bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A20: Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A
Authors: Hubert Christopher G. , Bradley Robert K. , Ding Yu , Chad Toledo M. , Skutt-Kakaria Kyobi , Girard Emily J. , Davison Jerry , Berndt Jason , Corrin Philip , Basom Ryan , Delrow Jeffery J. , Webb Thomas , Pollard Steven M. , Lee Jeongwu , Olson James M. , Paddison Patrick J. 
Published: August 2014

Abstract
To identify key regulators of human brain tumor maintenance and initiation, we performed multiple genome-wide RNAi screens in patient-derived glioblastoma multiforme (GBM) stem cells (GSCs). These screens identified the PHD-finger domain protein PHF5A as differentially required for GSC expansion gene, as compared to untransformed neural stem cells (NSCs) and fibroblasts. Given PHF5A's known involvement in facilitating interactions between the U2 snRNP complex and ATP-dependent helicases, we examined cancer-specific roles in RNA splicing. We find that in GSCs, but not untransformed controls, PHF5A facilitates recognition of exons with unusual C-rich 3' splice sites in thousands of essential genes. PHF5A knockdown in GSCs, but not untransformed NSCs, astrocytes, or fibroblasts, inhibited splicing of these genes, leading to cell cycle arrest and loss of viability. Notably, pharmacologic inhibition of U2 snRNP activity phenocopied PHF5A knockdown both in GSCs and in multiple genetically transformed cell types, suggesting that a cancer-specific requirement for PHF5A activity may be generalizable to a wide range of cancers. Furthermore, PHF5A inhibition compromises GSC tumor formation in vivo and dramatically inhibits the growth of established GBM patient-derived xenograft tumors. Together, this work demonstrates an additional mechanism for maintaining splicing fidelity in cancer cells and also suggests that PHF5A activity may provide new in-roads for novel anti-GBM therapeutic strategies.
Citation Format: Christopher G. Hubert, Robert K. Bradley, Yu Ding, Toledo M. Chad, Kyobi Skutt-Kakaria, Emily J. Girard, Jerry Davison, Jason Berndt, Philip Corrin, Ryan Basom, Jeffery J. Delrow, Thomas Webb, Steven M. Pollard, Jeongwu Lee, James M. Olson, Patrick J. Paddison. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A20.
Abstract A23: Genome-wide discovery of synthetic lethal interactions in PTEN-deficient human mammary epithelial cells
Authors: Tang Yew Chung , McPherson John , Tan Elisabeth , Goh Germaine , Bard Frederic , Rozen Steve 
Published: August 2014

Abstract
PTEN is one of the most frequently dysregulated tumor suppressor genes in human cancers, and PTEN deficiency is common in breast tumors, particularly those that belong to the aggressive basal-like breast cancer (BLBC) subtype. Because the BLBC subtype is itself very heterogeneous and basal-like tumors lack expression of cancer drug targets like HER2, there is currently no targeted therapy available for effective treatment. To systematically and comprehensively explore potential vulnerabilities in PTEN-deficient BLBC, we sought to discover genes that are synthetic lethal to PTEN loss using a functional genomics approach. We carried out a synthetic lethal siRNA screen in a pair of isogenic cell lines: an untransformed, non-tumorigenic human mammary epithelial cell line with molecular characteristics that closely mimic BLBCs (MCF10A), and a derivative cell line that harbored a targeted deletion of exon 2 in the PTEN gene (MCF10A-PTEN-/-). For greater sensitivity in detecting synthetic lethal effects, we used a high content screening system to determine total cell numbers by direct counting of stained cell nuclei after siRNA knock-down. Through the discovery of synthetic lethal interactions in these PTEN-deficient cell lines, we aim to identify novel components of the PTEN signaling network and uncover vulnerabilities in PTEN-deficient tumors. We first completed a pilot screen of kinase and phosphatase genes and identified synthetic lethal hits which were subsequently confirmed using multiple siRNA sequences for each gene. Our top candidate synthetic lethal genes were not directly involved in the PI3K-Akt signaling pathway, consistent with studies showing that therapeutic targeting of the PI3K pathway in PTEN-deficient cancers is not always effective. Using the strongest hit from the pilot screen as a positive synthetic lethal control, we further completed a whole-genome screen in the same pair of isogenic cell lines. We are currently validating the top candidate synthetic lethal genes and will explore if these putative synthetic lethal interactions are present in other PTEN-deficient breast cancer cell lines belonging to the BLBC subtype.
Citation Format: Yew Chung Tang, John McPherson, Elisabeth Tan, Germaine Goh, Frederic Bard, Steve Rozen. Genome-wide discovery of synthetic lethal interactions in PTEN-deficient human mammary epithelial cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A23.
Abstract A27: Dissecting the functional landscape of triple-negative breast cancer
Authors: Maxfield Kimberly , Prat Aleix , Corcoran Kathleen , Whitehurst Angelique 
Published: August 2014

