bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract C72: Combined pan-RAF and MEK inhibition overcomes multiple resistance mechanisms to selective RAF inhibitors
Authors: Whittaker Steven R. , Cowley Glenn S. , Wagner Steve , Luo Flora , Root David E. , Garraway Levi A. 
Published: May 2016

Abstract
Background
RAF and MEK inhibitors are efficacious in BRAF mutant melanoma but not in BRAF mutant colorectal cancer (CRC). To understand the underlying mechanisms of this difference we performed an RNA interference screen to identify loss of function events that sensitize CRC cells to RAF inhibition by PLX4720.
Methods
A pooled lentiviral library encoding 90,000 shRNAs, targeting 16,500 genes was transduced into the PLX4720-resistant, BRAF mutant RKO CRC cell line. The shRNA-infected cells were split into two experimental arms treated with either PLX4720 or DMSO. After 16 population doublings, the abundance of each shRNA was determined by PCR amplification and deep sequencing of the barcoded shRNA pool. The log-fold change in shRNA reads in the drug-treated condition was calculated relative to the vehicle control. RNAi gene enrichment (RIGER) was employed to rank genes that promoted sensitivity to PLX4720. Candidate genes were validated individually and their effects on cell proliferation, survival and MAPK pathway inhibition assessed.
Results
Genes involved in maintaining MAPK pathway activity scored prominently in our screen. Knockdown of MET, SHP2, SHOC2 and CRAF by shRNA sensitized cells to PLX4720. Efforts to suppress cell proliferation via single agent pan-RAF or MEK inhibition were more effective across melanoma and colorectal cancer cell lines than PLX4720. Strikingly, combined pan-RAF and MEK inhibition elicited a synergistic response in cell lines showing intrinsic resistance to PLX4720 associated with NF1 or KRAS mutation.
Conclusions
Resistance to BRAF inhibition is mediated by reactivation of the MAPK pathway in a CRAF-dependent manner. Pan-RAF inhibitors synergize with MEK inhibitors to suppress proliferation and induce apoptosis in both BRAF mutant, PLX4720-resistant cell lines and also in KRAS mutant cell lines. Pan-RAF inhibitors are progressing into clinical trials and our data support their use in combination with MEK inhibitors.
Citation Format: Steven R. Whittaker, Glenn S. Cowley, Steve Wagner, Flora Luo, David E. Root, Levi A. Garraway. Combined pan-RAF and MEK inhibition overcomes multiple resistance mechanisms to selective RAF inhibitors. [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 C72.
Abstract C73: A drug-modifier whole-genome shRNA screen identifies novel synthetic lethal interactions with PI3K inhibition in breast cancer
Authors: Zwang Yaara , Chen Casandra , Genomic Perturbation Platform The Broad Institute , Hahn William C. 
Published: May 2016

