PubMed

Front Pharmacol. 2023 Aug 11;14:1213602. doi: 10.3389/fphar.2023.1213602. eCollection 2023.ABSTRACTWuwei Shexiang Pill (WSP) is a Tibetan traditional medicine, which has been demonstrated to exhibit potent anti-inflammatory and anti-gout effects. However, the specific pharmacological mechanism is not elucidated clearly. In the present study, liquid chromatography-mass spectrometry (LC-MS)-based metabolomics was applied to investigate the alteration of serum metabolites induced by WSP treatment in MSU-induced gouty rats. Subsequently, bioinformatics was utilized to analyze the potential metabolic pathway of the anti-gout effect of WSP. The pharmacodynamic data discovered that WSP could ameliorate ankle swelling and inflammatory cell infiltration, as well as downregulate the protein expression of IL-1β, p-NF-κB p65, and NLRP3 in the synovial membrane and surrounding tissues of gouty ankles. LC-MS-based metabolomics revealed that there were 30 differential metabolites in the serum between sham-operated rats and gouty ones, which were mainly involved in the metabolism of fructose and mannose, primary bile acid biosynthesis, and cholesterol metabolism. However, compared to the model group, WSP treatment upregulated 11 metabolic biomarkers and downregulated 31 biomarkers in the serum. KEGG enrichment analysis found that 27 metabolic pathways contributed to the therapeutic action of WSP, including linoleic acid metabolism, phenylalanine metabolism, and pantothenate and CoA biosynthesis. The comprehensive analysis-combined network pharmacology and metabolomics further revealed that the regulatory network of WSP against gout might be attributed to 11 metabolites, 7 metabolic pathways, 39 targets, and 49 active ingredients of WSP. In conclusion, WSP could ameliorate the inflammation of the ankle in MSU-induced gouty rats, and its anti-gout mechanism might be relevant to the modulation of multiple metabolic pathways, such as linoleic acid metabolism, phenylalanine metabolism, and pantothenate and CoA biosynthesis. This study provided data support for the secondary development of Chinese traditional patent medicine.PMID:37637422 | PMC:PMC10450745 | DOI:10.3389/fphar.2023.1213602

Front Pharmacol. 2023 Aug 11;14:1212634. doi: 10.3389/fphar.2023.1212634. eCollection 2023.ABSTRACTObjective: Trabectedin is an anti-cancer drug commonly used for the treatment of patients with metastatic soft tissue sarcoma (mSTS). Despite its recognized efficacy, significant variability in pharmacological response has been observed among mSTS patients. To address this issue, this pharmacometabolomics study aimed to identify pre-dose plasma metabolomics signatures that can explain individual variations in trabectedin pharmacokinetics and overall clinical response to treatment. Methods: In this study, 40 mSTS patients treated with trabectedin administered by 24 h-intravenous infusion at a dose of 1.5 mg/m2 were enrolled. The patients' baseline plasma metabolomics profiles, which included derivatives of amino acids and bile acids, were analyzed using multiple reaction monitoring LC-MS/MS together with their pharmacokinetics profile of trabectedin. Multivariate Partial least squares regression and univariate statistical analyses were utilized to identify correlations between baseline metabolite concentrations and trabectedin pharmacokinetics, while Partial Least Squares-Discriminant Analysis was employed to evaluate associations with clinical response. Results: The multiple regression model, derived from the correlation between the AUC of trabectedin and pre-dose metabolomics, exhibited the best performance by incorporating cystathionine, hemoglobin, taurocholic acid, citrulline, and the phenylalanine/tyrosine ratio. This model demonstrated a bias of 4.6% and a precision of 17.4% in predicting drug AUC, effectively accounting for up to 70% of the inter-individual pharmacokinetic variability. Through the use of Partial least squares-Discriminant Analysis, cystathionine and hemoglobin were identified as specific metabolic signatures that effectively distinguish patients with stable disease from those with progressive disease. Conclusions: The findings from this study provide compelling evidence to support the utilization of pre-dose metabolomics in uncovering the underlying causes of pharmacokinetic variability of trabectedin, as well as facilitating the identification of patients who are most likely to benefit from this treatment.PMID:37637412 | PMC:PMC10450632 | DOI:10.3389/fphar.2023.1212634

