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Synthetic Lethal Screens As a Means to Understand and Treat MYC-Driven Cancers

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Synthetic Lethal Screens As a Means to Understand and Treat MYC-Driven Cancers Downloaded from http://perspectivesinmedicine.cshlp.org/ on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Synthetic Lethal Screens as a Means to Understand and Treat MYC-Driven Cancers Silvia Cermelli1, In Sock Jang2, Brady Bernard3, and Carla Grandori1 1Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 2SAGE Bionetworks, Seattle, Washington 98109 3Institute for Systems Biology, Seattle, Washington 98109 Correspondence: [email protected] Although therapeutics against MYC could potentially be used against a wide range of human cancers, MYC-targeted therapies have proven difficult to develop. The convergence of break- throughs in human genomics and in gene silencing using RNA interference (RNAi) have recently allowed functional interrogation of the genome and systematic identification of synthetic lethal interactions with hyperactive MYC. Here, we focus on the pathways that have emerged through RNAi screens and present evidence that a subset of genes showing synthetic lethality with MYC are significantly interconnected and linked to chromatin and transcriptional processes, as well as to DNA repair and cell cycle checkpoints. Other syn- thetic lethal interactions with MYC point to novel pathways and potentially broaden the repertoire of targeted therapies. The elucidation of MYC synthetic lethal interactions is still in its infancy, and how these interactions may be influenced by tissue-specific programs and by concurrent genetic change will require further investigation. Nevertheless, we predict that these studies may lead the way to novel therapeutic approaches and new insights into the role of MYC in cancer. sing a synthetic lethal RNA interference ap- of MYC-SL genes has the potential to halt can- Uproach, several groups have recently iden- cers driven by aberrant MYC expression, while tified genes whose function is selectively re- sparing normal tissues. In fact, by selecting for www.perspectivesinmedicine.org quired for the survival of MYC-overexpressing genetic interactions that occur only in the con- cells (Kessler et al. 2012; Liu et al. 2012; Toyo- text of MYC overexpression, the proliferation of shima et al. 2012). Analysis of these genes, re- normal cells, where MYC function is tightly reg- ferred to as MYC-synthetic lethal (MYC-SL) ulated, may not be affected. Here, we highlight genes, provides new insights into cellular path- MYC synthetic lethal genes and networks that ways that contribute to the fitness of cells with have emerged from RNA interference screens, aberrant MYC expression. Moreover MYC-SL and we describe their relationship to known genes provide a menu of possible therapeutic and novel functions of MYC. Finally, we discuss targets, potentially circumventing the difficul- therapeutic implications and challenges sur- ties inherent in targeting MYC itself. Inhibition rounding the exploitation of synthetic lethal Editors: Chi V. Dang and Robert N. Eisenman Additional Perspectives on MYC and the Pathway to Cancer available at www.perspectivesinmedicine.org Copyright # 2014 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a014209 Cite this article as Cold Spring Harb Perspect Med 2014;4:a014209 1 Downloaded from http://perspectivesinmedicine.cshlp.org/ on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press S. Cermelli et al. interactions in clinical settings of MYC-driven of synthetic lethality are negative digenic inter- cancers. actions, wherein the combination of mutations in two different genes leads to a significant loss of fitness from the expected additive effects of LEARNING FROM YEAST GENETIC the individual phenotypes. Synthetic lethality NETWORKS defines an extreme form of negative genetic in- In Saccharomyces cerevisiae (S. cerevisiae) and teraction, as, for example, when mutations in other single-cell organisms, systematic ge- two otherwise nonessential genes lead to cell nome-wide mapping of both positive and neg- death. The graphical representation in Figure 1A ative genetic interactions that affect cell viability illustrates the concept of synthetic lethality ap- have been performed (for review, see Dixon plied to MYC-overexpressing cells. In this in- et al. 2009; Costanzo et al. 2012). Positive inter- stance, the first aberration is the presence of actions describe double mutants whose fitness is MYC overexpression, achieved by either a retro- increased relative to the effect of each individual viral vector or through expression of a condi- mutation, and are often defined as suppressing tional MYC–ER fusion. When loss of function or rescuing mutations. Of relevance to the topic of a second gene is achieved, the