Next Issue
Volume 14, April
Previous Issue
Volume 14, February
 
 

Metabolites, Volume 14, Issue 3 (March 2024) – 45 articles

Cover Story (view full-size image): Vertical transmission of metabolites from mother to child influences early disease phenotypes. This study examines mother–child metabolite transmission, using machine learning to distinguish true mother–child dyads from non-dyads. Techniques include random forests (RFs), light gradient boosting machines (LGBM), and logistic regression (Elasticnet), analyzing metabolite concentrations in maternal plasma at 24 weeks of gestation and children’s plasma at 6 months. We quantified vertical transfer propensity, improving mother–child match accuracy. RF emerged as the top model, identifying perfluorooctanoic acid (PFOA) among the key transferred metabolites. This study confirms and expands our understanding of maternal influence on the child’s metabolome, demonstrating machine learning’s potential in exploring metabolic interactions. View this paper
  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.
Order results
Result details
Section
Select all
Export citation of selected articles as:
14 pages, 4946 KiB  
Article
Isobaric Tags for Relative and Absolute Quantitation-Based Proteomics Analysis Revealed Proteins Involved in Drought Response during the Germination Stage in Faba Bean
by Changyan Liu, Fangwen Yang, Li Li, Xuesong Han, Hongwei Chen, Aihua Sha and Chunhai Jiao
Metabolites 2024, 14(3), 175; https://doi.org/10.3390/metabo14030175 - 21 Mar 2024
Viewed by 637
Abstract
The faba bean, a significant cool-season edible legume crop, is susceptible to drought during the germination stage. Research regarding the genetic regulation of drought tolerance throughout this stage in the faba bean is limited. The differentially expressed proteins (DEPs) in faba beans between [...] Read more.
The faba bean, a significant cool-season edible legume crop, is susceptible to drought during the germination stage. Research regarding the genetic regulation of drought tolerance throughout this stage in the faba bean is limited. The differentially expressed proteins (DEPs) in faba beans between the drought-tolerant variety C105 and the drought-sensitive variant E1 during seed germination were identified in this work, accomplished through isobaric tags for relative and absolute quantitation (iTRAQ) analysis. A total of 3827 proteins were identified in the two varieties of germinating seeds. Compared to those of variety E1, an increase in 108 DEPs and a decrease in 61 DEPs were observed in variety C105 under drought. Conversely, in the control group, variety C105 showed 108 significantly upregulated DEPs and 55 significantly downregulated DEPs. GO and KEGG analyses showed that the DEPs associated with glutathione metabolism and protein processing demonstrated significant increases in response to drought stress. Protein–protein interaction (PPI) analysis unveiled three closely connected functional modules of protein translation, DNA replication, and post-translational modification, originating from 22 DEPs derived from the germination period of two varieties under drought stress. To verify the proteomic function, we selected three differentially expressed protein coding genes, which were overexpressed or silenced in tobacco, thereby enhancing the drought resistance of tobacco. This was accompanied via altered levels of superoxide dismutase or peroxidase in transgenic plants under drought stress. The possible mechanism for drought tolerance in germinating seeds of faba bean involves increasing protein translation, decreasing DNA replication, and modifying chromatin. These findings offer invaluable insights into the reaction mechanism in response to drought stress in faba beans. The identified DEPs could be utilized in faba bean breeding initiatives to manage drought. Full article
(This article belongs to the Section Plant Metabolism)
Show Figures

Figure 1

18 pages, 1984 KiB  
Article
Relationships and Mendelian Randomization of Gut Microbe-Derived Metabolites with Metabolic Syndrome Traits in the METSIM Cohort
by Sahereh Mirzaei, Holli A. DeVon, Rita M. Cantor, Arjen J. Cupido, Calvin Pan, Sung Min Ha, Lilian Fernandes Silva, James R. Hilser, Jaana Hartiala, Hooman Allayee, Federico E. Rey, Markku Laakso and Aldons J. Lusis
Metabolites 2024, 14(3), 174; https://doi.org/10.3390/metabo14030174 - 20 Mar 2024
Viewed by 906
Abstract
The role of gut microbe-derived metabolites in the development of metabolic syndrome (MetS) remains unclear. This study aimed to evaluate the associations of gut microbe-derived metabolites and MetS traits in the cross-sectional Metabolic Syndrome In Men (METSIM) study. The sample included 10,194 randomly [...] Read more.
The role of gut microbe-derived metabolites in the development of metabolic syndrome (MetS) remains unclear. This study aimed to evaluate the associations of gut microbe-derived metabolites and MetS traits in the cross-sectional Metabolic Syndrome In Men (METSIM) study. The sample included 10,194 randomly related men (age 57.65 ± 7.12 years) from Eastern Finland. Levels of 35 metabolites were tested for associations with 13 MetS traits using lasso and stepwise regression. Significant associations were observed between multiple MetS traits and 32 metabolites, three of which exhibited particularly robust associations. N-acetyltryptophan was positively associated with Homeostatic Model Assessment for Insulin Resistant (HOMA-IR) (β = 0.02, p = 0.033), body mass index (BMI) (β = 0.025, p = 1.3 × 10−16), low-density lipoprotein cholesterol (LDL-C) (β = 0.034, p = 5.8 × 10−10), triglyceride (0.087, p = 1.3 × 10−16), systolic (β = 0.012, p = 2.5 × 10−6) and diastolic blood pressure (β = 0.011, p = 3.4 × 10−6). In addition, 3-(4-hydroxyphenyl) lactate yielded the strongest positive associations among all metabolites, for example, with HOMA-IR (β = 0.23, p = 4.4 × 10−33), and BMI (β = 0.097, p = 5.1 × 10−52). By comparison, 3-aminoisobutyrate was inversely associated with HOMA-IR (β = −0.19, p = 3.8 × 10−51) and triglycerides (β = −0.12, p = 5.9 × 10−36). Mendelian randomization analyses did not provide evidence that the observed associations with these three metabolites represented causal relationships. We identified significant associations between several gut microbiota-derived metabolites and MetS traits, consistent with the notion that gut microbes influence metabolic homeostasis, beyond traditional risk factors. Full article
(This article belongs to the Special Issue Role of Gut-Derived Metabolites in Health and Disease)
Show Figures

Figure 1

16 pages, 6181 KiB  
Review
Matrix- and Surface-Assisted Laser Desorption/Ionization Mass Spectrometry Methods for Urological Cancer Biomarker Discovery—Metabolomics and Lipidomics Approaches
by Adrian Arendowski
Metabolites 2024, 14(3), 173; https://doi.org/10.3390/metabo14030173 - 20 Mar 2024
Viewed by 825
Abstract
Urinary tract cancers, including those of the bladder, the kidneys, and the prostate, represent over 12% of all cancers, with significant global incidence and mortality rates. The continuous challenge that these cancers present necessitates the development of innovative diagnostic and prognostic methods, such [...] Read more.
Urinary tract cancers, including those of the bladder, the kidneys, and the prostate, represent over 12% of all cancers, with significant global incidence and mortality rates. The continuous challenge that these cancers present necessitates the development of innovative diagnostic and prognostic methods, such as identifying specific biomarkers indicative of cancer. Biomarkers, which can be genes, proteins, metabolites, or lipids, are vital for various clinical purposes including early detection and prognosis. Mass spectrometry (MS), particularly soft ionization techniques such as electrospray ionization (ESI) and laser desorption/ionization (LDI), has emerged as a key tool in metabolic profiling for biomarker discovery, due to its high resolution, sensitivity, and ability to analyze complex biological samples. Among the LDI techniques, matrix-assisted laser desorption/ionization (MALDI) and surface-assisted laser desorption/ionization (SALDI) should be mentioned. While MALDI methodology, which uses organic compounds as matrices, is effective for larger molecules, SALDI, based on the various types of nanoparticles and nanostructures, is preferred for smaller metabolites and lipids due to its reduced spectral interference. This study highlights the application of LDI techniques, along with mass spectrometry imaging (MSI), in identifying potential metabolic and lipid biomarkers for urological cancers, focusing on the most common bladder, kidney, and prostate cancers. Full article
Show Figures

