Comprehensive Metabolomic Analysis Research Articles

Seasonal variation of metabolites in Kimchi cabbage: utilizing metabolomics based machine learning for cultivation season and taste discrimination

AbstractKimchi cabbage, a staple in South Korean cuisine, exhibits taste variations depending on the season of cultivation, with significant implications for kimchi production quality. In this study, we conducted comprehensive metabolomic analyses of kimchi cabbage grown in diverse environments throughout the year. We identified 15 primary metabolites, 10 glucosinolates, and 12 hydrolysates, providing valuable insights into the metabolic composition of kimchi cabbage. Using this data, we developed predictive models for taste and quality differentiation in kimchi cabbage based on the season of cultivation. Three regression models, including Orthogonal Partial Least Squares regression (OPLS), Partial Least Squares (PLS) regression, and Random Forest regression, were employed to predict seasonal variation. The models exhibited high accuracy, with R2 values ranging from 0.77 to 0.95, indicating their potential for distinguishing seasonal differences. Notably, hydroxyglucobrassicin, 5-oxoproline, and inositol consistently emerged as significant metabolites across all models. Additionally, we developed regression models for predicting sweetness and bitterness in kimchi cabbage. Metabolites such as malic acid, fructose, and glucose were positively correlated with sweetness, while neoglucobrassicin and glucobrassicin were negatively correlated. Conversely, metabolites like glucoerucin and glucobrassicin were positively correlated with bitterness, while malic acid and sucrose were negatively correlated. These findings provide a valuable foundation for understanding the metabolic basis of taste variation in kimchi cabbage and offer practical applications for improving kimchi production quality. By incorporating more varieties and multi-year data, future research aims to develop even more accurate predictive models for kimchi cabbage taste and quality, ultimately contributing to the consistency of kimchi production. Graphical Abstract

Comprehensive transcriptomic and metabolomic analysis of porcine intestinal epithelial cells after PDCoV infection

IntroductionPorcine deltacoronavirus (PDCoV), an emerging swine enteropathogenic coronavirus with worldwide distribution, mainly infects newborn piglets with severe diarrhea, vomiting, dehydration, and even death, causing huge economic losses to the pig industry. However, the underlying pathogenic mechanisms of PDCoV infection and the effects of PDCoV infection on host transcripts and metabolites remain incompletely understood.MethodsThis study investigated a combined transcriptomic and metabolomic analysis of porcine intestinal epithelial cells (IPEC-J2) following PDCoV infection by LC/MS and RNA-seq techniques. A total of 1,401 differentially expressed genes and 254 differentially accumulated metabolites were detected in the comparison group of PDCoV-infected vs. mock-infected.Results and discussionWe found that PDCoV infection regulates gene sets associated with multiple signaling pathways, including the neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction, MAPK signaling pathway, chemokine signaling pathway, ras signaling pathway and so on. Besides, the metabolomic results showed that biosynthesis of cofactors, nucleotide metabolism, protein digestion and absorption, and biosynthesis of amino acid were involved in PDCoV infection. Moreover, integrated transcriptomics and metabolomics analyses revealed the involvement of ferroptosis in PDCoV infection, and exogenous addition of the ferroptosis activator erastin significantly inhibited PDCoV replication. Overall, these unique transcriptional and metabolic reprogramming features may provide a better understanding of PDCoV-infected IPEC-J2 cells and potential targets for antiviral treatment.

Combined full-length transcriptomic and metabolomic analysis reveals the molecular mechanisms underlying nutrients and taste components development in Primulina juliae

BackgroundPrimulina juliae has recently emerged as a novel functional vegetable, boasting a significant biomass and high calcium content. Various breeding strategies have been employed to the domestication of P. juliae. However, the absence of genome and transcriptome information has hindered the research of mechanisms governing the taste and nutrients in this plant. In this study, we conducted a comprehensive analysis, combining the full-length transcriptomics and metabolomics, to unveil the molecular mechanisms responsible for the development of nutrients and taste components in P. juliae.ResultsWe obtain a high-quality reference transcriptome of P. juliae by combing the PacBio Iso-seq and Illumina sequencing technologies. A total of 58,536 cluster consensus sequences were obtained, including 28,168 complete protein coding transcripts and 8,021 Long Non-coding RNAs. Significant differences were observed in the composition and content of compounds related to nutrients and taste, particularly flavonoids, during the leaf development. Our results showed a decrease in the content of most flavonoids as leaves develop. Malate and succinate accumulated with leaf development, while some sugar metabolites were decreased. Furthermore, we identified the different accumulation of amino acids and fatty acids, which are associated with taste traits. Moreover, our transcriptomic analysis provided a molecular basis for understanding the metabolic variations during leaf development. We identified 4,689 differentially expressed genes in the two developmental stages, and through a comprehensive transcriptome and metabolome analysis, we discovered the key structure genes and transcription factors involved in the pathways.ConclusionsThis study provides a high-quality reference transcriptome and reveals molecular mechanisms associated with the development of nutrients and taste components in P. juliae. These findings will enhance our understanding of the breeding and utilization of P. juliae as a vegetable.