Abstract
The PI3K pathway is frequently activated in tumors, and was previously shown to be essential for tumorigenesis and tumor cell survival. Never the less, the main response to PI3K inhibition is cytostatic, therefore retaining a significant reservoir of tumor cells with a capability to re-grow and acquire resistance. Our goal is to identify genes that exhibit a synthetic lethal interaction with PI3K inhibition, namely, converting the response to PI3K inhibition from cytostatic to cytotoxic. To this end, we conducted a positive-selection whole-genome shRNA screen in a breast cancer cell line bearing a PI3K activating mutation, also exhibiting a robust cytostatic response to PI3K inhibition. Cells were infected with a pooled shRNA library consisting of 98K shRNAs, targeting ∼17K genes. Following selection, cells were either left untreated, or treated with a PI3K inhibitor (GDC0941) for 2-5 days. Based on cleaved-PARP staining, apoptotic cells were sorted by flow cytometry, and sequenced to identify the shRNAs in the sorted population. We ranked shRNAs according to the significance of their relative occurrence between non-treated and treated samples, thereby identifying shRNAs that induce cell death only upon PI3K inhibition.
We validated potential hit genes using an arrayed viability assay, in which we included multiple shRNAs targeting each of the genes. Using seed-control shRNAs and rescue experiments, we confirmed on-target effects of the identified shRNAs, collectively targeting 5 genes. We further confirmed the relevance of the identified genes by testing the shRNAs in additional PI3K-activated breast cancer cell-lines, and in combination with additional PI3K-pathway inhibitors. Interestingly, the effect of the identified genes was specific to inhibition of the PI3K pathway, and was not observed upon unrelated growth inhibition.
All together, we identified five genes that exhibit robust synthetic lethal interaction with PI3K inhibition in breast cancer, of which 2 genes are protein kinases, PIM2 and ZAK, thus are potential co-targets with PI3K.
Citation Format: Yaara Zwang, Casandra Chen, The Broad Institute Genomic Perturbation Platform, William C. Hahn. A drug-modifier whole-genome shRNA screen identifies novel synthetic lethal interactions with PI3K inhibition in breast cancer. [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 C73.
Abstract C81: Identification of novel synergistic targets for rational drug combinations with PI3 kinase inhibitors using siRNA synthetic lethality screening against GBM
Authors: Kim Yong-Wan 
Published: May 2016

Abstract
Several small molecules that inhibit the PI3 kinase (PI3K)-Akt signaling pathway are in clinical development. Although many of these molecules have been effective in preclinical models, it remains unclear whether this strategy alone will be sufficient to interrupt the molecular events initiated and maintained by signaling along the pathways because of the activation of other pathways that compensate for the inhibition of the targeted kinase. In this study, we performed a synthetic lethality screen to identify genes or pathways whose inactivation, in combination with the PI3K inhibitors PX-866 and NVPBEZ-235, might result in a lethal phenotype in glioblastoma multiforme (GBM) cells. We screened GBM cells (U87, U251, and T98G) with a large-scale, short hairpin RNA library (GeneNet), which contains 43 800 small interfering RNA sequences targeting 8500 well-characterized human genes. To decrease off-target effects, we selected overlapping genes among the 3 cell lines that synergized with PX- 866 to induce cell death. To facilitate the identification of potential targets, we used a GSE4290 dataset and The Cancer Genome Atlas GBM dataset, identifying 15 target genes overexpressed in GBM tissues. We further analyzed the selected genes using Ingenuity Pathway Analysis software and showed that the 15 genes were closely related to cancer-promoting pathways, and a highly interconnected network of aberrations along the MYC, P38MAPK, and ERK signaling pathways were identified. Our findings suggest that inhibition of these pathways might increase tumor sensitivity to PX-866 and therefore represent a potential clinical therapeutic strategy.
[This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MEST) (NRF-2013R1A1A2063115) and the MSIP(Ministry of Science, ICT and Future Planning), Korea, under the “IT Consilience Creative Program” (IITP-2015-R0346-15-1008) supervised by the IITP (Institute for Information & Communications Technology Promotion)]
Citation Format: Yong-Wan Kim. Identification of novel synergistic targets for rational drug combinations with PI3 kinase inhibitors using siRNA synthetic lethality screening against GBM. [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 C81.
Abstract C89: The small molecule inhibitor 4SC-202 controls aberrant HH signaling in cancer
Authors: Kohlhof Hella , Gruber Wolfgang , Vitt Daniel , Aberger Fritz , Prenzel Tanja 
Published: May 2016