Figure 1

12 pages, 578 KiB  
Article
Association between Protein Intake and Diabetes Complications Risk Following Incident Type 2 Diabetes: The EPIC-Potsdam Study
by Elif Inan-Eroglu, Olga Kuxhaus, Franziska Jannasch, Daniela V. Nickel and Matthias B. Schulze
Metabolites 2024, 14(3), 172; https://doi.org/10.3390/metabo14030172 - 19 Mar 2024
Viewed by 761
Abstract
Our knowledge about the connection between protein intake and diabetes-related complications comes largely from studies among those already diagnosed with type 2 diabetes (T2D). However, there is a lack of information on whether changing protein intake after diabetes diagnosis affects complications risk. We [...] Read more.
Our knowledge about the connection between protein intake and diabetes-related complications comes largely from studies among those already diagnosed with type 2 diabetes (T2D). However, there is a lack of information on whether changing protein intake after diabetes diagnosis affects complications risk. We aimed to explore the association between protein intake (total, animal, and plant) and vascular complications in incident T2D patients considering pre-diagnosis intake and changes in intake after diagnosis. This prospective cohort study included 1064 participants from the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam cohort who developed T2D during follow-up (physician-verified). Dietary protein intake was measured with a food frequency questionnaire at baseline and follow-up. We included physician-reported incident diabetes complications (myocardial infarction, stroke, nephropathy, and neuropathy). A total of 388 participants developed complications, 82 macrovascular complications, and 343 microvascular complications. Substituting carbohydrates with protein showed a trend towards lower complications risk, although this association was not statistically significant (hazard ratio (HR) for 5% energy (E) substitution: 0.83; 95% confidence intervals (CI): 0.60–1.14). Increasing protein intake at the expense of carbohydrates after diabetes diagnosis was not associated with total and microvascular complications (HR for 5% E change substitution: 0.98; 95% CI: 0.89–1.08 and HR for 5% E change substitution: 1.02; 95% CI: 0.92–1.14, respectively). Replacing carbohydrates with protein did not elevate the risk of diabetes complications in incident T2D cases. Full article
(This article belongs to the Special Issue Impact of Macronutrients on Metabolism)
Show Figures

Figure 1

14 pages, 1813 KiB  
Review
The Noncanonical Functions of Metabolites in Tumor Progression
by Siyang Wu, Yijun Qi and Weiwei Yang
Metabolites 2024, 14(3), 171; https://doi.org/10.3390/metabo14030171 - 19 Mar 2024
Viewed by 677
Abstract
Metabolic reprogramming has emerged as a prominent hallmark of cancer, characterized by substantial alterations in nutrient uptake and intracellular metabolic pathways. Consequently, intracellular metabolite concentrations undergo significant changes which can contribute to tumorigenesis through diverse mechanisms. Beyond their classical roles in regulating metabolic [...] Read more.
Metabolic reprogramming has emerged as a prominent hallmark of cancer, characterized by substantial alterations in nutrient uptake and intracellular metabolic pathways. Consequently, intracellular metabolite concentrations undergo significant changes which can contribute to tumorigenesis through diverse mechanisms. Beyond their classical roles in regulating metabolic pathway flux, metabolites exhibit noncanonical functions that play a crucial role in tumor progression. In this review, we delve into the nonclassical functions of metabolites in the context of tumor progression, with a particular focus on their capacity to modulate gene expression and cell signaling. Furthermore, we discuss the potential exploitation of these nonclassical functions in the enhancement of cancer therapy. Full article
(This article belongs to the Section Endocrinology and Clinical Metabolic Research)
Show Figures

Figure 1

16 pages, 4416 KiB  
Article
Elucidation and Regulation of Tyrosine Kinase Inhibitor Resistance in Renal Cell Carcinoma Cells from the Perspective of Glutamine Metabolism
by Kento Morozumi, Yoshihide Kawasaki, Tomonori Sato, Masamitsu Maekawa, Shinya Takasaki, Shuichi Shimada, Takanari Sakai, Shinichi Yamashita, Nariyasu Mano and Akihiro Ito
Metabolites 2024, 14(3), 170; https://doi.org/10.3390/metabo14030170 - 19 Mar 2024
Viewed by 730
Abstract
Tyrosine kinase inhibitors (TKIs) play a crucial role in the treatment of advanced renal cell carcinoma (RCC). However, there is a lack of useful biomarkers for assessing treatment efficacy. Through urinary metabolite analysis, we identified the metabolites and pathways involved in TKI resistance [...] Read more.
Tyrosine kinase inhibitors (TKIs) play a crucial role in the treatment of advanced renal cell carcinoma (RCC). However, there is a lack of useful biomarkers for assessing treatment efficacy. Through urinary metabolite analysis, we identified the metabolites and pathways involved in TKI resistance and elucidated the mechanism of TKI resistance. To verify the involvement of the identified metabolites obtained from urine metabolite analysis, we established sunitinib-resistant RCC cells and elucidated the antitumor effects of controlling the identified metabolic pathways in sunitinib-resistant RCC cells. Through the analysis of VEGFR signaling, we aimed to explore the mechanisms underlying the antitumor effects of metabolic control. Glutamine metabolism has emerged as a significant pathway in urinary metabolite analyses. In vitro and in vivo studies have revealed the antitumor effects of sunitinib-resistant RCC cells via knockdown of glutamine transporters. Furthermore, this antitumor effect is mediated by the control of VEGFR signaling via PTEN. Our findings highlight the involvement of glutamine metabolism in the prognosis and sunitinib resistance in patients with advanced RCC. Additionally, the regulating glutamine metabolism resulted in antitumor effects through sunitinib re-sensitivity in sunitinib-resistant RCC. Our results are expected to contribute to the more effective utilization of TKIs with further improvements in prognosis through current drug therapies. Full article
(This article belongs to the Special Issue Drug Metabolism and New Drug Development for Cancers)
Show Figures

Figure 1

9 pages, 905 KiB  
Article
Effect of Adding Apolipoprotein B Testing on the Prevalence of Dyslipidemia and Risk of Cardiovascular Disease in the Korean Adult Population
by Rihwa Choi, Sang Gon Lee and Eun Hee Lee
Metabolites 2024, 14(3), 169; https://doi.org/10.3390/metabo14030169 - 18 Mar 2024
Viewed by 719
Abstract
Traditional lipid parameters—including total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and non-HDL-C (calculated as TC minus HDL-C)—have long been used as indicators of cardiovascular disease (CVD) risk. The laboratory records of 9604 Korean adults who underwent traditional [...] Read more.
Traditional lipid parameters—including total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and non-HDL-C (calculated as TC minus HDL-C)—have long been used as indicators of cardiovascular disease (CVD) risk. The laboratory records of 9604 Korean adults who underwent traditional lipid panel tests (TC, TG, and HDL), as well as ApoB testing, were analyzed to evaluate the prevalence of dyslipidemia and high CVD risk (utilizing the NCEP ATP III criteria for traditional lipid panels and various ApoB test cutoffs recommended by international guidelines (145 mg/dL, 130 mg/dL, and 100 mg/dL)). The overall prevalence of dyslipidemia, as determined by traditional lipid panel criteria, was 27.4%. Utilizing the ApoB cutoffs of 145 mg/dL, 130 mg/dL, and 100 mg/dL resulted in prevalence figures of 5.3%, 11.0%, and 36.3%, respectively. The concordance in dyslipidemia classification between traditional lipid tests and ApoB at cutoffs of 145 mg/dL, 130 mg/dL, and 100 mg/dL was 78.4%, 81.3%, and 74.7%, respectively. Up to 17.5% of participants, based on an ApoB cutoff of ≥100 mg/dL, exhibited isolated high ApoB in the absence of traditional lipid test anomalies. Incorporating ApoB testing could enhance the identification of Koreans at high CVD risk. Full article
(This article belongs to the Special Issue Lipid Biomarkers and Cardiometabolic Diseases)
Show Figures

Figure 1

19 pages, 2194 KiB  
Article
Application of Clinical Blood Metabogram to Type 2 Diabetes Mellitus
by Petr G. Lokhov, Elena E. Balashova, Oxana P. Trifonova, Dmitry L. Maslov, Ekaterina A. Shestakova, Marina V. Shestakova and Ivan I. Dedov
Metabolites 2024, 14(3), 168; https://doi.org/10.3390/metabo14030168 - 18 Mar 2024
Viewed by 718
Abstract
The clinical blood metabogram (CBM) was developed to match a tailored analysis of the blood metabolome to the time, cost, and reproducibility constraints of clinical laboratory testing. By analyzing the main blood metabolite groups, CBM offers clinically relevant information about the intake of [...] Read more.
The clinical blood metabogram (CBM) was developed to match a tailored analysis of the blood metabolome to the time, cost, and reproducibility constraints of clinical laboratory testing. By analyzing the main blood metabolite groups, CBM offers clinically relevant information about the intake of low-molecular substances into the organism, humoral regulation, liver function, amino acid level, and the lipid and carbohydrate metabolism. The purpose of this work was to investigate the relevance of using the CBM in patients with diabetes mellitus. For this, a CBM was obtained for 18 healthy individuals, 12 individuals with prediabetes, and 64 individuals with type 2 diabetes mellitus, separated into groups according to fasting blood glucose and oral glucose tolerance tests. The results showed that the CBM reveals diabetes-associated metabolic alterations in the blood, including changes in the levels of carbohydrates, ketone bodies, eicosanoids, phospholipids, and amino acids, which are consistent with the scientific data available to date. The CBM enabled the separation of diabetic patients according to their metabolic metabotypes, providing both a general overview of their metabolic alterations and detailing their individual metabolic characteristics. It was concluded that the CBM is a precise and clinically applicable test for assessing an individual’s metabolic status in diabetes mellitus for diagnostic and treatment purposes. Full article
(This article belongs to the Collection Advances in Metabolomics)
Show Figures