Abstract
Our group employed a pangenomic loss of function screening approach to systematically dissect the molecular architecture that functionally supports Triple Negative Breast Cancer (TNBC). Given that treatment options for this disease are typically limited to cytotoxic therapies, we applied a paclitaxel-based synthetic lethal approach to identify those molecular components that modulate chemoresponsiveness. To account for heterogeneity within the patient population, we screened 4 triple negative tumor-derived breast cancer cell lines that represent the spectrum of TNBC oncogenic aberrations and chemoresponse profiles. We also accounted for the two molecular subtypes, Claudin-Low and Basal-Like, that comprise the majority of TNBC cases. These screens revealed a number of core modulators of tumor cell viability and paclitaxel-induced cellular stress that have not been previously appreciated for supporting TNBC biology at the cell autonomous level. For example, this strategy implicated AMPK family member, SIK2, as a key nutrient sensor that may inhibit excessive autophagy. Inhibition of SIK2 leads to enhanced autophagic flux and a loss of cell viability in a variety of TNBC genetic backgrounds. In addition, we discovered the signaling supported by the cytokine receptor, CXCR3, and its ligand, CXCL9, to be repurposed to promote mitotic fidelity and thus, tumor cell fitness specifically in the Basal-Like TNBC molecular subtype. Finally, we uncovered a requirement for the transcription factor, ZNF165, in specifying the gene expression profiles activated by TGFβ signaling. In particular, the TGFβ target protein, SERPINE1, is required to promote prosurvival signaling in the Claudin-Low TNBC molecular subtype. Given that the expression of ZNF165 is otherwise restricted to the male testes, ZNF165 may represent a mechanism by which tumors engage anomaly-expressed proteins to promote survival. Taken together, we have uncovered novel tumor cell vulnerabilities in TNBC that could be therapeutically leveraged to enhance current therapeutic approaches.
Citation Format: Kimberly Maxfield, Aleix Prat, Kathleen Corcoran, Angelique Whitehurst. Dissecting the functional landscape of triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A27.
Abstract A30: NF-kB activating peptides identified in genetic screen cooperate with Ras transformation by suppression of p53 linking inflammation to carcinogenesis
Authors: Natarajan Venkatesh , Komarov Andrei P. , Chenchik Alex , Gudkov Andrei V. 
Published: August 2014

