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Metabolomics in Health and Disease 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 April 2024) | Viewed by 10142

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Dr. Ana Varela Coelho

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Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
Interests: proteomics; metabolomics; mass spectrometry; host-pathogen interaction; tissue/organ regeneration; marine organisms; antimicrobials; echinoderms
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Special Issue Information

Dear Colleagues,

Metabolomics is the systematic quantification of a large part of the metabolites of a biological system (cell, tissue, organ, biological fluid, or organism) at a specific point in time. Based on the goal of the determination, metabolomics might be divided into untargeted (aiming to determine the largest part of the metabolome) or targeted (focused on the specific quantification of a selected part of the metabolome).

Mass spectrometry and nuclear magnetic resonance spectroscopy are the gold standard techniques for metabolomics. In the particular case of mass spectrometry, we can find a wealth of instrumental configurations. In addition, alternative techniques—either standalone or in combination with mass spectrometry—have also been tested for metabolomic studies. Notable examples are ion mobility spectrometry, Raman spectroscopy, infrared spectroscopy, and others.

Since metabolomics analysis generates large-scale and complex datasets, data analysis is crucial to extract biologically relevant information. Many metabolomics studies feature moderate sample counts, extremely high dimensional datasets, and complex experimental designs that require careful use of advanced statistics and machine learning.

Metabolomics is considered to provide a close link to the organism’s phenotype. Thus, alterations in the metabolome can be used as biomarkers for diagnosis, prognosis, or evolution monitoring of a wide range of diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, or rare diseases. Additionally, metabolomics can provide useful information regarding the mechanism underlying the pathological status. For all these reasons, metabolomics have become one of the most promising tools in health and disease.

This Special Issue, “Metabolomics in Health and Disease”, aims to provide a summary of the field and to explore the application of metabolomics for diagnosis, prognosis, and/or mechanism elucidation in different diseases using either human samples or animal models for disease. We warmly welcome original research and review articles dealing with these aspects.

Dr. Ana Varela Coelho
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Keywords

biomarkers
mass spectrometry
NMR
alternative analytical platforms for metabolomics
data processing workflows
computational biomarker discovery
volatile metabolomics
cancer
neurodegenerative diseases
cardiovascular diseases
epidemiology
rare diseases

Published Papers (7 papers)

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Research

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20 pages, 4803 KiB

Open AccessArticle

Insights into the Serum Metabolic Adaptations in Response to Inspiratory Muscle Training: A Metabolomic Approach Based on ¹H NMR and UHPLC-HRMS/MS

by Alex Castro, Aparecida M. Catai, Patrícia Rehder-Santos, Étore F. Signini, Raphael Martins de Abreu, Claudio Donisete Da Silva, Carla Cristina Dato, Regina V. Oliveira and Antônio G. Ferreira

Int. J. Mol. Sci. 2023, 24(23), 16764; https://doi.org/10.3390/ijms242316764 - 25 Nov 2023

Viewed by 1301

Abstract

Inspiratory muscle training (IMT) is known to promote physiological benefits and improve physical performance in endurance sports activities. However, the metabolic adaptations promoted by different IMT prescribing strategies remain unclear. In this work, a longitudinal, randomized, double-blind, sham-controlled, parallel trial was performed to investigate the effects of 11 weeks (3 days·week⁻¹) of IMT at different exercise intensities on the serum metabolomics profile and its main regulated metabolic pathways. Twenty-eight healthy male recreational cyclists (30.4 ± 6.5 years) were randomized into three groups: sham (6 cm·H₂O of inspiratory pressure, n = 7), moderate-intensity (MI group, 60% maximal inspiratory pressure (MIP), n = 11) and high-intensity (HI group, 85–90% MIP, n = 10). Blood serum samples were collected before and after 11 weeks of IMT and analyzed by ¹H NMR and UHPLC-HRMS/MS. Data were analyzed using linear mixed models and metabolite set enrichment analysis. The ¹H NMR and UHPLC-HRMS/MS techniques resulted in 46 and 200 compounds, respectively. These results showed that ketone body metabolism, fatty acid biosynthesis, and aminoacyl-tRNA biosynthesis were upregulated after IMT, while alpha linolenic acid and linoleic acid metabolism as well as biosynthesis of unsaturated fatty acids were downregulated. The MI group presented higher MIP, Tryptophan, and Valine levels but decreased 2-Hydroxybutyrate levels when compared to the other two studied groups. These results suggest an increase in the oxidative metabolic processes after IMT at different intensities with additional evidence for the upregulation of essential amino acid metabolism in the MI group accompanied by greater improvement in respiratory muscle strength. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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14 pages, 2086 KiB

Open AccessArticle

Human Serum and Salivary Metabolomes: Diversity and Closeness

by Elena Ferrari, Mariana Gallo, Alberto Spisni, Rita Antonelli, Marco Meleti and Thelma A. Pertinhez