Figure 1

12 pages, 473 KiB  
Article
Resting Metabolic Rate and Substrate Utilization during Energy and Protein Availability in Male and Female Athletes
by Mahmoud M. A. Abulmeaty, Ali Almajwal, Mervat Elsayed, Heba Hassan, Thamer Alsager and Zaid Aldossari
Metabolites 2024, 14(3), 167; https://doi.org/10.3390/metabo14030167 - 17 Mar 2024
Viewed by 1547
Abstract
Active athletes frequently develop low energy (LEA) and protein availabilities (LPA) with consequent changes in the vital metabolic processes, especially resting metabolic rate (RMR) and substrate utilization. This study investigated the association of energy and protein intakes with RMR and substrate utilization in [...] Read more.
Active athletes frequently develop low energy (LEA) and protein availabilities (LPA) with consequent changes in the vital metabolic processes, especially resting metabolic rate (RMR) and substrate utilization. This study investigated the association of energy and protein intakes with RMR and substrate utilization in male and female athletes and those with LEA and LPA. Sixty athletes (35% female, 26.83 ± 7.12 y) were enrolled in this study. Anthropometric measurements and body composition analysis were reported to estimate fat-free mass (eFFM). Dietary intakes were recorded by two-day multiple-pass 24 h recall records and three-day food records and then analyzed by food processor software to calculate protein intake (PI) and energy intake (EI). Indirect calorimetry was used to measure RMR and percentages of substrate utilization. Activity–energy expenditure (AEE) was assessed by using an Actighrphy sensor for three days. Energy availability was calculated using the following formula (EA = EI − AEE/eFFM). The correlation of EI and PI with RMR and substrate utilization was tested with Pearson correlation. In the LEA group, both EI and PI correlated positively with RMR (r = 0.308, 0.355, respectively, p < 0.05). In addition, EI showed a positive correlation with the percentage of fat utilization. In the male and sufficient-PA groups, PI correlated positively with the RMR and negatively with the percentage of protein utilization. In conclusion, the percentage of LEA is markedly prevalent in our sample, with a higher prevalence among males. Athletes with LEA had lower fat utilization and lower RMR, while those with sufficient PA showed lower protein utilization with excessive PI. These findings may explain the metabolic responses in the cases of LEA and LPA. Full article
(This article belongs to the Special Issue Resting Metabolic Rate and Health)
Show Figures

Figure 1

25 pages, 4295 KiB  
Review
Reproductive Enhancement through Phytochemical Characteristics and Biological Activities of Date Palm Pollen: A Comprehensive Review on Potential Mechanism Pathways
by Saad Salhi, Abdellatif Rahim, Mouad Chentouf, Hasnaa Harrak, Jean Loup Bister, Naima Hamidallah and Bouchra El Amiri
Metabolites 2024, 14(3), 166; https://doi.org/10.3390/metabo14030166 - 14 Mar 2024
Viewed by 819
Abstract
Infertility represents a significant global health challenge affecting both men and women. Despite regular unprotected sexual intercourse, approximately 15% of couples of reproductive age struggle to conceive within 12 months, with 10% of infertility cases attributed to unknown causes worldwide. As a result, [...] Read more.
Infertility represents a significant global health challenge affecting both men and women. Despite regular unprotected sexual intercourse, approximately 15% of couples of reproductive age struggle to conceive within 12 months, with 10% of infertility cases attributed to unknown causes worldwide. As a result, numerous studies have turned their attention to exploring the use of natural products for the prevention and treatment of infertility. Among these natural remedies is date palm pollen (DPP), a male reproductive powder derived from the blossoms of the Phoenix dactylifera L. palm tree, which has a long history of use as a dietary supplement, particularly as an aphrodisiac and fertility enhancer for both men and women. This review critically examines the diverse components of DPP, including metabolites, proteins, amino acids, fatty acids, to elucidate its potential impact on human reproduction. The analysis thoroughly assesses the composition of DPP in relation to its effects on enhancing reproductive processes and delves into its traditional uses and therapeutic benefits in male fertility, such as the enhancement of sexual desire, semen quality, and hormonal equilibrium. Similarly, it explores the influence of DPP on female fertility, emphasizing its potential to improve factors such as lubrication, desire, ovulation, and hormonal balance. Overall, this review underscores the potential of DPP as a natural remedy for addressing reproductive disorders. Full article
(This article belongs to the Section Plant Metabolism)
Show Figures

