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Special Issue "Animal and Cellular Models in Metabolomics Research Volume 2"

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Animal Metabolism".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 7330

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Special Issue Editors

Dr. Michal Ciborowski

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Guest Editor

Clinical Research Centre, Medical University of Bialystok, 15-089 Białystok, Poland
Interests: metrabolomics; mass spectrometry; diabetes and oncolody
Special Issues, Collections and Topics in MDPI journals

Dr. Joanna Godzien

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Guest Editor

Clinical Research Centre, Medical University of Bialystok, 15-089 Białystok, Poland
Interests: LC-MS metabolomics; lipidomics; metabolites annotation and diabetes
Special Issues, Collections and Topics in MDPI journals

Dr. Stanislaw Deja

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Guest Editor

Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8828, USA
Interests: metabolomics; stable isotope tracers; metabolic flux analysis; computational models of metabolism and liver metabolism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolomics, an essential tool of modern biochemical research, is no longer solely a hypothesis-generating platform, but rather is extensively used in hypothesis testing studies. Progress in gene manipulation techniques allows the turning on and off of particular enzymatic functions in a cell- or tissue-specific manner. High-throughput cell culture and animal model studies are increasingly popular. While many metabolic questions can be answered under well-controlled cell culture conditions, the true test is the transition from the dish to in vivo models.

We therefore invite research and review articles devoted to the various cell and animal models used in metabolic studies. The focus of this Special Issue involves technical approaches and the translation from cell to animal metabolic models. The topics include but are not limited to the use of cell culture and animal models in the exploration of single cell metabolism, high-throughput metabolomics, and the use of stable isotope tracers for metabolic flux analysis. Studies using genetic manipulations or in vivo dietary and pharmacological interventions are particularly welcome. Studies applying in vitro/in vivo imaging of metabolites with the use of DNP-NMR and MRI are highly anticipated. Finally, protocols describing experimental guidelines are also encouraged.

This Special Issue is open for submissions now. A proper extension may be granted, please kindly let us know in advance. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the Special Issue website.

Dr. Michal Ciborowski
Dr. Joanna Godzien
Dr. Stanislaw Deja
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.

Keywords

Cell culture models
Animal models
Animal microbiome
Tumour xenografts
Targeted and untargeted metabolomics
Metabolic flux analysis (MFA)
Metabolic imaging DNP-NMR

Published Papers (7 papers)

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Research

Open AccessArticle

Effects of Saline-Alkaline Stress on Metabolome, Biochemical Parameters, and Histopathology in the Kidney of Crucian Carp (Carassius auratus)

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Metabolites 2023, 13(2), 159; https://doi.org/10.3390/metabo13020159 - 20 Jan 2023

Viewed by 452

Abstract

The salinization of the water environment caused by human activities and global warming has increased which has brought great survival challenges to aquatic animals. Crucian carp (Carassius auratus) is an essential freshwater economic fish with superior adaptability to saline-alkali water. However, the physiological regulation mechanism of crucian carp adapting to saline-alkali stress remains still unclear. In this study, crucian carp were exposed to freshwater or 20, 40, and 60 mmol/L NaHCO₃ water environments for 30 days, the effects of saline-alkali stress on the kidney were evaluated by histopathology, biochemical assays and metabolomics analysis from renal function, antioxidant capacity and metabolites level. Our results showed different degrees of kidney damage at different exposure concentrations, which were characterized by glomerular atrophy and swelling, renal tubular degranulation, obstruction and degeneration, renal interstitial edema, renal cell proliferation and necrosis. Saline-alkali stress could change the levels of several physiological parameters with renal function and antioxidant capacity, including creatinine (CREA), urea nitrogen (BUN), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA). In addition, metabolomics analysis showed that differential metabolites (DMs) were involved in various metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, aminoacyl-tRNA biosynthesis, purine metabolism, glycerophospholipid metabolism, sphingolipid metabolism, glycolysis/gluconeogenesis and the TCA cycle. In general, our study revealed that saline-alkaline stress could cause significant changes in renal function and metabolic profiles, and induce severe damage in the crucian carp kidney through destroying the anti-oxidant system and energy homeostasis, inhibiting protein and amino acid catabolism, as well as disordering purine metabolism and lipid metabolism. This study could contribute to a deeper understanding the adverse effects of saline-alkali stress on crucian carp kidney and the regulatory mechanism in the crucian carp of saline-alkali adaptation at the metabolic level. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