Untargeted serum and gastric metabolomics and network pharmacology analysis reveal the superior efficacy of zingiberis rhizoma recens-/euodiae fructus-processed Coptidis Rhizoma on gastric ulcer rats

Ethnopharmacological relevanceZingiberis rhizoma recens-/wine-/euodiae fructus-processed Coptidis Rhizoma (CR, zCR/wCR/eCR) are the commonly used processed products of CR in clinic. After being processed with different excipients, the efficacy of CR will change accordingly. I.e., wCR could resolve excessive heat of the upper energizer, zCR could eliminate gastric heat and harmonize the stomach, eCR could smooth the liver and harmonize the stomach. However, the underlying mechanisms were still unclear. Aim of the studyTo further verify the differential efficacy of the three processed CR products and compare the mechanisms on gastric ulcer. Material and methodsFirst, a GU model, whose onset is closely related to the heat in stomach and the disharmony between liver and stomach, was established, and the therapeutic effects of zCR/wCR/eCR/CR were evaluated by pathologic observation and measurement of cytokine levels. Second, metabolomics analysis and network pharmacology were conducted to reveal the differential intervening mechanism of zCR/eCR on GU. Third, the predicted mechanisms from metabolomics analysis and network pharmacology were validated using western blotting, flow cytometry and immunofluorescence. ResultszCR/wCR/eCR/CR could alleviate the pathologic damage to varying degrees. In metabolomics research, fewer metabolic pathways were enriched in serum samples, and most of them were also present in the results of gastric tissue samples. The gastroprotective, anti-inflammatory, antioxidant, and anti-apoptotic effects of zCR/wCR/eCR/CR might be due to their interference on histidine, arachidonic acid, and glycerophospholipids metabolism. Quantitative results indicated that zCR/eCR had a better therapeutic effect than wCR/CR in treating GU. A comprehensive analysis of metabolomics and network pharmacology revealed that zCR and eCR exerted anti-GU effects via intervening in five core targets, including AKT, TNF, IL6, IL1B and PPARG. In the validation experiment, zCR/eCR could significantly reverse the abnormal expression of proteins related to apoptosis, inflammation, oxidative stress, gastric function, as well as the PI3K/AKT signaling pathways. ConclusionzCR and eCR could offer gastroprotective benefits by resisting inflammation and apoptosis, inhibiting gastric-acid secretion, as well as strengthening gastric mucosal defense and antioxidant capacity. Integrating network pharmacology and metabolomics analysis could reveal the acting mechanism of drugs and promote the development of medications to counteract GU.

Hazard assessment of hexagonal boron nitride and hexagonal boron nitride reinforced thermoplastic polyurethane composites using human skin and lung cells

Hexagonal boron nitride (hBN) is an emerging two-dimensional material attracting considerable attention in the industrial sector given its innovative physicochemical properties. Potential risks are associated mainly with occupational exposure where inhalation and skin contact are the most relevant exposure routes for workers. Here we aimed at characterizing the effects induced by composites of thermoplastic polyurethane (TPU) and hBN, using immortalized HaCaT skin keratinocytes and BEAS-2B bronchial epithelial cells. The composite was abraded using a Taber® rotary abraser and abraded TPU and TPU-hBN were also subjected to photo-Fenton-mediated degradation mimicking potential weathering across the product life cycle. Cells were exposed to the materials for 24 h (acute exposure) or twice per week for 4 weeks (chronic exposure) and evaluated with respect to material internalization, cytotoxicity, and proinflammatory cytokine secretion. Additionally, comprehensive mass spectrometry-based proteomics and metabolomics (secretomics) analyses were performed. Overall, despite evidence of cellular uptake of the material, no significant cellular and/or protein expression profiles alterations were observed after acute or chronic exposure of HaCaT or BEAS-2B cells, identifying only few pro-inflammatory proteins. Similar results were obtained for the degraded materials. These results support the determination of hazard profiles associated with cutaneous and pulmonary hBN-reinforced polymer composites exposure.

