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Published in final edited form as: J Invest Dermatol. 2016 May 7;136(7):1330–1336. doi: 10.1016/j.jid.2016.03.006

Searching for the Chokehold of NRAS Mutant Melanoma

Christian Posch 1,2,3, Igor Vujic 1,3, Babak Monshi 3, Martina Sanlorenzo 1,4, Felix Weihsengruber 3, Klemens Rappersberger 3, Susana Ortiz-Urda 1
PMCID: PMC4921268  NIHMSID: NIHMS786100  PMID: 27160069

Abstract

Up to 18% of melanomas harbor mutations in the neuroblastoma rat-sarcoma homolog (NRAS). Yet, decades of research aimed to interfere with oncogenic RAS signaling have been largely disappointing and have not resulted in meaningful clinical outputs. Recent advances in disease modeling, structural biology, and an improved understanding of RAS cycling as well as RAS signaling networks have renewed hope for developing strategies to selectively block hyperactive RAS function. This review discusses direct and indirect blocking of activated RAS with a focus on current and potential future therapeutic approaches for NRAS mutant melanoma.

INTRODUCTION

A central regulator of prosurvival signaling in the mitogen-activated protein kinase (MAPK) pathway is rat-sarcoma homolog (RAS). The four highly homologous members of the RAS protein family neuroblastoma-, Harvey-, and Kirsten-RAS (NRAS, HRAS, KRAS4A, KRAS4B) are ubiquitously expressed and control cellular proliferation, differentiation, and survival (Cox et al., 2014; Malumbres and Barbacid, 2003). Dysregulated RAS signaling, mainly mediated by oncogenic mutations, is found in about one-third of all cancers with NRAS being most frequently mutant in melanoma (18%) (Lee et al., 2011; Roberts and Der, 2007). Hence, the NRAS protein would be an attractive target for melanoma therapy; however, decades of research aimed toward direct blocking of the mutant oncogene in vivo have been largely unsuccessful. To date, indirect inhibition of mutant RAS by downstream pathway interference is one of the clinically most promising strategies (Ascierto et al., 2013; Carlino et al., 2014; Kwong et al., 2012; Tolcher et al., 2015; Vu and Aplin, 2014). In addition, recent discoveries indicate that RAS activity is also increased by loss of function mutations in the negative regulator of RAS, NF1, which is mutated in approximately 14% of patients with melanoma (Cancer Genome Atlas Network, 2015; Krauthammer et al., 2015). Such discoveries not only highlight the importance of RAS signaling in melanoma but also have the potential to open up new avenues for indirect targeting of NRAS activity.

Latest developments in systems and molecular biology highlight that targeting of mutant RAS is not a dead end; instead, it needs to be revisited systematically. Recently launched programs, such as “The RAS Initiative” by the National Cancer Institute (http://RasCentral.org), reflect researchers’ optimism to advance therapy for RAS mutant malignancies (Thompson, 2013).

This review aims to give an overview of recent discoveries in direct and indirect targeting of mutant RAS proteins with a focus on NRAS mutant melanoma and discusses opportunities and limitations for their future clinical application.

BACKGROUND—NRAS FUNCTION

RAS proteins function as small GTPases with low intrinsic catalytic activity, transducing signals from membrane localized receptor tyrosine kinases (RTKs) to the nucleus. Cycling of the RAS protein between a GTP-bound active state and a GDP-bound inactive state is catalyzed by guanine nucleotide exchange factors (GEFs), such as SOS1, and GTPase activating proteins (GAPs), such as NF1 (Bos et al., 2007; Plowman and Hancock, 2005; Rajalingam et al., 2007). The docking sites for effector proteins, such as rapidly accelerated fibrosarcoma (RAF) and phosphatidylinositol-3-kinases (PI3K), are located in the “effector lobe,” whereas the “allosteric lobe” contains affinity hot spots for direct interaction with membrane components. Hotspots for membrane localization and the C-terminal hypervariable region distinguish the structures of the otherwise highly homologous RAS family members and are important loci for post-translational (lipid) modifications (Buhrman et al., 2010; Gorfe et al., 2008) (Figure 1).

