PubMed

J Exp Clin Cancer Res. 2024 Jul 29;43(1):210. doi: 10.1186/s13046-024-03135-3.ABSTRACTBACKGROUND: It has been proposed that anti-angiogenesis therapy could induce tumor "vascular normalization" and further enhance the efficacy of chemotherapy, radiotherapy, target therapy, and immunotherapy for nearly twenty years. However, the detailed molecular mechanism of this phenomenon is still obscure.METHOD: Overexpression and knockout of CCL28 in human lung adenocarcinoma cell line A549 and murine lung adenocarcinoma cell line LLC, respectively, were utilized to establish mouse models. Single-cell sequencing was performed to analyze the proportion of different cell clusters and metabolic changes in the tumor microenvironment (TME). Immunofluorescence and multiplex immunohistochemistry were conducted in murine tumor tissues and clinical biopsy samples to assess the percentage of pericytes coverage. Primary pericytes were isolated from lung adenocarcinoma tumor tissues using magnetic-activated cell sorting (MACS). These pericytes were then treated with recombinant human CCL28 protein, followed by transwell migration assays and RNA sequencing analysis. Changes in the secretome and metabolome were examined, and verification of retinoic acid metabolism alterations in pericytes was conducted using quantitative real-time PCR, western blotting, and LC-MS technology. Chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) was employed to validate the transcriptional regulatory ability and affinity of RXRα to specific sites at the ANGPT1 promoter.RESULTS: Our study showed that after undergoing anti-angiogenesis treatment, the tumor exhibited a state of ischemia and hypoxia, leading to an upregulation in the expression of CCL28 in hypoxic lung adenocarcinoma cells by the hypoxia-sensitive transcription factor CEBPB. Increased CCL28 could promote tumor vascular normalization through recruiting and metabolic reprogramming pericytes in the tumor microenvironment. Mechanistically, CCL28 modified the retinoic acid (RA) metabolism and increased ANGPT1 expression via RXRα in pericytes, thereby enhancing the stability of endothelial cells.CONCLUSION: We reported the details of the molecular mechanisms of "vascular normalization" after anti-angiogenesis therapy for the first time. Our work might provide a prospective molecular marker for guiding the clinical arrangement of combination therapy between anti-angiogenesis treatment and other therapies.PMID:39075504 | DOI:10.1186/s13046-024-03135-3

BMC Med. 2024 Jul 29;22(1):309. doi: 10.1186/s12916-024-03529-2.ABSTRACTBACKGROUND: Exposure to famine in the prenatal period is associated with an increased risk of metabolic disease, including obesity and type 2 diabetes. We employed nuclear magnetic resonance (NMR) metabolomic profiling to identify the metabolic changes that are associated with survival of prenatal famine exposure during the Dutch Famine at the end of World War II and subsequently assess their link to disease.METHODS: NMR metabolomics data were generated from serum in 480 individuals prenatally exposed to famine (mean 58.8 years, 0.5 SD) and 464 controls (mean 57.9 years, 5.4 SD). We tested associations of prenatal famine exposure with levels of 168 individual metabolic biomarkers and compared the metabolic biomarker signature of famine exposure with those of 154 common diseases.RESULTS: Prenatal famine exposure was associated with higher concentrations of branched-chain amino acids ((iso)-leucine), aromatic amino acid (tyrosine), and glucose in later life (0.2-0.3 SD, p < 3 × 10-3). The metabolic biomarker signature of prenatal famine exposure was positively correlated to that of incident type 2 diabetes from the UK Biobank (r = 0.77, p = 3 × 10-27), also when re-estimating the signature of prenatal famine exposure among individuals without diabetes (r = 0.67, p = 1 × 10-18). Remarkably, this association extended to 115 common diseases for which signatures were available (0.3 ≤ r ≤ 0.9, p < 3.2 × 10-4). Correlations among metabolic signatures of famine exposure and disease outcomes were attenuated when the famine signature was adjusted for body mass index.CONCLUSIONS: Prenatal famine exposure is associated with a metabolic biomarker signature that strongly resembles signatures of a diverse set of diseases, an observation that can in part be attributed to a shared involvement of obesity.PMID:39075494 | DOI:10.1186/s12916-024-03529-2

