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

Characterization of the metabolomic profile of renal cell carcinoma by high resolution magic angle spinning proton magnetic resonance spectroscopy

Fri, 20/10/2023 - 12:00
Urol Oncol. 2023 Oct 19:S1078-1439(23)00305-8. doi: 10.1016/j.urolonc.2023.09.005. Online ahead of print.ABSTRACTBACKGROUND: Renal cell carcinoma (RCC) is a metabolic disease, with subtypes exhibiting aberrations in different metabolic pathways. Metabolomics may offer greater sensitivity for revealing disease biology. We investigated the metabolomic profile of RCC using high-resolution magic angle spinning (HRMAS) proton magnetic resonance spectroscopy (1HMRS).METHODS: Surgical tissue samples were obtained from our frozen tissue bank, collected from radical or partial nephrectomy. Specimens were fresh-frozen, then stored at -80 °C until analysis. Tissue HRMAS-1HMRS was performed. A MatLab-based curve fitting program was used to process the spectra to produce relative intensities for 59 spectral regions of interest (ROIs). Comparisons of the metabolomic profiles of various RCC histologies and benign tumors, angiomyolipoma, and oncocytoma, were performed. False discovery rates (FDR) were used from the response screening to account for multiple testing; ROIs with FDR p < 0.05 were considered potential predictors of RCC. Wilcoxon rank sum test was used to compare median 1HMRS relative intensities for those metabolites that may differentiate between RCC and benign tumor. Logistic regression determined odds ratios for risk of malignancy based on the abundance of each metabolite.RESULTS: Thirty-eight RCC (16 clear cell, 11 papillary, 11 chromophobe), 10 oncocytomas, 7 angiomyolipomas, and 13 adjacent normal tissue specimens (matched pairs) were analyzed. Candidate metabolites for predictors of malignancy based on FDR p-values include histidine, phenylalanine, phosphocholine, serine, phosphocreatine, creatine, glycerophosphocholine, valine, glycine, myo-inositol, scyllo-inositol, taurine, glutamine, spermine, acetoacetate, and lactate. Higher levels of spermine, histidine, and phenylalanine at 3.15 to 3.13 parts per million (ppm) were associated with decreased risk of RCC (OR 4 × 10-5, 95% CI 7.42 × 10-8, 0.02), while 2.84 to 2.82 ppm increased the risk of malignant pathology (OR 7158.67, 95% CI 6.3, 8.3 × 106). The specific metabolites characterizing this region remain to be identified. Tumor stage did not affect metabolomic profile of malignant tumors, suggesting that metabolites are dependent on histologic subtype.CONCLUSIONS: HRMAS-1HMRS identified metabolites that may predict RCC. We demonstrated that those in the 3.14 to 3.13 ppm ROI were present in lower levels in RCC, while higher levels of metabolites in the 2.84 to 2.82 ppm ROI were associated with substantially increased risk of RCC. Further research in a larger population is required to validate these findings.PMID:37863744 | DOI:10.1016/j.urolonc.2023.09.005

Characteristics of gut microbiota and metabolic phenotype in patients with major depressive disorder based on multi-omics analysis

Fri, 20/10/2023 - 12:00
J Affect Disord. 2023 Oct 18:S0165-0327(23)01294-6. doi: 10.1016/j.jad.2023.10.104. Online ahead of print.ABSTRACTDepression is a chronic, relapsing mental illness, often accompanied by loss of appetite, increased fatigue, insomnia and poor concentration. Here, we performed serum and urine metabolomics and fecal 16S rDNA sequencing studies on 57 unmedicated patients with major depressive disorder (MDD) and 57 healthy controls to characterize the metabolic and flora profile of MDD patients. We observed significant differences in serum and urinary metabolome between MDD patients and healthy individuals. Specifically, glycerophospholipid metabolism, primary bile acid biosynthesis and linoleic acid metabolism were significantly disordered in serum, and aminoacyl-tRNA biosynthesis, arginine biosynthesis, purine metabolism, phenylalanine metabolism, alanine, aspartate and glutamate metabolism, and pyrimidine metabolism were significantly impaired in urine. On this basis, we identified four potential diagnostic biomarkers for carnitine and four fatty acid classes in serum and urine, respectively. In addition, we observed significant disturbances of the gut microbiota in MDD patients. Spearman correlation analysis showed that imbalances in the gut microbiota were associated with metabolic disturbances, suggesting an important role of the gut microbiota in the pathogenesis of MDD. Our study provides a theoretical basis for further understanding of the pathogenesis of depression and for future clinical diagnosis and screening, as well as a basis for targeting the gut flora to optimize its structure for the prevention and treatment of depression.PMID:37863362 | DOI:10.1016/j.jad.2023.10.104