Mar Life Sci Technol. 2023 Jul 29;5(3):400-414. doi: 10.1007/s42995-023-00187-w. eCollection 2023 Aug.ABSTRACTMany marine bacteria are difficult to culture because they are dormant, rare or found in low-abundances. Enrichment culturing has been widely tested as an important strategy to isolate rare or dormant microbes. However, many more mechanisms remain uncertain. Here, based on 16S rRNA gene high-throughput sequencing and metabolomics technology, it was found that the short-chain fatty acids (SCFAs) in metabolites were significantly correlated with uncultured bacterial groups during enrichment cultures. A pure culture analysis showed that the addition of SCFAs to media also resulted in high efficiency for the isolation of uncultured strains from marine sediments. As a result, 238 strains belonging to 10 phyla, 26 families and 82 species were successfully isolated. Some uncultured rare taxa within Chlorobi and Kiritimatiellaeota were successfully cultured. Amongst the newly isolated uncultured microbes, most genomes, e.g. bacteria, possess SCFA oxidative degradation genes, and these features might aid these microbes in better adapting to the culture media. A further resuscitation analysis of a viable but non-culturable (VBNC) Marinilabiliales strain verified that the addition of SCFAs could break the dormancy of Marinilabiliales in 5 days, and the growth curve test showed that the SCFAs could shorten the lag phase and increase the growth rate. Overall, this study provides new insights into SCFAs, which were first studied as resuscitation factors in uncultured marine bacteria. Thus, this study can help improve the utilisation and excavation of marine microbial resources, especially for the most-wanted or key players.SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00187-w.PMID:37637259 | PMC:PMC10449756 | DOI:10.1007/s42995-023-00187-w

Front Microbiol. 2023 Aug 10;17:1218595. doi: 10.3389/fmicb.2023.1232846. eCollection 2023.ABSTRACTBACKGROUND: Polygonatum sibiricum is an understory economic plant, and its dried rhizome is a traditional Chinese medicine. The purpose of this study was to connect the quality improvement of the understory plant P. sibiricum with specific microorganisms.METHODS: Amplicon and metabolome sequencing were conducted for P. sibiricum interplanted under three types of trees and in the field, and the relationship between the microbiome and secondary metabolism was explored.RESULTS: Principal component analysis (PCA) divided field cultivated and understory interplanted groups into two classes. A total of 95 different metabolites were found, with four expression patterns. The alpha diversity of rhizosphere bacteria and endosphere fungi in the understory interplanted group was significantly higher than that in the farmland cultivated group. There were 276 different rhizosphere microorganism genera among the four groups; however, only 33 different endosphere genera were observed, indicating that endophytic microbial diversity was relatively stable within the P. sibiricum rhizome, especially for endosphere bacteria. Cointertia analysis (CoIA) suggested that the metabolite changes in P. sibiricum induced by interplanting under different trees were more strongly affected by rhizosphere microorganisms than by endosphere microorganisms. In addition, the interactions between rhizosphere microorganisms and metabolites in the farmland group were weakened compared with those in the underplanted groups. Canonical correspondence analysis (CCA) showed that Aspergillus and Ellin6067 had the greatest influence on the metabolites. Myrmecridium, as a shared microbe in the rhizosphere and endosphere, had interaction effects with the largest number of microbes.CONCLUSION: This study revealed the interactions between the microbes and metabolites in P. sibiricum and systematically explored the mechanism underlying their correlation, which was mediated by the understory interplanting mode. This study provides feasible strategies for improving the medicinal value of P. sibiricum by regulating microorganisms.PMID:37637191 | PMC:PMC10449124 | DOI:10.3389/fmicb.2023.1232846

Front Oncol. 2023 Aug 11;13:1192448. doi: 10.3389/fonc.2023.1192448. eCollection 2023.ABSTRACTINTRODUCTION: Diffuse intrinsic pontine glioma (DIPG), recently reclassified as a subtype of diffuse midline glioma, is a highly aggressive brainstem tumor affecting children and young adults, with no cure and a median survival of only 9 months. Conventional treatments are ineffective, highlighting the need for alternative therapeutic strategies such as cellular immunotherapy. However, identifying unique and tumor-specific cell surface antigens to target with chimeric antigen receptor (CAR) or T-cell receptor (TCR) therapies is challenging.METHODS: In this study, a multi-omics approach was used to interrogate patient-derived DIPG cell lines and to identify potential targets for immunotherapy.RESULTS: Through immunopeptidomics, a range of targetable peptide antigens from cancer testis and tumor-associated antigens as well as peptides derived from human endogenous retroviral elements were identified. Proteomics analysis also revealed upregulation of potential drug targets and cell surface proteins such as Cluster of differentiation 27 (CD276) B7 homolog 3 protein (B7H3), Interleukin 13 alpha receptor 2 (IL-13Rα2), Human Epidermal Growth Factor Receptor 3 (HER2), Ephrin Type-A Receptor 2 (EphA2), and Ephrin Type-A Receptor 3 (EphA3).DISCUSSION: The results of this study provide a valuable resource for the scientific community to accelerate immunotherapeutic approaches for DIPG. Identifying potential targets for CAR and TCR therapies could open up new avenues for treating this devastating disease.PMID:37637064 | PMC:PMC10455951 | DOI:10.3389/fonc.2023.1192448

