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

Spatial metabolomics reveals skeletal myofiber subtypes

Fri, 03/02/2023 - 12:00
Sci Adv. 2023 Feb 3;9(5):eadd0455. doi: 10.1126/sciadv.add0455. Epub 2023 Feb 3.ABSTRACTSkeletal muscle myofibers are heterogeneous in their metabolism. However, metabolomic profiling of single myofibers has remained difficult. Mass spectrometry imaging (MSI) is a powerful tool for imaging molecular distributions. In this work, we optimized the workflow of matrix-assisted laser desorption/ionization (MALDI)-based MSI from cryosectioning to metabolomics data analysis to perform high-spatial resolution metabolomic profiling of slow- and fast-twitch myofibers. Combining the advantages of MSI and liquid chromatography-MS (LC-MS), we produced spatial metabolomics results that were more reliable. After the combination of high-spatial resolution MSI and LC-MS metabolomic analysis, we also discovered a new subtype of superfast type 2B myofibers that were enriched for fatty acid oxidative metabolism. Our technological workflow could serve as an engine for metabolomics discoveries, and our approach has the potential to provide critical insights into the metabolic heterogeneity and pathways that underlie fundamental biological processes and disease states.PMID:36735792 | DOI:10.1126/sciadv.add0455

Picornavirus infection enhances aspartate by the SLC38A8 transporter to promote viral replication

Fri, 03/02/2023 - 12:00
PLoS Pathog. 2023 Feb 3;19(2):e1011126. doi: 10.1371/journal.ppat.1011126. Online ahead of print.ABSTRACTFoot-and-mouth disease, a class of animal diseases, is caused by foot-and-mouth disease virus (FMDV). The metabolic changes during FMDV infection remain unclear. Here, PK-15 cells, serum, and tonsils infected with FMDV were analyzed by metabolomics. A total of 284 metabolites in cells were significantly changed after FMDV infection, and most of them belong to amino acids and nucleotides. Further studies showed that FMDV infection significantly enhanced aspartate in vitro and in vivo. The amino acid transporter solute carrier family 38 member 8 (SLC38A8) was responsible for FMDV-upregulated aspartate. Enterovirus 71 (EV71) and Seneca Valley virus (SVV) infection also enhanced aspartate by SLC38A8. Aspartate aminotransferase activity was also elevated in FMDV-, EV71-, and SVV-infected cells, which may lead to reversible transition between the TCA cycle and amino acids synthesis. Aspartate and SLC38A8 were essential for FMDV, EV71, and SVV replication in cells. In addition, aspartate and SLC38A8 also promoted FMDV and EV71 replication in mice. Detailed analysis indicated that FMDV infection promoted the transfer of mTOR to lysosome to enhance interaction between mTOR and Rheb, and activated PI3K/AKT/TSC2/Rheb/mTOR/p70S6K1 pathway to promote viral replication. The mTORC1 signaling pathway was responsible for FMDV-induced SLC38A8 protein expression. For the first time, our data identified metabolic changes during FMDV infection. These data identified a novel mechanism used by FMDV to upregulate aspartate to promote viral replication and will provide new perspectives for developing new preventive strategies.PMID:36735752 | DOI:10.1371/journal.ppat.1011126

Association of plasma metabolites and diagnostic imaging findings with hepatic lipidosis in bearded dragons (Pogona vitticeps) and effects of gemfibrozil therapy

Fri, 03/02/2023 - 12:00
PLoS One. 2023 Feb 3;18(2):e0274060. doi: 10.1371/journal.pone.0274060. eCollection 2023.ABSTRACTOBJECTIVES: To evaluate the association between plasma metabolites, biochemical analytes, diagnostic imaging findings, and the histologic diagnosis of hepatic lipidosis in bearded dragons. To assess the effects of gemfibrozil therapy on hepatic lipid accumulation and associated diagnostic tests.ANIMALS: Fourteen bearded dragons (Pogona vitticeps) with varying severity of hepatic lipid accumulation (with and without hepatic lipidosis) were included.PROCEDURES: Animals underwent coelomic ultrasound, computed tomography (CT) scans, and coelioscopic hepatic biopsies. Clinical pathology tests included lipidologic tests, hepatic biomarkers, and mass spectrometry-based metabolomics. Animals were medicated with gemfibrozil 6mg/kg orally once a day for 2 months in a randomized blinded clinical trial prior to repeating previous diagnostic testing.RESULTS: Hounsfield units on CT were negatively associated with increased hepatic vacuolation, while ultrasound and gross evaluation of the liver were not reliable. Beta-hydroxybutyric-acid (BHBA) concentrations were significantly associated with hepatic lipidosis. Metabolomics and lipidomics data found BHBA and succinic acid to be potential biomarkers for diagnosing hepatic lipidosis in bearded dragons. Succinic acid concentrations were significantly lower in the gemfibrozil treatment group. There was a tendency for improvement in the biomarkers and reduced hepatic fat in bearded dragons with hepatic lipidosis when treated with gemfibrozil, though the improvement was not statistically significant.CONCLUSIONS: These findings provide information on the antemortem assessment of hepatic lipidosis in bearded dragons and paves the way for further research in diagnosis and treatment of this disease.PMID:36735707 | DOI:10.1371/journal.pone.0274060