Assessing stress responses in potherb mustard (Brassica juncea var. multiceps) exposed to a synergy of microplastics and cadmium: Insights from physiology, oxidative damage, and metabolomics

Fri, 20/10/2023 - 12:00
Sci Total Environ. 2023 Oct 18:167920. doi: 10.1016/j.scitotenv.2023.167920. Online ahead of print.ABSTRACTBoth microplastics (MPs) and cadmium (Cd) are common contaminants in farmland systems, is crucial for assessing their risks for human health and environment, and little research has focused on stress responses mechanisms of crops exposed to the combined pollution. The present study investigated the impact of polyethylene (PE) and polypropylene (PP) microplastics (MPs), in combination with Cd, on the physiological and metabolomic changes as well as rhizosphere soil of potherb mustard. Elevated levels of PEMPs and PPMPs were found to impede nutrient uptake in plants while promoting premature flowering, and the concomitant effect is lower crop yields. The substantial improvement in Cd bioavailability facilitated by MPs in rhizosphere soil, especially in high concentrations of MPs, then elevated bioavailability of Cd contributed to promoted Cd accumulation in plants, with distinct effects depending on the type and concentration of MPs. The presence of MPs Combined exposure to high concentrations of MPs and Cd resulted in alterations in plant physiology and metabolomics, including decreased biomass and photosynthetic parameters, elevated levels of reactive oxygen species primarily H2O2, increased antioxidant enzyme activities, and modifications in metabolite profiles. Overall, our study assessed the potential impact on food security (the availability of cadmium to plant) and crops stress responses regarding the contamination of MPs and Cd, providing new insights for future risk assessment in agriculture.PMID:37863229 | DOI:10.1016/j.scitotenv.2023.167920

Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil

Fri, 20/10/2023 - 12:00
Sci Total Environ. 2023 Oct 18:167832. doi: 10.1016/j.scitotenv.2023.167832. Online ahead of print.ABSTRACTGenotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.PMID:37863223 | DOI:10.1016/j.scitotenv.2023.167832

Integration of 16S rRNA gene sequencing and LC/MS-based metabolomic analysis of early biomarkers of acute stroke in Tibetan miniature pigs

Fri, 20/10/2023 - 12:00
J Microbiol Methods. 2023 Oct 18:106846. doi: 10.1016/j.mimet.2023.106846. Online ahead of print.ABSTRACTAcute ischaemic stroke (AIS) is a complex, systemic, pathological, and physiological process. Systemic inflammatory responses and disorders of the gut microbiome contribute to increased mortality and disability following AIS. We conducted 16S high-throughput sequencing and ultra-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry-based non-targeted metabolomic analyses of the plasma from a Tibetan miniature pig middle cerebral artery occlusion (MCAO) model. A significant decrease in the abundance of Firmicutes and a significant increase in the abundance of Actinobacteria were observed after the onset of AIS. Among the plasma metabolites, the levels of phospholipids and amino acids were considerably altered. Loading values and differential metabolite-bacterial group association analyses of the metabolome and microbiome indicated a correlation between the microbiome and metabolome of Tibetan miniature pigs after MCAO. Furthermore, significant changes were observed in the ABC transporter pathway and purine metabolism in the gut microbiome-plasma metabolome during the early stage of AIS. Kyoto Encyclopaedia of Genes and Genomes enrichment analysis showed that arginine, proline, and cyanoamino acid metabolism was upregulated while ABC transporter metabolism pathway and carbohydrate digestion and absorption were substantially downregulated. The results of this study suggest that AIS affects the gut microbiota and plasma metabolites in Tibetan miniature pigs and that faecal microbiota transplantation could be a potential therapeutic approach for AIS.PMID:37863204 | DOI:10.1016/j.mimet.2023.106846

