PubMed

Int J Mol Sci. 2023 Jan 23;24(3):2249. doi: 10.3390/ijms24032249.ABSTRACTLarge-scale high throughput metabolomic technologies are indispensable components of systems biology in terms of discovering and defining the metabolite parts of the system. However, the lack of a plant metabolite spectral library limits the metabolite identification of plant metabolomic studies. Here, we have created a plant metabolite spectral library using 544 authentic standards, which increased the efficiency of identification for untargeted metabolomic studies. The process of creating the spectral library was described, and the mzVault library was deposited in the public repository for free download. Furthermore, based on the spectral library, we describe a process of creating a pseudo-targeted method, which was applied to a proof-of-concept study of Arabidopsis leaf extracts. As authentic standards become available, more metabolite spectra can be easily incorporated into the spectral library to improve the mzVault package.PMID:36768571 | DOI:10.3390/ijms24032249

Int J Mol Sci. 2023 Jan 23;24(3):2234. doi: 10.3390/ijms24032234.ABSTRACTFood allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.PMID:36768555 | DOI:10.3390/ijms24032234

Int J Mol Sci. 2023 Jan 22;24(3):2209. doi: 10.3390/ijms24032209.ABSTRACTThaumatin-like proteins (TLPs), a family of proteins with high sequence similarity to thaumatin, are shown to be involved in plant defense, and are thus classified into the pathogenesis related protein family 5. Ammopiptanthus nanus is a rare evergreen broad-leaved shrub distributed in the temperate zone of Central Asia, which has a high tolerance to low-temperature stress. To characterize A. nanus TLPs and understand their roles in low-temperature response in A. nanus, a comprehensive analysis of the structure, evolution, and expression of TLP family proteins was performed. A total of 31 TLP genes were detected in the A. nanus genome, and they were divided into four groups based on their phylogenetic positions. The majority of the AnTLPs contained the conserved cysteine residues and were predicted to have the typical three-dimensional structure of plant TLPs. The primary modes of gene duplication of the AnTLP family genes were segmental duplication. The promoter regions of most AnTLP genes contain multiple cis-acting elements related to environmental stress response. Gene expression analysis based on transcriptome data and fluorescence quantitative PCR analysis revealed that several AnTLP genes were involved in cold-stress response. We further showed that a cold-induced AnTLP gene, AnTLP13, was localized in apoplast, and heterologous expression of the AnTLP13 in Escherichia coli and yeast cells and tobacco leaves enhanced low-temperature stress tolerance when compared with the control cells or seedlings. Our study provided important data for understanding the roles of TLPs in plant response to abiotic stress.PMID:36768531 | DOI:10.3390/ijms24032209

Int J Mol Sci. 2023 Jan 22;24(3):2186. doi: 10.3390/ijms24032186.ABSTRACTCholesterol efflux capacity (CEC) is of interest given its potential relationship with several important clinical conditions including Alzheimer's disease. The inactivation of the APOE locus in mouse models supports the idea that it is involved in determining the CEC. With that in mind, we examine the impact of the plasma metabolome profile and the APOE genotype on the CEC in cognitively healthy elderly subjects. The study subjects were 144 unrelated healthy individuals. The plasma CEC was determined by exposing cultured mouse macrophages treated with BODIPY-cholesterol to human plasma. The metabolome profile was determined using NMR techniques. Multiple regression was performed to identify the most important predictors of CEC, as well as the NMR features most strongly associated with the APOE genotype. Plasma 3-hydroxybutyrate was the variable most strongly correlated with the CEC (r = 0.365; p = 7.3 × 10-6). Male sex was associated with a stronger CEC (r = -0.326, p = 6.8 × 10-5). Most of the NMR particles associated with the CEC did not correlate with the APOE genotype. The NMR metabolomics results confirmed the APOE genotype to have a huge effect on the concentration of plasma lipoprotein particles as well as those of other molecules including omega-3 fatty acids. In conclusion, the CEC of human plasma was associated with ketone body concentration, sex, and (to a lesser extent) the other features of the plasma lipoprotein profile. The APOE genotype exerted only a weak effect on the CEC via the modulation of the lipoprotein profile. The APOE locus was associated with omega-3 fatty acid levels independent of the plasma cholesterol level.PMID:36768512 | DOI:10.3390/ijms24032186

