High expression of p110α is correlated with worse treatment outcomes of neuroblastoma patients
To gain insight into the function of class IA PI3K isoforms in neuroblastoma, we analyzed the gene expression data from primary neuroblastoma samples via the R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl). We first compared the correlations between the different catalytic class IA PI3K isoforms and the neuroblastoma prognosis. The Kaplan–Meier analysis showed that high expression of PIK3CA was associated with poor overall survival in patients (Fig. 1a), while high PIK3CB or PIK3CD levels indicated more favorable overall survival probability (Fig. 1b, c). Similarly, event-free survival probability is also lower in the PIK3CA high, PIK3CB low, and PIK3CD low groups in the Kaplan–Meier analysis (Additional file 1: Fig. S1a–c). PIK3CA, indeed, was expressed at higher levels in neuroblastoma tissues than in normal tissues, including the adrenal gland (Fig. 1d). Moreover, PIK3CA expression is higher in the high-risk group than in the low-risk group (Fig. 1e). In the International Neuroblastoma Staging System (INSS)-stage stratified neuroblastoma samples, we found that higher PIK3CA expression was highly correlated to the more advanced stages (Fig. 1f).
PI3K activation in neuroblastoma cells is predominantly mediated by p110α but not by p110β or p110δ
In addition to the differential correlation of class IA PI3K isoforms with neuroblastoma patient outcomes, we tried to determine the isoform dependence of neuroblastoma to PI3Ks. The efficacy of PI3K inhibitors with distinct isoform specificity was compared in neuroblastoma cells (Fig. 2a). Considering the importance of MYCN and ALK during neuroblastoma tumorigenesis, cell lines with specific genetic alterations of MYCN and ALK have been included (Additional file 1: Fig. S2a). Five MYCN amplified cell lines (LA1-5S, IMR-32, BE(2)C, LAN-5, and KELLY) and three non-MYCN amplified cell lines (SH-SY5Y, NBL-S, and SK-N-AS) were selected to examine the cytotoxicity of different class IA PI3K inhibitors. Among these cell lines, SH-SY5Y and KELLY harbor ALKF1174L mutation, while LAN-5 carries ALKR1275Q mutant, and LA1-5s cells do not express ALK. The endogenous expression of ALK and MYCN in these cell lines was also evaluated in our assay to confirm the different levels of the two genes in the selected neuroblastoma cell lines (Additional file 1: Fig. S2b, c). MYCN is highly expressed in LAN-5, KELLY, BE(2)C, and IMR-32, while ALK is highly expressed in LAN-5, IMR-32, KELLY, NBL-S, and SH-SY5Y cell lines.
We found that copanlisib effectively inhibited cell viability of all the tested neuroblastoma cell lines (Fig. 2b). With IC50 values less than 1 µM in the cell lines, it is the most effective among the three p110α inhibitors in treating neuroblastoma cells (Additional file 1: Fig. S3). Another pan-PI3K inhibitor, pictilisib, was also cytotoxic to these neuroblastoma cell lines but less effective than copanlisib, as revealed by the inhibitory curve (Fig. 2c), despite that pictilisib treated NBL-S, IMR-32, and LA1-5s failed to reach 50% of inhibition due to its poor solubility (data not shown). Notably, cell viability of tested neuroblastoma cells could be reduced by less than 5 μM alpelisib (p110α-selective inhibitor) treatment (Fig. 2d). However, blocking p110β with TGX-221 or inhibiting p110δ with idelalisib could not affect cell proliferation of all tested neuroblastoma cell lines until the treatment concentration reached 10 μM (Fig. 2e, f), suggesting the reliance of neuroblastoma cell growth on p110α.
To further validate the inhibitory impacts of these PI3K inhibitors on neuroblastoma cells, we performed colony formation assays. Consistent with the cell viability data above, the three inhibitors targeting p110α showed potent inhibitory effects on both NBL-S and KELLY cells in colony formation (Fig. 3a–d). Alpelisib was less effective than the two pan-inhibitors, but it still reduced the cell colonies by more than 50% in the two cell lines (Fig. 3a–d). However, isoform-selective inhibitors targeting either p110β or p110δ did not apparently suppress the colony formation of NBL-S and KELLY cells (Fig. 3a–d). In addition, attenuation of p110α by the siRNAs also suppressed the growth of KELLY cells (Fig. 3e). Consistently, p110α overexpression increased cell growth in IMR-32 cells as well (Fig. 3f), confirming the specificity of p110α inhibitor treatments.
