Showing papers on "Urea cycle published in 2023"
TL;DR: This article showed that SIRT4 decarbamylates OTCCP-K307 and inactivates OTC in an NAD+-dependent manner, and showed that the decarboramylase decouples amino acid sufficiency and regulates ammonia removal.
Abstract: Ammonia production via glutamate dehydrogenase is inhibited by SIRT4, a sirtuin that displays both amidase and non-amidase activities. The processes underlying the regulation of ammonia removal by amino acids remain unclear. Here, we report that SIRT4 acts as a decarbamylase that responds to amino acid sufficiency and regulates ammonia removal. Amino acids promote lysine 307 carbamylation (OTCCP-K307) of ornithine transcarbamylase (OTC), which activates OTC and the urea cycle. Proteomic and interactome screening identified OTC as a substrate of SIRT4. SIRT4 decarbamylates OTCCP-K307 and inactivates OTC in an NAD+-dependent manner. SIRT4 expression was transcriptionally upregulated by the amino acid insufficiency-activated GCN2-eIF2α-ATF4 axis. SIRT4 knockout in cultured cells caused higher OTCCP-K307 levels, activated OTC, elevated urea cycle intermediates and urea production via amino acid catabolism. Sirt4 ablation decreased male mouse blood ammonia levels and ameliorated CCl4-induced hepatic encephalopathy phenotypes. We reveal that SIRT4 safeguards cellular ammonia toxicity during amino acid catabolism.
1 citations
TL;DR: In this article , a multi-platform strategy was implemented to evaluate the long-term immuno-metabolic consequences of burn injury combining metabolite, lipoprotein, and cytokine panels.
Abstract: Introduction Burn injury in children causes prolonged systemic effects on physiology and metabolism leading to increased morbidity and mortality, yet much remains undefined regarding the metabolic trajectory towards specific health outcomes. Methods A multi-platform strategy was implemented to evaluate the long-term immuno-metabolic consequences of burn injury combining metabolite, lipoprotein, and cytokine panels. Plasma samples from 36 children aged 4–8 years were collected 3 years after a burn injury together with 21 samples from non-injured age and sex matched controls. Three different 1H Nuclear Magnetic Resonance spectroscopic experiments were applied to capture information on plasma low molecular weight metabolites, lipoproteins, and α-1-acid glycoprotein. Results Burn injury was characterized by underlying signatures of hyperglycaemia, hypermetabolism and inflammation, suggesting disruption of multiple pathways relating to glycolysis, tricarboxylic acid cycle, amino acid metabolism and the urea cycle. In addition, very low-density lipoprotein sub-components were significantly reduced in participants with burn injury whereas small-dense low density lipoprotein particles were significantly elevated in the burn injured patient plasma compared to uninjured controls, potentially indicative of modified cardiometabolic risk after a burn. Weighted-node Metabolite Correlation Network Analysis was restricted to the significantly differential features (q <0.05) between the children with and without burn injury and demonstrated a striking disparity in the number of statistical correlations between cytokines, lipoproteins, and small molecular metabolites in the injured groups, with increased correlations between these groups. Discussion These findings suggest a ‘metabolic memory’ of burn defined by a signature of interlinked and perturbed immune and metabolic function. Burn injury is associated with a series of adverse metabolic changes that persist chronically and are independent of burn severity and this study demonstrates increased risk of cardiovascular disease in the long-term. These findings highlight a crucial need for improved longer term monitoring of cardiometabolic health in a vulnerable population of children that have undergone burn injury.
1 citations
TL;DR: In this paper , the authors demonstrate that host's urea cycle metabolism is significantly activated during colorectal tumorigenesis, accompanied by the absence of beneficial bacteria with ureolytic capacity, such as Bifidobacterium.
1 citations
TL;DR: ACER-001 as discussed by the authors is a novel formulation of NaPBA with polymer coated pellets in suspension, which is designed to briefly mask the unpleasant bitter taste of PA and is being developed as a treatment option for patients with urea cycle disorders.
TL;DR: In this article , a review of neuroimaging findings, including those of 1H-MRS, of IEMs focusing on intoxication disorders such as urea cycle disorders, aminoacidopathies, and organic acidopathies which can result in acute lifethreatening metabolic decompensation or crisis.
Abstract: Although there are many types of inborn errors of metabolism (IEMs) affecting the central nervous system, also referred to as neurometabolic disorders, individual cases are rare, and their diagnosis is often challenging. However, early diagnosis is mandatory to initiate therapy and prevent permanent long-term neurological impairment or death. The clinical course of IEMs is very diverse, with some diseases progressing to acute encephalopathy following infection or fasting while others lead to subacute or slowly progressive encephalopathy. The diagnosis of IEMs relies on biochemical and genetic tests, but neuroimaging studies also provide important clues to the correct diagnosis and enable the conditions to be distinguished from other, more common causes of encephalopathy, such as hypoxia-ischemia. Proton magnetic resonance spectroscopy (1H-MRS) is a powerful, non-invasive method of assessing neurological abnormalities at the microscopic level and can measure in vivo brain metabolites. The present review discusses neuroimaging findings, including those of 1H-MRS, of IEMs focusing on intoxication disorders such as urea cycle disorders, aminoacidopathies, and organic acidopathies, which can result in acute life-threatening metabolic decompensation or crisis.
