PubMed

Mol Metab. 2023 Mar 28:101716. doi: 10.1016/j.molmet.2023.101716. Online ahead of print.ABSTRACTOBJECTIVES: The non-essential amino acids serine, glycine, and alanine, as well as diverse sphingolipid species, are implicated in inherited neuro-retinal disorders and are metabolically linked by serine palmitoyltransferase (SPT), a key enzyme in membrane lipid biogenesis. To gain insight into the pathophysiological mechanisms linking these pathways to neuro-retinal diseases we compared patients diagnosed with two metabolically intertwined diseases: macular telangiectasia type II (MacTel), hereditary sensory autonomic neuropathy type 1 (HSAN1), or both.METHODS: We performed targeted metabolomic analyses of amino acids and broad sphingolipids in sera from a cohort of MacTel (205), HSAN1 (25) and Control (151) participants.RESULTS: MacTel patients exhibited broad alterations of amino acids, including changes in serine, glycine, alanine, glutamate, and branched-chain amino acids reminiscent of diabetes. MacTel patients had elevated 1-deoxysphingolipids but reduced levels of complex sphingolipids in circulation. A mouse model of retinopathy indicates dietary serine and restriction can drive this depletion in complex sphingolipids. HSAN1 patients exhibited elevated serine, lower alanine, and a reduction in canonical ceramides and sphingomyelins compared to controls. Those patients diagnosed with both HSAN1 and MacTel showed the most significant decrease in circulating sphingomyelins.CONCLUSIONS: These results highlight metabolic distinctions between these two diseases, emphasize the importance of membrane lipids in the progression of MacTel, and suggest distinct therapeutic approaches.PMID:36997154 | DOI:10.1016/j.molmet.2023.101716

J Ethnopharmacol. 2023 Mar 28:116430. doi: 10.1016/j.jep.2023.116430. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula chronicled in Shang Han Lun, is safe and effective for treatment of ulcerative colitis (UC).AIM OF THE STUDY: To investigate the effect of HQD against dextran sulfate sodium (DSS)-induced UC mice by regulating gut microbiota and metabolites, and further explore the mechanism of fatty acid metabolism on macrophage polarization.MATERIALS AND METHODS: Based on 3% dextran sulfate sodium (DSS)-induced UC mice model, clinical symptoms observation (body weight, DAI, and colon length) and histological inspection were used to evaluate the efficacy of HQD and fecal microbiota transplantation (FMT) from HQD-treated mice. The gut microbiota and metabolites were detected by 16S rRNA sequencing and metabolomics analysis. The parameters of fatty acid metabolism, macrophage polarization, and FFAR1/FFAR4-AMPK-PPARα pathway were analyzed by immunofluorescence analysis, western blotting, and real-time PCR. Then, the effects of FFAR1 and FFAR4 on macrophage polarization were examined by agonists based on LPS-induced RAW264.7 cell model.RESULTS: The results showed that FMT, like HQD, ameliorated UC by improving weight loss, restoring colon length, and reducing DAI scores and histopathological scores. Besides, HQD and FMT both enhanced the richness of gut microbiota, and modulated intestinal bacteria and metabolites to achieve a new balance. Untargeted metabolomics analysis revealed that fatty acids, especially long-chain fatty acids (LCFAs), dominated in HQD against DSS-induced UC by regulating the gut microenvironment. Further, FMT and HQD recovered the expression of fatty acid metabolism-related enzymes, and simultaneously activated FFAR1/FFAR4-AMPK-PPARα pathway but suppressed NF-κB pathway. Combined with cell experiment, HQD and FMT promoted macrophage polarization from M1 toward M2, which were well associated with anti-inflammatory cytokines and combined with the activated FFAR4.CONCLUSIONS: The mechanism of HQD against UC was related to regulating fatty acid metabolism to mediate M2 macrophage polarization by activating the FFAR4-AMPK-PPARα pathway.PMID:36997133 | DOI:10.1016/j.jep.2023.116430

