Combined Inactivation of MYC and K-Ras Oncogenes Reverses Tumorigenesis in Lung Adenocarcinomas and Lymphomas

Background Conditional transgenic models have established that tumors require sustained oncogene activation for tumor maintenance, exhibiting the phenomenon known as “oncogene-addiction.” However, most cancers are caused by multiple genetic events making it difficult to determine which oncogenes or combination of oncogenes will be the most effective targets for their treatment. Methodology/Principal Findings To examine how the MYC and K-rasG12D oncogenes cooperate for the initiation and maintenance of tumorigenesis, we generated double conditional transgenic tumor models of lung adenocarcinoma and lymphoma. The ability of MYC and K-rasG12D to cooperate for tumorigenesis and the ability of the inactivation of these oncogenes to result in tumor regression depended upon the specific tissue context. MYC-, K-rasG12D- or MYC/K-rasG12D-induced lymphomas exhibited sustained regression upon the inactivation of either or both oncogenes. However, in marked contrast, MYC-induced lung tumors failed to regress completely upon oncogene inactivation; whereas K-rasG12D-induced lung tumors regressed completely. Importantly, the combined inactivation of both MYC and K-rasG12D resulted more frequently in complete lung tumor regression. To account for the different roles of MYC and K-rasG12D in maintenance of lung tumors, we found that the down-stream mediators of K-rasG12D signaling, Stat3 and Stat5, are dephosphorylated following conditional K-rasG12D but not MYC inactivation. In contrast, Stat3 becomes dephosphorylated in lymphoma cells upon inactivation of MYC and/or K-rasG12D. Interestingly, MYC-induced lung tumors that failed to regress upon MYC inactivation were found to have persistent Stat3 and Stat5 phosphorylation. Conclusions/Significance Taken together, our findings point to the importance of the K-Ras and associated down-stream Stat effector pathways in the initiation and maintenance of lymphomas and lung tumors. We suggest that combined targeting of oncogenic pathways is more likely to be effective in the treatment of lung cancers and lymphomas.


Introduction
Cancer is largely caused by the summation of activated oncogenes and inactivated tumor-suppressors that occur in a permissive epigenetic milieu resulting in various pathologic features: autonomous proliferation, immortalization, blocked differentiation, the induction of angiogenesis, capacity for invasion, resistance to apoptosis and genomic instability [1]. Transgenic mouse models have been a valuable means to identify cooperating oncogenic events relevant to human tumorigenesis. A classic example is the forced coexpression of c-myc and v-Ha-ras oncogenes in vivo resulting in a strongly synergistic tumorigenesis phenotype [2]. MYC encodes a transcription factor that regulates the expression of a multitude of genes involved in regulating cellular proliferation and growth and when overexpressed results in the prototypical pathologic features of cancer as described above [3,4]. K-ras encodes a low-molecular weight GTP-binding protein responsible for transmitting signals from receptor tyrosine kinases to downstream modulators of cell growth and survival [5,6] and has been shown to stabilize the MYC protein [7]. Thus, MYC and ras cooperate to induce tumorigenesis through multiple mechanisms.
Since most human cancers are genetically complex and are associated with the activation of more than one oncogene, strategies targeting multiple oncogenes appear to be a logical approach for the treatment of human cancers [1,37,38]. Notably, elegant studies illustrated that breast adenocarcinomas induced by conditional MYC overexpression but that also subsequently develop mutations in K-Ras fail to undergo sustained regression upon MYC inactivation [16,17]. These results suggest that the combined inactivation of both MYC and mutant Ras may be more effective in inducing sustained tumor regression. However, to date it has not been directly examined if the coordinate inactivation of both MYC and mutant Ras would be more effective in inducing sustained tumor regression.
To study how MYC and K-ras G12D cooperate for the initiation and maintenance of tumorigenesis, we have generated double conditional transgenic mouse models of lymphoma and lung adenocarcinoma. MYC-, K-ras G12D -or MYC/K-ras G12D -induced lymphomas exhibited sustained regression upon single or double oncogene inactivation. Interestingly, in contrast to most MYCinduced tumor models, MYC-induced lung tumors were not oncogene-addicted; whereas K-ras G12D inactivation did induce complete tumor regression in K-ras G12D -induced lung tumors. Furthermore, the combined inactivation of MYC and K-ras G12D was associated with reversible lung tumorigenesis. In addition, we observed that down stream K-Ras effector, Stat3, was downregulated upon oncogene inactivation in lung tumors and lymphomas that regressed. However, non-regressing MYCinduced lung tumors were found to have aberrantly active Stat3 signaling. These data have important implications for treatment strategies where use of multiple targeted agents is being considered and highlight the significance of the K-Ras and Stat pathways for tumorigenesis and tumor maintenance.

