Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Discovery of AHCY as an Off-Target of Doxorubicin by Integrative Analysis of Photoaffinity Labeling Chemoproteomics and Untargeted Metabolomics

Tue, 29/11/2022 - 12:00
Anal Chem. 2022 Nov 29. doi: 10.1021/acs.analchem.2c03377. Online ahead of print.ABSTRACTTarget identification is critically important for understanding the mechanism of action of drugs. Here, we reported a new strategy for deconvolution of drug targets (or off-targets) with photoaffinity labeling chemoproteomics in combination with untargeted metabolomics by using doxorubicin (DOX) as a model. The DOX-derived photoaffinity probes were prepared and applied to capture DOX-interacting proteins in living cells. The captured DOX-interacting proteins were then identified by label-free quantitative proteomics. Totally, 151 significant proteins were identified with high confidence (fold change >4, p-value < 0.005). The gene ontology enrichment analysis suggested that the proteins were mainly involved in carbon metabolism, citrate cycle, fatty acid metabolism, and metabolic pathways. Therefore, untargeted metabolomics was applied to quantify the significantly altered metabolites in cells upon drug treatment. The pathway enrichment analysis suggested that DOX mainly interrupted with the processes of pyrimidine and purine metabolism, carbon metabolism, methionine metabolism, and phosphatidylcholine biosynthesis. Integrative analysis of chemoproteomics and metabolomics indicated that adenosylhomocysteinase (AHCY) is a new target (off-target) of DOX leading to the accumulation of S-adenosyl homocysteine. This deduced DOX target was confirmed by the cellular thermal shift assay, affinity competitive pull-down assay, biochemical assay, and siRNA knock down experiments. Our result suggested that AHCY is the uncovered off-target of DOX.PMID:36445716 | DOI:10.1021/acs.analchem.2c03377

Production of Antimicrobial Compounds by Homologous and Heterologous Expression

Tue, 29/11/2022 - 12:00
Methods Mol Biol. 2023;2601:55-73. doi: 10.1007/978-1-0716-2855-3_4.ABSTRACTNatural product discovery campaigns aim to identify compounds with the desired bioactivity, for example, metabolites with antibiotic activity. The major driver of many projects is still the finding of bioactive extracts, which will be followed up to isolate the activity-causing agent as pure compound. However, nowadays also additional strategies can be used to increase the probability of success. Metabolomic approaches indicate chemical novelty, and genomics allow identification of putative biosynthetic gene clusters (BGCs) of interest, even though the corresponding metabolite is unknown. Whatever the entry to the campaign is, at one point the scientists need to have the desired compound in hand to analyze it in detail. Hence, expression must be achieved to yield the compound of interest, either to link it to the corresponding putative BGC or to overcome the bottleneck of sparse compound supply. Therefore, homologous and heterologous expression approaches are feasible ways forward to increase production yield, shorten fermentation time, or to get BGCs expressed at all for which no suitable fermentation condition was identified.In this chapter, expression approaches in bacteria are described to biosynthesize compounds of interest. Homologous expression, by genetic manipulation of the original Streptomyces producer strain, and heterologous expression in the microbial workhorse Escherichia coli are exemplified.PMID:36445579 | DOI:10.1007/978-1-0716-2855-3_4

Metabolomic analysis of combined exposure to microplastics and methylmercury in the brackish water flea Diaphanosoma celebensis

