MS-based Analysis Research Articles

Amplified Drought Alters Leaf Litter Metabolome, Slows Down Litter Decomposition, and Modifies Home Field (Dis)Advantage in Three Mediterranean Forests.

In Mediterranean ecosystems, the projected rainfall reduction of up to 30% may alter plant–soil interactions, particularly litter decomposition and Home Field Advantage (HFA). We set up a litter transplant experiment in the three main forests encountered in the northern part of the Medi-terranean Basin (dominated by either Quercus ilex, Quercus pubescens, or Pinus halepensis) equipped with a rain exclusion device, allowing an increase in drought either throughout the year or concentrated in spring and summer. Senescent leaves and needles were collected under two precipitation treatments (natural and amplified drought plots) at their “home” forest and were left to decompose in the forest of origin and in other forests under both drought conditions. MS-based metabolomic analysis of litter extracts combined with multivariate data analysis enabled us to detect modifications in the composition of litter specialized metabolites, following amplified drought treatment. Amplified drought altered litter quality and metabolomes, directly slowed down litter decomposition, and induced a loss of home field (dis)advantage. No indirect effect mediated by a change in litter quality on decomposition was observed. These results may suggest major alterations of plant–soil interactions in Mediterranean forests under amplified drought conditions.

Assessment of a Large-Scale Unbiased Malignant Pleural Effusion Proteomics Study of a Real-Life Cohort.

Simple SummaryPleural effusion (PE) occurs as a consequence of various pathologies. Malignant effusion due to lung cancer is one of the most frequent causes. A method for accurate differentiation of malignant from benign PE is an unmet clinical need. Proteomics profiling of PE has shown promising results. However, mass spectrometry (MS) analysis typically involves the tedious elimination of abundant proteins before analysis, and clinical annotation of proteomics profiled cohorts is limited. This study compares the proteomes of malignant PE and nonmalignant PE, identifies lung cancer malignant markers in agreement with other studies, and identifies markers strongly associated with patient survival.Background: Pleural effusion (PE) is common in advanced-stage lung cancer patients and is related to poor prognosis. Identification of cancer cells is the standard method for the diagnosis of a malignant PE (MPE). However, it only has moderate sensitivity. Thus, more sensitive diagnostic tools are urgently needed. Methods: The present study aimed to discover potential protein targets to distinguish malignant pleural effusion (MPE) from other non-malignant pathologies. We have collected PE from 97 patients to explore PE proteomes by applying state-of-the-art liquid chromatography-mass spectrometry (LC-MS) to identify potential biomarkers that correlate with immunohistochemistry assessment of tumor biopsy or with survival data. Functional analyses were performed to elucidate functional differences in PE proteins in malignant and benign samples. Results were integrated into a clinical risk prediction model to identify likely malignant cases. Sensitivity, specificity, and negative predictive value were calculated. Results: In total, 1689 individual proteins were identified by MS-based proteomics analysis of the 97 PE samples, of which 35 were diagnosed as malignant. A comparison between MPE and benign PE (BPE) identified 58 differential regulated proteins after correction of the p-values for multiple testing. Furthermore, functional analysis revealed an up-regulation of matrix intermediate filaments and cellular movement-related proteins. Additionally, gene ontology analysis identified the involvement of metabolic pathways such as glycolysis/gluconeogenesis, pyruvate metabolism and cysteine and methionine metabolism. Conclusion: This study demonstrated a partial least squares regression model with an area under the curve of 98 and an accuracy of 0.92 when evaluated on the holdout test data set. Furthermore, highly significant survival markers were identified (e.g., PSME1 with a log-rank of 1.68 × 10−6).

Serum peptidome profiles immune response of COVID-19 Vaccine administration.

BackgroundCoronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused significant loss of life and property. In response to the serious pandemic, recently developed vaccines against SARS-CoV-2 have been administrated to the public. Nevertheless, the research on human immunization response against COVID-19 vaccines is insufficient. Although much information associated with vaccine efficacy, safety and immunogenicity has been reported by pharmaceutical companies based on laboratory studies and clinical trials, vaccine evaluation needs to be extended further to better understand the effect of COVID-19 vaccines on human beings.MethodsWe performed a comparative peptidome analysis on serum samples from 95 participants collected at four time points before and after receiving CoronaVac. The collected serum samples were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to profile the serum peptides, and also subjected to humoral and cellular immune response analyses to obtain typical immunogenicity information.ResultsSignificant difference in serum peptidome profiles by MALDI-TOF MS was observed after vaccination. By supervised statistical analysis, a total of 13 serum MALDI-TOF MS feature peaks were obtained on day 28 and day 42 of vaccination. The feature peaks were identified as component C1q receptor, CD59 glycoprotein, mannose-binding protein C, platelet basic protein, CD99 antigen, Leucine-rich alpha-2-glycoprotein, integral membrane protein 2B, platelet factor 4 and hemoglobin subunits. Combining with immunogenicity analysis, the study provided evidence for the humoral and cellular immune responses activated by CoronaVac. Furthermore, we found that it is possible to distinguish neutralizing antibody (NAbs)-positive from NAbs-negative individuals after complete vaccination using the serum peptidome profiles by MALDI-TOF MS together with machine learning methods, including random forest (RF), partial least squares-discriminant analysis (PLS-DA), linear support vector machine (SVM) and logistic regression (LR).ConclusionsThe study shows the promise of MALDI-TOF MS-based serum peptidome analysis for the assessment of immune responses activated by COVID-19 vaccination, and discovered a panel of serum peptides biomarkers for COVID-19 vaccination and for NAbs generation. The method developed in this study can help not only in the development of new vaccines, but also in the post-marketing evaluation of developed vaccines.

Untangling the Extracellular Matrix of Idiopathic Epiretinal Membrane: A Path Winding among Structure, Interactomics and Translational Medicine.

Idiopathic epiretinal membranes (iERMs) are fibrocellular sheets of tissue that develop at the vitreoretinal interface. The iERMs consist of cells and an extracellular matrix (ECM) formed by a complex array of structural proteins and a large number of proteins that regulate cell–matrix interaction, matrix deposition and remodelling. Many components of the ECM tend to produce a layered pattern that can influence the tractional properties of the membranes. We applied a bioinformatics approach on a list of proteins previously identified with an MS-based proteomic analysis on samples of iERM to report the interactome of some key proteins. The performed pathway analysis highlights interactions occurring among ECM molecules, their cell receptors and intra- or extracellular proteins that may play a role in matrix biology in this special context. In particular, integrin β1, cathepsin B, epidermal growth factor receptor, protein-glutamine gamma-glutamyltransferase 2 and prolow-density lipoprotein receptor-related protein 1 are key hubs in the outlined protein–protein cross-talks. A section on the biomarkers that can be found in the vitreous humor of patients affected by iERM and that can modulate matrix deposition is also presented. Finally, translational medicine in iERM treatment has been summed up taking stock of the techniques that have been proposed for pharmacologic vitreolysis.

Astragaloside IV promotes pharmacological effect of Descurainia sophia seeds on isoproterenol-induced cardiomyopathy in rats by synergistically modulating the myosin motor.

