A New View into the Regulation of Purine Metabolism: The Purinosome

A novel framework for industrial pesticide effluent assessment: Integrating chemical screening, multi-endpoint responses and literature-based validation

Industrial pesticide effluents pose substantial risks to aquatic ecosystems, yet comprehensive understanding of their toxicological impacts remains limited. This study presents an integrated approach to evaluate the ecological risks of pesticide manufacturing effluents through chemical screening and multi-endpoints biological responses. Using zebrafish embryos as a model organism, we demonstrated that effluent discharge point (EDP) sample induced 100 % mortality, while diluted samples exhibited significant developmental toxicity, cardiovascular injury, immunosuppression, and behavioral alterations. Non-targeted metabolomics analysis revealed the molecular mechanisms underlying these toxic responses. Through chemical screening and targeted quantification, we identified three predominant azole fungicides - propiconazole (2.11 μg/L), hexaconazole (13.3 μg/L), and tebuconazole (18.66 μg/L) - that exhibited synergistic toxicity. Notably, our innovative meta-analysis framework based on literature data validated the toxicological profiles of detected compounds, providing an efficient alternative to conventional bioassays. This study establishes a comprehensive framework for assessing industrial effluent toxicity and demonstrates the value of integrating chemical analysis with biological responses for environmental risk assessment.

Exploring the fate of 6PPD in zebrafish (Danio rerio): Understanding toxicokinetics, biotransformation mechanisms, and metabolomic profiling at environmentally relevant levels

In recent years, N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) has attracted significant attention in environmental science, yet its behavior in biological systems remains poorly understood. This study involved a 28-day zebrafish exposure experiment at three concentrations (2, 20, and 200 μg/L), to investigate its physiologically based toxicokinetic (PBTK) properties, the formation of biotransformation products, and the metabolic characteristics of liver tissue. The results indicated that the liver and intestines are key organs for 6PPD accumulation, with tissue-specific distribution patterns. The biotransformation of 6PPD in the liver involves various phase I and phase II metabolic reactions, including hydroxylation, N-dealkylation, and sulfation processes. Furthermore, Metabolomics analysis revealed substantial changes in both the diversity and abundance of liver metabolites with increasing 6PPD concentrations, particularly in key biological processes such as lipid metabolism, amino acid metabolism, and redox balance. Notably, significant disruptions in sphingolipid and glycerophospholipid pathways suggest 6PPD may impair membrane fluidity and stability, potentially leading to membrane damage and dysfunction. Overall, this study provides crucial insights into the biological behavior of 6PPD in zebrafish, contributing essential knowledge for its ecotoxicological evaluation.

Characteristic noise of offshore wind turbine impacts the behavior and muscle physiology of sea cucumber Apostichopus japonicus

Sea cucumbers plays a crucial role in maintaining ecological balance through their unique behaviors and physiological functions. However, the noise from offshore wind turbines disrupts the habitat environment of the sea cucumber, potentially altering their behavior and physiology. Nevertheless, limited research exists on how noise from offshore wind turbines affects the sea cucumbers. In our study, we explored the effects of specific wind turbine noise frequencies on the behavior and muscle metabolism of sea cucumbers through four experimental groups: control, 125 Hz, 250 Hz, and 2500 Hz. Statistical analysis of the sea cucumber's ingestion rate, fecal production rate, step frequency and total step length showed that low-frequency noise (125 Hz and 250 Hz) significantly enhanced their locomotion and feeding activity compared to the control group. Further examination demonstrated that low-frequency noise significantly changed the metabolic products in sea cucumber's muscles, altering levels of nine metabolites, excluding tetraazecyclododecane tetraacetic acid. Furthermore, four key metabolic pathways showed marked alterations: pantothenate and CoA biosynthesis, glycerophospholipid metabolism, pyrimidine metabolism, and purine metabolism. These findings demonstrate that sea cucumbers adapt behaviorally and metabolically to anthropogenic noise disturbances.

Identification of the Third Patient With PAICS Deficiency Harbouring the p.(Lys53Arg) Recurrent Variant, Extending the Phenotype Diversity

Phosphoribosylaminoimidazole carboxylase (PAICS) deficiency, caused by biallelic variants in PAICS gene, is an inborn error of de novo purine synthesis. Only two patients from a consanguineous family have been reported, with multiple congenital malformations, resulting in early neonatal death. Molecular analysis identified a homozygous p.(Lys53Arg) missense variant. We report the third case of PAICS deficiency in a 7 years old boy, presenting with polymalformative syndrome, but normal neurodevelopment. We report malformations not previously described in PAICS deficiency, notably congenital cardiopathy, and support the consistency of skeletal and oesophageal defects. Genome Sequencing identified the homozygous pathogenic variant p.(Lys53Arg), suggesting a recurrent variant in PAICS. A probable recurrence of PAICS deficiency occurred in a sibling, with a similar polymalformative syndrome antenatally diagnosed, but could not be confirmed molecularly. We further delineate the phenotype of PAICS deficiency and provide new insights concerning prognosis, notably in terms of neurodevelopment.

How purine metabolites impact reproduction

Purine metabolism is one of the core biochemical processes essential for cell survival and function. During development, purines are involved in germ cell development, ovarian function, and pregnancy outcomes. Here, we discuss the relationships between purine metabolism and reproductive health, offering insights into the future directions of the field.

Purine Metabolism and Dystonia: Perspectives of a Long-Promised Relationship

Dystonia research focuses on the identification of converging biological pathways, allowing to define molecular drivers that serve as treatment targets. We summarize evidence supporting the concept that aberrations in purine metabolism intersect with dystonia pathogenesis. The recent discovery of IMPDH2-related dystonia introduced a gain-of-function paradigm in purinergic system defects, offering new perspectives to understand purine-pool imbalances in brain diseases. We discuss commonalities between known dystonia-linked mechanisms and mechanisms emerging from studies of purine metabolism disorders including Lesch-Nyhan disease. Together, we hypothesize that a greater appreciation of the relevance of purine perturbances in dystonia can offer fresh avenues for therapeutic intervention. ANN NEUROL 2025;97:809-825.

Effect of Fumonisin B1 and Hydrolyzed FB1 Exposure on Intestinal and Hepatic Toxicity in BALB/c Mice

Fumonisins, a class of mycotoxins, pose significant health risks due to widespread contamination. The presence of masked mycotoxins complicates risk assessments because of insufficient regulation and potential toxicity as well as in vivo transformation. This study aims to compare the toxic effects of continuous exposure to fumonisin B1 (FB1) and hydrolyzed FB1 (HFB1) on the gut-liver axis in mice. After 21 d of exposure to FB1 and HFB1, the distributions of FB1 and its metabolites in mice were analyzed, and their effects on intestinal morphology, gut microbial diversity, short-chain fatty acids (SCFAs), inflammatory factors, and hippocampal metabolites were assessed. The results revealed that the highest concentrations of FB1 (61.87%) and HFB1 (53.56%) were detected in the cecum, followed by the colon. Exposure to FB1 and HFB1 resulted in compromised intestinal integrity, villi atrophy, elevated levels of inflammatory factors, and decreased total SCFAs. Both FB1 and HFB1 led to a significant reduction in the Firmicutes to Bacteroides ratio. Blood biochemical analysis and liver metabolomics indicated that FB1 and HFB1 also induced disturbances in the liver homeostasis. The complex correlations observed between the metabolomic and microbiota results underscore the involvement of the gut-liver axis in the disruption induced by these two mycotoxins. These findings highlight the systemic effects of FB1 and HFB1 on liver and gut health, providing valuable insights for further research into their mechanisms and health implications.

Structure-based principles underlying ligand recognition of xanthine-II riboswitch

Riboswitches are conserved RNA elements that specifically recognize the cognate metabolites and regulate downstream gene expression involved in the metabolic pathways. To date, two classes of xanthine-responsive riboswitches involved in xanthine homeostasis have been identified. The recently reported xanthine-II riboswitch originates from guanine riboswitch family, featuring a single U-to-G mutation and several nucleotide insertions. Here, we report the complex structure of xanthine-II riboswitch bound to xanthine. The tertiary structure of xanthine-II riboswitch adopts a three-way junction scaffold similar to that of guanine riboswitch. However, the distinctive mutation and insertions in xanthine-II riboswitch facilitate the formation of a highly specific binding pocket for xanthine, distinguishing it from guanine riboswitches. Xanthine is bound in the junction region, forming a base triple with C64 and the mutant nucleotide G37, and is sandwiched by one base pair U8-A38 and one base triple A7-C36-U65. Structural alignment and ligand recognition specificity of the xanthine-II riboswitch are further verified by ligand-binding assays of structure-based mutation using isothermal titration calorimetry. Furthermore, leveraging the ligand specificity of the xanthine-II riboswitch, we develop a highly specific and sensitive biosensor for xanthine detection by fusing xanthine-II riboswitch with Pepper fluorogenic aptamer, highlighting the potential applications of xanthine-II riboswitch in diagnosing diseases related to xanthine metabolism disorders.