Tue, 29/11/2022 - 12:00
Environ Geochem Health. 2022 Nov 29. doi: 10.1007/s10653-022-01435-1. Online ahead of print.ABSTRACTOwing to their widespread distribution and high bioaccumulation, microplastics (MPs) and mercury (Hg) are considered major threats to the ocean. MP interacts with Hg because of its high adsorption properties. However, their toxicological interactions with marine organisms, especially combined effects at the molecular level, are poorly understood. This study investigated the single and combined effects of MP and Hg on the metabolic profile of the brackish water flea Diaphanosoma celebensis. A total of 238 metabolites were significantly affected by MP, Hg, or MP + Hg. Metabolite perturbation patterns showed that toxicity of Hg and MP + Hg was similar and that of MP was not significant. Among the 223 metabolites affected by Hg, profiles of 32 unannotated metabolites were significantly different from those of MP + Hg, and combined effects of MP + Hg decreased the effect of Hg on 25 of these metabolites. Only 11 annotated metabolites were significantly affected by Hg or MP + Hg and were related to carbohydrate, lipid, vitamin, and ecdysteroid metabolism. Ten metabolites were decreased by Hg and MP + Hg and were not significantly different between the exposure groups. Enrichment analysis showed that galactose, starch, and sucrose metabolism were the most affected pathways. These findings suggest that MP has negligible toxic effect, and Hg can induce energy depletion, membrane damage, and disruption of growth, development, and reproduction. Although the impact of MP was negligible, the combined effects of MP + Hg could be metabolite specific. This study provides better understanding of the combined effects of MP and Hg on marine organisms.PMID:36445536 | DOI:10.1007/s10653-022-01435-1

Immunometabolic Analysis of Synovial Fluid from Juvenile Idiopathic Arthritis Patients

Tue, 29/11/2022 - 12:00
Immunohorizons. 2022 Nov 1;6(11):768-778. doi: 10.4049/immunohorizons.2200052.ABSTRACTJuvenile idiopathic arthritis (JIA) is an inflammatory rheumatic disorder. Polymorphonuclear neutrophils (PMNs) are present in JIA synovial fluid (SF), but with variable frequency. SF PMNs in JIA were previously shown to display high exocytic but low phagocytic and immunoregulatory activities. To further assess whether the degree of SF neutrophilia associated with altered immune responses in JIA, we collected SF and blood from 16 adolescent JIA patients. SF and blood leukocytes were analyzed by flow cytometry. SF and plasma were used for immune mediator quantification and metabolomics. Healthy donor blood T cells were cultured in SF to evaluate its immunoregulatory activities. PMN and T cell frequencies were bimodal in JIA SF, delineating PMN high/T cell low (PMNHigh) and PMN low/T cell high (PMNLow) samples. Proinflammatory mediators were increased in SF compared with plasma across patients, and pro- and anti-inflammatory mediators were further elevated in PMNHigh SF. Compared to blood, SF PMNs showed increased exocytosis and programmed death-1/programmed death ligand-1 expression, and SF PMNs and monocytes/macrophages had increased surface-bound arginase-1. SPADE analysis revealed SF monocyte/macrophage subpopulations coexpressing programmed death-1 and programmed death ligand-1, with higher expression in PMNHigh SF. Healthy donor T cells showed reduced coreceptor expression when stimulated in PMNHigh versus PMNLow SF. However, amino acid metabolites related to the arginase-1 and IDO-1 pathways did not differ between the two groups. Hence, PMN predominance in the SF of a subset of JIA patients is associated with elevated immune mediator concentration and may alter SF monocyte/macrophage phenotype and T cell activation, without altering immunoregulatory amino acids.PMID:36445361 | DOI:10.4049/immunohorizons.2200052

Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era

Tue, 29/11/2022 - 12:00
OMICS. 2022 Nov 23. doi: 10.1089/omi.2022.0137. Online ahead of print.ABSTRACTThe majority of processes that occur in daily cell life are modulated by hundreds to thousands of dynamic protein-protein interactions (PPI). The resulting protein complexes constitute a tangled network that, with its continuous remodeling, builds up highly organized functional units. Thus, defining the dynamic interactome of one or more proteins allows determining the full range of biological activities these proteins are capable of. This conceptual approach is poised to gain further traction and significance in the current postgenomic era wherein the treatment of severe diseases needs to be tackled at both genomic and PPI levels. This also holds true for COVID-19, a multisystemic disease affecting biological networks across the biological hierarchy from genome to proteome to metabolome. In this overarching context and the current historical moment of the COVID-19 pandemic where systems biology increasingly comes to the fore, cross-linking mass spectrometry (XL-MS) has become highly relevant, emerging as a powerful tool for PPI discovery and characterization. This expert review highlights the advanced XL-MS approaches that provide in vivo insights into the three-dimensional protein complexes, overcoming the static nature of common interactomics data and embracing the dynamics of the cell proteome landscape. Many XL-MS applications based on the use of diverse cross-linkers, MS detection methods, and predictive bioinformatic tools for single proteins or proteome-wide interactions were shown. We conclude with a future outlook on XL-MS applications in the field of structural proteomics and ways to sustain the remarkable flexibility of XL-MS for dynamic interactomics and structural studies in systems biology and planetary health.PMID:36445175 | DOI:10.1089/omi.2022.0137

