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

DNA damage-induced senescence is associated with metabolomic reprogramming in breast cancer cells

Wed, 27/09/2023 - 12:00
Biochimie. 2023 Sep 25:S0300-9084(23)00248-1. doi: 10.1016/j.biochi.2023.09.021. Online ahead of print.ABSTRACTSenescence due to exogenous and endogenous stresses triggers metabolic reprogramming and is associated with many pathologies, including cancer. In solid tumors, senescence promotes tumorigenesis, facilitates relapse, and changes the outcomes of anti-cancer therapies. Hence, cellular and molecular mechanisms regulating senescent pathways make attractive therapeutic targets. Cancer cells undergo metabolic reprogramming to sustain the growth-arrested state of senescence. In the present study, we aimed to understand the metabolic reprogramming in MCF-7 breast tumor cells in response to two independent inducers of DNA damage-mediated senescence, including ionizing radiation and doxorubicin. Increased DNA double-strand breaks, as demonstrated by γH2AX staining, showed a senescence phenotype, with expression of senescence-associated β-galactosidase accompanied by the upregulation of p21 and p16 in both groups. Further, untargeted analysis of the senescence-related extracellular metabolome profile of MCF-7 cells showed significantly reduced concentrations of carnitine and pantothenic acid and increased levels of S-adenosylhomocysteine in doxorubicin-treated cells, indicating the accumulation of ROS mediated DNA damage and impaired mitochondrial membrane potential. Similarly, a significant decline in the creatine level was observed in radiation-exposed cells, suggesting an increase in oxidative stress-mediated DNA damage. Our study, therefore, provides key effectors of the metabolic changes in doxorubicin and radiation-induced early senescence in MCF-7 breast cancer cells.PMID:37758157 | DOI:10.1016/j.biochi.2023.09.021

Fibre-rich diet attenuates chemotherapy-related neuroinflammation in mice

Wed, 27/09/2023 - 12:00
Brain Behav Immun. 2023 Sep 25:S0889-1591(23)00282-9. doi: 10.1016/j.bbi.2023.09.018. Online ahead of print.ABSTRACTThe gastrointestinal microbiota has received increasing recognition as a key mediator of neurological conditions with neuroinflammatory features, through its production of the bioactive metabolites, short-chain fatty acids (SCFAs). Although neuroinflammation is a hallmark shared by the neuropsychological complications of chemotherapy (including cognitive impairment, fatigue and depression), the use of microbial-based therapeutics has not previously been studied in this setting. Therefore, we aimed to investigate the effect of a high fibre diet known to modulate the microbiota, and its associated metabolome, on neuroinflammation caused by the common chemotherapeutic agent 5-fluorouracil (5-FU). Twenty-four female C57Bl/6 mice were treated with 5-FU (400 mg/kg, intraperitoneal, i.p.) or vehicle control, with or without a high fibre diet (constituting amylose starch; 4.7 % crude fibre content), given one week prior to 5-FU and until study completion (16 days after 5-FU). Faecal pellets were collected longitudinally for 16S rRNA gene sequencing and terminal SCFA concentrations of the caecal contents were quantified using gas chromatography-mass spectrometry (GC-MS). Neuroinflammation was determined by immunofluorescent analysis of astrocyte density (GFAP). The high fibre diet significantly altered gut microbiota composition, increasing the abundance of Bacteroidaceae and Akkermansiaceae (p < 0.0001 and p = 0.0179) whilst increasing the production of propionate (p = 0.0097). In the context of 5-FU, the diet reduced GFAP expression in the CA1 region of the hippocampus (p < 0.0001) as well as the midbrain (p = 0.0216). Astrocyte density negatively correlated with propionate concentrations and the abundance of Bacteroidaceae and Akkermansiaceae, suggesting a relationship between neuroinflammatory and gastrointestinal markers in this model. This study provides the first evidence of the neuroprotective effects of fibre via dietary intake in alleviating the neuroimmune changes seen in response to systemically administered 5-FU, indicating that the microbiota-gut-brain axis is a targetable mediator to reduce the neurotoxic effects of chemotherapy treatment.PMID:37757978 | DOI:10.1016/j.bbi.2023.09.018

Goat mammary gland metabolism: An integrated omics analysis to unravel seasonal weight loss tolerance