Metabolite Profiling and Biological Activity Assessment of Paeonia ostii Anthers and Pollen Using UPLC-QTOF-MS.

Paeonia ostii is an important economic oil and medicinal crop. Its anthers are often used to make tea in China with beneficial effects on human health. However, the metabolite profiles, as well as potential biological activities of P. ostii anthers and the pollen within anthers have not been systematically analyzed, which hinders the improvement of P. ostii utilization. With comprehensive untargeted metabolomic analysis using UPLC-QTOF-MS, we identified a total of 105 metabolites in anthers and pollen, mainly including phenylpropanoids, polyketides, organic acids, benzenoids, lipids, and organic oxygen compounds. Multivariate statistical analysis revealed the metabolite differences between anthers and pollen, with higher carbohydrates and flavonoids content in pollen and higher phenolic content in anthers. Meanwhile, both anthers and pollen extracts exhibited antioxidant activity, antibacterial activity, α-glucosidase and α-amylase inhibitory activity. In general, the anther stage of S4 showed the highest biological activity among all samples. This study illuminated the metabolites and biological activities of anthers and pollen of P. ostii, which supports the further utilization of them.

A comprehensive analysis of metabolomics and lipidomics in areca nut mediated oral submucous fibrosis progression through LCMS and Raman spectroscopy

AbstractHabitual consumption of areca/betel nut in Southeast Asia has been associated with oral submucous fibrosis (OSMF) and its malignant transformation to oral squamous cell carcinoma. The current study aimed to assess the molecular alterations in fibroblast cell lines after treatment with areca nut. Areca nut extract (ANE) was prepared and characterized for its active ingredient, arecoline. ANE‐treated cells were subjected to cell viability, proliferation, migration, morphologic changes, and transcript of OSMF genes (col1a1, col1a2, hsp47, timp1, timp2, timp3, and timp4). Further, liquid chromatography–mass spectrometry (LCMS) of cell lysate and Raman microspectroscopy (RMS) of fixed cells were performed for metabolomics/lipidomics and biomolecular alterations in the nucleus and periphery of ANE‐treated cells. We compared and integrated the data from both techniques and observed that the cells treated with ANE mimicked OSMF and could be used as an in vitro model. LCMS showed a significant alteration in 17 metabolites and 165 lipid molecules in the cells treated with ANE. Further, 40 molecules in the nucleus and 29 in the periphery were found to be altered in these cells when subjected to RMS. Molecules associated with pathways such as the transfer of acetyl groups into mitochondria, amino sugar metabolism, and the Warburg effect were modulated the most upon ANE treatment. Acetyl CoA was found to be common in most of the altered pathways. Besides, the pathways affecting carbohydrate metabolism were also altered significantly. Targeting these molecules and pathways can help to prevent the malignant transformation of OSMF.

Integrated metabolome and transcriptome analyses reveal the role of BoGSTF12 in anthocyanin accumulation in Chinese kale (Brassica oleracea var. alboglabra)

BackgroundThe vivid red, purple, and blue hues that are observed in a variety of plant fruits, flowers, and leaves are produced by anthocyanins, which are naturally occurring pigments produced by a series of biochemical processes occurring inside the plant cells. The purple-stalked Chinese kale, a popular vegetable that contains anthocyanins, has many health benefits but needs to be investigated further to identify the genes involved in the anthocyanin biosynthesis and translocation in this vegetable.ResultsIn this study, the purple- and green-stalked Chinese kale were examined using integrative transcriptome and metabolome analyses. The content of anthocyanins such as cyanidin-3-O-(6″-O-feruloyl) sophoroside-5-O-glucoside, cyanidin-3,5-O-diglucoside (cyanin), and cyanidin-3-O-(6″-O-p-hydroxybenzoyl) sophoroside-5-O-glucoside were considerably higher in purple-stalked Chinese kale than in its green-stalked relative. RNA-seq analysis indicated that 23 important anthocyanin biosynthesis genes, including 3 PAL, 2 C4H, 3 4CL, 3 CHS, 1 CHI, 1 F3H, 2 FLS, 2 F3’H, 1 DFR, 3 ANS, and 2 UFGT, along with the transcription factor BoMYB114, were significantly differentially expressed between the purple- and green-stalked varieties. Results of analyzing the expression levels of 11 genes involved in anthocyanin production using qRT-PCR further supported our findings. Association analysis between genes and metabolites revealed a strong correlation between BoGSTF12 and anthocyanin. We overexpressed BoGSTF12 in Arabidopsis thaliana tt19, an anthocyanin transport mutant, and this rescued the anthocyanin-loss phenotype in the stem and rosette leaves, indicating BoGSTF12 encodes an anthocyanin transporter that affects the accumulation of anthocyanins.ConclusionThis work represents a key step forward in our understanding of the molecular processes underlying anthocyanin production in Chinese kale. Our comprehensive metabolomic and transcriptome analyses provide important insights into the regulatory system that controls anthocyanin production and transport, while providing a foundation for further research to elucidate the physiological importance of the metabolites found in this nutritionally significant vegetable.