MYC inactivation alone fails to induce regression of lung cancer
To examine the role of MYC in the initiation and maintenance of tumorigenesis, transgenic mice were generated that exhibit conditional expression of the human c-MYC oncogene (referred to as MYC from now on) by crossing TetO-MYC transgenic mice [15] with the CCSP-rtTA transgenic line [39] generating CCSP-rtTA/ TetO-MYC mice (now termed CM; see Figure 1A). The CCSP-rtTA mouse line contains the Clara cell secretory protein (CCSP or CC10) promoter which drives expression of the reverse tetracycline transactivating protein (rtTA) in lung Clara cells, alveolar Type II pneumocytes and some other non-ciliated bronchial and bronchiolar epithelial cells [23,39]. To verify conditional regulation, CM mice were examined for MYC expression using quantitative real-time polymerase chain reaction (qRT-PCR). The addition of doxycycline induced expression of MYC transcripts 380-fold in the lung with no appreciable expression in non-induced lung tissue or induced liver ( Figure 1B). Similar to previous reports using the CCSP-rtTA line, the kinetics of inactivation revealed background MYC expression by 3-days after doxycycline withdrawal [23,39]. Examination for MYC protein revealed similar robust inducible regulation by western blotting ( Figure 1C) and immunohistochemical (IHC) analysis in CM lung tissue ( Figure 1D-E). Notably, two target genes of MYC, ornithine decarboxylase (ODC) and nucleolin [3], were found to exhibit expression that was coordinately regulated in a conditional manner as expected from a functional MYC protein ( Figure S1). Thus, we have developed a conditional model for the expression of MYC in the lung.
Induction of MYC in the lung epithelium by the administration of doxycycline in the drinking water of CM mice uniformly resulted in tumorigenesis (Figure 2A) that on histologic examination were consistent with adenomas or adenocarcinomas ( Figure 2C-D) [40]. Tumors were composed of cuboidal to columnar cells lining alveoli frequently containing vacuolated tumor cells, multiple nucleoli and mitoses. Using the consensus classification system as developed by Yu and colleagues, these tumors would be classified as adenoma-mixed subtype (1.2.1.2.3) and adenocarcinoma-NOS (1.2.3.2.5) [40]. Activated tumor cells stained intensely for MYC protein by IHC analysis ( Figure 2J) and were TTF-1 positive as expected (data not shown). To enhance detection and allow serial monitoring of lung tumors during growth and following interventions in our study, micro-computed tomography (mCT) was performed on cohorts of mice for the detection of millimeter sized lesions ( Figure 2B). CM mice developed tumors with a median latency of 52 weeks as detected by mCT screening usually well before clinical signs developed. CM mice usually developed 1-2 dominant tumors that were located more centrally in the mediastinum ( Figure 2B). Thus, MYC induction by the CCSP promoter is sufficient to induce lung adenocarcinomas.
To simulate MYC targeted treatment and evaluate if MYC inactivation was sufficient to reverse lung tumorigenesis, doxycycline treatment was removed to suppress expression of the transgene. Surprisingly, 98% (n = 51) of tumor bearing CM mice did not exhibit complete tumor regression following doxycycline withdrawal as demonstrated by gross examination on necropsy, radiographically and/or histologically ( Figure 2E-H). Only 1 out of 8 CM mice demonstrated volumetric tumor regression greater than 60% by radiographic exam following 6 weeks of doxycycline withdrawal (and see below). A trivial explanation for doxycyclineindependent tumor viability could be either the aberrant expression of MYC independent of doxycycline or endogenous upregulation of murine c-Myc. To address this possibility qRT-PCR and IHC were performed on tissue from mice in which MYC was inactivated but the tumors had not regressed. No transgene or protein expression of MYC were detected (Figure 2I-K and data not shown, n = 6). Since the anti-MYC antibody used for IHC in our study also cross reacts with murine c-Myc, we concluded that these tumors also had not upregulated endogenous c-Myc ( Figure 2J-K). Taken together these results suggest continuously activated CM mice develop lung tumors that become independent of MYC for tumor maintenance.
MYC and K-ras G12D cooperation for tumorigenesis is dependent on tissue type We were surprised to find that CM tumors were independent of MYC, since a multitude of previous studies have demonstrated that MYC-induced tumors exhibit complete tumor regression upon MYC inactivation [13][14][15]17,21,22]. Studies demonstrated a subset of breast tumors induced by MYC overexpression that fail to undergo sustained regression upon MYC inactivation have mutations in K-Ras [16,17]. To evaluate in our conditional lung model if MYC and K-Ras cooperate, we utilized a conditional mutant K-ras G12D line previously described, CCSP-rtTA/TetO-Kras G12D (now called CR) [23]. CM and CR were then used to produce the bi-conditional animals CCSP-rtTA/TetO-MYC/TetO-K-ras G12D (or CMR), which upon doxycycline administration simultaneously overexpress both oncogenes under the control of the CCSP promoter in lung and as described below in lung tumors ( Figure S2). At 3-4 weeks of age cohorts of CM, CR and CMR mice were treated with doxycycline and screened using physical exam and mCT screening. As described above, CM mice developed lung tumors with a median latency of 52 weeks ( Figure 3A). Upon doxycycline treatment, CR mice developed lung adenocarcinomas with a median latency of 26 weeks. Surprisingly, CMR mice developed lung adenomas and adenocarcinomas ( Figure 4A) with a latency of 36 weeks similar to the CR mice ( Figure 3A; not significantly different by log-rank analysis, p.0.05). Thus, in the setting of adult lung epithelium MYC and K-ras G12D failed to cooperate to induce accelerated tumorigenesis.
We were surprised that the conditional MYC and K-ras G12D oncogenes did not cooperate to induce lung tumorigenesis. To evaluate if these transgenes would cooperate in another tissue setting, we induced expression of either oncogene alone or together in lymphocytes utilizing an Em-SR-tTA line (data not shown). In contrast to what we observed in the lung, we found that MYC (LM) was a much more potent oncogene than K-ras G12D (LR) at inducing lymphomas with a median latency of tumor onset of 13 weeks versus more than 100 weeks ( Figure 3B; p,0.0001 by log rank). Moreover, we found that MYC and K-ras G12D cooperate to induce tumorigenesis with a reduced median latency of 5 weeks (all curves different, p,0.0001 by log rank). Thus, MYC and Kras G12D cooperate to induce lymphoma but not lung adenocarcinoma.

