1
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Gelová Z, Ingles-Prieto A, Bohstedt T, Frommelt F, Chi G, Chang YN, Garcia J, Wolf G, Azzollini L, Tremolada S, Scacioc A, Hansen JS, Serrano I, Droce A, Bernal JC, Burgess-Brown NA, Carpenter EP, Dürr KL, Kristensen P, Geertsma ER, Štefanić S, Scarabottolo L, Wiedmer T, Puetter V, Sauer DB, Superti-Furga G. Protein Binder Toolbox for Studies of Solute Carrier Transporters. J Mol Biol 2024; 436:168665. [PMID: 38878854 DOI: 10.1016/j.jmb.2024.168665] [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: 03/05/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Transporters of the solute carrier superfamily (SLCs) are responsible for the transmembrane traffic of the majority of chemical substances in cells and tissues and are therefore of fundamental biological importance. As is often the case with membrane proteins that can be heavily glycosylated, a lack of reliable high-affinity binders hinders their functional analysis. Purifying and reconstituting transmembrane proteins in their lipidic environments remains challenging and standard approaches to generate binders for multi-transmembrane proteins, such as SLCs, channels or G protein-coupled receptors (GPCRs) are lacking. While generating protein binders to 27 SLCs, we produced full length protein or cell lines as input material for binder generation by selected binder generation platforms. As a result, we obtained 525 binders for 22 SLCs. We validated the binders with a cell-based validation workflow using immunofluorescent and immunoprecipitation methods to process all obtained binders. Finally, we demonstrated the potential applications of the binders that passed our validation pipeline in structural, biochemical, and biological applications using the exemplary protein SLC12A6, an ion transporter relevant in human disease. With this work, we were able to generate easily renewable and highly specific binders against SLCs, which will greatly facilitate the study of this neglected protein family. We hope that the process will serve as blueprint for the generation of binders against the entire superfamily of SLC transporters.
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Affiliation(s)
- Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julio Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Andreea Scacioc
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aida Droce
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Saša Štefanić
- Nanobody Service Facility, University of Zurich, AgroVet-Strickhof, Eschikon, Switzerland
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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2
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Redeker KEM, Brockmöller J. Several orphan solute carriers functionally identified as organic cation transporters: Substrates specificity compared with known cation transporters. J Biol Chem 2024; 300:107629. [PMID: 39098524 PMCID: PMC11406361 DOI: 10.1016/j.jbc.2024.107629] [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: 05/29/2024] [Revised: 07/10/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
Organic cations comprise a significant part of medically relevant drugs and endogenous substances. Such substances need organic cation transporters for efficient transfer via cell membranes. However, the membrane transporters of most natural or synthetic organic cations are still unknown. To identify these transporters, genes of 10 known OCTs and 18 orphan solute carriers (SLC) were overexpressed in HEK293 cells and characterized concerning their transport activities with a broad spectrum of low molecular weight substances emphasizing organic cations. Several SLC35 transporters and SLC38A10 significantly enhanced the transport of numerous relatively hydrophobic organic cations. Significant organic cation transport activities have been found in gene families classified as transporters of other substance classes. For instance, SLC35G3 and SLC38A10 significantly accelerated the uptake of several cations, such as clonidine, 3,4-methylenedioxymethamphetamine, and nicotine, which are known as substrates of a thus far genetically unidentified proton/organic cation antiporter. The transporters SLC35G4 and SLC35F5 stood out by their significantly increased choline uptake, and several other SLC transported choline together with a broader spectrum of organic cations. Overall, there are many more polyspecific organic cation transporters than previously estimated. Several transporters had one predominant substrate but accepted some other cationic substrates, and others showed no particular preference for one substrate but transported several organic cations. The role of these transporters in biology and drug therapy remains to be elucidated.
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Affiliation(s)
- Kyra-Elisa Maria Redeker
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany.
| | - Jürgen Brockmöller
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany
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3
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Patil S, Borisov O, Scherer N, Wirth C, Schlosser P, Wuttke M, Ehret S, Hannibal L, Eckardt KU, Hunte C, Neubauer B, Köttgen A, Köttgen M. The membrane transporter SLC25A48 enables transport of choline into human mitochondria. Kidney Int 2024:S0085-2538(24)00526-X. [PMID: 39084256 DOI: 10.1016/j.kint.2024.06.022] [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: 12/03/2023] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024]
Abstract
Choline has important physiological functions as a precursor for essential cell components, signaling molecules, phospholipids, and the neurotransmitter acetylcholine. Choline is a water-soluble charged molecule requiring transport proteins to cross biological membranes. Although transporters continue to be identified, membrane transport of choline is incompletely understood and knowledge about choline transport into intracellular organelles such as mitochondria remains limited. Here we show that SLC25A48 imports choline into human mitochondria. Human loss-of-function mutations in SLC25A48 show impaired choline transport into mitochondria and are associated with elevated urine and plasma choline levels. Thus, our studies may have implications for understanding and treating conditions related to choline metabolism.
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Affiliation(s)
- Suraj Patil
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Oleg Borisov
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Nora Scherer
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Christophe Wirth
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Sandra Ehret
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Luciana Hannibal
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; BIOSS-Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Björn Neubauer
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Michael Köttgen
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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4
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Colson C, Wang Y, Atherton J, Su X. SLC45A4 encodes a mitochondrial putrescine transporter that promotes GABA de novo synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604788. [PMID: 39091866 PMCID: PMC11291067 DOI: 10.1101/2024.07.23.604788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We developed a metabolomic-transcriptomic association analysis, and we found that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrated that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the mitochondrial membrane to facilitate GABA production. Taken together, our results revealed a new biochemical mechanism where SLC45A4 controls GABA production.
