PubMed

BMC Bioinformatics. 2022 Nov 28;22(Suppl 10):632. doi: 10.1186/s12859-022-04964-9.ABSTRACTBACKGROUND: Cancers are genetically heterogeneous, so anticancer drugs show varying degrees of effectiveness on patients due to their differing genetic profiles. Knowing patient's responses to numerous cancer drugs are needed for personalized treatment for cancer. By using molecular profiles of cancer cell lines available from Cancer Cell Line Encyclopedia (CCLE) and anticancer drug responses available in the Genomics of Drug Sensitivity in Cancer (GDSC), we will build computational models to predict anticancer drug responses from molecular features.RESULTS: We propose a novel deep neural network model that integrates multi-omics data available as gene expressions, copy number variations, gene mutations, reverse phase protein array expressions, and metabolomics expressions, in order to predict cellular responses to known anti-cancer drugs. We employ a novel graph embedding layer that incorporates interactome data as prior information for prediction. Moreover, we propose a novel attention layer that effectively combines different omics features, taking their interactions into account. The network outperformed feedforward neural networks and reported 0.90 for [Formula: see text] values for prediction of drug responses from cancer cell lines data available in CCLE and GDSC.CONCLUSION: The outstanding results of our experiments demonstrate that the proposed method is capable of capturing the interactions of genes and proteins, and integrating multi-omics features effectively. Furthermore, both the results of ablation studies and the investigations of the attention layer imply that gene mutation has a greater influence on the prediction of drug responses than other omics data types. Therefore, we conclude that our approach can not only predict the anti-cancer drug response precisely but also provides insights into reaction mechanisms of cancer cell lines and drugs as well.PMID:36443676 | DOI:10.1186/s12859-022-04964-9

BMC Bioinformatics. 2022 Nov 28;23(1):508. doi: 10.1186/s12859-022-05068-0.ABSTRACTBACKGROUND: Comprehensive metabolomic analyses have been conducted in various institutes and a large amount of metabolomic data are now publicly available. To help fully exploit such data and facilitate their interpretation, metabolomic data obtained from different facilities and different samples should be integrated and compared. However, large-scale integration of such data for biological discovery is challenging given that they are obtained from various types of sample at different facilities and by different measurement techniques, and the target metabolites and sensitivities to detect them also differ from study to study.RESULTS: We developed iDMET, a network-based approach to integrate metabolomic data from different studies based on the differential metabolomic profiles between two groups, instead of the metabolite profiles themselves. As an application, we collected cancer metabolomic data from 27 previously published studies and integrated them using iDMET. A pair of metabolomic changes observed in the same disease from two studies were successfully connected in the network, and a new association between two drugs that may have similar effects on the metabolic reactions was discovered.CONCLUSIONS: We believe that iDMET is an efficient tool for integrating heterogeneous metabolomic data and discovering novel relationships between biological phenomena.PMID:36443658 | DOI:10.1186/s12859-022-05068-0

BMC Plant Biol. 2022 Nov 29;22(1):549. doi: 10.1186/s12870-022-03939-5.ABSTRACTBACKGROUND: Salicylic acid (SA) is a major plant hormone that mediates the defence pathway against pathogens. SA accumulates in highly variable amounts depending on the plant-pathogen system, and several enzyme activities participate in the restoration of its levels. Gentisic acid (GA) is the product of the 5-hydroxylation of SA, which is catalysed by S5H, an enzyme activity regarded as a major player in SA homeostasis. GA accumulates at high levels in tomato plants infected by Citrus Exocortis Viroid (CEVd), and to a lesser extend upon Pseudomonas syringae DC3000 pv. tomato (Pst) infection.RESULTS: We have studied the induction of tomato SlS5H gene by different pathogens, and its expression correlates with the accumulation of GA. Transient over-expression of SlS5H in Nicotiana benthamiana confirmed that SA is processed by SlS5H in vivo. SlS5H-silenced tomato plants were generated, displaying a smaller size and early senescence, together with hypersusceptibility to the necrotrophic fungus Botrytis cinerea. In contrast, these transgenic lines exhibited an increased defence response and resistance to both CEVd and Pst infections. Alternative SA processing appears to occur for each specific pathogenic interaction to cope with SA levels. In SlS5H-silenced plants infected with CEVd, glycosylated SA was the most discriminant metabolite found. Instead, in Pst-infected transgenic plants, SA appeared to be rerouted to other phenolics such as feruloyldopamine, feruloylquinic acid, feruloylgalactarate and 2-hydroxyglutarate.CONCLUSION: Using SlS5H-silenced plants as a tool to unbalance SA levels, we have studied the re-routing of SA upon CEVd and Pst infections and found that, despite the common origin and role for SA in plant pathogenesis, there appear to be different pathogen-specific, alternate homeostasis pathways.PMID:36443652 | DOI:10.1186/s12870-022-03939-5