Graphical abstract

12 pages, 267 KiB  
Article
The Effect of Dietary Protein Hydrolysate from Black Soldier Fly Larvae and Schizochytrium on Palatability, Nutrient Metabolites and Health Status in Beagle Dogs
by Yu Wei, Lingfeng Xue, Deying Ma, Yuxiao Weng, Mingkang Liu, Luyang Li, Ziyi Dai, Ziyun Zhao, Haifeng Wang and Xiao Xu
Metabolites 2024, 14(3), 165; https://doi.org/10.3390/metabo14030165 - 14 Mar 2024
Viewed by 727
Abstract
Protein hydrolysate from black soldier fly larvae (BSFP) has garnered great attention with its lower allergenicity, high amount of essential amino acids, and small bioactive peptides. Schizochytrium is a promising alternative source of n-3 FUFA because it has enriched docosahexaenoic acid (DHA, C22: [...] Read more.
Protein hydrolysate from black soldier fly larvae (BSFP) has garnered great attention with its lower allergenicity, high amount of essential amino acids, and small bioactive peptides. Schizochytrium is a promising alternative source of n-3 FUFA because it has enriched docosahexaenoic acid (DHA, C22: 6). The aim of this study was to assess palatability, the presence of diarrhea, plasma biochemistry panels, anti-oxidative and anti-inflammatory effects, and immune function in beagle dogs when supplementing a mixture of protein hydrolysate from black soldier fly larvae and schizochytrium (BSFPs) into their diets. Experiment I: 24 young beagle dogs (16 males and 8 females; 4–5 months; BW: 6.40 ± 0.15 kg) were randomly divided into four groups: (1) control (CON), (2) 5% BSFPs, (3) 10% BSFPs, (4) 15% BSFPs. Their body weights and fecal scores were recorded, and blood samples were collected for analysis. Experiment II: three diets containing 5%, 10%, and 15% BSFPs were evaluated by comparing them with a basal diet (CON) to evaluate palatability. These results suggested that a lower presence of diarrhea existed in the BSFP diet than the CON diet (p < 0.05). Three treatment groups remarkably increased their total protein (TP) and albumin (ALB) contents and decreased their concentrations of triglyceride (TG) and total cholesterol (TC) in plasma (p < 0.05). Moreover, the 5% and 15% BSFPs groups had a higher calcium (CA) content in plasma, and the activities of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) and contents of creatinine (CREA) and urea nitrogen (BUN) were significantly reduced by supplementing BSFP in their diets (p < 0.05). Their anti-oxidative enzyme activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) were dramatically enhanced, and their malondialdehyde (MDA) concentrations were remarkably reduced (p < 0.05). Immunoglobulin A and G (IgA and IgG) concentrations in the plasma in the 10% and 15% BSFPs groups were significantly increased (p < 0.05). Furthermore, lower interleukin-8 (IL-8) contents were shown in the BSFP diets than the CON diet (p < 0.05). Similarly, the diets supplemented with BSFPs exhibited a positive effect on palatability (p < 0.05). To sum up, the diets supplemented with BSFPs significantly enhanced palatability, immune function, and anti-oxidative and anti-inflammatory capacity to alleviate diarrhea and improve the general health of the beagle dogs. Full article
(This article belongs to the Section Animal Metabolism)
14 pages, 1926 KiB  
Article
Serum Uric Acid/Serum Creatinine Ratio and Cardiovascular Mortality in Diabetic Individuals—The Uric Acid Right for Heart Health (URRAH) Project
by Lanfranco D’Elia, Maria Masulli, Pietro Cirillo, Agostino Virdis, Edoardo Casiglia, Valerie Tikhonoff, Fabio Angeli, Carlo Maria Barbagallo, Michele Bombelli, Federica Cappelli, Rosario Cianci, Michele Ciccarelli, Arrigo F. G. Cicero, Massimo Cirillo, Raffaella Dell’Oro, Giovambattista Desideri, Claudio Ferri, Loreto Gesualdo, Cristina Giannattasio, Guido Grassi, Guido Iaccarino, Luciano Lippa, Francesca Mallamaci, Alessandro Maloberti, Stefano Masi, Alberto Mazza, Alessandro Mengozzi, Maria Lorenza Muiesan, Pietro Nazzaro, Paolo Palatini, Gianfranco Parati, Roberto Pontremoli, Fosca Quarti-Trevano, Marcello Rattazzi, Gianpaolo Reboldi, Giulia Rivasi, Elisa Russo, Massimo Salvetti, Giuliano Tocci, Andrea Ungar, Paolo Verdecchia, Francesca Viazzi, Massimo Volpe, Claudio Borghi and Ferruccio Gallettiadd Show full author list remove Hide full author list
Metabolites 2024, 14(3), 164; https://doi.org/10.3390/metabo14030164 - 14 Mar 2024
Viewed by 780
Abstract
Several studies have detected a direct association between serum uric acid (SUA) and cardiovascular (CV) risk. In consideration that SUA largely depends on kidney function, some studies explored the role of the serum creatinine (sCr)-normalized SUA (SUA/sCr) ratio in different settings. Previously, the [...] Read more.
Several studies have detected a direct association between serum uric acid (SUA) and cardiovascular (CV) risk. In consideration that SUA largely depends on kidney function, some studies explored the role of the serum creatinine (sCr)-normalized SUA (SUA/sCr) ratio in different settings. Previously, the URRAH (URic acid Right for heArt Health) Study has identified a cut-off value of this index to predict CV mortality at 5.35 Units. Therefore, given that no SUA/sCr ratio threshold for CV risk has been identified for patients with diabetes, we aimed to assess the relationship between this index and CV mortality and to validate this threshold in the URRAH subpopulation with diabetes; the URRAH participants with diabetes were studied (n = 2230). The risk of CV mortality was evaluated by the Kaplan–Meier estimator and Cox multivariate analysis. During a median follow-up of 9.2 years, 380 CV deaths occurred. A non-linear inverse association between baseline SUA/sCr ratio and risk of CV mortality was detected. In the whole sample, SUA/sCr ratio > 5.35 Units was not a significant predictor of CV mortality in diabetic patients. However, after stratification by kidney function, values > 5.35 Units were associated with a significantly higher mortality rate only in normal kidney function, while, in participants with overt kidney dysfunction, values of SUA/sCr ratio > 7.50 Units were associated with higher CV mortality. The SUA/sCr ratio threshold, previously proposed by the URRAH Study Group, is predictive of an increased risk of CV mortality in people with diabetes and preserved kidney function. While, in consideration of the strong association among kidney function, SUA, and CV mortality, a different cut-point was detected for diabetics with impaired kidney function. These data highlight the different predictive roles of SUA (and its interaction with kidney function) in CV risk, pointing out the difference in metabolic- and kidney-dependent SUA levels also in diabetic individuals. Full article
(This article belongs to the Special Issue Exploring Uric Acid and Beyond)
Show Figures

Figure 1

14 pages, 1948 KiB  
Article
In Silico Analysis of Novel Bacterial Metabolites with Anticancer Activities
by Pfariso Maumela and Mahloro Hope Serepa-Dlamini
Metabolites 2024, 14(3), 163; https://doi.org/10.3390/metabo14030163 - 13 Mar 2024
Viewed by 822
Abstract
Resistance to anticancer therapeutics is a major global concern. Thus, new anticancer agents should be aimed against novel protein targets to effectively mitigate the increased resistance. This study evaluated the potential of secondary metabolites from a bacterial endophyte, as new anticancer agents, against [...] Read more.
Resistance to anticancer therapeutics is a major global concern. Thus, new anticancer agents should be aimed against novel protein targets to effectively mitigate the increased resistance. This study evaluated the potential of secondary metabolites from a bacterial endophyte, as new anticancer agents, against a novel protein target, fibroblast growth factor. In silico genomic characterization of the Bacillus sp. strain MHSD_37 was used to identify potential genes involved in encoding secondary metabolites with biological activity. The strain was also exposed to stress and liquid chromatography–mass spectrometry used for the identification and annotation of secondary metabolites of oligopeptide class with anticancer activity. Selected metabolites were evaluated for their anticancer activity through molecular docking and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties analysis. Phylogenetic analysis revealed that strain MHSD_37 shared close evolutionary relationships with Bacillus at the species level, with no identified relationships at the sub-species level. Both in silico genomic characterization and spectrometry analysis identified secondary metabolites with potential anticancer activity. Molecular docking analysis illustrated that the metabolites formed complexes with the target protein, fibroblast growth factor, which were stabilized by hydrogen bonds. Moreover, the ADMET analysis showed that the metabolites passed the toxicity test for use as a potential drug. Thereby, Bacillus sp. strain MHSD_37 is a potential novel strain with oligopeptide metabolites that can be used as new anticancer agents against novel protein targets. Full article
Show Figures

Figure 1

7 pages, 642 KiB  
Case Report
Balancing Risks and Benefits: Sodium-Glucose Cotransporter 2 Inhibitors and the Risk of Diabetic Ketoacidosis
by Jan P. Kleinjan, Justin Blom, André P. van Beek, Hjalmar R. Bouma and Peter R. van Dijk
Metabolites 2024, 14(3), 162; https://doi.org/10.3390/metabo14030162 - 13 Mar 2024
Viewed by 904
Abstract
Sodium-glucose cotransporter-2 inhibitors (SGLT2is) are a new class of drugs that have been proven beneficial in the management of diabetes, chronic kidney disease, and heart failure and in the mitigation of cardiovascular risk. The benefits of SGLT2i therapy have led to the rapid [...] Read more.
Sodium-glucose cotransporter-2 inhibitors (SGLT2is) are a new class of drugs that have been proven beneficial in the management of diabetes, chronic kidney disease, and heart failure and in the mitigation of cardiovascular risk. The benefits of SGLT2i therapy have led to the rapid adoption of these drugs in clinical guidelines. Since the introduction of these drugs, concerns have arisen, as diabetic ketoacidosis (DKA) unexpectedly occurred in patients treated with SGLT2i. DKA is an infrequent but serious complication of SGLT2i therapy, and is potentially preventable. The risk factors for the development of SGLT2i-associated DKA are inappropriate dose reductions of insulin, the dietary restriction of carbohydrates, and factors that may increase insulin demand such as excessive alcohol intake and major surgery. Moreover, the risk of SGLT2i-associated DKA is higher in persons with type 1 diabetes. It is crucial that both patients and healthcare providers are aware of the risks of SGLT2i-associated DKA. In an effort to encourage safe prescribing of this effective class of drugs, we present two cases that illustrate the risks of SGLT2i therapy with regard to the development of DKA. Full article
(This article belongs to the Special Issue Metabolism in Diabetes Progression and Diabetic Complications)
Show Figures

Figure 1

19 pages, 5352 KiB  
Article
Palmitate Compromises C6 Astrocytic Cell Viability and Mitochondrial Function
by Luisa O. Schmitt, Antonella Blanco, Sheila V. Lima, Gianni Mancini, Natalia F. Mendes, Alexandra Latini and Joana M. Gaspar
Metabolites 2024, 14(3), 161; https://doi.org/10.3390/metabo14030161 - 12 Mar 2024
Viewed by 833
Abstract
Consumption of high-fat diets (HFD) is associated with brain alterations, including changes in feeding behavior, cognitive decline, and dementia. Astrocytes play a role in HFD-induced neuroinflammation and brain dysfunction; however, this process is not entirely understood. We hypothesized that exposure to saturated fatty [...] Read more.
Consumption of high-fat diets (HFD) is associated with brain alterations, including changes in feeding behavior, cognitive decline, and dementia. Astrocytes play a role in HFD-induced neuroinflammation and brain dysfunction; however, this process is not entirely understood. We hypothesized that exposure to saturated fatty acids can compromise astrocyte viability and mitochondrial function. The C6 (astrocytes) cell line was treated with palmitate or stearate (200 µM and 400 µM) for 6 h. Cell viability, morphology, inflammatory markers, and oxidative stress were evaluated. To assess mitochondrial function, various parameters were measured (membrane potential, mass, respiration, and complex activities). We observed that 6 h of treatment with 400 µM palmitate decreased cell viability, and treatment with 200 µM palmitate changed the astrocyte morphology. Palmitate increased inflammatory markers (TNF-α and IL6) but did not induce oxidative stress. Palmitate significantly decreased the mitochondrial membrane potential and mitochondrial mass. Complex I activity also decreased in palmitate-treated cells; however, no changes were observed in mitochondrial respiration. In conclusion, palmitate, a saturated fatty acid, induces inflammation and impairs mitochondrial function, leading to reduced astrocytic cell viability and changes in cellular morphology. Our study provides valuable insights into the potential mechanisms underlying the relationship between saturated fatty acids, astrocytes, and mitochondrial function in obesity-related brain dysfunction. Full article
(This article belongs to the Section Nutrition and Metabolism)
Show Figures

