Nucleotide Metabolism Pathways Research Articles

Abstract 4426: Targeting MCT1 and PFKFB3 provokes synthetic lethality in small cell lung cancer

Abstract Small cell lung cancer (SCLC) is the third most common lung cancer and is extremely aggressive and highly metastatic. SCLC responds to radiation and standard platinum-based chemotherapy, yet this is invariably followed by relapse and the rapid emergence of lethal chemoresistant disease. Hence, SCLC has been declared a recalcitrant malignancy by NCI, and there is an urgent need to identify new and actionable therapeutic vulnerabilities. Unbiased metabolomic and shotgun and activity-based proteomic analyses of NSCLC and SCLC patient derived tumor tissues, PDX and a panel of cell lines revealed marked upregulation of glycolytic and nucleotide metabolic pathways in SCLC. Further, unbiased screens with metabolic inhibitors revealed selective sensitivity of SCLC cells to the MCT1 lactate transporter inhibitor SR13800 and to the PFKFB3 inhibitor PFK15, and that combined treatment provokes rapid apoptosis. Metabolic, flux and molecular analyses revealed that MCT1 inhibition (MCT1i) or loss in SCLC cells impairs glycolysis and triggers rapid increases in intracellular lactate that then diminish, and this is driven by the induction of lactate dehydrogenase-B (LDH-B) that oxidizes lactate into pyruvate. This is accompanied by a marked shift in the NAD+ to NADH ratio towards NADH, and increased pyruvate dehydrogenase (PDH) activity and OXPHOS. Further, MCT1 inhibition provoked increases in the Aspartate-Malate and DHAP-SnG3P shuttles, which restored the NAD+/NADH balance in the cytosol. In contrast, treatment of SCLC cells with PFKFB3 inhibitors (PFKFB3i) leads to inhibition of PDH activity, a collapse in OXPHOS and increases in lactate efflux that are due to flux of glucose through pentose phosphate pathway and re-entry into glycolysis via 3-phosphoglygerate (3-PGA). Combined MCT1/PFKFB3 inhibition amplifies metabolic alterations provoked by both MCT1i and PFKFB3i, triggering a collapse in both glycolysis and OXPHOS. Similarly, inhibition or silencing of enzymes that drive the Aspartate-Malate and DHAP-SnG3P shuttles, or inhibition of the mitochondrial pyruvate transporter, provoked metabolic collapse and cell death following inhibition or loss of MCT1. Finally, SCLC xenografts and primary SCLC CDX treated with a combination of SR13800 and PFK15 showed improved survival compared to vehicle or monotherapy treatments. Thus, co-targeting adaptive metabolic circuits provoked by inhibition of MCT1 and PFKFB3 provokes synthetic lethality in SCLC, supporting the notion that inhibition of these metabolic chokepoints will be an effective strategy for treatment of this lethal malignancy. Citation Format: Antony Herold Prabhu, Kristen Scott, Paul Stewart, Daniel Grass, Mario Fernandez, Dalia Ercan, John Koomen, Thomas Bannister, Charles Rudin, Gina DeNicola, Eric Haura, John Cleveland. Targeting MCT1 and PFKFB3 provokes synthetic lethality in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4426.

Rare red cell enzymopathies in the Indian population: A comprehensive review

Red blood cell enzyme deficiencies are a rare category of hemolytic anaemia that typically present in children with varying degrees of hemolysis, indirect hyperbilirubinemia and splenomegaly. Glucose 6-phosphate dehydrogenase (G6PD) is the most common enzyme deficiency, followed by pyruvate kinase deficiency (PKD). This article aims to understand the pathophysiology of the rare enzymopathies due to deficiencies in the Embden-Meyerhoff pathway, glutathione metabolism, hexose monophosphate shunt and nucleotide metabolism pathway, and to study the incidence, clinical symptoms, diagnostic strategy, and management of enzyme deficiencies in the Indian patients. Most red blood cell (RBC) enzyme deficiencies are inherited in an autosomal recessive fashion except for G6PD, and phosphoglycerate kinase deficiency which has X-linked inheritance. Presentation depends on the representation of the enzyme on different tissues of the body, hence some enzyme deficiencies may present with neurological or muscular manifestations. In patients with suspected hemolytic anaemia, complete blood count and peripheral smear help in differentiating from hemoglobinopathies, etc. To clinch the diagnosis enzyme levels and genetic testing may be required. These tests guide antenatal diagnosis in subsequent pregnancies. Management of RBC enzymopathies depends on the predominant symptoms and severity of hemolysis. Patients with marked hemolysis require regular blood transfusions and hence appropriate chelation therapy. Hematopoeitic stem cell transplant is attempted in patients with severe spectrum with variable results. Newer drugs, including mitapivat have proven to be beneficial in adults with PKD and ongoing trials in children are showing promising results.

