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

Phenotypic and Metabolomic Characterization of 3D Lung Cell Cultures Exposed to Airborne Particulate Matter from Three Air Quality Network Stations in Catalonia

Thu, 10/11/2022 - 12:00
Toxics. 2022 Oct 22;10(11):632. doi: 10.3390/toxics10110632.ABSTRACTAir pollution constitutes an environmental problem that it is known to cause many serious adverse effects on the cardiovascular and respiratory systems. The chemical characterization of particulate matter (PM) is key for a better understanding of the associations between chemistry and toxicological effects. In this work, the chemical composition and biological effects of fifteen PM10 air filter samples from three air quality stations in Catalonia with contrasting air quality backgrounds were investigated. Three-dimensional (3D) lung cancer cell cultures were exposed to these sample extracts, and cytotoxicity, reactive oxygen species (ROS) induction, metabolomics, and lipidomics were explored. The factor analysis method Multivariate Curve Resolution-Alternating Least-Squares (MCR-ALS) was employed for an integrated interpretation of the associations between chemical composition and biological effects, which could be related to urban traffic emission, biomass burning smoke, and secondary aerosols. In this pilot study, a novel strategy combining new approach methodologies and chemometrics provided new insights into the biomolecular changes in lung cells associated with different sources of air pollution. This approach can be applied in further research on air pollution toxicity to improve our understanding of the causality between chemistry and its effects.PMID:36355924 | DOI:10.3390/toxics10110632

What's New in the Diagnosis of Periprosthetic Joint Infections: Focus on Synovial Fluid Biomarkers

Thu, 10/11/2022 - 12:00
Trop Med Infect Dis. 2022 Nov 7;7(11):355. doi: 10.3390/tropicalmed7110355.ABSTRACTPeriprosthetic joint infections are some of the leading causes of revision prosthetic surgery, accounting for 25% of failed total knee replacements and 15% of failed total hip replacements. The search for a biomarker that, together with clinical and radiological findings, could improve the management of such patients is currently a significant challenge for orthopaedic surgeons. Synovial fluid is a viscous and mucinous substance produced by the synovium, a specialized connective tissue that lines diarthrodial joints. Synovial fluid is an ultrafiltrate of plasma but also contains proteins secreted from the surrounding tissues, including the articular cartilage and synovium. Therefore, synovial fluid represents a source of disease-related proteins that could be used as potential biomarkers in several articular diseases. Based on these findings, the study of synovial fluid has been gaining increasing importance in recent years. This review aims to assess the accuracy and the limitations of the most promising synovial fluid biomarkers-i.e., Alpha-Defensin, Leukocyte Esterase, C-Reactive Protein, Interleukin-6, Calprotectin, Presepsin and Neopterin-in the diagnosis of PJI. Special attention will be given to emerging synovial biomarkers, which could soon be important in diagnosing PJIs.PMID:36355897 | DOI:10.3390/tropicalmed7110355

Evaluation of Formalin-Fixed and FFPE Tissues for Spatially Resolved Metabolomics and Drug Distribution Studies

Thu, 10/11/2022 - 12:00
Pharmaceuticals (Basel). 2022 Oct 23;15(11):1307. doi: 10.3390/ph15111307.ABSTRACTFixation of samples is broadly used prior to the histological evaluation of tissue samples. Though recent reports demonstrated the ability to use fixed tissues for mass spectrometry imaging (MSI) based proteomics, glycomics and tumor classification studies, to date comprehensive evaluation of fixation-related effects for spatially resolved metabolomics and drug disposition studies is still missing. In this study we used matrix assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) MSI to investigate the effect of formalin-fixation and formalin-fixation combined with paraffin embedding on the detectable metabolome including xenobiotics. Formalin fixation was found to cause significant washout of polar molecular species, including inorganic salts, amino acids, organic acids and carnitine species, oxidation of endogenous lipids and formation of reaction products between lipids and fixative ingredients. The slow fixation kinetics under ambient conditions resulted in increased lipid hydrolysis in the tissue core, correlating with the time-dependent progression of the fixation. Paraffin embedding resulted in subsequent partial removal of structural lipids resulting in the distortion of the elucidated biodistributions.PMID:36355479 | DOI:10.3390/ph15111307