Integrating proteomics and metabolomics to elucidate the molecular network regulating of inosine monophosphate-specific deposition in Jingyuan chicken

Fri, 20/10/2023 - 12:00
Poult Sci. 2023 Sep 23;102(12):103118. doi: 10.1016/j.psj.2023.103118. Online ahead of print.ABSTRACTInosine monophosphate (IMP) plays a significant role in meat taste, yet the molecular mechanisms controlling IMP deposition in muscle tissues still require elucidation. The present study systematically and comprehensively explores the molecular network governing IMP deposition in different regions of Jingyuan chicken muscle. Two muscle groups, the breast and leg, were examined as test materials. Using nontargeted metabolomic sequencing, we screened and identified 20 metabolites that regulate IMP-specific deposition. We maintained regular author and institution formatting, used clear, objective, and value-neutral language, and avoided biased or emotional language. We followed a consistent footnote style and formatting features and used precise word choice with technical terms where appropriate. Out of these, 5 were identified as significant contributors to the regulation of IMP deposition. We explained technical term abbreviations when first used and ensured a logical flow of information with causal connections between statements. The results indicate that PGM1, a key enzyme involved in synthesis, is higher in the breast muscle compared to the leg muscle, which may provide an explanation for the increased deposition of IMP in the breast muscle. We aimed for a clear structure with logical progression, avoided filler words, and ensured grammatical correctness. The activity of key enzymes (PKM2, AK1, AMPD1) involved in this process was higher in the breast muscle than in the leg muscle. In the case of IMP degradation metabolism, the activity of its participating enzyme (PurH) was lower in the breast muscle than in the leg muscle. These findings suggest that the increased deposition of IMP in Jingyuan chickens' breast muscle may result from elevated metabolism and reduced catabolism of key metabolites. In summary, a metaomic strategy was utilized to assess the molecular network regulation mechanism of IMP-specific deposition in various segments of Jingyuan chicken. These findings provide insight into genetic improvement and molecular breeding of meat quality traits for top-notch broilers.PMID:37862870 | DOI:10.1016/j.psj.2023.103118

Publisher Correction: Inhibition of fatty acid oxidation enables heart regeneration in adult mice

Fri, 20/10/2023 - 12:00
Nature. 2023 Oct 20. doi: 10.1038/s41586-023-06755-5. Online ahead of print.NO ABSTRACTPMID:37863963 | DOI:10.1038/s41586-023-06755-5

Structural basis for recruitment of TASL by SLC15A4 in human endolysosomal TLR signaling

Fri, 20/10/2023 - 12:00
Nat Commun. 2023 Oct 20;14(1):6627. doi: 10.1038/s41467-023-42210-9.ABSTRACTToll-like receptors (TLRs) are a class of proteins that play critical roles in recognizing pathogens and initiating innate immune responses. TASL, a recently identified innate immune adaptor protein for endolysosomal TLR7/8/9 signaling, is recruited by the lysosomal proton-coupled amino-acid transporter SLC15A4, and then activates IRF5, which in turn triggers the transcription of type I interferons and cytokines. Here, we report three cryo-electron microscopy (cryo-EM) structures of human SLC15A4 in the apo monomeric and dimeric state and as a TASL-bound complex. The apo forms are in an outward-facing conformation, with the dimeric form showing an extensive interface involving four cholesterol molecules. The structure of the TASL-bound complex reveals an unprecedented interaction mode with solute carriers. During the recruitment of TASL, SLC15A4 undergoes a conformational change from an outward-facing, lysosomal lumen-exposed state to an inward-facing state to form a binding pocket, allowing the N-terminal helix of TASL to be inserted into. Our findings provide insights into the molecular basis of regulatory switch involving a human solute carrier and offers an important framework for structure-guided drug discovery targeting SLC15A4-TASL-related human autoimmune diseases.PMID:37863913 | DOI:10.1038/s41467-023-42210-9

