Metabolites

17 pages, 2527 KiB

Open AccessArticle

Explainable Artificial Intelligence Paves the Way in Precision Diagnostics and Biomarker Discovery for the Subclass of Diabetic Retinopathy in Type 2 Diabetics

by Fatma Hilal Yagin, Seyma Yasar, Yasin Gormez, Burak Yagin, Abdulvahap Pinar, Abedalrhman Alkhateeb and Luca Paolo Ardigò

Metabolites 2023, 13(12), 1204; https://doi.org/10.3390/metabo13121204 - 18 Dec 2023

Cited by 11 | Viewed by 2562

Abstract

Diabetic retinopathy (DR), a common ocular microvascular complication of diabetes, contributes significantly to diabetes-related vision loss. This study addresses the imperative need for early diagnosis of DR and precise treatment strategies based on the explainable artificial intelligence (XAI) framework. The study integrated clinical, [...] Read more.

Diabetic retinopathy (DR), a common ocular microvascular complication of diabetes, contributes significantly to diabetes-related vision loss. This study addresses the imperative need for early diagnosis of DR and precise treatment strategies based on the explainable artificial intelligence (XAI) framework. The study integrated clinical, biochemical, and metabolomic biomarkers associated with the following classes: non-DR (NDR), non-proliferative diabetic retinopathy (NPDR), and proliferative diabetic retinopathy (PDR) in type 2 diabetes (T2D) patients. To create machine learning (ML) models, 10% of the data was divided into validation sets and 90% into discovery sets. The validation dataset was used for hyperparameter optimization and feature selection stages, while the discovery dataset was used to measure the performance of the models. A 10-fold cross-validation technique was used to evaluate the performance of ML models. Biomarker discovery was performed using minimum redundancy maximum relevance (mRMR), Boruta, and explainable boosting machine (EBM). The predictive proposed framework compares the results of eXtreme Gradient Boosting (XGBoost), natural gradient boosting for probabilistic prediction (NGBoost), and EBM models in determining the DR subclass. The hyperparameters of the models were optimized using Bayesian optimization. Combining EBM feature selection with XGBoost, the optimal model achieved (91.25 ± 1.88) % accuracy, (89.33 ± 1.80) % precision, (91.24 ± 1.67) % recall, (89.37 ± 1.52) % F1-Score, and (97.00 ± 0.25) % the area under the ROC curve (AUROC). According to the EBM explanation, the six most important biomarkers in determining the course of DR were tryptophan (Trp), phosphatidylcholine diacyl C42:2 (PC.aa.C42.2), butyrylcarnitine (C4), tyrosine (Tyr), hexadecanoyl carnitine (C16) and total dimethylarginine (DMA). The identified biomarkers may provide a better understanding of the progression of DR, paving the way for more precise and cost-effective diagnostic and treatment strategies. Full article

(This article belongs to the Special Issue Novel Approaches for Metabolomics in Drugs and Biomarkers Discovery)

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37 pages, 3316 KiB

Open AccessReview

Metabolomics: An Emerging “Omics” Platform for Systems Biology and Its Implications for Huntington Disease Research

by Sumeyya Akyol, Nadia Ashrafi, Ali Yilmaz, Onur Turkoglu and Stewart F. Graham

Metabolites 2023, 13(12), 1203; https://doi.org/10.3390/metabo13121203 - 18 Dec 2023

Cited by 3 | Viewed by 2452

Abstract

Huntington’s disease (HD) is a progressive, fatal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. The precise mechanisms of HD progression are poorly understood; however, it is known that there is an expansion of the trinucleotide cytosine-adenine-guanine (CAG) repeat in the Huntingtin [...] Read more.

Huntington’s disease (HD) is a progressive, fatal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. The precise mechanisms of HD progression are poorly understood; however, it is known that there is an expansion of the trinucleotide cytosine-adenine-guanine (CAG) repeat in the Huntingtin gene. Important new strategies are of paramount importance to identify early biomarkers with predictive value for intervening in disease progression at a stage when cellular dysfunction has not progressed irreversibly. Metabolomics is the study of global metabolite profiles in a system (cell, tissue, or organism) under certain conditions and is becoming an essential tool for the systemic characterization of metabolites to provide a snapshot of the functional and pathophysiological states of an organism and support disease diagnosis and biomarker discovery. This review briefly highlights the historical progress of metabolomic methodologies, followed by a more detailed review of the use of metabolomics in HD research to enable a greater understanding of the pathogenesis, its early prediction, and finally the main technical platforms in the field of metabolomics. Full article

(This article belongs to the Special Issue Hunting of Huntington's Disease)

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17 pages, 36002 KiB

Open AccessArticle

Tetraenone A: A New β-Ionone Derivative from Tetraena aegyptia

by Ahmed Ashour, Asmaa E. Sherif, Selwan M. El-Sayed, Ji-Young Kim, Dae Sik Jang, Abtin Anvari, Abdelbasset A. Farahat, Sabrin R. M. Ibrahim, Gamal A. Mohamed, Bayan E. Ainousah, Raghad F. Aljohani, Razan R. Al-Hejaili, Rahaf H. Khoja, Ahmed H. E. Hassan and Ahmed A. Zaki

Metabolites 2023, 13(12), 1202; https://doi.org/10.3390/metabo13121202 - 18 Dec 2023

Viewed by 1919

Abstract

In this study, the chemical investigation of Tetraena aegyptia (Zygophyllaceae) led to the identification of a new megastigmene derivative, tetraenone A ((2S, 5R, 6R, 7E)-2-hydroxy-5,6-dihydro-β-ionone) (1), along with (3S, 5R [...] Read more.

In this study, the chemical investigation of Tetraena aegyptia (Zygophyllaceae) led to the identification of a new megastigmene derivative, tetraenone A ((2S, 5R, 6R, 7E)-2-hydroxy-5,6-dihydro-β-ionone) (1), along with (3S, 5R, 6S, 7E)-3-hydroxy-5,6-epoxy-5,6-dihydro-β-ionone- (2), 3,4-dihydroxy-cinnamyl alcohol-4-glucoside (3), 3β,19α-dihydroxy-ursan-28-oic acid (4), quinovic acid (5), p-coumaric acid (6), and ferulic acid (7), for the first time. The chemical structures of 1–7 were confirmed by analysis of their 1D and 2D NMR and HRESIMS spectra and by their comparison with the relevant literature. The absolute configurations of 1 and 2 were assigned based on NOESY interactions and ECD spectra. Conformational analysis showed that 1 existed exclusively in one of the two theoretically possible chair conformers with a predominant s-trans configuration for the 3-oxobut-1-en-1-yl group with the ring, while the half-chair conformer had a pseudo-axial hydroxy group that was predominant over the other half-chair conformation. Boat conformations were not among the most stable conformations, and the s-trans isomerism was in favor of s-cis configuration. In silico investigation revealed that 1 and 2 had more favorable binding interactions with M^pro rather than with TMPRSS2. Accordingly, molecular dynamic simulations were performed on the complexes of compounds 1 and 2 with M^pro to explore the stability of their interaction with the target protein structure. Compounds 1 and 2 might offer a possible starting point for developing covalent inhibitors of M^pro of SARS-CoV-2. Full article

(This article belongs to the Special Issue Extraction, Characterization, Chemical Composition and Biological Activity of Natural Metabolites)

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15 pages, 8228 KiB

Open AccessArticle

Effect of Garlic Straw with Silage Corn Stalks on Hu Sheep Rumen Fermentation and Microbial Community In Vitro

by Yangyang Shen, Jianli Zhang, Hongbing Gui, Huili Wang, Yinxia Li, Jun Zhang, Shaoxian Cao, Jifeng Zhong, Yong Qian and Chunhua Meng

Metabolites 2023, 13(12), 1201; https://doi.org/10.3390/metabo13121201 - 17 Dec 2023

Cited by 1 | Viewed by 1596

Abstract

Garlic, an important economic crop, provides nutrient-rich straw. When appropriately balanced with silage corn stalks, it is a high-quality forage resource. However, studies on the impact of garlic straw with silage corn stalks on Hu sheep’s digestive metabolism and rumen microbiota are scarce. [...] Read more.

