Abstract PR06: Systematic genetic interaction maps reveal synthetic-lethal vulnerabilities in leukemia and multiple myeloma
Authors: Kampmann Martin , Acosta-Alvear Diego , Bassik Michael C. , Chen Yuwen , Walter Peter , Weissman Jonathan S. 
Published: August 2014

Systematic, high-density mapping of genetic interactions is a powerful approach to elucidate functional pathways and reveal synthetic lethal gene pairs, and has successfully been applied in microorganisms. We have recently developed a functional genomics platform that enables the construction of high-density genetic interaction maps in mammalian cells (Bassik*, Kampmann* et al. Cell 152, Feb. 14, 2013 *Equal contribution). In a first step, we conduct pooled primary screens using an ultracomplex shRNA library that targets each protein-coding gene with 25 independent shRNAs and contains &gt;1,000 negative control shRNAs. This strategy enables us to robustly identify hit genes and shRNAs that target them effectively, while minimizing the identification of false-positive hits which has plagued many genome-wide RNAi screens. In a second step, we construct and screen a double-shRNA library that targets all pairwise combination of hit genes to contruct a high-density genetic interaction map. Our approach enables us to determine 100,000s of genetic interactions in a single experiment.

Here, we present the application of our platform to identify synthetic-lethal vulnerabilities in the stress response network of leukemia and multiple myeloma cells. Stress response pathways, including the endoplasmic reticulum stress response (unfolded protein response), heat shock, hypoxia and oxidative stress responses, and the associated induction of autophagy, have been shown to play important roles in cancer cell survival, drug resistance and disease progression. The goal of the research presented here is to systematically characterize vulnerabilities in the stress response network of cancer cells, and in particular, to identify synthetic-lethal vulnerabilities that are potential novel targets for combination drug therapy. We conducted our first experiments in two human cell lines derived from hematologic cancers, K562 (leukemia) and RPMI-8226 (multiple myeloma), for which we determined genetic vulnerabilities and their genetic interactions in the absence and presence of stress-inducing agents. We discovered previously unknown genetic vulnerabilities, several of which are considered “druggable”. We externally validated several of the synthetic-lethal vulnerabilities we identified by demonstrating synergistic effects of drug combinations targeting these gene pairs. Intriguingly, expression levels of several vulnerabilities we identified are prognostic of patient survival in a published multiple myeloma clinical trial.

We are in the process of testing the therapeutic potential of targeting the synthetic-lethal vulnerabilities we identified in the multiple myeloma stress response network in primary patient cells and in multiple myeloma mouse models.

This abstract is also presented as Poster A15.

Citation Format: Martin Kampmann, Diego Acosta-Alvear, Michael C. Bassik, Yuwen Chen, Peter Walter, Jonathan S. Weissman. Systematic genetic interaction maps reveal synthetic-lethal vulnerabilities in leukemia and multiple myeloma. [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 PR06.