Combined MYC/K-ras G12D inactivation induces complete tumor regression
We speculated that in our MYC-induced lung tumors, activation of the Ras signaling pathway may provide a means to bypass the requirement for MYC, as has been previously suggested [16,17]. To directly test this hypothesis, we simulated double targeted treatment of MYC and K-ras G12D using dual conditional CMR tumor laden mice by inactivating both oncogenes ( Figure 4B-F) and then comparing similarly to the single CM and CR mice. Serial mCT imaging was performed on cohorts of CR, CM and CMR lung tumor bearing mice prior to and following oncogene-inactivation was performed ( Figure 5A). CR mouse tumors demonstrated complete lung tumor regression following oncogene inactivation, as has been described previously (n = 11; Figure 5A-B) [23]. In marked contrast, CM tumors failed to regress completely, as described above (n = 8; Figure 5A-B). Tumor bearing CMR mice on the whole exhibited tumor regression intermediate to that of the CR and CM mice following dual oncogene-inactivation of MYC and K-ras G12D oncogenes (n = 10; Figure 5A-B). However as predicted, 40% of the individual CMR-induced lung tumors analyzed showed complete tumor regression equal to those from CR mice following doxycycline withdrawal ( Figure 5B). By qRT-PCR and IHC, we confirmed that MYC, transgenic K-ras G12D and endogenous K-Ras were not expressed in the inactivated CMR lung tumors and CMR tumors were indeed inactivated for both oncogenes ( Figure 4B-F). Altogether, these data suggest that activation of the K-Ras signaling pathway is an essential rate-limiting event during lung tumorigenesis. Moreover, our observation that the combined inactivation of both MYC and K-ras G12D induced lung tumor regression more effectively suggests that the K-Ras pathway may be an important target for the treatment of lung cancer.
From these results, we speculated that K-Ras may be mutated in MYC-induced lung tumors, as has been observed in MYCinduced breast tumors [16,17,20]. To address this possibility, we sequenced three MYC-inactivated CM tumors (or derived cell lines) for mutations in K-Ras but were unable to detect any hotspot activating mutations ( Figure S3). Therefore, activating mutations of K-ras were not a common occurrence and was not an explanation for MYC independence in our lung model, in contrast to what has been previously reported for breast cancer [16,17,20]. Other components of the K-Ras effector pathway were obvious next candidates and were investigated as described below.
Notably, in the lymphoma model, inactivation of MYC (LM Off), K-ras G12D (LR Off) or MYC/K-ras G12D together (LMR Off) were each able to induce complete regression of lymphomas and extend tumor free survival ( Figure 5C; no difference by log rank analysis, p.0.05). For lymphomas, inactivation of MYC or Kras G12D alone or both MYC/K-ras G12D induced reversible tumorigenesis. In contrast, single K-ras G12D and dual MYC/K-ras G12D inactivation induced reversible lung tumorigenesis, but MYC inactivation alone failed to reverse tumorigenesis. Thus, whether MYC induces reversible tumorigenesis alone is dependent upon the specific tumor context.

