PubMed

Diabetes Res Clin Pract. 2023 Feb 16:110578. doi: 10.1016/j.diabres.2023.110578. Online ahead of print.ABSTRACTAIMS: To uncover novel candidate metabolomic and lipidomic biomarkers in newly-diagnosed type 1 diabetes (T1DM) after achieving optimal glucose control.METHODS: Comprehensive lipidomic and metabolomic analysis was performed in serum of 12 adults with T1DM at onset and after achieving optimal glycemic control (HbA1c <7%) (after 2-6 months).RESULTS: After intensive therapy, subjects (mean age 25.2 years, 58.3% men) showed decreases in blood glucose (p<0.001), HbA1c [11.5% (9.2 - 13.4) to 6.2% (5.2 - 6.7); p<0.001] and changes in 51 identified lipids. Among these changes, we found that triglycerides (TG) containing medium chain fatty acids (TG45:0, TG47:1), sphingomyelins (SM) (SM(d18:2/20:0), SM42:4)), and phosphatidylcholines (PC) (PC(O-26:2), PC(O-30:0), PC(O-32:0), PC(O-42:6), PC(O-44:5), PC(O-38:3), PC(O-33:0), PC(O-46:8), PC(O-44:6), PC(O-40:3), PC(O-42:4), PC(O-46:7), PC(O-46:6), PC(O-44:5), PC(O-42:3), PC(O-44:4)) decreased; whereas PC(35:1), PC(37:1) and TG containing longer chain fatty acids (TG(52:1), TG(55:7), TG(51:2), TG(53:3), TG52:2), TG(53:2), TG(57:3), TG(61:3), TG(61:2) increased. Further, dihydro O-acylceramide (18:1/18:0/16:0), diacylglycerophosphoethanolamine (PE(34:1)), diacylglycerophosphoinositol (PI(38:6), and dihydrosphingomyelins (dihydroSM(36:0), dihydroSM(40:0), dihydroSM(41:0), dihydroSM(42:0)) increased. Uric acid, mannitol, and mannitol-1-acetate levels also increased.CONCLUSIONS: Our data uncovered potential favorable changes in the metabolism of glycerophospholipids, glycerolipids, and sphingolipids in new-onset T1DM after achieving optimal glycemic control. Further research on their potential role in developing diabetes-related complications is needed.PMID:36804334 | DOI:10.1016/j.diabres.2023.110578

Chemosphere. 2023 Feb 15:138166. doi: 10.1016/j.chemosphere.2023.138166. Online ahead of print.ABSTRACTThe increasing application of engineered nanomaterials (ENMs) unavoidably leads to environmental release and biological exposure. Understanding the potential hazards of ENMs on crops is essential for appropriate utilization and management. Herein, rice seedlings were hydroponically exposed to molybdenum sulfide (MoS2, a typical ENM) nanosheets at 5-20 mg/L for 7 days and then depurated for another 7 days in a fresh culture medium. Exposure to MoS2 triggered irreversible reductions in root length (by 26.3%-69.9%) and tip number (by 22.2%-66.0%). Integration of biochemical assays, transcriptomic and metabolomics found that oxidative stress induced by MoS2 in roots was persistent, whereas the activation of aquaporins, ionic transportation, and energy synthesis was normalized due to the recovery of nutrient uptake. The down-regulated levels of genes and metabolites associated with peroxidases, hemicellulose synthesis, expansins, and auxins caused persistent structural damages (sclerosis and rupture) of root cell walls. Approximately 64.5%-84.8% of internalized MoS2 nanosheets were degraded, and the successive up-regulation of genes encoding cytochrome P450s and glutathione S-transferases reflected the biotransformation and detoxification of MoS2 in the depuration period. These findings provide novel insights into the persistence and recovery of MoS2 phytotoxicity, which will help advance the risk assessment of MoS2 application on environment.PMID:36804254 | DOI:10.1016/j.chemosphere.2023.138166