Behav Brain Res. 2023 Mar 28:114411. doi: 10.1016/j.bbr.2023.114411. Online ahead of print.ABSTRACTKratom (M. speciosa Korth) is an herbal plant native to Southeast Asia. The leaves have been widely used to alleviate pain and opioid withdrawal symptoms. However, the increasing trend of recreational use of kratom among youth is concerning because substance abuse may render the adolescent brain more susceptible to neuropathological processes, causing dramatic consequences that persist into adulthood. Therefore, the present study aimed to investigate the long-term effects of mitragynine, the main alkaloid and lyophilized kratom decoction (LKD) exposure during adolescence on cognitive behaviours and brain metabolite profiles in adult rats. Adolescent male Sprague-Dawley rats were given mitragynine (3, 10 or 30mg/kg) or LKD orally for 15 consecutive days during postnatal days 31-45 (PND31-45). Behavioural testing was performed during adulthood (PND70-84) and the brains were subjected to metabolomic analysis. The results show that a high dose of mitragynine impaired long-term object recognition memory. Social behaviour and spatial learning were not affected, but both mitragynine and LKD impaired reference memory. Brain metabolomic study revealed several altered metabolic pathways that may be involved in the cognitive behavioural effects of LKD and mitragynine exposure. These pathways include arachidonic acid, taurine and hypotaurine, pantothenate and CoA biosynthesis, and tryptophan metabolism, while the N-isovalerylglycine was identified as the potential biomarker. In summary, adolescent kratom exposure can cause long-lasting cognitive behavioural deficits and alter brain metabolite profiles that are still evident in adulthood. This finding also indicates that the adolescent brain is vulnerable to the impact of early kratom use.PMID:36997094 | DOI:10.1016/j.bbr.2023.114411

Food Chem Toxicol. 2023 Mar 28:113747. doi: 10.1016/j.fct.2023.113747. Online ahead of print.ABSTRACTThis research aimed to explore the protective effect of quercetin against nephrotoxicity induced by four organophosphate pesticide mixtures (PM) using untargeted metabolomics technology in rat kidneys. Sixty male Wistar rats were randomly divided into six groups: control, low-dose quercetin treated (10 mg/kg. bw), high-dose quercetin treated (50 mg/kg. bw), PM-treated, and two dosages of quercetin + PM-treated. Metabolomics results showed that 17 differential metabolites were identified in the PM-treated group, and pathway analysis revealed that renal metabolic disorders include purine metabolism, glycerophospholipid metabolism, and vitamin B6 metabolism. When high-dose quercetin and PM-treated were administered to rats concurrently, the intensities of differential metabolites were substantially restored (p < 0.01), suggesting that quercetin can improve renal metabolic disorders caused by organophosphate pesticides (OPs). Mechanistically, quercetin could regulate the purine metabolism disorder and endoplasmic reticulum stress (ERS)-mediated autophagy induced by OPs by inhibiting XOD activity. Moreover, quercetin inhibits PLA2 activity to regulate glycerophospholipid metabolism and it could also exert antioxidant and anti-inflammatory effects to correct vitamin B6 metabolism in rat kidneys. Taken together, the high dose of quercetin (50 mg/kg.bw) has a certain protective effect on OPs-induced nephrotoxicity in rats, which provides a theoretical basis for quercetin against nephrotoxicity caused by OPs.PMID:36997054 | DOI:10.1016/j.fct.2023.113747