Single-dose pharmacokinetics of telmisartan oral solution and effect of feeding in dogs

Thu, 10/11/2022 - 12:00
J Vet Pharmacol Ther. 2022 Nov 10. doi: 10.1111/jvp.13104. Online ahead of print.ABSTRACTTelmisartan is an angiotensin II receptor blocker that has great potential to improve the treatment of hypertension, proteinuria, and cardiovascular disease in dogs. A feline-approved telmisartan oral solution (TOS) is available, but this formulation has not been evaluated in dogs. The aims of this study were to establish the pharmacokinetics of telmisartan administered as TOS and determine the effect of feeding on drug absorption in dogs. In a cross-over design, seven healthy dogs received 1 mg/kg telmisartan orally as TOS with or without food and underwent serial measurement of plasma telmisartan concentrations over 24 h. Bioequivalence of TOS administered with vs. without food was assessed by the 90% confidence interval method for maximum concentration (Cmax ), and the observed and extrapolated areas under the curve (AUC0-t and AUC0-∞ ). The mean ratios of these parameters were 0.97 (CI 0.74-1.27), 0.92 (0.81-1.03), and 0.90 (0.82-1.00), respectively. Feeding methods were not bioequivalent based on Cmax due to interindividual variation. These results suggest that TOS can be given to dogs with or without food but should be administered in the same way consistently. Additional pharmacokinetic and pharmacodynamic studies are warranted to confirm this recommendation and establish the therapeutic targets for telmisartan in dogs.PMID:36355449 | DOI:10.1111/jvp.13104

Dysregulated lipid synthesis by oncogenic IDH1 mutation is a targetable synthetic lethal vulnerability

Thu, 10/11/2022 - 12:00
Cancer Discov. 2022 Nov 10:CD-21-0218. doi: 10.1158/2159-8290.CD-21-0218. Online ahead of print.ABSTRACTIsocitrate dehydrogenase 1 and 2 (IDH) are mutated in multiple cancers and drive production of (R)-2-hydroxyglutarate (2HG). We identified a lipid synthesis enzyme (acetyl CoA carboxylase 1, ACC1) as a synthetic lethal target in mutant IDH1 (mIDH1), but not mIDH2, cancers. Here, we analyzed the metabolome of primary acute myeloid leukemia (AML) blasts and identified a mIDH1-specific reduction in fatty acids. mIDH1 also induced a switch to beta-oxidation indicating reprogramming of metabolism towards a reliance on fatty acids. Compared to mIDH2, mIDH1 AML displayed depletion of NADPH with defective reductive carboxylation that was not rescued by the mIDH1-specific inhibitor ivosidenib. In xenograft models, a lipid-free diet markedly slowed the growth of mIDH1 AML, but not healthy CD34+ HSPCs or mIDH2 AML. Genetic and pharmacologic targeting of ACC1 resulted in growth inhibition of mIDH1 cancers, not reversible by ivosidenib. Critically, pharmacologic targeting of ACC1 improved sensitivity of mIDH1 AML to venetoclax.PMID:36355448 | DOI:10.1158/2159-8290.CD-21-0218

Metabolomic Profiling to Understand Chondrocyte Metabolism

Thu, 10/11/2022 - 12:00
Methods Mol Biol. 2023;2598:141-156. doi: 10.1007/978-1-0716-2839-3_11.ABSTRACTMetabolism has long been recognized as a critical physiological process necessary to maintain homeostasis in all types of cells including the chondrocytes of articular cartilage. Alterations in metabolism in disease and metabolic adaptation to physiological stimuli such as mechanical loading are increasingly recognized as important for understanding musculoskeletal systems such as synovial joints. Metabolomics is an emerging technique that allows quantitative measurement of thousands of small molecule metabolites that serve as both products and reactants to myriad reactions of cellular biochemistry. This protocol describes procedures to perform metabolomic profiling on chondrocytes and other tissues and fluids within the synovial joint.PMID:36355290 | DOI:10.1007/978-1-0716-2839-3_11

