lamiaa , He Xiaolong , Beck William T. 
Published: August 2012

Abstract
While chemotherapy is the second-line of therapy for the treatment of epithelial ovarian cancer (EOC) after surgery, drug resistance constitutes a significant obstacle to achieving a complete response in many patients. There is a clear unmet need for new treatments for EOC patients. We have shown that PTB is frequently overexpressed and associated with malignancy in EOC (He et al, Clin Cancer Res, 10:4652-60, 2004, He et al, Oncogene 30:356-65, 2011). PTB knockdown via RNA interference significantly impairs EOC cell growth in vitro and in vivo, as well as invasiveness and colony formation in soft agar in vitro (He et al, Oncogene 26:4961-8, 2007). PTB or hnRNP-I is a splicing factor that regulates alternative pre-mRNA splicing, and has been implicated in metabolic, cytoskeletal, and cell membrane changes in cancer cells. In this study, we used A2780 cell lines carrying doxycycline (doxy)-inducible PTB shRNA. We characterized stable transfectants of A2780 cells that carry shRNA against PTB and cells carry a non-targeting control shRNA. In a 48 h MTT cytotoxicity assay, knockdown of PTB inhibited cell growth. When cells with PTB knockdown were treated with carboplatin or paclitaxel, drugs used as current standard of care in EOC, we observed 3- to 6-fold increases in drug sensitivity compared to the vector control. To rule out any drug-drug interaction (e.g., doxy-paclitaxel) (Foroodi et al, Anticancer Drugs 2009 20:115-22) in our assay, we evaluated the kinetics of the inducible knockdown system by western blot. We found that a 120 h doxy treatment was optimal to insure full depletion of PTB, and after doxy removal PTB suppression lasted 48 h more before recovering to its basal level. Based on those data, we performed all the cytotoxicity experiments within 48 h without exposing cells to both doxy and drug at once, and thereby avoiding drug-drug interactions. Findings here support the idea that PTB and other splicing factors may be novel drug targets in the treatment of ovarian cancer. (Support in part by NCI grants R01 CA40570 and R01 CA138762 [to WTB], by OCRF [to XH], and by UIC.)
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2932. doi:1538-7445.AM2012-2932
Abstract 2933: Synthetic lethal screening: A pathway for rational combinatorial therapies for cancer
Authors: Axelrod Mark J. , Gioeli Daniel G. , Weber Michael J. 
Published: August 2012

Abstract
We hypothesize that many cases of both intrinsic and acquired resistance to single agent targeted cancer drugs occur due to the activation of compensatory signaling pathways. Combination therapies targeting both the primary and compensatory pathways may be able to produce more robust and durable responses. To identify these compensatory pathways and rationally construct combination therapies, we performed a synthetic lethal screen of 420 targeted small molecule inhibitor combinations on 17 cancer cell lines, yielding over 5500 combinatorial tests. We identified both novel and expected synergistic combinations. Among the expected combinations was the combination of inhibitors of EGF Receptor with inhibitors of PI3 Kinase. Because this combination is currently being evaluated in clinical trials, we have focused on examination of the cellular and molecular mechanism(s) of the synthetic lethality. We found that inhibition of PI3 Kinase led to increased ERK activation, and conversely that inhibition of MEK resulted in increased signaling through the PI3 Kinase pathway. Flow cytometric analysis revealed that this synergistic cytotoxicity is both due to a robust apoptotic response to combination treatment measured by caspase 3 cleavage and also a decrease in proliferation upon combination treatment measured by BrdU incorporation. Using Reverse Phase Protein Arrays, we identified phosphorylation of ribosomal protein S6 as a molecular biomarker of synergistic cytotoxicity with these agents. To determine whether this biomarker reflects a mechanistic node in the signaling network, we tested pharmacological inhibition of 70 kD ribosomal protein S6 kinase (p70S6K) and found only modest cytotoxicity, but also robust activation of ERK1 and 2. This increase could be blocked by the addition of a pharmacological inhibitor of the EGF Receptor, suggesting a negative feedback loop between p70S6K and the EGF Receptor. Combined treatment with p70S6K and EGF Receptor inhibitors resulted in synergistic cytotoxicity. Currently, we are identifying the node between EGF Receptor and p70S6K signaling that could be responsible for this synthetic lethality. Additionally, we are conducting xenograft studies using inhibitors of this pathway that are currently in clinical trials, to test the efficacy of this drug combination in vivo.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2933. doi:1538-7445.AM2012-2933