bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A64: Human epidermal growth factor receptor 2 (HER2) directly binds and activates focal adhesion kinase (FAK) to promote oncogenesis
Authors: Marlowe Timothy , Figel Sheila , Lenzo Felicia , Golubovskaya Vita , Kurenova Elena , Tropsha Alexander , Cance William 
Published: May 2016

Abstract
Introduction: Human epidermal growth factor receptor 2 (HER2) is known to require focal adhesion kinase (FAK) for cellular transformation, tumor growth, invasion, and metastasis. FAK is overexpressed in nearly all types of human cancer, serving as a molecular scaffold protein to integrate oncogenic growth factor receptors with focal adhesion proteins. We have identified a novel direct protein-protein interaction between HER2 and FAK. In this study, we investigated whether the HER2-FAK direct interaction is required for HER2-dependent oncogenesis and its potential as a novel drug target.
Methods: We have taken a multidisciplinary approach (biophysics, biochemistry, molecular modeling, structural biology, and molecular biology) to map the HER2-FAK binding interface and to study the functional aspects of the interaction.
Results: Our data indicated that the N-lobe of the HER2 kinase domain directly interacts with the F1 lobe of the FAK FERM domain. In addition, molecular modeling studies have identified a putative HER2-FAK interface suitable for the binding of small molecule inhibitors. Site-directed mutagenesis studies validated this binding interface. Functional data indicated that HER2 directly transphosphorylated FAK at key tyrosine residues, Y397, Y861, and Y925, irrespective of FAK kinase activity. Additionally, kinome reprogramming analysis revealed upregulation of HER2 signaling and maintenance of FAK phosphorylation after FAK-kinase inhibitor treatment. Finally, cellular data suggested that loss of the HER2-FAK interaction, but not FAK-kinase activity, resulted in a defect in Heregulin β1-stimulated cell migration/invasion.
Conclusion: We have identified a direct interaction between HER2 and FAK that is required for HER2-dependent oncogenic signaling and is amenable to targeting by small molecule therapeutics. In addition, this interaction mediated a novel drug resistance mechanism whereby HER2 rescued and maintained FAK activation under FAK-kinase inhibition.
Citation Format: Timothy Marlowe, Sheila Figel, Felicia Lenzo, Vita Golubovskaya, Elena Kurenova, Alexander Tropsha, William Cance. Human epidermal growth factor receptor 2 (HER2) directly binds and activates focal adhesion kinase (FAK) to promote oncogenesis. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A64.
Abstract B161: Chemoproteomic profiling for target identification using chloroalkane derivatized compounds
Authors: Ford Michael , Jones Richard , Amunugama Ravi , Daniels Danette , Ohana Rachel , Levin Sergiy , Kirkland Thomas , Urh Marjeta , Wood Keith 
Published: May 2016

Abstract
Chemoproteomic technologies enable the quantitative and qualitative profiling of small molecule protein interactions. Here we report a new approach utilizing a chloroalkane (CA) capture tag which can be chemically attached to small molecules to enable the isolation of their respective protein targets through selective capture onto an immobilized HaloTag protein.
We have combined our chemoproteomics workflow with multiplexed chemical labeling methods to enable the analysis of dose dependent target engagement studies in a single LC-MS/MS experiment. Here we demonstrate this workflow using BIRB796-CA, a modified kinase inhibitor.
Target enrichment experiments were performed by incubating HEK293 cells with the BIRB-CA. Cells were then lysed and the BIRB-CA, together with the bound targets, was rapidly captured onto immobilized HaloTag protein. Unmodified compound was used to competitively elute putative interacting proteins. To study dose dependent effects on the protein interaction profile, cells were incubated with multiple mixtures of BIRB and BIRB-CA at varying relative concentrations. The eluted proteins were processed using SDS-PAGE and in-gel digestion. Digested material was labeled with Tandem Mass Tags (TMT) 10plex reagents and analyzed using nanoscale LC-MS/MS coupled with a Q Exactive mass spectrometer (Thermo). Protein identification was performed with MaxQuant (MaxQuant.org) and data validation and visualization was performed using Perseus (Perseus-framework.org).
We tested this chemoproteomics workflow using the interaction of MAP kinases (MAPK) with BIRB796, an allosteric kinase inhibitor. Treatment of LPS simulated THP-1 cells with BIRB796 and BIRB-CA revealed minimal impact of the CA modification on the inhibition of TNFα secretion. The interaction of BIRB-CA with known BIRB targets MAPK13, MAPK12, MAPK9 and MAPK14 has been confirmed using label free quantitative proteomic profiling. We have optimized the TMT labeling method for minimal losses and sample processing steps. We are applying the TMT method to BIRB-CA and control pull downs and extending this workflow to include the BIRB/BIRB-CA titration samples. Here we will use post-acquisition data processing of the BIRB/BIRB-CA titration pull down data to assess compound binding characteristics with the inferred extension to compounds with unknown binding specificities.
Citation Format: Michael Ford, Richard Jones, Ravi Amunugama, Danette Daniels, Rachel Ohana, Sergiy Levin, Thomas Kirkland, Marjeta Urh, Keith Wood. Chemoproteomic profiling for target identification using chloroalkane derivatized compounds. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B161.
Abstract B41: The gelatinases-stimuli nanoparticles reverse docetaxel resistance and epithelial to mesenchymal transition in lung cancer cell line
Authors: Liu Qin , Li Rutian , Liu Baorui 
Published: May 2016