Figure 1. Conceptual schema of NRAS cycling and mutation hotspots.

Figure 1

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(a) Wild-type NRAS cycles between an inactive GDP bound and an active GTP bound state. Upstream signals trigger the activation of NRAS which is regulated by GEFs (such as SOS1). NRAS deactivation is catalyzed by GAPs (such as NF1). (b) NRAS mutations are located at codon 12/13, affecting the P-loop (Walker A motif) of the protein. Mutations at codon 61 impair the intrinsic catalytic activity of NRAS located in the switch II domain of the protein. (c) Mutant NRAS impairs normal protein cycling, locking the protein in its active GTP bound state. GAP, GTPase activating protein; GDP, guanosine diphosphate; GEF, guanine nucleotide exchange factors; GTP, guanosine triphosphate; HVR, hypervariable region; NRAS, neuroblastoma rat-sarcoma homolog; RTK, receptor tyrosine kinases; SWI/II, switch I/II.

The mutational hotspots of NRAS are codon 61 (approximately 85% of cases) and to a much smaller extent codons 12 and 13 (Hodis et al., 2012). While mutant NRAS(Q61) disrupts the GTPase activity of RAS, locking it in its active conformation, NRAS(G12) and NRAS(G13) mutations affect the Walker A-motif (p-loop) of the protein, thus decreasing its sensitivity to GAPs (Curtin et al., 2005; Fedorenko et al., 2013; Smith et al., 2013) (Figure 1). Mutations in G12/13 and Q61 can all be described as activating, yet, they affect the NRAS protein in distinct ways. Small differences in intrinsic hydrolysis rate and minimal conformational changes, which have for the most part been disregarded as biologically irrelevant, impact (mutation specific) changes in downstream pathway activation and RAS cycling (Burd et al., 2014; Smith et al., 2013). These differences in RAS-structure and RAS-dependent signaling are central elements of recent research projects (Buhrman et al., 2011; Nussinov et al., 2013).

DIRECT TARGETING OF MUTANT NRAS

Mutations in NRAS favor the formation of GTP-bound, active RAS proteins (Bos et al., 2007). Similar to kinase inhibitors, which compete with ATP, attempts to directly target RAS have been designed to compete for GTP binding; however, because of the picomolar affinity of GTP toward RAS (in contrast to micromolar affinity of ATP toward kinases) and the high abundance of intracellular GTP, it has been challenging to discover such inhibitors with broad anti-RAS activity.

We understand that more defined approaches are needed. Ideally, inhibitors would target the activating substitution itself to achieve high selectivity and specificity. This is possible as recently exemplified in preclinical models of codon 12 mutant KRAS: Because the intrinsic catalytic capacity of mutant RAS(G12) is not affected, the mutant protein displays a balanced equilibrium of GDP and GTP bound states. This presents an opportunity to use GDP analogs that slowly but steadily trap RAS in its inactive state. These compounds covalently and specifically bind to cysteine-12 in G12C mutants and block the activation of downstream signaling mediators of RAS including v-akt murine thymoma viral oncogene homolog (AKT) and extracellular signal-regulated kinase (ERK) (Fetics et al., 2015; Lim et al., 2014; Ostrem et al., 2013). Even though this research has been carried out in models of oncogenic KRAS, it is likely that, such compounds will also specifically block codon G12C mutant NRAS given the high structural similarities in the effector lobe of RAS proteins. In melanoma, NRAS(G12) mutants are rare and comparable strategies for inhibiting the majority of codon 61 mutants have not been described to date; however, these findings remind us that mutation-specific direct targeting of RAS can be achieved, which is a concept that has largely been abandoned after decades of unsuccessful attempts.