30 Jun 2023
TL;DR: Wang et al. as discussed by the authors explored the altered metabolic pathways for esophageal squamous cell carcinoma (ESCC) through joint-pathway analysis of differentially expressed metabolites and genes, which revealed the altered amino acid metabolism, especially arginine and proline metabolism, as the most significant metabolic characteristic in ESCC.
Abstract: Abstract Introduction: Metabolic reprogramming plays a crucial role in tumor development by modifying tumor cell metabolism, which was also found in esophageal squamous cell carcinoma (ESCC). Objectives This study aims to explore the altered metabolic pathways for ESCC through joint-pathway analysis of differentially expressed metabolites and genes. Methods Differentially expressed metabolites in ESCC were collected from published tissue-based metabolomics studies. Differentially expressed genes in ESCC were obtained using bioinformatic analysis of online ESCC transcriptome data. Then, joint-pathway analysis was performed to explore the altered metabolic pathways in ESCC. Immunohistochemistry (IHC) staining and arginine-deprivation experiments were conducted to verified the key enzymes in metabolic pathway and their potential function in ESCC. Results A total of 9 tissue-based metabolomics studies revealed 495 differentially expressed metabolites in ESCC. Enrichment analysis of the 69 high-frequency metabolites, defined as reported by over 2 studies, showed that the top enriched pathways were urea cycle, arginine and proline metabolism and ammonia recycling. Besides, bioinformatic analysis of a dataset (GSE53625) showed 2679 differentially expressed genes in ESCC. Joint-pathway analysis illustrated that the top 5 significantly altered metabolic pathways were glycerolipid metabolism, ascorbate and aldarate metabolism, histidine metabolism, arginine and proline metabolism, and linoleic acid metabolism. IHC staining and arginine-deprivation experiments revealed the up-regulating of arginine transporter (CAT1) and characteristic of arginine-dependent proliferation in ESCC. Conclusions This study revealed the altered amino acid metabolism, especially arginine and proline metabolism, as the most significant metabolic characteristic in ESCC. However, further functional study is needed.
TL;DR: In this article , the authors evaluated the nitrite and nitrate content, thiobarbituric acid-reactive substances (TBARS), carbonyl protein content and a panel of cytokines in plasma sample of 14 patients.
TL;DR: In this article , a 23-year-old female presented four days postpartum to the emergency department (ED) obtunded and declined to the point of requiring intubation. Labs revealed hyperammonemia, and she was subsequently found to have CTLN1.
Abstract: Introduction Citrullinemia type 1 (CTLN1) is a urea cycle disorder caused by defective argininosuccinate synthetase leading to impaired ammonia elimination. Urea cycle disorders are typically diagnosed on neonatal screening but rarely can lie dormant until a metabolic stressor causes initial onset of symptoms in adulthood. Case Report A 23-year-old female presented four days postpartum to the emergency department (ED) obtunded and declined to the point of requiring intubation. Labs revealed hyperammonemia, and she was subsequently found to have CTLN1. Conclusion Urea cycle disorders presenting in adulthood are a rare etiology for the common ED complaint of altered mental status. The low incidence makes these treatable disorders easy to overlook leading to potentially significant morbidity and mortality. Therefore, it is important to recognize the risk factors that can trigger an acute metabolic derangement. This case highlights common risk factors for metabolic stress, possible presenting symptoms, and the positive outcome achievable when recognized and treated in a timely fashion.
TL;DR: In this article , spatial metabolomics analyses of the kidney tissue were conducted to further explore perturbations in kidney oxidative metabolism in T1D, showing impaired TCA cycle turnover using 11C acetate PET and lower proximal tubular transcripts.
