GPX4 is a potential therapeutic target in AML and has possible prognostic relevance
To evaluate the therapeutic potential of targeting ferroptosis-regulating genes including GPX4 in a variety of cancer cell lines, we analyzed Cancer Dependency Map (DepMap) datasets using shinyDepMap [22], a tool that combines CRISPR and shRNA screening data of 423 cancer cell lines. This tool enabled us to predict the essentiality of genes of interest across cancer cell lines as well as the selectivity of the gene essentiality among distinct cell types. In particular, we investigated ferroptosis suppressor genes annotated on FerrDb, a manually curated database of ferroptosis regulators and their disease associations [23] [24] (FerrDb V2, last access; 8/13/2022). GPX4 was the second-ranked gene with the high essentiality among the top 10 ferroptosis suppressors (efficacy score; X = -1.21), following MTOR as the top (X = -1.454) (Fig. 1A). In addition, the selectivity of GPX4 (selectivity score; Y = 0.799) was much higher than that of MTOR (Y= 0.076), indicating that the essentiality of GPX4 is more cell line–specific. Importantly, when the cell lines were grouped by tumor type, AML was among those that are highly dependent on GPX4 (Fig. 1B). Of note, consistently, MTOR exhibits high dependency not only in AML but more prominently in other tumor types (Fig. S1A). These analyses suggest that targeting GPX4 may have specific roles in AML.
We next evaluated the potential impact of GPX4 on the survival of AML patients, utilizing a dataset from The Cancer Genome Atlas (TCGA), and found that high GPX4 expression was associated with shorter patient survival (Fig. 1C and Fig. S1B–D). A multivariate Cox proportional hazard model adjusted for age, gender, and cytogenetic risk groups also revealed a significant association between higher GPX4 expression and shorter survival (Fig. 1D). These results are consistent with previous reports [25] [26] and suggest GPX4 as a novel prognostic factor in AML patients.
GPX4 inhibition induces ferroptosis in AML cells in vitro and in vivo
To test the anti-leukemia effects of the pharmacological inhibition of GPX4, we utilized ML210 [27, 28], to date a well-established, proteome-wide specific inhibitor of GPX4. Protein expression levels of GPX4 were determined and found variable among 11 AML cell lines (Fig. 2A). Next, we determined GPX4 inhibition–induced cell death as the percentage of cells positive for annexin V and/or DAPI to capture both apoptotic and non-apoptotic cell death including ferroptosis. In OCI-AML3 cells, ML210 increased both, annexin V–positive and DAPI-positive fractions, which were effectively suppressed by the lipophilic antioxidants liproxstatin-1 (Lip1) and a-tocopherol (aToc) as well as the iron chelator deferoxamine (DFO) (Fig. 2B). These data indicate that, although annexin V is usually used as a marker of apoptosis, annexin V–positive AML cells that result from GPX4 inhibition are ferroptotic. This is consistent with previous findings demonstrating that lipid peroxidation upon ferroptosis can cause phosphatidylserine externalization without caspase activation [29]. Consequently, the pan-caspase inhibitor z-VAD-FMK did not inhibit ML210-induced cell death (Fig. 2C and Fig. S2A, B). Lip1, aToc, and DFO consistently suppressed ML210-induced lipid peroxidation, which was detected with C11-BODIPY (Fig. 2D). The iron-dependent lipid peroxidation and cell death induced by ML210 were confirmed in MOLM-13 and OCI-AML2 cells as well (Fig. S2C-F).
Next, we evaluated the efficacy of ML210 across 11 AML cell lines. Sub-micromolar concentrations of ML210 induced cell death in most cell lines (Fig. 2E). Pearson correlation analysis revealed a negative correlation between ML210 sensitivity and GPX4 protein expression level (Fig. 2F), which suggests that GPX4 expression levels are potential predictors of AML cell sensitivity to GPX4 inhibition. To further assess the effects of endogenous GPX4 level on ferroptosis, we supplemented cell culture media with selenium to enhance GPX4 biosynthesis. Supplementing culture media with seleno-L-methionine (SLM) increased GPX4 expression levels in OCI-AML3 and MOLM-13 cells (Fig. S2G). We further generated Doxycycline (Dox)-inducible short hairpin RNA (shRNA) constructs to knockdown eukaryotic elongation factor, selenocysteine-tRNA specific (EEFSEC), which is required for selenoprotein translation [30]. The Dox-induced knockdown of EEFSEC abrogated SLM-induced GPX4 upregulation (Fig. S2H), confirming that GPX4 upregulation occurs through increased protein synthesis of GPX4. As expected, AML cells cultured in SLM-supplemented media are resistant to ML210 (Fig. S2I).
We also assessed ML210 sensitivity in TP53-mutant AML cell lines, which served as an in vitro model of one of the most clinically challenging genetic subtypes of AML. ML210 exerted its anti-leukemia effects independently of TP53 mutational status, as it had similar efficacy among isogenic MOLM-13 cells with TP53 deletion or hotspot mutations (Fig. 2G). The knockdown of mutant TP53 in Kasumi-1 cells harboring the TP53R248H mutation did not alter sensitivity to ML210 (Fig. 2H). Taken together, ML210 exerts anti-leukemia effects independently of TP53 mutation status.