Descurainia sophia seeds (DS), Astragalus mongholicus (AM), and their formulas are widely used to treat heart failure caused by various cardiac diseases in traditional Chinese medicine practice. However, the molecular mechanism of action of DS and AM has not been completely understood. Herein, we first used mass spectrometry coupled to UPLC to characterize the chemical components of DS and AM decoctions, then applied MS-based quantitative proteomic analysis to profile protein expression in the heart of rats with isoproterenol-induced cardiomyopathy (ISO-iCM) before and after treated with DS alone or combined with AM, astragaloside IV (AS4), calycosin-7-glucoside (C7G), and Astragalus polysaccharides (APS) from AM. We demonstrated for the first time that DS decoction alone could reverse the most of differentially expressed proteins in the heart of the rats with ISO-iCM, including the commonly recognized biomarkers natriuretic peptides (NPPA) of cardiomyopathy and sarcomeric myosin light chain 4 (MYL4), relieving ISO-iCM in rats, but AM did not pronouncedly improve the pharmacological efficiency of DS. Significantly, we revealed that AS4 remarkably promoted the pharmacological potency of DS by complementarily reversing myosin motor MYH6/7, and further downregulating NPPA and MYL4. In contrast, APS reduced the efficiency of DS due to upregulating NPPA and MYL4. These findings not only provide novel insights to better understanding in the combination principle of traditional Chinese medicine but also highlight the power of mass spectrometric proteomics strategy combined with conventional pathological approaches for the traditional medicine research.

LC-MS-based lipidomic analysis of liver tissue sample from spontaneously hypertensive rats treated with extract hawthorn fruits.

At present, many experiments provide support for the cardiovascular protective effect of hawthorn (Crataegus oxyacantha) flower, leaf and fruit extracts. The aim of this study was to investigate the intervention mechanism of hawthorn fruit extract on spontaneously hypertensive rats (SHR) and its effect on their lipid metabolic pattern. After SHR was intervened by hawthorn extract (1.08 g/kg/d) for 6 weeks, the blood pressure and liver histopathology of rats were evaluated. An UHPLC-Q Extractive metabolomics approach was used to collect information on rat liver lipid metabolites, combined with multivariate data analysis to identify significantly different substances and potential biomarkers through mass spectrometry and database searches. Histomorphology of the liver was partially restored in the hawthorn-treated group. Hawthorn extract interferes with sphingolipid metabolism, glycerophospholipid metabolism and glycerolipids metabolism, improving partially disturbed metabolic pathways. This study showed that hawthorn could partially restore liver histomorphology and has anti-hypertensive effect by regulating lipid metabolism.

Human RNase 4 improves mRNA sequence characterization by LC-MS/MS.

With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography–mass spectrometry (LC–MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of mRNA with site-specific endoribonucleases to generate pools of short oligonucleotides that are then amenable to MS-based sequence analysis. Here, we showed that the uridine-specific human endoribonuclease hRNase 4 improves mRNA sequence coverage, in comparison with the benchmark enzyme RNase T1, by producing a larger population of uniquely mappable cleavage products. We deployed hRNase 4 to characterize mRNAs fully substituted with 1-methylpseudouridine (m1Ψ) or 5-methoxyuridine (mo5U), as well as mRNAs selectively depleted of uridine–two key strategies to reduce synthetic mRNA immunogenicity. Lastly, we demonstrated that hRNase 4 enables direct assessment of the 5′ cap incorporation into in vitro transcribed mRNA. Collectively, this study highlights the power of hRNase 4 to interrogate mRNA sequence, identity, and modifications by LC–MS/MS.

LC-MS-Based Urine Metabolomics Analysis for the Diagnosis and Monitoring of Medulloblastoma.

Medulloblastoma (MB) is the most common type of brain cancer in pediatric patients. Body fluid biomarkers will be helpful for clinical diagnosis and treatment. In this study, liquid chromatography–mass spectrometry (LC–MS)-based metabolomics was used to identify specific urine metabolites of MB in a cohort, including 118 healthy controls, 111 MB patients, 31 patients with malignant brain cancer, 51 patients with benign brain disease, 29 MB patients 1 week postsurgery and 80 MB patients 1 month postsurgery. The results showed an apparent separation for MB vs. healthy controls, MB vs. benign brain diseases, and MB vs. other malignant brain tumors, with AUCs values of 0.947/0.906, 0.900/0.873, and 0.842/0.885, respectively, in the discovery/validation group. Among all differentially identified metabolites, 4 metabolites (tetrahydrocortisone, cortolone, urothion and 20-oxo-leukotriene E4) were specific to MB. The analysis of these 4 metabolites in pre- and postoperative MB urine samples showed that their levels returned to a healthy state after the operation (especially after one month), showing the potential specificity of these metabolites for MB. Finally, the combination of two metabolites, tetrahydrocortisone and cortolone, showed diagnostic accuracy for distinguishing MB from non-MB, with an AUC value of 0.851. Our data showed that urine metabolomics might be used for MB diagnosis and monitoring.