Metabolic and Microbial Community Engineering for Four-Carbon Dicarboxylic Acid Production from CO<sub>2</sub>-Derived Glycogen in the <em>Cyanobacterium Synechocystis</em> sp. PCC6803

Tue, 29/11/2022 - 12:00
ACS Synth Biol. 2022 Nov 29. doi: 10.1021/acssynbio.2c00379. Online ahead of print.ABSTRACTThe four-carbon (C4) dicarboxylic acids, fumarate, malate, and succinate, are the most valuable targets that must be exploited for CO2-based chemical production in the move to a sustainable low-carbon future. Cyanobacteria excrete high amounts of C4 dicarboxylic acids through glycogen fermentation in a dark anoxic environment. The enhancement of metabolic flux in the reductive TCA branch in the Cyanobacterium Synechocystis sp. PCC6803 is a key issue in the C4 dicarboxylic acid production. To improve metabolic flux through the anaplerotic pathway, we have created the recombinant strain PCCK, which expresses foreign ATP-forming phosphoenolpyruvate carboxykinase (PEPck) concurrent with intrinsic phosphoenolpyruvate carboxylase (Ppc) overexpression. Expression of PEPck concurrent with Ppc led to an increase in C4 dicarboxylic acids by autofermentation. Metabolome analysis revealed that PEPck contributed to an increase in carbon flux from hexose and pentose phosphates into the TCA reductive branch. To enhance the metabolic flux in the reductive TCA branch, we examined the effect of corn-steep liquor (CSL) as a nutritional supplement on C4 dicarboxylic acid production. Surprisingly, the addition of sterilized CSL enhanced the malate production in the PCCK strain. Thereafter, the malate and fumarate excreted by the PCCK strain are converted into succinate by the CSL-settling microorganisms. Finally, high-density cultivation of cells lacking the acetate kinase gene showed the highest production of malate and fumarate (3.2 and 2.4 g/L with sterilized CSL) and succinate (5.7 g/L with non-sterile CSL) after 72 h cultivation. The present microbial community engineering is useful for succinate production by one-pot fermentation under dark anoxic conditions.PMID:36445137 | DOI:10.1021/acssynbio.2c00379

Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic <em>Aromatoleum aromaticum</em> EbN1<sup>T</sup>

Tue, 29/11/2022 - 12:00
mSystems. 2022 Nov 29:e0068522. doi: 10.1128/msystems.00685-22. Online ahead of print.ABSTRACTMembers of the genus Aromatoleum thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O2 respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied. Their substrate-dependent regulation showed differing degrees of specificity, ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, the transcript and protein formation were essentially constitutive, contrasted by that of anoxia-specific versus oxia-specific metabolite profiles. The matrix factorization of transcriptomic data revealed that the anaerobic modules accounted for most of the variance across the degradation network. The respiration network appeared to be constitutive, both on the transcript and protein levels, except for nitrate reductase (with narGHI expression occurring only under nitrate-reducing conditions). The anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as by NarXL (all constitutively formed). The resequencing and functional reannotation of the genome fostered a genome-scale metabolic model, which is comprised of 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, with which 4-hydroxybenzoate was exported. Taken together, the combination of multi-omics, growth physiology, and a metabolic model advanced our knowledge of an environmentally relevant microorganism that differs significantly from other bacterial model strains. IMPORTANCE Aromatic compounds are abundant constituents not only of natural organic matter but also of bulk industrial chemicals and fuel components of environmental concern. Considering the widespread occurrence of redox gradients in the biosphere, facultative anaerobic degradation specialists can be assumed to play a prominent role in the natural mineralization of organic matter and in bioremediation at contaminated sites. Surprisingly, differential multi-omics profiling of the A. aromaticum EbN1T studied here revealed relaxed regulatory stringency across its four main physiological modi operandi (i.e., O2-independent and O2-dependent degradation reactions versus denitrification and O2 respiration). Combining multi-omics analyses with a genome-scale metabolic model aligned with measured growth performances establishes A. aromaticum EbN1T as a systems-biology model organism and provides unprecedented insights into how this bacterium functions on a holistic level. Moreover, this experimental platform invites future studies on eco-systems and synthetic biology of the environmentally relevant betaproteobacterial Aromatoleum/Azoarcus/Thauera cluster.PMID:36445109 | DOI:10.1128/msystems.00685-22

