Pyrimidine Metabolism Pathways Research Articles

Transcriptome analysis reveals key genes and pathways associated with heat stress in Pleurotus pulmonarius.

Pleurotus pulmonarius is a medium temperature edible mushroom, and its yield and quality are severely affected by high temperature. However, the molecular mechanism of Pleurotus pulmonarius response to heat stress remains unknown. In this study, transcriptome sequencing and analysis of Pleurotus pulmonarius mycelia under heat stress were performed, related differentially expressed genes (DEGs) were verified by fluorescence quantitative PCR (qPCR) and the reduced glutathione content was detected. 5906 DEGs, including 1086 upregulated and 4820 downregulated, were identified by RNA-Seq. GO analysis revealed that DEGs were mainly enriched in the pathways of Aminoacyl-tRNA biosynthesis, pyrimidine metabolism, arginine and proline metabolism, fructose and mannose metabolism, and glutathione metabolism. qPCR analysis showed that the expression of ggt decreased after heat stress treatment, while gst2 and gst3 increased. The glutathione content in mycelia after heat stress was significantly higher than that in the control group. These results suggest that glutathione metabolism may play an important role in the response to heat stress. Our study will provide a molecular-level perspective on fungal response to heat stress and a basis for research on fungal environmental response and molecular breeding.

Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1

Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.

Microbiome profiling and Co-metabolism pathway analysis in cervical cancer patients with acute radiation enteritis

BackgroundIntestinal bacteria significantly contribute to the metabolism of intestinal epithelial tissues. As the occurrence and development of radiation enteritis (RE) depend on the “co-metabolism” microenvironment formed by the host and intestinal microbiota, which involves complex influencing factors and strong correlations, ordinary techniques struggle to fully explain the underlying mechanisms. However, given that it is based on systems biology, metabolomics analysis is well-suited to address these issues. This study aimed to analyze the metabolomic changes in urine, serum, and fecal samples during volumetric modulated arc therapy (VMAT) for cervical cancer and screen for characteristic metabolites of severe acute radiation enteritis (SARE) and RE. MethodsWe enrolled 50 patients who received radiotherapy for cervical cancer. Urine, serum, and fecal samples of patients were collected at one day before radiotherapy and the second week, fourth week, and sixth week after the start of radiotherapy. Control group samples were collected during the baseline period. Differential metabolites were identified by metabolomics analysis; co-metabolic pathways were clarified. We used the mini-SOM library for incorporating characteristic metabolites, and established metabolite classification models for predicting SARE and RE. ResultsUrine and serum sample data showed remarkable clustering effect; metabolomics data of the fecal supernatant were evidently disturbed. Patient sample analyses during VMAT revealed the following. Urine samples: Downregulation of the pyrimidine and riboflavin metabolism pathways as well as initial upregulation followed by downregulation of arginine and proline metabolism pathways and the arginine biosynthesis pathway. Fecal samples: Upregulation of linoleic acid and phenylalanine metabolic pathways and initial downregulation followed by upregulation of arachidonic acid (AA) metabolic pathways. Serum samples: Initial upregulation followed by downregulation of the arginine biosynthesis pathway and downregulation of glutathione, AA, and arginine and proline metabolic pathways. ConclusionPatients with cervical cancer exhibited characteristic metabolic pathways and characteristic metabolites predicting RE and SARE were screened out. An effective RE mini-SOM classification model was successfully established.

Postharvest quality and metabolism changes of daylily flower buds treated with hydrogen sulfide during storage

Daylily flower buds are a good source of nutrients and contain lots of bioactive compounds, but they are subject to deterioration after harvest, which limits the taste and consumer satisfaction. Hydrogen sulfide (H2S) has been regarded as an important gaseous signaling molecule, which could prolong postharvest freshness of fruits and vegetables. The present study aims to investigate the effects of H2S on postharvest quality and metabolism changes of daylily flower buds during storage. The results showed that 3.2 mM NaHS (H2S donor) effectively inhibited weight loss, blooming and decay of daylily during storage. H2S application markedly reduced the accumulation of malondialdehyde and H2O2. H2S treatment also delayed the loss of total protein and antioxidant glutathione, and maintained the activities of antioxidant enzymes superoxide dismutase and catalase at higher level compared to control group. Widely targeted metabolomics identified various differentially accumulated metabolites (DAMs) during storage and with H2S treatment of daylily. These DAMs largely distributed in the classes of amino acids, organic acids, sugars and alcohols, terpenoids. A special focus was given to 303 common DAMs between the comparison of CK0 vs. CK6 and CK6 vs. T6, of which the DAMs were mainly enriched in the KEGG pathways of monobactam biosynthesis, pyrimidine metabolism, glycine, serine and threonine metabolism, arginine biosynthesis, pentose and glucuronate interconversions. Four DAMs including Cytidine 5′-Monophosphate, Fumaric Acid, Hydroxypyruvic Acid, 2′-Deoxycytidine-5′-Monophosphoric Acid exhibited great downregulation during storage, and H2S treatment dramatically recovered their relative contents. This study indicated that H2S treatment offers the potential to preserve the quality of daylily flower buds and extend their postharvest life.

