PubMed

Methods Mol Biol. 2023;2636:43-53. doi: 10.1007/978-1-0716-3012-9_3.ABSTRACTRetinal ganglion cell (RGC) axon regeneration in mammals can be stimulated through gene knockouts, pharmacological agents, and biophysical stimulation. Here we present a fractionation method to isolate regenerating RGC axons for downstream analysis using immunomagnetic separation of cholera toxin subunit B (CTB)-bound RGC axons. After optic nerve tissue dissection and dissociation, conjugated CTB is used to bind preferentially to regenerated RGC axons. Anti-CTB antibodies crosslinked to magnetic sepharose beads are used to isolate CTB-bound axons from a nonbound fraction of extracellular matrix and neuroglia. We provide a method of verifying fractionation by immunodetection of conjugated CTB and the RGC marker, Tuj1 (β-tubulin III). These fractions can be further analyzed with lipidomic methods, such as LC-MS/MS to gather fraction-specific enrichments.PMID:36881294 | DOI:10.1007/978-1-0716-3012-9_3

J Plant Res. 2023 Mar 7. doi: 10.1007/s10265-023-01446-8. Online ahead of print.ABSTRACTPinellia ternata (Thunb.) Breit. is an important traditional Chinese medicinal herb and very sensitive to high temperatures. To gain a better understanding of flavonoid biosynthesis under heat stress in P. ternata, we performed integrated analyses of metabolome and transcriptome data. P. ternata plants were subjected to a temperature of 38 °C, and samples were collected after 10 d of treatment. A total of 502 differential accumulated metabolites and 5040 different expressed transcripts were identified, with flavonoid biosynthesis predominantly enriched. Integrated metabolomics and transcriptome analysis showed that high temperature treatment upregulated the expression of CYP73A and downregulated the expression of other genes (such as HCT, CCoAOMT, DFR1, DFR2), which might inhibit the biosynthesis of the downstream metabolome, including such metabolites as chlorogenic acid, pelargonidin, cyanidin, and (-)-epigallocatechin in the flavonoid biosynthesis pathway. The transcription expression levels of these genes were validated by real-time PCR. Our results provide valuable insights into flavonoid composition and accumulation patterns and the candidate genes participating in the flavonoid biosynthesis pathways under heat stress in P. ternata.PMID:36881276 | DOI:10.1007/s10265-023-01446-8

Amino Acids. 2023 Mar 7. doi: 10.1007/s00726-023-03258-5. Online ahead of print.ABSTRACTAdiposity is an important determinant of blood metabolites, but little is known about the variations of blood amino acids according to general and central adiposity status among Chinese population. This study included 187 females and 322 males who were cancer-free subjects randomly selected from two cohorts in Shanghai, China. Participants' plasma concentrations of amino acids were measured by ultra-performance liquid chromatography coupled to tandem mass spectrometry. Linear regression models were used to examine the cross-sectional correlations between general and central adiposity and amino acid levels. A total of 35 amino acids in plasma were measured in this study. In females, alanine, aspartic acid and pyroglutamic acid were positively correlated with general adiposity. In males, glutamic acid, aspartic acid, valine and pyroglutamic acid showed positive correlations, and glutamine, serine and glycine showed negative correlations with both general and central adiposity; phenylalanine, isoleucine and leucine were positively correlated and N-phenylacetylglutamine was negatively correlated with general adiposity; asparagine was negatively correlated with central adiposity. In summary, general adiposity and central adiposity were correlated with the concentrations of specific plasma amino acids among cancer-free female and male adults in China. Adiposity-metabolite characteristics and relationships should be considered when studying blood biomarkers for adiposity-related health outcomes.PMID:36881189 | DOI:10.1007/s00726-023-03258-5