In vitro antiplasmodial activity-directed investigation and UPLC–MS fingerprint of promising extracts and fractions from Terminalia ivorensis A. Chev. and Terminalia brownii Fresen.

Ethnopharmacological significanceMedicinal plants from the Terminalia genus are widely used as remedies against many infectious diseases, including malaria. As such, Terminalia ivorensis A. Chev. and Terminalia brownii Fresen. are famous due to their usefulness in traditional medicines to treat malaria and yellow fever. However, further information is needed on the extent of anti-Plasmodium potency of extracts and fractions from these plants and their phytochemical profile. Aim of the studyThis study was designed to investigate the in vitro antiplasmodial activity and to determine the chemical profile of promising extracts and fractions from T. ivorensis and T. brownii stem bark. Materials and methodsCrude aqueous, ethanolic, methanolic, hydroethanolic and ethyl acetate extracts were prepared by maceration from the stem barks of T. brownii and T. ivorensis. They were subsequently tested against chloroquine-sensitive (Pf3D7) and multidrug-resistant (PfDd2) strains of P. falciparum using the parasite lactate dehydrogenase (PfLDH) assay. Extracts showing very good activity on both plasmodial strains were further fractionated using column chromatography guided by evidence of antiplasmodial activity. All bioactive extracts and fractions were screened for their cytotoxicity on Vero and Raw cell lines using the resazurin-based assay and on erythrocytes using the hemolysis assay. The phytochemical profiles of selected potent extracts and fractions were determined by UPLC–QTOF-MS analysis. ResultsOf the ten extracts obtained from both plant species, nine showed inhibitory activity against both P. falciparum strains (Pf3D7 and PfDd2), with median inhibitory concentration (IC50) values ranging from 0.13 μg/ml to 10.59 μg/ml. Interestingly, the aqueous extract of T. ivorensis (TiW) and methanolic extract of T. brownii (TbM) displayed higher antiplasmodial activities against both strains (IC50 0.13–1.43 μg/ml) and high selectivity indices (SI > 100). Their fractionation led to two fractions from T. ivorensis and two from T. brownii that showed very promising antiplasmodial activity (IC50 0.15–1.73 μg/mL) and SI greater than 100. The hemolytic assay confirmed the safety of crude extracts and fractions on erythrocytes. UPLC–MS-based phytochemical analysis of the crude aqueous extract of T. ivorensis showed the presence of ellagic acid (1) and leucodelphidin (2), while analysis of the crude methanol extract of T. brownii showed the presence of ellagic acid (1), leucodelphinidin (2), papyriogenin D (3), dihydroactinidiolide (4) and miltiodiol (5). ConclusionsThe extracts and fractions from T. ivorensis and T. brownii showed very good antiplasmodial activity, thus supporting the traditional use of the two plants in the treatment of malaria. Chemical profiling of the extracts and fractions led to the identification of chemical markers and the known antimalarial compound ellagic acid. Further isolation and testing of other pure compounds from the active fractions could lead to the identification of potent antiplasmodial compounds.

