PubMed

Front Plant Sci. 2024 Apr 24;15:1355832. doi: 10.3389/fpls.2024.1355832. eCollection 2024.ABSTRACTLycium barbarum L., commonly known as wolfberry, is not only a traditional Chinese medicine but also a highly nutritious food. Its main nutrients include L. barbarum polysaccharide, flavonoid polyphenols, carotenoids, alkaloids, and other compounds, demonstrating its wide application value. This study investigated the effects of nitrogen application on the accumulation of the main nutrients and metabolites in wolfberry fruits under three different nitrogen application rates, namely, N1 (20% nitrogen (N) reduction, 540 kg·ha-2), N2 (medium N, 675 kg·ha-2), and N3 (20% nitrogen increase, 810 kg·ha-2,which is a local conventional nitrogen application amount.). Additionally, due to continuous branching, blossoming, and fruiting of wolfberry plants during the annual growth period, this research also explored the variation in nutritional composition among different harvesting batches. The contents of total sugar and polysaccharide in wolfberry fruit were determined by Fehling reagent method and phenol-sulfuric acid method, respectively;The content of betaine in fruit was determined by high-performance liquid chromatography,and the flavonoids and carotene in the wolfberry fruits were determined by spectrophotometry. Analysis of data over three consecutive years revealed that as nitrogen application increased, the total sugar content in wolfberry fruits initially decreased and then increased. The levels of L. barbarum polysaccharides, total flavonoids, and total carotenoids initially increased and then decreased, while the betaine content consistently increased. Different picking batches significantly impacted the nutrient content of wolfberry fruits. Generally, the first batch of summer wolfberry fruits had greater amounts of total sugar and flavonoids, whereas other nutrients peaked in the third batch. By employing a broadly targeted metabolomics approach, 926 different metabolites were identified. The top 20 differentially abundant metabolites were selected for heatmap generation, revealing that the contents of L-citrulline, 2-methylglutaric acid, and adipic acid increased proportionally to the nitrogen gradient. Conversely, the dibutyl phthalate and 2, 4-dihydroxyquinoline contents significantly decreased under high-nitrogen conditions. The remaining 15 differentially abundant metabolites, kaempferol-3-O-sophorosid-7-O-rhamnoside, trigonelline, and isorhamnosid-3-O-sophoroside, initially increased and then decreased with increasing nitrogen levels. Isofraxidin, a common differentially abundant metabolite across all treatments, is a coumarin that may serve as a potential biomarker for wolfberry fruit response to nitrogen. Differentially abundant metabolites were analyzed for GO pathway involvement, revealing significant enrichment in metabolic pathways and biosynthesis of secondary metabolites under different nitrogen treatments. In conclusion, a nitrogen application of 675 kg·ha-2, 20% less than the local farmers' actual application, was most beneficial for the quality of four-year-old Ningqi 7 wolfberry fruits. Consumers who purchase wolfberry-dried fruit for health benefits should not consider only the first batch of summer wolfberry fruits. These results offer a broader perspective for enhancing the quality and efficiency of the wolfberry industry.PMID:38721340 | PMC:PMC11076786 | DOI:10.3389/fpls.2024.1355832

Front Vet Sci. 2024 Apr 24;11:1340849. doi: 10.3389/fvets.2024.1340849. eCollection 2024.ABSTRACTINTRODUCTION: Pigs are often used to study the intestinal development of newborns, particularly as preterm pig models that mimic the intestinal growth of human preterm infants. Neonatology's study of delivery mode's impact on neonatal development is crucial.METHODS: We established 14 newborn pigs delivered via cesarean sections (C-section, at 113 days of gestational age, CS group) and 8 naturally born pigs were used as controls (at 114 days of gestational age, NF group). The impact of two alternative delivery procedures (C-section and natural birth) on the levels of short-chain fatty acids (SCFAs) and organic acids in the hepatic and intestines of newborn pigs were compared using metabolomics. The underlying molecular pathways are examined at the "protein-metabolite" level by integrating proteomic data.RESULTS: The findings demonstrated that the mode of delivery changed the metabolism of SCFAs in newborn pigs, perhaps by affecting the physiology levels of cyclic intermediates such as lactate and malate in the pyruvate metabolic pathway. Additionally, by participating in the fatty acid metabolism pathway, two distinct proteins (FASN and HSD17B4) may impact the physiological concentration of these tiny metabolites.DISCUSSION: In conclusion, this study provided reliable animal model data for understanding the physiological SCFA metabolic information and its affecting mechanism of large-gestational age preterm infants.PMID:38721154 | PMC:PMC11076856 | DOI:10.3389/fvets.2024.1340849

