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Metabolomics : Official Journal of the... Aug 2023Head and neck cancer (HNC) is the fifth most common cancer globally. Diagnosis at early stages are critical to reduce mortality and improve functional and esthetic... (Review)
Review
INTRODUCTION
Head and neck cancer (HNC) is the fifth most common cancer globally. Diagnosis at early stages are critical to reduce mortality and improve functional and esthetic outcomes associated with HNC. Metabolomics is a promising approach for discovery of biomarkers and metabolic pathways for risk assessment and early detection of HNC.
OBJECTIVES
To summarize and consolidate the available evidence on metabolomics and HNC in plasma/serum, saliva, and urine.
METHODS
A systematic search of experimental research was executed using PubMed and Web of Science. Available data on areas under the curve was extracted. Metabolic pathway enrichment analysis were performed to identify metabolic pathways altered in HNC. Fifty-four studies were eligible for data extraction (33 performed in plasma/serum, 15 in saliva and 6 in urine).
RESULTS
Metabolites with high discriminatory performance for detection of HNC included single metabolites and combination panels of several lysoPCs, pyroglutamate, glutamic acid, glucose, tartronic acid, arachidonic acid, norvaline, linoleic acid, propionate, acetone, acetate, choline, glutamate and others. The glucose-alanine cycle and the urea cycle were the most altered pathways in HNC, among other pathways (i.e. gluconeogenesis, glycine and serine metabolism, alanine metabolism, etc.). Specific metabolites that can potentially serve as complementary less- or non-invasive biomarkers, as well as metabolic pathways integrating the data from the available studies, are presented.
CONCLUSION
The present work highlights utility of metabolite-based biomarkers for risk assessment, early detection, and prognostication of HNC, as well as facilitates incorporation of available metabolomics studies into multi-omics data integration and big data analytics for personalized health.
Topics: Humans; Alanine; Body Fluids; Glucose; Head and Neck Neoplasms; Metabolomics
PubMed: 37644353
DOI: 10.1007/s11306-023-02038-2 -
The American Journal of Gastroenterology Mar 2024The results from 2 phase 3 studies, through 2 years, in chronic hepatitis B infection showed tenofovir alafenamide (TAF) had similar efficacy to tenofovir disoproxil... (Randomized Controlled Trial)
Randomized Controlled Trial
INTRODUCTION
The results from 2 phase 3 studies, through 2 years, in chronic hepatitis B infection showed tenofovir alafenamide (TAF) had similar efficacy to tenofovir disoproxil fumarate (TDF) with superior renal and bone safety. We report updated results through 5 years.
METHODS
Patients with HBeAg-negative or HBeAg-positive chronic hepatitis B infection with or without compensated cirrhosis were randomized (2:1) to TAF 25 mg or TDF 300 mg once daily in double-blind (DB) fashion for up to 3 years, followed by open-label (OL) TAF up to 8 years. Efficacy (antiviral, biochemical, and serologic), resistance (deep sequencing of polymerase/reverse transcriptase and phenotyping), and safety, including renal and bone parameters, were evaluated by pooled analyses.
RESULTS
Of 1,298 randomized and treated patients, 866 receiving TAF (DB and OL) and 432 receiving TDF with rollover to OL TAF at year 2 (n = 180; TDF→TAF3y) or year 3 (n = 202; TDF→TAF2y) were included. Fifty (4%) TDF patients who discontinued during DB were excluded. At year 5, 85%, 83%, and 90% achieved HBV DNA <29 IU/mL (missing = failure) in the TAF, TDF→TAF3y, and TDF→TAF2y groups, respectively; no patient developed TAF or TDF resistance. Median estimated glomerular filtration rate (by using Cockcroft-Gault) declined <2.5 mL/min, and mean declines of <1% in hip and spine bone mineral density were seen at year 5 in the TAF group; patients in the TDF→TAF groups had improvements in these parameters at year 5 after switching to OL TAF.
DISCUSSION
Long-term TAF treatment resulted in high rates of viral suppression, no resistance, and favorable renal and bone safety.
