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Cell Death and Survival

Targeting CDK1 and MEK/ERK Overcomes Apoptotic Resistance in BRAF-Mutant Human Colorectal Cancer

Peng Zhang, Hisato Kawakami, Weizhen Liu, Xiangyu Zeng, Klaus Strebhardt, Kaixiong Tao, Shengbing Huang and Frank A. Sinicrope
DOI: 10.1158/1541-7786.MCR-17-0404 Published March 2018

Abstract

The BRAFV600E mutation occurs in approximately 8% of human colorectal cancers and is associated with therapeutic resistance that is due, in part, to reactivation of MEK/ERK signaling cascade. Recently, pathway analysis identified cyclin-dependent kinase 1 (CDK1) upregulation in a subset of human BRAFV600E colorectal cancers. Therefore, it was determined whether CDK1 antagonism enhances the efficacy of MEK inhibition in BRAFV600E colorectal cancer cells. BRAFV600E colorectal cancer cell lines expressing CDK1 were sensitized to apoptosis upon siRNA knockdown or small-molecule inhibition with RO-3306 (CDK1 inhibitor) or dinaciclib (CDK1, 2, 5, 9 inhibitors). Combination of RO-3306 or dinaciclib with cobimetinib (MEK inhibitor) cooperatively enhanced apoptosis and reduced clonogenic survival versus monotherapy. Cells isogenic or ectopic for BRAFV600E displayed resistance to CDK1 inhibitors, as did cells with ectopic expression of constitutively active MEK. CDK1 inhibitors induced a CASP8-dependent apoptosis shown by caspase-8 restoration in deficient NB7 cells that enhanced dinaciclib-induced CASP3 cleavage. CDK inhibitors suppressed pro-CASP8 phosphorylation at S387, as shown by drug withdrawal, which restored p-S387 and increased mitosis. In a colorectal cancer xenograft model, dinaciclib plus cobimetinib produced significantly greater tumor growth inhibition in association with a caspase-dependent apoptosis versus either drug alone. The Cancer Genome Atlas (TCGA) transcriptomic dataset revealed overexpression of CDK1 in human colorectal cancers versus normal colon. Together, these data establish CDK1 as a novel mediator of apoptosis resistance in BRAFV600E colorectal cancers whose combined targeting with a MEK/ERK inhibitor represents an effective therapeutic strategy.

Implications: CDK1 is a novel mediator of apoptosis resistance in BRAFV600E colorectal cancers whose dual targeting with a MEK inhibitor may be therapeutically effective. Mol Cancer Res; 16(3); 378–89. ©2017 AACR.

Introduction

Colorectal cancer is the second leading cause of cancer-related mortality in the United States (1). BRAFV600E mutations are detected in 8% of human colorectal cancers where they are associated with poor prognosis and treatment resistance (2–6). To date, no effective therapeutic options are available for patients with these tumors. A subset of colorectal cancers with frequent BRAFV600E mutations display the CpG island methylator phenotype (CIMP) with epigenetic inactivation of the MLH1 mismatch repair gene and p16(Ink4a), a negative regulator of cyclin-dependent kinase 1 (CDK1; ref. 7). BRAFV600E results in constitutive activation of the MAPK pathway (8, 9). In contrast with metastatic melanoma, where BRAF inhibitors produce high rates of initial tumor response (10, 11), colorectal cancers demonstrate resistance to these inhibitors in clinical trials (2). The observed resistance is due, in part, to rebound activation of EGFR that activates downstream MAPK signaling mediated by MEK (12–16). In preclinical models, dual inhibition of BRAF and MEK produces more potent tumor growth inhibition than did monotherapy and markedly improved efficacy in patients with metastatic melanoma that led to approval of cobimetinib combined with vemurafenib by the FDA for treatment of this malignancy (17). However, dual inhibition of BRAF and MEK only modestly increased efficacy in patients with metastatic BRAFV600E colorectal cancer (18), suggesting the importance of nonredundant resistance mechanisms.

Recent data suggest that biological subdivisions exist within BRAFV600E colorectal cancers as these tumors could be separated by pathway analysis into two subtypes based on gene expression, one of which shows upregulation of CDK1 (19). CDKs are serine/threonine kinases that regulate the cell cycle by interacting with specific cell-cycle–regulatory cyclins. CDK1 is the only essential CDK (20) and functions to promote the G2–M transition and regulates G1 progression and the G1–S transition (21, 22). Unrestricted cell proliferation, one of the hallmarks of malignant tumors, is often driven by alterations in CDK activity. Altered CDK expression and/or activity is observed in many human cancers (23, 24). In addition to cell-cycle regulation, CDK1 may regulate apoptosis by caspase phosphorylation (25), including the inhibitory phosphorylation of caspase-8 shown by the Strebhardt laboratory (26). Targeting CDK1 can be achieved by the selective CDK1 inhibitor R0-3306 and the nonselective CDK inhibitor dinaciclib that is undergoing evaluation in clinical trials. Dinaciclib (formerly SCH727965) is a potent inhibitor of CDK 1, 2, 5, and 9 with 50% inhibitory concentrations in the nanomolar range (27). In preclinical studies, dinaciclib has been shown to arrest cell-cycle progression, induce activation of caspase-8, -9 and related apoptosis, and inhibit tumor growth in multiple types of cancer (17, 27–30). In addition, early-phase clinical trials have shown that this drug was well tolerated (31) and has significant single-agent activity against relapsed and refractory chronic lymphocytic leukemia (31) and multiple myeloma (32), supporting its potential for the treatment of human malignancies.