Garlic, an important economic crop, provides nutrient-rich straw. When appropriately balanced with silage corn stalks, it is a high-quality forage resource. However, studies on the impact of garlic straw with silage corn stalks on Hu sheep’s digestive metabolism and rumen microbiota are scarce. In this study, different addition ratios of garlic straw and silage corn stalks were utilized for in vitro experiments. We designed six experimental groups (CON, G0, G20, G40, G60, G80, and G100) based on varying ratios of garlic straw to silage corn stalks. Rumen microbiota was analyzed through 16S rRNA sequencing. Nutrient composition analysis indicated that garlic straw’s relative feeding value (RFV) closely resembled that of silage corn stalks. After 24 h of fermentation, dry matter digestibility and in vitro gas production significantly increased, reaching peak values at a 60% addition ratio. Furthermore, volatile fatty acids (VFAs) such as acetic, propionic, and butyric acid exhibited elevated contents, with the highest yields observed at 60% inclusion. At the genus level, Prevotella, Rikenellaceae RC9 gut group, and Succiniclasticum were identified as the dominant bacterial groups. The gas production test showed a significant decrease in the G80 group compared to others. Microbial analysis revealed a higher abundance of Prevotella in G80 compared to G20, offering valuable insights for reducing greenhouse gas emissions from ruminant animals. Finally, this study predicted the impact of garlic straw with silage corn stalks’ addition on Hu sheep’s metabolic pathways and biological functions of the rumen microbiota. This research highlights the potential for effectively utilizing garlic straw as a feed resource for Hu sheep and proposes a rational proportion for combining garlic straw with silage corn stalks. Full article

(This article belongs to the Section Animal Metabolism)

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17 pages, 1239 KiB

Open AccessArticle

How Supplementation with SOD-Rich Plant Extract, Combined with Gliadin, Can Affect Oxidative Stress Markers and Zonulin Levels in Exercise-Induced Oxidative Stress

by Olina Dudašova Petrovičova, Ivan Stanković, Brižita Ðordević, Violeta Dopsaj, Neda Milinković and Milivoj Dopsaj

Metabolites 2023, 13(12), 1200; https://doi.org/10.3390/metabo13121200 - 17 Dec 2023

Cited by 1 | Viewed by 1817

Abstract

A randomized, double-blind, placebo-controlled study was conducted to investigate the influence of supplementation with a superoxide dismutase (SOD)-rich plant extract on markers of oxidative stress, zonulin levels and the performance of elite athletes. Participants were 30 international-level rowers, divided into an experimental group [...] Read more.

A randomized, double-blind, placebo-controlled study was conducted to investigate the influence of supplementation with a superoxide dismutase (SOD)-rich plant extract on markers of oxidative stress, zonulin levels and the performance of elite athletes. Participants were 30 international-level rowers, divided into an experimental group (n = 15) and a control group (n = 15). The rowers performed a maximal effort incremental test on a rowing ergometer at the beginning and at the end of the study. Markers of oxidative stress (total antioxidant status (TAS), total oxidant status (TOS), oxidative stress index (OSI), superoxide dismutase (SOD), glutathione peroxidase (GPx), advanced oxidation protein products (AOPPs), malondialdehyde (MDA), sulfhydryl (SH) groups, bilirubin, uric acid, albumin and zonulin) were determined in serum. A lower TOS (p = 0.010) and OSI (p = 0.004), a lower MDA (p = 0.001) and a higher level of SH groups (p = 0.031) were observed in the experimental group after supplementation. Physical performance was evaluated through metabolic efficiency, taking lactate levels and power output on the ergometer into account. After 6 weeks of supplementation, the relative increase in metabolic efficiency at a 4 mmol/L lactate concentration and maximal effort was significantly higher in the experimental group (p = 0.004 and p = 0.015, respectively). These results suggest that supplementation with a SOD-rich extract promotes lower oxidative stress, better antioxidant protection and, consequently, the better work performance of athletes. Full article

(This article belongs to the Special Issue Metabolomic Advances in Promoting Exercise-Induced Metabolic Changes)

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11 pages, 3601 KiB

Open AccessArticle

md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases

by Huan Jin and Hunter N. B. Moseley

Metabolites 2023, 13(12), 1199; https://doi.org/10.3390/metabo13121199 - 17 Dec 2023

Cited by 6 | Viewed by 1307

Abstract

A major challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. The md_harmonize package utilizes a neighborhood-specific graph coloring [...] Read more.

A major challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. The md_harmonize package utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on a compound’s chemical structure. The resulting harmonized compounds and reactions can be used for various downstream analyses, including the construction of atom-resolved metabolic networks and models for metabolic flux analysis. Parts of the md_harmonize package have been optimized using a variety of computational techniques to allow certain NP-complete problems handled by the software to be tractable for these specific use-cases. The software is available on GitHub and through the Python Package Index, with end-user documentation hosted on GitHub Pages. Full article

(This article belongs to the Section Bioinformatics and Data Analysis)

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13 pages, 1036 KiB

Open AccessArticle

Blood Serum and Drainage Microbial and Mitochondrial Metabolites in Patients after Surgery for Pancreatic Cancer

by Maria Getsina, Nikolay Tsyba, Petr Polyakov, Natalia Beloborodova and Ekaterina Chernevskaya

Metabolites 2023, 13(12), 1198; https://doi.org/10.3390/metabo13121198 - 15 Dec 2023

Cited by 1 | Viewed by 1576

Abstract

Pancreatic cancer (PC) has the highest mortality rate of all major cancers in the world despite improvements in clinical care and an understanding of the biology of pancreatic cancer. A study of 64 patients with verified pancreatic cancer who underwent surgery was included. [...] Read more.

Pancreatic cancer (PC) has the highest mortality rate of all major cancers in the world despite improvements in clinical care and an understanding of the biology of pancreatic cancer. A study of 64 patients with verified pancreatic cancer who underwent surgery was included. Sampling was carried out at three points: before surgery and on days 1–3 after surgery and 5–7 days after surgery. Drainage fluid collection was taken from the drains installed intraoperatively one day after surgery. Tyrosine and phenylalanine metabolites and two mitochondrial metabolites, namely succinic and fumaric acids, were identified and quantified by GC-MS in the serum of healthy donors and patients. Differences in the metabolomic profile were found between the patients and healthy people. A statistically significant decrease in the level of p-hydroxyphenyllactic acid (p-HPhLA), the amount of sum 3 sepsis-associated metabolites (Σ 3AMM), as well as fumaric and succinic acids in patients was observed. It was also noted that p-hydroxyphenyllactic acid in the preoperative period may be considered as a predictor of complications and longer postoperative recovery. Full article

(This article belongs to the Special Issue Metabolic Profiling of Aromatic Compounds)

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11 pages, 2134 KiB

Open AccessArticle

Breath Analysis for Lung Cancer Early Detection—A Clinical Study

by Zhunan Jia, Velmurugan Thavasi, Thirumalai Venkatesan and Pyng Lee

Metabolites 2023, 13(12), 1197; https://doi.org/10.3390/metabo13121197 - 12 Dec 2023

Cited by 3 | Viewed by 2512

Abstract

This clinical study presents a comprehensive investigation into the utility of breath analysis as a non-invasive method for the early detection of lung cancer. The study enrolled 14 lung cancer patients, 14 non-lung cancer controls with diverse medical conditions, and 3 tuberculosis (TB) [...] Read more.

This clinical study presents a comprehensive investigation into the utility of breath analysis as a non-invasive method for the early detection of lung cancer. The study enrolled 14 lung cancer patients, 14 non-lung cancer controls with diverse medical conditions, and 3 tuberculosis (TB) patients for biomarker discovery. Matching criteria including age, gender, smoking history, and comorbidities were strictly followed to ensure reliable comparisons. A systematic breath sampling protocol utilizing a BIO-VOC sampler was employed, followed by VOC analysis using Thermal Desorption–Gas Chromatography–Mass Spectrometry (TD-GC/MS). The resulting VOC profiles were subjected to stringent statistical analysis, including Orthogonal Projections to Latent Structures—Discriminant Analysis (OPLS-DA), Kruskal–Wallis test, and Receiver Operating Characteristic (ROC) analysis. Notably, 13 VOCs exhibited statistically significant differences between lung cancer patients and controls. The combination of eight VOCs (hexanal, heptanal, octanal, benzaldehyde, undecane, phenylacetaldehyde, decanal, and benzoic acid) demonstrated substantial discriminatory power with an area under the curve (AUC) of 0.85, a sensitivity of 82%, and a specificity of 76% in the discovery set. Validation in an independent cohort yielded an AUC of 0.78, a sensitivity of 78%, and a specificity of 64%. Further analysis revealed that elevated aldehyde levels in lung cancer patients’ breath could be attributed to overactivated Alcohol Dehydrogenase (ADH) pathways in cancerous tissues. Addressing methodological challenges, this study employed a matching of physiological and pathological confounders, controlled room air samples, and standardized breath sampling techniques. Despite the limitations, this study’s findings emphasize the potential of breath analysis as a diagnostic tool for lung cancer and suggest its utility in differentiating tuberculosis from lung cancer. However, further research and validation are warranted for the translation of these findings into clinical practice. Full article

(This article belongs to the Section Endocrinology and Clinical Metabolic Research)

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12 pages, 2625 KiB

Open AccessArticle

Metabolic Alterations in NADSYN1-Deficient Cells

by Nils W. F. Meijer, Johan Gerrits, Susan Zwakenberg, Fried J. T. Zwartkruis, Nanda M. Verhoeven-Duif and Judith J. M. Jans

Metabolites 2023, 13(12), 1196; https://doi.org/10.3390/metabo13121196 - 12 Dec 2023

Viewed by 1683

Abstract

NAD synthetase 1 (encoded by the gene NADSYN1) is a cytosolic enzyme that catalyzes the final step in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) from tryptophan and nicotinic acid. NADSYN1 deficiency has recently been added to the spectrum of congenital NAD+ deficiency [...] Read more.