We then treated primary cells derived from AML patients (n = 13) or healthy bone marrow donors (n = 12) with ML210. AML patients included those who relapsed after or developed resistance to multiple regimens and/or those with TP53 mutations (Table S1). Most of the primary AML samples tested were sensitive to ML210 (Fig. 2I and S2J). Three samples showed resistance to ML210, but we could not identify any common features explaining the resistance, including prior regimens, cytogenetics, or mutations. Independently, cell death induced in primary cells from healthy bone marrow donors (HD) was significantly lower than that induced in patient samples.
We next introduced Dox-inducible shRNAs targeting GPX4 (shGPX4) into OCI-AML3 cells (OCI-AML3-shGPX4-1 or -2 cells) (Fig. 3A). Treatment with Dox for 96 hours resulted in lipid peroxidation, followed by cell death induction at 120 hours (Fig. 3B, C and Fig. S3A), demonstrating that GPX4 downregulation induces lipid peroxidation prior to the cell death. The findings were confirmed in MOLM-13 cells and OCI-AML2 cells transfected with the same shRNAs (Fig. 3D, E and Fig. S3B, C). In addition, GPX4 knockdown sensitized OCI-AML3-shGPX4-1 and -2 cells to ML210 at a dose that were not effective by itself (Fig. 3F), consistent with the aforementioned negative correlation between GPX4 protein expression and sensitivity to GPX4 inhibition.
To determine the anti-leukemia effect of GPX4 inhibition in vivo, we labeled OCI-AML3-shGPX4-2 cells with luciferase and transplanted them into NSG mice. After engraftment was confirmed by bioluminescent imaging (BLI) (Fig. S3D), the mice were given regular water (vehicle) or tetracycline water to knockdown GPX4 in leukemia cells. Tetracycline treatment significantly prolonged mouse survival (median survival 74 days vs 55 days), confirming that GPX4 inhibition exerts anti-leukemia effects in vivo (Fig. 3G).
Cell death induced by GPX4 knockdown was abrogated by Lip1 and aToc but not by DFO (Fig. S3E-F), likely because of the low concentration of DFO used in these assays. The maximal tolerable dose of DFO in AML cell lines (4 µM for OCI-AML3 cells) (Fig. S3G) was much lower than those used in previous studies of ferroptosis in cancers other than leukemia (up to 100 µM) [6, 31]. Thus, the inherent anti-leukemia effects of DFO present a limitation in determining the protective effects of iron chelation against GPX4 inhibition–induced ferroptosis in AML cells. In fact, Lip1 completely blocked cell death induced by a high concentration (>20 times the EC50) of ML210, whereas DFO did not (Fig. S3H), suggesting that low-dose DFO blocks ferroptosis less efficiently than Lip1 does. Indeed, lipid peroxidation in OCI-AML3-shGPX4 cells (Fig. 3B, Fig. S3A) was more potent than that induced by ML210 in OCI-AML3 cells (Fig. 2D). Therefore, we speculate that the degree of ferroptosis induced by GPX4 inhibition in our genetic knockdown models was greater than that which could be rescued by low-dose DFO.
Mitochondrial lipid peroxidation and electron transport chain complexes regulate AML cell ferroptosis
Because mitochondria are the centers of cellular redox and iron metabolism, we next investigated the involvement of mitochondria in AML cell ferroptosis. Morphologically, evaluation by transmission electron microscopy showed that, compared with control cells, ML210-treated OCI-AML3 cells had smaller mitochondria with an electron-dense mitochondrial matrix (Fig. 4A). This is consistent with previous ferroptosis studies in non-leukemia models [6, 32]. ML210-treated OCI-AML3 cells also had disorganized cristae with “vesicular” morphology, a phenomenon similar to the finding reported to occur during apoptosis induction in HeLa cells [33]. Functionally, ML210 increased mitochondrial superoxide production, which was largely blocked by Lip1, aToc, and DFO, in AML cells (Fig. 4B, C, Fig. S4A, B). This suggests that the mitochondrial superoxide induced by GPX4 inhibition is mostly iron-dependent lipid peroxidation. Indeed, flow cytometry with MitoPerOx staining, which specifically detects lipid peroxidation in mitochondria, revealed that ML210 consistently increased mitochondrial lipid peroxidation (Fig. 4D). Dox-induced GPX4 knockdown also increased mitochondrial superoxide production and lipid peroxidation in OCI-AML3 cells (Fig. 4E and Fig. S4C) and MOLM-13 cells (Fig. S4D).