Int. J. Mol. Sci. 2023, 24(23), 16603; https://doi.org/10.3390/ijms242316603 - 22 Nov 2023

Viewed by 711

Abstract

Saliva, which contains molecular information that may reflect an individual’s health status, has become a valuable tool for discovering biomarkers of oral and general diseases. Due to the high vascularization of the salivary glands, there is a molecular exchange between blood and saliva. However, the composition of saliva is complex and influenced by multiple factors. This study aimed to investigate the possible relationships between the salivary and serum metabolomes to gain a comprehensive view of the metabolic phenotype under physiological conditions. Using ¹H-NMR spectroscopy, we obtained the serum metabolite profiles of 20 healthy young individuals and compared them with the metabolomes of parotid, submandibular/sublingual, and whole-saliva samples collected concurrently from the same individuals using multivariate and univariate statistical analysis. Our results show that serum is more concentrated and less variable for most of the shared metabolites than the three saliva types. While we found moderate to strong correlations between serum and saliva concentrations of specific metabolites, saliva is not simply an ultrafiltrate of blood. The intense oral metabolism prevents very strong correlations between serum and salivary concentrations. This study contributes to a better understanding of salivary metabolic composition, which is crucial for utilizing saliva in laboratory diagnostics. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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17 pages, 3661 KiB

Open AccessArticle

Untargeted Lipidomics Study of Bipolar Disorder Patients in Serbia

by Milka Jadranin, Nataša Avramović, Zoran Miladinović, Aleksandra Gavrilović, Ljubica Tasic, Vele Tešević and Boris Mandić

Int. J. Mol. Sci. 2023, 24(22), 16025; https://doi.org/10.3390/ijms242216025 - 07 Nov 2023

Viewed by 823

Abstract

The Lipidomic profiles of serum samples from patients with bipolar disorder (BD) and healthy controls (C) were explored and compared. The sample cohort included 31 BD patients and 31 control individuals. An untargeted lipidomics study applying liquid chromatography (LC) coupled with high-resolution mass spectrometry (HRMS) was conducted to achieve the lipid profiles. Multivariate statistical analyses (principal component analysis and partial least squares discriminant analysis) were performed, and fifty-six differential lipids were confirmed in BD and controls. Our results pointed to alterations in lipid metabolism, including pathways of glycerophospholipids, sphingolipids, glycerolipids, and sterol lipids, in BD patient sera. This study emphasized the role of lipid pathways in BD, and comprehensive research using the LC-HRMS platform is necessary for future application in the diagnosis and improvement of BD treatments. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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23 pages, 6222 KiB

Open AccessArticle

Anti-Inflammatory Activity of Black Soldier Fly Oil Associated with Modulation of TLR Signaling: A Metabolomic Approach

by Hadas Richter, Ofer Gover and Betty Schwartz

Int. J. Mol. Sci. 2023, 24(13), 10634; https://doi.org/10.3390/ijms241310634 - 25 Jun 2023

Cited by 5 | Viewed by 2243

Abstract

Dietary intervention in the treatment of ulcerative colitis involves, among other things, modifications in fatty acid content and/or profile. For example, replacing saturated long chain fatty acids with medium chain fatty acids (MCFAs) has been reported to ameliorate inflammation. The Black Soldier Fly Larvae’s (BSFL) oil is considered a sustainable dietary ingredient rich in the MCFA C12:0; however, its effect on inflammatory-related conditions has not been studied until now. Thus, the present study aimed to investigate the anti-inflammatory activity of BSFL oil in comparison to C12:0 using TLR4- or TLR2-activated THP-1 and J774A.1 cell lines and to assess its putative protective effect against dextran sulfate sodium (DSS)-induced acute colitis in mice. BSFL oil and C12:0 suppressed proinflammatory cytokines release in LPS-stimulated macrophages; however, only BSFL oil exerted anti-inflammatory activity in Pam3CSK4-stimulated macrophages. Transcriptome analysis provided insight into the possible role of BSFL oil in immunometabolism switch, involving mTOR signaling and an increase in PPAR target genes promoting fatty acid oxidation, exhibiting a discrepant mode of action compared to C12:0 treatment, which mainly affected cholesterol biosynthesis pathways. Additionally, we identified anti-inflammatory eicosanoids, oxylipins, and isoprenoids in the BSFL oil that may contribute to an orchestrated anti-inflammatory response. In vivo, a BSFL oil-enriched diet (20%) ameliorated the clinical signs of colitis, as indicated by improved body weight recovery, reduced colon shortening, reduced splenomegaly, and an earlier phase of secretory IgA response. These results indicate the novel beneficial use of BSFL oil as a modulator of inflammation. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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27 pages, 10252 KiB

Open AccessArticle

LC-MS/MS-Based Serum Metabolomics and Transcriptome Analyses for the Mechanism of Augmented Renal Clearance

by Yidan Wang, Yifan Luo, Shu Yang, Mingyan Jiang and Yang Chu

Int. J. Mol. Sci. 2023, 24(13), 10459; https://doi.org/10.3390/ijms241310459 - 21 Jun 2023

