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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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2
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Brands J, Bravo S, Jürgenliemke L, Grätz L, Schihada H, Frechen F, Alenfelder J, Pfeil C, Ohse PG, Hiratsuka S, Kawakami K, Schmacke LC, Heycke N, Inoue A, König G, Pfeifer A, Wachten D, Schulte G, Steinmetzer T, Watts VJ, Gomeza J, Simon K, Kostenis E. A molecular mechanism to diversify Ca 2+ signaling downstream of Gs protein-coupled receptors. Nat Commun 2024; 15:7684. [PMID: 39227390 PMCID: PMC11372221 DOI: 10.1038/s41467-024-51991-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024] Open
Abstract
A long-held tenet in inositol-lipid signaling is that cleavage of membrane phosphoinositides by phospholipase Cβ (PLCβ) isozymes to increase cytosolic Ca2+ in living cells is exclusive to Gq- and Gi-sensitive G protein-coupled receptors (GPCRs). Here we extend this central tenet and show that Gs-GPCRs also partake in inositol-lipid signaling and thereby increase cytosolic Ca2+. By combining CRISPR/Cas9 genome editing to delete Gαs, the adenylyl cyclase isoforms 3 and 6, or the PLCβ1-4 isozymes, with pharmacological and genetic inhibition of Gq and G11, we pin down Gs-derived Gβγ as driver of a PLCβ2/3-mediated cytosolic Ca2+ release module. This module does not require but crosstalks with Gαs-dependent cAMP, demands Gαq to release PLCβ3 autoinhibition, but becomes Gq-independent with mutational disruption of the PLCβ3 autoinhibited state. Our findings uncover the key steps of a previously unappreciated mechanism utilized by mammalian cells to finetune their calcium signaling regulation through Gs-GPCRs.
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Affiliation(s)
- Julian Brands
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
- Research Training Group 1873, University of Bonn, Bonn, Germany
| | - Sergi Bravo
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Lars Jürgenliemke
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
- Research Training Group 2873, University of Bonn, Bonn, Germany
| | - Lukas Grätz
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Schihada
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Fabian Frechen
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Judith Alenfelder
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Cy Pfeil
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
- Research Training Group 1873, University of Bonn, Bonn, Germany
- Amsterdam Institute for Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Paul Georg Ohse
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Suzune Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, 153-8505, Japan
| | - Luna C Schmacke
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nina Heycke
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Gabriele König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Dagmar Wachten
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Gunnar Schulte
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Torsten Steinmetzer
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Drug Discovery, Purdue University, West Lafayette, IN, USA
| | - Jesús Gomeza
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Katharina Simon
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131, Padova, Italy
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
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3
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Neřoldová M, Stuchlík A. Chemogenetic Tools and their Use in Studies of Neuropsychiatric Disorders. Physiol Res 2024; 73:S449-S470. [PMID: 38957949 PMCID: PMC11412350 DOI: 10.33549/physiolres.935401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Chemogenetics is a newly developed set of tools that allow for selective manipulation of cell activity. They consist of a receptor mutated irresponsive to endogenous ligands and a synthetic ligand that does not interact with the wild-type receptors. Many different types of these receptors and their respective ligands for inhibiting or excitating neuronal subpopulations were designed in the past few decades. It has been mainly the G-protein coupled receptors (GPCRs) selectively responding to clozapine-N-oxide (CNO), namely Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), that have been employed in research. Chemogenetics offers great possibilities since the activity of the receptors is reversible, inducible on demand by the ligand, and non-invasive. Also, specific groups or types of neurons can be selectively manipulated thanks to the delivery by viral vectors. The effect of the chemogenetic receptors on neurons lasts longer, and even chronic activation can be achieved. That can be useful for behavioral testing. The great advantage of chemogenetic tools is especially apparent in research on brain diseases since they can manipulate whole neuronal circuits and connections between different brain areas. Many psychiatric or other brain diseases revolve around the dysfunction of specific brain networks. Therefore, chemogenetics presents a powerful tool for investigating the underlying mechanisms causing the disease and revealing the link between the circuit dysfunction and the behavioral or cognitive symptoms observed in patients. It could also contribute to the development of more effective treatments.