Wed, 27/09/2023 - 12:00
J Proteomics. 2023 Sep 25:105009. doi: 10.1016/j.jprot.2023.105009. Online ahead of print.ABSTRACTSeasonal weight loss (SWL), is a major limitation to animal production. In the Canary Islands, there are two dairy goat breeds with different levels of tolerance to SWL: Majorera (tolerant) and Palmera (susceptible). Our team has studied the response of these breeds to SWL using different Omics. The objective of this study was to integrate such results in a data driven approach and using dedicated tools, namely the DIABLO software. The outputs of our analysis mainly separate unrestricted from restricted goats. Metabolites behave as "hub" molecules, grouping interactions with several genes and proteins. Unrestricted goats upregulated protein synthesis, along with arginine catabolism and adipogenesis pathways, which are related with higher anabolic rates and a larger proportion of secretory tissue, in agreement with their higher milk production. Contrarily, restricted goats seemingly increased the synthesis of acetyl-CoA through serine and acetate conversion into pyruvate. This may have occurred to increase fatty acid synthesis and/or to use them as an energy source in detriment to glucose, which was more available in the diet of unrestricted goats. Lastly, restricted Palmera upregulated the expression of PEBP4 and GPD1 genes compared to all other groups, which might support their use as putative biomarkers for SWL susceptibility. SIGNIFICANCE: Seasonal weight loss (SWL) is a major issue influencing animal production in the tropics and Mediterranean. By studying its impact on the mammary gland of resilient and susceptible dairy goat breeds, using Omics, we aim at surveying the tissue for possible biomarkers that reflect these traits. In this study, data integration of three Omics (transcriptomics, proteomics and metabolomics) was performed using bioinformatic tools, to relate putative biomarkers and evaluate all three levels of information; in a novel approach. This information can enhance selection programs, lowering the impact of SWL on food production systems.PMID:37757955 | DOI:10.1016/j.jprot.2023.105009

Regulatory mechanisms of submerged macrophyte on bacterial community recovery in decabromodiphenyl ether contaminated sediment: Microbiological and metabolomic perspectives

Wed, 27/09/2023 - 12:00
Environ Pollut. 2023 Sep 25:122616. doi: 10.1016/j.envpol.2023.122616. Online ahead of print.ABSTRACTPolybrominated diphenyl ether contamination in sediments poses serious threats to human health and ecological safety. Despite the broad application of submerged macrophytes for remediating pollutants, their regulatory influence on bacterial communities in contaminated sediments remains unclear. Herein, we analyzed the effects of decabromodiphenyl ether (BDE-209) and Hydrilla verticillata on sediment bacterial community and function using 16S rRNA gene sequencing and sediment metabolomics. Results showed that BDE-209 significantly inhibited sediment bacterial diversity and metabolic functions. It also enhanced bacterial interactions and altered both the bacterial community and metabolite composition. Uridine and inosine were critical metabolites that positively co-occurred with bacterial taxa inhibited by BDE-209. Notably, planting H. verticillata effectively alleviated the adverse impacts of BDE-209 by reducing its residuals, increasing the total organic carbon, and modifying metabolic profiles. Such mitigation was evidenced by enhancing bacterial diversity, restoring metabolic functions, and attenuating bacterial interactions. However, mitigation effectiveness depended on treatment time. Additionally, propionic acid, palmitic acid, and palmitoleic acid may facilitate the restoration of phylum Proteobacteria and class Planctomycetacia in H. verticillata planted sediment. Together, these findings improve understanding of BDE-209's impacts on aquatic ecosystems and provide valuable insights for ecological restoration using submerged macrophytes.PMID:37757929 | DOI:10.1016/j.envpol.2023.122616

Effects of food-borne docosahexaenoic acid supplementation on bone lead mobilisation, mitochondrial function and serum metabolomics in pre-pregnancy lead-exposed lactating rats