Hortic Res. 2023 Feb 21;10(4):uhad028. doi: 10.1093/hr/uhad028. eCollection 2023 Apr.ABSTRACTTea is one of the most popular healthy and non-alcoholic beverages worldwide. Tea anthracnose is a disease in tea mature leaves and ultimately affects yield and quality. Colletotrichum camelliae is a dominant fungal pathogen in the tea field that infects tea plants in China. The pathogenic factors of fungus and the susceptible factors in the tea plant are not known. In this work, we performed molecular and genetic studies to observe a cerato-platanin protein CcCp1 from C. camelliae, which played a key role in fungal pathogenicity. △CcCp1 mutants lost fungal virulence and reduced the ability to produce conidia. Transcriptome and metabolome were then performed and analysed in tea-susceptible and tea-resistant cultivars, Longjing 43 and Zhongcha 108, upon C. camelliae wild-type CCA and △CcCp1 infection, respectively. The differentially expressed genes and the differentially accumulated metabolites in tea plants were clearly overrepresented such as linolenic acid and linoleic acid metabolism, glycerophospholipid metabolism, phenylalanine biosynthesis and metabolism, biosynthesis of flavonoid, flavone and flavonol etc. In particular, the accumulation of jasmonic acid was significantly increased in the susceptible cultivar Longjing 43 upon CCA infection, in the fungal CcCp1 protein dependent manner, suggesting the compound involved in regulating fungal infection. In addition, other metabolites in the glycerophospholipid and phenylalanine pathway were observed in the resistant cultivar Zhongcha 108 upon fungal treatment, suggesting their potential role in defense response. Taken together, this work indicated C. camelliae CcCp1 affected the tea plant lipid metabolism pathway to promote disease while the lost function of CcCp1 mutants altered the fungal virulence and plant response.PMID:37090093 | PMC:PMC10117433 | DOI:10.1093/hr/uhad028

Enzyme Microb Technol. 2023 Feb 11;165:110212. doi: 10.1016/j.enzmictec.2023.110212. Online ahead of print.ABSTRACTTo solve the insufficient availability of mogrol, an 11α-hydroxy aglycone of mogrosides in Siraitia grosvenorii, snailase was employed as the enzyme to completely deglycosylate LHG extract containing 50% mogroside V. Other commonly used glycosidases performed less efficiently. Response surface methodology was conducted to optimize the productivity of mogrol, which peaked at 74.7% in an aqueous reaction. In view of the differences in water-solubility between mogrol and LHG extract, we employed an aqueous-organic system for the snailase-catalyzed reaction. Of five tested organic solvents, toluene performed best and was relatively well tolerated by snailase. After optimization, biphasic medium containing 30% toluene (v/v) could produce a high-quality mogrol (98.1% purity) at a 0.5 L scale with a production rate of 93.2% within 20 h. This toluene-aqueous biphasic system would not only provide sufficient mogrol to construct future synthetic biology systems for the preparation of mogrosides, but also facilitate the development of mogrol-based medicines.PMID:36804180 | DOI:10.1016/j.enzmictec.2023.110212

Am J Transplant. 2023 Feb;23(2):272-277. doi: 10.1016/j.ajt.2022.11.011. Epub 2023 Jan 12.ABSTRACTIntestinal commensals can exert immunomodulatory effects on the host, with beneficial or detrimental consequences depending on underlying diseases. We have previously correlated longer survival of minor mismatched skin grafts in mice with the presence of an intestinal commensal bacterium, Alistipes onderdonkii. In this study, we investigated its sufficiency and mechanism of action. Oral administration of A onderdonkii strain DSM19147 but not DSM108265 was sufficient to prolong minor mismatched skin graft survival through inhibition of tumor necrosis factor production. Through metabolomic and metagenomic comparisons between DSM19147 and DSM108265, we identified candidate gene products associated with the anti-inflammatory effect of DSM19147. A onderdonkii DSM19147 can lower inflammation both at a steady state and after transplantation and may serve as an anti-inflammatory probiotic beneficial for transplant recipients.PMID:36804134 | DOI:10.1016/j.ajt.2022.11.011