Abstract 3875: De novo spatial proteomic profiling of immune synapses using machine learning-guided microscoop

Abstract The spatial proteome of the immune synapse (IS) between a target cell and a lymphocyte is fundamentally important to understand the mechanism of cell-mediated immunity for both immuno-oncology and therapeutic applications. In this research, we used Microscoop, a fully-automatic microscope system integrated with a machine learning-based algorithm, to best determine ISs for proteomic mapping. We used Raji B cells as antigen-presenting cells (APCs) and induced the formation of ISs by incubating with Jurkat T cells. Multiple IS images were applied to train our algorithm using convolution neural network-based deep learning. A sequential process including fluorescence imaging, deep learning-enabled pattern generation, and photochemical labeling was implemented to achieve spatial-specific biotinylation of the IS proteins. Moreover, Microscoop is capable to repeat the process automatically on thousands of fields of view to label sufficient immune-synaptic proteins with biotin-tag for further enrichment allowing protein identification with mass spectrometry. We have successfully labeled and isolated proteins from spatially reorganized interfaces between T cells and APCs. Following MS-based proteomic analysis, several hundreds of proteins were identified, including the proteins known to be specifically associated with T-cell receptor (TCR) activation such as LCK, one of the major factors involved in TCR signaling at ISs. More interestingly, we identified several proteins novel for ISs, including proteins involved in phosphatidylinositol signaling. Our data showcases the capability of subcellular de novo spatial proteomics of the Microscoop technology, revealing novel factors responsible for initiating the immune response of a lymphocyte and shedding light on immune checkpoint signaling and tumor immunotherapy. Citation Format: You-Pi Liu, Weng Man Chong, Harry Huang, Yi-De Chen, Chia-Wen Chung, Hsiao-Jen Chang, Chih-Wei Chang, Jung-Chi Liao. De novo spatial proteomic profiling of immune synapses using machine learning-guided microscoop [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3875.

Tibolone Pre-Treatment Ameliorates the Dysregulation of Protein Translation and Transport Generated by Palmitic Acid-Induced Lipotoxicity in Human Astrocytes: A Label-Free MS-Based Proteomics and Network Analysis.

Excessive accumulation and release of fatty acids (FAs) in adipose and non-adipose tissue are characteristic of obesity and are associated with the leading causes of death worldwide. Chronic exposure to high concentrations of FAs such as palmitic acid (pal) is a risk factor for developing different neurodegenerative diseases (NDs) through several mechanisms. In the brain, astrocytic dysregulation plays an essential role in detrimental processes like metabolic inflammatory state, oxidative stress, endoplasmic reticulum stress, and autophagy impairment. Evidence shows that tibolone, a synthetic steroid, induces neuroprotective effects, but its molecular mechanisms upon exposure to pal remain largely unknown. Due to the capacity of identifying changes in the whole data-set of proteins and their interaction allowing a deeper understanding, we used a proteomic approach on normal human astrocytes under supraphysiological levels of pal as a model to induce cytotoxicity, finding changes of expression in proteins related to translation, transport, autophagy, and apoptosis. Additionally, tibolone pre-treatment showed protective effects by restoring those same pal-altered processes and increasing the expression of proteins from cell survival processes. Interestingly, ARF3 and IPO7 were identified as relevant proteins, presenting a high weight in the protein-protein interaction network and significant differences in expression levels. These proteins are related to transport and translation processes, and their expression was restored by tibolone. This work suggests that the damage caused by pal in astrocytes simultaneously involves different mechanisms that the tibolone can partially revert, making tibolone interesting for further research to understand how to modulate these damages.

From non-targeted to targeted GC\u2013MS metabolomics strategy for identification of TCM preparations containing natural and artificial musk

BackgroundMoschus is a rare and precious natural medicine. Due to the properties of resources scarcity and expensive price of natural musk, artificial musk has been developed as substitute materials in some prescriptions. Rapid and accurate identification of natural or artificial musk in complex traditional Chinese medicine (TCM) preparations is also a challenge.MethodA strategy from non-targeted to targeted gas chromatography-mass spectrometry (GC–MS) metabolomics was developed for discrimination of natural and artificial musk. Firstly, GC–MS-based non-targeted analysis combined with chemometrics was used to find the potential chemical markers to distinguish natural musk and artificial musk. Subsequently, targeted metabolomics was used to analyze musk in preparations with multiple reaction monitoring (MRM) mode by use gas chromatography coupled with triple quadrupole mass spectrometry (GC-QQQ MS).ResultsTwo chemical markers named prasterone and androsterone have been selected and could be detected in all Compound Pien Tze Huang preparations (CPZHs) containing artificial musk, while the CPZHs containing natural musk did not detect two markers with S/N (signal to noise ratio) less than 3.ConclusionOur work provides an applicable approach to select the practical chemical markers for the assessment of musk in preparations to realize the traceability of musk in TCM and improve the quality control of musk-containing preparations.