Front Plant Sci. 2023 Aug 10;14:1114398. doi: 10.3389/fpls.2023.1114398. eCollection 2023.ABSTRACTHemp (Cannabis sativa L.) is a widely researched industrial crop with a variety of applications in the pharmaceutical, nutraceutical, food, cosmetic, textile, and materials industries. Although many of these applications are related to its chemical composition, the chemical diversity of the hemp metabolome has not been explored in detail and new metabolites with unknown properties are likely to be discovered. In the current study, we explored the chemical diversity of the hemp seed metabolome through an untargeted metabolomic study of 52 germplasm accessions to 1) identify new metabolites and 2) link the presence of biologically important molecules to specific accessions on which to focus on in future studies. Multivariate analysis of mass spectral data demonstrated large variability of the polar chemistry profile between accessions. Five main groups were annotated based on their similar metabolic fingerprints. The investigation also led to the discovery of a new compound and four structural analogues, belonging to a previously unknown chemical class in hemp seeds: cinnamic acid glycosyl sulphates. Although variability in the fatty acid profiles was not as marked as the polar components, some accessions had a higher yield of fatty acids, and variation in the ratio of linoleic acid to α-linolenic acid was also observed, with some varieties closer to 3:1 (reported as optimal for human nutrition). We found that that cinnamic acid amides and lignanamides, the main chemical classes of bioactive metabolites in hemp seed, were more concentrated in the Spanish accession Kongo Hanf (CAN58) and the French accession CAN37, while the Italian cultivar Eletta Campana (CAN48) demonstrated the greatest yield of fatty acids. Our results indicate that the high variability of bioactive and novel metabolites across the studied hemp seed accessions may influence claims associated with their commercialization and inform breeding programs in cultivar development.PMID:37636102 | PMC:PMC10449600 | DOI:10.3389/fpls.2023.1114398

Front Plant Sci. 2023 Aug 11;14:1192235. doi: 10.3389/fpls.2023.1192235. eCollection 2023.ABSTRACTMetabolomics refers to the technology for the comprehensive analysis of metabolites and low-molecular-weight compounds in a biological system, such as cells or tissues. Metabolites play an important role in biological phenomena through their direct involvement in the regulation of physiological mechanisms, such as maintaining cell homeostasis or signal transmission through protein-protein interactions. The current review aims provide a framework for how the integrated analysis of metabolites, their functional actions and inherent biological information can be used to understand biological phenomena related to the regulation of metabolites and how this information can be applied to safety assessments of crops created using biotechnology. Advancement in technology and analytical instrumentation have led new ways to examine the convergence between biology and chemistry, which has yielded a deeper understanding of complex biological phenomena. Metabolomics can be utilized and applied to safety assessments of biotechnology products through a systematic approach using metabolite-level data processing algorithms, statistical techniques, and database development. The integration of metabolomics data with sequencing data is a key step towards improving additional phenotypical evidence to elucidate the degree of environmental affects for variants found in genome associated with metabolic processes. Moreover, information analysis technology such as big data, machine learning, and IT investment must be introduced to establish a system for data extraction, selection, and metabolomic data analysis for the interpretation of biological implications of biotechnology innovations. This review outlines the integrity of metabolomics assessments in determining the consequences of genetic engineering and biotechnology in plants.PMID:37636096 | PMC:PMC10451086 | DOI:10.3389/fpls.2023.1192235

Front Plant Sci. 2023 Aug 11;14:1233191. doi: 10.3389/fpls.2023.1233191. eCollection 2023.ABSTRACTCannabis sativa L. is a plant with a wide range of potential medicinal applications. In recent years, polyploidy has gained attention as a potential strategy for rapidly improving C. sativa, which, unlike other modern crops, has not yet benefitted from this established biotechnological application. Currently, no reports on high THCA and CBDA drug-type polyploid cultivars have been published. Moreover, it still needs to be clarified if different cultivars react similarly to polyploidization. For these reasons, we set out to evaluate and compare the phenotype and chemotype of three high Δ9-tetrahydrocannabinolic acid (THCA) and one high cannabidiolic acid (CBDA) drug-type cultivars in their diploid, triploid and tetraploid state through agronomic and metabolomic approaches. Our observations on plant morphology revealed a significant increase in plant height and leaf size with increasing ploidy levels in a cultivar-dependent manner. In contrast, cannabinoids were negatively affected by polyploidization, with the concentration of total cannabinoids, THCA, CBDA and cannabigerolic acid (CBGA) decreasing significantly in higher ploidy levels across all four cultivars. Headspace analysis of volatiles revealed that total volatile content decreased in triploids. On the other hand, tetraploids reacted differently depending on the cultivars. Two THCA dominant cultivars showed an increase in concentrations, while in the other two cultivars, concentrations decreased. Additionally, several rare compounds not present in diploids appeared in higher ploidy levels. Moreover, in one high THCA cultivar, a couple of elite tetraploid genotypes for cannabinoid and volatile production were identified, highlighting the role of cultivar and genotypic variability as an important factor in Cannabis sativa L. polyploids. Overall, our observations on plant morphology align with the giga phenotype observed in polyploids of other plant species. The decrease in cannabinoids and volatiles production in triploids have relevant implications regarding their commercial use. On the other hand, this study found that tetraploidization is a suitable approach to improve Cannabis sativa L. medicinal potential, although the response is cultivar and genotype-dependent. This work lays the ground for further improving, evaluating and harnessing Cannabis sativa L. chemical diversity by the breeding, biotechnological and pharmaceutical sectors.PMID:37636092 | PMC:PMC10455935 | DOI:10.3389/fpls.2023.1233191