Abstract
Introduction: 4SC-202, a clinical stage inhibitor of LSD1 and HDAC1, 2 and 3 was investigated to identify its unique mechanism to target cancer cells by controlling aberrant Hedgehog signaling. Experiments: 4SC-202 is an oral available epigenetic modulator exhibiting a combined inhibition of the lysine specific demethylase LSD1 (KDM1A) and histone deacetylases HDAC1, 2 and 3. 4SC-202's impact on Hedgehog signaling activity was tested in a SMO-dependent setting and in a SMO-independent setting. Therefore, Hedgehog signaling in DAOY cells was either activated by addition of sHH or Smoothened agonist or by stable depletion of SUFU for instrinsic, SMO-independent signaling. Pathway activity was determined by the expression of the effector protein GLI and primary target genes. SMO-independent Hedgehog signaling can be driven as well by growth factors like TGF-ß as demonstrated for the pancreatic cancer cell line PANC1. Therefore, 4SC-202's impact on spheroid formation and protein expression was tested in PANC1 cells. Results: Compared to HDAC inhibitors like Vorinostat, LSD1 inhibitors like OGL-002 and Hedgehog inhibitors targeting SMO like Vismodegib, 4SC-202 was able to inhibit canonical as well as non-canonical GLI-driven Hedgehog signaling. Additionally, 4SC-202 was able to prevent spheroid formation of pancreatic cancer cells and inhibit TGF-ß driven signaling in PANC1 cells.
Conclusion: Aberrant activity of the Hedgehog signaling pathway has been implicated in the development, progression and relapse of different cancer entities. Especially the interaction of tumor cells and the microenvironment is driven by SMO-independent Hedgehog signals and therefore Hedgehog inhibitors targeting SMO like Vismodegib were not able to demonstrate clinical benefit in SMO-independent Hedgehog driven cancer types like PDAC. The unique feature of 4SC-202 to control both SMO-dependent and SMO-independent HH signaling provides the opportunity to demonstrate activity in Hedgehog driven entities in further clinical investigations. 4SC-202 was safe and well tolerated in a phase I clinical trial (TOPAS) in patients with advanced hematological diseases. With a disease control rate of 83%, one partial responder treated for 8 months and one complete responder treated for 28 months, patients benefited from 4SC-202 treatment and hints of activity could be demonstrated.
Citation Format: Hella Kohlhof, Wolfgang Gruber, Daniel Vitt, Fritz Aberger, Tanja Prenzel. The small molecule inhibitor 4SC-202 controls aberrant HH signaling in cancer. [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 C89.
Abstract C94: Dual downregulation of Myc and AR with a sphingosine kinase-2 inhibitor prevents prostate cancer progression
Authors: Schrecengost Randy S. , Keller Staci , Schiewer Matthew , Knudsen Karen , Smith Charles 
Published: May 2016

Abstract
The bioactive sphingolipid sphingosine-1-phosphate (S1P) drives several hallmark processes of cancer, making the enzymes that synthesize S1P, i.e. sphingosine kinase 1 and 2 (SK1 and SK2), important targets for cancer drug development. ABC294640 is a first-in-class SK2 inhibitor that effectively inhibits cancer cell growth in vitro and in vivo. Given that AR and Myc are two of the most widely implicated oncogenes in prostate cancer (PCa), and that sphingolipids impact signaling by both proteins, the potential for using ABC294640 in the treatment of PCa was evaluated. This study demonstrates that ABC294640 abrogates signaling pathways requisite for PCa growth and proliferation. Key findings validate that ABC294640 treatment of early stage and advanced PCa models downregulate Myc and AR expression and activity. This corresponds with significant inhibition of growth, proliferation, and cell-cycle progression. Finally, oral administration of ABC294640 was found to dramatically impede xenograft tumor growth. Together, these results support the hypotheses that SK2 activity is required for PCa function and that ABC294640 represents a new pharmacological agent for treatment of early stage and aggressive PCa.
Citation Format: Randy S. Schrecengost, Staci Keller, Matthew Schiewer, Karen Knudsen, Charles Smith. Dual downregulation of Myc and AR with a sphingosine kinase-2 inhibitor prevents prostate cancer progression. [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 C94.
Abstract C96: Thyroid hormone induced Beta-catenin-dependent proliferation in colorectal cancer cells
Authors: Lin Hung-Yun 
Published: May 2016

