bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract C136: Identification of selective cancer cytotoxic modulators of phosphodiesterase 3a by predictive chemogenomics
Authors: de Waal Lucian , Lewis Timothy A. , Rees Matthew G. , Tsherniak Aviad , Wu Xiaoyun , Choi Peter S. , Gechijian Lara , Hartigan Christina , Faloon Patrick W. , Hickey Mark J. , Tolliday Nicola , Carr Steven A. , Clemons Paul A. , Munoz Benito , Wagner Bridget K. , Shamji Alykhan F. , Koehler Angela N. , Schenone Monica , Burgin Alex B. , Schreiber Stuart L. , Greulich Heidi , Meyerson Matthew
Published: May 2016

High cancer death rates indicate the need for new anti-cancer therapeutic agents. Approaches to discover new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identify phosphodiesterase 3A modulators as cell-selective cancer cytotoxic compounds by phenotypic compound library screening and target deconvolution by predictive chemogenomics. We found that sensitivity to 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one, or DNMDP, across 766 cancer cell lines correlates with expression of the phosphodiesterase 3A gene, PDE3A. Like DNMDP, a subset of known PDE3A inhibitors kill selected cancer cells while others do not. Furthermore, PDE3A depletion leads to DNMDP resistance. We demonstrate that DNMDP binding to PDE3A promotes an interaction between PDE3A and Schlafen 12 (SLFN12), suggesting a neomorphic activity. Co-expression of SLFN12 with PDE3A correlates with DNMDP sensitivity, while depletion of SLFN12 results in decreased sensitivity to DNMDP. Our results implicate PDE3A modulators as candidate cancer therapeutic agents and demonstrate the power of predictive chemogenomics in small-molecule discovery.

Citation Format: Lucian de Waal, Timothy A. Lewis, Matthew G. Rees, Aviad Tsherniak, Xiaoyun Wu, Peter S. Choi, Lara Gechijian, Christina Hartigan, Patrick W. Faloon, Mark J. Hickey, Nicola Tolliday, Steven A. Carr, Paul A. Clemons, Benito Munoz, Bridget K. Wagner, Alykhan F. Shamji, Angela N. Koehler, Monica Schenone, Alex B. Burgin, Stuart L. Schreiber, Heidi Greulich, Matthew Meyerson. Identification of selective cancer cytotoxic modulators of phosphodiesterase 3a by predictive chemogenomics. [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 C136.
Abstract C151: Systematic discovery of cancer dependencies through deep coverage pshRNA screens
Authors: Schlabach Michael , Billy Eric , Mavrakis Konstantinos , Hoffman Greg , Schmelzle Tobias , Hofmann Francesco , Keen Nicholas , Stegmeier Frank , Sellers William
Published: May 2016

Large scale cancer genome sequencing efforts, such as TCGA, revealed the landscape of genomic alterations across many tumor types, but the functional relevance of these alterations and genetic interdependencies cannot be fully assessed from these datasets. Thus, functional genomic screens, such as pooled shRNA 9pshRNA) screens, hold great promise to systematically identify cancer dependencies. However, RNAi discovery screens have been plagued by off target effects causing false positive results and possibly masking on-target effects. In order to address the previous problems with RNAi screens for cancer target discovery, we conducted a large scale pshRNA screening campaign targeting 7500 genes at a depth of 20 shRNAs per gene, across more than 300 cell lines of the cancer cell line encyclopedia (CCLE). The substantial shRNA and cell line depth in this screen significantly increased the robustness of results relative to previous published screens, and allowed the more robust identification of cancer dependencies. Moreover, integration of those growth phenotypes with known features of the cancer cell line encyclopedia (CCLE) enabled the identification of biomarkers (genetic, epigenetic, or proteomic) that correlate with sensitivity, and thus permitted discovery of synthetic lethal relationships. The increased depth provides a robust data set that can be used to find and validate new drug targets as well as infer pathway membership of novel genes by simple phenotypic similarity. The findings of this screen will be presented here.

