Background: CDK4/6 inhibitors (CDK4/6i) palbociclib (palbo) and abemaciclib (abema) have significantly improved outcomes in patients with hormonal receptor positive (HR+)/human epidermal growth factor receptor negative (HER2-) breast cancer. Yet almost 20% of patients never respond to treatment and all patients eventually develop acquired resistance. In vitro palbo and abema have different affinities for CDK4/6 and other cellular kinases, and in vivo they have different toxicity profiles. At present there are no clinically validated biomarkers to determine CDK4/6i sensitivity or resistance. Further it is not clear if and how to choose between the CDK4/6i for optimal outcomes. In this study, using 13C-isotopically enriched glucose we sought to identify metabolic changes associated with palbo and abema treatment in sensitive and resistant cell lines. Methods: MCF-7 cells (wild-type), palbociclib resistant cells (PDR) and abemaciclib resistant cells (ABR) treated with DMSO, palbo or abema were incubated for 24hrs in DMEM supplemented with 13C-glucose. After the incubation, cells were harvested, metabolites were extracted and analyzed via 1D and 2D NMR spectroscopy. Biological triplicates were prepared for each condition. Results: In wild-type MCF-7 cells treated with palbo or abema significant metabolite changes were observed compared to DMSO. In both palbo and abema treatment a marked decrease in nucleotide metabolites was observed, which is consistent with the ability of CDK4/6i to prevent cell cycle progression. In abema treated cells there was also significant decrease in metabolites involved in the serine-glycine pathway, which was not observed in the palbo treated cells. Palbo and abema treated cells were easily distinguishable via hierarchical clustering. PDR and ABR also had distinct metabolic profiles when they were maintained with palbo and abema, respectively or if the drugs were removed. Notably the serine-glycine pathway was increased in ABR cells but decreased in PDR cells. In PDR cells we observed an increase in glucose-1-phosphate and shift towards galactose/glycogen metabolism. Conclusions: Using cell line models we were able to demonstrate that glucose metabolism is altered in palbo and abema treatment and that resistance to each drug may activate different metabolic pathways. To the best of our knowledge this is the first direct evidence of palbo-specific and abema-specific metabolite signatures. We are assessing whether the results of these in vitro studies translate to clinical samples. If so, the altered metabolites could lead to biomarkers that correlate with response and resistance for specific CDK4/6i. Further, we are exploring if by targeting the pathways associated with resistance, we can restore CDK4/6i sensitivity. This could lead to novel therapeutic targets or treatment regimens that improve patient outcomes. Citation Format: Chandrashekhar Honrao, Kanchan Sonkar, Cristina Guarducci, Agostina Nardone, Wen Ma, Srihari Raghavendra Rao, Chen Dong, Leo Rodrigues, Rinath Jeselsohn, Elizabeth O'Day. Isotopic tracing reveals distinct metabolic changes with palbociclib or abemaciclib treatment & resistance in breast cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5802.
Background: Cyclin-dependent kinase 4/6 inhibitors (CKD4/6i) have demonstrated clinical utility extending progression-free survival (PFS) and overall survival (OS) for advanced hormone receptor positive and HER2 negative (HR+/HER2-) breast cancer patients. The efficacy in early-stage breast cancer (eBC) is unclear, with conflicting results from adjuvant CDK4/6i trials on invasive disease-free survival. Thus, there is a critical need to identify biomarkers of response (BoR) to determine which, if any, eBC patients could benefit from this treatment. This BoR could also stratify advanced BC patients for likelihood to respond to CDK4/6i. Metabolism is influenced by both genome and environment, and changes in the metabolome can be correlated with drug responsiveness. Thus, metabolite BoRs may serve to identify eBC patients for which CDK4/6i would offer a therapeutic benefit.Methods: Plasma and serum samples from 50 early-stage ER+/HER2- breast cancer patients, treated with neoadjuvant CDK4/6 inhibitor palbociclib (palbo) and aromatase inhibitor (AI) anastrozole on NeoPalAna trial (ClinicalTrials.gov identifier NCT01723774), were collected from treatment-naïve patients (BL) and 3 consecutive time points: anastrozole,1 mg daily for 4 weeks (C1D1), anastrozole plus palbo,125 mg daily, for 15 days (C1D15), and for 4-5 months before surgery (SURG). Metabolites were extracted from all samples via methanol and chloroform precipitation and quantified using an unbiased, non-destructive, nuclear magnetic resonance (NMR)-based profiling platform (Olaris®, Inc., Waltham, MA). Statistical analysis and machine learning was used to identify differential metabolites and generate predictive models. A separate validation set of samples was collected from a subset of patients (N=6) who received an additional cycle of palbo treatment prior to surgery to assess model accuracy. Results: Non-parametric differential expression analysis of BL/C1D1, BL/C1D15, and C1D1/C1D15 identified 53 ,97, and 90 differential NMR resonances in plasma (p<0.05) and 36, 34, and 25 differential NMR resonances in serum (p<0.05), respectively. Based on the proliferative marker Ki67 levels at C1D15, 37 patients were classified as responders (Ki67≤2.7%) and 6 patients as non-responders (Ki67>2.7%). Analysis of the responder (R) and non-responder (NR) groups identified that 13 plasma and 14 serum resonances (21 unique resonances and 6 overlapping) were differentially expressed (p<0.05) at C1D1. Many of the differential resonances could be mapped back to amino acid metabolites including several branched chain amino acids such as leucine, valine, and isoleucine, and positively charged amino acids such as lysine. A Olaris® BoR score was generated using 5 differential resonances that had an AUC of 0.931 (training set) and 100% accuracy when predicting palbo-response in a blinded test set (N=6).Conclusion: The differential metabolites identified from matching plasma and serum samples suggest that, compared to serum, plasma has a better representation of the metabolic changes associated with palbo treatment-response. While comparing samples from R and NR patients, amino acids were found to be consistently altered in both serum and plasma before palbo treatment. In addition, a BoR model based on select metabolites could precisely stratify palbo-response in a blinded dataset. A larger independent validation cohort is ongoing. Citation Format: Chen Dong, Shana Thomas, Chandrashekhar Honrao, Leonardo O. Rodrigues, Nathalie Tessier, Bo Zhang, Souzan Sanati, Kiran Vij, Brenda J. Ernst, Karen S. Anderson, Mateusz Opyrchal, Foluso Ademuyiwa, Lindsay L. Peterson, Matthew P. Goetz, Donald Northfelt, Elizabeth O'Day, Cynthia Ma. Identifying a metabolite signature that correlates with tumor proliferation in early-stage breast cancer patients treated with CDK4/6 inhibitors from matched plasma and serum samples [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-13-20.
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