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PROTAC-mediated CDK degradation differentially impacts cancer cell cycles due to heterogeneity in kinase dependencies

Abstract

Background

Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibition yields differential cellular responses in multiple tumor models due to redundancy in cell cycle. We investigate whether the differential requirements of CDKs in multiple cell lines function as determinant of response to pharmacological agents that target these kinases.

Methods

We utilized proteolysis-targeted chimeras (PROTACs) that are conjugated with palbociclib (Palbo-PROTAC) to degrade both CDK4 and CDK6. FN-POM was synthesized by chemically conjugating pomalidomide moiety with a multi-kinase inhibitor, FN-1501. Patient derived PDAC organoids and PDX model were utilized to investigate the effect of FN-POM in combination with palbociclib.

Results

Palbo-PROTAC mediates differential impact on cell cycle in different tumor models, indicating that the dependencies to CDK4 and 6 kinases are heterogenous. Cyclin E overexpression uncouples cell cycle from CDK4/6 and drives resistance to palbo-PROTAC. Elevated expression of P16INK4A antagonizes PROTAC-mediated degradation of CDK4 and 6. FN-POM degrades cyclin E and CDK2 and inhibits cell cycle progression in P16INK4A-high tumor models. Combination of palbociclib and FN-POM cooperatively inhibit tumor cell proliferation via RB activation.

Conclusion

Resistance to CDK4/6 inhibition could be overcome by pharmacologically limiting Cyclin E/CDK2 complex and proves to be a potential therapeutic approach.

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Fig. 1: Cellular response to different palbociclib-PROTACS.
Fig. 2: Differential effects of BSJ-02-162 in a panel of cell lines.
Fig. 3: Resistance to BSJ-02-162 via CCNE1 and CDKN2A overexpression.
Fig. 4: Cellular response to FN-POM in a panel of cell lines.
Fig. 5: Cellular response to FN-POM in combination with palbociclib.

Data availability

Data sharing not applicable to this paper as no datasets were generated or analyzed during the current study. The synthesis scheme and the structural characterization of the new chemical molecule are available in this published paper and its supplementary information.

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Acknowledgements

The author thank all members of the laboratory group and colleagues in the discussion and preparation of the paper. Dr Nathanael S. Gray (Stanford) kindly provided the PROTACS, BSJ-02-162 and BSJ-03-201. Dr Jianxin Wang (Roswell Park Cancer Center) generated the Oncoprint for the cell lines.

Funding

The research was supported by a grant to AKW and ESK from National Cancer Institute (CA247362 and CA267467).

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Contributions

Study concept and design: VK, SMR, KB, ESK, and AKW. Acquisition of data: VK, ZG, BJ, BZ. Analysis and interpretation of data: VK, SMR, ESK, and AKW. Study supervision: ESK and AKW.

Corresponding author

Correspondence to Erik S. Knudsen.

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Competing interests

Dr ESK and Dr AKW have received research funding from Eli Lilly, Novartis and Pfizer over the last 5 years. There is no current research support from these entities and the study was written in the absence of input from any pharmaceutical company.

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Kumarasamy, V., Gao, Z., Zhao, B. et al. PROTAC-mediated CDK degradation differentially impacts cancer cell cycles due to heterogeneity in kinase dependencies. Br J Cancer 129, 1238–1250 (2023). https://doi.org/10.1038/s41416-023-02399-4

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