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Hadfield CM, Walker JK, Arnatt C, McCommis KS. Computational structural prediction and chemical inhibition of the human mitochondrial pyruvate carrier protein heterodimer complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594520. [PMID: 39071381 PMCID: PMC11275797 DOI: 10.1101/2024.05.16.594520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The mitochondrial pyruvate carrier (MPC) plays a role in numerous diseases including neurodegeneration, metabolically dependent cancers, and the development of insulin resistance. Several previous studies in genetic mouse models or with existing inhibitors suggest that inhibition of the MPC could be used as a viable therapeutic strategy in these diseases. However, the MPC's structure is unknown, making it difficult to screen for and develop therapeutically viable inhibitors. Currently known MPC inhibitors would make for poor drugs due to their poor pharmacokinetic properties, or in the case of the thiazolidinediones (TZDs), off-target specificity for peroxisome-proliferator activated receptor gamma (PPARγ) leads to unwanted side effects. In this study, we develop several structural models for the MPC heterodimer complex and investigate the chemical interactions required for the binding of these known inhibitors to MPC and PPARγ. Based on these models, the MPC most likely takes on outward-facing (OF) and inward-facing (IF) conformations during pyruvate transport, and inhibitors likely plug the carrier to inhibit pyruvate transport. Although some chemical interactions are similar between MPC and PPARγ binding, there is likely enough difference to reduce PPARγ specificity for future development of novel, more specific MPC inhibitors.
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Affiliation(s)
- Christy M Hadfield
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine
| | - John K Walker
- Department of Pharmacology & Physiology, Saint Louis University School of Medicine
- Department of Chemistry, Saint Louis University
| | - Chris Arnatt
- Department of Pharmacology & Physiology, Saint Louis University School of Medicine
- Department of Chemistry, Saint Louis University
| | - Kyle S McCommis
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine
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2
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Colca JR, Tanis SP, Kletzien RF, Finck BN. Insulin sensitizers in 2023: lessons learned and new avenues for investigation. Expert Opin Investig Drugs 2023; 32:803-811. [PMID: 37755339 DOI: 10.1080/13543784.2023.2263369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
INTRODUCTION 'Insulin sensitizers' derived discoveries of the Takeda Company in 1970s. Pioglitazone remains the best in class with beneficial pleiotropic pharmacology, although use is limited by tolerability issues. Various attempts to expand out of this class assumed the primary molecular target was the transcription factor, PPARγ. Findings over the last 10 years have identified new targets of thiazolidinediones (TZDs) that should alter the drug discovery paradigm. AREAS COVERED We review structural classes of experimental insulin sensitizer drugs, some of which have attained limited approval in some markets. The TZD pioglitazone, originally approved in 1999 as a secondary treatment for type 2 diabetes, has demonstrated benefit in apparently diverse spectrums of disease from cardiovascular to neurological issues. New TZDs modulate a newly identified mitochondrial target (the mitochondrial pyruvate carrier) to reprogram metabolism and produce insulin sensitizing pharmacology devoid of tolerability issues. EXPERT OPINION Greater understanding of the mechanism of action of insulin sensitizing drugs can expand the rationale for the fields of treatment and potential for treatment combinations. This understanding can facilitate the registration and broader use of agents with that impact the pathophysiology that underlies chronic metabolic diseases as well as host responses to environmental insults including pathogens, insulin sensitizer, MPC, mitochondrial target, metabolic reprogramming, chronic and infectious disease.