Abstract: In abstract 2023-A-3497-Diabetes, we show impaired TCA cycle turnover using 11C acetate PET and lower proximal tubular transcripts of TCA cycle enzymes by single-cell RNA sequencing of kidney biopsies in young adults with T1D vs. healthy controls (HC). Spatial metabolomics analyses of the kidney tissue were conducted to further explore perturbations in kidney oxidative metabolism in T1D. Matrix-assisted laser desorption/ionization-mass spectrometry imaging-based spatial metabolomics was used to analyze metabolites in situ (spatial resolution: 20 μm) in kidney tissues from 8 participants with T1D and preserved kidney function and 5 HC. Univariate analysis (t-test or Wilcoxon Mann Whitney test) demonstrated that 36 of 456 METASPACE annotated metabolites were altered (P<0.05) in T1D vs. HC. Partial least squares-discriminant analysis (PLS-DA) and heatmaps showed clearly separated clusters of metabolites. To identify the most significant discriminators for T1D, a variable importance in projection (VIP) plot from PLS-DA model was applied. Of the top 15 metabolites, two TCA cycle intermediates, succinic acid (m/z 117.0193, -H; P = 0.016) and malic acid (m/z 133.0142, -H; P = 0.026), were reduced in kidney tissues of participants with T1D. Pathway analysis revealed that the TCA cycle, mitochondrial electron transport chain, glutamate metabolism, malate-aspartate shuttle, and purine pathway were the dominant metabolic pathways perturbed in T1D kidney tissue. Spatial metabolomics comparing T1D kidney biopsies vs. HC reveal alterations of TCA cycle intermediates indicating mitochondrial dysfunction in the subclinical stages of diabetic kidney disease. The spatial metabolomics data are consistent with the data from transcriptomics and stable isotope tracing analysis in a subset of same participants. Further analysis with pathologic features will identify potential pathways linked to disease development.
G.Zhang: None. C.Birznieks: None. I.De boer: Advisory Panel; AstraZeneca, Boehringer Ingelheim and Eli Lilly Alliance, Boehringer Ingelheim International GmbH, Otsuka America Pharmaceutical, Inc., Bayer Inc., Consultant; George Clinical, Gilead Sciences, Inc., Medscape, Research Support; Dexcom, Inc. J.A.Schaub: None. K.J.Nadeau: None. V.Nair: None. F.Alakwaa: None. P.J.Mccown: None. A.Naik: Advisory Panel; CareDx. L.Pyle: None. D.Blondin: None. L.Liu: None. G.Richard: None. M.Kretzler: Research Support; Lilly, Boehringer Ingelheim Inc., Traveere Pharmaceuticals, Novo Nordisk, certa, Chinook Therapeutics Inc., Janssen Research & Development, LLC, AstraZeneca, Moderna, Inc., Gilead Sciences, Inc., Regeneron, Ionis Pharmaceuticals, Angioin, Renalytix. P.Bjornstad: Advisory Panel; AstraZeneca, Novo Nordisk, Lilly, Horizon Therapeutics plc, Boehringer Ingelheim (Canada) Ltd., LG Chem, Consultant; Bayer Inc., Bristol-Myers Squibb Company. K.Sharma: Advisory Panel; Reata Pharmaceuticals, Inc., Otsuka America Pharmaceutical, Inc. I.M.Tamayo: None. N.Garcia ponce de leon: None. T.B.Vigers: None. K.L.Tommerdahl: None. R.G.Nelson: None. P.E.Ladd: None. T.Alexandrov: None.
National Institutes of Health (UH3DK114920); JDRF (2-SRA-2019-845-S-B); Diabetes Research Center (P30DK116073)
TL;DR: In this paper , the liver of largemouth bass were exposed to total ammonia nitrogen of 0 mg/L for 3 and 7 days, respectively, and the expression of genes involved in glycogen metabolism, tricarboxylic acid cycle, lipid metabolism, and urea cycle pathways were investigated.
Abstract: Elevated environmental ammonia leads to respiratory disorders and metabolic dysfunction in most fish species, and the majority of research has concentrated on fish behavior and gill function. Prior studies have rarely shown the molecular mechanism of the largemouth bass hepatic response to ammonia loading. In this experiment, 120 largemouth bass were exposed to total ammonia nitrogen of 0 mg/L or 13 mg/L for 3 and 7 days, respectively. Histological study indicated that ammonia exposure severely damaged fish liver structure, accompanied by increased serum alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase activity. RT-qPCR results showed that ammonia exposure down-regulated the expression of genes involved in glycogen metabolism, tricarboxylic acid cycle, lipid metabolism, and urea cycle pathways, whereas it up-regulated the expression of genes involved in gluconeogenesis and glutamine synthesis pathways. Thus, ammonia was mainly converted to glutamine in the largemouth bass liver during ammonia stress, which was rarely further used for urea synthesis. Additionally, transcriptome results showed that ammonia exposure also led to the up-regulation of the oxidative phosphorylation pathway and down-regulation of the mitogen-activated protein kinase signaling pathway in the liver of largemouth bass. It is possible that the energy supply of oxidative phosphorylation in the largemouth bass liver was increased during ammonia exposure, which was mediated by the MAPK signaling pathway.
TL;DR: Shirani et al. as mentioned in this paper quantitatively analyzed the proteomes of fibrolamellar hepatocellular carcinoma (FLC) patients to find pathways that are changed in FLC.
