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Here, we present a protocol to accurately and reliably measure metabolites in rare cell types. Technical improvements, including a modified sheath fluid for cell sorting and the generation of relevant blank samples, enable a comprehensive quantification of metabolites with an input of only 5000 cells per sample.
Cellular function critically depends on metabolism, and the function of the underlying metabolic networks can be studied by measuring small molecule intermediates. However, obtaining accurate and reliable measurements of cellular metabolism, particularly in rare cell types like hematopoietic stem cells, has traditionally required pooling cells from multiple animals. A protocol now enables researchers to measure metabolites in rare cell types using only one mouse per sample while generating multiple replicates for more abundant cell types. This reduces the number of animals that are required for a given project. The protocol presented here involves several key differences over traditional metabolomics protocols, such as using 5 g/L NaCl as a sheath fluid, sorting directly into acetonitrile, and utilizing targeted quantification with rigorous use of internal standards, allowing for more accurate and comprehensive measurements of cellular metabolism. Despite the time required for the isolation of single cells, fluorescent staining, and sorting, the protocol can preserve differences among cell types and drug treatments to a large extent.
Metabolism is an essential biological process that occurs in all living cells. Metabolic processes involve a vast network of biochemical reactions that are tightly regulated and interconnected, allowing cells to produce energy and synthesize essential biomolecules1. To understand the function of metabolic networks, researchers measure the levels of small molecule intermediates within cells. These intermediates serve as important indicators of metabolic activity and can reveal critical insights into cellular function.
Mass spectrometry (MS) is the most popular choice for the specific detection of metabolites in comple....
Breeding and husbandry of all mice used for this protocol were conducted in a conventional animal facility at the Max Planck Institute for Immunobiology and Epigenetics (MPI-IE) according to the regulations of the local authorities (Regierungspräsidium Freiburg). Mice were euthanized with CO2 and cervical dislocation by FELASA B-trained personnel following guidelines and regulations approved by the animal welfare committee of the MPI-IE and the local authorities. No animal experimentation was performed, a.......
FACS sorting enables the isolation of clean populations of different cell types from the same cell suspension (Figure 2 and Figure 3). The specificity of this method relies on the staining of the different cell types with specific surface markers (for example, B cells and T cells from the spleen) or specific combinations of surface markers (for example HSCs and MPPs). Staining of intracellular markers typically requires permeabilization of the cell membrane. Thi.......
The most critical steps for successful implementation of targeted metabolomics using this protocol are 1) a robust staining and gating strategy that will yield clean cell populations 2) precise handling of liquid volumes, 3) reproducible timing of all experimental steps, in particular all steps prior to metabolite extraction. Ideally, all samples belonging to one experiment should be processed and measured in one batch to minimize batch effects22. For larger experiments, we suggest collecting cell.......
The authors would like to thank the animal facility of the Max Planck Institute of Immunobiology and Epigenetics for providing the animals used in this study.
....Name | Company | Catalog Number | Comments |
13C yeast extract | Isotopic Solutions | ISO-1 | |
40 µm cell strainer | Corning | 352340 | |
Acetonitrile, LC-MS grade | VWR | 83640.32 | |
ACK lysis buffer | Gibco | 104921 | Alternatively: Lonza, Cat# BP10-548E |
Adenosine diphosphate (ADP) | Sigma Aldrich | A2754 | |
Adenosine monophosphate (AMP) | Sigma Aldrich | A1752 | |
Adenosine triphosphate (ATP) | Sigma Aldrich | A2383 | |
Ammonium Carbonate, HPLC grade | Fisher Scientific | A/3686/50 | |
Atlantis Premier BEH Z-HILIC column (100 x 2.1 mm, 1.7 µm) | Waters | 186009982 | |
B220-A647 | Invitrogen | 103226 | |
B220-PE/Cy7 | BioLegend | 103222 | RRID:AB_313005 |
CD11b-PE/Cy7 | BioLegend | 101216 | RRID:AB_312799 |
CD150-BV605 | BioLegend | 115927 | RRID:AB_11204248 |
CD3-PE | Invitrogen | 12-0031-83 | |
CD48-BV421 | BioLegend | 103428 | RRID:AB_2650894 |
CD4-PE/Cy7 | BioLegend | 100422 | RRID:AB_2660860 |
CD8a-PE/Cy7 | BioLegend | 100722 | RRID:AB_312761 |
cKit-PE | BioLegend | 105808 | RRID:AB_313217 |
Dynabeads Untouched Mouse CD4 Cells Kit | Invitrogen | 11415D | |
FACSAria III | BD | ||
Gr1-PE/Cy7 | BioLegend | 108416 | RRID:AB_313381 |
Heat sealing foil | Neolab | Jul-18 | |
Isoleucine | Sigma Aldrich | 58880 | |
JetStream ESI Source | Agilent | G1958B | |
Leucine | Sigma Aldrich | L8000 | |
Medronic acid | Sigma Aldrich | M9508-1G | |
Methanol, LC-MS grade | Carl Roth | HN41.2 | |
NaCl | Fluka | 31434-1KG | |
PBS | Sigma Aldrich | D8537 | |
Sca1-APC/Cy7 | BioLegend | 108126 | RRID:AB_10645327 |
TER119-PE/Cy7 | BioLegend | 116221 | RRID:AB_2137789 |
Triple Quadrupole Mass Spectrometer | Agilent | 6495B | |
Twin.tec PCR plate 96 well LoBind skirted | Eppendorf | 30129512 | |
UHPLC Autosampler | Agilent | G7157B | |
UHPLC Column Thermostat | Agilent | G7116B | |
UHPLC Pump | Agilent | G7120A | |
UHPLC Sample Thermostat | Agilent | G4761A |
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