Purinosomes as a therapeutic target in hepatocellular carcinoma: insights and opportunities

The formation of purinosomes, dynamic complexes involved in de novo purine biosynthesis, has been recognized as a critical process for cell growth. Although their upregulation in cancer cells suggests their potential as a therapeutic target, the specific role of purinosomes in hepatocellular carcinoma (HCC) remains uncertain. The purinosome score was found to have prognostic value. Enrichment analyses indicated a connection between purinosome-related genes and cell cycle regulation. Moreover, our research has demonstrated a correlation between the upregulation of genes associated with purinosomes and the enhanced formation of purinosomes in Huh-7 cells. Pyrimethamine has been identified as a promising therapeutic option for targeting purinosome to exert anti-cancer effects. Furthermore, the purinosome score exhibited an positive relationship with the response to immunotherapy. It may guide the stratification of liver cancer patients and screen for populations that may benefit from immunotherapy. This study examines the prognostic and predictive value of purinosome in liver cancer, suggesting that targeting purinosome formation with pyrimethamine or immunotherapy could benefit patients with high purinosome scores.

Resilience and vulnerabilities of tumor cells under purine shortage stress

Purine metabolism is a promising therapeutic target in cancer; however how cancer cells respond to purine shortage,particularly their adaptation and vulnerabilities, remains unclear. Using the recently developed purine shortage-inducing prodrug DRP-104 and genetic approaches, we investigated these responses in prostate, lung and glioma cancer models. We demonstrate that when de novo purine biosynthesis is compromised, cancer cells employ microtubules to assemble purinosomes, multi-protein complexes of de novo purine biosynthesis enzymes that enhance purine biosynthesis efficiency. While this process enables tumor cells to adapt to purine shortage stress, it also renders them more susceptible to the microtubule-stabilizing chemotherapeutic drug Docetaxel. Furthermore, we show that although cancer cells primarily rely on de novo purine biosynthesis, they also exploit Methylthioadenosine Phosphorylase (MTAP)-mediated purine salvage as a crucial alternative source of purine supply, especially under purine shortage stress. In support of this finding, combining DRP-104 with an MTAP inhibitor significantly enhances tumor suppression in prostate cancer (PCa) models in vivo. Finally, despite the resilience of the purine supply machinery, purine shortage-stressed tumor cells exhibit increased DNA damage and activation of the cGAS-STING pathway, which may contribute to impaired immunoevasion and provide a molecular basis of the previously observed DRP-104-induced anti-tumor immunity. Together, these findings reveal purinosome assembly and purine salvage as key mechanisms of cancer cell adaptation and resilience to purine shortage while identifying microtubules, MTAP, and immunoevasion deficits as therapeutic vulnerabilities.

Combined transcriptomics and metabolomics analyses reveal the molecular mechanism of heat tolerance in Pichia kudriavzevii

Introduction

Pichia kudriavzevii is a prevalent non-Saccharomyces cerevisiae yeast in baijiu brewing. The aim of this study was to isolate a high temperature resistant Pichia kudriavzevii strain from the daqu of strong flavor baijiu and to elucidate its molecular mechanism.

Methods

Growth activity was assessed at temperatures of 37°C, 40°C, 45°C, and 50°C. Morphological changes were observed by scanning electron microscopy at 37°C, 45°C, and 50°C. Subsequent analysis of the transcriptomics and metabolomics was undertaken to elucidate the molecular mechanism of heat tolerance.

Results

The strain was able to tolerate high temperature of 50°C, undergoing substantial morphological alterations. Gene ontology (GO) analysis of the transcriptomics revealed that differentially expressed genes (DEGs) were enriched in pathways such as ATP biosynthesis process and mitochondrion; Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that DEGs were up regulated in oxidative phosphorylation. Utilising liquid chromatograph-mass spectrometer, a total of 463 cationic differential metabolites and 352 anionic differential metabolites were detected and screened for differential substances that were closely related to heat tolerance (NAD+ and ADP); KEGG analysis showed that metabolites were up regulated in purine metabolism. Furthermore, correlation analyses of transcriptomics-metabolomics demonstrated a strong positive correlation between the metabolites NAD+ and ADP, and multiple DEGs of the oxidative phosphorylation pathway.

Discussion

These results suggest that the heat tolerant strain can be able to counteract high temperature environment by up regulating energy metabolism (especially oxidative phosphorylation) to increase ATP production.

SAM transmethylation pathway and adenosine recycling to ATP are essential for systemic regulation and immune response

During parasitoid wasp infection, activated immune cells of Drosophila melanogaster larvae release adenosine to conserve nutrients for immune response. S-adenosylmethionine (SAM) is a methyl group donor for most methylations in the cell and is synthesized from methionine and ATP. After methylation, SAM is converted to S-adenosylhomocysteine, which is further metabolized to adenosine and homocysteine. Here, we show that the SAM transmethylation pathway is up-regulated during immune cell activation and that the adenosine produced by this pathway in immune cells acts as a systemic signal to delay Drosophila larval development and ensure sufficient nutrient supply to the immune system. We further show that the up-regulation of the SAM transmethylation pathway and the efficiency of the immune response also depend on the recycling of adenosine back to ATP by adenosine kinase and adenylate kinase. We therefore hypothesize that adenosine may act as a sensitive sensor of the balance between cell activity, represented by the sum of methylation events in the cell, and nutrient supply. If the supply of nutrients is insufficient for a given activity, adenosine may not be effectively recycled back into ATP and may be pushed out of the cell to serve as a signal to demand more nutrients.

Phase separation of the PRPP amidotransferase into dynamic condensates promotes de novo purine synthesis in yeast

De novo purine synthesis (DPS) is up-regulated under conditions of high purine demand to ensure the production of genetic materials and chemical energy, thereby supporting cell proliferation. However, the regulatory mechanisms governing DPS remain unclear. We herein show that PRPP amidotransferase (PPAT), the rate-limiting enzyme in DPS, forms dynamic and motile condensates in Saccharomyces cerevisiae cells under a purine-depleted environment. The formation and maintenance of condensates requires phase separation, which is driven by target of rapamycin complex 1 (TORC1)-induced ribosome biosynthesis. The self-assembly of PPAT molecules facilitates condensate formation, with intracellular PRPP and purine nucleotides both regulating this self-assembly. Moreover, molecular dynamics simulations suggest that clustering-mediated PPAT activation occurs through intermolecular substrate channeling. Cells unable to form PPAT condensates exhibit growth defects, highlighting the physiological importance of condensation. These results indicate that PPAT condensation is an adaptive mechanism that regulates DPS in response to both TORC1 activity and cellular purine demands.

Endoplasmic Reticulum Stress and Its Role in Metabolic Reprogramming of Cancer

Background/Objectives: Endoplasmic reticulum (ER) stress occurs when ER homeostasis is disrupted, leading to the accumulation of misfolded or unfolded proteins. This condition activates the unfolded protein response (UPR), which aims to restore balance or trigger cell death if homeostasis cannot be achieved. In cancer, ER stress plays a key role due to the heightened metabolic demands of tumor cells. This review explores how metabolomics can provide insights into ER stress-related metabolic alterations and their implications for cancer therapy. Methods: A comprehensive literature review was conducted to analyze recent findings on ER stress, metabolomics, and cancer metabolism. Studies examining metabolic profiling of cancer cells under ER stress conditions were selected, with a focus on identifying potential biomarkers and therapeutic targets. Results: Metabolomic studies highlight significant shifts in lipid metabolism, protein synthesis, and oxidative stress management in response to ER stress. These metabolic alterations are crucial for tumor adaptation and survival. Additionally, targeting ER stress-related metabolic pathways has shown potential in preclinical models, suggesting new therapeutic strategies. Conclusions: Understanding the metabolic impact of ER stress in cancer provides valuable opportunities for drug development. Metabolomics-based approaches may help identify novel biomarkers and therapeutic targets, enhancing the effectiveness of antitumor therapies.

Emilia sonchifolia (L.) DC. inhibits the growth of Methicillin-Resistant Staphylococcus epidermidis by modulating its physiology through multiple mechanisms

Bloodstream infections (BSIs) are a public health concern, causing substantial morbidity and mortality. Staphylococcus epidermidis (S. epidermidis) is a leading cause BSIs. Antibiotics targeting S. epidermidis have been the mainstay of treatment for BSIs, however their efficacy is diminishing in combating with drug-resistant bacteria. Therefore, alternative treatments for antibiotic-resistant infections are urgently required. Studies have demonstrated that certain traditional Chinese medicine (TCM) exhibit notable antimicrobial activity and can help mitigate bacterial resistance. Among these, The ethanol extract of Emilia sonchifolia (L.) DC (E. sonchifolia) (10 g crude drug/1 g extract ) exhibits a noteworthy anti-methicillin-resistant S. epidermidis (MRSE) effect. This study explores antibacterial activity and underlying mechanisms of E. sonchifolia against MRSE. The antibacterial activity of E. sonchifolia against MRSE was assessed in vitro by measuring the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The MRSE-induced mouse BSIs model was used to evaluate the antibacterial activity of E. sonchifolia in vivo. Proteomic and transcriptomic analyses were performed to elucidate the underlying antibacterial mechanisms. The MIC and MBC values of E. sonchifolia against MRSE were 5 mg/mL and 20 mg/mL, respectively. In vivo, E. sonchifolia effectively treated MRSE-induced BSIs. Additionally, proteomic and transcriptomic analyses revealed considerable down-regulation of purine metabolism, that were associated with oxidative stress and cell wall synthesis. The enzyme linked immunosorbent assay(ELISA) results showed decreased levels of inosine monophosphate (IMP), Adenosine monophosphate(AMP) and guanine monophosphate (GMP), indicating inhibited purine metabolism. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis confirmed bacterial cell wall damage. E. sonchifolia exerts antibacterial effects by inhibiting purine metabolism, promoting bacterial oxidative stress, and impairing cell wall synthesis. These findings provide novel insights into the mechanistic understanding of E. sonchifolia's efficacy against MRSE, offering potential strategies for managing MRSE infections.