Abstract:
In fibrolamellar hepatocellular carcinoma (FLC), hyperammonemic encephalopathy is a common occurrence and occasionally causes death. Using mass spectrometry, we quantitatively analyzed the proteomes of FLC patient’s tumor and adjacent normal, to find pathways that are changed in FLC. These data identified multiple proteins that were altered in the proteome, among these, enzymes involved in metabolism of ammonia. These results were confirmed with immunofluorescence demonstrating that these alterations occur in all tumor cells. These results suggest that FLC cells have defects in the two primary ammonia detoxification pathways in the liver, which are responsible for detoxification of 70% of the ammonia in the body: 1) consumption of ammonia by glutamine synthetase (GLUL), and 2) addition of ammonia by ornithine carbamoyltransferase (OTC) to the urea cycle. Additionally, they also generate extra ammonia because of upregulation of glutaminase (GLS). This was tested with a targeted metabolomics of the reactants and products of these enzymes. The results were consistent with both a loss of the two pathways for consumption of ammonia activation of a pathway for generating ammonia. This production of ammonia is consistent with the observation that surgical resection of fibrolamellar reduces the ammonia in patients. All FLC patients with hyperammonemic encephalopathy and documented urine test results showed increased urinary orotic acid, evidence of blockage of the OTC pathway. This study implies that hyperammonemic encephalopathy in FLC may require alternatives to commonly used therapies.
Citation Format: Mahsa Shirani, Solomon Levin, Michael D. Tomasini, James Knox, Bassem Shebl, David Requena, Jackson Clark, Søren Heissel, Hanan Alwaseem, Rodrigo Surjan, Ron Lahasky, Henrik Molina, Barbara Lyons, Rachael D. Migler, Philip Coffino, Sanford M. Simon. Urea cycle metabolism is disturbed in Fibrolamellar carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6729.
TL;DR: In this paper , a high-throughput functional assay for human OTC and individually measured the impact of 1,570 variants, 84% of all SNV-accessible missense mutations, demonstrated that their assay distinguishes known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation.
Abstract: Deleterious mutations in the X-linked gene encoding ornithine transcarbamylase (OTC) cause the most common urea cycle disorder, OTC deficiency. This rare but highly actionable disease can present with severe neonatal onset in males or with later onset in either sex. Individuals with neonatal onset appear normal at birth but rapidly develop hyperammonemia, which can progress to cerebral edema, coma, and death, outcomes ameliorated by rapid diagnosis and treatment. Here, we develop a high-throughput functional assay for human OTC and individually measure the impact of 1,570 variants, 84% of all SNV-accessible missense mutations. Comparison to existing clinical significance calls, demonstrated that our assay distinguishes known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation. This functional stratification allowed us to identify score ranges corresponding to clinically relevant levels of impairment of OTC activity. Examining the results of our assay in the context of protein structure further allowed us to identify a 13 amino acid domain, the SMG loop, whose function appears to be required in human cells but not in yeast. Finally, inclusion of our data as PS3 evidence under the current ACMG guidelines, in a pilot reclassification of 34 variants with complete loss of activity, would change the classification of 22 from variants of unknown significance to clinically actionable likely pathogenic variants. These results illustrate how large-scale functional assays are especially powerful when applied to rare genetic diseases.
TL;DR: In this article , the authors performed a retrospective study of children with UCD seen in the period 2000-2021, where data was collected on clinical onset, hyperammonemia severity, evolution and liver transplantation.
Abstract: Urea cycle disorders (UCD) are inborn errors of metabolism caused by deficiency of enzymes required to convert nitrogen from ammonia into urea. Current paradigms of treatment focus on dietary manipulations, ammonia scavenger drugs, and liver transplantation. The aim of this study was to describe the characteristics and indication of liver transplantation in UCD in a tertiary hospital. We performed a retrospective study of children with UCD seen in the period 2000–2021. Data was collected on clinical onset, hyperammonemia severity, evolution and liver transplantation. There were 33 patients in the study period, whose diagnosis were: ornithine transcarbamylase (OTC, n = 20, 10 females), argininosuccinate synthetase (ASS, n = 6), carbamylphosphate synthetase 1 (CPS1, n = 4), argininosuccinate lyase (ASL, n = 2) and N-acetylglutamate synthetase (NAGS, n = 1) deficiency. Thirty one were detected because of clinical symptoms (45% with neonatal onset). The other 2 were diagnosed being presymptomatic, by neonatal/family screening. Neonatal forms (n = 14) were more severe, all of them presented during the first week of life as severe hyperammonemia (mean peak 1,152 µmol/L). Seven patients died (6 at debut) and all survivors received transplantation. There was no mortality among the late forms. Of the 27 patients who did not die in the neonatal period, 16 (59%) received liver transplantationwith 100% survival, normal protein tolerance and usual need of citrulline supplementation. The transplant's metabolic success was accompanied by neurologic sequelae in 69%, but there was no progression of brain damage. Decision of continuous medical treatment in 11 patients appeared to be related with preserved neurodevelopment and fewer metabolic crises.