Int J Mol Sci. 2023 Jan 21;24(3):2167. doi: 10.3390/ijms24032167.ABSTRACTCardiomyopathy is the leading cause of death in patients with muscular dystrophy (MD). Tranilast, a widely used anti-allergic drug, has displayed inhibitory activity against the transient receptor potential cation channel subfamily V member 2 and improved cardiac function in MD patients. To identify urinary biomarkers that assess improved cardiac function after tranilast administration, we performed a urinary metabolomic study focused on oxidative fatty acids. Accompanying the clinical trial of tranilast, urine specimens were collected over 24 weeks from MD patients with advanced heart failure. Urinary levels of tetranor-PGDM (tetranor-prostaglandin D metabolite), a metabolite of prostaglandin D2, significantly decreased 12 weeks after tranilast administration and were correlated with BNP. These results suggest that prostaglandin-mediated inflammation, which increases with the pathological progression of heart failure in MD patients, was attenuated. Urinary prostaglandin E3 (PGE3) levels significantly increased 4 weeks after tranilast administration. There were positive correlations between the urinary levels of PGE3 and 8-hydroxy-2'-deoxyguanosine, an oxidative stress marker. High PGE3 levels may have a protective effect against cardiomyopathy in MD patients with high oxidative stress. Although further validation studies are necessary, urinary tetranor-PGDM and PGE3 levels may help the current understanding of the extent of advanced heart failure in patients with MD after tranilast administration.PMID:36768491 | DOI:10.3390/ijms24032167

Transl Stroke Res. 2023 Feb 11. doi: 10.1007/s12975-023-01137-5. Online ahead of print.ABSTRACTBACKGROUND AND PURPOSE: Ischemic stroke is a heterogeneous disease with various etiologies. The current subtyping process is complicated, time-consuming, and costly. Metabolite-based biomarkers have the potential to improve classification and deliver optimal treatments. We here aimed to identify novel, targeted metabolomics-based biomarkers to discriminate between large-artery atherosclerosis (LAA) and cardioembolic (CE) stroke.METHODS: We acquired serum samples and clinical data from a hospital-based acute stroke registry (ischemic stroke within 3 days from symptom onset). We included 346 participants (169 LAA, 147 CE, and 30 healthy older adults) and divided them into training and test sets. Targeted metabolomic analysis was performed using quantitative and quality-controlled liquid chromatography with tandem mass spectrometry. A multivariate regression model using metabolomic signatures was created that could independently distinguish between LAA and CE strokes.RESULTS: The training set (n = 193) identified metabolomic signatures that were different in patients with LAA and CE strokes. Six metabolomic biomarkers, i.e., lysine, serine, threonine, kynurenine, putrescine, and lysophosphatidylcholine acyl C16:0, could discriminate between LAA and CE stroke after adjusting for sex, age, body mass index, stroke severity, and comorbidities. The enhanced diagnostic power of key metabolite combinations for discriminating between LAA and CE stroke was validated using the test set (n = 123).CONCLUSIONS: We observed significant differences in metabolite profiles in LAA and CE strokes. Targeted metabolomics may provide enhanced diagnostic yield for stroke subtypes. The pathophysiological pathways of the identified metabolites should be explored in future studies.PMID:36764997 | DOI:10.1007/s12975-023-01137-5

