1
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Zhang LM, Zeng T, Zhang BR, Zhang QJ, Gao SJ, Zhu YL, Liu MW. Mendelian randomization combined with single-cell sequencing data analysis of chemokines and chemokine receptors and key genes and molecular mechanisms associated with epilepsy. Neuroreport 2025; 36:467-486. [PMID: 40298633 PMCID: PMC12080367 DOI: 10.1097/wnr.0000000000002168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Accepted: 02/26/2025] [Indexed: 04/30/2025]
Abstract
OBJECTIVE To explore the functions and potential regulatory mechanisms of chemokine and chemokine receptor (CCR)-related genes in epilepsy. METHODS CCRs were identified as candidate genes and their causal relationship with epilepsy was rigorously evaluated via Mendelian randomization analysis. Subsequently, single-cell RNA sequencing (scRNA-seq) data were analyzed to identify and classify cell clusters into distinct types based on cellular annotation. Differential expression analysis was conducted to pinpoint key genes by overlapping the candidate gene set with differentially expressed genes (DEGs). Furthermore, potential therapeutic drugs for epilepsy were predicted, offering novel avenues for disease management and treatment. RESULTS In total, 6395 DEGs were identified across the six cell clusters. After their intersection, CCRL2, XCL2, CXCR5, CXCL1, and CX3CR1 were pinpointed as key genes. Microglia, T cells, B cells, and macrophages have been emerged as critical cells. Furthermore, CXCL1 was regulated by hsa-miR-570-3p and hsa-miR-532-5p. Notably, CXCR5, CXCL1, and CX3CR1 were associated with 27 drug compounds. This comprehensive study leveraged scRNA-seq and transcriptomic data to elucidate the roles of CCR-related genes in epilepsy. Notably, CCRL2, XCL2, CXCR5, CXCL1,and CX3CR1 were identified as key genes implicated in epilepsy, whereas microglia, T cells, B cells, and macrophages were recognized as critical contributors to the development of epilepsy. CONCLUSIONS Regulating the expression of CCRL2, XCL2, CXCR5, CXCL1, and CX3CR1, along with the activity of these immune cells may offer therapeutic potential for the alleviation of epilepsy.
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Affiliation(s)
- Lin-Ming Zhang
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Tao Zeng
- Department of Neurology, The Pearl River Hospital Affiliated to Southern Medical University, Guangzhou, Guangdong, China
| | - Bing-ran Zhang
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Qiu-juan Zhang
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Shu-ji Gao
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yan-lin Zhu
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Ming-wei Liu
- Department of Emergency, Dali Bai Autonomous Prefecture People’s Hospital, Dali, Yunnan, China
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2
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Ogger PP, Murray PJ. Dissecting inflammation in the immunemetabolomic era. Cell Mol Life Sci 2025; 82:182. [PMID: 40293552 PMCID: PMC12037969 DOI: 10.1007/s00018-025-05715-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 04/11/2025] [Accepted: 04/12/2025] [Indexed: 04/30/2025]
Abstract
The role of immune metabolism, specific metabolites and cell-intrinsic and -extrinsic metabolic states across the time course of an inflammatory response are emerging knowledge. Targeted and untargeted metabolomic analysis is essential to understand how immune cells adapt their metabolic program throughout an immune response. In addition, metabolomic analysis can aid to identify pathophysiological patterns in inflammatory disease. Here, we discuss new metabolomic findings within the transition from inflammation to resolution, focusing on three key programs of immunity: Efferocytosis, IL-10 signaling and trained immunity. Particularly the tryptophan-derived metabolite kynurenine was identified as essential for efferocytosis and inflammation resolution as well as a potential biomarker in diverse inflammatory conditions. In summary, metabolomic analysis and integration with transcriptomic and proteomic data, high resolution imaging and spatial information is key to unravel metabolic drivers and dependencies during inflammation and progression to tissue-repair.
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Affiliation(s)
- Patricia P Ogger
- Immunoregulation Research Group, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Peter J Murray
- Immunoregulation Research Group, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
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3
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Vachias C, Tourlonias C, Grelée L, Gueguen N, Renaud Y, Venugopal P, Richard G, Pouchin P, Brasset E, Mirouse V. Gap junctions allow transfer of metabolites between germ cells and somatic cells to promote germ cell growth in the Drosophila ovary. PLoS Biol 2025; 23:e3003045. [PMID: 39965028 PMCID: PMC11864552 DOI: 10.1371/journal.pbio.3003045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/26/2025] [Accepted: 01/29/2025] [Indexed: 02/20/2025] Open
Abstract
Gap junctions allow the exchange of small molecules between cells. How this function could be used to promote cell growth is not yet fully understood. During Drosophila ovarian follicle development, germ cells, which are surrounded by epithelial somatic cells, undergo massive growth. We found that this growth depends on gap junctions between these cell populations, with a requirement for Innexin4 and Innexin2, in the germ cells and the somatic cells, respectively. Translatomic analyses revealed that somatic cells express enzymes and transporters involved in amino acid metabolism that are absent in germ cells. Among them, we identified a putative amino acid transporter required for germline growth. Its ectopic expression in the germline can partially compensate for its absence or the one of Innexin2 in somatic cells. Moreover, affecting either gap junctions or the import of some amino acids in somatic cells induces P-bodies in the germ cells, a feature usually associated with an arrest of translation. Finally, in somatic cells, innexin2 expression and gap junction assembly are regulated by the insulin receptor/PI3K kinase pathway, linking the growth of the two tissues. Overall, these results support the view that metabolic transfer through gap junction promotes cell growth and illustrate how such a mechanism can be integrated into a developmental program, coupling growth control by extrinsic systemic signals with the intrinsic coordination between cell populations.
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Affiliation(s)
- Caroline Vachias
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Camille Tourlonias
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Louis Grelée
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Nathalie Gueguen
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Parvathy Venugopal
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Graziella Richard
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Pierre Pouchin
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Emilie Brasset
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
| | - Vincent Mirouse
- Université Clermont Auvergne, Institute of Genetics, Reproduction and Development (iGReD), UMR CNRS 6293—INSERM U1103, Faculté de Médecine, Clermont-Ferrand, France
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4
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Dyachenko EI, Bel’skaya LV. Transmembrane Amino Acid Transporters in Shaping the Metabolic Profile of Breast Cancer Cell Lines: The Focus on Molecular Biological Subtype. Curr Issues Mol Biol 2024; 47:4. [PMID: 39852119 PMCID: PMC11763447 DOI: 10.3390/cimb47010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 12/20/2024] [Accepted: 12/24/2024] [Indexed: 01/26/2025] Open
Abstract
Amino acid metabolism in breast cancer cells is unique for each molecular biological subtype of breast cancer. In this review, the features of breast cancer cell metabolism are considered in terms of changes in the amino acid composition due to the activity of transmembrane amino acid transporters. In addition to the main signaling pathway PI3K/Akt/mTOR, the activity of the oncogene c-Myc, HIF, p53, GATA2, NF-kB and MAT2A have a direct effect on the amino acid metabolism of cancer cells, their growth and proliferation, as well as the maintenance of homeostatic equilibrium. A distinctive feature of luminal subtypes of breast cancer from TNBC is the ability to perform gluconeogenesis. Breast cancers with a positive expression of the HER2 receptor, in contrast to TNBC and luminal A subtype, have a distinctive active synthesis and consumption of fatty acids. It is interesting to note that amino acid transporters exhibit their activity depending on the pH level inside the cell. In the most aggressive forms of breast cancer or with the gradual progression of the disease, pH will also change, which will directly affect the metabolism of amino acids. Using the cell lines presented in this review, we can trace the characteristic features inherent in each of the molecular biological subtypes of breast cancer and develop the most optimal therapeutic targets.
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Affiliation(s)
| | - Lyudmila V. Bel’skaya
- Biochemistry Research Laboratory, Omsk State Pedagogical University, 644099 Omsk, Russia;
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5
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Nanga RPR, Wiers CE, Elliott MA, Wilson NE, Liu F, Cao Q, Swago S, Jacobs PS, Armbruster R, Reddy D, Baur JA, Witschey WR, Detre JA, Reddy R. Acute nicotinamide riboside supplementation increases human cerebral NAD + levels in vivo. Magn Reson Med 2024; 92:2284-2293. [PMID: 39044608 PMCID: PMC11436296 DOI: 10.1002/mrm.30227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/30/2024] [Accepted: 07/01/2024] [Indexed: 07/25/2024]
Abstract
PURPOSE The purpose of this study was to determine the effect of acute nicotinamide riboside (NR) supplementation on cerebral nicotinamide adenine dinucleotide (NAD+) levels in the human brain in vivo by means of downfield proton MRS (DF 1H MRS). METHODS DF 1H MRS was performed on 10 healthy volunteers in a 7.0 T MRI scanner with spectrally selective excitation and spatially selective localization to determine cerebral NAD+ levels on two back-to-back days: once after an overnight fast (baseline) and once 4 h after oral ingestion of nicotinamide riboside (900 mg). Additionally, two more baseline scans were performed following the same paradigm to assess test-retest reliability of the NAD+ levels in the absence of NR. RESULTS NR supplementation increased mean NAD+ concentration compared to the baseline (0.458 ± 0.053 vs. 0.392 ± 0.058 mM; p < 0.001). The additional two baseline scans demonstrated no differences in mean NAD+ concentrations (0.425 ± 0.118 vs. 0.405 ± 0.082 mM; p = 0.45), and no difference from the first baseline scan (F(2, 16) = 0.907; p = 0.424). CONCLUSION These preliminary results confirm that acute NR supplementation increases cerebral NAD+ levels in healthy human volunteers and shows the promise of DF 1H MRS utility for robust detection of NAD+ in humans in vivo.