NAD synthetase 1 (encoded by the gene NADSYN1) is a cytosolic enzyme that catalyzes the final step in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) from tryptophan and nicotinic acid. NADSYN1 deficiency has recently been added to the spectrum of congenital NAD+ deficiency disorders. To gain insight into the metabolic consequences of NADSYN1 deficiency, the encoding gene was disrupted in A549 and HEK293T cells, and the metabolome was profiled in the presence of different NAD+ precursors, including tryptophan, nicotinamide and nicotinic acid. We demonstrate that when precursors of the NAD+ salvage pathway in the form of nicotinamide become limiting, NADSYN1 deficiency results in a decline in intracellular NAD+ levels even in the presence of other potential NAD+ sources such as tryptophan and nicotinic acid. As a consequence, alterations in 122 and 69 metabolites are observed in NADSYN1-deficient A549 and HEK293T cells compared to the wild-type cell line (FC > 2 and p < 0.05). We thus show that NADSYN1 deficiency results in a metabolic phenotype characterized by alterations in glycolysis, the TCA cycle, the pentose phosphate pathway, and the polyol pathway. Full article

(This article belongs to the Special Issue Diagnostic and Therapeutic Monitoring for Neurometabolic Disorders)

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13 pages, 6829 KiB

Open AccessArticle

SlbHLH22-Induced Hypertrophy Development Is Related to the Salt Stress Response of the GTgamma Gene in Tomatoes

by Baolu Cui, Min Yu, Jiaojiao Bai and Zhiguo Zhu

Metabolites 2023, 13(12), 1195; https://doi.org/10.3390/metabo13121195 - 11 Dec 2023

Viewed by 1442

Abstract

Hypertrophy development induced by the overexpression of SlbHLH22 (also called SlUPA-like) was susceptible to Xanthomonas in tomatoes. Transcriptome and metabolome analyses were performed on the hypertrophy leaves of a SlbHLH22-overexpressed line (OE) and wild type (WT) to investigate the molecular mechanism. [...] Read more.

Hypertrophy development induced by the overexpression of SlbHLH22 (also called SlUPA-like) was susceptible to Xanthomonas in tomatoes. Transcriptome and metabolome analyses were performed on the hypertrophy leaves of a SlbHLH22-overexpressed line (OE) and wild type (WT) to investigate the molecular mechanism. Metabolome analysis revealed that six key metabolites were over-accumulated in the OE, including Acetylserine/O-Acetyl-L-serine, Glucono-1,5-lactone, Gluconate, 2-Oxoglutarate, and Loganate, implying that the OE plants increased salt or oxidant resistance under normal growth conditions. The RNA-seq analysis showed the changed expressions of downstream genes involved in high-energy consumption, photosynthesis, and transcription regulation in OE lines, and we hypothesized that these biological processes were related to the GTgamma subfamily of trihelix factors. The RT-PCR results showed that the expressions of the GTgamma genes in tomatoes, i.e., SlGT-7 and SlGT-36, were suppressed in the hypertrophy development. The expression of the GTgamma gene was downregulated by salinity, indicating a coordinated role of GTgamma in hypertrophy development and salt stress. Further research showed that both SlGT-7 and SlGT-36 were highly expressed in leaves and could be significantly induced by abscisic acid (ABA). The GTgamma protein had a putative phosphorylation site at S⁹⁶. These results suggested GTgamma’s role in hypertrophy development by increasing the salt resistance. Full article

(This article belongs to the Special Issue Plant Metabolic Genetic Engineering)

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18 pages, 2784 KiB

Open AccessArticle

Searching for New Biomarkers to Assess COVID-19 Patients: A Pilot Study

by Nikolay V. Goncharov, Piotr P. Avdonin, Natalia G. Voitenko, Polina A. Voronina, Polina I. Popova, Artemy V. Novozhilov, Maria S. Blinova, Victoria S. Popkova, Daria A. Belinskaia and Pavel V. Avdonin

Metabolites 2023, 13(12), 1194; https://doi.org/10.3390/metabo13121194 - 10 Dec 2023

Viewed by 1637

Abstract

During the initial diagnosis of urgent medical conditions, which include acute infectious diseases, it is important to assess the severity of the patient’s clinical state as quickly as possible. Unlike individual biochemical or physiological indicators, derived indices make it possible to better characterize [...] Read more.

During the initial diagnosis of urgent medical conditions, which include acute infectious diseases, it is important to assess the severity of the patient’s clinical state as quickly as possible. Unlike individual biochemical or physiological indicators, derived indices make it possible to better characterize a complex syndrome as a set of symptoms, and therefore quickly take a set of adequate measures. Recently, we reported on novel diagnostic indices containing butyrylcholinesterase (BChE) activity, which is decreased in COVID-19 patients. Also, in these patients, the secretion of von Willebrand factor (vWF) increases, which leads to thrombosis in the microvascular bed. The objective of this study was the determination of the concentration and activity of vWF in patients with COVID-19, and the search for new diagnostic indices. One of the main objectives was to compare the prognostic values of some individual and newly derived indices. Patients with COVID-19 were retrospectively divided into two groups: survivors (n = 77) and deceased (n = 24). According to clinical symptoms and computed tomography (CT) results, the course of disease was predominantly moderate in severity. The first blood sample (first point) was taken upon admission to the hospital, the second sample (second point)—within 4–6 days after admission. Along with the standard spectrum of biochemical indicators, BChE activity (BChEa or BChEb for acetylthiocholin or butyrylthiocholin, respectively), malondialdehyde (MDA), and vWF analysis (its antigen level, AGFW, and its activity, ActWF) were determined and new diagnostic indices were derived. The pooled sensitivity, specificity, and area under the receiver operating curve (AUC), as well as Likelihood ratio (LR) and Odds ratio (OR) were calculated. The level of vWF antigen in the deceased group was 1.5-fold higher than the level in the group of survivors. Indices that include vWF antigen levels are superior to indices using vWF activity. It was found that the index [Urea] × [AGWF] × 1000/(BChEb × [ALB]) had the best discriminatory power to predict COVID-19 mortality (AUC = 0.91 [0.83, 1.00], p < 0.0001; OR = 72.0 [7.5, 689], p = 0.0002). In addition, [Urea] × 1000/(BChEb × [ALB]) was a good predictor of mortality (AUC = 0.95 [0.89, 1.00], p < 0.0001; OR = 31.5 [3.4, 293], p = 0.0024). The index [Urea] × [AGWF] × 1000/(BChEb × [ALB]) was the best predictor of mortality associated with COVID-19 infection, followed by [Urea] × 1000/(BChEb × [ALB]). After validation in a subsequent cohort, these two indices could be recommended for diagnostic laboratories. Full article

(This article belongs to the Special Issue Advances in Understanding Altered Metabolism in SARS-CoV-2 Infection)

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16 pages, 3038 KiB

Open AccessArticle

Altitudinal Variation on Metabolites, Elements, and Antioxidant Activities of Medicinal Plant Asarum

by Liben Pan, Nan Yang, Yushu Sui, Yi Li, Wen Zhao, Liqiu Zhang, Liqiang Mu and Zhonghua Tang

Metabolites 2023, 13(12), 1193; https://doi.org/10.3390/metabo13121193 - 9 Dec 2023

Cited by 5 | Viewed by 1801

Abstract

Asarum (Asarum sieboldii Miq. f. seoulense (Nakai) C. Y. Cheng et C. S. Yang) is a medicinal plant that contains asarinin and sesamin, which possess extensive medicinal value. The adaptation and distribution of Asarum’s plant growth are significantly affected by altitude. [...] Read more.