Front Plant Sci. 2023 Aug 10;14:1150854. doi: 10.3389/fpls.2023.1150854. eCollection 2023.ABSTRACTCitrus fruits are cultivated around the world, and they face drought stress frequently during their growth and development. Previous studies showed that citrus plants biosynthesized flavonoid compounds in response to abiotic stress. In this study, we have quantified 37 flavonoid compounds from the leaves of three distinct citrus species including sour orange (drought-tolerant), pummelo 'Majia you pummelo' (drought-sensitive), and lemon (drought-sensitive). The 37 flavonoids consisted of 12 flavones, 10 flavonols, 6 flavanones, 5 isoflavanones, and 1 each for chalcone, flavanol, flavanonol, and flavone glycoside. Drought stress differentially altered the flavonoid metabolism in drought-tolerant and drought-sensitive citrus species. The kaempferol 3-neohesperidoside was 17-fold higher in sour orange (124.41 nmol/L) after 18 days of drought stress than lemon (7.33 nmol/L). In sour orange, neohesperidin (69.49 nmol/L) was 1,407- and 37-fold higher than pummelo and lemon, respectively. In sour orange, some flavonoids were significantly increased, such as vitexin, neohesperidin, cynaroside, hyperoside, genistin, kaempferol 3-neohesperidoside, eriocitrin, and luteolin, in response to drought stress, whereas in lemon, these flavonoids were significantly decreased or not altered significantly in response to drought stress. Moreover, the total contents of flavonoids and antioxidant activity were increased in sour orange as compared with pummelo and lemon. The genes associated with flavonoid biosynthesis (PAL, CHI, FLS, GT1, F3H, F3'M, C4H, 4CL, FLS, FG2, FG3, and CYP81E1) were more highly expressed in sour orange leaves than in pummelo and lemon after drought stress. These outcomes showed that pummelo and lemon failed to biosynthesize antioxidant flavonoids to cope with the prolonged drought stress, whereas the sour orange biosynthesized fortified flavonoid compounds with increased antioxidant activity to detoxify the harmful effects of reactive oxygen species produced during drought stress.PMID:37636085 | PMC:PMC10450343 | DOI:10.3389/fpls.2023.1150854

iScience. 2023 Aug 3;26(9):107538. doi: 10.1016/j.isci.2023.107538. eCollection 2023 Sep 15.ABSTRACTLiver fibrosis, a rising cause of chronic liver diseases, could eventually develop into cirrhosis and liver failure. Current diagnosis of liver fibrosis relies on pathological examination of hepatic tissues acquired from percutaneous biopsy, which may produce invasive injuries. Here, for non-invasive assessment of liver fibrosis, we applied comparative multi-omics in non-human primates (rhesus macaques) and subsequent serum biopsy in human patients. Global transcriptomics showed significant gene enrichment of metabolism process, in parallel with oxidative stress and immune responses in fibrotic primates. Targeted metabolomics were concordant with transcriptomic patterns, identifying elevated lipids and porphyrin metabolites during hepatic fibrosis. Importantly, liquid biopsy results validated that specific metabolites in the serum (e.g., biliverdin) were highly diagnostic to distinguish human patients from healthy controls. Findings describe the interconnected transcriptional and metabolic network in primate liver fibrosis and provide potential indices for non-invasive detection of liver fibrosis in humans.PMID:37636059 | PMC:PMC10448158 | DOI:10.1016/j.isci.2023.107538

