Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Effects of resveratrol on changes in trimethylamine-N-oxide and circulating cardiovascular factors following exercise training among older adults

Thu, 13/06/2024 - 12:00
Exp Gerontol. 2024 Jun 11:112479. doi: 10.1016/j.exger.2024.112479. Online ahead of print.ABSTRACTPURPOSE: Trimethylamine-N-oxide (TMAO) is a gut-derived metabolite associated with cardiovascular disease (CVD). In preclinical and observational studies, resveratrol and exercise training have been suggested as potential strategies to reduce the systemic levels of TMAO. However, evidence from experimental studies in humans remains unknown. This project examined the dose-dependent effects of a combined resveratrol intervention with exercise training on circulating TMAO and other related metabolite signatures in older adults with high CVD risk.METHODS: Forty-one older adults [mean (±SD) age of 72.1 (6.8) years] participated in a 12-week supervised center-based, multi-component exercise training intervention [2×/week; 80 min/session] and were randomized to one of two resveratrol dosages [Low: 500 vs. High:1000 mg/day] or a cellulose-based placebo. Serum/plasma were collected at baseline and post-intervention and evaluated for TMAO and associated analytes.RESULTS: After the 12-week intervention, TMAO concentration increased over time, regardless of treatment [mean (±SD) Placebo: 11262 (±3970); Low:13252 (±1193); High: 12661(±3359) AUC; p = 0.04]. Each resveratrol dose produced different changes in metabolite signatures. Low dose resveratrol upregulated metabolites associated with bile acids biosynthesis (i.e., glycochenodeoxycholic acid, glycoursodeoxycholic acid, and glycocholic acid). High dose resveratrol modulated metabolites enriched for glycolysis, and pyruvate, propanoate, β-alanine, and tryptophan metabolism. Different communities tightly correlated to TMAO and resveratrol metabolites were associated with the lipid and vascular inflammatory clinical markers [|r| > 0.4, p < 0.05].CONCLUSION: These findings suggest a distinct dose-dependent adaptation response to resveratrol supplementation on circulating metabolite signatures but not on TMAO among high-risk CVD older adults when combined with an exercise training intervention.PMID:38871236 | DOI:10.1016/j.exger.2024.112479

Effects of three Huanglian-derived polysaccharides on the gut microbiome and fecal metabolome of high-fat diet/streptozocin-induced type 2 diabetes mice

Thu, 13/06/2024 - 12:00
Int J Biol Macromol. 2024 Jun 11:133060. doi: 10.1016/j.ijbiomac.2024.133060. Online ahead of print.ABSTRACTPlant-derived polysaccharides are important components for biological functions. The objective of this study is to study the mechanisms by which polysaccharides from three Huanglian (Rhizome Coptidis, HL) of Coptis chinensis, C. deltoidea, and Coptis teeta affect type 2 diabetes mellitus (T2DM) by analyzing the gut microbiome and their metabolites. A long-term high-fat diet (HFD) combined with streptozocin (STZ) induction was used to construct the T2DM mice model. The histopathology of liver, pancreas, and colon, biochemical indexes related to mice were determined to assess the ameliorative effects of these three HL polysaccharides (HLPs) on T2DM. The results indicated that oral HLPs improved hyperglycemia, insulin resistance, blood lipid levels, and β-cell function. Further, HLPs elevated the growth of advantageous beneficial bacteria within the gut microbiota and raised the concentrations of short-chain fatty acids (SCFAs), particularly butyric acid. Metabolic analyses showed that HLPs ameliorated the effects of T2DM on microbial-derived metabolites and related metabolic pathways, especially the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan. In the combined analysis, many associations of T2DM-related biochemical indicators with gut microbes and their metabolites were extracted, which suggested the important role of gut microbiome and fecal metabolome in the amelioration of type 2 diabetes mellitus by HLPs.PMID:38871107 | DOI:10.1016/j.ijbiomac.2024.133060

Metformin-induced changes in the gut microbiome and plasma metabolome are associated with cognition in men