In this report, we determined the contribution of CDK1 to apoptosis resistance in BRAF-mutant colorectal cancer cells, and examined whether CDK antagonism by genetic or pharmacologic means can enhance the efficacy of MEK inhibition. We demonstrate that targeting CDK1 is an effective strategy to enhance the efficacy of MEK inhibition in mutant BRAF colorectal cancer cell lines and tumor xenografts. The relevance of CDK1 as a therapeutic target in human colorectal cancers was confirmed in The Cancer Genome Atlas (TCGA) transcriptomic datasets (33).

Materials and Methods

Cell culture, drugs, and reagents

BRAF-mutant (HT-29, RKO, VACO432 and WiDr), KRAS-mutant (DLD1, SW620), and BRAF/KRAS wild-type (DiFi) human colorectal cancer cell lines, as well as the melanoma cell line A375, were obtained from the ATCC. Isogenic RKO [A19 (BRAFV600E/−/−), T29 (BRAFWT/−/−)] and VACO432 [parental (BRAFV600E/−), VT1 (BRAFWT/−)] human colorectal cancer cell lines were obtained from Dr. B. Vogelstein [Genetic Resources Core Facility (GRCF), Johns Hopkins University, Baltimore, MD]. Neuroblastoma NB7 cell line was used. All cell lines were tested and authenticated by the ATCC using short tandem repeat analysis. Cell lines were also routinely tested for Mycoplasma contamination every 3 months with a MycoAlert Mycoplasma detection set (Lonza). For isogenic BRAF cells, GRCF uses a short tandem repeat profiling for authentication. Cells were maintained as monolayers in RPMI medium (Invitrogen, catalog no. 11875) supplemented with 10% FBS as well as 1% antibiotic–antimycotic (Invitrogen, catalog no. 15240). HEK293T cells, used for lentivirus production, were grown in high-glucose DMEM (Sigma, catalog no. D5796) with the same supplementation as above.

Cells were treated with cobimetinib (GDC-0973/XL-518; Active Biochem, catalog no. A-1180) at indicated doses and times alone or combined with R0-3306 (Sigma, SML0569) or dinaciclib (Sellekchem, catalog no. S2768) in the presence or absence of a caspase-8 inhibitor, z-IETK-FMK (R&D Systems). Drugs were dissolved in DMSO, prepared as stock solutions, aliquoted, and then stored at −20°C. Drugs were later diluted in growth medium at the time of treatment. Carrier-free human recombinant TRAIL was purchased from R&D Systems. For immunoblotting, primary antibodies included mouse anti-p16 (BD Biosciences, catalog no. 550834), mouse anti-caspase-8 (BD Biosciences, catalog no. 551242), and tubulin (Sigma, T4026). A mouse anti-p-caspase-8-s387 was produced in the laboratory of K. Strebhardt. All other antibodies were purchased from Cell Signaling Technology.

Ectopic gene expression by lentiviral and retroviral delivery

pBabePuro3-p16Flag was purchased from Addgene (#24934). Lentiviral BRAFV600Ewas described previously (34). Lentiviral constitutive MEK (ERK2–L4A–MEK1 fusion, MEKDD) was generated by subcloning cDNA fragments [pCMV-myc-ERK2-L4A-MEK1 fusion, Addgene #39197] into vector pCDH1-puro-2HA. Production in HEK293T cells and transduction of pseudo-typed lentivirus or retrovirus into target cells were performed utilizing a standard procedure, as described previously (35). A puromycin-resistant pool of cells was produced by eliminating nontransduced cells using puromycin (Sigma; catalog no. P8833) at 48 hours posttransduction.

Transfection of siRNA

CDK1 and ERK1/2 siRNA were purchased from Cell Signaling Technology (catalog no. 3500, 6560); AllStars Negative Control siRNA was obtained from Qiagen (catalog no. SI03650318). Cells were seeded 1 day before transfection in medium without antibiotics to allow 30%–50% confluence at transfection. Lipofectamine RNAi Max (Invitrogen, catalog no. 13778150) and siRNA were each diluted in Opti-MEM medium (Invitrogen). The resulting two solutions were then mixed and incubated to enable complex formation. Cells were then transfected by adding the RNAi–Lipofectamine complex dropwise to medium to achieve a siRNA concentration of 100 nmol/L. Cells were then incubated at 37°C and knockdown efficiency was examined at 48 hours posttransfection.

