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Kerhoas M, Le Vée M, Carteret J, Jouan E, Tastet V, Bruyère A, Huc L, Fardel O. Inhibition of human drug transporter activities by succinate dehydrogenase inhibitors. CHEMOSPHERE 2024; 358:142122. [PMID: 38663675 DOI: 10.1016/j.chemosphere.2024.142122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/02/2024]
Abstract
Succinate dehydrogenase inhibitors (SDHIs) are widely-used fungicides, to which humans are exposed and for which putative health risks are of concern. In order to identify human molecular targets for these environmental chemicals, the interactions of 15 SDHIs with activities of main human drug transporters implicated in pharmacokinetics were investigated in vitro. 5/15 SDHIs, i.e., benzovindiflupyr, bixafen, fluxapyroxad, pydiflumetofen and sedaxane, were found to strongly reduce activity of the renal organic anion transporter (OAT) 3, in a concentration-dependent manner (with IC50 values in the 1.0-3.9 μM range), without however being substrates for OAT3. Moreover, these 5/15 SDHIs decreased the membrane transport of estrone-3 sulfate, an endogenous substrate for OAT3, and sedaxane was predicted to inhibit in vivo OAT3 activity in response to exposure to the acceptable daily intake (ADI) dose. In addition, pydiflumetofen strongly inhibited the renal organic cation transporter (OCT) 2 (IC50 = 2.0 μM) and benzovindiflupyr the efflux pump breast cancer resistance protein (BCRP) (IC50 = 3.9 μM). Other human transporters, including organic anion transporting polypeptide (OATP) 1B1 and OATP1B3 as well as multidrug and toxin extrusion protein (MATE) 1 and MATE2-K were moderately or weakly inhibited by SDHIs, whereas P-glycoprotein, multidrug resistance-associated protein (MRP), OCT1 and OAT1 activities were not or only marginally impacted. Then, some human drug transporters, especially OAT3, constitute molecular targets for SDHIs. This could have toxic consequences, notably with respect to levels of endogenous compounds and metabolites substrates for the considered transporters or to potential SDHI-drug interactions. This could therefore contribute to putative health risk of these fungicides.
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Affiliation(s)
- Marie Kerhoas
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Marc Le Vée
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Jennifer Carteret
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Elodie Jouan
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Valentin Tastet
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Arnaud Bruyère
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Laurence Huc
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France; Laboratoire Interdisciplinaire Sciences Innovations Sociétés (LISIS), INRAE/CNRS/Université Gustave Eiffel, F-Marne-La-Vallée, France
| | - Olivier Fardel
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
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Angarita-Rodríguez A, González-Giraldo Y, Rubio-Mesa JJ, Aristizábal AF, Pinzón A, González J. Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets. Int J Mol Sci 2023; 25:365. [PMID: 38203536 PMCID: PMC10778851 DOI: 10.3390/ijms25010365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Control theory, a well-established discipline in engineering and mathematics, has found novel applications in systems biology. This interdisciplinary approach leverages the principles of feedback control and regulation to gain insights into the complex dynamics of cellular and molecular networks underlying chronic diseases, including neurodegeneration. By modeling and analyzing these intricate systems, control theory provides a framework to understand the pathophysiology and identify potential therapeutic targets. Therefore, this review examines the most widely used control methods in conjunction with genomic-scale metabolic models in the steady state of the multi-omics type. According to our research, this approach involves integrating experimental data, mathematical modeling, and computational analyses to simulate and control complex biological systems. In this review, we find that the most significant application of this methodology is associated with cancer, leaving a lack of knowledge in neurodegenerative models. However, this methodology, mainly associated with the Minimal Dominant Set (MDS), has provided a starting point for identifying therapeutic targets for drug development and personalized treatment strategies, paving the way for more effective therapies.