Figure 1

9 pages, 1796 KiB  
Communication
Evaluation of Oil-Absorbing Film for Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging (IDESI-MSI) on Biological Samples
by Jiedong Li, Ruolun Wei, Yifan Meng and Richard N. Zare
Metabolites 2024, 14(3), 160; https://doi.org/10.3390/metabo14030160 - 11 Mar 2024
Viewed by 793
Abstract
Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging (IDESI-MSI) has proven to be a robust and reliable tool for chemically imaging biological samples such as fungi, animal tissues, and plants, but the choice of the imprint substrate is crucial. It must effectively transfer maximum [...] Read more.
Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging (IDESI-MSI) has proven to be a robust and reliable tool for chemically imaging biological samples such as fungi, animal tissues, and plants, but the choice of the imprint substrate is crucial. It must effectively transfer maximum amounts of species from the sample while preserving the original spatial distribution of detected molecules. In this study, we explored the potential of utilizing an oil-absorbing film, known for its soft nature and excellent lipophilicity, as an imprint substrate for IDESI-MSI on biological samples. To assess the transfer efficiency of the amounts of molecules and molecular patterns, we conducted experiments using mouse brain tissue. The result shows that more than 90% of the analytes can be transferred to the oil-absorbing film from the original tissue. A comparison of IDESI-MSI results between the oil-absorbing film and the original tissue demonstrates the material’s capability to transfer most molecules from the original tissue and retain images of different analytes with high spatial fidelity. We extended our investigation to plant imaging, where we applied IDESI-MSI to a cross-section of okra. The oil-absorbing film exhibited promise in this context as well. These findings suggest that IDESI-MSI utilizing the oil-absorbing film holds potential across various research fields, including biological metabolism, chemistry, and clinical research, making this technique widely applicable. Full article
Show Figures

Figure 1

16 pages, 2227 KiB  
Article
Metabolomics and Lipidomics Analyses Aid Model Classification of Type 2 Diabetes in Non-Human Primates
by Peining Tao, Stacey Conarello, Thomas P. Wyche, Nanyan Rena Zhang, Keefe Chng, John Kang and Theodore R. Sana
Metabolites 2024, 14(3), 159; https://doi.org/10.3390/metabo14030159 - 09 Mar 2024
Viewed by 969
Abstract
Type 2 diabetes (T2D) is a global public health issue characterized by excess weight, abdominal obesity, dyslipidemia, hyperglycemia, and a progressive increase in insulin resistance. Human population studies of T2D development and its effects on systemic metabolism are confounded by many factors that [...] Read more.
Type 2 diabetes (T2D) is a global public health issue characterized by excess weight, abdominal obesity, dyslipidemia, hyperglycemia, and a progressive increase in insulin resistance. Human population studies of T2D development and its effects on systemic metabolism are confounded by many factors that cannot be controlled, complicating the interpretation of results and the identification of early biomarkers. Aged, sedentary, and overweight/obese non-human primates (NHPs) are one of the best animal models to mimic spontaneous T2D development in humans. We sought to identify and distinguish a set of plasma and/or fecal metabolite biomarkers, that have earlier disease onset predictability, and that could be evaluated for their predictability in subsequent T2D studies in human cohorts. In this study, a single plasma and fecal sample was collected from each animal in a colony of 57 healthy and dysmetabolic NHPs and analyzed for metabolomics and lipidomics. The samples were comprehensively analyzed using untargeted and targeted LC/MS/MS. The changes in each animal’s disease phenotype were monitored using IVGTT, HbA1c, and other clinical metrics, and correlated with their metabolic profile. The plasma and fecal lipids, as well as bile acid profiles, from Healthy, Dysmetabolic (Dys), and Diabetic (Dia) animals were compared. Following univariate and multivariate analyses, including adjustments for weight, age, and sex, several plasma lipid species were identified to be significantly different between these animal groups. Medium and long-chain plasma phosphatidylcholines (PCs) ranked highest at distinguishing Healthy from Dys animals, whereas plasma triglycerides (TG) primarily distinguished Dia from Dys animals. Random Forest (RF) analysis of fecal bile acids showed a reduction in the secondary bile acid glycoconjugate, GCDCA, in diseased animals (AUC 0.76[0.64, 0.89]). Moreover, metagenomics results revealed several bacterial species, belonging to the genera Roseburia, Ruminococcus, Clostridium, and Streptococcus, to be both significantly enriched in non-healthy animals and associated with secondary bile acid levels. In summary, our results highlight the detection of several elevated circulating plasma PCs and microbial species associated with fecal secondary bile acids in NHP dysmetabolic states. The lipids and metabolites we have identified may help researchers to differentiate individual NHPs more precisely between dysmetabolic and overtly diabetic states. This could help assign animals to study groups that are more likely to respond to potential therapies where a difference in efficacy might be anticipated between early vs. advanced disease. Full article
(This article belongs to the Special Issue Metabolic Biomarkers and Gut Microbiota in Adults with Prediabetes)
Show Figures

Graphical abstract

20 pages, 4742 KiB  
Protocol
Unravel the Supremacy of Klebsiella variicola over Native Microbial Strains for Aroma-Enhancing Compound Production in Reconstituted Tobacco Concentrate through Metagenomic Analysis
by Shen Huang, Li Zhu, Ke Wang, Xinlong Zhang, Duobin Mao and Aamir Rasool
Metabolites 2024, 14(3), 158; https://doi.org/10.3390/metabo14030158 - 08 Mar 2024
Viewed by 853
Abstract
Sensory attributes strongly influence consumers’ preferences for products. The inoculation of the Klebsiella variicola H8 strain in a reconstituted tobacco leaf concentrate (RTLC) solution increased neutral aroma-enhancing compound (NAEC) production by 45%, decreased the nicotine level by 25%, decreased the water-soluble total sugar [...] Read more.
Sensory attributes strongly influence consumers’ preferences for products. The inoculation of the Klebsiella variicola H8 strain in a reconstituted tobacco leaf concentrate (RTLC) solution increased neutral aroma-enhancing compound (NAEC) production by 45%, decreased the nicotine level by 25%, decreased the water-soluble total sugar content by ~36%, and improved the sensory quality by 5.71%. The production of NAECs such as dihydrokiwi lactone (DHKL: 192.86%), 1,2,3,4-tetrahydro-1,1,6-trimethylnaphthalene (THTMN: 177.77%), 2,4-di-tert-butylphenol (DTBP: 25%), 4-oxoisofolkone (OIFK: 116.66%,) 1,9-heptadecadiene-4,6-diyn-3-ol (HDD: 116.67%), β-damastrone (BDS: 116.67), and megastigmatrienone A (MSTA: 116.67%) was increased. A metagenomics analysis of the microbial community in the fermented RTLC (FRTLC) was performed to elucidate the mechanism by which NAECs were produced. As a result, 24 groups of functional genes were identified, and among them, five families of carbohydrate-active enzymes, (i) glycoside hydrolase (GH), (ii) glycosyltransferase (GT), (iii) polysaccharide lyase (PL), (iv) carbohydrate esterase (CE), and (v) auxiliary active enzyme (AA), were found to be positively correlated with the production of NAECs. However, among the GHs, the GHs annotated from the H8 strain chromosome displayed the highest relative abundance and a positive correlation with the production of NAECs. Specifically, the GH13-14, GH13-20, GH13-38, GH13-25, GH13-10, GH42, and GH28 genes of the H8 strain were relatively more abundant and were key contributors to the production of NAECs. The correlation analyses revealed that the H8 strain plays a leading role among all the microorganisms in FRTLC in the production of NAECs. Our findings support the application of Klebsiella variicola in NAEC production and a reduction in nicotine content in tobacco products. Full article
(This article belongs to the Section Plant Metabolism)
Show Figures

