ATM inhibition synergizes with fenofibrate in high grade serous ovarian cancer cells

Abstract

While therapies targeting deficiencies in the homologous recombination (HR) pathway are emerging as the standard treatment for high grade serous ovarian cancer (HGSOC) patients, this strategy is limited to the ~50% of patients with a deficiency in this pathway. Therefore, patients with HR-proficient tumors are likely to be resistant to these therapies and require alternative strategies. We found that the HR gene Ataxia Telangiectasia Mutated (ATM) is wildtype and its activity is upregulated in HGSOC compared to normal fallopian tube tissue. Interestingly, multiple pathways related to metabolism are inversely correlated with ATM expression in HGSOC specimens, suggesting that combining ATM inhibition with metabolic drugs would be effective. Analysis of FDA-approved drugs from the Dependency Map demonstrated that ATM-low cells are more sensitive to fenofibrate, a PPARα agonist that affects multiple cellular metabolic pathways. Consistently, PPARα signaling is associated with ATM expression. We validated that combined inhibition of ATM and treatment with fenofibrate is synergistic in multiple HGSOC cell lines by inducing senescence. Together, our results suggest that metabolic changes induced by ATM inhibitors are a potential target for the treatment of HGSOC.

Keywords: Biochemistry; Bioinformatics; Cancer research; Cell biology; Cellular metabolism; Cellular senescence; Drug combinations; Homologous recombination; Metabolite; Molecular biology; PPARa.

Figure 1

ATM is wildtype and upregulated in high grade serous ovarian cancer patients. (A) Analysis of ATM alterations in TCGA PanCancer Atlas Studies. (B) Analysis of ATM alterations in TCGA HGSOC studies. (C) Total ATM protein expression in normal fallopian tube and HGSOC specimens. ns = not significant. (D) Phosphorylated ATM (S1981) protein expression in normal fallopian tube and HGSOC specimens. ∗p < 0.001.

Figure 2

Low ATM expression correlates with increased metabolic gene signatures and sensitivity to fenofibrate. (A) Spearman's correlation in HGSOC (TCGA, PanCancer Atlas) between ATM mRNA and other gene expression values was obtained from the standard co-expression analysis performed using cBioportal, and GSEA was performed. Negative NES means enrichment of expression in HGSOC specimens with lower ATM expression. (B) Volcano plot of FDA-approved drugs in ATM-low vs. ATM-high cell lines from depmap.org (see Materials and Methods for details on how cell lines were divided by ATM protein expression). Line represents p-value<0.05.

Figure 3

PPARα expression is associated with ATM expression in cell lines and HGSOC patient specimens. (A) Correlation between ATM and PPARA (encoding PPARα) expression in cell lines from Dependency Map. (B) Correlation between of ATM and PPARA expression in HGSOC patient specimens from TCGA.

Figure 4

Combined inhibition of ATM and treatment with fenofibrate is synergistic in HGSOC cell lines. (A–B) ATM wildtype Ovcar3 and Ovcar10 cells were treated with the ATM inhibitors KU60019 (A) or AZD0156 (B) or the PPARα agonist fenofibrate alone or in combination for 3 days and colonies were stained with crystal violet. n = 3/group, one of 3 experiments is shown. ∗p < 0.001 (C) Cell death was assessed by 7AAD staining. n = 3/group, one of 3 experiments is shown. Data represent mean ± SEM. (D) SA-β-Gal and PML body staining. n = 3/group, one of 3 experiments is shown. Data represent mean ± SEM. ∗p < 0.001. (E) Immunoblot analysis of lamin B1 (uncropped images: Ovcar3: Figure S1; Ovcar10: Figure S2). β-actin was used as a loading control (uncropped images: Ovcar3: Figure S3; Ovcar10: Figure S4). One of 3 experiments is shown.

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