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Open AccessArticle

In Vitro Animal Model for Estimating the Time since Death with Attention to Early Postmortem Stage

Anna Niemcunowicz-Janica

and

Michal Ciborowski

Metabolites 2023, 13(1), 26; https://doi.org/10.3390/metabo13010026 - 23 Dec 2022

Viewed by 614

Abstract

Estimating the postmortem interval (PMI) has remained the subject of investigations in forensic medicine for many years. Every kind of death results in changes in metabolites in body tissues and fluids due to lack of oxygen, altered circulation, enzymatic reactions, cellular degradation, and cessation of anabolic production of metabolites. Metabolic changes may provide markers determining the time since death, which is challenging in current analytical and observation-based methods. The study includes metabolomics analysis of blood with the use of an animal model to determine the biochemical changes following death. LC-MS is used to fingerprint postmortem porcine blood. Metabolites, significantly changing in blood after death, are selected and identified using univariate statistics. Fifty-one significant metabolites are found to help estimate the time since death in the early postmortem stage. Hypoxanthine, lactic acid, histidine, and lysophosphatidic acids are found as the most promising markers in estimating an early postmortem stage. Selected lysophosphatidylcholines are also found as significantly increased in blood with postmortal time, but their practical utility as PMI indicators can be limited due to a relatively low increasing rate. The findings demonstrate the great potential of LC-MS-based metabolomics in determining the PMI due to sudden death and provide an experimental basis for applying this attitude in investigating various mechanisms of death. As we assume, our study is also one of the first in which the porcine animal model is used to establish PMI metabolomics biomarkers. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

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Open AccessArticle

Sinomenine Ameliorates Colitis-Associated Cancer by Modulating Lipid Metabolism via Enhancing CPT1A Expression

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Metabolites 2022, 12(10), 946; https://doi.org/10.3390/metabo12100946 - 05 Oct 2022

Viewed by 784

Abstract

Colitis-associated cancer (CAC), arising from long-lasting intestinal inflammation, is a common type of colorectal cancer. Sinomenine (SIN), the major active compound of Sinomenium acutum, displays excellent antitumor activity. In modern pharmacological research, SIN has been proved to arrest proliferation of human colon cancer cells in vitro, but its functional role and specific mechanism in CAC were still elusive. This study explored the molecular mechanism of SIN on CAC. The results showed that orally administered SIN could decrease the occurrence and development of CAC. Metabolomics results revealed SIN could reprogram metabolism in CAC mice by reversing 34 endogenous metabolites. Importantly, the most prominent metabolic alteration was lipid metabolism. Mechanistically, SIN improved lipid metabolism by enhancing the expression of CPT1A in CAC mice. Moreover, the inhibitory effect of SIN on the proliferation of human colon cancer cells was blunted via CPT1A inhibitor. The results of this study added further evidence of the molecular mechanisms that allow SIN to exert anti-CAC effect by facilitating lipid metabolism and reaffirmed its potential and distinctive role as a chemopreventive agent in CAC. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

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Open AccessArticle

The Quantitative Profiling of Oxylipins from Arachidonic Acid by LC-MS/MS in Feces at Birth 3 Days and 21 Days of Piglets

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Metabolites 2022, 12(8), 702; https://doi.org/10.3390/metabo12080702 - 28 Jul 2022

Viewed by 787

Abstract

Oxylipins (also called eicosanoids) are enzymatically or nonenzymatically generated by oxidation of arachidonic acid (ARA) and are major mediators of ARA effects in the body. Previous studies demonstrated the importance of ARA in infant growth, brain development, immune response, and health. With the developments in lipidomic methodologies, it is important for exploring more ARA-deprived oxylipins to better understand the physiological functions of ARA. The concentrations of oxylipins in feces were determined from days 3 to 21 postnatally of suckling piglets in vivo. Feces were collected at two critical time points of the suckling piglets (3d and 21d after birth) and about 48 oxylipins were analyzed by using a target metabolomics approach based on Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). Here, 21 oxylipins were derived from ARA, and 11 differential oxylipins (Log2|fold change| ≥ 1.0) at birth 3d and 21d were identified. Particularly, 12-HETE was more abundant in feces at birth 3 days rather than 21 days. Considering that 12-HETE was a racemic mixture of stereoisomers containing the S and R enantiomers, we further detected the concentrations of 12(S)-HETE and 12(R)-HETE between the two time points by chiral LC-MS/MS analysis. There was no significant difference in the concentrations of 12(S)-HETE and 12(R)-HETE. It was showed that ARA - derived oxylipins might be related to the physiological changes of piglets during growing. Our results provided new information for describing the physiological changes of the piglets over the suckling period. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

