Abstract B20: Discovery of combination therapies in a pan-cancer context through functional complementarity and convergence analysis of oncogenic drivers
Inherent genetic alterations and tissue-specific variations in cancer present a range of unique vulnerabilities which can be targeted by precision cancer therapies. An understanding of these alterations is a crucial first step in developing novel therapeutic hypotheses in a personalized context. An unbiased method to correlate responses to treatment with small-molecules is cancer cell line (CCL) sensitivity profiling. This allows the understanding of single-agent therapies and associated mechanisms of resistance by employing unbiased combination screening. However, performing such studies in a principled manner to understa...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Murugadoss, K., Kellis, M. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract A20: Depletion of replication factor MCM7 is synthetically lethal to oncogenic KRAS expression
Colorectal cancer (CRC) is a substantial cause of death in the western world. With KRAS being one of the most frequently altered oncogenes in CRC, it is an obvious target for cancer therapy. But despite enormous efforts over the past three decades to target mutated RAS, not a single drug has made it to the clinic.In order to find vulnerabilities of KRAS mutant cells, we performed a shRNA-based screen. We used CaCo2 cells (wild type for KRAS/BRAF/PIK3CA) with doxycycline (DOX) inducible expression of the oncogenic KRASG12V as a model system. The custom-designed shRNA library comprised 121 selected genes encoding signaling p...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Gastl, B., Klotz-Noack, K., Klinger, B., Zuber, J., Blüthgen, N., Schäfer, R., Sers, C. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract A19: Exploring genetic interactions in haploid human cells
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...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Blomen, V. A., Brummelkamp, T. R. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR18: Leveraging synthetic lethality to target convergent therapeutic resistance
Our laboratory uses genomic and pharmacological methods to define the pathways of resistance to targeted anticancer therapies. Toward this end, we recently developed a technique in which engineered lentiviral cDNAs encoding activators of major oncogenic signaling pathways are introduced into cells and then profiled to identify those capable of conferring resistance to drugs. In parallel, we have also developed analogous loss-of-function screening approaches based on CRISPR/Cas9 gene editing, and have used these approaches to map the pathways supporting intrinsic resistance to targeted therapies. Using these tools in conjun...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Wood, K. C. Tags: Resistance against Drug Combinations: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA18: Mechanistic participation of cancer testes antigens in tumor initiation and progression
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...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Whitehurst, A. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Oral Presentations - Invited Abstracts Source Type: research
Abstract B18: Mechanisms of regulation and synthetic lethal strategies against PALB2 and APRIN, two DNA double-strand break repair proteins
One typical mechanism to promote genomic instability, a hallmark of cancer, is to inactivate tumor suppressors, such as PALB2. It has recently been reported that mutations in PALB2 increase the risk of breast cancer by 8-9 fold. PALB2 was identified BRCA2 interacting protein, essential for BRCA2 anchorage to nuclear structures and for its function in double-strand break repair. Inherited mutations in PALB2 are associated with a predisposition for ovarian, breast and pancreatic cancers. The basis of the tumorigenic potential of PALB2 is thought to be related to functions in homologous recombination. Therefore, the regulatio...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Couturier, A. M., Buisson, R., Pauty, J., Rodrigue, A., Caron, M.-C., Coulombe, Y., Joshi, N., Zou, L., Masson, J.-Y. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract A18: Predicting synergistic drug combinations from genomic features and single-agent response profiles
Drug combinations promise to improve clinical responses and/or forestall drug resistance. To capitalize on this promise, we need to know which drugs to combine, and whom to give them to based on the genetic or pathological features of their disease. However, accomplishing this goal has been precluded by the infeasibility of performing comprehensive drug-combination studies across thousands of cellular contexts. We hypothesized that the basal gene-transcription state of cancer cell lines, in concert with the response profiles of hundreds of single-agent small molecules, might be leveraged to nominate synergistic drug combin...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Rees, M. G., Brenan, L., Walker, A., Johannessen, C. M. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR17: Single-cell analysis reveals an adaptive, slowly-dividing, de-differentiated, drug-resistant cell state selectively inhibitable by drug combinations
In this study, we monitor the responses of BRAFV600E melanoma cells to RAF/MEK inhibitors at the single-cell level in real time using time-lapse live-cell imaging, and then analyze the resulting cell states using transcriptional, biochemical and phenotypic profiling. We found that exposure of tumor cells to RAF/MEK inhibitors elicits heterogeneous and time-variable responses in which some cells die, some arrest and a fraction of slowly-cycling cells adapts to drug, adopting a reversible drug-resistance phenotype characterized by up-regulation of markers of neural crest, a melanocyte precursor, including NGFR (the low affin...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Fallahi-Sichani, M., Becker, V., Izar, B., Baker, G. J., Lin, J.-R., Boswell, S. A., Garraway, L. A., Sorger, P. K. Tags: Resistance against Drug Combinations: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA17: Synthetic-lethal strategies for MYC-driven cancers