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Affiliation(s)
- Ravi Prakash Reddy Nanga
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Corinde E. Wiers
- Department of Psychiatry, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Mark A. Elliott
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Neil E. Wilson
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Fang Liu
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Quy Cao
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Sophie Swago
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA
| | - Paul S. Jacobs
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA
| | - Ryan Armbruster
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA
| | - Damodara Reddy
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Joseph A. Baur
- Department of Physiology, Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Walter R. Witschey
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - John A. Detre
- Department of Neurology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Ravinder Reddy
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
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6
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Knol MGE, Wulfmeyer VC, Müller RU, Rinschen MM. Amino acid metabolism in kidney health and disease. Nat Rev Nephrol 2024; 20:771-788. [PMID: 39198707 DOI: 10.1038/s41581-024-00872-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2024] [Indexed: 09/01/2024]
Abstract
Amino acids form peptides and proteins and are therefore considered the main building blocks of life. The kidney has an important but under-appreciated role in the synthesis, degradation, filtration, reabsorption and excretion of amino acids, acting to retain useful metabolites while excreting potentially harmful and waste products from amino acid metabolism. A complex network of kidney transporters and enzymes guides these processes and moderates the competing concentrations of various metabolites and amino acid products. Kidney amino acid metabolism contributes to gluconeogenesis, nitrogen clearance, acid-base metabolism and provision of fuel for tricarboxylic acid cycle and urea cycle intermediates, and is thus a central hub for homeostasis. Conversely, kidney disease affects the levels and metabolism of a variety of amino acids. Here, we review the metabolic role of the kidney in amino acid metabolism and describe how different diseases of the kidney lead to aberrations in amino acid metabolism. Improved understanding of the metabolic and communication routes that are affected by disease could provide new mechanistic insights into the pathogenesis of kidney diseases and potentially enable targeted dietary or pharmacological interventions.
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Affiliation(s)
- Martine G E Knol
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- III Department of Medicine, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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7
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Barroso IG, Canettieri CK, Ferreira C, Terra WR. Protein digestion and amino acid absorption mechanisms along the midgut of Musca domestica larvae. Comp Biochem Physiol B Biochem Mol Biol 2024; 275:111045. [PMID: 39532249 DOI: 10.1016/j.cbpb.2024.111045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 11/02/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024]
Abstract
A model of protein digestion and peptide and amino acid absorption along the midgut of Musca domestica larvae was proposed and supported by RNA-Seq analyses, protein bioinformatics, microvillar-membrane-enriched midgut proteomics, and enzymatic activities. Peptidase genes are highly expressed in the posterior midgut (PM), whereas those for cathepsins have expression limited to the middle midgut (MM). MM has the lowest levels of gene expression of almost all peptidases but has high expression of genes for membrane-bound serine endopeptidases. The anterior midgut (AM) has intermediate expression values of serine endopeptidase and aminopeptidase (AP) genes and low expression of carboxypeptidases (CPs). Gene expression and peptidase activities were usually consistent for putative intracellular and membrane-bound enzymes. However, secreted peptidase gene expression and activities have divergent values, especially in the PM, which may be due to the countercurrent water flux causing enzyme recycling, thus decreasing their excretion. Data suggest that Trys and APs act in the AM. In the acidic MM, lysozymes kill microorganisms found in the diet, releasing proteins digested by cathepsins D, which may also digest Trys coming from the AM. Finally, highly active serine endopeptidases, CPs, dipeptidases, and APs complete protein digestion in PM. Absorption of peptides and amino acids coupled to protons may occur along the midgut, especially in PM, as occurs for facilitated amino acid transport. Absorption with sodium ions is probably restricted to AM and PM. Our findings provide valuable insights into the protein digestion and amino acid absorption mechanism in M. domestica larvae.
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Affiliation(s)
- Ignacio G Barroso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil
| | - Carolina K Canettieri
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil
| | - Clelia Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil
| | - Walter R Terra
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil.
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8
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Surrer DB, Schüsser S, König J, Fromm MF, Gessner A. Transport of aromatic amino acids l-tryptophan, l-tyrosine, and l-phenylalanine by the organic anion transporting polypeptide (OATP) 3A1. FEBS J 2024; 291:4732-4743. [PMID: 39206635 DOI: 10.1111/febs.17255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/11/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Amino acids are important for cellular metabolism. Their uptake across the plasma membrane is mediated by transport proteins. Despite the fact that the organic anion transporting polypeptide 4C1 (OATP4C1, Uniprot: Q6ZQN7) mediates transport of l-arginine and l-arginine derivatives, other members of the OATP family have not been characterized as amino acid transporters. The OATP family member OATP3A1 (gene symbol SLCO3A1, Uniprot: Q9UIG8) is ubiquitously expressed in human cells and highly expressed in many cancer tissues and cell lines. However, only a few substrates are known for OATP3A1. Accordingly, knowledge about its biological relevance is restricted. Our aim was to identify new substrates of OATP3A1 to gain insights into its (patho-)physiological function. In an LC-MS-based untargeted metabolomics assay using untreated OATP3A1-overexpressing HEK293 cells and control cells, we identified several amino acids as potential substrates of OATP3A1. Subsequent uptake experiments using exogenously added substrates revealed OATP3A1-mediated transport of l-tryptophan, l-tyrosine, and l-phenylalanine with 194.8 ± 28.7% (P < 0.05), 226.2 ± 18.7% (P < 0.001), and 235.2 ± 13.5% (P < 0.001), respectively, in OATP3A1-overexpressing cells compared to control cells. Furthermore, kinetic transport parameters (Km values) were determined (Trp = 61.5 ± 14.2 μm, Tyr = 220.8 ± 54.5 μm, Phe = 234.7 ± 20.6 μm). In summary, we identified the amino acids l-tryptophan, l-tyrosine, and l-phenylalanine as new substrates of OATP3A1. These findings could be used for a better understanding of (patho-)physiological processes involving increased demand of amino acids, where OATP3A1 should be considered as an important uptake transporter of l-tryptophan, l-tyrosine, and l-phenylalanine.
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Affiliation(s)
- Daniela B Surrer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Sarah Schüsser
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Jörg König
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Martin F Fromm
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Arne Gessner
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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9
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Sukka SR, Ampomah PB, Darville LNF, Ngai D, Wang X, Kuriakose G, Xiao Y, Shi J, Koomen JM, McCusker RH, Tabas I. Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution. Nat Metab 2024; 6:1736-1755. [PMID: 39242914 PMCID: PMC11734744 DOI: 10.1038/s42255-024-01115-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 07/24/2024] [Indexed: 09/09/2024]
Abstract
Macrophage efferocytosis prevents apoptotic cell (AC) accumulation and triggers inflammation-resolution pathways. The mechanisms linking efferocytosis to resolution often involve changes in macrophage metabolism, but many gaps remain in our understanding of these processes. We now report that efferocytosis triggers an indoleamine 2,3-dioxygenase-1 (IDO1)-dependent tryptophan (Trp) metabolism pathway that promotes several key resolution processes, including the induction of pro-resolving proteins, such interleukin-10, and further enhancement of efferocytosis. The process begins with upregulation of Trp transport and metabolism, and it involves subsequent activation of the aryl hydrocarbon receptor (AhR) by the Trp metabolite kynurenine (Kyn). Through these mechanisms, macrophage IDO1 and AhR contribute to a proper resolution response in several different mouse models of efferocytosis-dependent tissue repair, notably during atherosclerosis regression induced by plasma low-density lipoprotein (LDL) lowering. These findings reveal an integrated metabolism programme in macrophages that links efferocytosis to resolution, with possible therapeutic implications for non-resolving chronic inflammatory diseases, notably atherosclerosis.
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Affiliation(s)
- Santosh R Sukka
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
| | - Patrick B Ampomah
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Lancia N F Darville
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David Ngai
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Xiaobo Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - George Kuriakose
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yuling Xiao
- Center for Nanomedicine and Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jinjun Shi
- Center for Nanomedicine and Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Robert H McCusker
- Department of Animal Sciences, Integrative Immunology and Behavior Program and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ira Tabas
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Departments of Physiology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
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10
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Ren C, Zhang S, Chen Y, Deng K, Kuang M, Gong Z, Zhang K, Wang P, Huang P, Zhou Z, Gong A. Exploring nicotinamide adenine dinucleotide precursors across biosynthesis pathways: Unraveling their role in the ovary. FASEB J 2024; 38:e23804. [PMID: 39037422 DOI: 10.1096/fj.202400453r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/31/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Natural Nicotinamide Adenine Dinucleotide (NAD+) precursors have attracted much attention due to their positive effects in promoting ovarian health. However, their target tissue, synthesis efficiency, advantages, and disadvantages are still unclear. This review summarizes the distribution of NAD+ at the tissue, cellular and subcellular levels, discusses its biosynthetic pathways and the latest findings in ovary, include: (1) NAD+ plays distinct roles both intracellularly and extracellularly, adapting its distribution in response to requirements. (2) Different precursors differs in target tissues, synthetic efficiency, biological utilization, and adverse effects. Importantly: tryptophan is primarily utilized in the liver and kidneys, posing metabolic risks in excess; nicotinamide (NAM) is indispensable for maintaining NAD+ levels; nicotinic acid (NA) constructs a crucial bridge between intestinal microbiota and the host with diverse functions; nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) increase NAD+ systemically and can be influenced by delivery route, tissue specificity, and transport efficiency. (3) The biosynthetic pathways of NAD+ are intricately intertwined. They provide multiple sources and techniques for NAD+ synthesis, thereby reducing the dependence on a single molecule to maintain cellular NAD+ levels. However, an excess of a specific precursor potentially influencing other pathways. In addition, Protein expression analysis suggest that ovarian tissues may preferentially utilize NAM and NMN. These findings summarize the specific roles and potential of NAD+ precursors in enhancing ovarian health. Future research should delve into the molecular mechanisms and intervention strategies of different precursors, aiming to achieve personalized prevention or treatment of ovarian diseases, and reveal their clinical application value.