Tumor regression is associated with the dephosphorylation of Stat3
Our results suggested that the K-Ras signaling pathway is crucial for both the initiation and maintenance of lung tumorigenesis. Important upstream and downstream regulators of the K-Ras pathway are the epidermal growth factor receptor (EGFR) and Erk1/2, Akt1 and Stat3/5, respectively [27,[41][42][43][44][45][46][47][48][49][50]. The upstream effector, EGFR, was not found to be phosphorylated in any of our MYC-or K-ras G12D -induced lung tumors by IHC (data not shown) and as described previously for K-Rasinduced lung tumors [27]. As expected, we observed phosphorylation of Erk1/2 in K-ras G12D -induced tumors decrease upon Kras G12D inactivation (CR; Figure 6A). However, there was no evidence for phosphorylated-Erk1/2 staining by IHC in MYCinduced lung tumors. Analogously we observed phospho-Akt1 staining in the CR lung tumors decrease upon K-ras G12D inactivation ( Figure 6B). We observed only minimal changes in the phosphorylation of Akt1 in CM lung tumors upon inactivation of MYC. K-ras G12D -induced lung tumors exhibited robust conditional Stat3 and Stat5 phosphorylation that was dependent on K-ras G12D activation ( Figure 6C-D). In contrast, MYC-induced tumors had cells that stained highly positive for both phospho-Stat3 and phospho-Stat5, and a large proportion of highly positive phospho-Stat3 and phospho-Stat5 cells remained after MYC inactivation ( Figure 6C-D).
Surprisingly, whereas single K-ras G12D -induced lung tumors exhibited a high degree of Stat5 phosphorylation, dual MYC/Kras G12D -induced lung tumors did not (compare Figures 6C and 7A). CMR lung tumors did show a high degree of Stat3 phosphorylation that decreased upon simultaneous inactivation of both MYC/K-ras G12D in persistent lung tumors ( Figure 7B). Thus, Kras G12D -or dual MYC/K-ras G12D -initiated lung tumors demonstrated a decrease in Stat3 phosphorylation upon oncogene inactivation that was associated with reversible tumorigenesis.
Next, we examined the consequences of MYC and/or K-ras G12D inactivation in lymphoma. LM, LR, and LMR lymphoma cells all exhibited phosphorylation of Stat3 that decreased upon inactivation of MYC and/or K-ras G12D (Figure 8A-B). In contrast, despite the fact that LM, LR, and LMR lymphomas all regress upon MYC and/or K-ras G12D inactivation, phospho-Stat5 decreased upon MYC, but not K-ras G12D or dual MYC/K-ras G12D inactivation. Collectively our results illustrate that for both MYC/Kras G12D -induced lung tumors and lymphomas dephosphorylation of Stat 3 is correlated with the ability of oncogene inactivation to induce tumor regression.

