bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A19: Exploring genetic interactions in haploid human cells
Authors: Blomen Vincent A. , Brummelkamp Thijn R. 
Published: December 2017

Abstract
Gene-associated phenotypes often depend on the activity of other genes resulting in genetic interactions. In model organisms, the large-scale generation of combinations of mutations has resulted in the identification of genetic interactions and provided insights into their contribution to complex phenotypes. Here we use haploid human cells combined with genome-wide mutagenesis to study genetic interactions. We have made a synthetic lethality network using query genes acting in the secretory pathway and observe that human genes frequently engage in genetic interactions. Beyond cell lethality, we search for genes, which upon loss deregulate cellular processes such as signaling pathways. Genetic modifier approaches in those mutants reveals back-up mechanisms or genetic networks contributing to the phenotype of interest. This provides a much-needed window into the robust genetic networks governing human cells.
Citation Format: Vincent A. Blomen, Thijn R. Brummelkamp. Exploring genetic interactions in haploid human cells [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A19.
Abstract A38: Genome-wide CRISPR-Cas9 screens reveal modulators of temozolomide sensitivity in glioblastoma
Authors: MacLeod Graham , Rajakulendran Nishani , Hart Traver , Yu Helen , Dirks Peter B. , Angers Stephane 
Published: December 2017

Abstract
Glioblastoma (GBM) is a prevalent and highly lethal form of primary brain tumour. Presently, median survival time for GBM patients is only 15 months and thus improved treatment methods are in great need. Treatment of GBM consists of surgery, radiotherapy and the chemotherapeutic agent temozolomide (TMZ). Unfortunately, many GBMs are refractory to TMZ and most others ultimately develop resistance leading to localized disease recurrence and brain tumor invasion. With the aim of identifying new therapeutic targets for GBM we performed genome-wide CRISPR-Cas9 screens to identify genes that modulate TMZ sensitivity in GBM. The TKO library of single-guide RNAs (gRNAs) targeting over 89,000 exons in 17,232 human genes was used to screen a panel of 5 patient-derived human GBM stem cell (GSC) lines. GSCs treated with DMSO were grown in parallel with GSCs treated with either a lethal, or sub-lethal dose of TMZ. Next-generation sequencing was used to identify gRNAs that were increased/decreased in abundance in TMZ treated pools of cells.
Positive selection screening revealed that loss of key components of the mismatch repair pathway–MLH1, MSH2, MSH6 and PMS2 confers resistance to lethal doses of TMZ, as has previously been observed in GBM patients. Negative selection screening using sub-lethal doses of TMZ showed that loss of a conserved set of 15 genes that conferred TMZ hypersensitivity in four MGMT-negative GSC lines while the lone MGMT-positive GSC line in our set had a completely different set of hypersensitivity genes. Functional annotation revealed enrichment for genes involved in multiple DNA repair pathways, most prominently Fanconi Anemia and interstrand cross-link repair. Further studies validated that deletion of either member of the MCM8/9 helicase complex sensitizes GBM cells to TMZ and characterized the previously undescribed gene ZC3H7A which was revealed to be a cytoplasmic, stress-granule associated protein. In addition, our results revealed that in drug resistant MGMT expressing GSCs, TMZ resistance can be restored via the PARP inhibitor ABT-888.
In conclusion, our results have identified a core set of genes that can be targeted to increase sensitivity to the chemotherapeutic agent TMZ responsive GBMs and elucidated opportunities for restoring TMZ sensitivity in resistant GBMs. These genes, many of which are targetable enzymes represent promising therapeutic targets for increasing efficacy of chemotherapy and decreasing lethality in GBM.
Citation Format: Graham MacLeod, Nishani Rajakulendran, Traver Hart, Helen Yu, Peter B. Dirks, Stephane Angers. Genome-wide CRISPR-Cas9 screens reveal modulators of temozolomide sensitivity in glioblastoma [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A38.
Abstract B21: CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions
Authors: Munoz Diana , Stegmeier Frank P. , Schlabach Michael 
Published: December 2017

