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Jiao H, Kalsbeek A, Yi CX. Microglia, circadian rhythm and lifestyle factors. Neuropharmacology 2024; 257:110029. [PMID: 38852838 DOI: 10.1016/j.neuropharm.2024.110029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
Microglia, a vital homeostasis-keeper of the central nervous system, perform critical functions such as synaptic pruning, clearance of cellular debris, and participation in neuroinflammatory processes. Recent research has shown that microglia exhibit strong circadian rhythms that not only actively regulate their own immune activity, but also affect neuronal function. Disruptions of the circadian clock have been linked to a higher risk of developing a variety of diseases. In this article we will provide an overview of how lifestyle factors impact microglial function, with a focus on disruptions caused by irregular sleep-wake patterns, reduced physical activity, and eating at the wrong time-of-day. We will also discuss the potential connection between these lifestyle factors, disrupted circadian rhythms, and the role of microglia in keeping brain health. This article is part of the Special Issue on "Microglia".
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Affiliation(s)
- Han Jiao
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam, the Netherlands; Department of Clinical Chemistry, Laboratory of Endocrinology, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
| | - Andries Kalsbeek
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam, the Netherlands; Department of Clinical Chemistry, Laboratory of Endocrinology, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
| | - Chun-Xia Yi
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam, the Netherlands; Department of Clinical Chemistry, Laboratory of Endocrinology, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Netherlands Institute for Neuroscience, Amsterdam, the Netherlands.
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2
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Feng J, Huang Z, Cui C, Zhao M, Feng Y. Synthesis, taste characteristics and taste mechanism of N-lactoyl leucine from soy sauce using sensory analysis and UPLC-MS/MS. Food Chem 2024; 454:139670. [PMID: 38820630 DOI: 10.1016/j.foodchem.2024.139670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/19/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
Recently, amino acid derivatives gradually gained attention, but studies on N-lactoyl-leucine (Lac-Leu) and N-lactoyl-isoleucine (Lac-Ile) are limited. This study aims to explore the contributions of Lac-Leu and Lac-Ile to soy sauce. Lac-Leu and Lac-Ile were synthesized via enzymatic synthesis method catalyzed by Tgase. The mixed solutions containing Lac-Leu were found to have greater taste improvement than those containing Lac-Ile. Sensory evaluation indicated the sour, bitter, and astringent taste of Lac-Leu in water as well as its kokumi, astringent, and umami-enhancing taste in MSG solution. The taste threshold and umami-enhancing threshold of Lac-Leu measured by TDA and cTDA, respectively, were 0.08 mg/mL and 0.16 mg/mL. Molecular docking of Lac-Leu and Lac-Ile with the kokumi receptor CaSR and the umami receptors T1R1 and T1R3 indicated that Lac-Leu had higher affinities with receptors than Lac-Ile. These findings demonstrated the underlying contribution Lac-Leu made to soy sauce, indicating its potential to improve the flavor quality of soy sauce.
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Affiliation(s)
- Junwei Feng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Zikun Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Chun Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Yunzi Feng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China.
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3
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van Wegberg AMJ, van der Weerd JC, Engelke UFH, Coene KLM, Jahja R, Bakker SJL, Huijbregts SCJ, Wevers RA, Heiner-Fokkema MR, van Spronsen FJ. The clinical relevance of novel biomarkers as outcome parameter in adults with phenylketonuria. J Inherit Metab Dis 2024; 47:624-635. [PMID: 38556470 DOI: 10.1002/jimd.12732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024]
Abstract
Recent studies in PKU patients identified alternative biomarkers in blood using untargeted metabolomics. To test the added clinical value of these novel biomarkers, targeted metabolomics of 11 PKU biomarkers (phenylalanine, glutamyl-phenylalanine, glutamyl-glutamyl-phenylalanine, N-lactoyl-phenylalanine, N-acetyl-phenylalanine, the dipeptides phenylalanyl-phenylalanine and phenylalanyl-leucine, phenylalanine-hexose conjugate, phenyllactate, phenylpyruvate, and phenylacetate) was performed in stored serum samples of the well-defined PKU patient-COBESO cohort and a healthy control group. Serum samples of 35 PKU adults and 20 healthy age- and sex-matched controls were analyzed using ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry. Group differences were tested using the Mann-Whitney U test. Multiple linear regression analyses were performed with these biomarkers as predictors of (neuro-)cognitive functions working memory, sustained attention, inhibitory control, and mental health. Compared to healthy controls, phenylalanine, glutamyl-phenylalanine, N-lactoyl-phenylalanine, N-acetyl-phenylalanine, phenylalanine-hexose conjugate, phenyllactate, phenylpyruvate, and phenylacetate were significant elevated in PKU adults (p < 0.001). The remaining three were below limit of detection in PKU and controls. Both phenylalanine and N-lactoyl-phenylalanine were associated with DSM-VI Attention deficit/hyperactivity (R2 = 0.195, p = 0.039 and R2 = 0.335, p = 0.002, respectively) of the ASR questionnaire. In addition, N-lactoyl-phenylalanine showed significant associations with ASR DSM-VI avoidant personality (R2 = 0.265, p = 0.010), internalizing (R2 = 0.192, p = 0.046) and externalizing problems (R2 = 0.217, p = 0.029) of the ASR questionnaire and multiple aspects of the MS2D and FI tests, reflecting working memory with R2 between 0.178 (p = 0.048) and 0.204 (p = 0.033). Even though the strength of the models was not considered strong, N-lactoyl-phenylalanine outperformed phenylalanine in its association with working memory and mental health outcomes.
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Affiliation(s)
- A M J van Wegberg
- Division of Metabolic Diseases, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, The Netherlands
| | - J C van der Weerd
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - U F H Engelke
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - K L M Coene
- Laboratory of Clinical Chemistry and Hematology, Máxima Medical Centre, Veldhoven, The Netherlands
| | - R Jahja
- Division of Metabolic Diseases, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, The Netherlands
| | - S J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, The Netherlands
| | - S C J Huijbregts
- Department of Clinical Child and Adolescent Studies-Neurodevelopmental Disorders, Faculty of Social Sciences, Leiden University, Leiden, The Netherlands
| | - R A Wevers
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M R Heiner-Fokkema
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - F J van Spronsen
- Division of Metabolic Diseases, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, The Netherlands
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Hoogstraten CA, Schirris TJJ, Russel FGM. Unlocking mitochondrial drug targets: The importance of mitochondrial transport proteins. Acta Physiol (Oxf) 2024; 240:e14150. [PMID: 38666512 DOI: 10.1111/apha.14150] [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: 10/04/2023] [Revised: 03/02/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024]
Abstract
A disturbed mitochondrial function contributes to the pathology of many common diseases. These organelles are therefore important therapeutic targets. On the contrary, many adverse effects of drugs can be explained by a mitochondrial off-target effect, in particular, due to an interaction with carrier proteins in the inner membrane. Yet this class of transport proteins remains underappreciated and understudied. The aim of this review is to provide a deeper understanding of the role of mitochondrial carriers in health and disease and their significance as drug targets. We present literature-based evidence that mitochondrial carrier proteins are associated with prevalent diseases and emphasize their potential as drug (off-)target sites by summarizing known mitochondrial drug-transporter interactions. Studying these carriers will enhance our knowledge of mitochondrial drug on- and off-targets and provide opportunities to further improve the efficacy and safety of drugs.
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Affiliation(s)
- Charlotte A Hoogstraten
- Department of Pharmacy, Division of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tom J J Schirris
- Department of Pharmacy, Division of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans G M Russel
- Department of Pharmacy, Division of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
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Becker A, Filipp M, Lantz C, Glinton K, Thorp EB. HIF-1α is Required to Differentiate the Neonatal Macrophage Secretome from Adults. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.591000. [PMID: 38712137 PMCID: PMC11071477 DOI: 10.1101/2024.04.24.591000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The immune response to stress diverges with age, with neonatal macrophages implicated in tissue regeneration versus tissue scarring and maladaptive inflammation in adults. Integral to the macrophage stress response is the recognition of hypoxia and pathogen-associated molecular patterns (PAMPs), which are often coupled. The age-specific, cell-intrinsic nature of this stress response remains vague. To uncover age-defined divergences in macrophage crosstalk potential after exposure to hypoxia and PAMPs, we interrogated the secreted proteomes of neonatal versus adult macrophages via non-biased mass spectrometry. Through this approach, we newly identified age-specific signatures in the secretomes of neonatal versus adult macrophages in response to hypoxia and the prototypical PAMP, lipopolysaccharide (LPS). Neonatal macrophages polarized to an anti-inflammatory, regenerative phenotype protective against apoptosis and oxidative stress, dependent on hypoxia inducible transcription factor-1α ( HIF-1α). In contrast, adult macrophages adopted a pro-inflammatory, glycolytic phenotypic signature consistent with pathogen killing. Taken together, these data uncover fundamental age and HIF-1α dependent macrophage programs that may be targeted to calibrate the innate immune response during stress and inflammation.
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Li VL, Xiao S, Schlosser P, Scherer N, Wiggenhorn AL, Spaas J, Tung ASH, Karoly ED, Köttgen A, Long JZ. SLC17 transporters mediate renal excretion of Lac-Phe in mice and humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.589815. [PMID: 38659895 PMCID: PMC11042375 DOI: 10.1101/2024.04.18.589815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
N-lactoyl-phenylalanine (Lac-Phe) is a lactate-derived metabolite that suppresses food intake and body weight. Little is known about the mechanisms that mediate Lac-Phe transport across cell membranes. Here we identify SLC17A1 and SLC17A3, two kidney-restricted plasma membrane-localized solute carriers, as physiologic urine Lac-Phe transporters. In cell culture, SLC17A1/3 exhibit high Lac-Phe efflux activity. In humans, levels of Lac-Phe in urine exhibit a strong genetic association with the SLC17A1-4 locus. Urine Lac-Phe levels are also increased following a Wingate sprint test. In mice, genetic ablation of either SLC17A1 or SLC17A3 reduces urine Lac-Phe levels. Despite these differences, both knockout strains have normal blood Lac-Phe and body weights, demonstrating that urine and plasma Lac-Phe pools are functionally and biochemically de-coupled. Together, these data establish SLC17 family members as the physiologic urine transporters for Lac-Phe and uncover a biochemical pathway for the renal excretion of this signaling metabolite.
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7
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Pfeffer T, Krug SM, Kracke T, Schürfeld R, Colbatzky F, Kirschner P, Medert R, Freichel M, Schumacher D, Bartosova M, Zarogiannis SG, Muckenthaler MU, Altamura S, Pezer S, Volk N, Schwab C, Duensing S, Fleming T, Heidenreich E, Zschocke J, Hell R, Poschet G, Schmitt CP, Peters V. Knock-out of dipeptidase CN2 in human proximal tubular cells disrupts dipeptide and amino acid homeostasis and para- and transcellular solute transport. Acta Physiol (Oxf) 2024; 240:e14126. [PMID: 38517248 DOI: 10.1111/apha.14126] [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: 08/24/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024]
Abstract
AIM Although of potential biomedical relevance, dipeptide metabolism has hardly been studied. We found the dipeptidase carnosinase-2 (CN2) to be abundant in human proximal tubules, which regulate water and solute homeostasis. We therefore hypothesized, that CN2 has a key metabolic role, impacting proximal tubular transport function. METHODS A knockout of the CN2 gene (CNDP2-KO) was generated in human proximal tubule cells and characterized by metabolomics, RNA-seq analysis, paracellular permeability analysis and ion transport. RESULTS CNDP2-KO in human proximal tubule cells resulted in the accumulation of cellular dipeptides, reduction of amino acids and imbalance of related metabolic pathways, and of energy supply. RNA-seq analyses indicated altered protein metabolism and ion transport. Detailed functional studies demonstrated lower CNDP2-KO cell viability and proliferation, and altered ion and macromolecule transport via trans- and paracellular pathways. Regulatory and transport protein abundance was disturbed, either as a consequence of the metabolic imbalance or the resulting functional disequilibrium. CONCLUSION CN2 function has a major impact on intracellular amino acid and dipeptide metabolism and is essential for key metabolic and regulatory functions of proximal tubular cells. These findings deserve in vivo analysis of the relevance of CN2 for nephron function and regulation of body homeostasis.