Discussion
Targeting single oncogenes is not likely to be effective in all cases for the treatment of human cancers [38,51]. Murine models provide a preclinical strategy to identify which combination of oncogenes are most likely to be effective [30,52]. To our knowledge, our study is the first to examine experimentally using conditional transgenic model systems if the combined inactivation of two oncogenes is more likely to be effective in the treatment of cancer in situ. Using our models we interrogate the role of MYC and K-ras G12D alone or in combination for the initiation and maintenance of lung and hematopoietic tumorigenesis. The inactivation of K-ras G12D but not MYC could induce complete tumor regression in lung adenocarcinomas; whereas in marked contrast, single K-ras G12D -or MYC-inactivation both succeeded in inducing sustained regression in lymphomas. However, the combined inactivation of both K-ras G12D and MYC was capable The double conditional oncogene animals (CMR, n = 25) had a median latency that were no different than the single CR animals by log-rank analysis suggesting that K-ras G12D was epistatic to MYC for lung tumorigenesis. A syngenic control cohort consisting of wildtype mice, those with MYC/K-ras G12D (without CCSP), CCSP alone, or K-ras G12D alone were fed water and never developed lung tumors (n = 8). Tumor Free Survival was scored by serial mCT imaging of animals following addition of doxycycline at 3-4 weeks of age. (B) Kaplan-Meir analysis of Tumor Free Survival for oncogene-induced lymphomagenesis. MYC-induced lymphomas (LM, n = 26) arose with a median latency of 13 weeks after conditional oncogene activation. In contrast, less than half of the mice developed lymphoma after 100 weeks of conditional Kras G12D activation (LR, n = 25). The double conditional oncogene animals (LMR, n = 22) had a median latency that was significantly different than either single oncogene line (5 weeks, p, = 0.0001 by log rank), suggesting that K-ras G12D and MYC were cooperative for lymphomagenesis. Control animals fed water never developed tumors (n = 6). Tumor Free Survival was scored when animals were moribund with tumor. doi:10.1371/journal.pone.0002125.g003 of inducing complete regression in both lung tumors and lymphomas.
Our data highlight two important considerations in targeted therapeutics: first, initiation of tumorigenesis by a specific oncogene does not mean inactivation of that specific oncogene will be sufficient to induce tumor regression; and second, that the consequences of the inactivation of a particular oncogene are pointedly dependent on tissue context. Specifically, we have demonstrated that the K-Ras pathway and its down-stream effector Stat3 are correlated with the ability of K-ras G12D or MYC to initiate lung tumorigenesis and that down regulation of the K-Ras/Stat pathway is strongly correlated with lung tumor and lymphoma To rule out the possibility that the double oncogene-induced lung tumors had developed doxycycline (or TetO)-dysregulated MYC or K-ras G12D expression, inactivated double oncogene-induced lung tumors were examined for spurious expression of MYC and K-ras G12D at the mRNA and/or protein level. qRT-PCR analysis of double oncogene-induced lung tumors from CMR mice that had been inactivated (doxycycline removed from drinking water) for 2-9 weeks demonstrated lack of expression of the MYC transgene in contrast to a MYC-induced tumor that had never been inactivated. Immunohistochemical analysis (performed like Figure 1D) on similar (C) inactivated double oncogene-induced tumors also showed lack of MYC transgene product and endogenous murine MYC protein compared to a (D) MYC-activated tumor. qRT-PCR analysis of double oncogeneinduced lung tumors from CMR mice that had been inactivated demonstrated no expression of the (E) K-ras G12D transgene or upregulation of (F) endogenous murine K-ras (. = 3-9 tumors for . = 3 mice per experiment). doi:10.1371/journal.pone.0002125.g004 regression. We conclude that the K-Ras/Stat3 pathways have a dominant role in the initiation and maintenance of lung tumors. Our experimental model system re-examines the classic experiments first demonstrating the cooperation between c-myc and v-Ha-ras for malignant transformation in vivo [2]. Identical to previous results using conventional transgenic models [2], MYC and K-ras G12D cooperated to induce tumorigenesis in lymphocytes (compare LM, LR and LMR mice; Figure 3B). In contrast, MYC . Oncogene inactivation in mice with K-ras G12D -induced lymphoma resulted in tumor regression and increased median survival by 12 weeks (LR OFF, n = 5). Inactivating both MYC/K-ras G12D together also resulted in tumor regression and increased median survival by 5 weeks. There is no significant