J Steroid Biochem Mol Biol. 2023 Mar 28:106305. doi: 10.1016/j.jsbmb.2023.106305. Online ahead of print.ABSTRACTThe incidence of central precocious puberty (CPP) in boys is rising, but lack of effective molecular biomarkers often leads to delayed treatment and thus the terrible clinical complications in adulthood. This study aims to identify the specific-biomarkers of CPP boys and understand the gender-related differences in metabolic characteristics of CPP. The specific-biomarkers of CPP boys were identified from serum and their combination was optimized by cross-metabolomics combined with linear discriminant analysis effect size analysis after age correction. The differences in metabolic characteristics between boys and girls with CPP were explored by cross-metabolomics and weighted gene co-expression network analysis. Results show that CPP activated in advance the HPG axis and induced gender-related clinical phenotypes. Seven serum metabolites were identified as specific-biomarkers of CPP boys, including acetoacetate, aspartate, choline, creatinine, myo-inositol, N,N-dimethylglycine and N-Acetyl-glycoprotein. The combination of aspartate, choline, myo-inositol and creatinine achieved an optimized diagnosis, where AUC is 0.949, prediction accuracy for CPP boys is 91.1%, and the average accuracy is 0.865. The metabolic disorders of CPP boys mainly involve in glycerophospholipid metabolism, and synthesis and degradation of ketone bodies. Betaine, glutamine, isoleucine, lactate, leucine, lysine, pyruvate, α-&β-glucose were identified as gender-related biomarkers for CPP, and they are mainly involved in glycolysis/gluconeogenesis, pyruvate metabolism, and alanine, aspartate and glutamate metabolism. Biomarkers combination provides a promising diagnostic potential for CPP boy with a favorite sensitivity and specificity. In addition, the differences of metabolic characteristics between boys and girls with CPP will contribute to the development of individualized clinical treatments in CPP.PMID:36997004 | DOI:10.1016/j.jsbmb.2023.106305

Metabolism. 2023 Mar 28:155552. doi: 10.1016/j.metabol.2023.155552. Online ahead of print.ABSTRACTBACKGROUND: High-Fructose Corn Syrup (HFCS), a sweetener rich in glucose and fructose, is nowadays widely used in beverages and processed foods; its consumption has been correlated to the emergence and progression of Non-Alcoholic Fatty Liver Disease (NAFLD). Nevertheless, the molecular mechanisms by which HFCS impacts hepatic metabolism remain scarce, especially in the context of obesity. Besides, the majority of current studies focuses either on the detrimental role of fructose in hepatic steatosis or compare separately the additive impact of fructose versus glucose in high fat diet-induced NAFLD.AIM: By engaging combined omics approaches, we sought to characterize the role of HFCS in obesity-associated NAFLD and reveal molecular processes, which mediate the exaggeration of steatosis under these conditions.METHODS: Herein, C57BL/6 mice were fed a normal-fat-diet (ND), a high-fat-diet (HFD) or a HFD supplemented with HFCS (HFD-HFCS) and upon examination of their metabolic and NAFLD phenotype, proteomic, lipidomic and metabolomic analyses were conducted to identify HFCS-related molecular alterations of the hepatic metabolic landscape in obesity.RESULTS: Although HFD and HFD-HFCS mice displayed comparable obesity, HFD-HFCS mice showed aggravation of hepatic steatosis, as analysis of the lipid droplet area in liver sections revealed (12,15 % of total section area in HFD vs 22,35 % in HFD-HFCS), increased NAFLD activity score (3,29 in HFD vs 4,86 in HFD-HFCS) and deteriorated hepatic insulin resistance, as compared to the HFD mice. Besides, the hepatic proteome of HFD-HFCS mice was characterized by a marked upregulation of 5 core proteins implicated in de novo lipogenesis (DNL), while an increased phosphatidyl-cholines(PC)/phosphatidyl-ethanolamines(PE) ratio (2.01 in HFD vs 3.04 in HFD-HFCS) was observed in the livers of HFD-HFCS versus HFD mice. Integrated analysis of the omics datasets indicated that Tricarboxylic Acid (TCA) cycle overactivation is likely contributing towards the intensification of steatosis during HFD-HFCS-induced NAFLD.CONCLUSION: Our results imply that HFCS significantly contributes to steatosis aggravation during obesity-related NAFLD, likely deriving from DNL upregulation, accompanied by TCA cycle overactivation and deteriorated hepatic insulin resistance.PMID:36996933 | DOI:10.1016/j.metabol.2023.155552