Full title: Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging

Fri, 03/02/2023 - 12:00
Rapid Commun Mass Spectrom. 2023 Feb 3:e9486. doi: 10.1002/rcm.9486. Online ahead of print.ABSTRACTRATIONALE: Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge.METHODS: In order to better understand the spatial distribution of ancient proteins preserved within teeth, we apply Matrix Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explore the spatial distribution of four proteins (collagen type I, of which chains alpha -1 and 2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6).RESULTS: We successfully identify ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observe that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein.CONCLUSIONS: While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we demonstrate that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.PMID:36735645 | DOI:10.1002/rcm.9486

Metabolomic Markers of Ultra-Processed Food and Incident CKD

Fri, 03/02/2023 - 12:00
Clin J Am Soc Nephrol. 2023 Jan 13. doi: 10.2215/CJN.0000000000000062. Online ahead of print.ABSTRACTBACKGROUND: High ultra-processed food consumption is associated with higher risk of CKD. However, there is no biomarker for ultra-processed food, and the mechanism through which ultra-processed food is associated with CKD is not clear. Metabolomics can provide objective biomarkers of ultra-processed food and provide important insights into the mechanisms by which ultra-processed food is associated with risk of incident CKD. Our objective was to identify serum metabolites associated with ultra-processed food consumption and investigate whether ultra-processed food-associated metabolites are prospectively associated with incident CKD.METHODS: We used data from 3751 Black and White men and women (aged 45-64 years) in the Atherosclerosis Risk in Communities study. Dietary intake was assessed using a semiquantitative 66-item food frequency questionnaire, and ultra-processed food was classified using the NOVA classification system. Multivariable linear regression models were used to identify the association between 359 metabolites and ultra-processed food consumption. Cox proportional hazards models were used to investigate the prospective association of ultra-processed food-associated metabolites with incident CKD.RESULTS: Twelve metabolites (saccharine, homostachydrine, stachydrine, N2, N2-dimethylguanosine, catechol sulfate, caffeine, 3-methyl-2-oxovalerate, theobromine, docosahexaenoate, glucose, mannose, and bradykinin) were significantly associated with ultra-processed food consumption after controlling for false discovery rate <0.05 and adjusting for sociodemographic factors, health behaviors, eGFR, and total energy intake. The 12 ultra-processed food-related metabolites significantly improved the prediction of ultra-processed food consumption (difference in C statistics: 0.069, P<1×10-16). Higher levels of mannose, glucose, and N2, N2-dimethylguanosine were associated with higher risk of incident CKD after a median follow-up of 23 years.CONCLUSIONS: We identified 12 serum metabolites associated with ultra-processed food consumption and three of them were positively associated with incident CKD. Mannose and N2, N2-dimethylguanosine are novel markers of CKD that may explain observed associations between ultra-processed food and CKD.PMID:36735499 | DOI:10.2215/CJN.0000000000000062

Reconstruction of Glutathione Metabolism in the Neuronal Model of Rotenone-Induced Neurodegeneration Using Mass Isotopologue Analysis with Hydrophilic Interaction Liquid Chromatography-Zeno High-Resolution Multiple Reaction Monitoring