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Affiliation(s)
- M Neřoldová
- Laboratory of Neurophysiology of Memory, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic. E-mail:
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Thompson MD, Reiner-Link D, Berghella A, Rana BK, Rovati GE, Capra V, Gorvin CM, Hauser AS. G protein-coupled receptor (GPCR) pharmacogenomics. Crit Rev Clin Lab Sci 2024:1-44. [PMID: 39119983 DOI: 10.1080/10408363.2024.2358304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/03/2023] [Accepted: 05/18/2024] [Indexed: 08/10/2024]
Abstract
The field of pharmacogenetics, the investigation of the influence of one or more sequence variants on drug response phenotypes, is a special case of pharmacogenomics, a discipline that takes a genome-wide approach. Massively parallel, next generation sequencing (NGS), has allowed pharmacogenetics to be subsumed by pharmacogenomics with respect to the identification of variants associated with responders and non-responders, optimal drug response, and adverse drug reactions. A plethora of rare and common naturally-occurring GPCR variants must be considered in the context of signals from across the genome. Many fundamentals of pharmacogenetics were established for G protein-coupled receptor (GPCR) genes because they are primary targets for a large number of therapeutic drugs. Functional studies, demonstrating likely-pathogenic and pathogenic GPCR variants, have been integral to establishing models used for in silico analysis. Variants in GPCR genes include both coding and non-coding single nucleotide variants and insertion or deletions (indels) that affect cell surface expression (trafficking, dimerization, and desensitization/downregulation), ligand binding and G protein coupling, and variants that result in alternate splicing encoding isoforms/variable expression. As the breadth of data on the GPCR genome increases, we may expect an increase in the use of drug labels that note variants that significantly impact the clinical use of GPCR-targeting agents. We discuss the implications of GPCR pharmacogenomic data derived from the genomes available from individuals who have been well-phenotyped for receptor structure and function and receptor-ligand interactions, and the potential benefits to patients of optimized drug selection. Examples discussed include the renin-angiotensin system in SARS-CoV-2 (COVID-19) infection, the probable role of chemokine receptors in the cytokine storm, and potential protease activating receptor (PAR) interventions. Resources dedicated to GPCRs, including publicly available computational tools, are also discussed.
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Affiliation(s)
- Miles D Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - David Reiner-Link
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Berghella
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brinda K Rana
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valerie Capra
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Caroline M Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Thompson MD, Percy ME, Cole DEC, Bichet DG, Hauser AS, Gorvin CM. G protein-coupled receptor (GPCR) gene variants and human genetic disease. Crit Rev Clin Lab Sci 2024; 61:317-346. [PMID: 38497103 DOI: 10.1080/10408363.2023.2286606] [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: 05/24/2023] [Revised: 08/28/2023] [Accepted: 11/19/2023] [Indexed: 03/19/2024]
Abstract
Genetic variations in the genes encoding G protein-coupled receptors (GPCRs) can disrupt receptor structure and function, which can result in human genetic diseases. Disease-causing mutations have been reported in at least 55 GPCRs for more than 66 monogenic diseases in humans. The spectrum of pathogenic and likely pathogenic variants includes loss of function variants that decrease receptor signaling on one extreme and gain of function that may result in biased signaling or constitutive activity, originally modeled on prototypical rhodopsin GPCR variants identified in retinitis pigmentosa, on the other. GPCR variants disrupt ligand binding, G protein coupling, accessory protein function, receptor desensitization and receptor recycling. Next generation sequencing has made it possible to identify variants of uncertain significance (VUS). We discuss variants in receptors known to result in disease and in silico strategies for disambiguation of VUS such as sorting intolerant from tolerant and polymorphism phenotyping. Modeling of variants has contributed to drug development and precision medicine, including drugs that target the melanocortin receptor in obesity and interventions that reverse loss of gonadotropin-releasing hormone receptor from the cell surface in idiopathic hypogonadotropic hypogonadism. Activating and inactivating variants of the calcium sensing receptor (CaSR) gene that are pathogenic in familial hypocalciuric hypercalcemia and autosomal dominant hypocalcemia have enabled the development of calcimimetics and calcilytics. Next generation sequencing has continued to identify variants in GPCR genes, including orphan receptors, that contribute to human phenotypes and may have therapeutic potential. Variants of the CaSR gene, some encoding an arginine-rich region that promotes receptor phosphorylation and intracellular retention, have been linked to an idiopathic epilepsy syndrome. Agnostic strategies have identified variants of the pyroglutamylated RF amide peptide receptor gene in intellectual disability and G protein-coupled receptor 39 identified in psoriatic arthropathy. Coding variants of the G protein-coupled receptor L1 (GPR37L1) orphan receptor gene have been identified in a rare familial progressive myoclonus epilepsy. The study of the role of GPCR variants in monogenic, Mendelian phenotypes has provided the basis of modeling the significance of more common variants of pharmacogenetic significance.