Front Mol Biosci. 2023 Aug 10;10:1232233. doi: 10.3389/fmolb.2023.1232233. eCollection 2023.ABSTRACTRalstonia solanacearum, one of the most destructive crop pathogens worldwide, causes bacterial wilt disease in a wide range of host plants. The major component of the outer membrane of Gram-negative bacteria, lipopolysaccharides (LPS), has been shown to function as elicitors of plant defense leading to the activation of signaling and defense pathways in several plant species. LPS from a R. solanacearum strain virulent on tomato (LPSR. sol.), were purified, chemically characterized, and structurally elucidated. The lipid A moiety consisted of tetra- to hexa-acylated bis-phosphorylated disaccharide backbone, also decorated by aminoarabinose residues in minor species, while the O-polysaccharide chain consisted of either linear tetrasaccharide or branched pentasaccharide repeating units containing α-L-rhamnose, N-acetyl-β-D-glucosamine, and β-L-xylose. These properties might be associated with the evasion of host surveillance, aiding the establishment of the infection. Using untargeted metabolomics, the effect of LPSR. sol. elicitation on the metabolome of Solanum lycopersicum leaves was investigated across three incubation time intervals with the application of UHPLC-MS for metabolic profiling. The results revealed the production of oxylipins, e.g., trihydroxy octadecenoic acid and trihydroxy octadecadienoic acid, as well as several hydroxycinnamic acid amide derivatives, e.g., coumaroyl tyramine and feruloyl tyramine, as phytochemicals that exhibit a positive correlation to LPSR. sol. treatment. Although the chemical properties of these metabolite classes have been studied, the functional roles of these compounds have not been fully elucidated. Overall, the results suggest that the features of the LPSR. sol. chemotype aid in limiting or attenuating the full deployment of small molecular host defenses and contribute to the understanding of the perturbation and reprogramming of host metabolism during biotic immune responses.PMID:37635940 | PMC:PMC10450222 | DOI:10.3389/fmolb.2023.1232233

Anim Nutr. 2023 May 26;14:383-402. doi: 10.1016/j.aninu.2023.05.009. eCollection 2023 Sep.ABSTRACTIntensive production can cause immunological stress in commercial broilers. Chlorogenic acid (CGA) regulates the intestinal microbiota, barrier function, and immune function in chickens. As complex interrelations regulate the dynamic interplay between gut microbiota, the host, and diverse health outcomes, the aim of this study was to elucidate the immunoregulatory mechanisms of CGA using multi-omics approaches. A total of 240 one-day-old male broilers were assigned to a 2 × 2 factorial design with 2 CGA levels (0 or 500 mg/kg) either with or without dexamethasone (DEX) injection for a 21-day experimental period. Therefore, there were 4 dietary treatments: control, DEX, CGA, and DEX + CGA, with 6 replicates per treatment. CGA supplementation improved (P < 0.05) growth performance, jejunal morphology, jejunal barrier function, and immune function in DEX-treated broilers. Moreover, in DEX + CGA-treated broilers, the increase in gut microbiome diversity (P < 0.05) was consistent with a change in taxonomic composition, especially in the Clostridiales vadin BB60_group. Additionally, the levels of short-chain fatty acids increased remarkably (P < 0.01) after CGA supplementation. This was consistent with the Kyoto Encyclopedia of Genes and Genomes analysis results that the "pyruvate fermentation to butanoate" pathway was more enriched (P < 0.01) in the DEX + CGA group than in the DEX group. Proteomics revealed that CGA treatment increased the expression of several health-promoting proteins, thymosin beta (TMSB4X) and legumain (LGMN), which were verified by multiple reaction monitoring. Metabolomics revealed that CGA treatment increased the expression of health-promoting metabolites (2,4-dihydroxy benzoic acid and homogentisic acid). Proteomic and metabolic analyses showed that CGA treatment regulated the peroxisome proliferator-activated receptor (PPAR) and mitogen-activated protein kinase (MAPK) pathways. Western blotting results support these findings. Pearson's correlation analyses showed correlations (P < 0.01) between altered immune function, jejunal barrier function, different microbiota, proteins, and metabolites parameters. Overall, our data indicate that CGA treatment increased growth performance and improved the immunological functions of DEX-treated broilers by regulating gut microbiota and the PPAR and MAPK pathways. The results offer novel insights into a CGA-mediated improvement in immune function and intestinal health.PMID:37635925 | PMC:PMC10448031 | DOI:10.1016/j.aninu.2023.05.009

Front Mol Neurosci. 2023 Aug 10;16:1201073. doi: 10.3389/fnmol.2023.1201073. eCollection 2023.ABSTRACTINTRODUCTION: Parkinson's disease (PD) is a representative neurodegenerative disease, and its diagnosis relies on the evaluation of clinical manifestations or brain neuroimaging in the absence of a crucial noninvasive biomarker. Here, we used non-targeted metabolomics profiling to identify metabolic alterations in the colon and plasma samples of Proteus mirabilis (P. mirabilis)-treated mice, which is a possible animal model for investigating the microbiota-gut-brain axis.METHODS: We performed gas chromatography-mass spectrometry to analyze the samples and detected metabolites that could reflect P. mirabilis-induced disease progression and pathology.RESULTS AND DISCUSSION: Pattern, correlation and pathway enrichment analyses showed significant alterations in sugar metabolism such as galactose metabolism and fructose and mannose metabolism, which are closely associated with energy metabolism and lipid metabolism. This study indicates possible metabolic factors for P. mirabilis-induced pathological progression and provides evidence of metabolic alterations associated with P. mirabilis-mediated pathology of brain neurodegeneration.PMID:37635904 | PMC:PMC10447900 | DOI:10.3389/fnmol.2023.1201073