A previous study using mouse embryonic fibroblasts (MEFs) demonstrated that the mitochondria-targeting antioxidant mitoquinone mesylate (MitoQ) is far less potent than the non-targeting antioxidant decylubiquinone (DecylQ) in protecting cells from GPX4 inhibition–induced ferroptosis [34]. This suggests that ferroptosis usually arises from a redox imbalance in cytoplasm but not in mitochondria. We confirmed that the concentration of MitoQ required to block ML210-induced cell death was more than 5-fold that of DecylQ in MEFs (Fig. 4F). In contrast, and unexpectedly, MitoQ was as potent as DecylQ in blocking ferroptosis in OCI-AML3 cells treated with ML210 (Fig. 4G), suggesting that AML cell ferroptosis is regulated predominantly by mitochondrial, rather than cytoplasmic, lipid peroxidation. In addition to MitoQ, MitoTEMPO, another mitochondria-targeted antioxidant, also blocked cell death caused by ML210 treatment or by Dox-induced GPX4 knockdown, further supporting the mitochondrial regulation of ferroptosis in AML cells (Fig. 4H, I and Fig. S4E, F).
Next, to investigate the role of mitochondrial respiration, the center of mitochondrial redox metabolism, in AML cell ferroptosis, we utilized HL-60-Rho0 cells, which were established by chronically exposing HL-60 cells to ethidium bromide to specifically deplete mitochondrial DNA and thus render them deficient of mitochondrial respiration [35]. Immunoblot analysis revealed that Rho0 cells had non-detectable levels of electron transport chain (ETC) complex proteins (subunits in complexes I, II, III, and IV) but unchanged levels of GPX4 expression (Fig. 4J). Both mitochondrial DNA–encoded proteins (UQCRC2 and MTCO1) and nuclear DNA–encoded proteins (SDHB and NDUFB8) were depleted in Rho0 cells, which indicates that the loss of mitochondrial DNA–encoded ETC subunits results in defects across the complexes. This is supported by a recent report of proteome-wide analysis of 143B-Rho0 cells [36]. Notably, HL-60-Rho0 cells are nearly 10 times as sensitive to ML210 as their wild type (WT) controls (HL-60-RhoWT) (Fig. 5K). This was unexpected because the original report that defined ferroptosis showed that the sensitivity of Rho0 cells was similar to that of control cells in 143B cells [6]. Furthermore, prominent mitochondrial lipid peroxidation was induced in Rho0 cells by almost 10-fold lower concentration of ML210 when compared to RhoWT cells, confirming that Rho0 cells are more sensitive to GPX4 inhibition–induced mitochondrial lipid peroxidation in the AML cell line (Fig. 5L). These data suggest that the intact protein expressions of ETC complex proteins protects AML cells from GPX4 inhibition–mediated ferroptosis, perhaps uniquely in AML cells.
GPX4 inhibition–mediated ferroptosis is synergistically enhanced by hyperactivation of mitochondrial caseinolytic protease P
Given Rho0 AML cells’ higher ferroptosis sensitivity, we investigated the therapeutic potential of a combination of ferroptosis induction and ETC downregulation in AML. We previously demonstrated that the hyperactivation of the mitochondrial protease caseinolytic protease P (ClpP) by imipridones (ONC201 or ONC212) induces the degradation of multiple ETC subunits to disrupt mitochondrial respiration and exerts cancer-selective lethality [37]. Indeed, the combination of ML210 and ONC201 induced synergistic cell death in OCI-AML2 and MOLM-13 cells (Fig. 5A). The combinatorial anti-leukemia effect was associated with the cumulative induction of lipid peroxidation and mitochondrial superoxide production (Fig. 5B, C). Synergistic cell death was also observed for the majority of primary AML cells tested, as determined by combination indexes (Fig. 5D). Importantly, primary cells from healthy bone marrow donors exhibit significantly less cell death upon the combinatorial treatment compared to AML cells (Fig. 5E, and Fig. S5A).
Furthermore, synergistic cell death was induced when the genetic activation of ClpP using a Dox-inducible CLPP-Y118A hyperactivated mutant was combined with ML210 and when Dox-inducible GPX4 knockdown was combined with ONC201 and ONC212 (Fig. 5F–H, Fig. S5B, C). Supporting these findings, our re-analysis of a previously published CRISPR screening data of NALM6 leukemia cells treated with imipridones [38] revealed GPX4 to be one of the top hits; knockdown of GPX4 sensitized cells to ClpP hyperactivation (Fig. 5I). In addition to GPX4, genes essential for selenoprotein synthesis (SEPSECS, EEFSEC, PSTK, SEPHS2) [39] were also top hits, suggesting that the inhibition of GPX4’s function as a selenoprotein is important for the synthetic lethality of GPX4 inhibition and ClpP hyperactivation. We also found that ClpP hyperactivation by ONC201 upregulates GPX4 protein expression (Fig. 5J). These findings are consistent with a previous study demonstrating upregulation of GPX4 by ETC inhibition [40], suggesting that GPX4 exerts a cell-protective response against mitochondrial proteotoxic stress in AML cells. ClpP hyperactivation sensitized ETC-intact RhoWT cells to GPX4 inhibition, but the synergism was not exerted in Rho0 cells (Fig. 5K). This indicates that the induced synergism depends on ETC, which also supports the notion that the regulated protein expression of ETC subunits helps protect cells from ferroptosis.