The Integration of Transcriptome and Metabolome Analyses Provides Insights into the Determinants of the Wood Properties in Toona ciliata.

Toona ciliata, also known as Chinese mahogany, is a high-quality and fast-growing wood species with a high economic value. The wood properties of T. ciliata of different provenances vary significantly. In this study, we conducted comprehensive transcriptome and metabolome analyses of red and non-red T. ciliata wood cores of different provenances to compare their wood properties and explore the differential metabolites and genes that govern the variation in their wood properties. Through combined analyses, three differential genes and two metabolites were identified that are possibly related to lignin synthesis. The lignin content in wood cores from T. ciliata of different provenances shows significant variation following systematic measurement and comparisons. The gene Tci09G002190, one of the three differential genes, was identified as a member of the CAD (Cinnamyl alcohol dehydrogenase) gene family of T. ciliata, which is associated with lignin synthesis. Our data provide insights into the determinants of the wood properties in T. ciliata, providing a solid foundation for research into the subsequent mechanisms of the formation of T. ciliata wood.

Serum metabolism alteration behind different etiology, diagnosis, and prognosis of disorders of consciousness

BackgroundPatients with disorders of consciousness (DoC) exhibit varied revival outcomes based on different etiologies and diagnoses, the mechanisms of which remain largely unknown. The fluctuating clinical presentations in DoC pose challenges in accurately assessing consciousness levels and prognoses, often leading to misdiagnoses. There is an urgent need for a deeper understanding of the physiological changes in DoC and the development of objective diagnostic and prognostic biomarkers to improve treatment guidance.MethodsTo explore biomarkers and understand the biological processes, we conducted a comprehensive untargeted metabolomic analysis on serum samples from 48 patients with DoC. Patients were categorized based on etiology (TBI vs. non-TBI), CRS-R scores, and prognosis. Advanced analytical techniques, including PCA and OPLS-DA models, were employed to identify differential metabolites.ResultsOur analysis revealed a distinct separation in metabolomic profiles among the different groups. The primary differential metabolites distinguishing patients with varying etiologies were predominantly phospholipids, with a notable decrease in glycerophospholipids observed in the TBI group. Patients with higher CRS-R scores exhibited a pattern of impaired carbohydrate metabolism coupled with enhanced lipid metabolism. Notably, serum concentrations of both LysoPE and PE were reduced in patients with improved outcomes, suggesting their potential as prognostic biomarkers.ConclusionsOur study underscores the critical role of phospholipid metabolism in the brain’s metabolic alterations in patients with DoC. It identifies key biomarkers for diagnosis and prognosis, offering insights that could lead to novel therapeutic targets. These findings highlight the value of metabolomic profiling in understanding and potentially treating DoC.

Proteomic and metabolomic characterization of bone, liver, and lung metastases in plasma of breast cancer patients.

Breast cancer (BC) is the second leading cause of cancer-related deaths among women, primarily due to metastases to other organs rather than the primary tumor. In this study, a comprehensive analysis of plasma proteomics and metabolomics was conducted on a cohort of 51 BC patients. Potential biomarkers were screened by the Least Absolute Shrinkage and Selection Operator (LASSO) regression and Random Forest algorithm. Additionally, enzyme-linked immunosorbent assay (ELISA) kits and untargeted metabolomics were utilized to validate the prognostic biomarkers in an independent cohort. In the study, extracellular matrix (ECM)-related functional enrichments were observed to be enriched in BC cases with bone metastases. Proteins dysregulated in retinol metabolism in liver metastases and leukocyte transendothelial migration in lung metastases were also identified. Machine learning models identified specific biomarker panels for each metastasis type, achieving high diagnostic accuracy with area under the curve (AUC) of 0.955 for bone, 0.941 for liver, and 0.989 for lung metastases. For bone metastasis, biomarkers such as leucyl-tryptophan, LysoPC(P-16:0/0:0), FN1, and HSPG2 have been validated. dUDP, LPE(18:1/0:0), and aspartylphenylalanine have been confirmed for liver metastasis. For lung metastasis, dUDP, testosterone sulfate, and PE(14:0/20:5) have been established.

