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Open AccessArticle

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

1
Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany
2
Department of Surgery, Robert-Bosch Hospital, 70376 Stuttgart, Germany
3
Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, 72074 Tuebingen, Germany
4
Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, 72074 Tuebingen, Germany
*
Author to whom correspondence should be addressed.
These authors have contributed equally to this work.
Metabolites 2020, 10(12), 494; https://doi.org/10.3390/metabo10120494
Received: 25 September 2020 / Revised: 25 November 2020 / Accepted: 27 November 2020 / Published: 1 December 2020
(This article belongs to the Special Issue Metabolomics Methodologies and Applications II)
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/injection) in the presence of an 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 the 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-methylcytidine, 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. View Full-Text
Keywords: metabolomics; lipidomics; metabolic profiling; organoids; colorectal cancer; QTOF; LC-MS metabolomics; lipidomics; metabolic profiling; organoids; colorectal cancer; QTOF; LC-MS
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MDPI and ACS Style

Neef, S.K.; Janssen, N.; Winter, S.; Wallisch, S.K.; Hofmann, U.; Dahlke, M.H.; Schwab, M.; Mürdter, T.E.; Haag, M. Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS. Metabolites 2020, 10, 494. https://doi.org/10.3390/metabo10120494

AMA Style

Neef SK, Janssen N, Winter S, Wallisch SK, Hofmann U, Dahlke MH, Schwab M, Mürdter TE, Haag M. Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS. Metabolites. 2020; 10(12):494. https://doi.org/10.3390/metabo10120494

Chicago/Turabian Style

Neef, Sylvia K.; Janssen, Nicole; Winter, Stefan; Wallisch, Svenja K.; Hofmann, Ute; Dahlke, Marc H.; Schwab, Matthias; Mürdter, Thomas E.; Haag, Mathias. 2020. "Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS" Metabolites 10, no. 12: 494. https://doi.org/10.3390/metabo10120494

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