Thu, 13/06/2024 - 12:00
Metabolism. 2024 Jun 11:155941. doi: 10.1016/j.metabol.2024.155941. Online ahead of print.ABSTRACTBACKGROUND: An altered gut microbiome characterized by reduced abundance of butyrate producing bacteria and reduced gene richness is associated with type 2 diabetes (T2D). An important complication of T2D is increased risk of cognitive impairment and dementia. The biguanide metformin is a commonly prescribed medication for the control of T2D and metformin treatment has been associated with a significant reduction in the risk of dementia and improved cognition, particularly in people with T2D.AIM: To investigate the associations of metformin use with cognition exploring potential mechanisms by analyzing the gut microbiome and plasma metabolome using shotgun metagenomics and HPLC-ESI-MS/MS, respectively.METHODS: We explored two independent cohorts: an observational study (Aging Imageomics) and a phase IV, randomized, double-blind, parallel-group, randomized pilot study (MEIFLO). From the two studies, we analyzed four study groups: (1) individuals with no documented medical history or medical treatment (n = 172); (2) people with long-term T2D on metformin monotherapy (n = 134); (3) people with long-term T2D treated with oral hypoglycemic agents other than metformin (n = 45); (4) a newly diagnosed T2D subjects on metformin monotherapy (n = 22). Analyses were also performed stratifying by sex.RESULTS: Several bacterial species belonging to the Proteobacteria (Escherichia coli) and Verrucomicrobia (Akkermansia muciniphila) phyla were positively associated with metformin treatment, while bacterial species belonging to the Firmicutes phylum (Romboutsia timonensis, Romboutsia ilealis) were negatively associated. Due to the consistent increase in A. muciniphila and decrease in R.ilealis in people with T2D subjects treated with metformin, we investigated the association between this ratio and cognition. In the entire cohort of metformin-treated T2D subjects, the A.muciniphila/R.ilealis ratio was not significantly associated with cognitive test scores. However, after stratifying by sex, the A.muciniphila/R. ilealis ratio was significantly and positively associated with higher memory scores and improved memory in men. Metformin treatment was associated with an enrichment of microbial pathways involved in the TCA cycle, and butanoate, arginine, and proline metabolism in both cohorts. The bacterial genes involved inarginine metabolism, especially in production of glutamate (astA, astB, astC, astD, astE, putA), were enriched following metformin intake. In agreement, in the metabolomics analysis, metformin treatment was strongly associated with the amino acid proline, a metabolite involved in the metabolism of glutamate.CONCLUSIONS: The beneficial effects of metformin may be mediated by changes in the composition of the gut microbiota and microbial-host-derived co-metabolites.PMID:38871078 | DOI:10.1016/j.metabol.2024.155941

Artemisia argyi essential oil alleviates asthma by regulating 5-LOX-CysLTs and IDO-1-KYN pathway: insights from metabolomics

Thu, 13/06/2024 - 12:00
J Ethnopharmacol. 2024 Jun 11:118458. doi: 10.1016/j.jep.2024.118458. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Artemisia argyi essential oil (AAEO) is a traditional herbal remedy for asthma. However, the potential effect of AAEO on asthma has not been elucidated.AIM OF THE STUDY: To investigate the protective properties of AAEO upon asthma and elucidate its mechanism.MATERIALS AND METHODS: The effects of AAEO in asthma were assessed by histology and biochemical analysis. Then, we integrated real-time reverse transcription-quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, immunohistochemistry and metabolomics analysis to reveal its mechanism.RESULTS: In vivo, AAEO reduced the counts of white blood cells (WBCs) and cytokines in bronchoalveolar lavage fluid (BALF), ameliorated pathologic alterations in lung tissues, and inhibited secretion of OVA-sIgE and muc5ac. Metabolomics results showed that AAEO can exert therapeutic effects on asthmatic mice by regulating disordered arachidonic acid metabolism and tryptophan metabolism. Further studies shown that AAEO inhibited the expression of 5-LOX and reduced the accumulation of CysLTs in mice. Meanwhile, AAEO promoted the activity of IDO-1, facilitated the conversion of tryptophan to kynurenine, and regulated the imbalance of Treg/Th17 immunity. Immunohistochemical results showed that AAEO promoted the expression of IDO-1. RT-qPCR results showed that AAEO promoted the expression of IL-10 and Foxp3 mRNA, and inhibited the expression of IL-17A and RORγt mRNA, thus regulated the imbalance of Treg/Th17 immunity and exerted its therapeutic effects.CONCLUSION: AAEO treatment not only attenuates the clinical symptoms of asthma but is also involved in regulating lung tissue metabolism. The anti-asthmatic activity of AAEO may be achieved by reprogramming 5-LOX-CysLTs and IDO-1-KYN pathways.PMID:38871010 | DOI:10.1016/j.jep.2024.118458