Abstract
Chronic inflammatory conditions are frequently linked to increased risk of carcinogenesis. The transcription factor NF-kappa B acts as a central component of signaling pathways governing the inflammatory response. NF-kB is also constitutively activated in several tumors. While the tumor promoting inflammatory effects are largely attributed to activation of NFκB signaling in tumor milieu, it is unclear whether activation of inflammatory pathway alone can initiate tumorigenesis. The mechanism by which constitutive activation of NF-kB contributes to carcinogenesis remains elusive. We hypothesized that constitutive activation of NFkB by proinflammatory agents renders p53 incapable of opposing oncogene induced transformation. As pharmacological activation of NF-kB in normal cells is prone to transient effects due to feedback regulation, we performed an unbiased genetic screen for proinflammatory peptides in an NFκB-GFP reporter cell line using a lentiviral trimer peptide library spanning the coding regions of 800 extracellular ligands. We identified several pro-inflammatory peptides whose expression lead to robust activation of NFκB signaling. Suppression of p53 has been shown to be the only criteria to be met to override ras oncogene induced senescence in rodent fibroblasts, which prompted us to test the NFκB activating peptides in this model. Here, we show that indeed, these NF-kB activating peptides cooperate with oncogenic RasV12 to induce transformation in both in rat fibroblast cell line REF52 and primary mouse embryonic fibroblasts (MEFs) through r p53. Further, these Ras transformed fibroblast cells formed tumors in nude mice. Thus, pro-inflammatory genetic elements that activate NF-kappa B pathway can override Ras induced senescence to facilitate cellular transformation underscoring the importance of NFκB inhibitors in preventing initiation of tumerigenesis.
Citation Format: Venkatesh Natarajan, Andrei P. Komarov, Alex Chenchik, Andrei V. Gudkov. NF-kB activating peptides identified in genetic screen cooperate with Ras transformation by suppression of p53 linking inflammation to carcinogenesis. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A30.
Abstract A33: Optimizing NGS-based shRNA screening experiments and data analysis
Authors: Yu Jiyang , Gao Ying , Zhong Wenyang , Chen Lei , Apanovitch Donald , Follettie Max , Rejto Paul , Arndt Kim 
Published: August 2014

Abstract
Pooled small hairpin RNA (shRNA) screening emerges as a powerful tool for loss-of-function studies in mammalian cells and searching for novel or synthetic lethality-based therapeutic targets of human tumors. Next-generation sequencing (NGS) is becoming a standard technology to read out hairpin representations with high resolution and allowance of massive multiplexing. However, the extraction of robust biological signals from high-throughput NGS-based shRNA screening (shSeq) data remains challenging due to low knock-down efficacy and off-target effects of shRNAs, sequencing errors, artificial mutations, etc. In this presentation, based on our in vitro shSeq screens in human cancer cells by Illumia MiSeq, we report a discovery of an unexpected recurrent distribution pattern of identified hairpin counts across number of allowed mismatches during read deconvolution. By exhaustive analysis of within and between-group noise, we develop a procedure to optimize both experimental and analytical parameters for shSeq screens and suggest a set of default parameters that perform well consistently. We observe that over 10% of recovered hairpin reads have at least one mismatch from the reference sequence, which cannot be explained by sequencing error only. We also notice that there are more mismatched reads at later time point than at initial one. And computational analysis of such dynamic process reflects higher evolutionary mutation rate (&gt;10^-5) in cancer cells than common sense (~10^-9). Artificial mutations that might cause a high percentage of mismatches are further explored and interesting mutation patterns are identified.
Citation Format: Jiyang Yu, Ying Gao, Wenyang Zhong, Lei Chen, Donald Apanovitch, Max Follettie, Paul Rejto, Kim Arndt. Optimizing NGS-based shRNA screening experiments and data analysis. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A33.
Abstract A41: Exploiting synthetic lethal interactions in the DNA damage response area and beyond in drug discovery
Authors: Wappett Mark , Ward Richard , Fisher Paul , Bradford James , Dry Jonathan , O'Connor Mark , Lau Alan , Durant Steve 
Published: August 2014

Abstract
Building upon the exciting precedent exemplified by olaparib in the PARP-BRCA axis, we aim to identify and exploit further synthetic lethal (SL) interactions within and beyond the DNA damage response (DDR) area. To facilitate with this search, we have developed a method implemented as an in silico algorithm that uses gene expression and mutation data to detect putative SL interactions in cell lines and cancer tissue across The Cancer Genome Atlas (TCGA). This approach has detected relatively rare signatures including those described in the literature, for example ATM and ATR. The algorithm has also revealed potentially novel in silico SL gene pairs outside of DDR involving frequently mutated tumor suppressor genes linked to targets that AstraZeneca has previously developed selective compounds against. We are validating an attractive selection of these in vitro using appropriate cell lines, siRNA and small molecule inhibitors.
Citation Format: Mark Wappett, Richard Ward, Paul Fisher, James Bradford, Jonathan Dry, Mark O'Connor, Alan Lau, Steve Durant. Exploiting synthetic lethal interactions in the DNA damage response area and beyond in drug discovery. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A41.
Abstract B05: Targeting nonapoptotic cell death in chemoresistant patient-derived breast cancer cells
Authors: Vaden Rachel M. , Gligorich Keith M. , Shelton Dawne N. , Wang Guoying , Matsen Cindy B. , Looper Ryan E. , Sigman Matthew S. , Welm Bryan E. 
Published: August 2014