Topics: Humans; Tenofovir; Hepatitis B, Chronic; Male; Female; Alanine; Middle Aged; Antiviral Agents; Adenine; Adult; Double-Blind Method; Bone Density; Glomerular Filtration Rate; Hepatitis B virus; Drug Resistance, Viral; Treatment Outcome; Kidney; Viral Load; Hepatitis B e Antigens
PubMed: 37561058
DOI: 10.14309/ajg.0000000000002468 -
Cell Reports Sep 2023In ribosome-associated quality control (RQC), nascent polypeptides produced by interrupted translation are modified with C-terminal polyalanine tails ("Ala-tails") that...
In ribosome-associated quality control (RQC), nascent polypeptides produced by interrupted translation are modified with C-terminal polyalanine tails ("Ala-tails") that function outside ribosomes to induce ubiquitylation by E3 ligases Pirh2 (p53-induced RING-H2 domain-containing) or CRL2 (Cullin-2 RING ligase2)-KLHDC10. Here, we investigate the molecular basis of Ala-tail function using biochemical and in silico approaches. We show that Pirh2 and KLHDC10 directly bind to Ala-tails and that structural predictions identify candidate Ala-tail-binding sites, which we experimentally validate. The degron-binding pockets and specific pocket residues implicated in Ala-tail recognition are conserved among Pirh2 and KLHDC10 homologs, suggesting that an important function of these ligases across eukaryotes is in targeting Ala-tailed substrates. Moreover, we establish that the two Ala-tail-binding pockets have convergently evolved, either from an ancient module of bacterial provenance (Pirh2) or via tinkering of a widespread C-degron-recognition element (KLHDC10). These results shed light on the recognition of a simple degron sequence and the evolution of Ala-tail proteolytic signaling.
Topics: Humans; Alanine; Binding Sites; Proteolysis; Ubiquitin-Protein Ligases; Ubiquitination; Carrier Proteins
PubMed: 37676773
DOI: 10.1016/j.celrep.2023.113100 -
Reviews in the Neurosciences Jan 2024Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder. Mutations in and the resulting hexanucleotide repeat (GGGGCC)... (Review)
Review
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder. Mutations in and the resulting hexanucleotide repeat (GGGGCC) expansion (HRE) has been identified as a major cause of familial ALS, accounting for about 40 % of familial and 6 % of sporadic cases of ALS in Western patients. The pathological outcomes of HRE expansion in ALS have been recognized as the results of two mechanisms that include both the toxic gain-of-function and loss-of-function of C9ORF72. The gain of toxicity results from RNA and dipeptide repeats (DPRs). The HRE can be bidirectionally transcribed into RNA foci, which can bind to and disrupt RNA splicing, transport, and translation. The DPRs that include poly-glycine-alanine, poly-glycine-proline, poly-glycine- arginine, poly-proline-alanine, and poly-proline-arginine can induce toxicity by direct binding and sequestrating other proteins to interfere rRNA synthesis, ribosome biogenesis, translation, and nucleocytoplasmic transport. The C9ORF72 functions through binding to its partners-Smith-Magenis chromosome regions 8 (SMCR8) and WD repeat-containing protein (WDR41). Loss of C9ORF72 function results in impairment of autophagy, deregulation of autoimmunity, increased stress, and disruption of nucleocytoplasmic transport. Further insight into the mechanism in C9ORF72 HRE pathogenesis will facilitate identifying novel and effective therapeutic targets for ALS.
Topics: Humans; Amyotrophic Lateral Sclerosis; C9orf72 Protein; Proteins; Dipeptides; RNA; Arginine; Alanine; Glycine; Proline
PubMed: 37525497
DOI: 10.1515/revneuro-2023-0060 -
Scientific Reports Jul 2023Disordered sleep is a global social problem and an established significant risk factor for psychological and metabolic diseases. We profiled non-targeted metabolites in...