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Affiliation(s)
- Caifang Ren
- School of Medicine, Jiangsu University, Zhenjiang, China
- Hematological Disease Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Shuang Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yanyan Chen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Kaiping Deng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Meiqian Kuang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zihao Gong
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ke Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Panqi Wang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Pan Huang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhengrong Zhou
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Aihua Gong
- School of Medicine, Jiangsu University, Zhenjiang, China
- Hematological Disease Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
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11
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Benjamin C, Crews R. Nicotinamide Mononucleotide Supplementation: Understanding Metabolic Variability and Clinical Implications. Metabolites 2024; 14:341. [PMID: 38921475 PMCID: PMC11205942 DOI: 10.3390/metabo14060341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Recent years have seen a surge in research focused on NAD+ decline and potential interventions, and despite significant progress, new discoveries continue to highlight the complexity of NAD+ biology. Nicotinamide mononucleotide (NMN), a well-established NAD+ precursor, has garnered considerable interest due to its capacity to elevate NAD+ levels and induce promising health benefits in preclinical models. Clinical trials investigating NMN supplementation have yielded variable outcomes while shedding light on the intricacies of NMN metabolism and revealing the critical roles played by gut microbiota and specific cellular uptake pathways. Individual variability in factors such as lifestyle, health conditions, genetics, and gut microbiome composition likely contributes to the observed discrepancies in clinical trial results. Preliminary evidence suggests that NMN's effects may be context-dependent, varying based on a person's physiological state. Understanding these nuances is critical for definitively assessing the impact of manipulating NAD+ levels through NMN supplementation. Here, we review NMN metabolism, focusing on current knowledge, pinpointing key areas where further research is needed, and outlining future directions to advance our understanding of its potential clinical significance.
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12
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Lautrup S, Hou Y, Fang EF, Bohr VA. Roles of NAD + in Health and Aging. Cold Spring Harb Perspect Med 2024; 14:a041193. [PMID: 37848251 PMCID: PMC10759992 DOI: 10.1101/cshperspect.a041193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
NAD+, the essential metabolite involved in multiple reactions such as the regulation of cellular metabolism, energy production, DNA repair, mitophagy and autophagy, inflammation, and neuronal function, has been the subject of intense research in the field of aging and disease over the last decade. NAD+ levels decline with aging and in some age-related diseases, and reduction in NAD+ affects all the hallmarks of aging. Here, we present an overview of the discovery of NAD+, the cellular pathways of producing and consuming NAD+, and discuss how imbalances in the production rate and cellular request of NAD+ likely contribute to aging and age-related diseases including neurodegeneration. Preclinical studies have revealed great potential for NAD+ precursors in promotion of healthy aging and improvement of neurodegeneration. This has led to the initiation of several clinical trials with NAD+ precursors to treat accelerated aging, age-associated dysfunctions, and diseases including Alzheimer's and Parkinson's. NAD supplementation has great future potential clinically, and these studies will also provide insight into the mechanisms of aging.
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Affiliation(s)
- Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway
| | - Yujun Hou
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway
- The Norwegian Centre on Healthy Ageing (NO-Age), Oslo, Norway
| | - Vilhelm A Bohr
- DNA Repair Section, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
- Danish Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
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Shu H, Zhang J, Cheng D, Zhao X, Ma Y, Zhang C, Zhang Y, Jia Z, Liu Z. The Role of Proton-Coupled Amino Acid Transporter 2 (SLC36A2) in Cold-Induced Thermogenesis of Mice. Nutrients 2023; 15:3552. [PMID: 37630739 PMCID: PMC10458080 DOI: 10.3390/nu15163552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Brown adipocytes mainly utilize glucose and fatty acids to produce energy, which play key roles in thermogenesis. Furthermore, brown adipocytes also utilize other substrates, such as amino acids, for energy expenditure in various conditions. Here, we report the new physiological roles of proton-coupled amino acid transporters, SLC36A2 and SLC36A3, on global energy metabolism. The relative mRNA expression levels of both Slc36a2 and Slc36a3 were all highest in brown adipose tissue. We then generated global Slc36a2 and Slc36a3 knockout mice to investigate their functions in metabolism. Neither loss of Slc36a2 nor Slc36a3 affected the body weight and body composition of the mice. Slc36a2 knockout mice exhibited increased oxygen consumption during the daytime. After cold treatment, inhibition of Slc36a2 significantly decreased the mass of brown adipose tissue compared to wildtype mice, while it lowered the expression level of Cpt1a. Moreover, the serum lipid levels and liver mass were also decreased in Slc36a2 knockout mice after cold treatment. On the contrary, Slc36a3 knockout impaired glucose tolerance and up-regulated serum LDL-cholesterol concentration. Thus, SLC36A2 and SLC36A3 play central and different roles in the energy metabolism of the mice.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhihao Jia
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou 215123, China; (H.S.); (J.Z.); (Y.M.); (Y.Z.)
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou 215123, China; (H.S.); (J.Z.); (Y.M.); (Y.Z.)
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14
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Guo C, Huang Q, Wang Y, Yao Y, Li J, Chen J, Wu M, Zhang Z, E M, Qi H, Ji P, Liu Q, Zhao D, Su H, Qi W, Li X. Therapeutic application of natural products: NAD + metabolism as potential target. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 114:154768. [PMID: 36948143 DOI: 10.1016/j.phymed.2023.154768] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Nicotinamide adenine dinucleotide (NAD+) metabolism is involved in the entire physiopathological process and is critical to human health. Long-term imbalance in NAD+ homeostasis is associated with various diseases, including non-alcoholic fatty liver disease, diabetes mellitus, cardiovascular diseases, neurodegenerative disorders, aging, and cancer, making it a potential target for effective therapeutic strategies. Currently, several natural products that target NAD+ metabolism have been widely reported to have significant therapeutic effects, but systematic summaries are lacking. PURPOSE To summarize the latest findings on the prevention and treatment of various diseases through the regulation of NAD+ metabolism by various natural products in vivo and in vitro models, and evaluate the toxicities of the natural products. METHODS PubMed, Web of Science, and ScienceDirect were searched using the keywords "natural products sources," "toxicology," "NAD+ clinical trials," and "NAD+," and/or paired with "natural products" and "diseases" for studies published within the last decade until January 2023. RESULTS We found that the natural products mainly include phenols (curcumin, cyclocurcumin, 4-hydroxybenzyl alcohol, salvianolic acid B, pterostilbene, EGCG), flavonoids (pinostrobin, apigenin, acacetin, tilianin, kaempferol, quercetin, isoliquiritigenin, luteolin, silybin, hydroxysafflor yellow A, scutellarin), glycosides (salidroside), quinones (emodin, embelin, β-LAPachone, shikonin), terpenoids (notoginsenoside R1, ginsenoside F2, ginsenoside Rd, ginsenoside Rb1, ginsenoside Rg3, thymoquinone, genipin), pyrazines (tetramethylpyrazine), alkaloids (evodiamine, berberine), and phenylpropanoids (ferulic acid). These natural products have antioxidant, energy-producing, anti-inflammatory, anti-apoptotic and anti-aging effects, which mainly influence the NAMPT/NAD+/SIRT, AMPK/SIRT1/PGC-1α, Nrf2/HO-1, PKCs/PARPs/NF-κB, and AMPK/Nrf2/mTOR signaling pathways, thereby regulating NAD+ metabolism to prevent and treat various diseases. These natural products have been shown to be safe, tolerable and have fewer adverse effects in various in vivo and in vitro studies and clinical trials. CONCLUSION We evaluated the toxic effects of natural products and summarized the available clinical trials on NAD+ metabolism, as well as the recent advances in the therapeutic application of natural products targeting NAD+ metabolism, with the aim to provide new insights into the treatment of multiple disorders.
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Affiliation(s)
- Chen Guo
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Qingxia Huang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China; Research Center of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130021, China
| | - Yisa Wang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Yao Yao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Jing Li
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Jinjin Chen
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Mingxia Wu
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Zepeng Zhang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China; Research Center of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130021, China
| | - Mingyao E
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Hongyu Qi
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Peng Ji
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Qing Liu
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Daqing Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Hang Su
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Wenxiu Qi
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China.
| | - Xiangyan Li
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China.