Citation Format: Michael Schlabach, Eric Billy, Konstantinos Mavrakis, Greg Hoffman, Tobias Schmelzle, Francesco Hofmann, Nicholas Keen, Frank Stegmeier, William Sellers. Systematic discovery of cancer dependencies through deep coverage pshRNA screens. [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 C151.
Abstract C156: GPCRs as potential therapeutic targets in pancreatic cancer-associated fibroblasts
Authors: Zhou Shu , Chang Sarah , McCann Thalia , French Randall , Lowy Andrew M. , Insel Paul A.
Published: May 2016

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense fibrotic stromal matrix, composed of activated fibroblasts (PFs)/stellate cells (PSCs), immune/inflammatory cells and other cell types. This unique tumor microenvironment is increasingly recognized as a key mediator of PDAC progression and drug resistance. Targeting the tumor stroma may thus be a therapeutic approach for PDAC. Pancreatic cancer-associated fibroblasts (CAFs), myofibroblast-like cells that produce extracellular matrix proteins, are responsible for the desmoplasia in PDAC. PSCs and PFs are the key progenitors of CAFs. Blocking the activity of CAFs may be a means to improve the therapy and prognosis of PDAC. We hypothesized that G protein-coupled receptors (GPCRs) expressed by pancreatic CAFs are potential therapeutic targets for PDAC. To begin to test this hypothesis, we used an unbiased GPCRomic array approach to identify and quantify the GPCRs expressed by pancreatic CAFs. We discovered that 104 GPCRs have shared expression in CAFs from the primary tumors of five patients; 35 of those GPCRs had at least a 2-fold increased expression in CAFs compared to both PSCs and PFs. An orphan GPCR that we term Orphan 1 is one of the most highly up-regulated GPCRs in CAFs. We found that: 1) co-culture of PSCs with a PDAC cell line (ASPC-1) increases expression of fibrotic markers and Orphan 1 GPCR; 2) Transfection of Orphan 1 GPCR in PSCs increases the expression of fibrotic markers; 3) siRNA knockdown of Orphan 1 in CAFs decreases fibrotic marker expression and cytokine secretion. We conclude that GPCRomics can identify GPCRs that regulate pancreatic CAFs. One such GPCR, Orphan 1, contributes to pro-fibrotic activities in CAFs and is a potential therapeutic target to blunt the fibrosis associated with pancreatic cancer.

Citation Format: Shu Zhou, Sarah Chang, Thalia McCann, Randall French, Andrew M. Lowy, Paul A. Insel. GPCRs as potential therapeutic targets in pancreatic cancer-associated fibroblasts. [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 C156.
Abstract C157: Syndecan1 is required for oncogenic Kras-driven PDAC tumorigenesis and maintenance
Authors: Yao Wantong , Ying Haoqiang , Draetta Giulio
Published: May 2016

Although the universal presence of KRAS mutations and their critical role in human pancreatic ductal adenocarcinoma (PDAC) designates it as an ideal therapeutic target, oncogenic KRAS (KRAS*) is still regarded as ‘undruggable’ to date. Therefore, to identify therapeutic points of intervention, it is critical to understand the impact of KRAS*-mediated pathways on in vivo tumor pathogenesis. We have recently generated an inducible KrasG12D-driven (iKRAS*) mouse PDAC model and established a critical role for sustained KRAS* activity in tumor maintenance, providing a model to characterize pathways required for KRAS*-dependent tumorigenicity. Cell surface proteins are relatively accessible and can not only provide candidates for biomarker discovery, but also be utilized as therapeutic targets. To characterize the KRAS*-specific organization of cell surface proteins for the development of possible diagnostic or therapeutic tools, we conducted an unbiased surfaceome analyses of tumor cells in the presence and absence of KRAS* signaling using the iKRAS* mouse PDAC model. Syndecans (SDC), a family of heparin sulfate proteoglycans, were identified as candidates whose membrane expression is correlated with KRAS* activity. SDC1 expression is increased in premalignant and malignant pancreatic lesions of primary human PDAC and various KRAS*-driven pancreatic cancer mouse models. In addition, SDC1 expression is specifically upregulated in response to KRAS* induction in acinar-ductal metaplasia (ADM) and early pancreatic intraepithelial neoplasia (PanIN), but not in cerulin-induced chromic pancretitis. Moreover, SDC1 membrane expression was abolished upon KRAS* extinction in PDAC cells and our data indicated that MAPK pathway, but not PI3K pathway, is important for KRAS*-mediated SDC1 surface localization. To further study the role of SDC1 in KRAS*-driven pancreatic cancers, SDC1 knockout mouse model was generated and crossed with LSL-KrasG12D-PDAC models. Our preliminary data indicated that genetic ablation of SDC1 expression effectively suppressed KRAS*-driven PDAC initiation and progression. The mechanisms of KRAS*-mediated SDC1 membrane localization and its impact on PDAC initiation and progression is being further explored. SDC1 might potentially be the drug target and diagnostic marker for PDAC.