Untargeted MS-Based Metabolomics Analysis of the Responses to Drought Stress in Quercus ilex L. Leaf Seedlings and the Identification of Putative Compounds Related to Tolerance

The effect and responses to drought stress were analyzed in Quercus ilex L. seedlings using a nontargeted metabolomic approach, implementing the approaches of previous studies in which other -omics platforms, transcriptomics, and proteomics were employed. This work aimed to characterize the Q. ilex leaf metabolome, determining possible mechanisms and molecular markers of drought tolerance and identifying putative bioactive compounds. Six-month-old seedling leaves subjected to drought stress imposed by water withholding under high-temperature and irradiance conditions were collected when leaf fluorescence decreased by 20% (day 17) and 45% (day 24) relative to irrigated seedlings. A total of 3934 compounds were resolved, with 616 being variable and 342 identified, which belonged to five chemical families. Out of the identified compounds, 33 were variable, mostly corresponding to amino acids, carboxylic acids, benzenoids, flavonoids and isoprenoids. Epigallocatechin, ellagic acid, pulegone, indole-3-acrylic acid and dihydrozeatin-O-glucoside were up-accumulated under drought conditions at both sampling times. An integrated multi-omics analysis of phenolic compounds and related enzymes was performed, revealing that some enzymes involved in the flavonoid pathways (chalcone synthase, anthocyanidin synthase and anthocyanidin reductase) were up-accumulated at day 24 in non-irrigated seedlings. Some putative markers of tolerance to drought in Q. ilex are proposed for assisting breeding programs based on the selection of elite genotypes.

Front Cover Picture: Engineering CYP153AM.aq to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening (ChemCatChem 6/2022)

The Front Cover shows an alkylamine molecule about to enter an enzyme through its substrate tunnel, which is currently under construction. In their Research Article, L. R. Rapp et al. describe dodecylamine as a P450 wild-type inhibitor that could be accepted as a novel substrate by engineering the enzyme's entrance tunnel using a simple MS-based rapid-flow analysis technique. By combining experimental and computational work, the effects of the mutations on the substrate tunnel architectures were demonstrated. The results demonstrate the great potential of enzyme engineering beyond the active site to open the catalytic space to new groups of molecules or even alter inhibition. More information can be found in the Research Article by L. R. Rapp et al.

A novel panel of yeast assays for the assessment of thiamin and its biosynthetic intermediates in plant tissues.

Summary Thiamin (or thiamine), known as vitamin B1, represents an indispensable component of human diets, being pivotal in energy metabolism. Thiamin research depends on adequate vitamin quantification in plant tissues. A recently developed quantitative liquid chromatography–tandem mass spectrometry (LC–MS/MS) method is able to assess the level of thiamin, its phosphorylated entities and its biosynthetic intermediates in the model plant Arabidopsis thaliana, as well as in rice. However, their implementation requires expensive equipment and substantial technical expertise. Microbiological assays can be useful in deter‐mining metabolite levels in plant material and provide an affordable alternative to MS‐based analysis.Here, we evaluate, by comparison to the LC–MS/MS reference method, the potential of a carefully chosen panel of yeast assays to estimate levels of total vitamin B1, as well as its biosynthetic intermediates pyrimidine and thiazole in Arabidopsis samples.The examined panel of Saccharomyces cerevisiae mutants was, when implemented in microbiological assays, capable of correctly assigning a series of wild‐type and thiamin biofortified Arabidopsis plant samples.The assays provide a readily applicable method allowing rapid screening of vitamin B1 (and its biosynthetic intermediates) content in plant material, which is particularly useful in metabolic engineering approaches and in germplasm screening across or within species.