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15
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Li W, Ling L, Xiang L, Ding P, Yue W. Identification and validation of a risk model and molecular subtypes based on tryptophan metabolism-related genes to predict the clinical prognosis and tumor immune microenvironment in lower-grade glioma. Front Cell Neurosci 2023; 17:1146686. [PMID: 36925967 PMCID: PMC10011102 DOI: 10.3389/fncel.2023.1146686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Background Lower-grade glioma (LGG) is one of the most common malignant tumors in the central nervous system (CNS). Accumulating evidence have demonstrated that tryptophan metabolism is significant in tumor. Therefore, this study aims to comprehensively clarify the relationship between tryptophan metabolism-related genes (TRGs) and LGGs. Methods The expression level of TRGs in LGG and normal tissues was first analyzed. Next, the key TRGs with prognostic value and differential expression in LGGs were identified using the least absolute shrinkage and selection operator (LASSO) regression analysis. Subsequently, a risk model was constructed and Consensus clustering analysis was conducted based on the expression level of key TRGs. Then, the prognostic value, clinicopathological factors, and tumor immune microenvironment (TIME) characteristics between different risk groups and molecular subtypes were analyzed. Finally, the expression, prognosis, and TIME of each key TRGs were analyzed separately in LGG patients. Results A total of 510 patients with LGG from The Cancer Genome Atlas (TCGA) dataset and 1,152 normal tissues from the Genotype-Tissue Expression (GTEx) dataset were included to evaluate the expression level of TRGs. After LASSO regression analysis, we identified six key TRGs and constructed a TRGs risk model. The survival analysis revealed that the risk model was the independent predictor in LGG patients. And the nomogram containing risk scores and independent clinicopathological factors could accurately predict the prognosis of LGG patients. In addition, the results of the Consensus cluster analysis based on the expression of the six TRGs showed that it could classify the LGG patients into two distinct clusters, with significant differences in prognosis, clinicopathological factors and TIME between these two clusters. Finally, we validated the expression, prognosis and immune infiltration of six key TRGs in patients with LGG. Conclusion This study demonstrated that tryptophan metabolism plays an important role in the progression of LGG. In addition, the risk model and the molecular subtypes we constructed not only could be used as an indicator to predict the prognosis of LGG patients but also were closely related to the clinicopathological factors and TIME of LGG patients. Overall, our study provides theoretical support for the ultimate realization of precision treatment for patients with LGG.
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Affiliation(s)
- Wenxia Li
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China
| | - Ling Ling
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Lei Xiang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Peng Ding
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China
| | - Wei Yue
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China.,Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
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16
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Yuan Z, Zhou Q, Cai L, Pan L, Sun W, Qumu S, Yu S, Feng J, Zhao H, Zheng Y, Shi M, Li S, Chen Y, Zhang X, Zhang MQ. SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment. Nat Methods 2021; 18:1223-1232. [PMID: 34608315 DOI: 10.1038/s41592-021-01276-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
Spatial metabolomics can reveal intercellular heterogeneity and tissue organization. Here we report on the spatial single nuclear metabolomics (SEAM) method, a flexible platform combining high-spatial-resolution imaging mass spectrometry and a set of computational algorithms that can display multiscale and multicolor tissue tomography together with identification and clustering of single nuclei by their in situ metabolic fingerprints. We first applied SEAM to a range of wild-type mouse tissues, then delineated a consistent pattern of metabolic zonation in mouse liver. We further studied the spatial metabolic profile in the human fibrotic liver. We discovered subpopulations of hepatocytes with special metabolic features associated with their proximity to the fibrotic niche, and validated this finding by spatial transcriptomics with Geo-seq. These demonstrations highlighted SEAM's ability to explore the spatial metabolic profile and tissue histology at the single-cell level, leading to a deeper understanding of tissue metabolic organization.
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Affiliation(s)
- Zhiyuan Yuan
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China
| | - Qiming Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lesi Cai
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Lin Pan
- Institute of Clinical Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Weiliang Sun
- Institute of Clinical Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Shiwei Qumu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friend Hospital, National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Si Yu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Shao Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China. .,The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing, China.
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China. .,Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX, USA.
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17
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Du J, Zhu S, Lim RR, Chao JR. Proline metabolism and transport in retinal health and disease. Amino Acids 2021; 53:1789-1806. [PMID: 33871679 PMCID: PMC8054134 DOI: 10.1007/s00726-021-02981-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/10/2021] [Indexed: 12/11/2022]
Abstract
The retina is one of the most energy-demanding tissues in the human body. Photoreceptors in the outer retina rely on nutrient support from the neighboring retinal pigment epithelium (RPE), a monolayer of epithelial cells that separate the retina and choroidal blood supply. RPE dysfunction or cell death can result in photoreceptor degeneration, leading to blindness in retinal degenerative diseases including some inherited retinal degenerations and age-related macular degeneration (AMD). In addition to having ready access to rich nutrients from blood, the RPE is also supplied with lactate from adjacent photoreceptors. Moreover, RPE can phagocytose lipid-rich outer segments for degradation and recycling on a daily basis. Recent studies show RPE cells prefer proline as a major metabolic substrate, and they are highly enriched for the proline transporter, SLC6A20. In contrast, dysfunctional or poorly differentiated RPE fails to utilize proline. RPE uses proline to fuel mitochondrial metabolism, synthesize amino acids, build the extracellular matrix, fight against oxidative stress, and sustain differentiation. Remarkably, the neural retina rarely imports proline directly, but it uptakes and utilizes intermediates and amino acids derived from proline catabolism in the RPE. Mutations of genes in proline metabolism are associated with retinal degenerative diseases, and proline supplementation is reported to improve RPE-initiated vision loss. This review will cover proline metabolism in RPE and highlight the importance of proline transport and utilization in maintaining retinal metabolism and health.
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Affiliation(s)
- Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV, 26506, USA. .,Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA. .,One Medical Center Dr, WVU Eye Institute, PO Box 9193, Morgantown, WV, 26505, USA.
| | - Siyan Zhu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV, 26506, USA.,Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Rayne R Lim
- Department of Ophthalmology, University of Washington, Seattle, WA, 98109, USA
| | - Jennifer R Chao
- Department of Ophthalmology, University of Washington, Seattle, WA, 98109, USA
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18
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Feng S, Zacharioudaki E, Millen K, Bray SJ. The SLC36 transporter Pathetic is required for neural stem cell proliferation and for brain growth under nutrition restriction. Neural Dev 2020; 15:10. [PMID: 32741363 PMCID: PMC7398078 DOI: 10.1186/s13064-020-00148-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/16/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Drosophila neuroblasts (NBs) are neural stem cells whose maintenance relies on Notch activity. NBs proliferate throughout larval stages to generate a large number of adult neurons. Their proliferation is protected under conditions of nutrition restriction but the mechanisms responsible are not fully understood. As amino acid transporters (Solute Carrier transporters, SLCs), such as SLC36, have important roles in coupling nutrition inputs to growth pathways, they may have a role in this process. For example, an SLC36 family transporter Pathetic (Path) that supports body size and neural dendrite growth in Drosophila, was identified as a putative Notch target in genome-wide studies. However, its role in sustaining stem cell proliferation and maintenance has not been investigated. This study aimed to investigate the function of Path in the larval NBs and to determine whether it is involved in protecting them from nutrient deprivation. METHODS The expression and regulation of Path in the Drosophila larval brain was analysed using a GFP knock-in allele and reporter genes containing putative Notch regulated enhancers. Path function in NB proliferation and overall brain growth was investigated under different nutrition conditions by depleting it from specific cell types in the CNS, using mitotic recombination to generate mutant clones or by directed RNA-interference. RESULTS Path is expressed in both NBs and glial cells in the Drosophila CNS. In NBs, path is directly targeted by Notch signalling via Su(H) binding at an intronic enhancer, PathNRE. This enhancer is responsive to Notch regulation both in cell lines and in vivo. Loss of path in neural stem cells delayed proliferation, consistent with it having a role in NB maintenance. Expression from pathNRE was compromised in conditions of amino acid deprivation although other Notch regulated enhancers are unaffected. However, NB-expressed Path was not required for brain sparing under amino acid deprivation. Instead, it appears that Path is important in glial cells to help protect brain growth under conditions of nutrient restriction. CONCLUSIONS We identify a novel Notch target gene path that is required in NBs for neural stem cell proliferation, while in glia it protects brain growth under nutrition restriction.
