CRAF mutations in lung cancer can be oncogenic and predict sensitivity to combined type II RAF and MEK inhibition

Two out of 41 non-small cell lung cancer patients enrolled in a clinical study were found with a somatic CRAF mutation in their tumor, namely CRAFP261A and CRAFP207S. To our knowledge, both mutations are novel in lung cancer and CRAFP261A has not been previously reported in cancer. Expression of CRAFP261A in HEK293T cells and BEAS-2B lung epithelial cells led to increased ERK pathway activation in a dimer-dependent manner, accompanied with loss of CRAF phosphorylation at the negative regulatory S259 residue. Moreover, stable expression of CRAFP261A in mouse embryonic fibroblasts and BEAS-2B cells led to anchorage-independent growth. Consistent with a previous report, we could not observe a gain-of-function with CRAFP207S. Type II but not type I RAF inhibitors suppressed the CRAFP261A-induced ERK pathway activity in BEAS-2B cells, and combinatorial treatment with type II RAF inhibitors and a MEK inhibitor led to a stronger ERK pathway inhibition and growth arrest. Our findings suggest that the acquisition of a CRAFP261A mutation can provide oncogenic properties to cells, and that such cells are sensitive to combined MEK and type II RAF inhibitors. CRAF mutations should be diagnostically and therapeutically explored in lung and perhaps other cancers.


Introduction
The RAF kinase family, which consists of three isoforms, ARAF, BRAF, and CRAF (RAF1), transmit signal from RAS to MEK along the RAS/RAF/MEK/ERK molecular pathway [1]. RAF kinase family members share three conserved regions (CR1-CR3) [1]. The kinase activity of CRAF is higher than ARAF but lower than BRAF [1,2]. BRAF and CRAF germline mutations have been previously described in rasopathies [2][3][4]. Somatic BRAF mutations have been detected in~8% of human tumors including nonsmall cell lung cancer (NSCLC) (5%) and melanoma (~50%), whereas CRAF mutations are very rarely reported in cancer [1,3]. With the emergence of genome-wide nextgeneration sequencing, somatic CRAF mutations in cancer appear to occur more frequently than previously considered [4][5][6]. We performed whole exome sequencing of 41 available paired tumor/matched normal tissue samples derived from a prospective cohort of "strictly non-smoking" or "formerly limited smoking" NSCLC patients and detected two CRAF mutations, namely CRAF P261A and CRAF P207S (manuscript in preparation). To our knowledge, these CRAF mutations have never been reported in lung cancer. One of these mutations, CRAF P261A , is located in conserved region CR2 and has never been reported in human cancer. However, a CRAF P261A germline mutation was reported in Noonan syndrome (rasopathy) and its characterization revealed that it activates the ERK pathway at higher levels compared with CRAF WT [7].
The other mutation, CRAF P207S , located at a nonconserved region between CR1 and CR2, was previously identified in a fibrosarcoma cell line and reported as incapable of activating the ERK pathway at higher levels than wild-type CRAF and its role as an oncogene remained undetermined [2].
Predicting the efficacy of RAF inhibitors in targeting mutated CRAF is still a challenge. A melanoma-derived oncogenic CRAF mutation (CRAF R391W ), which signals as a dimer, is reported to be resistant to Vemurafenib (a type I RAF inhibitor) [12]. Of note, acquisition of mutations at S259 or adjacent residues of CRAF including P261 [13] has also been described as one of the resistance-conferring mechanisms to type I RAF inhibitor therapy in mutant BRAF V600E melanomas [13]. In contrast, lung cancerderived mutations at S259 and S257 CRAF have been shown to predict sensitivity to Sorafenib, a type II RAF and multiple kinase inhibitor [6].
In the present work, we investigated the "actionability" of these lung cancer-derived CRAF mutations with ERK pathway inhibitors (RAF and MEK inhibitors) and further determined the comparative efficacy of two classes of RAF inhibitors in targeting these mutations.

Results and discussion
CRAF P261A but not CRAF P207S increases ERK pathway activity in a dimer-dependent manner To determine whether CRAF P261A and CRAF P207S mutations can induce ERK pathway activation at higher levels compared with the wild-type CRAF, we introduced CRAF P261A and CRAF P207S mutations into the wild-type CRAF coding sequence by site-directed mutagenesis and transiently expressed the mutant CRAF recombinant proteins in HEK293T and BEAS-2B cells. As shown in Fig. 1a, b, the expression of CRAF P261A led to increased MEK and ERK activation in both HEK293T and BEAS-2B cellular models. The enhanced MEK and ERK activity induced by CRAF P261A was less pronounced in BEAS-2B cells, which could be explained by a lesser transfection efficiency of BEAS-2B cells as opposed to HEK293T cells. It was previously reported that phosphorylation of CRAF at S338 is crucial for its activation, linking it to cancer progression [14][15][16], whereas phosphorylation at residue S259 (a negative regulatory site adjacent to P261) is essential for CRAF auto-inhibition [10,17]. In all tested conditions we observed that increased ERK pathway activity induced by CRAF P261A was accompanied by a clear decline in S259-CRAF phosphorylation levels ( Fig. 1a, b). In contrast, no marked increase in S338-CRAF phosphorylation levels was observed (Fig. 1a, b).