J Appl Toxicol. 2024 Jul 29. doi: 10.1002/jat.4680. Online ahead of print.ABSTRACTFood contaminates, such as insecticide, may influence the toxicity of nanoparticles (NPs) to intestine. The present study investigated the combined toxicity of TiO2 NPs and fipronil to male mouse intestine. Juvenile mice (8 weeks) were orally exposed to 5.74 mg/kg TiO2 NPs, 2.5 mg/kg fipronil, or both, once a day, for 5 days. We found that both TiO2 NPs and fipronil induced some pathological changes in intestines, accompanying with defective autophagy, but these effects were not obviously enhanced after TiO2 NP and fipronil co-exposure. Fipronil promoted Ti accumulation but induced minimal impact on other trace elements in TiO2 NP-exposed intestines. Metabolomics data revealed that the exposure altered metabolite profiles in mouse intestines, and two KEGG pathways, namely, ascorbate and aldarate metabolism (mmu00053) and glutathione metabolism (mmu00480), were only statistically significantly changed after TiO2 NP and fipronil co-exposure. Five metabolites, including 2-deoxy-D-erythro-pentofuranose 5-phosphate, 5alpha-cholestanol, beta-D-glucopyranuronic acid, elaidic acid, and isopentadecanoic acid, and maltotriose, were more significantly up-regulated after the co-exposure, whereas trisaccharide and xylonolactone were only significantly down-regulated by the co-exposure. We concluded that fipronil had minimal impact to enhance the toxicity of TiO2 NPs to mouse intestines but altered metabolite profiles.PMID:39075329 | DOI:10.1002/jat.4680

Sci Rep. 2024 Jul 29;14(1):17425. doi: 10.1038/s41598-024-68306-w.ABSTRACTThe analysis of the differences in metabolic profiles between naturally Ophiocordyceps sinensis (NO) and cultivated Ophiocordyceps sinensis (CO) is an essential process for the medicinal value mining of Ophiocordyceps sinensis. Non-targeted metabolomics was used to compare the differences in metabolite composition and abundance between NO and CO. Total metabolite composition found that NO is rich in organic acids and derivatives, and CO is rich in lipids and lipid-like molecules. HCA found that organooxygen compounds, cinchona alkaloid, and fatty acyls had different abundances in NO and CO. The variable importance in projection value and quantitative analysis of metabolites found that NO was rich in l-iditol, malate, linoleic acid, and oleic acid; CO is rich in sucrose, perseitol, hydroquinidine, nonanoic acid, 1-hydroxy-2-naphthoic acid, hymol-β-d-glucoside, and gly-his-lys. these compounds have the potential to be biomarkers of NO and CO. KEGG enrichment analysis showed that ascorbate and aldarate metabolism, carbon metabolism, pyrimidine metabolism, and fatty acid biosynthesis were the most different metabolic pathways between NO and CO. Therefore, the analysis of the characteristics of NO and CO metabolites has reference value for finding their different medicinal functions.PMID:39075220 | DOI:10.1038/s41598-024-68306-w

Sci Rep. 2024 Jul 29;14(1):17435. doi: 10.1038/s41598-024-68478-5.ABSTRACTAdlay millet seeds are well known for excellent health benefits. However, using fungal fermentation to improve their nutritional and functional constituents and the underlying mechanisms has not been thoroughly investigated. Herein, we used Rhizopus oryzae as starter and applied metabolomics combining with quantitative verification to understand the changes of the nutritional and functional profiles of adlay millet seeds. Results showed that a total of 718 metabolites from 18 compound classes were identified. The fermentation with R. oryzae varied 203 differential metabolites, of which 184 became more abundant and 19 got less abundant, and many components such as amino acids, nucleotides, vitamins, flavonoids, terpenoids, and phenols significantly increased after the fermentation process. Interestingly, we found that R. oryzae synthesized high levels of two important beneficial compounds, S-adenosylmethionine (SAMe) and β-Nicotinamide mononucleotide (β-NMN), with their contents increased from 0.56 to 370.26 μg/g and 0.55 to 8.32 μg/g, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of enriched metabolites revealed the amino acid metabolic pathways were important for conversion of the primary and secondary metabolites. Specifically, aspartate can up-regulate the biosynthesis of SAMe and β-NMN. These findings improved our understanding into the effects of R. oryzae fermentation on enhancing the nutritional and functional values of cereal foods.PMID:39075211 | DOI:10.1038/s41598-024-68478-5