Nat Metab. 2022 Nov 28. doi: 10.1038/s42255-022-00689-4. Online ahead of print.ABSTRACTThe branched-chain aminotransferase isozymes BCAT1 and BCAT2, segregated into distinct subcellular compartments and tissues, initiate the catabolism of branched-chain amino acids (BCAAs). However, whether and how BCAT isozymes cooperate with downstream enzymes to control BCAA homeostasis in an intact organism remains largely unknown. Here, we analyse system-wide metabolomic changes in BCAT1- and BCAT2-deficient mouse models. Loss of BCAT2 but not BCAT1 leads to accumulation of BCAAs and branched-chain α-keto acids (BCKAs), causing morbidity and mortality that can be ameliorated by dietary BCAA restriction. Through proximity labelling, isotope tracing and enzymatic assays, we provide evidence for the formation of a mitochondrial BCAA metabolon involving BCAT2 and branched-chain α-keto acid dehydrogenase. Disabling the metabolon contributes to BCAT2 deficiency-induced phenotypes, which can be reversed by BCAT1-mediated BCKA reamination. These findings establish a role for metabolon formation in BCAA metabolism in vivo and suggest a new strategy to modulate this pathway in diseases involving dysfunctional BCAA metabolism.PMID:36443523 | DOI:10.1038/s42255-022-00689-4

Nat Microbiol. 2022 Nov 28. doi: 10.1038/s41564-022-01266-x. Online ahead of print.ABSTRACTDespite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.PMID:36443458 | DOI:10.1038/s41564-022-01266-x

Anal Bioanal Chem. 2022 Nov 28. doi: 10.1007/s00216-022-04384-x. Online ahead of print.ABSTRACTLiquid chromatography mass spectrometry (LC-MS) has emerged as a mainstream strategy for metabolomics analyses. One advantage of LC-MS is that it can serve both as a biomarker discovery tool and as a platform for clinical diagnostics. Consequently, it offers an exciting opportunity to potentially transition research studies into real-world clinical tools. One important distinction between research versus diagnostics-based applications of LC-MS is throughput. Clinical LC-MS must enable quantitative analyses of target molecules in hundreds or thousands of samples each day. Currently, the throughput of these clinical applications is limited by the chromatographic gradient lengths, which-when analyzing complex metabolomics samples-are difficult to conduct in under ~ 3 min per sample without introducing serious quantitative analysis problems. To address this shortcoming, we developed sequential quantification using isotope dilution (SQUID), an analytical strategy that combines serial sample injections into a continuous isocratic mobile phase to maximize throughput. SQUID uses internal isotope-labelled standards to correct for changes in LC-MS response factors over time. We show that SQUID can detect microbial polyamines in human urine specimens (lower limit of quantification; LLOQ = 106 nM) with less than 0.019 normalized root mean square error. Moreover, we show that samples can be analyzed in as little as 57 s. We propose SQUID as a new, high-throughput LC-MS tool for quantifying small sets of target biomarkers across large cohorts.PMID:36443449 | DOI:10.1007/s00216-022-04384-x

