CPZ alters pivotal signal transduction pathways in GBM cells
The genomic complexity of GBM makes it extremely difficult to predict therapeutic vulnerabilities based only on molecular analyses at a genetic level. Indeed, at a steady state and under environmental pressures, the large spectrum of genomic lesions results in the functional downstream integration of several aberrant signaling pathways in individual GBM patients. Therefore, we sought to use the RPPA to analyze the pathway-level effects of CPZ on GBM cells. To this end, we selected 49 endpoints (The list of the antibodies employed is available as raw data, see below), mainly implicated in autophagy and metabolism, and measured the effects of CPZ treatment in GBM cells in vitro.
Interestingly, consistent with the biological diversity of GBM, we found that CPZ treatment either hindered or fueled diverse targets in individual cell lines (Figure 1 and Figure S1). Nonetheless, regardless of the dose or timing of the effects produced in anchorage-dependent GBM cells and neurospheres, CPZ treatment led to increased autophagic response, i.e., increased phosphorylation of LKB1 pS428, AMPK-a pT172 and Ac-CoA Carboxylase pS79 (Figure 1A), consistent with our previous report (13), and a concomitant reduction of signaling targets involved in the PI3K–mTOR metabolic network, resulting, in particular, in an early decrease of phosphorylated AKT pT308 (2 h) and ultimately of c-Myc levels (8 h). Of note, the levels of phosphorylated AKT were substantially decreased by CPZ (Figure 1B). Finally, we found that several analyzed targets showed co-regulation patterns in a cell- and time-dependent manner, further demonstrating the complex signaling network scenario of GBM (Figure S1).
Identification of cellular factors as putative targets of CPZ in GBM
Along with RPPA, we employed ABPP+MS to intercept cellular factors as potential direct targets of CPZ in GBM cells. Experiments conducted using a kinase enrichment procedure via an insoluble ATP probe allowed us to identify, by MS analysis, the PKM2 isoform in the U-87 MG GBM cells and TS#1 neurospheres as a factor whose binding to ATP was hindered by the addition of increasing CPZ concentrations (Figure S2 A-C).
These results uncovered a potential interference of CPZ with the PKM2 isoform of PK. To validate these results, we analyzed the effects of CPZ on several cellular and molecular processes involving PKM2.
Interference of CPZ with GBM energy metabolism
Since PK is a key regulatory enzyme of the glycolytic pathway, we determined the glycolytic rate in the anchorage-dependent U-87 MG and U-251 MG GBM cell lines using the glycolytic rate acute stress test (ECAR and OCR) performed on a Seahorse XFp platform. This technology allows real-time measurement of the derivative of the amount of H+ ions released from cells, which is assumed to represent the extracellular lactate concentration. Representative graphs are shown in Figure 2. After baseline determination, cells were additioned sequentially with CPZ (red lines) or solvent for control (black lines), rotenone (which blocks ATP production from NADH oxidation) plus antimycin A (AA, a mitochondrial electron transport inhibitor) and, finally, with 2-deoxy-D-glucose (2-DG, a glycolytic poison). In all controls, rotenone plus AA elicited the glycolytic reserve, i.e., the glycolytic boost to compensate for the pharmacologically-induced collapse of ATP production. Finally, the addition of 2-DG dropped the glycolytic rate. As far as ECAR was concerned, the addition of CPZ produced a significant and immediate glycolytic impairment in the U-87 MG and U-251 MG cells, further rendering them less sensitive to the glycolytic boost induced by rotenone plus AA. On the other hand, RPE-1 neuro-epithelial non-cancer cells appeared substantially unaffected by CPZ (Figure 2A). The drug also inhibited OCR in U-87 MG and U-251 MG GBM cells, while this parameter was unchanged in the RPE-1 non-cancer cells (Figure 2B).
These results outline the ability of CPZ to swiftly interfere with ECAR and OCR in GBM cells while affecting the RPE-1 cells to a lesser extent.
CPZ increases intracellular pyruvate amount in GBM cells
Subsequently, we investigated whether the impairment in GBM lactate production elicited by CPZ was associated with a concomitant variation in the intracellular amount of pyruvate. For this purpose, we incubated GBM cells in the presence of CPZ (or vehicle for controls) for 10 min for the U-87 MG, U-251 MG and RPE-1 cells and 20 min for the TS#1 and TS#163 neurospheres. Cells were washed, lysed, and then the pyruvate amount was determined enzymatically. As a reference, in the same experimental set, cells were incubated with DASA-58, a small molecule known to act as an allosteric activator of PKM2 by inducing its tetramerization and, consequently, its enzyme activity within the glycolytic pathway, thus increasing intracellular pyruvate amount (19). Exposure to CPZ or DASA-58 significantly increased intracellular pyruvate content in all four GBM cells, whereas no significant variations were observed in RPE-1 non-cancer cells (Figure 3).
These results concerning extracellular lactate release and intracellular pyruvate amount evoke an active role of CPZ in reprogramming glucose catabolism in GBM cells, likely via an allosteric activation (tetramerization) of PKM2. Overall, a decrease in the Warburg effect could be envisaged.