TL;DR: In this article , the authors used a cognitive battery to expose the cognitive deficits in asymptomatic carriers of OTCD, an X-linked disorder that results in a dysfunctional mitochondrial enzyme, which prevents the synthesis of citrulline from carbamoyl phosphate and ornithine.
01 May 2023
TL;DR: In this article , 13C-labeled sodium acetate was applied to 47 subjects (10 healthy subjects, 28 symptomatic patients, 9 asymptomatic carriers) to evaluate a practical method to quantify 13Curea production as a marker for urea cycle function.
TL;DR: In this paper , the authors used penalized regression to model the relationship between genetic variants and day 0 metabolite level, and then performed a metabolite-wide colocalization scan to associate the genetically regulated component of metabolite expression with ALT elevation.
Abstract: Acetaminophen (APAP) is the most common cause liver injury following alcohol in US patients. Predicting liver injury and subsequent hepatic regeneration in patients taking therapeutic doses of APAP may be possible using new 'omic methods such as metabolomics and genomics. Multi'omic techniques increase our ability to find new mechanisms of injury and regeneration.We used metabolomic and genomic data from a randomized controlled trial of patients administered 4 g of APAP per day for 14 days or longer with blood samples obtained at 0 (baseline), 4, 7, 10, 13 and 16 days. We used the highest ALT as the clinical outcome to be predicted in our integrated analysis. We used penalized regression to model the relationship between genetic variants and day 0 metabolite level, and then performed a metabolite-wide colocalization scan to associate the genetically regulated component of metabolite expression with ALT elevation. Genome-wide association study (GWAS) analyses were conducted for ALT elevation and metabolite level using linear regression, with age, sex, and the first five principal components included as covariates. Colocalization was tested via a weighted sum test.Out of the 164 metabolites modeled, 120 met the criteria for predictive accuracy and were retained for genetic analyses. After genomic examination, eight metabolites were found to be under genetic control and predictive of ALT elevation due to therapeutic acetaminophen. The metabolites were: 3-oxalomalate, allantoate, diphosphate, L-carnitine, L-proline, maltose, and ornithine. These genes are important in the tricarboxylic acid cycle (TCA), urea breakdown pathway, glutathione production, mitochondrial energy production, and maltose metabolism.This multi'omic approach can be used to integrate metabolomic and genomic data allowing identification of genes that control downstream metabolites. These findings confirm prior work that have identified mitochondrial energy production as critical to APAP induced liver injury and have confirmed our prior work that demonstrate the importance of the urea cycle in therapeutic APAP liver injury.
TL;DR: In this article , the authors investigated whether exposure to PFAS was associated with the global, untargeted metabolome and found associations between plasma PFAS and perturbations in lipid and amino acid metabolites in both mothers and children.
TL;DR: In this article , a 2-day-old male neonate was diagnosed with ornithine transcarbamylase deficiency presenting hyperammonemia and severe heart failure after total anomalous pulmonary venous connection repair.
Abstract: Abstract Ornithine transcarbamylase deficiency is an X-linked disorder which results in the accumulation of ammonia causing irritability and vomiting. Acute hyperammonemia requires rapid and intensive intervention. However, as those clinical features are non-specific and commonly seen in peri-operative situation, ornithine transcarbamylase deficiency could be difficult to diagnose prior to and post-emergency cardiac surgery. We report a 2-day-old male neonate who was diagnosed with ornithine transcarbamylase deficiency presenting hyperammonemia and severe heart failure after total anomalous pulmonary venous connection repair.
01 Jan 2023
TL;DR: In this article , the detailed regulation of CPS1 transcription in order to maintain urea cycle in acute liver failure (ALF) remains largely unknown, but it has been shown that the rate-limiting enzyme carbamoyl phosphate synthetase I (CPS1) can be used to regulate CPS1 in ALF.
Abstract: Background and Aims Disruption of the urea cycle results in hyperammonemia and thus causes hepatic encephalopathy (HE), a lethal complication of acute liver failure (ALF). A complete urea cycle requires six enzymes, including the rate-limiting enzyme carbamoyl phosphate synthetase I (CPS1). To date, the detailed regulation of CPS1 transcription in order to maintain urea cycle in ALF remains largely unknown.
TL;DR: In this article , the effects of different doses of squalene on the enzymes, intermediates, and molecules of the urea cycle, in order to determine if Squalene has beneficial effects among groups of people with Type 2 diabetes mellitus.