Wed, 27/09/2023 - 12:00
Environ Pollut. 2023 Sep 25:122613. doi: 10.1016/j.envpol.2023.122613. Online ahead of print.ABSTRACTLarge bone lead (Pb) resulting from high environmental exposure during childhood is an important source of endogenous Pb during pregnancy and lactation. Docosahexaenoic acid (DHA) attenuates Pb toxicity, however, the effect of DHA on bone Pb mobilisation during lactation has not been investigated. We aimed to study the effects of DHA supplementation during pregnancy and lactation on bone Pb mobilisation during lactation and its potential mechanisms. Weaning female rats were randomly divided into control (0.05% sodium acetate) and Pb-exposed (0.05% Pb acetate) groups, after a 4-week exposure by ad libitum drinking and a subsequent 4-week washout period, all female rats were mated with healthy males until pregnancy. Then exposed rats were randomly divided into Pb and Pb + DHA groups, and the latter was given a 0.14% DHA diet, while the remaining groups were given normal feed until the end of lactation. Pb and calcium levels, bone microarchitecture, bone turnover markers, mitochondrial function and serum metabolomics were analyzed. The results showed that higher blood and bone Pb levels were observed in the Pb group compared to the control, and there was a significant negative correlation between blood and bone Pb. Also, Pb increased trabecular bone loss along with slightly elevated serum C-telopeptide of type I collagen (CTX-I) levels. However, DHA reduced CTX-I levels and improved trabecular bone microarchitecture. Metabolomics showed that Pb affected mitochondrial function, which was further demonstrated in bone tissue by significant reductions in ATP levels, Na+-K+-ATPase, Ca2+-Mg2+-ATPase and CAT activities, and elevated levels of MDA, IL-1β and IL-18. However, these alterations were partially mitigated by DHA. In conclusion, DHA supplementation during pregnancy and lactation improved bone Pb mobilisation and mitochondrial dysfunction in lactating rats induced by pre-pregnancy Pb exposure, providing potential means of mitigating bone Pb mobilisation levels during lactation, but the mechanism still needs further study.PMID:37757928 | DOI:10.1016/j.envpol.2023.122613

cfOmics: a cell-free multi-Omics database for diseases

Wed, 27/09/2023 - 12:00
Nucleic Acids Res. 2023 Sep 27:gkad777. doi: 10.1093/nar/gkad777. Online ahead of print.ABSTRACTLiquid biopsy has emerged as a promising non-invasive approach for detecting, monitoring diseases, and predicting their recurrence. However, the effective utilization of liquid biopsy data to identify reliable biomarkers for various cancers and other diseases requires further exploration. Here, we present cfOmics, a web-accessible database (https://cfomics.ncRNAlab.org/) that integrates comprehensive multi-omics liquid biopsy data, including cfDNA, cfRNA based on next-generation sequencing, and proteome, metabolome based on mass-spectrometry data. As the first multi-omics database in the field, cfOmics encompasses a total of 17 distinct data types and 13 specimen variations across 69 disease conditions, with a collection of 11345 samples. Moreover, cfOmics includes reported potential biomarkers for reference. To facilitate effective analysis and visualization of multi-omics data, cfOmics offers powerful functionalities to its users. These functionalities include browsing, profile visualization, the Integrative Genomic Viewer, and correlation analysis, all centered around genes, microbes, or end-motifs. The primary objective of cfOmics is to assist researchers in the field of liquid biopsy by providing comprehensive multi-omics data. This enables them to explore cell-free data and extract profound insights that can significantly impact disease diagnosis, treatment monitoring, and management.PMID:37757861 | DOI:10.1093/nar/gkad777

Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease

Wed, 27/09/2023 - 12:00
Plant Physiol Biochem. 2023 Sep 12;203:108033. doi: 10.1016/j.plaphy.2023.108033. Online ahead of print.ABSTRACTLeaf scald caused by the bacteria Xanthomonas albilineans is one of the major concerns to sugarcane production. To breed for resistance, mechanisms underlying plant-pathogen interaction need deeper investigations. Herein, we evaluated sugarcane defense responses against X. albilineans using molecular and biochemical approaches to assess pathogen-triggered ROS, phytohormones and metabolomics in two contrasting sugarcane genotypes from 0.5 to 144 h post-inoculation (hpi). In addition, the infection process was monitored using TaqMan-based quantification of X. albilineans and the disease symptoms were evaluated in both genotypes after 15 d post-inoculation (dpi). The susceptible genotype presented a response to the infection at 0.5 hpi, accumulating defense-related metabolites such as phenolics and flavonoids with no significant defense responses thereafter, resulting in typical symptoms of leaf scald at 15 dpi. The resistant genotype did not respond to the infection at 0.5 hpi but constitutively presented higher levels of salicylic acid and of the same metabolites induced by the infection in the susceptible genotype. Moreover, two subsequent pathogen-induced metabolic responses at 12 and 144 hpi were observed only in the resistant genotype in terms of amino acids, quinic acids, coumarins, polyamines, flavonoids, phenolics and phenylpropanoids together with an increase of hydrogen peroxide, ROS-related genes expression, indole-3-acetic-acid and salicylic acid. Multilevel approaches revealed that constitutive chemical composition and metabolic reprogramming hampers the development of leaf scald at 48 and 72 hpi, reducing the disease symptoms in the resistant genotype at 15 dpi. Phenylpropanoid pathway is suggested as a strong candidate marker for breeding sugarcane resistant to leaf scald.PMID:37757720 | DOI:10.1016/j.plaphy.2023.108033