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Affiliation(s)
- Miles D Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, ON, Canada
| | - Maire E Percy
- Departments of Physiology and Obstetrics & Gynaecology, University of Toronto, Toronto, ON, Canada
| | - David E C Cole
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Daniel G Bichet
- Department of Physiology and Medicine, Hôpital du Sacré-Coeur, Université de Montréal, QC, Canada
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline M Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, West Midlands, UK
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6
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Gao M, Ooms JF, Leurs R, Vischer HF. Histamine H 3 Receptor Isoforms: Insights from Alternative Splicing to Functional Complexity. Biomolecules 2024; 14:761. [PMID: 39062475 PMCID: PMC11274711 DOI: 10.3390/biom14070761] [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: 05/31/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing significantly enhances the diversity of the G protein-coupled receptor (GPCR) family, including the histamine H3 receptor (H3R). This post-transcriptional modification generates multiple H3R isoforms with potentially distinct pharmacological and physiological profiles. H3R is primarily involved in the presynaptic inhibition of neurotransmitter release in the central nervous system. Despite the approval of pitolisant for narcolepsy (Wakix®) and daytime sleepiness in adults with obstructive sleep apnea (Ozawade®) and ongoing clinical trials for other H3R antagonists/inverse agonists, the functional significance of the numerous H3R isoforms remains largely enigmatic. Recent publicly available RNA sequencing data have confirmed the expression of multiple H3R isoforms in the brain, with some isoforms exhibiting unique tissue-specific distribution patterns hinting at isoform-specific functions and interactions within neural circuits. In this review, we discuss the complexity of H3R isoforms with a focus on their potential roles in central nervous system (CNS) function. Comparative analysis across species highlights evolutionary conservation and divergence in H3R splicing, suggesting species-specific regulatory mechanisms. Understanding the functionality of H3R isoforms is crucial for the development of targeted therapeutics. This knowledge will inform the design of more precise pharmacological interventions, potentially enhancing therapeutic efficacy and reducing adverse effects in the treatment of neurological and psychiatric disorders.
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Affiliation(s)
| | | | | | - Henry F. Vischer
- Amsterdam Institute of Molecular and Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands; (M.G.); (J.F.O.); (R.L.)
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7
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Khani S, Topel H, Kardinal R, Tavanez AR, Josephrajan A, Larsen BDM, Gaudry MJ, Leyendecker P, Egedal NM, Güller AS, Stanic N, Ruppert PMM, Gaziano I, Hansmeier NR, Schmidt E, Klemm P, Vagliano LM, Stahl R, Duthie F, Krause JH, Bici A, Engelhard CA, Gohlke S, Frommolt P, Gnad T, Rada-Iglesias A, Pradas-Juni M, Schulz TJ, Wunderlich FT, Pfeifer A, Bartelt A, Jastroch M, Wachten D, Kornfeld JW. Cold-induced expression of a truncated adenylyl cyclase 3 acts as rheostat to brown fat function. Nat Metab 2024; 6:1053-1075. [PMID: 38684889 DOI: 10.1038/s42255-024-01033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/25/2024] [Indexed: 05/02/2024]
Abstract
Promoting brown adipose tissue (BAT) activity innovatively targets obesity and metabolic disease. While thermogenic activation of BAT is well understood, the rheostatic regulation of BAT to avoid excessive energy dissipation remains ill-defined. Here, we demonstrate that adenylyl cyclase 3 (AC3) is key for BAT function. We identified a cold-inducible promoter that generates a 5' truncated AC3 mRNA isoform (Adcy3-at), whose expression is driven by a cold-induced, truncated isoform of PPARGC1A (PPARGC1A-AT). Male mice lacking Adcy3-at display increased energy expenditure and are resistant to obesity and ensuing metabolic imbalances. Mouse and human AC3-AT are retained in the endoplasmic reticulum, unable to translocate to the plasma membrane and lack enzymatic activity. AC3-AT interacts with AC3 and sequesters it in the endoplasmic reticulum, reducing the pool of adenylyl cyclases available for G-protein-mediated cAMP synthesis. Thus, AC3-AT acts as a cold-induced rheostat in BAT, limiting adverse consequences of cAMP activity during chronic BAT activation.