Abstract: Background: Type 2 diabetes mellitus is a chronic disease that diminishes the body’s ability to regulate glucose levels due to the lack of insulin produced. In recent studies, squalene has been reported to have beneficial effects for diabetic patients, especially within the liver where the urea cycle takes place.Objective: Our main goal was to evaluate the molecular effects of different doses of squalene on the enzymes, intermediates, and molecules of the urea cycle, in order to determine if squalene has beneficial effects among groups of people with type 2 diabetes mellitus. The enzymes and molecules that are being studied are ornithine transcarbamylase (OTC), arginosuccinate synthetase (ASS), arginase, carbamoyl-phosphate synthetase 1 (CSP1), urea, aspartate, and ammonium ion (NH4+).Methods: In this study, healthy volunteers were categorized as the healthy control (group 1) and volunteers with type 2 diabetes mellitus were selected. The patients with diabetes were divided up into 4 groups. Group 2 consists of the patients that will not be treated with squalene. Groups 3, 4, 5 were treated with 200, 400, 600 mg, respectively. The patients were treated with their respective amounts every 14 days for the duration of 84 days. The enzymes and molecules were measured on days 1, 14, 28, 56, and 84.Results: The squalene-treated diabetic groups were compared to group 2, who was not treated with any squalene to determine the differences between the parameters. Throughout the 84 days, it was observed that NH4+ or ammonium molecules decreased in all treated diabetic patients with high statistical difference (P < 0.05). For the majority of the diabetic patients treated with squalene, there was also a decrease in aspartate. The other parameters did not have consistent significant differences (P > 0.05).Conclusion: Based on the findings of this study, the addition of various doses of squalene to a diabetic patient’s diet decreased the amount of ammonium and aspartate in the body. As ammonium is the direct product of the urea cycle, it is evident that squalene does play a key role in reducing the amount of ammonium in a diabetic patient to a healthier level.Keywords: Diabetes mellitus, urea cycle, enzyme, metabolite, squalene.
TL;DR: In this article , the authors used data mining approaches to identify tumor types that exhibit aberrant overexpression of NAGS, CPS1, and citrin genes, and evaluated factors that may contribute to increased expression of the three genes and their products in tumors.
Abstract: Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 (CPS1) and SLC25A13 (citrin) genes has been associated with faster proliferation of tumor cells due to metabolic reprogramming that increases the activity of the CAD complex and pyrimidine biosynthesis. N-acetylglutamate (NAG), produced by NAG synthase (NAGS), is an essential activator of CPS1. Although NAGS is expressed in lung cancer derived cell lines, expression of the NAGS gene and its product was not evaluated in tumors with aberrant expression of CPS1 and citrin. We used data mining approaches to identify tumor types that exhibit aberrant overexpression of NAGS, CPS1, and citrin genes, and evaluated factors that may contribute to increased expression of the three genes and their products in tumors. Median expression of NAGS, CPS1, and citrin mRNA was higher in glioblastoma multiforme (GBM), glioma, and stomach adenocarcinoma (STAD) samples compared to the matched normal tissue. Median expression of CPS1 and citrin mRNA was higher in the lung adenocarcinoma (LUAD) sample while expression of NAGS mRNA did not differ. High NAGS expression was associated with an unfavorable outcome in patients with glioblastoma and GBM. Low NAGS expression was associated with an unfavorable outcome in patients with LUAD. Patterns of DNase hypersensitive sites and histone modifications in the upstream regulatory regions of NAGS, CPS1, and citrin genes were similar in liver tissue, lung tissue, and A549 lung adenocarcinoma cells despite different expression levels of the three genes in the liver and lung. Citrin gene copy numbers correlated with its mRNA expression in glioblastoma, GBM, LUAD, and STAD samples. There was little overlap between NAGS, CPS1, and citrin sequence variants found in patients with respective deficiencies, tumor samples, and individuals without known rare genetic diseases. The correlation between NAGS, CPS1, and citrin mRNA expression in the individual glioblastoma, GBM, LUAD, and STAD samples was very weak. These results suggest that the increased cytoplasmic supply of either carbamylphosphate, produced by CPS1, or aspartate may be sufficient to promote tumorigenesis, as well as the need for an alternative explanation of CPS1 activity in the absence of NAGS expression and NAG.
TL;DR: La Spina et al. as mentioned in this paper have shown that inhibition of the mitochondrial chaperone TRAP1, a master metabolic regulator, hampers MPNST cell tumorigenicity.