Integrated transcriptomic, proteomic and metabolomic analysis provides new insights into tetracycline stress tolerance in pumpkin

Fri, 20/10/2023 - 12:00
Environ Pollut. 2023 Oct 18:122777. doi: 10.1016/j.envpol.2023.122777. Online ahead of print.ABSTRACTThe aim of this study was to conduct transcriptomic, proteomic, and metabolomic analysis to provide a comprehensive view of plant response to tetracycline stress. Pumpkin seeds were cultured for 7 days without or with tetracycline at 10 mg/L. Pumpkin roots showed excessive growth inhibition, but not yet strong growth restraining in cotylendons. Tetracycline affected the abundance of metabolites related to flavonoid biosynthesis and amino acid metabolism. Main changes of metabolites in flavonoid biosynthesis were consistent with mRNA changes. Amino acid changes are mainly mediated by proteins or mRNAs. To be specific, tetracycline treatment increased the levels of rutin, caffeate, cinnamaldehyde, 4-hydroxycinnamic acid, ferulic acid, naringenin, apigenin, luteolin, (-)-epigallocatechin, astragalin, L-serine, and glutathione and the transcript levels related to these compounds; and decreased the levels of indole pyruvate, indole acetaldehyde, L-arginine, S-adenosylhomocysteine, L-glutamine, and gamma-glutamylcysteine and the transcript levels related to these compounds. Tetracycline treatment also increased the levels of oxoglutaric acid, L-glutamic acid, gamma-aminobutyric acid, and gamma-glutamylalanine and enzymes involved in their production; and decreased the levels of L-isoleucine, L-valine, and L-leucine and enzymes involved in their production. We elucidated several biological processes (e.g. phenylpropanoid/flavonoid biosynthesis pathways, amino acid metabolic pathways) that were altered by tetracycline, and provided a multi-omic perspective on the mechanisms underlying the response to tetracycline stress in pumpkin roots. We provide a useful reference for the development of environmental quality management methods.PMID:37863256 | DOI:10.1016/j.envpol.2023.122777

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring

Fri, 20/10/2023 - 12:00
Cancer Cell. 2023 Oct 16:S1535-6108(23)00328-8. doi: 10.1016/j.ccell.2023.09.012. Online ahead of print.ABSTRACTTumor microbiota can produce active metabolites that affect cancer and immune cell signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome features that affect chemoradiation response in patients with cervical cancer using a combined approach of deep microbiome sequencing, targeted bacterial culture, and in vitro assays. We identify that an obligate L-lactate-producing lactic acid bacterium found in tumors, Lactobacillus iners, is associated with decreased survival in patients, induces chemotherapy and radiation resistance in cervical cancer cells, and leads to metabolic rewiring, or alterations in multiple metabolic pathways, in tumors. Genomically similar L-lactate-producing lactic acid bacteria commensal to other body sites are also significantly associated with survival in colorectal, lung, head and neck, and skin cancers. Our findings demonstrate that lactic acid bacteria in the tumor microenvironment can alter tumor metabolism and lactate signaling pathways, causing therapeutic resistance. Lactic acid bacteria could be promising therapeutic targets across cancer types.PMID:37863066 | DOI:10.1016/j.ccell.2023.09.012

A new insight into mechanism of colchicine poisoning based on untargeted metabolomics

