Finding and Drugging the Vulnerabilities of RAS-Dependent Cancers
2009; Cell Press; Volume: 137; Issue: 5 Linguagem: Inglês
10.1016/j.cell.2009.05.011
ISSN1097-4172
Autores Tópico(s)Cancer therapeutics and mechanisms
ResumoKinase inhibitors have ushered in the era of targeted therapy, but their utility to date is primarily limited to cancers bearing oncogenic kinase mutations. Two papers in this issue (Luo et al., 2009Luo J. Emanuele M.J. Li D. Creighton C.J. Schlabach M.R. Westbrook T.F. Wong K. Elledge S.J. Cell. 2009; (this issue)Google Scholar, Scholl et al., 2009Scholl C. Fröhling S. Dunn I.F. Schinzel A.C. Barbie D.A. Kim S.Y. Silver S.J. Tamayo P. Wadlow R.C. Ramaswamy S. et al.Cell. 2009; (this issue)PubMed Google Scholar) could change this landscape by uncovering kinase-specific vulnerabilities in tumors with RAS mutations. Kinase inhibitors have ushered in the era of targeted therapy, but their utility to date is primarily limited to cancers bearing oncogenic kinase mutations. Two papers in this issue (Luo et al., 2009Luo J. Emanuele M.J. Li D. Creighton C.J. Schlabach M.R. Westbrook T.F. Wong K. Elledge S.J. Cell. 2009; (this issue)Google Scholar, Scholl et al., 2009Scholl C. Fröhling S. Dunn I.F. Schinzel A.C. Barbie D.A. Kim S.Y. Silver S.J. Tamayo P. Wadlow R.C. Ramaswamy S. et al.Cell. 2009; (this issue)PubMed Google Scholar) could change this landscape by uncovering kinase-specific vulnerabilities in tumors with RAS mutations. The success of kinase inhibitors in treating cancers bearing mutations in kinases has fueled a growing transformation of the cancer drug development enterprise into one informed by cancer genomics. The new mantra, quite simply, is that cancers bearing oncogenic mutations in a kinase are dependent on that kinase for growth and survival. With rare exception, patients with such tumors have derived significant benefit (that is, their tumors shrink) when treated with an inhibitor of that mutant kinase. The probability of success in such patients is so high that drug discovery programs can (and should) be launched when a new kinase mutation is discovered in a subset of human cancers. The drugs that emerge are anticipated to be active as single agents when studied in appropriate patients and can rapidly advance through clinical development. Yet, this may not be the only promising approach to discover new therapeutic targets. In this issue, Luo et al., 2009Luo J. Emanuele M.J. Li D. Creighton C.J. Schlabach M.R. Westbrook T.F. Wong K. Elledge S.J. Cell. 2009; (this issue)Google Scholar and Scholl et al., 2009Scholl C. Fröhling S. Dunn I.F. Schinzel A.C. Barbie D.A. Kim S.Y. Silver S.J. Tamayo P. Wadlow R.C. Ramaswamy S. et al.Cell. 2009; (this issue)PubMed Google Scholar report the use of large-scale RNA interference screens to probe the vulnerabilities of cancer cells expressing oncogenic K-RAS. The confidence born of the success with kinase inhibitors provides much of the rationale for the Cancer Genome Atlas, the national effort to resequence the genomes of several hundred tumors of each major human cancer (Cancer Genome Atlas Research Network, 2008Cancer Genome Atlas Research NetworkNature. 2008; 455: 1061-1068Crossref PubMed Scopus (5223) Google Scholar). Of course, this encyclopedic approach is costly and may yield few new leads. At least one new mutant (and presumably druggable) cancer target, isocitrate dehydrogenase 1 gene (IDH1), has emerged from an independent glioblastoma resequencing project (Parsons et al., 2008Parsons D.W. Jones S. Zhang X. Lin J.C. Leary R.J. Angenendt P. Mankoo P. Carter H. Siu I.M. Gallia G.L. et al.Science. 2008; 321: 1807-1812Crossref PubMed Scopus (4186) Google Scholar). However, its utility as a drug target remains unclear, given recent evidence suggesting that mutant IDH1 has a tumor suppressor rather than an oncogenic function (Yan et al., 2009Yan H. Parsons D.W. Jin G. McLendon R. Rasheed B.A. Yuan W. Kos I. Batinic-Haberle I. Jones S. Riggins G.J. et al.N. Engl. J. Med. 2009; 360: 765-773Crossref PubMed Scopus (3664) Google Scholar). The Cancer Genome Atlas also has the broader goal of generating a complete map of all genomic alterations in human cancer. But with rare exceptions, such as IDH1, few discoveries are anticipated to generate immediately actionable drug targets. For common but currently undruggable cancer mutations in oncogenes, such as RAS, and tumor suppressors, such as PTEN and TP53, the Cancer Genome Atlas may provide little translational insight. One alternative is to screen for synthetic lethality to identify druggable targets that are uniquely required by tumor cells but not normal cells (Kaelin, 2005Kaelin Jr., W.G. Nat. Rev. Cancer. 