Metabolomics and NMR

Thu, 10/11/2022 - 12:00
Handb Exp Pharmacol. 2022 Nov 11. doi: 10.1007/164_2022_616. Online ahead of print.ABSTRACTThe purpose of this manuscript will be to convince the reader to dive deeper into NMR spectroscopy and prevent the technique from being just another "black-box" in the lab. We will try to concisely highlight interesting topics and supply additional references for further exploration at each stage. The advantages of delving into the technique will be shown. The secondary objective, i.e., avoiding common problems before starting, will hopefully then become clear. Lastly, we will emphasize the spectrometer information needed for manuscript reporting to allow reproduction of results and confirm findings.PMID:36355220 | DOI:10.1007/164_2022_616

Advancements in Pulsed Stable Isotope-Resolved Metabolomics

Thu, 10/11/2022 - 12:00
Handb Exp Pharmacol. 2022 Nov 11. doi: 10.1007/164_2022_621. Online ahead of print.ABSTRACTThe understanding of biochemical processes of metabolism is gained through the measurement of the concentration of intermediates and the rate of metabolite conversion. However, the measurement of metabolite concentrations does not give a full representation of this dynamic system. To understand the kinetics of metabolism, the system must be described and quantified in terms of metabolite flow as a function of time. In order to measure the metabolite flow, or more precisely the metabolic flux through a biological system, substrates of the cell are labelled with stable isotopes. The usage of these substrates by the cell leads to the incorporation of the isotopes into downstream intermediates.The most important metabolic pathways are encompassed in the central carbon metabolism (CCM). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the central carbon metabolism "is the most basic aspect of life". It includes all metabolites and enzymatic reactions within: glycolysis and gluconeogenesis, pentose phosphate pathway (PPP), tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), amino acids and nucleotide metabolic pathways. Some molecules are at the crossroad of metabolic pathways, interconnecting diverse metabolic and therefore functional outcomes. Labelling these nodal metabolites and analysing their isotopic composition allows the precise determination of the metabolic flow within the biochemical networks that they are in.Application of stable isotope labelled substrates allows the measurement of metabolic flux through a biochemical pathway. The rapid turnover of metabolites in pathways requires pulse-feeding cells with a labelled substrate. This method allows for the determination of different cell states. For example, the action of a drug from immediate impact until the compensatory response of the metabolic system (cell, organs, organisms). Pulsed labelling is an elegant way to analyse the action of small molecules and drugs and enables the analysis of regulatory metabolic processes in short time scales.PMID:36355219 | DOI:10.1007/164_2022_621

Interrogating the Metabolomic Profile of Amyotrophic Lateral Sclerosis in the Post-Mortem Human Brain by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) Mass Spectrometry Imaging (MSI)

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 10;12(11):1096. doi: 10.3390/metabo12111096.ABSTRACTAmyotrophic lateral sclerosis (ALS) is an idiopathic, fatal neurodegenerative disease characterized by progressive loss of motor function with an average survival time of 2-5 years after diagnosis. Due to the lack of signature biomarkers and heterogenous disease phenotypes, a definitive diagnosis of ALS can be challenging. Comprehensive investigation of this disease is imperative to discovering unique features to expedite the diagnostic process and improve diagnostic accuracy. Here, we present untargeted metabolomics by mass spectrometry imaging (MSI) for comparing sporadic ALS (sALS) and C9orf72 positive (C9Pos) post-mortem frontal cortex human brain tissues against a control cohort. The spatial distribution and relative abundance of metabolites were measured by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI for association to biological pathways. Proteomic studies on the same patients were completed via LC-MS/MS in a previous study, and results were integrated with imaging metabolomics results to enhance the breadth of molecular coverage. Utilizing METASPACE annotation platform and MSiPeakfinder, nearly 300 metabolites were identified across the sixteen samples, where 25 were identified as dysregulated between disease cohorts. The dysregulated metabolites were further examined for their relevance to alanine, aspartate, and glutamate metabolism, glutathione metabolism, and arginine and proline metabolism. The dysregulated pathways discussed are consistent with reports from other ALS studies. To our knowledge, this work is the first of its kind, reporting on the investigation of ALS post-mortem human brain tissue analyzed by multiomic MSI.PMID:36355179 | DOI:10.3390/metabo12111096