difference between inactivating MYC/K-ras G12D together vs K-ras G12D alone (log rank analysis p = 0.4849). Relapse free survival was scored when mice were moribund with tumor burden. doi:10.1371/journal.pone.0002125.g005 failed to cooperate with K-ras G12D to induce lung adenocarcinomas (compare CM, CR and CMR mice; Figure 3A). Thus, whether or not MYC and K-ras G12D functionally cooperate to activate critical tumor promoting pathways appears to depend upon the specific tissue context. In lung adenocarcinomas induced by MYC and/or K-ras G12D , tumors exhibited activation of the K-Ras/Stat3 signaling pathway. Apparently, MYC activation is not capable of initiating lung tumorigenesis without activation of the mediators of the K-Ras/Stat3 pathway, perhaps accounting for why MYC does not appear to cooperate with K-ras G12D to induce lung tumorigenesis. For lung tumorigenesis, there must be an essential role for activation of the K-Ras pathway or downstream mediators such as the Stat pathway. Similarly, the combined inactivation of MYC and K-ras G12D was now capable of reversing lung tumorigenesis in contrast to MYC-induced lung tumors, because under these circumstances the K-Ras pathway and presumably the downstream Stat3 pathway can be conditionally inactivated.
Notably, our results are highly consistent with several elegant studies that illustrated that mutation of the K-Ras pathway in breast tumorigenesis can reduce the dependence of tumors on sustained MYC overexpression [16,17,20]. We acknowledge that the differences seen between tumor initiation and maintenance could be secondary to differences in the expression of MYC and Kras from the two different tissue specific promoters and/or may be confined to the particular genetic background of the mice used in our study. Nevertheless, we speculate that the combined inactivation of both the MYC and K-Ras pathways in these breast tumor models will also result in complete tumor regression.
In our lung tumor model system other genes are likely to be somatically activated in the EGFR/BRAF/KRAS pathway or parallel pathways that may also contribute to the escape from the requirement of MYC expression. This is evidenced in our study by the inactivated CM ( Figure 6) and CMR (Figure 7) lung tumors that did not demonstrate aberrant signaling in any of the pathways we examined. Possible candidates to undergo such mutations include a multitude of gene products described in studies of human lung tumors [53][54][55][56][57][58][59][60][61][62], some of these studies have implicated the EGFR/IL-6/Stat3 pathway in the pathogenesis of lung adenocarcinomas [43,49,50,[61][62][63]. Stat3 and Stat5 transcription factors have been widely implicated in the pathogenesis of tumors [64,65] and are known to be downstream targets of K-Ras [27,44,[48][49][50]. Phosphorylation of Stat3/5 promotes homotetramerization, followed by nuclear translocation and increased transcription of target genes critical for cell growth, survival, and angiogenesis [64,65]. Persistent activation of Stat3/5 was found in the majority of our inactivated MYC-induced lung tumors, as evidenced by elevated phosphorylation and nuclear localization by IHC ( Figure 6C-D). Consistent with a role of Stat3/5 in oncogene-addiction, phosphorylation of Stat3/5 has been shown to diminish in tumor cells undergoing apoptosis upon oncogene inactivation in vitro [41,42]. Phosphorylated Stat3/5 appears to be particularly important for survival of human lung adenocarcinoma cells harboring certain EGFR mutations [43,49,62]. Similar to the lung cancer mouse models described above, in these EGFR mutated lung cancers behave in an oncogene-addicted fashion following treatment with EGFR tyrosine kinase inhibitors [33,63].
Our observations illustrate that the combined inactivation of multiple oncogenes is more likely to be effective to treat some cancers [30,38,51,52]. The potential of targeting multiple oncogenic pathways in the treatment of human cancer has recently been illustrated in brain tumor cell lines in vitro [38]. The identification of the best gene products to therapeutically target in cancers is very likely to be much more complicated than simply identifying the genes mutated in a given tumor, as has recently been illustrated in human lung cancer patients who become resistant to tyrosine kinase inhibitors [37,51]. In this work, we illustrate that even the knowledge of the oncogene that initiated tumorigenesis is not necessarily sufficient to identify a gene  product whose inactivation will result in tumor regression. The generation of transgenic mice with multiple conditional oncogenes is a tractable preclinical platform to define the combination of oncogenic targets most likely to be effective in the treatment of cancer.

