Dataset Information

Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS

ABSTRACT: As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by LC-QTOF-MS facing the challenge of capturing metabolic information from minimal sample amount (< 500 cells/injection) in the presence of extracellular matrix (ECM). The best procedure of the tested protocols included ultrasonic metabolite extraction with acetonitrile/methanol/water (2:2:1, v/v/v) without ECM removal. To eliminate ECM-derived background signals, we implemented a data filtering procedure based on p-value and fold change cut-offs which retained features with signal intensities >120% compared to matrix-derived signals present in blank samples. As a proof-of-concept, the method was applied to examine the early metabolic response of colorectal cancer organoids to 5-fluorouracil treatment. Statistical analysis revealed dose-dependent changes in the metabolic profiles of treated organoids including elevated levels of 2'-deoxyuridine, 2'-O-methylcytidin, inosine and 1-methyladenosine and depletion of 2'-deoxyadenosine and specific phospholipids. In accordance with the mechanism of action of 5-fluorouracil, changed metabolites are mainly involved in purine and pyrimidine metabolism. The novel protocol provides a first basis for the assessment of metabolic drug response phenotypes in 3D organoid models.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - hilic, Liquid Chromatography MS - positive - reverse phase, Liquid Chromatography MS - negative - hilic

SUBMITTER: Sylvia Karin Neef

PROVIDER: MTBLS2130 | MetaboLights | 2021-10-12

REPOSITORIES: MetaboLights

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Dataset's files

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			Action	DRS
	MTBLS2130	Other
	FILES	Other
	a_MTBLS2130_LC-MS_negative_hilic_metabolite_profiling.txt	Txt
	a_MTBLS2130_LC-MS_negative_reverse-phase_metabolite_profiling.txt	Txt
	a_MTBLS2130_LC-MS_positive_hilic_metabolite_profiling.txt	Txt

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Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS.

Neef Sylvia K SK Janssen Nicole N Winter Stefan S Wallisch Svenja K SK Hofmann Ute U Dahlke Marc H MH Schwab Matthias M Mürdter Thomas E TE Haag Mathias M

Metabolites 20201201 12

As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) facing the challenge of capturing metabolic information from a minimal sample amount (<500 cells/in ...[more]

PMID: 33271860

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