DNA Authentication and Chemical Analysis of <em>Psilocybe</em> Mushrooms Reveal Widespread Misdeterminations in Fungaria and Inconsistencies in Metabolites

Tue, 29/11/2022 - 12:00
Appl Environ Microbiol. 2022 Nov 29:e0149822. doi: 10.1128/aem.01498-22. Online ahead of print.ABSTRACTThe mushroom genus Psilocybe is best known as the core group of psychoactive mushrooms, yet basic information on their diversity, taxonomy, chemistry, and general biology is still largely lacking. In this study, we reexamined 94 Psilocybe fungarium specimens, representing 18 species, by DNA barcoding, evaluated the stability of psilocybin, psilocin, and their related tryptamine alkaloids in 25 specimens across the most commonly vouchered species (Psilocybe cubensis, Psilocybe cyanescens, and Psilocybe semilanceata), and explored the metabolome of cultivated P. cubensis. Our data show that, apart from a few well-known species, the taxonomic accuracy of specimen determinations is largely unreliable, even at the genus level. A substantial quantity of poor-quality and mislabeled sequence data in public repositories, as well as a paucity of sequences derived from types, further exacerbates the problem. Our data also support taxon- and time-dependent decay of psilocybin and psilocin, with some specimens having no detectable quantities of them. We also show that the P. cubensis metabolome possibly contains thousands of uncharacterized compounds, at least some of which may be bioactive. Taken together, our study undermines commonly held assumptions about the accuracy of names and presence of controlled substances in fungarium specimens identified as Psilocybe spp. and reveals that our understanding of the chemical diversity of these mushrooms is largely incomplete. These results have broader implications for regulatory policies pertaining to the storage and sharing of fungarium specimens as well as the use of psychoactive mushrooms for recreation and therapy. IMPORTANCE The therapeutic use of psilocybin, the active ingredient in "magic mushrooms," is revolutionizing mental health care for a number of conditions, including depression, posttraumatic stress disorder (PTSD), and end-of-life care. This has spotlighted the current state of knowledge of psilocybin, including the organisms that endogenously produce it. However, because of international regulation of psilocybin as a controlled substance (often included on the same list as cocaine and heroin), basic research has lagged far behind. Our study highlights how the poor state of knowledge of even the most fundamental scientific information can impact the use of psilocybin-containing mushrooms for recreational or therapeutic applications and undermines critical assumptions that underpin their regulation by legal authorities. Our study shows that currently available chemical studies are mainly inaccurate, irreproducible, and inconsistent, that there exists a high rate of misidentification in museum collections and public databases rendering even names unreliable, and that the concentration of psilocybin and its tryptamine derivatives in three of the most commonly collected Psilocybe species (P. cubensis, P. cyanescens, and P. semilanceata) is highly variable and unstable in museum specimens spanning multiple decades, and our study generates the first-ever insight into the highly complex and largely uncharacterized metabolomic profile for the most commonly cultivated magic mushroom, P. cubensis.PMID:36445079 | DOI:10.1128/aem.01498-22

A shift towards succinate-producing Prevotella in the ruminal microbiome challenged with monensin