Comparative Transcriptome Profiles of the Response of Mycelia of the Genus Morchella to Temperature Stress: An Examination of Potential Resistance Mechanisms.

Temperature and moisture belong to the most important environmental factors affecting the growth and development of fungi. However, the effect of temperature on the mycelia of the edible Morchella mushrooms has not been determined. Here, a comprehensive analysis was performed to determine the influence of culture temperature on 13 strains of mycelia of three Morchella species (Morchella sextelata, Morchella septimelata, and Morchella importuna) at 5 °C, 10 °C, 15 °C, 20 °C, 25 °C, and 30 °C. The mycelial branching and growth rate data showed that 15-20 °C was a suitable temperature range for the mycelial growth of the 13 Morchella strains. RNA sequences revealed that a total of 2843, 2404, 1973, 1572, and 1866 differentially expressed genes (DEGs) were identified at 5 °C, 10 °C, 15 °C, 25 °C, and 30 °C compared with 20 °C. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis further indicated that the purine nucleotide and tyrosine metabolism pathways were crucial for mycelium development. Moreover, the enrichment of autophagy of mitochondria, regulation of cell morphogenesis, and piecemeal microautophagy of the nuclei at 25 °C (vs. 20 °C) indicated the damage caused by heat stress in Morchella mycelia. Notably, a total of four unique module eigengenes (MEs) were identified through a weighted gene coexpression network analysis (WGCNA). Among them, 2293 genes in the turquoise module were significantly positively correlated with temperature (r = 0.946, p < 0.001), whereas 739 genes in the blue module were significantly negatively correlated with temperature (r = -0.896, p < 0.001), suggesting that the effect of high temperatures on mycelial genes was significantly greater than that of low temperatures. Moreover, the coexpression network indicated that high culture temperatures accelerated the oxidative stress response and energy metabolism in mycelia, while upregulation of purine nucleotide catabolism and ribosomal protein-related genes were improved by low-temperature tolerance. In addition, the upregulated expression of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), and heat shock protein (HSP) genes in mycelia was associated with reactive oxygen species (ROS)-mediated damage at high temperatures. Overall, this study provides an important theoretical basis and application value for optimizing Morchella cultivation techniques.

Multi-omics analyses uncover metabolic signatures and gene expression profiles of interstitial cystitis/bladder pain syndrome.

We explore molecular and metabolic pathways involved in interstitial cystitis (IC) with integrating multi-omics analysis for identifying potential diagnostic and therapeutic targets. Mouse models of IC/bladder pain syndrome (BPS) were established by intraperitoneal injection of cyclophosphamide and bladder tissue samples were collected for metabolomics and transcriptome analysis. We found a total of 82 and 145 differential metabolites in positive ion modes and negative ion modes, respectively. Glycerophospholipid metabolism, choline metabolism in cancer, and nucleotide metabolism pathways were significantly enriched in the IC/BPS group. Transcriptome analysis demonstrated that 1069 upregulated genes and 1087 downregulated genes were detected. Importantly, the stronger enrichment for cell cycle pathway was observed in IC/BPS than that in normal bladder tissue, which may be involved in the process of bladder remodeling. Moreover, the inflammatory response and inflammatory factors related pathways were enriched in the IC/BPS group. Our findings provide critical directions for further exploration of the molecular pathology underlying IC/BPS.

Dynamic changes of volatile compounds and small molecule compounds during curing and drying processes of Megalobrama amblycephala

SummaryIn this study, the changes in volatile compounds, lipids, and small molecule compounds during the curing and drying processes were examined. The results showed that lipid oxidation was enhanced during curing and drying processes. A total of fifty‐two types of volatile compounds in the dry‐cured fish were detected, and the contents of alcohols (such as 3‐methyl‐1‐butanol, 1‐octen‐3‐ol), ketones (such as 2‐heptanone, 2‐octanone), and aldehydes (such as 3‐methylbutyraldehyde, hexanal, nonanal, decanal) were increased during curing and drying processes. A total of 812 metabolites were identified. The metabolites in linoleate, arachidonate, nucleotide, amino acid, and other metabolic pathways showed significant differences between drying stage and curing stage. The oxidative degradation of arachidonate acid, linoleate acid, and amino acid may contribute to the changes in volatile compounds during the curing and drying stages. Seven compounds including shikimic acid, carnitine C5: DC, carnitine C7: DC, 2‐hydroxybutanoic acid, 3‐hydroxybutanoic acid, malonic acid, and methylmalonic acid could be key small molecule compounds in curing and drying processing. These findings are valuable for understanding the mechanisms underlying flavour changes occurring during fish curing and drying processes.

