Abstract A10: CRISPR-AnalyzeR (caR): Web-based, interactive and exploratory analysis and documentation of pooled CRISPR/Cas9 screens
Since the availability of the CRISPR/Cas9 gene editing technique, pooled CRISPR/Cas9 screens have become a powerful and versatile tool for the investigation of functional genomics in a variety of organisms. Pooled CRISPR/Cas9 screens are cost-effective and do not require lab automation, which allows even small labs to perform genome-wide genetic perturbation screens. The analysis of such screens so far requires in-depth knowledge in either bioinformatics or data analysis as there is a limited availability of end-to-end data analysis pipelines (Li et al., 2014; Winter et al., 2015). Moreover, the explorative analysis of scr...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Winter, J., Schwering, M., Rauscher, B., Heigwer, F., Boutros, M. Tags: New Technology and Bioinformatics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR09: Harnessing synthetic lethality to predict clinical outcomes of cancer treatment
Conclusions: ISLE is predictive of the patients' response for the majority of current cancer drugs. Of paramount importance, the predictions of ISLE are based on SLi between (potentially) all genes in the cancer genome, thus prioritizing treatments for patients whose tumors do not bear specific actionable mutations in cancer driver genes, offering a novel approach to precision-based cancer therapy. The predictive performance of ISLE is likely to further improve with the expected rapid accumulation of additional cancer omics and clinical phenotypic data.Citation Format: Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Dikla A...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Lee, J. S., Das, A., Jerby-Arnon, L., Atias, D., Amzallag, A., Benes, C. H., Golan, T., Ruppin, E. Tags: New Technology and Bioinformatics: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA09: Genome-wide CRISPR screens illuminate lymphoma pathogenesis and therapeutic resistance
While the genetic aberrations in cancer cells have been revealing, many malignant phenotypes are regulated by genes that are not genetically altered. To gain insight into these pathways, we have employed genome-wide genetic screens using CRISPR-Cas9 technology. In one type of screen, lentiviral libraries expressing small guide RNAs (sgRNAs) are used to direct the endonuclease Cas9 to particular genomic locations, leading to the cutting and inactivation of the targeted gene. An alternative approach, called CRISPRi, uses a catalytically-dead Cas9 isoform fused to a KRAB transcriptional repressor domain. sgRNAs are used to gu...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Staudt, L. M. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Oral Presentations - Invited Abstracts Source Type: research
Abstract A09: Decomposing Oncogenic Transcriptional Signatures to Generate Maps of RAS/MAPK Cellular States
The systematic sequencing of the cancer genome has provided a powerful framework for identifying genetic alterations in cancer. However, a deeper understanding of the functional consequences of these alterations is necessary to guide appropriate therapeutic strategies. Here, we describe Onco-GPS (OncoGenic Positioning System), a data-driven analysis framework, and associated experimental and computational methodology, to organize individual tumor samples with shared oncogenic alterations onto a reference map defined by their underlying cellular states. Using this approach, we generated series of RAS/MAPK sub-signatures tha...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Kim, J. W., Hahn, W. C., Mesirov, J., Tamayo, P. Tags: New Technology and Bioinformatics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR08: Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type
We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbation coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with multiplexed guide RNAs in two cell lines, testing 23,652 combinations. Numerous therapeutically relevant interactions were identified, most private to one cell line. These patterns replicated with combinatorial drugs at 80% precision. Thus, cellular context will be critical to synthetic-lethal therapies.Here, we combined multiplex targeting with array-based oligonucleotide synthesis to create dual-gRNA libraries covering up to...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Shen, J. P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Kreisberg, J., Ideker, T., Mali, P. Tags: Other Topics: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA08: Systematic interrogation of cancer dependencies
Although we now have a draft view of the genetic alterations that occur in human cancer, the number of mutations found at low frequency and the molecular heterogeneity of most cancers makes identifying genes that contribute to cancer phenotypes challenging. Determining the function of genes altered in cancer genomes is essential to develop new therapeutic approaches. To complement these genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed systematic studies to interrogate rare alleles ...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Hahn, W. C. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Oral Presentations - Invited Abstracts Source Type: research
Abstract A08: in vivo CRISPR screening enables precision medicine by identifying novel drug combinations and modeling anticancer drug sensitivity
Identifying novel targets to synergistically improve the efficacy of existing chemotherapy is a major goal in cancer research. Here, we report in vivo CRISPR knockout (KO) screening in a patient derived xenograft (PDX) model of pancreatic cancer to identify genes that mediate the resistance to trametinib, an inhibitor of the MEK signaling pathway, which is aberrantly active in pancreatic cancers due to oncogenic KRAS mutations. The screening and subsequent genetic as well as in vitro and in vivo pharmacological validations identified a set of kinetochore function genes whose depletion is synthetic lethal with MEK inhibitio...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: ADLI, M. Tags: New Technology and Bioinformatics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR07: Collateral sensitivity in chemotherapy resistance
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 preclinica...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Dalin, S., Zhao, B., Hemann, M. T. Tags: Other Topics: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA07: Defining, Optimizing, and Altering the Specificities of CRISPR-Cas Nucleases