Fri, 20/10/2023 - 12:00
Phytomedicine. 2023 Oct 6;122:155122. doi: 10.1016/j.phymed.2023.155122. Online ahead of print.ABSTRACTBACKGROUND: Colchicine (COL) is a well-known plant-derived mitogenic toxin that has been widely applied for the treatment of immune system diseases and various cancers. However, its clinical use is severely limited by frequent occurrence of poisoning accidents, and the mechanism of COL poisoning is not clear yet.PURPOSE: The present study aimed to unveil how COL works as a toxin based on untargeted metabolomics analysis of animal models and clinical human case.METHODS: KM mice orally administered COL were used to establish poisoning models, and plasma samples were collected for untargeted metabolomics analysis. The data mining was performed to screen dose-dependent differences and disturbed metabolic pathways. The blood samples collected from clinical COL poisoning human case at various time points during treatment period were further analyzed to investigate the temporal changes in the metabolic disposition of COL in vivo and also verify the findings from mice. Finally, the expression of key pathways was evaluated by ELISA and Western blotting analysis.RESULTS: Histological examination demonstrated systemic toxicity of COL poisoning in mice. Metabolite profiling analysis of plasma samples from model mice and clinical case both revealed that COL poisoning could significantly disturb in vivo metabolism of amino acid and lipid metabolism by the FXR/AMPK signal pathway. Quantitative monitoring of the metabolic process of COL further demonstrated that it could be greatly ameliorated with the rapid metabolic transformation of COL in vivo, which thus may be an effective detoxification pathway for COL poisoning.CONCLUSION: The findings of the present study provided new insight into the molecular mechanism of COL poisoning, thus helpful for guiding reasonable application of this phytotoxin.PMID:37863002 | DOI:10.1016/j.phymed.2023.155122

Insight into the effect of cultivar and altitude on the identification of EnshiYulu tea grade in untargeted metabolomics analysis

Fri, 20/10/2023 - 12:00
Food Chem. 2023 Oct 14;436:137768. doi: 10.1016/j.foodchem.2023.137768. Online ahead of print.ABSTRACTThe accurate identification of tea grade is crucial to the quality control of tea. However, existing methods lack sufficient generalization ability in identifying tea grades due to the effect of temporal and spatial factors. In this study, we analyzed the effect of cultivar and altitude on EnshiYulu (ESYL) tea grades and established a robust model to evaluate their quality. Principal component analysis (PCA) revealed that differences in variety and elevation can mask grade differences. Orthogonal projection to latent structure-discriminant analysis (OPLS-DA) was used for grade identification of samples from different altitudes. For ESYL tea samples above and below 800 m altitude, 75 and 35 grade differentiated metabolites were discovered, with 14 common differentiated metabolites. Based on reconstructed OPLS-DA models, the grades of multi-altitude sources ESYL were discriminated with a rate > 85%. These results demonstrate the potential of a grade discrimination model based on common differential metabolites, which exhibits generalization ability.PMID:37862999 | DOI:10.1016/j.foodchem.2023.137768

Combined effects of temperature and emersion-immersion cycles on metabolism and bioenergetics of the Pacific oyster Crassostrea (Magallana) gigas

Fri, 20/10/2023 - 12:00
Mar Environ Res. 2023 Oct 16;192:106231. doi: 10.1016/j.marenvres.2023.106231. Online ahead of print.ABSTRACTLife on tidal coasts presents physiological major challenges for sessile species. Fluctuations in oxygen and temperature can affect bioenergetics and modulate metabolism and redox balance, but their combined effects are not well understood. We investigated the effects of intermittent hypoxia (12h/12h) in combination with different temperature regimes (normal (15 °C), elevated (30 °C) and fluctuating (15 °C water/30 °C air)) on the Pacific oyster Crassostrea (Magallana) gigas. Fluctuating temperature led to energetic costly metabolic rearrangements and accumulation of proteins in oyster tissues. Elevated temperature led to high (60%) mortality and oxidative damage in survivors. Normal temperature had no major negative effects but caused metabolic shifts. Our study shows high plasticity of oyster metabolism in response to oxygen and temperature fluctuations and indicates that metabolic adjustments to oxygen deficiency are strongly modulated by the ambient temperature. Co-exposure to constant elevated temperature and intermittent hypoxia demonstrates the limits of this adaptive metabolic plasticity.PMID:37862760 | DOI:10.1016/j.marenvres.2023.106231