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Open AccessArticle

Comparative Metabolomics of Small Molecules Specifically Expressed in the Dorsal or Ventral Marginal Zones in Vertebrate Gastrula

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Metabolites 2022, 12(6), 566; https://doi.org/10.3390/metabo12060566 - 20 Jun 2022

Cited by 2 | Viewed by 1290

Abstract

Many previous studies have reported the various proteins specifically secreted as inducers in the dorsal or ventral regions in vertebrate gastrula. However, little is known about the effect on cell fate of small molecules below 1000 Da. We therefore tried to identify small molecules specifically expressed in the dorsal marginal zone (DMZ) or ventral marginal zone (VMZ) in vertebrate gastrula. Small intracellular and secreted molecules were detected using explants and supernatant samples. Hydrophilic metabolites were analyzed by capillary ion chromatography–mass spectrometry and liquid chromatography–mass spectrometry, and lipids were analyzed by supercritical fluid chromatography–tandem mass spectrometry. In total, 190 hydrophilic metabolites and 396 lipids were identified. The DMZ was found to have high amounts of glycolysis- and glutathione metabolism-related metabolites in explants, and the VMZ was richer in purine metabolism-related metabolites. We also discovered some hydrophilic metabolites and lipids differentially contained in the DMZ or VMZ. Our research would contribute to a deeper understanding of the cellular physiology that regulates early embryogenesis. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

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Open AccessCommunication

Sanitary Conditions on the Farm Alters Fecal Metabolite Profile in Growing Pigs

Soumya K. Kar

Marinus F. W. te Pas

Leo Kruijt

, Jacques J. M. Vervoort,

Alfons J. M. Jansman

and

Dirkjan Schokker

Metabolites 2022, 12(6), 538; https://doi.org/10.3390/metabo12060538 - 11 Jun 2022

Viewed by 1092

Abstract

The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrasting sanitary conditions and the associated subclinical health status of pigs. We analyzed fecal metabolite profiles by nuclear magnetic resonance (¹H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions differed in fecal metabolites related to the degradation of dietary starch, metabolism of the gut microbiome, and degradation of components of animal (host) origin. The metabolites that differed significantly (FDR < 0.1) were from metabolic processes involved in either maintaining nutrient digestive capacity, including purine metabolism, energy metabolism, bile acid breakdown and recycling, or immune system metabolism. The results show that the fecal metabolite profiles reflect the sanitary conditions under which the pigs are kept. The fecal metabolite profiles closely resembled the profiles of metabolites found in the colon of pigs. Fecal valerate and kynurenic acid could potentially be used as “non-invasive” biomarkers of immune or inflammatory status that could form the basis for monitoring subclinical health status in pigs. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

Open AccessArticle

High Resolution Magic Angle Spinning Proton NMR Study of Alzheimer’s Disease with Mouse Models

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Metabolites 2022, 12(3), 253; https://doi.org/10.3390/metabo12030253 - 17 Mar 2022

Cited by 1 | Viewed by 1475

Abstract

Alzheimer’s disease (AD) is a crippling condition that affects millions of elderly adults each year, yet there remains a serious need for improved methods of diagnosis. Metabolomic analysis has been proposed as a potential methodology to better investigate and understand the progression of this disease; however, studies of human brain tissue metabolomics are challenging, due to sample limitations and ethical considerations. Comprehensive comparisons of imaging measurements in animal models to identify similarities and differences between aging- and AD-associated metabolic changes should thus be tested and validated for future human non-invasive studies. In this paper, we present the results of our highresolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) studies of AD and wild-type (WT) mouse models, based on animal age, brain regions, including cortex vs. hippocampus, and disease status. Our findings suggest the ability of HRMAS NMR to differentiate between AD and WT mice using brain metabolomics, which potentially can be implemented in in vivo evaluations. Full article

(This article belongs to the Special Issue Animal and Cellular Models in Metabolomics Research Volume 2)

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