Figure 1

19 pages, 1443 KiB  
Review
Integrative Multiomics Approach to Skin: The Sinergy between Individualised Medicine and Futuristic Precision Skin Care?
by Angelica Dessì, Roberta Pintus, Vassilios Fanos and Alice Bosco
Metabolites 2024, 14(3), 157; https://doi.org/10.3390/metabo14030157 - 07 Mar 2024
Viewed by 890
Abstract
The skin is a complex ecosystem colonized by millions of microorganisms, the skin microbiota, which are crucial in regulating not only the physiological functions of the skin but also the metabolic changes underlying the onset of skin diseases. The high microbial colonization together [...] Read more.
The skin is a complex ecosystem colonized by millions of microorganisms, the skin microbiota, which are crucial in regulating not only the physiological functions of the skin but also the metabolic changes underlying the onset of skin diseases. The high microbial colonization together with a low diversity at the phylum level and a high diversity at the species level of the skin is very similar to that of the gastrointestinal tract. Moreover, there is an important communication pathway along the gut–brain–skin axis, especially associated with the modulation of neurotransmitters by the microbiota. Therefore, it is evident that the high complexity of the skin system, due not only to the genetics of the host but also to the interaction of the host with resident microbes and between microbe and microbe, requires a multi-omics approach to be deeply understood. Therefore, an integrated analysis, with high-throughput technologies, of the consequences of microbial interaction with the host through the study of gene expression (genomics and metagenomics), transcription (transcriptomics and meta-transcriptomics), and protein production (proteomics and meta-proteomics) and metabolite formation (metabolomics and lipidomics) would be useful. Although to date very few studies have integrated skin metabolomics data with at least one other ‘omics’ technology, in the future, this approach will be able to provide simple and fast tests that can be routinely applied in both clinical and cosmetic settings for the identification of numerous skin diseases and conditions. It will also be possible to create large archives of multi-omics data that can predict individual responses to pharmacological treatments and the efficacy of different cosmetic products on individual subjects by means of specific allotypes, with a view to increasingly tailor-made medicine. In this review, after analyzing the complexity of the skin ecosystem, we have highlighted the usefulness of this emerging integrated omics approach for the analysis of skin problems, starting with one of the latest ‘omics’ sciences, metabolomics, which can photograph the expression of the genome during its interaction with the environment. Full article
(This article belongs to the Special Issue Preclinical and Clinical Application of Metabolomics in Medicine)
Show Figures

Graphical abstract

18 pages, 2032 KiB  
Article
Daily Injection of the β2 Adrenergic Agonist Clenbuterol Improved Muscle Glucose Metabolism, Glucose-Stimulated Insulin Secretion, and Hyperlipidemia in Juvenile Lambs Following Heat-Stress-Induced Intrauterine Growth Restriction
by Rachel L. Gibbs, James A. Wilson, Rebecca M. Swanson, Joslyn K. Beard, Zena M. Hicks, Haley N. Beer, Eileen S. Marks-Nelson, Ty B. Schmidt, Jessica L. Petersen and Dustin T. Yates
Metabolites 2024, 14(3), 156; https://doi.org/10.3390/metabo14030156 - 07 Mar 2024
Viewed by 911
Abstract
Stress-induced fetal programming diminishes β2 adrenergic tone, which coincides with intrauterine growth restriction (IUGR) and lifelong metabolic dysfunction. We determined if stimulating β2 adrenergic activity in IUGR-born lambs would improve metabolic outcomes. IUGR lambs that received daily injections of saline or [...] Read more.
Stress-induced fetal programming diminishes β2 adrenergic tone, which coincides with intrauterine growth restriction (IUGR) and lifelong metabolic dysfunction. We determined if stimulating β2 adrenergic activity in IUGR-born lambs would improve metabolic outcomes. IUGR lambs that received daily injections of saline or the β2 agonist clenbuterol from birth to 60 days were compared with controls from pair-fed thermoneutral pregnancies. As juveniles, IUGR lambs exhibited systemic inflammation and robust metabolic dysfunction, including greater (p < 0.05) circulating TNFα, IL-6, and non-esterified fatty acids, increased (p < 0.05) intramuscular glycogen, reduced (p < 0.05) circulating IGF-1, hindlimb blood flow, glucose-stimulated insulin secretion, and muscle glucose oxidation. Daily clenbuterol fully recovered (p < 0.05) circulating TNFα, IL-6, and non-esterified fatty acids, hindlimb blood flow, muscle glucose oxidation, and intramuscular glycogen. Glucose-stimulated insulin secretion was partially recovered (p < 0.05) in clenbuterol-treated IUGR lambs, but circulating IGF-1 was not improved. Circulating triglycerides and HDL cholesterol were elevated (p < 0.05) in clenbuterol-treated IUGR lambs, despite being normal in untreated IUGR lambs. We conclude that deficient β2 adrenergic regulation is a primary mechanism for several components of metabolic dysfunction in IUGR-born offspring and thus represents a potential therapeutic target for improving metabolic outcomes. Moreover, benefits from the β2 agonist were likely complemented by its suppression of IUGR-associated inflammation. Full article
(This article belongs to the Special Issue Unlocking the Mysteries of Muscle Metabolism in the Animal Sciences)
Show Figures

Figure 1

15 pages, 1752 KiB  
Review
Pesticides: Unintended Impact on the Hidden World of Gut Microbiota
by Asghar Ali and Khalid I. AlHussaini
Metabolites 2024, 14(3), 155; https://doi.org/10.3390/metabo14030155 - 07 Mar 2024
Viewed by 1436
Abstract
A vast range of pesticides have been routinely employed for plant protection throughout the last few decades. Pesticides can enter non-target organisms in various ways, posing health hazards. Exposure to different environmental pollutants, including pesticides, can affect the human gut flora. Metabolites generated [...] Read more.
A vast range of pesticides have been routinely employed for plant protection throughout the last few decades. Pesticides can enter non-target organisms in various ways, posing health hazards. Exposure to different environmental pollutants, including pesticides, can affect the human gut flora. Metabolites generated from the gut microbiota play an essential role in the host’s health by regulating metabolic homeostasis. A disruption in this equilibrium can lead to the emergence of numerous illnesses and their etiology. Pesticides have been shown in a few recent studies to harm the host’s gut microbiome. As a result, there is an urgent need to investigate the impact of pesticides on gut microbiota-mediated immunity. Metabolic alterations in the host may give a better understanding of pesticide-induced harm. This review highlights the potential consequences of pesticide exposure on gut microbiota composition and function, mainly focusing on how it might alter the production of secondary metabolites with potential downstream implications for host health. Full article
(This article belongs to the Section Environmental Metabolomics)
Show Figures

Figure 1

17 pages, 1971 KiB  
Review
Machine Learning to Predict Enzyme–Substrate Interactions in Elucidation of Synthesis Pathways: A Review
by Luis F. Salas-Nuñez, Alvaro Barrera-Ocampo, Paola A. Caicedo, Natalie Cortes, Edison H. Osorio, Maria F. Villegas-Torres and Andres F. González Barrios
Metabolites 2024, 14(3), 154; https://doi.org/10.3390/metabo14030154 - 07 Mar 2024
Viewed by 1114
Abstract
Enzyme–substrate interactions play a fundamental role in elucidating synthesis pathways and synthetic biology, as they allow for the understanding of important aspects of a reaction. Establishing the interaction experimentally is a slow and costly process, which is why this problem has been addressed [...] Read more.
Enzyme–substrate interactions play a fundamental role in elucidating synthesis pathways and synthetic biology, as they allow for the understanding of important aspects of a reaction. Establishing the interaction experimentally is a slow and costly process, which is why this problem has been addressed using computational methods such as molecular dynamics, molecular docking, and Monte Carlo simulations. Nevertheless, this type of method tends to be computationally slow when dealing with a large search space. Therefore, in recent years, methods based on artificial intelligence, such as support vector machines, neural networks, or decision trees, have been implemented, significantly reducing the computing time and covering vast search spaces. These methods significantly reduce the computation time and cover broad search spaces, rapidly reducing the number of interacting candidates, as they allow repetitive processes to be automated and patterns to be extracted, are adaptable, and have the capacity to handle large amounts of data. This article analyzes these artificial intelligence-based approaches, presenting their common structure, advantages, disadvantages, limitations, challenges, and future perspectives. Full article
(This article belongs to the Section Pharmacology and Drug Metabolism)
Show Figures