Abstract
CRISPR/Cas9 has emerged as a transformative new tool to systematically probe gene function. In this study, we compare the performance of CRISPR to RNAi-based loss-of-function screens for the identification of cancer dependencies by performing parallel deep-coverage shRNA and CRISPR screens targeting 2722 genes across several cancer cell lines. CRISPR-based dropout screens identified more lethal genes compared to RNAi in all five cancer models, indicating that the identification of many cellular dependencies may require full gene inactivation, as induced by CRISPR but not RNAi. However, in two aneuploid cancer models we found that all genes within highly amplified regions, including non-expressed genes, scored as lethal by CRISPR, revealing an unanticipated class of false-positive hits in CRISPR-based screens. Using a CRISPR tiling array that encompassed all possible sgRNAs against the coding regions of 139 genes, sgRNAs targeting essential domains provide the most robust dropout phenotypes, suggesting that this approach might be used to define the protein domains that are required for cancer dependence. Collectively, these findings demonstrate the utility of CRISPR-based screens in the identification of cancer-dependent genes, but also reveal the need to carefully control for false-positive results especially in chromosomally unstable cancer lines.
Note: This abstract was not presented at the conference.
Citation Format: Diana Munoz, Frank P. Stegmeier, Michael Schlabach. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B21.
Abstract B27: Identifying therapeutic combinations with EGFR-targeted therapy through the generation of genome-wide CRISPR-Cas9 knockout libraries in oral cancer cell lines
Authors: Ludwig Megan , Birkeland Andrew , Nimmagadda Sai , Foltin Sue , Jiang Hui , Carey Thomas , Brenner John Chad 
Published: December 2017

Abstract
Oral squamous cell carcinoma (OSCC) remains a disease with poor survival. With recent characterization of the mutational landscape of OSCCs, there is great potential for personalized targeted therapies. However, to date utilization of targeted therapies in OSCC have had limited success with anti-EGFR therapy. Combinations of targeted therapies, which may have greater efficacy by inhibiting compensatory pathways, have not been well studied. To identify synergistic combinations with EGFR-targeted therapy, we introduced Genome-scale CRISPR-Cas9 Knock-Out (GeCKO) libraries into OSCC cell lines. CRISPR-Cas9 generates individual genetic knockouts through targeted gene editing, and by using a pool of CRISPRs targeting over 18,000 genes we can perform genome-scale screening for synergistic targetable pathways. Upon selection of the OSCC GeCKO pool, we identified that knockouts of genes in the FGFR pathway caused sensitivity to the EGFR inhibitor gefitinib. We further investigated the possible synergistic effect of dual EGFR and FGFR inhibition with resazurin viability assays in 14 of our OSCC models. We found 6/14 (43%) of the models were responsive to the combination of EGFR and FGFR inhibition, indicating that the FGFR pathway could be an alternate mechanism of resistance to EGFR-targeted therapy. For further investigation of this combination, we again used CRISPR-Cas9 to generate an EGFR knockout (KO) OSCC cell line. This EGFR KO cell line retains sensitivity to FGFR inhibitors, and we expect that this cell line will be a useful tool in further evaluating the compensatory mechanism of the FGFR pathway. OSCC remains a common and frequently lethal cancer with great potential for the development of personalized targeted therapies. Here, we describe the use of genome-wide CRISPR-Cas9 library to discover the synergistic combination of EGFR and FGFR inhibition. Further investigation suggests the FGFR pathway as a common compensatory mechanism to EGFR inhibition. We hope to use this approach to identify additional compensatory mechanisms of resistance to targeted therapies with the eventual goal of translating these findings to clinic.
Citation Format: Megan Ludwig, Andrew Birkeland, Sai Nimmagadda, Sue Foltin, Hui Jiang, Thomas Carey, John Chad Brenner. Identifying therapeutic combinations with EGFR-targeted therapy through the generation of genome-wide CRISPR-Cas9 knockout libraries in oral cancer cell lines [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B27.
Abstract B30: Novel targets for combination therapy in EGFR mutated NSCLC
Authors: Drobnitzky Neele , Patel Agata , Mumin Amalina , Cahill Fiona , Lourenco Luiza Madia , Olyha Samantha , Corbacioglu Sureyya , Jiang Yanyan , Ryan Anderson J. 
Published: December 2017

Abstract
Non-small cell lung cancer (NSCLC) patients with activating mutations in the epidermal growth factor receptor (EGFR) gene generally show good responses to therapy with EGFR tyrosine kinase inhibitors (EGFR-TKIs). Unfortunately resistance emerges during treatment, driven by different mechanisms. Mutation-driven mechanisms are becoming well understood and include secondary mutations in the EGFR (T790M for 1st generation EGFR-TKIs and C797S for 3rd generation EGFR-TKIs) and activating mutations in NRAS. On the other hand, non-mutation based resistance mechanisms are less well understood but may involve activation of alternative, potentially targetable signalling pathways.
To identify alternative signalling pathways and potential combination targets, we performed a bioactive small molecule (n=1902) screen to identify targets that could delay the emergence of resistance to sustained inhibition of EGFR in EGFR-mutant NSCLC cells.
9 out of 186 target classes were significantly enriched (p&lt; 0.05) within the top 2.5 % of screen compounds, when ranked for their ability to sensitise cells to the 3rd generation EGFR-TKI AZD9291. We identified expected hits such as AKT, PI3K and mTOR but also novel targets.
To prioritise targets for in vivo validation, compounds were tested in 3D-spheroids, which have a complex microenvironment, providing a more tumour-like model. Most compounds were more cytotoxic in 3D compared to 2D when used individually, preventing or slowing down spheroid growth. EGFR-TKI combination effects in 3D varied when compared to 2D-models. FAK inhibition was less effective in spheroids compared to 2D. AKT or MEK inhibitors showed marked effects in combination, further delaying spheroid growth under EGFR-TKI treatment but also inhibited spheroid growth when used on their own. Inhibitors of novel targets were identified that showed promising combination effects even at sub-toxic single-agent doses.
Our data identify new candidates for combination therapy with EGFR-TKIs and suggest that 3D-spheroids may be a useful approach for prioritising combinations for in vivo studies.
Citation Format: Neele Drobnitzky, Agata Patel, Amalina Mumin, Fiona Cahill, Luiza Madia Lourenco, Samantha Olyha, Sureyya Corbacioglu, Yanyan Jiang, Anderson J. Ryan. Novel targets for combination therapy in EGFR mutated NSCLC [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B30.
Abstract IA14: Understanding the complex biology of KRAS mutant cancers using genetic screens
Authors: L Tina 
Published: December 2017