Cited by 2 | Viewed by 1042

Abstract

Augmented Renal Clearance (ARC) refers to the increased renal clearance of circulating solute in critically ill patients. In this study, the analytical research method of transcriptomics combined with metabolomics was used to study the pathogenesis of ARC at the transcriptional and metabolic levels. In transcriptomics, 534 samples from 5 datasets in the Gene Expression Omnibus database were analyzed and 834 differential genes associated with ARC were obtained. In metabolomics, we used Ultra-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry to determine the non-targeted metabolites of 102 samples after matching propensity scores, and obtained 45 differential metabolites associated with ARC. The results of the combined analysis showed that purine metabolism, arginine biosynthesis, and arachidonic acid metabolism were changed in patients with ARC. We speculate that the occurrence of ARC may be related to the alteration of renal blood perfusion by LTB4R, ARG1, ALOX5, arginine and prostaglandins E2 through inflammatory response, as well as the effects of CA4, PFKFB2, PFKFB3, PRKACB, NMDAR, glutamate and cAMP on renal capillary wall permeability. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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18 pages, 6026 KiB

Open AccessArticle

Comprehensive Insight into Colorectal Cancer Metabolites and Lipids for Human Serum: A Proof-of-Concept Study

by Kinjal Bhatt, Titziana Orlando, Marie-Alice Meuwis, Edouard Louis, Pierre-Hugues Stefanuto and Jean-François Focant

Int. J. Mol. Sci. 2023, 24(11), 9614; https://doi.org/10.3390/ijms24119614 - 01 Jun 2023

Cited by 2 | Viewed by 1999

Abstract

Colorectal cancer (CRC) ranks as the third most frequently diagnosed cancer and the second leading cause of cancer-related deaths. The current endoscopic-based or stool-based diagnostic techniques are either highly invasive or lack sufficient sensitivity. Thus, there is a need for less invasive and more sensitive screening approaches. We, therefore, conducted a study on 64 human serum samples representing three different groups (adenocarcinoma, adenoma, and control) using cutting-edge GC×GC–LR/HR-TOFMS (comprehensive two-dimensional gas chromatography coupled with low/high-resolution time-of-flight mass spectrometry). We analyzed samples with two different specifically tailored sample preparation approaches for lipidomics (fatty acids) (25 μL serum) and metabolomics (50 μL serum). In-depth chemometric screening with supervised and unsupervised approaches and metabolic pathway analysis were applied to both datasets. A lipidomics study revealed that specific PUFA (ω-3) molecules are inversely associated with increased odds of CRC, while some PUFA (ω-6) analytes show a positive correlation. The metabolomics approach revealed downregulation of amino acids (alanine, glutamate, methionine, threonine, tyrosine, and valine) and myo-inositol in CRC, while 3-hydroxybutyrate levels were increased. This unique study provides comprehensive insight into molecular-level changes associated with CRC and allows for a comparison of the efficiency of two different analytical approaches for CRC screening using same serum samples and single instrumentation. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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Review

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17 pages, 737 KiB

Open AccessReview

A Systematic Review on Metabolomics Analysis in Hearing Impairment: Is It a Possible Tool in Understanding Auditory Pathologies?

by Rita Malesci, Martina Lombardi, Vera Abenante, Federica Fratestefano, Valeria Del Vecchio, Anna Rita Fetoni and Jacopo Troisi

Int. J. Mol. Sci. 2023, 24(20), 15188; https://doi.org/10.3390/ijms242015188 - 14 Oct 2023

Cited by 1 | Viewed by 1393

Abstract

With more than 466 million people affected, hearing loss represents the most common sensory pathology worldwide. Despite its widespread occurrence, much remains to be explored, particularly concerning the intricate pathogenic mechanisms underlying its diverse phenotypes. In this context, metabolomics emerges as a promising approach. Indeed, lying downstream from molecular biology’s central dogma, the metabolome reflects both genetic traits and environmental influences. Furthermore, its dynamic nature facilitates well-defined changes during disease states, making metabolomic analysis a unique lens into the mechanisms underpinning various hearing impairment forms. Hence, these investigations may pave the way for improved diagnostic strategies, personalized interventions and targeted treatments, ultimately enhancing the clinical management of affected individuals. In this comprehensive review, we discuss findings from 20 original articles, including human and animal studies. Existing literature highlights specific metabolic changes associated with hearing loss and ototoxicity of certain compounds. Nevertheless, numerous critical issues have emerged from the study of the current state of the art, with the lack of standardization of methods, significant heterogeneity in the studies and often small sample sizes being the main limiting factors for the reliability of these findings. Therefore, these results should serve as a stepping stone for future research aimed at addressing the aforementioned challenges. Full article

(This article belongs to the Special Issue Metabolomics in Health and Disease 2.0)

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