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Affiliation(s)
- Andrea Angarita-Rodríguez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
| | - Juan J. Rubio-Mesa
- Departamento de Estadística, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Andrés Felipe Aristizábal
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
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Ermakov VS, Granados JC, Nigam SK. Remote effects of kidney drug transporter OAT1 on gut microbiome composition and urate homeostasis. JCI Insight 2023; 8:e172341. [PMID: 37937647 PMCID: PMC10721261 DOI: 10.1172/jci.insight.172341] [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: 05/17/2023] [Accepted: 09/12/2023] [Indexed: 11/09/2023] Open
Abstract
The organic anion transporter OAT1 (SLC22A6, originally identified as NKT) is a multispecific transporter responsible for the elimination by the kidney of small organic anions that derive from the gut microbiome. Many are uremic toxins associated with chronic kidney disease (CKD). OAT1 is among a group of "drug" transporters that act as hubs in a large homeostatic network regulating interorgan and interorganismal communication via small molecules. The Remote Sensing and Signaling Theory predicts that genetic deletion of such a key hub in the network results in compensatory interorganismal communication (e.g., host-gut microbe dynamics). Recent metabolomics data from Oat1-KO mice indicate that some of the most highly affected metabolites derive from bacterial tyrosine, tryptophan, purine, and fatty acid metabolism. Functional metagenomic analysis of fecal 16S amplicon and whole-genome sequencing revealed that loss of OAT1 was impressively associated with microbial pathways regulating production of urate, gut-derived p-cresol, tryptophan derivatives, and fatty acids. Certain changes, such as alterations in gut microbiome urate metabolism, appear compensatory. Thus, Oat1 in the kidney appears to mediate remote interorganismal communication by regulating the gut microbiome composition and metabolic capability. Since OAT1 function in the proximal tubule is substantially affected in CKD, our results may shed light on the associated alterations in gut-microbiome dynamics.
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Affiliation(s)
| | | | - Sanjay K. Nigam
- Department of Pediatrics, and
- Department of Medicine, Division of Nephrology, University of California, San Diego (UCSD), La Jolla, California, USA
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Caetano-Pinto P, Stahl SH. Renal Organic Anion Transporters 1 and 3 In Vitro: Gone but Not Forgotten. Int J Mol Sci 2023; 24:15419. [PMID: 37895098 PMCID: PMC10607849 DOI: 10.3390/ijms242015419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Organic anion transporters 1 and 3 (OAT1 and OAT3) play a crucial role in kidney function by regulating the secretion of multiple renally cleared small molecules and toxic metabolic by-products. Assessing the activity of these transporters is essential for drug development purposes as they can significantly impact drug disposition and safety. OAT1 and OAT3 are amongst the most abundant drug transporters expressed in human renal proximal tubules. However, their expression is lost when cells are isolated and cultured in vitro, which is a persistent issue across all human and animal renal proximal tubule cell models, including primary cells and cell lines. Although it is well known that the overall expression of drug transporters is affected in vitro, the underlying reasons for the loss of OAT1 and OAT3 are still not fully understood. Nonetheless, research into the regulatory mechanisms of these transporters has provided insights into the molecular pathways underlying their expression and activity. In this review, we explore the regulatory mechanisms that govern the expression and activity of OAT1 and OAT3 and investigate the physiological changes that proximal tubule cells undergo and that potentially result in the loss of these transporters. A better understanding of the regulation of these transporters could aid in the development of strategies, such as introducing microfluidic conditions or epigenetic modification inhibitors, to improve their expression and activity in vitro and to create more physiologically relevant models. Consequently, this will enable more accurate assessment for drug development and safety applications.
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Affiliation(s)
- Pedro Caetano-Pinto
- Department of Urology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
| | - Simone H. Stahl
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, 310 Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK;
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Zheng S, Zhou L, Hoene M, Peter A, Birkenfeld AL, Weigert C, Liu X, Zhao X, Xu G, Lehmann R. A New Biomarker Profiling Strategy for Gut Microbiome Research: Valid Association of Metabolites to Metabolism of Microbiota Detected by Non-Targeted Metabolomics in Human Urine. Metabolites 2023; 13:1061. [PMID: 37887386 PMCID: PMC10608496 DOI: 10.3390/metabo13101061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023] Open
Abstract
The gut microbiome is of tremendous relevance to human health and disease, so it is a hot topic of omics-driven biomedical research. However, a valid identification of gut microbiota-associated molecules in human blood or urine is difficult to achieve. We hypothesize that bowel evacuation is an easy-to-use approach to reveal such metabolites. A non-targeted and modifying group-assisted metabolomics approach (covering 40 types of modifications) was applied to investigate urine samples collected in two independent experiments at various time points before and after laxative use. Fasting over the same time period served as the control condition. As a result, depletion of the fecal microbiome significantly affected the levels of 331 metabolite ions in urine, including 100 modified metabolites. Dominating modifications were glucuronidations, carboxylations, sulfations, adenine conjugations, butyrylations, malonylations, and acetylations. A total of 32 compounds, including common, but also unexpected fecal microbiota-associated metabolites, were annotated. The applied strategy has potential to generate a microbiome-associated metabolite map (M3) of urine from healthy humans, and presumably also other body fluids. Comparative analyses of M3 vs. disease-related metabolite profiles, or therapy-dependent changes may open promising perspectives for human gut microbiome research and diagnostics beyond analyzing feces.