Abstract
Apart from identifying synthetic lethal genes, genetic screens have the potential to reveal much about the basic biology of cell lines. We utilize two techniques, one analytical and one experimental, to demonstrate how genetic screens can also reveal which pathways are on in cell lines and what are the phenotypic consequences of pathway perturbation. First, we apply a clustering analysis of genome-scale CRISPR screening data to map out active pathways in cancer cell lines and to discover novel members of signaling transduction pathways and protein complexes. Secondly, we performed a combinatorial siRNA screen that knocks out multiple genes at once and measures five functional parameters to comprehensively describe the effects of pathway inhibition. Application of these two techniques to KRAS mutant cancer cell lines reveals a trove of biological information that highlights the vast heterogeneity of this disease and subtype-specific opportunities for therapeutic intervention.
Citation Format: Tina L. Understanding the complex biology of KRAS mutant cancers using genetic screens [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr IA14.
Abstract IA18: Mechanistic participation of cancer testes antigens in tumor initiation and progression
Authors: Whitehurst Angelique 
Published: December 2017

Abstract
Tumors frequently activate genes whose expression is otherwise biased to the testis, collectively known as cancer-testis antigens (CTAs). The extent to which the anomalous expression of CTAs represents epiphenomenon or confers tumorigenic traits is unknown. To gain a systems level view of CTA activity, we implemented a multidimensional functional genomics approach that incorporated seven different phenotypic assays in 11 distinct disease settings. This analysis identified 16 CTAs that are essential for tumor cell viability and 10 CTAs that are pathological drivers of HIF, WNT or TGFb signaling. In particular, we discovered that Fetal and Adult Testis Expressed 1 (FATE1), is a key survival factor in multiple oncogenic backgrounds. FATE1's mechanism of action is to prevent the accumulation of the stress sensing, BH3-only protein, BIK, thereby permitting viability in the presence of toxic stimuli. Importantly, FATE1 expression correlates with significantly decreased survival time in colorectal and lung cancer patients. We also found that the CTA, ZNF165, promotes TGFb signaling by directly inhibiting the expression of negative feedback regulatory pathways. This action is essential for survival of triple negative breast cancer (TNBC) cells in vitro and in vivo. Given these robust phenotypes, we hypothesize that ectopically expressed testes proteins can buttress deviant tumor cell processes that promote tumor initiation and progression.
Citation Format: Angelique Whitehurst. Mechanistic participation of cancer testes antigens in tumor initiation and progression [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr IA18.
Abstract PR04: A CRISPR-based genetic interaction map identifies synergistic drug combinations for cancer
Authors: Han Kyuho , Jeng Edwin , Hess Gaelen , Morgens David , Li Amy , Bassik Michael 
Published: December 2017

Abstract
Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers. Although millions of drug combinations might be created by repurposing existing drugs, direct screening of these combinations is infeasible. Here, we designed a scalable CRISPR-based double knockout (CDKO) system to generate a mammalian genetic interaction (GI) map at unprecedented scale, comprised of 490,000 double-sgRNAs directed against 21,321 pairs of drug targets. We first developed an efficient strategy for cloning and sequencing the libraries, as well as a robust statistical scoring method for calculating GIs from CRISPR-deleted gene pairs. We then extensively validated this system by identifying known and novel genetic interactions in the ricin pathway, and compared the GIs to known protein-protein interactions (PPIs). Using this validated system, we searched for rare synthetic lethal drug target pairs in K562 leukemia cells and identified a number of potent combinations for which corresponding drugs exhibit synergistic killing. Together, this work demonstrates an effective strategy to screen synergistic drug combinations in high throughput, and a powerful CRISPR-based tool to dissect functional genetic interaction networks.
Citation Format: Kyuho Han, Edwin Jeng, Gaelen Hess, David Morgens, Amy Li, Michael Bassik. A CRISPR-based genetic interaction map identifies synergistic drug combinations for cancer [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR04.
Abstract PR07: Collateral sensitivity in chemotherapy resistance
Authors: Dalin Simona , Zhao Boyang , Hemann Michael T. 
Published: December 2017