To examine whether PI3K inhibitors modulate the cell cycle of neuroblastoma cells, the cell cycle distribution was assessed upon the treatment of different inhibitors. As we expected, p110α inhibitors significantly increase the G0/G1 phase arrest in neuroblastoma cells (Fig. 3g, h). Of note, compared with the control, over 20% increase in the G0/G1 phase was induced by copanlisib treatment in NBL-S and KELLY cells (Fig. 3g, h and Additional file 1: Fig. S4b, h). The treatment of pictilisib also caused G0/G1 phase arrest in NBL-S and KELLY cells, increasing around 25% and 20% in G0/G1 proportion, respectively (Fig. 3g, h and Additional file 1: Fig. S4c, i). Similar to copanlisib and pictilisib, alpelisib caused more than 10% increment of G0/G1 phase cells (Fig. 3g, h and Additional file 1: Fig. S4d, j). Conversely, p110β or p110δ inhibitor could not affect the cell cycle in both tested cell lines (Fig. 3g, h and Additional file 1: Fig. S4e, f, k, l).
We next examined the activation of the PI3K signaling pathway under the treatment of different PI3K inhibitors. In agreement with the inhibition of neuroblastoma cell growth, the three p110α inhibitors suppressed the downstream signaling of PI3K in neuroblastoma cells (Fig. 4a–c). The activation of PI3K signaling could be largely blocked by 40 nM of copanlisib treatment in NBL-S and SH-SY5Y cells (Fig. 4a and Additional file 1: Fig. S5a, b). Pictilisib at 40 nM significantly affected the phosphorylation of both AKT and the downstream effector S6 (Fig. 4b and Additional file 1: Fig S5c, d). Alpelisib also evidently suppressed the phosphorylation of AKT and S6 at 0.2 μM (Fig. 4c and Additional file 1: Fig. S5 e, f), whereas no apparent reduction in the activation of AKT was detected upon the treatment of p110β inhibitor TGX-221 (Fig. 4d and Additional file 1: Fig. S5g, h). P110δ inhibitor idelalisib could barely inhibit the signaling pathway at concentrations less than 1.0 μM and failed to suppress the activation of the AKT at 5 μM treatment in SH-SY5Y cells (Fig. 4e and Additional file 1: Fig. S5i, j). Using siRNAs to inhibit p110α expression also downregulated the activation of AKT and S6 (Fig. 4f), suggesting the major role of p110α in PI3K signaling in neuroblastoma.
Although both pan-PI3K inhibitors (copanlisib and pictilisib) in our study were more effective than p110α selective inhibitor alpelisib in vitro, the inhibition on neuroblastoma cell growth by alpelisib was not further enhanced by either TGX-221 or idelalisib (Additional file 1: Fig. S6a, b), suggesting that p110α is the prevailing catalytic isoform in neuroblastoma cells among the class IA PI3Ks. This notion was further supported by examining the PI3K signaling pathway activation when the cells were treated by either alpelisib alone or combined with TGX-221 and idelalisib (Additional file 1: Fig. S6c).
p110α inhibitors suppress the growth of neuroblastoma xenografts
To evaluate the efficacy of the PI3K inhibitors in the treatment of neuroblastoma in vivo, neuroblastoma xenografts in BALB/c nude mice were established and treated with copanlisib or alpelisib. As expected, copanlisib significantly suppressed the growth of neuroblastoma xenografts (Fig. 5a, b) with no differences in the body weight during the treatment period (Fig. 5c), suggesting the mild toxicity of the inhibitor. Similar tumor growth inhibition could be detected when treating the mice with alpelisib (Fig. 5d–f). Furthermore, tumor cells stained positive with pH3 in copanlisib-treated or alpelisib-treated tumor samples were reduced by 41% and 22% respectively, compared with those in vehicle-treated counterparts (Fig. 5g–j), indicating the critical role of p110α in the tumor formation of neuroblastoma. In line with this observation, copanlisib and alpelisib treatment also decreased pH3 levels in the neuroblastoma xenografts (Fig. 5k–n).
p110α inhibition enhances the suppressive effects of ALK inhibitors on neuroblastoma cells
We next studied the underlying mechanisms of the growth suppression of neuroblastoma induced by these p110α inhibitors. MYCN amplification is a genetic cause of neuroblastoma, and it was reported that inhibition of the PI3K-AKT-mTOR signaling pathway could inhibit neuroblastoma growth by destabilizing MYCN [19]. We also confirmed that MYCN-amplified cell lines, such as KELLY, LA1-5s, and BE(2)C, were relatively sensitive to PI3K inhibitors (Fig. 2b–d). On the other hand, according to the survival analysis from the R2 database, in patients without MYCN amplification, high expression of PIK3CA was associated with poor outcomes (Fig. 6a). Non-MYCN amplified neuroblastoma cells (NBL-S, SH-SY5Y, and SK-N-AS) also responded to the presence of p110α inhibitors (Fig. 2b–d). These data suggested the existence of other oncogenic targets mediated by the PI3K signaling pathway in neuroblastoma.