Another approach to specifically block RAS family members is targeting the allosteric lobe and hypervariable region in which K-, N-, and H-RAS differ the most. Such inhibitors would thus not distinguish between the wild-type and the mutant protein; instead, they would functionally deplete one isoform, which appears to be biologically tolerable, at least in animal models (Stephen et al., 2014).

Interfering with the membrane association of RAS also reduces protein activity. Blocking farnesylation, a post-translational modification step essential for RAS binding to the cell membrane, showed promising results in preclinical models of mutant HRAS (Liu et al., 1998); however, clinical testing of farnesyltransferase inhibitors in K- and N-RAS mutant malignancies failed to provide a benefit for patients. This was later discovered to be due to alternative lipid modifications mediated by the related enzyme geranylgeranyltransferase that functionally substitutes for farnesylation (Whyte et al., 1997). Similarly, inhibitors of posttranslational palmitoylation, such as palmostatin B, which also aim to disrupt the membrane localization of RAS, were effective in preclinical models of NRAS mutant cells but have not (yet) translated into clinical applications (Vujic et al., 2016; Xu et al., 2012). The clinical value of targeting other post-translational modifications of RAS such as phosphorylation, nitrosylation, monoubiquitination, and acetylation, which mainly affect the subcellular localization of the protein, is currently unknown.

Activated RAS proteins form complexes with regulators controlling RAS cycling (GEFs, GAPs) and effectors mediating downstream signaling (RAF, RAS related GTP binding protein [RAL], PI3K, and others). Peptide library screens identified compounds that interfere with the binding of RAS to son of sevenless homolog 1 (SOS1), one of the most prominent RAS-GEFs. These molecules reduce RAS activation and subsequent MAPK pathway signaling (Patgiri et al., 2011; Sun et al., 2012). Yet, it remains unknown to which extent GEFs contribute to mutant RAS activation and if compounds targeting RAS-GEF interactions might be beneficial in the context of the mutant protein. Another study identified compounds that block RAS-GTP binding to the downstream mediator CRAF, using a computer-based screen (Shima et al., 2013). The design of molecules that selectively occupy these RAS binding sites has been challenging, and small molecules reported thus far only bind weakly to RAS. Similar to studies mentioned above, most research was carried out in models of mutant HRAS and KRAS, and it remains unclear whether such findings hold promise for NRAS mutant melanoma.

Direct targeting of mutant NRAS can also be achieved by genetic silencing using small interfering RNAs, which prevent translation of the NRAS protein. This technique is widely used to abolish mutant NRAS signaling in experimental models (Eskandarpour et al., 2005; Jaiswal et al., 2009). The overarching problem with using small interfering RNAs clinically is their fast degradation in vivo, a limitation that might be solved in the future using nanotechnology-based small interfering RNAs-delivery systems (Davis et al., 2010).

Indirect NRAS targeting—pathway interference

Monotherapy

Assuming that it is impossible to design clinically effective, direct inhibitors of RAS, research has explored concepts of indirect targeting by blocking downstream mediators of RAS. The most investigated signaling cascades in NRAS mutant melanoma are the MAPK, PI3K/mammalian target of rapamycin (mTOR), and cell-cycle pathways (Figure 2) (Hodis et al., 2012; Kwong et al., 2012; Posch et al., 2013).

Figure 2. Conceptual schema highlighting some of the most studied pathways involved in signaling of NRAS mutant melanoma.

Figure 2

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Horizontal inhibition refers to targeting of signaling members within different pathways, such as combinations of MEK/AKT, MEK/PI3K, MEK/CDK4, and MEK/Plk1. Vertical inhibition refers to targeting of signaling members within one pathway. This approach is currently investigated by combinatorial targeting of MEK/ERK in the MAPK pathway. MAPK, mitogen-activated protein kinase; MEK, MAPK/ERK kinase; NRAS, neuroblastoma rat-sarcoma homolog.