Response, resistance, and recovery of gut bacteria to human-targeted drug exposure

Thu, 13/06/2024 - 12:00
Cell Host Microbe. 2024 Jun 12;32(6):786-793. doi: 10.1016/j.chom.2024.05.009.ABSTRACTSurvival strategies of human-associated microbes to drug exposure have been mainly studied in the context of bona fide pathogens exposed to antibiotics. Less well understood are the survival strategies of non-pathogenic microbes and host-associated commensal communities to the variety of drugs and xenobiotics to which humans are exposed. The lifestyle of microbial commensals within complex communities offers a variety of ways to adapt to different drug-induced stresses. Here, we review the responses and survival strategies employed by gut commensals when exposed to drugs-antibiotics and non-antibiotics-at the individual and community level. We also discuss the factors influencing the recovery and establishment of a new community structure following drug exposure. These survival strategies are key to the stability and resilience of the gut microbiome, ultimately influencing the overall health and well-being of the host.PMID:38870896 | DOI:10.1016/j.chom.2024.05.009

The influences of extraction methods on the chemical constituents of Lyonia ovalifolia (wall.) Drude and intracellular protective effects based on metabolomics analysis

Thu, 13/06/2024 - 12:00
Food Chem. 2024 Jun 8;456:140031. doi: 10.1016/j.foodchem.2024.140031. Online ahead of print.ABSTRACTLyonia ovalifolia (Wall.) Drude (LO) is mainly distributed in China with health benefits. In this study, LO buds (LOB) were extracted by ultrasonic extraction (UE) with or without ultra-high-pressure (UHP-UE), microwave (MW-UE), subcritical (SC-UE) techniques. The metabolomic result showed that a total of 960 chemical compounds and 117 differential compounds were identified from LOB extracts. The UHP-UE extract was rich in total polyphenol and flavonoid contents, followed by MW-UE, UE and SC-UE extracts, respectively. All LOB extracts increased superoxide dismutase (SOD) and catalase (CAT) activities, and glutathione (GSH) content, decreased reactive oxygen species (ROS) accumulation, levels of interleukin-6 (IL-6), interleukin-1β (IL-1β), tumor necrosis factor -α (TNF-α), and nitric oxide (NO), and alleviated apoptosis in cells. The cellular protective effect was UHP-UE > MW-UE > UE > SC-UE. This study revealed that higher pressure and lower temperature may be key factors for increasing bioactivities of LOB extracts.PMID:38870821 | DOI:10.1016/j.foodchem.2024.140031

Flavonoid localization in soybean seeds: Comparative analysis of wild (Glycine soja) and cultivated (Glycine max) varieties

Thu, 13/06/2024 - 12:00
Food Chem. 2024 May 29;456:139883. doi: 10.1016/j.foodchem.2024.139883. Online ahead of print.ABSTRACTWild soybean (Glycine soja) is known for its high flavonoid contents, yet the distribution of flavonoids in the seeds is not well understood. Herein, we utilized matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and metabolomics methods to systematically investigate flavonoid differences in the seed coats and embryos of G. soja and G. max. The results of flavonoid profiles and total flavonoid content analyses revealed that flavonoid diversity and abundance in G. soja seed coats were significantly higher than those in G. max whereas the levels were similar in embryos. Specifically, 23 unique flavonoids were identified in the seed coats of G. soja, including procyanidins, epicatechin derivatives, and isoflavones. Using MALDI-MSI, we further delineated the distribution of the important flavonoids in the cotyledons, hypocotyls, and radicles of the two species. These findings imply that G. soja holds considerable breeding potential to enhance the nutritional and stress resistance traits of G. max.PMID:38870803 | DOI:10.1016/j.foodchem.2024.139883

A new chemical derivatization reagent sulfonyl piperazinyl for the quantification of fatty acids using LC-MS/MS