Effects of microplastics and phenanthrene on gut microbiome and metabolome alterations in the marine medaka Oryzias melastigma

Wed, 27/09/2023 - 12:00
J Hazard Mater. 2023 Sep 23;461:132620. doi: 10.1016/j.jhazmat.2023.132620. Online ahead of print.ABSTRACTPlastic pollution of the oceans is increasing, and toxic interactions between microplastics (MPs) and organic pollutants have become a major environmental concern. However, the combined effects of organic pollutants and MPs on microbiomes and metabolomes have not been studied extensively. In the present study, to evaluate whether MPs and phenanthrene (Phe) act synergistically in the guts of marine medaka (Oryzias melastigma), we performed toxicity assessments, 16 S rRNA gene sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. Our investigations revealed increased toxicity induced by Phe, as well as disturbances in gut microbiota (known as dysbiosis) when MPs were present. Furthermore, combined exposure to Phe and MPs resulted in greater alterations to microbiota composition and metabolite profiles. Notably, MP exposure was distinctly associated with the abundance of Shewanella and Spongiibacteraceae, while Phe exposure was associated with the abundance of Marimicrobium. Among key microbiota, Marimicrobium and Roseibacillus were significantly correlated with metabolites responsible for coenzyme A and glycerophospholipid metabolism in medaka. These results suggest that interactions between Phe and MPs may have significant effects on the gut microbiota and metabolism of aquatic organisms and underscore the importance of acknowledging the interplay between MPs and contaminants in aquatic environments.PMID:37757554 | DOI:10.1016/j.jhazmat.2023.132620

Objective measures of smoking and caffeine intake and the risk of adverse pregnancy outcomes

Wed, 27/09/2023 - 12:00
Int J Epidemiol. 2023 Sep 28:dyad123. doi: 10.1093/ije/dyad123. Online ahead of print.ABSTRACTBACKGROUND: In pregnancy, women are encouraged to cease smoking and limit caffeine intake. We employed objective definitions of smoking and caffeine exposure to assess their association with adverse outcomes.METHODS: We conducted a case cohort study within the Pregnancy Outcome Prediction study to analyse maternal serum metabolomics in samples from 12, 20, 28 and 36 weeks of gestational age. Objective smoking status was defined based on detectable cotinine levels at each time point and objective caffeine exposure was based on tertiles of paraxanthine levels at each time point. We used logistic and linear regression to examine the association between cotinine, paraxanthine and the risk of pre-eclampsia, spontaneous pre-term birth (sPTB), fetal growth restriction (FGR), gestational diabetes mellitus and birthweight.RESULTS: There were 914 and 915 women in the smoking and caffeine analyses, respectively. Compared with no exposure to smoking, consistent exposure to smoking was associated with an increased risk of sPTB [adjusted odds ratio (aOR) = 2.58, 95% CI: 1.14 to 5.85)] and FGR (aOR = 4.07, 95% CI: 2.14 to 7.74) and lower birthweight (β = -387 g, 95% CI: -622 g to -153 g). On univariate analysis, consistently high levels of paraxanthine were associated with an increased risk of FGR but that association attenuated when adjusting for maternal characteristics and objective-but not self-reported-smoking status.CONCLUSIONS: Based on objective data, consistent exposure to smoking throughout pregnancy was strongly associated with sPTB and FGR. High levels of paraxanthine were not independently associated with any of the studied outcomes and were confounded by smoking.PMID:37759082 | DOI:10.1093/ije/dyad123