Citation Format: Wantong Yao, Haoqiang Ying, Giulio Draetta. Syndecan1 is required for oncogenic Kras-driven PDAC tumorigenesis and maintenance. [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 C157.
Abstract C168: A two stage prospective clinical trial with irofulven treatment targeting a selected subgroup of castration- and docetaxel resistant prostate cancer patients
Authors: Knudsen Steen , Jensen Thomas , Hansen Anker , Buhl Ulla , Rasmussen Annie , Pratt Bruce , Asaithambi Arun , Brünner Nils , Jensen Peter Buhl
Published: May 2016

Irofulven, a DNA damaging semi -synthetic analog of Illudin S (phytotoxin from Omphalotus illudins, jack-o'-lantern mushroom) which in the body is activated by prostaglandin reductase, has shown promising clinical activity in a range of cancer forms but the objective response rates were too low to justify further clinical development. Of particular interest is that irofulven may not be a substrate of the mdr-1 drug efflux pump and thereby potentially active in prostate cancer patients with acquired resistance to docetaxel. We have now developed an irofulven responsive predictor which is based on gene expression data by comparing associations between gene expression profiles and growth inhibition in a panel of cell lines treated with irofulven. A second step has included filtering the identified gene expression profile against mRNA expression from a collection of 3200 human tumors. Only genes being differentially expressed in the clinical tumor material were retained in the model. A total of 205 mRNA's were selected for the final irofulven responsive profile. The profile can be converted to a single score of predicted irofulven responsiveness. We are now initiating a prospective clinical trial (Simon's two stage design) in selected patients with castration - and docetaxel resistant prostate cancer and with a favorable irofulven responsive profile. We are screening 600 prostate cancer samples (FFPE tissue) in order to select the 10% of patients with the highest likelihood of benefit from irofulven treatment. Primary end-points are objective response rate and changes in serum PSA.

Citation Format: Steen Knudsen, Thomas Jensen, Anker Hansen, Ulla Buhl, Annie Rasmussen, Bruce Pratt, Arun Asaithambi, Nils Brünner, Peter Buhl Jensen. A two stage prospective clinical trial with irofulven treatment targeting a selected subgroup of castration- and docetaxel resistant prostate cancer patients. [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 C168.
Abstract C173: Anti-PD-L1 antibody-based IL-15 immunocytokine has enhanced antitumor immunity
Authors: Wu Yan , Zhong Zhaojing , Martomo Stella , Lu Dan , Polonskaya Zhanna , Luna Xenia , Zhang Haifan , Zhang Zhikai , Wang Zhun , Liu Leo , Patel Jeegar , Tonra James , Li Henry , Witte Larry , Waksal Sam , Zhu Zhenping
Published: May 2016

Immune checkpoint antagonists to PD-1/PD-L1 and immunostimulating cytokines such as IL-15 have shown success to some extent in certain clinical settings across multiple cancer types. However, the full potential of the checkpoint inhibitor is limited due to impaired overall antitumor immunity, and cytokine as single agent has insufficient half-life and systemic toxicities due to the lack of target specificity. To overcome these challenging hurdles, we developed a bifunctional fusion protein, KD-033, composed of an antibody specific for PD-L1 and complex of IL-15Rα sushi domain/IL-15 as a novel immunotherapeutic agent for achieving better antitumor efficacy. Previously, we presented the generation and characteristics of a prototype of bifunctional fusion protein and its potential of in vivo antitumor activity. Here, we report a genetically modified fusion protein that has enhanced immunological activity and capability to achieve stronger antitumor efficacy in tumor models in comparison with either single agent. Our data indicate that the improved bifunctional fusion protein has favorable thermal stability and can be efficiently expressed in mammalian cells. The bifunctional fusion protein has higher affinity to PD-L1, silenced binding activity to Fc receptors and better ability to increase the secretion of Th1 cytokine, i.e. gamma IFN and the cytotoxicity of CD8 T-cells and NK cells to tumor cells as assessed in immunological assays. In preclinical study, KD033 had stronger anti-tumor efficacy in controlling primary tumor growth and prolonging the survival of tumor bearing mice in a number of mouse tumor models including those aggressive tumor models. Furthermore, the PD-L1 targeted bifunctional protein had significantly less cytokine-related toxicity when compared to non-targeted full IgG/IL-15Rα sushi domain/IL-15 fusion protein in vivo. These results demonstrate that KD033 has the capacity of targeting IL-15-stimulated innate and adaptive immune effectors into local tumor sites, thereby effectively controlling tumor progression while having minimized potential adverse effect in vivo. The preclinical studies of the novel immunotherapeutics warrant further investigation towards the clinical development of the bifunctional immunotherapeutic agent for cancer treatment.