Apoptosis assay

Apoptosis was analyzed by Annexin V+ staining and quantified by flow cytometry as described previously (36). Briefly, cells were treated with the study drugs for a prespecified duration. After drug treatment, TrypLE Express Enzyme without phenol red (Invitrogen) was used to detach adherent cells that were then combined with floating cells. The cell pellet from centrifugation was rinsed three times in cold PBS. Then, cells were resuspended in 1× Annexin V binding solution (BD Biosciences, catalog no. 556454) and stained with Annexin V conjugated with FITC (BD Biosciences, catalog no. 556419). The proportion of Annexin V–labeled cells was quantified by flow cytometry.

Immunoblotting

Protein samples were prepared in a lysis buffer [5 mmol/L MgCl2, 137 mmol/L KCl, 1 mmol/L EDTA, 1 mmol/L EGTA, 1% CHAPS, 10 mmol/L HEPES (pH 7.5)] supplemented with a protease inhibitor cocktail and a phosphatase inhibitor cocktail 2 (both from Sigma), normalized using NanoDrop measurement (NanoDrop Technologies) or Bio-Rad protein assay (catalog no. 500-0006). Samples were denatured in LDS sample buffer (Invitrogen) supplemented with 2-Mercaptoethanol (Bio-Rad) and then loaded onto 10% or 14% SDS-PAGE gels followed by electrophoretic transfer onto a polyvinylidene difluoride membrane (Bio-Rad). The membrane was blocked with 0.2% I-Block (Applied Biosystems) in PBS-T (PBS containing 0.1% Tween 20) and incubated with the primary antibodies in PBS-T containing 0.2% I-Block overnight at 4°C or at room temperature for 3 hours. The membranes were then incubated with a secondary antibody in PBS-T containing 0.2% I-Block conjugated to alkaline phosphatase, and then developed with CDP-Star substrate (Applied Biosystems).

Clongenic assay

Cells were seeded into 6-well plates at a density of 200 cells per well. After attachment, the cells were treated with drugs for 12 hours. Drugs were removed by replacing with fresh growth medium. After incubation for 8–10 days, cells grown as colonies were visualized by fixation in 10% methanol/10% acetic acid and staining with 0.5% crystal violet in 10% methanol. Each condition was performed in triplicate. Colony area was computed using the ImageJ plugin ColonyArea (37).

Gene expression analysis

TCGA RNA-Seq and associated somatic mutation data (in VCF format) together with the metadata for 478 human colorectal cancers and 41 normal colonic tissue samples (33) were downloaded using GDC data portal (https://gdc.cancer.gov/access-data/gdc-data-portal). The VCF file was utilized to classify RNA-Seq samples from human colorectal cancers as being mutated for BRAF or KRAS or wild-type for both genes. Log transformation of normalized gene expression in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was performed. In the colorectal cancers, a Pearson correlation coefficient was computed between expression of CDK1 and p16(INK4a) genes. The R ggplot2 package was utilized for data plotting (38).

Colorectal cancer tumor xenograft model

Five-week-old male BALB/c mice were purchased from Beijing HFK Bioscience and received sterilized food and acidified water daily under pathogen-free conditions. RKO colorectal cancer cells were grown in vitro and then 106 cells (in 0.1 mL Hanks balanced solution) were injected subcutaneously into the left dorsal flanks of each mouse. When mean tumor volume reached 100–150 mm3, mice were randomly divided into four groups: vehicle (n = 8), dinaciclib (n = 8), cobimetinib (n = 8), and combination of dinaciclib plus cobimetinib (n = 8). Dinaciclib was administered as 40 mg/kg (2% DMSO/30% PEG 300/ddH2O) by intraperitoneal injection 3× per week for 3 weeks. Cobimetinib was administered by oral gavage at 15 mg/kg (5% DMSO/30% PEG 300/5% Tween 80/ddH2O) 3× per week for 3 weeks. Tumor volume and body weight were measured 3× per week postimplantation. Tumor volume was determined using the following formula: length × width2 × 0.5.

After 3 weeks of treatment, mice were euthanized and xenograft tumor tissues were immediately harvested. Tissues were divided into those snap frozen with subsequent protein extraction for immunoblotting, and those fixed in 10% neutral buffered formalin and embedded in paraffin for IHC. Five-micron-thick sections were cut and used for IHC staining performed according to the manufacturer's instructions. For IHC, primary antibodies used included rabbit anti-cleaved caspase-8, -3, and anti-Ki-67 (all from Cell Signaling Technology). All animal experiments were performed in accordance with guidelines of the Animal Care Facility of the Huazhong University of Science and Technology (Wuhan, China).

Statistical analysis

Apoptosis data in cell culture experiments derived from Annexin V data, clonogenic survival assays, and tumor volumes in murine xenograft models were expressed as mean ± SD. All cell culture experiments were performed in triplicate. Data were analyzed using the Student t test (two-tailed). A P value of <0.05 was considered statistically significant. Methods used to analyze gene expression data in human tissue samples from the TCGA datasets are described above.