Psychopharmacology (Berl). 2023 Mar 7. doi: 10.1007/s00213-023-06348-0. Online ahead of print.ABSTRACTRATIONALE: Parkinson's disease (PD) is a chronic and progressive neurodegenerative disorder. Increasing evidence suggests the role of the gut-microbiota-brain axis in the pathogenesis of PD. Mesenchymal stem-cell-derived microvesicles (MSC-MVs) have emerged as a therapeutic potential for neurological disorders over the last years.OBJECTIVE: The objective of this study was to investigate whether MSC-MVs could improve PD-like neurotoxicity in mice after administration of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).RESULTS: MPTP-induced reductions in the dopamine transporter and tyrosine hydroxylase expressions in the striatum and substantia nigra (SNr) were attenuated after a subsequent single administration of MSC-MVs. Increases in the phosphorylated α-synuclein (p-α-Syn)/α-Syn ratio in the striatum, SNr, and colon after MPTP injection were also attenuated after MSC-MVs injection. Furthermore, MSC-MVs restored MPTP-induced abnormalities of the gut microbiota composition. Interestingly, positive correlations between the genus Dubosiella and the p-α-Syn/α-Syn ratio were observed in the brain and colon, suggesting their roles in the gut-microbiota-brain communication. Moreover, MSC-MVs attenuated MPTP-induced reduction of the metabolite, 3,6-dihydroxy-2-[3-methoxy-4-(sulfooxy)phenyl]-7-(sulfinooxy)-3,4-dihydro-2H-1-benzopyran-5-olate, in the blood. Interestingly, a negative correlation between this compound and the p-α-Syn/α-Syn ratio was observed in the brain and colon.CONCLUSIONS: These data suggest that MSC-MVs could ameliorate MPTP-induced neurotoxicity in the brain and colon via the gut-microbiota-brain axis. Therefore, MSC-MVs would have a new therapeutic potential for neurological disorders such as PD.PMID:36881113 | DOI:10.1007/s00213-023-06348-0

Aging (Albany NY). 2023 Feb 24;15(4):1039-1051. doi: 10.18632/aging.204528. Online ahead of print.ABSTRACTPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a poor prognosis. Reprogramming of amino acid metabolism is one of the characteristics of PDAC, in which arginine metabolism is significantly altered in PDAC cells and is involved in important signaling pathways. Current studies have identified arginine deprivation as a potential strategy for PDAC treatment. In this study, we performed Liquid Chromatograph Mass Spectrometer (LC-MS)-based non-targeted metabolomic analysis on PDAC cell lines with stable Rio Kinase 3 (RIOK3) knockdown and PDAC tissues with different RIOK3 expressions and found that RIOK3 expression was significantly correlated with arginine metabolism in PDAC. Subsequent RNA sequencing (RNA-Seq) and Western blot analysis showed that RIOK3 knockdown significantly inhibited the expression of arginine transporter solute carrier family 7 member 2 (SLC7A2). Further studies revealed that RIOK3 promoted arginine uptake, mechanistic target of rapamycin complex 1 (mTORC1) activation, cell invasion, and metastasis in PDAC cells via SLC7A2. Finally, we found that patients with high expression of both RIOK3 and infiltrating Treg cells had a worse prognosis. Overall, our study found that RIOK3 in PDAC cells promotes arginine uptake and mTORC1 activation through upregulation of SLC7A2 expression, and also provides a new therapeutic target for therapeutic strategies targeting arginine metabolism.PMID:36880835 | DOI:10.18632/aging.204528

Integr Zool. 2023 Mar 7. doi: 10.1111/1749-4877.12710. Online ahead of print.ABSTRACTThe harsh environment in the Tibetan plateau, the highest place in the world, poses thermoregulatory challenges and hypoxic stress to animals. The impacts of plateau environment on animal physiology and reproduction include external factors such as strong ultraviolet radiation and low temperature, and internal factors such as animal metabolites and gut microbiota. However, it remains unclear how plateau pika adapt to high altitudes through the combination of serum metabolites and gut microbiota. To this end, we captured 24 wild plateau pikas at the altitudes of 3400 m, 3600 m, or 3800 m a.s.l. in a Tibetan alpine grassland. Using the machine learning algorithms (random forest), we identified five biomarkers of serum metabolites indicative of the altitudes, i.e., dihydrotestosterone, homo-L-arginine, alpha-ketoglutaric-acid, serotonin and threonine, which were related to body weight, reproduction, and energy metabolism of pika. Those metabolic biomarkers were positively correlated with Lachnospiraceae_ Agathobacter, Ruminococcaceae, or Prevotellaceae_Prevotella, suggesting the close relationship between metabolites and gut microbiota. By identifying the metabolic biomarkers and gut microbiota analysis, we reveal the mechanisms of adaptation to high altitudes in plateau pika. This article is protected by copyright. All rights reserved.PMID:36880690 | DOI:10.1111/1749-4877.12710