Sci Rep. 2024 Jul 29;14(1):17423. doi: 10.1038/s41598-024-67177-5.ABSTRACTInflammation is an important factor in Alzheimer's disease (AD). An NMR measurement in plasma, glycoprotein acetyls (GlycA), captures the overall level of protein production and glycosylation implicated in systemic inflammation. With its additional advantage of reducing biological variability, GlycA might be useful in monitoring the relationship between peripheral inflammation and brain changes relevant to AD. However, the associations between GlycA and these brain changes have not been fully evaluated. Here, we performed Spearman's correlation analyses to evaluate these associations cross-sectionally and determined whether GlycA can inform AD-relevant longitudinal measurements among participants in the Alzheimer's Disease Neuroimaging Initiative (n = 1506), with additional linear models and stratification analyses to evaluate the influences of sex or diagnosis status and confirm findings from Spearman's correlation analyses. We found that GlycA was elevated in AD patients compared to cognitively normal participants. GlycA correlated negatively with multiple concurrent regional brain volumes in females diagnosed with late mild cognitive impairment (LMCI) or AD. Baseline GlycA level was associated with executive function decline at 3-9 year follow-up in participants diagnosed with LMCI at baseline, with similar but not identical trends observed in the future decline of memory and entorhinal cortex volume. Results here indicated that GlycA is an inflammatory biomarker relevant to AD pathogenesis and that the stage of LMCI might be relevant to inflammation-related intervention.PMID:39075118 | DOI:10.1038/s41598-024-67177-5

NPJ Breast Cancer. 2024 Jul 29;10(1):65. doi: 10.1038/s41523-024-00664-0.ABSTRACTTherapeutic resistance presents a significant hurdle in combating inflammatory breast cancer (IBC), adding to the complexity of its management. To investigate these mechanisms, we conducted a comprehensive analysis using transcriptomic and proteomic profiling in a preclinical model alone with correlates of treatment response in IBC patients. This included SUM149 cell lines derived from treatment-naïve patients, along with acquired drug resistance (rSUM149) and others in a state of resistance reversal (rrSUM149), aiming to uncover drug resistance networks. We identified specific ribosomal proteins associated with acquiring resistance. These correlated with elevated levels of molecular markers such as pERK, CDK1, XIAP, and SOD2. While resistance reversal in rrSUM149 cells largely normalized the expression profile, VIPER analysis revealed persistent alterations in ribosomal process-related proteins (AGO2, Exportin 1, RPL5), suggesting their continued involvement in drug resistance. Moreover, genes linked to ribosomal processes were significantly enriched (P < 0.001) among overexpressed genes in IBC patients (n = 87) who exhibited a pathological complete response (pCR) to neoadjuvant chemotherapy. Given the common hyperactivation of MAPK in IBC tumors, including rSUM149, we evaluated Merestinib, a multikinase inhibitor in clinical trials. It effectively targeted pERK and peIF4E pathways, suppressed downstream targets, induced cell death in drug-resistant rSUM149 cells, and showed synergistic effects with another tyrosine kinase inhibitor (Lapatinib) in parental cells. This underscores its significant impact on protein synthesis signaling, crucial for combating translational dependence in cancer cells. In summary, our study elucidates adaptive changes in IBC cells in response to therapy and treatment pauses, guiding precision medicine approaches for this challenging cancer type.PMID:39075068 | DOI:10.1038/s41523-024-00664-0