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Affiliation(s)
- Tilman Pfeffer
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
- Tissue Bank of the German Center for Infection Research (DZIF), Partner Site Heidelberg, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Susanne M Krug
- Clinical Physiology/Nutritional Medicine, Charité-Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Tamara Kracke
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Robin Schürfeld
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Florian Colbatzky
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Philip Kirschner
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Dagmar Schumacher
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Maria Bartosova
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Sotiris G Zarogiannis
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center (KiTZ), University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), EMBL and University of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Sandro Altamura
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center (KiTZ), University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), EMBL and University of Heidelberg, Heidelberg, Germany
| | - Silvia Pezer
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Volk
- Tissue Bank of the National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Constantin Schwab
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Internal Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Elena Heidenreich
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Claus P Schmitt
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Verena Peters
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
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8
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Scott B, Day EA, O'Brien KL, Scanlan J, Cromwell G, Scannail AN, McDonnell ME, Finlay DK, Lynch L. Metformin and feeding increase levels of the appetite-suppressing metabolite Lac-Phe in humans. Nat Metab 2024; 6:651-658. [PMID: 38499765 PMCID: PMC11052712 DOI: 10.1038/s42255-024-01018-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
Metformin, a widely used first-line treatment for type 2 diabetes (T2D), is known to reduce blood glucose levels and suppress appetite. Here we report a significant elevation of the appetite-suppressing metabolite N-lactoyl phenylalanine (Lac-Phe) in the blood of individuals treated with metformin across seven observational and interventional studies. Furthermore, Lac-Phe levels were found to rise in response to acute metformin administration and post-prandially in patients with T2D or in metabolically healthy volunteers.
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Affiliation(s)
- Barry Scott
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Emily A Day
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Katie L O'Brien
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - John Scanlan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Grace Cromwell
- Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Aine Ni Scannail
- Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marie E McDonnell
- Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Lydia Lynch
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.
- Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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9
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TeSlaa T. Metformin induces a Lac-Phe gut-brain signalling axis. Nat Metab 2024; 6:603-605. [PMID: 38499764 DOI: 10.1038/s42255-024-01014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Affiliation(s)
- Tara TeSlaa
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
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10
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Xiao S, Li VL, Lyu X, Chen X, Wei W, Abbasi F, Knowles JW, Tung ASH, Deng S, Tiwari G, Shi X, Zheng S, Farrell L, Chen ZZ, Taylor KD, Guo X, Goodarzi MO, Wood AC, Chen YDI, Lange LA, Rich SS, Rotter JI, Clish CB, Tahir UA, Gerszten RE, Benson MD, Long JZ. Lac-Phe mediates the effects of metformin on food intake and body weight. Nat Metab 2024; 6:659-669. [PMID: 38499766 PMCID: PMC11062621 DOI: 10.1038/s42255-024-00999-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 01/30/2024] [Indexed: 03/20/2024]
Abstract
Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. There is ongoing debate about the mechanisms that mediate metformin's effects on energy balance. Here, we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite N-lactoyl-phenylalanine (Lac-Phe) in cells, in mice and two independent human cohorts. Metformin drives Lac-Phe biosynthesis through the inhibition of complex I, increased glycolytic flux and intracellular lactate mass action. Intestinal epithelial CNDP2+ cells, not macrophages, are the principal in vivo source of basal and metformin-inducible Lac-Phe. Genetic ablation of Lac-Phe biosynthesis in male mice renders animals resistant to the effects of metformin on food intake and body weight. Lastly, mediation analyses support a role for Lac-Phe as a downstream effector of metformin's effects on body mass index in participants of a large population-based observational cohort, the Multi-Ethnic Study of Atherosclerosis. Together, these data establish Lac-Phe as a critical mediator of the body weight-lowering effects of metformin.
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Affiliation(s)
- Shuke Xiao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xudong Chen
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Fahim Abbasi
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua W Knowles
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Alan Sheng-Hwa Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Gaurav Tiwari
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Laurie Farrell
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark D Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA.
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Wei W, Lyu X, Markhard AL, Fu S, Mardjuki RE, Cavanagh PE, Zeng X, Rajniak J, Lu N, Xiao S, Zhao M, Moya-Garzon MD, Truong SD, Chou JCC, Wat LW, Chidambaranathan-Reghupaty S, Coassolo L, Xu D, Shen F, Huang W, Ramirez CB, Jang C, Svensson KJ, Fischbach MA, Long JZ. A PTER-dependent pathway of taurine metabolism linked to energy balance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586194. [PMID: 38562797 PMCID: PMC10983888 DOI: 10.1101/2024.03.21.586194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Taurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans1-3. In endogenous taurine metabolism, dedicated enzymes are involved in biosynthesis of taurine from cysteine as well as the downstream derivatization of taurine into secondary taurine metabolites4,5. One such taurine metabolite is N-acetyltaurine6. Levels of N-acetyltaurine are dynamically regulated by diverse physiologic perturbations that alter taurine and/or acetate flux, including endurance exercise7, nutritional taurine supplementation8, and alcohol consumption6,9. While taurine N-acetyltransferase activity has been previously detected in mammalian cells6,7, the molecular identity of this enzyme, and the physiologic relevance of N-acetyltaurine, have remained unknown. Here we show that the orphan body mass index-associated enzyme PTER (phosphotriesterase-related)10 is the principal mammalian taurine N-acetyltransferase/hydrolase. In vitro, recombinant PTER catalyzes bidirectional taurine N-acetylation with free acetate as well as the reverse N-acetyltaurine hydrolysis reaction. Genetic ablation of PTER in mice results in complete loss of tissue taurine N-acetyltransferase/hydrolysis activities and systemic elevation of N-acetyltaurine levels. Upon stimuli that increase taurine levels, PTER-KO mice exhibit lower body weight, reduced adiposity, and improved glucose homeostasis. These phenotypes are recapitulated by administration of N-acetyltaurine to wild-type mice. Lastly, the anorexigenic and anti-obesity effects of N-acetyltaurine require functional GFRAL receptors. Together, these data uncover enzymatic control of a previously enigmatic pathway of secondary taurine metabolism linked to energy balance.
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Affiliation(s)
- Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Andrew L. Markhard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Sipei Fu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Rachel E. Mardjuki
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Xianfeng Zeng
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jakub Rajniak
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Shuke Xiao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Meng Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Maria Dolores Moya-Garzon
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Steven D. Truong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | | | - Lianna W. Wat
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Saranya Chidambaranathan-Reghupaty
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Laetitia Coassolo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Fangfang Shen
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Wentao Huang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cuauhtemoc B. Ramirez
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Katrin J. Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael A Fischbach
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
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12
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Rogers RS, Sharma R, Shah HB, Skinner OS, Guo XA, Panda A, Gupta R, Durham TJ, Shaughnessy KB, Mayers JR, Hibbert KA, Baron RM, Thompson BT, Mootha VK. Circulating N-lactoyl-amino acids and N-formyl-methionine reflect mitochondrial dysfunction and predict mortality in septic shock. Metabolomics 2024; 20:36. [PMID: 38446263 PMCID: PMC10917846 DOI: 10.1007/s11306-024-02089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/11/2024] [Indexed: 03/07/2024]
Abstract
INTRODUCTION Sepsis is a highly morbid condition characterized by multi-organ dysfunction resulting from dysregulated inflammation in response to acute infection. Mitochondrial dysfunction may contribute to sepsis pathogenesis, but quantifying mitochondrial dysfunction remains challenging. OBJECTIVE To assess the extent to which circulating markers of mitochondrial dysfunction are increased in septic shock, and their relationship to severity and mortality. METHODS We performed both full-scan and targeted (known markers of genetic mitochondrial disease) metabolomics on plasma to determine markers of mitochondrial dysfunction which distinguish subjects with septic shock (n = 42) from cardiogenic shock without infection (n = 19), bacteremia without sepsis (n = 18), and ambulatory controls (n = 19) - the latter three being conditions in which mitochondrial function, proxied by peripheral oxygen consumption, is presumed intact. RESULTS Nine metabolites were significantly increased in septic shock compared to all three comparator groups. This list includes N-formyl-L-methionine (f-Met), a marker of dysregulated mitochondrial protein translation, and N-lactoyl-phenylalanine (lac-Phe), representative of the N-lactoyl-amino acids (lac-AAs), which are elevated in plasma of patients with monogenic mitochondrial disease. Compared to lactate, the clinical biomarker used to define septic shock, there was greater separation between survivors and non-survivors of septic shock for both f-Met and the lac-AAs measured within 24 h of ICU admission. Additionally, tryptophan was the one metabolite significantly decreased in septic shock compared to all other groups, while its breakdown product kynurenate was one of the 9 significantly increased. CONCLUSION Future studies which validate the measurement of lac-AAs and f-Met in conjunction with lactate could define a sepsis subtype characterized by mitochondrial dysfunction.
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Affiliation(s)
- Robert S Rogers
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA.
| | - Rohit Sharma
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hardik B Shah
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | | | | | - Rahul Gupta
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Timothy J Durham
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Kelsey B Shaughnessy
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Jared R Mayers
- Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, MA, USA
| | - Kathryn A Hibbert
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca M Baron
- Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, MA, USA
| | - B Taylor Thompson
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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13
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Chmielewska K, Vittorio S, Gervasoni S, Dzierzbicka K, Inkielewicz-Stepniak I, Vistoli G. Human carnosinases: A brief history, medicinal relevance, and in silico analyses. Drug Discov Today 2024; 29:103860. [PMID: 38128717 DOI: 10.1016/j.drudis.2023.103860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Carnosine, an endogenous dipeptide, has been found to have a plethora of medicinal properties, such as antioxidant, antiageing, and chelating effects, but with one downside: a short half-life. Carnosinases and two hydrolytic enzymes, which remain enigmatic, are responsible for these features. Hence, here we emphasize why research is valuable for better understanding crucial concepts like ageing, neurodegradation, and cancerogenesis, given that inhibition of carnosinases might significantly prolong carnosine bioavailability and allow its further use in medicine. Herein, we explore the literature regarding carnosinases and present a short in silico analysis aimed at elucidating the possible recognition pattern between CN1 and its ligands.