Toxicol Lett. 2023 Mar 28:S0378-4274(23)00111-X. doi: 10.1016/j.toxlet.2023.03.009. Online ahead of print.ABSTRACTINTRODUCTION: Acetyl-coenzyme A carboxylase (ACCase) inhibition is an attractive herbicide target. However, issues with fetal developmental toxicity identified at the late stages of the development process can halt progression of previously promising candidates.OBJECTIVES: To select and verify predictive lipid biomarkers of ACCase inhibition activity in vivo using liver samples obtained from early stage 7 day repeat dose studies in non-pregnant female Han Wistar rats that could be translated to developmental toxicity endpoints discovered during late-stage studies to provide an early screening tool.METHODS: Liver samples from eight rat repeat dose studies, exposed to six ACCase inhibitors from three different chemistries and one alternative mode of action (MoA) that also perturbs lipid biochemistry, were analysed using liquid chromatography - high resolution accurate mass - mass spectrometry. Multivariate and univariate data analysis methods were used for biomarker discovery and validation.RESULTS: A biomarker signature consisting of sixteen lipids biomarkers were selected. Verification of the signature as indicative of ACCase inhibition was established by demonstrating consistent perturbations in the biomarkers using two different ACCase inhibitor chemistries and the lack thereof with an alternate MoA. The fold change profile pattern was predictive of which test substance doses would or would not cause developmental toxicity.CONCLUSION: A strategy for selecting and verifying a robust signature of lipid biomarkers for predicting a toxicological end point has been described and demonstrated. Differences in lipidomic profiles correlated with developmental toxicity suggesting that indicators of a molecular initiation event resulting in pup developmental toxicity can be predicted from short term, toxicity studies conducted in non-pregnant adult female Han Wistar rats.PMID:36996930 | DOI:10.1016/j.toxlet.2023.03.009

Chemosphere. 2023 Mar 28:138539. doi: 10.1016/j.chemosphere.2023.138539. Online ahead of print.ABSTRACTThe potential risks of anti-cancer drugs such as capecitabine have attracted considerable attention due to their continuous release. Understanding the response of removal performance and protective mechanism to the presence of emerging contaminants is crucial for the application of anammox techniques in wastewater treatment. Capecitabine affected the nitrogen removal performance slightly in the activity experiment. Due to bio-adsorption and biodegradation, up to 64-70% of the capecitabine can be removed effectively. However, 10 mg/L of capecitabine significantly decreased the removal efficiency of capecitabine and total nitrogen at repeated load of capecitabine. Metabolomic analysis revealed the metabolites 5'-deoxy-5-fluorocytidine and alpha-fluoro-beta-alanine, while metagenomic analysis confirmed the biodegradation pathway and underlying gene distribution. The potentially protective mechanisms of the system against capecitabine were the increased heterotrophic bacteria and secretion of sialic acid. Blast analysis confirmed the presence of potential genes involved in the complete biosynthesis pathway of sialic acid in anammox bacteria, some of which are also found in Nitrosomonas, Thauera, and Candidatus Promineofilum.PMID:36996924 | DOI:10.1016/j.chemosphere.2023.138539

Cell. 2023 Mar 24:S0092-8674(23)00215-5. doi: 10.1016/j.cell.2023.02.037. Online ahead of print.ABSTRACTLittle is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.PMID:36996814 | DOI:10.1016/j.cell.2023.02.037

Biomed Pharmacother. 2023 Mar 28;162:114578. doi: 10.1016/j.biopha.2023.114578. Online ahead of print.ABSTRACTBACKGROUND: The peptide hormone relaxin has potent anti-fibrotic and anti-inflammatory properties in various organs, including the kidneys. However, the protective effects of relaxin in the context of diabetic kidney complications remain controversial. Here, we aimed to evaluate the effects of relaxin treatment on key markers of kidney fibrosis, oxidative stress, and inflammation and their subsequent impact on bile acid metabolism in the streptozotocin-induced diabetes mouse model.METHODS AND RESULTS: Male mice were randomly allocated to placebo-treated control, placebo-treated diabetes or relaxin-treated diabetes groups (0.5 mg/kg/d, final 2 weeks of diabetes). After 12 weeks of diabetes or sham, the kidney cortex was harvested for metabolomic and gene expression analyses. Diabetic mice exhibited significant hyperglycaemia and increased circulating levels of creatine, hypoxanthine and trimethylamine N-oxide in the plasma. This was accompanied by increased expression of key markers of oxidative stress (Txnip), inflammation (Ccl2 and Il6) and fibrosis (Col1a1, Mmp2 and Fn1) in the diabetic kidney cortex. Relaxin treatment for the final 2 weeks of diabetes significantly reduced these key markers of renal fibrosis, inflammation, and oxidative stress in diabetic mice. Furthermore, relaxin treatment significantly increased the levels of bile acid metabolites, deoxycholic acid and sodium glycodeoxycholic acid, which may in part contribute to the renoprotective action of relaxin in diabetes.CONCLUSION: In summary, this study shows the therapeutic potential of relaxin and that it may be used as an adjunctive treatment for diabetic kidney complications.PMID:36996678 | DOI:10.1016/j.biopha.2023.114578