Abstract
Drug resistance is a main obstacle for the successful cancer therapy. Emerging evidence suggests that miR-200c functions as an effective cancer stem cells (CSCs) inhibitor and restores sensitivity to microtubule-targeting drugs. In the present work, we engineered the intelligent gelatinases-stimuli nanoparticles (NPs) to co-delivery miR-200c and antitumor drug docetaxel (DOC) to verify their synergetic effects on inhibition of CSCs and cancer cells. After tumor cells were treated with miR-200c NPs, miR-200c and its targeted gene TUBB3 expression were evaluated. The effects of (miR-200c+DOC) NPs on docetaxel-resistant lung cancer cells viability as well as the expression of E-cadherin and CD44 were studied. We found that the (miR-200c+DOC) NPs significantly overcome DOC resistance, possibly by elevated miR-200c expression,low TUBB3 level, and reversed the EMT through upregulation E-cadherin and inhibition lung CSCs. The (miR-200c+DOC) NPs may provide a new modality for co-delivery of nucleic acid and drugs to inhibit CSCs and reverse drug resistance.
Citation Format: Qin Liu, Rutian Li, Baorui Liu. The gelatinases-stimuli nanoparticles reverse docetaxel resistance and epithelial to mesenchymal transition in lung cancer cell line. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B41.
Abstract C105: DNA damage response deficiency (DDRD) in breast cancer is associated with a STING-dependent innate immune response
Authors: Parkes Eileen E. , Walker Steven M. , McCabe Nuala , Taggart Laura E. , Hill Laura , McCloskey Karen D. , Buckley Niamh E. , Salto-Tellez Manuel , Mullan Paul B. , Harkin D. P. , Kennedy Richard D. 
Published: May 2016

Abstract
Background
In breast cancer the presence of an immune infiltration has been recognised as a prognostic factor, however the mechanisms underpinning this response are not clearly defined. Previously we identified a gene expression signature that defines a DNA damage response defective (DDRD) molecular subgroup in breast cancer, that is enriched for BRCA1 and 2 mutations, and has a good outcome following DNA-damaging chemotherapy. Importantly, this DDRD subgroup is associated with up-regulation of type I Interferon-related genes. We therefore investigated the mechanism activating this immune response in the context of abnormal DNA repair.
Results
IHC analysis demonstrated that both intra-tumoral and stromal CD8+ and CD4+ T cell infiltration were associated with DDRD positive breast tumors. The CXCL10 and CCL5 cytokines were shown to be significantly up-regulated in DDRD positive breast tumours and in tissue culture models for the DDRD molecular subgroup. Furthermore, conditioned media from DDRD positive cell lines stimulated inward migration of peripheral blood mononuclear cells, when compared to media from DDRD negative cells, indicating the presence of active cytokines. We identified constitutive activation of the innate immune pathway STING/TBK1/IRF3 specifically in DDRD positive cells when compared to DDRD negative cells and found that binding of the DNA sensor cGAS to cytosolic Histone H3 was required for this immune response. Treatment of HeLa cells with DNA damaging chemotherapies but not taxanes resulted in STING-dependent expression of CXCL10 and CCL5 cytokines.
Conclusion
We have identified that the STING/TBK1/IRF3 immune pathway is activated by endogenous DNA damage in DDRD breast cancers and may explain lymphocytic infiltration observed in this subtype of breast tumours. These data suggest that the DDRD signature can identify an innate immune response to DNA damage in breast cancer, which may have therapeutic applications for immune targeted therapies.
Citation Format: Eileen E. Parkes, Steven M. Walker, Nuala McCabe, Laura E. Taggart, Laura Hill, Karen D. McCloskey, Niamh E. Buckley, Manuel Salto-Tellez, Paul B. Mullan, D. P. Harkin, Richard D. Kennedy. DNA damage response deficiency (DDRD) in breast cancer is associated with a STING-dependent innate immune response. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C105.
Abstract C112: Cabozantinib eradicates advanced murine prostate cancer by activating anti-tumor innate immunity
Authors: Patnaik Akash , Swanson Kenneth , Signoretti Sabina , Ye Huihui , Csizmadia Eva , Novak Jesse , Gehring Marina , Helenius Katja , Pyzer Athalia , Montaser Laleh , Wang Lily , Elemento Olivier , Levantini Elena , Clohessy John , Asara John , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn , Avigan David , Balk Steven , Cantley Lewis 
Published: May 2016