Thu, 13/06/2024 - 12:00
Talanta. 2024 Jun 6;277:126378. doi: 10.1016/j.talanta.2024.126378. Online ahead of print.ABSTRACTIn our previous study, a chemical derivatization reagent named 5-(dimethylamino) naphthalene-1-sulfonyl piperazine (Dns-PP) was developed to enhance the chromatographic retention and the mass spectrometric response of free fatty acids (FFAs) in reversed-phase liquid chromatography coupled with electrospray ionization-mass spectrometry (RPLC-ESI-MS). However, Dns-PP exhibited strong preferences for long-chain FFAs, with limited improvement for short- or medium-chain FFAs. In this study, a new series of labeling reagents targeting FFAs were designed, synthesized, and evaluated. Among these reagents, Tmt-PP (N2, N2, N4, N4-tetramethyl-6-(4-(piperazin-1-ylsulfonyl) phenyl)-1,3,5-triazine-2,4-diamine) exhibited the best MS response and was selected for further evaluations. We compared Tmt-PP with Dns-PP and four commonly used carboxyl labeling reagents from existing studies, demonstrating the advantages of Tmt-PP. Further comparisons between Tmt-PP and Dns-PP in measuring FFAs from biological samples revealed that Tmt-PP labeling enhanced the MS response for about 80 % (30/38) of the measured FFAs, particularly for short- and medium-chain FFAs. Moreover, Tmt-PP labeling significantly improved the chromatographic retention of short-chain FFAs. To ensure accurate quantification, we developed a stable isotope-labeled Tmt-PP (i.e., d12-Tmt-PP) to react with chemical standards and serve as one-to-one internal standards (IS). The method was validated for accuracy, precision, sensitivity, linearity, stability, extraction efficiency, as well as matrix effect. Overall, this study introduced a new chemical derivatization reagent Tmt-PP (d12-Tmt-PP), providing a sensitive and accurate option for quantifying FFAs in biological samples.PMID:38870757 | DOI:10.1016/j.talanta.2024.126378

Antioxidant inactivated yeast: High potential of non-Saccharomyces specific metabolome

Thu, 13/06/2024 - 12:00
Talanta. 2024 May 29;277:126340. doi: 10.1016/j.talanta.2024.126340. Online ahead of print.ABSTRACTUnderstanding the contribution of new natural sources of antioxidant compounds to the stability of wines is of great interest in a context of reduction of sulfites. Here, we investigated the antioxidant potential of selected inactivated non-Saccharomyces yeast (INSY) along with related chemical fingerprints, using combined untargeted UHPLC-Q-ToF MS and DPPH analyses. 4 INSY species were compared to a reference inactivated Saccharomyces cerevisiae yeast (ISY) selected for its high antioxidant capacity. Our results show that, all the INSY can accumulate GSH during the specific production process with yields ranging from +170 % to +360 % compared to the corresponding classical production process. The principal component analysis of the 3511 ions detected by UHPLC-Q-ToF-MS clearly grouped INSY by species, independently of the production process. One INSY exhibited equivalent antioxidant capacity to the control ISY, but with a GSH concentration four times lower (4.73 ± 0.09 mg/g against 20.95 ± 0.34 mg/g, respectively). 73 specific ions presenting strong and significant spearman correlation (rho < -0.6, p-value < 0.05) with the DPPH scores, clustered the most antioxidant INSY and the control Saccharomyces in different groups, indicating that the antioxidant capacity of these two products should be driven by different pools of compounds. These results point out that, GSH alone is not relevant to explain the antioxidant capacity of INSY soluble fractions and other more reactive compounds must be considered, which opens an avenue for the selection new species with great enological potential.PMID:38870756 | DOI:10.1016/j.talanta.2024.126340

Trichodelphinine A alleviates pulmonary fibrosis by inhibiting collagen synthesis via NOX4-ARG1/TGF-β signaling pathway