Metabolomic interference induced by short-chain chlorinated paraffins in human normal hepatic cells

Short-chain chlorinated paraffins (SCCPs) are an emerging class of persistent organic pollutants (POPs) that are widely detected in environmental matrices and human samples. Because of their environmental persistence, long-range transport potential, bioaccumulation potential, and biotoxicity, SCCPs pose a significant threat to human health. In this study, metabolomics technology was applied to reveal the metabolomic interference in human normal hepatic (L02) cells after exposure to low (1 μg/L), moderate (10 μg/L), and high (100 μg/L) doses of SCCPs. Principal component analysis (PCA) and metabolic effect level index (MELI) values showed that all three SCCP doses caused notable metabolic perturbations in L02 cells. A total of 72 metabolites that were annotated by MS/MS and matched with the experimental spectra in the Human Metabolome Database (HMDB) or validated by commercially available standards were selected as differential metabolites (DMs) across all groups. The low-dose exposure group shared 33 and 36 DMs with the moderate- and high-dose exposure groups, respectively. The moderate-dose exposure group shared 46 DMs with the high-dose exposure group. In addition, 33 DMs were shared among the three exposure groups. Among the 72 DMs, 9, 9, and 45 metabolites participated in the amino acid, nucleotide, and lipid metabolism pathways, respectively. The results of pathway enrichment analysis showed that the most relevant metabolic pathways affected by SCCPs were the lipid metabolism, fatty acid β-oxidation, and nucleotide metabolism pathways, and that compared with low-dose exposure, moderate- and high-dose SCCP exposures caused more notable perturbations of these metabolic pathways in L02 cells. Exposure to SCCPs perturbed glycerophospholipid and sphingolipid metabolism. Significant alterations in the levels of phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins indicated SCCP-induced biomembrane damage. SCCPs inhibited fatty acid β-oxidation by decreasing the levels of short- and medium-chain acylcarnitines in L02 cells, indicating that the energy supplied by fatty acid oxidation was reduced in these cells. Furthermore, compared with low- and moderate-dose SCCPs, high-dose SCCPs produced a significantly stronger inhibition of fatty acid β-oxidation. In addition, SCCPs perturbed nucleotide metabolism. The higher hypoxanthine levels observed in L02 cells after SCCP exposures indicate that SCCPs may induce several adverse effects, including hypoxia, reactive oxygen species production, and mutagenesis in L02 cells.

Key biological processes and essential genes for Proteus mirabilis biofilm development inhibition by protocatechuic acid

Proteus mirabilis is an opportunistic pathogen linked to human urinary tract infections, and is potentially present as a foodborne pathogen within poultry products, including broiler chickens. This report outlines the inhibitory impacts of protocatechuic acid (PCA) on P. mirabilis isolated from a broiler slaughterhouse in China as well as its biofilm. This investigation encompasses assays related to motility and adhesion, bacterial metabolic activity, extracellular polymer (EPS) production, and scavenging capacity. The findings demonstrated that PCA reduced biofilm formation by 61 %. Transcriptomics findings identified that PCA limited the expression of genes like PstS that promote adhesin formation, rbsA and RcsB that alter bacterial chemotaxis, lipopolysaccharide synthesis genes LpxA and EptB, and cell wall synthesis genes MurF and MrdA, and affects the Regulator of Capsule Synthesis (RCS) two-component modulation system. Weighted gene co-expression network analysis (WGCNA) was conducted to identify the core genes. Furthermore, the binding sites of PCA to cytochrome oxidases cydA and cydB, two subunits of ATP synthase atpI and atpH, and ftsZ, which regulate bacterial division, were predicted via molecular docking. Metabolome analysis determined that PCA critically influenced coenzyme A biosynthesis, nucleotide metabolism, alanine, aspartic acid, and glutamate metabolic pathways of P. mirabilis. Therefore, PCA impacts metabolism within bacteria via various pathways, limiting the levels of extracellular polymer and bacterial viability to hinder biofilm formation. Additionally, we prepared an antibacterial plastic film containing protocatechuic acid using PVA as the monomer and CNC as the reinforcing agent. We examined the mechanical and antibacterial properties of this film. When used to wrap chicken, it reduced the total number of colonies, slowed the deterioration of chicken, and maintained the freshness of chicken. In conclusion, the information outlined in this study complements our comprehension of P. mirabilis inhibition by PCA and provides clues for the reduction of foodborne infections associated with P. mirabilis.

Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions.

Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.

Integrated bioinformatics analysis of nucleotide metabolism based molecular subtyping and biomarkers in lung adenocarcinoma.

Lung adenocarcinoma (LUAD), a predominant subtype of non-small cell lung cancers, continues to challenge treatment outcomes due to its heterogeneity and complex tumor microenvironment (TME). Dysregulation in nucleotide metabolism has been identified as a significant factor in tumorigenesis, suggesting its potential as a therapeutic target. This study analyzed LUAD samples from The Cancer Genome Atlas (TCGA) using Non-negative Matrix Factorization (NMF) clustering, Weighted Correlation Network Analysis (WGCNA), and various machine learning techniques. We investigated the role of nucleotide metabolism in relation to clinical features and immune microenvironment through large-scale data analysis and single-cell sequencing. Using in vivo and in vitro experiments such as RT-qPCR, Western Blot, immunohistochemistry, and subcutaneous tumor formation in mice, we further validated the functions of key nucleotide metabolism genes in cell lines and animals. Nucleotide metabolism genes classified LUAD patients into two distinct subtypes with significant prognostic differences. The 'C1' subtype associated with active nucleotide metabolism pathways showed poorer prognosis and a more aggressive tumor phenotype. Furthermore, a nucleotide metabolism-related score (NMRS) calculated from the expression of 28 key genes effectively differentiated between patient outcomes and predicted associations with oncogenic pathways and immune responses. By integrating various immune infiltration algorithms, we delineated the associations between nucleotide metabolism signature genes and the tumor microenvironment, and characterized their distribution differences at the cellular level by analyzing single-cell sequencing dataset related to immunochemotherapy. Finally, we demonstrated the differential expression of the key nucleotide metabolism gene AUNIP acts as an oncogene to promote LUAD cell proliferation and is associated with tumor immune infiltration. The study underscores the pivotal role of nucleotide metabolism in LUAD progression and prognosis, highlighting the NMRS as a valuable biomarker for clinical outcomes and therapeutic responses. Specifically, AUNIP functions as a critical oncogene, offering a promising target for novel treatment strategies in LUAD.

Transcriptome Analysis Reveals the Response of Cryptomeria japonica to Feeding Stress of Dendrolimus houi Lajonquière Larvae

The Japanese fir, Cryptomeria japonica, is ecologically and commercially vital in China. However, infestations by Dendrolimus houi Lajonquière larvae cause widespread dieback, mimicking mechanical damage effects, with unclear differential impacts and mechanisms. To address this, 6th instar larvae of D. houi were introduced to three-year-old C. japonica seedlings to induce pest infestation, while mechanical damage and non-infested pests were controlled. Then, next-generation sequencing techniques were employed, and transcriptome sequencing was conducted to analyze the distinct damage mechanisms responding to C. japonica. This study revealed 10,412 DEGs between pest infestation and controls and 5535 DEGs comparing pest infestation to mechanical damage. Functional enrichment analysis highlighted the involvement of these DEGs in crucial processes such as photosynthesis, amino acid and nucleotide metabolism, flavonoid biosynthesis, and plant hormone signaling pathways. In particular, 786 unique DEGs were discerned in pest-infested samples. Key enriched pathways, such as pyruvate and propionate metabolism, were pinpointed, with flavonoid biosynthesis potentially closely linked to pest-feeding inductions. These findings provided valuable insights into the molecular responses of C. japonica to D. houi infestation, laying the foundation for future research aimed at developing pest-resistant varieties of Japanese fir.