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Affiliation(s)
- Klaudia Chmielewska
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Serena Vittorio
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy; Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | | | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
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14
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Suciu I, Delp J, Gutbier S, Suess J, Henschke L, Celardo I, Mayer TU, Amelio I, Leist M. Definition of the Neurotoxicity-Associated Metabolic Signature Triggered by Berberine and Other Respiratory Chain Inhibitors. Antioxidants (Basel) 2023; 13:49. [PMID: 38247474 PMCID: PMC10812665 DOI: 10.3390/antiox13010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
To characterize the hits from a phenotypic neurotoxicity screen, we obtained transcriptomics data for valinomycin, diethylstilbestrol, colchicine, rotenone, 1-methyl-4-phenylpyridinium (MPP), carbaryl and berberine (Ber). For all compounds, the concentration triggering neurite degeneration correlated with the onset of gene expression changes. The mechanistically diverse toxicants caused similar patterns of gene regulation: the responses were dominated by cell de-differentiation and a triggering of canonical stress response pathways driven by ATF4 and NRF2. To obtain more detailed and specific information on the modes-of-action, the effects on energy metabolism (respiration and glycolysis) were measured. Ber, rotenone and MPP inhibited the mitochondrial respiratory chain and they shared complex I as the target. This group of toxicants was further evaluated by metabolomics under experimental conditions that did not deplete ATP. Ber (204 changed metabolites) showed similar effects as MPP and rotenone. The overall metabolic situation was characterized by oxidative stress, an over-abundance of NADH (>1000% increase) and a re-routing of metabolism in order to dispose of the nitrogen resulting from increased amino acid turnover. This unique overall pattern led to the accumulation of metabolites known as biomarkers of neurodegeneration (saccharopine, aminoadipate and branched-chain ketoacids). These findings suggest that neurotoxicity of mitochondrial inhibitors may result from an ensemble of metabolic changes rather than from a simple ATP depletion. The combi-omics approach used here provided richer and more specific MoA data than the more common transcriptomics analysis alone. As Ber, a human drug and food supplement, mimicked closely the mode-of-action of known neurotoxicants, its potential hazard requires further investigation.
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Affiliation(s)
- Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
- Graduate School of Chemical Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Johannes Delp
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Simon Gutbier
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Julian Suess
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Lars Henschke
- Graduate School of Chemical Biology, University of Konstanz, 78464 Konstanz, Germany
- Department of Molecular Genetics, University of Konstanz, 78464 Konstanz, Germany
| | - Ivana Celardo
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Thomas U. Mayer
- Department of Molecular Genetics, University of Konstanz, 78464 Konstanz, Germany
| | - Ivano Amelio
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
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15
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Fernandes Silva L, Hokkanen J, Vangipurapu J, Oravilahti A, Laakso M. Metabolites as Risk Factors for Diabetic Retinopathy in Patients With Type 2 Diabetes: A 12-Year Follow-up Study. J Clin Endocrinol Metab 2023; 109:100-106. [PMID: 37560996 PMCID: PMC10735554 DOI: 10.1210/clinem/dgad452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/29/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023]
Abstract
CONTEXT Diabetic retinopathy (DR) is a specific microvascular complication in patients with diabetes and the leading cause of blindness. Recent advances in omics, especially metabolomics, offer the possibility identifying novel potential biomarkers for DR. OBJECTIVE The aim was to identify metabolites associated with DR. METHODS We performed a 12-year follow-up study including 1349 participants with type 2 diabetes (1021 without DR, 328 with DR) selected from the METSIM cohort. Individuals who had retinopathy before the baseline study were excluded (n = 63). The diagnosis of retinopathy was based on fundus photography examination. We performed nontargeted metabolomics profiling to identify metabolites. RESULTS We found 17 metabolites significantly associated with incident DR after adjustment for confounding factors. Among amino acids, N-lactoyl isoleucine, N-lactoyl valine, N-lactoyl tyrosine, N-lactoyl phenylalanine, N-(2-furoyl) glycine, and 5-hydroxylysine were associated with an increased risk of DR, and citrulline with a decreased risk of DR. Among the fatty acids N,N,N-trimethyl-5-aminovalerate was associated with an increased risk of DR, and myristoleate (14:1n5), palmitoleate (16:1n7), and 5-dodecenoate (12:1n7) with a decreased risk of DR. Sphingomyelin (d18:2/24:2), a sphingolipid, was significantly associated with a decreased risk of DR. Carboxylic acid maleate and organic compounds 3-hydroxypyridine sulfate, 4-vinylphenol sulfate, 4-ethylcatechol sulfate, and dimethyl sulfone were significantly associated with an increased risk of DR. CONCLUSION Our study is the first large population-based longitudinal study to identify metabolites for DR. We found multiple metabolites associated with an increased and decreased risk for DR from several different metabolic pathways.
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Affiliation(s)
- Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jenna Hokkanen
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anniina Oravilahti
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Department of Internal Medicine, Kuopio University Hospital, 70211 Kuopio, Finland
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16
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Ikeda Y, Fujii J. The Emerging Roles of γ-Glutamyl Peptides Produced by γ-Glutamyltransferase and the Glutathione Synthesis System. Cells 2023; 12:2831. [PMID: 38132151 PMCID: PMC10741565 DOI: 10.3390/cells12242831] [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: 10/24/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
L-γ-Glutamyl-L-cysteinyl-glycine is commonly referred to as glutathione (GSH); this ubiquitous thiol plays essential roles in animal life. Conjugation and electron donation to enzymes such as glutathione peroxidase (GPX) are prominent functions of GSH. Cellular glutathione balance is robustly maintained via regulated synthesis, which is catalyzed via the coordination of γ-glutamyl-cysteine synthetase (γ-GCS) and glutathione synthetase, as well as by reductive recycling by glutathione reductase. A prevailing short supply of L-cysteine (Cys) tends to limit glutathione synthesis, which leads to the production of various other γ-glutamyl peptides due to the unique enzymatic properties of γ-GCS. Extracellular degradation of glutathione by γ-glutamyltransferase (GGT) is a dominant source of Cys for some cells. GGT catalyzes the hydrolytic removal of the γ-glutamyl group of glutathione or transfers it to amino acids or to dipeptides outside cells. Such processes depend on an abundance of acceptor substrates. However, the physiological roles of extracellularly preserved γ-glutamyl peptides have long been unclear. The identification of γ-glutamyl peptides, such as glutathione, as allosteric modulators of calcium-sensing receptors (CaSRs) could provide insights into the significance of the preservation of γ-glutamyl peptides. It is conceivable that GGT could generate a new class of intercellular messaging molecules in response to extracellular microenvironments.
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Affiliation(s)
- Yoshitaka Ikeda
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata City 990-9585, Japan
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17
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Li S, Guo R, Wang J, Zheng X, Zhao S, Zhang Z, Yu W, Li S, Zheng P. The effect of blood flow restriction exercise on N-lactoylphenylalanine and appetite regulation in obese adults: a cross-design study. Front Endocrinol (Lausanne) 2023; 14:1289574. [PMID: 38116312 PMCID: PMC10728722 DOI: 10.3389/fendo.2023.1289574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Background N-lactoylphenylalanine (Lac-Phe) is a new form of "exerkines" closely related to lactate (La), which may be able to inhibit appetite. Blood flow restriction (BFR) can lead to local tissue hypoxia and increase lactate accumulation. Therefore, this study investigated the effects of combining Moderate-intensity Continuous Exercise (MICE) with BFR on Lac-Phe and appetite regulation in obese adults. Methods This study employed the cross-design study and recruited 14 obese adults aged 18-24 years. The participants were randomly divided into three groups and performed several tests with specific experimental conditions: (1) M group (MICE without BFR, 60%VO2max, 200 kJ); (2) B group (MICE with BFR, 60%VO2max, 200 kJ); and (3) C group (control session without exercise). Participants were given a standardized meal 60 min before exercise and a ad libitum 60 min after exercise. In addition, blood and Visual Analogue Scale (VAS) were collected before, immediately after, and 1 hour after performing the exercise. Results No significant difference in each index was detected before exercise. After exercise, the primary differential metabolites detected in the M and B groups were xanthine, La, succinate, Lac-Phe, citrate, urocanic acid, and myristic acid. Apart from that, the major enrichment pathways include the citrate cycle, alanine, aspartate, and glutamate metabolism. The enhanced Lac-Phe and La level in the B group was higher than M and C groups. Hunger of the B group immediately after exercise substantially differed from M group. The total ghrelin, glucagon-like peptide-1 and hunger in the B group 1 hour after exercise differed substantially from M group. The results of calorie intake showed no significant difference among the indexes in each group. Conclusions In conclusion, this cross-design study demonstrated that the combined MICE and BFR exercise reduced the appetite of obese adults by promoting the secretion of Lac-Phe and ghrelin. However, the exercise did not considerably affect the subsequent ad libitum intake.
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Affiliation(s)
- Shuoqi Li
- School of Sports Science, Nantong University, Nantong, China
| | - Rong Guo
- School of Foreign Languages, Ludong University, Yantai, China
| | - Juncheng Wang
- Department of Physical Education, Ocean University of China, Qingdao, China
| | - Xinyu Zheng
- Department of Physical Education, Ocean University of China, Qingdao, China
| | - Shuo Zhao
- Department of Physical Education, Ocean University of China, Qingdao, China
| | - Zhiru Zhang
- Department of Physical Education, Ocean University of China, Qingdao, China
| | - Wenbing Yu
- Department of Physical Education, Ocean University of China, Qingdao, China
| | - Shiming Li
- Department of Physical Education, Ocean University of China, Qingdao, China
| | - Peng Zheng
- Department of Physical Education, Ocean University of China, Qingdao, China
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18
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Hao M, Qin Y, Li Y, Tang Y, Ma Z, Tan J, Jin L, Wang F, Gong X. Metabolome subtyping reveals multi-omics characteristics and biological heterogeneity in major psychiatric disorders. Psychiatry Res 2023; 330:115605. [PMID: 38006718 DOI: 10.1016/j.psychres.2023.115605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023]
Abstract
Growing evidence suggests that major psychiatric disorders (MPDs) share common etiologies and pathological processes. However, the diagnosis is currently based on descriptive symptoms, which ignores the underlying pathogenesis and hinders the development of clinical treatments. This highlights the urgency of characterizing molecular biomarkers and establishing objective diagnoses of MPDs. Here, we collected untargeted metabolomics, proteomics and DNA methylation data of 327 patients with MPDs, 131 individuals with genetic high risk and 146 healthy controls to explore the multi-omics characteristics of MPDs. First, differential metabolites (DMs) were identified and we classified MPD patients into 3 subtypes based on DMs. The subtypes showed distinct metabolomics, proteomics and DNA methylation signatures. Specifically, one subtype showed dysregulation of complement and coagulation proteins, while the DNA methylation showed abnormalities in chemical synapses and autophagy. Integrative analysis in metabolic pathways identified the important roles of the citrate cycle, sphingolipid metabolism and amino acid metabolism. Finally, we constructed prediction models based on the metabolites and proteomics that successfully captured the risks of MPD patients. Our study established molecular subtypes of MPDs and elucidated their biological heterogeneity through a multi-omics investigation. These results facilitate the understanding of pathological mechanisms and promote the diagnosis and prevention of MPDs.
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Affiliation(s)
- Meng Hao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China
| | - Yue Qin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China; International Human Phenome Institutes, Shanghai, China
| | - Yanqing Tang
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Zehan Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China; International Human Phenome Institutes, Shanghai, China
| | - Fei Wang
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China; Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China.
| | - Xiaohong Gong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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19
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Xiao S, Li VL, Lyu X, Chen X, Wei W, Abbasi F, Knowles JW, Deng S, Tiwari G, Shi X, Zheng S, Farrell L, Chen ZZ, Taylor KD, Guo X, Goodarzi MO, Wood AC, Ida Chen YD, Lange LA, Rich SS, Rotter JI, Clish CB, Tahir UA, Gerszten RE, Benson MD, Long JZ. Lac-Phe mediates the anti-obesity effect of metformin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565321. [PMID: 37961394 PMCID: PMC10635077 DOI: 10.1101/2023.11.02.565321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. The mechanisms that mediate metformin's effects on energy balance remain incompletely defined. Here we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite Lac-Phe in mice as well as in two independent human cohorts. In cell culture, metformin drives Lac-Phe biosynthesis via inhibition of complex I, increased glycolytic flux, and intracellular lactate mass action. Other biguanides and structurally distinct inhibitors of oxidative phosphorylation also increase Lac-Phe levels in vitro. Genetic ablation of CNDP2, the principal biosynthetic enzyme for Lac-Phe, in mice renders animals resistant to metformin's anorexigenic and anti-obesity effects. Mediation analyses also support a role for Lac-Phe in metformin's effect on body mass index in humans. These data establish the CNDP2/Lac-Phe pathway as a critical mediator of the effects of metformin on energy balance.