Thu, 13/06/2024 - 12:00
Phytomedicine. 2024 May 23;132:155755. doi: 10.1016/j.phymed.2024.155755. Online ahead of print.ABSTRACTBACKGROUND: Pulmonary fibrosis, a progressive and fatal lung disease with no effective treatment medication, is characterized by lung remodeling and fibroblastic foci caused by an oxidative imbalance with an overloading deposition of collagen. Trichodelphinine A, a hetisine-type C20-diterpenoid alkaloid, was found anti-fibrotic activity in vitro, but its effect and mechanism on pulmonary fibrosis still unknown.PURPOSE: Our study aimed to investigate and validate the anti-fibrotic properties of trichodelphinine A in pulmonary fibrosis animals induced by bleomycin (BLM), and its mechanism whether via NOX4-ARG1/TGF-β signaling pathway.METHODS: The anti-fibrotic effects of trichodelphinine A were evaluated using BLM-induced rats through indicators of lung histopathology and collagen synthesis. Dynamic metabolomics evaluated the metabolic disorder and therapeutic effect of trichodelphinine A. The interaction between trichodelphinine A and NOX4 receptor was confirmed using CETSA and molecular dynamics experiments. Molecular biology experiments were conducted in NOX4 gene knockout mice to investigate the intervention effect of trichodelphinine A.RESULTS: Trichodelphinine A could suppress histopathologic changes, collagen deposition and proinflammatory cytokine release pulmonary fibrosis in bleomycin induced rats. Dynamic metabolomics studies revealed that trichodelphinine A could correct endogenous metabolic disorders of arachidonic acid, arginine and proline during fibrosis development, which revealed that the regulation of oxidative stress and amino acid metabolism targeting NOX4 and ARG1 may be the main pharmacological mechanisms of trichodelphinine A on pulmonary fibrosis. We further determined that trichodelphinine A inhibited over oxidative stress and collagen deposition by suppressing Nrf2-keap1 and ARG1-OAT signaling pathways, respectively. Molecular dynamics studies showed that trichodelphinine A was directly binds with NOX4, in which PHE354 and THR355 residues of NOX4 are critical binding sites for trichodelphinine A. Mechanistic validation in cells or mice with NOX4 knockout or silencing suggested that the anti-fibrotic effects of trichodelphinine A depended on inhibition of NOX4 to suppress ARG1/OAT activation and TGF-β/Smads signaling pathway.CONCLUSION: Collectively, our findings indicate a powerful anti-fibrotic function of trichodelphinine A in pulmonary fibrosis via targeting NOX4. NOX4 mediates the activation of ARG1/OAT to regulate arginase-proline metabolism, and promotes TGF-β/Smads signaling pathway, thereby affecting the collagen synthesis in pulmonary fibrosis, which is a novel finding and indicates that inhibition of NOX4 is a novel therapeutic strategy for pulmonary fibrosis.PMID:38870750 | DOI:10.1016/j.phymed.2024.155755

Bacteroidales reduces growth rate through serum metabolites and cytokines in Chinese Ningdu yellow chickens

Thu, 13/06/2024 - 12:00
Poult Sci. 2024 May 25;103(8):103905. doi: 10.1016/j.psj.2024.103905. Online ahead of print.ABSTRACTIncreasing evidence has indicated that the gut microbiome plays an important role in chicken growth traits. However, the cecal microbial taxa associated with the growth rates of the Chinese Ningdu yellow chickens are unknown. In this study, shotgun metagenomic sequencing was used to identify cecal bacterial species associated with the growth rate of the Chinese Ningdu yellow chickens. We found that nine cecal bacterial species differed significantly between high and low growth rate chickens, including three species (Succinatimonas hippei, Phocaeicola massiliensis, and Parabacteroides sp. ZJ-118) that were significantly enriched in high growth rate chickens. We identified six Bacteroidales that were significantly enriched in low growth rate chickens, including Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium which were key biomarkers in differentiating high and low growth rate chickens and were associated with alterations in the functional taxa of the cecal microbiome. Untargeted serum metabolome analysis revealed that 8 metabolites showing distinct enrichment patterns between high and low growth rate chickens, including triacetate lactone and N-acetyl-a-neuraminic acid, which were at higher concentrations in low growth rate chickens and were positively and significantly correlated with Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium. Furthermore, the results suggest that serum cytokines, such as IL-5, may reduce growth rate and are related to changes in serum metabolites and gut microbes (e.g., Barnesiella sp. An22 and Barnesiella sp. ET7). These results provide important insights into the effects of the cecal microbiome, serum metabolism and cytokines in Ningdu yellow chickens.PMID:38870614 | DOI:10.1016/j.psj.2024.103905

Beneficial effects of melatonin on boar sperm motility and kinematics are mediated by MT1 receptor