Food Chem. 2023 Mar 15;418:135959. doi: 10.1016/j.foodchem.2023.135959. Online ahead of print.ABSTRACTWheat flour is one of the most prevalent foodstuffs for human consumption, and novel strategies are underway to enhance its nutritional properties. This work evaluated wholegrain flours from bread wheat lines with different amylose/amylopectin ratios through in vitro starch digestion and large intestine fermentation. High-amylose flours presented a higher resistant starch content and lower starch hydrolysis index. Moreover, UHPLC-HRMS metabolomics was carried out to determine the profile of the resulting in vitro fermentates. The multivariate analysis highlighted distinctive profiles between the flours derived from the different lines compared to the wild type. Peptides, glycerophospholipids, polyphenols, and terpenoids were identified as the main markers of the discrimination. The high-amylose flour fermentates showed the richest bioactive profile, containing stilbenes, carotenoids, and saponins. Present findings pave the way toward applying high-amylose flours to design novel functional foods.PMID:36996655 | DOI:10.1016/j.foodchem.2023.135959

J Pharm Biomed Anal. 2023 Mar 27;229:115369. doi: 10.1016/j.jpba.2023.115369. Online ahead of print.ABSTRACTCurrently, drugs are limited to treating pediatric pneumonia in clinical practice. It is urgent to find one new precise prevention and control therapy. The dynamically changing biomarkers during the development of pediatric pneumonia could help diagnose this disease, determine its severity, assess the risk of future events, and guide its treatment. Dexamethasone has been recognized as an effective agent with anti-inflammatory activity. However, its mechanisms against pediatric pneumonia remain unclear. In this study, spatial metabolomics was used to reveal the potential and characteristics of dexamethasone. Specifically, bioinformatics was first applied to find the critical biomarkers of differential expression in pediatric pneumonia. Subsequently, Desorption Electrospray Ionization mass spectrometry imaging-based metabolomics screened the differential metabolites affected by dexamethasone. Then, a gene-metabolite interaction network was built to mark functional correlation pathways for exploring integrated information and core biomarkers related to the pathogenesis and etiology of pediatric pneumonia. Further, these were validated by molecular biology and targeted metabolomics. As a result, genes of Cluster of Differentiation19, Fc fragment of IgG receptor IIb, Cluster of Differentiation 22, B-cell linker, Cluster of Differentiation 79B and metabolites of Triethanolamine, Lysophosphatidylcholine(18:1(9Z)), Phosphatidylcholine(16:0/16:0), phosphatidylethanolamine(O-18:1(1Z)/20:4(5Z,8Z,11Z,14Z)) were identified as the critical biomarkers in pediatric pneumonia. B cell receptor signaling pathway and glycerophospholipid metabolism were integrally analyzed as the main pathways of these biomarkers. The above data were illustrated using a Lipopolysaccharides-induced lung injury juvenile rat model. This work will provide evidence for the precise treatment of pediatric pneumonia.PMID:36996615 | DOI:10.1016/j.jpba.2023.115369