Graphical abstract

22 pages, 762 KiB  
Review
Interleukins: Pathogenesis in Non-Alcoholic Fatty Liver Disease
by Saira Rafaqat, Sanja Gluscevic, Filiz Mercantepe, Sana Rafaqat and Aleksandra Klisic
Metabolites 2024, 14(3), 153; https://doi.org/10.3390/metabo14030153 - 06 Mar 2024
Cited by 1 | Viewed by 849
Abstract
Inflammatory cytokines have been implicated as crucial contributors to the onset and progression of non-alcoholic fatty liver disease (NAFLD). The exact mechanisms by which interleukins (ILs) contribute to NAFLD may vary, and ongoing research is aimed at understanding the specific roles of different [...] Read more.
Inflammatory cytokines have been implicated as crucial contributors to the onset and progression of non-alcoholic fatty liver disease (NAFLD). The exact mechanisms by which interleukins (ILs) contribute to NAFLD may vary, and ongoing research is aimed at understanding the specific roles of different ILs in the pathogenesis of this condition. In addition, variations in environmental factors and genetics in each individual can influence the onset and/or progression of NAFLD. The lack of clinical studies related to the potential therapeutic properties of IL-1 inhibitors currently does not allow us to conclude their validity as a therapeutic option, although preclinical studies show promising results. Further studies are needed to elucidate their beneficial properties in NAFLD treatment. Full article
(This article belongs to the Special Issue New Biomarkers for Diagnostics in Metabolic Diseases)
Show Figures

Figure 1

11 pages, 1367 KiB  
Case Report
Integrating Genome Sequencing and Untargeted Metabolomics in Monozygotic Twins with a Rare Complex Neurological Disorder
by Rulan Shaath, Aljazi Al-Maraghi, Haytham Ali, Jehan AlRayahi, Adam D. Kennedy, Karen L. DeBalsi, Sura Hussein, Najwa Elbashir, Sujitha S. Padmajeya, Sasirekha Palaniswamy, Sarah H. Elsea, Ammira A. Akil, Noha A. Yousri and Khalid A. Fakhro
Metabolites 2024, 14(3), 152; https://doi.org/10.3390/metabo14030152 - 04 Mar 2024
Viewed by 909
Abstract
Multi-omics approaches, which integrate genomics, transcriptomics, proteomics, and metabolomics, have emerged as powerful tools in the diagnosis of rare diseases. We used untargeted metabolomics and whole-genome sequencing (WGS) to gain a more comprehensive understanding of a rare disease with a complex presentation affecting [...] Read more.
Multi-omics approaches, which integrate genomics, transcriptomics, proteomics, and metabolomics, have emerged as powerful tools in the diagnosis of rare diseases. We used untargeted metabolomics and whole-genome sequencing (WGS) to gain a more comprehensive understanding of a rare disease with a complex presentation affecting female twins from a consanguineous family. The sisters presented with polymicrogyria, a Dandy–Walker malformation, respiratory distress, and multiorgan dysfunctions. Through WGS, we identified two rare homozygous variants in both subjects, a pathogenic variant in ADGRG1(p.Arg565Trp) and a novel variant in CNTNAP1(p.Glu910Val). These genes have been previously associated with autosomal recessive polymicrogyria and hypomyelinating neuropathy with/without contractures, respectively. The twins exhibited symptoms that overlapped with both of these conditions. The results of the untargeted metabolomics analysis revealed significant metabolic perturbations relating to neurodevelopmental abnormalities, kidney dysfunction, and microbiome. The significant metabolites belong to essential pathways such as lipids and amino acid metabolism. The identification of variants in two genes, combined with the support of metabolic perturbation, demonstrates the rarity and complexity of this phenotype and provides valuable insights into its underlying mechanisms. Full article
(This article belongs to the Section Endocrinology and Clinical Metabolic Research)
Show Figures

Figure 1

16 pages, 2886 KiB  
Article
In Vitro Astroglial Dysfunction Induced by Neurotoxins: Mimicking Astrocytic Metabolic Alterations of Alzheimer’s Disease
by Jéssica Taday, Fernanda Telles Fróes, Marina Seady, Carlos Alberto Gonçalves and Marina Concli Leite
Metabolites 2024, 14(3), 151; https://doi.org/10.3390/metabo14030151 - 01 Mar 2024
Viewed by 923
Abstract
Astrocytes play fundamental roles in the maintenance of brain homeostasis. The dysfunction of these cells is widely associated with brain disorders, which are often characterized by variations in the astrocyte protein markers GFAP and S100B, in addition to alterations in some of its [...] Read more.
Astrocytes play fundamental roles in the maintenance of brain homeostasis. The dysfunction of these cells is widely associated with brain disorders, which are often characterized by variations in the astrocyte protein markers GFAP and S100B, in addition to alterations in some of its metabolic functions. To understand the role of astrocytes in neurodegeneration mechanisms, we induced some of these metabolic alterations, such as energy metabolism, using methylglyoxal (MG) or fluorocitrate (FC); and neuroinflammation, using lipopolysaccharide (LPS) and streptozotocin (STZ), which is used for inducing Alzheimer’s disease (AD) in animal models. We showed that MG, LPS, STZ and FC similarly caused astrocyte dysfunction by increasing GFAP and reducing S100B secretion. In the context of AD, STZ caused an amyloid metabolism impairment verified by increases in Aβ1-40 peptide content and decreases in the amyloid degradation enzymes, IDE and NEP. Our data contribute to the understanding of the role of astrocytes in brain injury mechanisms and suggest that STZ is suitable for use in vitro models for studying the role of astrocytes in AD. Full article
(This article belongs to the Special Issue Energy Metabolism in Neurodegenerative Diseases)
Show Figures

Graphical abstract

16 pages, 2027 KiB  
Article
Transcriptome in Liver of Periparturient Dairy Cows Differs between Supplementation of Rumen-Protected Niacin and Rumen-Protected Nicotinamide
by Yuanjie Zhang, Rongrong Li, Xue’er Du, Zhijie Cui, Xingwei Jiang, Lamei Wang, Junhu Yao, Shimin Liu, Jianguo Wang, Chuanjiang Cai and Yangchun Cao
Metabolites 2024, 14(3), 150; https://doi.org/10.3390/metabo14030150 - 01 Mar 2024
Viewed by 903
Abstract
To investigate the difference between rumen-protected niacin (RPN) and rumen-protected nicotinamide (RPM) in the transcriptome of genes relating to the lipid metabolism of the liver of periparturient dairy cows, 10 healthy Chinese Holstein cows were randomly divided into two groups and fed diets [...] Read more.
To investigate the difference between rumen-protected niacin (RPN) and rumen-protected nicotinamide (RPM) in the transcriptome of genes relating to the lipid metabolism of the liver of periparturient dairy cows, 10 healthy Chinese Holstein cows were randomly divided into two groups and fed diets supplemented with 18.4 g/d RPN or 18.7 g/d RPM, respectively. The experiment lasted from 14 days before to 21 days after parturition. Liver biopsies were taken 21 days postpartum for transcriptomic sequencing. In addition, human LO2 cells were cultured in a medium containing 1.6 mmol/L of non-esterified fatty acids and 1 mmol/L niacin (NA) or 2 mmol/L nicotinamide (NAM) to verify the expression of the 10 genes selected from the transcriptomic analysis of the liver biopsies. The expression of a total of 9837 genes was detected in the liver biopsies, among which 1210 differentially expressed genes (DEGs) were identified, with 579 upregulated and 631 downregulated genes. These DEGs were associated mainly with lipid metabolism, oxidative stress, and some inflammatory pathways. Gene ontology (GO) enrichment analysis showed that 355 DEGs were enriched in 38 GO terms. The differences in the expression of these DEGs between RPN and RPM were predominantly related to the processes of steroid catabolism, steroid hydroxylase, monooxygenase activity, oxidoreductase activity, hemoglobin binding, and ferric iron binding, which are involved mainly in lipid anabolism and redox processes. The expressions of FADS2, SLC27A6, ARHGAP24, and THRSP in LO2 cells were significantly higher (p < 0.05) while the expressions of BCO2, MARS1, GARS1, S100A12, AGMO, and OSBPL11 were significantly lower (p < 0.05) on the NA treatment compared to the NAM treatment, indicating that NA played a role in liver metabolism by directly regulating fatty acid anabolism and transport, inflammatory factor expression, and oxidative stress; and NAM functioned more as a precursor of nicotinamide adenine dinucleotide (NAD, coenzyme I) and nicotinamide adenine dinucleotide phosphate (NADP, coenzyme II) to participate indirectly in biological processes such as ether lipid metabolism, cholesterol metabolism, energy metabolism, and other processes. Full article
(This article belongs to the Special Issue Nutrition and Metabolism in Animals)
Show Figures