Fri, 03/02/2023 - 12:00
Anal Chem. 2023 Feb 3. doi: 10.1021/acs.analchem.2c04231. Online ahead of print.ABSTRACTAccurate reconstruction of metabolic pathways is an important prerequisite for interpreting metabolomics changes and understanding the diverse biological processes in disease models. A tracer-based metabolomics strategy utilizes stable isotope-labeled precursors to resolve complex pathways by tracing the labeled atom(s) to downstream metabolites through enzymatic reactions. Isotope enrichment analysis is informative and achieved by counting total labeled atoms and acquiring the mass isotopologue distribution (MID) of the intact metabolite. However, quantitative analysis of labeled metabolite substructures/moieties (MS2 fragments) can offer more valuable insights into the reaction connections through measuring metabolite transformation. In order to acquire the isotopic labeling information at the intact metabolite and moiety level simultaneously, we developed a method that couples hydrophilic interaction liquid chromatography (HILIC) with Zeno trap-enabled high-resolution multiple reaction monitoring (MRMHR). The method enabled accurate and reproducible MID quantification for intact metabolites as well as their fragmented moieties, with notably high sensitivity in the MS2 fragmentation mode based on the measurement of 13C- or 15N-labeled cellular samples. The method was applied to human-induced pluripotent stem cell-derived neurons to trace the fate of 13C/15N atoms from D-13C6-glucose/L-15N2-glutamine added to the media. With the MID analysis of both intact metabolites and fragmented moieties, we validated the pathway reconstruction of de novo glutathione synthesis in mid-brain neurons. We discovered increased glutathione oxidization from both basal and newly synthesized glutathione pools under neuronal oxidative stress. Furthermore, the significantly decreased de novo glutathione synthesis was investigated and associated with altered activities of several key enzymes, as evidenced by suppressed glutamate supply via glucose metabolism and a diminished flux of glutathione synthetic reaction in the neuronal model of rotenone-induced neurodegeneration.PMID:36735349 | DOI:10.1021/acs.analchem.2c04231

Oral administration of silver nanomaterials affects the gut microbiota and metabolic profile altering the secretion of 5-HT in mice

Fri, 03/02/2023 - 12:00
J Mater Chem B. 2023 Feb 3. doi: 10.1039/d2tb02756a. Online ahead of print.ABSTRACTDue to their excellent antibacterial ability, silver nanomaterials (Ag NMs) are the most frequently used nanomaterials. Their widespread use introduces the risk of human ingestion. However, the potential toxicity of Ag NMs to the gut microbiota and their metabolic profile are yet to be fully explored. In this study, we examined the effects of Ag NMs after oral administration (0.5 mg kg-1 and 2.5 mg kg-1, 14 and 28 days) on gut homeostasis by integrating tissue imaging, 16s rRNA gene sequencing and metabolomics techniques. We uncovered that silver nanoparticles (Ag NPs) and silver nanowires (Ag NWs) altered the structure (inhibiting the proliferation of Gram-negative bacteria) and decreased the diversity of gut microbiota in mice after short-term (14 days) exposure, while the microbial community tended to recover after long-term exposure (28 days), indicating that the resistance and resilience of the gut microbiome may pose a defense against the interference by reactive, exogenous nanomaterials. Interestingly, even though the gut microbiota structure recovered after 28 days of exposure, the gut metabolites significantly changed, showing increased 1H-indole-3-carboxylic acid and elevated levels of 5-HT in the gut and blood. Collectively, our results provide a piece of evidence on the association between the ingestion of exogenous nanoparticles and gut homeostasis, especially the metabolic profile of the host. This work thus provides additional insights for the continued investigation of the adverse effects of silver nanomaterials on biological hosts.PMID:36734837 | DOI:10.1039/d2tb02756a

Integration of transcriptomics and metabonomics revealed the protective effects of hemp seed oil against methionine-choline-deficient diet-induced non-alcoholic steatohepatitis in mice

Fri, 03/02/2023 - 12:00
Food Funct. 2023 Feb 3. doi: 10.1039/d2fo03054c. Online ahead of print.ABSTRACTNon-alcoholic steatohepatitis (NASH) is a chronic liver disease with few therapeutic options available currently. Hemp seed oil extracted from the seeds of hemp (Cannabis sativa L.) has significant nutritional and biological properties due to the unique composition of polyunsaturated fatty acids and various antioxidant compounds. However, little is known about the beneficial effects and molecular mechanisms of hemp seed oil on NASH. Here, the hepatoprotective effects of hemp seed oil on methionine-choline-deficient (MCD) diet-induced NASH in C57BL/6 mice were explored via integration of transcriptomics and metabolomics. Hemp seed oil could improve hepatic steatosis, inflammation and fibrosis in mice with MCD diet-induced NASH. In a nuclear magnetic resonance (NMR)-based metabonomic study, the hepatic and urinary metabolic profiles of mice supplemented with hemp seed oil showed a tendency to recover to healthy controls compared to those of NASH mice. Eight potential biomarkers associated with NASH in both liver tissue and urine were restored to near normal levels by administration of hemp seed oil. The proposed pathways were mainly involved in pyrimidine metabolism, one-carbon metabolism, amino acid metabolism, glycolysis and the tricarboxylic acid (TCA) cycle. Hepatic transcriptomics based on Illumina RNA-Seq sequencing showed that hemp seed oil exerted anti-NASH activities by regulating multiple signaling pathways, e.g., downregulation of the TNF signaling pathway, the IL-17 signaling pathway, the MAPK signaling pathway and the NF-κB signaling pathway, which played a pivotal role in the pathogenesis of NASH. In particular, integration of metabonomic and transcriptomic results suggested that hemp seed oil could attenuate NASH-related liver fibrosis by inhibition of glutaminolysis. These results provided new insights into the hepatoprotective effects of hemp seed oil against MCD diet-induced NASH and hemp seed oil might have potential as an effective therapy for NASH.PMID:36734470 | DOI:10.1039/d2fo03054c