Predictive metabolomic signatures for safety assessment of three plastic nanoparticles using intestinal organoids

Nanoplastic particles are pervasive environmental contaminants with potential health risks, while mouse intestinal organoids provide accurate in vitro models for studying these interactions. Metabolomics, especially through LC-MS, enables detailed cellular response studies, and there's a novel interest in comparing metabolic changes across nanoparticle species using gut organoids. This study used a mouse intestinal organoid combined with cell model to explore the differences in metabolites and toxicity mechanisms induced by exposure to three nanoplastics (PS, PTFE, and PMMA). The results showed that PS, PTFE, and PMMA exposure reduced mitochondrial membrane potential, intracellular ROS accumulation and oxidative stress, and inhibited the AKT/mTOR signaling pathway. Non-targeted metabolomics results confirmed that three types of nanoplastic particles regulate cellular status by regulating fatty acid metabolism, nucleotide metabolism, necroptosis and autophagy pathways. More importantly, these representative metabolites were further validated in model groups after mouse intestinal organoids and HCT116 cells were exposed to the respective NPs, indicating that organoid metabolomics results can be used to effectively predict toxicity. Untargeted metabolomics is sensitive enough to detect subtle metabolomic changes when functional cellular analysis shows no significant differences. Overall, our study reveals the underlying metabolic mechanism of NPs-induced intestinal organoid toxicity and provides new insights into the possible adverse consequences of NPs.

Microbiota-mediated metabolic perturbations in the gut and brain of mice after microplastic exposure

Microplastics (MPs), emerging environmental toxicants, have drawn attention because of their wide distribution in the environment. Exposure to MPs induces gut microbiota dysbiosis, intestinal barrier dysfunction, metabolic perturbations, and neurotoxicity in different rodents. However, the relationship between MPs, gut microbiota, and the metabolome of the gut and brain in mice remains unclear. In this study, female C57BL/6 mice were orally gavaged with vehicle, 200 nm MP, and 800 nm MP three times per week for four weeks. Cecal contents were collected for gut microbiota analysis using 16S rRNA gene sequencing. Intestinal and brain tissues from mice were used to determine metabolic profiles using liquid chromatography-mass spectrometry (LC-MS). The results showed that MP altered microbiota composition, accompanied by metabolic perturbations in the mouse gut and brain. Specifically, Firmicutes and Bacteroidetes were suggested to be important phyla for MP exposure, partially dominating further metabolite alterations. Simultaneously, MP-induced metabolic profiles were associated with energy homeostasis and bile acid, nucleotide, and carnitine metabolic pathways. The results of the mediation analysis further revealed an MP-microbiota-metabolite relationship. Our results indicate that MPs can induce gut dysbiosis and disturb metabolic dysfunction in the mouse brain and/or intestine. Integrative omics approaches have the potential to monitor MP-induced molecular responses in various organs and systematically elucidate the complex mechanisms of human health effects.

Changes in quality characteristics and metabolites composition of wheat under different storage temperatures

The quality variation of wheat post harvesting is strongly affected by storage temperature. Low temperature storage can alleviate the quality deterioration in wheat after harvest. However, the mechanism regarding metabonomics analysis between different storage temperatures in postharvest wheat remains poorly understood. Here, we analyzed the changes in wet gluten content, fatty acid values, Catalase (CAT) activity, alpha-amylase activity, pasting properties changes, as well as the differentially expressed key metabolites in wheat, stored at 15, 20, and 30 °C for 180 days. In our study, wheat storage, processing, and edible quality remained steady at 15 °C and 20 °C storage temperatures, and wheat quality drastically degraded at 30 °C. Through non-targeted metabolomics analysis, carbohydrate metabolism, fatty acid metabolism, amino acid metabolism, and nucleotide metabolism pathways were proven to be involved in wheat storage. Specifically, gamma-glu-cys and 4-trimethylammoniobutanoic acid were up-regulated; adenine, l-gluconic acid, linoleic acid, 13(s)-HPODE, 9(s)-HPODE, 9-OxoODE, n-acetyl-l-glutamic acid, and trans-2,3-dihydroxycinnamate were down-regulated at 15 °C and 20 °C. These substances helped maintain the stability of cellular structures within the wheat kernel. The study's findings revealed the low-temperature impact mechanism on high moisture wheat from the perspective of metabolite changes. This may provide a scientific basis for the efficient preservation of wheat.

Metabolomics reveals the mechanism of action of meropenem and amikacin combined in the treatment of Pseudomonas aeruginosa.