Asarum (Asarum sieboldii Miq. f. seoulense (Nakai) C. Y. Cheng et C. S. Yang) is a medicinal plant that contains asarinin and sesamin, which possess extensive medicinal value. The adaptation and distribution of Asarum’s plant growth are significantly affected by altitude. Although most studies on Asarum have concentrated on its pharmacological activities, little is known about its growth and metabolites with respect to altitude. In this study, the physiology, ionomics, and metabolomics were investigated and conducted on the leaves and roots of Asarum along an altitude gradient, and the content of its medicinal components was determined. The results showed that soil pH and temperature both decreased along the altitude, which restricts the growth of Asarum. The accumulation of TOC, Cu, Mg, and other mineral elements enhanced the photosynthetic capacity and leaf plasticity of Asarum in high-altitude areas. A metabolomics analysis revealed that, at high altitude, nitrogen metabolism in leaves was enhanced, while carbon metabolism in roots was enhanced. Furthermore, the metabolic pathways of some phenolic substances, including syringic acid, vanillic acid, and ferulic acid, were altered to enhance the metabolism of organic acids. The study uncovered the growth and metabolic responses of Asarum to varying altitudes, providing a theoretical foundation for the utilization and cultivation of Asarum. Full article

(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)

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22 pages, 557 KiB

Open AccessReview

Metabolic and Other Endocrine Elements with Regard to Lifestyle Choices: Focus on E-Cigarettes

by Andrei Osman, Gabriel Sebastian Petrescu, Mihaela Jana Tuculină, Ionela Teodora Dascălu, Cristina Popescu, Anca-Ștefania Enescu, Constantin Dăguci, Anca-Pati Cucu, Claudiu Nistor and Mara Carsote

Metabolites 2023, 13(12), 1192; https://doi.org/10.3390/metabo13121192 - 8 Dec 2023

Viewed by 2468

Abstract

Our objective was to overview recent data on metabolic/endocrine disorders with respect to e-cigarette (e-cig) use. This is a narrative review; we researched English, full-length, original articles on PubMed (between January 2020 and August 2023) by using different keywords in the area of [...] Read more.

Our objective was to overview recent data on metabolic/endocrine disorders with respect to e-cigarette (e-cig) use. This is a narrative review; we researched English, full-length, original articles on PubMed (between January 2020 and August 2023) by using different keywords in the area of metabolic/endocrine issues. We only included original clinical studies (n = 22) and excluded case reports and experimental studies. 3 studies (N1 = 22,385; N2 = 600,046; N3 = 5101) addressed prediabetes risk; N1 showed a 1.57-fold increased risk of dual vs. never smokers, a higher risk that was not confirmed in N2 (based on self-reported assessments). Current non-smokers (N1) who were dual smokers still have an increased odd of prediabetes (a 1.27-fold risk increase). N3 and another 2 studies addressed type 2 diabetes mellitus (DM): a lower prevalence of DM among dual users (3.3%) vs. cigarette smoking (5.9%) was identified. 6 studies investigated obesity profile (4 of them found positive correlations with e-cig use). One study (N4 = 373,781) showed that e-cig use was associated with obesity in the general population (OR = 1.6, 95%CI: 1.3–2.1, p < 0.05); another (N5 = 7505, 0.82% were e-cig-only) showed that obesity had a higher prevalence in dual smokers (51%) vs. cig-only (41.2%, p < 0.05), while another (N6 = 3055) found that female (not male) e-cig smokers had higher body mass index vs. non-smokers. Data on metabolic syndrome (MS) are provided for dual smokers (n = 2): one case–control study found that female dual smokers had higher odds of MS than non-smokers. The need for awareness with respect to potential e-cig-–associated medical issues should be part of modern medicine, including daily anamnesis. Whether the metabolic/endocrine frame is part of the general picture is yet to be determined. Surveillance protocols should help clinicians to easily access the medical background of one subject, including this specific matter of e-cig with/without conventional cigarettes smoking and other habits/lifestyle elements, especially when taking into consideration metabolism anomalies. Full article

(This article belongs to the Topic Metabolic Syndrome, Biomarkers and Lifestyles)

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28 pages, 3033 KiB

Open AccessArticle

Key Therapeutic Targets to Treat Hyperglycemia-Induced Atherosclerosis Analyzed Using a Petri Net-Based Model

by Agnieszka Rybarczyk, Dorota Formanowicz and Piotr Formanowicz

Metabolites 2023, 13(12), 1191; https://doi.org/10.3390/metabo13121191 - 8 Dec 2023

Cited by 2 | Viewed by 1640

Abstract

Chronic superphysiological glucose concentration is a hallmark of diabetes mellitus (DM) and a cause of damage to many types of cells. Atherosclerosis coexists with glucose metabolism disturbances, constituting a significant problem and exacerbating its complications. Atherosclerosis in DM is accelerated, so it is [...] Read more.

Chronic superphysiological glucose concentration is a hallmark of diabetes mellitus (DM) and a cause of damage to many types of cells. Atherosclerosis coexists with glucose metabolism disturbances, constituting a significant problem and exacerbating its complications. Atherosclerosis in DM is accelerated, so it is vital to slow its progression. However, from the complex network of interdependencies, molecules, and processes involved, choosing which ones should be inhibited without blocking the pathways crucial for the organism’s functioning is challenging. To conduct this type of analysis, in silicotesting comes in handy. In our study, to identify sites in the network that need to be blocked to have an inhibitory effect on atherosclerosis in hyperglycemia, which is toxic for the human organism, we created a model using Petri net theory and performed analyses. We have found that blocking isoforms of protein kinase C (PKC)—PKC

β

and PKC

γ

—in diabetic patients can contribute to the inhibition of atherosclerosis progression. In addition, we have discovered that aldose reductase inhibition can slow down atherosclerosis progression, and this has been shown to reduce PKC (

β

and

γ

) expression in DM. It has also been observed that diminishing oxidative stress through the inhibitory effect on the AGE-RAGE axis may be a promising therapeutic approach in treating hyperglycemia-induced atherosclerosis. Moreover, the blockade of NADPH oxidase, the key enzyme responsible for the formation of reactive oxygen species (ROS) in blood vessels, only moderately slowed down atherosclerosis development. However, unlike aldose reductase blockade, or direct PKC (

β

and

γ

), the increased production of mitochondrial ROS associated with mitochondrial dysfunction effectively stopped after NADPH oxidase blockade. The results obtained may constitute the basis for further in-depth research. Full article

(This article belongs to the Special Issue Application of Metabolomics in Toxicology Research)

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26 pages, 890 KiB

Open AccessReview

Modulation of MicroRNAs and Exosomal MicroRNAs after Dietary Interventions for Obesity and Insulin Resistance: A Narrative Review

by Karla G. Hernández-Gómez, Azalia Avila-Nava, Luis E. González-Salazar, Lilia G. Noriega, Aurora E. Serralde-Zúñiga, Rocio Guizar-Heredia, Isabel Medina-Vera, Ana Ligia Gutiérrez-Solis, Nimbe Torres, Armando R. Tovar and Martha Guevara-Cruz

Metabolites 2023, 13(12), 1190; https://doi.org/10.3390/metabo13121190 - 7 Dec 2023

Cited by 4 | Viewed by 2115

Abstract

MicroRNAs (miRNAs) are small noncoding RNAs approximately 22 nucleotides in length. Their main function is to regulate gene expression at the posttranscriptional level by inhibiting the translation of messenger RNAs (mRNAs). miRNAs originate in the cell nucleus from specific genes, where they can [...] Read more.