Dietary Effect of <em>Clostridium autoethanogenum</em> Protein on Growth, Intestinal Histology and Flesh Lipid Metabolism of Largemouth Bass (<em>Micropterus salmoides</em>) Based on Metabolomics

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 9;12(11):1088. doi: 10.3390/metabo12111088.ABSTRACTClostridium autoethanogenum protein (CAP) is a new single-cell protein explored in aquatic feeds in recent years. This study investigated the dietary effects of CAP replacing fishmeal (FM) on the growth, intestinal histology and flesh metabolism of largemouth bass (Micropterus salmoides). In a basal diet containing 700 g/kg of FM, CAP was used to substitute 0%, 15%, 30%, 45%, 70% and 100% of dietary FM to form six isonitrogenous diets (Con, CAP-15, CAP-30, CAP-45, CAP-70, CAP-100) to feed largemouth bass (80.0 g) for 12 weeks. Only the CAP-100 group showed significantly lower weight gain (WG) and a higher feed conversion ratio (FCR) than the control (p &lt; 0.05). A broken-line analysis based on WG and FCR showed that the suitable replacement of FM with CAP was 67.1-68.0%. The flesh n-3/n-6 polyunsaturated fatty acid, intestinal protease activity, villi width and height in the CAP-100 group were significantly lower than those in the control group (p &lt; 0.05). The Kyoto Encyclopedia of Genes and Genomes analysis showed that the metabolic pathway in flesh was mainly enriched in the "lipid metabolic pathway", "amino acid metabolism", "endocrine system" and "carbohydrate metabolism". In conclusion, CAP could successfully replace 67.1-68.0% of dietary FM, while the complete substitution decreased the growth, damaged the intestinal morphology and down-regulated the lipid metabolites.PMID:36355171 | DOI:10.3390/metabo12111088

Isotopic Tracer for Absolute Quantification of Metabolites of the Pentose Phosphate Pathway in Bacteria

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 9;12(11):1085. doi: 10.3390/metabo12111085.ABSTRACTThe pentose phosphate pathway (PPP) plays a key role in many metabolic functions, including the generation of NADPH, biosynthesis of nucleotides, and carbon homeostasis. In particular, the intermediates of PPP have been found to be significantly perturbed in bacterial metabolomic studies. Nonetheless, detailed analysis to gain mechanistic information of PPP metabolism remains limited as most studies are unable to report on the absolute levels of the metabolites. Absolute quantification of metabolites is a prerequisite to study the details of fluxes and its regulations. Isotope tracer or labeling studies are conducted in vivo and in vitro and have significantly improved the analysis and understanding of PPP. Due to the laborious procedure and limitations in the in vivo method, an in vitro approach known as Group Specific Internal Standard Technology (GSIST) has been successfully developed to measure the absolute levels of central carbon metabolism, including PPP. The technique adopts derivatization of an experimental sample and a corresponding internal standard with isotope-coded reagents to provide better precision for accurate identification and absolute quantification. In this review, we highlight bacterial studies that employed isotopic tracers as the tagging agents used for the absolute quantification analysis of PPP metabolites.PMID:36355168 | DOI:10.3390/metabo12111085

Physiological and Metabolic Adaptation to Heat Stress at Different Altitudes in Yaks