Results

Dual inhibition of CDK1 and MEK enhances cell death in BRAF-mutant colorectal cancer cells

Colorectal cancers with mutant BRAF show constitutive activation of the MAPK pathway that promotes unrestricted cell proliferation (8). Rebound MAPK activation has been observed in cancer cells with BRAFV600E and is believed to represent a key mechanism of treatment resistance (12–16). In a panel of colorectal cancer cells with BRAFV600E, we observed that treatment with the MEK inhibitor cobimetinib can more potently suppress p-ERK and induce BIM and PARP cleavage compared with treatment with the BRAF inhibitor vemurafenib (Fig. 1A). Furthermore, we previously found that cobimetinib produced more sustained inhibition of downstream pERK activity than did the varamefinib, although it did not induce significant apoptosis in these colorectal cancer cells (34). Cobimetinib induced the proapoptotic BH3-only BIM protein, as has been shown for other MEK/ERK inhibitors (39), whose induction was due to suppression of ERK-mediated phosphorylation that blocks proteasome-mediated BIM degradation, as previously shown by our laboratory (40).

Figure 1.
Figure 1.

Inhibition of CDK1 enhances cell death induction by cobimetinib in BRAF-mutant colorectal cancer cells. A, A panel of BRAF mutant colorectal cancer cells and A375 melanoma cells were treated with cobimetinib (Cobi) or vemurafenib for 48 hours and expression of pERK1/2 and apoptosis-related proteins were determined by immunoblotting. Basal levels of CDK1 expression were examined in colorectal cancer cell lines with mutant or wild-type BRAF or KRAS genes. B, RKO and HT29 cells were transiently transfected with siRNA against CDK1 versus nontargeting control siRNA. After treatment with cobimetinib for 24 or 48 hours, immunoblotting using designated antibodies or Annexin V labeling was performed, respectively; *, P < 0.05. In HT29 and WiDr colorectal cancer cells with siRNA knockdown of ERK1/2, expression of CDK1, pERK1/2 and ERK1/2 was detected by immunoblotting. Tubulin was probed as a loading control. C, RKO and HT29 cell lines were treated with cobimetinib, R0-3306 (CDK1 inhibitor), or their combination for 24 hours. Cell lysates were collected and subjected to immunoblotting for pERK1/2, ERK1/2, CDK1, pH2Ax, and cleaved caspase-3 or PARP. Cells were treated with same drugs for 48 hours and apoptosis was analyzed by Annexin V labeling followed by quantification using flow cytometry; **, P < 0.002. D, Cells were seeded in 6-well plates at a density of 200 cells per well and allowed to attach overnight. Cells were then treated with designated drugs for 12 hours followed by replacement of media and continued incubation for 8–10 days. Colonies were stained and a percentage of colony area was quantified (see Materials and Methods). Results represent mean ± SD from triplicate experiments (*, P < 0.02; **, P < 0.005).

Recent data indicate that many BRAF-mutant colorectal cancers show cell-cycle dysregulation with upregulation of CDK1 (19). We detected abundant CDK1 expression in multiple human colorectal cancer cell lines, including those with BRAFV600E (Fig. 1A). To investigate whether CDK1 can confer apoptosis resistance, we determined whether CDK1 inhibition can enhance cobimetinib-induced apoptosis in BRAFV600E colorectal cancer cells. To test this hypothesis, we performed gene knockdown of CDK1 by siRNA that was shown to increase cobimetinib-induced cleavage of PARP, caspase-3, and double-strand DNA damage (pH2Ax) concurrent with enhanced Annexin V labeling compared with control siRNA cells (Fig. 1B). Addition of the selective CDK1 inhibitor RO-3306 to cobimetinib was shown to enhance apoptosis induction shown by cleavage of PARP, caspase-3, and an increase in pH2Ax that was accompanied by increased Annexin V labeling in RKO and HT29 cell lines (Fig. 1C). The effect of the drug combination on long-term cell viability was examined by clonogenic survival assay. The combination of R0-3306 and cobimetinib suppressed colony formation to a greater extent compared with either drug alone (Fig. 1D). Interestingly, cobimetinib suppressed CDK1 expression (Fig. 1B and C) that was due to MEK/ERK inhibition shown clearly in WiDr cells with knockdown of ERK (Fig. 1B). Together, these results indicate that CDK1 inhibition can significantly enhance cobimetinib-induced apoptosis in BRAF-mutant colorectal cancer cell lines.

We also examined the ability of the CDK inhibitor dinaciclib to enhance apoptosis induction by cobimetinib in BRAFV600E colorectal cancer cells. The combination of dinaciclib with cobimetinib enhanced caspase-3 cleavage, induced pH2Ax, and increased the proportion of RKO cells undergoing apoptosis in a dose-dependent manner (Fig. 2A). While cobimetinib or dinaciclib monotherapy reduced colony formation, the drug combination did so to a greater extent in both RKO and HT29 cell lines. Specifically, the colony area formed by cells treated with the drug combination was reduced by approximately 50% compared with either drug alone (Fig. 2B and C).

Figure 2.
Figure 2.