Abstract
The current 5-year survival rate across all cancers is only 68%. The ability of tumors to develop resistance to chemotherapy is a major factor keeping survival rates down. Understanding the evolutionary paths tumors take towards resistance will aid in creating drug regimens designed to avoid resistant tumor states. Research in bacteria suggests that a specific type of drug pair, where resistance to each drug confers sensitivity to the other drug, can slow evolution toward drug resistance. This drug pair relationship, termed collateral sensitivity, has not been systematically investigated in cancer. Here, using a preclinical Eμ-myc; Arf-/- murine model of Burkitt lymphoma we investigate collateral sensitivities in this malignancy. We derived resistant cell lines in vitro by treating the parental cell line with dose escalating concentrations of doxorubicin or cisplatin. We screened a subset of these resistant cell lines against a panel of drugs and found several collateral sensitivities conferred by doxorubicin or cisplatin resistance. We are currently investigating the mechanism of one of these collateral sensitivities. We plan to derive cell lines resistant to a variety of other chemotherapies to learn about collateral sensitivities across many chemotherapeutics. Collateral sensitivity is a promising avenue towards rationally designing combination therapies that reduce the emergence of chemotherapy resistant disease.
Citation Format: Simona Dalin, Boyang Zhao, Michael T. Hemann. Collateral sensitivity in chemotherapy resistance [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR07.
Abstract PR10: ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling
Authors: Yu Jiyang , Silva Jose M. , Califano Andrea 
Published: December 2017

Abstract
Motivation: Functional genomics (FG) screens, using RNAi or CRISPR technology, have become a standard tool for systematic, genome-wide loss-of-function studies for therapeutic target discovery. As in many large-scale assays, however, off-target effects, variable reagents' potency, and experimental noise must be accounted for appropriately control for false positives. Indeed, rigorous statistical analysis of high-throughput FG screening data remains challenging, particularly when integrative analyses are used to combine multiple sh/sgRNAs targeting the same gene in the library.
Method: We use large RNAi and CRISPR repositories that are publicly available to evaluate a novel meta-analysis approach for FG screens via Bayesian hierarchical modeling, ScreenBEAM (Screening Bayesian Evaluation and Analysis Method).
Results: Results from our analysis show that the proposed strategy, which seamlessly combines all available data, robustly outperforms classical algorithms developed for microarray data sets as well as recent approaches designed for next generation sequencing technologies (NGS). Remarkably, the ScreenBEAM algorithm works well even when the quality of FG screens is relatively low, which accounts for about 80-95% of the public datasets.
Availability: R package and source code are available at: https://github.com/jyyu/ScreenBEAM.
Citation Format: Jiyang Yu, Jose M. Silva, Andrea Califano. ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR10.
Abstract PR13: CRISPRi screening with targeted therapeutics classifies functional long non-coding RNAs in DLBCL
Authors: Webster Dan E. , Phelan James D. , Kasbekar Monica , Shaffer Arthur L. , Staudt Louis M. 
Published: December 2017

Abstract
While tens of thousands of lncRNAs have been detected in the human genome, the functional significance of the majority of these genes remain untested. Here, we use CRISPR interference (CRISPRi) loss-of-function screening combined with targeted drug treatment to identify oncogenic and tumor suppressive lncRNAs. Integrative analysis of 417 primary human tumor and cell line RNA-seq datasets from Diffuse Large B Cell Lymphoma (DLBCL) identified 1,276 intergenic lncRNA candidates, including 59 de novo assembled transcripts. CRISPRi screening in a genetically diverse panel of 4 DLBCL cell lines identified known ABC DLBCL protein-coding oncogenes (BTK, CD79A) and demonstrated oncogenic function of 247 lncRNAs including MIR155HG and MALAT1. To assign functionally-related pathways to unknown lncRNAs, we performed this CRISPRi screen in the context of drugs with known targets: Ibrutinib (BTK), JQ1 (BRD4), and Etoposide (TOP2A). Significant synergy or resistance to drug treatment was observed with 54 lncRNAs. This ongoing work demonstrates a high-throughput pipeline for functional classification of lncRNAs using synthetic lethality screening in cancer.
Citation Format: Dan E. Webster, James D. Phelan, Monica Kasbekar, Arthur L. Shaffer, III, Louis M. Staudt. CRISPRi screening with targeted therapeutics classifies functional long non-coding RNAs in DLBCL [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR13.