Comprehensive Metabolomic Analysis of Human Heart Tissue Enabled by Parallel Metabolite Extraction and High-Resolution Mass Spectrometry.

The heart contracts incessantly and requires a constant supply of energy, utilizing numerous metabolic substrates, such as fatty acids, carbohydrates, lipids, and amino acids, to supply its high energy demands. Therefore, a comprehensive analysis of various metabolites is urgently needed for understanding cardiac metabolism; however, complete metabolome analyses remain challenging due to the broad range of metabolite polarities, which makes extraction and detection difficult. Herein, we implemented parallel metabolite extractions and high-resolution mass spectrometry (MS)-based methods to obtain a comprehensive analysis of the human heart metabolome. To capture the diverse range of metabolite polarities, we first performed six parallel liquid-liquid extractions (three monophasic, two biphasic, and one triphasic) of healthy human donor heart tissue. Next, we utilized two complementary MS platforms for metabolite detection: direct-infusion ultrahigh-resolution Fourier-transform ion cyclotron resonance (DI-FTICR) and high-resolution liquid chromatography quadrupole time-of-flight tandem MS (LC-Q-TOF-MS/MS). Using DI-FTICR MS, 9644 metabolic features were detected where 7156 were assigned a molecular formula and 1107 were annotated by accurate mass assignment. Using LC-Q-TOF-MS/MS, 21,428 metabolic features were detected where 285 metabolites were identified based on fragmentation matching against publicly available libraries. Collectively, 1340 heart metabolites were identified in this study, which span a wide range of polarities including polar (benzenoids, carbohydrates, and nucleosides) as well as nonpolar (phosphatidylcholines, acylcarnitines, and fatty acids) compounds. The results from this study will provide critical knowledge regarding the selection of appropriate extraction and MS detection methods for the analysis of the diverse classes of human heart metabolites.

Metabolomic profiling of maternal plasma identifies inverse associations of acetate and urea with anti-SARS-CoV-2 antibody titers following COVID-19 vaccination during pregnancy.

We conducted a comprehensive metabolomic analysis of plasma samples obtained from pregnant women who displayed varying post-vaccination antibody titers after receiving mRNA-1273-SARS-CoV-2 vaccines. The study involved 62 pregnant women, all of whom had been vaccinated after reaching 24weeks of gestation. To quantify post-vaccination plasma antibody titers, we employed binding antibody units (BAU) in accordance with the World Health Organization International Standard. Subsequently, we classified the study participants into three distinct BAU/mL categories: those with high titers (above 2000), medium titers (ranging from 1000 to 2000), and low titers (below 1000). Plasma metabolomic profiling was conducted using 1H nuclear magnetic resonance spectroscopy, and the obtained data were correlated with the categorized antibody titers. Notably, in pregnant women exhibiting elevated anti-SARS-CoV-2 antibody titers, reduced plasma concentrations of acetate and urea were observed. A significant negative correlation between these compounds and antibody titers was also evident. An analysis of metabolomics pathways revealed significant inverse associations between antibody titers and four distinct amino acid metabolic pathways: (1) biosynthesis of phenylalanine, tyrosine, and tryptophan; (2) biosynthesis of valine, leucine, and isoleucine; (3) phenylalanine metabolism; and (4) degradation of valine, leucine, and isoleucine. Additionally, an association between the synthesis and degradation pathways of ketone bodies was evident. In conclusion, we identified different metabolic pathways that underlie the diverse humoral responses triggered by COVID-19 mRNA vaccines during pregnancy. Our data hold significant implications for refining COVID-19 vaccination approaches in expectant mothers. KEY MESSAGES : Anti-SARS-CoV-2 antibody titers decline as the number of days since COVID-19 vaccination increases. Anti-SARS-CoV-2 antibody titers are inversely associated with acetate, a microbial-derived metabolite, and urea. Amino acid metabolism is significantly associated with SARS-CoV-2 antibody titers.