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5
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Digles D, Ingles-Prieto A, Dvorak V, Mocking TAM, Goldmann U, Garofoli A, Homan EJ, Di Silvio A, Azzollini L, Sassone F, Fogazza M, Bärenz F, Pommereau A, Zuschlag Y, Ooms JF, Tranberg-Jensen J, Hansen JS, Stanka J, Sijben HJ, Batoulis H, Bender E, Martini R, IJzerman AP, Sauer DB, Heitman LH, Manolova V, Reinhardt J, Ehrmann A, Leippe P, Ecker GF, Huber KVM, Licher T, Scarabottolo L, Wiedmer T, Superti-Furga G. Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily. Front Pharmacol 2024; 15:1401599. [PMID: 39050757 PMCID: PMC11267547 DOI: 10.3389/fphar.2024.1401599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024] Open
Abstract
With over 450 genes, solute carriers (SLCs) constitute the largest transporter superfamily responsible for the uptake and efflux of nutrients, metabolites, and xenobiotics in human cells. SLCs are associated with a wide variety of human diseases, including cancer, diabetes, and metabolic and neurological disorders. They represent an important therapeutic target class that remains only partly exploited as therapeutics that target SLCs are scarce. Additionally, many small molecules reported in the literature to target SLCs are poorly characterized. Both features may be due to the difficulty of developing SLC transport assays that fulfill the quality criteria for high-throughput screening. Here, we report one of the main limitations hampering assay development within the RESOLUTE consortium: the lack of a resource providing high-quality information on SLC tool compounds. To address this, we provide a systematic annotation of tool compounds targeting SLCs. We first provide an overview on RESOLUTE assays. Next, we present a list of SLC-targeting compounds collected from the literature and public databases; we found that most data sources lacked specificity data. Finally, we report on experimental tests of 19 selected compounds against a panel of 13 SLCs from seven different families. Except for a few inhibitors, which were active on unrelated SLCs, the tested inhibitors demonstrated high selectivity for their reported targets. To make this knowledge easily accessible to the scientific community, we created an interactive dashboard displaying the collected data in the RESOLUTE web portal (https://re-solute.eu). We anticipate that our open-access resources on assays and compounds will support the development of future drug discovery campaigns for SLCs.
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Affiliation(s)
- Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tamara A. M. Mocking
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Garofoli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Evert J. Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | - Felix Bärenz
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | - Antje Pommereau
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | - Yasmin Zuschlag
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | - Jasper F. Ooms
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Jeppe Tranberg-Jensen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jesper S. Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Josefina Stanka
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Helena Batoulis
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Eckhard Bender
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Riccardo Martini
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - David B. Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | - Alexander Ehrmann
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Kilian V. M. Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Thomas Licher
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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6
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Hushmandi K, Einollahi B, Saadat SH, Lee EHC, Farani MR, Okina E, Huh YS, Nabavi N, Salimimoghadam S, Kumar AP. Amino acid transporters within the solute carrier superfamily: Underappreciated proteins and novel opportunities for cancer therapy. Mol Metab 2024; 84:101952. [PMID: 38705513 PMCID: PMC11112377 DOI: 10.1016/j.molmet.2024.101952] [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: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Solute carrier (SLC) transporters, a diverse family of membrane proteins, are instrumental in orchestrating the intake and efflux of nutrients including amino acids, vitamins, ions, nutrients, etc, across cell membranes. This dynamic process is critical for sustaining the metabolic demands of cancer cells, promoting their survival, proliferation, and adaptation to the tumor microenvironment (TME). Amino acids are fundamental building blocks of cells and play essential roles in protein synthesis, nutrient sensing, and oncogenic signaling pathways. As key transporters of amino acids, SLCs have emerged as crucial players in maintaining cellular amino acid homeostasis, and their dysregulation is implicated in various cancer types. Thus, understanding the intricate connections between amino acids, SLCs, and cancer is pivotal for unraveling novel therapeutic targets and strategies. SCOPE OF REVIEW In this review, we delve into the significant impact of amino acid carriers of the SLCs family on the growth and progression of cancer and explore the current state of knowledge in this field, shedding light on the molecular mechanisms that underlie these relationships and highlighting potential avenues for future research and clinical interventions. MAJOR CONCLUSIONS Amino acids transportation by SLCs plays a critical role in tumor progression. However, some studies revealed the tumor suppressor function of SLCs. Although several studies evaluated the function of SLC7A11 and SLC1A5, the role of some SLC proteins in cancer is not studied well. To exert their functions, SLCs mediate metabolic rewiring, regulate the maintenance of redox balance, affect main oncogenic pathways, regulate amino acids bioavailability within the TME, and alter the sensitivity of cancer cells to therapeutics. However, different therapeutic methods that prevent the function of SLCs were able to inhibit tumor progression. This comprehensive review provides insights into a rapidly evolving area of cancer biology by focusing on amino acids and their transporters within the SLC superfamily.
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Affiliation(s)
- Kiavash Hushmandi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Behzad Einollahi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Hassan Saadat
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - E Hui Clarissa Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Marzieh Ramezani Farani
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Elena Okina
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yun Suk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6, Vancouver, BC, Canada
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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7
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Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nat Commun 2024; 15:4380. [PMID: 38782905 PMCID: PMC11116522 DOI: 10.1038/s41467-024-48569-7] [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: 08/14/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane. Cells expressing great ape SLC22A10 orthologs exhibit significant accumulation of estradiol-17β-glucuronide, unlike those expressing human SLC22A10. Sequence alignments reveal a proline at position 220 in humans, which is a leucine in great apes. Replacing proline with leucine in SLC22A10-P220L restores plasma membrane localization and uptake function. Neanderthal and Denisovan genomes show proline at position 220, akin to modern humans, indicating functional loss during hominin evolution. Human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220, while in great apes, its orthologs transport sex steroid conjugates. Characterizing SLC22A10 across species sheds light on its biological role, influencing organism development and steroid homeostasis.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Luis Ferrández-Peral
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pol Alentorn-Moron
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352, Copenhagen, Denmark
| | - Merve Ceylan
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Virginia M Artegoitia
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA, 95616, USA
| | - Giovanni Lara
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Jacques Dainat
- Joint Research Unit for Infectious Diseases and Vectors Ecology Genetics Evolution and Control (MIVEGEC), University of Montpellier, French National Center for Scientific Research (CNRS 5290), French National Research Institute for Sustainable Development (IRD 224), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, US
| | - Colin M Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Finn D Wolfreys
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - John A Capra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - John W Newman
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA, 95616, USA
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG, Centro Nacional de Analisis Genomico, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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8
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Chidley C, Darnell AM, Gaudio BL, Lien EC, Barbeau AM, Vander Heiden MG, Sorger PK. A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments. Nat Cell Biol 2024; 26:825-838. [PMID: 38605144 PMCID: PMC11098743 DOI: 10.1038/s41556-024-01402-1] [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: 05/23/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Blocking the import of nutrients essential for cancer cell proliferation represents a therapeutic opportunity, but it is unclear which transporters to target. Here we report a CRISPR interference/activation screening platform to systematically interrogate the contribution of nutrient transporters to support cancer cell proliferation in environments ranging from standard culture media to tumours. We applied this platform to identify the transporters of amino acids in leukaemia cells and found that amino acid transport involves high bidirectional flux dependent on the microenvironment composition. While investigating the role of transporters in cystine starved cells, we uncovered a role for serotonin uptake in preventing ferroptosis. Finally, we identified transporters essential for cell proliferation in subcutaneous tumours and found that levels of glucose and amino acids can restrain proliferation in that environment. This study establishes a framework for systematically identifying critical cellular nutrient transporters, characterizing their function and exploring how the tumour microenvironment impacts cancer metabolism.