Tue, 29/11/2022 - 12:00
Proteomics. 2022 Nov 28:e2200121. doi: 10.1002/pmic.202200121. Online ahead of print.ABSTRACTThe time-resolved impact of monensin on the active rumen microbiome was studied in a rumen-simulating technique (Rusitec) with metaproteomic and metabolomic approaches. Monensin treatment caused a decreased fiber degradation potential that was observed by the reduced abundance of proteins assigned to fibrolytic bacteria and glycoside hydrolases, sugar transporters and carbohydrate metabolism. Decreased proteolytic activities resulted in reduced amounts of ammonium as well as branched-chain fatty acids. The family Prevotellaceae exhibited increased resilience in the presence of monensin, with a switch of the metabolism from acetate to succinate production. Prevotella species harbor a membrane bound electron transfer complex, which drives the reduction of fumarate to succinate, which is the substrate for propionate production in the rumen habitat. Besides the increased succinate production, a concomitant depletion of methane concentration was observed upon monensin exposure. Our study demonstrates that Prevotella sp. shifts its metabolism successfully in response to monensin exposure and Prevotellaceae represents the key bacterial family stabilizing the rumen microbiota during exposure to monensin. This article is protected by copyright. All rights reserved.PMID:36444514 | DOI:10.1002/pmic.202200121

Comprehensive proteomic and metabolomic analysis uncover the response of okra to drought stress

Tue, 29/11/2022 - 12:00
PeerJ. 2022 Nov 23;10:e14312. doi: 10.7717/peerj.14312. eCollection 2022.ABSTRACTThe response of okra to drought stress is very complicated, and the molecular mechanisms underlying this process remains ambiguous up to now. In this study, different degrees of water-stress responses of okra leaf were explained by using transcriptomics and metabolomic approaches. The photosynthesis and glycometabolism in okra leaf were both adversely affected by drought stress, leading to inhibition of the carbohydrate metabolic process, and then influencing the secondary plant metabolism. Further, drought stress disturbed amino acid metabolism, especially for the tyrosine-derived pathway as well as arginine and proline metabolism, which have been shown to be significantly enriched under water withholding conditions based on multi-omics conjoint analysis (transcriptome, proteome and metabolome). In-depth analysis of the internal linkages between differentially expressed transcripts, proteins, and metabolites decidedly indicate that tyrosine metabolism could confer tolerance to drought stress by influencing carbon and nitrogen metabolism. These findings provide a whole framework of the regulation and relationships of major transcripts and peptides related to secondary metabolism, particularly, the role of critical proteins and metabolite involved in the change of amino acid metabolism in response to drought stress.PMID:36444379 | PMC:PMC9700456 | DOI:10.7717/peerj.14312

Metabolomic and transcriptomic analyses provide insights into metabolic networks during cashew fruit development and ripening

Tue, 29/11/2022 - 12:00
Food Chem. 2023 Mar 15;404(Pt B):134765. doi: 10.1016/j.foodchem.2022.134765. Epub 2022 Oct 29.ABSTRACTCashew nut is a popular food around the world. The high-resolution profiles and dynamics of metabolomes in cashew fruits are poorly understood till now. In this study, we analyzed the temporal metabolome of cashew nut via a non-targeted method based on UHPLC-Q-Exactive-MS, and analyzed that of cashew apple via a widely targeted method based on UHPLC-QTRAP-MS/MS (MRM). Furthermore, we performed integrative analyses of temporal metabolome and transcriptome data, characterized the accumulation of specific metabolites, and identified the transcriptional changes during cashew fruit development. Specifically, we found that phosphatidylinositol species were the predominant fractions in the unsaturated glycerophospholipids, and we identified a transcription factor that was the potential regulator of phosphatidylinositol biosynthesis. Analysis of cashew apple revealed metabolic genes and transcription factors involved in sugar biosynthesis. Taken together, our results provide insights into metabolic networks during cashew fruit development and generate a valuable resource for further cashew breeding studies.PMID:36444096 | DOI:10.1016/j.foodchem.2022.134765

Effects of heat-treated starch and protein from foxtail millet (Setaria italica) on type 2 diabetic mice