Abstract
Several kinase inhibitors targeting aberrant signaling pathways in tumor cells have been deployed in cancer therapy. However, their impact on the tumor immune microenvironment remains poorly understood. The tyrosine kinase inhibitor cabozantinib showed striking responses in early phase clinical trials, particularly in cancer patients with bone metastases. Here we show that cabozantinib rapidly eradicates invasive, poorly-differentiated PTEN/p53 deficient murine prostate cancer. This was associated with increased neutrophil chemotactic factor expression, including CXCL12 and HMGB1 production by tumor cells, and robust infiltration of neutrophils into the tumor. Critically, cabozantinib-induced tumor clearance in mice was abolished by antibody-mediated granulocyte depletion or HMGB1 neutralization or blockade of neutrophil chemotaxis with the CXCR4 inhibitor, plerixafor. Collectively, these results demonstrate that cabozantinib triggers neutrophil-mediated anti-tumor innate immune response that results in tumor clearance.
(Manuscript submitted to Science)
Citation Format: Akash Patnaik, Kenneth Swanson, Sabina Signoretti, Huihui Ye, Eva Csizmadia, Jesse Novak, Marina Gehring, Katja Helenius, Athalia Pyzer, Laleh Montaser, Lily Wang, Olivier Elemento, Elena Levantini, John Clohessy, John Asara, Kathleen Kelly, Pier Paolo Pandolfi, Jacalyn Rosenblatt, David Avigan, Steven Balk, Lewis Cantley. Cabozantinib eradicates advanced murine prostate cancer by activating anti-tumor innate immunity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C112.
Abstract C116: Concomitant blockade of glucose uptake and paracrine HGF signaling uncovers the metabolic vulnerability of KRAS-mutant colorectal tumors
Authors: Mira Alessia , Michieli Paolo 
Published: May 2016

Abstract
Mutations in KRAS and over-expression of MET, the hepatocyte growth factor (HGF) receptor, are both negative prognostic factors for colorectal cancer (CRC). We studied the KRAS-MET interplay using human isogenic CRC cells with defined KRAS status and human HGF knock-in SCID mice, thereby reproducing species-specific HGF-MET paracrine signaling. We show that KRAS-mutant CRC cells display an extraordinary high glycolytic rate that makes them ‘addicted’ to glycolysis. When glucose availability is scarce or upon drug-mediated impairment of glucose metabolism, KRAS-mutant cells rapidly undergo apoptosis, unless ‘salvaged’ by micro-environment-borne HGF, which permits their survival by enhancing glucose influx, sustaining glycolysis and activating autophagy, thus improving energetic efficiency and preventing a mitotic catastrophe. In an orthotopic model of metastatic CRC using human HGF knock-in SCID mice and human KRAS-mutant CRC cells, combined pharmacological blockade of glucose metabolism and of HGF/MET signaling resulted in synthetic lethality and achieved superior tumor inhibition and metastasis suppression compared to metabolism-active drugs or HGF/MET inhibitors alone. In the same system, paracrine HGF signaling also protected KRAS-mutant tumors against anti-angiogenic therapy, which caused more dramatic and less specific metabolic stress by depriving tumors of both nutrients and oxygen. However, in contrast to selective glucose metabolism impairment, anti-angiogenic therapy exacerbated tumor hypoxia, promoted HGF-dependent metastatic dissemination and gave rise to acquired resistance. These results indicate that selective impairment of glucose metabolism is a much safer and effective approach to target KRAS-mutant CRC metabolic vulnerability compared to angiogenesis inhibition. They also show that microenvironment-borne HGF is a major source of resistance to anti-tumor therapies that cause metabolic stress to cancer cells. Considering that angiogenesis inhibition is the only biological therapy currently available for KRAS-mutant tumors, the data generated by this study open new perspectives for the treatment of this highly aggressive cancer type.
Citation Format: Alessia Mira, Paolo Michieli. Concomitant blockade of glucose uptake and paracrine HGF signaling uncovers the metabolic vulnerability of KRAS-mutant colorectal tumors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C116.
Abstract C154: Integrated genomics approach to identify driver alterations
Authors: Chandrani Pratik , Upadhyay Pawan , Iyer Prajish , Tanna Mayur , Shetty Madhur , Gorantala Raghuram Venkata , Oak Ninad , Singh Ankita , Chaubal Rohan , Ramteke Manoj , Gupta Sudeep , Dutt Amit 
Published: May 2016