Front Nutr. 2024 Apr 24;11:1371995. doi: 10.3389/fnut.2024.1371995. eCollection 2024.ABSTRACTBACKGROUND: Chronic kidney disease (CKD) is a common public health problem, which is characterized as impairment of renal function. The associations between blood metabolites and renal function remained unclear. This study aimed to assess the causal effect of various circulation metabolites on renal function based on metabolomics.METHODS: We performed a two-sample Mendelian randomization (MR) analysis to estimate the causality of genetically determined metabolites on renal function. A genome-wide association study (GWAS) of 486 metabolites was used as the exposure, while summary-level data for creatinine-based estimated glomerular filtration rate (eGFR) or CKD occurrence were set the outcomes. Inverse variance weighted (IVW) was used for primary causality analysis and other methods including weight median, MR-egger, and MR-PRESSO were applied as complementary analysis. Cochran Q test, MR-Egger intercept test, MR-PRESSO global test and leave-one-out analysis were used for sensitivity analysis. For the identified metabolites, reverse MR analysis, linkage disequilibrium score (LDSC) regression and multivariable MR (MVMR) analysis were performed for further evaluation. The causality of the identified metabolites on renal function was further validated using GWAS data for cystatin-C-based eGFR. All statistical analyses were performed in R software.RESULTS: In this MR analysis, a total of 44 suggestive associations corresponding to 34 known metabolites were observed. After complementary analysis and sensitivity analysis, robust causative associations between two metabolites (betaine and N-acetylornithine) and renal function were identified. Reverse MR analysis showed no causal effects of renal function on betaine and N-acetylornithine. MVMR analysis revealed that genetically predicted betaine and N-acetylornithine could directly influence independently of each other. The causal effects of betaine and N-acetylornithine were also found on cystatin-C-based eGFR.CONCLUSION: Our study provided evidence to support the causal effects of betaine and N-acetylornithine on renal function. These findings required further investigations to conduct mechanism exploration and drug target selection of these identified metabolites.PMID:38721027 | PMC:PMC11078220 | DOI:10.3389/fnut.2024.1371995

Front Pharmacol. 2024 Apr 24;15:1343755. doi: 10.3389/fphar.2024.1343755. eCollection 2024.ABSTRACTPurpose: The prevalence of non-alcoholic fatty liver disease (NAFLD) and its related mortality is increasing at an unprecedented rate. Traditional Chinese medicine (TCM) has been shown to offer potential for early prevention and treatment of NAFLD. The new mechanism of "Shenling Baizhu San" (SLBZS) is examined in this study for the prevention and treatment of NAFLD at the preclinical level. Methods: Male C57BL/6J mice were randomly divided into three groups: normal diet (ND), western diet + CCl4 injection (WDC), and SLBZS intervention (WDC + SLBZS). Body weights, energy intake, liver enzymes, pro-inflammatory factors, and steatosis were recorded in detail. Meanwhile, TPH1, 5-HT, HTR2A, and HTR2B were tested using qRT-PCR or ELISA. Dynamic changes in the gut microbiota and metabolites were further detected through the 16S rRNA gene and untargeted metabolomics. Results: SLBZS intervention for 6 weeks could reduce the serum and liver lipid profiles, glucose, and pro-inflammatory factors while improving insulin resistance and liver function indexes in the mice, thus alleviating NAFLD in mice. More importantly, significant changes were found in the intestinal TPH-1, 5-HT, liver 5-HT, and related receptors HTR2A and HTR2B. The 16S rRNA gene analysis suggested that SLBZS was able to modulate the disturbance of gut microbiota, remarkably increasing the relative abundance of probiotics (Bifidobacterium and Parvibacter) and inhibiting the growth of pro-inflammatory bacteria (Erysipelatoclostridium and Lachnoclostridium) in mice with NAFLD. Combined with metabolomics in positive- and negative-ion-mode analyses, approximately 50 common differential metabolites were selected via non-targeted metabolomics detection, which indicated that the targeting effect of SLBZS included lipid metabolites, bile acids (BAs), amino acids (AAs), and tryptophan metabolites. In particular, the lipid metabolites 15-OxEDE, vitamin D3, desoxycortone, and oleoyl ethanol amide were restored by SLBZS. Conclusion: Integrating the above results of multiple omics suggests that SLBZS ameliorates NAFLD via specific gut microbiota, gut-derived 5-HT, and related metabolites to decrease fat accumulation in the liver and inflammatory responses.PMID:38720776 | PMC:PMC11076757 | DOI:10.3389/fphar.2024.1343755