Tue, 29/11/2022 - 12:00
Food Chem. 2023 Mar 15;404(Pt B):134735. doi: 10.1016/j.foodchem.2022.134735. Epub 2022 Oct 28.ABSTRACTFoxtail millet and its components have hypoglycemic effects on mice, but the role of starch and protein in millet in these effects is unclear. The present study investigated the impact of heat-treated foxtail millet starch and protein on type 2 diabetic mice and the underlying mechanisms, including the influence of gut microbiota and serum metabolic profile. In diabetic mice, the consumption of heat-treated foxtail millet starch and protein reduced, respectively, fasting blood glucose 18.52% and 26.33% and insulin levels 12.22% and 15.96%. In addition, heat-treated foxtail millet starch and protein altered the gut microbiota composition, enriched the abundance of probiotics and short-chain fatty acids producing bacteria, reduced harmful bacteria, and increased fecal short-chain fatty acids concentration. Heat-treated foxtail millet protein had greater effects on gut microbiota composition, whereas heat-treated foxtail millet starch had greater effects on metabolic function. The hypoglycemic potential of heat-treated foxtail millet starch and protein was associated with the modulation of both gut microbiota and serum metabolic profile.PMID:36444094 | DOI:10.1016/j.foodchem.2022.134735

Microplastics reduce nitrogen uptake in peanut plants by damaging root cells and impairing soil nitrogen cycling

Tue, 29/11/2022 - 12:00
J Hazard Mater. 2023 Feb 5;443(Pt B):130384. doi: 10.1016/j.jhazmat.2022.130384. Epub 2022 Nov 11.ABSTRACTMicroplastic (MP) pollution severely impairs the sustainable development of modern agriculture. However, the mechanisms underlying the effects of MP contaminants on nutrient cycles in agroecosystems are poorly understood. In this study, we examined the impacts of two types of MPs, polypropylene (PP) and rubber crumb (RC), on nitrogen (N) transformation and N cycling in soil-peanut system. High concentrations of PP (1% w/w) and RC (1% w/w) inhibited vegetative growth and N uptake in peanut plants by damaging root cells and disturbing soil N cycling. These MPs damaged the plasma membranes of root cells and caused oxidative stress, as evidenced by the decreased number of xylem vessels, which in turn inhibited N uptake by roots. Integrated metagenomic and metabolomic analyses revealed that the differential soil metabolite levels in response to MP treatment affected the microbial community structure in the rhizosphere and the expression of key N cycling-related genes, resulting in altered N transformation and the decreased availability of N in rhizosphere soil. These findings provide the first evidence of the effects of MPs on N uptake in peanut plants and shed light on the importance of rational management of MPs for crop growth and yield in agroecosystems.PMID:36444071 | DOI:10.1016/j.jhazmat.2022.130384

Polysaccharides from red kidney bean alleviating hyperglycemia and hyperlipidemia in type 2 diabetic rats via gut microbiota and lipid metabolic modulation

Tue, 29/11/2022 - 12:00
Food Chem. 2023 Mar 15;404(Pt A):134598. doi: 10.1016/j.foodchem.2022.134598. Epub 2022 Oct 14.ABSTRACTCrude polysaccharides extracted from red kidney bean (RK) display significant antidiabetic activity in type 2 diabetic mice, but the underlying mechanism and the core functional component has not been elucidated. In this study, the antidiabetic effect and mechanism of RK are investigated by serum metabolomics and high-throughput sequencing. In addition, the key component was identified by evaluating the improvement on glucose and lipid homeostasis in type 2 diabetic rats. Our data indicated that RK relieved the symptoms of hyperglycemia, hyperlipidemia in STZ-induced diabetic rats. RK not only improved the metabolic disturbance by regulating the biosynthesis of unsaturated fatty acids, but also modified gut microbiota composition by selectively enriching in key genera of Bacteroides, Phascolarctobacterium, Succinivibrio, Blautia. We further found the purified polysaccharides (RKP) were identified as the core biofunctional component in RK. Our present studies provide evidence that RKP are potential effective dietary supplement for type 2 diabetic individuals.PMID:36444040 | DOI:10.1016/j.foodchem.2022.134598

Metabolite profiling and identification of novel umami compounds in the chaya leaves of two species using multiplatform metabolomics