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Affiliation(s)
- Shiyun Feng
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Evanthia Zacharioudaki
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Kat Millen
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Sarah J Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
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19
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Kulikova V, Shabalin K, Nerinovski K, Yakimov A, Svetlova M, Solovjeva L, Kropotov A, Khodorkovskiy M, Migaud ME, Ziegler M, Nikiforov A. Degradation of Extracellular NAD + Intermediates in Cultures of Human HEK293 Cells. Metabolites 2019; 9:E293. [PMID: 31795381 PMCID: PMC6950141 DOI: 10.3390/metabo9120293] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 01/06/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential redox carrier, whereas its degradation is a key element of important signaling pathways. Human cells replenish their NAD contents through NAD biosynthesis from extracellular precursors. These precursors encompass bases nicotinamide (Nam) and nicotinic acid and their corresponding nucleosides nicotinamide riboside (NR) and nicotinic acid riboside (NAR), now collectively referred to as vitamin B3. In addition, extracellular NAD+ and nicotinamide mononucleotide (NMN), and potentially their deamidated counterparts, nicotinic acid adenine dinucleotide (NAAD) and nicotinic acid mononucleotide (NAMN), may serve as precursors of intracellular NAD. However, it is still debated whether nucleotides enter cells directly or whether they are converted to nucleosides and bases prior to uptake into cells. Here, we studied the metabolism of extracellular NAD+ and its derivatives in human HEK293 cells using normal and serum-free culture medium. Using medium containing 10% fetal bovine serum (FBS), mono- and dinucleotides were degraded to the corresponding nucleosides. In turn, the nucleosides were cleaved to their corresponding bases. Degradation was also observed in culture medium alone, in the absence of cells, indicating that FBS contains enzymatic activities which degrade NAD+ intermediates. Surprisingly, NR was also rather efficiently hydrolyzed to Nam in the absence of FBS. When cultivated in serum-free medium, HEK293 cells efficiently cleaved NAD+ and NAAD to NMN and NAMN. NMN exhibited rather high stability in cell culture, but was partially metabolized to NR. Using pharmacological inhibitors of plasma membrane transporters, we also showed that extracellular cleavage of NAD+ and NMN to NR is a prerequisite for using these nucleotides to maintain intracellular NAD contents. We also present evidence that, besides spontaneous hydrolysis, NR is intensively metabolized in cell culture by intracellular conversion to Nam. Our results demonstrate that both the cultured cells and the culture medium mediate a rather active conversion of NAD+ intermediates. Consequently, in studies of precursor supplementation and uptake, the culture conditions need to be carefully defined.
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Affiliation(s)
- Veronika Kulikova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (V.K.); (M.S.); (L.S.); (A.K.)
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia; (A.Y.); (M.K.)
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg 194223, Russia
| | - Konstantin Shabalin
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia;
| | - Kirill Nerinovski
- Department of Nuclear Physics Research Methods, St. Petersburg State University, St. Petersburg 199034, Russia;
| | - Alexander Yakimov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia; (A.Y.); (M.K.)
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia;
| | - Maria Svetlova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (V.K.); (M.S.); (L.S.); (A.K.)
| | - Ljudmila Solovjeva
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (V.K.); (M.S.); (L.S.); (A.K.)
| | - Andrey Kropotov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (V.K.); (M.S.); (L.S.); (A.K.)
| | - Mikhail Khodorkovskiy
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia; (A.Y.); (M.K.)
| | - Marie E. Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA;
| | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway;
| | - Andrey Nikiforov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (V.K.); (M.S.); (L.S.); (A.K.)
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20
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Kulikova VA, Gromyko DV, Nikiforov AA. The Regulatory Role of NAD in Human and Animal Cells. BIOCHEMISTRY (MOSCOW) 2018; 83:800-812. [PMID: 30200865 DOI: 10.1134/s0006297918070040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) and its phosphorylated form NADP are the major coenzymes in the redox reactions of various essential metabolic pathways. NAD+ also serves as a substrate for several families of regulatory proteins, such as protein deacetylases (sirtuins), ADP-ribosyltransferases, and poly(ADP-ribose) polymerases, that control vital cell processes including gene expression, DNA repair, apoptosis, mitochondrial biogenesis, unfolded protein response, and many others. NAD+ is also a precursor for calcium-mobilizing secondary messengers. Proper regulation of these NAD-dependent metabolic and signaling pathways depends on how efficiently cells can maintain their NAD levels. Generally, mammalian cells regulate their NAD supply through biosynthesis from the precursors delivered with the diet: nicotinamide and nicotinic acid (vitamin B3), as well as nicotinamide riboside and nicotinic acid riboside. Administration of NAD precursors has been demonstrated to restore NAD levels in tissues (i.e., to produce beneficial therapeutic effects) in preclinical models of various diseases, such as neurodegenerative disorders, obesity, diabetes, and metabolic syndrome.
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Affiliation(s)
- V A Kulikova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - D V Gromyko
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - A A Nikiforov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
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21
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Fan SJ, Goberdhan DCI. PATs and SNATs: Amino Acid Sensors in Disguise. Front Pharmacol 2018; 9:640. [PMID: 29971004 PMCID: PMC6018406 DOI: 10.3389/fphar.2018.00640] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/29/2018] [Indexed: 11/30/2022] Open
Abstract
Solute Carriers (SLCs) are involved in the transport of substances across lipid bilayers, including nutrients like amino acids. Amino acids increase the activity of the microenvironmental sensor mechanistic Target of Rapamycin Complex 1 (mTORC1) to promote cellular growth and anabolic processes. They can be brought in to cells by a wide range of SLCs including the closely related Proton-assisted Amino acid Transporter (PAT or SLC36) and Sodium-coupled Neutral Amino acid Transporter (SNAT or SLC38) families. More than a decade ago, the first evidence emerged that members of the PAT family can act as amino acid-stimulated receptors, or so-called "transceptors," connecting amino acids to mTORC1 activation. Since then, further studies in human cell models have suggested that other PAT and SNAT family members, which share significant homology within their transmembrane domains, can act as transceptors. A paradigm shift has also led to the PATs and SNATs at the surface of multiple intracellular compartments being linked to the recruitment and activation of different pools of mTORC1. Much focus has been on late endosomes and lysosomes as mTORC1 regulatory hubs, but more recently a Golgi-localized PAT was shown to be required for mTORC1 activation. PATs and SNATs can also traffic between the cell surface and intracellular compartments, with regulation of this movement providing a means of controlling their mTORC1 regulatory activity. These emerging features of PAT and SNAT amino acid sensors, including the transceptor mechanism, have implications for the pharmacological inhibition of mTORC1 and new therapeutic interventions.
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Affiliation(s)
| | - Deborah C. I. Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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22
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Müller F, Sharma A, König J, Fromm MF. Biomarkers for In Vivo Assessment of Transporter Function. Pharmacol Rev 2018; 70:246-277. [PMID: 29487084 DOI: 10.1124/pr.116.013326] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Drug-drug interactions are a major concern not only during clinical practice, but also in drug development. Due to limitations of in vitro-in vivo predictions of transporter-mediated drug-drug interactions, multiple clinical Phase I drug-drug interaction studies may become necessary for a new molecular entity to assess potential drug interaction liabilities. This is a resource-intensive process and exposes study participants, who frequently are healthy volunteers without benefit from study treatment, to the potential risks of a new drug in development. Therefore, there is currently a major interest in new approaches for better prediction of transporter-mediated drug-drug interactions. In particular, researchers in the field attempt to identify endogenous compounds as biomarkers for transporter function, such as hexadecanedioate, tetradecanedioate, coproporphyrins I and III, or glycochenodeoxycholate sulfate for hepatic uptake via organic anion transporting polypeptide 1B or N1-methylnicotinamide for multidrug and toxin extrusion protein-mediated renal secretion. We summarize in this review the currently proposed biomarkers and potential limitations of the substances identified to date. Moreover, we suggest criteria based on current experiences, which may be used to assess the suitability of a biomarker for transporter function. Finally, further alternatives and supplemental approaches to classic drug-drug interaction studies are discussed.
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Affiliation(s)
- Fabian Müller
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (F.M., J.K., M.F.F.); and Department of Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riß, Germany (F.M., A.S.)
| | - Ashish Sharma
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (F.M., J.K., M.F.F.); and Department of Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riß, Germany (F.M., A.S.)
| | - Jörg König
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (F.M., J.K., M.F.F.); and Department of Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riß, Germany (F.M., A.S.)
| | - Martin F Fromm
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (F.M., J.K., M.F.F.); and Department of Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riß, Germany (F.M., A.S.)
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Abstract
The overall goal of radiogenomics is the identification of genomic markers that are predictive for the development of adverse effects resulting from cancer treatment with radiation. The principal rationale for a focus on toxicity in radiogenomics is that for many patients treated with radiation, especially individuals diagnosed with early-stage cancers, the survival rates are high, and therefore a substantial number of people will live for a significant period of time beyond treatment. However, many of these patients could suffer from debilitating complications resulting from radiotherapy. Work in radiogenomics has greatly benefited from creation of the Radiogenomics Consortium (RGC) that includes investigators at multiple institutions located in a variety of countries. The common goal of the RGC membership is to share biospecimens and data so as to achieve large-scale studies with increased statistical power to enable identification of relevant genomic markers. A major aim of research in radiogenomics is the development of a predictive instrument to enable identification of people who are at greatest risk for adverse effects resulting from cancer treatment using radiation. It is anticipated that creation of a predictive assay characterized by a high level of sensitivity and specificity will improve precision radiotherapy and assist patients and their physicians to select the optimal treatment for each individual.
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Affiliation(s)
- Barry S Rosenstein
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
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24
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Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs. Genomics 2017; 110:171-179. [PMID: 28943389 DOI: 10.1016/j.ygeno.2017.09.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/16/2022]
Abstract
In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level. A total of 8, 23 and 20 significant SNPs were associated with TNB, NBA, and LWB, respectively, and these significant SNPs accounted for 62.78%, 79.75%, and 58.79% of genetic variance. Furthermore, 1 (SSC14: 16314857), 4 (SSC1: 81986236, SSC1: 66599775, SSC1: 161999013, and SSC1: 267883107), and 5 (SSC9: 29030061, SSC2: 32368561, SSC5: 110375350, SSC13: 45619882 and SSC13: 45647829) significant SNPs for TNB, NBA, and LWB were inferred to be novel loci. At SSC1, the AIM1 and FOXO3 genes were found to be associated with NBA; these genes increase ovarian reproductive capacity and follicle number and decrease gonadotropin levels. The genes SLC36A4 and INTU are involved in cell growth, cytogenesis and development were found to be associated with LWB. These significant SNPs can be used as an indication for regions in the Sus scrofa genome for variability in litter traits, but further studies are expected to confirm causative mutations.