J Agric Food Chem. 2023 Mar 30. doi: 10.1021/acs.jafc.3c01014. Online ahead of print.ABSTRACTPomegranate peel polyphenols (PPPs) and inulin have been reported to have lipid-lowering effects. Here, the effects of PPPs combined with inulin on obesity traits and the change of the gut microbiota, short-chain fatty acids (SCFAs), and serum metabolomics profiles in rats with a high-fat diet (HFD) were investigated. According to the experimental results, PPPs were most effective in reducing the body weight and serum and liver lipid levels. Besides, PPPs ameliorated the disorder of gut microbiota, in particular, the enrichment of SCFA producers, such as Lactobacillus, Roseburia, Christensenellaceae_R-7_group, Ruminococcaceae_UCG-005, Bacteroides, and Allobaculum, and the depletion of the Blautia and unclassified Lachnospiraceae population. PPPs also regulated the levels of metabolites changed by HFD feeding via tryptophan metabolism, valine, leucine, and isoleucine biosynthesis, and arachidonic acid metabolism pathways. The correlation analysis showed that PPPs remitted HFD-induced elevation in triglycerides (TGs), interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-α) levels and lowered high-density lipoprotein (HDL) levels through regulating the gut microbiota, SCFAs, and related metabolites. These findings elucidated that PPPs have a good anti-obesity effect. This study extends the understanding of PPP effects on high-fat-induced obesity, which includes the relationship among gut microbiota, SCFAs, serum metabolites, and TG-, IL-6- and TNF-α- lowering and HDL-elevating functions.PMID:36996454 | DOI:10.1021/acs.jafc.3c01014

Anal Chem. 2023 Mar 30. doi: 10.1021/acs.analchem.2c04201. Online ahead of print.ABSTRACTToxicity testing is currently undergoing a paradigm shift from examining apical end points such as death, to monitoring sub-lethal toxicity in vivo. In vivo nuclear magnetic resonance (NMR) spectroscopy is a key platform in this endeavor. A proof-of-principle study is presented which directly interfaces NMR with digital microfluidics (DMF). DMF is a "lab on a chip" method allowing for the movement, mixing, splitting, and dispensing of μL-sized droplets. The goal is for DMF to supply oxygenated water to keep the organisms alive while NMR detects metabolomic changes. Here, both vertical and horizontal NMR coil configurations are compared. While a horizontal configuration is ideal for DMF, NMR performance was found to be sub-par and instead, a vertical-optimized single-sided stripline showed most promise. In this configuration, three organisms were monitored in vivo using 1H-13C 2D NMR. Without support from DMF droplet exchange, the organisms quickly showed signs of anoxic stress; however, with droplet exchange, this was completely suppressed. The results demonstrate that DMF can be used to maintain living organisms and holds potential for automated exposures in future. However, due to numerous limitations of vertically orientated DMF, along with space limitations in standard bore NMR spectrometers, we recommend future development be performed using a horizontal (MRI style) magnet which would eliminate practically all the drawbacks identified here.PMID:36996326 | DOI:10.1021/acs.analchem.2c04201

PLoS Comput Biol. 2023 Mar 30;19(3):e1010690. doi: 10.1371/journal.pcbi.1010690. Online ahead of print.ABSTRACTWe analyzed large-scale post-translational modification (PTM) data to outline cell signaling pathways affected by tyrosine kinase inhibitors (TKIs) in ten lung cancer cell lines. Tyrosine phosphorylated, lysine ubiquitinated, and lysine acetylated proteins were concomitantly identified using sequential enrichment of post translational modification (SEPTM) proteomics. Machine learning was used to identify PTM clusters that represent functional modules that respond to TKIs. To model lung cancer signaling at the protein level, PTM clusters were used to create a co-cluster correlation network (CCCN) and select protein-protein interactions (PPIs) from a large network of curated PPIs to create a cluster-filtered network (CFN). Next, we constructed a Pathway Crosstalk Network (PCN) by connecting pathways from NCATS BioPlanet whose member proteins have PTMs that co-cluster. Interrogating the CCCN, CFN, and PCN individually and in combination yields insights into the response of lung cancer cells to TKIs. We highlight examples where cell signaling pathways involving EGFR and ALK exhibit crosstalk with BioPlanet pathways: Transmembrane transport of small molecules; and Glycolysis and gluconeogenesis. These data identify known and previously unappreciated connections between receptor tyrosine kinase (RTK) signal transduction and oncogenic metabolic reprogramming in lung cancer. Comparison to a CFN generated from a previous multi-PTM analysis of lung cancer cell lines reveals a common core of PPIs involving heat shock/chaperone proteins, metabolic enzymes, cytoskeletal components, and RNA-binding proteins. Elucidation of points of crosstalk among signaling pathways employing different PTMs reveals new potential drug targets and candidates for synergistic attack through combination drug therapy.PMID:36996232 | DOI:10.1371/journal.pcbi.1010690