JCO Precis Oncol. 2024 Jul;8:e2400260. doi: 10.1200/PO.24.00260.ABSTRACTPURPOSE: Intense androgen deprivation therapy (ADT) with androgen receptor pathway inhibitors (ARPIs) before radical prostatectomy (RP) produced favorable pathologic responses in approximately 20% of patients. The molecular reason for the low rate of response remains unclear. Lipid metabolism is known to influence androgen receptor signaling and ARPI efficacy. The aim of the study was to identify circulating lipid profiles associated with ADT/ARPI resistance in localized prostate cancer.MATERIALS AND METHODS: Two independent experimental approaches were used. Experiment 1: Post hoc analysis of the association between plasma lipidomic profiles and ADT/ARPI response was performed on patients (n = 104) from two phase II trials of neoadjuvant ADT/ARPI. Response to ADT/ARPI was defined by pathologic response. Experiment 2: Patient-derived tumor explants from RP (n = 105) were cultured in enzalutamide for 48 hours. Explant response to enzalutamide was evaluated against pre-RP plasma lipidomic profiles (n = 105) and prostate tissue lipidomic profiles (n = 36). Response was defined by Ki67 (cell proliferation marker) fold difference between enzalutamide and vehicle-treated explants. In both experiments, associations between lipid profiles and ADT/ARPI response were analyzed by latent class analysis.RESULTS: Pretreatment plasma lipid profiles classified each experimental cohort into two groups with differences in ADT/ARPI response rates. The response rates of the groups were 9.6% versus 29% in experiment 1 (chi-squared test P = .012) and 49% versus 70% in experiment 2 (chi-squared test P = .037). In both experiments, the group with a higher incidence of ADT/ARPI resistance had higher plasma levels of sphingomyelin, glycosylceramides, free fatty acids, acylcarnitines, cholesterol esters, and alkyl/alkenyl-phosphatidylcholine and lower plasma levels of triacylglycerols, diacylglycerols, and phosphoethanolamine (t-test P < .05).CONCLUSION: Pretreatment circulating lipid profiles are associated with ADT/ARPI resistance in localized cancer in both human cohorts and explant models.PMID:39074346 | DOI:10.1200/PO.24.00260

J Agric Food Chem. 2024 Jul 29. doi: 10.1021/acs.jafc.4c03524. Online ahead of print.ABSTRACTA recently published untargeted metabolomics approach toward marker compounds of cocoa germination revealed and identified 12-hydroxyjasmonic acid sulfate, (+)-catechin, and (-)-epicatechin as the most downregulated compounds and two hydroxymethylglutaryl glucosides (HMG gluc) A and B, among others, as the decisive upregulated compounds in the germinated material. These findings were quantitatively evaluated using ultrahigh-performance liquid chromatography-tandem mass spectrometry not only in previously examined sample material but also in a vastly expanded array of cocoa samples of different provenience and process and in cocoa products such as cocoa liquor and chocolate. Hereby, yields of newly identified HMG gluc derivatives could be determined in raw, fermented, germinated, and alternatively processed cocoa, and isomers of HMG gluc A and B could be established as key process indicators. Based on unsupervised clustering and supervised classification, models could identify germinated samples in testing sets consisting of raw, fermented, and germinated samples.PMID:39074251 | DOI:10.1021/acs.jafc.4c03524