MicroRNAs (miRNAs) are small noncoding RNAs approximately 22 nucleotides in length. Their main function is to regulate gene expression at the posttranscriptional level by inhibiting the translation of messenger RNAs (mRNAs). miRNAs originate in the cell nucleus from specific genes, where they can perform their function. However, they can also be found in serum, plasma, or other body fluids travelling within vesicles called exosomes and/or bound to proteins or other particles such as lipoproteins. miRNAs can form complexes outside the cell where they are synthesized, mediating paracrine and endocrine communication between different tissues. In this way, they can modulate the gene expression and function of distal cells. It is known that the expression of miRNAs can be affected by multiple factors, such as the nutritional or pathological state of the individual, or even in conditions such as obesity, insulin resistance, or after any dietary intervention. In this review, we will analyse miRNAs whose expression and circulation are affected in conditions of obesity and insulin resistance, as well as the changes generated after a dietary intervention, with the purpose of identifying new possible biomarkers of early response to nutritional treatment in these conditions. Full article

(This article belongs to the Special Issue Novel Biomarkers for Cardiovascular Disease in Patients with Diabetes)

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16 pages, 1524 KiB

Open AccessArticle

In Silico and In Vivo Evaluation of the Maqui Berry (Aristotelia chilensis (Mol.) Stuntz) on Biochemical Parameters and Oxidative Stress Markers in a Metabolic Syndrome Model

by Emily Leonela Castillo-García, Ana Lizzet Cossio-Ramírez, Óscar Arturo Córdoba-Méndez, Marco A. Loza-Mejía, Juan Rodrigo Salazar, Edwin Chávez-Gutiérrez, Guadalupe Bautista-Poblet, Nadia Tzayaka Castillo-Mendieta, Diego A. Moreno, Cristina García-Viguera, Rodolfo Pinto-Almazán, Julio César Almanza-Pérez, Juan Manuel Gallardo and Christian Guerra-Araiza

Metabolites 2023, 13(12), 1189; https://doi.org/10.3390/metabo13121189 - 7 Dec 2023

Cited by 1 | Viewed by 2820

Abstract

Metabolic syndrome (MetS) is a complex disease that includes metabolic and physiological alterations in various organs such as the heart, pancreas, liver, and brain. Reports indicate that blackberry consumption, such as maqui berry, has a beneficial effect on chronic diseases such as cardiovascular [...] Read more.

Metabolic syndrome (MetS) is a complex disease that includes metabolic and physiological alterations in various organs such as the heart, pancreas, liver, and brain. Reports indicate that blackberry consumption, such as maqui berry, has a beneficial effect on chronic diseases such as cardiovascular disease, obesity, and diabetes. In the present study, in vivo and in silico studies have been performed to evaluate the molecular mechanisms implied to improve the metabolic parameters of MetS. Fourteen-day administration of maqui berry reduces weight gain, blood fasting glucose, total blood cholesterol, triacylglycerides, insulin resistance, and blood pressure impairment in the diet-induced MetS model in male and female rats. In addition, in the serum of male and female rats, the administration of maqui berry (MB) improved the concentration of MDA, the activity of SOD, and the formation of carbonyls in the group subjected to the diet-induced MetS model. In silico studies revealed that delphinidin and its glycosylated derivatives could be ligands of some metabolic targets such as α-glucosidase, PPAR-α, and PPAR-γ, which are related to MetS parameters. The experimental results obtained in the study suggest that even at low systemic concentrations, anthocyanin glycosides and aglycones could simultaneously act on different targets related to MetS. Therefore, these molecules could be used as coadjuvants in pharmacological interventions or as templates for designing new multitarget molecules to manage patients with MetS. Full article

(This article belongs to the Special Issue Hormones and Metabolic Syndrome: Importance of Hormones in the Epidemiology, Physiopathology and Treatment of Metabolic Disorders)

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14 pages, 2262 KiB

Open AccessArticle

Miltiradiene Production by Cytoplasmic Metabolic Engineering in Nicotiana benthamiana

by Xiangxiang Ren, Chuhang Lin, Yanbo Huang, Tao Su, Juan Guo and Lei Yang

Metabolites 2023, 13(12), 1188; https://doi.org/10.3390/metabo13121188 - 6 Dec 2023

Cited by 1 | Viewed by 1856

Abstract

Plant natural products are important sources of innovative drugs, but the extraction and isolation of medicinal natural products from plants is challenging as these compounds have complex structures that are difficult to synthesize chemically. Therefore, utilizing heterologous expression systems to produce medicinal natural [...] Read more.

Plant natural products are important sources of innovative drugs, but the extraction and isolation of medicinal natural products from plants is challenging as these compounds have complex structures that are difficult to synthesize chemically. Therefore, utilizing heterologous expression systems to produce medicinal natural products in plants is a novel, environmentally friendly, and sustainable method. In this study, Nicotiana benthamiana was used as the plant platform to successfully produce miltiradiene, the key intermediate of tanshinones, which are the bioactive constituents of the Chinese medicinal plant Salvia miltiorrhiza. The yield of miltiradiene was increased through cytoplasmic engineering strategies combined with the enhancement of isoprenoid precursors. Additionally, we discovered that overexpressing SmHMGR alone accelerated apoptosis in tobacco leaves. Due to the richer membrane systems and cofactors in tobacco compared to yeast, tobacco is more conducive to the expression of plant enzymes. Therefore, this study lays the foundation for dissecting the tanshinone biosynthetic pathway in tobacco, which is essential for subsequent research. Additionally, it highlights the potential of N. benthamiana as an alternative platform for the production of natural products in plants. Full article

(This article belongs to the Special Issue Identification of Secondary Metabolites by Multi-Omics Methods)

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16 pages, 3922 KiB

Open AccessSystematic Review

Olive Oil Polyphenols Improve HDL Cholesterol and Promote Maintenance of Lipid Metabolism: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

by Roberta Zupo, Fabio Castellana, Pasquale Crupi, Addolorata Desantis, Mariangela Rondanelli, Filomena Corbo and Maria Lisa Clodoveo

Metabolites 2023, 13(12), 1187; https://doi.org/10.3390/metabo13121187 - 6 Dec 2023

Cited by 7 | Viewed by 3542

Abstract

In 2011, the European Food Safety Authority (EFSA) accorded a health claim to olive oil polyphenols in that they protected LDL particles from oxidative damage. However, limited scientific evidence has so far failed to confer any claim of function on the maintenance of [...] Read more.

In 2011, the European Food Safety Authority (EFSA) accorded a health claim to olive oil polyphenols in that they protected LDL particles from oxidative damage. However, limited scientific evidence has so far failed to confer any claim of function on the maintenance of normal lipid metabolism. We performed a systematic review and meta-analysis of human RCTs, evaluating the effect of olive oil polyphenol administration on lipid profiles. Previous literature was acquired from six electronic databases until June 2023. A total of 75 articles were retrieved and screened for inclusion criteria, which resulted in the selection of 10 RCTs that evaluated the effect of daily exposure to olive oil polyphenols on serum lipids in adults. Meta-analyses were built by tertiles of outcomes, as follows: low (0–68 mg/kg), medium (68–320 mg/kg), and high (320–600 mg/kg) polyphenols for HDL and LDL cholesterol (HDL-C and LDL-C, respectively), and low (0–59.3 mg/kg), medium (59.3–268 mg/kg), and high (268–600 mg/kg) polyphenols for total cholesterol (TC). The study protocol was registered on PROSPERO (registration code: CRD42023403383). The study design was predominantly cross-over (n = 8 of 10) but also included parallel (n = 2 of 10). The study population was predominantly European and healthy. Daily consumption of olive oil polyphenols did not affect TC levels and only slightly significantly reduced LDL-C, with WMD statistically significant only for high daily consumption of olive oil polyphenols (WMD −4.28, 95%CI −5.78 to −2.77). Instead, our data found a statistically significant HDL-C enhancing effect (WMD pooled effect model: 1.13, 95%CI 0.45; 1.80, heterogeneity 38%, p = 0.04) with WMD by daily exposure level showing a statistically significant improvement effect for low (WMD 0.66, 95%CI 0.10–1.23), medium (WMD 1.36, 95%CI 0.76–1.95), and high (WMD 1.13, 95%CI 0.45–1.80) olive oil polyphenol consumptions. Olive oil polyphenols contribute toward maintaining lipid metabolism. Thus, food labeling regulations should stress this health feature of olive oil, whereby a declaration of the olive oil polyphenol content should be added to products on the market. Consumers need to be aware of the quality and possible health effects of any products they consume, and enforcement of nutrition labels offers the best way of providing this information. Full article

(This article belongs to the Special Issue Epidemiology, Nutrition and Metabolism)

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15 pages, 1925 KiB

Open AccessArticle

Targeting Longevity Gene SLC13A5: A Novel Approach to Prevent Age-Related Bone Fragility and Osteoporosis

by Grit Zahn, Hannes A. Baukmann, Jasmine Wu, Jens Jordan, Andreas L. Birkenfeld, Naomi Dirckx and Marco F. Schmidt

Metabolites 2023, 13(12), 1186; https://doi.org/10.3390/metabo13121186 - 6 Dec 2023

Cited by 1 | Viewed by 2540

Abstract

Reduced expression of the plasma membrane citrate transporter SLC13A5, also known as INDY, has been linked to increased longevity and mitigated age-related cardiovascular and metabolic diseases. Citrate, a vital component of the tricarboxylic acid cycle, constitutes 1–5% of bone weight, binding to [...] Read more.