Metabolome alterations in Clonorchis sinensis after treatment with tribendimidine and praziquante in vivo

Tribendimidine (TBD) is a broad-spectrum anthelmintic drug that is also significantly effective in treating clonorchiasis. In this study, the altered metabolomes of Clonorchis sinensis (C. sinensis) in rats after TBD administration were quantified by using ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC–MS/MS) and gas chromatography-mass spectrometry (GC–MS) to explore the possible active sites of TBD against clonorchiasis through altered metabolites and metabolic pathway analysis, and the results are expected to provide a target for the future design of anti-Clonorchis sinensis drugs. The worm burden reduction rate and scanning electron microscopy demonstrated that praziquantel (PZQ, positive control drug) and TBD had significant effects on C. sinensis in rats after treatment at a single dose of 200 mg/kg for 24 h. For the MS-based metabolomic analysis, a total of 173 standard metabolites (126 amino acids, 10 phospholipids and 37 fatty acids) were utilized as a reference metabolite database for metabolome identification. In total, 32 amino acids, 71 phospholipids and 27 fatty acids were detected in the C. sinensis of each group. Among these metabolites, 10 amino acids were significantly decreased in both drug-treated groups. Four lysophosphatidyl cholines (LPCs), six lysophosphatidyl ethanolamines (LPEs) and one phosphatidyl inositol (PI) were significantly increased after treatment with TBD. There were no significant changes in fatty acids among the control group and the two drug-treated groups. The results indicated that TBD administration caused a decrease in amino acids involved in the metabolic pathways of energy consumption and an increase in lysophospholipids, which are the hydrolysis products of phospholipase2 (PLA2) in the phospholipid metabolic pathways. The increased lysophospholipid content can destroy the cell membrane, increase membrane permeability, and even cause exposure to internal antigens that can be attacked by host antibodies. Perhaps the destroyed membrane, the exposed internal antigens and the consumed energy are the cause of the damage and death of C. sinensis after TBD administration. This is an interesting problem that can be examined in future research.

Inorganic Matrices Assisted Laser Desorption/Ionization Mass Spectrometry for Metabolic Analysis in Biofluids.

Metabolic analysis in biofluids interprets the end products in the bioprocess, emerging as an irreplaceable disease diagnosis and monitoring platform. Laser desorption/ionization mass spectrometry (LDI MS)-based metabolic analysis holds great potential for clinical applications in terms of high throughput, rapid signal readout, and minimal sample preparation. There are two essential elements to construct the LDI MS-based metabolic analysis: 1) well-designed nanomaterials as matrices; 2) machine learning algorithms for data analysis. This review highlights the development of various inorganic matrices to comprehend the advantages of LDI MS in metabolite detection and the recent diagnostic applications based on target metabolite detection and untargeted metabolic fingerprints in biological fluids.

Metabolomic Profiles of the Creeping Wood Sorrel Oxalis corniculata in Radioactively Contaminated Fields in Fukushima: Dose-Dependent Changes in Key Metabolites.