Inhibition of fatty acid oxidation enables heart regeneration in adult mice

Wed, 27/09/2023 - 12:00
Nature. 2023 Sep 27. doi: 10.1038/s41586-023-06585-5. Online ahead of print.ABSTRACTPostnatal maturation of cardiomyocytes is characterized by a metabolic switch from glycolysis to fatty acid oxidation, chromatin reconfiguration and exit from the cell cycle, instating a barrier for adult heart regeneration1,2. Here, to explore whether metabolic reprogramming can overcome this barrier and enable heart regeneration, we abrogate fatty acid oxidation in cardiomyocytes by inactivation of Cpt1b. We find that disablement of fatty acid oxidation in cardiomyocytes improves resistance to hypoxia and stimulates cardiomyocyte proliferation, allowing heart regeneration after ischaemia-reperfusion injury. Metabolic studies reveal profound changes in energy metabolism and accumulation of α-ketoglutarate in Cpt1b-mutant cardiomyocytes, leading to activation of the α-ketoglutarate-dependent lysine demethylase KDM5 (ref. 3). Activated KDM5 demethylates broad H3K4me3 domains in genes that drive cardiomyocyte maturation, lowering their transcription levels and shifting cardiomyocytes into a less mature state, thereby promoting proliferation. We conclude that metabolic maturation shapes the epigenetic landscape of cardiomyocytes, creating a roadblock for further cell divisions. Reversal of this process allows repair of damaged hearts.PMID:37758950 | DOI:10.1038/s41586-023-06585-5

Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets

Wed, 27/09/2023 - 12:00
Nat Commun. 2023 Sep 27;14(1):6030. doi: 10.1038/s41467-023-41442-z.ABSTRACTInfluenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.PMID:37758692 | DOI:10.1038/s41467-023-41442-z

Insights into bacterial community metatranscriptome and metabolome in river water influenced by palm oil mill effluent final discharge

Wed, 27/09/2023 - 12:00
J Appl Microbiol. 2023 Sep 26:lxad219. doi: 10.1093/jambio/lxad219. Online ahead of print.ABSTRACTAIMS: This study aimed to investigate the effect of palm oil mill effluent (POME) final discharge on the active bacterial composition, gene expression, and metabolite profiles in the receiving rivers to establish a foundation for identifying potential biomarkers for monitoring POME pollution in rivers.METHODS AND RESULTS: The POME final discharge, upstream (unpolluted by POME) and downstream (effluent receiving point) parts of the rivers from two sites were physicochemically characterised. The taxonomic and gene profiles were then evaluated using de novo metatranscriptomics, while the metabolites were detected using qualitative metabolomics. A similar bacterial community structure in the POME final discharge samples from both sites was recorded, but their composition varied. Redundancy analysis showed that several families, particularly Comamonadaceae and Burkholderiaceae (Pr(>F) = 0.028), were positively correlated with biochemical oxygen demand (BOD5) and chemical oxygen demand (COD). The results also showed significant enrichment of genes regulating various metabolisms in the POME-receiving rivers, with methane, carbon fixation pathway and amino acids among the predominant metabolisms identified (FDR < 0.05, PostFC > 4, PPDE > 0.95). This was further validated through qualitative metabolomics whereby amino acids were detected as the predominant metabolites.CONCLUSIONS: The results suggest that genes regulating amino acid metabolism have significant potential for developing effective biomonitoring and bioremediation strategies in river water influenced by POME final discharge, fostering a sustainable palm oil industry.PMID:37757470 | DOI:10.1093/jambio/lxad219

Discovery of Triazinone Derivatives as Novel, Specific, and Direct NLRP3 Inflammasome Inhibitors for the Treatment of DSS-Induced Ulcerative Colitis

Wed, 27/09/2023 - 12:00
J Med Chem. 2023 Sep 27. doi: 10.1021/acs.jmedchem.3c00696. Online ahead of print.ABSTRACTNLRP3 is an intracellular sensor protein that causes inflammasome formation and pyroptosis in response to a wide range of stimuli. Aberrant activation of NLRP3 inflammasome has been implicated in various chronic inflammatory diseases, making it a promising target for therapeutic intervention. In this work, a series of novel triazinone inhibitors of NLRP3 inflammasome were designed and synthesized. Compound L38 was identified for its excellent activity and acceptable metabolic stability among 41 compounds. Additionally, mechanism studies indicated that L38 inhibited NLRP3 inflammasome activation and pyroptosis by suppressing gasdermin D cleavage, ASC oligomerization, and NLRP3 inflammasome assembly while leaving mitochondrial ROS production, lysosome damage, and chloride/potassium efflux unaffected. Further investigation revealed that L38 could bind to the NACHT domain to exert inflammatory properties. Importantly, L38 exhibited positive therapeutic effects in DSS-induced ulcerative colitis mouse model. Taken together, this study presents a promising inhibitor of NLRP3 inflammasome deserving further investigation.PMID:37756547 | DOI:10.1021/acs.jmedchem.3c00696

Oxidized Low-Density Lipoprotein Accumulation Suppresses Glycolysis and Attenuates the Macrophage Inflammatory Response by Diverting Transcription from the HIF-1α to the Nrf2 Pathway