PLoS One. 2024 Jul 29;19(7):e0307757. doi: 10.1371/journal.pone.0307757. eCollection 2024.ABSTRACTFeline chronic enteropathies (FCE), include food-responsive-enteropathy (FRE), inflammatory bowel disease (IBD), and low-grade intestinal T-cell lymphoma (LGITL), and are common causes of chronic gastrointestinal signs in cats. Distinguishing between different subgroups of FCE can be challenging due to the frequent overlap of anamnestic, clinical, and laboratory data. While dysregulation in lipid metabolism has been reported in humans and dogs with chronic IBD, similar changes in cats are not yet completely understood. Assessing the fatty acid (FA) profile of red blood cell (RBC) membranes offers a valuable method for evaluating the quantity and quality of structural and functional molecular components in the membranes. Therefore, this study aimed to examine the FA composition of RBC membranes in FCE in comparison to healthy cats (HC). Gas-chromatography was used to quantitatively analyze a cluster of 11 FA, and based on these results, parameters of lipid homeostasis and enzyme activity indexes were calculated. A total of 41 FCE cats (17 FRE, 15 IBD, 9 LGITL) and 43 HC were enrolled. In FCE cats, the values of docosapentaenoic acid (p = 0.0002) and docosahexaenoic acid (p = 0.0246), were significantly higher, resulting in an overall increase in ω-3 polyunsaturated fatty acids (PUFA) (p = 0.006), and that of linoleic acid (p = 0.0026) was significantly lower. Additionally, FCE cats exhibited an increased PUFA balance (p = 0.0019) and Δ6-desaturase index (p = 0.0151), along with a decreased ω-6/ω-3 ratio (p = 0.0019). No differences were observed among cats affected by FRE, IBD and LGITL. Like humans and dogs, the results of this study indicate that FCE cats also display changes in their FA lipid profile at the level of the RBC membrane. The non-invasive analysis of RBC membrane shows promise as a potential tool for gaining a better understanding of lipid imbalances in this disease.PMID:39074116 | DOI:10.1371/journal.pone.0307757

Plant J. 2024 Jul 29. doi: 10.1111/tpj.16952. Online ahead of print.ABSTRACTPlant immune regulation is complex. In addition to proteins, lipid molecules play critical roles in modulating immune responses. The mutant pi4kβ1,2 is mutated in two phosphatidylinositol 4-kinases PI4Kβ1 and β2 involved in the biosynthesis of phosphatidylinositol 4-phosphate (PI4P). The mutant displays autoimmunity, short roots, aberrant root hairs, and a heightened sensitivity to ER stress. In a forward genetic screen designed to dissect pi4kβ1,2 autoimmunity, we found that Orosomucoid-like 1 (ORM1) is required for the phenotypes of pi4kβ1,2, including short root and ER stress sensitivity. The orm1 mutations lead to increased long-chain base and ceramide levels in the suppressors. We also found that the basic region/leucine Zipper motif (bZIP) 28 and 60 transcription factors, central regulators of ER stress response, are required for its autoimmunity and root defect. In comparison, the defense-related phytohormones salicylic acid (SA) and N-hydroxypipecolic acid (NHP) are required for its autoimmunity but plays a minor role in its root phenotypes. Further, we found that wild-type plants overexpressing ORM1 are autoimmune, displaying short roots and increased ceramide levels. The autoimmunity of the ORM1 overexpression lines is dependent on SA, NHP, and bZIP60. As ORM1 is a known negative regulator of sphingolipid biosynthesis, our study uncovers a balancing role between PIs and sphingolipids in regulating immunity and ER stress responses in pi4kβ1,2.PMID:39074039 | DOI:10.1111/tpj.16952

Bioinformatics. 2024 Jul 29:btae488. doi: 10.1093/bioinformatics/btae488. Online ahead of print.ABSTRACTSUMMARY: Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and extracellular substrates and products. A single tool is available to non-computational biologists to calculate extracellular fluxes, but it is hardly interoperable and is limited to a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any growth model and is interoperable by design. PhysioFit includes some of the most common growth models, and advanced users can implement additional models to calculate extracellular fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative kinetics. PhysioFit can be used as a Python library and offers a graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines.AVAILABILITY AND IMPLEMENTATION: PhysioFit v3 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/PhysioFit/ and https://physiofit.readthedocs.io/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.PMID:39073885 | DOI:10.1093/bioinformatics/btae488