Mass Spectrometry Imaging Unveils the Metabolic Effect of 6PPD-Quinone in Exposed Mice

N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q) has gained widespread attention as an emerging significant environmental contaminant, but its biochemical toxicity in mammals remains inadequately explored. In this study, the systemic toxicological effects of 6PPD-Q in mouse models exposed to both high and low doses were investigated. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) was applied to evaluate its effects on major organs, including the liver, kidneys, spleen, and testes. Notably, both high and low doses caused similar multiorgan metabolic disturbances, with significant changes in antioxidant levels, highlighting oxidative stress as a key factor in 6PPD-Q-induced damage. Further results revealed that 6PPD-Q disrupts critical metabolic pathways, including glutathione metabolism, ascorbic acid metabolism, energy metabolism, and amino acid metabolism, which are associated with systemic oxidative stress, immune dysfunction, and disruptions in liver, kidney and testis. This study provides important insights into the mechanisms of 6PPD-Q toxicity and underscores the need for further research to assess its potential health risks, which could guide future environmental policies and human health risk assessments.

Activation of Imprinted Gene PW1 Promotes Cardiac Fibrosis After Ischemic Injury

BACKGROUND

Cardiac fibrosis, characterized by excessive extracellular matrix (ECM) deposition in the myocardium, is an important target for heart disease treatments. Pw1 (paternally expressed gene 3) is an imprinted gene expressed from the paternal allele, and de novo purine biosynthesis (DNPB) is a crucial pathway for nucleotide synthesis. However, the roles of PW1 and DNPB in ECM production by cardiac fibroblasts during myocardial ischemia are not yet understood.

METHODS

To induce myocardial damage, we performed left anterior descending coronary artery ligation. We generated Pw1CreER-2A-eGFP and Pw12A-CreER knock-in mouse lines to evaluate the expression of the 2 Pw1 alleles in normal and injured hearts. Bisulfite sequencing was used to analyze the DNA methylation of the Pw1 imprinting control region. We identified the phosphoribosylformylglycinamidine synthase (Pfas) gene, encoding the DNPB enzyme PFAS, as a direct target of PW1 using chromatin immunoprecipitation sequencing and real-time quantitative polymerase chain reaction. The role of DNPB in ECM production and cardiac fibrosis after injury was examined in vitro using cultured cardiac fibroblasts and in vivo with Pfas-deficient mice.

RESULTS

Our study demonstrates that myocardial infarction reduces DNA methylation at the imprinting control region of the maternally imprinted gene Pw1, triggering a switch from monoallelic imprinting to biallelic expression of Pw1 in cardiac fibroblasts. In activated cardiac fibroblasts, increased Pw1 expression promotes purine biosynthesis and induces ECM production by transcriptionally activating the DNPB factor Pfas. We identified that DNPB is essential for ECM production in activated fibroblasts and that loss of Pfas in fibroblasts limits cardiac fibrosis and improves heart function after injury.

CONCLUSIONS

This study demonstrates that Pw1 imprinting is disrupted after injury and reveals a novel role for the downstream target PFAS in ECM production and cardiac fibrogenesis. Targeting the PW1/PFAS signaling pathway presents a promising therapeutic strategy for improving cardiac repair after injury.

Gut microbiota as a new target for hyperuricemia: A perspective from natural plant products

BACKGROUND

Hyperuricemia, a prevalent chronic metabolic disorder caused by purine metabolism disturbances, is characterized by elevated serum uric acid (UA) levels. Prolonged hyperuricemia can cause severe complications such as gout or kidney damage. However, the toxic side effects of and adverse reactions to UA-lowering drugs are becoming increasingly prominent. Therefore, new targets and drugs for hyperuricemia are needed.

PURPOSE

This review aims to summarize recent research progress on the prevention and treatment mechanisms for gut microbiota-hyperuricemia from the perspective of plant-derived natural products.

METHODS

Data from PubMed, Web of Science, ScienceDirect, and the CNKI databases spanning from January 2020 to December 2024 were reviewed. The aim of this study is to categorize and summarize the relevant mechanisms through which natural products improve hyperuricemia via the gut microbiota. The retrieved data followed PRISMA criteria (Preferred Reporting Items for Systematic reviews and Meta-Analyses).

RESULTS

Regulating gut microbiota as a treatment for hyperuricemia. Targeting the gut microbiota could reduce host UA levels by promoting purine degradation, reducing UA production, and increasing UA excretion. Moreover, the gut microbiota also exerts anti-inflammatory and antioxidant effects that alleviate complications such as renal damage caused by hyperuricemia. Due to their diverse sources, multicomponent synergy, multitarget effects, and minimal side effects, plant-derived natural products have been extensively utilized in the management of hyperuricemia. Especially, utilizing natural products from plants to regulate the gut microbiota has become a new strategy for reducing UA levels.

CONCLUSION

This review comprehensively summarizes recent advances in understanding the preventive and therapeutic mechanisms of plant-derived natural products in ameliorating hyperuricemia and its comorbidities through gut microbiota modulation. This review contributes a novel perspective for the development of safer and more efficacious UA-lowering products.

Genetic control over biogenic crystal morphogenesis in zebrafish

Organisms evolve mechanisms that regulate the properties of biogenic crystals to support a wide range of functions, from vision and camouflage to communication and thermal regulation. Yet, the mechanism underlying the formation of diverse intracellular crystals remains enigmatic. Here we unravel the biochemical control over crystal morphogenesis in zebrafish iridophores. We show that the chemical composition of the crystals determines their shape, particularly through the ratio between the nucleobases guanine and hypoxanthine. We reveal that these variations in composition are genetically controlled through tissue-specific expression of specialized paralogs, which exhibit remarkable substrate selectivity. This orchestrated combination grants the organism with the capacity to generate a broad spectrum of crystal morphologies. Overall, our findings suggest a mechanism for the morphological and functional diversity of biogenic crystals and may, thus, inspire the development of genetically designed biomaterials and medical therapeutics.

Metabolomic and gene networks approaches reveal the role of mitochondrial membrane proteins in response of human melanoma cells to THz radiation

Terahertz (THz) radiation has gained attention due to technological advancements, but its biological effects remain unclear. We investigated the impact of 2.3 THz radiation on SK-MEL-28 cells using metabolomic and gene network analysis. Forty metabolites, primarily related to purine, pyrimidine synthesis and breakdown pathways, were significantly altered post-irradiation. Lipids, such as ceramides and phosphatidylcholines, were also affected. Gene network reconstruction and analysis identified key regulators of the enzymes involved in biosynthesis and degradation of significantly altered metabolites. Mitochondrial membrane components, such as the respiratory chain complex, the proton-transporting ATP synthase complex, and components of lipid rafts reacted to THz radiation. We propose that THz radiation induces reversible disruption of the lipid raft macromolecular structure, thereby altering mitochondrial molecule transport while maintaining protein integrity, which explains the high cell survival rate. Our findings enhance the understanding of THz biological effects and emphasize the role of membrane components in the cellular response to THz radiation.

Combined exposure effects: Multilevel impact analysis of cycloxaprid and microplastics on Penaeus vannamei

In real environments, multiple pollutants often coexist, so studying the impact of a single pollutant does not fully reflect the actual situation. Cycloxaprid, a new neonicotinoid pesticide, poses significant ecological risks due to its unique mechanism and widespread distribution in aquatic environments. Additionally, the ecological effects of microplastics, another common environmental pollutant, cannot be overlooked. This study explored the ecotoxicological effects of cycloxaprid and microplastics, both alone and in combination, on Penaeus vannamei over 28 days. The results revealed significant physiological impacts, with notable changes in the shrimp immune system and hepatopancreatic energy and lipid metabolism. Key findings include alterations in hemocyanin, nitric oxide, and phenol oxidase levels, along with disturbances in Na+/K+-, Ca2+-, and Mg2+-ATPase activities. Additionally, neural signaling disruptions were evidenced by fluctuations in acetylcholine, dopamine, and acetylcholinesterase levels. Transcriptomic analysis revealed the profound influence of these pollutants on gene expression and metabolic processes in the hepatopancreas and nervous system. This comprehensive assessment underlines the potential growth impacts on shrimp and underscores the ecological risks of cycloxaprid and microplastics, offering insights for future risk assessments and biomarker identification.