Heliyon. 2024 Apr 27;10(9):e30452. doi: 10.1016/j.heliyon.2024.e30452. eCollection 2024 May 15.ABSTRACTParkinson's disease (PD) is a prevalent neurodegenerative disorder with a poorly understood etiology. An accurate diagnosis of idiopathic PD remains challenging as misdiagnosis is common in routine clinical practice. Moreover, current therapeutics focus on symptomatic management rather than curing or slowing down disease progression. Therefore, identification of potential PD biomarkers and providing a better understanding of the underlying disease pathophysiology are urgent. Herein, hydrophilic interaction liquid chromatography-mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-TOF MS) based metabolomics approaches were used to profile the serum metabolome of 50 patients with different stages of idiopathic PD (early, mid and advanced) and 45 age-matched controls. Levels of 57 metabolites including cysteine-S-sulfate and N-acetyl tryptophan were significantly higher in patients with PD compared to controls, with lower amounts of additional 51 metabolites including vanillic acid, and N-acetylaspartic acid. Xanthines, including caffeine and its downstream metabolites, were lowered in patients with PD relative to controls indicating a potential role caffeine and its metabolites against neuronal damage. Seven metabolites, namely cysteine-S-sulfate, 1-methylxanthine, vanillic acid, N-acetylaspartic acid, 3-N-acetyl tryptophan, 5-methoxytryptophol, and 13-HODE yielded a ROC curve with a high classification accuracy (AUC 0.977). Comparison between different PD stages showed that cysteine-S-sulfate levels were significantly increasing with the advancement of PD stages while LPI 20:4 was significantly decreasing with disease progression. Our findings provide new biomarker candidates to assist in the diagnosis of PD and monitor its progression. Unusual metabolites like cysteine-S-sulfate might point to therapeutic targets that could enhance the development of novel PD treatments, such as NMDA antagonists.PMID:38720721 | PMC:PMC11077040 | DOI:10.1016/j.heliyon.2024.e30452

J Anim Sci. 2024 May 9:skae126. doi: 10.1093/jas/skae126. Online ahead of print.ABSTRACTInfertility or subfertility impacts approximately 5% and 15% of dairy and beef heifers (Bos taurus), respectively. Heifers that do not produce a calf within an optimum window of time have a significant negative impact on the profitability and sustainability of the cattle industry. Selection of heifers based on their fertility potential remains a challenge yet to be resolved. Here, we tested the hypothesis that heifers of different fertility potential have differing metabolome signatures in their plasma. We obtained blood from Bos taurus heifers at their first artificial insemination and processed the samples to separate the plasma. The heifers were classified based on their reproductive outcome as fertile (pregnant and delivered a calf after their first artificial insemination (AI)) or sub-fertile (Angus heifers: no pregnancy after two AI and exposure to a bull; Holstein heifers: no pregnancy by the third AI). We tested the relative abundance of 140 metabolites obtained from 22 heifers (Angus fertile n = 5, Angus sub-fertile n = 7, Holstein fertile N = 5, Holstein sub-fertile N = 5). The metabolite 2-Dehydro-D-gluconate (C6H10O7) was significantly more abundant in the plasma of sub-fertile heifers in both breeds (1.4-fold, false discovery rate <0.1). In the context that a small proportion of circulating metabolites in the plasma were quantified in this study, the results show that the metabolomic profile in the blood stream may be associated with heifer fertility potential.PMID:38720650 | DOI:10.1093/jas/skae126

BMC Gastroenterol. 2024 May 8;24(1):158. doi: 10.1186/s12876-024-03246-3.ABSTRACTBACKGROUND: Primary sclerosing cholangitis (PSC) is a complex disease with pathogenic mechanisms that remain to be elucidated. Previous observational studies with small sample sizes have reported associations between PSC, dyslipidemia, and gut microbiota dysbiosis. However, the causality of these associations is uncertain, and there has been no systematic analysis to date.METHODS: The datasets comprise data on PSC, 179 lipid species, and 412 gut microbiota species. PSC data (n = 14,890) were sourced from the International PSC Study Group, while the dataset pertaining to plasma lipidomics originated from a study involving 7174 Finnish individuals. Data on gut microbiota species were derived from the Dutch Microbiome Project study, which conducted a genome-wide association study involving 7738 participants. Furthermore, we employed a two-step Mendelian randomization (MR) analysis to quantify the proportion of the effect of gut microbiota-mediated lipidomics on PSC.RESULTS: Following a rigorous screening process, our MR analysis revealed a causal relationship between higher levels of gene-predicted Phosphatidylcholine (O-16:1_18:1) (PC O-16:1_18:1) and an increased risk of developing PSC (inverse variance-weighted method, odds ratio (OR) 1.30, 95% confidence interval (CI) 1.03-1.63). There is insufficient evidence to suggest that gene-predicted PSC impacts the levels of PC O-16:1_18:1 (OR 1.01, 95% CI 0.98-1.05). When incorporating gut microbiota data into the analysis, we found that Eubacterium rectale-mediated genetic prediction explains 17.59% of the variance in PC O-16:1_18:1 levels.CONCLUSION: Our study revealed a causal association between PC O-16:1_18:1 levels and PSC, with a minor portion of the effect mediated by Eubacterium rectale. This study aims to further explore the pathogenesis of PSC and identify promising therapeutic targets. For patients with PSC who lack effective treatment options, the results are encouraging.PMID:38720308 | DOI:10.1186/s12876-024-03246-3