Environ Toxicol. 2023 Mar 7. doi: 10.1002/tox.23763. Online ahead of print.ABSTRACTMicroplastics (MPs) and nanoplastics (NPs) are novel environmental pollutants that are ubiquitous in the environment and everyday life. NPs can easily enter the tissues and have more significant potential health risks due to their smaller diameter. Previous studies have shown that NPs can induce male reproductive toxicity, but the detailed mechanisms remain uncertain. In this study, intragastric administration treated mice with polystyrene NPs (PS-NPs, 50, and 90 nm) at 3 and 15 mg/mL/day doses for 30 days. Then, the fresh fecal samples were collected from those mice that the exposure doses of 50 nm PS-NPs at 3 mg/mL/day and 90 nm at 15 mg/mL/day for subsequent investigations of 16S rRNA and metabolomics according to significant toxicological effects (Sperm number, viability, abnormality, and testosterone level). The conjoint analysis findings indicated that PS-NPs disrupted the homeostasis of the gut microbiota, metabolism, and male reproduction, suggesting that abnormal gut microbiota-metabolite pathways may be important in PS-NPs-induced male reproductive toxicity. Meanwhile, the common differential metabolites such as 4-deoxy-Erythronic acid, 8-iso-15-keto-PGE2, apo-10'-violaxanthin, beta-D-glucosamine, isokobusone, oleamide, oxoadipic acid, sphingosine induced by 50 and 90 nm PS-NPs might be used as biomarkers to explore PS-NPs-induced male reproductive toxicity. In addition, this study systematically demonstrated that nano-scale PS-NPs induced male reproductive toxicity via the crosstalk of gut microbiota and metabolites. It also provided valuable insights into the toxicity of PS-NPs, which was conducive to reproductive health risk assessment for public health prevention and treatment.PMID:36880397 | DOI:10.1002/tox.23763

J Inherit Metab Dis. 2023 Mar 7. doi: 10.1002/jimd.12604. Online ahead of print.ABSTRACTMaple syrup urine disease (MSUD) is rare autosomal recessive metabolic disorder caused by the dysfunction of the mitochondrial branched-chain 2-ketoacid dehydrogenase (BCKD) enzyme complex leading to massive accumulation of branched-chain amino and 2-keto acids. MSUD management, based on a life-long strict protein restriction with non-toxic amino acids oral supplementation represents an unmet need as it is associated with a poor quality of life, and does not fully protect from acute life-threatening decompensations or long-term neuropsychiatric complications. Orthotopic liver transplantation is a beneficial therapeutic option, which shows that restoration of only a fraction of whole-body BCKD enzyme activity is therapeutic. MSUD is thus an ideal target for gene therapy. We and others have tested AAV gene therapy in mice for two of the three genes involved in MSUD, BCKDHA and DBT. In this study, we developed a similar approach for the third MSUD gene, BCKDHB. We performed the first characterization of a Bckdhb-/- mouse model, which recapitulates the severe human phenotype of MSUD with early-neonatal symptoms leading to death during the first week of life with massive accumulation of MSUD biomarkers. Based on our previous experience in Bckdha-/- mice, we designed a transgene carrying the human BCKDHB gene under the control of a ubiquitous EF1α promoter, encapsidated in an AAV8 capsid. Injection in neonatal Bckdhb-/- mice at 1014 vg/kg achieved long-term rescue of the severe MSUD phenotype of Bckdhb-/- mice. These data further validate the efficacy of gene therapy for MSUD opening perspectives towards clinical translation. This article is protected by copyright. All rights reserved.PMID:36880392 | DOI:10.1002/jimd.12604