Transgenic mice
The TetO-c-MYC and CCSP-rtTa transgenic lines generated for these experiments was described previously [15]. The Em-tTA, and K-ras4b G12D transgenic lines were kindly provided by H. Bujard (Universitä t Heidelberg, Germany), and H. Varmus (Memorial Sloan-Kettering Cancer Center, New York), respectively. Mice were mated and screened by PCR as below. MYC and/or K-ras G12D expression was activated in the CM, CR, and CMR lung lines by administering doxycycline (Sigma) to the drinking water weekly [100 mg/mL] starting at the age of 3-4 weeks. All procedures were performed in accordance with APLAC protocols and animals were housed in a pathogen-free environment.

Oncogene Inactivation
Lung mice were followed by micro-computed tomography (microCT) scans for a total of 16 weeks. Serial microCT scans were performed at 210, 26, 22, 0, 2 and 6 weeks relative to oncogene inactivation occurring at time point ''0''. Oncogenes were inactivated in the CM, CR and CMR cohorts in week 10 by removing doxycycline from the animals' drinking water. Oncogenes were inactivated in the LM, LR and LMR cohorts by injecting mice with 100 mg of doxycycline in PBS IP and adding doxycycline [100 mg/ml] to the drinking water weekly.

PCR genotyping
DNA was isolated from mouse tails using the Qiaprep DNeasy kit (Qiagen) in accordance with the manufacturer's directions. The CCSP-rtTA segment was detected using the following primers: CCSP-F 59-ACTGCCCATTGCCCAAACAC-39 and CCSP-R 59-AAAATCTTGCCAGCTTTCCCC-39 (yielding a 440 bp product). The TetO-Myc construct was detected with the following primers: Myc-F 59-TAGTGAACCGTCAGATCGCCTG-39 and Myc-R 59-TTTGATGAAGGTCTCGTCGTCC-39 (yielding a 450 bp product). TetO-K-ras G12D and Em-SR-tTA werescreened as described previously [23]. DNA was amplified using the following PCR protocol: 94uC denaturation for 2 minutes followed by 35 cycles of 94uC for 15 seconds, 59uC annealing for 30 seconds, and 72uC for 30 seconds, followed by a 5 minute extension at 72uC. PCR products were resolved on a 1.5% gel.

SYBER-green quantitative RT-PCR and RT-PCR
Total RNA was isolated from tissue using the Strataprep total RNA Miniprep Kit (Stratagene) according to the manufacturer's directions. Samples were treated with RQ1 RNase-Free DNase (Promega) and RT-PCR was performed using Superscript One- Step RT-PCR (Life Technologies) for 35 cycles with an annealing temperature of 57uC with 0.25 mg of total RNA per sample. Control reactions were run using Taq polymerase without RT enzyme (Perkin Elmer). cDNA was generated from 1 mg of total RNA using the Superscript II kit (Invitrogen Technologies). 50 mg of cDNA equivalents were amplified for the transcript described below in an ABI-prism 7700 (Perkin Elmer Applied Biosystems) for 40 cycles using SYBR green PCR Master mix (Perkin Elmer Applied Biosystems) according to manufacturer's directions. PCR reactions were performed in at least triplicate in a final volume of 20 mL. Thermal cycling conditions were: 95uC for 10 minutes, followed by 40 cycles of 95uC for 15 seconds, 57uC for 30 seconds, 72uC for 30 seconds, and a dissociation stage consisting of 95uC for 15 seconds, 60uC for 15 seconds, and 95uC for 15 seconds. Following amplification, the data was processed with the analysis program Sequence Detection Systems v2.2.2 (Applied Biosystems). For each sample, the level of RNA for the genes of interest was standardized to the level of ubiquitin within that sample; subsequently, the level of a transcript of interest was normalized to the expression of that transcript in wildtype lung. Primers for qRT-PCR were the following: transgenic K-ras exon 4b (K-ras4bfwd 5-CAAGGACAAGGTGTACAGTTATGTGACT-3) and downstream primer mp-1 pA (mp-1-real time-rev 5-GGCAT-CTGCTCCTGCTTTTG-3); endogenous K-ras4b 3UTR (K-ras-4b-UTR-fwd 5-GCAGGGTTGGGCCTTACAT-3 and K-ras-4b-UTR