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Affiliation(s)
- Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin L Gaudio
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Evan C Lien
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna M Barbeau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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9
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White B, Swietach P. What can we learn about acid-base transporters in cancer from studying somatic mutations in their genes? Pflugers Arch 2024; 476:673-688. [PMID: 37999800 PMCID: PMC11006749 DOI: 10.1007/s00424-023-02876-y] [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: 09/25/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Acidosis is a chemical signature of the tumour microenvironment that challenges intracellular pH homeostasis. The orchestrated activity of acid-base transporters of the solute-linked carrier (SLC) family is critical for removing the end-products of fermentative metabolism (lactate/H+) and maintaining a favourably alkaline cytoplasm. Given the critical role of pH homeostasis in enabling cellular activities, mutations in relevant SLC genes may impact the oncogenic process, emerging as negatively or positively selected, or as driver or passenger mutations. To address this, we performed a pan-cancer analysis of The Cancer Genome Atlas simple nucleotide variation data for acid/base-transporting SLCs (ABT-SLCs). Somatic mutation patterns of monocarboxylate transporters (MCTs) were consistent with their proposed essentiality in facilitating lactate/H+ efflux. Among all cancers, tumours of uterine corpus endometrial cancer carried more ABT-SLC somatic mutations than expected from median tumour mutation burden. Among these, somatic mutations in SLC4A3 had features consistent with meaningful consequences on cellular fitness. Definitive evidence for ABT-SLCs as 'cancer essential' or 'driver genes' will have to consider microenvironmental context in genomic sequencing because bulk approaches are insensitive to pH heterogeneity within tumours. Moreover, genomic analyses must be validated with phenotypic outcomes (i.e. SLC-carried flux) to appreciate the opportunities for targeting acid-base transport in cancers.
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Affiliation(s)
- Bobby White
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
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10
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Gorostiola González M, Rakers PRJ, Jespers W, IJzerman AP, Heitman LH, van Westen GJP. Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities. Int J Mol Sci 2024; 25:3698. [PMID: 38612509 PMCID: PMC11011372 DOI: 10.3390/ijms25073698] [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: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets.
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Affiliation(s)
- Marina Gorostiola González
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
| | - Pepijn R. J. Rakers
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
| | - Willem Jespers
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
| | - Adriaan P. IJzerman
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
| | - Laura H. Heitman
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
| | - Gerard J. P. van Westen
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
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11
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Boytsov D, Madej GM, Horn G, Blaha N, Köcher T, Sitte HH, Siekhaus D, Ziegler C, Sandtner W, Roblek M. Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Proc Natl Acad Sci U S A 2024; 121:e2319686121. [PMID: 38507452 PMCID: PMC10990142 DOI: 10.1073/pnas.2319686121] [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: 11/10/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Orphan solute carrier (SLC) represents a group of membrane transporters whose exact functions and substrate specificities are not known. Elucidating the function and regulation of orphan SLC transporters is not only crucial for advancing our knowledge of cellular and molecular biology but can potentially lead to the development of new therapeutic strategies. Here, we provide evidence for the biological function of a ubiquitous orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing Protein 1 (MFSD1), which has remained phylogenetically unassigned. Targeted metabolomics revealed that dipeptides containing either lysine or arginine residues accumulate in lysosomes of cells lacking MFSD1. Whole-cell patch-clamp electrophysiological recordings of HEK293-cells expressing MFSD1 on the cell surface displayed transport affinities for positively charged dipeptides in the lower mM range, while dipeptides that carry a negative net charge were not transported. This was also true for single amino acids and tripeptides, which MFSD1 failed to transport. Our results identify MFSD1 as a highly selective lysosomal lysine/arginine/histidine-containing dipeptide exporter, which functions as a uniporter.
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Affiliation(s)
- Danila Boytsov
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
| | - Gregor M. Madej
- Department of Biophysics II/Structural Biology, University of Regensburg, RegensburgDE-93053, Germany
| | - Georg Horn
- Department of Biophysics II/Structural Biology, University of Regensburg, RegensburgDE-93053, Germany
| | - Nadine Blaha
- Vienna BioCenter Core Facilities, Metabolomics, Vienna BioCenter, ViennaAT-1030, Austria
| | - Thomas Köcher
- Vienna BioCenter Core Facilities, Metabolomics, Vienna BioCenter, ViennaAT-1030, Austria
| | - Harald H. Sitte
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
- Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, AmmanJO-19328, Jordan
- Center for Addiction Research and Science, Medical University of Vienna, ViennaAT-1090, Austria
| | - Daria Siekhaus
- Institute of Science and Technology Austria, KlosterneuburgAT-3400, Austria
| | - Christine Ziegler
- Department of Biophysics II/Structural Biology, University of Regensburg, RegensburgDE-93053, Germany
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
| | - Marko Roblek
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
- Institute of Science and Technology Austria, KlosterneuburgAT-3400, Austria
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12
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Koe JC, Parker SJ. The posttranslational regulation of amino acid transporters is critical for their function in the tumor microenvironment. Curr Opin Biotechnol 2024; 85:103022. [PMID: 38056204 DOI: 10.1016/j.copbio.2023.103022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 12/08/2023]
Abstract
Amino acid transporters (AATs) facilitate nutrient uptake and nutrient exchange between cancer and stromal cells. The posttranslational modification (PTM) of transporters is an important mechanism that tumor-associated cells use to dynamically regulate their function and stability in response to microenvironmental cues. In this review, we summarize recent findings that demonstrate the significance of N-glycosylation, phosphorylation, and ubiquitylation for the function of AATs. We also highlight powerful approaches that hijack the PTM machinery that could be used as therapeutics or tools to modulate transporter activity.
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Affiliation(s)
- Jessica C Koe
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Seth J Parker
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada; British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.