Cancer Med. 2023 Mar 7. doi: 10.1002/cam4.5759. Online ahead of print.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) is aggressive liver cancer. Despite advanced imaging and other diagnostic measures, HCC in a significant portion of patients had reached the advanced stage at the first diagnosis. Unfortunately, there is no cure for advanced HCC. As a result, HCC is still a leading cause of cancer death, and there is a pressing need for new diagnostic markers and therapeutic targets.METHODS: We investigated sulfotransferase 1C2 (SUTL1C2), which we recently showed was overexpressed in human HCC cancerous tissues. Specifically, we analyzed the effects of SULT1C2 knockdown on the growth, survival, migration, and invasiveness of two HCC cell lines, i.e., HepG2 and Huh7 cells. We also studied the transcriptomes and metabolomes in the two HCC cell lines before and after SULT1C2 knockdown. Based on the transcriptome and metabolome data, we further investigated the SULT1C2 knockdown-mediated shared changes, i.e., glycolysis and fatty acid metabolism, in the two HCC cell lines. Finally, we performed rescue experiments to determine whether the inhibitory effects of SULT1C2 knockdown could be rescued via overexpression.RESULTS: We showed that SULT1C2 overexpression promoted the growth, survival, migration, and invasiveness of HCC cells. In addition, SULT1C2 knockdown resulted in a wide range of gene expression and metabolome changes in HCC cells. Moreover, analysis of shared alterations showed that SULT1C2 knockdown significantly suppressed glycolysis and fatty acid metabolism, which could be rescued via SULT1C2 overexpression.CONCLUSIONS: Our data suggest that SULT1C2 is a potential diagnostic marker and therapeutic target for human HCC.PMID:36880364 | DOI:10.1002/cam4.5759

Plant J. 2023 Mar 7. doi: 10.1111/tpj.16160. Online ahead of print.ABSTRACTPlant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1-week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated ~81% of the fragmented peaks versus ~6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed ~37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bioanalytical Resource website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.PMID:36880270 | DOI:10.1111/tpj.16160

Br Poult Sci. 2023 Mar 7. doi: 10.1080/00071668.2022.2154638. Online ahead of print.ABSTRACT1. In this study, transcriptomics and metabolomics were used to analyse changes in gene expression and metabolites in the liver of 70-d-old mule ducks after 10 and 20 d of continuous overfeeding.2. In the free-feeding group, 995 differentially expressed genes and 51 metabolites (VIP>1, P<0.05) were detected in the early stage, and 3,448 differentially expressed genes and 55 metabolites (VIP>1, P<0.05) were detected in the later stage. There were 775 differentially expressed genes and 47 metabolites (VIP>1, P<0.05) detected in the early stage of the overfeeding group, and 6,719 differentially expressed genes and 57 metabolites (VIP>1, P<0.05) detected in the later stage.3. There were no significant differences between the early stage in the overfeeding and free-feeding groups at the transcriptional and metabolic levels. Oleic acid and palmitic acid synthesis increased in the early stage of the overfeeding and free-feeding groups, however, these were inhibited in the late stage. Fatty acid oxidation and β-oxidation pathways were inhibited and insulin resistance was enhanced significantly in the late overfeeding stage.4. In the early stage, the digestion and absorption of fat in the overfeeding and free-feeding groups were enhanced. In the later stage, the ability to store triglyceride in the overfeeding group was greater than in the free-feeding group.5. The expression of nuclear factor κB (NFκB), a key inflammatory factor, was inhibited in the late stage of overfeeding, while arachidonic acid (AA), a metabolite with anti-inflammatory properties, increased in the late stage of overfeeding to inhibit the inflammatory effects caused by excessive lipid accumulation. These results add to the understanding of the mechanism of production of fatty liver in mule ducks and facilitate the development of treatments for non-alcoholic fatty liver disease.PMID:36880206 | DOI:10.1080/00071668.2022.2154638