Metabolomics. 2023 Mar 30;19(4):31. doi: 10.1007/s11306-023-02001-1.ABSTRACTINTRODUCTION: Technological advancements enabled the analyses of limited sample volumes on 1H NMR. Manual spectral profiling of the data is, however, complex, and timely.OBJECTIVE: To evaluate the performance of BAYESIL for automated identification and quantification of 1H NMR spectra of limited volume samples.METHOD: Aliquots of a pooled African elephant serum sample were analyzed using standard and reduced volumes. Performance was evaluated on confidence scores, non-detects and laboratory CV.RESULTS: Of the 47 compounds detected, 28 had favorable performances. The approach could differentiate samples based on biological variation.CONCLUSIONS: BAYESIL is valuable for limited sample 1H NMR data analyses.PMID:36995481 | DOI:10.1007/s11306-023-02001-1

Anal Chem. 2023 Mar 30. doi: 10.1021/acs.analchem.2c05807. Online ahead of print.ABSTRACTGlioblastoma (GBM) is an incurable brain cancer with a median survival of less than two years from diagnosis. The standard treatment of GBM is multimodality therapy comprising surgical resection, radiation, and chemotherapy. However, prognosis remains poor, and there is an urgent need for effective anticancer drugs. Since different regions of a single GBM contain multiple cancer subpopulations ("intra-tumor heterogeneity"), this likely accounts for therapy failure as certain cancer cells can escape from immune surveillance and therapeutic threats. Here, we present metabolomic data generated using the Orbitrap secondary ion mass spectrometry (OrbiSIMS) technique to investigate brain tumor metabolism within its highly heterogeneous tumor microenvironment. Our results demonstrate that an OrbiSIMS-based untargeted metabolomics method was able to discriminate morphologically distinct regions (viable, necrotic, and non-cancerous) within single tumors from formalin-fixed paraffin-embedded tissue archives. Specifically, cancer cells from necrotic regions were separated from viable GBM cells based on a set of metabolites including cytosine, phosphate, purine, xanthine, and 8-hydroxy-7-methylguanine. Moreover, we mapped ubiquitous metabolites across necrotic and viable regions into metabolic pathways, which allowed for the discovery of tryptophan metabolism that was likely essential for GBM cellular survival. In summary, this study first demonstrated the capability of OrbiSIMS for in situ investigation of GBM intra-tumor heterogeneity, and the acquired information can potentially help improve our understanding of cancer metabolism and develop new therapies that can effectively target multiple subpopulations within a tumor.PMID:36995369 | DOI:10.1021/acs.analchem.2c05807

mSystems. 2023 Mar 30:e0009223. doi: 10.1128/msystems.00092-23. Online ahead of print.ABSTRACTZymomonas mobilis is an industrially relevant aerotolerant anaerobic bacterium that can convert up to 96% of consumed glucose to ethanol. This highly catabolic metabolism could be leveraged to produce isoprenoid-based bioproducts via the methylerythritol 4-phosphate (MEP) pathway, but we currently have limited knowledge concerning the metabolic constraints of this pathway in Z. mobilis. Here, we performed an initial investigation of the metabolic bottlenecks within the MEP pathway of Z. mobilis using enzyme overexpression strains and quantitative metabolomics. Our analysis revealed that 1-deoxy-d-xylulose 5-phosphate synthase (DXS) represents the first enzymatic bottleneck in the Z. mobilis MEP pathway. DXS overexpression triggered large increases in the intracellular levels of the first five MEP pathway intermediates, of which the buildup in 2-C-methyl-d-erythritol 2,4-cyclodiphosphate (MEcDP) was the most substantial. The combined overexpression of DXS, 4-hydroxy-3-methylbut-2-enyl diphosphate (HMBDP) synthase (IspG), and HMBDP reductase (IspH) mitigated the bottleneck at MEcDP and mobilized carbon to downstream MEP pathway intermediates, indicating that IspG and IspH activity become the primary pathway constraints during DXS overexpression. Finally, we overexpressed DXS with other native MEP enzymes and a heterologous isoprene synthase and showed that isoprene can be used as a carbon sink in the Z. mobilis MEP pathway. By revealing key bottlenecks within the MEP pathway of Z. mobilis, this study will aid future engineering efforts aimed at developing this bacterium for industrial isoprenoid production. IMPORTANCE Engineered microorganisms have the potential to convert renewable substrates into biofuels and valuable bioproducts, which offers an environmentally sustainable alternative to fossil-fuel-derived products. Isoprenoids are a diverse class of biologically derived compounds that have commercial applications as various commodity chemicals, including biofuels and biofuel precursor molecules. Thus, isoprenoids represent a desirable target for large-scale microbial generation. However, our ability to engineer microbes for the industrial production of isoprenoid-derived bioproducts is limited by an incomplete understanding of the bottlenecks in the biosynthetic pathway responsible for isoprenoid precursor generation. In this study, we combined genetic engineering with quantitative analyses of metabolism to examine the capabilities and constraints of the isoprenoid biosynthetic pathway in the industrially relevant microbe Zymomonas mobilis. Our integrated and systematic approach identified multiple enzymes whose overexpression in Z. mobilis results in an increased production of isoprenoid precursor molecules and mitigation of metabolic bottlenecks.PMID:36995223 | DOI:10.1128/msystems.00092-23