J Med Virol. 2022 Nov 28. doi: 10.1002/jmv.28355. Online ahead of print.ABSTRACTThe genetic association of COVID-19 with its complications has not been fully understood. This study aimed to identify variants and haplotypes of candidate genes implicated in COVID-19 related traits by combining the literature review and pathway analysis. In order to explore such genes, the protein-protein interactions and relevant pathways of COVID-19-associated genes were assessed. A number of variants on candidate genes were identified from genome-wide association studies (GWASs) which were associated with COVID-19 related traits (p˂10-6 ). Haplotypic blocks were assessed using haplotypic structures among the 1000 Genomes Project (r2 ≥0.8, D'≥0.8). Further functional analyses were performed on the selected variants. The results demonstrated that a group of variants in ACE and AGT genes were significantly correlated with COVID-19 related traits. Three haplotypes were identified to be involved in the blood metabolites levels and the development of blood pressure. Functional analyses revealed that most GWAS index variants were expression quantitative trait loci (eQTL) and had transcription factor binding sites, exonic splicing enhancers, or silencer activities. Furthermore, the proxy haplotype variants, rs4316, rs4353, rs4359, and three variants, namely rs2493133, rs2478543, and rs5051, were associated with blood metabolite and systolic blood pressure, respectively. These variants exerted more regulatory effects compared with other GWAS variants. The present study indicates that the genetic variants and candidate haplotypes of COVID-19 related genes are associated with blood pressure and blood metabolites. However, further observational studies are warranted to confirm these results. This article is protected by copyright. All rights reserved.PMID:36443248 | DOI:10.1002/jmv.28355

Anim Sci J. 2022 Jan;93(1):e13785. doi: 10.1111/asj.13785.ABSTRACTEctopic fat is defined by the deposition of adipose tissue within non-adipose tissue such as skeletal muscle. Japanese Black cattle (Wagyu) are characterized by the ability to accumulate high amounts of intramuscular adipose tissue. Obese conditions enhance the accumulation of ectopic fat. This review shows the effects of subcutaneous and visceral fat distribution on Wagyu intramuscular adipogenesis. Obese conditions also stimulate the macrophage infiltration into adipose tissues. Adipose tissue macrophages have reported to regulate adipose tissue growth and ectopic fat accumulation in humans and rodents. Wagyu is characterized by the higher capacity for intramuscular adipogenesis than Holsteins. This review discusses the depot-specific effects of macrophage infiltration among subcutaneous, visceral, and intramuscular adipose tissue on intramuscular adipogenesis in Wagyu and Holstein cattle. Recently, metabolome analysis has been used to identify obesity-related biomarkers by comparing the biological samples between lean and obese patients. This review introduces the metabolomic profiles of plasma and intramuscular adipose tissue between Wagyu and Holsteins.PMID:36443236 | DOI:10.1111/asj.13785

Anal Chim Acta. 2023 Jan 2;1237:340583. doi: 10.1016/j.aca.2022.340583. Epub 2022 Nov 6.ABSTRACTHydrogen sulfide is a toxic gas but also established as a naturally occurring gaseous signaling molecule in humans, playing key physiological roles with particular involvement in lung disease including COVID-19. Thiosulfate is the conventional biomarker of hydrogen sulfide and is excreted in human urine at low micromolar levels. Thiosulfate is amenable to detection by the element-selective inductively coupled plasma tandem mass spectrometry (ICPMS/MS), but sulfur speciation in human samples at trace levels is challenging due to the high complexity of human sulfur metabolome and the utility of this detector under such settings has not been demonstrated. We report a method for thiosulfate determination in human urine at trace physiological levels by HPLC-ICPMS/MS. The method involved one-step derivatization to improve chromatographic behavior followed by direct injection. The instrumental limit of detection was 1.4 μg S L-1 (0.02 μM or 0.1 pmol). In a group of samples from volunteers (n = 24), measured thiosulfate concentrations in the diluted urine matrix were down to 8.0 μg S L-1 with a signal-to-noise ratio >10. The method was validated for recovery (80-110%), repeatability (RSD% <5%), and linearity (r2 = 0.9999, at a tested working concentration range of 0.01-1.0 mg S L-1), and the accuracy was assessed by comparing with HPLC-ESIMS/MS which showed agreement within ±20%. This work demonstrates the applicability of HPLC-ICPMS/MS for sulfur speciation at trace levels in a matrix with complex sulfur metabolome as human urine and provides a sensitive method for the determination of the hydrogen sulfide biomarker.PMID:36442947 | DOI:10.1016/j.aca.2022.340583