Microbiol Res. 2023 Feb 14;270:127334. doi: 10.1016/j.micres.2023.127334. Online ahead of print.ABSTRACTCotton leaf worm (Spodoptera littoralis) is a pest that produces important losses in horticultural and ornamental crops in greenhouse, being classified as quarantine pest A2 by EPPO. One of the strategies proposed to control agricultural pests in a health and environmentally friendly way is biological control with entomopathogenic fungi. The genus of filamentous fungi Trichoderma includes different species with direct (infection, antibiosis, anti-feeding, etc.) and indirect (systemic activation of plant defenses) insecticidal capacity, however, the species T. hamatum has never been described previously as entomopathogenic. In this work, the entomopathogenic capacity of T. hamatum on S. littoralis L3 larvae was analyzed by applying spores and fungal filtrates (topically and orally). Infection by spores was compared with the commercial entomopathogenic fungus Beauveria bassiana, obtaining similar results with respect to the production of larval mortality. Oral application of spores reported high mortality and fungal colonization of larvae, however, T. hamatum did not show chitinase activity when grown in the presence of S. littoralis tissues. Therefore, infection of S. littoralis larvae by T. hamatum is through natural openings such as mouth, anus or spiracles. With respect to the application of filtrates, only those obtained from the liquid culture of T. hamatum in contact with S. littoralis tissues reported a significant reduction in larval growth. Metabolomic analysis of the filtrates determined that the filtrate with insecticidal capacity presented the siderophore rhizoferrin in large quantities, which could be responsible for this activity. However, the production of this siderophore had never been previously described in Trichoderma and its insecticidal capacity was unknown. In conclusion, T. hamatum presents entomopathogenic capacity against S. littoralis larvae through the application of spores and filtrates, and both ways could be the basis for the development of efficient bioinsecticides against the pest.PMID:36804128 | DOI:10.1016/j.micres.2023.127334

Cell Metab. 2023 Feb 16:S1550-4131(23)00010-4. doi: 10.1016/j.cmet.2023.01.010. Online ahead of print.ABSTRACTThe efficacy of immunotherapy is limited by the paucity of T cells delivered and infiltrated into the tumors through aberrant tumor vasculature. Here, we report that phosphoglycerate dehydrogenase (PHGDH)-mediated endothelial cell (EC) metabolism fuels the formation of a hypoxic and immune-hostile vascular microenvironment, driving glioblastoma (GBM) resistance to chimeric antigen receptor (CAR)-T cell immunotherapy. Our metabolome and transcriptome analyses of human and mouse GBM tumors identify that PHGDH expression and serine metabolism are preferentially altered in tumor ECs. Tumor microenvironmental cues induce ATF4-mediated PHGDH expression in ECs, triggering a redox-dependent mechanism that regulates endothelial glycolysis and leads to EC overgrowth. Genetic PHGDH ablation in ECs prunes over-sprouting vasculature, abrogates intratumoral hypoxia, and improves T cell infiltration into the tumors. PHGDH inhibition activates anti-tumor T cell immunity and sensitizes GBM to CAR T therapy. Thus, reprogramming endothelial metabolism by targeting PHGDH may offer a unique opportunity to improve T cell-based immunotherapy.PMID:36804058 | DOI:10.1016/j.cmet.2023.01.010