Wed, 27/09/2023 - 12:00
J Immunol. 2023 Sep 27:ji2300293. doi: 10.4049/jimmunol.2300293. Online ahead of print.ABSTRACTLipid accumulation in macrophages (Mφs) is a hallmark of atherosclerosis, yet how lipid accumulation affects inflammatory responses through rewiring of Mφ metabolism is poorly understood. We modeled lipid accumulation in cultured wild-type mouse thioglycolate-elicited peritoneal Mφs and bone marrow-derived Mφs with conditional (Lyz2-Cre) or complete genetic deficiency of Vhl, Hif1a, Nos2, and Nfe2l2. Transfection studies employed RAW264.7 cells. Mφs were cultured for 24 h with oxidized low-density lipoprotein (oxLDL) or cholesterol and then were stimulated with LPS. Transcriptomics revealed that oxLDL accumulation in Mφs downregulated inflammatory, hypoxia, and cholesterol metabolism pathways, whereas the antioxidant pathway, fatty acid oxidation, and ABC family proteins were upregulated. Metabolomics and extracellular metabolic flux assays showed that oxLDL accumulation suppressed LPS-induced glycolysis. Intracellular lipid accumulation in Mφs impaired LPS-induced inflammation by reducing both hypoxia-inducible factor 1-α (HIF-1α) stability and transactivation capacity; thus, the phenotype was not rescued in Vhl-/- Mφs. Intracellular lipid accumulation in Mφs also enhanced LPS-induced NF erythroid 2-related factor 2 (Nrf2)-mediated antioxidative defense that destabilizes HIF-1α, and Nrf2-deficient Mφs resisted the inhibitory effects of lipid accumulation on glycolysis and inflammatory gene expression. Furthermore, oxLDL shifted NADPH consumption from HIF-1α- to Nrf2-regulated apoenzymes. Thus, we postulate that repurposing NADPH consumption from HIF-1α to Nrf2 transcriptional pathways is critical in modulating inflammatory responses in Mφs with accumulated intracellular lipid. The relevance of our in vitro models was established by comparative transcriptomic analyses, which revealed that Mφs cultured with oxLDL and stimulated with LPS shared similar inflammatory and metabolic profiles with foamy Mφs derived from the atherosclerotic mouse and human aorta.PMID:37756544 | DOI:10.4049/jimmunol.2300293

Labile Metabolite Profiling in Human Blood Using Phosphorus NMR Spectroscopy

Wed, 27/09/2023 - 12:00
Anal Chem. 2023 Sep 27. doi: 10.1021/acs.analchem.3c03040. Online ahead of print.ABSTRACTPhosphorus metabolites occupy a unique place in cellular function as critical intermediates and products of cellular metabolism. Human blood is the most widely used biospecimen in the clinic and in the metabolomics field, and hence an ability to profile phosphorus metabolites in blood, quantitatively, would benefit a wide variety of investigations of cellular functions in health and diseases. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the two premier analytical platforms used in the metabolomics field. However, detection and quantitation of phosphorus metabolites by MS can be challenging due to their lability, high polarity, structural isomerism, and interaction with chromatographic columns. The conventionally used 1H NMR, on the other hand, suffers from poor resolution of these compounds. As a remedy, 31P NMR promises an important alternative to both MS and 1H NMR. However, numerous challenges including the instability of phosphorus metabolites, their chemical shift sensitivity to solvent composition, pH, salt, and temperature, and the lack of identified metabolites have so far restricted the scope of 31P NMR. In the current study, we describe a method to analyze nearly 25 phosphorus metabolites in blood using a simple one-dimensional (1D) NMR spectrum. Establishment of the identity of unknown metabolites involved a combination of (a) comprehensively analyzing an array of 1D and two-dimensional (2D) 1H/31P homonuclear and heteronuclear NMR spectra of blood; (b) mapping the central carbon metabolic pathway; (c) developing and using 1H and 31P spectral and chemical shift databases; and finally (d) confirming the putative metabolite peaks with spiking using authentic compounds. The resulting simple 1D 31P NMR-based method offers an ability to visualize and quantify the levels of intermediates and products of multiple metabolic pathways, including central carbon metabolism, in one step. Overall, the findings represent a new dimension for blood metabolite analysis and are anticipated to greatly impact the blood metabolomics field.PMID:37756488 | DOI:10.1021/acs.analchem.3c03040