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Affiliation(s)
- Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (S.Z.); (L.Z.); (X.L.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (S.Z.); (L.Z.); (X.L.); (X.Z.)
| | - Miriam Hoene
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tuebingen, Germany; (M.H.); (A.P.); (C.W.)
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tuebingen, Germany; (M.H.); (A.P.); (C.W.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 90451 Neuherberg, Germany
| | - Andreas L. Birkenfeld
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 90451 Neuherberg, Germany
- Internal Medicine 4, University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Cora Weigert
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tuebingen, Germany; (M.H.); (A.P.); (C.W.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 90451 Neuherberg, Germany
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (S.Z.); (L.Z.); (X.L.); (X.Z.)
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (S.Z.); (L.Z.); (X.L.); (X.Z.)
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (S.Z.); (L.Z.); (X.L.); (X.Z.)
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tuebingen, Germany; (M.H.); (A.P.); (C.W.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 90451 Neuherberg, Germany
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Abstract
Homeostasis is a prerequisite for health. When homeostasis becomes disrupted, dysfunction occurs. This is especially the case for the gut microbiota, which under normal conditions lives in symbiosis with the host. As there are as many microbial cells in and on our body as human cells, it is unlikely they would not contribute to health or disease. The gut bacterial metabolism generates numerous beneficial metabolites but also uremic toxins and their precursors, which are transported into the circulation. Barrier function in the intestine, the heart, and the kidneys regulates metabolite transport and concentration and plays a role in inter-organ and inter-organism communication via small molecules. This communication is analyzed from the perspective of the remote sensing and signaling theory, which emphasizes the role of a large network of multispecific, oligospecific, and monospecific transporters and enzymes in regulating small-molecule homeostasis. The theory provides a systems biology framework for understanding organ cross talk and microbe-host communication involving metabolites, signaling molecules, nutrients, antioxidants, and uremic toxins. This remote small-molecule communication is critical for maintenance of homeostasis along the gut-heart-kidney axis and for responding to homeostatic perturbations. Chronic kidney disease is characterized by gut dysbiosis and accumulation of toxic metabolites. This slowly impacts the body, affecting the cardiovascular system and contributing to the progression of kidney dysfunction, which in its turn influences the gut microbiota. Preserving gut homeostasis and barrier functions or restoring gut dysbiosis and dysfunction could be a minimally invasive way to improve patient outcomes and quality of life in many diseases, including cardiovascular and kidney disease.
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Affiliation(s)
- Griet Glorieux
- Nephrology Unit, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Gent, Belgium (G.G., R.V., F.V.)
| | - Sanjay K Nigam
- Department of Pediatrics (S.K.N.), University of California San Diego, La Jolla, CA
- Division of Nephrology, Department of Medicine (S.K.N.), University of California San Diego, La Jolla, CA
| | - Raymond Vanholder
- Nephrology Unit, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Gent, Belgium (G.G., R.V., F.V.)
| | - Francis Verbeke
- Nephrology Unit, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Gent, Belgium (G.G., R.V., F.V.)