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Affiliation(s)
- Shuke Xiao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Veronica L. Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xudong Chen
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Fahim Abbasi
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua W. Knowles
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Gaurav Tiwari
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Laurie Farrell
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Alexis C. Wood
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | | | - Usman A. Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mark D. Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
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20
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Löding S, Andersson U, Kaaks R, Schulze MB, Pala V, Urbarova I, Amiano P, Colorado-Yohar SM, Guevara M, Heath AK, Chatziioannou AC, Johansson M, Nyberg L, Antti H, Björkblom B, Melin B. Altered plasma metabolite levels can be detected years before a glioma diagnosis. JCI Insight 2023; 8:e171225. [PMID: 37651185 PMCID: PMC10619434 DOI: 10.1172/jci.insight.171225] [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: 04/06/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Genetic and metabolic changes in tissue and blood are reported to occur several years before glioma diagnosis. Since gliomas are currently detected late, a liquid biopsy for early detection could affect the quality of life and prognosis of patients. Here, we present a nested case-control study of 550 prediagnostic glioma cases and 550 healthy controls from the Northern Sweden Health and Disease study (NSHDS) and the European Prospective Investigation into Cancer and Nutrition (EPIC) study. We identified 93 significantly altered metabolites related to glioma development up to 8 years before diagnosis. Out of these metabolites, a panel of 20 selected metabolites showed strong disease correlation and a consistent progression pattern toward diagnosis in both the NSHDS and EPIC cohorts, and they separated future cases from controls independently of biological sex. The blood metabolite panel also successfully separated both lower-grade glioma and glioblastoma cases from controls, up to 8 years before diagnosis in patients within the NSHDS cohort and up to 2 years before diagnosis in EPIC. Pathway enrichment analysis detected metabolites related to the TCA cycle, Warburg effect, gluconeogenesis, and cysteine, pyruvate, and tyrosine metabolism as the most affected.
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Affiliation(s)
| | - Ulrika Andersson
- Biobank Reserach Unit, and
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Valeria Pala
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ilona Urbarova
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Pilar Amiano
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Ministry of Health of the Basque Government, Public Health Laboratory in Gipuzkoa, San Sebastián, Spain
- Epidemiology of Chronic and Comunnicable Diseases Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Sandra M. Colorado-Yohar
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Epidemiology, Murcia Regional Health Council, IMIB, Murcia, Spain
- Research Group on Demography and Health, National Faculty of Public Health, University of Antioquia, Medellín, Colombia
| | - Marcela Guevara
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Institute of Public and Labor Health and Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Alicia K. Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | | | | | - Lars Nyberg
- Department of Radiation Sciences, Diagnositc Radiology, and
- Department of Integrative Medical Biology (IMB), Umeå University, Umeå, Sweden
| | | | | | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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21
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Vu HM, Mohammad HB, Nguyen TNC, Lee JH, Do Y, Sung JY, Lee SH, Kim MS. Quantitative proteomic analysis of bronchoalveolar lavage fluids from patients with small cell lung cancers. Proteomics Clin Appl 2023; 17:e2300011. [PMID: 36807835 DOI: 10.1002/prca.202300011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023]
Abstract
PURPOSE Small cell lung cancer (SCLC) is one of the malignant cancers with aggressive progression and poor prognosis. Bronchoalveolar lavage fluid (BALF) has been arising recently as a potential source of biomarkers for lung cancers. In this study, we performed quantitative BALF proteomic analysis to identify potential biomarkers for SCLC. EXPERIMENTAL DESIGN BALF were collected from tumor-bearing lungs and non-tumor lungs of five SCLC patients. Then, BALF proteomes were prepared for a TMT-based quantitative mass spectrometry analysis. Differentially expressed proteins (DEP) were identified when considering individual variation. Potential SCLC biomarker candidates were validated by immunohistochemistry (IHC). A public database of multiple SCLC cell lines was used to evaluate the correlation of these markers with SCLC subtypes and chemo-drug responses. RESULTS We identified 460 BALF proteins in SCLC patients and observed considerable individual variation among the patients. Immunohistochemical analysis and bioinformatics resulted in the identification of CNDP2 and RNPEP as potential subtype markers for ASCL1 and NEUROD1, respectively. In addition, CNDP2 was found to be positively correlated with responses to etoposide, carboplatin, and irinotecan. CONCLUSIONS AND CLINICAL RELEVANCE BALF is an emerging source of biomarkers, making it useful for the diagnosis and prognosis of lung cancers. We characterized the proteomes of paired BALF samples collected from tumor-bearing and non-tumor lungs of SCLC patients. Several proteins were found elevated in tumor-bearing BALF, and especially CNDP2 and RNPEP appeared to be potential indicators for ASLC1-high and NEUROD1-high subtypes of SCLC, respectively. The positive correlation of CNDP2 with chemo-drug responses would help to make decisions for treatment of SCLC patients. These putative biomarkers could be comprehensively investigated for a clinical use towards precision medicine.
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Affiliation(s)
- Hung M Vu
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Hazara Begum Mohammad
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Thy N C Nguyen
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Jun Hyung Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Yeji Do
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Ji-Youn Sung
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Hyeun Lee
- Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
- New Biology Research Center, DGIST, Daegu, Republic of Korea
- Center for Cell Fate Reprogramming and Control, DGIST, Daegu, Republic of Korea
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22
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Kowalski K, Marciniak P, Rychlik L. Proteins from toad's parotoid macroglands: do they play a role in gland functioning and chemical defence? Front Zool 2023; 20:21. [PMID: 37328749 DOI: 10.1186/s12983-023-00499-8] [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: 03/02/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Parotoid gland secretion of bufonid toads is a rich source of toxic molecules that are used against predators, parasites and pathogens. Bufadienolides and biogenic amines are the principal compounds responsible for toxicity of parotoid secretion. Many toxicological and pharmacological analyses of parotoid secretions have been performed, but little is known about the processes related to poison production and secretion. Therefore, our aim was to investigate protein content in parotoids of the common toad, Bufo bufo, to understand the processes that regulate synthesis and excretion of toxins as well as functioning of parotoid macroglands. RESULTS Applying a proteomic approach we identified 162 proteins in the extract from toad's parotoids that were classified into 11 categories of biological functions. One-third (34.6%) of the identified molecules, including acyl-CoA-binding protein, actin, catalase, calmodulin, and enolases, were involved in cell metabolism. We found many proteins related to cell division and cell cycle regulation (12.0%; e.g. histone and tubulin), cell structure maintenance (8.4%; e.g. thymosin beta-4, tubulin), intra- and extracellular transport (8.4%), cell aging and apoptosis (7.3%; e.g. catalase and pyruvate kinase) as well as immune (7.0%; e.g. interleukin-24 and UV excision repair protein) and stress (6.3%; including heat shock proteins, peroxiredoxin-6 and superoxide dismutase) response. We also identified two proteins, phosphomevalonate kinase and isopentenyl-diphosphate delta-isomerase 1, that are involved in synthesis of cholesterol which is a precursor for bufadienolides biosynthesis. STRING protein-protein interaction network predicted for identified proteins showed that most proteins are related to metabolic processes, particularly glycolysis, stress response and DNA repair and replication. The results of GO enrichment and KEGG analyses are also consistent with these findings. CONCLUSION This finding indicates that cholesterol may be synthesized in parotoids, and not only in the liver from which is then transferred through the bloodstream to the parotoid macroglands. Presence of proteins that regulate cell cycle, cell division, aging and apoptosis may indicate a high epithelial cell turnover in parotoids. Proteins protecting skin cells from DNA damage may help to minimize the harmful effects of UV radiation. Thus, our work extends our knowledge with new and important functions of parotoids, major glands involved in the bufonid chemical defence.
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Affiliation(s)
- Krzysztof Kowalski
- Department of Vertebrate Zoology and Ecology, Faculty of Biological and Veterinary Sciences, Institute of Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
| | - Paweł Marciniak
- Department of Animal Physiology and Developmental Biology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Leszek Rychlik
- Department of Systematic Zoology, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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23
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Trans-10, cis-12 conjugated linoleic acid- and caloric restriction-mediated upregulation of CNDP2 expression in white adipose tissue in rodents, with implications in feeding and obesity. J Nutr Biochem 2023; 114:109269. [PMID: 36641073 DOI: 10.1016/j.jnutbio.2023.109269] [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: 07/05/2022] [Revised: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
Certain dietary supplements such as trans-10, cis-12 conjugated linoleic acid (t10-c12 CLA), and diets including caloric-restricted diets can promote weight loss in certain animal models and humans. A very recent study showed that exercise induces the biosynthesis of N-lactoyl-phenylalanine (Lac-Phe), a circulating signaling metabolite that suppresses feeding and obesity selectively in mice fed with a high-fat diet, and that cytosolic nonspecific dipeptidase 2 (CNDP2) catalyzes the synthesis of Lac-Phe from lactate (Lac) and phenylalanine (Phe). In this in silico study, we found that two anti-obesity strategies, namely treatment with t10-c12 CLA and caloric restriction, increase CNDP2 expression in adipose tissue in mice and rats, respectively. We showed that the effect of t10-c12 CLA on CNDP2 expression might be isomer-specific. We hypothesized that these t10-c12 CLA treatment- or caloric-restricted diet-mediated increases in CNDP2 expression might contribute to their anti-obesity effects, possibly due to increased Lac-Phe levels and ultimately due to Lac-Phe-mediated decreases in daily food consumption, reduced body weight and fat mass. A better understanding of the regulation of CNDP2 expression in diverse tissues in mammals might be of high importance in the treatment of obesity, considering its role in the synthesis of Lac-Phe, a metabolite that decreases body weight and fat mass selectively in mice fed with a high-fat diet. Further research is needed to find out how these two strategies lead to the upregulation of CNDP2 expression and whether this increased expression of CNDP2 might translate to reduced body weight and fat mass through higher Lac-Phe levels.
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24
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Wu J, Zhao J, Zhou Y, Cui C, Xu J, Li L, Feng Y. Discovery of N-l-Lactoyl-l-Trp as a Bitterness Masker via Structure-Based Virtual Screening and a Sensory Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2082-2093. [PMID: 36689686 DOI: 10.1021/acs.jafc.2c07807] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
N-Lactoyl-amino acid derivatives (N-Lac-AAs) are of increasing interest as potential taste-active compounds. The complexity and diversity of N-Lac-AAs pose a significant challenge to the effective discovery of taste-active N-Lac-AAs. Therefore, a structure-based virtual screening was used to identify taste-active N-Lac-AAs. Virtual screening results showed that N-lactoyl-hydrophobic amino acids had a higher affinity for taste receptors, specifically N-l-Lac-l-Trp. And then, N-l-Lac-l-Trp was synthesized in yields of 22.3% by enzymatic synthesis in the presence of l-lactate and l-Trp, and its chemical structure was confirmed by MS/MS and one-dimensional (1D) and two-dimensional (2D) NMR. Sensory evaluation revealed that N-l-Lac-l-Trp had a significant taste-masking effect on quinine, d-salicin, caffeine, and l-Trp, particularly l-Trp and caffeine. N-l-Lac-l-Trp had a better masking effect on the higher concentration of bitter compounds. It reduced the bitterness of caffeine (500 mg/L) and l-Trp (1000 mg/L) by approximately 20 and 26%, respectively. The result of the ligand-receptor interaction and a quantum mechanical analysis showed that N-l-Lac-l-Trp increased the binding affinity to the bitter receptor mainly through hydrogen bonding and lowering the electrostatic potential.