Abstract
Thyroid hormone has been shown to induce proliferation of a variety of human cancer cell lines via a cell surface binding site on integrin αvβ3. Clinical studies indicate that thyroid hormone may support the growth of brain tumor, breast cancer, head-and-neck cancer, renal cell carcinoma and several other cancers. The effect of microenvironmental thyroid hormone on the growth of colorectal cancer has not been investigated fully. Numerous evidences suggest that the Wnt/β-catenin pathway, which is involved in both normal and oncogenic developments of the gut, is associated with thyroid hormone and its downstream signaling. The study is therefore aimed to look at the role of thyroid hormone, thyroxine (T4) on colon cancer progression through β-catenin activation.
Materials and Methods: The effect of T4 in two APC mutant colon cancer cell lines HT-29 and Colo205 cells and one APC wild type colon cancer HCT116 cells were studied. MTT assays were performed to evaluate cell proliferation under different concentrations of T4. Relative mRNA and protein expressions of relevant genes were examined using qPCR and Western blotting, respectively.
Results: T4 (10−8 to 10−6 M) induced proliferation in colorectal cancer HT-29 cells, HCT116 cells and Colo205 cells in a concentration-dependent manner. In HT29 and Colo205 cancer cell lines, the expressions of β-catenin and HMGA2 were not significantly altered by the application of T4. Alternatively, T4 increased accumulation of nuclear β-catenin and HMGA2 in HT-29 cells. Nuclear β-catenin and message were elevated by T4 in Colo205 cells. On the other hand, in addition to the cell proliferation and nuclear accumulation of β-catenin and HMGA2, T4 (10−8-10−6 M) induced the expression of β-catenin and HMGA2 in HCT116 cells. The expression of genes involved in proliferation was enhanced by thyroxine treatment.
Conclusions: T4 promoted proliferation in colon cancer HT-29, Colo205 and HCT116 cells. The effect of T4 in colon cancer involved nuclear distribution of β-catenin and its activation. However, the different phenotypes of APC affected the accumulation of nuclear β-catenin and HMGA2 induced by T4. Further study concerning detailed mechanisms is required to elucidate the role of thyroid hormone in colon cancer progression. By understanding the mechanisms behind the pathogenic effects of thyroid hormone, we will propose and develop new treatment approaches to colorectal cancers.
Citation Format: Hung-Yun Lin. Thyroid hormone induced Beta-catenin-dependent proliferation in colorectal cancer cells. [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 C96.
Abstract C98: Selective estrogen mimics (SEMs) for the treatment of tamoxifen resistant breast cancer
Authors: Patel Hitisha , Xiong Rui , Gutgesell Lauren , Zhao Jiong , Molloy Mary Ellen , Tonetti Debra , Thatcher Gregory R.J 
Published: May 2016