Adrenal pheochromocytoma impacts three main pathways: cysteine-methionine, pyrimidine, and tyrosine metabolism.

Pheochromocytomas and paragangliomas (PPGLs) cause symptoms by altering the circulation levels of catecholamines and peptide hormones. Currently, the diagnosis of PPGLs relies on diagnostic imaging and the detection of catecholamines. In this study, we used ultra-performance liquid chromatography (UPLC)/quadrupole time-of-flight mass spectrometry (Q-TOF MS) analysis to identify and measure the perioperative differential metabolites in the plasma of adrenal pheochromocytoma patients. We identified differentially expressed genes by comparing the transcriptomic data of pheochromocytoma with the normal adrenal medulla. Through conducting two steps of metabolomics analysis, we identified 111 differential metabolites between the healthy group and the patient group, among which 53 metabolites were validated. By integrating the information of differential metabolites and differentially expressed genes, we inferred that the cysteine-methionine, pyrimidine, and tyrosine metabolism pathways were the three main metabolic pathways altered by the neoplasm. The analysis of transcription levels revealed that the tyrosine and cysteine-methionine metabolism pathways were downregulated in pheochromocytoma, whereas the pyrimidine pathway showed no significant difference. Finally, we developed an optimized diagnostic model of two metabolites, L-dihydroorotic acid and vanylglycol. Our results for these metabolites suggest that they may serve as potential clinical biomarkers and can be used to supplement and improve the diagnosis of pheochromocytoma.

Identification of Key Factors in Cartilage Tissue During the Progression of Osteoarthritis Using a Non-targeted Metabolomics Strategy

AbstractThis research was to reveal the key factors in the progression of osteoarthritis (OA) using non-targeted metabolomics and to find targeted therapies for patients with OA. Twenty-two patients with knee OA scheduled for total knee arthroplasty were divided into two groups: Kellgren–Lawrence (KL) grade 3 (n = 16) and grade 4 (n = 6), according to plain X-rays of the knee. After the operation, the cartilages of femur samples were analyzed using non-targeted metabolomics. When compared with grade 3 patients, the levels of choline, 2-propylpiperidine, rhamnose, and monomethyl glutaric acid were higher; while 1-methylhistamine, sphingomyelin (SM) (d18:1/14:0), zeranol, 3- (4-hydroxyphenyl)-1-propanol, 5-aminopentanamide, dihydrouracil, 2-hydroxypyridine, and 3-amino-2-piperidone were lower in grade 4 patients. Furthermore, some metabolic pathways were found to be significantly different in two groups such as the pantothenate and coenzyme A (CoA) biosynthesis pathway, the glycerophospholipid metabolism pathway, histidine metabolism pathway, lysine degradation pathway, glycine, serine and threonine metabolism pathway, fructose and mannose metabolism pathway, the pyrimidine metabolism pathway, and beta-alanine metabolism pathway. This work used non-targeted metabolomics and screened out differential metabolites and metabolic pathways, providing a reliable theoretical basis for further study of specific markers and their specific pathways in the progression of OA.

MX1 and UBE2L6 are potential metaflammation gene targets in both diabetes and atherosclerosis.