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13
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Grandits M, Ecker GF. Ligand- and Structure-based Approaches for Transmembrane Transporter Modeling. Curr Drug Res Rev 2024; 16:81-93. [PMID: 37157206 PMCID: PMC11340286 DOI: 10.2174/2589977515666230508123041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 05/10/2023]
Abstract
The study of transporter proteins is key to understanding the mechanism behind multidrug resistance and drug-drug interactions causing severe side effects. While ATP-binding transporters are well-studied, solute carriers illustrate an understudied family with a high number of orphan proteins. To study these transporters, in silico methods can be used to shed light on the basic molecular machinery by studying protein-ligand interactions. Nowadays, computational methods are an integral part of the drug discovery and development process. In this short review, computational approaches, such as machine learning, are discussed, which try to tackle interactions between transport proteins and certain compounds to locate target proteins. Furthermore, a few cases of selected members of the ATP binding transporter and solute carrier family are covered, which are of high interest in clinical drug interaction studies, especially for regulatory agencies. The strengths and limitations of ligand-based and structure-based methods are discussed to highlight their applicability for different studies. Furthermore, the combination of multiple approaches can improve the information obtained to find crucial amino acids that explain important interactions of protein-ligand complexes in more detail. This allows the design of drug candidates with increased activity towards a target protein, which further helps to support future synthetic efforts.
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Affiliation(s)
- Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
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14
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Kondo S, Miyake M. Simultaneous Prediction Method for Intestinal Absorption and Metabolism Using the Mini-Ussing Chamber System. Pharmaceutics 2023; 15:2732. [PMID: 38140073 PMCID: PMC10747201 DOI: 10.3390/pharmaceutics15122732] [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: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Many evaluation tools for predicting human absorption are well-known for using cultured cell lines such as Caco-2, MDCK, and so on. Since the combinatorial chemistry and high throughput screening system, pharmacological assay, and pharmaceutical profiling assay are mainstays of drug development, PAMPA has been used to evaluate human drug absorption. In addition, cultured cell lines from iPS cells have been attracting attention because they morphologically resemble human intestinal tissues. In this review, we used human intestinal tissues to estimate human intestinal absorption and metabolism. The Ussing chamber uses human intestinal tissues to directly assay a drug candidate's permeability and determine the electrophysiological parameters such as potential differences (PD), short circuit current (Isc), and resistance (R). Thus, it is an attractive tool for elucidating human intestinal permeability and metabolism. We have presented a novel prediction method for intestinal absorption and metabolism by utilizing a mini-Ussing chamber using human intestinal tissues and animal intestinal tissues, based on the transport index (TI). The TI value was calculated by taking the change in drug concentrations on the apical side due to precipitation and the total amounts accumulated in the tissue (Tcorr) and transported to the basal side (Xcorr). The drug absorbability in rank order, as well as the fraction of dose absorbed (Fa) in humans, was predicted, and the intestinal metabolism of dogs and rats was also predicted, although it was not quantitative. However, the metabolites formation index (MFI) values, which are included in the TI values, can predict the evaluation of intestinal metabolism and absorption by using ketoconazole. Therefore, the mini-Ussing chamber, equipped with human and animal intestinal tissues, would be an ultimate method to predict intestinal absorption and metabolism simultaneously.
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Affiliation(s)
- Satoshi Kondo
- Department of Drug Metabolism and Pharmacokinetics, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 460-10 Kagasuno Kawauchi-cho, Tokushima 771-0192, Japan;
- Department of Drug Safety Research, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 460-10 Kagasuno Kawauchi-cho, Tokushima 771-0192, Japan
| | - Masateru Miyake
- Business Integrity and External Affairs, Otsuka Pharmaceutical Co., Ltd., 2-16-4 Konan, Minato-ku, Tokyo 108-8242, Japan
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15
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Alam S, Doherty E, Ortega-Prieto P, Arizanova J, Fets L. Membrane transporters in cell physiology, cancer metabolism and drug response. Dis Model Mech 2023; 16:dmm050404. [PMID: 38037877 PMCID: PMC10695176 DOI: 10.1242/dmm.050404] [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] [Indexed: 12/02/2023] Open
Abstract
By controlling the passage of small molecules across lipid bilayers, membrane transporters influence not only the uptake and efflux of nutrients, but also the metabolic state of the cell. With more than 450 members, the Solute Carriers (SLCs) are the largest transporter super-family, clustering into families with different substrate specificities and regulatory properties. Cells of different types are, therefore, able to tailor their transporter expression signatures depending on their metabolic requirements, and the physiological importance of these proteins is illustrated by their mis-regulation in a number of disease states. In cancer, transporter expression is heterogeneous, and the SLC family has been shown to facilitate the accumulation of biomass, influence redox homeostasis, and also mediate metabolic crosstalk with other cell types within the tumour microenvironment. This Review explores the roles of membrane transporters in physiological and malignant settings, and how these roles can affect drug response, through either indirect modulation of sensitivity or the direct transport of small-molecule therapeutic compounds into cells.
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Affiliation(s)
- Sara Alam
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Emily Doherty
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Paula Ortega-Prieto
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Julia Arizanova
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Louise Fets
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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16
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Grotehans N, McGarry L, Nolte H, Xavier V, Kroker M, Narbona‐Pérez ÁJ, Deshwal S, Giavalisco P, Langer T, MacVicar T. Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression. EMBO J 2023; 42:e113256. [PMID: 37439264 PMCID: PMC10505918 DOI: 10.15252/embj.2022113256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023] Open
Abstract
Replication of the mitochondrial genome and expression of the genes it encodes both depend on a sufficient supply of nucleotides to mitochondria. Accordingly, dysregulated nucleotide metabolism not only destabilises the mitochondrial genome, but also affects its transcription. Here, we report that a mitochondrial nucleoside diphosphate kinase, NME6, supplies mitochondria with pyrimidine ribonucleotides that are necessary for the transcription of mitochondrial genes. Loss of NME6 function leads to the depletion of mitochondrial transcripts, as well as destabilisation of the electron transport chain and impaired oxidative phosphorylation. These deficiencies are rescued by an exogenous supply of pyrimidine ribonucleosides. Moreover, NME6 is required for the maintenance of mitochondrial DNA when the access to cytosolic pyrimidine deoxyribonucleotides is limited. Our results therefore reveal an important role for ribonucleotide salvage in mitochondrial gene expression.
