Summary of Study ST004262

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002689. The data can be accessed directly via it's Project DOI: 10.21228/M82R9H This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST004262
Study Title	The lipidome of drug-resistant glioblastoma persister cells.
Study Summary	This study aimed to determine mechanisms through which glioblastoma stem cells acquire a drug-resistant phenotype. A small proportion of glioblastoma stem cells survive chemotherapy and radiotherapy, creating a drug-resistant persister cell population that resumes proliferation after the cessation of drug treatment. The specific experiment profiled the lipidome of glioblastoma stem cells that survive treatment with the anti-microtubule agent CMPD1. Glioblastoma stem cell line RKI1 was treated for 14 days with 25 micromolar CMPD1 to generate drug-resistant persister cells, replacing the cell culture medium every 3 days (n = 3). At day 14 of treatment, the CMPD1-treated cells were collected for lipid extraction and lipidomic analysis. The drug-resistant persister cells were compared to control cells grown in RKI1 growth medium and collected prior to drug-treatment (n = 3). The drug-resistant persister cells displayed significantly decreased levels of ceramide and cholesterol, and increased sphingomyelin and diacylgylcerol, indicative of membrane remodelling that may allow the cells to survive chemotherapy. Further investigation indicated that the reduced cholesterol content provides a point of metabolic vulnerability to eliminate the drug resistant persister cells.
Institute	University of Sydney
Department	School of Medical Sciences
Last Name	Don
First Name	Anthony
Address	Office 3210, D17 Charles Perkins Centre, Camperdown, NSW, 2006
Email	anthony.don@sydney.edu.au
Phone	+612 8627 5578
Submit Date	2025-09-29
Num Groups	2
Total Subjects	6
Study Comments	Control and drug-treated RKI1 glioblastoma cells
Publications	Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-10-10
Release Version	1

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Treatment:

Treatment ID:	TR004424
Treatment Summary:	RKI1 cells (1.5 × 10^4 cells/cm2) were grown in 10 cm2 dishes and treated with CMPD1 (25 μM) for 14 days. Every 3 days, the media containing CMPD1 was replaced. At Day 14, three independent cultures of drug tolerant persister (DTP) cells were collected for lipidomic analysis. Control cells were RKI1 cells grown in culture medium without CMPD1 (1.5 x 10^5 cells in 10 cm2 dishes). Three independent cultures of the cells were used. RKI1 cells are cultured in KnockOut DMEM/F-12 basal medium kit with neural supplement, EGF (20 ng/mL) and FGF-β (10 ng/mL) (ThermoFisher Scientific, Cat# 579 A1050901). GlutaMAX-ICTS (2 mM) (ThermoFisher Scientific, Cat# A1286001) and Antibiotic- Antimycotic (ThermoFisher Scientific, Cat# 15240112) were also added. Adherent cells were plated on flasks coated with 0.15% in PBS MatriGel Matrix (Corning Life Sciences, Cat# BDAA356237), incubated at 37 °C, 5% CO2.

Treatment ID:

TR004424

Treatment Summary:

RKI1 cells (1.5 × 10^4 cells/cm2) were grown in 10 cm2 dishes and treated with CMPD1 (25 μM) for 14 days. Every 3 days, the media containing CMPD1 was replaced. At Day 14, three independent cultures of drug tolerant persister (DTP) cells were collected for lipidomic analysis. Control cells were RKI1 cells grown in culture medium without CMPD1 (1.5 x 10^5 cells in 10 cm2 dishes). Three independent cultures of the cells were used. RKI1 cells are cultured in KnockOut DMEM/F-12 basal medium kit with neural supplement, EGF (20 ng/mL) and FGF-β (10 ng/mL) (ThermoFisher Scientific, Cat# 579 A1050901). GlutaMAX-ICTS (2 mM) (ThermoFisher Scientific, Cat# A1286001) and Antibiotic- Antimycotic (ThermoFisher Scientific, Cat# 15240112) were also added. Adherent cells were plated on flasks coated with 0.15% in PBS MatriGel Matrix (Corning Life Sciences, Cat# BDAA356237), incubated at 37 °C, 5% CO2.