Thu, 13/06/2024 - 12:00
Theriogenology. 2024 Jun 8;226:95-103. doi: 10.1016/j.theriogenology.2024.06.003. Online ahead of print.ABSTRACTMelatonin, a hormone synthesized in various tissues, plays a crucial role in modulating sperm characteristics, yet its protective function on boar sperm remains poorly understood. This study aimed to investigate the expression and localization of melatonin-related proteins (AANAT, ASMT, MT1, MT2, and NQO2) in pig tissues, assess the impact of melatonin on pig sperm motility parameters and quality, and elucidate the underlying molecular mechanisms. Our results revealed widespread expression of AANAT, ASMT, MT1, MT2, and NQO2 proteins in pig tissues, particularly in the testis. Specific localization patterns were observed in Leydig cells, reproductive epithelium, and columnar epithelium cells in the testis and cauda epididymis. Additionally, melatonin membrane receptors MT1 and MT2 were detected in boar sperm. Melatonin treatment significantly enhanced boar sperm motility parameters and quality, particularly with 10 nM melatonin treatment. Inhibition of the MT1 receptor, but not the MT2 receptor, resulted in decreased sperm motility, highlighting the pivotal role of the MT1 receptor in mediating melatonin's effects on boar sperm. Metabolomic analysis revealed significant alterations in sperm metabolites following melatonin supplementation, particularly in amino acid metabolism. Overall, our findings provide comprehensive insights into melatonin's mechanisms in improving boar sperm quality, suggesting its potential as a therapeutic agent for enhancing male fertility.PMID:38870584 | DOI:10.1016/j.theriogenology.2024.06.003

Neuroforensomics: metabolites as valuable biomarkers in cerebrospinal fluid of lethal traumatic brain injuries

Thu, 13/06/2024 - 12:00
Sci Rep. 2024 Jun 13;14(1):13651. doi: 10.1038/s41598-024-64312-0.ABSTRACTTraumatic brain injury (TBI) is a ubiquitous, common sequela of accidents with an annual prevalence of several million cases worldwide. In forensic pathology, structural proteins of the cellular compartments of the CNS in serum and cerebrospinal fluid (CSF) have been predominantly used so far as markers of an acute trauma reaction for the biochemical assessment of neuropathological changes after TBI. The analysis of endogenous metabolites offers an innovative approach that has not yet been considered widely in the assessment of causes and circumstances of death, for example after TBI. The present study, therefore, addresses the question whether the detection of metabolites by liquid-chromatography-mass spectrometry (LC/MS) analysis in post mortem CSF is suitable to identify TBI and to distinguish it from acute cardiovascular control fatalities (CVF). Metabolite analysis of 60 CSF samples collected during autopsies was performed using high resolution (HR)-LC/MS. Subsequent statistical and graphical evaluation as well as the calculation of a TBI/CVF quotient yielded promising results: numerous metabolites were identified that showed significant concentration differences in the post mortem CSF for lethal acute TBI (survival times up to 90 min) compared to CVF. For the first time, this forensic study provides an evaluation of a new generation of biomarkers for diagnosing TBI in the differentiation to other causes of death, here CVF, as surrogate markers for the post mortem assessment of complex neuropathological processes in the CNS ("neuroforensomics").PMID:38871842 | DOI:10.1038/s41598-024-64312-0

Untargeted metabolomics reveal signatures of a healthy lifestyle

Thu, 13/06/2024 - 12:00
Sci Rep. 2024 Jun 13;14(1):13630. doi: 10.1038/s41598-024-64561-z.ABSTRACTThis cross-sectional study investigated differences in the plasma metabolome in two groups of adults that were of similar age but varied markedly in body composition and dietary and physical activity patterns. Study participants included 52 adults in the lifestyle group (LIFE) (28 males, 24 females) and 52 in the control group (CON) (27 males, 25 females). The results using an extensive untargeted ultra high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) metabolomics analysis with 10,535 metabolite peaks identified 486 important metabolites (variable influence on projections scores of VIP ≥ 1) and 16 significantly enriched metabolic pathways that differentiated LIFE and CON groups. A novel metabolite signature of positive lifestyle habits emerged from this analysis highlighted by lower plasma levels of numerous bile acids, an amino acid profile characterized by higher histidine and lower glutamic acid, glutamine, β-alanine, phenylalanine, tyrosine, and proline, an elevated vitamin D status, higher levels of beneficial fatty acids and gut microbiome catabolism metabolites from plant substrates, and reduced levels of N-glycan degradation metabolites and environmental contaminants. This study established that the plasma metabolome is strongly associated with body composition and lifestyle habits. The robust lifestyle metabolite signature identified in this study is consistent with an improved life expectancy and a reduced risk for chronic disease.PMID:38871777 | DOI:10.1038/s41598-024-64561-z

