Multivariate analysis of NMR‐based metabolomic data

Debik, Julia; Sangermani, Matteo; Wang, Feng; Madssen, Torfinn Støve; Giskeødegård, Guro F.

doi:10.1002/nbm.4638

Cited by 29 publications

(19 citation statements)

References 146 publications

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“…A mass spectrometry-based untargeted metabolomic analysis approach was applied to assess the metabolic changes triggered by a sublethal concentration of AgNPs in the two lifeforms. To provide a global perspective of the meta-bolomes under each condition, we performed a PCA analysis [ 45 ]. Both the planktonic and biofilm control groups diverged, indicating differences in their basal metabolome ( Figure 3 a and Figure 5 ).…”

Section: Discussionmentioning

confidence: 99%

Metabolomic Profiling of the Responses of Planktonic and Biofilm Vibrio cholerae to Silver Nanoparticles

et al. 2022

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Vibrio cholerae causes cholera and can switch between planktonic and biofilm lifeforms, where biofilm formation enhances transmission, virulence, and antibiotic resistance. Due to antibiotic microbial resistance, new antimicrobials including silver nanoparticles (AgNPs) are being studied. Nevertheless, little is known about the metabolic changes exerted by AgNPs on both microbial lifeforms. Our objective was to evaluate the changes in the metabolomic profile of V. cholerae planktonic and biofilm cells in response to sublethal concentrations of AgNPs using MS2 untargeted metabolomics and chemoinformatics. A total of 690 metabolites were quantified among all groups. More metabolites were significantly modulated in planktonic cells (n = 71) compared to biofilm (n = 37) by the treatment. The chemical class profiles were distinct for both planktonic and biofilm, suggesting a phenotype-dependent metabolic response to the nanoparticles. Chemical enrichment analysis showed altered abundances of oxidized fatty acids (FA), saturated FA, phosphatidic acids, and saturated stearic acid in planktonic cells treated with AgNPs, which hints at a turnover of the membrane. In contrast, no chemical classes were enriched in the biofilm. In conclusion, this study suggests that the response of V. cholerae to silver nanoparticles is phenotype-dependent and that planktonic cells experience a lipid remodeling process, possibly related to an adaptive mechanism involving the cell membrane.

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Section: Discussionmentioning

confidence: 99%

Metabolomic Profiling of the Responses of Planktonic and Biofilm Vibrio cholerae to Silver Nanoparticles

et al. 2022

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“…Typically, these analyses will assist in identifying differential significant metabolites (or metabolite features) in datasets. Details on various possibilities of handling NMR-based metabolomics data can be consulted elsewhere ( Blaise et al, 2021 ; Debik et al, 2022 ). Beyond statistical treatment, web-based tools like MetaboAnalyst ( Chong et al, 2018 ) allow to visualise metabolomics data in an user-friendly way, and are able to perform additional tasks, as for example pathway enrichment analysis ( Wieder et al, 2021 ).…”

Section: Computational Tools and Resourcesmentioning

confidence: 99%

Studying Metabolism by NMR-Based Metabolomics

Moco

2022

Front. Mol. Biosci.

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During the past few decades, the direct analysis of metabolic intermediates in biological samples has greatly improved the understanding of metabolic processes. The most used technologies for these advances have been mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. NMR is traditionally used to elucidate molecular structures and has now been extended to the analysis of complex mixtures, as biological samples: NMR-based metabolomics. There are however other areas of small molecule biochemistry for which NMR is equally powerful. These include the quantification of metabolites (qNMR); the use of stable isotope tracers to determine the metabolic fate of drugs or nutrients, unravelling of new metabolic pathways, and flux through pathways; and metabolite-protein interactions for understanding metabolic regulation and pharmacological effects. Computational tools and resources for automating analysis of spectra and extracting meaningful biochemical information has developed in tandem and contributes to a more detailed understanding of systems biochemistry. In this review, we highlight the contribution of NMR in small molecule biochemistry, specifically in metabolic studies by reviewing the state-of-the-art methodologies of NMR spectroscopy and future directions.

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“…In metabolomics, it is therefore common practice to use multivariate statistical tools to compare cells that are cultured under different conditions or exposed to different interventions without the need for normalization to biomass. 14 While this relaxes the requirements for analytical accuracy, the precision must be sufficient to allow reproducible comparisons of specimens. The same applies to metabolic analysis of organoids.…”

Section: Analysis Of Mr Spectra From Extracts and Hr Masmentioning

confidence: 99%

Metabolic profiling of colorectal cancer organoids: A comparison between high‐resolution magic angle spinning magnetic resonance spectroscopy and solution nuclear magnetic resonance spectroscopy of polar extracts

et al. 2022

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Patient‐derived cancer cells cultured in vitro are a cornerstone of cancer metabolism research. More recently, the introduction of organoids has provided the research community with a more versatile model system. Physiological structure and organization of the cell source tissue are maintained in organoids, representing a closer link to in vivo tumor models. High‐resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) is a commonly applied analytical approach for metabolic profiling of intact tissue, but its use has not been reported for organoids. The aim of the current work was to compare the performance of HR MAS MRS and extraction‐based nuclear magnetic resonance (NMR) in metabolic profiling of wild‐type and tumor progression organoids (TPOs) from human colon cancer, and further to investigate how the sequentially increased genetic alterations of the TPOs affect the metabolic profile. Sixteen metabolites were reliably identified and quantified both in spectra based on NMR of extracts and HR MAS MRS of intact organoids. The metabolite concentrations from the two approaches were highly correlated (r = 0.94), and both approaches were able to capture the systematic changes in metabolic features introduced by the genetic alterations characteristic of colorectal cancer progression (e.g., increased levels of lactate and decreased levels of myo‐inositol and phosphocholine with an increasing number of mutations). The current work highlights that HR MAS MRS is a well‐suited method for metabolic profiling of intact organoids, with the additional benefit that the nondestructive nature of HR MAS enables subsequent recovery of the organoids for further analyses based on nucleic acids or proteins.

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Multivariate analysis of NMR‐based metabolomic data

Cited by 29 publications

References 146 publications

Metabolomic Profiling of the Responses of Planktonic and Biofilm Vibrio cholerae to Silver Nanoparticles

Metabolomic Profiling of the Responses of Planktonic and Biofilm Vibrio cholerae to Silver Nanoparticles

Studying Metabolism by NMR-Based Metabolomics

Metabolic profiling of colorectal cancer organoids: A comparison between high‐resolution magic angle spinning magnetic resonance spectroscopy and solution nuclear magnetic resonance spectroscopy of polar extracts

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