Abstract
Breast cancer (BC) is the most prevalent malignancy in women, with hormone receptor-positive, HER2-negative (HR+/HER2−) tumors representing ~70% of cases. While CDK4/6 inhibitors (CDK4/6i) combined with endocrine therapy have transformed treatment for metastatic HR+/HER2− BC, acquired resistance remains a major obstacle. Using HR+/HER2− BC models with acquired resistance to the CDK4/6 inhibitors Palbociclib or Ribociclib, we uncovered a metabolic vulnerability in highly resistant clones, mediated by mTORC1 hyperactivation and autophagy suppression. Gene expression profiling revealed enrichment of glycolysis and mTORC1 pathways in CDK4/6i-resistant cells, which manifested as heightened sensitivity to the metabolic inhibitors Metformin and Dichloroacetate (DCA). Mechanistically, mTORC1 overactivation impaired autophagy via ULK1-Ser757 phosphorylation, as confirmed by LC3 flux assays, leaving resistant cells unable to adapt to energy stress. Treatment with metabolic drugs triggered AMPK activation, ACC inhibition, and PARP cleavage, culminating in apoptosis. Clinically, immunohistochemical analysis of a BC cohort revealed a significant correlation between mTORC1 activity (p4E-BP1T37/46) and autophagy suppression (p62 accumulation), supporting the translational relevance of this axis. Our findings propose mTORC1-mediated autophagy defects as a biomarker for metabolic vulnerability in CDK4/6i-resistant BC, offering a rationale for targeting these tumors with metabolic therapies to overcome resistance.
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Data availability
All data generated or analyzed during this study are included in this published article (and its supplementary figures). The following source western blot data are provided with this paper: uncropped images for for Figs. 3d, 4c and 4d. The GSEA data generated and analyzed for this paper are available at BioStudies with accession code E-MTAB-15265.
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Acknowledgements
We extend our gratitude to Marina Föth, Sigrid Bischofsberger, and Viktoria Wischmann for their experimental contributions and technical assistance. We also thank the members of our lab for their valuable discussions and advice.
Funding
NG was supported by the Clinician Scientist Program (SUCCESS-Program) of Philipps University Marburg and the UniversityHospital of Giessen and Marburg (UKGM), as well as the Clinical Trialist Program (SUCCESS meets MSNZ) of the Department ofMedicine. NG received research funding from the Deutsche Forschungsgemeinschaft (DFG) (GRK 2573/2 – 2024), the UniversityMedical Center Giessen and Marburg (UKGM) (Grant 3/2022 MR to NG), the von Behring-Röntgen Foundation (Grant 70_0027 toNG), the PE Kempkes Foundation (Grant 01/2021 to NG), and the Medical Foundation (Grant 04/2021 to NG). Open Access funding enabled and organized by Projekt DEAL.
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NG and TS jointly planned and supervised the study. NG generated CDK4/6 inhibitor-resistant clones. LvW performed most experiments with contributions from NG, AS and MWitt. NG, LvW and JT-S prepared and analyzed samples using HTG EdgeSeq. M.M. performed GSEA analyses. BMP and CD provided breast cancer tissue microarrays and clinical data. LvW and A-SL performed immunohistochemistry and statistical analysis of the tissue microarrays. TW, UW, TS and NG provided resources. M Wanzel, SG, TW and UW provided essential intellectual and conceptual input. LvW, NG and TS analyzed data, performed statistics and wrote the manuscript. All authors have read and approved the final manuscript.
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CD received personal fees from Novartis, Roche, MSD Oncology, Daiichi Sankyo, AstraZeneca, Molecular Health, and Merck, all outside the submitted work. CD is cofounder of Sividon Diagnostics. In addition, CD has a patent on VMScope digital pathology software with royalties paid; a patent WO2020109570A1—cancer immunotherapy pending; and patents WO2015114146A1 and WO2010076322A1—therapy response issued. PJ reports research grant and travel expenses from GILEAD Sciences GmbH out-side the submitted work. NH declares to be GBG Forschungs GmbH employee. GBG Forschungs GmbH reports financial funding from AstraZeneca and Myriad during the conduct of the study; received funding for research grants from Abbvie, Amgen, AstraZeneca, BMS, Daiichi-Sankyo, Gilead, Molecular Health, Stemline Menarini, Celgene/BMS, Novartis, Pfizer and Roche (paid to the institution); GBG Forschungs GmbH has licensing fees from VMscope GmbH. In addition, GBG Forschungs GmbH has a patent EP21152186.9 pending, a patent EP19808852.8 pending, and a patent EP14153692.0 pending. The other authors declare no conflicts of interest.
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Immunohistochemical staining and evaluation of breast cancer patient tissue samples were approved by the Ethics Committee of the Charité (Ethics Opinion No. EA1/139/05) and conducted in accordance with the Declaration of Helsinki. Written informed consent was obtained from all patients for the use of their tissue samples in this study.
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von Wichert, L., Stroh, A., Witt, M. et al. mTOR-driven autophagy suppression defines metabolic vulnerability in CDK4/6 inhibitor-resistant HR+/HER2− breast cancer. Cell Death Dis (2026). https://doi.org/10.1038/s41419-026-08496-5
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DOI: https://doi.org/10.1038/s41419-026-08496-5