Biochem Pharmacol. 2023 Feb 17:115458. doi: 10.1016/j.bcp.2023.115458. Online ahead of print.ABSTRACTOncogene FLT3 internal tandem duplication (FLT3-ITD) mutation accounts for 30% of acute myeloid leukaemia (AML) cases and induces transformation. Previously, we found that E2F transcription factor 1 (E2F1) was involved in AML cell differentiation. Here, we reported that E2F1 expression was aberrantly upregulated in AML patients, especially in AML patients carrying FLT3-ITD. E2F1 knockdown inhibited cell proliferation and increased cell sensitivity to chemotherapy in cultured FLT3-ITD-positive AML cells. E2F1-depleted FLT3-ITD+ AML cells lost their malignancy as shown by the reduced leukaemia burden and prolonged survival in NOD-PrkdcscidIl2rgem1/Smoc mice receiving xenografts. Additionally, FLT3-ITD-driven transformation of human CD34+ hematopoietic stem and progenitor cells was counteracted by E2F1 knockdown. Mechanistically, FLT3-ITD enhanced the expression and nuclear accumulation of E2F1 in AML cells. Further study using chromatin immunoprecipitation-sequencing and metabolomics analyses revealed that ectopic FLT3-ITD promoted the recruitment of E2F1 on genes encoding key enzymatic regulators of purine metabolism and thus supported AML cell proliferation. Together, this study demonstrates that E2F1-activated purine metabolism is a critical downstream process of FLT3-ITD in AML and a potential target for FLT3-ITD+ AML patients.PMID:36803956 | DOI:10.1016/j.bcp.2023.115458

J Transl Med. 2023 Feb 20;21(1):132. doi: 10.1186/s12967-023-03985-z.ABSTRACTBACKGROUND: Osteosarcoma is the most common malignant tumor in bone and its prognosis has reached a plateau in the past few decades. Recently, metabolic reprogramming has attracted increasing attention in the field of cancer research. In our previous study, P2RX7 has been identified as an oncogene in osteosarcoma. However, whether and how P2RX7 promotes osteosarcoma growth and metastasis through metabolic reprogramming remains unexplored.METHODS: We used CRISPR/Cas9 genome editing technology to establish P2RX7 knockout cell lines. Transcriptomics and metabolomics were performed to explore metabolic reprogramming in osteosarcoma. RT-PCR, western blot and immunofluorescence analyses were used to determine gene expression related to glucose metabolism. Cell cycle and apoptosis were examined by flowcytometry. The capacity of glycolysis and oxidative phosphorylation were assessed by seahorse experiments. PET/CT was carried out to assess glucose uptake in vivo.RESULTS: We demonstrated that P2RX7 significantly promotes glucose metabolism in osteosarcoma via upregulating the expression of genes related to glucose metabolism. Inhibition of glucose metabolism largely abolishes the ability of P2RX7 to promote osteosarcoma progression. Mechanistically, P2RX7 enhances c-Myc stabilization by facilitating nuclear retention and reducing ubiquitination-dependent degradation. Furthermore, P2RX7 promotes osteosarcoma growth and metastasis through metabolic reprogramming in a predominantly c-Myc-dependent manner.CONCLUSIONS: P2RX7 plays a key role in metabolic reprogramming and osteosarcoma progression via increasing c-Myc stability. These findings provide new evidence that P2RX7 might be a potential diagnostic and/or therapeutic target for osteosarcoma. Novel therapeutic strategies targeting metabolic reprogramming appear to hold promise for a breakthrough in the treatment of osteosarcoma.PMID:36803784 | DOI:10.1186/s12967-023-03985-z

Gut Microbes. 2023 Jan-Dec;15(1):2178794. doi: 10.1080/19490976.2023.2178794.ABSTRACTAn individual's immune and metabolic status is coupled to their microbiome. Probiotics offer a promising, safe route to influence host health, possibly via the microbiome. Here, we report an 18-week, randomized prospective study that explores the effects of a probiotic vs. placebo supplement on 39 adults with elevated parameters of metabolic syndrome. We performed longitudinal sampling of stool and blood to profile the human microbiome and immune system. While we did not see changes in metabolic syndrome markers in response to the probiotic across the entire cohort, there were significant improvements in triglycerides and diastolic blood pressure in a subset of probiotic arm participants. Conversely, the non-responders had increased blood glucose and insulin levels over time. The responders had a distinct microbiome profile at the end of the intervention relative to the non-responders and placebo arm. Importantly, diet was a key differentiating factor between responders and non-responders. Our results show participant-specific effects of a probiotic supplement on improving parameters of metabolic syndrome and suggest that dietary factors may enhance stability and efficacy of the supplement.PMID:36803658 | DOI:10.1080/19490976.2023.2178794