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25
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Lin WY, Williams CR, Yan C, Parrish JZ. Functions of the SLC36 transporter Pathetic in growth control. Fly (Austin) 2016; 9:99-106. [PMID: 26735916 DOI: 10.1080/19336934.2015.1129089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Neurons exhibit extreme diversity in size, but whether large neurons have specialized mechanisms to support their growth is largely unknown. Recently, we identified the SLC36 transporter Pathetic (Path) as a factor required for extreme dendrite growth in neurons. Path is broadly expressed, but only neurons with large dendrite arbors or small neurons that are forced to grow large require path for their growth. To gain insight into the basis of growth control by path, we generated additional alleles of path and further examined the apparent specificity of growth defects in path mutants. Here, we confirm our prior finding that loss of path function imposes an upper limit on neuron growth, and additionally report that path likely limits overall neurite length rather than dendrite length alone. Using a GFP knock-in allele of path, we identify additional tissues where path likely functions in nutrient sensing and possibly growth control. Finally, we demonstrate that path regulates translational capacity in a cell type that does not normally require path for growth, suggesting that path may confer robustness on growth programs by buffering translational output. Altogether, these studies suggest that Path is a nutrient sensor with widespread function in Drosophila.
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Affiliation(s)
- Wen-Yang Lin
- a Department of Biology ; University of Washington ; Seattle , WA USA
| | - Claire R Williams
- a Department of Biology ; University of Washington ; Seattle , WA USA
| | - Connie Yan
- a Department of Biology ; University of Washington ; Seattle , WA USA
| | - Jay Z Parrish
- a Department of Biology ; University of Washington ; Seattle , WA USA
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26
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Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R, Le KT, Deelen P, Ricaño-Ponce I, Schoffelen T, Jansen AF, Swertz MA, Withoff S, van de Vosse E, van Deuren M, van de Veerdonk F, Zhernakova A, van der Meer JW, Xavier RJ, Franke L, Joosten LA, Wijmenga C, Kumar V, Netea MG. A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell 2016; 167:1099-1110.e14. [DOI: 10.1016/j.cell.2016.10.017] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/04/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022]
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27
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Recent Advances in Understanding Amino Acid Sensing Mechanisms that Regulate mTORC1. Int J Mol Sci 2016; 17:ijms17101636. [PMID: 27690010 PMCID: PMC5085669 DOI: 10.3390/ijms17101636] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 11/25/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) is the central regulator of mammalian cell growth, and is essential for the formation of two structurally and functionally distinct complexes: mTORC1 and mTORC2. mTORC1 can sense multiple cues such as nutrients, energy status, growth factors and hormones to control cell growth and proliferation, angiogenesis, autophagy, and metabolism. As one of the key environmental stimuli, amino acids (AAs), especially leucine, glutamine and arginine, play a crucial role in mTORC1 activation, but where and how AAs are sensed and signal to mTORC1 are not fully understood. Classically, AAs activate mTORC1 by Rag GTPases which recruit mTORC1 to lysosomes, where AA signaling initiates. Plasma membrane transceptor L amino acid transporter 1 (LAT1)-4F2hc has dual transporter-receptor function that can sense extracellular AA availability upstream of mTORC1. The lysosomal AA sensors (PAT1 and SLC38A9) and cytoplasmic AA sensors (LRS, Sestrin2 and CASTOR1) also participate in regulating mTORC1 activation. Importantly, AAs can be sensed by plasma membrane receptors, like G protein-coupled receptor (GPCR) T1R1/T1R3, and regulate mTORC1 without being transported into the cells. Furthermore, AA-dependent mTORC1 activation also initiates within Golgi, which is regulated by Golgi-localized AA transporter PAT4. This review provides an overview of the research progress of the AA sensing mechanisms that regulate mTORC1 activity.
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Fan SJ, Snell C, Turley H, Li JL, McCormick R, Perera SMW, Heublein S, Kazi S, Azad A, Wilson C, Harris AL, Goberdhan DCI. PAT4 levels control amino-acid sensitivity of rapamycin-resistant mTORC1 from the Golgi and affect clinical outcome in colorectal cancer. Oncogene 2016; 35:3004-15. [PMID: 26434594 PMCID: PMC4705441 DOI: 10.1038/onc.2015.363] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/14/2015] [Accepted: 08/28/2015] [Indexed: 12/26/2022]
Abstract
Tumour cells can use strategies that make them resistant to nutrient deprivation to outcompete their neighbours. A key integrator of the cell's responses to starvation and other stresses is amino-acid-dependent mechanistic target of rapamycin complex 1 (mTORC1). Activation of mTORC1 on late endosomes and lysosomes is facilitated by amino-acid transporters within the solute-linked carrier 36 (SLC36) and SLC38 families. Here, we analyse the functions of SLC36 family member, SLC36A4, otherwise known as proton-assisted amino-acid transporter 4 (PAT4), in colorectal cancer. We show that independent of other major pathological factors, high PAT4 expression is associated with reduced relapse-free survival after colorectal cancer surgery. Consistent with this, PAT4 promotes HCT116 human colorectal cancer cell proliferation in culture and tumour growth in xenograft models. Inducible knockdown in HCT116 cells reveals that PAT4 regulates a form of mTORC1 with two distinct properties: first, it preferentially targets eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1), and second, it is resistant to rapamycin treatment. Furthermore, in HCT116 cells two non-essential amino acids, glutamine and serine, which are often rapidly metabolised by tumour cells, regulate rapamycin-resistant mTORC1 in a PAT4-dependent manner. Overexpressed PAT4 is also able to promote rapamycin resistance in human embryonic kidney-293 cells. PAT4 is predominantly associated with the Golgi apparatus in a range of cell types, and in situ proximity ligation analysis shows that PAT4 interacts with both mTORC1 and its regulator Rab1A on the Golgi. These findings, together with other studies, suggest that differentially localised intracellular amino-acid transporters contribute to the activation of alternate forms of mTORC1. Furthermore, our data predict that colorectal cancer cells with high PAT4 expression will be more resistant to depletion of serine and glutamine, allowing them to survive and outgrow neighbouring normal and tumorigenic cells, and potentially providing a new route for pharmacological intervention.
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Affiliation(s)
- S-J Fan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - C Snell
- Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - H Turley
- Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - J-L Li
- Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - R McCormick
- Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - S M W Perera
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - S Heublein
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - S Kazi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - A Azad
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - C Wilson
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - A L Harris
- Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - D C I Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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29
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Abstract
Cell metabolism and growth are matched to nutrient availability via the amino-acid-regulated mechanistic target of rapamycin complex 1 (mTORC1). Transporters have emerged as important amino acid sensors controlling mTOR recruitment and activation at the surface of multiple intracellular compartments. Classically, this has involved late endosomes and lysosomes, but now, in a recent twist, also the Golgi apparatus. Here we propose a model in which specific amino acids in assorted compartments activate different mTORC1 complexes, which may have distinct drug sensitivities and functions. We will discuss the implications of this for mTORC1 function in health and disease.
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Affiliation(s)
- Deborah C I Goberdhan
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK.
| | - Clive Wilson
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Adrian L Harris
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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30
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Nikiforov A, Kulikova V, Ziegler M. The human NAD metabolome: Functions, metabolism and compartmentalization. Crit Rev Biochem Mol Biol 2015; 50:284-97. [PMID: 25837229 PMCID: PMC4673589 DOI: 10.3109/10409238.2015.1028612] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The metabolism of NAD has emerged as a key regulator of cellular and organismal homeostasis. Being a major component of both bioenergetic and signaling pathways, the molecule is ideally suited to regulate metabolism and major cellular events. In humans, NAD is synthesized from vitamin B3 precursors, most prominently from nicotinamide, which is the degradation product of all NAD-dependent signaling reactions. The scope of NAD-mediated regulatory processes is wide including enzyme regulation, control of gene expression and health span, DNA repair, cell cycle regulation and calcium signaling. In these processes, nicotinamide is cleaved from NAD+ and the remaining ADP-ribosyl moiety used to modify proteins (deacetylation by sirtuins or ADP-ribosylation) or to generate calcium-mobilizing agents such as cyclic ADP-ribose. This review will also emphasize the role of the intermediates in the NAD metabolome, their intra- and extra-cellular conversions and potential contributions to subcellular compartmentalization of NAD pools.