Clin Lab Med. 2023 Mar;43(1):99-114. doi: 10.1016/j.cll.2022.09.021.ABSTRACTAdvancements in technology have improved biomarker discovery in the field of heart failure (HF). What was once a slow and laborious process has gained efficiency through use of high-throughput omics platforms to phenotype HF at the level of genes, transcripts, proteins, and metabolites. Furthermore, improvements in artificial intelligence (AI) have made the interpretation of large omics data sets easier and improved analysis. Use of omics and AI in biomarker discovery can aid clinicians by identifying markers of risk for developing HF, monitoring care, determining prognosis, and developing druggable targets. Combined, AI has the power to improve HF patient care.PMID:36764811 | DOI:10.1016/j.cll.2022.09.021

Anal Chim Acta. 2023 Mar 15;1246:340863. doi: 10.1016/j.aca.2023.340863. Epub 2023 Jan 20.ABSTRACTSupercritical fluid chromatography (SFC) is often coupled with electrospray ionization mass spectrometry (ESI-MS) for analyte detection because of its detection capability to a wide range of chemical properties. However, MS sensitivity is highly dependent on the chromatographic conditions, so that it is important to understand the ionization mechanism to determine the optimal chromatographic conditions. The ionization mechanism in SFC/ESI-MS is different to that of liquid chromatography because of the use of CO2 as a mobile phase. Some studies have suggested that alkoxycarbonic acids are formed in the mixture of CO2 and the alcohol modifier, and these species contribute to ionization in CO2-assisted SFC/ESI-MS. Therefore, in this study, we investigated CO2-assisted ESI to test this hypothesis, and we confirmed that methoxylcarbonic acid is generated in CO2/methanol mixtures and contributed to ion generation and detection because it acts as a proton donor in positive-ion mode. However, methoxylcarbonic acid interfered with ionization in negative-ion mode. Addition of ammonium acetate, which is often added to the modifier for negative ion detection in SFC/MS analysis, did not contribute to the recovery of MS sensitivity, although it tended to suppress the formation of metoxylcarbonic acid. This is likely due to ion suppression and neutralization of the negative sites of the analytes by anions or cations derived from ammonium acetate in the negative ion mode. Thus, additive-free methanol/CO2 was the most suitable mobile phase for obtaining high sensitivity in SFC/MS. To demonstrate the practicality of these findings, we tested our optimal mobile phase selection for pesticide analysis. In addition, we tested the addition of 0, 1, and 5 mM ammonium formate to the modifier and make-up solvent, and found that the addition of 1 mM ammonium formate gave the best results in pesticides analysis. In SFC/MS, salt is often added to improve separation or prevent desorption, but our findings suggest that the concentration of salt must be kept as low as possible to achieve highly sensitive MS detection. The results of this study reveal the best selection of the optimal conditions for the modifier and make-up solvent for CO2-assisted SFC/MS analysis and will be useful for the method development in SFC/MS.PMID:36764769 | DOI:10.1016/j.aca.2023.340863