Tue, 29/11/2022 - 12:00
Food Chem. 2023 Mar 15;404(Pt A):134564. doi: 10.1016/j.foodchem.2022.134564. Epub 2022 Oct 12.ABSTRACTChaya (Cnidoscolus chayamansa and C. aconitifolius) is a fast-growing medicinal plant, and its leaves exhibit a strong umami taste. Here metabolite variation and umami-related compounds in the leaves of two chaya species were determined using a multiplatform untargeted-metabolomics approach, electronic tongue, and in silico screening. Metabolite profiles varied between the leaves of the two species and among leaf maturation stages. Young leaves exhibited the highest umami taste intensity, followed by mature and old leaves. Partial least square regression and computational molecular docking analyses revealed five potent umami substances (quinic acid, trigonelline, alanyl-tyrosine, leucyl-glycyl-proline, and leucyl-aspartyl-glutamine) and three known umami compounds (l-glutamic acid, pyroglutamic acid, and 5'-adenosine monophosphate). The five substances were validated as novel umami compounds using electronic tongue assay; leucyl-glycyl-proline exhibited synergism with monosodium glutamate, thereby enhancing the umami taste. Thus, substances contributing to the taste of chaya leaves were successfully identified.PMID:36444036 | DOI:10.1016/j.foodchem.2022.134564

Metabolomics and lipidomics profiles related to intramuscular fat content and flavor precursors between Laiwu and Yorkshire pigs

Tue, 29/11/2022 - 12:00
Food Chem. 2023 Mar 15;404(Pt A):134699. doi: 10.1016/j.foodchem.2022.134699. Epub 2022 Oct 19.ABSTRACTChinese indigenous pig breeds have higher intramuscular fat content (IMF) and better meat quality than Western commercial pigs. The differential metabolites and lipids in the skeletal muscle associated with IMF contents and meat flavor in Laiwu and Yorkshire pigs were investigated in this study. As a result, 113 differential metabolites and 54 differential lipids were discovered. Lipidomics revealed that the Laiwu pig had a fast lipid droplet formation and contained more triglyceride than the Yorkshire pig, which was corresponded to its high IMF contents. Both the lipidomics and metabolomics results indicated that the Laiwu pig had a higher mitochondrial content and aerobic respiration, due to its larger percentage of oxidative fibers. In addition, differential metabolites, such as oxoglutaric acid, fumarate, and l-aspartate, were thought to be important flavor precursors contributing to the Laiwu pig's improved pork taste.PMID:36444028 | DOI:10.1016/j.foodchem.2022.134699

Tea polyphenol and epigallocatechin gallate ameliorate hyperlipidemia via regulating liver metabolism and remodeling gut microbiota

Tue, 29/11/2022 - 12:00
Food Chem. 2023 Mar 15;404(Pt A):134591. doi: 10.1016/j.foodchem.2022.134591. Epub 2022 Oct 14.ABSTRACTHyperlipidemia can directly cause metabolic diseases that seriously endanger disorder and metabolism and gut health. Tea polyphenol (TP) and epigallocatechin gallate (EGCG) was found to improve blood lipid levels and gut microbiota. This study aimed to investigate the effects of TP and EGCG on alleviating hyperlipidemia and liver fat accumulation with physiology, genomics, and metabolomics. Results showed that both TP and EGCG reduced body weight, and TP showed advantages in the decrease of serum cholesterol and triglycerides in hyperlipidemic rats induced by the high-fat diet. Moreover, EGCG may protect liver function via reducing the glycerophospholipids increased by high-fat diet intervention. TP remodeled the gut microbiota composition and enriched the abundance of beneficial bacteria (Bacteroides, Faecalibacterium, Parabacteroides, Akkermansia), and EGCG may improve gut health via promoting the acid-producing bacteria (such as Butyricimonas, Desulfovibrio). The above results provided new insights into the hypolipidemic mechanism of TP and EGCG.PMID:36444016 | DOI:10.1016/j.foodchem.2022.134591

Inhaled Corticosteroid-Induced Adrenal Suppression in Patients With Asthma Detected by Metabolomic Profiling

Tue, 29/11/2022 - 12:00
J Allergy Clin Immunol Pract. 2022 Oct;10(10):2774-2775. doi: 10.1016/j.jaip.2022.08.004. Epub 2022 Oct 7.NO ABSTRACTPMID:36444000 | DOI:10.1016/j.jaip.2022.08.004

Two effective models based on comprehensive lipidomics and metabolomics can distinguish BC versus HCs, and TNBC versus Non-TNBC