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Affiliation(s)
- Sajjad Khani
- Institute for Genetics, University of Cologne, Cologne, Germany
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Hande Topel
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Ronja Kardinal
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ana Rita Tavanez
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Ajeetha Josephrajan
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | | | - Michael James Gaudry
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Philipp Leyendecker
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Nadia Meincke Egedal
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Aylin Seren Güller
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Natasa Stanic
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Phillip M M Ruppert
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | | | - Elena Schmidt
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Paul Klemm
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Lara-Marie Vagliano
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Rainer Stahl
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Fraser Duthie
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jens-Henning Krause
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ana Bici
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Gohlke
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Peter Frommolt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Gnad
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Marta Pradas-Juni
- Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Copenhagen, Denmark
| | - Tim Julius Schulz
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | | | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Alexander Bartelt
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Molecular Metabolism and Sabri Ülker Center for Metabolic Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dagmar Wachten
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany.
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark.
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8
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Gao M, Dekker ME, Leurs R, Vischer HF. Pharmacological characterization of seven human histamine H 3 receptor isoforms. Eur J Pharmacol 2024; 968:176450. [PMID: 38387718 DOI: 10.1016/j.ejphar.2024.176450] [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: 12/06/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
The histamine H3 receptor (H3R) regulates as a presynaptic G protein-coupled receptor the release of histamine and other neurotransmitters in the brain, and is consequently a potential therapeutic target for neuronal disorders. The human H3R encodes for seven splice variants that vary in the length of intracellular loop 3 and/or the C-terminal tail but are all able to induce heterotrimeric Gi protein signaling. The last two decades H3R drug discovery and lead optimization has been exclusively focused on the 445 amino acids-long reference isoform H3R-445. In this study, we pharmacologically characterized for the first time all seven H3R isoforms by determining their binding affinities for reference histamine H3 receptor agonists and inverse agonists. The H3R-453, H3R-415, and H3R-413 isoforms display similar binding affinities for all ligands as the H3R-445. However, increased agonist binding affinities were observed for the three shorter isoforms H3R-329, H3R-365, and H3R-373, whereas inverse agonists such as the approved anti-narcolepsy drug pitolisant (Wakix®) displayed significantly decreased binding affinities for the latter two isoforms. This opposite change in binding affinity of agonist versus inverse agonists on H3R-365 and H3R-373 is associated with their higher constitutive activity in a cAMP biosensor assay as compared to the other five isoforms. The observed differences in pharmacology between longer and shorter H3R isoforms should be considered in future drug discovery programs.
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Affiliation(s)
- Meichun Gao
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands
| | - Mabel E Dekker
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands
| | - Rob Leurs
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands.
| | - Henry F Vischer
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands.
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9
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Fasciani I, Petragnano F, Wang Z, Edwards R, Telugu N, Pietrantoni I, Zabel U, Zauber H, Grieben M, Terzenidou ME, Di Gregorio J, Pellegrini C, Santini S, Taddei AR, Pohl B, Aringhieri S, Carli M, Aloisi G, Marampon F, Charlesworth E, Roman A, Diecke S, Flati V, Giorgi F, Amicarelli F, Tobin AB, Scarselli M, Tokatlidis K, Rossi M, Lohse MJ, Annibale P, Maggio R. The C-terminus of the prototypical M2 muscarinic receptor localizes to the mitochondria and regulates cell respiration under stress conditions. PLoS Biol 2024; 22:e3002582. [PMID: 38683874 PMCID: PMC11093360 DOI: 10.1371/journal.pbio.3002582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/14/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
Muscarinic acetylcholine receptors are prototypical G protein-coupled receptors (GPCRs), members of a large family of 7 transmembrane receptors mediating a wide variety of extracellular signals. We show here, in cultured cells and in a murine model, that the carboxyl terminal fragment of the muscarinic M2 receptor, comprising the transmembrane regions 6 and 7 (M2tail), is expressed by virtue of an internal ribosome entry site localized in the third intracellular loop. Single-cell imaging and import in isolated yeast mitochondria reveals that M2tail, whose expression is up-regulated in cells undergoing integrated stress response, does not follow the normal route to the plasma membrane, but is almost exclusively sorted to the mitochondria inner membrane: here, it controls oxygen consumption, cell proliferation, and the formation of reactive oxygen species (ROS) by reducing oxidative phosphorylation. Crispr/Cas9 editing of the key methionine where cap-independent translation begins in human-induced pluripotent stem cells (hiPSCs), reveals the physiological role of this process in influencing cell proliferation and oxygen consumption at the endogenous level. The expression of the C-terminal domain of a GPCR, capable of regulating mitochondrial function, constitutes a hitherto unknown mechanism notably unrelated to its canonical signaling function as a GPCR at the plasma membrane. This work thus highlights a potential novel mechanism that cells may use for controlling their metabolism under variable environmental conditions, notably as a negative regulator of cell respiration.