EMBO J. 2023 Aug 28:e112814. doi: 10.15252/embj.2022112814. Online ahead of print.ABSTRACTThe regulation of autophagy initiation is a key step in autophagosome biogenesis. However, our understanding of the molecular mechanisms underlying the stepwise assembly of ATG proteins during this process remains incomplete. The Rab GTPase Ypt1/Rab1 is recognized as an essential autophagy regulator. Here, we identify Atg23 and Atg17 as binding partners of Ypt1, with their direct interaction proving crucial for the stepwise assembly of autophagy initiation complexes. Disruption of Ypt1-Atg23 binding results in significantly reduced Atg9 interactions with Atg11, Atg13, and Atg17, thus preventing the recruitment of Atg9 vesicles to the phagophore assembly site (PAS). Likewise, Ypt1-Atg17 binding contributes to the PAS recruitment of Ypt1 and Atg1. Importantly, we found that Ypt1 is phosphorylated by TOR at the Ser174 residue. Converting this residue to alanine blocks Ypt1 phosphorylation by TOR and enhances autophagy. Conversely, the Ypt1S174D phosphorylation mimic impairs both PAS recruitment and activation of Atg1, thus inhibiting subsequent autophagy. Thus, we propose TOR-mediated Ypt1 as a multifunctional assembly factor that controls autophagy initiation via its regulation of the stepwise assembly of ATG proteins.PMID:37635626 | DOI:10.15252/embj.2022112814

Lab Invest. 2023 Aug 25:100243. doi: 10.1016/j.labinv.2023.100243. Online ahead of print.ABSTRACTRenal amyloidosis is a rare condition caused by the progressive accumulation of misfolded proteins within glomeruli, vessels and interstitium, causing functional decline and requiring prompt treatment due to its significant morbidity and mortality. Congo Red (CR) stain on renal biopsy is the gold standard for the diagnosis, but the need for polarized light is limiting the digitization of this nephropathology field. This study explores the feasibility and reliability of CR fluorescence on virtual slide (CRFvs) evaluating the diagnostic accuracy and proposing an automated digital pipeline for its assessment. Whole slide images (WSI) from 154 renal biopsies with CR were scanned through Texas red fluorescence filter (Nanozoomer S60, Hamamatsu) at the digital Nephropathology Center of IRCCS San Gerardo, Monza, Italy, were evaluated double blinded for the detection and quantification through Amyloid Score (AS) and a custom ImageJ pipeline was built to automatically detect amyloid containing regions. Inter-observer agreement for CRFvs was optimal (k=0.90, 95%CI=0.81-0.98), with even better concordance when consensus-based CRFvs evaluation was compared to the standard CR birefringence (BR, k=0.98, 95%CI=0.93-1). Excellent performance was achieved in the assessment of AS overall by CRFvs (Wk=0.70, 95%CI=0.08-1), especially within the interstitium (Wk=0.60, 95%CI=0.35-0.84), overcoming the misinterpretation of interstitial and capsular collagen birefringence. The application of an automated digital pathology pipeline (Streamlined Pipeline for Amyloid detection through congo red fluorescence Digital Analysis, SPADA) further increased the performance of pathologists, leading to a complete concordance with the standard BR. This study represents an initial step in the validation of CRFvs, demonstrating its general reliability in a digital nephropathology center. The computational method used in this study has the potential to facilitate the integration of spatial omics and artificial intelligence tools for the diagnosis of amyloidosis, streamlining its detection process.PMID:37634845 | DOI:10.1016/j.labinv.2023.100243