Cyclosporine A-induced systemic metabolic perturbations in rats: A comprehensive metabolome analysis

A better understanding of cyclosporine A (CsA)-induced nephro- and hepatotoxicity at the molecular level is necessary for safe and effective use. Utilizing a sophisticated study design, this study explored metabolic alterations after long-term CsA treatment in vivo. Rats were exposed to CsA with 4, 10, and 25 mg/kg for 4 weeks and then sacrificed to obtain liver, kidney, urine, and serum for untargeted metabolomics analysis. Differential network analysis was conducted to explore the biological relevance of metabolites significantly altered by toxicity-induced disturbance. Dose-dependent toxicity was observed in all biospecimens. The toxic effects were characterized by alterations of metabolites related to energy metabolism and cellular membrane composition, which could lead to the cholestasis-induced accumulation of bile acids in the tissues. The unfavorable impacts were also demonstrated in the serum and urine. Intriguingly, phenylacetylglycine was increased in the kidney, urine, and serum treated with high doses versus controls. Differential correlation network analysis revealed the strong correlations of deoxycytidine and guanosine with other metabolites in the network, which highlighted the influence of repeated CsA exposure on DNA synthesis. Overall, prolonged CsA administration had system-level dose-dependent effects on the metabolome in treated rats, suggesting the need for careful usage and dose adjustment.

Ophthalmate is a new regulator of motor functions via CaSR: Implications for movement disorders.

Dopamine's role as the principal neurotransmitter in motor functions has long been accepted. We broaden this conventional perspective by demonstrating the involvement of non-dopaminergic mechanisms. In mouse models of Parkinson's Disease (PD), we observed that L-DOPA elicited a substantial motor response even when its conversion to dopamine was blocked by inhibiting the enzyme aromatic amino acid decarboxylase (AADC). Remarkably, the motor activity response to L-DOPA in the presence of an AADC inhibitor (NSD1015) showed a delayed onset, yet greater intensity and longer duration, peaking at 7 hours, compared to when L-DOPA was administered alone. This suggests an alternative pathway or mechanism, independent of dopamine signaling, mediating the motor functions. We sought to determine the metabolites associated with the pronounced hyperactivity observed, using comprehensive metabolomics analysis. Our results revealed that the peak in motor activity induced by NSD1015/L-DOPA in PD mice is associated with a surge (20-fold) in brain levels of the tripeptide ophthalmic acid (OA, also known as ophthalmate in its anionic form). Interestingly, we found that administering ophthalmate directly to the brain rescued motor deficits in PD mice in a dose-dependent manner. We investigated the molecular mechanisms underlying ophthalmate's action and discovered, through radioligand binding and cAMP-luminescence assays, that ophthalmate binds to and activates the calcium-sensing receptor (CaSR). Additionally, our findings demonstrated that a CaSR antagonist inhibits the motor-enhancing effects of ophthalmate, further solidifying the evidence that ophthalmate modulates motor functions through the activation of the CaSR. The discovery of ophthalmate as a novel regulator of motor function presents significant potential to transform our understanding of brain mechanisms of movement control and the therapeutic management of related disorders.

Abstract 1471: A novel mouse model of upper tract urothelial carcinoma influenced by gut microbiota

