Targeting human apurinic/apyrimidinic endonuclease 1 (APE1) in phosphatase and tensin homolog (PTEN) deficient melanoma cells for personalized therapy.

Rachel Abbotts,Claire Seedhouse,David M Wilson,Rosalyn Jewell,Srinivasan Madhusudan,Faye Elliott,Jérémie Nsengimana,Graham Ball,Anton Simeonov,Poulam M Patel,Ajit Jadhav,Jon Laye,Christy Walker,Anna Grabowska,Julia Newton-Bishop,David J Maloney

doi:10.18632/oncotarget.1926

Abstract

Phosphatase and tensin homolog (PTEN) loss is associated with genomic instability. APE1 is a key player in DNA base excision repair (BER) and an emerging drug target in cancer. We have developed small molecule inhibitors against APE1 repair nuclease activity. In the current study we explored a synthetic lethal relationship between PTEN and APE1 in melanoma. Clinicopathological significance of PTEN mRNA and APE1 mRNA expression was investigated in 191 human melanomas. Preclinically, PTEN-deficient BRAF-mutated (UACC62, HT144, and SKMel28), PTEN-proficient BRAF-wildtype (MeWo), and doxycycline-inducible PTEN-knockout BRAF-wildtype MeWo melanoma cells were DNA repair expression profiled and investigated for synthetic lethality using a panel of four prototypical APE1 inhibitors. In human tumours, low PTEN mRNA and high APE1 mRNA was significantly associated with reduced relapse free and overall survival. Pre-clinically, compared to PTEN-proficient cells, PTEN-deficient cells displayed impaired expression of genes involved in DNA double strand break (DSB) repair. Synthetic lethality in PTEN-deficient cells was evidenced by increased sensitivity, accumulation of DSBs and induction of apoptosis following treatment with APE1 inhibitors. We conclude that PTEN deficiency is not only a promising biomarker in melanoma, but can also be targeted by a synthetic lethality strategy using inhibitors of BER, such as those targeting APE1.

Highlights

Base excision repair (BER) is a critical and highly conserved mechanism for the repair of damage induced by alkylation and oxidation of DNA, including by chemotherapy and ionising radiation [1]
Phosphatase and tensin homolog (PTEN) is a key regulator of the anti-apoptotic PI3K/ Akt pathway [15], and emerging evidence suggests a role in DNA repair [19,20,21]
A number of recent studies provide compelling evidence that nuclear PTEN may have essential roles in DNA repair [40, 41], and that PTEN deficiency may be targeted in a synthetic lethality approach by inhibitors of single strand break repair (SSBR) [24]

Summary

Introduction

Base excision repair (BER) is a critical and highly conserved mechanism for the repair of damage induced by alkylation and oxidation of DNA, including by chemotherapy and ionising radiation [1]. Abasic sites ( known as apurinic/apyrimidinic or AP sites) are cytotoxic obligate repair intermediates generated during BER and processed by human apurinic/apyrimidinic endonuclease 1 (APE1). APE1 cleaves the phosphodiester DNA backbone 5’ to the AP site prior to further processing via either the short patch or the long patch BER pathway. SiRNA-mediated APE1 downregulation induces AP site accumulation and is associated with hypersensitivity to DNA damaging agents, including alkylators and ionising radiation [1]. Exposure to alkylating agents causes upregulation of endogenous APE1 levels, suggesting a role in the development of treatment resistance [5]. APE1 expression in human tumours may have prognostic or predictive significance in patients [1]

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Results

Conclusion