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 8;12(11):1082. doi: 10.3390/metabo12111082.ABSTRACTYaks have strong adaptability to extremely cold and hypoxic conditions but are susceptible to high ambient temperature when yaks are raised in low-altitude areas during the high-temperature season. Twenty-four adult male yaks with similar weights and ages were randomly divided into TN (Thermoneutral, altitude = 3464 m), LHS (Light heat stress, altitude = 1960 m), and MHS (Medium heat stress, altitude = 906 m) groups to evaluate adaptation strategies to HS. Non-targeted and targeted metabolomics were applied to investigate the effects of different extents of HS on yaks. LHS- and MHS-yaks showed higher rectal temperatures and respiratory rates than TN-yaks. MHS-yaks had higher levels of red blood cells (RBCs), hemoglobin (Hb), whole blood relative index of middle shear at a shear rate of 5 S-1 (WMS), whole blood relative index of high shear at a shear rate of 200 S-1 (WHS), Casson viscosity (CV), middle shear flow resistance at a shear rate of 5 S-1 (MSFR), and high shear flow resistance at a shear rate of 200 S-1 (HSFR) as compared to TN- and LHS-yaks. Differential metabolites and metabolic pathways, including fatty acid metabolism, lipid metabolism, glucose metabolism, and amino acid metabolism, were altered by HS. Metabolites in the glucose metabolism pathway in LHS- and MHS-yaks were lower than those in TN-yaks. However, LHS-yaks showed higher levels of metabolites in the HIF-1 signaling pathway compared to TN- and MHS-yaks. Most of the tricarboxylic acid cycle (TCA) intermediates and fatty acids were significantly decreased in MHS-yaks compared to the other two groups. As a whole, yaks raised at a low altitude (25.6 °C) suffered from severe HS, but they adapted to HS with vasodilatation for dissipating heat and the increased antioxidants and metabolite levels of energy substrates.PMID:36355165 | DOI:10.3390/metabo12111082

Plasma Metabolomic and Lipidomic Profiling of Metabolic Dysfunction-Associated Fatty Liver Disease in Humans Using an Untargeted Multiplatform Approach

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 8;12(11):1081. doi: 10.3390/metabo12111081.ABSTRACTMetabolic dysfunction-associated fatty liver disease (MAFLD) is a complex disorder that is implicated in dysregulations in multiple biological pathways, orchestrated by interactions between genetic predisposition, metabolic syndromes and environmental factors. The limited knowledge of its pathogenesis is one of the bottlenecks in the development of prognostic and therapeutic options for MAFLD. Moreover, the extent to which metabolic pathways are altered due to ongoing hepatic steatosis, inflammation and fibrosis and subsequent liver damage remains unclear. To uncover potential MAFLD pathogenesis in humans, we employed an untargeted nuclear magnetic resonance (NMR) spectroscopy- and high-resolution mass spectrometry (HRMS)-based multiplatform approach combined with a computational multiblock omics framework to characterize the plasma metabolomes and lipidomes of obese patients without (n = 19) or with liver biopsy confirmed MAFLD (n = 63). Metabolite features associated with MAFLD were identified using a metabolome-wide association study pipeline that tested for the relationships between feature responses and MAFLD. A metabolic pathway enrichment analysis revealed 16 pathways associated with MAFLD and highlighted pathway changes, including amino acid metabolism, bile acid metabolism, carnitine shuttle, fatty acid metabolism, glycerophospholipid metabolism, arachidonic acid metabolism and steroid metabolism. These results suggested that there were alterations in energy metabolism, specifically amino acid and lipid metabolism, and pointed to the pathways being implicated in alerted liver function, mitochondrial dysfunctions and immune system disorders, which have previously been linked to MAFLD in human and animal studies. Together, this study revealed specific metabolic alterations associated with MAFLD and supported the idea that MAFLD is fundamentally a metabolism-related disorder, thereby providing new perspectives for diagnostic and therapeutic strategies.PMID:36355164 | DOI:10.3390/metabo12111081

Multi-Omics Investigation into Acute Myocardial Infarction: An Integrative Method Revealing Interconnections amongst the Metabolome, Lipidome, Glycome, and Metallome

