Special Issue "From Samples to Insights into Metabolism for Precision Medicine"

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: 15 September 2023 | Viewed by 1446

Special Issue Editors

Institut d’Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
Interests: precision medicine; clinical applications; metabolomics; volatilomics; MS; NMR; QA/QC; ion mobility spectrometry; MEMS; data learning; meta-analysis; ethics; ML; scientific dissemination
Denali Therapeutics, South San Francisco, CA, USA
Interests: precision medicine; patient phenotyping; metabolomics; lipidomics; data mining; clinical biomarker development; clinical trials
Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 452 McCallum Bldg, 1918 University Blvd, Birmingham, AL 35294, USA
Interests: bile acids; polyphenols; metabolomics; NMR; mass spectrometry

Special Issue Information

Dear Colleagues,

Large-scale metabolomics studies are gaining interest, as is the need to develop metabolome-wide association studies (MWAS). Large-scale initiatives such as NIH “All of Us” and extensive clinical studies will provide the metabolomics community with more reliable biomarkers of specific diseases. However, the path to achieving MWAS as a precision medicine tool for clinics needs to be paved, following the FAIR principles.

We will cover all steps to achieve reliable and cost-effective MWAS for precision medicine with the current Special Issue. Specifically:

1) Samples and Experimentally related issues: Biofluid collection and preservation, including POC devices; the need for fast, robust, and reliable high throughput methods; strategies for removing multiple batch variations (internal standards, QC’s, statistically, RUV algorithms); raw spectra processing issues (larger files, different formats).

2) Meta-data collection: Informed consent and data protection (such as HIPPA) compliances; public and digital health collaborations (personalized tools); minimum of anthropometrical, prescription and health status data needed.

3) Progression of Profiling to Identification: Metabolites identification to support iterative downstream investigations; appropriate levels of compound identification (MSI); software tools for processing and identification; the need to report databases used (in silico, public or in-house libraries).

4) Insights of the Metabolism: Statistic (univariate vs. multivariate) and normalization in MWAS; pathway analysis validity for biological fluids (as opposed to cells or tissue); data reporting for further re-analysis with meta-analysis; repositories needed for MWAS; reliability of MWAS results.

Dr. Raquel Cumeras
Dr. Jung H. Suh
Prof. Dr. Stephen Barnes
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • large scale metabolomics
  • biofluid collection and preservation
  • high throughput screening methods
  • batch variations
  • raw spectras processing issues
  • informed consent and data protection
  • public and digital health collaborations (personalized tools)
  • clinical metadata
  • metabolites identification
  • software tools for processing and identification
  • metabolism
  • large-scale statistic and normaltization
  • pathway analysis
  • data reporting
  • meta-analysis
  • large-scale repositiories

Published Papers (1 paper)

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Development of an Untargeted Metabolomics Strategy to Study the Metabolic Rewiring of Dendritic Cells upon Lipopolysaccharide Activation
Metabolites 2023, 13(3), 311; https://doi.org/10.3390/metabo13030311 - 21 Feb 2023
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Dendritic cells (DCs) are essential immune cells for defense against external pathogens. Upon activation, DCs undergo profound metabolic alterations whose precise nature remains poorly studied at a large scale and is thus far from being fully understood. The goal of the present work [...] Read more.
Dendritic cells (DCs) are essential immune cells for defense against external pathogens. Upon activation, DCs undergo profound metabolic alterations whose precise nature remains poorly studied at a large scale and is thus far from being fully understood. The goal of the present work was to develop a reliable and accurate untargeted metabolomics workflow to get a deeper insight into the metabolism of DCs when exposed to an infectious agent (lipopolysaccharide, LPS, was used to mimic bacterial infection). As DCs transition rapidly from a non-adherent to an adherent state upon LPS exposure, one of the leading analytical challenges was to implement a single protocol suitable for getting comparable metabolomic snapshots of those two cellular states. Thus, a thoroughly optimized and robust sample preparation method consisting of a one-pot solvent-assisted method for the simultaneous cell lysis/metabolism quenching and metabolite extraction was first implemented to measure intracellular DC metabolites in an unbiased manner. We also placed special emphasis on metabolome coverage and annotation by using a combination of hydrophilic interaction liquid chromatography and reverse phase columns coupled to high-resolution mass spectrometry in conjunction with an in-house developed spectral database to identify metabolites at a high confidence level. Overall, we were able to characterize up to 171 unique meaningful metabolites in DCs. We then preliminarily compared the metabolic profiles of DCs derived from monocytes of 12 healthy donors upon in vitro LPS activation in a time-course experiment. Interestingly, the resulting data revealed differential and time-dependent activation of some particular metabolic pathways, the most impacted being nucleotides, nucleotide sugars, polyamines pathways, the TCA cycle, and to a lesser extent, the arginine pathway. Full article
(This article belongs to the Special Issue From Samples to Insights into Metabolism for Precision Medicine)
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