Abstract
The development of anti-cancer therapeutics that target non-apoptotic pathways has received increasing attention from the scientific community in recent years. The prevalence of chemoresistance and the characterization of defective apoptotic pathways in cancer has promoted interest in the expansion of current therapeutic regimens to include drugs that induce non-apoptotic cell death. From a phenotypic screen we have identified a small molecule named C6 that induces caspase-independent, non-apoptotic cell death in chemoresistant patient-derived breast cancer cells. Additionally, C6 is also selectively cytotoxic against cancer cells compared to normal mammary epithelial cells. In an effort to characterize this small molecule's mechanism of action and identify relevant biological pathways that might be used as therapeutic drug targets, we have utilized a photoaffinity pull-down strategy to identify biological binding partners of C6. Our photoaffinity pull-down studies have revealed Mitsugumin 23 (MG23), an endoplasmic reticulum-bound transmembrane protein capable of ion channel formation, as a binding partner for C6. Additionally, we have identified a metabolic component of C6-induced cell death through the use of mitochondrial respiration measurements, metabolomic analyses, and mitochondrial transmission electron microscopy (TEM) imaging. Metabolic studies have identified mitochondrial respiration defects, excess lactic acid production, and gross changes in mitochondrial morphology as a result of C6 treatment. Collectively, our findings suggest a role for ionic imbalance and subsequent metabolic disruption in this form of caspase-independent cell death. Our ongoing work is focused on further mechanistic characterization of this non-apoptotic pathway as a potential target for breast cancer drug development.
Citation Format: Rachel M. Vaden, Keith M. Gligorich, Dawne N. Shelton, Guoying Wang, Cindy B. Matsen, Ryan E. Looper, Matthew S. Sigman, Bryan E. Welm. Targeting nonapoptotic cell death in chemoresistant patient-derived breast cancer cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B05.
Abstract B18: High-dimensional combinations of cancer drugs to induce synthetic lethality in colorectal cancer
Authors: Horn Thomas , Zhang Xiaobin , Ho Samuel , Garraway Levi , Schlegel Robert , Caponigro Giordano , Lehar Joseph 
Published: August 2014

Abstract
Cancers are inherently robust biological systems with many compensation mechanisms and genetic redundancies allowing them to escape treatments and become resistant. Theoretically, such complex systems can become fragile when perturbed by multiple attacks. Here, we systematically tested whether pairwise combinations of compounds targeting critical oncogenic pathways in colorectal cancer cells can combine to inhibit their growth or even kill them. Some combinations targeting growth pathways showed synergies in a broad spectrum of genetic backgrounds even when the single agents had more specific effects. Guided by the pairwise combination screening, we identified higher-dimensional combinations that not only showed broad synergy but could also drive cytostatic combination responses into synthetic lethality.
Citation Format: Thomas Horn, Xiaobin Zhang, Samuel Ho, Levi Garraway, Robert Schlegel, Giordano Caponigro, Joseph Lehar. High-dimensional combinations of cancer drugs to induce synthetic lethality in colorectal cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B18.
Abstract B25: Inhibition of autocrine signaling as a strategy to target tumor-initiating breast cancer cells
Authors: Scheel Christina , Dragoi Diana , Eaton Elinor Ng , Sophia Hsin-Jung Li , Reinhardt Ferenc , Weinberg Robert A. 
Published: August 2014