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 8;12(11):1080. doi: 10.3390/metabo12111080.ABSTRACTAcute myocardial infarction (AMI) is a leading cause of mortality and morbidity worldwide. This work aims to investigate the translational potential of a multi-omics study (comprising metabolomics, lipidomics, glycomics, and metallomics) in revealing biomechanistic insights into AMI. Following the N-glycomics and metallomics studies performed by our group previously, untargeted metabolomic and lipidomic profiles were generated and analysed in this work via the use of a simultaneous metabolite/lipid extraction and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis workflow. The workflow was applied to blood plasma samples from AMI cases (n = 101) and age-matched healthy controls (n = 66). The annotated metabolomic (number of features, n = 27) and lipidomic (n = 48) profiles, along with the glycomic (n = 37) and metallomic (n = 30) profiles of the same set of AMI and healthy samples were integrated and analysed. The integration method used here works by identifying a linear combination of maximally correlated features across the four omics datasets, via utilising both block-partial least squares-discriminant analysis (block-PLS-DA) based on sparse generalised canonical correlation analysis. Based on the multi-omics mapping of biomolecular interconnections, several postulations were derived. These include the potential roles of glycerophospholipids in N-glycan-modulated immunoregulatory effects, as well as the augmentation of the importance of Ca-ATPases in cardiovascular conditions, while also suggesting contributions of phosphatidylethanolamine in their functions. Moreover, it was shown that combining the four omics datasets synergistically enhanced the classifier performance in discriminating between AMI and healthy subjects. Fresh and intriguing insights into AMI, otherwise undetected via single-omics analysis, were revealed in this multi-omics study. Taken together, we provide evidence that a multi-omics strategy may synergistically reinforce and enhance our understanding of diseases.PMID:36355163 | DOI:10.3390/metabo12111080

Metabolomics Characterization of Scleractinia Corals with Different Life-History Strategies: A Case Study about <em>Pocillopora meandrina</em> and <em>Seriatopora hystrix</em> in the South China Sea

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 8;12(11):1079. doi: 10.3390/metabo12111079.ABSTRACTLife-history strategies play a critical role in susceptibility to environmental stresses for Scleractinia coral. Metabolomics, which is capable of determining the metabolic responses of biological systems to genetic and environmental changes, is competent for the characterization of species' biological traits. In this study, two coral species (Pocillopora meandrina and Seriatopora hystrix in the South China Sea) with different life-history strategies ("competitive" and "weedy") were targeted, and untargeted mass spectrometry metabolomics combined with molecular networking was applied to characterize their differential metabolic pathways. The results show that lyso-platelet activating factors (lyso-PAFs), diacylglyceryl carboxyhydroxymethylcholine (DGCC), aromatic amino acids, and sulfhydryl compounds were more enriched in P. meandrina, whereas new phospholipids, dehydrated phosphoglycerol dihydroceramide (de-PG DHC), monoacylglycerol (MAG), fatty acids (FA) (C &lt; 18), short peptides, and guanidine compounds were more enriched in S. hystrix. The metabolic pathways involved immune response, energy metabolism, cellular membrane structure regulation, oxidative stress system, secondary metabolite synthesis, etc. While the immune system (lysoPAF) and secondary metabolite synthesis (aromatic amino acids and sulfhydryl compounds) facilitates fast growth and resistance to environmental stressors of P. meandrina, the cell membrane structure (structural lipids), energy storage (storage lipids), oxidative stress system (short peptides), and secondary metabolite synthesis (guanidine compounds) are beneficial to the survival of S. hystrix in harsh conditions. This study contributes to the understanding of the potential molecular traits underlying life-history strategies of different coral species.PMID:36355162 | DOI:10.3390/metabo12111079

Proteomic and Metabolomic Evaluation of Insect- and Herbicide-Resistant Maize Seeds