consequences A Viability/growth MYCWT MYC+ MYCWT siMYC-SL MYC+ genes B 100 www.perspectivesinmedicine.org Weak 50 viability (%) + MYC Hits Strong 50 100 MYCWT viability (%) Figure 1. Graphical representation of synthetic lethal interactions applied to MYC overexpression. (A)Growth/ viability of normal cells expressing endogenously controlled levels of MYCWT (gray) in comparison with cells overexpressing MYC (blue, MYCþ). A gene is here defined as “synthetic lethal” with MYC overexpression if its knockdown minimally impacts viability/growth in the control cells, MYCWT, while leading to loss of viability in MYCþ cells. (B) Schematic of results obtained from arrayed siRNA screening. Although most of the siRNAs similarly affect MYCWTand MYCþ cells, with a gradient illustrating the lower abundance of highly toxic siRNAs, a small subset confers selective growth inhibition in MYCþ (blue oval). “Strong” hits lead to a dramatic loss of viability (below 20%) in contrast to “weak” hits, also referred to as “synthetic sick” (see text for details). 2 Cite this article as Cold Spring Harb Perspect Med 2014;4:a014209 Downloaded from http://perspectivesinmedicine.cshlp.org/ on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press MYC-Driven Cancers for cell viability in normal cells versus MYC- because the methodology had yet to be devel- overexpressing cells enable the identification of oped for efficient gene targeting and functional genes showing a “synthetic lethal” or “synthetic interrogation in cell culture. Thus, synthetic sick” interaction (Fig. 1B). From these studies, lethality in mammalian cells had only been ob- both potential candidate therapeutic targets as served via a candidate hypothesis-driven pro- well as insights into MYC-induced vulnera- cess, verified by time-consuming intercross- bilities and functionally linked pathways have es of knockout mouse mutant strains (Gurley emerged. and Kemp 2001) or availability of mutant cells. In yeast, positive interactions are frequently Only recently has a systematic testing of gene– observed among genes whose products physi- gene interactions, or “functional genomics,” be- cally interact, whereas negative interactions gen- come feasible in mammalian cells as a conse- erally occur between genes working within par- quence of the convergence of three major break- allel biological pathways. In fact, many genes throughs: (1) knowledge of the human genome; affecting DNA repair processes show synthetic (2) the discovery of RNA interference, which lethal interactions, perhaps reflecting the evolu- enabled the targeting of virtually all protein- tion of robust buffering systems that ensure coding genes; and (3) the availability of robot- DNA stability. The example of synthetic lethal ics equipment to achieve truly massive parallel interaction between BRCA mutants and PARP testing, in a single query, of thousands of gene fits this model because both genes act in parallel knockdowns, as shown in Figure 1A and B. to repair DNA breaks through homologous The availability of unbiased, high-throughput recombination. Accordingly, PARP inhibitors empirical testing enables the construction of have exquisite efficacy toward cancers that carry large-scale functional networks centered on homozygous loss-of-function mutations in the known oncogenes. BRCA gene (McCabe et al. 2005; Fong et al. 2009). The high therapeutic window of PARP OVERVIEW OF RNA INTERFERENCE inhibitors is likely due to the minimal toxicity to SCREENS noncancerous tissues harboring one or two functional copies of the BRCA gene, thus retain- Synthetic lethal screens in mammalian cells ide- ing some capacity to repair DNA breaks under ally use isogenic systems where the only diffe- PARP inhibition. The example of BRCA and rence between two cell types is the mutation of a PARP interaction is consistent with the relative- single gene, such as amplification of an onco- ly high frequency of synthetic lethality among gene or mutation of a tumor suppressor. In the functionally related genes (18%–25%), in con- case of MYC, screens have used MYC overex- www.perspectivesinmedicine.org trast to its rarity among unrelated genes (,1%) pression, which reflects the alteration observed (Dixon et al. 2009). In fact, unbiased genetic in many cancers (Nesbit et al. 1999). The screen mapping has enabled the assignment of novel by Toyoshima et al. (2012) used primary hu- functions to genes included in networks based man-foreskin fibroblasts (HFFs) where MYC on genetic interactions as shown in yeast (Dixon was constitutively expressed through a retroviral et al. 2009) and illustrated here for MYC. These vector. HFFs provide a unique cell background novel interactions point to unexpected drug tar- where oncogene activation does not induce gets and shed new light on MYC-mediated tu- senescence (Benanti and Galloway
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