2005; 5: 689-698Crossref PubMed Scopus (1014) Google Scholar). Two general strategies can be envisioned: (1) chemical screens in which compounds are found that specifically kill tumor cells, but these “hits” generally require extensive additional work to define their protein targets, and (2) RNA interference screens in which “hits” immediately define a new drug target that, in some cases, can be aggressively pursued with conventional enzyme-based drug discovery approaches. Pilot studies using both strategies have been reported, but none of the discoveries from these early screens are known to have progressed to drug development programs. Therefore, in contrast to the impressive track record of targets emerging from studies of the human cancer oncogenome, the probability of clinical success with targets emerging from synthetic lethal screens is unknown. Based on two papers in the current issue of Cell, we may get an answer soon. The two independent teams, led by Gilliland and Elledge respectively, identify two kinases—STK33 (serine/threonine kinase 33) and PLK1 (polo-like kinase 1)—in screens for synthetic lethality using short hairpin RNAs (shRNAs) in human cancer cells expressing mutant K-RAS (Scholl et al., 2009Scholl C. Fröhling S. Dunn I.F. Schinzel A.C. Barbie D.A. Kim S.Y. Silver S.J. Tamayo P. Wadlow R.C. Ramaswamy S. et al.Cell. 2009; (this issue)PubMed Google Scholar, Luo et al., 2009Luo J. Emanuele M.J. Li D. Creighton C.J. Schlabach M.R. Westbrook T.F. Wong K. Elledge S.J. Cell. 2009; (this issue)Google Scholar). The translational implications of both reports are important and immediate. K-RAS is among the most commonly mutated human cancer genes, and inhibitors of STK33 and PLK1 should be relatively straightforward to identify via standard chemical approaches. Indeed, preclinical PLK1 inhibitors have already been described (McInnes et al., 2005McInnes C. Mezna M. Fischer P.M. Curr. Top. Med. Chem. 2005; 5: 181-197Crossref PubMed Scopus (103) Google Scholar, Steegmaier et al., 2007Steegmaier M. Hoffmann M. Baum A. Lenart P. Petronczki M. Krssak M. Gurtler U. Garin-Chesa P. Lieb S. Quant J. et al.Curr. Biol. 2007; 17: 316-322Abstract Full Text Full Text PDF PubMed Scopus (622) Google Scholar). Clinical trials of such inhibitors in patients with K-RAS mutant tumors could, in principle, begin in 1–2 years. There are important technical differences between the screens conducted by the two groups that may impact the broader application of shRNA screening by the cancer research community (Figure 1). Gilliland and colleagues screened ∼5000 shRNAs targeting ∼1000 genes across a panel of eight human cancer cell lines (4 K-RAS wild-type and 4 K-RAS mutant) using a well-by-well approach in which the biological effects of each hairpin are scored individually (Scholl et al., 2009Scholl C. Fröhling S. Dunn I.F. Schinzel A.C. Barbie D.A. Kim S.Y. Silver S.J. Tamayo P. Wadlow R.C. Ramaswamy S. et al.Cell. 2009; (this issue)PubMed Google Scholar). Annotation of “hits” that score only across the four K-RAS mutant lines yields a small list of genes that include K-RAS (as expected) and STK33 at the top. Additional studies in several diverse biological systems confirm the synthetic lethal association of STK33 with K-RAS, which, remarkably, appears to be specific for K-RAS and does not extend to H-RAS or N-RAS mutant tumor lines. Furthermore, a few cell lines not previously known to bear K-RAS mutations score as STK33-dependent and are found upon closer inspection to bear previously unappreciated K-RAS mutations at atypical codons. Although clearly powerful, such large-scale well-by-well screening (at least 160,000 wells for a screen limited to 1000 genes run in quadruplicate) requires a high-throughput platform run by specialized personnel. Cost will preclude the academic community from easily expanding this approach to other undruggable cancer mutations as well as scaling it for whole genome screens. In contrast, Elledge and colleagues use a pooled screening approach whereby a library of ∼75,000 shRNAs targeting ∼30,000 mRNA transcripts from ∼12,000 genes is introduced into a K-RAS mutant cancer cell line as well as an isogenic wild-type KRAS control (Luo et al., 2009Luo J. Emanuele M.J. Li D. Creighton C.J. Schlabach M.R. Westbrook T.F. Wong K. Elledge S.J. Cell. 2009; (this issue)Google Scholar). shRNAs targeting ∼400 genes are selectively depleted from the library (as