J Am Soc Mass Spectrom. 2022 Nov 28. doi: 10.1021/jasms.2c00296. Online ahead of print.ABSTRACTIdentification and further characterization of antibody charge variants is a crucial step during biopharmaceutical drug development, particularly with regard to the increasing complexity of novel antibody formats. As a standard analytical approach, manual offline fractionation of charge variants by cation-exchange chromatography followed by comprehensive analytical testing is applied. These conventional workflows are time-consuming and labor-intensive and overall reach their limits in terms of chromatographic separation of enhanced structural heterogeneities raised from new antibody formats. For these reasons, we aimed to develop an alternative online characterization strategy for charge variant characterization of a therapeutic bispecific antibody by online mD-LC-MS at middle-up (2D-LC-MS) and bottom-up (4D-LC-MS) level. Using the implemented online mD-LC-MS approach, all medium- and even low-abundant product variants previously identified by offline fraction experiments and liquid chromatography mass spectrometry could be monitored. The herein reported automated online mD-LC-MS methodology therefore represents a complementary and in part alternative approach for analytical method validation including multiattribute monitoring (MAM) strategies by mass spectrometry, offering various benefits including increased throughput and reduced sample handling and combined protein information at intact protein and peptide level.PMID:36442848 | DOI:10.1021/jasms.2c00296

J Nutr Biochem. 2022 Nov 25:109239. doi: 10.1016/j.jnutbio.2022.109239. Online ahead of print.ABSTRACTHealth effects of dairy fats (DF) are difficult to evaluate, as DF intakes are hard to assess epidemiologically and DF have heterogeneous compositions that influence biological responses. We set out to find biomarkers of DF intake and assess biological response to a summer DF diet (R2), a winter DF diet (R3), and a R3 supplemented with calcium (R4) compared to a plant-fat-based diet (R1) in a randomized clinical trial (n=173) and a 2-year study in mildly metabolically disturbed downsized pigs (n=32). Conventional clinical measures were completed by LC/MS plasma metabolomics/lipidomics. The measured effects were modeled as biological functions to facilitate interpretation. DF intakes in pigs specifically induced a U-shaped metabolic trajectory, reprogramming metabolism to close to its initial status after a one-year turnaround. Twelve lipid species repeatably predicted DF intakes in both pigs and humans (6.6% errors). More broadly, in pigs, quality of DF modulated the time-related biological response (R2: 30 regulated functions, primarily at 6 months; R3: 26 regulated functions, mostly at 6-12 months; R4: 43 regulated functions, mostly at 18 months). Despite this heterogeneity, 9 functions overlapped under all 3 DF diets in both studies, related to a restricted area of amino acids metabolism, cofactors, nucleotides and xenobiotic pathways and the microbiota. In conclusion, over the long-term, DF reprograms metabolism to close to its initial biological status in metabolically-disrupted pigs. Quality of the DF modulates its metabolic influence, although some effects were common to all DF. A resilient signature of DF consumption found in pigs was validated in humans.PMID:36442717 | DOI:10.1016/j.jnutbio.2022.109239

Int J Biol Macromol. 2022 Nov 25:S0141-8130(22)02815-X. doi: 10.1016/j.ijbiomac.2022.11.257. Online ahead of print.ABSTRACTRheumatoid arthritis (RA) is an autoimmune disease affected patients' quality of life severely. Our previous study found Lycium barbarum polysaccharide (LBP) alleviated RA, but it remains unknown whether gut microbiota is necessary for the alleviation. Here, RA models were established in rats with microbiota and rats treated by antibiotic cocktail, and LBP was applied for the intervention on rats. The biochemical test, 16S rDNA sequencing and metabolome analysis were applied to analyze the effects of LBP on gut microbiota, their metabolites and hosts. Results showed the LBP intervention improved RA by inhibiting pro-inflammatory cytokines IL-1α, IL-1β, TNF-α and IL-6 only in rats with microbiota, but not in pseudo-germ-free rats. The abundance of specific bacteria, including Romboutsia, Lactobacillus, Turicibacter, Clostridium_sensu_stricto_1, Faecalibacterium and Adlercreutzia, and several metabolites, including O-desmethylangolensin, 3-hydroxydodecanedioic acid, N-formyl-L-methionine, suberic acid, (S)-oleuropeic acid, prolyl-histidine, 13,14-dihydro PGF-1a, (R)-pelletierine and short-chain fatty acids increased only in RA rats with microbiota after the intervention. Our results suggest that intestinal bacteria are necessary for LBP alleviating RA alleviation. The fermentation metabolite acts on the host instead of LBP itself, which may be the reason for the improvement of RA.PMID:36442555 | DOI:10.1016/j.ijbiomac.2022.11.257