Dinaciclib enhances cobimetinib-induced cell death in BRAF-mutant colorectal cancer cells. A, RKO cells were treated with increasing doses of dinaciclib (Dina) alone or combined with cobimetinib for 24 hours. Immunoblotting was performed for detection of PARP and caspase-3 cleavage as well as DNA double-strand breaks using pH2Ax. Treatment-induced apoptosis was analyzed by Annexin V labeling; **, P < 0.003. B and C, Clonogenic survival was determined in RKO and HT-29 cells that were treated with dinaciclib, cobimetnib, or their combination for 12 hours. Colony percent area was then quantified and results are shown as mean ± SD from triplicate experiments; **, P < 0.006.

Mutant BRAF–mediated MEK/ERK activation attenuates apoptosis induction by CDK inhibitors

Dual inhibition of CDK1 and MEK/ERK signaling cooperatively enhanced apoptosis induction (Figs. 1 and 2), suggesting that these two pathways act interdependently to confer apoptosis resistance. Ectopic expression of mutant BRAF or constitutively active MEK each increased MEK/ERK signaling indicated by increased pERK expression, and attenuated dinaciclib-induced DNA damage (pH2Ax), cleavage of caspase-3 and PARP (Fig. 3A), and apoptosis shown by Annexin V labeling (Fig. 3B). Using isogenic cells that differ only in number of mutant BRAF alleles, we found that RKO cells with one (A19) or two copies (RKO parental) of mutant BRAF (vs. WT allele only, T29) conferred resistance to R0-3306, as shown by attenuation of pH2Ax and cleaved caspase-3 and PARP (Fig. 3C). Together, these data support the strategy of dual targeting of CDK1 and MEK/ERK pathways to overcome BRAF-mediated apoptosis resistance.

Figure 3.
Figure 3.

BRAFV600E or constitutively active MEK/ERK confer resistance to apoptosis induction by CDK inhibitors. A, BRAFV600E or a fusion of MEK1–ERK2 (ERK2-L4A-MEK1) versus empty vector was ectopically expressed in VACO432 VT1 cells. Cells were exposed to dinaciclib or vehicle for 24 hours and then probed for cleavage of caspase-3 and PARP as well as pH2Ax by immunoblotting. B, Cells were treated with vehicle or dinaciclib at the indicated doses (24 hours) and apoptosis induction was examined by Annexin V labeling. C, Isogenic RKO colorectal cancer cell lines that differ in number of mutant BRAF alleles [parental (BRAFV600E/V600E/WT), A19 (BRAFV600E/−/−), and T29 (BRAFwt/−/−)] were treated with RO-3306 versus vehicle for 48 hours. Cell lysates were prepared and then probed with antibodies against CDK1, pERK1/2, ERK1/2, pH2Ax, and cleaved PARP and caspase-3 by immunoblotting.

Caspase-8 mediates apoptosis induced by inhibition of CDK1 and MEK/ERK signaling

Caspase-8 is a key cell death regulator and procaspase-8 is known to be regulated during the cell cycle through the inhibitory action of CDK1/cyclin B1 (41). We determined whether inhibition of MEK/ERK signaling can activate caspase-8. Cobimetinib treatment inhibited pERK expression that was associated with an increase in caspase-8 cleavage and pH2Ax expression in HT29 and WiDr colorectal cancer cell lines (Fig. 4A). Similar promotion of caspase-8 cleavage and DNA damage were found in untreated cells with ERK1/2 siRNA (Fig. 4A), which also suppressed CDK1 (Fig. 1B). Given that CDK1 was shown to phosphorylate caspase-8 at S387 (p-C8-S387; ref. 41), we tested the ability of CDK1 inhibitors to reduce this inhibitory phosphorylation event. Because the basal level of p-C8-S837 is difficult for detection, we performed drug withdrawal experiments. Withdrawal of R0-3306 or dinaciclib was each shown to upregulate p-C8-S387 expression that was accompanied by restoration of mitosis (shown by pH3S10; Fig. 4B). These findings suggest that CDK1 inhibitors can induce apoptosis by reducing caspase-8 phosphorylation. The ability of caspase-8 to mediate dinaciclib-induced apoptosis was confirmed by ectopic caspase-8 expression in caspase-8–deficient NB7 cells that was shown to increase both dinaciclib- and TRAIL-induced caspase-3 and PARP cleavage (Fig. 4C). Further support for the dependence of apoptosis on caspase-8 activation was achieved using the caspase-8 inhibitor, Z-IETD-FMK, that attenuated apoptosis (Annexin V+ cells) induced by dinaciclib ± cobimetinib (Fig. 4C). Similarly, Z-IETD-FMK reduced DNA damage, cleavage of caspase-8 and -3, and attenuated Annexin V+ labeling induced by the combination of R0-3306 plus cobimetinib in colorectal cancer cells (Fig. 4D).

Figure 4.
Figure 4.