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Affiliation(s)
| | | | | | - Brian N Finck
- Department of Medicine, Center for Human Nutrition, Washington University in St Louis, Euclid Ave, MO, USA
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3
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Musa M, Zeppieri M, Atuanya GN, Enaholo ES, Topah EK, Ojo OM, Salati C. Nutritional Factors: Benefits in Glaucoma and Ophthalmologic Pathologies. Life (Basel) 2023; 13:1120. [PMID: 37240765 PMCID: PMC10222847 DOI: 10.3390/life13051120] [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: 03/07/2023] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023] Open
Abstract
Glaucoma is a chronic optic neuropathy that can lead to irreversible functional and morphological damage if left untreated. The gold standard therapeutic approaches in managing patients with glaucoma and limiting progression include local drops, laser, and/or surgery, which are all geared at reducing intraocular pressure (IOP). Nutrients, antioxidants, vitamins, organic compounds, and micronutrients have been gaining increasing interest in the past decade as integrative IOP-independent strategies to delay or halt glaucomatous retinal ganglion cell degeneration. In our minireview, we examine the various nutrients and compounds proposed in the current literature for the management of ophthalmology diseases, especially for glaucoma. With respect to each substance considered, this minireview reports the molecular and biological characteristics, neuroprotective activities, antioxidant properties, beneficial mechanisms, and clinical studies published in the past decade in the field of general medicine. This study highlights the potential benefits of these substances in glaucoma and other ophthalmologic pathologies. Nutritional supplementation can thus be useful as integrative IOP-independent strategies in the management of glaucoma and in other ophthalmologic pathologies. Large multicenter clinical trials based on functional and morphologic data collected over long follow-up periods in patients with IOP-independent treatments can pave the way for alternative and/or coadjutant therapeutic options in the management of glaucoma and other ocular pathologies.
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Affiliation(s)
- Mutali Musa
- Department of Optometry, University of Benin, Benin City 300238, Edo State, Nigeria
| | - Marco Zeppieri
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
| | | | | | - Efioshiomoshi Kings Topah
- Department of Optometry, Faculty of Allied Health Sciences, College of Health Sciences Bayero University, Kano 700006, Kano State, Nigeria
| | - Oluwasola Michael Ojo
- School of Optometry and Vision Sciences, College of Health Sciences, University of Ilorin, Ilorin 240003, Kwara State, Nigeria
| | - Carlo Salati
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
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4
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Mallet D, Goutaudier R, Barbier EL, Carnicella S, Colca JR, Fauvelle F, Boulet S. Re-routing Metabolism by the Mitochondrial Pyruvate Carrier Inhibitor MSDC-0160 Attenuates Neurodegeneration in a Rat Model of Parkinson's Disease. Mol Neurobiol 2022; 59:6170-6182. [PMID: 35895232 DOI: 10.1101/2022.01.17.476616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/10/2022] [Indexed: 05/25/2023]
Abstract
A growing body of evidence supports the idea that mitochondrial dysfunction might represent a key feature of Parkinson's disease (PD). Central regulators of energy production, mitochondria, are also involved in several other essential functions such as cell death pathways and neuroinflammation which make them a potential therapeutic target for PD management. Interestingly, recent studies related to PD have reported a neuroprotective effect of targeting mitochondrial pyruvate carrier (MPC) by the insulin sensitizer MSDC-0160. As the sole point of entry of pyruvate into the mitochondrial matrix, MPC plays a crucial role in energetic metabolism which is impacted in PD. This study therefore aimed at providing insights into the mechanisms underlying the neuroprotective effect of MSDC-0160. We investigated behavioral, cellular, and metabolic impact of chronic MSDC-0160 treatment in unilateral 6-OHDA PD rats. We evaluated mitochondrially related processes through the expression of pivotal mitochondrial enzymes in dorsal striatal biopsies and the level of metabolites in serum samples using nuclear magnetic resonance spectroscopy (NMR)-based metabolomics. MSDC-0160 treatment in unilateral 6-OHDA rats improved motor behavior, decreased dopaminergic denervation, and reduced mTOR activity and neuroinflammation. Concomitantly, MSDC-0160 administration strongly modified energy metabolism as revealed by increased ketogenesis, beta oxidation, and glutamate oxidation to satisfy energy needs and maintain energy homeostasis. MSDC-0160 exerts its neuroprotective effect through reorganization of multiple pathways connected to energy metabolism.
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Affiliation(s)
- David Mallet
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Raphael Goutaudier
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Emmanuel L Barbier
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
- Université Grenoble Alpes Inserm, US17, CNRS, UMS, 3552, CHU Grenoble Alpes IRMaGe, Grenoble, France
| | - Sebastien Carnicella
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Jerry R Colca
- Metabolic Solutions Development Company, Kalamazoo, MI, 49007, USA
| | - Florence Fauvelle
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
- Université Grenoble Alpes Inserm, US17, CNRS, UMS, 3552, CHU Grenoble Alpes IRMaGe, Grenoble, France
| | - Sabrina Boulet
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France.