The treatment of Pseudomonas aeruginosa infection often involves the combined use of β-lactam and aminoglycoside antibiotics. In this study, we employed metabolomic analysis to investigate the mechanism responsible for the synergistic activities of meropenem/amikacin combination therapy against multidrug-resistant P. aeruginosa strains harboring OXA-50 and PAO genes. Antibiotic concentrations for meropenem (2 mg/L) monotherapy, amikacin (16 mg/L) monotherapy, and meropenem/amikacin (2/16 mg/L) combination therapy were selected based on clinical breakpoint considerations. Metabolomic analysis revealed significant alterations in relevant metabolites involved in bacterial cell membrane and cell wall synthesis within 15 min of combined drug administration. These alterations encompassed various metabolic pathways, including fatty acid metabolism, peptidoglycan synthesis, and lipopolysaccharide metabolism. Furthermore, at 1 h and 4 h, the combination therapy exhibited significant interference with amino acid metabolism, nucleotide metabolism, and central carbon metabolism pathways, including the tricarboxylic acid cycle and pentose phosphate pathway. In contrast, the substances affected by single drug administration at 1 h and 4 h demonstrated a noticeable reduction. Meropenem/amikacin combination resulted in notable perturbations of metabolic pathways essential for survival of P. aeruginosa, whereas monotherapies had comparatively diminished impacts.

Modulating Metabolic Reprogramming By Phosphoglycerate Dehydrogenase (PHGDH) Inhibitors in Omipalisib-Refractory AML

Background: Numerous reports indicated the significance of the PI3K/AKT/mTOR signaling pathway in AML. Up to now, there is no FDA-approved PI3K/AKT/mTOR inhibitors available for patients with acute myeloid leukemia (AML). Recently, we demonstrated that PI3K/mTOR dual inhibitor omipalisib had a potent anti-leukemic effect, but it could not completely eliminate leukemia cells in a subcutaneous murine model. To explore the refractory features of omipalisib, we established several OCI-AML3 sublines refractory to omipalisib by an in vivo selection procedure. The OCI-AML3-R cell line was the most refractory one and showed cross-resistance to another PI3K/mTOR inhibitor dactolisib and multi-tyrosine kinase inhibitor dasatinib, in addition to omipalisib. Several genes associated with multidrug-resistance, ABCC1, ABCC2, ABCB1, ABCG2, MDR1, and MRP1, did not express significant difference between OCI-AML3 and OCI-AML3-R. Aims: To investigate the molecular mechanisms of OCI-AML3-R using transcriptomics and metabolomics analysis, and to explore potential therapeutic strategies from both in vitro and in vivo aspects. Methods: OCI-AML3 and OCI-AML3-R leukemia cell lines were used in this study. MTS assay was performed to assess cell viability and proliferation. The differential expression genes (DEGs) were examined using RNA-seq (Illumina NovaSeq 6000). Metabolomic analysis was conducted by the C-SCOPE service using capillary electrophoresis mass spectrometry CE-TOFMS and CE-QqQMS with Agilent 6460 TripleQuad LC/MS (HMT, Yamagata, Japan). Q-RT-PCR was used for mRNA quantification. Immunoblotting were used to clarify the variations of total- and phosphor-proteins. Flow cytometry was used for apoptosis and mitochondrial ROS content analysis. OCI-AML3-R xenograft models in nude mice were used for scrutinizing efficacy of PHGDH inhibitor in vivo. The protocol for the xenograft experiments was approved by the IACUC, National Taiwan University. Results: A total of 1946 DEGs between OCI-AML3 and OCI-AML3-R cells were identified with the selection criteria of p&amp;lt; 0.05 and [log 2 (fold change)]&amp;gt; 1 or &amp;lt;1, of which 477 and 1469 DEGs were up- and down-regulated, respectively. g:Profiler was used for functional enrichment analysis and revealed that NFkB signaling-related pathways ( p&amp;lt; 0.001), cell cycle-related pathways ( p&amp;lt; 0.001), and nucleotide metabolic pathways ( p&amp;lt; 0.001) were enriched in OCI-AML3-R. Q-RT-PCR confirmed that a series of genes related to pentose phosphate pathway (PPP; TKT and 6PGD), serine synthesis pathway (SSP; PHGDH and PSAT1), purine synthesis and folate/methionine cycle ( PAICS, SHMT2, MTHFD2, and MTHFD1L) were increased in OCI-AML3-R cells. Among them, PHGDH and PSAT1 increased the most, 4.75x and 11.38x, respectively. A total of 103 metabolites were screened out by metabolomic analysis, 58 of which showed significant differences between OCI-AML3 and OCI-AML3-R cells ( p&amp;lt; 0.05). Metabolite enrichment analysis also revealed that the purine metabolism, urea cycle, glycolysis/gluconeogenesis, and several amino acid metabolism pathways were enriched in OCI-AML3-R cells. A comprehensive overview of metabolites in glycolysis and TCA cycle in OCI-AML3-R cells revealed significantly increased levels of PRPP and serine, as well as steady-state levels of glycine, folate, and several purine metabolites. These results indicated that a reprogramming of glucose metabolism towards the PPP and SSP in OCI-AML3-R cells was noted. Based on these results, we proposed targeting the PPP and SSP as a therapeutic approach for omipalisib-refractory AML. The PHGDH inhibitors, WQ-2101 and NCT-503, showed strong anti-leukemic effects in OCI-AML3-R with an IC 50 of 26.17 and 16.81 μM, respectively, while the G6PD inhibitor 6-AN had limited effect. The PHGDH inhibitors increased mitochondrial ROS levels and induced apoptosis in OCI-AML3-R. Additionally, in vivo experiment showed that treatment with NCT-503 significantly prolonged mouse survival and inhibited tumor growth in a dose-dependent manner without adverse effects on body weight. Summary/Conclusion: Transcriptomic and metabolomic analyses revealed that OCI-AML3-R upregulated PPP and SSP, leading to increased nucleotide synthesis, which contribute cell growth and survival. Targeting PHGDH could significantly suppress omipalisib-refractory in AML and may have implications for future clinical trials.