Whole-cell MALDI-ToF MS coupled with untargeted metabolomics facilitates investigations of microbial chemical interactions

Fri, 03/02/2023 - 12:00
Chembiochem. 2023 Feb 3. doi: 10.1002/cbic.202200802. Online ahead of print.ABSTRACTThe emergence of drug resistant pathogens necessitates development of new countermeasures. In this regard, the introduction of probiotics to directly attack or competitively exclude pathogens presents a useful strategy. Application of this approach requires an understanding of how a probiotic and its target pathogen interact. A key means of probiotic-pathogen interaction involves the production of small molecules called natural products (NPs). Here, we report use of whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry for characterization of NP production by candidate probiotics (mouse airway microbiome isolates) when co-cultured with respiratory pathogen Burkholderia. We found that a Bacillus velezensis strain inhibits growth of and elicits NP production by B. thailandensis. Dereplication of known NPs detected in the metabolome of this B. velezensis strain suggests that a previously unannotated bioactive compound is involved. Thus, we present use of whole-cell MALDI as a broadly applicable method for screening of NP composition of microbial co-cultures, which can be combined with other -omics methods for characterization of probiotic-pathogen, and other microbe-microbe, interactions.PMID:36734186 | DOI:10.1002/cbic.202200802

Wet-food diet promotes the recovery from surgery of castration and control of body weight in adult young cats

Fri, 03/02/2023 - 12:00
J Anim Sci. 2023 Feb 3:skad039. doi: 10.1093/jas/skad039. Online ahead of print.ABSTRACTInappropriate dietary management may lead to delayed recovery from castration surgery and significant weight gain in cats after castration. Wet canned food often exhibits more advantageous characteristics than dry food (e.g., higher palatability and digestibility, and lower energy density). This study compared the effects of canned and dry food on surgical recovery and weight management in cats after castration. Eighteen healthy cats (weighed 4.33 ± 1.04 kg and aged 18-months old) were allocated to one of the two dietary treatments (N = 9/group), dry (CON) and canned food (CAN) balanced for sex and initial BW. Cats were fed ad libitum for 7 weeks, including one week before surgery (week 0) and 6 weeks after surgery (week 1 to 6). Daily dry matter intake (DMI), and weekly body weight (BW) and body condition score (BCS) was obtained. Feces were collected for measuring nutrient digestibility and concentrations of short-chain fatty acids (SCFA) and branched-chain fatty acids (BCFA). Physical pain and wound surface assessment were performed at week 1. Blood was also collected intermittently for measuring biochemical indices and untargeted metabolomics analysis. Results indicated that BW, BCS and daily DMI in CON group increased (P < 0.05) over time after castration, but were maintained relatively stable in CAN group. Cats in CAN group exhibited less pain-related behavior as reflected by lower score of comfort (P < 0.05) and vocalization (P < 0.10), improved wound surface assessment (P < 0.10), lower level of lipase (P < 0.10) and ratio of blood urea nitrogen/serum creatinine (BUN/SC; P < 0.05), and higher level of superoxide dismutase (SOD; P < 0.05) in week 1 than CON cats. Meanwhile, the CAN group had significantly higher concentration of immunoglobulin G (IgG) on day 5 and 7, and higher level of high-density lipoprotein cholesterol (HDL-C; P < 0.10) but lower triglyceride (TG; P < 0.05) than CON group on day 20 and 48. Fecal total and most individual SCFA increased significantly from week 1 to week 6 regardless of diet, but the increase of butyric acid over time only occurred in CON group (P < 0.05). Also, serum metabolomic analysis revealed differential metabolic pathways between the two groups. Overall, compared with the dry food, the canned food tested in our study promoted cat wound recovery by reducing pain and increasing immune and antioxidative capacity after sterilizing surgery, and helped to maintain healthy body condition in cats after castration.PMID:36734030 | DOI:10.1093/jas/skad039