Reduced expression of the plasma membrane citrate transporter SLC13A5, also known as INDY, has been linked to increased longevity and mitigated age-related cardiovascular and metabolic diseases. Citrate, a vital component of the tricarboxylic acid cycle, constitutes 1–5% of bone weight, binding to mineral apatite surfaces. Our previous research highlighted osteoblasts’ specialized metabolic pathway facilitated by SLC13A5 regulating citrate uptake, production, and deposition within bones. Disrupting this pathway impairs bone mineralization in young mice. New Mendelian randomization analysis using UK Biobank data indicated that SNPs linked to reduced SLC13A5 function lowered osteoporosis risk. Comparative studies of young (10 weeks) and middle-aged (52 weeks) osteocalcin-cre-driven osteoblast-specific Slc13a5 knockout mice (Slc13a5^cKO) showed a sexual dimorphism: while middle-aged females exhibited improved elasticity, middle-aged males demonstrated enhanced bone strength due to reduced SLC13A5 function. These findings suggest reduced SLC13A5 function could attenuate age-related bone fragility, advocating for SLC13A5 inhibition as a potential osteoporosis treatment. Full article

(This article belongs to the Special Issue I'm Not Dead Yet in Metabolic Regulation)

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16 pages, 2531 KiB

Open AccessArticle

Oleic Acid Metabolism in Response to Glucose in C. elegans

by Andre F. C. Vieira, Mark A. Xatse, Sofi Y. Murray and Carissa Perez Olsen

Metabolites 2023, 13(12), 1185; https://doi.org/10.3390/metabo13121185 - 6 Dec 2023

Viewed by 1929

Abstract

A key response to glucose stress is an increased production of unsaturated fatty acids to balance the increase in saturated fatty acids in the membrane. The C. elegans homolog of stearoyl-CoA desaturase, FAT-7, introduces the first double bond into saturated C18 fatty acids [...] Read more.

A key response to glucose stress is an increased production of unsaturated fatty acids to balance the increase in saturated fatty acids in the membrane. The C. elegans homolog of stearoyl-CoA desaturase, FAT-7, introduces the first double bond into saturated C18 fatty acids yielding oleic acid, and is a critical regulatory point for surviving cold and glucose stress. Here, we incorporated ¹³C stable isotopes into the diet of nematodes and quantified the ¹³C-labelled fatty acid using GC-MS and HPLC/MS-MS to track its metabolic response to various concentrations of glucose. Previous work has analyzed the membrane composition of C. elegans when responding to mild glucose stress and showed few alterations in the overall fatty acid composition in the membrane. Here, in nematodes exposed to higher concentrations of glucose, a specific reduction in oleic acid and linoleic acid was observed. Using time courses and stable isotope tracing, the response of fatty acid metabolism to increasing levels of glucose stress is characterized, revealing the funneling of monounsaturated fatty acids to preserve the abundance of polyunsaturated fatty acids. Taken together, higher levels of glucose unveil a specific reduction in oleic and linolenic acid in the metabolic rewiring required to survive glucose stress. Full article

(This article belongs to the Section Lipid Metabolism)

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12 pages, 619 KiB

Open AccessReview

From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates

by Riadh Cheddadi, Venkata Yeramilli and Colin Martin

Metabolites 2023, 13(12), 1184; https://doi.org/10.3390/metabo13121184 - 5 Dec 2023

Viewed by 1937

Abstract

The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, [...] Read more.

The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, it was believed that each individual harbored unique microbial communities acquired early in life, evolving over the course of their lifetime, with little acknowledgment of any prenatal microbial development, but recent research challenges this belief. The neonatal microbiome’s onset, influenced by factors like delivery mode and maternal health, remains a subject of intense debate, hinting at potential intrauterine microbial processes. In-depth research reveals associations between microbiome profiles and specific health outcomes, ranging from obesity to neurodevelopmental disorders. Understanding these diverse microbiome profiles is essential for unraveling the intricate relationships between the microbiome and health outcomes. Full article

(This article belongs to the Special Issue Natural Metabolites on Gut Microbiome Modulation)

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14 pages, 723 KiB

Open AccessReview

Once upon a Time Oral Microbiota: A Cinderella or a Protagonist in Autism Spectrum Disorder?

by Michele Mussap, Paola Beretta, Elena Esposito and Vassilios Fanos

Metabolites 2023, 13(12), 1183; https://doi.org/10.3390/metabo13121183 - 5 Dec 2023

Cited by 2 | Viewed by 2481

Abstract

Autism spectrum disorder (ASD) is a neurodevelopmental disorder evolving over the lifetime of individuals. The oral and gut microbial ecosystems are closely connected to each other and the brain and are potentially involved in neurodevelopmental diseases. This narrative review aims to identify all [...] Read more.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder evolving over the lifetime of individuals. The oral and gut microbial ecosystems are closely connected to each other and the brain and are potentially involved in neurodevelopmental diseases. This narrative review aims to identify all the available evidence emerging from observational studies focused on the role of the oral microbiome in ASD. A literature search was conducted using PubMed and the Cochrane Library for relevant studies published over the last ten years. Overall, in autistic children, the oral microbiota is marked by the abundance of several microbial species belonging to the Proteobacteria phylum and by the depletion of species belonging to the Bacteroidetes phylum. In mouse models, the oral microbiota is marked by the abundance of the Bacteroidetes phylum. Oral dysbiosis in ASD induces changes in the human metabolome, with the overexpression of metabolites closely related to the pathogenesis of ASD, such as acetate, propionate, and indoles, together with the underexpression of butyrate, confirming the central role of tryptophan metabolism. The analysis of the literature evidences the close relationship between oral dysbiosis and autistic core symptoms; the rebuilding of the oral and gut ecosystems by probiotics may significantly contribute to mitigating the severity of ASD symptoms. Full article

(This article belongs to the Special Issue Preclinical and Clinical Application of Metabolomics in Medicine)

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21 pages, 389 KiB

Open AccessReview

Bridging the Gap from Enterotypes to Personalized Dietary Recommendations: A Metabolomics Perspective on Microbiome Research

by Madeline Bartsch, Andreas Hahn and Shoma Berkemeyer

Metabolites 2023, 13(12), 1182; https://doi.org/10.3390/metabo13121182 - 2 Dec 2023

Cited by 4 | Viewed by 2867

Abstract

Advances in high-throughput DNA sequencing have propelled research into the human microbiome and its link to metabolic health. We explore microbiome analysis methods, specifically emphasizing metabolomics, how dietary choices impact the production of microbial metabolites, providing an overview of studies examining the connection [...] Read more.

Advances in high-throughput DNA sequencing have propelled research into the human microbiome and its link to metabolic health. We explore microbiome analysis methods, specifically emphasizing metabolomics, how dietary choices impact the production of microbial metabolites, providing an overview of studies examining the connection between enterotypes and diet, and thus, improvement of personalized dietary recommendations. Acetate, propionate, and butyrate constitute more than 95% of the collective pool of short-chain fatty acids. Conflicting data on acetate’s effects may result from its dynamic signaling, which can vary depending on physiological conditions and metabolic phenotypes. Human studies suggest that propionate has overall anti-obesity effects due to its well-documented chemistry, cellular signaling mechanisms, and various clinical benefits. Butyrate, similar to propionate, has the ability to reduce obesity by stimulating the release of appetite-suppressing hormones and promoting the synthesis of leptin. Tryptophan affects systemic hormone secretion, with indole stimulating the release of GLP-1, which impacts insulin secretion, appetite suppression, and gastric emptying. Bile acids, synthesized from cholesterol in the liver and subsequently modified by gut bacteria, play an essential role in the digestion and absorption of dietary fats and fat-soluble vitamins, but they also interact directly with intestinal microbiota and their metabolites. One study using statistical methods identified primarily two groupings of enterotypes Bacteroides and Ruminococcus. The Prevotella-dominated enterotype, P-type, in humans correlates with vegetarians, high-fiber and carbohydrate-rich diets, and traditional diets. Conversely, individuals who consume diets rich in animal fats and proteins, typical in Western-style diets, often exhibit the Bacteroides-dominated, B-type, enterotype. The P-type showcases efficient hydrolytic enzymes for plant fiber degradation but has limited lipid and protein fermentation capacity. Conversely, the B-type features specialized enzymes tailored for the degradation of animal-derived carbohydrates and proteins, showcasing an enhanced saccharolytic and proteolytic potential. Generally, models excel at predictions but often struggle to fully elucidate why certain substances yield varied responses. These studies provide valuable insights into the potential for personalized dietary recommendations based on enterotypes. Full article