BMC Genomics. 2024 May 8;25(1):454. doi: 10.1186/s12864-024-10357-4.ABSTRACTBACKGROUND: In response to seasonal cold and food shortage, the Xizang plateau frogs, Nanorana parkeri (Anura: Dicroglossidae), enter a reversible hypometabolic state where heart rate and oxygen consumption in skeletal muscle are strongly suppressed. However, the effect of winter hibernation on gene expression and metabolic profiling in these two tissues remains unknown. In the present study, we conducted transcriptomic and metabolomic analyses of heart and skeletal muscle from summer- and winter-collected N. parkeri to explore mechanisms involved in seasonal hibernation.RESULTS: We identified 2407 differentially expressed genes (DEGs) in heart and 2938 DEGs in skeletal muscle. Enrichment analysis showed that shared DEGs in both tissues were enriched mainly in translation and metabolic processes. Of these, the expression of genes functionally categorized as "response to stress", "defense mechanisms", or "muscle contraction" were particularly associated with hibernation. Metabolomic analysis identified 24 and 22 differentially expressed metabolites (DEMs) in myocardium and skeletal muscle, respectively. In particular, pathway analysis showed that DEMs in myocardium were involved in the pentose phosphate pathway, glycerolipid metabolism, pyruvate metabolism, citrate cycle (TCA cycle), and glycolysis/gluconeogenesis. By contrast, DEMs in skeletal muscle were mainly involved in amino acid metabolism.CONCLUSIONS: In summary, natural adaptations of myocardium and skeletal muscle in hibernating N. parkeri involved transcriptional alterations in translation, stress response, protective mechanisms, and muscle contraction processes as well as metabolic remodeling. This study provides new insights into the transcriptional and metabolic adjustments that aid winter survival of high-altitude frogs N. parkeri.PMID:38720264 | DOI:10.1186/s12864-024-10357-4

BMC Plant Biol. 2024 May 8;24(1):380. doi: 10.1186/s12870-024-05101-9.ABSTRACTBACKGROUND: Soybean (Glycine max), a vital grain and oilseed crop, serves as a primary source of plant protein and oil. Soil salinization poses a significant threat to soybean planting, highlighting the urgency to improve soybean resilience and adaptability to saline stress. Melatonin, recently identified as a key plant growth regulator, plays crucial roles in plant growth, development, and responses to environmental stress. However, the potential of melatonin to mitigate alkali stress in soybeans and the underlying mechanisms remain unclear.RESULTS: This study investigated the effects of exogenous melatonin on the soybean cultivar Zhonghuang 13 under alkaline stress. We employed physiological, biochemical, transcriptomic, and metabolomic analyses throughout both vegetative and pod-filling growth stages. Our findings demonstrate that melatonin significantly counteracts the detrimental effects of alkaline stress on soybean plants, promoting plant growth, photosynthesis, and antioxidant capacity. Transcriptomic analysis during both growth stages under alkaline stress, with and without melatonin treatment, identified 2,834 and 549 differentially expressed genes, respectively. These genes may play a vital role in regulating plant adaptation to abiotic stress. Notably, analysis of phytohormone biosynthesis pathways revealed altered expression of key genes, particularly in the ARF (auxin response factor), AUX/IAA (auxin/indole-3-acetic acid), and GH3 (Gretchen Hagen 3) families, during the early stress response. Metabolomic analysis during the pod-filling stage identified highly expressed metabolites responding to melatonin application, such as uteolin-7-O-(2''-O-rhamnosyl)rutinoside and Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside, which helped alleviate the damage caused by alkali stress. Furthermore, we identified 183 differentially expressed transcription factors, potentially playing a critical role in regulating plant adaptation to abiotic stress. Among these, the gene SoyZH13_04G073701 is particularly noteworthy as it regulates the key differentially expressed metabolite, the terpene metabolite Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside. WGCNA analysis identified this gene (SoyZH13_04G073701) as a hub gene, positively regulating the crucial differentially expressed metabolite of terpenoids, Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside. Our findings provide novel insights into how exogenous melatonin alleviates alkali stress in soybeans at different reproductive stages.CONCLUSIONS: Integrating transcriptomic and metabolomic approaches, our study elucidates the mechanisms by which exogenous melatonin ameliorates the inhibitory effects of alkaline stress on soybean growth and development. This occurs through modulation of biosynthesis pathways for key compounds, including terpenes, flavonoids, and phenolics. Our findings provide initial mechanistic insights into how melatonin mitigates alkaline stress in soybeans, offering a foundation for molecular breeding strategies to enhance salt-alkali tolerance in this crop.PMID:38720246 | DOI:10.1186/s12870-024-05101-9