Arch Dermatol Res. 2024 Jul 29;316(8):494. doi: 10.1007/s00403-024-03217-4.ABSTRACTSeveral studies have indicated a potential causal relationship between plasma standard lipids, such as high-density lipoprotein-cholesterol (HDL-C), low-density lipoprotein-cholesterol (LDL-C), triglycerides (TG), and total cholesterol (TC), and psoriasis. However, few studies have offered causal evidence of lipid species beyond these standard lipids. We conducted an analysis using a genome-wide association study (GWAS) dataset comprising 179 lipid species, including 13 types across four major categories, to identify instrumental variables (IVs) associated with plasma lipids. We utilized two GWAS datasets from the IEU and Finngen for psoriasis vulgaris as the outcome. A two-sample Mendelian randomization (MR) analysis was used to explore the causal relationship between 179 lipid species and psoriasis vulgaris in two datasets. Lipid species showing causal association in both psoriasis datasets were compared for overlap. Our study identified potential causal relationships between six lipid species and psoriasis vulgaris: phosphatidylcholine (16:1_18:2), phosphatidylcholine (18:0_18:2), phosphatidylcholine (18:1_20:4), phosphatidylethanolamine (16:0_18:2), phosphatidylinositol (18:0_20:3), and triacylglycerol (50:1). In summary, elevated plasma levels of phosphatidylcholine (16:1_18:2), phosphatidylcholine (18:0_18:2), phosphatidylethanolamine (16:0_18:2), phosphatidylinositol (18:0_20:3), and triacylglycerol (50:1) may increase the risk of psoriasis vulgaris. Conversely, plasma phosphatidylcholine (18:1_20:4) may play a protective role against psoriasis vulgaris.PMID:39073618 | DOI:10.1007/s00403-024-03217-4

Metabolomics. 2024 Jul 29;20(4):88. doi: 10.1007/s11306-024-02145-8.ABSTRACTINTRODUCTION: Food intake biomarkers are used to estimate dietary exposure; however, selecting a single biomarker to evaluate a specific dietary component is difficult due to the overlap of diverse compounds from different foods. Therefore, combining two or more biomarkers can increase the sensitivity and specificity of food intake estimates.OBJECTIVE: This study aimed to evaluate the ability of metabolite panels to distinguish between self-reported fruit consumers and non-consumers among participants in the Longitudinal Study of Adult Health.MATERIALS AND METHODS: A total of 93 healthy adults of both sexes were selected from the Longitudinal Study of Adult Health. A 24-h dietary recall was obtained using the computer-assisted 24-h food recall GloboDiet software, and 24-h urine samples were collected from each participant. Metabolites were identified in urine using liquid chromatography coupled with high-resolution mass spectrometry by comparing their exact mass and fragmentation patterns using free-access databases. Multivariate receiver operating characteristic curve (ROC) analysis and partial least squares discriminant analysis were used to verify the ability of the metabolite combination to classify daily and non-daily fruit consumers. Fruit intake was identified using a 24 h dietary recall (24 h-DR).RESULTS: Bananas, grapes, and oranges are included in the summary. The panel of biomarkers exhibited an area under the curve (AUC) > 0.6 (Orange AUC = 0.665; Grape AUC = 0.622; Bananas AUC = 0.602; All fruits AUC = 0.679; Citrus AUC = 0.693) and variable importance projection score > 1.0, and these were useful for assessing the sensitivity and predictability of food intake in our population.CONCLUSION: A panel of metabolites was able to classify self-reported fruit consumers with strong predictive power and high specificity and sensitivity values except for banana and total fruit intake.PMID:39073486 | DOI:10.1007/s11306-024-02145-8

Mol Omics. 2024 Jul 29. doi: 10.1039/d4mo00015c. Online ahead of print.ABSTRACTLiquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) untargeted metabolomics has become the gold standard for the profiling of low-molecular-weight compounds. Recently, this discipline has raised great interest in forensic sciences, especially in the field of toxicology and for post-mortem interval estimation. The current study aims at evaluating three extraction protocols and two LC-MS/MS assays run in both positive and negative modes, to identify the most suitable method to conduct post-mortem metabolomic profiling of bone tissue. A fragment of the anterior tibia of a 82 years-old male sampled from a human taphonomy facility was powdered via freeze-milling. The powdered sub-samples were extracted in five replicates per protocol. Methods tested were (I) a biphasic chloroform-methanol-water protocol, (II) a single phase methanol-water protocol, and (III) a single phase methanol-acetonitrile-water protocol. LC-MS/MS analyses were carried out via high performance liquid chromatography, either on hydrophilic interaction (HILIC) or on reversed-phase (C18) columns in both positive and negative ionisation modes, coupled with a Q-TOF mass spectrometer. Results suggest that the highest consistency between replicates and quality control samples was obtained with the single phase extractions (i.e., methanol-acetonitrile-water), whilst the ideal combination of instrumental set up HILIC chromatography in positive ionisation mode and of C18 chromatography in negative ionisation mode. For the purpose of forensic investigations, a combination of a single phase extraction and the two aforementioned chromatographic and mass spectrometry modes could represent an ideal set up for obtaining bone metabolomic profiles from taphonomically altered bones.PMID:39073399 | DOI:10.1039/d4mo00015c