Stress exposure in the mdx mouse model of Duchenne muscular dystrophy provokes a widespread metabolic response

Duchenne muscular dystrophy is a severe neuromuscular wasting disease that is caused by a primary defect in dystrophin protein and involves organism-wide comorbidities such as cardiomyopathy, metabolic and mitochondrial dysfunction, and nonprogressive cognitive impairments. Physiological stress exposure in the mdx mouse model of Duchenne muscular dystrophy results in phenotypic abnormalities that include locomotor inactivity, hypotension, and increased morbidity. Severe and lethal stress susceptibility in mdx mice corresponds to metabolic dysfunction in several coordinated metabolic pathways within dystrophin-deficient skeletal muscle, as well as prolonged elevation in mdx plasma corticosterone levels that extends beyond the wild-type (WT) stress response. Here, we performed a targeted mass spectrometry-based plasma metabolomics screen focused on biological stress pathways in healthy and dystrophin-deficient mdx mice exposed to mild scruff stress. One-third of the stress-relevant metabolites interrogated displayed significant elevation or depletion in mdx plasma after scruff stress and were restored to WT levels by skeletal muscle-specific dystrophin expression. The metabolic pathways of mdx mice altered by scruff stress are associated with regulation of the hypothalamic-pituitary-adrenal axis, locomotor tone, neurocognitive function, redox metabolism, cellular bioenergetics, and protein catabolism. Our data suggest that a mild stress triggers an exaggerated, multi-system metabolic response in mdx mice.

Metabolic pathways of Alternative Lengthening of Telomeres in pan-carcinoma

Alternative Lengthening of Telomeres (ALT) is a telomerase-independent mechanism deployed by several aggressive cancers to maintain telomere length. This contributes to their malignancy and resistance to conventional therapies. In prior studies, we have identified key proteins linked to the ALT process using multi-omic data integration strategies. In this work, we combined metabolomic datasets with our earlier results to identify targetable metabolic pathways for ALT-positive tumors. 39 ALT-related proteins were found to interact with 42 different metabolites in our analysis. Additional networking analysis revealed a complex interaction between metabolites and ALT-related proteins, suggesting that pan-cancer oncogenes may have an impact on these pathways. Three metabolic pathways have been primarily related with the ALT mechanism: purine metabolism, cysteine and methionine metabolism, and nicotinate and nicotinamide metabolism. Lastly, we prioritized FDA-approved drugs (azathioprine, thioguanine, and mercaptopurine) that could target ALT-positive tumors through purine metabolism. This work provides a wide perspective of the metabolomic pathways associated with ALT and reveals potential therapeutic targets that require further experimental validation.

Metabolic Regulation in Acute Respiratory Distress Syndrome: Implications for Inflammation and Oxidative Stress

Acute respiratory distress syndrome (ARDS) is a severe and life-threatening pulmonary condition characterized by intense inflammation and disrupted oxygen exchange, which can lead to multiorgan failure. Recent findings have established ARDS as a systemic inflammatory disorder involving complex interactions between lung injury, systemic inflammation, and oxidative stress. This review examines the pivotal role of metabolic disturbances in the pathogenesis of ARDS, emphasizing their influence on inflammatory responses and oxidative stress. Common metabolic abnormalities in ARDS patients, including disruptions in carbohydrate, amino acid, and lipid metabolism, contribute significantly to the disease's severity. These metabolic dysfunctions interplay with systemic inflammation and oxidative stress, further exacerbating lung injury and worsening patient outcomes. By analyzing the regulatory mechanisms of various metabolites implicated in ARDS, we underscore the potential of targeting metabolic pathways as a therapeutic approach. Such interventions could help attenuate inflammation and oxidative stress, presenting a promising strategy for ARDS treatment. Additionally, we review potential drugs that modulate metabolic pathways, providing valuable insights into the etiology of ARDS and potential therapeutic directions. This comprehensive analysis enhances our understanding of ARDS and highlights the importance of metabolic regulation in the development of effective treatment strategies. Key findings from this review demonstrate that metabolic disturbances, particularly those affecting carbohydrate, amino acid, and lipid metabolism, play critical roles in amplifying inflammation and oxidative stress, underscoring the potential of metabolic-targeted therapies to improve patient outcomes.

Redox-dependent purine degradation triggers postnatal loss of cardiac regeneration potential

Postnatal cardiomyocyte cell cycle withdrawal is a critical step wherein the mammalian heart loses regenerative potential after birth. Here, we conducted interspecies multi-omic comparisons between the mouse heart and that of the opossum, which have different postnatal time-windows for cardiomyocyte cell cycle withdrawal. Xanthine metabolism was activated in both postnatal hearts in parallel with cardiomyocyte cell cycle arrest. The pentose phosphate pathway (PPP) which produces NADPH was found to decrease simultaneously. Postnatal myocardial tissues became oxidized accordingly, and administration of antioxidants to neonatal mice altered the PPP and suppressed the postnatal activation of cardiac xanthine metabolism. These results suggest a redox-driven postnatal switch from purine synthesis to degradation in the heart. Importantly, inhibition of xanthine metabolism in the postnatal heart extended postnatal duration of cardiomyocyte proliferation and maintained postnatal heart regeneration potential in mice. These findings highlight a novel role of xanthine metabolism as a redox-dependent metabolic regulator of cardiac regeneration potential.

Persistent Metabolic Changes Are Induced by 24 h Low-Dose Lead (Pb) Exposure in Zebrafish Embryos

Lead (Pb) is a heavy metal associated with a range of toxic effects. Relatively few studies attempt to understand the impact of lead on development from a mechanistic perspective. Danio rerio (zebrafish) embryos are a model organism for studying the developmental consequences of exposure to chemical agents. This study examined the metabolome of developing zebrafish embryos exposed to 5 ppb, 15 ppb, 150 ppb, and 1500 ppb Pb concentrations during the first 24 h post fertilization, followed by 24 h of unexposed development and harvest at 48 h. Untargeted metabolomics and multivariate analysis revealed that various Pb exposures differentially affected the embryonic metabolome. Pathway analyses showed the dysregulation of biopterin, purine, alanine, and aspartate metabolism. Inductively coupled plasma mass spectrometry demonstrated Pb accumulation in embryos. Additionally, decreases in oxidation-reduction ratios were observed in 5-150 ppb groups but not in the 1500 ppb exposure group. This finding, along with several metabolite abundances, suggests a hormetic effect of Pb concentrations on the developing zebrafish metabolome. Together, these data reveal persistent global changes in the embryonic metabolome, pin-point biomarkers for Pb exposure, unveil dose-dependent relationships, and reflect Pb-induced changes in cellular energy. This work highlights aberrant processes and persistent changes underlying low-dose heavy metal exposure during early development.

Estrogen-mediated inhibition of purine metabolism and cell cycle arrest as a novel therapeutic approach in colorectal cancer

Purine metabolism is upregulated in various cancers including colorectal cancer (CRC). While previous work has elucidated the role of estrogen (E2) in metabolic reprogramming and ATP production, the effect of E2 on purine metabolism remains largely unknown. Herein, the impact of E2 signalling on purine metabolism in CRC cells was investigated using metabolome and transcriptome profiling of cell extracts derived from E2-treated HCT-116 cells with intact or silenced estrogen receptor alpha (ERα). Purine metabolic pathway enrichment analysis showed that 27 genes in the de novo purine synthesis pathway were downregulated in E2-treated CRC cells. Downstream consequences of E2 treatment including the induction of DNA damage, cell cycle arrest, and apoptosis were all shown to be ERα-dependent. These findings demonstrate, for the first time, that E2 exerts a significant anti-growth and survival effect in CRC cells by targeting the purine synthesis pathway in a ERα-dependent manner, meriting further investigation of the therapeutic utility of E2 signalling in CRC.

Smooth muscle cell-specific CD47 deletion suppresses atherosclerosis

BACKGROUND

Recent smooth muscle cell (SMC)-lineage tracing and single-cell RNA sequencing (scRNA-seq) experiments revealed a significant role of SMC-derived cells in atherosclerosis development. Further, thrombospondin-1 (TSP1), a matricellular protein, and activation of its receptor cluster of differentiation (CD) 47 have been linked with atherosclerosis. However, the role of vascular SMC TSP1-CD47 signaling in regulating VSMC phenotype and atherogenesis remains unknown.

METHODS

We investigated the role of SMC CD47 activation by TSP1 in regulating VSMC phenotype and atherosclerosis development using various in vitro cell-based assays, molecular biological techniques, immunohistological approaches, reanalysis of publicly available scRNA-seq data, and cell-specific knockout mice.

RESULTS

We observed elevated TSP1 expression in human atherosclerotic vascular tissues and VSMCs. TSP1-treated VSMCs exhibited decreased expression of contractile SMC markers (ACTA2, CNN1, and TAGLN) and increased proliferation. Additional experiments and reanalysis of the scRNA-seq dataset showed CD47 as the major TSP1 receptor in VSMCs, with its expression increased in SMC-derived modulated cells of murine atherosclerotic arteries. Knockdown of CD47 gene in human VSMCs upregulated expression of contractile SMC markers and abrogated TSP1's effects on these genes. SMC-specific Cd47 deletion in mice suppressed atherosclerotic lesion formation, reduced macrophage accumulation, and decreased necrotic area. However, no significant differences were observed in weight gain, liver and adipose tissue mass, plasma total cholesterol, and fasting blood glucose between control and SMC-restricted Cd47-deficient mice. Further experiments demonstrated increased efferocytosis of apoptotic CD47-silenced VSMCs by macrophages.