J Proteomics. 2023 Feb 8:104836. doi: 10.1016/j.jprot.2023.104836. Online ahead of print.ABSTRACTSheep meat (encompassing lamb, hogget and mutton) is an important source of animal protein in many countries, with a unique flavour and sensory profile compared to other red meats. Flavour, colour and texture are the key quality attributes contributing to consumer liking of sheep meat. Over the last decades, various factors from 'farm to fork', including production system (e.g., age, breed, feeding regimes, sex, pre-slaughter stress, and carcass suspension), post-mortem manipulation and processing (e.g., electrical stimulation, ageing, packaging types, and chilled and frozen storage) have been identified as influencing different aspects of sheep meat quality. However conventional meat-quality assessment tools are not able to elucidate the underlying mechanisms and pathways for quality variations. Advances in broad-based analytical techniques have offered opportunities to obtain deeper insights into the molecular changes of sheep meat which may become biomarkers for specific variations in quality traits and meat authenticity. This review provides an overview on how omics techniques, especially proteomics (including peptidomics) and metabolomics (including lipidomics and volatilomics) are applied to elucidate the variations in sheep meat quality, mainly in loin muscles, focusing on colour, texture and flavour, and as tools for authentication. SIGNIFICANCE: From this review, we observed that attempts have been made to utilise proteomics and metabolomics techniques on sheep meat products for elucidating pathways of quality variations due to various factors. For instance, the improvement of colour stability and tenderness could be associated with the changes to glycolysis, energy metabolism and endogenous antioxidant capacity. Several studies identify proteolysis as being important, but potentially conflicting for quality as the enhanced proteolysis improves tenderness and flavour, while reducing colour stability. The use of multiple analytical methods e.g., lipidomics, metabolomics, and volatilomics, detects a wider range of flavour precursors (including both water and lipid soluble compounds) that underlie the possible pathways for sheep meat flavour evolution. The technological advancement in omics (e.g., direct analysis-mass spectrometry) could make analysis of the proteins, lipids and metabolites in sheep meat routine, as well as enhance the confidence in quality determination and molecular-based assurance of meat authenticity.PMID:36764652 | DOI:10.1016/j.jprot.2023.104836

Biol Psychiatry. 2023 Feb 8:S0006-3223(23)00055-0. doi: 10.1016/j.biopsych.2023.01.027. Online ahead of print.ABSTRACTBACKGROUND: Metabolic differences have been reported between individuals with and without Major Depressive Disorder (MDD), but their consistency and causal relevance has been unclear.METHODS: We conducted a metabolome-wide association study of MDD with 249 metabolomic measures available in UK Biobank (N = 29, 757). We then applied 2-sample bidirectional Mendelian Randomisation (MR) and colocalization analysis to identify potentially causal relationships between each metabolite and MDD.RESULTS: One hundred and ninety-one metabolites tested were significantly associated with MDD (PFDR < 0.05), which reduced to 129 after adjustment for likely confounders. Lower abundance of Omega-3 fatty acid measures and a higher Omega-6: Omega-3 ratio showed potentially causal effects on liability to MDD. There was no evidence of a causal effect of MDD on metabolite levels. Furthermore, genetic signals associated with Docosahexaenoic Acid colocalized with loci associated with MDD within the FADS gene cluster. Post-hoc MR of gene-transcript abundance within the FADS cluster demonstrated a causal association with MDD. In contrast, colocalization analysis did not suggest a single causal variant for both transcript abundance and MDD liability, but the likely existence of two variants in LD with one another.CONCLUSION: Our findings suggest that decreased Docosahexaenoic Acid and increased Omega-6: Omega-3 fatty acids ratio may be causally related to MDD. These findings provide further support for the causal involvement of fatty acids in MDD.PMID:36764567 | DOI:10.1016/j.biopsych.2023.01.027

Sci Total Environ. 2023 Feb 8:162101. doi: 10.1016/j.scitotenv.2023.162101. Online ahead of print.ABSTRACTPolystyrene nano-plastics (PS-NPs) can be accumulated in the food chain and can penetrate biological barriers to affect multiple physiological functions. However, the adverse effects of nano-plastics on mammals and the underlying mechanism still remain unknown. To fill the gaps, our study administrated low-dose PS-NPs (50 and 100 μg/L) for 24 consecutive weeks in rats. Behavioral and morphological evaluations were performed to assess the neurobehavoirs. A combined analysis of multiple omics was used to evaluate the dysfunctions of the gut-microbe-brain axis. After dihydrochalcone(NHDC) treatment in the PS-NPs rat model, the inflammation response and apoptosis process were assessed and proteomics was used to explore the underlying mechanism. Our results indicated that long-term exposure to low-dose PS-NPs could induce abnormal neurobehaviors and amygdaloid nucleus impairment, and stimulate inflammatory responses and apoptosis. Metagenomics results revealed that four microbial phyla including Proteobacteria, Firmicutes, Defferibacteres, and Bacteroidetes changed significantly compared to the control. Targeted metabolomics analysis in the feces showed alteration of 122 metabolites induced by the PS-NPs exposure, among which the content of dihydrocaffeic acid was significantly associated with the different microbial genera and pivotal differential metabolites in the amygdaloid nucleus. And NHDC treatment significantly alleviated PS-NP-induced neuroinflammation and apoptosis and the cyclic adenosine monophosphate(cAMP)/protein kinase A(PKA)/phosphorylated cAMP-response element binding protein(p-CREB)/plasma membrane calcium-transporting ATPase 2(Atp2b2) signaling pathway was identified in the proteomics. In conclusion, long-term exposure to low-dose PS-NPs has adverse effects on emotion through the dysregulation of the gut-brain axis, and dihydrocaffeic acid can alleviate these effects via the cAMP/PKA/p-CREB/Atp2b2 signaling pathway.PMID:36764550 | DOI:10.1016/j.scitotenv.2023.162101