High temperature stress induced oxidative stress, gut inflammation and disordered metabolome and microbiome in tsinling lenok trout

Fri, 20/10/2023 - 12:00
Ecotoxicol Environ Saf. 2023 Oct 18;266:115607. doi: 10.1016/j.ecoenv.2023.115607. Online ahead of print.ABSTRACTTsinling lenok trout (Brachymystax lenok tsinlingensis Li) is a species of cold-water salmon that faces serious challenges due to global warming. High temperature stress has been found to damage the gut integrity of cold-water fish, impacting their growth and immunity. However, limited research exists on the causal relationship between gut microbial disturbance and metabolic dysfunction in cold-water fish induced by high temperature stress. To address this gap, we conducted a study to investigate the effects of high temperature stress (24 °C) on the gut tissue structure, antioxidant capacity, gut microorganisms, and metabolome reactions of tsinling lenok trout. Our analysis using 16 S rDNA gene sequencing revealed significant changes in the gut microbial composition and metabolic profile. Specifically, the abundance of Firmicutes and Gemmatimonadetes decreased significantly with increasing temperature, while the abundance of Bacteroidetes increased significantly. Metabolic analysis revealed a significant decrease in the abundance of glutathione, which is synthesized from glutamate and glycine, under high temperature stress. Additionally, there was a notable reduction in the levels of adenosine, inosine, xanthine, guanosine, and deoxyguanosine, which are essential for DNA/RNA synthesis. Conversely, there was a significant increase in the abundance of D-glucose 6 P. Furthermore, high temperature stress adversely affects intestinal structure and barrier function. Our findings provide valuable insights into the mechanism of high temperature stress in cold-water fish and serve as a foundation for future research aimed at mitigating the decline in production performance caused by such stress.PMID:37862746 | DOI:10.1016/j.ecoenv.2023.115607

Divergent Skeletal Muscle Metabolomic Signatures of Different Exercise Training Modes Independently Predict Cardiometabolic Risk Factors

Fri, 20/10/2023 - 12:00
Diabetes. 2023 Oct 20:db230142. doi: 10.2337/db23-0142. Online ahead of print.ABSTRACTWe investigated the link between enhancement of insulin sensitivity (SI) (by hyperinsulinemiceuglycemic clamp) and muscle metabolites following 12-weeks of aerobic (high-intensity interval training, HIIT), resistance (RT), or combined (CT) exercise training in 52 lean healthy people. Muscle RNA-sequencing revealed a significant association between SI following both HIIT and RT and the branched chain amino acid (BCAA) metabolic pathway. Concurrent to increased expression and activity of branched chain ketoacid dehydrogenase enzyme, many muscle amino metabolites including BCAAs, glutamate, phenylalanine, aspartate, asparagine, methionine, and GABA increased by HIIT, supporting substantial impact of HIIT on amino acid metabolism. Short-chain C3 and C5 acylcarnitines were reduced in muscle by all three training modes, but unlike RT, both HIIT and CT increased TCA metabolites and cardiolipins, supporting greater mitochondrial activity by aerobic training. Conversely, RT and CT increased more plasma membrane phospholipids than HIIT, suggesting a resistance exercise effect on cellular membrane protection against environmental damage. Sex and age contributed modestly to the exerciseinduced changes in metabolites and their association to cardiometabolic parameters. Integrated transcriptomic and metabolomic analyses suggest various clusters of genes and metabolites are involved in distinct effects of HIIT, RT, and CT. These distinct metabolic signatures of different exercise modes independently link each type of exercise training to improved SI and cardiometabolic risk.PMID:37862464 | DOI:10.2337/db23-0142

The murine retinal pigment epithelium requires peroxisomal β-oxidation to maintain lysosomal function and prevent dedifferentiation