In contrast to CRAF P261A , CRAF P207S did not induce MEK and ERK phosphorylation at higher levels compared with CRAF WT (Fig. 1a, b). We postulated that CRAF P207S , like kinase-impaired BRAF mutants that allosterically activate their heterodimerization partner (CRAF), might function in co-operation with wild-type BRAF. Therefore, we overexpressed CRAF recombinant proteins in HEK293T cells together with BRAF WT . As shown in Fig. 1d, co-expression of BRAF together with CRAF P207S did not lead to increased MEK and ERK activation when compared with CRAF WT /BRAF co-transfectants (idem for CRAF P261A ).

CRAF P261A transforms mouse embryonic fibroblasts and human lung epithelial cells
To determine whether CRAF P207S and CRAF P261A mutations can induce anchorage-independent growth, a hallmark of carcinogenesis, we stably transduced lung epithelial cells (BEAS-2B) and mouse embryonic fibroblasts of two different origins (NIH3T3 [34] derived from Swiss 3T3 mice and another immortalized MEF [35] derived from C57BL/ 6J mice, hereafter mentioned as MEF), with lentiviral vectors bearing recombinant wild-type and mutant forms of CRAF. The anchorage-independent growth was determined using a soft agar colony-formation assay, which is considered as a stringent test for malignant transformation. As shown in Fig. 2a-c, the number of colonies formed after transducing BEAS-2B, NIH3T3, and MEF cells with CRAF P261A strongly increases when compared with CRAF WT transductions. We observed a 10.6-fold, 18.4-fold, and 25-fold increase in colony formation for respectively BEAS-2B, NIH3T3 (the least pronounced) and MEF stably transduced cells. Comparable results were not obtained when transducing cells with CRAF P207S (Fig. 2a, b). Indeed, CRAF P207S exhibited only a meagre transforming activity (Fig. 2a, b), which correlates with the observed lack of ERK pathway activation (Fig. 1a, b).
In addition, CRAF P261A not only generates more colonies but also clearly induces the formation of larger colonies ( Fig. 2d-f, Supplementary Fig. S1d and S1e) compared with CRAF WT . Interestingly, the capacity of CRAF P261A to form colonies in BEAS-2B was relatively high, as it was only four fold less than for the well-characterized BRAF V600E , which has been reported to rank among the highest ERK pathway activating BRAF mutants [22,23,36] (Supplementary Fig. S1a and S1e). We also tested CRAF S259A as a control, and consistent with two previous reports [6,37] we observed that this variant induces increased anchorage-independent growth in lung epithelial and MEFs ( Supplementary Fig. S1). CRAF P261A -induced ERK pathway activation is suppressed by type II inhibitors, but paradoxically increased by type I inhibitors Several studies have suggested that ERK pathway activating cancer-derived CRAF mutations are oncogenic, but their response to RAF inhibitors is still uncertain [4,6,13]. In this study, we first tested three RAF inhibitors (Dabrafenib, LY3009120, and AZ628) at the clinically relevant dose of 1 µM by measuring ERK pathway activity in BEAS-2B cells transiently expressing CRAF recombinant proteins. Dabrafenib is a type I RAF inhibitor (recently characterized as type 1.5 inhibitor [27]), which stabilizes the drug-bound RAF molecule in a DFG-in conformation [27]. AZ628 and LY3009120 are both type II RAF inhibitors and stabilize RAF in the DFG-out conformation [23,26,29]. Dabrafenib is Food and Drug Administration-approved for the treatment of V600E/K BRAF melanoma and has an affinity for CRAF as well [22,38]; LY3009120 has been recently tested clinicaly (phase I study) in mutant BRAF and KRAS cancers (NCT02014116), and AZ628 is an experimental RAF inhibitor.