The biological impacts of the Fukushima nuclear accident, in 2011, on wildlife have been studied in many organisms, including the pale grass blue butterfly and its host plant, the creeping wood sorrel Oxalis corniculata. Here, we performed an LC–MS-based metabolomic analysis on leaves of this plant collected in 2018 from radioactively contaminated and control localities in Fukushima, Miyagi, and Niigata prefectures, Japan. Using 7967 peaks detected by LC–MS analysis, clustering analyses showed that nine Fukushima samples and one Miyagi sample were clustered together, irrespective of radiation dose, while two Fukushima (Iitate) and two Niigata samples were not in this cluster. However, 93 peaks were significantly different (FDR < 0.05) among the three dose-dependent groups based on background, low, and high radiation dose rates. Among them, seven upregulated and 15 downregulated peaks had single annotations, and their peak intensity values were positively and negatively correlated with ground radiation dose rates, respectively. Upregulated peaks were annotated as kudinoside D (saponin), andrachcinidine (alkaloid), pyridoxal phosphate (stress-related activated vitamin B6), and four microbe-related bioactive compounds, including antibiotics. Additionally, two peaks were singularly annotated and significantly upregulated (K1R1H1; peptide) or downregulated (DHAP(10:0); decanoyl dihydroxyacetone phosphate) most at the low dose rates. Therefore, this plant likely responded to radioactive pollution in Fukushima by upregulating and downregulating key metabolites. Furthermore, plant-associated endophytic microbes may also have responded to pollution, suggesting their contributions to the stress response of the plant.

Antihypertensive effect and underlying mechanism of tripeptide NCW on spontaneously hypertensive rats using metabolomics analysis.

Tripeptide NCW identified in our previous study displayed a strong ACE inhibitory activity, but whether it has any antihypertensive effect in vivo remains unknown. Thus, in this study, we aimed to investigate the protective effects of tripeptide NCW in spontaneously hypertensive rats (SHRs) and to further figure out the serum metabolic profiling variations due to its oral administration via UPLC-Q-TOF-MS/MS-based metabolomics analysis to clarify the underlying hypotensive mechanism. After three weeks of oral administration, the tripeptide NCW-treated group (NCW/SHR group, 80 mg per kg BW per d) showed significantly reduced systolic and diastolic blood pressure by 48.08 ± 3.84 mmHg and 48.92 ± 5.77 mmHg, respectively. Additionally, a total of 25 blood pressure-related metabolites were identified as being significantly changed in SHRs given tripeptide NCW after three weeks. These 25 metabolites might be biomarkers that indicated that the tripeptide NCW exhibits antihypertensive activity via regulating bile acid metabolism, lipid metabolism, amino acid metabolism, purinergic signaling, pantothenate and CoA biosynthesis, and the citrate cycle. Collectively, tripeptide NCW has a protective effect on SHRs associated with serum metabolite abnormalities.

In vitro toxicity screening of amorphous silica nanoparticles using mitochondrial fraction exposure followed by MS-based proteomic analysis.

Silica nanoparticles (SiNPs) are used in consumer products, engineering and medical technologies. Attractive properties of SiNPs (e.g. size/surface-modification) enhance usage and thus the likelihood of environmental/human exposures. The assessment of health risks associated with exposures to SiNPs requires information on their relative potencies and toxicity mechanisms. In this work, phagocytic J774 cells were exposed to amorphous pristine (15, 30, 75 nm) and surface-modified (-NH2, -C3COOH, -C11COOH, -PEG) SiNP variants, and internalization was assessed by transmission electron microscopy (TEM), while cellular ATP was measured as a cytotoxicity endpoint. Furthermore, mitochondrial fractions from J774 cells were exposed to these SiNP variants (5, 15 μg mL-1), as well as two reference particles (SiNP 12 nm and TiO2), and proteomic changes were analyzed by mass spectrometry. Ingenuity Pathway Analysis was used to identify toxicity pathways. TEM analyses showed SiNP internalization and distribution along with some changes in mitochondrial structure. SiNP size- and surface-modification and chemical composition-related changes in mitochondrial proteins, including key proteins of the respiratory complex and oxidative stress, were evident based on high content mass spectrometry data. In addition, the dose-related decrease in cellular ATP levels in SiNP-exposed cells was consistent with related mitochondrial protein profiles. These findings suggest that physicochemical properties can be determinants of SiNP exposure-related mitochondrial effects, and mitochondrial exposures combined with proteomic analysis can be valuable as a new approach methodology in the toxicity screening of SiNPs for risk assessment, with added insight into related toxicity mechanisms.