Abstract
Several statistical tools have been developed to identify genes mutated at rates significantly higher than the background, indicative of positive selection, involving large sample cohort studies. However, studies involving relatively smaller sample sizes or single data-type genome wide analysis are inherently restricted due to their limited statistical power to identify low frequency genetic variation. We undertook integrated copy number, mutation and expression analyses of head and neck cancer cell lines assessing multiple levels of biological regulation in individual samples to enrich for driver events affected by two or more alterations. Besides identifying TP53, PTEN, HRAS and MET as major altered HNSCC hallmark genes, this analysis uncovered 34 novel candidate tumor suppressor and oncogenes altered by at least two types of alterations. Of these, we find a driver heterozygous truncating mutation in Nuclear receptor binding protein NRBP1, a pseudokinase, identical to that reported in other cancers and similar to activating mutant alleles in non-human model organisms. In addition to demonstrating the ability of integrated analyses to uncover biologically important genetic variation in relatively small datasets, we report for the first time, mutant NRBP1 is oncogenic when ectopically expressed in NIH 3T3 cells. We further show that knockdown of NRBP1 in oral carcinoma cell lines bearing such NRBP1 mutations inhibits transformation and survival. In over all, this approach could be of immense value for studies involving fewer or rare clinical specimen that are otherwise inherently restrictive due to the limited statistical power to detect alterations existing at lower frequency.
Citation Format: Pratik Chandrani, Pawan Upadhyay, Prajish Iyer, Mayur Tanna, Madhur Shetty, Raghuram Venkata Gorantala, Ninad Oak, Ankita Singh, Rohan Chaubal, Manoj Ramteke, Sudeep Gupta, Amit Dutt. Integrated genomics approach to identify driver alterations. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C154.
Abstract C160: An RNAi kinome screen identifies YES1 as a potential target for glioblastoma
Authors: Goel-Bhattacharya Surbhi , Sengupta Sejuti , Cochran Brent H. 
Published: May 2016

Abstract
Glioblastoma stem like cells (GSC) are known to have gene expression patterns and growth phenotypes more similar to the tumor of origin than do traditional glioma cell lines grown in serum. They also exhibit increased resistance to drugs and radiation and are likely to be responsible for tumor recurrence following therapy. As a result, it is important to identify therapeutic targets for these cells. Toward this end, we have conducted RNAi kinome screens in GSCs to identify genes that are required for their growth and survival. In addition, glioblastomas (GBM) often have significant regions of hypoxia and GSCs tend to be resistant to hypoxia. We have therefore conducted shRNA screens in both normoxic and hypoxic conditions and screened three independent patient derived GSC lines. Of 501 kinases screened, 8-11% were scored as hits with at least 2 shRNAs per kinase in each cell line, but only ∼2% were common hits for all the cell lines in both oxygen conditions. The majority of the hits were shared in both oxygen conditions, but about one sixth were specific to hypoxia in each of the cell lines. However, none of the hypoxia specific hits were common to all three cell lines. Several genes well known to have a role in GBM such as EGFR, CDK4 and KDR were scored as common hits. The non-receptor associated tyrosine kinase YES1 was scored as a novel hit common to all the three cell lines in both the oxygen conditions. YES1 is overexpressed in GBM and several other solid tumors. Depletion of YES1 expression by shRNA and CRISPR was found to be strongly growth inhibitory in GSCs suggesting that it could be a therapeutic target for GBM. Ongoing experiments include studying the mechanism of YES1 associated cell death.
Citation Format: Surbhi Goel- Bhattacharya, Sejuti Sengupta, Brent H. Cochran. An RNAi kinome screen identifies YES1 as a potential target for glioblastoma. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C160.
Abstract C161: CRISPR/Cas9 genome-wide gRNA library screening platform
Authors: Tedesco Donato , Diehl Paul , Makhanov Mikhail , Baron Sylvain , Suchkov Dmitry , Chenchik Alex 
Published: May 2016

Abstract
CRISPR/Cas9 gene knock-out technology can be used as a powerful tool for large-scale functional genomic analysis in mammalian cells. With the goal to establish a cost-effective functional genomics platform for the discovery of therapeutic targets, we developed a highly functional high throughput lentiviral gRNA/CRISPR screening platform, enabling scientists to perform pooled format genome-wide CRISPR/Cas9 genetic screens. Three 55K gRNA libraries were designed to cover the whole protein-encoding human genome with a redundancy of 8 gRNAs per gene. As supporting tools, we developed protocols, reagents, and software tools for hit validation and target prioritization.
Here we show the results of parallel genetic screens in a pair of isogenic CML cell lines (CML-R and CML-P), where the performance of CRISPR/Cas9 and RNAi screening platforms was compared for each cell line.
Citation Format: Donato Tedesco, Paul Diehl, Mikhail Makhanov, Sylvain Baron, Dmitry Suchkov, Alex Chenchik. CRISPR/Cas9 genome-wide gRNA library screening platform. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C161.