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Affiliation(s)
- Irene Fasciani
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Francesco Petragnano
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ziming Wang
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ruairidh Edwards
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Ilaria Pietrantoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Maria E. Terzenidou
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jacopo Di Gregorio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Silvano Santini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Anna R. Taddei
- Section of Electron Microscopy, Great Equipment Center, University of Tuscia, Viterbo, Italy
| | - Bärbel Pohl
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stefano Aringhieri
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Marco Carli
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Gabriella Aloisi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | | | - Eve Charlesworth
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | | | | | - Vincenzo Flati
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Franco Giorgi
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Fernanda Amicarelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Andrew B. Tobin
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Marco Scarselli
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Kostas Tokatlidis
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mario Rossi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Martin J. Lohse
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
- ISAR Bioscience Institute, Munich, Germany
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - Roberto Maggio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
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10
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Braga Emidio N, Small BM, Keller AR, Cheloha RW, Wingler LM. Nanobody-Mediated Dualsteric Engagement of the Angiotensin Receptor Broadens Biased Ligand Pharmacology. Mol Pharmacol 2024; 105:260-271. [PMID: 38164609 PMCID: PMC10877709 DOI: 10.1124/molpharm.123.000797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/15/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Dualsteric G protein-coupled receptor (GPCR) ligands are a class of bitopic ligands that consist of an orthosteric pharmacophore, which binds to the pocket occupied by the receptor's endogenous agonist, and an allosteric pharmacophore, which binds to a distinct site. These ligands have the potential to display characteristics of both orthosteric and allosteric ligands. To explore the signaling profiles that dualsteric ligands of the angiotensin II type 1 receptor (AT1R) can access, we ligated a 6e epitope tag-specific nanobody (single-domain antibody fragment) to angiotensin II (AngII) and analogs that show preferential allosteric coupling to Gq (TRV055, TRV056) or β-arrestin (TRV027). While the nanobody itself acts as a probe-specific neutral or negative allosteric ligand of N-terminally 6e-tagged AT1R, nanobody conjugation to orthosteric ligands had varying effects on Gq dissociation and β-arrestin plasma membrane recruitment. The potency of certain AngII analogs was enhanced up to 100-fold, and some conjugates behaved as partial agonists, with up to a 5-fold decrease in maximal efficacy. Nanobody conjugation also biased the signaling of TRV055 and TRV056 toward Gq, suggesting that Gq bias at AT1R can be modulated through molecular mechanisms distinct from those previously elucidated. Both competition radioligand binding experiments and functional assays demonstrated that orthosteric antagonists (angiotensin receptor blockers) act as non-competitive inhibitors of all these nanobody-peptide conjugates. This proof-of-principle study illustrates the array of pharmacological patterns that can be achieved by incorporating neutral or negative allosteric pharmacophores into dualsteric ligands. Nanobodies directed toward linear epitopes could provide a rich source of allosteric reagents for this purpose. SIGNIFICANCE STATEMENT: Here we engineer bitopic (dualsteric) ligands for epitope-tagged angiotensin II type 1 receptor by conjugating angiotensin II or its biased analogs to an epitope-specific nanobody (antibody fragment). Our data demonstrate that nanobody-mediated interactions with the receptor N-terminus endow angiotensin analogs with properties of allosteric modulators and provide a novel mechanism to increase the potency, modulate the maximal effect, or alter the bias of ligands.
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Affiliation(s)
- Nayara Braga Emidio
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Brandi M Small
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Amanda R Keller
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Ross W Cheloha
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Laura M Wingler
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
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11
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Wu Y, Zhang P, Fan H, Zhang C, Yu P, Liang X, Chen Y. GPR35 acts a dual role and therapeutic target in inflammation. Front Immunol 2023; 14:1254446. [PMID: 38035084 PMCID: PMC10687457 DOI: 10.3389/fimmu.2023.1254446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
GPR35 is a G protein-coupled receptor with notable involvement in modulating inflammatory responses. Although the precise role of GPR35 in inflammation is not yet fully understood, studies have suggested that it may have both pro- and anti-inflammatory effects depending on the specific cellular environment. Some studies have shown that GPR35 activation can stimulate the production of pro-inflammatory cytokines and facilitate the movement of immune cells towards inflammatory tissues or infected areas. Conversely, other investigations have suggested that GPR35 may possess anti-inflammatory properties in the gastrointestinal tract, liver and certain other tissues by curbing the generation of inflammatory mediators and endorsing the differentiation of regulatory T cells. The intricate role of GPR35 in inflammation underscores the requirement for more in-depth research to thoroughly comprehend its functional mechanisms and its potential significance as a therapeutic target for inflammatory diseases. The purpose of this review is to concurrently investigate the pro-inflammatory and anti-inflammatory roles of GPR35, thus illuminating both facets of this complex issue.