Abstract Introduction & Objective: Recently, it has been revealed that bladder cancer (BC) and upper tract urothelial carcinoma (UTUC) are biologically distinct diseases. Mouse models of BC carcinogenesis have been established using N-butyl-N-(4-hydro-oxybutyl) nitorosamine (BBN) for a long time, but there are few reports of UTUC carcinogenesis with high incidence. Therefore, the UTUC carcinogenesis mouse model is expected. The aim of this study is to establish a novel mouse model of UTUC carcinogenesis and to identify the characteristics of this model. Methods: We used two strains (C57BL/6 and BALB/c) of male and female mice and fed 0.05% BBN from 6 weeks old to the harvest day. Both sides of upper urinary tract from mice drinking BBN or tap water were subjected to whole exome sequencing and whole transcriptome sequencing (WTS) to assess its genetic similarity to human UTUC. Microbiome in gut were assessed by 16S ribosomal RNA gene sequencing (16S rRNA-seq). Metabolic differences in feces, serum and liver between UTUC mice and healthy mice were evaluated by comprehensive metabolomic analysis. Inflammatory mediators were assessed by quantitative polymerase chain reaction (qPCR). Results: Only BALB/c female showed higher incidence of UTUC than BC, while the other strains rarely had UTUC. This model showed SBS5-like mutational pattern. The frequent mutated gene list showed similarity to human UTUC. In terms of gene expression, this model belonged basal subtype. We detected 593 differentially expressed genes between cancerous side and non-cancerous side of upper urinary tract in this model, which could also classify human UTUC and adjacent normal samples. The cancerous side of upper urinary tract enriched several inflammation related pathways such as Nfkb and Tnf pathway. We validated the upregulation of inflammatory gene expression in upper urinary tract (Il6, Il1b, Tnfa, Relb) by qPCR (all: p < 0.05). 16S rRNA-seq revealed that Firmicutes was enriched in feces. Metabolomic analysis revealed that some amino acids in feces and FAD in serum were upregulated. Feeding with amino acid mediated diet changed gut environment. Firmicutes in feces and FAD in both feces and serum were downregulated consistently. This diet suppressed inflammatory gene expression in upper urinary tract (Il6, Il1b, Tnfa, Relb, Cd38, Tnfrsf1b and Kdm1a; all: p < 0.05). Finally, UTUC was disappeared but not BC in this model treated by BBN with amino acid mediated diet. Conclusion: We have established a novel mouse model developing UTUC with high incidence that genetically mimics human UTUC. In addition, amino acid mediated diet can change both microbiome and metabolome in gut of this model, downregulate host’s inflammatory reaction to BBN in upper urinary trat and suppress the UTUC carcinogenesis. Citation Format: Akinaru Yamamoto, Atsunari Kawashima, Kentaro Jingushi, Sassi Nesrine, Yuki Horibe, Akihiro Yoshimura, Masaru Tani, Liu Yutong, toshiki Oka, Yohei Okuda, toshihiro Uemura, Gaku Yamamichi, Yu Ishizuya, Yoshiyuki Yamamoto, Taigo Kato, Koji Hatano, Norio Nonomura. A novel mouse model of upper tract urothelial carcinoma influenced by gut microbiota [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1471.

Effect of glabridin combined with bakuchiol on UVB-induced skin damage and its underlying mechanism: An experimental study.

Research has demonstrated the anti-photoaging properties of glabridin and bakuchiol. The impact of glabridin, glabridin + bakuchiol, and bakuchiol on the levels of tumor necrosis factor alpha (TNF-α) and interleukin-1 beta (IL-1β) in mice skin fibroblasts was observed. Furthermore, we investigated the potential roles of fibronectin (FN), interferon-γ (IFN-γ), interleukin-22 (IL-22), and transforming growth factor-β (TGF-β) in the tissues, and evaluated their impact on the enzymatic levels in the skin. In conjunction with transcriptomic analysis, metabolomic profiling, and network pharmacology, all samples underwent comprehensive metabolomic and principal component analysis. The Venny2.1 method was utilized to identify variances in shared metabolites between the treatment group and the UVB group, as well as between the UVB group and the control group. Subsequently, a cluster heat map was generated to forecast and analyze metabolic pathways and targets. The outcomes from the hematoxylin and eosin and toluidine blue staining revealed that glabridin and bakuchiol markedly decreased dermal thickness and suppressed mast cell infiltration in photoaged mice. Immunohistochemistry and Elisa analysis revealed that glabridin and bakuchiol effectively attenuated the levels of pro-inflammatory factors, including IL-1β, tumor necrosis factor-α, IL-22, and IFN-γ. Furthermore, an increase in the levels of anti-inflammatory factors such as FN and TGF-β was also observed. The determination of the contents of superoxide dismutase, hydroxypropyltransferase and malondialdehyde in mice dorsal skin revealed that glabridin and bakuchiol not only elevated the levels of superoxide dismutase and hydroxyproline, but also reduced malondialdehyde content. Due to the limited number of shared differential metabolites exclusively within Kyoto Encyclopedia of Genes and Genomes, comprehensive pathway enrichment analysis was not feasible. This study demonstrates that glabridin and bakuchiol effectively impede photoaging and alleviate skin inflammation in mice.