(This article belongs to the Special Issue Metabolomics of Human Nutrition: The Dot of Human Nutrition and the Circle of Soil, Plants, Animals and Microbes in Relation to It)

16 pages, 3087 KiB

Open AccessArticle

Technical Report: A Comprehensive Comparison between Different Quantification Versions of Nightingale Health’s ¹H-NMR Metabolomics Platform

by Daniele Bizzarri, Marcel J. T. Reinders, Marian Beekman, P. Eline Slagboom, Erik B. van den Akker and on behalf of the BbmriNl

Metabolites 2023, 13(12), 1181; https://doi.org/10.3390/metabo13121181 - 30 Nov 2023

Cited by 4 | Viewed by 1681

Abstract

¹H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of ¹H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies [...] Read more.

¹H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of ¹H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies with repeated measures. Using data from BBMRI-NL consortium (~28,000 samples from 28 cohorts), we compared Nightingale data, originally released in 2014 and 2016, with a re-quantified version released in 2020, of which both versions were based on the same NMR spectra. Apart from two discontinued and twenty-three new analytes, we generally observe a high concordance between quantification versions with 73 out of 222 (33%) analytes showing a mean

ρ

> 0.9 across all cohorts. Conversely, five analytes consistently showed lower Spearman’s correlations (

ρ

< 0.7) between versions, namely acetoacetate, LDL-L, saturated fatty acids, S-HDL-C, and sphingomyelins. Furthermore, previously trained multi-analyte scores, such as MetaboAge or MetaboHealth, might be particularly sensitive to platform changes. Whereas MetaboHealth replicated well, the MetaboAge score had to be retrained due to use of discontinued analytes. Notably, both scores in the re-quantified data recapitulated mortality associations observed previously. Concluding, we urge caution in utilizing different platform versions to avoid mixing analytes, having different units, or simply being discontinued. Full article

(This article belongs to the Topic Biomarker Development and Application)

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23 pages, 3953 KiB

Open AccessArticle

Impact of Different Treatment Regimens and Timeframes in the Plasmatic Metabolic Profiling of Patients with Lung Adenocarcinoma

by Daniela Madama, David F. Carrageta, Bárbara Guerra-Carvalho, Maria F. Botelho, Pedro F. Oliveira, Carlos R. Cordeiro, Marco G. Alves and Ana M. Abrantes

Metabolites 2023, 13(12), 1180; https://doi.org/10.3390/metabo13121180 - 30 Nov 2023

Viewed by 1896

Abstract

In recent years, the treatment of advanced non-small cell lung cancer (NSCLC) has suffered a variety of alterations. Chemotherapy (CTX), immunotherapy (IT) and tyrosine kinase inhibitors (TKI) have shown remarkable results. However, not all patients with NSCLC respond to these drug treatments or [...] Read more.

In recent years, the treatment of advanced non-small cell lung cancer (NSCLC) has suffered a variety of alterations. Chemotherapy (CTX), immunotherapy (IT) and tyrosine kinase inhibitors (TKI) have shown remarkable results. However, not all patients with NSCLC respond to these drug treatments or receive durable benefits. In this framework, metabolomics has been applied to improve the diagnosis, treatment, and prognosis of lung cancer and particularly lung adenocarcinoma (AdC). In our study, metabolomics was used to analyze plasma samples from 18 patients with AdC treated with CTX or IT via ¹H-NMR spectroscopy. Relevant clinical information was gathered, and several biochemical parameters were also evaluated throughout the treatments. During the follow-up of patients undergoing CTX or IT, imaging control is recommended in order to assess the effectiveness of the therapy. This evaluation is usually performed every three treatments. Based on this procedure, all the samples were collected before the beginning of the treatment and after three and six treatments. The identified and quantified metabolites in the analyzed plasma samples were the following: isoleucine, valine, alanine, acetate, lactate, glucose, tyrosine, and formate. Multivariate/univariate statistical analyses were performed. Our data are in accordance with previous published results, suggesting that the plasma glucose levels of patients under CTX become higher throughout the course of treatment, which we hypothesize could be related to the tumor response to the therapy. It was also found that alanine levels become lower during treatment with CTX regimens, a fact that could be associated with frailty. NMR spectra of long responders’ profiles also showed similar results. Based on the results of the study, metabolomics can represent a potential option for future studies, in order to facilitate patient selection and the monitoring of therapy efficacy in treated patients with AdC. Further studies are needed to improve the prospective identification of predictive markers, particularly glucose and alanine levels, as well as confer guidance to NSCLC treatment and patient stratification, thus avoiding ineffective therapeutic strategies. Full article

(This article belongs to the Section Advances in Metabolomics)

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18 pages, 3765 KiB

Open AccessArticle

Solanaceae Glycoalkaloids Disturb Lipid Metabolism in the Tenebrio molitor Beetle

by Magdalena Joanna Winkiel, Szymon Chowański, Marek Gołębiowski, Sabino Aurelio Bufo and Małgorzata Słocińska

Metabolites 2023, 13(12), 1179; https://doi.org/10.3390/metabo13121179 - 30 Nov 2023

Cited by 4 | Viewed by 1767

Abstract

Glycoalkaloids (GAs) are produced naturally by plants and affect insect survivability and fertility. These compounds can be considered potential bioinsecticides; however, the mechanisms and effects of their action remain undiscovered. As lipids are essential molecules for the proper functioning of an insect organism, [...] Read more.

Glycoalkaloids (GAs) are produced naturally by plants and affect insect survivability and fertility. These compounds can be considered potential bioinsecticides; however, the mechanisms and effects of their action remain undiscovered. As lipids are essential molecules for the proper functioning of an insect organism, this research aimed to determine the effects of GAs on the lipid metabolism of the Tenebrio molitor beetle. Solanine, chaconine, tomatine, and tomato leaf extract were applied to larvae by injection at two concentrations, 10⁻⁸ and 10⁻⁵ M. Then, the tissue was isolated after 2 and 24 h to determine the levels of free fatty acids, sterols and esters using the GC–MS technique. Moreover, the triacylglyceride level and the activity of the key β-oxidation enzyme, 3-hydroxyacyl-CoA dehydrogenase (HADH), were measured. The results indicate that GAs affect the content and composition of lipid compounds in the beetles’ haemolymph and fat body. The effects depend on the GA concentrations, incubation time, and kind of tissue. Moreover, the tested compounds decrease HADH activity, especially in the fat body, which may affect energy production. To our knowledge, this is the first study concerning lipid metabolism in T. molitor after GA application. Our results provide some insights into that topic. Full article

(This article belongs to the Special Issue Insect Metabolism and Physiology)

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21 pages, 1203 KiB

Open AccessReview

Metabolomics to Understand Alterations Induced by Physical Activity during Pregnancy

by Ana Carolina Rosa da Silva, Anahita Yadegari, Velislava Tzaneva, Tarushika Vasanthan, Katarina Laketic, Jane Shearer, Shannon A. Bainbridge, Cory Harris and Kristi B. Adamo

Metabolites 2023, 13(12), 1178; https://doi.org/10.3390/metabo13121178 - 29 Nov 2023

Cited by 1 | Viewed by 2809

Abstract

Physical activity (PA) and exercise have been associated with a reduced risk of cancer, obesity, and diabetes. In the context of pregnancy, maintaining an active lifestyle has been shown to decrease gestational weight gain (GWG) and lower the risk of gestational diabetes mellitus [...] Read more.