Platelets. 2023 Dec;34(1):2182180. doi: 10.1080/09537104.2023.2182180.ABSTRACTBesides their proteome, platelets use, in all responses to the environmental cues, a huge and diverse family of hydrophobic and amphipathic small molecules involved in structural, metabolic and signaling functions; the lipids. Studying how platelet lipidome changes modulate platelet function is an old story constantly renewed through the impressive technical advances allowing the discovery of new lipids, functions and metabolic pathways. Technical progress in analytical lipidomic profiling by top-of-the-line approaches such as nuclear magnetic resonance and gas chromatography or liquid chromatography coupled to mass spectrometry enables either large-scale analysis of lipids or targeted lipidomics. With the support of bioinformatics tools and databases, it is now possible to investigate thousands of lipids over a concentration range of several orders of magnitude. The lipidomic landscape of platelets is considered a treasure trove, not only able to expand our knowledge of platelet biology and pathologies but also to bring diagnostic and therapeutic opportunities. The aim of this commentary article is to summarize the advances in the field and to highlight what lipidomics can tell us about platelet biology and pathophysiology.PMID:36880158 | DOI:10.1080/09537104.2023.2182180

Neurooncol Adv. 2022 Dec 13;5(1):vdac181. doi: 10.1093/noajnl/vdac181. eCollection 2023 Jan-Dec.ABSTRACTBACKGROUND: Primary central nervous system lymphoma (PCNSL) is a highly aggressive non-Hodgkin's B-cell lymphoma which normally treated by high-dose methotrexate (HD-MTX)-based chemotherapy. However, such treatment cannot always guarantee a good prognosis (GP) outcome while suffering several side effects. Thus, biomarkers or biomarker-based models that can predict PCNSL patient prognosis would be beneficial.METHODS: We first collected 48 patients with PCNSL and applied HPLC-MS/MS-based metabolomic analysis on such retrospective PCNSL patient samples. We then selected the highly dysregulated metabolites to build a logical regression model that can distinguish the survival time length by a scoring standard. Finally, we validated the logical regression model on a 33-patient prospective PCNSL cohort.RESULTS: Six metabolic features were selected from the cerebrospinal fluid (CSF) that can form a logical regression model to distinguish the patients with relatively GP (Z score ≤0.06) from the discovery cohort. We applied the metabolic marker-based model to a prospective recruited PCNSL patient cohort for further validation, and the model preformed nicely on such a validation cohort (AUC = 0.745).CONCLUSIONS: We developed a logical regression model based on metabolic markers in CSF that can effectively predict PCNSL patient prognosis before the HD-MTX-based chemotherapy treatments.PMID:36879663 | PMC:PMC9985165 | DOI:10.1093/noajnl/vdac181

J Oleo Sci. 2023;72(3):273-282. doi: 10.5650/jos.ess22164.ABSTRACTThe present study aimed to analyze the lipid profiles of three selected chicken eggs (Nixi, silky fowl, and ordinary eggs) from the market of China by an UPLC-Q-Exactive-MS based untargeted lipidomics approach. In total, 11 classes and 285 lipid molecular species were identified from the egg yolks. Glycerophospholipids (GPLs, 6 classes, 168 lipid species) are the most abundant lipids groups, followed by sphingolipids (3 classes, 50 lipid species), and two neutral lipid classes (TG and DG). Notably, two ethersubclass of GPLs (PC-e and PE-p) and 12 species of cerebrosides were firstly detected from the chicken eggs. Furthermore, multivariate statistical analysis was performed and the lipids profiles of the three types of eggs were well discriminated from each other by 30 predominant lipids species. The characteristic lipid molecules of the different kind of eggs were also screened out. This study provides a novel insight for better understanding the lipid profiles and nutritional values of different chicken eggs.PMID:36878581 | DOI:10.5650/jos.ess22164