Angew Chem Int Ed Engl. 2024 Jul 29:e202409220. doi: 10.1002/anie.202409220. Online ahead of print.ABSTRACTProtein homeostasis in bacteria is regulated by proteases such as the tetradecameric caseinolytic protease P (ClpP). Although substrates of ClpP have been successfully deciphered in genetically engineered cells, methods which directly trap processed proteins within native cells remain elusive. Here, we introduce an in situ trapping strategy which utilizes trifunctional probes that bind to the active site serine of ClpP and capture adjacent substrates with an attached photocrosslinking moiety. After enrichment using an alkyne handle, substrate deconvolution by mass spectrometry (MS) is performed. We show that our two traps bind substoichiometrically to ClpP, retain protease activity, exhibit unprecedented selectivity for Staphylococcus aureus ClpP in living cells and capture numerous known and novel substrates. The exemplary validation of trapped hits using a targeted proteomics approach confirmed the fidelity of this technology. In conclusion, we provide a novel chemical platform suited for the discovery of serine protease substrates beyond genetic engineering.PMID:39073273 | DOI:10.1002/anie.202409220

Parasite Immunol. 2024 Jul;46(7):e13056. doi: 10.1111/pim.13056.ABSTRACTCo-evolutionary adaptation of hookworms with their mammalian hosts has been selected for immunoregulatory excretory/secretory (E/S) products. However, it is not known whether, or if so, how host immunological status impacts the secreted profile of hematophagous adult worms. This study interrogated the impact of host Signal transducer and activator of transcription 6 (STAT6) expression during the experimental evolution of hookworms through the sequential passage of the life cycle in either STAT6 deficient or WT C57BL/6 mice. Proteomic analysis of E/S products by LC-MS showed increased abundance of 15 proteins, including myosin-3, related to muscle function, and aconitate hydratase, related to iron homeostasis. However, most E/S proteins (174 of 337 unique identities) were decreased, including those in the Ancylostoma-secreted protein (ASP) category, and metallopeptidases. Several identified proteins are established immune-modulators such as fatty acid-binding protein homologue, cystatin, and acetylcholinesterase. Enrichment analysis of InterPro functional categories showed down-regulation of Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 proteins (CAP), Astacin-like metallopeptidase, Glycoside hydrolase, and Transthyretin-like protein groups in STAT6 KO-adapted worms. Taken together, these data indicate that in an environment lacking Type 2 immunity, hookworms alter their secretome by reducing immune evasion proteins- and increasing locomotor- and feeding-associated proteins.PMID:39073185 | DOI:10.1111/pim.13056

CNS Neurosci Ther. 2024 Jul;30(7):e14887. doi: 10.1111/cns.14887.ABSTRACTAIMS: Neuroinflammation is a recognized contributor to cognitive disorders like Alzheimer's disease, with ferroptosis emerging as a novel mechanism underlying cognitive dysfunction associated with neuroinflammation. Insulin, pivotal in the central nervous system, holds promise for cognitive function enhancement. This study aimed to establish a cognitive impairment model through intracerebroventricular injection of lipopolysaccharide (LPS) and explore the impact of intracerebroventricular insulin injection on cognitive function in mice.METHODS: We employed diverse experimental techniques, including animal behavior testing, molecular assays, targeted metabolomics, nuclear medicine, and electron microscopy, to assess neurodegenerative changes, brain insulin resistance (IR), glucose uptake and metabolism, and ferroptosis. The model of cognitive impairment was induced via intracerebroventricular injection of LPS, followed by intracerebroventricular administration of insulin to evaluate its effects.RESULTS: Insulin treatment effectively mitigated LPS-induced cognitive decline and safeguarded against neuronal degeneration. Furthermore, insulin alleviated LPS-induced insulin resistance, enhanced glucose uptake in the hippocampus, and promoted the Pentose Phosphate Pathway (PPP) and nicotinamide adenine dinucleotide phosphate (NADPH) production. Additionally, insulin activated the glutathione (GSH)-glutathione peroxidase 4 (GPX4) pathway, reducing lipid peroxidation, and mitochondrial damage characteristic of LPS-induced ferroptosis in the hippocampus.CONCLUSION: Our findings underscore the therapeutic potential of insulin in alleviating LPS-induced cognitive impairment and ferroptosis by modulating glucose metabolism. This study offers a promising avenue for future interventions targeting cognitive decline.PMID:39073013 | DOI:10.1111/cns.14887