MSU crystal deposition contributes to inflammation and immune responses in gout remission

Wed, 27/09/2023 - 12:00
Cell Rep. 2023 Sep 26;42(10):113139. doi: 10.1016/j.celrep.2023.113139. Online ahead of print.ABSTRACTAs a prominent feature of gout, monosodium urate (MSU) crystal deposition induces gout flares, but its impact on immune inflammation in gout remission remains unclear. Using single-cell RNA sequencing (scRNA-seq), we characterize the transcription profiling of peripheral blood mononuclear cells (PBMCs) among intercritical remission gout, advanced remission gout, and normal controls. We find systemic inflammation in gout remission with MSU crystal deposition at the intercritical and advanced stages, evidenced by activated inflammatory pathways, strengthened inflammatory cell-cell interactions, and elevated arachidonic acid metabolic activity. We also find increased HLA-DQA1high classic monocytes and PTGS2high monocytes in advanced gout and overactivated CD8+ T cell subtypes in intercritical and advanced gout. Additionally, the osteoclast differentiation pathway is significantly enriched in monocytes, T cells, and B cells from advanced gout. Overall, we demonstrate systemic inflammation and distinctive immune responses in gout remission with MSU crystal deposition, allowing further exploration of the underlying mechanism and clinical significance in conversion from intercritical to advanced stage.PMID:37756161 | DOI:10.1016/j.celrep.2023.113139

Effect of the Probiotic <em>Bacillus subtilis</em> DE-CA9<sup>TM</sup> on Fecal Scores, Serum Oxidative Stress Markers and Fecal and Serum Metabolome in Healthy Dogs

Wed, 27/09/2023 - 12:00
Vet Sci. 2023 Sep 11;10(9):566. doi: 10.3390/vetsci10090566.ABSTRACTBACKGROUND: There is increasing interest in the use of Bacillus species as probiotics since their spore-forming ability favors their survival in the acidic gastric environment over other probiotic species. The subsequent germination of B. subtilis to their vegetative form allows for their growth in the small intestine and may increase their beneficial effect on the host. B. subtilis strains have also previously been shown to have beneficial effects in humans and production animals, however, no reports are available so far on their use in companion animals.STUDY DESIGN: The goal of this study was therefore to investigate the daily administration of 1 × 109 cfu DE-CA9TM orally per day versus placebo on health parameters, fecal scores, fecal microbiome, fecal metabolomics, as well as serum metabolomics and oxidative stress markers in ten healthy Beagle dogs in a parallel, randomized, prospective, placebo-controlled design over a period of 45 days.RESULTS: DE-CA9TM decreased the oxidative status compared to controls for advanced oxidation protein products (AOPP), thiobarbituric acid reactive substances (TBARS) and reactive oxygen metabolites (d-ROMS), suggesting an antioxidant effect of the treatment. Fecal metabolomics revealed a significant reduction in metabolites associated with tryptophan metabolism in the DE-CA9TM-treated group. DE-CA9TM also significantly decreased phenylalanine and homocysteine and increased homoserine and threonine levels. Amino acid metabolism was also affected in the serum metabolome, with increased levels of urea and cadaverine, and reductions in N-acetylornithine in DE-CA9TM compared to controls. Similarly, changes in essential amino acids were observed, with a significant increase in tryptophan and lysine levels and a decrease in homocysteine. An increase in serum guanine and deoxyuridine was also detected, with a decrease in beta-alanine in the animals that ingested DE-CA9TM.CONCLUSIONS: Data generated throughout this study suggest that the daily administration of 1 × 109 cfu of DE-CA9TM in healthy Beagle dogs is safe and does not affect markers of general health and fecal scores. Furthermore, DE-CA9TM administration had a potential positive effect on some serum markers of oxidative stress, and protein and lipid metabolism in serum and feces.PMID:37756088 | DOI:10.3390/vetsci10090566

Antagonistic Activity of Oroxylin A against <em>Fusarium graminearum</em> and Its Inhibitory Effect on Zearalenone Production