CPZ decreases nuclear PKM2 amount in GBM cells
We then evaluated CPZ-dependent changes in nuclear PKM2 amounts by confocal microscopy. We measured the mean fluorescence intensity of PKM2 signal in the nuclei following 48 h CPZ treatment. Figure 4 shows representative images of anchorage-dependent U-87 MG and U-251 MG GBM cells, TS#1 and TS#163 neurospheres and RPE-1 non-cancer cells, after staining with a fluorescent anti-PKM2 MoAb (green) and with DAPI to highlight nuclei (blue), respectively. For each cell line, PKM2 and merged PKM2 + DAPI staining in control cells and CPZ-treated cells is also shown. As a functional control, cells were also treated for 24 h with 30 mM DASA-58, which, as expected (19), reduced nuclear PKM2 amount likely by inducing its tetramerization. Histograms represent the average evaluation of PKM2 nuclear content in ≥150 nuclei for CTL and CPZ and ≥80 for DASA-58-treated cells. A significant nuclear PKM2 reduction was apparent for all the cell lines after treatment with CPZ or DASA-58. Notably, RPE-1 cells displayed an overall lower amount of nuclear PKM2 in untreated cells.
Effect of CPZ on the functional role of nuclear PKM2
A. CPZ alters the transcriptional pattern downstream of nuclear PKM2.
Dimeric PKM2 can translocate into the nucleus, where it associates with various transcription factors (20, 21). PKM2 downstream transcription pattern appeared modified when GBM cells were exposed to CPZ. In detail, c-MYC transcription appeared significantly down-regulated in 4/4 (U-87 MG, U-251 MG, TS#1 and TS#163) and CCND1 in 2/4 (U-87 MG and TS#163) GBM cell lines. Being both c-MYC and CCND1 mRNA expression under direct transcriptional control of PKM2 (22, 23), these results provide a functional link between CPZ and decreased PKM2 nuclear localization. In RPE-1 cells, no significant effects were detectable (Figure 5A).
B. CPZ influences nuclear PKM2 kinase activity.
Nuclear PKM2 phosphorylates STAT3 at the Y705 residue, which in turn activates MEK5 transcription, thus promoting oncogenesis (21, 24). Although CPZ did not affect total amounts of STAT3 protein in exposed GBM cells, western blot analysis showed a significant decrease in STAT3 pY705 (Figure 5B). These results are in line with both reduced PKM2 protein kinase activity and decreased amounts of PKM2 in the nuclear compartment. In the RPE-1 cell line, STAT3 protein, though expressed, appeared undetectable in its phosphorylated form. Representative western blot analyses of STAT3 and STAT3 pY705 in control and CPZ-treated cells are shown in Figure S3.
PKM2 is a relevant target of CPZ
To further investigate the interference of CPZ with PKM2 nuclear activity, we silenced PKM2 expression in two GBM cells (U-87 MG and TS#163) and assessed its nuclear activity. As compared to control siRNA, PKM2 silencing resulted in a remarkable reduction of PKM2 protein expression in U-87 MG GBM cells, in TS#163 neurospheres and in RPE-1 non-cancer cells, as evaluated via western blotting and RT-PCR (Figure S4). Under these conditions, we exposed U-87 MG and TS#163 GBM cells, either siRNA-control or PKM2-silenced, to CPZ and assessed gene expression of CCND1, cMYC, and also the STAT3 downstream gene MEK5. While CPZ downregulated the expression of these genes in siRNA control cells, the effect of the drug was significantly lower in siRNA-PKM2 cells. CCND1, cMYC, and MEK5 transcription in RPE-1 cells was less influenced by PKM2 silencing (Figure 5C). In all evaluated cases, the expression fold-changes in PKM2-silenced cells are referred to the corresponding untreated cells.
The clear drop of CPZ-dependent effects in siRNA-PKM2 GBM cells, points to PKM2 as a major cellular target of CPZ in these cells.
CPZ binds PKM2 tetramer in the same binding pocket used by other known activators
To identify the PKM2 amino acid residues that interact with the activators in the binding pocket, we analyzed in silico all the experimental structures related to PKM2 tetramer, complexed with activators already reported in PDB, to identify the PKM2 amino acid residues interacting with the activators in the binding pocket. This analysis evidenced that each PKM2 monomer binds a fructose 1,6-bisphosphate (FBP) molecule at an allosteric site located between three amino acid regions (431-437, 482-489, 514-522). In contrast, all the synthetic activators bind to another allosteric site located at the dimer interface of PKM2 and distinct from the FBP binding site (Table S2).
Molecular docking simulations were performed as reported in Materials and Methods. The more energetically stable structure of the obtained complex showed that two CPZ molecules fit into the binding pocket of the other activators (Figure 6A). Moreover, the protein-drug interaction appeared stabilized by four hydrophobic interactions, two H-bonds, four p-stacking interactions, and a halogen bond (Figure 6B).
Indeed, by comparing our CPZ/PKM2 complex with those already reported in PDB for other compounds, we can underline that the affinity energy of our complex falls within the range of values obtained for most complexes and higher only in the case of activators composed by a larger number of atoms and functional groups. Finally, our complex has the maximum number of π-stacking interactions compared with known PDB structures, as the CPZ molecule is a polycyclic aromatic compound containing a linear tricyclic system consisting of two benzene rings joined by a para-thiazine ring (Table S3).
Therefore, these results demonstrated a specific interaction between two CPZ molecules and PKM2 and support the ability of the drug to act as a PKM2 allosteric activator.