The coexistence of diabetes mellitus (DM) and atherosclerosis (AS) is widespread, although the explicit metabolism and metabolism-associated molecular patterns (MAMPs) responsible for the correlation are still unclear. Twenty-four genetically wild-type male Ba-Ma mini pigs were randomly divided into five groups distinguished by different combinations of 90 mg/kg streptozotocin (STZ) intravenous injection and high-cholesterol/lipid (HC) or high-lipid (HL) diet feeding for 9 months in total. Pigs in the STZ+HC and STZ+HL groups were injected with STZ first and then fed the HC or HL diet for 9 months. In contrast, pigs in the HC+STZ and HL+STZ groups were fed the HC or HL diet for 9 months and injected with STZ at 3 months. The controls were only fed a regular diet for 9 months. The blood glucose and abdominal aortic plaque observed through oil red O staining were used as evaluation indicators for successful modelling of DM and AS. A microarray gene expression analysis of all subjects was performed. Atherosclerotic lesions were observed only in the HC+STZ and STZ+HC groups. A total of 103 differentially expressed genes (DEGs) were identified as common between them. The most significantly enriched pathways of 103 common DEGs were influenza A, hepatitis C, and measles. The global and internal protein-protein interaction (PPI) networks of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The top 10 hub proteins, namely, ISG15, IRG6, IRF7, IFIT3, MX1, UBE2L6, DDX58, IFIT2, USP18, and IFI44L, drive aspects of DM and AS. MX1 and UBE2L6 were the intersection of internal and global PPI networks. The expression of MX1 and UBE2L6 was 507.22 ± 342.56 and 96.99 ± 49.92 in the HC+STZ group, respectively, which was significantly higher than others and may be linked to the severity of hyperglycaemia-related atherosclerosis. Further PPI network analysis of calcium/micronutrients, including MX1 and UBE2L6, consisted of 58 and 18 nodes, respectively. The most significantly enriched KEGG pathways were glutathione metabolism, pyrimidine metabolism, purine metabolism, and metabolic pathways. The global and internal PPI network of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The intersection of the nodes of internal and global PPI networks was MX1 and UBE2L6, suggesting their key role in the comorbidity mechanism of DM and AS. This inference was partly verified by the overexpression of MX1 and UBE2L6 in the HC+STZ group but not others. Further calcium- and micronutrient-related enriched KEGG pathway analysis supported that MX1 and UBE2L6 may affect the inflammatory response through micronutrient metabolic pathways, conceptually named metaflammation. Collectively, MX1 and UBE2L6 may be potential common biomarkers for DM and AS that may reveal metaflammatory aspects of the pathological process, although proper validation is still needed to determine their contribution to the detailed mechanism.

Research on mechanism of hypolipidemic effect of Massa Medicata Fermentata based on metabolomics

This paper aims to study the therapeutic effect of Massa Medicata Fermentata on hyperlipidemia model rats and investigate its mechanism of hypolipidemic effect with the help of non-targeted metabolomics. The mixed hyperlipidemia model rats were constructed by giving high-fat chow. After successful modeling, the rats were divided into the model group, pravastatin sodium group(4.4 mg·kg~(-1)), lipotropic group(0.1 g·kg~(-1)), high-dose group(2.4 g·kg~(-1)), medium-dose group(1.2 g·kg~(-1)), and low-dose group(0.6 g·kg~(-1)) of Massa Medicata Fermentata, and they were administered for four weeks once daily. An equal volume of ultrapure water was given to the blank group and model group. Serum lipid level and liver hematoxylin-eosin(HE) staining were used as indicators to estimate the intervention effect of Massa Medicata Fermentata on mixed hyperlipidemia, and the changes in metabolites in plasma of mixed hyperlipidemia model rats were analyzed by non-targeted metabolomics. The mechanism of the hypolipidemic effect of Massa Medicata Fermentata was analyzed through metabolite pathway enrichment. The results showed that compared with the model group, the Massa Medicata Fermentata administration group, especially the high-dose group, could significantly reduce the content of total cholesterol(TC), triglyceride(TG), and low-density lipoprotein cholesterol(LDL-c)(P<0.05 or P<0.01), and liver HE staining revealed that the number of adipocytes in the high-dose group was reduced to some extent. The potential biomarkers obtained by non-targeted metabolomics screening included glycerol 3-phosphate, sphingomyelin, sphingosine 1-phosphate, and deoxyuridine, which were mainly involved in the sphingolipid metabolism process, glycerophospholipid metabolism process, glycerol ester metabolism pathway, and pyrimidine metabolism pathway, totaling four possible metabolic pathways related to lipid metabolism. This study provides a reference for an in-depth investigation of the hypolipidemic mechanism of Massa Medicata Fermentata, which is of great significance for further promoting the clinical application of Massa Medicata Fermentata and increasing the indications.

Selenium Protects Yellow Catfish (Tachysurus fulvidraco) from Low-Temperature Damage via the Perspective Analysis of Metabolomics and Intestinal Microbes

The effects of selenium supplementation in Tachysurus fulvidraco (T. fulvidraco) on low-temperature stress are not known. In this study, 280 healthy T. fulvidraco were divided into two groups, the G0 group (a control group) and the T0 group (a selenium treatment group on a 0.22 mg/kg diet), for a 6-week feeding time. Then, low-temperature stress (water temperature dropped from 26 to 13 °C, with a rate of 1 °C/h) was administered after that. The feeding results showed that selenium increased the percent weight gain (PWG), specific growth rate (SGR), and survival rate (SR) of T. fulvidraco and decreased the feed conversion rate (FCR), but these differences were not significant (p > 0.05). Under low temperatures, selenium still has no significant effects on antioxidant indexes such as glutathione peroxidase (GSH-Px) activity, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content in serum (p > 0.05). However, metabolomic analysis revealed that selenium caused changes in lipids and lipid-like molles, organic acids and their derivatives, and fatty acyls. Choline, linoleic acid, and glycerophospholipid metabolism pathways; d-arginine and d-ornithine metabolism; valine, leucine, and isoleucine degradation; and biosynthesis pathways, as well as pyrimidine metabolism pathways, were activated to produce these metabolites to combat against this stress. In addition, selenium increased the diversity of intestinal microbes in T. fulvidraco and decreased the relative abundance of Plesiomonas. However, the combined analysis showed the intestinal microbe changes did not affect metabolite production. In summary, selenium activated lipid, carbohydrate, and amino acid metabolism for energy substance provision, reduced the oxidation and production of other harmful substances, and increased the intestinal microbe diversity of T. fulvidraco to improve resistance to low-temperature stress.

Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites

BackgroundLung cancer (LC) is one of the most devastating diseases worldwide, there is growing studies confirm the role of impaired lung function in LC susceptibility. Moreover, gut microbiota dysbiosis is associated with LC severity. Whether alterations in gut microbiota and metabolites are associated with long-term lung dysfunction in LC patients remain unclear. Our study aimed to analyze the risk factors in LC patients with impaired pulmonary function based on the characteristics of the gut microbiome and metabolites.MethodsFecal samples from 55 LC patients and 28 benign pulmonary nodules patients were collected. Pulmonary ventilation function was graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) method. LC patients were divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction. The fecal samples were analyzed using 16 S rRNA gene amplicon sequencing and metabolomics.ResultsThe gut microbiome composition between LC patients and benign pulmonary nodules patients presented clearly differences based on Partial Least Squares Discriminant Analysis (PLS-DA). Pulmonary ventilation function was positively correlated with LC tumor stage, the richness and diversity of the gut microbiota in LC patients with moderate or above pulmonary ventilation dysfunction increased significantly, characterized by increased abundance of Subdoligranulum and Romboutsia. The metabolomics analysis revealed 69 differential metabolites, which were mainly enriched in beta-Alanine metabolism, styrene degradation and pyrimidine metabolism pathway. The area under the curve (AUC) combining the gut microbiome and metabolites was 90% (95% CI: 79-100%), indicating that the two species and four metabolites might regarded as biomarkers to assess the prediction of LC patients with impaired pulmonary function.ConclusionsOur results showed that microbiome and metabolomics analyses provide important candidate to be used as clinically diagnostic biomarkers and therapeutic targets related to lung cancer with impaired pulmonary function.

Effects of continuous and pulse lead exposure on the swimming behavior of tadpoles revealed by brain-gut axis analysis

Lead (Pb) is present in aquatic environments with a continuous or pulse form due to the regular or irregular discharge of wastewater. These two modes of exposure result in different toxicological effects on aquatic animals. To compare the effects of Pb exposure mode on the swimming behavior of amphibian larvae, this study proposed a combination method to examine the brain-gut axis (gut bacteria, histopathology, metabolomics, and ethology) in order to evaluate the ecotoxic differences in Pelophylax nigromaculatus tadpoles (Gs 21–28) when exposed to continuous (CE100) versus pulse exposure (PE100) of environmental concentrations of Pb (100 μg/L). The results showed that: 1) CE100 significantly decreased the movement distance and swimming activity of the tadpoles compared to PE100 and the control, while there were no significant differences between the control group and PE100. 2) At the phyla level, compared to PE100, CE100 treatment significantly decreased the abundance of Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes and increased the abundance of Fusobacteria in the gut. At the genus level, compared to PE100, CE100 significantly increased the abundance of U114 and decreased the abundance of Anaerorhabdus, Exiguobacterium and Microbacterium. 3) Compared to PE100, CE100 changed the metabolites of the brain-gut axis pathway, such as quinolinic acid, L-valine, L-dopa, L-histidine, urocanic acid, L-threonine, γ-aminobutyric acid (GABA), L-glutamate (Glu), acetylcholine (Ach), L-tyrosine (Tyr), L-tryptophan (Trp), and levodopa (DOPA). 4) CE100 and PE100 played a repressive role in the histidine metabolism and tyrosine metabolism pathways and played a promoting role in the purine metabolism and pyrimidine metabolism pathways. This study provides a method for evaluating the toxic effects of heavy metal exposure via two different exposure modes (pulse versus continuous) which tadpoles may encounter in the natural environment from a combined study examining the brain-gut axis.