J Ethnopharmacol. 2023 Aug 25:117092. doi: 10.1016/j.jep.2023.117092. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Qingre Huashi (QRHS) formula is an empirical prescription for the treatment of Gan-Dan-Shi-Re syndrome (GDSR) syndrome in traditional Chinese medicine (TCM). GDSR is one of the typical TCM syndromes in chronic hepatitis B (CHB). However, little is known about the mechanism of the QRHS formula in treating CHB patients with GDSR. The biological basis of GDSR also remains largely unknown.AIM OF THE STUDY: GDSR mostly occurs in the acute and early stages of chronic liver disease. Effectively alleviating GDSR stalls disease development and benefits patients. The purpose of this study was to explore the molecular basis of GDSR in CHB and then study the mechanism of the QRHS formula treating GDSR using transcriptomics and metabolomics.MATERIALS AND METHODS: The transcriptome and metabolome of CHB patients with GDSR syndrome were detected using RNA microarray combined with ultra-high performance liquid chromatography/mass spectrometry and information mining. The potential biomarkers were identified from differentially expressed genes and metabolites, and the metabolic pathway was analyzed. We also investigated the callback of metabolic biomarkers after treatment with the QRHS formula, an empirical prescription for the treatment of GDSR syndrome. RT-PCR analysis was carried out in an independent patient cohort of CHB for validation.RESULTS: Four candidate genes-GPT2, HK2, DDIT3, and HIF1A-and 14 candidate metabolic biomarkers, including L-alpha-aminobutyric acid, selenomethionine, and fructose 1,6-bisphosphate, were identified and validated. All four transcripts of GPT2, HK2, DDIT3, and HIF1A were significantly differentially expressed between the GDSR and non-GDSR groups through independent microarray data and RT-PCR. After treatment with the QRHS formula, the clinical indexes and TCM syndrome were significantly improved, and the 14 disturbed biomarkers were obviously corrected. Three metabolic pathways were confirmed to be perturbed in CHB GDSR patients: alanine, aspartate, and glutamate metabolism, arginine biosynthesis, and aminoacyl-tRNA biosynthesis.CONCLUSION: Using integrated transcriptomic and targeted metabolomic methods, we identified the potential biomarkers and dysregulated metabolic pathways in CHB patients with GDSR syndrome, which was alleviated by the QRHS formula treatment. These results may provide the mechanism of metabolic dysregulation in GDSR syndrome as well as that underlying the curative effect of the QRHS formula.PMID:37634751 | DOI:10.1016/j.jep.2023.117092

J Ethnopharmacol. 2023 Aug 25:117083. doi: 10.1016/j.jep.2023.117083. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Cholestasis is the main manifestation of cholestatic liver disease, which has a risk of progression to end-stage liver disease. Gardeniae Fructus is the dried fruit of Gardeniae jasminoides Ellis, a plant of the Rubiaceae family. Gardeniae Fructus has shown therapeutic potential in cholestasis-related liver diseases and it is generally believed that Gardeniae Fructus ameliorates cholestasis, which could be related to its influence on bile acids (BAs) metabolism. However, the specific targets of Gardeniae Fructus and its impact on enterohepatic circulation of BAs have not yet been fully elucidated.AIM OF THE STUDY: To systematically elucidate the mechanism by which Gardenia extract (GE, total iridoids in Gardeniae Fructus, which contains the predominant and characteristic phytoconstituents of Gardeniae Fructus) ameliorates alpha-naphthylisothiocyanate (ANIT)-induced cholestatic liver injury.MATERIALS AND METHODS: Sprague-Dawley rats were orally administered water, obeticholic acid (OCA, 2 mg/kg), or GE (21 and 42 mg/kg) once daily for five days. On the third day, the model was established by administration of a single dose of ANIT (40 mg/kg) by oral gavage. Biochemical and pathological analyses, BA metabolomics, transcriptomics, and qRT-PCR were performed.RESULTS: The profile of BAs in serum and liver confirmed that GE attenuated ANIT-induced acute cholestasis by affecting BA metabolism in a dose-dependent manner. Liver transcriptomic analysis indicated that GE mainly influenced the primary bile acid (PBA) biosynthesis and bile secretion pathways. GE mainly affected PBA biosynthesis in liver by upregulating Cyp8b1 gene expression, thereby significantly reducing the level of total bile acids (TBA). GE mainly promoted PBA excretion from liver into duodenum by upregulating Fxr and Oatp1 gene expression, thereby increasing the excretion of PBA in feces, and inhibiting PBA in liver entering the blood by alternative routes to reduce TBA levels in serum and urine and improve the enterohepatic circulation of BAs.CONCLUSION: GE attenuated ANIT-induced hepatotoxicity and cholestasis in rats by upregulating Cyp8b1 expression to inhibit BA synthesis in the liver, while also promoting BA excretion via the intestinal-fecal route, and improving enterohepatic circulation of BAs.PMID:37634748 | DOI:10.1016/j.jep.2023.117083