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5
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Li L, Wen M, Run C, Wu B, OuYang B. Experimental Investigations on the Structure of Yeast Mitochondrial Pyruvate Carriers. MEMBRANES 2022; 12:membranes12100916. [PMID: 36295675 PMCID: PMC9608981 DOI: 10.3390/membranes12100916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 06/01/2023]
Abstract
Mitochondrial pyruvate carrier (MPC) transports pyruvate from the cytoplasm into the mitochondrial matrix to participate in the tricarboxylic acid (TCA) cycle, which further generates the energy for the physiological activities of cells. Two interacting subunits, MPC1 and MPC2 or MPC3, form a heterodimer to conduct transport function. However, the structural basis of how the MPC complex transports pyruvate is still lacking. Here, we described the detailed expression and purification procedures to obtain large amounts of yeast MPC1 and MPC2 for structural characterization. The purified yeast MPC1 and MPC2 were reconstituted in dodecylphosphocholine (DPC) micelles and examined using nuclear magnetic resonance (NMR) spectroscopy, showing that both subunits contain three α-helical transmembrane regions with substantial differences from what was predicted by AlphaFold2. Furthermore, the new protocol producing the recombinant MPC2 using modified maltose-binding protein (MBP) with cyanogen bromide (CNBr) cleavage introduced general way to obtain small membrane proteins. These findings provide a preliminary understanding for the structure of the MPC complex and useful guidance for further studies.
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Affiliation(s)
- Ling Li
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maorong Wen
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Changqing Run
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Mallet D, Goutaudier R, Barbier EL, Carnicella S, Colca JR, Fauvelle F, Boulet S. Re-routing Metabolism by the Mitochondrial Pyruvate Carrier Inhibitor MSDC-0160 Attenuates Neurodegeneration in a Rat Model of Parkinson's Disease. Mol Neurobiol 2022; 59:6170-6182. [PMID: 35895232 DOI: 10.1007/s12035-022-02962-9] [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: 02/14/2022] [Accepted: 07/10/2022] [Indexed: 11/29/2022]
Abstract
A growing body of evidence supports the idea that mitochondrial dysfunction might represent a key feature of Parkinson's disease (PD). Central regulators of energy production, mitochondria, are also involved in several other essential functions such as cell death pathways and neuroinflammation which make them a potential therapeutic target for PD management. Interestingly, recent studies related to PD have reported a neuroprotective effect of targeting mitochondrial pyruvate carrier (MPC) by the insulin sensitizer MSDC-0160. As the sole point of entry of pyruvate into the mitochondrial matrix, MPC plays a crucial role in energetic metabolism which is impacted in PD. This study therefore aimed at providing insights into the mechanisms underlying the neuroprotective effect of MSDC-0160. We investigated behavioral, cellular, and metabolic impact of chronic MSDC-0160 treatment in unilateral 6-OHDA PD rats. We evaluated mitochondrially related processes through the expression of pivotal mitochondrial enzymes in dorsal striatal biopsies and the level of metabolites in serum samples using nuclear magnetic resonance spectroscopy (NMR)-based metabolomics. MSDC-0160 treatment in unilateral 6-OHDA rats improved motor behavior, decreased dopaminergic denervation, and reduced mTOR activity and neuroinflammation. Concomitantly, MSDC-0160 administration strongly modified energy metabolism as revealed by increased ketogenesis, beta oxidation, and glutamate oxidation to satisfy energy needs and maintain energy homeostasis. MSDC-0160 exerts its neuroprotective effect through reorganization of multiple pathways connected to energy metabolism.
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Affiliation(s)
- David Mallet
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Raphael Goutaudier
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Emmanuel L Barbier
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France.,Université Grenoble Alpes Inserm, US17, CNRS, UMS, 3552, CHU Grenoble Alpes IRMaGe, Grenoble, France
| | - Sebastien Carnicella
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Jerry R Colca
- Metabolic Solutions Development Company, Kalamazoo, MI, 49007, USA
| | - Florence Fauvelle
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France.,Université Grenoble Alpes Inserm, US17, CNRS, UMS, 3552, CHU Grenoble Alpes IRMaGe, Grenoble, France
| | - Sabrina Boulet
- Université Grenoble Alpes Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France.