Proteomic analysis of N-glycosylation of the human placenta between preeclampsia and normal pregnancies

Protein N-glycosylation plays critical roles in modulating placental function, but little is known about N-glycoproteins in the human placenta and modifications in preeclampsia (PE). Here, we show a large, site-specific N-glycoproteome profiling study of PE and normal placenta using quantitative N-glycoproteomics based on mass spectrometry. The study identified disease signatures of altered N-glycoproteins and N-glycosylation site occupancy in PE and provided a system-level view of human placental N-glycoproteins and in vivo N-glycosylation sites. The study led to the discovery of a roster of glycoproteins with aberrant N-glycosylation levels associated with PE, including CD34, ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase family member 1), insulin-like growth factor binding protein (IGFBP3), and HYOU1 (hypoxia up-regulated 1). An emerging phenomenon that N-glycosylation is involved in several PE pathways, including cell adhesion molecules, PI3K-Akt signaling, pyrimidine metabolism, and metabolic pathways was revealed by pathway analysis of PE-associated aberrant glycoproteins. After enzymolysis, the proteins in each group were enriched with N-glycosylated peptides by lectin, the glycochain was excised by peptide N-glycosidase F (PNGase F) in H218O, and the glycosylated sites were analyzed by LC-MS/MS to achieve large-scale qualitative and quantitative analysis of N-glycosylated proteins. Our findings highlight the role of N-glycosylation in the pathogenesis of PE and provide new molecular and system-level insights for understanding and treating this disease.

Gut Microbiome and Metabolomics Study of Selenium-Enriched Kiwifruit Regulating Hyperlipidemia in Mice Induced by a High-Fat Diet.

Our previous study showed that as a substitute for statins, selenium-enriched kiwifruit (Se-Kiwi) might reduce blood lipids and protect the liver in Kunming mice, but the underlying mechanism remains unclear. Metabolic regulation of mammalian intestinal microflora plays an important role in obesity and related diseases induced by a high-fat diet (HFD). Here, samples of serum, liver, colon, and fresh feces from the Se-Kiwi-treated hyperlipidemia C57BL/6J mouse model were collected. Based on metabolome (UHPLC-Q-TOF MS) and gut microbiome (16S rDNA) analyses as well as the integrative analysis of physiological and biochemical indices and pathological data of mice, we aimed to systematically illustrate the gut microbiome and metabolomics mechanism of Se-Kiwi in HFD-induced hyperlipidemic mice. As a result, Se-Kiwi can significantly increase the abundance of potentially beneficial gut bacteria such as Parabacteroides, Bacteroides, and Allobaculum in the colon and improve hyperlipidemia by regulating the digestion and absorption of vitamins, pyrimidine metabolism, purine metabolism, and other metabolic pathways, which have been confirmed by the following fecal microbiota transplantation experiment. This process was significantly regulated by the Ada, Gda, Pank1, Ppara, Pparg, and Cd36 genes. These findings may provide a theoretical basis for the research and development of selenium-enriched functional foods in the treatment of hyperlipidemia.

Uridine Synthesis Is the Metabolic Vulnerability in Relapse-Associated B-ALL Cells with Active Pre-BCR Signaling

Relapse stubbornly continues to limit survival for children with B-cell progenitor acute lymphoblastic leukemia (B-ALL). B-ALL cells accumulate at the developmental checkpoint regulating the transition from pro-B to pre-B cells and express the pre-B cell receptor (preBCR). B-ALL samples have previously been categorized as preBCR positive and preBCR negative subtypes. We previously found that pre-B cells with active preBCR signaling are present at diagnosis and highly predictive of relapse, termed relapse predictive cells (RPCs) (Good et al. Nature Med 2018). Whole transcriptome sequencing of pre-B RPCs from patient samples demonstrated enrichment of gene signature pathways is involved in oxidative phosphorylation (OXPHOS), pyrimidine metabolism, and glycolysis pathways compared to pre-B cells from patients in complete remission. Thus, we hypothesized that RPCs have unique metabolic demands driven by their active signaling. Utilizing TARGET dataset, B-ALL patients were classified as preBCR high or low based on the sum of normalized counts of preBCR components and signaling molecules. Notably, preBCR high patients (top 25%ile) had inferior overall survival compared to preBCR low (bottom 75%ile; P=0.009). Further, preBCR high patients demonstrated enrichment for the metabolic gene signatures identified in RPCs. CyTOF analysis in primary B-ALL samples demonstrated increased expression of glycolysis (PFKFB4, ENO1, LDHA) and pentose phosphate pathway (G6PD, PGD) proteins in preB cells from patients destined to relapse compared to those in continued remission. These data support the link between a distinct metabolic state in preB cells associated with relapse. To investigate the metabolic state associated with the preBCR in B-ALL, we utilized cell line models (preBCR high: Nalm6, 697, Kasumi2; preBCR low: REH, Nalm16, RS4;11). We found that preBCR high cells are more metabolically active than preBCR low cells with significantly higher oxygen consumption rate and extracellular acidification rate. To identify their targetable dependencies, cells were starved of glucose or glutamine for 24 hours. Neither cell type was sensitive to glutamine starvation. However, preBCR high cells were uniquely vulnerable to glucose deprivation (killing effect 64% vs 25%, P=0.027) indicating a distinct need for glucose in preBCR high cells. To unravel the unique glucose dependency of preBCR high cells, we performed isotype tracing with U- 13C-glucose and U- 13C-glutamine. Both preBCR high and preBCR low cells use glutamine as the primary carbon source in the TCA cycle. However, glucose is primarily utilized for the pentose phosphate pathway and nucleotide synthesis in preBCR high cells, as evidenced by higher fractional 13C labeling in m+5 UTP, UDP and ATP. Uridine, but not other pyrimidines or purines, rescued preBCR high cells from glucose starvation, highlighting glucose-dependent uridine synthesis as the metabolic vulnerability of preBCR high cells. To target this dependency, we treated the cells with the dihydroorotate dehydrogenase (DHODH) inhibitor (BAY-2402234), which disrupts a crucial step in uridine synthesis. Remarkably, DHODH inhibition resulted in preferential killing in preBCR high but not preBCR low cells. Evaluation of the in vivo efficacy of DHODH inhibition in xenografts will be presented. Together, we found that preBCR high B-ALL cells are associated with relapse and are highly energetic, relying uniquely on glucose for survival to fuel the PPP and uridine synthesis. Inhibition of uridine synthesis is a novel strategy to target these treatment resistant and relapse-associated cells.