RAF kinases (A-, B-, and C-RAF) are validated effectors of RAS signaling. Several multikinase inhibitors with modest pan-RAF activity were developed but only showed minimal effects in patients with NRAS mutant melanoma (Eisen et al., 2006). More specific RAF inhibitors, such as vemurafenib and dabrafenib, which preferentially target the mutant BRAF(V600) protein, even caused worsening of NRAS mutant disease. This was later found to be due to paradoxical activation of ERK signaling in BRAF wild-type cells caused by enhanced dimerization, conformational changes, and trans-activation of RAF induced by these drugs, as well as the switch from BRAF to CRAF signaling when NRAS is mutant (Dumaz et al., 2006; Hatzivassiliou et al., 2010; Poulikakos et al., 2010). Yet, RAF inhibition in RAS mutant cells is not considered obsolete and compounds with increased anti-CRAF activity or inhibitors blocking RAF-dimerization are currently tested (Su et al., 2012).

Direct substrates of RAF are the highly homologous kinases MEK1 and MEK2. Inhibition of MAPK/ERK kinase (MEK) with specific, small molecules suppresses MAPK signaling and has shown promising results in patients with NRAS mutant melanoma. Notably, treatment with binimetinib, a selective MEK1/2 inhibitor, has resulted in a 20% objective response rate and prolonged overall survival for 3.7 months (Ascierto et al., 2013) (Supplementary Table S1 online). Still, the majority of patients did not benefit from MEK inhibitor therapy or rapidly developed resistance.

Exclusively blocking further downstream by targeting ERK1/2, the only well-validated substrate of MEK, is also ineffective in RAS mutant malignancies. Similar to MEK inhibitors, ERK inhibition releases feedback loops that activate RTKs, such as ERBB3, EGFR, and c-MET upstream of RAS (Carlino et al., 2014; Duncan et al., 2012; Fattore et al., 2013; Rebecca et al., 2014). Activated RTKs enhance the flux through the MAPK pathway and activate additional prosurvival cascades such as the PI3K, RAL, and PLC cascades among others.

It is now clear that the MAPK pathway is a complex network with multiple inputs and outputs. Even though RAF, MEK, and ERK comprise the core of MAPK signaling, we now understand that a one-directional picture of the pathway is insufficient to account for the diverse regulatory mechanisms that ensure mutant NRAS cell homeostasis.

Research also provides compelling evidence for the importance of PI3K signaling in NRAS-driven melanoma. PI3K is a substrate of RAS and can also be activated through non-RAS-mutant mechanisms, most importantly through a variety of RTKs (Pacold et al., 2000). The efficacy of available PI3K/mTOR inhibitors is mainly limited by a lack of a clear therapeutic window. Nonetheless, their value as anti-RAS drugs may be revisited, particularly in combination with inhibitors of other pathways (Greger et al., 2012; Posch et al., 2013).

Even though a role of RAL-GDS in NRAS melanomagenesis has been established, this pathway has not been studied extensively (Mishra et al., 2010; Zipfel et al., 2010). Like RAS, RAL-GTPases are similarly difficult targets for direct inhibition. Yet, indirect blockades of RAL-downstream molecules, such as TBK1, might have therapeutic value for NRAS-driven melanoma (Vu and Aplin, 2014).

Combinatorial therapy

The search for NRAS coextinction targets has become central in the development of RAS treatment regimens. The important role of MAPK signaling in NRAS mutant cancers and the fact that to date only MEK inhibitors have shown clinical activity in patients with NRAS mutant melanoma are the rationale for using MEK inhibitors as a cornerstone for combinational treatments (Supplementary Table S1). Two strategies can be defined for targeted combinatorial therapy: horizontal and vertical inhibition (Figure 2).