Physical activity (PA) and exercise have been associated with a reduced risk of cancer, obesity, and diabetes. In the context of pregnancy, maintaining an active lifestyle has been shown to decrease gestational weight gain (GWG) and lower the risk of gestational diabetes mellitus (GDM), hypertension, and macrosomia in offspring. The main pathways activated by PA include BCAAs, lipids, and bile acid metabolism, thereby improving insulin resistance in pregnant individuals. Despite these known benefits, the underlying metabolites and biological mechanisms affected by PA remain poorly understood, highlighting the need for further investigation. Metabolomics, a comprehensive study of metabolite classes, offers valuable insights into the widespread metabolic changes induced by PA. This narrative review focuses on PA metabolomics research using different analytical platforms to analyze pregnant individuals. Existing studies support the hypothesis that exercise behaviour can influence the metabolism of different populations, including pregnant individuals and their offspring. While PA has shown considerable promise in maintaining metabolic health in non-pregnant populations, our comprehension of metabolic changes in the context of a healthy pregnancy remains limited. As a result, further investigation is necessary to clarify the metabolic impact of PA within this unique group, often excluded from physiological research. Full article

(This article belongs to the Special Issue Metabolomic Advances in Promoting Exercise-Induced Metabolic Changes)

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21 pages, 7960 KiB

Open AccessArticle

In Vitro Anti-Oxidant, In Vivo Anti-Hyperglycemic, and Untargeted Metabolomics-Aided-In Silico Screening of Macroalgae Lipophilic Extracts for Anti-Diabetes Mellitus and Anti-COVID-19 Potential Metabolites

by Anggit Listyacahyani Sunarwidhi, Wahyu Rahmaniar, Eka Sunarwidhi Prasedya, Hasriaton Padmi, Sri Widyastuti, Kukuh Waseso Jati Pangestu, Bq Tri Khairina Ilhami, Ervina Handayani, Ni Wayan Putri Utami, Farreh Alan Maulana, Muhammad Syach Maulad Ichfa and Ari Hernawan

Metabolites 2023, 13(12), 1177; https://doi.org/10.3390/metabo13121177 - 27 Nov 2023

Cited by 1 | Viewed by 1863

Abstract

COVID-19 patients with comorbid DM face more severe outcomes, indicating that hyperglycemic conditions exacerbate SARS-CoV-2 infection. Negative side effects from existing hyperglycemia treatments have urged the need for safer compounds. Therefore, sourcing potential compounds from marine resources becomes a new potential approach. Algal [...] Read more.

COVID-19 patients with comorbid DM face more severe outcomes, indicating that hyperglycemic conditions exacerbate SARS-CoV-2 infection. Negative side effects from existing hyperglycemia treatments have urged the need for safer compounds. Therefore, sourcing potential compounds from marine resources becomes a new potential approach. Algal lipids are known to possess beneficial activities for human health. However, due to limitations in analyzing large amounts of potential anti-hyperglycemic and anti-COVID-19-related marine metabolites, there is an increasing need for new approaches to reduce risks and costs. Therefore, the main aim of this study was to identify potential compounds in macroalgae Sargassum cristaefolium, Tricleocarpa cylindrica, and Ulva lactuca lipophilic extracts for treating DM and COVID-19 by an integrated approach utilizing in vitro anti-oxidant, in vivo anti-hyperglycemic, and metabolomic-integrated in silico approaches. Among them, S. cristaefolium and T. cylindrica showed potential anti-hyperglycemic activity, with S. cristaefolium showing the highest anti-oxidant activity. A GC-MS-based untargeted metabolomic analysis was used to profile the lipophilic compounds in the extracts followed by an in silico molecular docking analysis to examine the binding affinity of the compounds to anti-DM and anti-COVID-19 targets, e.g., α-amylase, α-glucosidase, ACE2, and TMPRSS2. Notably, this study reveals for the first time that steroid-derived compounds in the macroalgae T. cylindrica had higher binding activity than known ligands for all the targets mentioned. Studies on drug likeliness indicate that these compounds possess favorable drug properties. These findings suggest the potential for these compounds to be further developed to treat COVID-19 patients with comorbid DM. The information in this study would be a basis for further in vitro and in vivo analysis. It would also be useful for the development of these candidate compounds into drug formulations. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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60 pages, 18089 KiB

Open AccessReview

Porokeratoses—A Comprehensive Review on the Genetics and Metabolomics, Imaging Methods and Management of Common Clinical Variants

by Paweł Pietkiewicz, Katarzyna Korecka, Natalia Salwowska, Ihor Kohut, Adarsha Adhikari, Monika Bowszyc-Dmochowska, Anna Pogorzelska-Antkowiak and Cristian Navarrete-Dechent

Metabolites 2023, 13(12), 1176; https://doi.org/10.3390/metabo13121176 - 26 Nov 2023

Cited by 8 | Viewed by 5703

Abstract

Porokeratosis is a heterogeneous group of keratinising disorders characterised by the presence of particular microscopic structural changes, namely the presence of the cornoid lamella. This structure develops as a consequence of a defective isoprenoid pathway, critical for cholesterol synthesis. Commonly recognised variants include [...] Read more.

Porokeratosis is a heterogeneous group of keratinising disorders characterised by the presence of particular microscopic structural changes, namely the presence of the cornoid lamella. This structure develops as a consequence of a defective isoprenoid pathway, critical for cholesterol synthesis. Commonly recognised variants include disseminated superficial actinic porokeratosis, disseminated superficial porokeratosis, porokeratosis of Mibelli, palmoplantar porokeratosis (including porokeratosis palmaris et plantaris disseminata and punctate porokeratosis), linear porokeratosis, verrucous porokeratosis (also known as genitogluteal porokeratosis), follicular porokeratosis and porokeratoma. Apart from the clinical presentation and epidemiology of each variant listed, this review aims at providing up-to-date information on the precise genetic background, introduces imaging methods facilitating the diagnosis (conventional and ultraviolet-induced fluorescence dermatoscopy, reflectance confocal microscopy and pathology), discusses their oncogenic potential and reviews the literature data on the efficacy of the treatment used, including the drugs directly targeting the isoprenoid–mevalonate pathway. Full article

(This article belongs to the Special Issue Lipid Expression and Metabolism Aberrations in Skin Diseases)

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Sex-Specific Relationships between HDL-Cholesterol Levels and 10-Year Mortality in Individuals with Atherosclerotic Cardiovascular Disease: A Nationwide Cohort Study of South Koreans

by Hyun Suk Yang, Ho Jin Jeong, Hyeongsu Kim, Seungho Lee and Mina Hur

Metabolites 2023, 13(12), 1175; https://doi.org/10.3390/metabo13121175 - 26 Nov 2023

Cited by 2 | Viewed by 1977

Abstract

Large epidemiological studies show U-shaped relationships between high-density lipoprotein cholesterol (HDL-C) levels and all-cause mortality in individuals without atherosclerotic cardiovascular diseases (ASCVD). Association in those with ASCVD by sex is unclear. We examined the association between HDL-C levels and 10-year all-cause mortality in [...] Read more.

Large epidemiological studies show U-shaped relationships between high-density lipoprotein cholesterol (HDL-C) levels and all-cause mortality in individuals without atherosclerotic cardiovascular diseases (ASCVD). Association in those with ASCVD by sex is unclear. We examined the association between HDL-C levels and 10-year all-cause mortality in subjects (≥40 years of age) with ASCVD using the 2010 National Health Insurance Service and the National Death Registry of Korea. We categorized HDL-C levels into three groups (low: <40 mg/dL for males, <50 mg/dL for females; high: 40–90 mg/dL for males, 50–90 mg/dL for females; extremely high: >90 mg/dL) and 10 mg/dL intervals. We conducted a sex-stratified and adjusted Cox proportional hazards analysis. Out of 1,711,548 individuals (54% female, mean age 61.4 years), 10-year mortality was observed in 218,252 (12.8%). Males had a higher mortality rate than females (16.2% vs. 9.8%; p < 0.001). When adjusting for age, body mass index, LDL-cholesterol, triglycerides, hypertension, diabetes, smoking, and alcohol consumption, the low and extremely high HDL-C groups had significantly higher hazard ratios for 10-year mortality compared to the high HDL-C group in males [1.183 (1.166–1.199), 1.359 (1.288–1.434)] and in females [1.153 (1.138–1.169), 1.095 (1.029–1.167)]. The frequency distribution bars for the 10-year mortality rate showed sex-specific nadirs of 50–59 mg/dL in males and 70–79 mg/dL in females. In this ASCVD cohort, the extremely high HDL-C (>90 mg/dL) group had 35.9% and 9.5% higher 10-year mortality risks than the high HDL-C group for males and females, respectively. There was a slightly U-shaped relationship between baseline HDL-C levels and a 10-year mortality rate, with earlier inflection in males than in females. Full article

(This article belongs to the Special Issue Lipid Biomarkers and Cardiometabolic Diseases)

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Metabolites, Volume 13, Issue 12 (December 2023) – 38 articles

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