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Translational Therapeutics

Targeting autophagy reverses de novo resistance in homologous recombination repair proficient breast cancers to PARP inhibition

Abstract

Background

Poly(ADP-ribose) polymerase inhibitors (PARPi) target tumours defective in homologous recombination (HR). Most BRCA-wild-type (WT) HR-proficient breast cancers are intrinsically resistant to PARP inhibitors, e.g., talazoparib. We evaluated the role of autophagy in this de novo resistance and determined the underlying mechanism to overcome this.

Methods

Autophagosome formation and autophagic flux were assessed by evaluating endogenous LC3-II levels and ectopic expression of EGFP-LC3 and mRFP-EGFP-LC3 in breast cancer cells. Autophagy-defective cells were generated by genetic depletion of BECN1, ATG5, p62/SQSTM1 and LAMP1 by using CRISPR-Cas9 double nickase system. The response of PARPi was evaluated in autophagy-proficient and -defective breast cancer cells and in xenograft SCID-mice model.

Results

Pro-survival autophagy was significantly enhanced upon talazoparib treatment in BRCA-WT breast cancer cell lines. Autophagy-deficient cells were hypersensitive to talazoparib. Targeting autophagy synergistically enhanced the therapeutic efficacy of talazoparib in BRCA1-WT breast cancer cells in vitro and in vivo xenograft tumour mouse model. Mechanistically, autophagy inhibition by chloroquine promoted deleterious NHEJ mediated DSB-repair, leading to extensive genomic instability and mitotic catastrophe.

Conclusions

Autophagy confers de novo resistance to PARP inhibitor, talazoparib. Autophagy inhibition improves the therapeutic outcome of PARPi treatment in preclinical mice model, bearing HR-proficient breast tumours, warranting its usage in the clinical settings.

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Fig. 1: BRCA-WT HR-proficient breast cancer cells are de novo resistant to talazoparib monotherapy.
Fig. 2
Fig. 3: Autophagic flux was enhanced in breast cancer cell lines in response to talazoparib.
Fig. 4: Autophagy confers intrinsic resistance to PARP inhibitor in BRCA1-WT HR-proficient breast cancer cells.
Fig. 5: Pharmacological inhibition of autophagy sensitises BRCA-WT breast cancer cells by promoting NHEJ.
Fig. 6: Pharmacological inhibition of autophagy sensitises BRCA1-WT MCF-7 tumour xenograft to PARPi treatment.

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Acknowledgements

We would like to acknowledge the central animal facility at Bhabha Atomic Research Centre, Mumbai. We would also like to thank R. Krishna Mohan, Jasraj Vaishnav and Unique Biodiagnostics Enterprises, Mumbai for their help in the conduct of animal experiments, HPLC and histopathology and biochemical analysis, respectively.

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G.P.B. and B.S.P. designed the experiments and wrote the paper. G.P.B., B.S.P. and B.S. performed the experiments. G.P.B., B.S. and B.S.P. contributed to data analysis and preparing and editing the paper.

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Correspondence to Birija Sankar Patro.

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No human-derived samples were used in this study and hence there is no human-specific ethical approval to report. All the animal experiments were performed upon receipt of approval from the institutional animal ethics committee (IAEC). Mice were maintained in BARC SCID mouse facility, and experiments were performed as per the institutional guidelines and regulations laid down by the BARC animal ethics committee.

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The authors agree to make the data in this paper publicly available on genuine request.

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The authors declare no competing interests.

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This work was supported financially by the internal funding of Bhabha Atomic Research Centre, Department of Atomic Energy, India.

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Pai Bellare, G., Saha, B. & Patro, B.S. Targeting autophagy reverses de novo resistance in homologous recombination repair proficient breast cancers to PARP inhibition. Br J Cancer 124, 1260–1274 (2021). https://doi.org/10.1038/s41416-020-01238-0

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