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Affiliation(s)
- Andrey Nikiforov
- a Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University , St. Petersburg , Russia .,b Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia , and
| | - Veronika Kulikova
- a Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University , St. Petersburg , Russia
| | - Mathias Ziegler
- c Department of Molecular Biology , University of Bergen , Bergen , Norway
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31
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Liu JC, Shen WC, Shih TC, Tsai CW, Chang WS, Cho DY, Tsai CH, Bau DT. The current progress and future prospects of personalized radiogenomic cancer study. Biomedicine (Taipei) 2015; 5:2. [PMID: 25705582 PMCID: PMC4328115 DOI: 10.7603/s40681-015-0002-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/05/2015] [Indexed: 12/14/2022] Open
Abstract
During the last twenty years, mounting studies have supported the hypothesis that there is a genetic component that plays an important role in clinically observed variability in individual tissue/organ toxicity after radiotherapy. We propose the term “Personalized Radiogenomics” for the translational study of individual genetic variations that may associate with or contribute to the responses of tissues to radiation therapy used in the treatment of all types of cancer. The missions of personalized radiogenomic research are 1) to reveal the related genes, proteins, and biological pathways responsible for non-tumor or tumor tissue toxicity resulting from radiotherapy that could be targeted with radio-sensitizing and/or radio-protective agents, and 2) to identify specific genetic markers that can be used in risk prediction and evaluation models before and after clinical cancer surgery. For the members of the Terry Fox Cancer Research Lab in China Medical University and Hospital, the long-term goal is to develop SNP-based risk models that can be used to stratify patients to more precisely tailored radiotherapy protocols. Worldwide, the field has evolved over the last two decades in parallel with rapid advances in genetic and genomic technology, moving step by step from narrowly focused candidate gene studies to large-scale, collaborative genome-wide association studies. This article will summarize the candidate gene association studies published so far from the Terry Fox Cancer Research Lab as well as worldwide on the risk of radiation-related cancers and highlight some wholegenome association studies showing feasibility in fulfilling the dream of personalized radiogenomic cancer therapy.
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Affiliation(s)
- Juhn-Cherng Liu
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan ; Graduate Institute of Clinical Medical Science, China Medical University, 404 Taichung, Taiwan
| | - Wu-Chung Shen
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan ; Department of Biomedical Imaging and Radiological Science, China Medical University, 404 Taichung, Taiwan
| | - Tzu-Ching Shih
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan ; Department of Biomedical Imaging and Radiological Science, China Medical University, 404 Taichung, Taiwan
| | - Chia-Wen Tsai
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan
| | - Wen-Shin Chang
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan
| | - Der-Yang Cho
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan
| | - Chang-Hai Tsai
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan
| | - Da-Tian Bau
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, No. 2, Yuh-Der Road, 404 Taichung, Taiwan ; Graduate Institute of Clinical Medical Science, China Medical University, 404 Taichung, Taiwan
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32
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Interferon-γ induces a tryptophan-selective amino acid transporter in human colonic epithelial cells and mouse dendritic cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:453-62. [DOI: 10.1016/j.bbamem.2014.10.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 01/29/2023]
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Kerns SL, West CML, Andreassen CN, Barnett GC, Bentzen SM, Burnet NG, Dekker A, De Ruysscher D, Dunning A, Parliament M, Talbot C, Vega A, Rosenstein BS. Radiogenomics: the search for genetic predictors of radiotherapy response. Future Oncol 2014; 10:2391-406. [PMID: 25525847 DOI: 10.2217/fon.14.173] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
'Radiogenomics' is the study of genetic variation associated with response to radiotherapy. Radiogenomics aims to uncover the genes and biologic pathways responsible for radiotherapy toxicity that could be targeted with radioprotective agents and; identify genetic markers that can be used in risk prediction models in the clinic. The long-term goal of the field is to develop single nucleotide polymorphism-based risk models that can be used to stratify patients to more precisely tailored radiotherapy protocols. The field has evolved over the last two decades in parallel with advances in genomics, moving from narrowly focused candidate gene studies to large, collaborative genome-wide association studies. Several confirmed genetic variants have been identified and the field is making progress toward clinical translation.
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Affiliation(s)
- Sarah L Kerns
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Sasaki S, Futagi Y, Kobayashi M, Ogura J, Iseki K. Functional characterization of 5-oxoproline transport via SLC16A1/MCT1. J Biol Chem 2014; 290:2303-11. [PMID: 25371203 DOI: 10.1074/jbc.m114.581892] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Thyrotropin-releasing hormone is a tripeptide that consists of 5-oxoproline, histidine, and proline. The peptide is rapidly metabolized by various enzymes. 5-Oxoproline is produced by enzymatic hydrolysis in a variety of peptides. Previous studies showed that 5-oxoproline could become a possible biomarker for autism spectrum disorders. Here we demonstrate the involvement of SLC16A1 in the transport of 5-oxoproline. An SLC16A1 polymorphism (rs1049434) was recently identified. However, there is no information about the effect of the polymorphism on SLC16A1 function. In this study, the polymorphism caused an observable change in 5-oxoproline and lactate transport via SLC16A1. The Michaelis constant (Km) was increased in an SLC16A1 mutant compared with that in the wild type. In addition, the proton concentration required to produce half-maximal activation of transport activity (K0.5, H (+)) was increased in the SLC16A1 mutant compared with that in the wild type. Furthermore, we examined the transport of 5-oxoproline in T98G cells as an astrocyte cell model. Despite the fact that 5-oxoproline is an amino acid derivative, Na(+)-dependent and amino acid transport systems scarcely contributed to 5-oxoproline transport. Based on our findings, we conclude that H(+)-coupled 5-oxoproline transport is mediated solely by SLC16A1 in the cells.
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Affiliation(s)
- Shotaro Sasaki
- From the Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo 060-0812 and
| | - Yuya Futagi
- From the Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo 060-0812 and
| | - Masaki Kobayashi
- From the Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo 060-0812 and
| | - Jiro Ogura
- From the Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo 060-0812 and
| | - Ken Iseki
- From the Laboratory of Clinical Pharmaceutics and Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo 060-0812 and the Department of Pharmacy, Hokkaido University Hospital, Sapporo 060-8648, Japan
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Matsui T, Noguchi K, Fukuda M. Dennd3 functions as a guanine nucleotide exchange factor for small GTPase Rab12 in mouse embryonic fibroblasts. J Biol Chem 2014; 289:13986-95. [PMID: 24719330 DOI: 10.1074/jbc.m113.546689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small GTPase Rab12 regulates mTORC1 (mammalian target of rapamycin complex 1) activity and autophagy through controlling PAT4 (proton/amino acid transporter 4) trafficking from recycling endosomes to lysosomes, where PAT4 is degraded. However, the precise regulatory mechanism of the Rab12-mediated membrane trafficking pathway remained to be determined because a physiological Rab12-GEF (guanine nucleotide exchange factor) had yet to be identified. In this study we performed functional analyses of Dennd3, which has recently been shown to possess a GEF activity toward Rab12 in vitro. The results showed that knockdown of Dennd3 in mouse embryonic fibroblast cells caused an increase in the amount of PAT4 protein, the same as Rab12 knockdown did, and knockdown of Dennd3 and overexpression of Dennd3 were found to result in an increase and a decrease, respectively, in the intracellular amino acid concentration. Dennd3 overexpression was also found to reduce mTORC1 activity and promoted autophagy in a Rab12-dependent manner. Unexpectedly, however, Dennd3 knockdown had no effect on mTORC1 activity or autophagy despite increasing the intracellular amino acid concentration. Further study showed that Dennd3 knockdown reduced Akt activity, and the reduction in Akt activity is likely to have canceled out amino acid-induced mTORC1 activation through PAT4. These findings indicated that Dennd3 not only functions as a Rab12-GEF but also modulates Akt signaling in mouse embryonic fibroblast cells.
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Affiliation(s)
- Takahide Matsui
- From the Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kenta Noguchi
- From the Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Mitsunori Fukuda
- From the Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells. Brain Res 2014; 1557:12-25. [PMID: 24530433 DOI: 10.1016/j.brainres.2014.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/05/2014] [Indexed: 11/23/2022]
Abstract
PAT4, the fourth member of the SLC36/proton dependent amino acid transporter (PAT) family, is a high-affinity, low capacity electroneutral transporter of neutral amino acids like proline and tryptophan. It has also been associated with the function of mTORC1, a complex in the mammalian target of rapamycin (mTOR) pathway. We performed in situ hybridization and immunohistological analysis to determine the expression profile of PAT4, as well as an RT-PCR study on tissue from mice exposed to leucine. We performed a phylogenetic analysis to determine the evolutionary origin of PAT4. The in situ hybridization and the immunohistochemistry on mouse brain sections and hypothalamic cells showed abundant PAT4 expression in the mouse brain intracellularly in both inhibitory and excitatory neurons, partially co-localizing with lysosomal markers and epithelial cells lining the ventricles. Its location in epithelial cells around the ventricles indicates a transport of substrates across the blood brain barrier. Phylogenetic analysis showed that PAT4 belongs to an evolutionary old family most likely predating animals, and PAT4 is the oldest member of that family.
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Alexander SPH, Benson HE, Faccenda E, Pawson AJ, Sharman JL, Spedding M, Peters JA, Harmar AJ. The Concise Guide to PHARMACOLOGY 2013/14: transporters. Br J Pharmacol 2013; 170:1706-96. [PMID: 24528242 PMCID: PMC3892292 DOI: 10.1111/bph.12450] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Concise Guide to PHARMACOLOGY 2013/14 provides concise overviews of the key properties of over 2000 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.12444/full. Transporters are one of the seven major pharmacological targets into which the Guide is divided, with the others being G protein-coupled receptors, ligand-gated ion channels, ion channels, catalytic receptors, nuclear hormone receptors and enzymes. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in previous Guides to Receptors and Channels. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and the Guide to Receptors and Channels, providing a permanent, citable, point-in-time record that will survive database updates.