Mol Brain. 2023 Feb 20;16(1):26. doi: 10.1186/s13041-023-01014-0.ABSTRACTBACKGROUND: Metabolites secreted by the gut microbiota may play an essential role in microbiota-gut-central nervous system crosstalk. In this study, we explored the changes occurring in the gut microbiota and their metabolites in patients with spinal cord injury (SCI) and analyzed the correlations among them.METHODS: The structure and composition of the gut microbiota derived from fecal samples collected from patients with SCI (n = 11) and matched control individuals (n = 10) were evaluated using 16S rRNA gene sequencing. Additionally, an untargeted metabolomics approach was used to compare the serum metabolite profiles of both groups. Meanwhile, the association among serum metabolites, the gut microbiota, and clinical parameters (including injury duration and neurological grade) was also analyzed. Finally, metabolites with the potential for use in the treatment of SCI were identified based on the differential metabolite abundance analysis.RESULTS: The composition of the gut microbiota was different between patients with SCI and healthy controls. At the genus level, compared with the control group, the abundance of UBA1819, Anaerostignum, Eggerthella, and Enterococcus was significantly increased in the SCI group, whereas that of Faecalibacterium, Blautia, Escherichia-Shigella, Agathobacter, Collinsella, Dorea, Ruminococcus, Fusicatenibacter, and Eubacterium was decreased. Forty-one named metabolites displayed significant differential abundance between SCI patients and healthy controls, including 18 that were upregulated and 23 that were downregulated. Correlation analysis further indicated that the variation in gut microbiota abundance was associated with changes in serum metabolite levels, suggesting that gut dysbiosis is an important cause of metabolic disorders in SCI. Finally, gut dysbiosis and serum metabolite dysregulation was found to be associated with injury duration and severity of motor dysfunction after SCI.CONCLUSIONS: We present a comprehensive landscape of the gut microbiota and metabolite profiles in patients with SCI and provide evidence that their interaction plays a role in the pathogenesis of SCI. Furthermore, our findings suggested that uridine, hypoxanthine, PC(18:2/0:0), and kojic acid may be important therapeutic targets for the treatment of this condition.PMID:36803646 | DOI:10.1186/s13041-023-01014-0

Microbiome. 2023 Feb 17;11(1):28. doi: 10.1186/s40168-023-01476-3.ABSTRACTBACKGROUND: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.RESULTS: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses.CONCLUSION: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User's guide of MetaboDirect are freely available through ( https://github.com/Coayala/MetaboDirect ) and ( https://metabodirect.readthedocs.io/en/latest/ ), respectively. Video Abstract.PMID:36803638 | DOI:10.1186/s40168-023-01476-3

Biomark Res. 2023 Feb 18;11(1):20. doi: 10.1186/s40364-023-00458-9.ABSTRACTBACKGROUND: Aging and diet are risks for metabolic diseases. Bile acid receptor farnesoid X receptor (FXR) knockout (KO) mice develop metabolic liver diseases that progress into cancer as they age, which is accelerated by Western diet (WD) intake. The current study uncovers the molecular signatures for diet and age-linked metabolic liver disease development in an FXR-dependent manner.METHODS: Wild-type (WT) and FXR KO male mice, either on a healthy control diet (CD) or a WD, were euthanized at the ages of 5, 10, or 15 months. Hepatic transcriptomics, liver, serum, and urine metabolomics as well as microbiota were profiled.RESULTS: WD intake facilitated hepatic aging in WT mice. In an FXR-dependent manner, increased inflammation and reduced oxidative phosphorylation were the primary pathways affected by WD and aging. FXR has a role in modulating inflammation and B cell-mediated humoral immunity which was enhanced by aging. Moreover, FXR dictated neuron differentiation, muscle contraction, and cytoskeleton organization in addition to metabolism. There were 654 transcripts commonly altered by diets, ages, and FXR KO, and 76 of them were differentially expressed in human hepatocellular carcinoma (HCC) and healthy livers. Urine metabolites differentiated dietary effects in both genotypes, and serum metabolites clearly separated ages irrespective of diets. Aging and FXR KO commonly affected amino acid metabolism and TCA cycle. Moreover, FXR is essential for colonization of age-related gut microbes. Integrated analyses uncovered metabolites and bacteria linked with hepatic transcripts affected by WD intake, aging, and FXR KO as well as related to HCC patient survival.CONCLUSION: FXR is a target to prevent diet or age-associated metabolic disease. The uncovered metabolites and microbes can be diagnostic markers for metabolic disease.PMID:36803569 | DOI:10.1186/s40364-023-00458-9