Int J Biol Macromol. 2022 Nov 25:S0141-8130(22)02808-2. doi: 10.1016/j.ijbiomac.2022.11.249. Online ahead of print.ABSTRACTPlant-derived monoterpene indole alkaloids (MIAs) from Uncaria rhynchophylla (UR) have huge medicinal properties in treating Alzheimer's disease, Parkinson's disease, and depression. Although many bioactive UR-MIA products have been isolated as drugs, their biosynthetic pathway remains largely unexplored. In this study, untargeted metabolome identified 79 MIA features in UR tissues (leaf, branch stem, hook stem, and stem), of which 30 MIAs were differentially accumulated among different tissues. Short time series expression analysis captured 58 pathway genes and 12 hub regulators responsible for UR-MIA biosynthesis and regulation, which were strong links with main UR-MIA features. Coexpression networks further pointed to two strictosidine synthases (UrSTR1/5) that were coregulated with multiple MIA-related genes and highly correlated with UR-MIA features (r > 0.7, P < 0.005). Both UrSTR1/5 catalyzed the formation of strictosidine with tryptamine and secologanin as substrates, highlighting the importance of key residues (UrSTR1: Glu309, Tyr155; UrSTR5: Glu295, Tyr141). Further, overexpression of UrSTR1/5 in UR hairy roots constitutively increased the biosynthesis of bioactive UR-MIAs (rhynchophylline, isorhynchophylline, corynoxeine, etc), whereas RNAi of UrSTR1/5 significantly decreased UR-MIA biosynthesis. Collectively, our work not only provides candidates for reconstituting the biosynthesis of bioactive UR-MIAs in heterologous hosts but also highlights a powerful strategy for mining natural product biosynthesis in medicinal plants.PMID:36442554 | DOI:10.1016/j.ijbiomac.2022.11.249

Int J Biol Macromol. 2022 Nov 25:S0141-8130(22)02790-8. doi: 10.1016/j.ijbiomac.2022.11.231. Online ahead of print.ABSTRACTIn this paper, we reported an excellent hypoglycemic effect of a Ganoderma lucidium polysaccharide F31 with efficacies between 45 and 54 %, approaching to that of liraglutide (52 %). Significantly, F31 reduced the body weight gains and food intakes. F31 decreased 4 key compounds, consisting of adenosine, adenosine, galactitol and glycerophosphocholine and elevated 8 key compounds, including arginine, proline, arachidonic acid, creatine, aspartic acid, leucine, phenylalanine and ornithine, which protected kidney function. Also, apoptosis was promoted by F31 in epididymal fat through increasing Caspase-3, Caspase-6 and Bax and decreasing Bcl-2. On 3 T3-L1 preadipocyte cells, F31 induced early apoptosis through reducing mitochondrial membrane potential. Finally, a molecular docking was performed to reveal a plausible cross-talk between kidney and epididymal fat through glycerophosphorylcholine-Bax axis. Overall, F31 alleviated hyperglycemia through kidney protection and adipocyte apoptosis in db/db mice. This work may provide novel insights into the hypoglycemic activity of polysaccharides.PMID:36442553 | DOI:10.1016/j.ijbiomac.2022.11.231

Food Chem. 2022 Nov 19;405(Pt B):134909. doi: 10.1016/j.foodchem.2022.134909. Online ahead of print.ABSTRACTCold is the best means of prolonging fruit storage. However, tropical fruit are susceptible to cold storage. The mode of action of mango fruit tolerance to suboptimal cold temperature of 7 or 10 °C after postharvest application of 8 mM phenylalanine was investigated using transcriptomic and metabolomic analyses of mango fruit during suboptimal cold storage. Phenylalanine-treated fruit had less chilling injuries-black spot and pitting electrolyte leakage,-and reduced decay after suboptimal cold storage. Phenylalanine treatment induced genes related to plant-pathogen interactions, plant hormone signal transduction, and the phenylpropanoid pathway, increasing the levels of the flavonoids quercetin and kaempferol glycosides and anthocyanins, and antioxidant content. Reduced oxidation led to lower lipid peroxidation, and a reduction in fatty acid-degradation products, e.g., volatile aldehydes. Treatment with phenylalanine, therefore, enhances chilling tolerance of mango fruit through regulation of metabolic and defense-related pathways, maintaining high levels of flavonoids, and antioxidants enzyme activity, and reducing H2O2 content, lipid peroxidation, and volatile aldehydes.PMID:36442247 | DOI:10.1016/j.foodchem.2022.134909