Horizontal inhibition

Horizontal inhibition refers to parallel targeting of multiple pathways. The most advanced horizontal combination for NRAS mutant melanoma is simultaneous MEK and CDK4 inhibition (Kwong et al., 2012). CDK4 is a serine/threonine kinase important for G1 cell-cycle progression that is controlled by the CDK inhibitor p16 (INK4a). Clinical testing of MEK/CDK4 inhibition showed activity in NRAS mutant melanoma; however, the majority of patients still did not respond. Current research suggests that the efficacy of this combination might be increased when tumor cells also have genetic aberrations increasing CDK4 activity such as loss of p16(INK4a) or amplifications of cyclin D1 (VanArsdale et al., 2015; Young et al., 2014). Another, yet experimental, combination blocking the MAPK and cell-cycle pathways targets MEK and the cell-cycle regulator Plk1, which effectively reduces growth of NRAS mutant melanoma xenografts independent of p16(INK4a) mutation status (Posch et al., 2015).

The rationale for dual inhibition of the MAPK and PI3K/mTOR pathways is supported by effective growth reduction of NRAS mutant melanoma in mouse models and the upregulation of PI3K/mTOR pathway members due to the release of negative feedback to RTKs after single MEK inhibitor treatment (Fattore et al., 2013; Jaiswal et al., 2009; Posch et al., 2013). However, with only a few patients experiencing stable disease as best response, combined targeting of MEK/AKT or MEK/PI3K did not meet preclinical expectations and was overall poorly tolerated (Greger et al., 2012; Juric et al., 2014; Tolcher et al., 2015). In addition, cotargeting of both PI3K and mTOR signaling molecules in combination with MEK inhibition might be necessary for effective NRAS mutant tumor shrinkage (Posch et al., 2013). An early phase clinical trial testing dactolisib, a dual PI3K/mTOR inhibitor, in combination with the MEK inhibitor binimetinib will offer insights into the clinical profile and efficacy of such a combination (Supplementary Table S1).

Inhibition of PI3K/mTOR pathway activity can potentially also be achieved by using high doses of metformin. Because metformin has been used for decades as an antidiabetic drug, has a known side effect profile, is cheap and generically available, this combination might be an interesting addition to current treatment modalities (Vujic et al., 2014).

The overactivation of the hepatocyte growth factor receptor (c-MET) in NRAS mutant melanoma prompted testing of the RAF kinase inhibitor sorafenib in combination with the c-MET inhibitor tivantinib. In a first clinical trial, 2 of 8 patients with NRAS mutant melanoma experienced complete or partial response; 2 additional patients had stable disease (Puzanov et al., 2015). Interestingly, indirect c-Met inhibition was reported in cancer cells treated with the cardiac glycoside digitoxin (Yang et al., 2013). Thus, it is possible that in the context of NRAS mutant melanoma, digitoxin (or derivates with comparable characteristics) could be used therapeutically.

Other inhibitor combinations using analogs of the mTORC1 inhibitor rapamycin (rapalogs) together with compounds affecting DNA repair/replication (carboplatin, cisplatin, gemcitabine), mitosis (paclitaxel), or angiogenesis (bevacizumab) are additional therapeutic approaches for patients with solid tumors including NRAS mutant melanoma (Algazi et al., 2015; Hauke et al., 2013; Mudigonda et al., 2016; Puzanov et al., 2015). The clinical activity of such combinations is yet to be fully explored.

Vertical inhibition

Vertical inhibition of a signaling pathway refers to the blockade of more than one signaling member within a single cascade. This concept has proved effective in BRAF mutant melanoma, where combined BRAF/MEK inhibition significantly prolongs overall survival compared with BRAF or MEK inhibition alone (Flaherty et al., 2012; Larkin et al., 2014). A similar concept might also be effective in NRAS mutant melanoma: As discussed, one of the mechanisms of resistance using MEK inhibitors in NRAS mutant melanoma is the reactivation or inability to fully suppress ERK signaling (Fedorenko et al., 2013). In preclinical studies, targeting of MEK and ERK in combination potently suppresses levels of phospho-ERK and induces apoptosis in NRAS mutant cells (Morris et al., 2013; Rebecca et al., 2014). Another approach for vertical pathway inhibition uses combined pan-RAF and MEK inhibition (Atefi et al., 2015). Similarly, single compound, dual RAF/MEK inhibitors are currently investigated for their potential therapeutic activity in RAS mutated malignancies, including melanoma (Wada et al., 2014).