Abstract
The epithelial-mesenchymal transition (EMT), a pleiotropic cellular program, has been associated with the acquisition of metastatic ability, self-renewal traits and resistance to chemotherapeutic drugs in breast cancer and other carcinomas. During normal development and tumor progression, this change in cell phenotype is induced by contextual signals that epithelial cells receive from their microenvironment, thereby promoting cellular heterogeneity. The signaling context responsible for inducing an EMT and maintaining the resulting cellular states has been unclear.
We describe three signaling pathways, involving transforming growth factor (TGF)-beta and canonical/beta-catenin dependent and noncanonical Wnt signaling, that collaborate to induce activation of the EMT program and thereafter function in an autocrine fashion to maintain the resulting mesenchymal and stem cell-like state. Importantly, the induction of the EMT program and associated autocrine signaling is partly enabled by the downregulation of endogenous inhibitors of autocrine signals secreted by epithelial cells prior EMT, indicating a homeostatic mechanism. These inhibitors include secreted frizzled-related protein 1 (SFRP1), which has been shown by others to be a rate-limiting determinant of Wnt signaling, and Bone Morphogenetic Proteins, which appear to inhibit TGF-beta signaling. Conversely, disruption of autocrine signaling by adding back endogenous inhibitors of autocrine signaling as recombinant proteins inhibits migration and self-renewal of breast cancer cells in vitro and reduces tumorigenicity and spontaneous metastasis in vivo.
Together, our results indicate that ongoing autocrine signaling is required for the maintenance of mesenchymal and stem cell traits in breast cancer cells. In the longer term, we intent to develop a cocktail small-molecule inhibitors to therapeutically interrupt multiple autocrine pathways, thereby forcing tumor-initiating cells of breast and other carcinomas to exit the mesenchymal, stem cell-like state. Since this cellular state is associated with resistance to chemotherapeutic drugs, we predict that such a treatment protocol might render breast cancer cells that have passed through an EMT more sensitive to standard chemotherapy, thereby serving as a therapeutic strategy to overcome tumor heterogeneity and relapse.
Citation Format: Christina Scheel, Diana Dragoi, Elinor Ng Eaton, Sophia Hsin-Jung Li, Ferenc Reinhardt, Robert A. Weinberg. Inhibition of autocrine signaling as a strategy to target tumor-initiating breast cancer cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B25.
Abstract B27: Probing synthetic lethal interactions with RAF inhibition in BRAF-mutant colorectal cancer
Authors: Whittaker Steven R. , Luo Flora , Hsiao Jessica , Cowley Glenn S. , Root David E. , Garraway Levi A. 
Published: August 2014

Abstract
Large-scale RNA interference screens have indicated that BRAF-mutant colorectal cancer (CRC) cell lines are dependent upon BRAF expression for proliferation. However, small molecule RAF inhibitors, such as vemurafenib, have so far failed to exhibit robust activity in clinical trials of patients with CRC, with a response rate of only 5%. Commensurate with this, CRC cell lines demonstrate intrinsic resistance to RAF inhibitors. Therefore, we designed an RNA interference screen to identify loss of function events that could synergize with pharmacologic RAF inhibition. We transduced a pooled lentiviral library encoding 90,000 shRNAs targeting over 16,500 genes into RAF-inhibitor-resistant RKO CRC cells. The shRNA-infected population was divided into two experimental arms, one treated with DMSO, the other treated with PLX4720. Following 16 population doublings, the abundance of each hairpin was assessed by PCR amplification of barcoded hairpin DNA, followed by massively parallel paired-end sequencing. The log-fold change in shRNA abundance between the PLX4720- and DMSO-treated controls was determined and RNAi gene enrichment (RIGER) used to rank individual shRNAs and nominate candidate genes that were required for survival of RKO cells exposed to PLX4720. We validated the 40 top-ranking genes that displayed synthetic lethality with RAF inhibition in an arrayed secondary screen. shRNAs targeting MET scored highly, consistent with recent reports implicating HGF-MET signaling in resistance to BRAF inhibition, validating our approach. Furthermore, we describe the characterization of additional genes that sensitize cells to inhibition of BRAF, suggesting novel therapeutic opportunities. By integrating these findings with other genomic and functional studies we aim to identify clinically actionable events that cause RAF-inhibitor resistance in colorectal cancers.
Citation Format: Steven R. Whittaker, Flora Luo, Jessica Hsiao, Glenn S. Cowley, David E. Root, Levi A. Garraway. Probing synthetic lethal interactions with RAF inhibition in BRAF-mutant colorectal cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B27.