Dabrafenib treatment of CRAF WT expressing BEAS-2B cells whether in the absence or presence of BRAF led to  [22]) in HEK293T cells do not result in higher (or lower) ERK pathway activation compared with single transfections (d). Forty-eight hours post-transfection cells were lysed and subjected to western blotting analysis to detect the indicated proteins (a, b, c, d). EV stands for empty vector. Lipofectamine was added in the mock condition paradoxical ERK pathway activation compared with dimethyl sulfoxide (DMSO) (vehicle) treatment ( Fig. 3a and Supplementary Fig. S2). As previously shown [1,21,25,32,39], when a type I RAF inhibitor (Dabrafenib) binds to one CRAF WT homodimer partner, the other dimer partner is transactivated, resulting in paradoxical ERK activation. Notably, a similar phenomenon was observed upon Dabrafenib treatment of cells expressing either CRAF P261A or CRAF P207S (Fig. 3a and Supplementary Fig. S1). In contrast, both AZ628 and LY3009120 suppressed ERK activity in CRAF P261A -and CRAF P207S -expressing cells in the presence or absence of BRAF and did not induce ERK paradoxical activity in CRAF WT -expressing cells (Fig. 3a and Supplementary Fig.  S2). The differential effect of type I vs. type II RAF inhibition can be explained by our observation that CRAF P261A relies on dimerization for downstream signaling. Indeed, the abolishment of ERK pathway signaling observed when CRAF P261A mutant proteins were rendered unable to dimerize suggests that only inhibitors that concomitantly block the kinase activity of both RAF dimer partners (=type II inhibitors) can suppress CRAF P261A -induced ERK pathway activation.
Interestingly, in CRAF P207S mono-transfectants, both AZ628 and LY3009120 induced a slight increase in p-MEK levels, which was not consistent with the observed decline The experiments were performed with three biological repeats and were represented as a bar chart (means ± SEM). d Representative whole well image of the nitro blue tetrazolium chloride stained MEF colonies after 16 days in culture. e Representative high-magnification images of the MEF colonies prior to staining. f Graphical representation of the relative size of the MEF colonies as determined with OpenCFU software [55]. Dots represent individual colonies (the three biological repeats are pooled), lines represent the means Fig. 3 CRAF P261A -induced ERK pathway activation is suppressed by type II RAF inhibitors. a BEAS-2B cells were transiently transfected with different CRAF expression vectors (wild type or mutant). Forty-eight hours post transfection, cells were treated for 2 h with DMSO, Dabrafenib (1 µM), or AZ628 (1 µM), or LY3009120 (1 µM), then lysed and subjected to western blotting analysis to detect the indicated proteins. b, c BEAS-2B cells were transiently transfected with CRAF P261A . Forty-eight hours post transfection, cells were treated for 2 h with DMSO, Vemurafenib, Dabrafenib, AZ628, LY3009120, or Sorafenib (drug concentrations are indicated). b Cells were lysed and subjected to western blotting analysis to detect the indicated proteins. c Graphical representation of the relative p-ERK signals (normalized to actin and DMSO group) based on at least two independent experiments as shown in b. Dots represent individual data points, lines represent the mean value ± SEM. d MEF cells stably expressing CRAF P261A were treated with DMSO, Vemurafenib, Dabrafenib, AZ628, LY3009120, or Sorafenib (all at 1 µM but Sorafenib at 5 µM) for a duration of 72 h. Cell viability was determined using CellTiter-Glo. The dots represent the means of the independent experiments, the horizontal lines with error bars represent the mean ± SEM of three independent experiments each performed at least in triplicate. Statistical significance was indicated by *** and represents a p-value < 0.001 in corresponding p-ERK levels (Fig. 3a). This phenomenon was not observed in the presence of BRAF WT (Supplementary Fig. S2). To further gain a broader insight into the link between the mode of RAF inhibition and the efficacy in suppressing CRAF P261A -induced ERK activity, we also tested (Fig. 3b, c) the clinically available Type I RAF inhibitor Vemurafenib as well as the relatively weak but clinically available Type II RAF inhibitor Sorafenib [29] (multiple kinase inhibitor). As for Dabrafenib, Vemurafenib caused paradoxical ERK activation. Also, Sorafenib activated the ERK pathway rather than inhibiting it at 1 µM, the concentration used for the other inhibitors. However, one should notice that 1 µM is a relatively low concentration for Sorafenib as the maximal plasma concentration of Sorafenib in patients reaches 10 to 21 µM [40][41][42]. Previous reports confirm that Sorafenib causes ERK paradoxical activation at low doses [43][44][45]. However, at higher doses (5 µM and 10 µM), Sorafenib caused ERK inhibition (Fig. 3b). Overall, LY3009120 exerted the strongest ERK pathway inhibition (Fig. 3a, b and Supplementary Fig. S2). These results were consistent with our observations regarding the growth inhibitory effect of the tested RAF inhibitors in MEFs transduced with CRAF P261A (Fig. 3d).