Front Immunol. 2023 Feb 16;14:1124910. doi: 10.3389/fimmu.2023.1124910. eCollection 2023.ABSTRACTINTRODUCTION: Lipopolysaccharide (LPS)-accelerated autoimmune glomerulonephritis (GN) in NZBWF1 mice is a preclinical model potentially applicable for investigating lipidome-modulating interventions against lupus. LPS can be expressed as one of two chemotypes: smooth LPS (S-LPS) or rough LPS (R-LPS) which is devoid of O-antigen polysaccharide sidechain. Since these chemotypes differentially affect toll-like receptor 4 (TLR4)-mediated immune cell responses, these differences may influence GN induction.METHODS: We initially compared the effects of subchronic intraperitoneal (i.p.) injection for 5 wk with 1) Salmonella S-LPS, 2) Salmonella R-LPS, or 3) saline vehicle (VEH) (Study 1) in female NZBWF1 mice. Based on the efficacy of R-LPS in inducing GN, we next used it to compare the impact of two lipidome-modulating interventions, ω-3 polyunsaturated fatty acid (PUFA) supplementation and soluble epoxide hydrolase (sEH) inhibition, on GN (Study 2). Specifically, effects of consuming ω-3 docosahexaenoic acid (DHA) (10 g/kg diet) and/or the sEH inhibitor 1-(4-trifluoro-methoxy-phenyl)-3-(1-propionylpiperidin-4-yl) urea (TPPU) (22.5 mg/kg diet ≈ 3 mg/kg/day) on R-LPS triggering were compared.RESULTS: In Study 1, R-LPS induced robust elevations in blood urea nitrogen, proteinuria, and hematuria that were not evident in VEH- or S-LPS-treated mice. R-LPS-treated mice further exhibited kidney histopathology including robust hypertrophy, hyperplasia, thickened membranes, lymphocytic accumulation containing B and T cells, and glomerular IgG deposition consistent with GN that was not evident in VEH- or SLPS-treated groups. R-LPS but not S-LPS induced spleen enlargement with lymphoid hyperplasia and inflammatory cell recruitment in the liver. In Study 2, resultant blood fatty acid profiles and epoxy fatty acid concentrations reflected the anticipated DHA- and TPPU-mediated lipidome changes, respectively. The relative rank order of R-LPS-induced GN severity among groups fed experimental diets based on proteinuria, hematuria, histopathologic scoring, and glomerular IgG deposition was: VEH/CON< R-LPS/DHA ≈ R-LPS/TPPU<<< R-LPS/TPPU+DHA ≈ R-LPS/CON. In contrast, these interventions had modest-to- negligible effects on R-LPS-induced splenomegaly, plasma antibody responses, liver inflammation, and inflammation-associated kidney gene expression.DISCUSSION: We show for the first time that absence of O-antigenic polysaccharide in R-LPS is critical to accelerated GN in lupus-prone mice. Furthermore, intervention by lipidome modulation through DHA feeding or sEH inhibition suppressed R-LPS-induced GN; however, these ameliorative effects were greatly diminished upon combining the treatments.PMID:36875087 | PMC:PMC9978350 | DOI:10.3389/fimmu.2023.1124910