Sci Total Environ. 2023 Feb 8:162110. doi: 10.1016/j.scitotenv.2023.162110. Online ahead of print.ABSTRACTThe potential adverse effects of progestins on aquatic organisms, especially non-target species, are of increasing concern worldwide. However, the effect and mechanism of progestin toxicity on aquatic invertebrates remain largely unexplored. In the present study, clams Mactra veneriformis were exposed to norgestrel (NGT, 0, 10, and 1000 ng/L), the dominant progestin detected in the aquatic environment, for 21 days. NGT accumulation, histology, transcriptome, and metabolome were assessed in the digestive gland. The bioconcentration factor (BCF) was 386 and 268 in the 10 ng/L NGT group and 1000 ng/L NGT group, respectively, indicating efficient accumulation of NGT in the clams. Histological analysis showed that NGT led to the swelling of epithelial cells and blurring of the basement membrane in the digestive gland. Differentially-expressed genes and KEGG pathway enrichment analysis using a transcriptomic approach suggested that NGT primarily disturbed the detoxification system, antioxidant defense, carbohydrate and amino acid metabolism, and steroid hormone metabolism, which was consistent with the metabolites analyzed using a metabolomic approach. Furthermore, we speculated that the oxidative stress caused by NGT resulted in histological damage to the digestive gland. This study showed that NGT caused adverse effects in the clams and sheds light on the mechanisms of progestin interference in aquatic invertebrates.PMID:36764532 | DOI:10.1016/j.scitotenv.2023.162110

Clin Chim Acta. 2023 Feb 8:117250. doi: 10.1016/j.cca.2023.117250. Online ahead of print.ABSTRACTBACKGROUND: Mucopolysaccharidoses (MPSs) are inherited genetic diseases caused by an absence or deficiency of lysosomal enzymes responsible for catabolizing glycosaminoglycans (GAGs). Undiagnosed patients, or those without adequate treatment in early life, can be severely and irreversibly affected by the disease. In this study, we applied liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based untargeted metabolomics to identify potential biomarkers for MPS disorders to better understand how MPS may affect the metabolome of patients.METHODS: Urine samples from 37 MPS patients (types I, II, III, IV, and VI; untreated and treated with enzyme replacement therapy (ERT)) and 38 controls were analyzed by LC-HRMS. Data were processed by an untargeted metabolomics workflow and submitted to multivariate statistical analyses to reveal significant differences between the MPS and control groups.RESULTS: A total of 12 upregulated metabolites common to all MPS types were identified. Dipeptides, amino acids and derivatives were upregulated in the MPS group compared to controls. N-acetylgalactosamines 4- or 6-sulfate, important constituents of GAGs, were also elevated in MPS patients, most prominently in those with MPS VI. Notably, treated patients exhibited lower levels of the aforementioned acylaminosugars than untreated patients in all MPS types.CONCLUSIONS: Untargeted metabolomics has enabled the detection of metabolites that could improve our understanding of MPS physiopathology. These potential biomarkers can be utilized in screening methods to support diagnosis and ERT monitoring.PMID:36764508 | DOI:10.1016/j.cca.2023.117250