Disordered sleep is a global social problem and an established significant risk factor for psychological and metabolic diseases. We profiled non-targeted metabolites in saliva from mouse models of chronic sleep disorder (CSD). We identified 288 and 55 metabolites using CE-FTMS and LC-TOFMS, respectively, among which concentrations of 58 (CE-FTMS) and three (LC-TOFMS) were significantly changed by CSD. Pathway analysis revealed that CSD significantly suppressed glycine, serine and threonine metabolism. Arginine and proline metabolic pathways were among those that were both upregulated and downregulated. Pathways of alanine, aspartate and glutamate metabolism, genetic information processing, and the TCA cycle tended to be downregulated, whereas histidine metabolism tended to be upregulated in mice with CSD. Pyruvate, lactate, malate, succinate and the glycemic amino acids alanine, glycine, methionine, proline, and threonine were significantly decreased, whereas 3-hydroxybutyric and 2-hydroxybutyric acids associated with ketosis were significantly increased, suggesting abnormal glucose metabolism in mice with CSD. Increases in the metabolites histamine and kynurenic acid that are associated with the central nervous system- and decreased glycine, might be associated with sleep dysregulation and impaired cognitive dysfunction in mice with CSD. Our findings suggested that profiling salivary metabolites could be a useful strategy for diagnosing CSD.
Topics: Male; Animals; Mice; Saliva; Sleep; Psychophysiology; Alanine; Chronic Disease; Disease Models, Animal; Fabaceae; Metabolome
PubMed: 37429932
DOI: 10.1038/s41598-023-38289-1 -
Biochemistry. Biokhimiia Aug 2023Using nutritional interventions to cure and manage psychiatric disorders is a promising tool. In this regard, accumulating documents support strong relationships between... (Review)
Review
Using nutritional interventions to cure and manage psychiatric disorders is a promising tool. In this regard, accumulating documents support strong relationships between the diet and brain health throughout the lifespan. Evidence from animal and human studies demonstrated that β-alanine (Beta-alanine; BA), a natural amino acid, provides several benefits in fight against cognitive decline promoting mental health. This review summarizes and reports state-of-the-art evidence on how BA affects cognitive health and argues existence of potential unrevealed biochemical mechanisms and signaling cascades. There is a growing body of evidence showing that BA supplement has a significant role in mental health mediating increase of the cell carnosine and brain-derived neurotrophic factor (BDNF) content. BDNF is one of the most studied neurotrophins in the mammalian brain, which activates several downstream functional cascades via the tropomyosin-related kinase receptor type B (TrkB). Activation of TrkB induces diverse processes, such as programmed cell death and neuronal viability, dendritic branching growth, dendritic spine formation and stabilization, synaptic development, cognitive-related processes, and synaptic plasticity. Carnosine exerts its main effect via its antioxidant properties. This critical antioxidant also scavenges hypochlorous acid (HOCl), another toxic species produced in mammalian cells. Carnosine regulates transcription of hundreds of genes related to antioxidant mechanisms by increasing expression of the nuclear erythroid 2-related factor 2 (Nrf2) and translocating Nrf2 to the nucleus. Another major protective effect of carnosine on the central nervous system (CNS) is related to its anti-glycating, anti-aggregate activities, anti-inflammatory, metal ion chelator activity, and regulation of pro-inflammatory cytokine secretion. These effects could be associated with the carnosine ability to form complexes with metal ions, particularly with zinc (Zn2+). Thus, it seems that BA via BDNF and carnosine mechanisms may improve brain health and cognitive function over the entire human lifespan.
Topics: Animals; Humans; Carnosine; Antioxidants; Brain-Derived Neurotrophic Factor; NF-E2-Related Factor 2; Cognition; beta-Alanine; Mammals
PubMed: 37758316
DOI: 10.1134/S0006297923080114 -
Advances in Colloid and Interface... Nov 2023The monolayer characteristics of selected N-alkanoyl substituted α-amino acid are studied with the objective to demonstrate the specific effect of the chemical...