Abstract:
Neurofibromatosis type 1 (NF1) is a tumor-predisposing genetic disorder caused by heterozygous mutations in the NF1 gene encoding for the tumor suppressor Neurofibromin. Biallelic NF1 inactivation in Schwann cells leads to the onset of neurofibromas, benign neoplasms that can cause severe medical complications and give rise to malignant peripheral nerve sheath tumors (MPNSTs), for which no treatment exists. Neurofibroma cells undergo bioenergetic changes required to sustain their malignant transformation. Our group has shown that inhibition of the mitochondrial chaperone TRAP1, a master metabolic regulator, hampers MPNST cell tumorigenicity. A growing number of evidence indicates that urea cycle (UC) dysregulation can redirect metabolic substrates to specific biosynthetic routes in many tumor cell types. We have found that a complete UC is absent in MPNST cell models, as they lack ornithine transcarbamylase (OTC), a key UC enzyme that converts ornithine into citrulline. In the absence of TRAP1, MPNST cells strongly reduce arginine levels and accumulate ornithine through the activity of the mitochondrial enzymes arginase 2 (ARG2) and ornithine aminotransferase (OAT). These changes can reverberate on glutamine and proline levels ultimately affecting extracellular matrix deposition, motility and ROS homeostasis, as well as on ornithine-dependent polyamine biosynthesis that can regulate cell growth and proliferation. Surprisingly, in the absence of TRAP1 MPNST cells also accumulate citrulline, even though they do not express either OTC or any nitric oxide synthase (NOS) isoform that converts arginine into citrulline. We ascribe citrulline production to the activity of dimethylarginine dimethylaminohydrolase (DDAH) enzymes, involved in the catabolism of asymmetric dimethylarginines. Induction of DDAHs indicates an elevated protein catabolism that could contribute to tune MPNST cell tumorigenicity. A thorough comprehension of the amino acid metabolism rewiring in NF1-related tumors may unveil new targetable liabilities of cancer cells to be exploited for the design of new effective therapeutic approaches.
Citation Format: Martina La Spina. Rewiring of amino acid metabolism in neurofibromatosis type 1-related tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3678.
TL;DR: In this paper , the effects of short-term high-fat diets on the brain are investigated by employing RNA sequencing and metabolomics profiling, and the results showed that the brain pathways upregulated from HFD-exposed brain tissues relative to control samples included oxidative stress, oxidized polyunsaturated fatty acids, amino acid metabolism (e.g., branched-chain amino acid catabolism, and lysine metabolism), and the gut microbiome.
Abstract: The chronic consumption of diets rich in saturated fats leads to obesity and associated metabolic disorders including diabetes and atherosclerosis. Intake of a high-fat diet (HFD) is also recognized to dysregulate neural functions such as cognition, mood, and behavior. However, the effects of short-term high-fat diets on the brain are elusive. Here, we investigated molecular changes in the mouse brain following an acute HFD for 10 days by employing RNA sequencing and metabolomics profiling. Aberrant expressions of 92 genes were detected in the brain tissues of acute HFD-exposed mice. The differentially expressed genes were enriched for various pathways and processes such as superoxide metabolism. In our global metabolomic profiling, a total of 59 metabolites were significantly altered by the acute HFD. Metabolic pathways upregulated from HFD-exposed brain tissues relative to control samples included oxidative stress, oxidized polyunsaturated fatty acids, amino acid metabolism (e.g., branched-chain amino acid catabolism, and lysine metabolism), and the gut microbiome. Acute HFD also elevated levels of N-acetylated amino acids, urea cycle metabolites, and uracil metabolites, further suggesting complex changes in nitrogen metabolism. The observed molecular events in the present study provide a valuable resource that can help us better understand how acute HFD stress impacts brain homeostasis.
03 Apr 2023
TL;DR: In this article , the relative quantities of the detected metabolites involved in glycolysis/glyconeogenesis (A), the urea cycle (B), pyrimidine metabolism (C), amino acid metabolism (D), and nicotinate and nicotinamide metabolism (E) are represented as bar graphs.
Abstract: <p>The relative quantities of the detected metabolites involved in glycolysis/glyconeogenesis (A), the urea cycle (B), pyrimidine metabolism (C), amino acid metabolism (D), and nicotinate and nicotinamide metabolism (E) are represented as bar graphs (from left to right: DEN group, DEN-0.03ACR group, DEN-0.06 group, and 0.06ACR group). N.D., not detected.</p>
TL;DR: In this paper , the authors applied a non-targeted metabolomic approach to identify Trichinella zimbabwensis biomarkers including metabolic response from sera of infected Sprague-Dawley rats.
Abstract: Trichinella infections have been documented globally and have been detected in wild and/or domestic animals except Antarctica. There is paucity of information in the metabolic responses of hosts during Trichinella infections and biomarkers for infection that can be used in the diagnosis of the disease. The current study aimed to apply a non-targeted metabolomic approach to identify Trichinella zimbabwensis biomarkers including metabolic response from sera of infected Sprague-Dawley rats. Fifty-four male Sprague-Dawley rats were randomly assigned into T. zimbabwensis infected group (n = 36) and the non-infected control (n = 18). Results from the study showed that the metabolic signature of T. zimbabwensis infection consists of enriched methyl histidine metabolism, disturbance of the liver urea cycle, impeded TCA cycle, and upregulation of gluconeogenesis metabolism. The observed disturbance in the metabolic pathways was attributed to the effects caused by the parasite during its migration to the muscles resulting in downregulation of amino acids intermediates in the Trichinella-infected animals, and therefore affecting energy production and degradation of biomolecules. It was concluded that T. zimbabwensis infection caused an upregulation of amino acids; pipecolic acid, histidine, and urea, and upregulation of glucose and meso-Erythritol. Moreover, T. zimbabwensis infection caused upregulation of the fatty acids, retinoic acid, and acetic acid. These findings highlight the potential of metabolomics as a novel approach for fundamental investigations of host-pathogen interactions as well as for disease progression and prognosis.