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Jamshidi N, Nigam KB, Nigam SK. Loss of the Kidney Urate Transporter, Urat1, Leads to Disrupted Redox Homeostasis in Mice. Antioxidants (Basel) 2023; 12:antiox12030780. [PMID: 36979028 PMCID: PMC10045411 DOI: 10.3390/antiox12030780] [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: 01/15/2023] [Revised: 02/28/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
High uric acid is associated with gout, hypertension, metabolic syndrome, cardiovascular disease, and kidney disease. URAT1 (SLC22A12), originally discovered in mice as Rst, is generally considered a very selective uric acid transporter compared to other closely-related kidney uric acid transporters such as OAT1 (SLC22A6, NKT) and OAT3 (SLC22A8). While the role of URAT1 in regulating human uric acid is well-established, in recent studies the gene has been linked to redox regulation in flies as well as progression of renal cell carcinoma. We have now identified over twenty metabolites in the Urat1 knockout that are generally distinct from metabolites accumulating in the Oat1 and Oat3 knockout mice, with distinct molecular properties as revealed by chemoinformatics and machine learning analysis. These metabolites are involved in seemingly disparate aspects of cellular metabolism, including pyrimidine, fatty acid, and amino acid metabolism. However, through integrative systems metabolic analysis of the transcriptomic and metabolomic data using a human metabolic reconstruction to build metabolic genome-scale models (GEMs), the cellular response to loss of Urat1/Rst revealed compensatory processes related to reactive oxygen species handling and maintaining redox state balances via Vitamin C metabolism and cofactor charging reactions. These observations are consistent with the increasingly appreciated role of the antioxidant properties of uric acid. Collectively, the results highlight the role of Urat1/Rst as a transporter strongly tied to maintaining redox homeostasis, with implications for metabolic side effects from drugs that block its function.
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Affiliation(s)
- Neema Jamshidi
- Department of Radiological Sciences, University of California, Los Angeles, CA 90095, USA
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA;
- Correspondence:
| | - Kabir B. Nigam
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02130, USA
| | - Sanjay K. Nigam
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA;
- Departments of Pediatrics and Medicine (Nephrology), University of California, San Diego, La Jolla, CA 92093, USA
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Granados JC, Ermakov V, Maity K, Vera DR, Chang G, Nigam SK. The kidney drug transporter OAT1 regulates gut microbiome-dependent host metabolism. JCI Insight 2023; 8:160437. [PMID: 36692015 PMCID: PMC9977316 DOI: 10.1172/jci.insight.160437] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023] Open
Abstract
Organic anion transporter 1 (OAT1/SLC22A6, NKT) is a multispecific drug transporter in the kidney with numerous substrates, including pharmaceuticals, endogenous metabolites, natural products, and uremic toxins. Here, we show that OAT1 regulates levels of gut microbiome-derived metabolites. We depleted the gut microbiome of Oat1-KO and WT mice and performed metabolomics to analyze the effects of genotype (KO versus WT) and microbiome depletion. OAT1 is an in vivo intermediary between the host and the microbes, with 40 of the 162 metabolites dependent on the gut microbiome also impacted by loss of Oat1. Chemoinformatic analysis revealed that the altered metabolites (e.g., indoxyl sulfate, p-cresol sulfate, deoxycholate) had more ring structures and sulfate groups. This indicates a pathway from gut microbes to liver phase II metabolism, to renal OAT1-mediated transport. The idea that multiple gut-derived metabolites directly interact with OAT1 was confirmed by in vitro transport and magnetic bead binding assays. We show that gut microbiome-derived metabolites dependent on OAT1 are impacted in a chronic kidney disease (CKD) model and human drug-metabolite interactions. Consistent with the Remote Sensing and Signaling Theory, our results support the view that drug transporters (e.g., OAT1, OAT3, OATP1B1, OATP1B3, MRP2, MRP4, ABCG2) play a central role in regulating gut microbe-dependent metabolism, as well as interorganismal communication between the host and microbiome.
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Affiliation(s)
| | | | - Koustav Maity
- Skaggs School of Pharmacy and Pharmaceutical Sciences
| | - David R. Vera
- Department of Radiology,,In Vivo Cancer and Molecular Imaging Program
| | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Sciences,,Department of Pharmacology, School of Medicine
| | - Sanjay K. Nigam
- Department of Pediatrics, and,Department of Medicine (Nephrology), UCSD, La Jolla, California, USA
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