CRAF P261A predicts sensitivity to the combination of LY3009120 and Trametinib
Combined MEK and BRAF targeting has shown superior efficacy in BRAF mutant cancers [18,22,23,38,39,[46][47][48][49]. We investigated whether similar effects are observed in the mutant CRAF context. MEK inhibitors are known to be ineffective or poorly effective in cells where ERK pathway activation is CRAF-mediated such as in mutant KRAS cells [50][51][52]. However, the MEK inhibitor Trametinib is known to be more efficient compared with several other MEK inhibitors in such cells [50]. As LY3009120 showed the highest ERK inhibitory effect among the RAF inhibitors we tested, we further studied the effect of Trametinib at the clinically relevant dose of 25 nM as a single agent and in combination with LY3009120. Trametinib single agent treatment of lung epithelial BEAS-2B cells expressing CRAF mutants alone and together with BRAF WT led to increased MEK phosphorylation ( Fig. 4a and Supplementary Fig. S3). However, increased MEK phosphorylation was not followed by increased ERK phosphorylation but by strong ERK inhibition. Other groups and we have previously described this phenomenon upon MEK inhibition in cells with CRAF-mediated ERK pathway activity [23,[50][51][52][53]. The ERK inhibitory effect of Trametinib alone was even stronger than for LY3009120 alone. Combination of LY3009120 and Trametinib led to an enhanced ERK inhibitory effect compared with single agent treatments, whether in the presence or absence of BRAF ( Fig. 4a and Supplementary Fig. S3). Notably, the presence of LY3009120 decreased the Trametinib-induced MEK phosphorylation (Fig. 4a).
Finally, we tested the growth inhibitory effect of Trametinib (10 nM) combined with LY3009120 (1 µM) or combined with Sorafenib (5 µM) in mouse embryonic fibroblasts expressing CRAF P261A . In both cases, Fig. 4 CRAF P261A predicts sensitivity to combination of LY3009120 and Trametinib. a BEAS-2B cells were transiently transfected with different CRAF expression vectors (wild type or mutant). Forty-eight hours post transfection, cells were treated for 2 h with DMSO, LY3009120 (1 µM), and/or Trametinib (25 nM), then lysed and subjected to western blotting analysis for the indicated proteins. b MEF cells stably expressing CRAF P261A were treated with DMSO, Sorafenib, LY3009120, Trametinib, and the combinations of Sorafenib (5 µM) or LY3009120 (1 µM) with Trametinib (10 nM), for a duration of 72 h. Cell viability was determined using CellTiter-Glo. The dots represent the means of the independent experiments, the horizontal lines with error bars represent the mean ± SEM of three independent experiments each performed at least in triplicate. Statistical significance was indicated by ** and ***, which represent p-values < 0.01 and 0.001, respectively combinatorial treatments resulted in reduced cell viability compared with single agent treatments (Fig. 4b). Trametinib plus LY3009120 produced stronger growth inhibitory effects compared with Trametinib plus Sorafenib (Fig. 4b).
Our findings predict sensitivity of cells with CRAF oncogene dependency to the combination of type II RAF and MEK inhibition.
In summary, two somatic CRAF mutations identified in a series of 41 NSCLC patients with a non-smoking history were examined for their ability to activate the MEK-ERK pathway and their therapeutic actionability with several pathway inhibitors. We show that one of these mutations (CRAF P261A ) strongly activates the MEK-ERK pathway, whereas the other mutation (CRAF P207S ) does not. The mode of RAF inhibition determines whether the ERK pathway will be suppressed or paradoxically activated in cells expressing the CRAF P261A mutation. Among the type II inhibitors tested, LY3009120 resulted in strongest ERK inhibitory effect. Moreover, combined LY3009120 and Trametinib (MEK inhibitor) treatment of cells expressing CRAF P261A even led to a stronger MEK and ERK inhibition. LY3009120 has shown promising preclinical efficacy in BRAF and KRAS mutant cells but the subsequent clinical trial (NCT02014116) exploring the efficacy of the inhibitor in melanoma, colon, NSCLC and pancreatic cancers led to poor pharmacodynamic responses in treated patients and discontinuation of the drug development [29,54].
Regarding CRAF P207S , our results show that this mutation does not activate the ERK pathway at higher levels compared with CRAF WT and does not transform the transduced cells. Further investigation is required to uncover whether CRAF P207S can deregulate other pathways and induce oncogenesis in co-operation with other protumorigenic events, or it is rather a passenger mutation. This study inspires discovery and characterization of CRAF mutations in lung and other cancers. Our results support the clinical exploration of the therapeutic exploitation of CRAF mutations in cancer [35].
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