Prog Neuropsychopharmacol Biol Psychiatry. 2023 Aug 25:110848. doi: 10.1016/j.pnpbp.2023.110848. Online ahead of print.ABSTRACTThe discovery of new biomarkers that can distinguish Alzheimer's disease (AD) from mild cognitive impairment (MCI) in the early stages will help to provide new diagnostic and therapeutic strategies and slow the transition from MCI to AD. Patients with AD may present with a concomitant metabolic disorder, such as diabetes, obesity, and dyslipidemia, as a risk factor for AD that may be involved in the onset of both AD pathology and cognitive impairment. Therefore, metabolite profiling, or metabolomics, can be very useful in diagnosing AD, developing new therapeutic targets, and evaluating both the course of treatment and the clinical course of the disease. In addition, studying the relationship between nutritional behavior and AD requires investigation of the role of conditions such as obesity, hypertension, dyslipidemia, and elevated glucose level. Based on this literature review, nutritional recommendations, including weight loss by reducing calorie and cholesterol intake and omega-3 fatty acid supplementation can prevent cognitive decline and dementia in the elderly. The underlying metabolic causes of the pathology and cognitive decline caused by AD and MCI are not well understood. In this review article, metabolomics biomarkers for diagnosis of AD and MCI and metabolic risk factors for cognitive decline in AD were evaluated.PMID:37634657 | DOI:10.1016/j.pnpbp.2023.110848

Int Immunopharmacol. 2023 Aug 25;124(Pt A):110832. doi: 10.1016/j.intimp.2023.110832. Online ahead of print.ABSTRACTGlutamine has anti-inflammatory properties as well as the ability to maintain the integrity of the intestinal barrier. In our previous study, we found that 1.0% glutamine promoted SIgA (secretory immunoglobulin A) synthesis in the gut via both T cell-dependent and non-dependent processes, as well as via the intestinal microbiota. The purpose of this study was to investigate whether the intestinal microbiota or microbial metabolites regulate SIgA synthesis. In the mouse model, supplementation with 1.0% glutamine had no significant effect on the intestinal microbiota, but KEGG function prediction showed the difference on microbiota metabolites. Therefore, in this study, untargeted metabolomics techniques were used to detect and analyze the metabolic changes of glutamine in intestinal luminal contents. Metabolomics showed that in the positive ion (POS) mode, a total of 1446 metabolic differentials (VIP ≥ 1, P < 0.05, FC ≥ 2 or FC ≤ 0.5) were annotated in samples treated with glutamine-supplemented group compared to control group, of which 922 were up-regulated and 524 down-regulated. In the negative ion (NEG) mode, 370 differential metabolites (VIP ≥ 1, P < 0.05, FC ≥ 2 or FC ≤ 0.5) were screened, of which 220 were up-regulated and 150 down-regulated. These differential metabolites mainly include bile secretion synthesis, ABC transporters, diterpenoids and other secondary metabolites. KEGG analysis showed that propionic acid metabolism, TCA cycle, endoplasmic reticulum protein processing, nitrogen metabolism and other metabolic pathways were active. The above metabolic pathways and differential metabolites have positive effects on intestinal development and intestinal immunity, and combined with our previous studies, we conclude that glutamine supplementation can may maintain intestinal homeostasis and improving intestinal immunity through intestinal microbial metabolites.PMID:37634449 | DOI:10.1016/j.intimp.2023.110832

J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Aug 12;1228:123849. doi: 10.1016/j.jchromb.2023.123849. Online ahead of print.ABSTRACTThe field of metabolomics based on mass spectrometry has grown considerably in recent years due to the need to detect and, above all, quantify a very large number of metabolites, simultaneously. Up to now, targeted multiplexed analysis on complex samples by Liquid Chromatography coupled with tandem Mass Spectrometry (LC-MS/MS) has relied almost exclusively on compound detection based on absolute retention times, as in the Scheduled-MRM (sMRM) approach. Those methods turn out to be poorly transferable from one instrument to another and result in a time-consuming and tedious method development involving a significant number of critical parameters that need specific re-optimisation. To address this challenge, we introduce a novel acquisition mode called scout-triggered MRM (stMRM). In stMRM, a marker transition is used to trigger MS analysis for a group of dependent target analytes. These marker transitions are strategically distributed throughout the chromatographic run, and the dependent analytes are associated based on their retention times. The result is a targeted assay that remains robust even in the presence of retention time shifts. A 3 to 5-fold increase in the number of detected transitions associated to plasma metabolites was obtained when transferring from a direct application of a published sMRM to a stMRM method. This significant improvement highlights the universal applicability of the stMRM method, as it can be implemented on any LC system without the need for extensive method development. We subsequently illustrate the robustness of stMRM in modified chromatographic elution conditions. Despite a large change in metabolite's selectivity, the multiplexed assay successfully recovered 70% of the monitored transitions when consequently modifying the gradient method. These findings demonstrate the versatility and adaptability of stMRM, opening new avenues for the development of highly multiplexed LC-MS/MS methods in metabolomics. These methods are characterized by their analytical transparency and straightforward implementation using existing literature data.PMID:37634392 | DOI:10.1016/j.jchromb.2023.123849