Legume-potato rotation affects soil physicochemical properties, enzyme activity, and rhizosphere metabolism in continuous potato cropping

BackgroundContinuous cropping can reduce soil quality and affect rhizosphere metabolism, ultimately reducing crop yield. Crop rotation can mitigate the damage caused by continuous cropping, but different crop rotation patterns respond differently to soil quality and rhizosphere metabolism. We investigated the effects of different cropping patterns on soil physicochemical properties, enzyme activities, microbial quantity, and rhizosphere metabolism of continuous potato cropping based on a long-term field study from 2018 to 2022. The experiment was set up with the following three treatments: potato (Solanum tuberosum L.)-potato-potato-potato-potato (CK), potato-potato-potato-pea (Pisum arvense L.)-potato (T1), and potato-potato-potato-faba bean (Vicia faba L.)-potato (T2).ResultsThe results showed that pea-potato rotation (T1) and faba bean-potato rotation (T2) significantly improved soil physicochemical properties and microbial quantity, enhanced enzyme activity, and increased yield by 21.19% and 28.38%, respectively, compared with the continuous potato crop. Non-targeted metabolomics analysis showed that the differential metabolites of pea-potato and faba bean-potato rotation were mainly nucleotides, organic acids and derivatives, and flavonoids compared to continuous potato cropping. These differential metabolites are mainly enriched in the ABC transporter, purine metabolism, pyrimidine metabolism, and phenylalanine metabolism pathways. Combined analyses showed that legume-potato rotations improved soil physicochemical properties, enzyme activities, and microbial quantity of continuous potato cropping, ultimately increasing tuber yields. In addition, correlation analyses showed that differential metabolites significantly enriched in purine and phenylalanine metabolism (l-Tyrosine, Trans-Cinnamic acid, Guanine, and Adenine) were also strongly associated with these measurements.ConclusionsTherefore, we conclude that legume-potato rotations modulate the abundance and function of rhizosphere metabolites and significantly alter the low molecular metabolite profile of the soil under continuous potato conditions. Some of these important metabolites may play a part in the cycling of nutrients in the soil, making its physicochemical properties and microbial quantity better, raising the activity of soil enzymes, and ultimately increasing the yield of potato tubers. The above results indicate that legume-potato rotation has a positive effect on continuous potato soils. It lays a solid foundation for revealing the complex molecular network and metabolic pathways of microbial communities in soil after legume crop rotation.Graphical

Tissue-specific toxic effects of nano-copper on zebrafish

Understanding the behavior and potential toxicity of copper nanoparticles (nano-Cu) in the aquatic environment is a primary way to assess their environmental risks. In this study, RNA-seq was performed on three different tissues (gills, intestines, and muscles) of zebrafish exposed to nano-Cu, to explore the potential toxic mechanism of nano-Cu on zebrafish. The results indicated that the toxic mechanism of nano-Cu on zebrafish was tissue-specific. Nano-Cu enables the CB1 receptor of the presynaptic membrane of gill cells to affect short-term synaptic plasticity or long-term synaptic changes (ECB-LTD) through DSI and DSE, causing dysfunction of intercellular signal transmission. Imbalance of de novo synthesis of UMP in intestinal cells and its transformation to UDP, UTP, uridine, and uracil, resulted in many functions involved in the pyrimidine metabolic pathway being blocked. Meanwhile, the toxicity of nano-Cu caused abnormal expression of RAD51 gene in muscle cells, which affects the repair of damaged DNA through Fanconi anemia and homologous recombination pathway, thus causing cell cycle disorder. These results provide insights for us to better understand the differences in toxicity of nano-Cu on zebrafish tissues and are helpful for a comprehensive assessment of nano-Cu's effects on aquatic organisms.