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Affiliation(s)
- Nils Grotehans
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Hendrik Nolte
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Moritz Kroker
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Soni Deshwal
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Thomas Langer
- Max Planck Institute for Biology of AgeingCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
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17
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Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. RESEARCH SQUARE 2023:rs.3.rs-3263845. [PMID: 37790518 PMCID: PMC10543398 DOI: 10.21203/rs.3.rs-3263845/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | | | - Pol Alentorn
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain; Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Merve Ceylan
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, P.O. Box 580, 75123, Uppsala, Sweden
| | - Megan L. Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Niklas Handin
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, P.O. Box 580, 75123, Uppsala, Sweden
| | - Virginia M. Artegoitia
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA 95616, USA
| | - Giovanni Lara
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Jacques Dainat
- Joint Research Unit for Infectious Diseases and Vectors Ecology Genetics Evolution and Control (MIVEGEC), University of Montpellier, French National Center for Scientific Research (CNRS 5290), French National Research Institute for Sustainable Development (IRD 224), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, UCSF Box 0775 1700 4th St, University of California, San Francisco, San Francisco, CA 94158, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF Box 2880 600 16th St, San Francisco, CA 94143, United States; Quantitative Biosciences Institute (QBI), University of California, San Francisco, 1700 4th St, San Francisco, CA, United States
| | - Colin M. Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - John A. Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Per Artursson
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, P.O. Box 580, 75123, Uppsala, Sweden
| | - John W. Newman
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA 95616, USA; Department of Nutrition, University of California, Davis, Davis, CA 95616, USA; UC Davis West Coast Metabolomics Center, Davis, CA 95616, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain; Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG, Centro Nacional de Analisis Genomico, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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18
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Schlessinger A, Zatorski N, Hutchinson K, Colas C. Targeting SLC transporters: small molecules as modulators and therapeutic opportunities. Trends Biochem Sci 2023; 48:801-814. [PMID: 37355450 PMCID: PMC10525040 DOI: 10.1016/j.tibs.2023.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023]
Abstract
Solute carrier (SLCs) transporters mediate the transport of a broad range of solutes across biological membranes. Dysregulation of SLCs has been associated with various pathologies, including metabolic and neurological disorders, as well as cancer and rare diseases. SLCs are therefore emerging as key targets for therapeutic intervention with several recently approved drugs targeting these proteins. Unlocking this large and complex group of proteins is essential to identifying unknown SLC targets and developing next-generation SLC therapeutics. Recent progress in experimental and computational techniques has significantly advanced SLC research, including drug discovery. Here, we review emerging topics in therapeutic discovery of SLCs, focusing on state-of-the-art approaches in structural, chemical, and computational biology, and discuss current challenges in transporter drug discovery.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Nicole Zatorski
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Colas
- University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria.
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19
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Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552553. [PMID: 37609337 PMCID: PMC10441401 DOI: 10.1101/2023.08.08.552553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | | | - Pol Alentorn
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain; Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Merve Ceylan
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, P.O. Box 580, 75123, Uppsala, Sweden
| | - Megan L. Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Niklas Handin
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, P.O. Box 580, 75123, Uppsala, Sweden
| | - Virginia M. Artegoitia
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA 95616, USA
| | - Giovanni Lara
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Jacques Dainat
- Joint Research Unit for Infectious Diseases and Vectors Ecology Genetics Evolution and Control (MIVEGEC), University of Montpellier, French National Center for Scientific Research (CNRS 5290), French National Research Institute for Sustainable Development (IRD 224), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, UCSF Box 0775 1700 4th St, University of California, San Francisco, San Francisco, CA 94158, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF Box 2880 600 16th St, San Francisco, CA 94143, United States; Quantitative Biosciences Institute (QBI), University of California, San Francisco, 1700 4th St, San Francisco, CA, United States
| | - Colin M. Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - John A. Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Per Artursson
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, P.O. Box 580, 75123, Uppsala, Sweden
| | - John W. Newman
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA 95616, USA; Department of Nutrition, University of California, Davis, Davis, CA 95616, USA; UC Davis West Coast Metabolomics Center, Davis, CA 95616, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain; Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG, Centro Nacional de Analisis Genomico, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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20
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Dvorak V, Superti-Furga G. Structural and functional annotation of solute carrier transporters: implication for drug discovery. Expert Opin Drug Discov 2023; 18:1099-1115. [PMID: 37563933 DOI: 10.1080/17460441.2023.2244760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
INTRODUCTION Solute carriers (SLCs) represent the largest group of membrane transporters in the human genome. They play a central role in controlling the compartmentalization of metabolism and most of this superfamily is linked to human disease. Despite being in general considered druggable and attractive therapeutic targets, many SLCs remain poorly annotated, both functionally and structurally. AREAS COVERED The aim of this review is to provide an overview of functional and structural parameters of SLCs that play important roles in their druggability. To do this, the authors provide an overview of experimentally solved structures of human SLCs, with emphasis on structures solved in complex with chemical modulators. From the functional annotations, the authors focus on SLC localization and SLC substrate annotations. EXPERT OPINION Recent progress in the structural and functional annotations allows to refine the SLC druggability index. Particularly the increasing number of experimentally solved structures of SLCs provides insights into mode-of-action of a significant number of chemical modulators of SLCs.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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21
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Schlosser P, Scherer N, Grundner-Culemann F, Monteiro-Martins S, Haug S, Steinbrenner I, Uluvar B, Wuttke M, Cheng Y, Ekici AB, Gyimesi G, Karoly ED, Kotsis F, Mielke J, Gomez MF, Yu B, Grams ME, Coresh J, Boerwinkle E, Köttgen M, Kronenberg F, Meiselbach H, Mohney RP, Akilesh S, Schmidts M, Hediger MA, Schultheiss UT, Eckardt KU, Oefner PJ, Sekula P, Li Y, Köttgen A. Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine. Nat Genet 2023:10.1038/s41588-023-01409-8. [PMID: 37277652 DOI: 10.1038/s41588-023-01409-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
The kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies of paired plasma and urine metabolomes may identify underlying processes. We conducted genome-wide studies of 1,916 plasma and urine metabolites and detected 1,299 significant associations. Associations with 40% of implicated metabolites would have been missed by studying plasma alone. We detected urine-specific findings that provide information about metabolite reabsorption in the kidney, such as aquaporin (AQP)-7-mediated glycerol transport, and different metabolomic footprints of kidney-expressed proteins in plasma and urine that are consistent with their localization and function, including the transporters NaDC3 (SLC13A3) and ASBT (SLC10A2). Shared genetic determinants of 7,073 metabolite-disease combinations represent a resource to better understand metabolic diseases and revealed connections of dipeptidase 1 with circulating digestive enzymes and with hypertension. Extending genetic studies of the metabolome beyond plasma yields unique insights into processes at the interface of body compartments.