Sci Rep. 2024 May 8;14(1):10546. doi: 10.1038/s41598-024-61067-6.ABSTRACTRadioiodine refractory (RAIR) patients do not benefit from iodine-131 therapy. Thus, timely identification of RAIR patients is critical for avoiding ineffective radioactive iodine therapy. In addition, determining the causes of iodine resistance will facilitate the development of novel treatment strategies. This study was comprised of 20 RAIR and 14 non-radioiodine refractory (non-RAIR) thyroid cancer patients. Liquid chromatography-mass spectrometry was used to identify differences in the serum metabolites of RAIR and non-RAIR patients. In addition, chemical assays were performed to determine the effects of the differential metabolites on iodine uptake. Metabolic pathway enrichment analysis of the differential metabolites revealed significant differences in the phenylalanine and tyrosine metabolic pathways. Notably, quinate and shikimic acid, metabolites of the tyrosine pathway, were significantly increased in the RAIR group. In contrast, the phenylalanine pathway metabolites, hippuric acid and 2-phenylacetamide, were markedly decreased in the RAIR group. Thyroid peroxidase plays an important role in catalyzing the iodination of tyrosine residues, while the ionic state of iodine promotes the iodination reaction. Quinate, shikimic acid, hippuric acid, and 2-phenylacetamide were found to be involved in the iodination of tyrosine, which is a key step in thyroid hormone synthesis. Specifically, quinate and shikimic acid were found to inhibit iodination, while hippuric acid and 2-phenylacetamide promoted iodination. Abnormalities in phenylalanine and tyrosine metabolic pathways are closely associated with iodine resistance. Tyrosine is required for thyroid hormone synthesis and could be a potential cause of iodine resistance.PMID:38719979 | DOI:10.1038/s41598-024-61067-6

Cell Death Differ. 2024 May 8. doi: 10.1038/s41418-024-01303-8. Online ahead of print.ABSTRACTNeuronal ferroptosis plays a key role in neurologic deficits post intracerebral hemorrhage (ICH). However, the endogenous regulation of rescuing ferroptotic neurons is largely unexplored. Here, we analyzed the integrated alteration of metabolomic landscape after ICH using LC-MS and MALDI-TOF/TOF MS, and demonstrated that aconitate decarboxylase 1 (Irg1) and its product itaconate, a derivative of the tricarboxylic acid cycle, were protectively upregulated. Deficiency of Irg1 or depletion of neuronal Irg1 in striatal neurons was shown to exaggerate neuronal loss and behavioral dysfunction in an ICH mouse model using transgenic mice. Administration of 4-Octyl itaconate (4-OI), a cell-permeable itaconate derivative, and neuronal Irg1 overexpression protected neurons in vivo. In addition, itaconate inhibited ferroptosis in cortical neurons derived from mouse and human induced pluripotent stem cells in vitro. Mechanistically, we demonstrated that itaconate alkylated glutathione peroxidase 4 (GPx4) on its cysteine 66 and the modification allosterically enhanced GPx4's enzymatic activity by using a bioorthogonal probe, itaconate-alkyne (ITalk), and a GPx4 activity assay using phosphatidylcholine hydroperoxide. Altogether, our research suggested that Irg1/itaconate-GPx4 axis may be a future therapeutic strategy for protecting neurons from ferroptosis post ICH.PMID:38719928 | DOI:10.1038/s41418-024-01303-8