Citation Format: Yan Wu, Zhaojing Zhong, Stella Martomo, Dan Lu, Zhanna Polonskaya, Xenia Luna, Haifan Zhang, Zhikai Zhang, Zhun Wang, Leo Liu, Jeegar Patel, James Tonra, Henry Li, Larry Witte, Sam Waksal, Zhenping Zhu. Anti-PD-L1 antibody-based IL-15 immunocytokine has enhanced antitumor 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 C173.
Abstract C203: Cracking the (ultra)structural biology of Scribble to understand its role as a cell polarity regulator and tumor suppressor protein
Authors: Lim Krystle YB , Caria Sofia , House Colin M. , Godde Nathan J. , Ogden Allison J. , Humbert Patrick O. , Kvansakul Marc
Published: May 2016

Cell polarity or cell asymmetry is crucial for the normal biological function of all metazoan cells. Loss of cell polarity disrupts cellular organization that represents one of the hallmarks of cancer progression. Scribble, a member of the core polarity SCRIB module is deregulated in many cancers such as breast cancer, cervical cancer and prostate cancer. Scribble is a member of the LAP family that consists of 16 Leucine Rich Repeats and 4 PSD-95/Discs-large/ZO-1 (PDZ) domains. The PDZ domains (4PDZ) in particular are important in Scribble's interactions with molecules that are involved in many crucial signaling pathways. We hypothesized that Scribble acts as a scaffold protein to orchestrate these interactions. Our aim is to decipher Scribble's mechanism of action through characterization of Scribble interactions with βPIX (PAK-interacting exchange factor beta), which is well establish in exocytosis and neuronal transmission. Herein, we used pull down assay, isothermal titration calorimetry and small angle X-ray scattering to unravel the interaction profile of the region of Scribble encoding for all four PDZ domains. Our study proposes a working model to illustrate how PDZ domains modulate Scribble and βPIX interactions.

Citation Format: Krystle YB Lim, Sofia Caria, Colin M. House, Nathan J. Godde, Allison J. Ogden, Patrick O. Humbert, Marc Kvansakul. Cracking the (ultra)structural biology of Scribble to understand its role as a cell polarity regulator and tumor suppressor protein. [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 C203.
Abstract C27: Activation of PKA induces a mesenchymal-to-epithelial transition and epigenetic reprogramming-mediated loss of tumor initiating ability
Authors: Pattabiraman Diwakar R. , Weinberg Robert A.
Published: May 2016

Cancer stem cells (CSCs) have emerged in recent years as important targets for cancer therapy owing to their elevated resistance to conventional chemotherapy as well as to tumor-initiating ability that enables them to seed new tumors and thereby drive clinical relapse. The epithelial-to-mesenchymal transition (EMT) is a cell-biological program that confers mesenchymal traits on both normal and neoplastic epithelial cells. By activating EMT programs, carcinoma cells acquire malignancy-associated traits and additionally may become converted into CSC-like cells, as has been shown in many cases. This association between the EMT program and the CSC state has presented an attractive opportunity for drug development and agents that preferentially target more mesenchymal carcinoma cells rather than their epithelial counterparts are highly sought. An alternative therapeutic approach is to convert CSCs to their non-stem cell counterparts through the induction of a mesenchymal-to-epithelial transition (MET). Here we observe that increases in intracellular levels of the second messenger 3'-5'-cyclic adenosine monophosphate (cAMP) and the subsequent activation of protein kinase A (PKA) induces an MET in mesenchymal human mammary epithelial cells and their neoplastic derivatives. The MET-induced differentiation is accompanied by a loss of stem-like properties and tumor-initiating ability, rendering the cells more sensitive to treatment with chemotherapeutic drugs such as doxorubicin and paclitaxel. Upon activation PKA phosphorylates and activates PHF2, a histone H3K9 demethylase, which relieves H3K9me2/3-mediated repression of epithelial genes. Genome-wide occupancy studies of PHF2 reveal that it interacts with numerous genomic loci, relieving their methylation-mediated silencing, enabling the access of epithelial loci to transcription machinery and ultimately, acquisition of an epithelial state. This works presents an attractive strategy to induce an MET through the activation of a histone demethylase that induces widespread epigenomic reprogramming and acquisition of an epithelial state that is more amenable to chemotherapeutic treatment.