Western blot analysis
Western analysis was performed using conventional techniques [66]. Tissues were disrupted and protein was isolated using a pestle and tube homogenizer in NP-40 lysis buffer. Equal protein was loaded in each lane, as quantitated by the Bicinchoninic Acid (BCA) Protein Assay (Pierce, Rockford, Illinois, United States). Proteins were electrophoresed on 10% Tris-HCl polyacrylamide gels at 100 V for 60 min and transferred on PVDF membranes at 100 V for 60 min. Blotting was then performed as directed by the antibody manufacturer. MYC protein expression was detected using the 9E10 antibody that recognizes human MYC (Santa Cruz Biotech.).

Computed Tomography
Micro-computed tomography (mCT) scans were performed on a custom GEHC (London, Ontario) RS150 cone-beam scanner, which uses a fixed anode with tungsten target source. Animals were anesthetized with 2% isofluorane in a nitrogen/oxygen mixture. Scans were performed at 97 mm resolution, using a 70 kV (40 mA) beam to acquire images at 286 radial views over 200 degrees around the subject. Four frames were exposed and averaged in each position. Data were corrected using the GEHC reconstruction utility and volumes generated using the same application, which were viewed using the GEHC Microview software.

Tumor Volume Measurements
We used the open source application, ITK-Snap, for segmentation of the lung nodules in three-dimensions [67]. The postprocessing of the segmented data provides the voxel counts and the volume (cubic millimeters) and displays the shape of the segmented structure. We calculated the volume of individual lung tumor nodules right before and 6 weeks following oncogene-inactivation. Volumes at 6 weeks were normalized relative to the volume before oncogene-inactivation and all values for a given genotype were averaged: CR, n = 11; CM, n = 8; and CMR, n = 10.
Intracellular phospho-protein detection using flow cytometry LM, LR, and LMR-lymphoma derived cell lines were treated with doxycyline in vitro. 1 million cells from each condition were fixed for 10 minutes in 1.6% paraformaldehyde at 37uC, permeabilized for 10 minutes in 100% methanol at room temperature, washed twice with PBS 1% BSA, then stained with 10 ul anti-Phospho-Stat 5: Alexa-488(BD Biosciences Pharmingen) or 10ul anti-Phospho-Stat 3: Alexa-488 (BD Biosciences Pharmingen) in 100 ul PBS 1% BSA, incubated for 30 minutes in the dark at room temperature. Finally, samples were washed once with PBS 1% BSA and then analyzed using a benchtop FACSCAN (Becton-Dickinson) flow cytometer. 10,000 ungated events were collected per sample and live cells were gated for analysis.

K-Ras mutation analysis
Total genomic DNA was harvested using DNeasy Blood & Tissue Kit (Qiagen) as directed by the manufacturer and PCR amplified using primers specific for K-Ras. PCR products were purified with a QIAquick column (Qiagen) as directed by the manufacturer and sequenced to detect point mutations at codons 12, 13, and 61.

Statistics
Survival graphs were generated by the product limit method of Kaplan and Meier and log-rank analysis was utilized for differences between proportions. Pair-wise and multiple comparisons were made using Mann-Whitney and Kruskal-Wallis nonparametric tests, respectively. Analysis was facilitated using Prism v5.0 by GraphPad. Figure S1 MYC transcriptional targets in the lung tumors. The canonical MYC transcriptional targets (A) ornithine decarboxylase (ODC) and (B) nucleolin were assayed by qRT-PCR as performed in Figure 1B. This pattern of MYC target expression supports the conditional and lung specific regulation of a functional MYC gene product in the bitransgenic CM mice. Found at: doi:10.1371/journal.pone.0002125.s001 (5.37 MB TIF) Figure S2 Lung specific co-expression of MYC and K-rasG12D transgenes in MYC/K-rasG12D mice. Genotype and lung specific expression of (A) MYC and (B) K-rasG12D transgenes were assayed by RT-PCR using cDNA templates generated from mRNA extracted from lung tumors of CM, CR and CMR mice. Minus reverse transcriptase (-RT) and water (H20) negative controls were performed concurrently. The -RT control shown was generated using the CMR mRNA.