Tue, 29/11/2022 - 12:00
Proteomics Clin Appl. 2022 Nov 28:e2200042. doi: 10.1002/prca.202200042. Online ahead of print.ABSTRACTBACKEGROUND: Lipidomics and metabolomics are closely related to tumor phenotypes, and serum lipoprotein subclasses and small-molecule metabolites are considered as promising biomarkers for breast cancer (BC) diagnosis. This study aimed to explore potential biomarker models based on lipidomic and metabolomic analysis that could distinguish BC from healthy controls (HCs) and triple-negative BC (TNBC) from non-TNBC.METHODS: Blood samples were collected from 114 patients with BC and 75 healthy controls (HCs). A total of 112 types of lipoprotein subclasses and 30 types of small-molecule metabolites in the serum were detected by 1 H-NMR. All lipoprotein subclasses and small-molecule metabolites were subjected to a three-step screening process in the order of significance (P < 0.05), univariate regression (P < 0.1), and lasso regression (non-zero coefficient). Discriminant models of BC versus HCs and TNBC versus non-TNBC were established using binary logistic regression.RESULTS: We developed a valid discriminant model based on three-biomarker panel (formic acid, TPA2, and L6TG) that could distinguish patients with BC from HCs. The area under the receiver operating characteristic curve (AUC) was 0.999 (95% confidence interval [CI]: 0.995-1.000) and 0.990 (95% CI: 0.959-1.000) in the training and validation sets, respectively. Based on the panel (D-dimer, CA15-3, CEA, L5CH, glutamine, and ornithine), a discriminant model was established to differentiate between TNBC and non-TNBC, with AUC of 0.892 (95% CI: 0.778-0.967) and 0.905 (95% CI: 0.754-0.987) in the training and validation sets, respectively.CONCLUSION: This study revealed lipidomic and metabolomic differences between BC versus HCs and TNBC versus non-TNBC. Two validated discriminatory models established against lipidomic and metabolomic differences can accurately distinguish BC from HCs and TNBC from non-TNBC.IMPACT: Two validated discriminatory models can be used for early BC screening and help BC patients avoid time-consuming, expensive, and dangerous BC screening. This article is protected by copyright. All rights reserved.PMID:36443927 | DOI:10.1002/prca.202200042

The effect of tacrolimus-induced toxicity on metabolic profiling in target tissues of mice

Tue, 29/11/2022 - 12:00
BMC Pharmacol Toxicol. 2022 Nov 28;23(1):87. doi: 10.1186/s40360-022-00626-x.ABSTRACTTacrolimus (Tac) is a common immunosuppressant that used in organ transplantation. However, its therapeutic index is narrow, and it is prone to adverse side effects, along with an increased risk of toxicity, namely, cardio-, nephro-, hepato-, and neurotoxicity. Prior metabolomic investigations involving Tac-driven toxicity primarily focused on changes in individual organs. However, extensive research on multiple matrices is uncommon. Hence, in this research, the authors systemically evaluated Tac-mediated toxicity in major organs, namely, serum, brain, heart, liver, lung, kidney, and intestines, using gas chromatography-mass spectrometry (GC-MS). The authors also employed multivariate analyses, including orthogonal projections to the latent structure (OPLS) and t-test, to screen 8 serum metabolites, namely, D-proline, glycerol, D-fructose, D-glucitol, sulfurous acid, 1-monopalmitin (MG (16:0/0:0/0:0)), glycerol monostearate (MG (0:0/18:0/0:0)), and cholesterol. Metabolic changes within the brain involved alterations in the levels of butanamide, tartronic acid, aminomalonic acid, scyllo-inositol, dihydromorphine, myo-inositol, and 11-octadecenoic acid. Within the heart, the acetone and D-fructose metabolites were altered. In the liver, D-glucitol, L-sorbose, palmitic acid, myo-inositol, and uridine were altered. In the lung, L-lactic acid, L-5-oxoproline, L-threonine, phosphoric acid, phosphorylethanolamine, D-allose, and cholesterol were altered. Lastly, in the kidney, L-valine and D-glucose were altered. Our findings will provide a systematic evaluation of the metabolic alterations in target organs within a Tac-driven toxicity mouse model.PMID:36443830 | DOI:10.1186/s40360-022-00626-x

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