Integration of Metabolomes and Transcriptomes Provides Insights into Morphogenesis and Maturation in Morchella sextelata.

True morels (Morchella, Pezizales) are a popular edible and medicinal fungus with great nutritional and economic value. The dynamics and regulatory mechanisms during the morphogenesis and maturation of morels are poorly understood. In this study, the metabolomes and transcriptomes of the mycelium (MY), primordium differentiation (PR), young fruiting body (YFB), and mature fruiting body (MFB) were comprehensively analyzed to reveal the mechanism of the morphogenesis and maturation of Morchella sextelata. A total of 748 differentially expressed metabolites (DEMs) and 5342 differentially expressed genes (DEGs) were detected, mainly enriched in the carbohydrate, amino acid, and lipid metabolism pathways, with the transition from the mycelium to the primordium being the most drastic stage at both the metabolic and transcriptional levels. The integrated metabolomics and transcriptomics highlighted significant correlations between the DEMs and DEGs, and specific amino acid and nucleotide metabolic pathways were significantly co-enriched, which may play key roles in morphological development and ascocarp maturation. A conceptual model of transcriptional and metabolic regulation was proposed during morphogenesis and maturation in M. sextelata for the first time, in which environmental factors activate the regulation of transcription factors, which then promote metabolic and transcriptional regulation from vegetative to reproductive growth. These results provide insights into the metabolic dynamics and transcriptional regulation during the morphogenesis and maturation of morels and valuable resources for future breeding enhancement and sustainable artificial cultivation.

Transcriptional reprogramming of nucleotide metabolism in response to altered pyrimidine availability in Arabidopsis seedlings.

In Arabidopsis seedlings, inhibition of aspartate transcarbamoylase (ATC) and de novo pyrimidine synthesis resulted in pyrimidine starvation and developmental arrest a few days after germination. Synthesis of pyrimidine nucleotides by salvaging of exogenous uridine (Urd) restored normal seedling growth and development. We used this experimental system and transcriptional profiling to investigate genome-wide responses to changes in pyrimidine availability. Gene expression changes at different times after Urd supplementation of pyrimidine-starved seedlings were mapped to major pathways of nucleotide metabolism, in order to better understand potential coordination of pathway activities, at the level of transcription. Repression of de novo synthesis genes and induction of intracellular and extracellular salvaging genes were early and sustained responses to pyrimidine limitation. Since de novo synthesis is energetically more costly than salvaging, this may reflect a reduced energy status of the seedlings, as has been shown in recent studies for seedlings growing under pyrimidine limitation. The unexpected induction of pyrimidine catabolism genes under pyrimidine starvation may result from induction of nucleoside hydrolase NSH1 and repression of genes in the plastid salvaging pathway, diverting uracil (Ura) to catabolism. Identification of pyrimidine-responsive transcription factors with enriched binding sites in highly coexpressed genes of nucleotide metabolism and modeling of potential transcription regulatory networks provided new insights into possible transcriptional control of key enzymes and transporters that regulate nucleotide homeostasis in plants.