Plant Physiol Biochem. 2023 Feb 4;196:507-519. doi: 10.1016/j.plaphy.2023.02.004. Online ahead of print.ABSTRACTThe sesquiterpene farnesene and the monoterpene citral are phytotoxic natural compounds characterized by a high similarity in macroscopic effects, suggesting an equal or similar mechanism of action when assayed at IC50 concentration. In the present study, a short-time experiment (24 and 48 h) using an imaging spectrofluorometer allowed us to monitor the in-vivo effects of the two molecules, highlighting that both terpenoids were similarly affecting all PSII parameters, even when the effects of citral were quicker in appearing than those of farnesene. The multivariate, univariate, and pathway analyses, carried out on untargeted-metabolomic data, confirmed a clear separation of the plant metabolome in response to the two treatments, whereas similarity in the affected pathways was observed. The main metabolites affected were amino acids and polyamine, which significantly accumulated in response to both treatments. On the contrary, a reduction in sugar content (i.e. glucose and sucrose) was observed. Finally, the in-silico studies demonstrated a similar mechanism of action for both molecules by interacting with DNA binding proteins, although differences concerning the affinity with the proteins with which they could potentially interact were also highlighted. Despite the similarities in macroscopic effects of these two molecules, the metabolomic and in-silico data suggest that both terpenoids share a similar but not equal mechanism of action and that the similar effects observed on the photosynthetic machinery are more imputable to a side effect of molecules-induced oxidative stress.PMID:36764266 | DOI:10.1016/j.plaphy.2023.02.004

Environ Int. 2023 Feb 4;172:107802. doi: 10.1016/j.envint.2023.107802. Online ahead of print.ABSTRACTDecabromodiphenyl ethane (DBDPE) as a widely used brominated flame retardant is harmful to human health due to its toxicity, including cardiovascular toxicity, reproductive toxicity, and hepatotoxicity. However, the knowledge of the long-term effects and structural and metabolic function influence on gut microbiota from DBDPE exposure remains limited. This study was mainly aimed at the gut microbiome and fecal metabolome of female rats and their offspring exposed to DBDPE in early life. 16S rRNA gene sequencing demonstrated that maternal DBDPE exposure could increase the α-diversity of gut microbiota in immature offspring while decreasing the abundance of Bifidobacterium, Clostridium, Muribaculum, Escherichia, and Lactobacillus in adult offspring. The nonmetric multidimensional scaling showed a consistency in the alternation of β-diversity between pregnant rats and their adult offspring. Furthermore, the short-chain fatty acids produced by gut microbiota dramatically increased in adult offspring after maternal DBDPE exposure, revealing that DBDPE treatment disrupted the gut microbial compositions and altered the gut community's metabolic functions. Untargeted metabolomics identified 41 differential metabolites and seven metabolic pathways between adult offspring from various groups. Targeted metabolomic showed that maternal high dose DBDPE exposure obviously decreased the level of glutathione, taurine, and l-carnitine in their adult offspring, which verified the correlation between weight loss and amino acid metabolites. An interesting link between some gut bacteria (especially the Firmicutes) and fecal metabolites demonstrated the shifts in gut microbiota may drive the metabolic process of fecal metabolites. The current findings provide new insight into long-term effects on human health.PMID:36764182 | DOI:10.1016/j.envint.2023.107802