Food Chem. 2022 Nov 23;405(Pt B):135026. doi: 10.1016/j.foodchem.2022.135026. Online ahead of print.ABSTRACTArabica roast coffee contains a substantial amount of water soluble atractyligenin-2-O-β-d-glucoside, which is ingested by consumption of coffee brew. Metabolomics data suggest this coffee compound is excreted as glucuronides, but the structures of conjugates have not been elucidated so far. We collected coffee drinkers' urine and isolated four metabolites by MS-guided liquid chromatographic fractionation. The structures were investigated by nuclear magnetic resonance (NMR) and time-of-flight mass spectrometry (ToF-MS) and identified as atractyligenin-19-O-β-d-glucuronide (M1), 2β-hydroxy-15-oxoatractylan-4α-carboxy-19-O-β-d-glucuronide (M2), and 2β-hydroxy-15-oxoatractylan-4α-carboxylic acid-2-O-β-d-glucuronide (M3). An unconjugated metabolite (M4) was confirmed as atractyligenin. We analyzed spot urines from n = 6 coffee drinking individuals and detected the metabolites M1, M2 and M4 in every sample, and M3 in four out of six samples, suggesting interindividual differences in metabolism.PMID:36442242 | DOI:10.1016/j.foodchem.2022.135026

Food Chem. 2022 Nov 15;405(Pt B):134968. doi: 10.1016/j.foodchem.2022.134968. Online ahead of print.ABSTRACTSuaeda salsa L. (Chenopodiaceae) is a wild vegetable distributed along the northern coast of China. Searching for potential agents with health benefits from S. salsa L. led to the identification of 14 flavonoids (1-14), eight phenolic acids (15-22), one coumarin (23), one benzoquinone (24), two sesquiterpenes (25, 26), and three lignins (27-29) from an aqueous ethanol (EtOH) extract of the above-ground whole plant using various column chromatographic methods. High-resolution electrospray ionization mass spectrometry (HRESIMS) analyses and nuclear magnetic resonance (1H and 13C NMR) spectroscopy were adopted to examine the structural properties of the compounds. To date, our study is the first to identify 20 compounds from this genus. Some compounds exhibited significant health benefits in zebrafish models. Compounds 2, 4, 23, and 28 significantly improved oxidative damage, while compounds 1-5, 7, 11, 13, 18, 19, and 23 significantly improved zebrafish lateral line neuromast inflammation. Additionally, compounds 1, 4, 8, 13, and 16 significantly promoted zebrafish angiogenesis, while compounds 3-5 and 18 significantly improved zebrafish arrhythmia. Furthermore, a flavonoid-targeted metabolomics study revealed that flavanone was the precursor of all of the flavonoids and had its highest accumulation in August, while the others showed their highest accumulation in September. Thus, the best time to harvest most of the bioactive polyphenols is during September. The present study revealed that the wild vegetable S. salsa L. might be developed as a potential cardioprotective functional food.PMID:36442239 | DOI:10.1016/j.foodchem.2022.134968