Citation Format: Diwakar R. Pattabiraman, Robert A. Weinberg. Activation of PKA induces a mesenchymal-to-epithelial transition and epigenetic reprogramming-mediated loss of tumor initiating ability. [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 C27.
Abstract C30: The 1,2-diaminocyclohexane carrier ligand in oxaliplatin induces p53-dependent transcriptional repression of factors involved in thymidylate biosynthesis
Authors: Kitao Hiroyuki , Kiyonari Shinichi , Iimori Makoto , Matsuoka Kazuaki , Morikawa-Ichinose Tomomi , Miura Daisuke , Niimi Shinichiro , Saeki Hiroshi , Oki Eiji , Maehara Yoshihiko
Published: May 2016

Platinum-based chemotherapeutic drugs are widely used as components of combination chemotherapy in the treatment of cancer. One such drug, oxaliplatin, exerts a synergistic effect against advanced colorectal cancer in combination with 5-FU and leucovorin. In the p53-proficient colorectal cancer cell line HCT116, oxaliplatin represses the expression of deoxyuridine triphosphatase (dUTPase), a ubiquitous pyrophosphatase that catalyzes the hydrolysis of dUTP to dUMP and inhibits dUTP-mediated cytotoxicity. However, the underlying mechanism of this activity has not been completely elucidated, and it remains unclear whether factors other than downregulation of dUTPase contribute to the synergistic effect of 5-FU and oxaliplatin. In this study, we found that oxaliplatin and dachplatin, platinum-based drugs containing the 1,2-diaminocyclohexane (DACH) carrier ligand, repressed the expression of nuclear isoform of dUTPase (DUT-N), whereas cisplatin and carboplatin did not. Oxaliplatin induced early p53 accumulation, upregulation of primary miR-34a transcript expression, and subsequent downregulation of E2F3 and E2F1. Nutlin-3a, which activates p53 non-genotoxically, had similar effects. Introduction of miR-34a mimic also repressed E2F1 and DUT-N expression, indicating that this miRNA plays a causative role. In addition to DUT-N, oxaliplatin repressed, in a p53-dependent manner, the expression of genes encoding enzymes involved in thymidylate biosynthesis. Consequently, oxaliplatin significantly decreased the level of dTTP in the dNTP pool in a p53-dependent manner. These data indicate that the DACH carrier ligand in oxaliplatin triggers signaling via the p53-miR-34a-E2F axis, leading to transcriptional regulation that ultimately results in accumulation of dUTP and reduced dTTP biosynthesis, potentially enhancing 5-FU cytotoxicity.

Citation Format: Hiroyuki Kitao, Shinichi Kiyonari, Makoto Iimori, Kazuaki Matsuoka, Tomomi Morikawa-Ichinose, Daisuke Miura, Shinichiro Niimi, Hiroshi Saeki, Eiji Oki, Yoshihiko Maehara. The 1,2-diaminocyclohexane carrier ligand in oxaliplatin induces p53-dependent transcriptional repression of factors involved in thymidylate biosynthesis. [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 C30.
Abstract C58: Small molecule inhibitors targeting the interaction of xeroderma pigmentosum group A protein with cisplatin-damaged DNA
Authors: VanderVere-Carozza Pamela S. , Gavande Navnath , Mishra Akaash , Turchi John J.
Published: May 2016

Targeting DNA repair and the DNA damage response for cancer therapy has recently gained increasing attention with inhibitors of the PI3-K-like kinases in early stage clinical trials. The utility of DNA repair inhibitors can be expanded by their use in combination treatment with DNA damaging chemotherapeutics including cisplatin. We have focused on directly targeting the DNA repair pathway responsible for repairing platinum-induced DNA damage, nucleotide excision repair (NER). We have selected the molecular target XPA, whose role is in the identification and verification of the sites of DNA damage. Clinical validation of XPA has been obtained where high XPA expression in lung, ovarian and lung cancer results in decreased efficacy of platinum therapy. We report the continued development of the X80 class of XPA small molecule inhibitors. In a two-step, iterative process we have identified critical structure activity relationships that have resulted in a 100-fold increase in potency with in vitro IC50 values below 1μM. Analyses of the SARs define the chemical and structural features that impact the interaction with XPA, cellular permeability and contribute to selectivity. Data demonstrate that the X80 class of inhibitors do not interact with DNA but directly bind the XPA protein. Recent production of a sub-fragment of the XPA protein will allow the identification of the direct binding domain to enable continued structure-based design of more potent XPA inhibitors.

Supported by NIH grants R01CA180710 and R41CA162648 to JJT.

Citation Format: Pamela S. VanderVere-Carozza, Navnath Gavande, Akaash Mishra, John J. Turchi. Small molecule inhibitors targeting the interaction of xeroderma pigmentosum group A protein with cisplatin-damaged DNA. [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 C58.
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

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

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

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

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

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

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

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

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

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.