Virulence. 2023 Feb 20:2180938. doi: 10.1080/21505594.2023.2180938. Online ahead of print.ABSTRACTStreptococcus agalactiae (GBS) is an important pathogenic bacteria that infected both of human and animals, causing huge economic loss. The increasing cases of antibiotic-resistant GBS impose challenges to treat such infection by antibiotics. Thus, it is highly demanded for the approach to tackle antibiotic resistance in GBS. In this study, we adopte a metabolomic approach to identify the metabolic signature of ampicillin-resistant GBS (AR-GBS) that ampicillin is the routine choice to treat infection by GBS. We find glycolysis is significantly repressed in AR-GBS, and fructose is the crucial biomarker. Exogenous fructose not only reverses ampicillin resistance in AR-GBS but also in clinic isolates including methicillin-resistant Staphylococcus aureus (MRSA) and NDM-1 expressing Escherichia coli. The synergistic effect is confirmed in a zebrafish infection model. Furthermore, we demonstrate that the potentiation by fructose is dependent on glycolysis that enhances ampicillin uptake and the expression of penicillin-binding proteins, the ampicillin target. Our study demonstrates a novel approach to combat antibiotic resistance in GBS.PMID:36803528 | DOI:10.1080/21505594.2023.2180938

BMC Plant Biol. 2023 Feb 21;23(1):103. doi: 10.1186/s12870-023-04130-0.ABSTRACTBACKGROUND: Plant growth regulators are chemicals that regulate plant growth and development, which can regulate hormonal balance and affect plant growth, thereby increasing crop yield and improving crop quality. Our studies have revealed a new compound, GZU001, which could be used as a plant growth regulator. This compound has been observed to affect root elongation in maize significantly. However, the exact mechanism of this phenomenon is still being investigated.RESULTS: Metabolomics and proteomics were used in unison in this study to explore the response pathway and regulation mechanism of GZU001 in promoting maize root elongation. From the appearance, we can see that both roots and plants of maize treated with GZU001 are significantly improved. Maize root metabolism revealed 101 differentially abundant proteins and 79 differentially expressed metabolites. The current study identified altered proteins and metabolites associated with physiological and biochemical processes. GZU001 treatment has been demonstrated to promote primary metabolism, essential for carbohydrates, amino acids, energy, and secondary metabolism. The result suggests that the stimulation of primary metabolism is beneficial for the growth and development of maize and plays a significant role in sustaining metabolism and growth.CONCLUSIONS: This study recorded the changes of related proteins and metabolites in maize roots after GZU001 treatment and provided evidence for this compound's action mode and mechanism in plants.PMID:36803498 | DOI:10.1186/s12870-023-04130-0