Effects of Biodegradable Liquid Film (BLF) on Cold Resistance in Grapevine Revealed by Metabolomic Analysis

Low temperatures are among the most important abiotic stresses, severely affecting vine growth and development. In order to overwinter safely, grape growers pay high labor costs, which are unsustainable in modern agriculture. Biodegradable liquid film (BLF) is an environmentally friendly material that assists grapevines to withstand the cold. In this experiment, Cabernet Sauvignon from Junding Winery was used as material for field trials. The regulatory effect of BLF on the cold resistance of grapevines was analyzed, and its mechanism of action was explored using metabolomics. The results showed that BLF significantly increased the activity of superoxide dismutase, the content of proline and ascorbic acid, reducing sugar, sucrose, and soluble sugar, and also decreased the content of malondialdehyde. In addition, BLF significantly increased the activity of invertase and decreased the activity of pectinase and phosphofructokinase. Metabolomics data showed that BLF improved cold resistance in grapevines by affecting lipids, flavonoids, amino acids, and nucleotide metabolic pathways.

The primary neurotoxic factor, Lansamide I, from Clausena lansium fruits and metabolic dysfunction invoked

Wampee (Clausena lansium) is a common fruit in South Asia. The pulp is a tasty food, and the seed is a typical traditional herb in China. However, we identified a primary toxic compound, Lansamide I, by NMR and X-ray diffraction of single-crystal. The compound occurred at 4.17 ± 0.16 mg/kg of dried seed and 0.08 ± 0.01 g/kg of fresh fruit. In our phenotype-based toxicity investigation, the compound caused decreased hatchability of zebrafish eggs, increased malformations such as enlarged yolk sacs and pericardial edema, and delayed body length development. Moreover, the compound also caused nerve cell damage and decreased locomotor activity. The compound caused an increase in peroxidation levels in vivo, with increases in both malondialdehyde and superoxide dismutase levels, but did not interfere with acetylcholinesterase levels. Metabolomic studies found that the compound caused significant up-regulation of 16 metabolites, mainly amino acids and peptides, which were involved in the nucleotide metabolism pathway and the betaine biosynthesis module. The qRT-PCR revealed that the substance interfered with the mRNA expression of tat and dctpp. These discoveries offer fresh perspectives on the toxicity mechanisms and metabolic response to the primary harmful molecules in wampee, which could inform the rational usage of wampee resources.

Integrated Transcriptomic and Metabolomics Analyses Reveal Molecular Responses to Cold Stress in Coconut (Cocos nucifera L.) Seedlings.

Coconut is an important tropical and subtropical fruit and oil crop severely affected by cold temperature, limiting its distribution and application. Thus, studying its low-temperature reaction mechanism is required to expand its cultivation range. We used growth morphology and physiological analyses to characterize the response of coconuts to 10, 20, and 30 d of low temperatures, combined with transcriptome and metabolome analysis. Low-temperature treatment significantly reduced the plant height and dry weight of coconut seedlings. The contents of soil and plant analyzer development (SPAD), soluble sugar (SS), soluble protein (SP), proline (Pro), and malondialdehyde (MDA) in leaves were significantly increased, along with the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the endogenous hormones abscisic acid (ABA), auxin (IAA), zeatin (ZR), and gibberellin (GA) contents. A large number of differentially expressed genes (DEGs) (9968) were detected under low-temperature conditions. Most DEGs were involved in mitogen-activated protein kinase (MAPK) signaling pathway-plant, plant hormone signal transduction, plant-pathogen interaction, biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism, carbon metabolism, starch and sucrose metabolism, purine metabolism, and phenylpropanoid biosynthesis pathways. Transcription factors (TFs), including WRKY, AP2/ERF, HSF, bZIP, MYB, and bHLH families, were induced to significantly differentially express under cold stress. In addition, most genes associated with major cold-tolerance pathways, such as the ICE-CBF-COR, MAPK signaling, and endogenous hormones and their signaling pathways, were significantly up-regulated. Under low temperatures, a total of 205 differentially accumulated metabolites (DAMs) were enriched; 206 DAMs were in positive-ion mode and 97 in negative-ion mode, mainly including phenylpropanoids and polyketides, lipids and lipid-like molecules, benzenoids, organoheterocyclic compounds, organic oxygen compounds, organic acids and derivatives, nucleosides, nucleotides, and analogues. Comprehensive metabolome and transcriptome analysis revealed that the related genes and metabolites were mainly enriched in amino acid, flavonoid, carbohydrate, lipid, and nucleotide metabolism pathways under cold stress. Together, the results of this study provide important insights into the response of coconuts to cold stress, which will reveal the underlying molecular mechanisms and help in coconut screening and breeding.