J Anim Sci Biotechnol. 2023 Mar 7;14(1):39. doi: 10.1186/s40104-022-00823-y.ABSTRACTBACKGROUND: Lipid metabolism differs significantly between grazing and stall-feeding lambs, affecting the quality of livestock products. As two critical organs of lipid metabolism, the differences between feeding patterns on rumen and liver metabolism remain unclear. In this study, 16S rRNA, metagenomics, transcriptomics, and untargeted metabolomics were utilized to investigate the key rumen microorganisms and metabolites, as well as liver genes and metabolites associated with fatty acid metabolism under indoor feeding (F) and grazing (G).RESULTS: Compared with grazing, indoor feeding increased ruminal propionate content. Using metagenome sequencing in combination with 16S rRNA amplicon sequencing, the results showed that the abundance of propionate-producing Succiniclasticum and hydrogenating bacteria Tenericutes was enriched in the F group. For rumen metabolism, grazing caused up-regulation of EPA, DHA and oleic acid and down-regulation of decanoic acid, as well as, screening for 2-ketobutyric acid as a vital differential metabolite, which was enriched in the propionate metabolism pathway. In the liver, indoor feeding increased 3-hydroxypropanoate and citric acid content, causing changes in propionate metabolism and citrate cycle, while decreasing the ETA content. Then, the liver transcriptome revealed that 11 lipid-related genes were differentially expressed in the two feeding patterns. Correlation analysis showed that the expression of CYP4A6, FADS1, FADS2, ALDH6A1 and CYP2C23 was significantly associated with the propionate metabolism process, suggesting that propionate metabolism may be an important factor mediating the hepatic lipid metabolism. Besides, the unsaturated fatty acids in muscle, rumen and liver also had a close correlation.CONCLUSIONS: Overall, our data demonstrated that rumen microbial-driven metabolite from grazing lambs potentially regulates multiple hepatic lipid-related genes, ultimately affecting body fatty acid metabolism.PMID:36879349 | DOI:10.1186/s40104-022-00823-y

Hum Genomics. 2023 Mar 6;17(1):18. doi: 10.1186/s40246-023-00465-9.ABSTRACTBACKGROUND: The metabolome is the best representation of cancer phenotypes. Gene expression can be considered a confounding covariate affecting metabolite levels. Data integration across metabolomics and genomics to establish the biological relevance of cancer metabolism is challenging. This study aimed to eliminate the confounding effect of metabolic gene expression to reflect actual metabolite levels in microsatellite instability (MSI) cancers.METHODS: In this study, we propose a new strategy using covariate-adjusted tensor classification in high dimensions (CATCH) models to integrate metabolite and metabolic gene expression data to classify MSI and microsatellite stability (MSS) cancers. We used datasets from the Cancer Cell Line Encyclopedia (CCLE) phase II project and treated metabolomic data as tensor predictors and data on gene expression of metabolic enzymes as confounding covariates.RESULTS: The CATCH model performed well, with high accuracy (0.82), sensitivity (0.66), specificity (0.88), precision (0.65), and F1 score (0.65). Seven metabolite features adjusted for metabolic gene expression, namely, 3-phosphoglycerate, 6-phosphogluconate, cholesterol ester, lysophosphatidylethanolamine (LPE), phosphatidylcholine, reduced glutathione, and sarcosine, were found in MSI cancers. Only one metabolite, Hippurate, was present in MSS cancers. The gene expression of phosphofructokinase 1 (PFKP), which is involved in the glycolytic pathway, was related to 3-phosphoglycerate. ALDH4A1 and GPT2 were associated with sarcosine. LPE was associated with the expression of CHPT1, which is involved in lipid metabolism. The glycolysis, nucleotide, glutamate, and lipid metabolic pathways were enriched in MSI cancers.CONCLUSIONS: We propose an effective CATCH model for predicting MSI cancer status. By controlling the confounding effect of metabolic gene expression, we identified cancer metabolic biomarkers and therapeutic targets. In addition, we provided the possible biology and genetics of MSI cancer metabolism.PMID:36879264 | DOI:10.1186/s40246-023-00465-9