Caspase-8 mediates apoptosis induced by inhibition of CDK1 and MEK/ERK signaling. A, MEK/ERK signaling was suppressed in HT29 and WiDr colorectal cancer cells by increasing doses of cobimetinib for 24 hours or by siRNA knockdown of ERK1/2 (48 hours). Detection of pERK1/2, ERK1/2, cleaved caspase-8, or pH2Ax was performed by immunoblotting. B, RKO cells were treated with RO-3306 (5 μmol/L) or dinaciclib (12.5 nmol/L) for 16 hours. The drug was then withdrawn and cells allowed to incubate in drug-free media for indicated times (0–3 hours). Phosphorylation of procaspase-8 at S387(p-C8-S387) and phosphorylation of the mitotic marker histone H3 at Ser10 (pH3S10) were then probed by immunoblotting. Caspase-8–deficient NB7 cells were used as a negative control for procaspase-8. C, Caspase-8 was reconstituted in caspase-8–deficient NB7 cells by ectopic expression. NB7 cells were then treated with TRAIL or dinaciblib for 24 hours and probed for cleavage of caspase-8, caspase-3, PARP, and expression of pH2Ax. Apoptosis induction by cobimetinib ± dinaciclib versus vehicle was analyzed by Annexin V staining in the presence or absence of the caspase-8 inhibitor, z-IETD-fmk (**, P < 0.002). D, HT29 and WiDr cells were treated with vehicle, cobimetinib (5 μmol/L), RO-3306 (5 μmol/L), or their combination for 48 hours in the presence/absence of z-IETD-fmk. Expression of designated proteins was examined in cell lysates by immunoblotting. Annexin V staining was performed to determine the effect of RO-3306 plus cobimetinib on apoptosis in the presence or absence of z-IETD-fmk (**, P < 0.002).

Combination of dinaciclib and cobimetinib enhance tumor growth inhibition in vivo

To evaluate the efficacy of our combinatorial strategy in vivo, we generated murine xenograft models using the BRAF-mutant RKO colorectal cancer cell line. Treatment of mice with intraperitoneal dinaciclib or oral cobimetinib was shown to significantly suppress tumor growth compared with vehicle. Furthermore, the drug combination was shown to inhibit tumor growth to a significantly greater extent compared with dinaciclib or cobimetinib (Fig. 5A and B). Drugs were well tolerated by the mice as indicated by the lack of significant changes in body weight of the mice in each group during the experimental period. Tumor growth inhibition in the xenograft model was accompanied by induction of apoptosis that was enhanced by the drug combination compared with monotherapy, as shown in tumor tissues analyzed by immunoblotting and IHC. Specifically, we observed an increase in cleaved caspase-8, -3, and PARP as well as increased pH2AX proteins in tumors treated with dinaciclib plus cobimentib compared with single drugs as shown by immunoblotting (Fig. 5C). Furthermore, IHC staining of tumor xenografts demonstrated cleavage of caspase-8 and -3 and inhibition of the cell proliferation marker Ki-67 in mice treated with the drug combination compared with monotherapy (Fig. 5D). Together, these results confirm our in vitro findings and suggest that cooperative apoptosis induction is a key mechanism of the antitumor effect of dual CDK1 and MEK inhibition.

Figure 5.
Figure 5.

Effect of cobimetinib plus dinaciclib on tumor growth in the RKO colorectal cancer xenograft model. A, Isolated tumor tissue size (left) and tumor volume measurements (right) are shown at termination of treatment (day 20) for each drug and vehicle control (n = 8 mice; *, P < 0.05). B, Tumor volume growth curve for mice treated with study drugs versus vehicle over time (days; *, P < 0.05). C, Immunoblot of representative tissue lysates prepared from fresh tumor tissues for each experimental group were analyzed for cleavage of caspase-8, caspase-3, PARP, and expression of p-ERK1/2, total ERK1/2 and pH2Ax. GAPDH served as protein loading control. D, Representative images of tumor tissues from drug- versus vehicle-treated mice were immunostained for cleaved caspase-8, caspase-3, Ki-67, and hematoxylin and eosin (H&E).

CDK1 is upregulated in human colorectal cancers

A schematic diagram shows the proposed mechanism by which CDK1 inhibition can antagonize inhibitory caspase-8 phosphorylation to promote apoptosis that is attenuated by BRAFV600Ein human colorectal cancer cells. Combined inhibition of CDK1 and MEK/ERK were shown to cooperatively enhance apoptosis induction in BRAFV600Ecolorectal cancer cells (Fig. 6A).

Figure 6.
Figure 6.

CDK1 mRNA expression in human colorectal cancers versus normal colonic tissue. A, Schematic diagram of proposed mechanism by which CDK1 promotes inhibitory caspase-8 phosphorylation and together with BRAFV600E signaling, confers resistance to apoptosis that can be reversed by combined inhibition of CDK1 and MEK/ERK. B,CDK1 gene expression data were extracted from TCGA RNA-Seq datasets for human colorectal cancers (N = 478) and compared with expression levels in normal colonic tissues (N = 41); P = 8.61925E−18. C, Colorectal cancer tissue samples were categorized based on mutant BRAF (N = 49), mutant KRAS (N = 177) or wild-type (WT) copies of both genes (N = 225) using associated metadata. CDK1 expression was then compared among these three colorectal cancer subgroups; P > 0.6. D, Association of CDK1 and p16(INK4a) expression were analyzed by linear regression and a Pearson correlation coefficient was computed (r = −0.19, P = 3.548e-05). E, CDK1 expression was compared in RKO cells with ectopic retroviral p16 expression versus empty vector. CDK1 expression was also compared in VACO432 VT1 [BRAFWT/−] cells with ectopic BRAFV600E versus empty vector, and in parental (BRAFV600E/V600E/WT) or isogenic RKO cells with a mutant [A19 (BRAFV600E/−/−)] or wild-type BRAF allele [T29 (BRAFwt/−/−)]. In these cells, MAFG and pERK expression were also probed.