Phytomedicine. 2023 Feb 4;112:154702. doi: 10.1016/j.phymed.2023.154702. Online ahead of print.ABSTRACTBACKGROUND: Nervonic acid (C24:1∆15, 24:1 ω-9, cis-tetracos-15-enoic acid; NA), a long-chain monounsaturated fatty acid, plays an essential role in prevention of metabolic diseases, and immune regulation, and has anti-inflammatory properties. As a chronic, immune-mediated inflammatory disease, ulcerative colitis (UC) can affect the large intestine. The influences of NA on UC are largely unknown.PURPOSE: The present study aimed to decipher the anti-UC effect of NA in the mouse colitis model. Specifically, we wanted to explore whether NA can regulate the levels of inflammatory factors in RAW264.7 cells and mouse colitis model.METHODS: To address the above issues, the RAW264.7 cell inflammation model was established by lipopolysaccharide (LPS), then the inflammatory factors tumor necrosis factor-α (TNF-α), Interleukin-6 (IL-6), Interleukin-1β (IL-1β), and Interleukin-10 (IL-10) were detected by Enzyme-linked immunosorbent assay (ELISA). The therapeutic effects of NA for UC were evaluated using C57BL/6 mice gavaged dextran sodium sulfate (DSS). Hematoxylin and eosin (H&E) staining, Myeloperoxidase (MPO) kit assay, ELISA, immunofluorescence assay, and LC-MS/MS were used to assess histological changes, MPO levels, inflammatory factors release, expression and distribution of intestinal tight junction (TJ) protein ZO-1, and metabolic pathways, respectively. The levels of proteins involved in the nuclear factor kappa-B (NF-κB) pathway in the UC were investigated by western blotting and RT-qPCR.RESULTS: In vitro experiments verified that NA could reduce inflammatory response and inhibit the activation of key signal pathways associated with inflammation in LPS-induced RAW264.7 cells. Further, results from the mouse colitis model suggested that NA could restore intestinal barrier function and suppress NF-κB signal pathways to ameliorate DSS-induced colitis. In addition, untargeted metabolomics analysis of NA protection against UC found that NA protected mice from colitis by regulating citrate cycle, amino acid metabolism, pyrimidine and purine metabolism.CONCLUSION: These results suggested that NA could ameliorate the secretion of inflammatory factors, suppress the NF-κB signaling pathway, and protect the integrity of colon tissue, thereby having a novel role in prevention or treatment therapy for UC. This work for the first time indicated that NA might be a potential functional food ingredient for preventing and treating inflammatory bowel disease (IBD).PMID:36764096 | DOI:10.1016/j.phymed.2023.154702

J Proteome Res. 2023 Feb 10. doi: 10.1021/acs.jproteome.2c00758. Online ahead of print.ABSTRACTProteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.PMID:36763818 | DOI:10.1021/acs.jproteome.2c00758

J Cell Sci. 2023 Feb 1;136(3):jcs260370. doi: 10.1242/jcs.260370. Epub 2023 Feb 10.ABSTRACTMitochondria and peroxisomes are dynamic signaling organelles that constantly undergo fission, driven by the large GTPase dynamin-related protein 1 (DRP1; encoded by DNM1L). Patients with de novo heterozygous missense mutations in DNM1L present with encephalopathy due to defective mitochondrial and peroxisomal fission (EMPF1) - a devastating neurodevelopmental disease with no effective treatment. To interrogate the mechanisms by which DRP1 mutations cause cellular dysfunction, we used human-derived fibroblasts from patients who present with EMPF1. In addition to elongated mitochondrial morphology and lack of fission, patient cells display lower coupling efficiency, increased proton leak and upregulation of glycolysis. Mitochondrial hyperfusion also results in aberrant cristae structure and hyperpolarized mitochondrial membrane potential. Peroxisomes show a severely elongated morphology in patient cells, which is associated with reduced respiration when cells are reliant on fatty acid oxidation. Metabolomic analyses revealed impaired methionine cycle and synthesis of pyrimidine nucleotides. Our study provides insight into the role of mitochondrial dynamics in cristae maintenance and the metabolic capacity of the cell, as well as the disease mechanism underlying EMPF1.PMID:36763487 | DOI:10.1242/jcs.260370