The monolayer characteristics of selected N-alkanoyl substituted α-amino acid are studied with the objective to demonstrate the specific effect of the chemical structure of the polar head group which is highlighted with the D- and L-enantiomers of the following selected examples: R-alanine, R-serine, R-threonine, R-allo-threonine, and R-aspartic acid (R = C, C). The thermodynamic effect of the head group variation is studied. Experimental π-A isotherms of the N-tetradecyl-L-alanine monolayers show similar behavior as those of usual amphiphiles. The -CH-group in R-alanine with the simplest head group structure is substituted by a -CH-OH group in R-serine and serine methylester and by a -CH- CH-OH group in R-threonine (or allo-threonine) and threonine methylester. The introduction of the methyl group in 3-position of serine (serine to 3-methyl-serine = threonine) shifts the characteristic temperatures by >20 K to lower values determined for N-C16-Dl-serine. The formation of the corresponding methylester decreases these temperatures by 15 K for serine with the shorter (C16) alkyl chain and only by ∼5 K for threonine with the longer chain (C18). The π-A curves of the enantiomeric and racemic allo-forms show similar features to those of N-stearoyl-threonine. The absolute T-values (disappearance of the LE/LC-transition) are 4-5 K larger compared with the corresponding N-stearoyl-threonines, but the ΔT between the enantiomeric (D) and the racemic (DL) forms is only slightly larger than that of N-stearoyl-threonine. Monolayers of different N-alkanoyl substituted α-amino acid amphiphiles have been mesoscopically characterized. Substantial topological differences are observable at the condensed phase domains of several amino acid amphiphiles, such as, N-palmitoyl aspartic acid, N-palmitoyl- or N-stearoyl serine methyl ester, N-stearoyltyrosine, N-palmitoyl or N-myristoyl alanine. Many fascinating domain shapes are found, but always the curvatures of the two enantiomeric forms are directed in an opposite sense. The domain shape of the 1:1 racemic mixtures is usually different, but very often oppositely curved texture elements are observable. GIXD is used to study the characteristic features of the lattice structure of condensed monolayer phases on the Angstrom scale. Specific for all structures is the large tilt angle with respect to the surface normal, which decreases only marginally by compression. The large size of the head groups and strong interactions between them dominate the monolayer structure. As presented for NC16 and N-C18-threonine, N-C16-DL -serine, N-C16-L -serine, NC16 DL -serine-ME, NC16 L -serine-ME, NC18 DL -threonine-ME, and NC18 L -threonine-ME the enantiomers form an oblique lattice structure (3 diffraction peaks), whereas two peaks are observed for the racemates forming NNN tilted orthorhombic structures. A complete phase diagram of mixed monolayers of the D- and L-enantiomers of N-stearoyl-threonine with two eutectic points at x ≈ 0.25 and x ≈ 0.75 is proposed. The quantum chemical semiempirical PM3 method is applied to calculate the thermodynamic and structural parameters of clusterization in finite and infinite clusters for N-alkanoyl-substituted alanine with n = 8-17 carbon atoms in the chain at the air/water interface with the aim to obtain a new theoretical verification of the experimental results.
Topics: Amino Acids; Aspartic Acid; Thermodynamics; Threonine; Alanine; Serine
PubMed: 37863015
DOI: 10.1016/j.cis.2023.103001 -
Nature Metabolism Nov 2023Glucose is the primary source of energy for the brain; however, it remains controversial whether, upon neuronal activation, glucose is primarily used by neurons for ATP...
Glucose is the primary source of energy for the brain; however, it remains controversial whether, upon neuronal activation, glucose is primarily used by neurons for ATP production or if it is partially oxidized in astrocytes, as proposed by the astrocyte-neuron lactate shuttle model for glutamatergic neurons. Thus, an in vivo picture of glucose metabolism during cognitive processes is missing. Here, we uncover in Drosophila melanogaster a glia-to-neuron alanine transfer involving alanine aminotransferase that sustains memory formation. Following associative conditioning, glycolysis in glial cells produces alanine, which is back-converted into pyruvate in cholinergic neurons of the olfactory memory center to uphold their increased mitochondrial needs. Alanine, as a mediator of glia-neuron coupling, could be an alternative to lactate in cholinergic systems. In parallel, a dedicated glial glucose transporter imports glucose specifically for long-term memory, by directly transferring it to neurons for use by the pentose phosphate pathway. Our results demonstrate in vivo the compartmentalization of glucose metabolism between neurons and glial cells during memory formation.