CONCLUSIONS

These findings suggest that CD47 plays a crucial role in regulating VSMC phenotype, and SMC-specific-Cd47 deletion suppresses atherosclerosis.

NEW AND NOTEWORTHY

VSMC phenotypic switching contributes to atherosclerosis development. The present study reports the novel observations that Cd47 levels are upregulated in phenotypically modulated SMCs within atherosclerotic arteries and targeted deletion of Cd47 specifically in SMCs attenuates atherosclerosis. Mechanistic in vitro investigations further showed that TSP1-CD47 signaling regulates VSMC phenotype. Therefore, targeting SMC CD47 represents a promising therapeutic target to suppress atherogenesis.

Failure to repair damaged NAD(P)H blocks de novo serine synthesis in human cells

BACKGROUND

Metabolism is error prone. For instance, the reduced forms of the central metabolic cofactors nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH), can be converted into redox-inactive products, NADHX and NADPHX, through enzymatically catalyzed or spontaneous hydration. The metabolite repair enzymes NAXD and NAXE convert these damaged compounds back to the functional NAD(P)H cofactors. Pathogenic loss-of-function variants in NAXE and NAXD lead to development of the neurometabolic disorders progressive, early-onset encephalopathy with brain edema and/or leukoencephalopathy (PEBEL)1 and PEBEL2, respectively.

METHODS

To gain insights into the molecular disease mechanisms, we investigated the metabolic impact of NAXD deficiency in human cell models. Control and NAXD-deficient cells were cultivated under different conditions, followed by cell viability and mitochondrial function assays as well as metabolomic analyses without or with stable isotope labeling. Enzymatic assays with purified recombinant proteins were performed to confirm molecular mechanisms suggested by the cell culture experiments.

RESULTS

HAP1 NAXD knockout (NAXDko) cells showed growth impairment specifically in a basal medium containing galactose instead of glucose. Surprisingly, the galactose-grown NAXDko cells displayed only subtle signs of mitochondrial impairment, whereas metabolomic analyses revealed a strong inhibition of the cytosolic, de novo serine synthesis pathway in those cells as well as in NAXD patient-derived fibroblasts. We identified inhibition of 3-phosphoglycerate dehydrogenase as the root cause for this metabolic perturbation. The NAD precursor nicotinamide riboside (NR) and inosine exerted beneficial effects on HAP1 cell viability under galactose stress, with more pronounced effects in NAXDko cells. Metabolomic profiling in supplemented cells indicated that NR and inosine act via different mechanisms that at least partially involve the serine synthesis pathway.

CONCLUSIONS

Taken together, our study identifies a metabolic vulnerability in NAXD-deficient cells that can be targeted by small molecules such as NR or inosine, opening perspectives in the search for mechanism-based therapeutic interventions in PEBEL disorders.

Cordycepin affects Streptococcus mutans biofilm and interferes with its metabolism

BACKGROUND

Streptococcus mutans (S. mutans) contributes to caries. The biofilm formed by S. mutans exhibits greater resistance to drugs and host immune defenses than the planktonic form of the bacteria. The objective of this study was to evaluate the anti-biofilm effect of cordycepin from the perspective of metabolomics.

METHODS

The minimum inhibitory concentration (MIC) was determined to evaluate the antimicrobial effect of cordycepin on planktonic S. mutans. The 24-h biofilm was treated with 128 µg/mL of cordycepin for 10 min at the 8- or 20-h time points. Biofilm biomass and metabolism were assessed using crystal violet and MTT assays and cordycepin cytotoxicity was evaluated in human oral keratinocytes (HOK) using CCK-8 assays. The live bacterial rate and the biofilm volume were assessed by confocal laser scanning microscopy. Metabolic changes in the biofilm collected at different times during with cordycepin were analyzed by metabolomics and verified by quantitative real-time PCR.

RESULTS

The results showed that treatment with 128 µg/mL cordycepin reduced both the biomass and metabolic activity of the biofilm without killing the bacteria, and cordycepin at this concentration showed good biocompatibility. Metabolomics analysis showed that differentially abundant metabolites following cordycepin treatment were mainly related to purine and nucleotide metabolism. After immediate treatment with cordycepin, genes related to purine and nucleotide metabolism were downregulated, and the levels of various metabolites changed significantly. However, the effect was reversible. After continuing culture for 4 h, the changes in genes and most metabolites were reversed, although the levels of 2'-deoxyadenosine, 2'-deoxyinosine, and adenine remained significantly different.

CONCLUSIONS

Cordycepin has the effect of anti-biofilm of S. mutans, mainly related to purine and nucleotide metabolism.

Elucidating the Mechanisms of Acquired Palbociclib Resistance via Comprehensive Metabolomics Profiling

Palbociclib is a cyclin-dependent kinase 4/6 inhibitor and a commonly used antitumor drug. Many cancers are susceptible to palbociclib resistance, however, the underlying metabolism mechanism and extent of resistance to palbociclib are unknown. In this study, LC-MS metabolomics was used to investigate the metabolite changes of colorectal cancer SW620 cells that were resistant to palbociclib. The study indicated that there were 76 metabolite expression differences between SW620 cells with palbociclib resistance and the parental SW620 cells involving amino acids, glutathione, ABC transporters, and so on. MetaboAnalyst 6.0 metabolic pathway analysis showed that arginine synthesis, β-alanine metabolism, and purine metabolism were disrupted. These results may provide potential clues to the metabolism mechanism of drug resistance in cancer cells that are resistant to palbociclib. Our study has the potential to contribute to the study of anti-palbociclib resistance.

Simultaneous determination of canonical purine metabolism using a newly developed HILIC-MS/MS in cultured cells

Purine metabolism acts as the core role in human metabolic network. It offers purine metabolites as raw material for building blocks in cell survival and proliferation. Purine metabolites are the most abundant metabolic substrates in organisms. There are few reports to simultaneously quantify canonical purine metabolism in cells. A novel hydrophilic interaction liquid chromatography coupled with mass spectrometry (HILIC-MS/MS) method was developed to simultaneously determine purines profile in biological samples. Chromatographic separation was achieved using a HILIC (Waters Xbridge™ Amide) column. Different optimizing chromatographic conditions and mass spectrometric parameters were tested in order to provide the best separation and the lowest limit of quantification (LLOQ) values for targeted metabolites. The validation was evaluated according to the Food and Drug Administration guidelines. The limit of determination (LOD) and the LOQ values were in the range of 0.02-8.33 ng mL-1 and 0.1-24.5 ng mL-1, respectively. All calibration curves displayed good linear relationship of with excellent correlation coefficient (r) ranging from 0.9943 to 0.9999. Both intra-day and inter-day variability were below 15 %, respectively. Trueness, expressed as relative error, was always within ±15 %. In addition, no derivatization procedure and ion-pair reagents are in need. The innovated approach demonstrates high sensitivity, strong specificity, and good repeatability, making it suitable for absolute quantitative studies of canonical purine metabolism in cultured cells.

Phlorizin ameliorates cognitive and behavioral impairments via the microbiota-gut-brain axis in high-fat and high-fructose diet-induced obese male mice

The long-term high-fat, high-sugar diet exacerbates type 2 diabetes mellitus (T2DM)-related cognitive impairments. Phlorizin, a well-studied natural compound found in apples and other plants, is recognized for its bioactive properties, including modulation of glucose and lipid metabolism. Despite its established role in mitigating metabolic disorders, the neuroprotective effects of phlorizin, particularly against diabetes-related cognitive dysfunction, have not been fully elucidated. Therefore, the present study aimed to investigate the effect of dietary supplementation of phlorizin on high-fat and high-fructose diet (HFFD)-induced cognitive dysfunction and evaluate the crucial role of the microbiota-gut-brain axis. We found that dietary supplementation of phlorizin for 14 weeks effectively prevented glucolipid metabolism disorder, spatial learning impairment, and memory impairment in HFFD mice. In addition, phlorizin improved the HFFD-induced decrease in synaptic plasticity, neuroinflammation, and excessive activation of microglia in the hippocampus. Transcriptomics analysis shows that the protective effect of phlorizin on cognitive impairment was associated with increased expression of neurotransmitters and synapse-related genes in the hippocampus. Phlorizin treatment alleviated colon microbiota disturbance, mainly manifested by an increase in gut microbiota diversity and the abundance of short-chain fatty acid (SCFA)-producing bacteria. The level of microbial metabolites, including SCFA, inosine 5'-monophosphate (IMP), and D (-)-beta-hydroxybutyric acid (BHB) were also significantly increased after phlorizin treatment. Integrating multiomics analysis observed tight connections between phlorizin-regulated genes, microbiota, and metabolites. Furthermore, removal of the gut microbiota via antibiotics treatment diminished the protective effect of phlorizin against HFFD-induced cognitive impairment, underscoring the critical role of the gut microbiota in mediating cognitive behavior. Importantly, supplementation with SCFA and BHB alone mimicked the regulatory effects of phlorizin on cognitive function. Therefore, phlorizin shows promise as a potential nutritional therapy for addressing cognitive impairment associated with metabolic disorders. Further research is needed to explore its effectiveness in preventing and alleviating neurodegenerative diseases.