Fri, 20/10/2023 - 12:00
Proc Natl Acad Sci U S A. 2023 Oct 24;120(43):e2301733120. doi: 10.1073/pnas.2301733120. Epub 2023 Oct 20.ABSTRACTRetinal pigment epithelium (RPE) cells have to phagocytose shed photoreceptor outer segments (POS) on a daily basis over the lifetime of an organism, but the mechanisms involved in the digestion and recycling of POS lipids are poorly understood. Although it was frequently assumed that peroxisomes may play an essential role, this was never investigated. Here, we show that global as well as RPE-selective loss of peroxisomal β-oxidation in multifunctional protein 2 (MFP2) knockout mice impairs the digestive function of lysosomes in the RPE at a very early age, followed by RPE degeneration. This was accompanied by prolonged mammalian target of rapamycin activation, lipid deregulation, and mitochondrial structural anomalies without, however, causing oxidative stress or energy shortage. The RPE degeneration caused secondary photoreceptor death. Notably, the deterioration of the RPE did not occur in an Mfp2/rd1 mutant mouse line, characterized by absent POS shedding. Our findings prove that peroxisomal β-oxidation in the RPE is essential for handling the polyunsaturated fatty acids present in ingested POS and shed light on retinopathy in patients with peroxisomal disorders. Our data also have implications for gene therapy development as they highlight the importance of targeting the RPE in addition to the photoreceptor cells.PMID:37862382 | DOI:10.1073/pnas.2301733120

Discovery of Modified Metabolites, Secondary Metabolites, and Xenobiotics by Structure-Oriented LC-MS/MS

Fri, 20/10/2023 - 12:00
Chem Res Toxicol. 2023 Oct 20. doi: 10.1021/acs.chemrestox.3c00209. Online ahead of print.ABSTRACTExogenous compounds and metabolites derived from therapeutics, microbiota, or environmental exposures directly interact with endogenous metabolic pathways, influencing disease pathogenesis and modulating outcomes of clinical interventions. With few spectral library references, the identification of covalently modified biomolecules, secondary metabolites, and xenobiotics is a challenging task using global metabolomics profiling approaches. Numerous liquid chromatography-coupled mass spectrometry (LC-MS) small molecule analytical workflows have been developed to curate global profiling experiments for specific compound groups of interest. These workflows exploit shared structural moiety, functional groups, or elemental composition to discover novel and undescribed compounds through nontargeted small molecule discovery pipelines. This Review introduces the concept of structure-oriented LC-MS discovery methodology and aims to highlight common approaches employed for the detection and characterization of covalently modified biomolecules, secondary metabolites, and xenobiotics. These approaches represent a combination of instrument-dependent and computational techniques to rapidly curate global profiling experiments to detect putative ions of interest based on fragmentation patterns, predictable phase I or phase II metabolic transformations, or rare elemental composition. Application of these methods is explored for the detection and identification of novel and undescribed biomolecules relevant to the fields of toxicology, pharmacology, and drug discovery. Continued advances in these methods expand the capacity for selective compound discovery and characterization that promise remarkable insights into the molecular interactions of exogenous chemicals with host biochemical pathways.PMID:37862059 | DOI:10.1021/acs.chemrestox.3c00209

Light-driven Metabolic Pathways in Non-photosynthetic Biohybrid Bacteria

Fri, 20/10/2023 - 12:00
Chembiochem. 2023 Oct 20:e202300572. doi: 10.1002/cbic.202300572. Online ahead of print.ABSTRACTBiomanufacturing via microorganisms relies on carbon substrates for molecular feedstocks and a source of energy to carry out enzymatic reactions. This creates metabolic bottlenecks and lowers the efficiency for substrate conversion. Nanoparticle biohybridization with proteins and whole cell surfaces can bypass the need for redox cofactor regeneration for improved secondary metabolite production in a non-specific manner. Here we propose using nanobiohybrid organisms (Nanorgs), intracellular protein-nanoparticle hybrids formed through the spontaneous coupling of core-shell quantum dots (QDs) with histidine-tagged enzymes in non-photosynthetic bacteria, for light-mediated control of bacterial metabolism. This proved to eliminate metabolic constrictions and replace glucose with light as the source of energy in Escherichia coli, with an increase of growth by 1.7-fold in 75 % reduced nutrient media. Metabolomic tracking through carbon isotope labeling confirmed flux shunting through targeted pathways, with accumulation of metabolites downstream of respective targets. Finally, application of Nanorgs with the Ehrlich pathway improved isobutanol titers/yield by 3.9-fold in 75 % less carbon source from E. coli strains with no genetic alterations. These results demonstrate the promise of Nanorgs for metabolic engineering and low-cost biomanufacturing.PMID:37861981 | DOI:10.1002/cbic.202300572

