Single cell metabolism: current and future trends

Ali, Ahmed; Davidson, Shawn M.; Fraenkel, Ernest; Gilmore, Ian S.; Hankemeier, Thomas; Kirwan, Jennifer; Lane, Andrew N.; Lanekoff, Ingela; Larion, Mioara; McCall, Laura-Isobel; Murphy, Michael; Sweedler, Jonathan V.; Zhu, Caigang

doi:10.1007/s11306-022-01934-3

Cited by 20 publications

(6 citation statements)

References 198 publications

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“…The development and increased accessibility of novel technologies will continue to yield breakthroughs in quantitative metabolomics studies. Techniques such as ion mobility or newly adapted ionization methods have become available, enabling new approaches like quantitative single‐cell analysis 143 , 144 , 145 or quantitative metabolic flux analysis. 146 , 147 For instance, ion mobility separation can help compensate for the lack of chromatographic separation in mass spectrometry imaging.…”

Section: Discussionmentioning

confidence: 99%

Challenges and recent advances in quantitative mass spectrometry‐based metabolomics

Ghafari,

Sleno

2024

Analytical Science Advances

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The field of metabolomics has gained tremendous interest in recent years. Whether the goal is to discover biomarkers related to certain pathologies or to better understand the impact of a drug or contaminant, numerous studies have demonstrated how crucial it is to understand variations in metabolism. Detailed knowledge of metabolic variabilities can lead to more effective treatments, as well as faster or less invasive diagnostics. Exploratory approaches are often employed in metabolomics, using relative quantitation to look at perturbations between groups of samples. Most metabolomics studies have been based on metabolite profiling using relative quantitation, with very few studies using an approach for absolute quantitation. Using accurate quantitation facilitates the comparison between different studies, as well as enabling longitudinal studies. In this review, we discuss the most widely used techniques for quantitative metabolomics using mass spectrometry (MS). Various aspects will be addressed, such as the use of external and/or internal standards, derivatization techniques, in vivo isotopic labelling, or quantitative MS imaging. The principles, as well as the associated limitations and challenges, will be described for each approach.

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Section: Discussionmentioning

confidence: 99%

Challenges and recent advances in quantitative mass spectrometry‐based metabolomics

Ghafari,

Sleno

2024

Analytical Science Advances

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“…A further challenge with all these studies is that none of them directly measured parasite metabolism in situ, within tissues. Improvements in the spatial resolution of imaging mass spectrometry and single-cell metabolomics may help partially address these concerns [65,66].…”

Section: Importance Of Exogenous Metabolites For T Cruzi During Mamma...mentioning

confidence: 99%

Small molecule mediators of host-T. cruzi-environment interactions in Chagas disease

Kwakye-Nuako,

Middleton,

McCall

2024

PLoS Pathog

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Small molecules (less than 1,500 Da) include major biological signals that mediate host-pathogen-microbiome communication. They also include key intermediates of metabolism and critical cellular building blocks. Pathogens present with unique nutritional needs that restrict pathogen colonization or promote tissue damage. In parallel, parts of host metabolism are responsive to immune signaling and regulated by immune cascades. These interactions can trigger both adaptive and maladaptive metabolic changes in the host, with microbiome-derived signals also contributing to disease progression. In turn, targeting pathogen metabolic needs or maladaptive host metabolic changes is an important strategy to develop new treatments for infectious diseases. Trypanosoma cruzi is a single-celled eukaryotic pathogen and the causative agent of Chagas disease, a neglected tropical disease associated with cardiac and intestinal dysfunction. Here, we discuss the role of small molecules during T. cruzi infection in its vector and in the mammalian host. We integrate these findings to build a theoretical interpretation of how maladaptive metabolic changes drive Chagas disease and extrapolate on how these findings can guide drug development.

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“…In recent years, technologies for high-resolution spatial “mapping” of metabolites have been advancing rapidly ( 117 ). The spatial resolution of Mass Spectrometry Imaging (MSI) technologies has been improving and currently reaching below 10-mm spatial resolution in some systems.…”

Section: Perspectivementioning

confidence: 99%

Plant and microbial sciences as key drivers in the development of metabolomics research

Aharoni

Goodacre

Fernie

2023

Proc. Natl. Acad. Sci. U.S.A.

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This year marks the 25th anniversary of the coinage of the term metabolome [S. G. Oliver et al ., Trends Biotech. 16 , 373–378 (1998)]. As the field rapidly advances, it is important to take stock of the progress which has been made to best inform the disciplines future. While a medical-centric perspective on metabolomics has recently been published [M. Giera et al ., Cell Metab. 34 , 21–34 (2022)], this largely ignores the pioneering contributions made by the plant and microbial science communities. In this perspective, we provide a contemporary overview of all fields in which metabolomics is employed with particular emphasis on both methodological and application breakthroughs made in plant and microbial sciences that have shaped this evolving research discipline from the very early days of its establishment. This will not cover all types of metabolomics assays currently employed but will focus mainly on those utilizing mass spectrometry–based measurements since they are currently by far the most prominent. Having established the historical context of metabolomics, we will address the key challenges currently facing metabolomics and offer potential approaches by which these can be faced. Most salient among these is the fact that the vast majority of mass features are as yet not annotated with high confidence; what we may refer to as definitive identification. We discuss the potential of both standard compound libraries and artificial intelligence technologies to address this challenge and the use of natural variance–based approaches such as genome-wide association studies in attempt to assign specific functions to the myriad of structurally similar and complex specialized metabolites. We conclude by stating our contention that as these challenges are epic and that they will need far greater cooperative efforts from biologists, chemists, and computer scientists with an interest in all kingdoms of life than have been made to date. Ultimately, a better linkage of metabolome and genome data will likely also be needed particularly considering the Earth BioGenome Project.

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Single cell metabolism: current and future trends

Cited by 20 publications

References 198 publications

Challenges and recent advances in quantitative mass spectrometry‐based metabolomics

Challenges and recent advances in quantitative mass spectrometry‐based metabolomics

Small molecule mediators of host-T. cruzi-environment interactions in Chagas disease

Plant and microbial sciences as key drivers in the development of metabolomics research

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