EXTH-17. TARGETING CTPS1 AND NUCLEOTIDE BIOSYNTHESIS PATHWAYS AS A NOVEL THERAPEUTIC APPROACH IN MYC-AMPLIFIED MEDULLOBLASTOMA

Abstract MYC-amplified medulloblastoma (MB) tumors are the deadliest of all subgroups with a < 50% 5-year overall survival rate. High risk patients receive large doses of chemo- and radio- therapy (CT/RT) with most survivors experiencing debilitating neurological and cognitive sequelae making the identification of novel targets of the utmost importance. Recent whole-genome CRISPR screening identified the enzyme CTPS1 and other components of the de novo pyrimidine metabolism cascade as a possible cancer-specific vulnerability in MYC-amplified MB. Our study tested targeted inhibitors of this pathway to identify rational combinations for translation to pre-clinical models. A stable of treatment-naïve, patient-derived models of MYC-amplified MB were used and treated with various de novo pyrimidine synthesis inhibitors alone and in novel combinations. Analysis of proliferation, cell survival, and downstream signaling were performed both in vitro and in vivo. Inhibition of CTPS1 led to a significant decrease in cell proliferation and alterations in cell cycle with minimal increases in cell death, suggest a cytostatic mechanism. Previous work has shown de novo pathway inhibition results in reduction of the dNTP pool, leading to activation of the DNA damage response (DDR), seizing the cell cycle. Interestingly, the DDR inhibitor prexasertib (CHKi) robustly targets MYC-amplified MB tumors in pre-clinical models. Combining CHKi and CTPS1 inhibitors yields significant tumor cytotoxicity both in vitro and in vivo. We further demonstrated robust synergy of CHKi with other clinically relevant de novo pyrimidine metabolism inhibitors. The results of this investigation confirm CTPS1 and the de novo pyrimidine metabolism pathway as targets in MYC-amplified MB and identifies a novel rational combination for treatment in patients.

PSI-6 Effects of a Postbiotic Program Consisting of Liquid and Solid Saccharomyces Cerevisiae Fermentation Products on Digestibility, Ruminal Fermentation, and Plasma Metabolome of Finishing Beef Steers

Abstract The objective of this study was to determine the effects of a postbiotic feeding program consisting of liquid and solid Saccharomyces cerevisiae fermentation products (SCFP) on digestibility, ruminal fermentation, and plasma metabolome of finishing beef steers. Eight Holstein steers (BW 467 ± 13.9 kg) equipped with rumen cannulas were used in a crossover design study, with 21-d per period and 7-d washout period in between periods. Steers were blocked based on initial BW to one of two treatments: 1) Control, basal diet only (CON), or 2) SCFP, one day feeding of LiquiCare RTU (Diamond V, dosed via rumen cannula at 11 mL/100 kg BW) followed by daily feeding of 12 g NaturSafe (Diamond V, top-dressed). Feed and fecal samples were collected during d 17 to 20 for determination of digestibility and fecal excretion of N, P, Cu and Zn using acid-insoluble ash as an internal marker. Blood samples were collected on d 21 before morning feeding. Rumen fluid samples were collected on d 0, 1, 2, 3, 5 and 21 at 0, 4, 8, or 12 h post morning feeding via rumen cannula. Results were analyzed with the GLIMMIX procedure of SAS 9.4 (SAS, 2022). BW, DMI and digestibility were not affected by treatment. There was a tendency of treatment by period interaction (P = 0.09) on feed efficiency, which was improved by feeding SCFP only in period 1. Feeding SCFP did not affect (P > 0.10) ruminal pH. Feeding SCFP tended to reduce ruminal lactate concentration on d 21 (0.09 vs. 0.02 mM, P = 0.10). Supplementing SCFP reduced ruminal NH3-N concentration on d 2 (4.24 vs. 7.31 mg/dL, P = 0.03) and d 21 (4.86 vs. 6.83 mg/dL, P = 0.04). By feeding SCFP, ruminal total VFA concentration was increased 4-h post-feeding on d 5 (139.7 vs. 126.7 mM, P = 0.01) and numerically increased 4-h post-feeding on d 21 (151.2 vs. 133.3 mM, P = 0.12). For VFA composition, no treatment differences were observed on day 21. However, feeding SCFP reduced (P = 0.01) propionate proportion and increased (P = 0.05) butyrate proportion on day 3. The enriched plasma metabolic pathways (P ≤ 0.05) by feeding SCFP are citric acid cycle, pyrimidine metabolism, glycolysis/gluconeogenesis, retinol metabolism, and inositol phosphate metabolism pathways. Overall, our results indicated potential benefits of the SCFP feeding program on improving ruminal fermentation, preventing acidosis and improving N utilization in the rumen. Furthermore, feeding SCFP enriched several important pathways in lipid, protein, and glucose metabolism, which may improve feed efficiency of energy and protein in finishing beef cattle.