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7
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Yiew NKH, Finck BN. The mitochondrial pyruvate carrier at the crossroads of intermediary metabolism. Am J Physiol Endocrinol Metab 2022; 323:E33-E52. [PMID: 35635330 PMCID: PMC9273276 DOI: 10.1152/ajpendo.00074.2022] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/04/2022] [Accepted: 05/18/2022] [Indexed: 11/22/2022]
Abstract
Pyruvate metabolism, a central nexus of carbon homeostasis, is an evolutionarily conserved process and aberrant pyruvate metabolism is associated with and contributes to numerous human metabolic disorders including diabetes, cancer, and heart disease. As a product of glycolysis, pyruvate is primarily generated in the cytosol before being transported into the mitochondrion for further metabolism. Pyruvate entry into the mitochondrial matrix is a critical step for efficient generation of reducing equivalents and ATP and for the biosynthesis of glucose, fatty acids, and amino acids from pyruvate. However, for many years, the identity of the carrier protein(s) that transported pyruvate into the mitochondrial matrix remained a mystery. In 2012, the molecular-genetic identification of the mitochondrial pyruvate carrier (MPC), a heterodimeric complex composed of protein subunits MPC1 and MPC2, enabled studies that shed light on the many metabolic and physiological processes regulated by pyruvate metabolism. A better understanding of the mechanisms regulating pyruvate transport and the processes affected by pyruvate metabolism may enable novel therapeutics to modulate mitochondrial pyruvate flux to treat a variety of disorders. Herein, we review our current knowledge of the MPC, discuss recent advances in the understanding of mitochondrial pyruvate metabolism in various tissue and cell types, and address some of the outstanding questions relevant to this field.
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Affiliation(s)
- Nicole K H Yiew
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, Missouri
| | - Brian N Finck
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, Missouri
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8
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Colca JR, Finck BN. Metabolic Mechanisms Connecting Alzheimer's and Parkinson's Diseases: Potential Avenues for Novel Therapeutic Approaches. Front Mol Biosci 2022; 9:929328. [PMID: 35782864 PMCID: PMC9243557 DOI: 10.3389/fmolb.2022.929328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's (AD) and Parkinson's Diseases (PD) are common neurodegenerative disorders growing in incidence and prevalence and for which there are no disease-modifying treatments. While there are considerable complexities in the presentations of these diseases, the histological pictures of these pathologies, as well as several rare genetic predispositions for each, point to the involvement of maladaptive protein processing and inflammation. Importantly, the common presentations of AD and PD are connected to aging and to dysmetabolism, including common co-diagnosis of metabolic syndrome or diabetes. Examination of anti-diabetic therapies in preclinical models and in some observational clinical studies have suggested effectiveness of the first generation insulin sensitizer pioglitazone in both AD and PD. Recently, the mitochondrial pyruvate carrier (MPC) was shown to be a previously unrecognized target of pioglitazone. New insulin sensitizers are in development that can be dosed to full engagement of this previously unappreciated mitochondrial target. Here we review molecular mechanisms that connect modification of pyruvate metabolism with known liabilities of AD and PD. The mechanisms involve modification of autophagy, inflammation, and cell differentiation in various cell types including neurons, glia, macrophages, and endothelium. These observations have implications for the understanding of the general pathology of neurodegeneration and suggest general therapeutic approaches to disease modification.