Capturing the antimicrobial profile of Paeonia officinalis, Jasminum officinale and Rosa damascene against methicillin resistant Staphylococcus aureus with metabolomics analysis and network pharmacology

Thu, 13/06/2024 - 12:00
Sci Rep. 2024 Jun 13;14(1):13621. doi: 10.1038/s41598-024-62369-5.ABSTRACTIn the current study, we evaluated the in vitro antibacterial efficacy of the roots' extracts of Jasminum officinale, Rosa damascene and Paeonia officinalis against MRSA (methicillin-resistant Staphylococcus aureus) by well diffusion technique. The root extract of P. officinalis exerted a potent anti-MRSA with MIC 0.4673 µg/ml, while both J. officinale and R. damascene exhibited very weak activity. Therefore, chemical profiling of the crude extract P. officinalis roots assisted by LC-HR-ESI-MS was performed and led to the dereplication of twenty metabolites of different classes, in which terpenes are the most abundant compounds. On a molecular level, network pharmacology was used to determine the targets of active metabolites to bacterial infections, particularly MRSA. Online databases PubChem, UniProt, STRING, and Swiss Target Prediction were used. In addition to using CYTOSCAPE software to display and analyze the findings, ShinyGO and FunRich tools were used to identify the gene enrichment analysis to the set of recognized genes. The results detected the identified metabolites were annotated by 254 targets. ALB, ACHE, TYMS, PRKCD, PLG, MMP9, MMP2, ERN1, EDNRA, BRD4 were found to be associated with MRSA infection. The top KEGG pathway was the vascular smooth muscle contraction pathway according to enrichment FDR. The present study suggested a possible implication of P. officinalis roots as a potent candidate having a powerful antibacterial activity against MRSA.PMID:38871725 | DOI:10.1038/s41598-024-62369-5

Comprehensive multi-omics analysis of breast cancer reveals distinct long-term prognostic subtypes

Thu, 13/06/2024 - 12:00
Oncogenesis. 2024 Jun 13;13(1):22. doi: 10.1038/s41389-024-00521-6.ABSTRACTBreast cancer (BC) is a leading cause of cancer-related death worldwide. The diverse nature and heterogeneous biology of BC pose challenges for survival prediction, as patients with similar diagnoses often respond differently to treatment. Clinically relevant BC intrinsic subtypes have been established through gene expression profiling and are implemented in the clinic. While these intrinsic subtypes show a significant association with clinical outcomes, their long-term survival prediction beyond 5 years often deviates from expected clinical outcomes. This study aimed to identify naturally occurring long-term prognostic subgroups of BC based on an integrated multi-omics analysis. This study incorporates a clinical cohort of 335 untreated BC patients from the Oslo2 study with long-term follow-up (>12 years). Multi-Omics Factor Analysis (MOFA+) was employed to integrate transcriptomic, proteomic, and metabolomic data obtained from the tumor tissues. Our analysis revealed three prominent multi-omics clusters of BC patients with significantly different long-term prognoses (p = 0.005). The multi-omics clusters were validated in two independent large cohorts, METABRIC and TCGA. Importantly, a lack of prognostic association to long-term follow-up above 12 years in the previously established intrinsic subtypes was shown for these cohorts. Through a systems-biology approach, we identified varying enrichment levels of cell-cycle and immune-related pathways among the prognostic clusters. Integrated multi-omics analysis of BC revealed three distinct clusters with unique clinical and biological characteristics. Notably, these multi-omics clusters displayed robust associations with long-term survival, outperforming the established intrinsic subtypes.PMID:38871719 | DOI:10.1038/s41389-024-00521-6

HPLC/ESI-QTOF-MS/MS based untargeted metabolomics authentication of Taxus media six tissues