TL;DR: In this article , a CITRIN knockout HepG2 cell line was generated using Clustered Regularly Interspaced Short Palindromic Repeats/Cas 9 genome editing technology to study metabolic and cell signaling defects in CD.
Abstract: Abstract Citrin deficiency (CD) is an inborn error of metabolism caused by loss-of-function of the mitochondrial aspartate/glutamate transporter, CITRIN, which is involved in both the urea cycle and malate–aspartate shuttle. Patients with CD develop hepatosteatosis and hyperammonemia but there is no effective therapy for CD. Currently, there are no animal models that faithfully recapitulate the human CD phenotype. Accordingly, we generated a CITRIN knockout HepG2 cell line using Clustered Regularly Interspaced Short Palindromic Repeats/Cas 9 genome editing technology to study metabolic and cell signaling defects in CD. CITRIN KO cells showed increased ammonia accumulation, higher cytosolic ratio of reduced versus oxidized form of nicotinamide adenine dinucleotide (NAD) and reduced glycolysis. Surprisingly, these cells showed impaired fatty acid metabolism and mitochondrial activity. CITRIN KO cells also displayed increased cholesterol and bile acid metabolism resembling those observed in CD patients. Remarkably, normalizing cytosolic NADH:NAD+ ratio by nicotinamide riboside increased glycolysis and fatty acid oxidation but had no effect on the hyperammonemia suggesting the urea cycle defect was independent of the aspartate/malate shuttle defect of CD. The correction of glycolysis and fatty acid metabolism defects in CITRIN KO cells by reducing cytoplasmic NADH:NAD+ levels suggests this may be a novel strategy to treat some of the metabolic defects of CD and other mitochondrial diseases.
TL;DR: In this paper , a proof-of-concept framework for integrating knowledge of metabolic interactions with real-life patient data before scaling up this approach is presented. But it is limited to two groups of well-studied and related metabolic pathways (the urea cycle and pyrimidine de-novo synthesis).
Abstract: Abstract Background Inherited Metabolic Disorders (IMDs) are rare diseases where one impaired protein leads to a cascade of changes in the adjacent chemical conversions. IMDs often present with non-specific symptoms, a lack of a clear genotype–phenotype correlation, and de novo mutations, complicating diagnosis. Furthermore, products of one metabolic conversion can be the substrate of another pathway obscuring biomarker identification and causing overlapping biomarkers for different disorders. Visualization of the connections between metabolic biomarkers and the enzymes involved might aid in the diagnostic process. The goal of this study was to provide a proof-of-concept framework for integrating knowledge of metabolic interactions with real-life patient data before scaling up this approach. This framework was tested on two groups of well-studied and related metabolic pathways (the urea cycle and pyrimidine de-novo synthesis). The lessons learned from our approach will help to scale up the framework and support the diagnosis of other less-understood IMDs. Methods Our framework integrates literature and expert knowledge into machine-readable pathway models, including relevant urine biomarkers and their interactions. The clinical data of 16 previously diagnosed patients with various pyrimidine and urea cycle disorders were visualized on the top 3 relevant pathways. Two expert laboratory scientists evaluated the resulting visualizations to derive a diagnosis. Results The proof-of-concept platform resulted in varying numbers of relevant biomarkers (five to 48), pathways, and pathway interactions for each patient. The two experts reached the same conclusions for all samples with our proposed framework as with the current metabolic diagnostic pipeline. For nine patient samples, the diagnosis was made without knowledge about clinical symptoms or sex. For the remaining seven cases, four interpretations pointed in the direction of a subset of disorders, while three cases were found to be undiagnosable with the available data. Diagnosing these patients would require additional testing besides biochemical analysis. Conclusion The presented framework shows how metabolic interaction knowledge can be integrated with clinical data in one visualization, which can be relevant for future analysis of difficult patient cases and untargeted metabolomics data. Several challenges were identified during the development of this framework, which should be resolved before this approach can be scaled up and implemented to support the diagnosis of other (less understood) IMDs. The framework could be extended with other OMICS data (e.g. genomics, transcriptomics), and phenotypic data, as well as linked to other knowledge captured as Linked Open Data.