Triple-helix β-glucan-based self-assemblies, synthesis, characterization and anticarcinogenic effect

Triple negative breast cancer (TNBC) seriously endangers women's life and health due to its high invasion and mortality. Reactive oxygen species (ROS) mediated tumor cells apoptosis is considered an effective anticancer approach. Herein, we designed a natural active triple helix β-Glucan (BFP) wrapped single walled carbon nanotubes (SWNTs)-loaded doxorubicin (DOX) self-assembly (BSD) via generating excess ROS to induce oxidative stress damage for TNBC therapy. BSD could directly consume glutathione (GSH) to promote ROS. In vitro results demonstrated that BSD exhibited obvious antitumor effects to breast cancer cells by promoting apoptosis. Un-targeted metabolomics under molecular level identified the specific metabolic targets and unveiled that BSD markedly disturbed multiple metabolic pathways, including purine metabolism, pentose phosphate pathway, glutathione metabolism pathways, amino sugar and nucleotide sugar metabolism and energy metabolism, led to the inhibition of DNA and RNA synthesis, the generation of ROS, the exacerbation of DNA damage, the disruption of cell membrane integrity and the decrease of ATP. In vitro and in vivo oxidative stress assays further verified that BSD significantly promoted intracellular oxidative stress and resulted in cell damage. This study provides theoretical basis for the development and screening of new drugs based on ROS therapy for TNBC.

Integrative Proteomics-Metabolomics of In Vitro Degeneration of Cardiovascular Cell Lines

Long-term cell culture is an important biological approach but is also characterized by degeneration in cellular morphology, proliferation rate, and function. To explore this phenomenon in a systematic way, we conducted an integrative proteomics-metabolomics measurement of two cardiovascular cell lines of AC16 and HUVECs. The 18th culturing passages, i.e., G18, showed as the turning points by cell metabolism profiles, in which the metabolomic changes demonstrated the dysfunction of energy, amino acid, and ribonucleotide metabolism metabolic pathways. Although active protein networks showed mitochondria abundance AC16 and oxidative/nitrative sensitive HUVECs indicated the different degeneration patterns, the G18 and G30 proteomics evidenced the senescence by processes of signal transduction, signaling by interleukins, programmed cell death, cellular responses to stimuli, cell cycle, mRNA splicing, and translation. Some crucial proteins (RPS8, HNRNPR, SOD2, LMNB1, PSMA1, DECR1, GOT2, OGDH, PNP, CBS, ATIC, and IMPDH2) and metabolites (L-glutamic acid, guanine, citric acid, guanosine, guanosine diphosphate, glucose 6-phosphate, and adenosine) that contributed to the dysregulation of cellular homeostasis are identified by using the integrative proteomic-metabolomic analysis, which highlighted the increased cellular instability. These findings illuminate some vital molecular processes when culturing serial passages, which contribute holistic viewpoints of in vitro biology with emphasis on the replicative senescence of cardiovascular cells.

Failure of metabolic checkpoint control during late-stage granulopoiesis drives neutropenia in reticular dysgenesis

ABSTRACT

Cellular metabolism is highly dynamic during hematopoiesis, yet the regulatory networks that maintain metabolic homeostasis during differentiation are incompletely understood. Herein, we have studied the grave immunodeficiency syndrome reticular dysgenesis caused by loss of mitochondrial adenylate kinase 2 (AK2) function. By coupling single-cell transcriptomics in samples from patients with reticular dysgenesis with a CRISPR model of this disorder in primary human hematopoietic stem cells, we found that the consequences of AK2 deficiency for the hematopoietic system are contingent on the effective engagement of metabolic checkpoints. In hematopoietic stem and progenitor cells, including early granulocyte precursors, AK2 deficiency reduced mechanistic target of rapamycin (mTOR) signaling and anabolic pathway activation. This conserved nutrient homeostasis and maintained cell survival and proliferation. In contrast, during late-stage granulopoiesis, metabolic checkpoints were ineffective, leading to a paradoxical upregulation of mTOR activity and energy-consuming anabolic pathways such as ribonucleoprotein synthesis in AK2-deficient cells. This caused nucleotide imbalance, including highly elevated adenosine monophosphate and inosine monophosphate levels, the depletion of essential substrates such as NAD+ and aspartate, and ultimately resulted in proliferation arrest and demise of the granulocyte lineage. Our findings suggest that even severe metabolic defects can be tolerated with the help of metabolic checkpoints but that the failure of such checkpoints in differentiated cells results in a catastrophic loss of homeostasis.

Bacterial purine metabolism modulates C. elegans development and stress tolerance via DAF-16

The purine metabolism is crucial for cellular function and is a conserved metabolic network from prokaryotes to humans. While extensively studied in microorganisms like yeast and bacteria, the impact of perturbing dietary intermediates from the purine biosynthesis on animal development and growth remains poorly understood. We utilized Caenorhabditis elegans as the metazoan model to investigate the mechanisms underlying this deficiency. Through a high-throughput screening of an Escherichia coli mutant library Keio collection, we identified 34 E. coli mutants that delay C. elegans development. Among these mutants, we found that E. coli purE gene is an essential genetic component that promotes host development in a dose-dependent manner. Further metabolites supplementation suggests that bacterial purE downstream metabolite 5-aminoimidazole-4-carboxamide ribotide (AICAR) can inhibit worm growth. Additionally, we found the FoxO transcription factor DAF-16 is indispensable in worm development delay induced by purE mutation, and observed increased nuclear accumulation of DAF-16 when fed E. coli purE- mutants, suggesting the role of DAF-16 in response to purE mutation. RNA-seq analysis and phenotypic assays revealed that worms fed the E. coli purE mutant exhibited elevated lifespan, thermotolerance, and pathogen resistance. These findings collectively suggest that certain intermediates in the bacterial purine biosynthesis can serve as a cue to modulate development and activate the defense response in the nematode C. elegans through DAF-16.

Targeting purine metabolism-related enzymes for therapeutic intervention: A review from molecular mechanism to therapeutic breakthrough

Purines are ancient metabolites with established and emerging metabolic and non-metabolic signaling attributes. The expression of purine metabolism-related genes is frequently activated in human malignancies, correlating with increased cancer aggressiveness and chemoresistance. Importantly, under certain stimulating conditions, the purine biosynthetic enzymes can assemble into a metabolon called "purinosomes" to enhance purine flux. Current evidence suggests that purine flux is regulated by a complex circuit that encompasses transcriptional, post-translational, metabolic, and association-dependent regulatory mechanisms. Furthermore, purines within the tumor microenvironment modulate cancer immunity through signaling mediated by purinergic receptors. The deregulation of purine metabolism has significant metabolic consequences, particularly hyperuricemia. Herbal-based therapeutics have emerged as valuable pharmacological interventions for the treatment of hyperuricemia by inhibiting the activity of hepatic XOD, modulating the expression of renal urate transporters, and suppressing inflammatory responses. This review summarizes recent advancements in the understanding of purine metabolism in clinically relevant malignancies and metabolic disorders. Additionally, we discuss the role of herbal interventions and the interaction between the host and gut microbiota in the regulation of purine homeostasis. This information will fuel the innovation of therapeutic strategies that target the disease-associated rewiring of purine metabolism for therapeutic applications.

SUMO-targeted Ubiquitin Ligases as crucial mediators of protein homeostasis in Candida glabrata

Candida glabrata is an opportunistic human pathogen, capable of causing severe systemic infections that are often resistant to standard antifungal treatments. To understand the importance of protein SUMOylation in the physiology and pathogenesis of C. glabrata, we earlier identified the components of SUMOylation pathway and demonstrated that the deSUMOylase CgUlp2 is essential for pathogenesis. In this work we show that the CgUlp2 is essential to maintain protein homeostasis via the SUMO-targeted ubiquitin ligase pathway. The dual loss of deSUMOylase and specific ubiquitin ligase, CgSlx8, results in heightened protein degradation, rendering the cells vulnerable to various stressors. This degradation affects crucial processes such as purine biosynthesis and compromises mitochondrial function in the mutants. Importantly, the absence of these ubiquitin ligases impedes the proliferation of C. glabrata in macrophages. These findings underscore the significance of SUMOylation and SUMO-mediated protein homeostasis as pivotal regulators of C. glabrata physiology and capacity to survive in host cells. Understanding these mechanisms could pave the way for the development of effective antifungal treatments.

Transcriptome-wide mapping of internal mRNA N7-methylguanosine in sporulated and unsporulated oocysts of Eimeria tenella reveals stage-specific signatures

BACKGROUND

Growing evidence indicates that N7-methylguanosine (m7G) modification plays critical roles in epigenetic regulation. However, no data regarding m7G modification are currently available in Eimeria tenella, a highly virulent species causing coccidiosis in chickens.

