Metabolomics-based mass spectrometry methods to analyze the chemical content of 3D organoid models

Abstract

Metabolomics, the study of metabolites present in biological samples, can provide a global view of sample state as well as insights into biological changes caused by disease or environmental interactions. Mass spectrometry (MS) is commonly used for metabolomics analysis given its high-throughput capabilities, high sensitivity, and capacity to identify multiple compounds in complex samples simultaneously. MS can be coupled to separation methods that can handle small volumes, making it well suited for analyzing the metabolome of organoids, miniaturized three-dimensional aggregates of stem cells that model in vivo organs. Organoids are being used in research efforts to study human disease and development, and in the design of personalized drug treatments. For organoid models to be useful, they need to recapitulate morphological and chemical aspects, such as the metabolome, of the parent tissue. This review highlights the separation- and imaging-based MS-based metabolomics methods that have been used to analyze the chemical contents of organoids. Future perspectives on how MS techniques can be optimized to determine the accuracy of organoid models and expand the field of organoid research are also discussed.

Fig. 1

Schematic illustrating several of the methods used for culturing organoids. These methods include (a) extracellular matrix scaffold, (b) bioreactor, (c) hanging drop, (d) low-adherent culture plate, and (e) magnetic levitation method. Adapted from ref with permission under Creative Commons Attribution (CC-BY 4.0) license (http://creativecommons.org/licenses/by/4.0/).

Fig. 2

Mass spectrometry (MS) techniques using organoid samples. Advantages for using mass spectrometry imaging and liquid chromatography (LC)-, gas chromatography (GC)-, and capillary electrophoresis (CE)-MS to measure the chemical components of three-dimensional organoid samples are compared.

Fig. 3

Detection of metabolites in organoids using GC-MS. (a) Metabolites detected in cerebral organoids with arrows indicating relative increase or decrease in CLN3 mutant organoids compared to the controls. Red = relative decrease compared to control. Green = relative increase compared to control. Asterisks indicate significantly deregulated metabolites. (b) The neurotransmitter GABA is significantly downregulated in CLN3 mutant organoids compared to control organoids. Adapted from ref. with permission under Creative Commons Attribution (CC-BY 4.0) license (http://creativecommons.org/licenses/by/4.0/).

Fig. 4

Multi-omic analysis of intestinal organoids provides a complete profile of cell-type enriched and depleted organoid cultures. (a) Multi-omic approaches require the combination of several assays. (b) Relative abundance of significantly changing metabolites in stem-cell enriched vs. stem-cell depleted intestinal organoids measured using MS metabolomics and lipidomics measurements. Significantly enriched pathways are indicated next to the corresponding cluster of metabolites. CV = stem-cell enriched organoids; ENR = organoids grown in regular culture media; EN = stem-cell depleted organoids. Adapted from ref. with permission under Creative Commons Attribution (CC-BY 4.0) license (http://creativecommons.org/licenses/by/4.0/).

Fig. 5

MALDI-MSI of colorectal tumor organoids reveals the time and concentration distribution dynamics of irinotecan. (a) MALDI-MSI intensity maps showing the time-dependent distribution of irinotecan in colorectal tumor organoid samples. (b) MALDI-MSI ion density maps showing the concentration-dependent distribution of 0, 20, and 40 μM irinotecan-treated colorectal tumor organoid samples. Adapted from ref. with permission from the American Chemical Society, copyright 2018.