Comprehensive analysis of transcriptomics and metabolomics to understand tail-suspension-induced myocardial injury in rat

Fri, 03/02/2023 - 12:00
Front Cardiovasc Med. 2023 Jan 17;9:1074257. doi: 10.3389/fcvm.2022.1074257. eCollection 2022.ABSTRACTBACKGROUND/AIMS: The effect and underlying mechanism of microgravity on myocardium still poorly understood. The present study aims to reveal the effect and underlying mechanism of tail-suspension-induced microgravity on myocardium of rats.METHODS: Tail-suspension was conducted to simulate microgravity in rats. Echocardiography assay was used to detect cardiac function. The cardiac weight index was measured. Hematoxylin and eosin (HE) staining and transmission electron microscopy assay were conducted to observe the structure of the tissues. RNA sequencing and non-targeted metabolomics was employed to obtain transcriptome and metabolic signatures of heart from tail-suspension-induced microgravity and control rats.RESULTS: Microgravity induced myocardial atrophy and decreased cardiac function in rats. Structure and ultrastructure changes were observed in myocardium of rats stimulated with microgravity. RNA sequencing for protein coding genes was performed and identified a total of 605 genes were differentially expressed in myocardium of rats with tail suspension, with 250 upregulated and 355 downregulated (P < 0.05 and | log2fold change| > 1). A total of 55 differentially expressed metabolites were identified between the two groups (VIP > 1 and P < 0.05) by the metabolic profiles of heart tissues from microgravity groups and control. Several major pathways altered aberrantly at both transcriptional and metabolic levels, including FoxO signaling pathway, Amyotrophic lateral sclerosis, Histidine metabolism, Arginine and proline metabolism.CONCLUSION: Microgravity can induce myocardial atrophy and decreases cardiac function in rats and the molecular alterations at the metabolic and transcriptomic levels was observed, which indicated major altered pathways in rats with tail suspension. The differentially expressed genes and metabolites-involved in the pathways maybe potential biomarkers for microgravity-induced myocardial atrophy.PMID:36733828 | PMC:PMC9886666 | DOI:10.3389/fcvm.2022.1074257

Improving flesh quality of grass carp (<em>Ctenopharyngodon idellus</em>) by completely replacing dietary soybean meal with yellow mealworm (<em>Tenebrio molitor</em>)

Fri, 03/02/2023 - 12:00
Anim Nutr. 2022 Dec 7;12:375-387. doi: 10.1016/j.aninu.2022.12.004. eCollection 2023 Mar.ABSTRACTIn order to find viable alternative protein sources for aquaculture, we evaluated the effect of partial or complete replacement of dietary soybean meal with yellow mealworm (TM) on the flesh quality of grass carp. In this study, 180 grass carp (511.85 ± 0.25 g) were fed 3 experimental diets in which 0% (CN), 30% (YM30) and 100% (YM100) dietary soybean meal was replaced by TM for 90 d. The results showed that growth performance, biological parameters and serum antioxidant capacity of grass carp were not affected by dietary TM (P > 0.05). Both muscle and whole body crude protein were obviously promoted with the increase of dietary TM (P < 0.05), and the concentration of heavy metal in muscle was not influenced (P > 0.05), indicating that food safety was not influenced by TM. Dietary TM improved muscle textural characteristics by elevating adhesiveness, springiness and chewiness in YM100 (P < 0.05). In addition, the muscle tenderness was significantly increased by declining the shear force (P < 0.05). The muscle fiber density in YM30 &YM100 and length of dark bands and sarcomeres in YM100 were obviously increased (P < 0.05). The expression of myf5, myog and myhc exhibited a significant upward trend with the increase of dietary TM (P < 0.05), which promoted fiber density, length of sarcomere and texture of grass carp muscle. According to the results of metabolomics, the arachidonate (ARA) and eicosapentaenoic acid (EPA) were notably elevated in YM30 and YM100, which indicated that the improvement of flesh quality of grass carp may contribute to the dietary TM influence on muscle lipid metabolism, especially the polyunsaturated fatty acids. In conclusion, TM can completely replace dietary soybean meal and improve the nutritional value of grass carp.PMID:36733784 | PMC:PMC9883186 | DOI:10.1016/j.aninu.2022.12.004

