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Combination of ZEN-3694 with CDK4/6 inhibitors reverses acquired resistance to CDK4/6 inhibitors in ER-positive breast cancer

Cancer Gene Therapy volume 29, pages 859–869 (2022)Cite this article

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Abstract

CDK4/6 inhibitors significantly prolong progression-free survival in patients with advanced hormone receptor-positive (HR+) HER2-negative breast cancer. Despite recent successes, patients acquire resistance, necessitating the development of additional novel therapeutic strategies. Bromodomain and extra-terminal domain (BET) proteins are key epigenetic regulators that interact with acetylated lysine (AcLys) residues of histones or transcription factors. BET proteins are directly involved in modulating estrogen receptor (ER) signaling and the cell cycle. Therefore, BET inhibitors can potentially offer new strategies in the treatment of advanced ER+ breast cancer. ZEN-3694 is an orally bioavailable small molecule BET inhibitor currently being evaluated in Phase 1/2 clinical trials (NCT03901469). To assess a potential combination strategy in a CDK4/6i resistant breast cancer population, we investigated the mechanism of action of ZEN-3694 combined with CDK4/6 inhibitors in the ER+ cell lines resistant to palbociclib or abemaciclib. Here, we describe that the combination of ZEN-3694 with CDK4/6i potently inhibits proliferation and induces apoptosis in CDK4/6i resistant cell lines. The resistance to both palbociclib and abemaciclib was associated with the strong upregulation of CDK6 and CCND1 protein levels, which was reversed by the ZEN-3694 treatment. Furthermore, RNAseq data and pathway analysis elucidated the combinatorial effects of ZEN-3694 with CDK4/6 inhibitors through significant downregulation of multiple pathways involved in cell cycle regulation, cellular growth, proliferation, apoptosis, inflammation, and cellular immune response. Our data indicate that ZEN-3694 has therapeutic potential in combination with CDK4/6 inhibitors in patients with advanced ER+ breast resistant to CDK4/6 inhibitors.

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Fig. 1: Developing CDK4/6i-resistant cell lines.
Fig. 2: ZEN-3694 inhibits proliferation of CDK4/6i sensitive and resistant ER+ breast cancer cell lines and inhibits markers of CDK4/6i-resistance.
Fig. 3: The combination of ZEN-3694 and abemaciclib synergistically inhibits proliferation and induces apoptosis in WT and CDK4/6i-resistant ER+ breast cancer cell lines.
Fig. 4
Fig. 5: Comparison of palbociclib and abemaciclib-resistant cell lines using RNAseq analysis.
Fig. 6: RNAseq and IPA analysis of ZEN-3694, CDK4/6i and combination treatments in CDK4/6i-resistant vs. parental MCF7 cell lines.

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Acknowledgements

We thank Laura Tsujikawa for her help with IPA® data upload and analysis. The work has been funded by Zenith Epigenetics.

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  1. Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, AB, T3E 6L1, Canada

    Olesya A. Kharenko, Reena G. Patel, Cyrus Calosing & Edward H. van der Horst

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  1. Olesya A. Kharenko
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  2. Reena G. Patel
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  3. Cyrus Calosing
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  4. Edward H. van der Horst
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RGP, CC, and OK conducted experiments, analyzed, and interpreted the data. OK and EvH conception and supervision of the study, wrote the paper. All authors corrected draft versions and approved the final version of the paper.

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Correspondence to Olesya A. Kharenko.

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The authors are the employees and shareholders of Zenith Epigenetics.

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Kharenko, O.A., Patel, R.G., Calosing, C. et al. Combination of ZEN-3694 with CDK4/6 inhibitors reverses acquired resistance to CDK4/6 inhibitors in ER-positive breast cancer. Cancer Gene Ther 29, 859–869 (2022). https://doi.org/10.1038/s41417-021-00375-9

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