BMC Bioinformatics. 2023 Feb 20;24(1):57. doi: 10.1186/s12859-023-05171-w.ABSTRACTBACKGROUND: The growing amount of high dimensional biomolecular data has spawned new statistical and computational models for risk prediction and disease classification. Yet, many of these methods do not yield biologically interpretable models, despite offering high classification accuracy. An exception, the top-scoring pair (TSP) algorithm derives parameter-free, biologically interpretable single pair decision rules that are accurate and robust in disease classification. However, standard TSP methods do not accommodate covariates that could heavily influence feature selection for the top-scoring pair. Herein, we propose a covariate-adjusted TSP method, which uses residuals from a regression of features on the covariates for identifying top scoring pairs. We conduct simulations and a data application to investigate our method, and compare it to existing classifiers, LASSO and random forests.RESULTS: Our simulations found that features that were highly correlated with clinical variables had high likelihood of being selected as top scoring pairs in the standard TSP setting. However, through residualization, our covariate-adjusted TSP was able to identify new top scoring pairs, that were largely uncorrelated with clinical variables. In the data application, using patients with diabetes (n = 977) selected for metabolomic profiling in the Chronic Renal Insufficiency Cohort (CRIC) study, the standard TSP algorithm identified (valine-betaine, dimethyl-arg) as the top-scoring metabolite pair for classifying diabetic kidney disease (DKD) severity, whereas the covariate-adjusted TSP method identified the pair (pipazethate, octaethylene glycol) as top-scoring. Valine-betaine and dimethyl-arg had, respectively, ≥ 0.4 absolute correlation with urine albumin and serum creatinine, known prognosticators of DKD. Thus without covariate-adjustment the top-scoring pair largely reflected known markers of disease severity, whereas covariate-adjusted TSP uncovered features liberated from confounding, and identified independent prognostic markers of DKD severity. Furthermore, TSP-based methods achieved competitive classification accuracy in DKD to LASSO and random forests, while providing more parsimonious models.CONCLUSIONS: We extended TSP-based methods to account for covariates, via a simple, easy to implement residualizing process. Our covariate-adjusted TSP method identified metabolite features, uncorrelated from clinical covariates, that discriminate DKD severity stage based on the relative ordering between two features, and thus provide insights into future studies on the order reversals in early vs advanced disease states.PMID:36803209 | DOI:10.1186/s12859-023-05171-w

Nano Lett. 2023 Feb 20. doi: 10.1021/acs.nanolett.3c00035. Online ahead of print.ABSTRACTOncogenic-driven lipogenic metabolism is a common hallmark of colorectal cancer (CRC) progression. Therefore, there is an urgent need to develop novel therapeutic strategies for metabolic reprogramming. Herein, the metabolic profiles in the plasma between CRC patients and paired healthy controls were compared using metabolomics assays. Matairesinol downregulation was evident in CRC patients, and matairesinol supplementation significantly represses CRC tumorigenesis in azoxymethane/dextran sulfate sodium (AOM/DSS) colitis-associated CRC mice. Matairesinol rewired lipid metabolism to improve the therapeutic efficacy in CRC by inducing mitochondrial damage and oxidative damage and blunting ATP production. Finally, matairesinol-loaded liposomes significantly promoted the enhanced antitumor activity of 5-Fu/leucovorin combined with oxaliplatin (FOLFOX) in CDX and PDX mouse models by restoring chemosensitivity to the FOLFOX regimen. Collectively our findings highlight matairesinol-mediated lipid metabolism reprogramming as a novel druggable strategy to restore CRC chemosensitivity, and this nanoenabled approach for matairesinol will improve the chemotherapeutic efficacy with good biosafety.PMID:36802650 | DOI:10.1021/acs.nanolett.3c00035