Genome Res. 2024 May 7. doi: 10.1101/gr.278684.123. Online ahead of print.ABSTRACTOmics methods are widely used in basic biology and translational medicine research. More and more omics data are collected to explain the impact of certain risk factors on clinical outcomes. To explain the mechanism of the risk factors, a core question is how to find the genes/proteins/metabolites that mediate their effects on the clinical outcome. Mediation analysis is a modeling framework to study the relationship between risk factors and pathological outcomes, via mediator variables. However, high-dimensional omics data are far more challenging than traditional data: (1) From tens of thousands of genes, can we overcome the curse of dimensionality to reliably select a set of mediators? (2) How do we ensure that the selected mediators are functionally consistent? (3) Many biological mechanisms contain nonlinear effects. How do we include nonlinear effects in the high-dimensional mediation analysis? (4) How do we consider multiple risk factors at the same time? To meet these challenges, we propose a new exploratory mediation analysis framework, medNet, which focuses on finding mediators through predictive modeling. We propose new definitions for predictive exposure, predictive mediator, and predictive network mediator, using a statistical hypothesis testing framework to identify predictive exposures and mediators. Additionally, two heuristic search algorithms are proposed to identify network mediators, essentially subnetworks in the genome-scale biological network that mediate the effects of single or multiple exposures. We applied medNet on a breast cancer data set and a metabolomics data set combined with food intake questionnaire data. It identified functionally consistent network mediators for the exposures' impact on the outcome, facilitating data interpretation.PMID:38719472 | DOI:10.1101/gr.278684.123

Anal Chim Acta. 2024 Jun 8;1307:342574. doi: 10.1016/j.aca.2024.342574. Epub 2024 Apr 13.ABSTRACTBACKGROUND: Metabolomics is nowadays considered one the most powerful analytical for the discovery of metabolic dysregulations associated with the insurgence of cancer, given the reprogramming of the cell metabolism to meet the bioenergetic and biosynthetic demands of the malignant cell. Notwithstanding, several challenges still exist regarding quality control, method standardization, data processing, and compound identification. Therefore, there is a need for effective and straightforward approaches for the untargeted analysis of structurally related classes of compounds, such as acylcarnitines, that have been widely investigated in prostate cancer research for their role in energy metabolism and transport and β-oxidation of fatty acids.RESULTS: In the present study, an innovative analytical platform was developed for the straightforward albeit comprehensive characterization of acylcarnitines based on high-resolution mass spectrometry, Kendrick mass defect filtering, and confirmation by prediction of their retention time in reversed-phase chromatography. In particular, a customized data processing workflow was set up on Compound Discoverer software to enable the Kendrick mass defect filtering, which allowed filtering out more than 90 % of the initial features resulting from the processing of 25 tumoral and adjacent non-malignant prostate tissues collected from patients undergoing radical prostatectomy. Later, a partial least square-discriminant analysis model validated by repeated double cross-validation was built on the dataset of 74 annotated acylcarnitines, with classification rates higher than 93 % for both groups, and univariate statistical analysis helped elucidate the individual role of the annotated metabolites.SIGNIFICANCE: Hydroxylation of short- and medium-chain minor acylcarnitines appeared to be a significant variable in describing tissue differences, suggesting the hypothesis that the neoplastic growth is linked to oxidation phenomena on selected metabolites and reinforcing the need for effective methods for the annotation of minor metabolites.PMID:38719419 | DOI:10.1016/j.aca.2024.342574

Br J Haematol. 2024 May 8. doi: 10.1111/bjh.19514. Online ahead of print.ABSTRACTImmune thrombocytopenia (ITP) is a highly heterogeneous autoimmune bleeding disorder characterized by low platelet counts due to an immune-mediated platelet destruction and impaired platelet production. The pathophysiology is multifactorial and remains to be fully unravelled. Consequently, disease trajectories and responses to therapeutics, despite the availability of multiple agents, can be unpredictable and differing between patients. There is an urgent need for the identification of diagnostic and therapeutic biomarkers, but this has proven to be challenging to achieve. To shed light on this, two studies in this issue of the British Journal of Haematology have recognized the opportunity of using high-throughput Omics technologies in ITP. Sun et al. performed proteomics, and Li et al. metabolomics, on bone marrow biopsy samples of patients with ITP. This was conducted using mass spectrometry and, due to the generation of large datasets, in combination with machine learning. These studies set the stage for further investigations exploring the high potential of multi-omics technologies in order to shed light on the heterogeneity in ITP, accelerating the path towards a much needed personalized medicine approach. Commentary on: Li et al. Metabolomics profile and machine learning prediction of treatment responses in immune thrombocytopenia: A prospective cohort study. Br J Haematol 2024 (Online ahead of print). doi: 10.1111/bjh.19391 Commentary on: Sun et al. Proteomics landscape and machine learning prediction of long-term response to splenectomy in primary immune thrombocytopenia. Br J Haematol 2024 (Online ahead of print). doi: 10.1111/bjh.19420.PMID:38719342 | DOI:10.1111/bjh.19514