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Affiliation(s)
- Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Nora Scherer
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Sara Monteiro-Martins
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefan Haug
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Burulça Uluvar
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | | | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Johanna Mielke
- Research and Early Development, Pharmaceuticals Division, Bayer AG, Wuppertal, Germany
| | - Maria F Gomez
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Lund, Sweden
| | - Bing Yu
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Morgan E Grams
- New York University Grossman School of Medicine, New York, NY, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eric Boerwinkle
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Köttgen
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Miriam Schmidts
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Freiburg University Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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22
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Stillhart C, Asteriadis A, Bocharova E, Eksteen G, Harder F, Kusch J, Tzakri T, Augustijns P, Matthys C, Vertzoni M, Weitschies W, Reppas C. The impact of advanced age on gastrointestinal characteristics that are relevant to oral drug absorption: An AGePOP review. Eur J Pharm Sci 2023; 187:106452. [PMID: 37098371 DOI: 10.1016/j.ejps.2023.106452] [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: 02/08/2023] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 04/27/2023]
Abstract
The purpose of this review is to summarize the current knowledge on three physiological determinants of oral drug absorption, i.e., gastric emptying, volumes and composition of luminal fluids, and intestinal permeability, in the advanced age population, so that potential knowledge gaps and directions for further research efforts are identified. Published data on gastric emptying rates in older people are conflicting. Also, there are significant knowledge gaps, especially on gastric motility and emptying rates of drugs and of non-caloric fluids. Compared with younger adults, volumes of luminal contents seem to be slightly smaller in older people. Our understanding on the impact of advanced age on luminal physicochemical characteristics is, at best, very limited, whereas the impact of (co)morbidities and geriatric syndromes in the advanced age population has not been addressed to date. The available literature on the effect of advanced age on intestinal permeability is limited, and should be approached with caution, primarily due to the limitations of the experimental methodologies used.
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Affiliation(s)
| | - Adam Asteriadis
- Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Ekaterina Bocharova
- Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Gabriel Eksteen
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Fritz Harder
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
| | - Jonas Kusch
- Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodora Tzakri
- Department of Biopharmaceutics and Pharmaceutical Technology, Center of Drug Absorption and Transport, University of Greifswald, Germany
| | - Patrick Augustijns
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
| | - Christophe Matthys
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium; Department of Endocrinology, University Hospitals Leuven, Leuven, Belgium
| | - Maria Vertzoni
- Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Werner Weitschies
- Department of Biopharmaceutics and Pharmaceutical Technology, Center of Drug Absorption and Transport, University of Greifswald, Germany
| | - Christos Reppas
- Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece.
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23
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Rebsamen M, Girardi E, Sedlyarov V, Scorzoni S, Papakostas K, Vollert M, Konecka J, Guertl B, Klavins K, Wiedmer T, Superti-Furga G. Gain-of-function genetic screens in human cells identify SLC transporters overcoming environmental nutrient restrictions. Life Sci Alliance 2022; 5:e202201404. [PMID: 36114003 PMCID: PMC9481932 DOI: 10.26508/lsa.202201404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
Solute carrier (SLC) transporters control fluxes of nutrients and metabolites across membranes and thereby represent a critical interface between the microenvironment and cellular and subcellular metabolism. Because of substantial functional overlap, the interplay and relative contributions of SLCs in response to environmental stresses remain poorly elucidated. To infer functional relationships between SLCs and metabolites, we developed a strategy to identify SLCs able to sustain cell viability and proliferation under growth-limiting concentrations of essential nutrients. One-by-one depletion of 13 amino acids required for cell proliferation enabled gain-of-function genetic screens using a SLC-focused CRISPR/Cas9-based transcriptional activation approach to uncover transporters relieving cells from growth-limiting metabolic bottlenecks. Among the transporters identified, we characterized the cationic amino acid transporter SLC7A3 as a gene that, when up-regulated, overcame low availability of arginine and lysine by increasing their uptake, whereas SLC7A5 was able to sustain cellular fitness upon deprivation of several neutral amino acids. Moreover, we identified metabolic compensation mediated by the glutamate/aspartate transporters SLC1A2 and SLC1A3 under glutamine-limiting conditions. Overall, this gain-of-function approach using human cells uncovered functional transporter-nutrient relationships and revealed that transport activity up-regulation may be sufficient to overcome environmental metabolic restrictions.
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Affiliation(s)
- Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefania Scorzoni
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Konstantinos Papakostas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuela Vollert
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Justyna Konecka
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Guertl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristaps Klavins
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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24
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A structure and evolutionary-based classification of solute carriers. iScience 2022; 25:105096. [PMID: 36164651 PMCID: PMC9508557 DOI: 10.1016/j.isci.2022.105096] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 09/04/2022] [Indexed: 11/22/2022] Open
Abstract
Solute carriers are an operationally defined diverse family of membrane proteins involved in the transport of nutrients, metabolites, xenobiotics, and drugs. Here, we provide an integrative classification of solute carriers by combining evolutionary information with proteome-wide structure models recently made available through the AlphaFold resource. Analyses of orthologous relations among 455 protein-coding genes currently classified as human solute carriers, over the fully sequenced genomes of 2,100 species, suggest no more than approximately 180 independent evolutionary origins. Structural comparative analyses provided further insight revealing a total of 24 structurally distinct transmembrane folds, increasing by approximately 40% the number of previously described SLC structural folds. In addition, a structural comparative analysis identified a new human solute carrier member and revealed details of noncanonical ones. Our analyses uncover new ancestral relations between solute carrier genes, provide insights into the evolution of remote homologs and a platform to test hypotheses of functional deorphanization.
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25
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Giacomini KM, Yee SW, Koleske ML, Zou L, Matsson P, Chen EC, Kroetz DL, Miller MA, Gozalpour E, Chu X. New and Emerging Research on Solute Carrier and ATP Binding Cassette Transporters in Drug Discovery and Development: Outlook From the International Transporter Consortium. Clin Pharmacol Ther 2022; 112:540-561. [PMID: 35488474 PMCID: PMC9398938 DOI: 10.1002/cpt.2627] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023]
Abstract
Enabled by a plethora of new technologies, research in membrane transporters has exploded in the past decade. The goal of this state-of-the-art article is to describe recent advances in research on membrane transporters that are particularly relevant to drug discovery and development. This review covers advances in basic, translational, and clinical research that has led to an increased understanding of membrane transporters at all levels. At the basic level, we describe the available crystal structures of membrane transporters in both the solute carrier (SLC) and ATP binding cassette superfamilies, which has been enabled by the development of cryogenic electron microscopy methods. Next, we describe new research on lysosomal and mitochondrial transporters as well as recently deorphaned transporters in the SLC superfamily. The translational section includes a summary of proteomic research, which has led to a quantitative understanding of transporter levels in various cell types and tissues and new methods to modulate transporter function, such as allosteric modulators and targeted protein degraders of transporters. The section ends with a review of the effect of the gut microbiome on modulation of transporter function followed by a presentation of 3D cell cultures, which may enable in vivo predictions of transporter function. In the clinical section, we describe new genomic and pharmacogenomic research, highlighting important polymorphisms in transporters that are clinically relevant to many drugs. Finally, we describe new clinical tools, which are becoming increasingly available to enable precision medicine, with the application of tissue-derived small extracellular vesicles and real-world biomarkers.