Plasma and serum metabolic analysis of healthy adults shows characteristic profiles by subjects’ sex and age

IntroductionPre-analytical factors like sex, age, and blood processing methods introduce variability and bias, compromising data integrity, and thus deserve close attention.ObjectivesThis study aimed to explore the influence of participant characteristics (age and sex) and blood processing methods on the metabolic profile.MethodA Thermo UPLC-TSQ-Quantiva-QQQ Mass Spectrometer was used to analyze 175 metabolites across 9 classes in 208 paired serum and lithium heparin plasma samples from 51 females and 53 males.ResultsComparing paired serum and plasma samples from the same cohort, out of the 13 metabolites that showed significant changes, 4 compounds related to amino acids and derivatives had lower levels in plasma, and 5 other compounds had higher levels in plasma. Sex-based analysis revealed 12 significantly different metabolites, among which most amino acids and derivatives and nitrogen-containing compounds were higher in males, and other compounds were elevated in females. Interestingly, the volcano plot also confirms the similar patterns of amino acids and derivatives higher in males. The age-based analysis suggested that metabolites may undergo substantial alterations during the 25-35-year age range, indicating a potential metabolic turning point associated with the age group. Moreover, a more distinct difference between the 25–35 and above 35 age groups compared to the below 25 and 25–35 age groups was observed, with the most significant compound decreased in the above 35 age groups.ConclusionThese findings may contribute to the development of comprehensive metabolomics analyses with confounding factor-based adjustment and enhance the reliability and interpretability of future large-scale investigations.

Integrated metabolomic and transcriptomic analysis reveals the mechanism of high polysaccharide content in tetraploid Dendrobium catenatum Lindl

Dendrobium catenatum Lindl (Orchidaceae) has high medicinal and economic value. Unfortunately, industrially-cultivated D. catenatum exhibits inferior medicinal quality in comparison with wild-harvested plant materials. Previously, we produced tetraploid D. catenatum germplasm in order to increase the production of bioactive compounds. However, although tetraploid D. catenatum contains a higher polysaccharide content than diploid D. catenatum, the molecular mechanism is still unknown. In this study, the polysaccharide content of tetraploid D. catenatum stems and leaves was studied alongside a comprehensive transcriptomic and metabolomic analysis. Overall, tetraploid D. catenatum contained a higher polysaccharide content (stem: 30.93%, leaf: 23.28%) than diploid D. catenatum (stem: 17.93%, leaf: 15.28%). Further analyses of differential metabolites and genes were carried out, targeting genes related to polysaccharide synthesis, metabolism, regulation, and transport. Functional enrichment analysis showed that tetraploid plants were highly enriched in transport- and metabolism-related pathways. Specifically, CesA/Csl, SWEET, and BGLU gene family members were upregulated in tetraploid plants. The results of this study suggest that enhanced polysaccharide transport may be the key driver of increased polysaccharide content in tetraploid D. catenatum. These results provide a foundation for further studies aimed at resolving the molecular mechanism of high polysaccharide content in tetraploid D. catenatum, as well as a theoretical basis for the breeding of new D. catenatum varieties.

Comprehensive metabolomics analysis reveals novel biomarkers and pathways in falsely suspected glutaric aciduria Type-1 newborns

BackgroundGlutaric aciduria type-1 (GA-1) is a rare metabolic disorder due to glutaryl coenzyme A dehydrogenase deficiency, causing elevated levels of glutaryl-CoA and its derivatives. GA-1 exhibits symptoms like macrocephaly, developmental delays, and movement disorders. Timely diagnosis through genetic testing and newborn screening is crucial. However, in some cases, transiently elevated level of glutarylcarnitine (C5DC) challenges accurate diagnosis, highlighting the need for alternative diagnostic methods, like mass spectrometry-based untargeted metabolomics, to identify additional biomarkers for distinguishing falsely suspected GA-1 from healthy newborns. MethodologyDBS samples from falsely suspected GA-1 newborns (n = 47) and matched control were collected through the NBS program. Untargeted metabolomics using liquid chromatography-high-resolution mass spectrometry (LC-HRMS) was performed to enable biomarker and pathway investigations for significantly altered metabolites. Results582 and 546 were up- and down-regulated metabolites in transient GA-1. 155 endogenous metabolites displayed significant variations compared to the control group. Furthermore, our data identified novel altered metabolic biomarkers, such as N-palmitoylcysteine, heptacarboxyporphyrin, 3-hydroxylinoleoylcarnitine, and monoacylglyceride (MG) (0:0/20:1/0:0), along with perturbed metabolic pathways like sphingolipid and thiamine metabolism associated with the transient elevated C5DC levels in DBS samples. ConclusionsA distinct metabolic pattern linked to the transient C5DC elevation in newborns was reported to enhance the prediction of the falsely positive cases, which could help avoiding unnecessary medical treatments and minimizing the financial burdens in the health sector.