To date, combined vertical inhibition of the PI3K/mTOR pathway in melanoma has only been investigated in BRAF mutant cells (Werzowa et al., 2011). Still, research suggests that dual PI3K/mTOR inhibition might also show activity in NRAS mutant melanoma (Posch et al., 2013; personal communication Schatton T).

Immunity and targeted therapy

Systemic therapy with targeted molecules also affects cells other than tumor cells, including immune cells. MEK inhibitors suppress MAPK signaling in all exposed cells, potentially dampening immune cell activity, too. Still, the successful use of single MEK inhibitors in NRAS mutant melanoma makes it appealing to test the effects of combined MEK and immune-checkpoint inhibition in patients with NRAS mutant melanoma. In contrast, compounds designed to target mutant BRAF(V600) cause paradox activation of ERK signaling in non-BRAF(V600) mutant cells. This can potentially be harnessed to augment MAPK activity and thus boost immune cell function in treatment combinations with immune-checkpoint inhibitors or adoptive cell immunotherapy (Koya et al., 2012).

CONCLUSION

NRAS mutations are common in melanoma and are associated with clinical features of poor biological behavior (Devitt et al., 2011; Jakob et al., 2012). Because of difficulties of direct NRAS targeting, interference with downstream signaling cascades is to date the most promising targeted therapeutic modality. It is likely that the complexity of NRAS signaling events and the genetic heterogeneity, such as low-activating BRAF mutations, loss of p16(INK4a) and MITF amplification, will require a diverse set of therapeutics for optimized patient care. Hence, studies investigating other than the discussed combinatorial regimens target ROCK, HSP90, NFkB, and Wnt signaling members and are essential to advance our understanding of mutant NRAS biology (Conrad et al., 2012; Feng et al., 2013; Haarberg et al., 2013; Vogel et al., 2015). To further complete our picture of RAS-driven melanoma growth, it will be necessary to also take into account other forms of RAS pathway activation, such as loss of function mutations in NF1, or copy number alterations of RAS itself.

To date most RAS research has been performed in models of mutant KRAS. The slight but distinct functional differences of RAS family members mandate dedicated NRAS research to further advance melanoma treatment. Recent developments in targeting oncogenic RAS function allow for an optimistic yet cautious outlook that effective targeted treatment of NRAS mutant melanoma can be achieved.

Supplementary Material

1

Acknowledgments

This study was supported by the National Cancer Institute of the National Institutes of Health under award number K08CA155035 and the Melanoma Research Alliance Young Investigator Award. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors are grateful to Timothy Dattels, the Max Kade Foundation, and the René Touraine Foundation for their generous support. They are also grateful to the Society for Dermatology and Venerology KA Rudolfstiftung. Further, the authors thank K. Hölbling, G. Posch, and R. Panzer-Grümayer for their support.

Abbreviation

ERK

extracellular signal-regulated kinase

GEF

guanine nucleotide exchange factor

HRAS

Harvey-rat-sarcoma homolog

KRAS

Kirsten-rat-sarcoma homolog

MAPK

mitogen-activated protein kinase

NRAS

neuroblastoma rat-sarcoma homolog

RAL

retinaldehyde

RAS

rat-sarcoma homolog

RTK

receptor tyrosine kinase

Footnotes

ORCID

Christian Posch: http://orcid.org/0000-0003-0296-3567

CONFLICT OF INTEREST

The authors state no conflict of interest.

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