MYC is an essential, pleiotropic transcription factor whose amplification or deregulated expression is one of the most commonly occurring events in cancer. Despite the importance of MYC as a therapeutic target, no available drugs directly inhibit MYC transcriptional activity. Our group has undertaken several orthogonal approaches to identify MYC-pathway directed synthetic-lethal interactions. Using cell-based and transgenic animal models we have identified new potential therapeutic targets. These include metabolic, cell cycle and novel kinase vulnerabilities of MYC-driven cancers that will be discussed.Citation Format: And...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Goga, A. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Oral Presentations - Invited Abstracts Source Type: research
Abstract B17: Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma
Renal medullary carcinoma is a rare kidney cancer that is primarily seen in adolescent and young adult African American patients with sickle cell trait. Prognosis is poor and treatment options are limited. We have developed several cell line models that recapitulate the primary and relapsed metastatic samples from a patient who succumbed to this disease. We have confirmed by whole exome sequencing that our models have sickle cell trait and loss of heterozygosity of the SMARCB1 loci, both hallmarks of this disease. By RNA-sequencing, we see a lack of SMARCB1 transcription. We have further shown dependency of our models to S...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Hong, A. L., Tseng, Y.-Y., Kynnap, B. D., Doshi, M. B., Sandoval, G., Oh, C., Sayeed, A., Shubhroz, G., Church, A. J., Keskula, P., Peng, A., Clemons, P. A., Tsherniak, A., Vazquez, F., Rodriguez-Galindo, C., Janeway, K. A., Garraway, L. A., Schreiber, S. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR16: A druggable transcriptional vulnerability in NRF2-dependent lung cancer
The b-ZIP transcription factor NRF2 is a master regulator of the cellular antioxidant response and frequently activated in Non-Small Cell Lung Cancers (NSCLCs). While direct pharmacological inhibition of NRF2 has proven challenging, its aberrant activation rewires metabolic and signaling networks in cancer cells that may create special vulnerabilities for therapeutic intervention. Here, we use chemical proteomics to map ligandable proteins in NRF2-activated NSCLC cells, leading to the discovery of metabolic and transcriptional pathways that are strictly regulated by NRF2. Principal among these was the orphan nuclear recept...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Bar-Peled, L., Kemper, E., Cravatt, B. Tags: Chemical Biology: Oral Presentations - Proffered Abstracts Source Type: research
Abstract IA16: Systematic mapping and modeling of genetic interaction networks in cancer cells
We have developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbation coupled to robust analysis of growth kinetics. To demonstrate this approach, we targeted all gene pairs among a set of 73 known cancer genes with multiplexed guide RNAs in two cell lines, testing 23,652 combinations. Numerous therapeutically relevant interactions are identified, most private to one cell line. In parallel, we are developing bioinformatic approaches that analyze genetic interactions to construct hierarchical models of cancer pathways. I will discuss means by which these hierarchical models can be u...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Ideker, T. Tags: New Technology and Bioinformatics: Oral Presentations - Invited Abstracts Source Type: research
Abstract B16: Epistatic mapping of signaling and chromatin regulators
Phenotypes are often not only based on the effect of a single gene, but are rather influenced by multiple genetic (also termed epistatic) interactions. Prominent examples are synthetic lethal interactions, where the individual loss-of-function of two genes does not lead to phenotypic alterations, whereas their simultaneous perturbation results in reduced fitness or even cell death. Previously, we have established large-scale genetic interaction mapping experiments in Drosophila cells that discovered a high-number of functional interactions of conserved factors. Here, we aim to create a platform to investigate epistatic int...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Henkel, L., Heigwer, F., Winter, J., Rauscher, B., Boutros, M. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract A16: Discovery and functional characterization of essential pathways in KRAS mutant cancers
KRAS oncogenes are present in 30% of all human cancers and are required for tumor development and maintenance and although clearly important efforts to target KRAS mutant tumors remains a major challenge. Several systematic approaches have been made to target these RAS-dependent cancers through small molecule screening and genome-scale RNAi screens to identify KRAS Synthetic Lethal (SL) genes. We applied and network based approached to integrate published KRAS SL screen data to uncover protein networks enriched with KRAS SL genes. We are using these proteins networks to generate a KRAS genetic interaction map (E-MAP) using...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Ku, A. A., Bandyopadhyay, S. Tags: Finding Synthetic Lethal Interactions through Functional Genomics: Poster Presentations - Proffered Abstracts Source Type: research
Abstract PR15: Rho-associated kinase 1 inhibition is synthetically lethal with von Hippel-Lindau deficiency in clear cell renal cell carcinoma
The objective of this study was to identify chemical compounds that are synthetically lethal with VHL deficiency in CC-RCC. An annotated chemical library, the library of pharmacologically active compounds (LOPAC), was screened in parallel on VHL-deficient RCC4 cells and RCC4VHL cells with re-introduced VHL. The ROCK inhibitor, Y-27632, was identified and validated for selective targeting of VHL-deficient CC-RCC in multiple genetic backgrounds by clonogenic assays. Downregulation of ROCK1 by small interfering RNA (siRNA) selectively reduced the colony forming ability of VHL-deficient CC-RCC, thus mimicking the effect of Y-2...
Source: Molecular Cancer Therapeutics - October 2, 2017 Category: Cancer & Oncology Authors: Thompson, J. M., Nguyen, Q. H., Singh, M., Pavesic, M. W., Nesterenko, I., Nelson, L. J., Liao, A., Razorenova, O. V. Tags: Chemical Biology: Oral Presentations - Proffered Abstracts Source Type: research