Wed, 27/09/2023 - 12:00
Toxins (Basel). 2023 Aug 31;15(9):535. doi: 10.3390/toxins15090535.ABSTRACTFusarium graminearum produces zearalenone (ZEA), a mycotoxin that is widely found in food and feed products and is toxic to humans and livestock. Piper sarmentosum extract (PSE) inhibits F. graminearum, and Oroxylin A appears to be a major antifungal compound in PSE. The aim of this study is to quantify the Oroxylin A content in PSE using UPLC-QTOF-MS/MS, and to investigate the antagonistic activity of Oroxylin A against F. graminearum and its inhibitory effect on ZEA production. The results indicate that Oroxylin A inhibits both fungal growth and ZEA production in a dose-dependent manner. Oroxylin A treatment downregulated the mRNA expression of zearalenone biosynthesis protein 1 (ZEB1) and zearalenone biosynthesis protein 2 (ZEB2). The metabolomics analysis of F. graminearum mycelia indicated that the level of ribose 5-phosphate (R5P) deceased (p < 0.05) after Oroxylin A treatment (64-128 ng/mL). Moreover, as the Oroxylin A treatment content increased from 64 to 128 ng/mL, the levels of cis-aconitate (p < 0.05) and fumarate (p < 0.01) were upregulated successively. A correlation analysis further showed that the decreased R5P level was positively correlated with ZEB1 and ZEB2 expression, while the increased cis-aconitate and fumarate levels were negatively correlated with ZEB1 and ZEB2 expression. These findings demonstrate the potential of Oroxylin A as a natural agent to control toxigenic fungi and their mycotoxin.PMID:37755961 | DOI:10.3390/toxins15090535

Untargeted Metabolomics Approach Correlated Enniatin B Mycotoxin Presence in Cereals with Kashin-Beck Disease Endemic Regions of China

Wed, 27/09/2023 - 12:00
Toxins (Basel). 2023 Aug 30;15(9):533. doi: 10.3390/toxins15090533.ABSTRACTKashin-Beck disease (KBD) is a multifactorial endemic disease that only occurs in specific Asian areas. Mycotoxin contamination, especially from the Fusarium spp., has been considered as one of the environmental risk factors that could provoke chondrocyte and cartilage damage. This study aimed to investigate whether new mycotoxins could be identified in KBD-endemic regions as a potential KBD risk factor. This was investigated on 292 barley samples collected in Tibet during 2009-2016 and 19 wheat samples collected in Inner Mongolia in 2006, as control, from KBD-endemic and non-endemic areas. The LC-HRMS(/MS) data, obtained by a general mycotoxin extraction technic, were interpreted by both untargeted metabolomics and molecular networks, allowing us to identify a discriminating compound, enniatin B, a mycotoxin produced by some Fusarium spp. The presence of Fusarium spp. DNA was detected in KBD-endemic area barley samples. Further studies are required to investigate the role of this mycotoxin in KBD development in vivo.PMID:37755959 | DOI:10.3390/toxins15090533

Multiplatform Metabolomics to Understand the Imidacloprid-Induced Toxicity in <em>Drosophila</em>

Wed, 27/09/2023 - 12:00
Chem Res Toxicol. 2023 Sep 27. doi: 10.1021/acs.chemrestox.3c00127. Online ahead of print.ABSTRACTNeonicotinoids, the class of insecticides used for crop protection, are subjected to vigilance due to their pernicious impacts. Imidacloprid (IMD) is one of the most representative insecticides of the neonicotinoid family, which has shown unfriendly consequences for non-target species. Metabolomics, a multidisciplinary approach, is being used in toxicological research to understand the metabolic responses to toxicant exposure by utilizing modern analytical techniques. Yet, no solitary analytical technique can cover the broad metabolite spectrum, but a multi-technique metabolomics platform can aid in analyzing the majority of the metabolites. In the present study, an effort has been made to identify the differential metabolites in Drosophila after exposure to IMD at 2.5 and 25 ng/mL using liquid chromatography-high-resolution mass spectrometry (LC-HRMS), gas chromatography-MS (GC-MS), and NMR-based untargeted metabolomics. Multivariate pattern recognition analysis helped in identifying/recognizing 19 (LC-HRMS), 7 (GC-MS), and 13 (NMR) differential metabolites mainly belonging to the category of amino acids, sugars, fatty acids, and organic acids. The pathway analysis of differential metabolites predominantly showed impact on aminoacyl-tRNA biosynthesis, amino acid metabolism, and glycerophospholipid metabolism. Among these, arginine and proline metabolism was observed to be the common metabolic pathway perturbed in Drosophila due to IMD exposure. The multiplatform metabolomics based on LC-HRMS, GC-MS, and NMR analysis with an advanced level of statistical analysis can provide insights into potential perturbations in the metabolome of IMD-exposed Drosophila.PMID:37755873 | DOI:10.1021/acs.chemrestox.3c00127

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