Integrative metabolome and transcriptome analyses reveal the molecular mechanism underlying variation in floral scent during flower development of <em>Chrysanthemum indicum</em> var. <em>aromaticum</em>

Fri, 03/02/2023 - 12:00
Front Plant Sci. 2022 Sep 15;13:919151. doi: 10.3389/fpls.2022.919151. eCollection 2022.ABSTRACTChrysanthemum indicum var. aromaticum (CIA) is an endemic plant that occurs only in the high mountain areas of the Shennongjia Forest District in China. The whole plant, in particular the flowers of CIA, have intense fragrance, making it a novel resource plant for agricultural, medicinal, and industrial applications. However, the volatile metabolite emissions in relation to CIA flower development and the molecular mechanisms underlying the generation of floral scent remain poorly understood. Here, integrative metabolome and transcriptome analyses were performed to investigate floral scent-related volatile compounds and genes in CIA flowers at three different developmental stages. A total of 370 volatile metabolites, mainly terpenoids and esters, were identified, of which 89 key differential metabolites exhibited variable emitting profiles during flower development. Transcriptome analysis further identified 8,945 differentially expressed genes (DEGs) between these samples derived from different flower developmental stages and KEGG enrichment analyses showed that 45, 93, and 101 candidate DEGs associated with the biosynthesis of phenylpropanoids, esters, and terpenes, respectively. Interestingly, significant DEGs involved into the volatile terpenes are only present in the MEP and its downstream pathways, including those genes encoding ISPE, ISPG, FPPS, GPPS, GERD, ND and TPS14 enzymes. Further analysis showed that 20 transcription factors from MYB, bHLH, AP2/EFR, and WRKY families were potentially key regulators affecting the expressions of floral scent-related genes during the CIA flower development. These findings provide insights into the molecular basis of plant floral scent metabolite biosynthesis and serve as an important data resources for molecular breeding and utilization of CIA plants in the future.PMID:36733600 | PMC:PMC9889088 | DOI:10.3389/fpls.2022.919151

KODAMA exploratory analysis in metabolic phenotyping

Fri, 03/02/2023 - 12:00
Front Mol Biosci. 2023 Jan 17;9:1070394. doi: 10.3389/fmolb.2022.1070394. eCollection 2022.ABSTRACTKODAMA is a valuable tool in metabolomics research to perform exploratory analysis. The advanced analytical technologies commonly used for metabolic phenotyping, mass spectrometry, and nuclear magnetic resonance spectroscopy push out a bunch of high-dimensional data. These complex datasets necessitate tailored statistical analysis able to highlight potentially interesting patterns from a noisy background. Hence, the visualization of metabolomics data for exploratory analysis revolves around dimensionality reduction. KODAMA excels at revealing local structures in high-dimensional data, such as metabolomics data. KODAMA has a high capacity to detect different underlying relationships in experimental datasets and correlate extracted features with accompanying metadata. Here, we describe the main application of KODAMA exploratory analysis in metabolomics research.PMID:36733493 | PMC:PMC9887019 | DOI:10.3389/fmolb.2022.1070394

High-fiber-diet-related metabolites improve neurodegenerative symptoms in patients with obesity with diabetes mellitus by modulating the hippocampal-hypothalamic endocrine axis

Fri, 03/02/2023 - 12:00
Front Neurol. 2023 Jan 17;13:1026904. doi: 10.3389/fneur.2022.1026904. eCollection 2022.ABSTRACTOBJECTIVE: Through transcriptomic and metabolomic analyses, this study examined the role of high-fiber diet in obesity complicated by diabetes and neurodegenerative symptoms.METHOD: The expression matrix of high-fiber-diet-related metabolites, blood methylation profile associated with pre-symptomatic dementia in elderly patients with type 2 diabetes mellitus (T2DM), and high-throughput single-cell sequencing data of hippocampal samples from patients with Alzheimer's disease (AD) were retrieved from the Gene Expression Omnibus (GEO) database and through a literature search. Data were analyzed using principal component analysis (PCA) after quality control and data filtering to identify different cell clusters and candidate markers. A protein-protein interaction network was mapped using the STRING database. To further investigate the interaction among high-fiber-diet-related metabolites, methylation-related DEGs related to T2DM, and single-cell marker genes related to AD, AutoDock was used for semi-flexible molecular docking.RESULT: Based on GEO database data and previous studies, 24 marker genes associated with high-fiber diet, T2DM, and AD were identified. Top 10 core genes include SYNE1, ANK2, SPEG, PDZD2, KALRN, PTPRM, PTPRK, BIN1, DOCK9, and NPNT, and their functions are primarily related to autophagy. According to molecular docking analysis, acetamidobenzoic acid, the most substantially altered metabolic marker associated with a high-fiber diet, had the strongest binding affinity for SPEG.CONCLUSION: By targeting the SPEG protein in the hippocampus, acetamidobenzoic acid, a metabolite associated with high-fiber diet, may improve diabetic and neurodegenerative diseases in obese people.PMID:36733447 | PMC:PMC9888315 | DOI:10.3389/fneur.2022.1026904