To establish CDK1 as a relevant therapeutic target in human colorectal cancers with mutant BRAF, we used public RNA-Seq datasets from TCGA to examine CDK1 gene expression. CDK1 mRNA was found to be significantly overexpressed in human colorectal cancer versus normal colonic tissue (Fig. 6B). As shown by normalized and log-transformed FPKM (log-FPKM], we found that the mean log-RPKM was approximately 3 in tumor compared with approximately 1.5 in normal colonic tissue. Similar levels of CDK1 expression were found among colorectal cancers with mutant versus wild-type copies of BRAF or KRAS genes (Fig. 6C). CDK1 expression has been shown to be negatively regulated by p16 at the posttranscriptional level by interaction of miR-410 or miR-650 with CDK1-3′UTR (42). p16(INK4a), which blocks cell-cycle progression from G1 to S phase, is epigenetically silenced along with MLH1 in colorectal cancers with CIMP (7). Consistent with this finding, we observed a negative correlation between the expression of p16(INK4a) and CDK1 (r, −0.19, P < 0.001) in TCGA datasets (Fig. 6D). To confirm this regulation, we ectopically expressed retroviral p16(INK4a) into RKO human colorectal cancer cells and observed reduced CDK1 protein expression (Fig. 6E). Consistent with our analysis of TCGA datasets, we found that neither ectopic BRAFV600E nor presence of mutant BRAFV600E alleles in isogenic RKO cells altered CDK1 expression, although pERK and the transcription factor MAFG were upregulated by mutant BRAF (Fig. 6E) consistent with published reports (7). MAFG is a transcriptional repressor that has been identified as a key factor required for MLH1 silencing and CIMP in colorectal cancers harboring BRAFV600E (7).

Discussion

Combined treatment with inhibitors of both BRAF and MEK only modestly improved response rates in patients with colorectal cancer (18), suggesting the need to target other pathways. Recent pathway analysis identified two subtypes of BRAFV600E human colorectal cancers, one of which shows prominent cell-cycle dysregulation (19). Using colorectal cancer cells lines with BRAFV600E that express CDK1, we made the novel observation that CDK1 can confer apoptosis resistance and that antagonism of CDK1 by genetic or pharmacologic means can significantly and cooperatively enhance apoptosis induction by cobimetinib that was also shown in long-term clonogenic survival assays. Interestingly, cobimetinib suppressed CDK1 expression due to its ability to inhibit MEK/ERK signaling as shown by ERK1/2 knockdown by siRNA. Dual inhibition of CDK1 and BRAF-mediated MEK/ERK signaling were required for effective tumor cell death given that cells with isogenic BRAFV600E versus wild-type alleles conferred resistance to cobimetinib-induced DNA damage and apoptosis in a gene dose-dependent manner. Ectopic BRAFV600E or constitutively active MEK were also shown to confer resistance to apoptosis induction by CDK inhibitors. These in vitro data demonstrate that a combinatorial strategy that targets both CDK1 and MEK signaling can overcome apoptosis resistance and, thereby, achieve tumor cell death in BRAF-mutant colorectal cancer cells. To demonstrate the clinical relevance of this strategy, we generated a murine tumor xenograft model of BRAFV600E colorectal cancer whereby the combination of dinaciclib and cobimetinib were shown to significantly suppress tumor growth to a greater extent than did either drug alone. Consistent with our in vitro findings, the drug combination induced a caspase-dependent apoptosis, including caspase-8 cleavage, in tumor xenografts that was enhanced compared with monotherapy. The relevance of CDK1 in the clinical behavior of human colorectal cancers has been shown by the finding that a high CDK1 nuclear to cytoplasmic expression ratio was associated with poor overall survival and was an independent risk factor for outcome (43). Further support for the use of dinaciclib in the treatment of refractory solid tumors, including those with mutant KRAS, derives from the finding that its combination with the pan-AKT inhibitor MK-2206 can strongly suppress tumor growth in murine orthotopic and patient-derived xenograft models of human pancreatic cancer (44).