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Affiliation(s)
- Jing Wu
- School of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Junpeng Zhao
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yubo Zhou
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chun Cui
- School of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| | - Jucai Xu
- School of Biotechnology and Health Sciences & International Healthcare Innovation Institute (Jiangmen), Wuyi University, Jiangmen 529020, China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yunzi Feng
- School of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
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25
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Aas V, Øvstebø R, Brusletto BS, Aspelin T, Trøseid AMS, Qureshi S, Eid DSO, Olstad OK, Nyman TA, Haug KBF. Distinct microRNA and protein profiles of extracellular vesicles secreted from myotubes from morbidly obese donors with type 2 diabetes in response to electrical pulse stimulation. Front Physiol 2023; 14:1143966. [PMID: 37064893 PMCID: PMC10098097 DOI: 10.3389/fphys.2023.1143966] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/09/2023] [Indexed: 04/18/2023] Open
Abstract
Lifestyle disorders like obesity, type 2 diabetes (T2D), and cardiovascular diseases can be prevented and treated by regular physical activity. During exercise, skeletal muscles release signaling factors that communicate with other organs and mediate beneficial effects of exercise. These factors include myokines, metabolites, and extracellular vesicles (EVs). In the present study, we have examined how electrical pulse stimulation (EPS) of myotubes, a model of exercise, affects the cargo of released EVs. Chronic low frequency EPS was applied for 24 h to human myotubes isolated and differentiated from biopsy samples from six morbidly obese females with T2D, and EVs, both exosomes and microvesicles (MV), were isolated from cell media 24 h thereafter. Size and concentration of EV subtypes were characterized by nanoparticle tracking analysis, surface markers were examined by flow cytometry and Western blotting, and morphology was confirmed by transmission electron microscopy. Protein content was assessed by high-resolution proteomic analysis (LC-MS/MS), non-coding RNA was quantified by Affymetrix microarray, and selected microRNAs (miRs) validated by real time RT-qPCR. The size and concentration of exosomes and MV were unaffected by EPS. Of the 400 miRs identified in the EVs, EPS significantly changed the level of 15 exosome miRs, of which miR-1233-5p showed the highest fold change. The miR pattern of MV was unaffected by EPS. Totally, about 1000 proteins were identified in exosomes and 2000 in MV. EPS changed the content of 73 proteins in exosomes, 97 in MVs, and of these four were changed in both exosomes and MV (GANAB, HSPA9, CNDP2, and ATP5B). By matching the EPS-changed miRs and proteins in exosomes, 31 targets were identified, and among these several promising signaling factors. Of particular interest were CNDP2, an enzyme that generates the appetite regulatory metabolite Lac-Phe, and miR-4433b-3p, which targets CNDP2. Several of the regulated miRs, such as miR-92b-5p, miR-320b, and miR-1233-5p might also mediate interesting signaling functions. In conclusion, we have used a combined transcriptome-proteome approach to describe how EPS affected the cargo of EVs derived from myotubes from morbidly obese patients with T2D, and revealed several new factors, both miRs and proteins, that might act as exercise factors.
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Affiliation(s)
- Vigdis Aas
- Department of Life Sciences and Health, Oslo Metropolitan University (OsloMet), Oslo, Norway
- *Correspondence: Vigdis Aas, ; Kari Bente Foss Haug,
| | - Reidun Øvstebø
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
| | | | - Trude Aspelin
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
| | | | - Saba Qureshi
- Department of Life Sciences and Health, Oslo Metropolitan University (OsloMet), Oslo, Norway
| | | | | | - Tuula A. Nyman
- Department of Immunology, University of Oslo, and Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Kari Bente Foss Haug
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
- *Correspondence: Vigdis Aas, ; Kari Bente Foss Haug,
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Exercise-Induced N-Lactoylphenylalanine Predicts Adipose Tissue Loss during Endurance Training in Overweight and Obese Humans. Metabolites 2022; 13:metabo13010015. [PMID: 36676940 PMCID: PMC9863672 DOI: 10.3390/metabo13010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Physical exercise is a powerful measure to prevent cardiometabolic diseases. However, the individual response to lifestyle interventions is variable and cannot, to date, be predicted. N-Lactoylphenylalanine (Lac-Phe) produced during exercise has recently been shown to mediate weight loss in obese mice. Lac-Phe could also contribute to, and potentially explain differences in, the effectiveness of exercise interventions in humans. Sedentary overweight and obese subjects completed an 8-week supervised endurance exercise intervention (n = 22). Before and after the intervention, plasma levels of Lac-Phe were determined by UHPLC-MS in the resting state and immediately after an acute bout of endurance exercise. Adipose tissue volume was quantified using MRI. Acute exercise caused a pronounced increase in Lac-Phe, both before and after the intervention. Higher levels of Lac-Phe after acute exercise were associated with a greater reduction in abdominal subcutaneous and, to a lower degree, visceral adipose tissue during the intervention. Lac-Phe produced during physical activity could contribute to weight loss by acting as a signaling molecule that regulates food intake, as previously shown in mice. Quantification of Lac-Phe during an exercise test could be employed as a tool to predict and potentially improve the individual response to exercise-based lifestyle interventions in overweight humans and those with obesity.
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27
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Philips O, Sultonova M, Blackmore B, Murphy JP. Understanding emerging bioactive metabolites with putative roles in cancer biology. Front Oncol 2022; 12:1014748. [PMID: 36249070 PMCID: PMC9557195 DOI: 10.3389/fonc.2022.1014748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulated metabolism in cancers is, by now, well established. Although metabolic adaptations provide cancers with the ability to synthesize the precursors required for rapid biosynthesis, some metabolites have direct functional, or bioactive, effects in human cells. Here we summarize recently identified metabolites that have bioactive roles either as post-translational modifications (PTMs) on proteins or in, yet unknown ways. We propose that these metabolites could play a bioactive role in promoting or inhibiting cancer cell phenotypes in a manner that is mostly unexplored. To study these potentially important bioactive roles, we discuss several novel metabolomic and proteomic approaches aimed at defining novel PTMs and metabolite-protein interactions. Understanding metabolite PTMs and protein interactors of bioactive metabolites may provide entirely new therapeutic targets for cancer.
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The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES). Metabolites 2022; 12:metabo12090787. [PMID: 36144194 PMCID: PMC9505353 DOI: 10.3390/metabo12090787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Non-O blood groups are associated with decreased insulin sensitivity and risk of type 2 diabetes. A recent study pinpointed the associations between ABO blood groups and gut microbiome, which may serve as potential mediators for the observed increased disease risks. We aimed to characterize associations between ABO haplotypes and insulin-related traits as well as potential mediating pathways. We assessed insulin homeostasis in African Americans (AAs; n = 109) and non-Hispanic whites (n = 210) from the Microbiome and Insulin Longitudinal Evaluation Study. The ABO haplotype was determined by six SNPs located in the ABO gene. Based on prior knowledge, we included 21 gut bacteria and 13 plasma metabolites for mediation analysis. In the white study cohort (60 ± 9 years, 42% male), compared to the O1 haplotype, A1 was associated with a higher Matsuda insulin sensitivity index, while a lower relative abundance of Bacteroides massiliensis and lactate levels. Lactate was a likely mediator of this association but not Bacteroides massiliensis. In the AAs group (57 ± 8 years, 33% male), we found no association between any haplotype and insulin-related traits. In conclusion, the A1 haplotype may promote healthy insulin sensitivity in non-Hispanic whites and lactate likely play a role in this process but not selected gut bacteria.
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Abstract
Lactate released from skeletal muscle during high-intensity exercise gives rise to a surge in circulating lactate-derived pseudo-dipeptide metabolites including N-lactoyl-phenylalanine (Lac-Phe). In a recent Nature paper, Li et al. use genetic and pharmacological evidence to now propose Lac-Phe to be an "exercise hormone" that suppresses appetite and obesity.
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Affiliation(s)
- Jens Lund
- Novo Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christoffer Clemmensen
- Novo Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Thue W Schwartz
- Novo Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Fox BW, Ponomarova O, Lee YU, Zhang G, Giese GE, Walker M, Roberto NM, Na H, Rodrigues PR, Curtis BJ, Kolodziej AR, Crombie TA, Zdraljevic S, Yilmaz LS, Andersen EC, Schroeder FC, Walhout AJM. C. elegans as a model for inter-individual variation in metabolism. Nature 2022; 607:571-577. [PMID: 35794472 PMCID: PMC9817093 DOI: 10.1038/s41586-022-04951-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 06/08/2022] [Indexed: 01/11/2023]
Abstract
Individuals can exhibit differences in metabolism that are caused by the interplay of genetic background, nutritional input, microbiota and other environmental factors1-4. It is difficult to connect differences in metabolism to genomic variation and derive underlying molecular mechanisms in humans, owing to differences in diet and lifestyle, among others. Here we use the nematode Caenorhabditis elegans as a model to study inter-individual variation in metabolism. By comparing three wild strains and the commonly used N2 laboratory strain, we find differences in the abundances of both known metabolites and those that have not to our knowledge been previously described. The latter metabolites include conjugates between 3-hydroxypropionate (3HP) and several amino acids (3HP-AAs), which are much higher in abundance in one of the wild strains. 3HP is an intermediate in the propionate shunt pathway, which is activated when flux through the canonical, vitamin-B12-dependent propionate breakdown pathway is perturbed5. We show that increased accumulation of 3HP-AAs is caused by genetic variation in HPHD-1, for which 3HP is a substrate. Our results suggest that the production of 3HP-AAs represents a 'shunt-within-a-shunt' pathway to accommodate a reduction-of-function allele in hphd-1. This study provides a step towards the development of metabolic network models that capture individual-specific differences of metabolism and more closely represent the diversity that is found in entire species.
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Affiliation(s)
- Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Olga Ponomarova
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yong-Uk Lee
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Gabrielle E Giese
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Melissa Walker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Huimin Na
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pedro R Rodrigues
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Aiden R Kolodziej
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - L Safak Yilmaz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
| | - Albertha J M Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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31
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Christa P, Dunkel A, Krauss A, Stark TD, Dawid C, Hofmann T. Discovery and Identification of Tastants and Taste-Modulating N-Acyl Amino Acid Derivatives in Traditional Korean Fermented Dish Kimchi Using a Sensomics Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7500-7514. [PMID: 35674110 DOI: 10.1021/acs.jafc.2c02623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sensory-guided fractionation by means of ultrafiltration and gel permeation chromatography followed by high-performance liquid chromatography, synthesis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) quantitation, and taste re-engineering experiments revealed taste-active and taste-enhancing compounds contributing to the umami, mouthful and complex taste profile of the fermented Korean dish, kimchi. Besides basic taste-active compounds, in particular, various N-acylated amino acids deriving from succinic acid and lactic acid imparted taste-modulating properties in food matrices. Taste threshold concentrations were determined to evaluate intrinsic and modulating effects. Quantitation of N-acylated amino acids in kimchi following synthesis revealed the presence of numerous derivatives showing taste-active properties. Sensory evaluation including recombination and partial addition experiments highlighted that both the N-lactoyl- and the N-succinoyl amino acid derivatives contribute to increasing the fullness, volume, and complexity of food matrices, whereas the latter directly contributes to the overall taste of kimchi in natural concentrations.
