Patient-derived organotypic tissue cultures as a platform to evaluate metabolic reprogramming in breast cancer patients

Teresa W-M Fan; Jing Yan; Carlos Frederico L Goncalves; Jahid M M Islam; Penghui Lin; Mohamed M Y Kaddah; Richard M Higashi; Andrew N Lane; Xiaoqin Wang; Caigang Zhu

doi:10.1016/j.jbc.2025.108495

Patient-derived organotypic tissue cultures as a platform to evaluate metabolic reprogramming in breast cancer patients

J Biol Chem. 2025 Apr 8;301(5):108495. doi: 10.1016/j.jbc.2025.108495. Online ahead of print.

Authors

Affiliations

¹ Center for Environmental and Systems Biochemistry (CESB), Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA. Electronic address: twmfan@gmail.com.
² F. Joseph Halcomb III, M.D. Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky, USA.
³ Center for Environmental and Systems Biochemistry (CESB), Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA.
⁴ Center for Environmental and Systems Biochemistry (CESB), Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA; Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications, Alexandria, Egypt.
⁵ Department of Radiology, University of Kentucky, Lexington, Kentucky, USA.
⁶ F. Joseph Halcomb III, M.D. Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky, USA. Electronic address: caigang.zhu@uky.edu.

PMID: 40209948
DOI: 10.1016/j.jbc.2025.108495

Abstract

Patient-derived organotypic tissue cultures (PD-OTC) are unique models for probing cancer metabolism and therapeutic responses. They retain patient tissue architectures/microenvironments that are difficult to recapitulate while affording comparison of cancer (CA) versus matched noncancer (NC) tissue responses to treatments. We have developed a long-term culturing method for fresh and cryopreserved PD-OTC of breast cancer patients bearing invasive ductal carcinoma. Five PD-OTC came from patients with treatment-naïve primary ER⁺/PR⁺/HER2^- tumors while one came from a patient with neoadjuvant therapy for locally metastatic ER^low/PR^-/HER2^- tumor. They all exhibited tissue outgrowth in 1 month with some CA OTC harboring isolatable organoids and fibroblasts. We interrogated reprogrammed metabolism in CA versus paired NC OTC with dual ²H₇-glucose/¹³C₅,¹⁵N₂-Gln tracers coupled with stable isotope-resolved metabolomic analysis. We noted variable activation of glycolysis, cataplerotic/anaplerotic Krebs cycle including reductive carboxylation, the pentose phosphate pathway, riboneogenesis, gluconeogenesis, de novo and salvage synthesis of purine/pyrimidine nucleotides, and ADP-ribosylation in CA PD-OTC. Altered metabolic activities were in part accountable by expression changes in key enzymes measured by reverse phase protein array profiling. Notably, Gln-fueled gluconeogenesis products were preferentially diverted to support purine nucleotide synthesis. When blocking this novel process with an inhibitor of phosphoenolpyruvate carboxykinase (3-mercaptopicolinic acid), metastatic, ER^low/PR^-/HER2^- CA OTC displayed compromised cellularity, reduced outgrowth, and disrupted growth/survival-supporting metabolism but the matched NC OTC did not. Thus, our PD-OTC culturing method not only promoted understanding of actual patient's tumor metabolism to uncover viable metabolic targets but also enabled target testing and elucidation of therapeutic efficacy.

Keywords: breast cancer; gluconeogenesis; nucleotide synthesis; patient-derived organotypic tissue cultures; reverse phase protein array; stable isotope-resolved metabolomics; tumor metabolic reprogramming.