J Lipid Res. 2024 May 6:100555. doi: 10.1016/j.jlr.2024.100555. Online ahead of print.ABSTRACTCYP46A1 is the CNS-specific cholesterol 24-hydroxylase that controls cholesterol elimination and turnover in the brain. In mouse models, pharmacologic CYP46A1 activation with low dose efavirenz (EFV) or by gene therapy mitigates the manifestations of various brain disorders, neurologic and non-neurologic, by affecting numerous, apparently unliked biological processes. Accordingly, CYP46A1 is emerging as a promising therapeutic target; however, the mechanisms underlying the multiplicity of the brain CYP46A1 activity effects are currently not understood. We proposed the chain reaction hypothesis, according to which CYP46A1 is important for the three primary (unifying) processes in the brain (sterol flux through the plasma membranes, acetyl-CoA and isoprenoid production), which in turn affect a variety of secondary processes. We already identified several processes secondary to changes in sterol flux and herein undertook a multiomics approach to compare the brain proteome, acetylproteome, and metabolome of 5XFAD mice (an Alzheimer's disease model), control and treated with low dose EFV. We found that the latter had increased production of phospholipids from the corresponding lysophospholipids and a globally increased protein acetylation (including histone acetylation). Apparently, these effects were secondary to increased acetyl-CoA production. Signaling of small GTPases due to their altered abundance or abundance of their regulators could be affected as well, potentially via isoprenoid biosynthesis. In addition, the omics data related differentially abundant molecules to other biological processes either reported previously or new. Thus, we obtained unbiased mechanistic insights and identified potential players mediating the multiplicity of the CYP46A1 brain effects and further detailed our chain reaction hypothesis.PMID:38719151 | DOI:10.1016/j.jlr.2024.100555

Fish Shellfish Immunol. 2024 May 6:109607. doi: 10.1016/j.fsi.2024.109607. Online ahead of print.ABSTRACTThe aim of this study was to investigate the effects of quercetin (QUE) on alleviating the negative effects of high soybean meal diet for spotted sea bass Lateolabrax maculatus. A healthy control group fed a 44% fishmeal diet was used, while the induction control group replaced 50% fishmeal with soybean meal. Subsequently, QUE was added at concentrations of 0.25, 0.50, 0.75, and 1.00 g/kg in the experimental groups. A total of 540 tailed spotted sea bass were randomly divided into 6 groups and fed the corresponding diet for 56 days. The results showed that 40% soybean meal significantly decreased the growth performance and immunity, increased the intestinal mucosal permeability, and caused damage to the intestinal tissue morphology; moreover, there were alterations observed in the composition of the intestinal microbiota, accompanied by detectable levels of saponins in the metabolites. However, the addition of QUE did not yield significant changes in growth performance; instead, it notably reduced the permeability of the intestinal mucosa, improved the body's immunity and the structural integrity of the intestinal tissue, increased the proportion of Proteobacteria, and enhanced the richness and diversity of intestinal microorganisms to a certain extent. In addition, QUE up-regulate the metabolism of amino acids and their derivatives and energy-related metabolites such as uridine and guanosine; furthermore, it appears to regulate transporters through the ABC transporters pathway to promote the absorption and utilization of QUE by enterocytes.PMID:38719096 | DOI:10.1016/j.fsi.2024.109607

Sci Total Environ. 2024 May 6:172892. doi: 10.1016/j.scitotenv.2024.172892. Online ahead of print.ABSTRACTOrganophosphate esters (OPEs) have been demonstrated to induce various forms of toxicity in aquatic organisms. However, a scarcity of evidence impedes the conclusive determination of whether OPEs manifest sex-dependent toxic effects. Here, we investigated the effects of tris (1-chloro-2-propyl) phosphate (TCPP) and resorcinol bis (diphenyl phosphate) (RDP) on the intestines of both female and male zebrafish. The results indicated that, in comparison to TCPP, RDP induced more pronounced intestinal microstructural damage and oxidative stress, particularly in male zebrafish. 16S rRNA sequencing and metabolomics revealed significant alterations in the species richness and oxidative stress-related metabolites in the intestinal microbiota of zebrafish under exposure to both TCPP and RDP, manifesting gender-specific effects. Based on differential species analysis, we defined invasive species and applied invasion theory to analyze the reasons for changes in the male fish intestinal community. Correlation analysis demonstrated that alien species may have potential effects on metabolism. Overall, this study reveals a pronounced gender-dependent impact on both the intestinal microbiota and metabolic disruptions of zebrafish due to OPEs exposure and offers a novel perspective on the influence of pollutants on intestinal microbial communities and metabolism.PMID:38719053 | DOI:10.1016/j.scitotenv.2024.172892