Phytochem Anal. 2024 Jul 28. doi: 10.1002/pca.3428. Online ahead of print.ABSTRACTINTRODUCTION: Stemona tuberosa Lour. (ST) is a significant traditional Chinese medicine (TCM) renowned for its antitussive and insecticidal properties. ST is commonly subjected to processing in clinical practice before being utilized as a medicinal substance. Currently, the customary technique for processing ST is honey-fried. Nevertheless, the specific variations in chemical constituents of ST before and after honey-fried remain unclear.OBJECTIVE: This work aimed to analyze the variations in chemical constituents of ST before and after honey-fried and to study the distribution of differential markers in the roots.METHODS: UPLC-Orbitrap Fusion MS combined with molecular network analysis was used to analyze the metabolome of ST and honey-fried ST (HST) and to screen the differential metabolites by multivariate statistical analysis. Spatial metabolomics was applied to study the distribution of differential metabolites by desorption electrospray ionization mass spectrometry imaging (DESI-MSI).RESULTS: The ST and HST exhibited notable disparities, with 56 and 61 chemical constituents found from each, respectively. After processing, the types of alkaloids decreased, and 12 differential metabolites were screened from the common compounds. The notable component variations were epibisdehydro-tuberostemonine J, neostenine, tuberostemonine, croomine, neotuberostemonine, and so forth. MSI visualized the spatial distribution of differential metabolites.CONCLUSIONS: Our research provided a rapid and effective visualization method for the identification and spatial distribution of metabolites in ST. Compared with the traditional method, this method offered more convincing data supporting the processing mechanism investigations of Stemona tuberosa from a macroscopic perspective.PMID:39072901 | DOI:10.1002/pca.3428

Eur J Neurosci. 2024 Jul 28. doi: 10.1111/ejn.16482. Online ahead of print.ABSTRACTBoth clinical diagnosis and neuropathological diagnosis are commonly used in literature to categorize individuals as Alzheimer's disease (AD) or non-AD in omics analyses. Whether these diagnostic strategies result in distinct profiles of molecular abnormalities is poorly understood. Here, we analysed one of the most commonly used AD omics datasets in the literature from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort and compared the two diagnosis strategies using brain transcriptome and metabolome by grouping individuals as non-AD and AD according to clinical or neuropathological diagnosis separately. Differentially expressed genes, associated pathways related with AD hallmarks and AD-related genes showed that the categorization based on neuropathological diagnosis more accurately reflects the disease state at the molecular level than the categorization based on clinical diagnosis. We further identified consensus biomarker candidates between the two diagnosis strategies such as 5-hydroxylysine, sphingomyelin and 1-myristoyl-2-palmitoyl-GPC as metabolite biomarkers and sphingolipid metabolism as a pathway biomarker, which could be robust AD biomarkers since they are independent of diagnosis strategies. We also used consensus AD and consensus non-AD individuals between the two diagnostic strategies to train a machine-learning based model, which we used to classify the individuals who were cognitively normal but diagnosed as AD based on neuropathological diagnosis (asymptomatic AD individuals). The majority of these individuals were classified as consensus AD patients for both omics data types. Our study provides a detailed characterization of both diagnostic strategies in terms of the association of the corresponding multi-omics profiles with AD.PMID:39072881 | DOI:10.1111/ejn.16482