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Affiliation(s)
- Jerry R. Colca
- Metabolic Solutions Development Company, Western Michigan University, Kalamazoo, MI, United States
| | - Brian N. Finck
- Washington University School of Medicine, St. Louis, MO, United States
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9
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Mitochondrial Metabolism behind Region-Specific Resistance to Ischemia-Reperfusion Injury in Gerbil Hippocampus. Role of PKCβII and Phosphate-Activated Glutaminase. Int J Mol Sci 2021; 22:ijms22168504. [PMID: 34445210 PMCID: PMC8395184 DOI: 10.3390/ijms22168504] [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: 07/01/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
Ischemic episodes are a leading cause of death worldwide with limited therapeutic interventions. The current study explored mitochondrial phosphate-activated glutaminase (GLS1) activity modulation by PKCβII through GC-MS untargeted metabolomics approach. Mitochondria were used to elucidate the endogenous resistance of hippocampal CA2-4 and dentate gyrus (DG) to transient ischemia and reperfusion in a model of ischemic episode in gerbils. In the present investigation, male gerbils were subjected to bilateral carotids occlusion for 5 min followed by reperfusion (IR). Gerbils were randomly divided into three groups as vehicle-treated sham control, vehicle-treated IR and PKCβII specific inhibitor peptide βIIV5-3-treated IR. Vehicle or βIIV5-3 (3 mg/kg, i.v.) were administered at the moment of reperfusion. The gerbils hippocampal tissue were isolated at various time of reperfusion and cell lysates or mitochondria were isolated from CA1 and CA2-4,DG hippocampal regions. Recombinant proteins PKCβII and GLS1 were used in in vitro phosphorylation reaction and organotypic hippocampal cultures (OHC) transiently exposed to NMDA (25 μM) to evaluate the inhibition of GLS1 on neuronal viability. PKCβII co-precipitates with GAC (GLS1 isoform) in CA2-4,DG mitochondria and phosphorylates GLS1 in vitro. Cell death was dose dependently increased when GLS1 was inhibited by BPTA while inhibition of mitochondrial pyruvate carrier (MPC) attenuated cell death in NMDA-challenged OHC. Fumarate and malate were increased after IR 1h in CA2-4,DG and this was reversed by βIIV5-3 what correlated with GLS1 activity increases and earlier showed elevation of neuronal death (Krupska et al., 2017). The present study illustrates that CA2-4,DG resistance to ischemic episode at least partially rely on glutamine and glutamate utilization in mitochondria as a source of carbon to tricarboxylic acid cycle. This phenomenon depends on modulation of GLS1 activity by PKCβII and remodeling of MPC: all these do not occur in ischemia-vulnerable CA1.
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10
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Cuesta-Astroz Y, Gischkow Rucatti G, Murgas L, SanMartín CD, Sanhueza M, Martin AJM. Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. Front Genet 2021; 12:649764. [PMID: 34394179 PMCID: PMC8355599 DOI: 10.3389/fgene.2021.649764] [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: 01/05/2021] [Accepted: 04/30/2021] [Indexed: 01/12/2023] Open
Abstract
Gene Regulatory Networks (GRNs) allow the study of regulation of gene expression of whole genomes. Among the most relevant advantages of using networks to depict this key process, there is the visual representation of large amounts of information and the application of graph theory to generate new knowledge. Nonetheless, despite the many uses of GRNs, it is still difficult and expensive to assign Transcription Factors (TFs) to the regulation of specific genes. ChIP-Seq allows the determination of TF Binding Sites (TFBSs) over whole genomes, but it is still an expensive technique that can only be applied one TF at a time and requires replicates to reduce its noise. Once TFBSs are determined, the assignment of each TF and its binding sites to the regulation of specific genes is not trivial, and it is often performed by carrying out site-specific experiments that are unfeasible to perform in all possible binding sites. Here, we addressed these relevant issues with a two-step methodology using Drosophila melanogaster as a case study. First, our protocol starts by gathering all transcription factor binding sites (TFBSs) determined with ChIP-Seq experiments available at ENCODE and FlyBase. Then each TFBS is used to assign TFs to the regulation of likely target genes based on the TFBS proximity to the transcription start site of all genes. In the final step, to try to select the most likely regulatory TF from those previously assigned to each gene, we employ GENIE3, a random forest-based method, and more than 9,000 RNA-seq experiments from D. melanogaster. Following, we employed known TF protein-protein interactions to estimate the feasibility of regulatory events in our filtered networks. Finally, we show how known interactions between co-regulatory TFs of each gene increase after the second step of our approach, and thus, the consistency of the TF-gene assignment. Also, we employed our methodology to create a network centered on the Drosophila melanogaster gene Hr96 to demonstrate the role of this transcription factor on mitochondrial gene regulation.