Sci Total Environ. 2024 May 6:172915. doi: 10.1016/j.scitotenv.2024.172915. Online ahead of print.ABSTRACTThe increasing trend regarding the use of plastics has arisen an exponential concern on the fate of their derived products to the environment. Among these derivatives, microplastics and nanoplastics (MNPs) have been featured for their associated environmental impact due to their low molecular size and high surface area, which has prompted their ubiquitous transference among all environmental interfaces. Due to the heterogenous chemical composition of MNPs, the study of these particles has focused a high number of studies, as a result of the myriad of associated physicochemical properties that contribute to the co-transference of a wide range of contaminants, thus becoming a major challenge for the scientific community. In this sense, both primary and secondary MNPs are well-known to be adscribed to industrial and urbanized areas, from which they are massively released to the environment through a multiscale level, involving the atmosphere, hydrosphere, and lithosphere. Consequently, much research has been conducted on the understanding of the interconnection between those interfaces, that motivate the spread of these contaminants to biological systems, being mostly represented by the biosphere, especially phytosphere and, finally, the anthroposphere. These findings have highlighted the potential hazardous risk for human health through different mechanisms from the environment, requiring a much deeper approach to define the real risk of MNPs exposure. As a result, there is a gap of knowledge regarding the environmental impact of MNPs from a high-throughput perspective. In this review, a metabolomics-based overview on the impact of MNPs to all environmental interfaces was proposed, considering this technology a highly valuable tool to decipher the real impact of MNPs on biological systems, thus opening a novel perspective on the study of these contaminants.PMID:38719035 | DOI:10.1016/j.scitotenv.2024.172915

Int J Biol Macromol. 2024 May 6:132103. doi: 10.1016/j.ijbiomac.2024.132103. Online ahead of print.ABSTRACTRhodotorula spp. has been studied as one powerful source for a novel cell factory with fast growth and its high added-value biomolecules. However, its inadequate genome and genomic annotation have hindered its widespread use in cosmetics and food industries. Rhodotorula glutinis QYH-2023, was isolated from rice rhizosphere soil, and the highest quality of the genome of the strain was obtained at chromosome level (18 chromosomes) than ever before in red yeast in this study. Comparative genomics analysis revealed that there are more key gene copies of carotenoids biosynthesis in R. glutinis QYH-2023 than other species of Rhodotorula spp. Integrated transcriptome and metabolome analysis revealed that lipids and carotenoids biosynthesis was significantly enriched during fermentation. Subsequent investigation revealed that the over-expression of the strain three genes related to carotenoids biosynthesis in Komagataella phaffii significantly promoted the carotenoid production. Furthermore, in vitro tests initially confirmed that the longer the fermentation period, the synthesized metabolites controlled by R. glutinis QYH-2023 genome had the stronger anti-inflammatory properties. All of the findings revealed a high-quality reference genome which highlight the potential of R. glutinis strains to be employed as chassis cells for biosynthesizing carotenoids and other active chemicals.PMID:38719011 | DOI:10.1016/j.ijbiomac.2024.132103

Environ Pollut. 2024 May 6:124116. doi: 10.1016/j.envpol.2024.124116. Online ahead of print.ABSTRACTBiodegradable plastics, such as poly(butylene adipate terephthalate) (PBAT) and polylactic acid (PLA), are potential alternatives to conventional polyethylene (PE), both of which are associated with the production of microplastics (MPs). However, the toxicity of these compounds on medicinal plants and their differential effects on plant morphophysiology remain unclear. This study supplemented soils with MPs sized at 200 μm at a rate of 1% w/w and incubated them for 50 days to investigate the impact of MPs on the growth and metabolites of dandelion (Taraxacum mongolicum Hand.-Mazz.). The results demonstrated that the investigated MPs decreased the growth of dandelion seedlings, induced oxidative stress, and altered the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase). Based on the comprehensive toxicity assessment results, the ecological toxicity was in the following order: PE MPs > PBAT MPs > PLA MPs. Metabolomics analyses revealed metabolic reprogramming in dandelion plants, leading to the enrichment of numerous differentially accumulated metabolites (DAMs) in the leaves. These pathways include carbohydrate metabolism, energy metabolism, and biosynthesis of secondary metabolites, suggesting that dandelions respond to MP stress by enhancing the activity of sugar, organic acid, and amino acid metabolic pathways. In addition, phenolic acids and flavonoids are critical for maintaining the balance in the antioxidant defense system. Our results provide substantial insights into the toxicity of biodegradable MPs to plants and shed light on plant defense and adaptation strategies. Further assessment of the safety of biodegradable MPs in terrestrial ecosystems is essential to provide guidance for environmentally friendly management.PMID:38718962 | DOI:10.1016/j.envpol.2024.124116