Integrative metabolomic and network pharmacological analysis reveals potential mechanisms of Cardamine circaeoides Hook.f. & Thomson in alleviating potassium oxonate-induced asymptomatic hyperuricemia in rats.

Cardamine circaeoides Hook.f. & Thomson (CC), a herb of the genus Cardamine (family Brassicaceae), has a rich historical usage in China for both culinary and medicinal purposes. It is distinguished by its remarkable ability to hyperaccumulate selenium (Se). CC has demonstrated efficacy in the prevention of metabolic disorders. However, investigations into the effects of CC on asymptomatic hyperuricemia remain scarce. The objective of this study is to elucidate the mechanism by which CC aqueous extract (CCE) exerts its anti-hyperuricemic effects on asymptomatic hyperuricemic rats induced by potassium oxonate (PO) by integrating metabolomics and network pharmacological analysis. Asymptomatic hyperuricemia was induced by feeding rats with PO (1000mg/kg) and CCE (0.75, 1.5, or 3g/kg) once daily for 30days. Various parameters, including body weight, uric acid (UA) levels, histopathology of renal tissue, and inflammatory factors (IL-1β, IL-6, IL-8, and TNF-α) were assessed. Subsequently, metabolomic analysis of kidney tissues was conducted to explore the effects of CCE on renal metabolites and the related pathways. Furthermore, network pharmacology was employed to explicate the mechanism of action of CCE components identified through UPLC-Q-TOF-MS analysis. Finally, metabolomic and network-pharmacology analyses were performed to predict crucial genes dysregulated in the disease model and rescued by CCE, which were then subjected to verification by RT-qPCR. The findings revealed that CCE significantly inhibited the UA levels from the 21stday to the 30thday. Moreover, CCE exhibited significant inhibition of IL-1β, IL-6, IL-8, and TNF-α levels in renal tissues. The dysregulation of 18 metabolites and the tyrosine, pyrimidine, cysteine, methionine, sphingolipid, and histidine metabolism pathways was prevented by CCE treatment. A joint analysis of targets predicted using the network pharmacology approach and the differential metabolites found in metabolics predicted 8 genes as potential targets of CCE, and 3 of them (PNP gene, JUN gene, and ADA gene) were verified at the mRNA level by RT-qPCR. We conclude that CCE has anti-hyperuricemia effects and alleviates renal inflammation in a rat model of hyperuricemia, and these efficacies are associated with the reversal of increased ADA, PNP, and JUN mRNA expression in renal tissues.

Perturbation and mechanism of non-antibiotic drug in regulating resistome and metabolome of anammox consortia: An overlooked and underrated cause of multiresistance

Given that antibiotic resistance genes (ARGs) become emerging pollutants, their accumulation and transfer caused by extensive use of antibiotic and non-antibiotic drugs raise concerns. In contrast, the impacts of non-antibiotic drugs have been largely overlooked, and their regulation mechanism in anammox system remains unclear. In this study, the single and combined effects of typical antibiotic (doxycycline) and non-antibiotic drug (propranolol) on anammox consortia were evaluated and compared from process performance, community succession, metabolic and gene regulation perspectives. Significant reduction in the nitrogen removal efficiency (49.0 ± 0.5%) was only observed in the anammox process stressed by propranolol and doxycycline, but it was reversible. Metabolome results showed that anammox consortia upregulated amino acid metabolism under propranolol stress, while the abundance of pyrimidine and purine metabolic pathways significantly increased under doxycycline and multidrug stress. Microorganisms adapted to these stresses by changing the utilization preference for metabolites. Metagenomic analyses indicated that doxycycline and propranolol induced the high frequency of gene transfer through increasing oxidative stress level, membrane permeability, pili and efflux pumps. Significant correlations between ARGs and mobile genetic elements (MGEs), especially intI1, demonstrated the conjugative transfer of ARGs. Furthermore, structural equation models showed that microbial community, bacterial metabolism, MGEs, reactive oxygen species (ROS) and corresponding SOS response were key driving factors for ARGs transfer in the anammox systems. These findings fill the gap in the effect of non-antibiotic drugs on anammox system and their regulation mechanism, which further provides a theoretical guidance for anammox-based process to treat multidrug-containing wastewater.