Abstract
Tamoxifen, an antagonist at estrogen receptor alpha (ERα) in breast tissue, and the prototypical selective estrogen receptor modulator (SERM), is the standard of care for many patients with ER-positive breast cancer. However, continued tamoxifen treatment increases the risk of endometrial cancer and half of ER-positive breast cancer patients do not respond or relapse on treatment with tamoxifen. Tamoxifen-resistant tumors are often ER-positive and endocrine-independent and therefore resistant to aromatase inhibitors. Recent clinical trials have shown the efficacy of estrogen in patients who have undergone exhaustive tamoxifen therapy. Therefore, we propose the development of small molecules that mimic the actions of estradiol in ER-positive breast cancer without the uterotrophic actions of estradiol and tamoxifen: Selective Estrogen Mimics (SEMs). Evidence suggest that a significant subset of ER-positive breast cancer, over-expressing PKCα, and tamoxifen-resistant cancers will respond to SEMs. In order to design and optimize SEMs, tamoxifen-resistant cell lines, MCF-7:5C, T47D: PKCα and T47D: Tam1 were studied. The activation of classical ERα signaling by the estrogen mimics was profiled in MCF-7 cells and cell viability in 2D culture was examined. In an effort to increase throughput and mimic the in vivoenvironment more closely, we assessed the SEMs in a new 3D spheroid model. It was found that in MCF-7:5C cells in 2D and T47D spheroids that SEM induced cell death was mediated by activation of ERα. SEMs caused decreased spheroid viability and growth in all three models of tamoxifen resistance. Extranuclear localization of ER after SEM treatment previously reported in matrigel assays and in vivo xenografts was also observed in spheroids. This emphasizes the capability of the 3D spheroids to replicate in vivo environments, making them a high-throughput translational assay of choice for drug discovery. Three promising SEMs were evaluated in xenograft models of TAM-resistant, PKCα overexpressing breast cancer. While E2 caused regression of these tumors, a significant increase in uterine weight as predicted was observed. More importantly, SEM treated mice had negligible increase in uterine weight underlining the enhanced safety of these molecules. These data suggest that development of SEMs that retain the beneficial properties of estrogen while limiting the side effects is a feasible strategy for the treatment of tamoxifen resistant breast cancer.
Citation Format: Hitisha Patel, Rui Xiong, Lauren Gutgesell, Jiong Zhao, Mary Ellen Molloy, Debra Tonetti, Gregory R.J Thatcher. Selective estrogen mimics (SEMs) for the treatment of tamoxifen resistant breast cancer. [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 C98.
Abstract CN05-01: The Cancer Cell Map Initiative: Mapping molecular networks for tumor stratification and treatment
Authors: Ideker Trey 
Published: May 2016

Abstract
Progress in DNA sequencing has revealed the startling complexity of cancer genomes, which typically carry thousands of somatic mutations. However, it remains unclear which are the key driver mutations or dependencies in a given cancer and how these influence pathogenesis and response to therapy. Although tumors of similar types and clinical outcomes can have patterns of mutations that are strikingly different, it is becoming apparent that these mutations recurrently hijack the same hallmark molecular pathways and networks. For this reason, it is likely that successful interpretation of cancer genomes will require comprehensive knowledge of the molecular networks under selective pressure in oncogenesis. I will discuss the creation of a new effort, The Cancer Cell Map Initiative (CCMI), aimed at systematically detailing these complex interactions among cancer genes and how they differ between diseased and healthy states. I will present recent progress that enables creation of these cancer cell maps across a range of tumor types and how they can be used to target networks disrupted in individual patients, significantly accelerating the development of precision medicine.
Citation Format: Trey Ideker. The Cancer Cell Map Initiative: Mapping molecular networks for tumor stratification and treatment. [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 CN05-01.
Abstract CN05-02: From the cancer landscape to personalized treatment
Authors: Wessels Lodewyk , Thijssen Bram , Jastrzebski Kathy , Beijersbergen Roderick 
Published: May 2016

Abstract
While many oncogenic drivers and drug resistance mechanisms have been discovered, it is generally unclear how these mechanisms interact to induce sensitivity or resistance in a cell line for a particular drug. To systematically unravel these mechanisms, we developed a combined computational and experimental approach based on high throughput datasets and show these can be employed to predict response to anti-cancer agents. Specifically, we characterized 30 breast cancer cell lines at the DNA, RNA and protein level, and measured the response to various inhibitors. We then constructed Bayesian models encompassing several of the important driver pathways and resistance mechanisms, which we extracted from the literature and knowledge bases. Subsequently we tested how well these models describe the available data. The models provide estimates of the relative contribution of each of the drivers and resistance mechanisms and allow estimation of latent variables such as ‘pathway activation'. We demonstrate the utility of the models by thoroughly analyzing which parts of the data cannot be explained even by fairly extensive models. This provides interesting new leads and narrows down which follow-up studies may be most fruitful to advance our understanding of drug response. The systematic, quantitative understanding of drug response gained from these models will contribute significantly towards precision medicine for individual cancer patients.
Citation Format: Lodewyk Wessels, Bram Thijssen, Kathy Jastrzebski, Roderick Beijersbergen. From the cancer landscape to personalized treatment. [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 CN05-02.