Respir Res. 2023 Mar 6;24(1):69. doi: 10.1186/s12931-023-02375-9.ABSTRACTBACKGROUND: Airway epithelium is the first barrier against environmental insults, and epithelial barrier dysfunction caused by cigarette smoke (CS) is particularly relevant to chronic obstructive pulmonary disease (COPD) progression. Our study was to determine whether Azithromycin (AZI) ameliorates CS-induced airway epithelial barrier dysfunction and the underlying mechanisms.METHODS: Primary bronchial epithelial cells (PBECs), human bronchial epithelial cells (HBECs), Sprague Dawley rats and nuclear factor erythroid 2-related factor 2 (Nrf2)-/- mice were pretreated with AZI and subsequently exposed to CS. Transepithelial electronic resistance (TEER), junction proteins as well as pro-inflammatory cytokines and apoptosis markers were examined to assess epithelial barrier dysfunction. Metabolomics study was applied to explore the underlying mechanism of AZI.RESULTS: CS-induced TEER decline and intercellular junction destruction, accompanied with inflammatory response and cell apoptosis in PBECs were restored by AZI dose-dependently, which were also observed in CS-exposed rats. Mechanistically, GSH metabolism pathway was identified as the top differentially impacted pathway and AZI treatment upregulated the activities of glutamate cysteine ligase (GCL) and the contents of metabolites in GSH metabolic pathway. Furthermore, AZI apparently reversed CS-induced Nrf2 suppression, and similar effects on airway epithelial barrier dysfunction were also found for Nrf2 agonist tert-butylhydroquinone and vitamin C. Finally, deletion of Nrf2 in both HBECs and C57BL/6N mice aggravated CS-induced GSH metabolism imbalance to disrupt airway epithelial barrier and partially deprived the effects of AZI.CONCLUSION: These findings suggest that the clinical benefits of AZI for COPD management are related with the protection of CS-induced airway epithelial barrier dysfunction via activating Nrf2/GCL/GSH pathway, providing potential therapeutic strategies for COPD.PMID:36879222 | DOI:10.1186/s12931-023-02375-9

Sci Rep. 2023 Mar 6;13(1):3695. doi: 10.1038/s41598-023-30892-6.ABSTRACTAlzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the formation of amyloid plaques implicated in neuronal death. Genetics, age, and sex are the risk factors attributed to AD. Though omics studies have helped to identify pathways associated with AD, an integrated systems analysis with the available data could help to understand mechanisms, potential biomarkers, and therapeutic targets. Analysis of transcriptomic data sets from the GEO database, and proteomic and metabolomic data sets from literature was performed to identify deregulated pathways and commonality analysis identified overlapping pathways among the data sets. The deregulated pathways included those of neurotransmitter synapses, oxidative stress, inflammation, vitamins, complement, and coagulation pathways. Cell type analysis of GEO data sets showed microglia, endothelial, myeloid, and lymphoid cells are affected. Microglia are associated with inflammation and pruning of synapses with implications for memory and cognition. Analysis of the protein-cofactor network of B2, B6, and pantothenate shows metabolic pathways modulated by these vitamins which overlap with the deregulated pathways from the multi-omics analysis. Overall, the integrated analysis identified the molecular signature associated with AD. Treatment with anti-oxidants, B2, B6, and pantothenate in genetically susceptible individuals in the pre-symptomatic stage might help in better management of the disease.PMID:36879094 | DOI:10.1038/s41598-023-30892-6

Nat Chem Biol. 2023 Mar 6. doi: 10.1038/s41589-023-01276-8. Online ahead of print.ABSTRACTNatural products research increasingly applies -omics technologies to guide molecular discovery. While the combined analysis of genomic and metabolomic datasets has proved valuable for identifying natural products and their biosynthetic gene clusters (BGCs) in bacteria, this integrated approach lacks application to fungi. Because fungi are hyper-diverse and underexplored for new chemistry and bioactivities, we created a linked genomics-metabolomics dataset for 110 Ascomycetes, and optimized both gene cluster family (GCF) networking parameters and correlation-based scoring for pairing fungal natural products with their BGCs. Using a network of 3,007 GCFs (organized from 7,020 BGCs), we examined 25 known natural products originating from 16 known BGCs and observed statistically significant associations between 21 of these compounds and their validated BGCs. Furthermore, the scalable platform identified the BGC for the pestalamides, demystifying its biogenesis, and revealed more than 200 high-scoring natural product-GCF linkages to direct future discovery.PMID:36879060 | DOI:10.1038/s41589-023-01276-8