Advances in mass spectrometry based single-cell metabolomics

Duncan, Kyle D.; Fyrestam, Jonas; Lanekoff, Ingela

doi:10.1039/c8an01581c

Cited by 196 publications

(128 citation statements)

References 62 publications

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“…This may be a further direction for increasing the information for AOP development to advance from the cellular to tissue and organ response. Remarkable developments have recently been made for single-cell proteomics and metabolomics (Yang et al 2019;Duncan et al 2019). However, compared to sequencing-based approaches, the applicability of these methods is still limited by the number of cells that can be profiled, or the number of biomolecules detected in parallel.…”

Section: Which Omics Layers To Use For Toxicological Research Questionsmentioning

confidence: 99%

Prospects and challenges of multi-omics data integration in toxicology

et al. 2020

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Exposure of cells or organisms to chemicals can trigger a series of effects at the regulatory pathway level, which involve changes of levels, interactions, and feedback loops of biomolecules of different types. A single-omics technique, e.g., transcriptomics, will detect biomolecules of one type and thus can only capture changes in a small subset of the biological cascade. Therefore, although applying single-omics analyses can lead to the identification of biomarkers for certain exposures, they cannot provide a systemic understanding of toxicity pathways or adverse outcome pathways. Integration of multiple omics data sets promises a substantial improvement in detecting this pathway response to a toxicant, by an increase of information as such and especially by a systemic understanding. Here, we report the findings of a thorough evaluation of the prospects and challenges of multi-omics data integration in toxicological research. We review the availability of such data, discuss options for experimental design, evaluate methods for integration and analysis of multi-omics data, discuss best practices, and identify knowledge gaps. Re-analyzing published data, we demonstrate that multi-omics data integration can considerably improve the confidence in detecting a pathway response. Finally, we argue that more data need to be generated from studies with a multi-omics-focused design, to define which omics layers contribute most to the identification of a pathway response to a toxicant.Archives of Toxicology (2020) 94:371-388Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Section: Which Omics Layers To Use For Toxicological Research Questionsmentioning

confidence: 99%

Prospects and challenges of multi-omics data integration in toxicology

et al. 2020

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“…65 Increased emphasis on studying immune cell metabolism in vivo, or in more sophisticated culture systems such as those provided by organoids, 107,108 is therefore warranted. In this general context, the application of advances in single-cell metabolomics 109 and spatial metabolomics [110][111][112][113] has the potential to greatly improve the resolution of future studies.…”

Section: Future Pros Pec Tsmentioning

confidence: 99%

Cell‐intrinsic metabolic regulation of mononuclear phagocyte activation: Findings from the tip of the iceberg

Bakker

Pearce

2020

Immunological Reviews

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We have only recently started to appreciate the extent to which immune cell activation involves significant changes in cellular metabolism. We are now beginning to understand how commitment to specific metabolic pathways influences aspects of cellular biology that are the more usual focus of immunological studies, such as activation-induced changes in gene transcription, post-transcriptional regulation of transcription, post-translational modifications of proteins, cytokine secretion, etc. Here, we focus on metabolic reprogramming in mononuclear phagocytes downstream of stimulation with inflammatory signals (such as LPS and IFNγ) vs alternative activation signals (IL-4), with an emphasis on work on dendritic cells and macrophages from our laboratory, and related studies from others. We cover aspects of glycolysis and its branching pathways (glycogen synthesis, pentose phosphate, serine synthesis, hexose synthesis, and glycerol 3 phosphate shuttle), the tricarboxylic acid pathway, fatty acid synthesis and oxidation, and mitochondrial biology. Although our understanding of the metabolism of mononuclear phagocytes has progressed significantly over the last 10 years, major challenges remain, including understanding the effects of tissue residence on metabolic programming related to cellular activation, and the translatability of findings from mouse to human biology. K E Y W O R D SThis is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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“…In vivo extraction and detection of compounds of biological and environmental interest from small living organisms and single cells is a challenging task due to reduced sample dimension, but it is of paramount importance to give an insight in microsize processes. In this context, ambient MS provides a straightforward strategy for direct analysis of individual organisms and single cells under ambient conditions [82,83].…”

Section: In Vivo Spme Extraction Of Cells and Simple Organismsmentioning

confidence: 99%

Recent Advances in In Vivo SPME Sampling

et al. 2020

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In vivo solid-phase microextraction (SPME) has been recently proposed for the extraction, clean-up and preconcentration of analytes of biological and clinical concern. Bioanalysis can be performed by sampling exo- or endogenous compounds directly in living organisms with minimum invasiveness. In this context, innovative and miniaturized devices characterized by both commercial and lab-made coatings for in vivo SPME tissue sampling have been proposed, thus assessing the feasibility of this technique for biomarker discovery, metabolomics studies or for evaluating the environmental conditions to which organisms can be exposed. Finally, the possibility of directly interfacing SPME to mass spectrometers represents a valuable tool for the rapid quali- and quantitative analysis of complex matrices. This review article provides a survey of in vivo SPME applications focusing on the extraction of tissues, cells and simple organisms. This survey will attempt to cover the state-of- the-art from 2014 up to 2019.

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Advances in mass spectrometry based single-cell metabolomics

Abstract: Single cell metabolomics using mass spectrometry can contribute to understanding biological activities in health and disease.

Cited by 196 publications

References 62 publications

Prospects and challenges of multi-omics data integration in toxicology

Prospects and challenges of multi-omics data integration in toxicology

Cell‐intrinsic metabolic regulation of mononuclear phagocyte activation: Findings from the tip of the iceberg

Recent Advances in In Vivo SPME Sampling

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