The mechanism by which CDK1 inhibitors can induce apoptosis is unknown; however, it has been shown that procaspase-8 is phosphorylated by CDK1/cyclin B1 on Ser-387 in cancer cell lines (41). Our data demonstrate that caspase-8 is a key mediator of cell death induction by the CDK1 inhibitors RO-3306 or dinaciclib. Caspase-8 is a key effector of cell death, particularly through the death receptor (DR)–mediated apoptotic pathway (45), although it can be activated independent of DRs as shown for paclitaxel (46). Although inhibition of caspase-8 attenuated apoptosis in response to combined targeting of CDK1 and MEK/ERK, this partial effect suggests that additional mechanisms besides caspase-8 signaling are likely to contribute. Our finding that withdrawal of R0-3306 or dinaciclib restored procaspase-8 phosphorylation at S387 is consistent with the ability of CDK1 to inhibit apoptosis by phosphorylation of procaspase-8. This event occurred in association with increased cell mitosis that is known to be regulated by CDK1 (47). Confirmation of the ability of caspase-8 to mediate dinaciblib-induced apoptosis was shown by reexpression of caspase-8 in caspase-8–deficient NB7 cells. Moreover, treatment of colon cancer xenografts with the combination of dinaciclib and cobimetinib promoted caspase-8 cleavage. Together, these data indicate the importance of caspase-8 activation in mediating cell death induction by CDK1 antagonists alone or in combination with cobimetinib.

We found that CDK1 was frequently overexpressed in human colorectal cancers relative to normal colonic tissues from TCGA datasets that was not limited to the BRAF-mutant subtype. However, ectopic BRAFV600E conferred resistance to apoptosis induced by CDK1 inhibitors that was further shown to be gene dose-dependent in BRAFV600E isogenic cells. These data indicate that CDK1 is a therapeutic target in human colorectal cancer and the susceptibility to CDK1 inhibition is regulated by mutant BRAF, which supports the rationale for the combinatorial strategy of targeting CDK1 and BRAF-mediated MEK/ERK signaling in BRAF-mutant colorectal cancer. Given that KRAS-mutant colorectal cancers also show aberrant activation of MEK/ERK signaling, the drug combination holds promise in this tumor subtype. We found a negative correlation between expression of CDK1 and p16(Ink4a) in TCGA datasets. CDK1 is known to be negatively regulated by p16 (42), and we confirmed that ectopic p16 can suppress CDK1 expression in BRAF-mutant colorectal cancer cells. Ectopic BRAFV600E did not increase CDK1 expression but was able to upregulate MAFG, a transcriptional repressor and target of CIMP that is frequently detected in colorectal cancers with mutant BRAF and deficient DNA mismatch repair (7).

In conclusion, we identify CDK1 as a novel mediator of apoptosis resistance in BRAF-mutant colorectal cancer cells whose antagonism by CDK1 inhibitors, including dinaciclib, was shown to significantly enhance the efficacy of cobimetinib both in vitro and in vivo that was shown to be mediated, in part, by caspase-8 activation. Mutant BRAF is a negative regulator of susceptibility to CDK1 inhibitors that supports combined inhibition of CDK1- and BRAFV600E-mediated MEK/ERK signaling in this tumor subtype. Frequent CDK1 overexpression in human colorectal cancers suggests its relevance as a therapeutic target. Taken together, our data support a novel combinatorial strategy to inhibit CDK1 and MEK for the treatment of BRAF-mutant colorectal cancer.

Disclosure of Potential Conflicts of Interest

F.A. Sinicrope is a consultant/advisory board member for Hoffmann La Roche. No potential conflicts of interest were disclosed by the other authors.

Authors' Contributions

Conception and design: P. Zhang, H. Kawakami, S. Huang, F.A. Sinicrope

Development of methodology: P. Zhang, H. Kawakami, W. Liu, K. Strebhardt, S. Huang, F.A. Sinicrope

Acquisition of data (provided animals, acquired and managed patients, provided facilities, etc.): P. Zhang, W. Liu, X. Zeng, K. Tao, S. Huang, F.A. Sinicrope

Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis): P. Zhang, H. Kawakami, W. Liu, K. Tao, S. Huang, F.A. Sinicrope

Writing, review, and/or revision of the manuscript: P. Zhang, H. Kawakami, K. Strebhardt, S. Huang, F.A. Sinicrope

Administrative, technical, or material support (i.e., reporting or organizing data, constructing databases): H. Kawakami, S. Huang, F.A. Sinicrope

Study supervision: S. Huang, F.A. Sinicrope

Acknowledgments

This study was supported, in part, by National Cancer Institute grant R01 CA210509 (to F.A. Sinicrope). Additional support was obtained from the National Natural Science Foundation of China (#81572413 to K.T, #81702386; to P. Zhang). P. Zhang was supported by the Scientific Research Training Program for Young Talents of Wuhan Union Hospital, PRC; his current address is Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

The authors express their gratitude to Mr. Matthew A. Bockol for downloading TCGA data.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

  • Received July 25, 2017.
  • Revision received October 13, 2017.
  • Accepted November 14, 2017.

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Targeting CDK1 and MEK/ERK Overcomes Apoptotic Resistance in BRAF-Mutant Human Colorectal Cancer
Peng Zhang, Hisato Kawakami, Weizhen Liu, Xiangyu Zeng, Klaus Strebhardt, Kaixiong Tao, Shengbing Huang and Frank A. Sinicrope
Mol Cancer Res March 1 2018 (16) (3) 378-389; DOI: 10.1158/1541-7786.MCR-17-0404
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