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Affiliation(s)
- Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Sook W. Yee
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Megan L. Koleske
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Ling Zou
- Pharmacokinetics and Drug MetabolismAmgen Inc.South San FranciscoCaliforniaUSA
| | - Pär Matsson
- Department of PharmacologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Eugene C. Chen
- Department of Drug Metabolism and PharmacokineticsGenentech, Inc.South San FranciscoCaliforniaUSA
| | - Deanna L. Kroetz
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Miles A. Miller
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Elnaz Gozalpour
- Drug Safety and MetabolismIMED Biotech UnitSafety and ADME Translational Sciences DepartmentAstraZeneca R&DCambridgeUK
| | - Xiaoyan Chu
- Department of ADME and Discovery ToxicologyMerck & Co. IncKenilworthNew JerseyUSA
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26
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Wright NJ, Lee SY. Recent advances on the inhibition of human solute carriers: Therapeutic implications and mechanistic insights. Curr Opin Struct Biol 2022; 74:102378. [PMID: 35487145 DOI: 10.1016/j.sbi.2022.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/03/2022]
Abstract
Solute carriers (SLCs) are membrane transport proteins tasked with mediating passage of hydrophilic molecules across lipid bilayers. Despite the extensive roles played in all aspects of human biology, SLCs remain vastly under-explored as therapeutic targets. In this brief review, we first discuss a few successful cases of drugs that exert their mechanisms of action through inhibition of human SLCs, and introduce select examples of human SLCs that have untapped therapeutic potential. We then highlight two recent structural studies which uncovered detailed structural mechanisms of inhibition exhibited against two different human major facilitator superfamily (MFS) transporters of clinical relevance.
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Affiliation(s)
- Nicholas J Wright
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA. https://twitter.com/@nick_rite
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
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27
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Sijben HJ, Superti-Furga G, IJzerman AP, Heitman LH. Targeting solute carriers to modulate receptor–ligand interactions. Trends Pharmacol Sci 2022; 43:358-361. [DOI: 10.1016/j.tips.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 10/19/2022]
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28
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Yee SW, Giacomini KM. Emerging Roles of the Human Solute Carrier 22 Family. Drug Metab Dispos 2021; 50:DMD-MR-2021-000702. [PMID: 34921098 PMCID: PMC9488978 DOI: 10.1124/dmd.121.000702] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/22/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022] Open
Abstract
The human Solute Carrier 22 family (SLC22), also termed the organic ion transporter family, consists of 28 distinct multi-membrane spanning proteins, which phylogenetically cluster together according to their charge specificity for organic cations (OCTs), organic anions (OATs) and organic zwitterion/cations (OCTNs). Some SLC22 family members are well characterized in terms of their substrates, transport mechanisms and expression patterns, as well as their roles in human physiology and pharmacology, whereas others remain orphans with no known ligands. Pharmacologically, SLC22 family members play major roles as determinants of the absorption and disposition of many prescription drugs, and several including the renal transporters, OCT2, OAT1 and OAT3 are targets for many clinically important drug-drug interactions. In addition, mutations in some of these transporters (SLC22A5 (OCTN2) and SLC22A12 (URAT1) lead to rare monogenic disorders. Genetic polymorphisms in SLC22 transporters have been associated with common human disease, drug response and various phenotypic traits. Three members in this family were deorphaned in very recently: SLC22A14, SLC22A15 and SLC22A24, and found to transport specific compounds such as riboflavin (SLC22A14), anti-oxidant zwitterions (SLC22A15) and steroid conjugates (SLC22A24). Their physiologic and pharmacological roles need further investigation. This review aims to summarize the substrates, expression patterns and transporter mechanisms of individual SLC22 family members and their roles in human disease and drug disposition and response. Gaps in our understanding of SLC22 family members are described. Significance Statement In recent years, three members of the SLC22 family of transporters have been deorphaned and found to play important roles in the transport of diverse solutes. New research has furthered our understanding of the mechanisms, pharmacological roles, and clinical impact of SLC22 transporters. This minireview provides overview of SLC22 family members of their physiologic and pharmacologic roles, the impact of genetic variants in the SLC22 family on disease and drug response, and summary of recent studies deorphaning SLC22 family members.
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Affiliation(s)
- Sook Wah Yee
- Bioengineering and Therapeutic Sciences, Univerity of California, San Francisco, United States
| | - Kathleen M Giacomini
- Bioengineering and Therapeutic Sciences, Univerity of California, San Francisco, United States
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29
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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30
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Pizzagalli MD, Bensimon A, Superti‐Furga G. A guide to plasma membrane solute carrier proteins. FEBS J 2021; 288:2784-2835. [PMID: 32810346 PMCID: PMC8246967 DOI: 10.1111/febs.15531] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022]
Abstract
This review aims to serve as an introduction to the solute carrier proteins (SLC) superfamily of transporter proteins and their roles in human cells. The SLC superfamily currently includes 458 transport proteins in 65 families that carry a wide variety of substances across cellular membranes. While members of this superfamily are found throughout cellular organelles, this review focuses on transporters expressed at the plasma membrane. At the cell surface, SLC proteins may be viewed as gatekeepers of the cellular milieu, dynamically responding to different metabolic states. With altered metabolism being one of the hallmarks of cancer, we also briefly review the roles that surface SLC proteins play in the development and progression of cancer through their influence on regulating metabolism and environmental conditions.
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Affiliation(s)
- Mattia D. Pizzagalli
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Giulio Superti‐Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Center for Physiology and PharmacologyMedical University of ViennaAustria
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31
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Li KC, Girardi E, Kartnig F, Grosche S, Pemovska T, Bigenzahn JW, Goldmann U, Sedlyarov V, Bensimon A, Schick S, Lin JMG, Gürtl B, Reil D, Klavins K, Kubicek S, Sdelci S, Superti-Furga G. Cell-surface SLC nucleoside transporters and purine levels modulate BRD4-dependent chromatin states. Nat Metab 2021; 3:651-664. [PMID: 33972798 PMCID: PMC7612075 DOI: 10.1038/s42255-021-00386-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
Metabolism negotiates cell-endogenous requirements of energy, nutrients and building blocks with the immediate environment to enable various processes, including growth and differentiation. While there is an increasing number of examples of crosstalk between metabolism and chromatin, few involve uptake of exogenous metabolites. Solute carriers (SLCs) represent the largest group of transporters in the human genome and are responsible for the transport of a wide variety of substrates, including nutrients and metabolites. We aimed to investigate the possible involvement of SLC-mediated solutes uptake and cellular metabolism in regulating cellular epigenetic states. Here, we perform a CRISPR-Cas9 transporter-focused genetic screen and a metabolic compound library screen for the regulation of BRD4-dependent chromatin states in human myeloid leukaemia cells. Intersection of the two orthogonal approaches reveal that loss of transporters involved with purine transport or inhibition of de novo purine synthesis lead to dysfunction of BRD4-dependent transcriptional regulation. Through mechanistic characterization of the metabolic circuitry, we elucidate the convergence of SLC-mediated purine uptake and de novo purine synthesis on BRD4-chromatin occupancy. Moreover, adenine-related metabolite supplementation effectively restores BRD4 functionality on purine impairment. Our study highlights the specific role of purine/adenine metabolism in modulating BRD4-dependent epigenetic states.
