Single-cell metabolomics by mass spectrometry: Advances, challenges, and future applications

Ali, Ahmed; Abouleila, Yasmine; Shimizu, Yoshihiro; Hiyama, Eiso; Emara, Samy; Mashaghi, Alireza; Hankemeier, Thomas

doi:10.1016/j.trac.2019.02.033

Cited by 80 publications

(51 citation statements)

References 107 publications

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“…Immunometabolism is an emerging field in biomedicine that explores the crosstalk between inflammatory processes and metabolic signaling. Metabolic profiling is increasingly used to find novel disease biomarkers that inform on disease activity and therapeutic outcomes [11,12], and provide insights into phenotypical variations between individual cells [13,14]. The importance of metabolic and immunometabolic processes in ocular surface diseases has been increasingly reported [15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Signaling lipids as diagnostic biomarkers for ocular surface cicatrizing conjunctivitis

et al. 2020

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Metabolomics has been applied to diagnose diseases, predict disease progression, and design therapeutic strategies in various areas of medicine. However, it remains to be applied to the ocular surface diseases, where biological samples are often of limited quantities. We successfully performed proof-of-concept metabolomics assessment of volume-limited cytology samples from a clinical form of chronic inflammatory cicatrizing conjunctivitis, i.e., ocular MMP and discovered metabolic changes of signaling lipid mediators upon disease onset and progression. The metabolomics assessment revealed active oxylipins, lysophospholipids, fatty acids, and endocannabinoids alterations, from which potential biomarkers linked to inflammatory processes were identified. Possible underlying mechanisms such as dysregulated enzyme activities (e.g., lipoxygenases, cytochrome P450, and phospholipases) were suggested which may be considered as potential therapeutic targets in future studies. Key messages & Metabolic profile of the ocular surface can be measured using impression cytology samples. & Metabolomics analysis of ocular pemphigoid is presented for the first time. & The metabolomics assessment of OCP patients revealed active oxylipins, lysophospholipids, fatty acids, and endocannabinoids alterations. & Several oxylipins are identified as diagnostic biomarkers for OCP.

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Section: Introductionmentioning

confidence: 99%

Signaling lipids as diagnostic biomarkers for ocular surface cicatrizing conjunctivitis

et al. 2020

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“…The resulting cell pellets were washed four times with 10 mL PBS before resuspending the washed cell pellets in PBS. After the floating cell suspension in 1 mL PBS was counted using a cell counter (Moxi Z, ASONE Co., Osaka, Japan), 1×10 5 cells were transferred to a 1.5-mL polypropylene Eppendorf tube.…”

Section: Cell Culture and Sample Preparationmentioning

confidence: 99%

“…In recent years, various technologies have been developed for obtaining data on hydrophilic metabolites at the tissue-or cell-specific level. 4,5) Matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) under a microscope, imaging mass spectrometry, and live single-cell mass spectrometry (LSCMS) are potential tools for single-cell metabolomics. [6][7][8] However, polar primary metabolites have not yet been identified from single-cells using these techniques.…”

Section: Introductionmentioning

confidence: 99%

An Analytical System for Single-Cell Metabolomics of Typical Mammalian Cells Based on Highly Sensitive Nano-Liquid Chromatography Tandem Mass Spectrometry

et al. 2020

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The rapid development of next-generation sequencing techniques has enabled single-cell genomic and transcriptomic analyses, which have revealed the importance of heterogeneity in biological systems. However, analytical methods to accurately identify and quantify comprehensive metabolites from single mammalian cells with a typical diameter of 10-20 µm are still in the process of development. The aim of this study was to develop a single-cell metabolomic analytical system based on highly sensitive nanoliquid chromatography tandem mass spectrometry (nano-LC-MS/MS) with multiple reaction monitoring. A packed nano-LC column (3-µm particle-size pentafluorophenylpropyl Discovery HSF5 of dimensions 100 µm i.d.×180 mm) was prepared using a slurry technique. The optimized nano-LC-MS/MS method showed 3-132-fold (average value, 26-fold) greater sensitivity than semimicro-LC-MS/MS, and the detection limits for several hydrophilic metabolites, including amino acids and nucleic acid related metabolites were in the sub-fmol range. By combining live single-cell sampling and nano-LC-MS/MS, we successfully detected 18 relatively abundant hydrophilic metabolites (16 amino acids and 2 nucleic acid related metabolites) from single HeLa cells (n=22). Based on single-cell metabolic profiles, the 22 HeLa cells were classified into three distinct subclasses, suggesting differences in metabolic function in cultured HeLa cell populations. Our single-cell metabolomic analytical system represents a potentially useful tool for in-depth studies focused on cell metabolism and heterogeneity.

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“…This is critical to the fundamental understanding of tumor biology and the design of therapeutic strategies. Nevertheless, considerable progress is being made via single cell analyses of genome, transcriptome [13,21,22,[40][41][42][43][44][45][46][47][48][49], proteome [50][51][52], and metabolome [8,[52][53][54][55][56][57]. Although spatially resolved single cell metabolism has long been studied by live cell microscopy, the number of metabolites that can be detected and quantified is very limited [58][59][60][61].…”

Section: Global Cell Typesmentioning

confidence: 99%

Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective

et al. 2020

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The tumor microenvironment (TME) comprises complex interactions of multiple cell types that determines cell behavior and metabolism such as nutrient competition and immune suppression. We discuss the various types of heterogeneity that exist in solid tumors, and the complications this invokes for studies of TME. As human subjects and in vivo model systems are complex and difficult to manipulate, simpler 3D model systems that are compatible with flexible experimental control are necessary for studying metabolic regulation in TME. Stable Isotope Resolved Metabolomics (SIRM) is a valuable tool for tracing metabolic networks in complex systems, but at present does not directly address heterogeneous metabolism at the individual cell level. We compare the advantages and disadvantages of different model systems for SIRM experiments, with a focus on lung cancer cells, their interactions with macrophages and T cells, and their response to modulators in the immune microenvironment. We describe the experimental set up, illustrate results from 3D cultures and co-cultures of lung cancer cells with human macrophages, and outline strategies to address the heterogeneous TME.

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Single-cell metabolomics by mass spectrometry: Advances, challenges, and future applications

Cited by 80 publications

References 107 publications

Signaling lipids as diagnostic biomarkers for ocular surface cicatrizing conjunctivitis

Signaling lipids as diagnostic biomarkers for ocular surface cicatrizing conjunctivitis

An Analytical System for Single-Cell Metabolomics of Typical Mammalian Cells Based on Highly Sensitive Nano-Liquid Chromatography Tandem Mass Spectrometry

Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective

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