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Affiliation(s)
- Yesid Cuesta-Astroz
- Colombian Institute of Tropical Medicine, CES University, Medellin, Colombia
| | | | - Leandro Murgas
- Laboratorio de Biologia de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Carol D SanMartín
- Departamento de Neurología y Neurocirugía, Hospital Clínico Universidad de Chile, Santiago, Chile.,Centro de Investigacíon Clínica Avanzada (CICA), Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Mario Sanhueza
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Alberto J M Martin
- Laboratorio de Biologia de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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11
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Anti-Warburg Effect of Melatonin: A Proposed Mechanism to Explain its Inhibition of Multiple Diseases. Int J Mol Sci 2021; 22:ijms22020764. [PMID: 33466614 PMCID: PMC7828708 DOI: 10.3390/ijms22020764] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Glucose is an essential nutrient for every cell but its metabolic fate depends on cellular phenotype. Normally, the product of cytosolic glycolysis, pyruvate, is transported into mitochondria and irreversibly converted to acetyl coenzyme A by pyruvate dehydrogenase complex (PDC). In some pathological cells, however, pyruvate transport into the mitochondria is blocked due to the inhibition of PDC by pyruvate dehydrogenase kinase. This altered metabolism is referred to as aerobic glycolysis (Warburg effect) and is common in solid tumors and in other pathological cells. Switching from mitochondrial oxidative phosphorylation to aerobic glycolysis provides diseased cells with advantages because of the rapid production of ATP and the activation of pentose phosphate pathway (PPP) which provides nucleotides required for elevated cellular metabolism. Molecules, called glycolytics, inhibit aerobic glycolysis and convert cells to a healthier phenotype. Glycolytics often function by inhibiting hypoxia-inducible factor-1α leading to PDC disinhibition allowing for intramitochondrial conversion of pyruvate into acetyl coenzyme A. Melatonin is a glycolytic which converts diseased cells to the healthier phenotype. Herein we propose that melatonin's function as a glycolytic explains its actions in inhibiting a variety of diseases. Thus, the common denominator is melatonin's action in switching the metabolic phenotype of cells.
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12
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Zhu H, Wan H, Wu L, Li Q, Liu S, Duan S, Huang Z, Zhang C, Zhang B, Xing C, Yuan Y. Mitochondrial pyruvate carrier: a potential target for diabetic nephropathy. BMC Nephrol 2020; 21:274. [PMID: 32664896 PMCID: PMC7362444 DOI: 10.1186/s12882-020-01931-5] [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: 03/10/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Background Mitochondrial dysfunction contributes to the pathogenesis of diabetic nephropathy (DN). Mitochondrial pyruvate carrier 1 (MPC1) and mitochondrial pyruvate carrier 2 (MPC2) play a bottleneck role in the transport of pyruvate into mitochondrial across the mitochondrial inner membrane. A previous study showed that increasing mitochondrial pyruvate carrier content might ameliorate diabetic kidney disease in db/db mice. However, the expression status of MPC1 and MPC2 in patients with DN is unclear. Methods Patients with primary glomerulonephropathy (PGN, n = 30), PGN with diabetes mellitus (PGN-DM, n = 30) and diabetic nephropathy (DN, n = 30) were included. MPC1 and MPC2 protein levels were examined by immunohistochemistry. The expression of MPC in different groups was evaluated by the Kruskal-Wallis test. Spearman’s rank correlation was performed for correlation analysis between MPC levels and clinical factors. Results Both MPC1 and MPC2 were localized in renal tubules. Levels of MPC1 and MPC2 were lower in DN patients than in PGN patients and in PGN patients with DM, whereas there were no differences in MPC1 and MPC2 levels among DN stage II to stage IV. Moreover, both MPC1 and MPC2 levels were significantly correlated with serum creatinine, BUN and eGFR in patients with DN, whereas no analogous trend was observed in nondiabetic kidney disease. Conclusions Our study indicated that MPC localized in renal tubules, which were significantly decreased in DN. MPC was associated with clinical features, especially those representing renal functions.
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Affiliation(s)
- Huanhuan Zhu
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Huiting Wan
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Lin Wu
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Qing Li
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Simeng Liu
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Suyan Duan
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Zhimin Huang
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Chengning Zhang
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Bo Zhang
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China
| | - Changying Xing
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China.
| | - Yanggang Yuan
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, P. R. of China.
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