METHODS

In the present study, we explore the distribution of internal messenger RNA (mRNA) m7G modification in sporulated and unsporulated oocysts of E. tenella as well as its potential biological functions during oocyst development using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and mRNA sequencing (mRNA-seq), and the mRNA-seq and MeRIP-seq data were verified by the quantitative reverse transcription polymerase chain reaction (RT-qPCR) and MeRIP-qPCR, respectively.

RESULTS

Our data showed that m7G peaks were detected throughout the whole mRNA body, and the coding DNA sequence (CDS) region displayed the most methylation modification. Compared with unsporulated oocysts, 7799 hypermethylated peaks and 1945 hypomethylated peaks were identified in sporulated oocysts. Further combined analysis of differentially methylated genes (DMGs) and differentially expressed genes (DEGs) showed that there was a generally positive correlation between m7G modification levels and gene transcript abundance. Unsurprisingly, the mRNA-seq and MeRIP-seq data showed good consistency with the results of the RT-qPCR and MeRIP-qPCR, respectively. Gene Ontology (GO) and pathway enrichment analysis of DEGs with altered m7G-methylated peaks were involved in diverse biological functions and pathways, including DNA replication, RNA transport, spliceosome, autophagy-yeast, and cAMP signaling pathway.

CONCLUSIONS

Altogether, our findings revealed the potential significance of internal m7G modification in E. tenella oocysts, providing some directions and clues for later in-depth research.

Regulation of Isoleucine on Colonic Barrier Function in Rotavirus-Infected Weanling Piglets and Analysis of Gut Microbiota and Metabolomics

Rotavirus (RV) is a significant contributor to diarrhea in both young children and animals, especially in piglets, resulting in considerable economic impacts on the global pig industry. Isoleucine (Ile), a branched-chain amino acid, is crucial for regulating nutrient metabolism and has been found to help mitigate diarrhea. This study aimed to assess the impact of isoleucine supplementation in feed on colonic barrier function, colonic microbiota, and metabolism in RV-infected weanling piglets. A total of thirty-two weaned piglets, aged 21 days, were randomly assigned to two dietary groups (each further divided into two subgroups, with eight replicates in each subgroup), receiving diets with either 0% or 1% isoleucine for a duration of 14 days. One group from each treatment was then challenged with RV, and the experimental period lasted for 19 days. The results showed that dietary Ile significantly increased the secretion of IL-4, IL-10, and sIgA in the colon of RV-infected weanling piglets (p < 0.05). In addition, Ile supplementation notably increased the expression of tight junction proteins, including Claudin-3, Occludin, and ZO-1 (p < 0.01), as well as the mucin protein MUC-1 in the colon of RV-infected weanling piglets (p < 0.05). Gut microbiota analysis revealed that dietary Ile increased the relative abundance of Prevotella and decreased the relative abundance of Rikenellaceae in the colons of RV-infected weanling piglets. Compared with the RV+CON, metabolic pathways in the RV+ILE group were significantly enriched in vitamin digestion and absorption, steroid biosynthesis, purine metabolism, pantothenate and CoA biosynthesis, cutin, suberine, and wax biosynthesis, as well as fatty acid biosynthesis, and unsaturated fatty acid biosynthesis. In conclusion, dietary Ile supplementation can improve immunity, colonic barrier function, colonic microbiota, and colonic metabolism of RV-infected weaned piglets. These findings provide valuable insights into the role of isoleucine in the prevention and control of RV.

The metabolic engineering of Escherichia coli for the high-yield production of hypoxanthine

BACKGROUND

Hypoxanthine, prevalent in animals and plants, is used in the production of food additives, nucleoside antiviral drugs, and disease diagnosis. Current biological fermentation methods synthesize quantities insufficient to meet industrial demands. Therefore, this study aimed to develop a strain capable of industrial-scale production of hypoxanthine.

RESULTS

De novo synthesis of hypoxanthine was achieved by blocking the hypoxanthine decomposition pathway, thus alleviating transcriptional repression and multiple feedback inhibition, and introducing a purine operon from Bacillus subtilis to construct a chassis strain. The effects of knocking out the IMP(Inosine 5'-monophosphate) branch on the growth status and titer of the strain were then investigated, and the effectiveness of adenosine deaminase and adenine deaminase was verified. Overexpressing these enzymes created a dual pathway for hypoxanthine synthesis, enhancing the metabolic flow of hypoxanthine synthesis and preventing auxotrophic strain formation. Introducing IMP-specific 5' -nucleotidase addressed the issue of adenylate accumulation. In addition, the metabolic flow of the guanine branch was dynamically regulated by the guaB gene. The supply of glutamine and aspartic acid precursors was enhanced by introducing an exogenous glnA mutant gene, overexpressing aspC, and replacing the weaker promoter to regulate the aspartic acid branching pathway. Ultimately, fermentation in a 5 L bioreactor for 48 h produced 30.6 g/L hypoxanthine, with a maximum real-time productivity of 1.4 g/L/h, the highest value of hypoxanthine production by microbial fermentation reported so far.

CONCLUSIONS

The intracellular purine biosynthesis pathway is extensive and regulated at multiple levels in cells. The IMP branch in the hypoxanthine synthesis pathway has a higher metabolic flux. The current challenge lies in systematically allocating the metabolic flux within the branch pathway to achieve substantial product accumulation. In this study, E. coli was used as the chassis strain to construct a dual pathway for IMP and AMP(Adenosine 5'-monophosphate) synergistic hypoxanthine synthesis and dynamically regulate the guanine branch pathway. Overall, our experimental efforts culminated in a high-yield, plasmid- and defect-free engineered hypoxanthine strain.

Carboxylation in de novo purine biosynthesis

De novo purine biosynthesis is one of two pathways for the synthesis of purine nucleotides that are critical for numerous biological processes, most notably nucleic acid replication. Within the pathway, there is only one carbon-carbon bond formation which is the carboxylation of 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). Interestingly, there are two unique pathways within purine biosynthesis to accomplish this transformation and this divergence is species specific. In humans and higher eukaryotes, CAIR is synthesized directly from AIR and carbon dioxide by the enzyme AIR carboxylase. In bacteria, yeast, fungi and plants, CAIR synthesis requires two steps. In the first, AIR is converted into the unstable carbamate, N5-CAIR by the enzyme N5-CAIR synthetase. N5-CAIR is then converted into CAIR by transfer of the CO2 group from N5 to C4. This is catalyzed by the enzyme N5-CAIR mutase. This divergence has provided a biochemical rationale for targeting CAIR synthesis in the development of antimicrobial agents, but recent studies have provided strong evidence that AIR carboxylase plays a critical role in several cancers. Given the significance of these enzymes as drug targets, methods to prepare and evaluate these enzymes is of interest. In this chapter, we have accumulated the most relevant assays and provided methods to synthesize the substrates and purify the enzymes.

Sustainable and Biosafe Approach to Control Potato Late Blight Using Mesoporous Silica Nanoparticles

Phytophthora infestans-induced potato late blight is considered the "cancer of the potato crop." In this work, mesoporous silica nanoparticles (MSNs) with ultrahigh specific surface area (786.28 m2/g) were synthesized, which significantly inhibited P. infestans compared with some commercial fungicides. Moreover, MSNs inhibited the growth and reproductive of P. infestans processes, including germination, sporangia infection, and zoospore release. MSNs targeted key biological pathways and induced a stress response in the P. infestans, leading to reactive oxygen species (•O2-, •OH, and 1O2) production and structural damage of sporangia. Pot experiments showed that MSNs are translocated from leaves to roots of potato plants, enhancing physiological and biochemical processes, alleviating drought stress, improving resistance to pathogens, and exhibiting soil microbe-friendly. This study systematically reveals the mechanism of MSNs to weaken the reproduction process of P. infestans and confirm the safety and feasibility of MSNs as a green and sustainable fungicide.

Probiotics as Potential Tool to Mitigate Nucleotide Metabolism Alterations Induced by DiNP Dietary Exposure in Danio rerio

Diisononyl phthalate, classified as endocrine disruptor, has been investigate to trigger lipid biosynthesis in both mammalian and teleostean animal models. Despite this, little is known about the effects of DiNP exposure at tolerable daily intake level and the possible mechanisms of its toxicity. Probiotics, on the other hand, were demonstrated to have beneficial effects on the organism's metabolism and recently emerged as a possible tool to mitigate the EDC toxicity. In the present study, using a metabolomic approach, the potential hepatic sex-related toxicity of DiNP was investigated in adult zebrafish together with the mitigating action of the probiotic formulation SLAB51, which has already demonstrated its ability to ameliorate gastrointestinal pathologies in animals including humans. Zebrafish were exposed for 28 days to 50 µg/kg body weight (bw)/day of DiNP (DiNP) through their diet and treated with 109 CFU/g bw of SLAB51 (P) and the combination of DiNP and SLAB51 (DiNP + P), and the results were compared to those of an untreated control group (C). DiNP reduced AMP, IMP, and GMP in the purine metabolism, while such alterations were not observed in the DiNP + P group, for which the phenotype overlapped that of C fish. In addition, in male, DiNP reduced UMP and CMP levels in the pyrimidine metabolism, while the co-administration of probiotic shifted the DiNP + P metabolic phenotype toward that of P male and closed to C male, suggesting the beneficial effects of probiotics also in male fish. Overall, these results provide the first evidence of the disruptive actions of DiNP on hepatic nucleotide metabolism and mitigating action of the probiotic to reduce a DiNP-induced response in a sex-related manner.