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Affiliation(s)
- Kai-Chun Li
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Enrico Girardi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sarah Grosche
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tea Pemovska
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Goldmann
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sandra Schick
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jung-Ming G Lin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Gürtl
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniela Reil
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristaps Klavins
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sara Sdelci
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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32
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Cinquetti R, Imperiali FG, Bozzaro S, Zanella D, Vacca F, Roseti C, Peracino B, Castagna M, Bossi E. Characterization of Transport Activity of SLC11 Transporters in Xenopus laevis Oocytes by Fluorophore Quenching. SLAS DISCOVERY 2021; 26:798-810. [PMID: 33825579 DOI: 10.1177/24725552211004123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Membrane proteins are involved in different physiological functions and are the target of pharmaceutical and abuse drugs. Xenopus laevis oocytes provide a powerful heterologous expression system for functional studies of these proteins. Typical experiments investigate transport using electrophysiology and radiolabeled uptake. A two-electrode voltage clamp is suitable only for electrogenic proteins, and uptake measurements require the existence of radiolabeled substrates and adequate laboratory facilities.Recently, Dictyostelium discoideum Nramp1 and NrampB were characterized using multidisciplinary approaches. NrampB showed no measurable electrogenic activity, and it was investigated in Xenopus oocytes by acquiring confocal images of the quenching of injected fluorophore calcein.This method is adequate to measure the variation in emitted fluorescence, and thus transporter activity indirectly, but requires long experimental procedures to collect statistically consistent data. Considering that optimal expression of heterologous proteins lasts for 48-72 h, a slow acquiring process requires the use of more than one batch of oocytes to complete the experiments. Here, a novel approach to measure substrate uptake is reported. Upon injection of a fluorophore, oocytes were incubated with the substrate and the transport activity measured, evaluating fluorescence quenching in a microplate reader. The technique permits the testing of tens of oocytes in different experimental conditions simultaneously, and thus the collection of significant statistical data for each batch, saving time and animals.The method was tested with different metal transporters (SLC11), DMT1, DdNramp1, and DdNrampB, and verified with the peptide transporter PepT1 (SLC15). Comparison with traditional methods (uptake, two-electrode voltage clamp) and with quenching images acquired by fluorescence microscopy confirmed its efficacy.
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Affiliation(s)
| | | | | | - Daniele Zanella
- University of Insubria, Varese, Lombardia, Italy.,The University of Alabama, Birmingham, AL, USA
| | - Francesca Vacca
- University of Insubria, Varese, Lombardia, Italy.,Italian Institute of Technology (IIT), Genova, Italy
| | | | | | | | - Elena Bossi
- University of Insubria, Varese, Lombardia, Italy
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33
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Girardi E, Agrimi G, Goldmann U, Fiume G, Lindinger S, Sedlyarov V, Srndic I, Gürtl B, Agerer B, Kartnig F, Scarcia P, Di Noia MA, Liñeiro E, Rebsamen M, Wiedmer T, Bergthaler A, Palmieri L, Superti-Furga G. Epistasis-driven identification of SLC25A51 as a regulator of human mitochondrial NAD import. Nat Commun 2020; 11:6145. [PMID: 33262325 PMCID: PMC7708531 DOI: 10.1038/s41467-020-19871-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022] Open
Abstract
About a thousand genes in the human genome encode for membrane transporters. Among these, several solute carrier proteins (SLCs), representing the largest group of transporters, are still orphan and lack functional characterization. We reasoned that assessing genetic interactions among SLCs may be an efficient way to obtain functional information allowing their deorphanization. Here we describe a network of strong genetic interactions indicating a contribution to mitochondrial respiration and redox metabolism for SLC25A51/MCART1, an uncharacterized member of the SLC25 family of transporters. Through a combination of metabolomics, genomics and genetics approaches, we demonstrate a role for SLC25A51 as enabler of mitochondrial import of NAD, showcasing the potential of genetic interaction-driven functional gene deorphanization.
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Affiliation(s)
- Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gennaro Agrimi
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giuseppe Fiume
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ismet Srndic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Gürtl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pasquale Scarcia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Maria Antonietta Di Noia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Eva Liñeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Luigi Palmieri
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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34
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Yee SW, Buitrago D, Stecula A, Ngo HX, Chien HC, Zou L, Koleske ML, Giacomini KM. Deorphaning a solute carrier 22 family member, SLC22A15, through functional genomic studies. FASEB J 2020; 34:15734-15752. [PMID: 33124720 DOI: 10.1096/fj.202001497r] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022]
Abstract
The human solute carrier 22A (SLC22A) family consists of 23 members, representing one of the largest families in the human SLC superfamily. Despite their pharmacological and physiological importance in the absorption and disposition of a range of solutes, eight SLC22A family members remain classified as orphans. In this study, we used a multifaceted approach to identify ligands of orphan SLC22A15. Ligands of SLC22A15 were proposed based on phylogenetic analysis and comparative modeling. The putative ligands were then confirmed by metabolomic screening and uptake assays in SLC22A15 transfected HEK293 cells. Metabolomic studies and transporter assays revealed that SLC22A15 prefers zwitterionic compounds over cations and anions. We identified eight zwitterions, including ergothioneine, carnitine, carnosine, gabapentin, as well as four cations, including MPP+ , thiamine, and cimetidine, as substrates of SLC22A15. Carnosine was a specific substrate of SLC22A15 among the transporters in the SLC22A family. SLC22A15 transport of several substrates was sodium-dependent and exhibited a higher Km for ergothioneine, carnitine, and carnosine compared to previously identified transporters for these ligands. This is the first study to characterize the function of SLC22A15. Our studies demonstrate that SLC22A15 may play an important role in determining the systemic and tissue levels of ergothioneine, carnosine, and other zwitterions.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Dina Buitrago
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Adrian Stecula
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Huy X Ngo
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ling Zou
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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