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Affiliation(s)
- Yetian Wu
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Pei Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Caiying Zhang
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Pengfei Yu
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Xinmiao Liang
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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12
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Li M, Qing R, Tao F, Xu P, Zhang S. Dynamic Dimerization of Chemokine Receptors and Potential Inhibitory Role of Their Truncated Isoforms Revealed through Combinatorial Prediction. Int J Mol Sci 2023; 24:16266. [PMID: 38003455 PMCID: PMC10671024 DOI: 10.3390/ijms242216266] [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: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Chemokine receptors play crucial roles in fundamental biological processes. Their malfunction may result in many diseases, including cancer, autoimmune diseases, and HIV. The oligomerization of chemokine receptors holds significant functional implications that directly affect their signaling patterns and pharmacological responses. However, the oligomerization patterns of many chemokine receptors remain poorly understood. Furthermore, several chemokine receptors have highly truncated isoforms whose functional role is not yet clear. Here, we computationally show homo- and heterodimerization patterns of four human chemokine receptors, namely CXCR2, CXCR7, CCR2, and CCR7, along with their interaction patterns with their respective truncated isoforms. By combining the neural network-based AlphaFold2 and physics-based protein-protein docking tool ClusPro, we predicted 15 groups of complex structures and assessed the binding affinities in the context of atomistic molecular dynamics simulations. Our results are in agreement with previous experimental observations and support the dynamic and diverse nature of chemokine receptor dimerization, suggesting possible patterns of higher-order oligomerization. Additionally, we uncover the strong potential of truncated isoforms to block homo- and heterodimerization of chemokine receptors, also in a dynamic manner. Our study provides insights into the dimerization patterns of chemokine receptors and the functional significance of their truncated isoforms.
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Affiliation(s)
- Mengke Li
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
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13
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Zhao F, Hang K, Zhou Q, Shao L, Li H, Li W, Lin S, Dai A, Cai X, Liu Y, Xu Y, Feng W, Yang D, Wang MW. Molecular basis of signal transduction mediated by the human GIPR splice variants. Proc Natl Acad Sci U S A 2023; 120:e2306145120. [PMID: 37792509 PMCID: PMC10576055 DOI: 10.1073/pnas.2306145120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 08/07/2023] [Indexed: 10/06/2023] Open
Abstract
Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a potential drug target for metabolic disorders. It works with glucagon-like peptide-1 receptor and glucagon receptor in humans to maintain glucose homeostasis. Unlike the other two receptors, GIPR has at least 13 reported splice variants (SVs), more than half of which have sequence variations at either C or N terminus. To explore their roles in endogenous peptide-mediated GIPR signaling, we determined the cryoelectron microscopy (cryo-EM) structures of the two N terminus-altered SVs (referred as GIPR-202 and GIPR-209 in the Ensembl database, SV1 and SV2 here, respectively) and investigated the outcome of coexpressing each of them in question with GIPR in HEK293T cells with respect to ligand binding, receptor expression, cAMP (adenosine 3,5-cyclic monophosphate) accumulation, β-arrestin recruitment, and cell surface localization. It was found that while both N terminus-altered SVs of GIPR neither bound to the hormone nor elicited signal transduction per se, they suppressed ligand binding and cAMP accumulation of GIPR. Meanwhile, SV1 reduced GIPR-mediated β-arrestin 2 responses. The cryo-EM structures of SV1 and SV2 showed that they reorganized the extracellular halves of transmembrane helices 1, 6, and 7 and extracellular loops 2 and 3 to adopt a ligand-binding pocket-occupied conformation, thereby losing binding ability to the peptide. The results suggest a form of signal bias that is constitutive and ligand-independent, thus expanding our knowledge of biased signaling beyond pharmacological manipulation (i.e., ligand specific) as well as constitutive and ligand-independent (e.g., SV1 of the growth hormone-releasing hormone receptor).