Lactate promotes the biofilm-to-invasive-planktonic transition in Salmonella enterica serovar Typhimurium via the de novo purine pathway

Salmonella enterica serovar Typhimurium (S. Typhimurium) infection triggers an inflammatory response that changes the concentration of metabolites in the gut impacting the luminal environment. Some of these environmental adjustments are conducive to S. Typhimurium growth, such as the increased concentrations of nitrate and tetrathionate or the reduced levels of Clostridia-produced butyrate. We recently demonstrated that S. Typhimurium can form biofilms within the host environment and respond to nitrate as a signaling molecule, enabling it to transition between sessile and planktonic states. To investigate whether S. Typhimurium utilizes additional metabolites to regulate its behavior, our study delved into the impact of inflammatory metabolites on biofilm formation. The results revealed that lactate, the most prevalent metabolite in the inflammatory environment, impedes biofilm development by reducing intracellular c-di-GMP levels, suppressing the expression of curli and cellulose, and increasing the expression of flagellar genes. A transcriptomic analysis determined that the expression of the de novo purine pathway increases during high lactate conditions, and a transposon mutagenesis genetic screen identified that PurA and PurG, in particular, play a significant role in the inhibition of curli expression and biofilm formation. Lactate also increases the transcription of the type III secretion system genes involved in tissue invasion. Finally, we show that the pyruvate-modulated two-component system BtsSR is activated in the presence of high lactate, which suggests that lactate-derived pyruvate activates BtsSR system after being exported from the cytosol. All these findings propose that lactate is an important inflammatory metabolite used by S. Typhimurium to transition from a biofilm to a motile state and fine-tune its virulence.IMPORTANCEWhen colonizing the gut, Salmonella enterica serovar Typhimurium (S. Typhimurium) adopts a dynamic lifestyle that alternates between a virulent planktonic state and a multicellular biofilm state. The coexistence of biofilm formers and planktonic S. Typhimurium in the gut suggests the presence of regulatory mechanisms that control planktonic-to-sessile transition. The signals triggering the transition of S. Typhimurium between these two lifestyles are not fully explored. In this work, we demonstrated that in the presence of lactate, the most dominant host-derived metabolite in the inflamed gut, there is a reduction of c-di-GMP in S. Typhimurium, which subsequently inhibits biofilm formation and induces the expression of its invasion machinery, motility genes, and de novo purine metabolic pathway genes. Furthermore, high levels of lactate activate the BtsSR two-component system. Collectively, this work presents new insights toward the comprehension of host metabolism and gut microenvironment roles in the regulation of S. Typhimurium biology during infection.

Metabolomic Alterations Associated with Phthalate Exposures among Pregnant Women in Puerto Rico

Although phthalate exposure has been linked with multiple adverse pregnancy outcomes, their underlying biological mechanisms are not fully understood. We examined associations between biomarkers of phthalate exposures and metabolic alterations using untargeted metabolomics in 99 pregnant women and 86 newborns [mean (SD) gestational age = 39.5 (1.5) weeks] in the PROTECT cohort. Maternal urinary phthalate metabolites were quantified using isotope dilution high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), while metabolic profiles in maternal and cord blood plasma were characterized via reversed-phase LC-MS. Multivariable linear regression was used in metabolome-wide association studies (MWAS) to identify individual metabolic features associated with elevated phthalate levels, while clustering and correlation network analyses were used to discern the interconnectedness of biologically relevant features. In the MWAS adjusted for maternal age and prepregnancy BMI, we observed significant associations between specific phthalates, namely, di(2-ethylhexyl) phthalate (DEHP) and mono(3-carboxypropyl) phthalate (MCPP), and 34 maternal plasma metabolic features. These associations predominantly included upregulation of fatty acids, amino acids, purines, or their derivatives and downregulation of ceramides and sphingomyelins. In contrast, fewer significant associations were observed with metabolic features in cord blood. Correlation network analysis highlighted the overlap of features associated with phthalates and those identified as differentiating markers for preterm birth in a previous study. Overall, our findings underscore the complex impact of phthalate exposures on maternal and fetal metabolism, highlighting metabolomics as a tool for understanding associated biological processes. Future research should focus on expanding the sample size, exploring the effects of phthalate mixtures, and validating identified metabolic features in larger, more diverse populations.

Metabolic changes induced by heavy metal copper exposure in human ovarian granulosa cells

Copper (Cu) is a common heavy metal and a hazardous environmental pollutant. Emerging epidemiological evidence suggests that Cu exposure is associated with female infertility, especially ovarian dysfunction. However, the mechanisms underlying ovarian toxicity remain poorly understood. Granulosa cells play crucial roles in follicle development and are the main target cells of environmental pollutants for ovarian toxicity. In this study, we investigated the effects of Cu exposure on human granulosa (KGN) cells by using cell biology and metabolomics methods, and explored the molecular mechanisms of Cu-induced cytotoxicity. We found that Cu reduced cell viability in a dose- and time-dependent manner. Then, metabolomic analyses led to the identification of 279, 368 and 466 differentially expressed metabolites (DEMs) in KGN cells exposed to 10, 60 and 240 μM Cu, respectively. Pathway enrichment analysis revealed that high Cu led to disturbances of glutathione metabolism, nucleotide metabolism, glycerophospholipid and ether lipid metabolism. Using cell biological assays, we found that exposure to high Cu significantly decreased the GSH/GSSG ratio and altered the activities of the antioxidant enzymes SOD and CAT. Exposure to high Cu significantly increased the level of mitochondrial ROS. These findings further supported the results revealed by metabolomic analysis and provided clues for elucidating the mechanism by which Cu interferes with the development of ovarian follicles.

Comparative metabolomic analysis of spaghetti meat and wooden breast in broiler chickens: unveiling similarities and dissimilarities

Introduction

Spaghetti meat (SM) and wooden breast (WB) are emerging myopathies in the breast meat of fast-growing broiler chickens. The purpose of the study was to investigate the metabolomic differences between normal (N), SM, and WB fillets 24 h postmortem.

Materials and methods

Eight chicken breasts for each experimental group were collected from a commercial processing plant. Supernatant from tissue homogenates were subjected to ultra-performance liquid chromatographytandem mass spectrometry (UPLC-MS) analysis.

Results and methods

A total of 3,090 metabolites were identified in the chicken breast meat. The comparison of WB and N showed 850 differential metabolites (P < 0.05), and the comparison of SM and N displayed 617 differential metabolites. The comparison of WB and SM showed 568 differential metabolites. The principal component analysis (PCA) plots showed a distinct separation between SM and N and between WB and N except for one sample, but SM and WB were not distinctly separated. Compared to N, 15-Hydroxyeicosatetraenoic acid (15-HETE) increased, and D-inositol-4-phosphate decreased in both SM and WB, indicating that cellular homeostasis and lipid metabolism can be affected in SM and WB. The abundance of nicotinamide adenine dinucleotide (NAD) + hydrogen (H) (NADH) was exclusively decreased between SM and N (P < 0.05). Purine metabolism was upregulated in SM and WB compared to N with a greater degree of upregulation in WB than SM. Folic acid levels decreased in SM and WB compared to N (P < 0.05). Steroid hormone biosynthesis was downregulated in SM compared to N (P < 0.05). Carbon metabolism was downregulated in SM and WB compared to N with greater degree of downregulation in WB than SM (P < 0.05). These data suggest both shared and unique metabolic alterations in SM and WB, indicating commonalities and differences in their underlying etiologies and meat quality traits. Dietary supplementation of deficient nutrients, such as NADH, folic acids, etc. and modulation of altered pathways in SM and WB would be strategies to reduce the incidence and severity of SM and WB.

Enantioselective toxicity effect and mechanisms of bifenthrin enantiomers on normal human hepatocytes

In recent decades, the toxicity of chiral pesticides to non-target organisms has attracted increasing attention. Cellular metabolic disorders are essential sensitive molecular initiating event for toxicological effects. BF is a typical chiral pesticide, and the liver is the main organ for BF accumulation. This study aimed to investigate the potential molecular mechanism of BF enantiomers' different toxic effects on L02 by a non-targeted metabolomic approach. Results revealed that the BF enantiomers exhibited different metabolic responses. In total, 51 and 36 differential metabolites were perturbed by 1S-cis-BF and 1R-cis-BF at the value of variable importance, respectively. When L02 were exposed to 1R-cis-BF, the significantly disturbed metabolic pathways were nicotinate and nicotinamide metabolism and pyrimidine metabolism. By comparison, more significantly perturbed metabolic pathways were received when the L02 were exposed to 1S-cis-BF, including glycine, serine and threonine metabolism, nicotinate and nicotinamide metabolism, arginine and proline metabolism, cysteine and methionine metabolism, glycerolipid metabolism, histidine metabolism, pyrimidine metabolism, amino sugar and nucleotide sugar metabolism and arginine biosynthesis. The results offer a new perspective in understanding the role of selective cytotoxicity of BF enantiomers, and help to evaluate the risk to human health at the enantiomeric level.