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Affiliation(s)
- Peter Christa
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Andreas Dunkel
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Alin Krauss
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Timo D Stark
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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Li VL, He Y, Contrepois K, Liu H, Kim JT, Wiggenhorn AL, Tanzo JT, Tung ASH, Lyu X, Zushin PJH, Jansen RS, Michael B, Loh KY, Yang AC, Carl CS, Voldstedlund CT, Wei W, Terrell SM, Moeller BC, Arthur RM, Wallis GA, van de Wetering K, Stahl A, Kiens B, Richter EA, Banik SM, Snyder MP, Xu Y, Long JZ. An exercise-inducible metabolite that suppresses feeding and obesity. Nature 2022; 606:785-790. [PMID: 35705806 PMCID: PMC9767481 DOI: 10.1038/s41586-022-04828-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 05/03/2022] [Indexed: 01/12/2023]
Abstract
Exercise confers protection against obesity, type 2 diabetes and other cardiometabolic diseases1-5. However, the molecular and cellular mechanisms that mediate the metabolic benefits of physical activity remain unclear6. Here we show that exercise stimulates the production of N-lactoyl-phenylalanine (Lac-Phe), a blood-borne signalling metabolite that suppresses feeding and obesity. The biosynthesis of Lac-Phe from lactate and phenylalanine occurs in CNDP2+ cells, including macrophages, monocytes and other immune and epithelial cells localized to diverse organs. In diet-induced obese mice, pharmacological-mediated increases in Lac-Phe reduces food intake without affecting movement or energy expenditure. Chronic administration of Lac-Phe decreases adiposity and body weight and improves glucose homeostasis. Conversely, genetic ablation of Lac-Phe biosynthesis in mice increases food intake and obesity following exercise training. Last, large activity-inducible increases in circulating Lac-Phe are also observed in humans and racehorses, establishing this metabolite as a molecular effector associated with physical activity across multiple activity modalities and mammalian species. These data define a conserved exercise-inducible metabolite that controls food intake and influences systemic energy balance.
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Affiliation(s)
- Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Yang He
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Hailan Liu
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Amanda L Wiggenhorn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Julia T Tanzo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Alan Sheng-Hwa Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Peter-James H Zushin
- Department of Nutrition and Toxicology, University of California Berkeley, Berkeley, CA, USA
| | - Robert S Jansen
- Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Basil Michael
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kang Yong Loh
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Andrew C Yang
- Department of Anatomy and the Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Christian S Carl
- August Krogh Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christian T Voldstedlund
- August Krogh Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benjamin C Moeller
- Maddy Equine Analytical Chemistry Laboratory, California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California at Davis, Davis, CA, USA
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Rick M Arthur
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Gareth A Wallis
- School of Sport, Exercise, and Rehabilitation Sciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Koen van de Wetering
- Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andreas Stahl
- Department of Nutrition and Toxicology, University of California Berkeley, Berkeley, CA, USA
| | - Bente Kiens
- August Krogh Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Erik A Richter
- August Krogh Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Steven M Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Yong Xu
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA.
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA.
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33
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Exercise molecule burns away hunger. Nature 2022; 606:655-656. [PMID: 35705863 DOI: 10.1038/d41586-022-01321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Effects of Acute and Chronic Resistance Exercise on the Skeletal Muscle Metabolome. Metabolites 2022; 12:metabo12050445. [PMID: 35629949 PMCID: PMC9142957 DOI: 10.3390/metabo12050445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 12/18/2022] Open
Abstract
Resistance training promotes metabolic health and stimulates muscle hypertrophy, but the precise routes by which resistance exercise (RE) conveys these health benefits are largely unknown. Aim: To investigate how acute RE affects human skeletal muscle metabolism. Methods: We collected vastus lateralis biopsies from six healthy male untrained volunteers at rest, before the first of 13 RE training sessions, and 45 min after the first and last bouts of RE. Biopsies were analysed using untargeted mass spectrometry-based metabolomics. Results: We measured 617 metabolites covering a broad range of metabolic pathways. In the untrained state RE altered 33 metabolites, including increased 3-methylhistidine and N-lactoylvaline, suggesting increased protein breakdown, as well as metabolites linked to ATP (xanthosine) and NAD (N1-methyl-2-pyridone-5-carboxamide) metabolism; the bile acid chenodeoxycholate also increased in response to RE in muscle opposing previous findings in blood. Resistance training led to muscle hypertrophy, with slow type I and fast/intermediate type II muscle fibre diameter increasing by 10.7% and 10.4%, respectively. Comparison of post-exercise metabolite levels between trained and untrained state revealed alterations of 46 metabolites, including decreased N-acetylated ketogenic amino acids and increased beta-citrylglutamate which might support growth. Only five of the metabolites that changed after acute exercise in the untrained state were altered after chronic training, indicating that training induces multiple metabolic changes not directly related to the acute exercise response. Conclusion: The human skeletal muscle metabolome is sensitive towards acute RE in the trained and untrained states and reflects a broad range of adaptive processes in response to repeated stimulation.
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35
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Wu J, Gao J, Lin J, Cui C, Li L, He S, Brennan C. Preparation and Taste Characteristics of Kokumi N-Lactoyl Phenylalanine in the Presence of Phenylalanine and Lactate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5396-5407. [PMID: 35452224 DOI: 10.1021/acs.jafc.2c00530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
N-l-Lactoyl phenylalanine (N-l-lactoyl-Phe) has been identified as a taste-active contributor in many fermented foods. However, its preparation, taste property, and content in foodstuffs are little known to date. In the current study, two preparation technologies of N-l-lactoyl-Phe including heating and enzymatic methods were investigated. Other investigations include its taste property and quantification in several fermented foods. The results indicated that the heating preparation and enzymatic preparation only produced N-l-lactoyl-Phe instead of N-d-lactoyl-Phe in the presence of l-lactate/d-lactate and l-phenylalanine (Phe). A high yield (58.0% ± 0.7%) of N-l-lactoyl-Phe was achieved under the following conditions: Phe, lactate, CaO, and water at molar ratios of 1:8:0.3:9 kept at 100 °C for 3 h. With nine enzymes, a maximum yield of 21.2% ± 0.3% was achieved in the aqueous solution under mild operating conditions: 0.18 M Phe, 0.90 M lactate, 5 g/L Debitrase HYW 20, pH 8, and 55 °C for 24 h. The sensory evaluation revealed that N-l-lactoyl-Phe in water enhanced the salty and umami intensity. It also enhanced the thickness, mouthfulness, and continuity of salt solution, model broth, and chicken broth, revealing that N-l-lactoyl-Phe was a kokumi-active compound. The kokumi thresholds of N-l-lactoyl-Phe in these solutions were 50, 50, and 25 mg/L, respectively. N-l-Lactoyl-Phe was quantified in traditional Chinese fermented foods as 30.12 ± 0.28 mg/kg in preserved pickles, 14.11 ± 0.14 mg/kg in soybean paste, 4.87 ± 0.16 mg/kg in fermented bean, 0.71 ± 0.11 mg/kg in rice vinegar, and 20.34 ± 0.18 mg/kg in soy sauce. These results revealed the potential of N-l-lactoyl-Phe as a taste enhancer, presenting a new opportunity for the food industry.
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Affiliation(s)
- Jing Wu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Jingrong Gao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Junjie Lin
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chun Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Shan He
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Charles Brennan
- School of Science STEM College, RMIT University, Melbourne 3000, Australia
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36
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Kadota Y, Yano A, Kawakami T, Sato M, Suzuki S. Metabolomic profiling of plasma from middle-aged and advanced-age male mice reveals the metabolic abnormalities of carnitine biosynthesis in metallothionein gene knockout mice. Aging (Albany NY) 2021; 13:24963-24988. [PMID: 34851303 PMCID: PMC8714139 DOI: 10.18632/aging.203731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022]
Abstract
Metallothionein (MT) is a family of low molecular weight, cysteine-rich proteins that regulate zinc homeostasis and have potential protective effects against oxidative stress and toxic metals. MT1 and MT2 gene knockout (MTKO) mice show shorter lifespans than wild-type (WT) mice. In this study, we aimed to investigate how MT gene deficiency accelerates aging. We performed comparative metabolomic analyses of plasma between MTKO and WT male mice at middle age (50-week-old) and advanced age (100-week-old) using liquid chromatography with time-of-flight mass spectrometry (LC-TOF-MS). The concentration of N6,N6,N6-trimethyl-L-lysine (TML), which is a metabolic intermediate in carnitine biosynthesis, was consistently higher in the plasma of MTKO mice compared to that of WT mice at middle and advanced age. Quantitative reverse transcription PCR (RT-PCR) analysis revealed remarkably lower mRNA levels of Tmlhe, which encodes TML dioxygenase, in the liver and kidney of male MTKO mice compared to that of WT mice. L-carnitine is essential for β-oxidation of long-chain fatty acids in mitochondria, the activity of which is closely related to aging. Our results suggest that reduced carnitine biosynthesis capacity in MTKO mice compared to WT mice led to metabolic disorders of fatty acids in mitochondria in MTKO mice, which may have caused shortened lifespans.
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Affiliation(s)
- Yoshito Kadota
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Asuka Yano
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Takashige Kawakami
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Masao Sato
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Shinya Suzuki
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
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37
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Metabolomic Analysis Reveals Changes in Plasma Metabolites in Response to Acute Cold Stress and Their Relationships to Metabolic Health in Cold-Acclimatized Humans. Metabolites 2021; 11:metabo11090619. [PMID: 34564435 PMCID: PMC8468536 DOI: 10.3390/metabo11090619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
Cold exposure results in activation of metabolic processes required for fueling thermogenesis, potentially promoting improved metabolic health. However, the metabolic complexity underlying this process is not completely understood. We aimed to analyze changes in plasma metabolites related to acute cold exposure and their relationship to cold-acclimatization level and metabolic health in cold-acclimatized humans. Blood samples were obtained before and acutely after 10–15 min of ice-water swimming (<5 °C) from 14 ice-water swimmers. Using mass spectrometry, 973 plasma metabolites were measured. Ice-water swimming induced acute changes in 70 metabolites. Pathways related to amino acid metabolism were the most cold-affected and cold-induced changes in several amino acids correlated with cold-acclimatization level and/or metabolic health markers, including atherogenic lipid profile or insulin resistance. Metabolites correlating with cold-acclimatization level were enriched in the linoleic/α-linolenic acid metabolic pathway. N-lactoyl-tryptophan correlated with both cold-acclimatization level and cold-induced changes in thyroid and parathyroid hormones. Acute cold stress in cold-acclimatized humans induces changes in plasma metabolome that involve amino acids metabolism, while the linoleic and α-linolenic acid metabolism pathway seems to be affected by regular cold exposure. Metabolites related to metabolic health, thermogenic hormonal regulators and acclimatization level might represent prospective molecular factors important in metabolic adaptations to regular cold exposure.