J Agric Food Chem. 2023 Feb 21. doi: 10.1021/acs.jafc.2c07709. Online ahead of print.ABSTRACTThis study aimed to investigate the amendatory effects of Fu brick tea aqueous extract (FTE) on constipation and its underlying molecular mechanism. The administration of FTE by oral gavage (100 and 400 mg/kg·bw) for 5 weeks significantly increased fecal water content, improved difficult defecation, and enhanced intestinal propulsion in loperamide (LOP)-induced constipated mice. FTE also reduced colonic inflammatory factors, maintained the intestinal tight junction structure, and inhibited colonic Aquaporins (AQPs) expression, thus normalizing the intestinal barrier and colonic water transport system of constipated mice. 16S rRNA gene sequence analysis results indicated that two doses of FTE increased the Firmicutes/Bacteroidota (F/B) ratio at the phylum level and increased the relative abundance of Lactobacillus from 5.6 ± 1.3 to 21.5 ± 3.4% and 28.5 ± 4.3% at the genus level, subsequently resulting in a significant elevation of colonic contents short-chain fatty acids levels. The metabolomic analysis demonstrated that FTE improved levels of 25 metabolites associated with constipation. These findings suggest that Fu brick tea has the potential to alleviate constipation by regulating gut microbiota and its metabolites, thereby improving the intestinal barrier and AQPs-mediated water transport system in mice.PMID:36802556 | DOI:10.1021/acs.jafc.2c07709

Rheumatology (Oxford). 2023 Feb 20:kead061. doi: 10.1093/rheumatology/kead061. Online ahead of print.ABSTRACTOBJECTIVE: Trained immunity (TI) is a de facto memory program of innate immune cells, characterized by immunometabolic and epigenetic changes sustaining enhanced production of cytokines. TI evolved as a protective mechanism against infections; however, inappropriate activation can cause detrimental inflammation and might be implicated in the pathogenesis of chronic inflammatory diseases. In this study, we investigated the role of TI in the pathogenesis of giant cell arteritis (GCA), a large-vessel vasculitis characterized by aberrant macrophage activation and excess cytokine production.METHODS: Monocytes from GCA patients and from age- and sex-matched healthy donors were subjected to polyfunctional studies, including cytokine production assays at baseline and following stimulation, intracellular metabolomics, chromatin immunoprecipitation-qPCR, and combined ATAC/RNA sequencing. Immunometabolic activation (i.e. glycolysis) was assessed in inflamed vessels of GCA patients with FDG-PET and immunohistochemistry (IHC), and the role of this pathway in sustaining cytokine production was confirmed with selective pharmacologic inhibition in GCA monocytes.RESULTS: GCA monocytes exhibited hallmark molecular features of TI. Specifically, these included enhanced IL-6 production upon stimulation, typical immunometabolic changes (e.g. increased glycolysis and glutaminolysis) and epigenetic changes promoting enhanced transcription of genes governing pro-inflammatory activation. Immunometabolic changes of TI (i.e. glycolysis) were a feature of myelomonocytic cells in GCA lesions and were required for enhanced cytokine production.CONCLUSIONS: Myelomonocytic cells in GCA activate TI programs sustaining enhanced inflammatory activation with excess cytokine production.PMID:36802235 | DOI:10.1093/rheumatology/kead061

Curr Protoc. 2023 Feb;3(2):e696. doi: 10.1002/cpz1.696.ABSTRACTGaucher disease (GD) is a lysosomal storage disorder caused by a deficiency of the enzyme beta-glucocerebrosidase. This leads to the accumulation of glycolipids in macrophages and ultimately results in tissue damage. Recent metabolomic studies highlighted several potential biomarkers in plasma specimens. In hopes of better understanding the distribution, importance, and clinical significance of these potential markers, a UPLC-MS/MS method was developed and validated to quantify lyso-Gb1 and six related analogs (with the following modifications on the sphingosine moiety: -C2 H4 (-28 Da), -C2 H4 +O (-12 Da), -H2 (-2 Da), -H2 +O (+14 Da), +O (+16 Da), and +H2 O (+18 Da)), sphingosylphosphorylcholine, and N-palmitoyl-O-phosphocholineserine in plasma specimens of treated and untreated patients. This 12-min UPLC-MS/MS method involves a purification step via solid-phase extraction followed by evaporation under nitrogen flow and resuspension in an organic mix compatible with HILIC chromatography. This method is currently used for research purposes and might be used for monitoring, prognostics, and follow-up. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.PMID:36802221 | DOI:10.1002/cpz1.696