ALK is often overexpressed or constitutively activated by gain-of-function mutations in neuroblastoma, and ALK inhibitors have been tested in clinical trial for neuroblastoma treatment. We found that expression of ALK and PIK3CA were positively correlated in neuroblastoma samples (Fig. 6b). To test whether the combination of ALK and p110α inhibitors could improve the neuroblastoma treatment, we performed cell viability assays in vitro. In our assays, the ALKwt carrying cell line NBL-S was sensitive to the first-generation ALK inhibitor (crizotinib) (IC50 value = 0.7934 μM) and the second-generation ALK inhibitor (NVP-TAE684) (IC50 value = 0.4996 μM) (Additional file 1: Fig. S7a, b). KELLY cells harbor ALKF1174L mutation (a crizotinib-resistant mutation), but they were sensitive to NVP-TAE684 (IC50 value = 0.09008 μM) (Additional file 1: Fig. S7c). In the combinatory tests, the inhibitory effects of ALK inhibitors (crizotinib and NVP-TAE684) on the growth of NBL-S cells were significantly enhanced by either alpelisib or copanlisib (Fig. 6c–f). Similarly, NVP-TAE684 also synergized with either copanlisib or alpelisib to suppress the growth of KELLY cells (Fig. 6g, h). These results provide a strong rationale for testing the combinational use of ALK and p110α inhibitors to treat neuroblastoma in the clinic.
Inhibition of PI3K activity reduced ALK by protein destabilization
PI3K-mediated signaling is one of the downstream signaling cascades upon ALK activation. We next examined whether ALK is regulated by the PI3K signaling reciprocally. As revealed in our experiments, p110α inhibitors suppressed PI3K signaling pathway and inhibited ALK expression in SH-SY5Y cells (Additional file 1: Fig. S7d, e). In a more detailed examination in NBL-S cells, ALK expression was decreased in a dose-dependent manner when treated with inhibitors of p110α but not p110β or p110δ (Fig. 6i). Similar results were obtained in BE(2)C cells expressing wild-type ALK (Additional file 1: Fig. S7f) and KELLY cells expressing oncogenic ALK mutant (Fig. 6j). Knockdown of p110α in neuroblastoma cells could also reduce ALK at the protein level (Fig. 6k–m), while overexpression of p110α upregulated ALK (Fig. 6n).
However, compared with the protein reduction in p110α-deficient NBL-S cells, the mRNA levels of ALK were only reduced in a mild manner (Fig. 7a and Additional file 1: Fig. S8a). In KELLY cells, knockdown of PIK3CA expression did not affect the ALK mRNA expression (Fig. 7b and Additional file 1: Fig. S8b). Moreover, inhibition of p110α activity using alpelisib could not downregulate ALK mRNA in KELLY cells (Fig. 7c). Consistent with previous results, the pan-PI3K inhibitor LY294002 also downregulated the ALK protein dose-dependently (Additional file 1: Fig. S9a), but no apparent decrease occurred at the mRNA levels upon the treatment of LY294002 (Additional file 1: Fig. S9b). Therefore, p110α likely affects the protein degradation rather than mRNA transcription of ALK. In cycloheximide (CHX) chase analysis of ALK degradation, the presence of copanlisib and alpelisib shortened the half-life of ALK protein significantly in NBL-S cells (Fig. 7d–g). In KELLY cells, the degradation of the ALKF1174L mutant was also enhanced upon the treatment of copanlisib and alpelisib (Fig. 7h–k). In line with these observations, ALK protein was degraded faster in the presence of LY294002 (Additional file 1: Fig. S9c, d). Consistently, the shortened half-life of ALK protein was also detected in both ALKwt (NBL-S) and ALKF1174L (SH-SY5Y) cells when p110α expression was inhibited by shRNA (Fig. 7l–o). Thus, inhibition of PI3K, at least in part, decreases ALK protein stability, and negatively attenuates the inputs of ALK oncogenic signaling (Fig. 7p).