Temporal metabolic profiling of bone healing in a caprine tibia segmental defect model

Fri, 03/02/2023 - 12:00
Front Vet Sci. 2023 Jan 17;9:1023650. doi: 10.3389/fvets.2022.1023650. eCollection 2022.ABSTRACTBone tissue engineering is an emerging field of regenerative medicine, with a wide array of biomaterial technologies and therapeutics employed. However, it is difficult to objectively compare these various treatments during various stages of tissue response. Metabolomics is rapidly emerging as a powerful analytical tool to establish broad-spectrum metabolic signatures for a target biological system. Developing an effective biomarker panel for bone repair from small molecule data would provide an objective metric to readily assess the efficacy of novel therapeutics in relation to natural healing mechanisms. In this study we utilized a large segmental bone defect in goats to reflect trauma resulting in substantial volumetric bone loss. Characterization of the native repair capacity was then conducted over a period of 12 months through the combination of standard (radiography, computed tomography, histology, biomechanics) data and ultra-high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) metabolic profiling. Standard metrics demonstrated that samples formed soft callus structures that later mineralized. Small molecule profiles showed distinct temporal patterns associated with the bone tissue repair process. Specifically, increased lactate and amino acid levels at early time points indicated an environment conducive to osteoblast differentiation and extracellular matrix formation. Citrate and pyruvate abundances increased at later time points indicating increasing mineral content within the defect region. Taurine, shikimate, and pantothenate distribution profiles appeared to represent a shift toward a more homeostatic remodeling environment with the differentiation and activity of osteoclasts offsetting the earlier deposition phases of bone repair. The generation of a comprehensive metabolic reference portfolio offers a potent mechanism for examining novel biomaterials and can serve as guide for the development of new targeted therapeutics to improve the rate, magnitude, and quality of bone regeneration.PMID:36733424 | PMC:PMC9886884 | DOI:10.3389/fvets.2022.1023650

Metabolomics profiling in prediction of chemo-immunotherapy efficiency in advanced non-small cell lung cancer

Fri, 03/02/2023 - 12:00
Front Oncol. 2023 Jan 17;12:1025046. doi: 10.3389/fonc.2022.1025046. eCollection 2022.ABSTRACTBACKGROUND: To explore potential metabolomics biomarker in predicting the efficiency of the chemo-immunotherapy in patients with advanced non-small cell lung cancer (NSCLC).METHODS: A total of 83 eligible patients were assigned to receive chemo-immunotherapy. Serum samples were prospectively collected before the treatment to perform metabolomics profiling analyses under the application of gas chromatography mass spectrometry (GC-MS). The key metabolites were identified using projection to latent structures discriminant analysis (PLS-DA). The key metabolites were used for predicting the chemo-immunotherapy efficiency in advanced NSCLC patients.RESULTS: Seven metabolites including pyruvate, threonine, alanine, urea, oxalate, elaidic acid and glutamate were identified as the key metabolites to the chemo-immunotherapy response. The receiver operating characteristic curves (AUC) were 0.79 (95% CI: 0.69-0.90), 0.60 (95% CI: 0.48-0.73), 0.69 (95% CI: 0.57-0.80), 0.63 (95% CI: 0.51-0.75), 0.60 (95% CI: 0.48-0.72), 0.56 (95% CI: 0.43-0.67), and 0.67 (95% CI: 0.55-0.80) for the key metabolites, respectively. A binary logistic regression was used to construct a combined biomarker model to improve the discriminating efficiency. The AUC was 0.86 (95% CI: 0.77-0.94) for the combined biomarker model. Pathway analyses showed that urea cycle, glucose-alanine cycle, glycine and serine metabolism, alanine metabolism, and glutamate metabolism were the key metabolic pathway to the chemo-immunotherapy response in patients with advanced NSCLC.CONCLUSION: Metabolomics analyses of key metabolites and pathways revealed that GC-MS could be used to predict the efficiency of chemo-immunotherapy. Pyruvate, threonine, alanine, urea, oxalate, elaidic acid and glutamate played a central role in the metabolic of PD patients with advanced NSCLC.PMID:36733356 | PMC:PMC9887290 | DOI:10.3389/fonc.2022.1025046