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38
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Sharma R, Reinstadler B, Engelstad K, Skinner OS, Stackowitz E, Haller RG, Clish CB, Pierce K, Walker MA, Fryer R, Oglesbee D, Mao X, Shungu DC, Khatri A, Hirano M, De Vivo DC, Mootha VK. Circulating markers of NADH-reductive stress correlate with mitochondrial disease severity. J Clin Invest 2021; 131:136055. [PMID: 33463549 DOI: 10.1172/jci136055] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial disorders represent a large collection of rare syndromes that are difficult to manage both because we do not fully understand biochemical pathogenesis and because we currently lack facile markers of severity. The m.3243A>G variant is the most common heteroplasmic mitochondrial DNA mutation and underlies a spectrum of diseases, notably mitochondrial encephalomyopathy lactic acidosis and stroke-like episodes (MELAS). To identify robust circulating markers of m.3243A>G disease, we first performed discovery proteomics, targeted metabolomics, and untargeted metabolomics on plasma from a deeply phenotyped cohort (102 patients, 32 controls). In a validation phase, we measured concentrations of prioritized metabolites in an independent cohort using distinct methods. We validated 20 analytes (1 protein, 19 metabolites) that distinguish patients with MELAS from controls. The collection includes classic (lactate, alanine) and more recently identified (GDF-15, α-hydroxybutyrate) mitochondrial markers. By mining untargeted mass-spectra we uncovered 3 less well-studied metabolite families: N-lactoyl-amino acids, β-hydroxy acylcarnitines, and β-hydroxy fatty acids. Many of these 20 analytes correlate strongly with established measures of severity, including Karnofsky status, and mechanistically, nearly all markers are attributable to an elevated NADH/NAD+ ratio, or NADH-reductive stress. Our work defines a panel of organelle function tests related to NADH-reductive stress that should enable classification and monitoring of mitochondrial disease.
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Affiliation(s)
- Rohit Sharma
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Bryn Reinstadler
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Kristin Engelstad
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Owen S Skinner
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Erin Stackowitz
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald G Haller
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Institute for Exercise and Environmental Medicine of Texas Health Presbyterian Hospital, Dallas, Texas, USA
| | | | | | - Melissa A Walker
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert Fryer
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Xiangling Mao
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Dikoma C Shungu
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Ashok Khatri
- Endocrine Division and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Darryl C De Vivo
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
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39
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Schmidt C, Wehsling M, Le Mignon M, Wille G, Rey Y, Schnellbaecher A, Zabezhinsky D, Fischer M, Zimmer A. Lactoyl leucine and isoleucine are bioavailable alternatives for canonical amino acids in cell culture media. Biotechnol Bioeng 2021; 118:3395-3408. [PMID: 33738790 PMCID: PMC8453549 DOI: 10.1002/bit.27755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/26/2021] [Accepted: 03/14/2021] [Indexed: 11/08/2022]
Abstract
Increasing demands for protein-based therapeutics such as monoclonal antibodies, fusion proteins, bispecific molecules, and antibody fragments require researchers to constantly find innovative solutions. To increase yields and decrease costs of next generation bioprocesses, highly concentrated cell culture media formulations are developed but often limited by the low solubility of amino acids such as tyrosine, cystine, leucine, and isoleucine, in particular at physiological pH. This study sought to investigate highly soluble and bioavailable derivatives of leucine and isoleucine that are applicable for fed-batch processes. N-lactoyl-leucine and N-lactoyl-isoleucine sodium salts were tested in cell culture media and proved to be beneficial to increase the overall solubility of cell culture media formulations. These modified amino acids proved to be bioavailable for various Chinese hamster ovary (CHO) cells and were suitable for replacement of canonical amino acids in cell culture feeds. The quality of the final recombinant protein was studied in bioprocesses using the derivatives, and the mechanism of cleavage was investigated in CHO cells. Altogether, both N-lactoyl amino acids represent an advantageous alternative to canonical amino acids to develop highly concentrated cell culture media formulations to support next generation bioprocesses.
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Affiliation(s)
| | | | | | - Gregor Wille
- Merck Life Science, Process Development, Buchs, Switzerland
| | - Yannick Rey
- Merck Life Science, Process Development, Buchs, Switzerland
| | | | | | - Markus Fischer
- Merck Life Science, Process Development, Buchs, Switzerland
| | - Aline Zimmer
- Merck Life Science, Upstream R&D, Darmstadt, Germany
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40
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Zhang Y, Li W, Chen TT, Yang Y, Wu MY, Luo JY, Gong Y, Zou L. Chemical Fingerprint Analysis and Ultra-Performance Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry-Based Metabolomics Study of the Protective Effect of Buxue Yimu Granule in Medical-Induced Incomplete Abortion Rats. Front Pharmacol 2020; 11:578217. [PMID: 33328985 PMCID: PMC7734354 DOI: 10.3389/fphar.2020.578217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/09/2020] [Indexed: 12/17/2022] Open
Abstract
Medical abortion is a common method to terminate an early pregnancy and often causes serious complications such as abnormal uterine bleeding and endometritis. Buxue Yimu granule (BYG) is a well-known traditional Chinese medicine prescription composed of five kinds of drugs and is widely used in gynecology and obstetrics. The aim of the present study was to establish the quality standard of BYG and investigate its protective effect on incomplete abortion. The chemical fingerprint of BYG was established by high performance liquid chromatography (HPLC). The major compounds of BYG were determined by ultra-performance liquid chromatography with triple quadrupole mass spectrometry. An incomplete abortion rat model was induced by intragastric administration of mifepristone (8.3 mg·kg-1) combined with misoprostol (100.0 μg·kg-1) during early pregnancy. The serum levels of human chorionic gonadotrophin (HCG), estradiol (E2), and progesterone (PG) were determined. The serum endogenous metabolites were analyzed by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS). Multivariate analysis, including partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA), was employed to analyze the metabolic profiles, and MetaboAnalyst was used to investigate the metabolic pathways. Furthermore, hematoxylin-eosin staining (HE) was used to evaluate the histopathological changes in uterine tissue. The expression levels of VEGFA and NF-κB were detected by immunohistochemistry. The results indicated that HPLC fingerprint analysis can be successfully used to assess the quality of BYG. The medical-induced incomplete abortion rats were clearly separated from control rats, and the biochemical changes were gradually restored to normal after administration of BYG. Moreover, 19 potential biomarkers, including N-lactoylleucine, 2-piperidinone, isobutyryl-l-carnitine, eicosapentaenoylcholine, LysoPC(14:0), LysoPC(20:5), physagulin C, LysoPC(18:3), leukotriene D5, deoxycholic acid 3-glucuronide, glycine, pregnanediol 3-O-glucuronide, LysoPC(18:2), LysoPC(17:0/0:0), N-acetyl-leukotriene E4, LysoPC(18:0), platelet-activating factor, LysoPA(24:1), and LysoPC(18:1), which were mainly related to the amino acids metabolism, lipids metabolism, and bile acid biosynthesis, were identified. Consequently, BYG exerts a potential protective role in the intervention of incomplete abortion by anti-inflammatory, promote endometrial repair, and regulate the metabolic disorders.
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Affiliation(s)
- Yan Zhang
- School of Medicine, Chengdu University, Chengdu, China
| | - Wei Li
- School of Medicine, Chengdu University, Chengdu, China
| | | | - Yong Yang
- School of Medicine, Chengdu University, Chengdu, China
| | - Meng-Yao Wu
- Department of Pharmacology, Zhuzhou Qianjin Pharmaceutical Co., Ltd., Zhuzhou, China
| | - Jie-Ying Luo
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Yun Gong
- Department of Pharmacology, Zhuzhou Qianjin Pharmaceutical Co., Ltd., Zhuzhou, China
| | - Liang Zou
- School of Medicine, Chengdu University, Chengdu, China.,Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
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41
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Borst P. Looking back at multidrug resistance (MDR) research and ten mistakes to be avoided when writing about ABC transporters in MDR. FEBS Lett 2020; 594:4001-4011. [PMID: 33111311 DOI: 10.1002/1873-3468.13972] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/31/2020] [Accepted: 10/16/2020] [Indexed: 12/19/2022]
Abstract
This paper presents a personal, selective, and sometimes critical retrospective of the history of ABC transporters in multidrug resistance (MDR) of cancer cells, overrepresenting discoveries of some early pioneers, long forgotten, and highlights of research in Amsterdam, mainly focussing on discoveries made with disruptions of ABC genes in mice (KO mice) and on the role of ABC transporters in causing drug resistance in a mouse model of mammary cancer. The history is complemented by a list of erroneous concepts often found in papers and grant applications submitted anno 2020.
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Affiliation(s)
- Piet Borst
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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42
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Gao W, Zhang Q, Su Y, Huang P, Lu X, Gong Q, Chen W, Xu R, Tian R. Multiomic analysis of a dried single-drop plasma sample using an integrated mass spectrometry approach. Analyst 2020; 145:6441-6446. [PMID: 32785396 DOI: 10.1039/d0an01149e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An easy-to-use and fast approach was developed for integrated proteomic and metabolic profiling in a dried single-drop plasma sample. Plasma collection, room temperature storage, and sample preparation for both proteins and metabolites were seamlessly integrated in one spintip device. MS-based multiomic profiling using the same nano LC-MS system identified more than 150 proteins and 160 metabolites from the 1 μL plasma sample in 6 hours. Further combination with micro-flow LC and targeted MS made it a promising approach for the fast profiling of molecular biomarkers with high sensitivity and accuracy.
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Affiliation(s)
- Weina Gao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.
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43
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Bacigalupa ZA, Rathmell WK. Beyond glycolysis: Hypoxia signaling as a master regulator of alternative metabolic pathways and the implications in clear cell renal cell carcinoma. Cancer Lett 2020; 489:19-28. [PMID: 32512023 PMCID: PMC7429250 DOI: 10.1016/j.canlet.2020.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/17/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022]
Abstract
The relationship between kidney cancer, specifically clear cell renal cell carcinoma (ccRCC), and the hypoxia signaling program has been extensively characterized. Its underlying role as the primary driver of the disease has led to the development of the most effective targeted therapies to date. Cellular responses to hypoxia or mutations affecting the von Hippel-Lindau (VHL) tumor suppressor gene stabilize the hypoxia inducible factor (HIF) transcription factors which then orchestrate elaborate downstream signaling events resulting in adaptations to key biological processes, such as reprogramming metabolism. The direct link of hypoxia signaling to glucose uptake and glycolysis has long been appreciated; however, the HIF family of proteins directly regulate many downstream targets, including other transcription factors with their own extensive networks. In this review, we will summarize our current understanding of how hypoxia signaling regulates other metabolic pathways and how this contributes to the development and progression of clear cell renal cell carcinomas.
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Affiliation(s)
- Zachary A Bacigalupa
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - W Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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44
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A new opening for the tricky untargeted investigation of natural and modified short peptides. Talanta 2020; 219:121262. [PMID: 32887153 DOI: 10.1016/j.talanta.2020.121262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022]
Abstract
Short peptides are of extreme interest in clinical and food research fields, nevertheless they still represent a crucial analytical issue. The main aim of this paper was the development of an analytical platform for a considerable advancement in short peptides identification. For the first time, short sequences presenting both natural and post-translationally modified amino acids were comprehensively studied thanks to the generation of specific databases. Short peptide databases had a dual purpose. First, they were employed as inclusion lists for a suspect screening mass-spectrometric analysis, overcoming the limits of data dependent acquisition mode and allowing the fragmentation of such low-abundance substances. Moreover, the databases were implemented in Compound Discoverer 3.0, a software dedicated to the analysis of short molecules, for the creation of a data processing workflow specifically dedicated to short peptide tentative identification. For this purpose, a detailed study of short peptide fragmentation pathways was carried out for the first time. The proposed method was applied to the study of short peptide sequences in enriched urine samples and led to the tentative identification more than 200 short natural and modified short peptides, the highest number ever reported.