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Affiliation(s)
- Fenghui Zhao
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Kaini Hang
- iHuman Institute, ShanghaiTech University, Shanghai201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Research Center for Deepsea Bioresources, Sanya, Hainan572025, China
| | - Lijun Shao
- iHuman Institute, ShanghaiTech University, Shanghai201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Hao Li
- Research Center for Deepsea Bioresources, Sanya, Hainan572025, China
| | - Wenzhuo Li
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Shi Lin
- Research Center for Deepsea Bioresources, Sanya, Hainan572025, China
| | - Antao Dai
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Xiaoqing Cai
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Yanyun Liu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing210023, China
| | - Yingna Xu
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Wenbo Feng
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- Research Center for Deepsea Bioresources, Sanya, Hainan572025, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing210023, China
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Research Center for Deepsea Bioresources, Sanya, Hainan572025, China
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo113-0033, Japan
- School of Pharmacy, Hainan Medical University, Haikou570228, China
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14
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Rees TA, Labastida-Ramírez A, Rubio-Beltrán E. Calcitonin/PAC 1 receptor splice variants: a blind spot in migraine research. Trends Pharmacol Sci 2023; 44:651-663. [PMID: 37543479 PMCID: PMC10529278 DOI: 10.1016/j.tips.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/08/2023] [Accepted: 07/08/2023] [Indexed: 08/07/2023]
Abstract
The neuropeptides calcitonin gene-related peptide (CGRP) and pituitary adenylate cyclase-activating polypeptide (PACAP) and their receptors are linked to migraine neurobiology. Recent antimigraine therapeutics targeting the signaling of these neuropeptides are effective; however, some patients respond suboptimally, indicating an incomplete understanding of migraine pathophysiology. The CGRP- and PACAP-responsive receptors can be differentially spliced. It is known that receptor splice variants can have different pathophysiological effects in other receptor-mediated pain pathways. Despite considerable knowledge on the structural and pharmacological differences of the CGRP- and PACAP-responsive receptor splice variants and their expression in migraine-relevant tissues, their role in migraine is rarely considered. Here we shine a spotlight on the calcitonin and PACAP (PAC1) receptor splice variants and examine what implications they may have for drug activity and design.
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Affiliation(s)
- Tayla A Rees
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Alejandro Labastida-Ramírez
- Headache Group, Wolfson Center for Age Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Eloisa Rubio-Beltrán
- Headache Group, Wolfson Center for Age Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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15
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Beets I, Zels S, Vandewyer E, Demeulemeester J, Caers J, Baytemur E, Courtney A, Golinelli L, Hasakioğulları İ, Schafer WR, Vértes PE, Mirabeau O, Schoofs L. System-wide mapping of peptide-GPCR interactions in C. elegans. Cell Rep 2023; 42:113058. [PMID: 37656621 PMCID: PMC7615250 DOI: 10.1016/j.celrep.2023.113058] [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: 11/15/2022] [Revised: 07/19/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
Neuropeptides and peptide hormones are ancient, widespread signaling molecules that underpin almost all brain functions. They constitute a broad ligand-receptor network, mainly by binding to G protein-coupled receptors (GPCRs). However, the organization of the peptidergic network and roles of many peptides remain elusive, as our insight into peptide-receptor interactions is limited and many peptide GPCRs are still orphan receptors. Here we report a genome-wide peptide-GPCR interaction map in Caenorhabditis elegans. By reverse pharmacology screening of over 55,384 possible interactions, we identify 461 cognate peptide-GPCR couples that uncover a broad signaling network with specific and complex combinatorial interactions encoded across and within single peptidergic genes. These interactions provide insights into peptide functions and evolution. Combining our dataset with phylogenetic analysis supports peptide-receptor co-evolution and conservation of at least 14 bilaterian peptidergic systems in C. elegans. This resource lays a foundation for system-wide analysis of the peptidergic network.
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Affiliation(s)
- Isabel Beets
- Department of Biology, KU Leuven, 3000 Leuven, Belgium.