J Chem Ecol. 2023 Feb 10. doi: 10.1007/s10886-023-01410-9. Online ahead of print.ABSTRACTSecondary plant chemistry mediates a variety of communication signals among species, playing a fundamental role in the evolutionary diversification of communities and ecosystems. Herein, we explored diet-mediated host plant effects on development and immune response of a generalist insect herbivore. Vanessa cardui (Nymphalidae) caterpillars were reared on leaves of three host plants that vary in secondary metabolites, Plantago lanceolata (Plantaginaceae), Taraxacum officinale (Asteraceae) and Tithonia diversifolia (Asteraceae). Insect development was evaluated by larval and pupal viabilities, survivorship, and development rate. Immune response was measured as phenoloxidase (PO) activity. Additionally, chemical profiles of the host plants were obtained by liquid chromatograph-mass spectrometry (LC-MS) and the discriminant metabolites were determined using a metabolomic approach. Caterpillars reared on P. lanceolata exhibited the highest larval and pupal viabilities, as well as PO activity, and P. lanceolata leaves were chemically characterized by the presence of iridoid glycosides, phenylpropanoids and flavonoids. Taraxacum officinale leaves were characterized mainly by the presence of phenylpropanoids, flavones O-glycoside and germacranolide-type sesquiterpene lactones; caterpillars reared on this host plant fully developed to the adult stage, however they exhibited lower larval and pupal viabilities compared to individuals reared on P. lanceolata. Conversely, caterpillars reared on T. diversifolia leaves, which contain phenylpropanoids, flavones and diverse furanoheliangolide-type sesquiterpene lactones, were not able to complete larval development and exhibited the lowest PO activity. These findings suggested that V. cardui have adapted to tolerate potentially toxic metabolites occurring in P. lanceolata (iridoid glycosides), however caterpillars were not able to cope with potentially detrimental metabolites occurring in T. diversifolia (furanoheliangolides). Therefore, we suggest that furanoheliangolide-type sesquiterpene lactones were responsible for the poor development and immune response observed for caterpillars reared on T. diversifolia.PMID:36763248 | DOI:10.1007/s10886-023-01410-9

Endocrinology. 2023 Feb 10:bqad026. doi: 10.1210/endocr/bqad026. Online ahead of print.ABSTRACTPheochromocytomas (PCC) and paragangliomas (PGL) are rare neuroendocrine tumors with limited curative treatment options outside of surgical resection. Patients with mutations in succinate dehydrogenase subunit B (SDHB) are at an increased risk of malignant and aggressive disease. As cation channels are associated with tumorigenesis, we studied the expression and activity of cation channels from the Degenerin superfamily in a progenitor cell line derived from a human PCC. hPheo1 wild-type (WT) and SDHB knockdown (KD) cells were studied to investigate whether epithelial sodium channels (ENaC) and acid-sensing ion channels (ASIC) are regulated by the activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). First, we performed targeted metabolomic studies and quantified changes in glycolysis pathway intermediates and citric acid cycle intermediates using hPheo1 WT cells and SDHB KD cells. Next, we performed protein biochemistry and electrophysiology studies to characterize the protein expression and activity, respectively, of these ion channels. Our western blot experiments show both ENaC alpha and ASIC1/2 are expressed in both hPheo1 WT and SDHB KD cells, with lower levels of a cleaved 60kDa form of ENaC in SDHB KD cells. Single-channel patch clamp studies corroborate these results and further indicate channel activity is decreased in SDHB KD cells. Additional experiments showed a more significant decreased membrane potential in SDHB KD cells which were sensitive to amiloride compared to WT cells. We provide evidence for the differential expression and activity of ENaC and ASIC hybrid channels in hPheo1 WT and SDHB KD cells providing an important area of investigation in understanding SDHB-related disease.PMID:36763043 | DOI:10.1210/endocr/bqad026