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45
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Yin J, Sun W, Li F, Hong J, Li X, Zhou Y, Lu Y, Liu M, Zhang X, Chen N, Jin X, Xue J, Zeng S, Yu L, Zhu F. VARIDT 1.0: variability of drug transporter database. Nucleic Acids Res 2020; 48:D1042-D1050. [PMID: 31495872 PMCID: PMC6943059 DOI: 10.1093/nar/gkz779] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
The absorption, distribution and excretion of drugs are largely determined by their transporters (DTs), the variability of which has thus attracted considerable attention. There are three aspects of variability: epigenetic regulation and genetic polymorphism, species/tissue/disease-specific DT abundances, and exogenous factors modulating DT activity. The variability data of each aspect are essential for clinical study, and a collective consideration among multiple aspects becomes crucial in precision medicine. However, no database is constructed to provide the comprehensive data of all aspects of DT variability. Herein, the Variability of Drug Transporter Database (VARIDT) was introduced to provide such data. First, 177 and 146 DTs were confirmed, for the first time, by the transporting drugs approved and in clinical/preclinical, respectively. Second, for the confirmed DTs, VARIDT comprehensively collected all aspects of their variability (23 947 DNA methylations, 7317 noncoding RNA/histone regulations, 1278 genetic polymorphisms, differential abundance profiles of 257 DTs in 21 781 patients/healthy individuals, expression of 245 DTs in 67 tissues of human/model organism, 1225 exogenous factors altering the activity of 148 DTs), which allowed mutual connection between any aspects. Due to huge amount of accumulated data, VARIDT made it possible to generalize characteristics to reveal disease etiology and optimize clinical treatment, and is freely accessible at: https://db.idrblab.org/varidt/ and http://varidt.idrblab.net/.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wen Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoxu Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying Zhou
- The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Yinjing Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mengzhi Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xue Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Na Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiuping Jin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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46
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Kim JT, Terrell SM, Li VL, Wei W, Fischer CR, Long JZ. Cooperative enzymatic control of N-acyl amino acids by PM20D1 and FAAH. eLife 2020; 9:55211. [PMID: 32271712 PMCID: PMC7145423 DOI: 10.7554/elife.55211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/21/2020] [Indexed: 12/28/2022] Open
Abstract
The N-acyl amino acids are a family of bioactive lipids with pleiotropic physiologic functions, including in energy homeostasis. Their endogenous levels are regulated by an extracellular mammalian N-acyl amino acid synthase/hydrolase called PM20D1 (peptidase M20 domain containing 1). Using an activity-guided biochemical approach, we report the molecular identification of fatty acid amide hydrolase (FAAH) as a second intracellular N-acyl amino acid synthase/hydrolase. In vitro, FAAH exhibits a more restricted substrate scope compared to PM20D1. In mice, genetic ablation or selective pharmacological inhibition of FAAH bidirectionally dysregulates intracellular, but not circulating, N-acyl amino acids. Dual blockade of both PM20D1 and FAAH reveals a dramatic and non-additive biochemical engagement of these two enzymatic pathways. These data establish FAAH as a second intracellular pathway for N-acyl amino acid metabolism and underscore enzymatic division of labor as an enabling strategy for the regulation of a structurally diverse bioactive lipid family.
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Affiliation(s)
- Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States
| | - Curt R Fischer
- Stanford ChEM-H, Stanford University, Stanford, United States
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
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47
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Walach J, Filzmoser P, Kouřil Š, Friedecký D, Adam T. Cellwise outlier detection and biomarker identification in metabolomics based on pairwise log ratios. JOURNAL OF CHEMOMETRICS 2020; 34:e3182. [PMID: 32189829 PMCID: PMC7063692 DOI: 10.1002/cem.3182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Data outliers can carry very valuable information and might be most informative for the interpretation. Nevertheless, they are often neglected. An algorithm called cellwise outlier diagnostics using robust pairwise log ratios (cell-rPLR) for the identification of outliers in single cell of a data matrix is proposed. The algorithm is designed for metabolomic data, where due to the size effect, the measured values are not directly comparable. Pairwise log ratios between the variable values form the elemental information for the algorithm, and the aggregation of appropriate outlyingness values results in outlyingness information. A further feature of cell-rPLR is that it is useful for biomarker identification, particularly in the presence of cellwise outliers. Real data examples and simulation studies underline the good performance of this algorithm in comparison with alternative methods.
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Affiliation(s)
- Jan Walach
- Institute of Statistics and Mathematical Methods in EconomicsTU WienViennaAustria
| | - Peter Filzmoser
- Institute of Statistics and Mathematical Methods in EconomicsTU WienViennaAustria
| | - Štěpán Kouřil
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and DentistryPalacký University OlomoucOlomoucCzech Republic
- Department of Clinical BiochemistryUniversity Hospital OlomoucOlomoucCzech Republic
| | - David Friedecký
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and DentistryPalacký University OlomoucOlomoucCzech Republic
- Department of Clinical BiochemistryUniversity Hospital OlomoucOlomoucCzech Republic
| | - Tomáš Adam
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and DentistryPalacký University OlomoucOlomoucCzech Republic
- Department of Clinical BiochemistryUniversity Hospital OlomoucOlomoucCzech Republic
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48
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Kim JT, Li VL, Terrell SM, Fischer CR, Long JZ. Family-wide Annotation of Enzymatic Pathways by Parallel In Vivo Metabolomics. Cell Chem Biol 2019; 26:1623-1629.e3. [PMID: 31587987 PMCID: PMC6874721 DOI: 10.1016/j.chembiol.2019.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/19/2019] [Accepted: 09/16/2019] [Indexed: 12/21/2022]
Abstract
Enzymes catalyze fundamental biochemical reactions that control cellular and organismal homeostasis. Here we present an approach for de novo biochemical pathway discovery across entire mammalian enzyme families using parallel viral transduction in mice and untargeted liquid chromatography-mass spectrometry. Applying this method to the M20 peptidases uncovers both known pathways of amino acid metabolism as well as a previously unknown CNDP2-regulated pathway for threonyl dipeptide catabolism. Ablation of CNDP2 in mice elevates threonyl dipeptides across multiple tissues, establishing the physiologic relevance of our biochemical assignments. Taken together, these data underscore the utility of parallel in vivo metabolomics for the family-wide discovery of enzymatic pathways.
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Affiliation(s)
- Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Curt R Fischer
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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49
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Barupal DK, Fiehn O. Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:97008. [PMID: 31557052 PMCID: PMC6794490 DOI: 10.1289/ehp4713] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Blood chemicals are routinely measured in clinical or preclinical research studies to diagnose diseases, assess risks in epidemiological research, or use metabolomic phenotyping in response to treatments. A vast volume of blood-related literature is available via the PubMed database for data mining. OBJECTIVES We aimed to generate a comprehensive blood exposome database of endogenous and exogenous chemicals associated with the mammalian circulating system through text mining and database fusion. METHODS Using NCBI resources, we retrieved PubMed abstracts, PubChem chemical synonyms, and PMC supplementary tables. We then employed text mining and PubChem crowdsourcing to associate phrases relating to blood with PubChem chemicals. False positives were removed by a phrase pattern and a compound exclusion list. RESULTS A query to identify blood-related publications in the PubMed database yielded 1.1 million papers. Matching a total of 15 million synonyms from 6.5 million relevant PubChem chemicals against all blood-related publications yielded 37,514 chemicals and 851,999 publications records. Mapping PubChem compound identifiers to the PubMed database yielded 49,940 unique chemicals linked to 676,643 papers. Analysis of open-access metabolomics papers related to blood phrases in the PMC database yielded 4,039 unique compounds and 204 papers. Consolidating these three approaches summed up to a total of 41,474 achiral structures that were linked to 65,957 PubChem CIDs and to over 878,966 PubMed articles. We mapped these compounds to 50 databases such as those covering metabolites and pathways, governmental and toxicological databases, pharmacology resources, and bioassay repositories. In comparison, HMDB, the Human Metabolome Database, links 1,075 compounds to blood-related primary publications. CONCLUSION This new Blood Exposome Database can be used for prioritizing chemicals for systematic reviews, developing target assays in exposome research, identifying compounds in untargeted mass spectrometry, and biological interpretation in metabolomics data. The database is available at http://bloodexposome.org. https://doi.org/10.1289/EHP4713.
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Affiliation(s)
- Dinesh Kumar Barupal
- National Institutes of Health (NIH) West Coast Metabolomics Center, Genome Center, University of California, Davis, Davis, California, USA
| | - Oliver Fiehn
- National Institutes of Health (NIH) West Coast Metabolomics Center, Genome Center, University of California, Davis, Davis, California, USA
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50
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Cyranka M, Veprik A, McKay EJ, van Loon N, Thijsse A, Cotter L, Hare N, Saibudeen A, Lingam S, Pires E, Larraufie P, Reimann F, Gribble F, Stewart M, Bentley E, Lear P, McCullagh J, Cantley J, Cox RD, de Wet H. Abcc5 Knockout Mice Have Lower Fat Mass and Increased Levels of Circulating GLP-1. Obesity (Silver Spring) 2019; 27:1292-1304. [PMID: 31338999 PMCID: PMC6658130 DOI: 10.1002/oby.22521] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/09/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE A previous genome-wide association study linked overexpression of an ATP-binding cassette transporter, ABCC5, in humans with a susceptibility to developing type 2 diabetes with age. Specifically, ABCC5 gene overexpression was shown to be strongly associated with increased visceral fat mass and reduced peripheral insulin sensitivity. Currently, the role of ABCC5 in diabetes and obesity is unknown. This study reports the metabolic phenotyping of a global Abcc5 knockout mouse. METHODS A global Abcc5-/- mouse was generated by CRISPR/Cas9. Fat mass was determined by weekly EchoMRI and fat pads were dissected and weighed at week 18. Glucose homeostasis was ascertained by an oral glucose tolerance test, intraperitoneal glucose tolerance test, and intraperitoneal insulin tolerance test. Energy expenditure and locomotor activity were measured using PhenoMaster cages. Glucagon-like peptide 1 (GLP-1) levels in plasma, primary gut cell cultures, and GLUTag cells were determined by enzyme-linked immunosorbent assay. RESULTS Abcc5-/- mice had decreased fat mass and increased plasma levels of GLP-1, and they were more insulin sensitive and more active. Recombinant overexpression of ABCC5 protein in GLUTag cells decreased GLP-1 release. CONCLUSIONS ABCC5 protein expression levels are inversely related to fat mass and appear to play a role in the regulation of GLP-1 secretion from enteroendocrine cells.
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Affiliation(s)
- Malgorzata Cyranka
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Anna Veprik
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Eleanor J. McKay
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Nienke van Loon
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Amber Thijsse
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Luke Cotter
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Nisha Hare
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Affan Saibudeen
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Swathi Lingam
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | | | - Pierre Larraufie
- Wellcome Trust‐MRC Institute of Metabolic ScienceAddenbrooke's HospitalCambridgeUK
| | - Frank Reimann
- Wellcome Trust‐MRC Institute of Metabolic ScienceAddenbrooke's HospitalCambridgeUK
| | - Fiona Gribble
- Wellcome Trust‐MRC Institute of Metabolic ScienceAddenbrooke's HospitalCambridgeUK
| | - Michelle Stewart
- MRC Harwell Institute, Genetics of Type 2 DiabetesMammalian Genetics Unit, Harwell CampusOxfordshireUK
| | - Elizabeth Bentley
- MRC Harwell Institute, Genetics of Type 2 DiabetesMammalian Genetics Unit, Harwell CampusOxfordshireUK
| | - Pamela Lear
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | | | - James Cantley
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Roger D. Cox
- MRC Harwell Institute, Genetics of Type 2 DiabetesMammalian Genetics Unit, Harwell CampusOxfordshireUK
| | - Heidi de Wet
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
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