Thu, 13/06/2024 - 12:00
Phytochem Anal. 2024 Jun 13. doi: 10.1002/pca.3403. Online ahead of print.ABSTRACTINTRODUCTION: Taxus media (Taxus × media Rehder) is renowned for its high paclitaxel content, serving as a major source for industrial paclitaxel production. In addition to paclitaxel, T. media contains a diverse range of metabolites, including flavonoids, alkaloids, and terpenoids, which have been shown to possess antioxidant, antibacterial, anti-inflammatory, and immunomodulatory effects. However, these compounds have not been thoroughly studied as key metabolites in T. media.OBJECTIVE: The untargeted metabolomics analysis of six T. media tissues provides new insights into the development and utilization of T. media metabolites.METHOD: The extracts from six tissues of T. media were analyzed and subjected to analysis using high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF-MS/MS) and chemometric techniques.RESULTS: Using a reliable HPLC-Q-TOF-MS/MS method, we identified 312 compounds in six T. media tissues, including 214 previously unreported in T. media. To identify characteristic compounds across different tissues, 34 metabolites were further screened. KEGG metabolic pathway analysis revealed that these compounds primarily occur in the metabolic pathways of terpene glycosides, flavans, and O-methylated flavonoids.CONCLUSION: This study initially utilized an HPLC-QTOF-MS/MS-based metabolomics approach to assess the metabolites in different tissues of T. media, providing a basis for their utilization and management.PMID:38870256 | DOI:10.1002/pca.3403

Feasibility of MALDI-MSI-Based Proteomics Using Bouin-Fixed Pathology Samples: Untapping the Goldmine of Nephropathology Archives

Thu, 13/06/2024 - 12:00
J Proteome Res. 2024 Jun 13. doi: 10.1021/acs.jproteome.4c00198. Online ahead of print.ABSTRACTThe application of innovative spatial proteomics techniques, such as those based upon matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technology, has the potential to impact research in the field of nephropathology. Notwithstanding, the possibility to apply this technology in more routine diagnostic contexts remains limited by the alternative fixatives employed by this ultraspecialized diagnostic field, where most nephropathology laboratories worldwide use bouin-fixed paraffin-embedded (BFPE) samples. Here, the feasibility of performing MALDI-MSI on BFPE renal tissue is explored, evaluating variability within the trypsin-digested proteome as a result of different preanalytical conditions and comparing them with the more standardized formalin-fixed paraffin-embedded (FFPE) counterparts. A large proportion of the features (270, 68.9%) was detected in both BFPE and FFPE renal samples, demonstrating only limited variability in signal intensity (10.22-10.06%). Samples processed with either fixative were able to discriminate the principal parenchyma regions along with diverse renal substructures, such as glomeruli, tubules, and vessels. This was observed when performing an additional "stress test", showing comparable results in both BFPE and FFPE samples when the distribution of several amyloid fingerprint proteins was mapped. These results suggest the utility of BFPE tissue specimens in MSI-based nephropathology research, further widening their application in this field.PMID:38869849 | DOI:10.1021/acs.jproteome.4c00198

Identification of Stress-Responsive Metabolites in Plants Using an Untargeted Metabolomics Approach

Thu, 13/06/2024 - 12:00
Methods Mol Biol. 2024;2832:171-182. doi: 10.1007/978-1-0716-3973-3_12.ABSTRACTStress can affect different groups of plant metabolites and multiple signaling pathways. Untargeted metabolomics enables the collection of whole-spectrum data for the entire metabolite content present in plant tissues at that point in time. We present a thorough approach for large-scale, untargeted metabolomics of plant tissues using reverse-phase liquid chromatography connected to high-resolution mass spectrometry (LC-MS) of dilute methanolic extract. MZmine is a specialized computer software that automates the alignment and baseline modification of all derived mass peaks across all samples, resulting in precise information on the relative abundance of hundreds of metabolites reflected by thousands of mass signals. Further processing with statistic and bioinformatic techniques will provide a comprehensive perspective of the variations and connections among groups of samples.PMID:38869795 | DOI:10.1007/978-1-0716-3973-3_12

The changes of intestinal microbiota and metabolomics during the inhibition of bladder cancer by liquiritigenin

Thu, 13/06/2024 - 12:00
J Asian Nat Prod Res. 2024 Jun 13:1-10. doi: 10.1080/10286020.2024.2366010. Online ahead of print.ABSTRACTLiquiritigenin is a natural medicine. However, its inhibitory effect and its potential mechanism on bladder cancer (BCa) remain to be explored. It was found that it could be visualized that the transplanted tumours in the low-dose liquiritigenin -treated group and the high-dose liquiritigenin -treated group were smaller than those in the model group. Liquiritigenin treatment led to alterations in Lachnoclostridium, Escherichia-Shigella, Alistipes and Akkermansia. Non-targeted metabolomics analysis showed that a total of multiple differential metabolites were identified between the model group and the high-dose liquiritigenin-treated group. This provides a new direction and rationale for the antitumour effects of liquiritigenin.PMID:38869213 | DOI:10.1080/10286020.2024.2366010

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