Sheng Wu Gong Cheng Xue Bao. 2023 Mar 25;39(3):1056-1069. doi: 10.13345/j.cjb.220548.ABSTRACTSteroids are a class of medicines with important physiological and pharmacological effects. In pharmaceutical industry, steroidal intermediates are mainly prepared through Mycobacteria transformation, and then modified chemically or enzymatically into advanced steroidal compounds. Compared with the "diosgenin-dienolone" route, Mycobacteria transformation has the advantages of abundant raw materials, cost-effective, short reaction route, high yield and environmental friendliness. Based on genomics and metabolomics, the key enzymes in the phytosterol degradation pathway of Mycobacteria and their catalytic mechanisms are further revealed, which makes it possible for Mycobacteria to be used as chassis cells. This review summarizes the progress in the discovery of steroid-converting enzymes from different species, the modification of Mycobacteria genes and the overexpression of heterologous genes, and the optimization and modification of Mycobacteria as chassis cells.PMID:36994571 | DOI:10.13345/j.cjb.220548

J Tradit Chin Med. 2023 Apr;43(2):274-285. doi: 10.19852/j.cnki.jtcm.20230201.001.ABSTRACTOBJECTIVE: To investigate the mechanism of deficiency syndrome (YDS) by analyzing the liver metabolomic characteristics of three different deficiency rat models METHODS: Following the TCM etiology, for clinical features and pathological manifestations of modern medicine, three kinds of animal models of deficiency were induced and replicated. Totally 48 Sprague-Dawley (SD) male rats were randomly divided into blank group, irritation induced model group, Fuzi-Ganjiang induced model group, and thyroxine-reserpine induced model group. After successful development of model, the ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry was carried out to detect metabolites in each group. The metabolites of rat liver were analyzed for the characteristics of their biomarkers. The pathway enrichment analysis and metabolic network construction were performed through various online databases including Metabolite Biology Role, Human Metabolome Database, MetaboAnalyst, and Kyoto Encyclopedia of Genes and Genomes.RESULTS: The SD rats in the experimental group showed symptoms like less weight gain, reduced diet and water intake, high body temperature, increased liver and kidney indexes, and abnormal liver and kidney tissue morphology. Moreover, the rats showed high increased levels of serum cyclic adenosine monophosphate, estradiol, alanine transaminase, and aspartate aminotransferase and decreased levels of cyclic guanosinc monophosphate and testosterone. We found four key interrelated metabolic pathways in the liver tissue metabolomics, including the biosynthesis of pantothenic acid and coenzyme A, and metabolism of alpha-linolenic acid metabolism, glycerophospholipid metabolism, and sphingolipid.CONCLUSION: The liver and kidney YDS is closely related to the biosynthesis of pantothenic acid and CoA and abnormal metabolism of α-linolenic acid, glycerophospholipid, and sphingolipid in SD rats.PMID:36994515 | DOI:10.19852/j.cnki.jtcm.20230201.001