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 7;12(11):1078. doi: 10.3390/metabo12111078.ABSTRACTLabel-free quantitative proteomic (LFQ) and widely targeted metabolomic analyses were applied in the safety evaluation of three genetically modified (GM) maize varieties, BBL, BFL-1, and BFL-2, in addition to their corresponding non-GM parent maize. A total of 76, 40, and 25 differentially expressed proteins (DEPs) were screened out in BBL, BFL-1, and BFL-2, respectively, and their abundance compared was with that in their non-GM parents. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most of the DEPs participate in biosynthesis of secondary metabolites, biosynthesis of amino acids, and metabolic pathways. Metabolomic analyses revealed 145, 178, and 88 differentially accumulated metabolites (DAMs) in the BBL/ZH58, BFL-1/ZH58, and BFL-2/ZH58×CH72 comparisons, respectively. KEGG pathway enrichment analysis showed that most of the DAMs are involved in biosynthesis of amino acids, and in arginine and proline metabolism. Three co-DEPs and 11 co-DAMs were identified in the seeds of these GM maize lines. The proteomic profiling of seeds showed that the GM maize varieties were not dramatically different from their non-GM control. Similarly, the metabolomic profiling of seeds showed no dramatic changes in the GM/non-GM maize varieties compared with the GM/GM and non-GM/non-GM maize varieties. The genetic background of the transgenic maize was found to have some influence on its proteomic and metabolomic profiles.PMID:36355161 | DOI:10.3390/metabo12111078

Metabolomic Study of a Rat Model of Retinal Detachment

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 7;12(11):1077. doi: 10.3390/metabo12111077.ABSTRACTRetinal detachment is a serious ocular disease leading to photoreceptor degeneration and vision loss. However, the mechanism of photoreceptor degeneration remains unclear. The aim of this study was to investigate the altered metabolism pathway and physiological changes after retinal detachment. Eight-week-old male SD rats were fed, and the model of retinal detachment was established by injecting hyaluronic acid into the retinal space. The rats were euthanized 3 days after RD, and the retinal tissues were sectioned for analysis. Untargeted lipid chromatography-mass spectrometry lipidomic was performed to analyze the metabolite changes. A total of 90 significant metabolites (34 in anionic and 56 in cationic models) were detected after retinal detachment. The main pathways were (1) histidine metabolism; (2) phenylalanine, tyrosine, and tryptophan biosynthesis; and (3) glycine, serine, and threonine metabolism. The key genes corresponding to each metabolic pathway were verified from the Gene Expression Omnibus (GEO) database of human retinal samples. The results indicated that the production of histamine by histidine decarboxylase from histidine reduced after RD (p &lt; 0.05). Xanthine, hypoxanthine, guanine, and guanosine decreased after RD (p &lt; 0.05). Decreased xanthine and hypoxanthine may reduce the antioxidant ability. The decreased guanosine could not provide enough sources for inosine monophosphate production. Tyrosine is an important neurotransmitter and was significantly reduced after RD (p &lt; 0.05). Citrate was significantly reduced with the increase of ATP-citrate lyase enzyme (ACLY) (p &lt; 0.05). We inferred that lipid oxidation might increase rather than lipid biogenesis. Thus, this study highlighted the main changes of metabolite and physiological process after RD. The results may provide important information for photoreceptor degeneration.PMID:36355160 | DOI:10.3390/metabo12111077

Revealing the Pathogenesis of Salt-Sensitive Hypertension in Dahl Salt-Sensitive Rats through Integrated Multi-Omics Analysis