Lysophospholipids and branched chain amino acids are associated with aging: a metabolomics-based study of Chinese adults

Fri, 03/02/2023 - 12:00
Eur J Med Res. 2023 Feb 2;28(1):58. doi: 10.1186/s40001-023-01021-w.ABSTRACTBACKGROUND: Aging is an inevitable process associated with impairments in multiple organ systems, which increases the risk of comorbidity and disability, and reduces the health-span. Metabolomics is a powerful tool in aging research, which can reflect the characteristics of aging at the level of terminal metabolism, and may contribute to the exploration of aging mechanisms and the formulation of anti-aging strategies.METHODS: To identify possible biomarkers and pathways associated with aging using untargeted metabolomics methods, we performed liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics profiling on serum samples from 32 older adults and 32 sex-matched young controls.RESULTS: Metabolite profiling could distinguish the two groups. Among the 349 metabolites identified, 80-including lysophospholipids whose levels gradually decline-are possible candidate aging biomarkers. Valine, leucine and isoleucine degradation and biosynthesis were important pathways in aging, with reduced levels of L-isoleucine (r = - 0.30, p = 0.017) and L-leucine (r = - 0.32, p = 0.010) observed in older adults.CONCLUSIONS: We preliminarily revealed the metabolite changes associated with aging in Chinese adults. Decreases in mitochondrial membrane-related lysophospholipids and dysfunction of branched-chain amino acid metabolism were determined to be the characteristics and promising research targets for aging.PMID:36732870 | DOI:10.1186/s40001-023-01021-w

Integrative multi-omics networks identify PKCδ and DNA-PK as master kinases of glioblastoma subtypes and guide targeted cancer therapy

Thu, 02/02/2023 - 12:00
Nat Cancer. 2023 Feb 2. doi: 10.1038/s43018-022-00510-x. Online ahead of print.ABSTRACTDespite producing a panoply of potential cancer-specific targets, the proteogenomic characterization of human tumors has yet to demonstrate value for precision cancer medicine. Integrative multi-omics using a machine-learning network identified master kinases responsible for effecting phenotypic hallmarks of functional glioblastoma subtypes. In subtype-matched patient-derived models, we validated PKCδ and DNA-PK as master kinases of glycolytic/plurimetabolic and proliferative/progenitor subtypes, respectively, and qualified the kinases as potent and actionable glioblastoma subtype-specific therapeutic targets. Glioblastoma subtypes were associated with clinical and radiomics features, orthogonally validated by proteomics, phospho-proteomics, metabolomics, lipidomics and acetylomics analyses, and recapitulated in pediatric glioma, breast and lung squamous cell carcinoma, including subtype specificity of PKCδ and DNA-PK activity. We developed a probabilistic classification tool that performs optimally with RNA from frozen and paraffin-embedded tissues, which can be used to evaluate the association of therapeutic response with glioblastoma subtypes and to inform patient selection in prospective clinical trials.PMID:36732634 | DOI:10.1038/s43018-022-00510-x

Fetal bovine serum, an important factor affecting the reproducibility of cell experiments

Thu, 02/02/2023 - 12:00
Sci Rep. 2023 Feb 2;13(1):1942. doi: 10.1038/s41598-023-29060-7.ABSTRACTFetal bovine serum (FBS) is a natural medium used in cell cultures containing the large amount of nutrients necessary for cell growth and is often used for in vitro cultures of animal cells. Although FBS plays a vital role in cell cultures, there are small molecules contained within FBS that remain unidentified, and their effects on cultured cells is poorly understood. Here, we report that different brands of FBS have varying influences on the background expression of IL-8, not TNFα and IL1β in epithelial cells. The endogenous small molecules in FBS and ERK pathways may contribute to these effects. In addition, FBS form the IL-8 stimulation and IL-8 non-responsive groups have different metabolome profiles. Overall, our study suggests that metabolites in FBS should be included in the quantitative considerations when conducting cell experiments, especially immune-related experiments, to improve the repeatability of experimental results in scientific papers; IL-8 could thus be an important factor in selecting FBS.PMID:36732616 | DOI:10.1038/s41598-023-29060-7

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