Anal Chem. 2022 Nov 28. doi: 10.1021/acs.analchem.2c03042. Online ahead of print.ABSTRACTThis work presents an advanced analytical platform for untargeted enantioselective amino acid analysis (eAAA) by comprehensive achiral × chiral 2D-LC hyphenated to ESI-QTOF-MS/MS utilizing data-independent SWATH (sequential window acquisition of all theoretical fragment-ion spectra) technology. The methodology involves N-terminal pre-column derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC; AccQ) as retention, selectivity, and MS tag, supporting retention and UV detection in RPLC (1D), chiral recognition, and thus enantioselectivity by the core-shell tandem column composed of a quinine carbamate weak anion exchanger (QN-AX) and a zwitterionic chiral ion-exchanger (ZWIX(+)) (2D) as well as the ionization efficiency during positive electrospray ionization due to a high proton affinity of the AQC label. Furthermore, the urea-type MS tag gives rise to the generation of AQC-tag characteristic signature fragments in MS2. The latter allows the chemoselective mass spectrometric filtering of targeted and untargeted N-derivatized amino acids or related labeled species. The chiral core-shell tandem column provides a complete enantioselective amino acid profile of all proteinogenic amino acids within 1 min, with full baseline separation of all enantiomers, but without resolution of isomeric Ile/allo-Ile (aIle)/Leu, which can be resolved by RPLC. The entire LC × LC separation occurs within a total run time of 60 min (1D), with the chiral 2D operated in gradient elution mode and a cycle time of 60 s. A strategy to mine the 2D-LC-SWATH data is presented and demonstrated for the qualitative eAAA of two peptide hydrolysate samples of therapeutic peptides containing common and uncommon as well as primary and secondary amino acids. Absolute configuration assignment of amino acids using template matching for all proteinogenic amino acids was made feasible due to method robustness and the inclusion of an isotopically labeled L-[U-13C15N]-AA standard. The quantification performance of this LC × LC-MS/MS assay was also evaluated. Accuracies were acceptable for the majority of AAs enabling AA composition determination in peptide hydrolysates simultaneously with configuration assignment, as exemplified by oxytocin. This methodology represents a step toward truly untargeted 2D enantioselective amino acid analysis and metabolomics.PMID:36442145 | DOI:10.1021/acs.analchem.2c03042

Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2214331119. doi: 10.1073/pnas.2214331119. Epub 2022 Nov 29.ABSTRACTHuman leukocyte antigen (HLA) molecules present small peptide antigens to T cells, thereby allowing them to recognize pathogen-infected and cancer cells. A central dogma over the last 50+ y is that peptide binding to HLA molecules is mediated by the docking of side chains of particular amino acids in the peptide into pockets in the HLA molecules in a conserved N- to C-terminal orientation. Whether peptides can be presented in a reversed C- to N-terminal orientation remains unclear. Here, we performed large-scale identification of peptides bound to HLA-DP molecules and observed that in addition to peptide binding in an N- to C-terminal orientation, in 9 out of 14 HLA-DP allotypes, reverse motifs are found, compatible with C- to N-terminal peptide binding. Moreover, we isolated high-avidity human cytomegalovirus (CMV)-specific HLA-DP-restricted CD4+ T cells from the memory repertoire of healthy donors and demonstrate that such T cells recognized CMV-derived peptides bound to HLA-DPB1*01:01 or *05:01 in a reverse C- to N-terminal manner. Finally, we obtained a high-resolution HLA-DPB1*01:01-CMVpp65(142-158) peptide crystal structure, which is the molecular basis for C- to N-terminal peptide binding to HLA-DP. Our results point to unique features of HLA-DP molecules that substantially broaden the HLA class II bound peptide repertoire to combat pathogens and eliminate cancer cells.PMID:36442096 | DOI:10.1073/pnas.2214331119

J Agric Food Chem. 2022 Nov 28. doi: 10.1021/acs.jafc.2c05925. Online ahead of print.ABSTRACTMicrobial action and moist-heat action are crucial factors that influence the piling fermentation (PF) of Pu-erh tea. However, their effects on the quality of Pu-erh tea remain unclear. In this study, the effects of spontaneous PF (SPPF) and sterile PF (STPF) on the chemical profile of Pu-erh tea were investigated for the first time, and sun-dried green tea was used as a raw material to determine the factors contributing to the unique quality of Pu-erh tea. The results indicated that the SPPF-processed samples had a stale and mellow taste, whereas the STPF-processed samples had a sweet and mellow taste. Through metabolomics-based analysis, 21 potential markers of microbial action (including kaempferol, quercetin, and dulcitol) and 10 potential markers of moist-heat action (including ellagic acid, β-glucogallin, and ascorbic acid) were screened among 186 differential metabolites. Correlation analysis with taste revealed that metabolites upregulated by moist-heat and microbial action were the main factors contributing to the staler mellow taste of the SPPF-processed samples and the sweeter mellow taste of the STPF-processed samples. Kaempferol, quercetin, d-glucuronic acid, and dulcitol were the main active substances formed under microbial action. This study provides new knowledge regarding the quality formation mechanism of Pu-erh tea.PMID:36441948 | DOI:10.1021/acs.jafc.2c05925