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Affiliation(s)
- Stephen PH Alexander
- School of Life Sciences, University of Nottingham Medical SchoolNottingham, NG7 2UH, UK
| | - Helen E Benson
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Elena Faccenda
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Adam J Pawson
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Joanna L Sharman
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | | | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of DundeeDundee, DD1 9SY, UK
| | - Anthony J Harmar
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
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38
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Schiöth HB, Roshanbin S, Hägglund MGA, Fredriksson R. Evolutionary origin of amino acid transporter families SLC32, SLC36 and SLC38 and physiological, pathological and therapeutic aspects. Mol Aspects Med 2013; 34:571-85. [PMID: 23506890 DOI: 10.1016/j.mam.2012.07.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 06/25/2012] [Indexed: 10/27/2022]
Abstract
About 25% of all solute carriers (SLCs) are likely to transport amino acids as their primary substrate. One of the major phylogenetic clusters of amino acid transporters from the SLC family is the β-family, which is part of the PFAM APC clan. The β-family includes three SLC families, SLC32, SLC36 and SLC38 with one, four and eleven members in humans, respectively. The most well characterized genes within these families are the vesicular inhibitory amino acid transporter (VIAAT, SLC32A1), PAT1 (SLC36A1), PAT2 (SLC36A2), PAT4 (SLC36A4), SNAT1 (SLC38A1), SNAT2 (SLC38A2), SNAT3 (SLC38A3), and SNAT4 (SLC38A4). Here we review the structural characteristics and functional role of these transporters. We also mined the complete protein sequence datasets for nine different genomes to clarify the evolutionary history of the β-family of transporters. We show that all three main branches of the this family are found as far back as green algae suggesting that genes from these families existed in the early eukaryote before the split of animals and plants and that they are present in most animal species. We also address the potential of further drug development within this field highlighting the important role of these transporters in neurotransmission and transport of amino acids as nutrients.
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Affiliation(s)
- Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden.
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Matsui T, Fukuda M. Rab12 regulates mTORC1 activity and autophagy through controlling the degradation of amino-acid transporter PAT4. EMBO Rep 2013; 14:450-7. [PMID: 23478338 DOI: 10.1038/embor.2013.32] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 02/16/2013] [Accepted: 02/19/2013] [Indexed: 12/22/2022] Open
Abstract
Autophagy is an evolutionarily conserved catabolic mechanism that targets intracellular molecules and damaged organelles to lysosomes. Autophagy is achieved by a series of membrane trafficking events, but their regulatory mechanisms are poorly understood. Here, we report small GTPase Rab12 as a new type of autophagic regulator that controls the degradation of an amino-acid transporter. Knockdown of Rab12 results in inhibition of autophagy and in increased activity of mTORC1 (mammalian/mechanistic target of rapamycin complex 1), an upstream regulator of autophagy. We also found that Rab12 promotes constitutive degradation of PAT4 (proton-coupled amino-acid transporter 4), whose accumulation in Rab12-knockdown cells modulates mTORC1 activity and autophagy. Our findings reveal a new mechanism of regulation of mTORC1 signalling and autophagy, that is, quality control of PAT4 by Rab12.
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Affiliation(s)
- Takahide Matsui
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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40
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Frølund S, Nøhr M, Holm R, Brodin B, Nielsen C. Potential involvement of the proton-coupled amino acid transporter PAT1 (SLC36A1) in the delivery of pharmaceutical agents. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50046-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Zebisch K, Brandsch M. Transport of L-proline by the proton-coupled amino acid transporter PAT2 in differentiated 3T3-L1 cells. Amino Acids 2012; 44:373-81. [PMID: 22711289 DOI: 10.1007/s00726-012-1340-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
Mechanism and substrate specificity of the proton-coupled amino acid transporter 2 (PAT2, SLC36A2) have been studied so far only in heterologous expression systems such as HeLa cells and Xenopus laevis oocytes. In this study, we describe the identification of the first cell line that expresses PAT2. We cultured 3T3-L1 cells for up to 2 weeks and differentiated the cells into adipocytes in supplemented media containing 2 μM rosiglitazone. During the 14 day differentiation period the uptake of the prototype PAT2 substrate L-[(3)H]proline increased ~5-fold. The macro- and microscopically apparent differentiation of 3T3-L1 cells coincided with their H(+) gradient-stimulated uptake of L-[(3)H]proline. Uptake was rapid, independent of a Na(+) gradient but stimulated by an inwardly directed H(+) gradient with maximal uptake occurring at pH 6.0. L-Proline uptake was found to be mediated by a transport system with a Michaelis constant (K(t)) of 130 ± 10 μM and a maximal transport velocity of 4.9 ± 0.2 nmol × 5 min(-1 )mg of protein(-1). Glycine, L-alanine, and L-tryptophan strongly inhibited L-proline uptake indicating that these amino acids also interact with the transport system. It is concluded that 3T3-L1 adipocytes express the H(+)-amino acid cotransport system PAT2.
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Affiliation(s)
- Katja Zebisch
- Biozentrum of the Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle, Germany
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42
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Proton-assisted amino acid transporter PAT1 complexes with Rag GTPases and activates TORC1 on late endosomal and lysosomal membranes. PLoS One 2012; 7:e36616. [PMID: 22574197 PMCID: PMC3344915 DOI: 10.1371/journal.pone.0036616] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/03/2012] [Indexed: 01/19/2023] Open
Abstract
Mammalian Target of Rapamycin Complex 1 (mTORC1) is activated by growth factor-regulated phosphoinositide 3-kinase (PI3K)/Akt/Rheb signalling and extracellular amino acids (AAs) to promote growth and proliferation. These AAs induce translocation of mTOR to late endosomes and lysosomes (LELs), subsequent activation via mechanisms involving the presence of intralumenal AAs, and interaction between mTORC1 and a multiprotein assembly containing Rag GTPases and the heterotrimeric Ragulator complex. However, the mechanisms by which AAs control these different aspects of mTORC1 activation are not well understood. We have recently shown that intracellular Proton-assisted Amino acid Transporter 1 (PAT1)/SLC36A1 is an essential mediator of AA-dependent mTORC1 activation. Here we demonstrate in Human Embryonic Kidney (HEK-293) cells that PAT1 is primarily located on LELs, physically interacts with the Rag GTPases and is required for normal AA-dependent mTOR relocalisation. We also use the powerful in vivo genetic methodologies available in Drosophila to investigate the regulation of the PAT1/Rag/Ragulator complex. We show that GFP-tagged PATs reside at both the cell surface and LELs in vivo, mirroring PAT1 distribution in several normal mammalian cell types. Elevated PI3K/Akt/Rheb signalling increases intracellular levels of PATs and synergistically enhances PAT-induced growth via a mechanism requiring endocytosis. In light of the recent identification of the vacuolar H+-ATPase as another Rag-interacting component, we propose a model in which PATs function as part of an AA-sensing engine that drives mTORC1 activation from LEL compartments.
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Thwaites DT, Anderson CMH. The SLC36 family of proton-coupled amino acid transporters and their potential role in drug transport. Br J Pharmacol 2012; 164:1802-16. [PMID: 21501141 DOI: 10.1111/j.1476-5381.2011.01438.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the solute carrier (SLC) 36 family are involved in transmembrane movement of amino acids and derivatives. SLC36 consists of four members. SLC36A1 and SLC36A2 both function as H(+) -coupled amino acid symporters. SLC36A1 is expressed at the luminal surface of the small intestine but is also commonly found in lysosomes in many cell types (including neurones), suggesting that it is a multipurpose carrier with distinct roles in different cells including absorption in the small intestine and as an efflux pathway following intralysosomal protein breakdown. SLC36A1 has a relatively low affinity (K(m) 1-10 mM) for its substrates, which include zwitterionic amino and imino acids, heterocyclic amino acids and amino acid-based drugs and derivatives used experimentally and/or clinically to treat epilepsy, schizophrenia, bacterial infections, hyperglycaemia and cancer. SLC36A2 is expressed at the apical surface of the human renal proximal tubule where it functions in the reabsorption of glycine, proline and hydroxyproline. SLC36A2 also transports amino acid derivatives but has a narrower substrate selectivity and higher affinity (K(m) 0.1-0.7 mM) than SLC36A1. Mutations in SLC36A2 lead to hyperglycinuria and iminoglycinuria. SLC36A3 is expressed only in testes and is an orphan transporter with no known function. SLC36A4 is widely distributed at the mRNA level and is a high-affinity (K(m) 2-3 µM) transporter for proline and tryptophan. We have much to learn about this family of transporters, but from current knowledge, it seems likely that their function will influence the pharmacokinetic profiles of amino acid-based drugs by mediating transport in both the small intestine and kidney.
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Affiliation(s)
- David T Thwaites
- Epithelial Research Group, Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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Abstract
Amino acids are essential building blocks of all mammalian cells. In addition to their role in protein synthesis, amino acids play an important role as energy fuels, precursors for a variety of metabolites and as signalling molecules. Disorders associated with the malfunction of amino acid transporters reflect the variety of roles that they fulfil in human physiology. Mutations of brain amino acid transporters affect neuronal excitability. Mutations of renal and intestinal amino acid transporters affect whole-body homoeostasis, resulting in malabsorption and renal problems. Amino acid transporters that are integral parts of metabolic pathways reduce the function of these pathways. Finally, amino acid uptake is essential for cell growth, thereby explaining their role in tumour progression. The present review summarizes the involvement of amino acid transporters in these roles as illustrated by diseases resulting from transporter malfunction.
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