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 7;12(11):1076. doi: 10.3390/metabo12111076.ABSTRACTSalt-induced renal metabolism dysfunction is an important mechanism of salt-sensitive hypertension. Given that the gut-liver axis is the first hit of a high-salt diet (HSD), we aimed to identify the extra-renal mechanism from hepatic metabolism and gut microbiota, and attempted to relieve the salt-induced metabolic dysfunctions by curcumin. Untargeted metabolomics analysis was performed to identify the changes in hepatic metabolic pathways, and integrated analysis was employed to reveal the relationship between hepatic metabolic dysfunction and gut microbial composition. HSD induced significant increase in fumaric acid, l-lactic acid, creatinine, l-alanine, glycine, and l-cysteine levels, and amino acids metabolism pathways associated with glycolysis were significantly altered, including alanine, aspartate, and glutamate metabolism; glycine, serine, and threonine metabolism, which were involved in the regulation of blood pressure. Integrated multi-omics analysis revealed that changes in Paraprevotella, Erysipelotrichaceae, and genera from Clostridiales are associated with metabolic disorders. Gene functional predication analysis based on 16S Ribosomal RNA sequences showed that the dysfunction in hepatic metabolism were correlated with enhanced lipopolysaccharide (LPS) biosynthesis and apoptosis in gut microbes. Curcumin (50 mg/kg/d) might reduce gut microbes-associated LPS biosynthesis and apoptosis, partially reverse metabolic dysfunction, ameliorate renal oxidative stress, and protect against salt-sensitive hypertension.PMID:36355159 | DOI:10.3390/metabo12111076

Mapping of Urinary Volatile Organic Compounds by a Rapid Analytical Method Using Gas Chromatography Coupled to Ion Mobility Spectrometry (GC-IMS)

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 5;12(11):1072. doi: 10.3390/metabo12111072.ABSTRACTVolatile organic compounds (VOCs) are a differentiated class of molecules, continuously generated in the human body and released as products of metabolic pathways. Their concentrations vary depending on pathophysiological conditions. They are detectable in a wide variety of biological samples, such as exhaled breath, faeces, and urine. In particular, urine represents an easily accessible specimen widely used in clinics. The most used techniques for VOCs detections are expensive and time-consuming, thus not allowing for rapid clinical analysis. In this perspective, the aim of this study is a comprehensive characterisation of the urine volatilome by the development of an alternative rapid analytical method. Briefly, 115 urine samples are collected; sample treatment is not needed. VOCs are detected in the urine headspace using gas chromatography coupled to ion mobility spectrometry (GC-IMS) by an extremely fast analysis (10 min). The method is analytically validated; the analysis is sensitive and robust with results comparable to those reported with other techniques. Twenty-three molecules are identified, including ketones, aldehydes, alcohols, and sulphur compounds, whose concentration is altered in several pathological states such as cancer and metabolic disorders. Therefore, it opens new perspectives for fast diagnosis and screening, showing great potential for clinical applications.PMID:36355153 | DOI:10.3390/metabo12111072

Human Milk from Tandem Feeding Dyads Does Not Differ in Metabolite and Metataxonomic Features When Compared to Single Nursling Dyads under Six Months of Age

Thu, 10/11/2022 - 12:00
Metabolites. 2022 Nov 4;12(11):1069. doi: 10.3390/metabo12111069.ABSTRACTGiven the long-term advantages of exclusive breastfeeding to infants and their mothers, there is both an individual and public health benefit to its promotion and support. Data on the composition of human milk over the course of a full period of lactation for a single nursling is sparse, but data on human milk composition during tandem feeding (feeding children of different ages from different pregnancies) is almost entirely absent. This leaves an important knowledge gap that potentially endangers the ability of parents to make a fully informed choice on infant feeding. We compared the metataxonomic and metabolite fingerprints of human milk samples from 15 tandem feeding dyads to that collected from ten exclusively breastfeeding single nursling dyads where the nursling is under six months of age. Uniquely, our cohort also included three tandem feeding nursling dyads where each child showed a preferential side for feeding-allowing a direct comparison between human milk compositions for different aged nurslings. Across our analysis of volume, total fat, estimation of total microbial load, metabolite fingerprinting, and metataxonomics, we showed no statistically significant differences between tandem feeding and single nursling dyads. This included comparisons of preferential side nurslings of different ages. Together, our findings support the practice of tandem feeding of nurslings, even when feeding an infant under six months.PMID:36355152 | DOI:10.3390/metabo12111069

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