Topics: Animals; Drosophila; Alanine; Drosophila melanogaster; Neuroglia; Glycolysis; Neurons; Glucose; Mitochondria; Lactic Acid
PubMed: 37932430
DOI: 10.1038/s42255-023-00910-y -
Respiratory Research Feb 2024Allergic diseases exert a considerable impact on global health, thus necessitating investigations into their etiology and pathophysiology for devising effective... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Allergic diseases exert a considerable impact on global health, thus necessitating investigations into their etiology and pathophysiology for devising effective prevention and treatment strategies. This study employs a Mendelian randomization (MR) analysis and meta-analysis to identify metabolite targets potentially associated with allergic diseases.
METHODS
A two-sample MR analysis was conducted to explore potential causal relationships between circulating and urinary metabolites and allergic diseases. Exposures were derived from a genome-wide association study (GWAS) of 486 circulating metabolites and a GWAS of 55 targeted urinary metabolites. Outcome data for allergic diseases, including atopic dermatitis (AD), allergic rhinitis (AR), and asthma, were obtained from the FinnGen biobank in Europe (cohort 1) and the Biobank Japan in Asia (cohort 2). MR results from both cohorts were combined using a meta-analysis.
RESULTS
MR analysis identified 50 circulating metabolites and 6 urinary metabolites in cohort 1 and 54 circulating metabolites and 2 urinary metabolites in cohort 2 as potentially causally related to allergic diseases. A meta-analysis of the MR results revealed stearoylcarnitine (OR 8.654; 95% CI 4.399-17.025; P = 4.06E-10) and 1-arachidonoylglycerophosphoinositol (OR 2.178; 95% CI 1.388-3.419; P = 7.15E-04) as the most reliable causal circulating metabolites for asthma and AR, respectively. Further, histidine (OR 0.734; 95% CI: 0.594-0.907; P = 0.004), tyrosine (OR 0.601; 95% CI: 0.380-0.952; P = 0.030), and alanine (OR 0.280; 95% CI: 0.125-0.628; P = 0.002) emerged as urinary metabolites with the greatest protective effects against asthma, AD, and AR, respectively.
CONCLUSIONS
Imbalances in numerous circulating and urinary metabolites may be implicated in the development and progression of allergic diseases. These findings have significant implications for the development of targeted strategies for the prevention and treatment of allergic diseases.
Topics: Humans; Genome-Wide Association Study; Mendelian Randomization Analysis; Asthma; Rhinitis, Allergic; Alanine
PubMed: 38378549
DOI: 10.1186/s12931-024-02720-6 -
Scientific Reports Sep 2023E3 ubiquitin ligases are critical to the protein degradation pathway by catalyzing the final step in protein ubiquitination by mediating ubiquitin transfer from E2...
E3 ubiquitin ligases are critical to the protein degradation pathway by catalyzing the final step in protein ubiquitination by mediating ubiquitin transfer from E2 enzymes to target proteins. Nedd4 is a HECT domain-containing E3 ubiquitin ligase with a wide range of protein targets, the dysregulation of which has been implicated in myriad pathologies, including cancer and Parkinson's disease. Towards the discovery of compounds disrupting the auto-ubiquitination activity of Nedd4, we developed and optimized a TR-FRET assay for high-throughput screening. Through selective screening of a library of potentially covalent compounds, compounds 25 and 81 demonstrated apparent IC values of 52 µM and 31 µM, respectively. Tandem mass spectrometry (MS/MS) analysis confirmed that 25 and 81 were covalently bound to Nedd4 cysteine residues (Cys182 and Cys867). In addition, 81 also adducted to Cys627. Auto-ubiquitination assays of Nedd4 mutants featuring alanine substitutions for each of these cysteines suggested that the mode of inhibition of these compounds occurs through blocking the catalytic Cys867. The discovery of these inhibitors could enable the development of therapeutics for various diseases caused by Nedd4 E3 ligase dysregulation.
Topics: Tandem Mass Spectrometry; Ubiquitination; Ubiquitin; Ubiquitin-Protein Ligases; Alanine; Cysteine
PubMed: 37749144
DOI: 10.1038/s41598-023-42997-z