Mechanism Exploration of Euphorbia fischeriana Steud. for Liver Cancer Based on Aspartic Acid Identification in Metabolomics

Fri, 20/10/2023 - 12:00
Chin J Integr Med. 2023 Oct 20. doi: 10.1007/s11655-023-3706-0. Online ahead of print.ABSTRACTOBJECTIVE: To investigate the anti-liver cancer effects and aspartic acid (Asp)-related action mechanism of Euphorbia fischeriana Steud. (Lang Du, LD).METHODS: The mice model of liver cancer was established by injection of H22 cells. After 5 days, mice were randomly divided into model group, sorafenib group (20 mg/kg), LD high-dose (LDH, 1.36 g/kg) group, LD medium-dose (LDM, 0.68 g/kg) group, and LD low-dose (LDL, 0.34 g/kg) group, 10 mice each group. Drugs were intragastrically administered to the mice once daily for 10 days, respectively. Body weight, tumor size and tumor weight were recorded. Hepatic index was calculated. Pathological changes of liver cancer tissues were evaluated by hematoxylin and eosin staining and TUNEL staining. Liquid chromatography-mass spectrometer was used to analyze different metabolites between the model and LDH groups.RESULTS: After LD treatment, tumor weight, tumor size and hepatic index were reduced compared with the model group. Necrocytosis and karyorrhexis of tumor cells were found. Moreover, 61 differential metabolites (18 up-regulated, 43 down-regulated) were affirmed and 20 pathways of KEGG (P<0.05) were gotten. In addition, Bel-7402, HepG2 and H22 cell viabilities were significantly increased after adding Asp into the medium. And then, the cell proliferation effect induced by Asp was ameliorated by LD.CONCLUSION: The anti-liver cancer efficacy of LD extract was validated in H22 mice model, and inhibition of Asp level might be the underlying mechanism.PMID:37861961 | DOI:10.1007/s11655-023-3706-0

Green Pea (<em>Pisum sativum</em> L.) Hull Polyphenol Extract Alleviates NAFLD through VB6/TLR4/NF-κB and PPAR Pathways

Fri, 20/10/2023 - 12:00
J Agric Food Chem. 2023 Oct 20. doi: 10.1021/acs.jafc.3c02337. Online ahead of print.ABSTRACTGreen pea hull is a processing byproduct of green pea and rich in polyphenols. Nonalcoholic fatty liver disease (NAFLD) is a chronic metabolic disease characterized by accumulation of lipids in the liver for which there are no effective treatment strategies. Here, a mouse model of NAFLD induced by a DSS+high-fat diet (HFD) was established to investigate the effect of green pea hull polyphenol extract (EGPH). The results show that EGPH relief of NAFLD was a combined effect, including reducing hepatic fat accumulation, improving antioxidant activity and blood lipid metabolism, and maintaining glucose homeostasis. Increased intestinal permeability aggravated NAFLD. Combined metabolomics and transcriptomic analysis showed that vitamin B6 is the key target substance for EGPH to alleviate NAFLD, and it may be the intestinal flora metabolite. After EGPH intervention, the level of vitamin B6 in mice was significantly increased, and more than 60% in the blood enters the liver, which activated or inhibited PPAR and TLR4/NF-κB signaling pathways to relieve NAFLD. Our research could be a win-win for expanding the use of green pea hull and the search for NAFLD prophylactic drugs.PMID:37861789 | DOI:10.1021/acs.jafc.3c02337

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