Figure 1

14 pages, 1963 KiB  
Article
Advancing Personalized Medicine by Analytical Means: Selection of Three Metabolites That Allows Discrimination between Glaucoma, Diabetes, and Controls
by David Bernal-Casas, Joan Serrano-Marín, Juan Sánchez-Navés, Josep M. Oller and Rafael Franco
Metabolites 2024, 14(3), 149; https://doi.org/10.3390/metabo14030149 - 29 Feb 2024
Viewed by 965
Abstract
This paper aimed at devising an intelligence-based method to select compounds that can distinguish between open-angle glaucoma patients, type 2 diabetes patients, and healthy controls. Taking the concentration of 188 compounds measured in the aqueous humour (AH) of patients and controls, linear discriminant [...] Read more.
This paper aimed at devising an intelligence-based method to select compounds that can distinguish between open-angle glaucoma patients, type 2 diabetes patients, and healthy controls. Taking the concentration of 188 compounds measured in the aqueous humour (AH) of patients and controls, linear discriminant analysis (LDA) was used to identify the right combination of compounds that could lead to accurate diagnosis. All possibilities, using the leave-one-out approach, were considered through ad hoc programming and in silico massive data production and statistical analysis. Our proof of concept led to the selection of four molecules: acetyl-ornithine (Ac-Orn), C3 acyl-carnitine (C3), diacyl C42:6 phosphatidylcholine (PC aa C42:6), and C3-DC (C4-OH) acyl-carnitine (C3-DC (C4-OH)) that, taken in combination, would lead to a 95% discriminative success. 100% success was obtained with a non-linear combination of the concentration of three of these four compounds. By discarding younger controls to adjust by age, results were similar although one control was misclassified as a diabetes patient. Methods based on the consideration of individual clinical chemical parameters have limitations in the ability to make a reliable diagnosis, stratify patients, and assess disease progression. Leveraging human AH metabolomic data, we developed a procedure that selects a minimal number of metabolites (3–5) and designs algorithms that maximize the overall accuracy evaluating both positive predictive (PPV) and negative predictive (NPV) values. Our approach of simultaneously considering the levels of a few metabolites can be extended to any other body fluid and has potential to advance precision medicine. Artificial intelligence is expected to use algorithms that use the concentration of three to five molecules to correctly diagnose diseases, also allowing stratification of patients and evaluation of disease progression. In addition, this significant advance shifts focus from a single-molecule biomarker approach to that of an appropriate combination of metabolites. Full article
(This article belongs to the Special Issue Advances in Metabolic Profiling of Biological Samples 2nd Edition)
Show Figures

Figure 1

14 pages, 2460 KiB  
Article
Diagnostic and Prognostic Performance of Metabolic Signatures in Pancreatic Ductal Adenocarcinoma: The Clinical Application of Quantitative NextGen Mass Spectrometry
by Paulo D’Amora, Ismael D. C. G. Silva, Steven S. Evans, Adam J. Nagourney, Katharine A. Kirby, Brett Herrmann, Daniela Cavalheiro, Federico R. Francisco, Paula J. Bernard and Robert A. Nagourney
Metabolites 2024, 14(3), 148; https://doi.org/10.3390/metabo14030148 - 29 Feb 2024
Viewed by 3252
Abstract
With 64,050 new diagnoses and 50,550 deaths in the US in 2023, pancreatic ductal adenocarcinoma (PDAC) is among the most lethal of all human malignancies. Early detection and improved prognostication remain critical unmet needs. We applied next-generation metabolomics, using quantitative tandem mass spectrometry [...] Read more.
With 64,050 new diagnoses and 50,550 deaths in the US in 2023, pancreatic ductal adenocarcinoma (PDAC) is among the most lethal of all human malignancies. Early detection and improved prognostication remain critical unmet needs. We applied next-generation metabolomics, using quantitative tandem mass spectrometry on plasma, to develop biochemical signatures that identify PDAC. We first compared plasma from 10 PDAC patients to 169 samples from healthy controls. Using metabolomic algorithms and machine learning, we identified ratios that incorporate amino acids, biogenic amines, lysophosphatidylcholines, phosphatidylcholines and acylcarnitines that distinguished PDAC from normal controls. A confirmatory analysis then applied the algorithms to 30 PDACs compared with 60 age- and sex-matched controls. Metabolic signatures were then analyzed to compare survival, measured in months, from date of diagnosis to date of death that identified metabolite ratios that stratified PDACs into distinct survival groups. The results suggest that metabolic signatures could provide PDAC diagnoses earlier than tumor markers or radiographic measures and offer insights into disease severity that could allow more judicious use of therapy by stratifying patients into metabolic-risk subgroups. Full article
(This article belongs to the Topic Biomarker Development and Application)
Show Figures

Figure 1

14 pages, 1569 KiB  
Article
Automated Spectrophotometric Assays for the Measurement of Ammonia and Bicarbonate in Saliva of Horses: Analytical Validation and Changes in Equine Gastric Ulcer Syndrome (EGUS)
by Alberto Muñoz-Prieto, Eva Llamas-Amor, María Dolores Contreras-Aguilar, Ignacio Ayala, María Martín Cuervo, José Joaquín Cerón and Sanni Hansen
Metabolites 2024, 14(3), 147; https://doi.org/10.3390/metabo14030147 - 28 Feb 2024
Viewed by 809
Abstract
Ammonia (NH3) and bicarbonate (HCO3) have been related to gastric ulcers in humans. Ammonia is considered a possible cause of gastric ulcers, whereas bicarbonate has a protective function. The presence of ulcers in the stomach of horses is defined [...] Read more.
Ammonia (NH3) and bicarbonate (HCO3) have been related to gastric ulcers in humans. Ammonia is considered a possible cause of gastric ulcers, whereas bicarbonate has a protective function. The presence of ulcers in the stomach of horses is defined as Equine Gastric Ulcer Syndrome (EGUS), which is a frequent disease in this species, and it has been associated with changes in saliva composition, such as in analytes related to inflammation, immune system and oxidative stress. The objectives of this study were (1) to perform an analytical validation of two automated spectrophotometric assays, one for ammonia and one for bicarbonate, in the horses’ saliva and (2) to evaluate their possible variations with EGUS. Analytical validation of the automated assays for ammonia and bicarbonate in the saliva of horses showed that both assays were precise and accurate. In addition, significantly higher values of ammonia and lower values of bicarbonate were found in the saliva of horses with EGUS compared to healthy horses. It can be concluded that ammonia and bicarbonate can be measured in the saliva of horses and that ammonia increases and bicarbonate decreases in this sample type could be related to the presence of EGUS in this species. Full article
(This article belongs to the Section Animal Metabolism)
Show Figures

Figure 1

39 pages, 1578 KiB  
Review
Plant-Derived Senotherapeutics for the Prevention and Treatment of Intervertebral Disc Degeneration and Aging
by Eleni Mavrogonatou and Dimitris Kletsas
Metabolites 2024, 14(3), 146; https://doi.org/10.3390/metabo14030146 - 28 Feb 2024
Viewed by 924
Abstract
Chronic low back pain, a major cause of disability with a great global socioeconomic impact, has been inextricably associated with intervertebral disc degeneration. On the other hand, an enhanced number of senescent cells has been identified in aged and degenerated intervertebral discs and [...] Read more.
Chronic low back pain, a major cause of disability with a great global socioeconomic impact, has been inextricably associated with intervertebral disc degeneration. On the other hand, an enhanced number of senescent cells has been identified in aged and degenerated intervertebral discs and their senescence-associated secretory phenotype (SASP) has been connected with qualitative/quantitative alterations in the extracellular matrix and ultimately with the disturbance of tissue homeostasis. Given that selective elimination of senescent cells (by the so-called senolytics) or amendment of their secretome towards a less catabolic/inflammatory phenotype (by molecules known as senomorphics) has been reported to alleviate symptoms of several age-associated diseases and to improve tissue quality during aging, here we will review the emerging role of senolytic and senomorphic agents derived from plants and natural products against intervertebral disc degeneration. The mode of action of these senotherapeutics, as well as the challenges in their practical application, will also be explicitly discussed in an attempt to direct their more targeted and effective use in exclusive or combinatorial therapeutic schemes for the prevention and/or treatment of disc degenerative disorders. Full article
Show Figures

Figure 1

Previous Issue
Next Issue
Back to TopTop