RNA-guided CRISPR-Cas nucleases are now widely used for research and are also being rapidly developed as novel therapeutics for various human diseases. In this talk, I will discuss methods developed by our group that enable unbiased, genome-wide assessment of off-target cleavage specificities of CRISPR-Cas nucleases in human cells. I will also summarize our efforts to use protein engineering to create CRISPR-Cas nuclease variants that robustly show substantially reduced off-target effects and/or altered DNA recognition specificities. Taken together, our results have yielded reagents, methods, and insights that will be impo...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Joung, J. K. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Oral Presentations - Invited Abstracts Source Type: research
Abstract B07: Analysis of allele specific expression in esophageal squamous cell carcinoma with combination of exome sequencing and mRNA Sequencing
In recent years, large-scale international studies have provide comprehensive catalogues of genomic alterations in cancers including Esophageal Squamous Cell Cancer(ESCC). They revealed that some gene associated with cell cycle/apoptosis pathway, NOTCH pathway, WNT pathway, such as TP53 and NOTCH1, harbored genetic abnormalities frequently. As the next step clinical sequencing studies are starting to evaluate efficacy of using targeted agents to patients with specific molecular aberrations.We performed exome sequencing and RNA sequencing for 25 Japanese patients with esophageal squamous cell carcinoma (ESCC) to provide a c...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Takahashi, M., Nakaoka, H., Akutsu, Y., Hanari, N., Murakami, K., Kano, M., Matsumoto, Y., Otsuka, R., Sekino, N., Yokoyama, M., Inoue, I., Matsubara, H. Tags: New Technology and Bioinformatics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR06: CRISPR screens identified drivers of endocrine resistance and synthetic lethal vulnerabilities in breast cancer
Estrogen receptor positive (ER+) breast cancer is treated with endocrine therapies, although in advanced disease therapeutic resistance almost invariably develops. Using genome-wide CRISPR screens we identified genes essential for the growth of ER+ breast cancers. More importantly, we also identified genes whose loss confers endocrine resistance. Notably the expression of c-src tyrosine kinase (CSK) is driven by estrogen yet loss of CSK promoted estrogen independent growth. A synthetic lethality screen for CSK loss identified the p21 protein-activated kinase (PAK2) which becomes activated by SRC-family kinases (SFK) in the...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Xiao, T., Li, W., Wang, X., Xu, H., Wu, Q., Jiang, P., Yang, J., Fei, T., Zang, C., Liao, Q., Rennhack, J., Andrechek, E., Li, N., Jeselsohn, R., Liu, S. X., Brown, M. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA06: Leveraging genome-wide CRISPR screens and synthetic lethal interactions for novel cancer therapeutics
Forward genetic screens with CRISPR-Cas9 genome editing enable high-resolution detection of genetic vulnerabilities in cancer cells. We conducted genome-wide CRISPR-Cas9 screens in RNF43 mutant pancreatic ductal adenocarcinoma (PDAC) cells, which rely on Wnt signaling for proliferation, and discovered a unique requirement for a Wnt signaling circuit engaging FZD5, one of the ten Frizzled receptors encoded in the human genome. Our results uncover an underappreciated level of context dependent specificity at the Wnt receptor level. We further derived a panel of recombinant antibodies that reports the expression of nine FZD p...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Angers, S. Tags: New Technology and Bioinformatics: Oral Presentations - Invited Abstracts Source Type: research
Abstract B06: HTSvis: An user-friendly application for analysis of arrayed high-throughput experiments by interactive data representations
The presented application HTSvis provides an user-interface tool for interactive analysis of arrayed high-throughput screening experiments. Arrayed formats are broadly used for cell-based screens which help to reveal mechanisms of complex diseases such as cancer. Technological advances allow to screen tens of thousands experimental conditions in a single experiments resulting in large datasets with complicated annotation files. Software packages for standardized analysis with a minimized programming effort have been developed accordingly. Even though such pipelines provide comprehensive analysis options, interpretation of ...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Scheeder, C., Heigwer, F., Boutros, M. Tags: New Technology and Bioinformatics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract IA05: Massively parallel search for synthetic lethal vulnerabilities using CRISPRi and CRISPRa
We present a robust technology enabling systematic investigation of the cellular consequences of repressing or inducing individual transcripts. We identify rules for specific targeting of transcriptional repressors (CRISPRi), typically achieving 90-99% knockdown with minimal off-target effects, and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9. Together they enable modulation of gene expression over a ~1000-fold range. Using these rules, we construct and validate genome-scale CRISPRi and CRISPRa libraries that enable systematic analysis of gene function including both essential and nonessential a...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Weissman, J. Tags: New Technology and Bioinformatics: Oral Presentations - Invited Abstracts Source Type: research
Abstract B05: Discovery, validation and targeting of novel synthetic lethal interactions in academic drug discovery
The identification of novel oncology targets for small molecule drug discovery is becoming increasingly challenging despite 10-15% of the human genome estimated to be druggable. The literature is an important source of novel targets; however, several recent reports by pharma and academia have indicated that approximately 11-55% of published studies are irreproducible. Moreover, oncology drug attrition rates are extremely poor, with 66% of candidates in Phase III clinical trials not achieving approval. This is reflected by increasing failure rates of drug development projects in Phase II, from 72% in 2006-2007 to 82% in 200...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: March, H. N., Chapman, P., Blaikley, E., Eberlein, C. A., Cockerill, M., Hitchin, S., Waddell, I. D., Ogilvie, D. Tags: New Technology and Bioinformatics: Poster Presentations - Proffered Abstracts Source Type: research