detected by barcode arrays) in K-RAS mutant cells after multiple population doublings and deemed candidate RAS synthetic lethals. Roughly a quarter of these “hits” were validated in a repeat screen, and a subset of these were then confirmed in another K-RAS mutant isogenic cell line pair, resulting in a list of 77 validated RAS synthetic lethal genes. Perhaps due to the greater scale (whole genome) relative to the Gilliland screen, no single “hit” emerges as an obvious top candidate. Rather, computational analysis of all “hits” reveals increased dependence of K-RAS mutant cells on the mitotic machinery (including the kinase PLK1) and the proteasome. As predicted from the shRNA analysis, K-RAS mutant cells are preferentially killed by clinical drugs, such as paclitaxel, which target mitotic spindle function, and a preclinical PLK1 inhibitor as well as by the proteasome inhibitor bortezomib. In addition to the translational implications for patients with K-RAS mutant cancers, these reports will spawn a series of investigations by RAS aficionados into why K-RAS mutant cells are dependent on STK33, PLK1, and the long list of other RAS synthetic lethal genes. Curiously, STK33 does not appear to be a component of the RAS signaling pathway and does not, on its own, score as an oncogene in transformation assays. Furthermore, there is no evidence of STK33 mutation or gene amplification in a limited analysis of human cancers. Rather, cells with mutant K-RAS appear to be rewired and, through that process, acquire unique dependence on STK33. It will be important to dissect the temporal and biochemical details of this rewiring, as well as the normal function of STK33. The enhanced dependence of K-RAS mutant cells on basic cellular functions such as the mitotic machinery and on the proteasome is consistent with growing evidence that cancer cells are stressed and must adapt to avoid stress-induced death that typically occurs in normal cells. Indeed, much recent work has established that some cancer cells are poised to die but are rescued by hyperexpression of prosurvival proteins and that this vulnerability can be exploited clinically with Bcl-2 antagonists such as ABT-737 (Cragg et al., 2009Cragg M.S. Harris C. Strasser A. Scott C.L. Nat. Rev. Cancer. 2009; 9: 321-326Crossref PubMed Scopus (142) Google Scholar, Letai, 2008Letai A.G. Nat. Rev. Cancer. 2008; 8: 121-132Crossref PubMed Scopus (433) Google Scholar). The ultimate validation of the synthetic lethal screening strategies outlined here will be evidence that patients with K-RAS mutant tumors benefit from treatment with STK33 or PLK1 inhibitors. Unfortunately we won't have the answer for many years. We already know that a few limited but dramatic clinical successes with kinase inhibitors helped launch a large scale assault on the cancer genome to define all cancer mutations. How long do we wait before launching a similar assault to define all cancer cell vulnerabilities? Synthetic Lethal Interaction between Oncogenic KRAS Dependency and STK33 Suppression in Human Cancer CellsScholl et al.CellMay 29, 2009In BriefAn alternative to therapeutic targeting of oncogenes is to perform “synthetic lethality” screens for genes that are essential only in the context of specific cancer-causing mutations. We used high-throughput RNA interference (RNAi) to identify synthetic lethal interactions in cancer cells harboring mutant KRAS, the most commonly mutated human oncogene. We find that cells that are dependent on mutant KRAS exhibit sensitivity to suppression of the serine/threonine kinase STK33 irrespective of tissue origin, whereas STK33 is not required by KRAS-independent cells. Full-Text PDF Open ArchiveA Genome-wide RNAi Screen Identifies Multiple Synthetic Lethal Interactions with the Ras OncogeneLuo et al.CellMay 29, 2009In BriefOncogenic mutations in the small GTPase Ras are highly prevalent in cancer, but an understanding of the vulnerabilities of these cancers is lacking. We undertook a genome-wide RNAi screen to identify synthetic lethal interactions with the KRAS oncogene. We discovered a diverse set of proteins whose depletion selectively impaired the viability of Ras mutant cells. Among these we observed a strong enrichment for genes with mitotic functions. We describe a pathway involving the mitotic kinase PLK1, the anaphase-promoting complex/cyclosome, and the proteasome that, when inhibited, results in prometaphase accumulation and the subsequent death of Ras mutant cells. Full-Text PDF Open Archive
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