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

Five patient-derived organotypic cultures from patients with treatment-naïve primary ER+/PR+/HER2- tumors while one came from a patient with neoadjuvant therapy for locally metastatic ERlow/PR-/HER2- tumor. They all exhibited tissue outgrowth in one 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. The data are provided as Excel spreadsheets for each patient. The entries comprise reduced data from FT-MS analyses in terms of identified compounds, their ion intensities for each isotopologue, injection volumes and derived normalized concentrations. These data can therefore be reanalyzed as desired., Dual stable isotope tracer treatment
Each patient’s OTC was replaced with a stable isotope tracer medium 2-3 weeks after culturing in BCOM. The tracer medium was composed of 0.68% (w/v) D7 (2H7)-glucose + 7.44 mM 13C5,15N2-Gln in BCOM and the treatment lasted for 2 (CZ016-017) or 3 days (CZ019-022). At tissue harvest, two small pieces of CZ016-017 OTC were cut for histology and live fluorescence spectroscopy while the rest were metabolically quenched in liquid N2 before further processing for SIRM analysis. The CZ019-022 OTC were processed similarly for histology and SIRM analysis.
Tissue and medium extraction
Frozen OTC were pulverized into 10 µm particles in liquid N2 with a SPEX 6775 Freezer/Mill (SPEX SamplePrep, Metuchen, NJ) to maximize metabolite extraction. Polar/non-polar metabolites and proteins were extracted simultaneously using the acetonitrile:H2O:chloroform (2:1.5:1, v/v) solvent partitioning method as described previously (16). Polar metabolite extracts were split and l..., # Patient-derived organotypic tissue cultures as a platform to evaluate metabolic reprogramming in breast cancer patients

Dataset DOI: [10.5061/dryad.4qrfj6qnm](10.5061/dryad.4qrfj6qnm)

## Description of the data and file structure

Five patient-derived organotypic cultures from patients with treatment-naïve primary ER+/PR+/HER2- tumors while one came from a patient with neoadjuvant therapy for locally metastatic ERlow/PR-/HER2- tumor. They all exhibited tissue outgrowth in one 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.  The data are provided as Excel spreadsheets for each patient.  The entries comprise reduced data from FT-MS analyses in terms of identified compounds, their ion intensities for each isotopologue, injection volumes and derived normalized concentrations.  These data can there..., Ethics Approval and Consent to Participate
All patients were consented prior to surgery for their tissue collection under the approved protocol of the University of Kentucky Institutional Review Board (IRB#44224, Total Cancer Care). The studies in this work abide by the Declaration of Helsinki principles.