| | - Sven Zels
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | | | - Jonas Demeulemeester
- The Francis Crick Institute, London NW1 1AT, UK; VIB - KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Jelle Caers
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Esra Baytemur
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Amy Courtney
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Petra E Vértes
- Department of Psychiatry, Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, UK
| | - Olivier Mirabeau
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Inserm U1224, Brain-Immune Communication Lab, 75015 Paris, France
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16
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Kim MA, Kim TH, Kannan P, Kho KH, Park K, Sohn YC. Functional Characterization of Gonadotropin-Releasing Hormone and Corazonin Signaling Systems in Pacific Abalone: Toward Reclassification of Invertebrate Neuropeptides. Neuroendocrinology 2023; 114:64-89. [PMID: 37703838 DOI: 10.1159/000533662] [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: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
INTRODUCTION The proposed evolutionary origins and corresponding nomenclature of bilaterian gonadotropin-releasing hormone (GnRH)-related neuropeptides have changed tremendously with the aid of receptor deorphanization. However, the reclassification of the GnRH and corazonin (CRZ) signaling systems in Lophotrochozoa remains unclear. METHODS We characterized GnRH and CRZ receptors in the mollusk Pacific abalone, Haliotis discus hannai (Hdh), by phylogenetic and gene expression analyses, bioluminescence-based reporter, Western blotting, substitution of peptide amino acids, in vivo neuropeptide injection, and RNA interference assays. RESULTS Two Hdh CRZ-like receptors (Hdh-CRZR-A and Hdh-CRZR-B) and three Hdh GnRH-like receptors (Hdh-GnRHR1-A, Hdh-GnRHR1-B, and Hdh-GnRHR2) were identified. In phylogenetic analysis, Hdh-CRZR-A and -B grouped within the CRZ-type receptors, whereas Hdh-GnRHR1-A/-B and Hdh-GnRHR2 clustered within the GnRH/adipokinetic hormone (AKH)/CRZ-related peptide-type receptors. Hdh-CRZR-A/-B and Hdh-GnRHR1-A were activated by Hdh-CRZ (pQNYHFSNGWHA-NH2) and Hdh-GnRH (pQISFSPNWGT-NH2), respectively. Hdh-CRZR-A/-B dually coupled with the Gαq and Gαs signaling pathways, whereas Hdh-GnRHR1-A was linked only with Gαq signaling. Analysis of substituted peptides, [I2S3]Hdh-CRZ and [N2Y3H4]Hdh-GnRH, and in silico docking models revealed that the N-terminal amino acids of the peptides are critical for the selectivity of Hdh-CRZR and Hdh-GnRHR. Two precursor transcripts for Hdh-CRZ and Hdh-GnRH peptides and their receptors were mainly expressed in the neural ganglia, and their levels increased in starved abalones. Injection of Hdh-CRZ peptide into abalones decreased food consumption, whereas Hdh-CRZR knockdown increased food consumption. Moreover, Hdh-CRZ induced germinal vesicle breakdown in mature oocytes. CONCLUSION Characterization of Hdh-CRZRs and Hdh-GnRHRs and their cognate peptides provides new insight into the evolutionary route of GnRH-related signaling systems in bilaterians.
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Affiliation(s)
- Mi Ae Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Tae Ha Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Priyadharshini Kannan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Kang Hee Kho
- Department of Fisheries Science, Chonnam National University, Yeosu, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Republic of Korea
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17
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Li C, Ma QY, Liu XQ, Li HD, Yu MJ, Xie SS, Ma WX, Chen Y, Wang JN, He RB, Bian HG, He Y, Gao L, Deng SS, Zang HM, Gong Q, Wen JG, Liu MM, Yang C, Chen HY, Li J, Lan HY, Jin J, Yao RS, Meng XM. Genetic and pharmacological inhibition of GRPR protects against acute kidney injury via attenuating renal inflammation and necroptosis. Mol Ther 2023; 31:2734-2754. [PMID: 37415332 PMCID: PMC10492025 DOI: 10.1016/j.ymthe.2023.06.016] [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: 02/16/2023] [Revised: 05/16/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023] Open
Abstract
Gastrin-releasing peptide (GRP) binds to its receptor (GRP receptor [GRPR]) to regulate multiple biological processes, but the function of GRP/GRPR axis in acute kidney injury (AKI) remains unknown. In the present study, GRPR is highly expressed by tubular epithelial cells (TECs) in patients or mice with AKI, while histone deacetylase 8 may lead to the transcriptional activation of GRPR. Functionally, we uncovered that GRPR was pathogenic in AKI, as genetic deletion of GRPR was able to protect mice from cisplatin- and ischemia-induced AKI. This was further confirmed by specifically deleting the GRPR gene from TECs in GRPRFlox/Flox//KspCre mice. Mechanistically, we uncovered that GRPR was able to interact with Toll-like receptor 4 to activate STAT1 that bound the promoter of MLKL and CCL2 to induce TEC necroptosis, necroinflammation, and macrophages recruitment. This was further confirmed by overexpressing STAT1 to restore renal injury in GRPRFlox/Flox/KspCre mice. Concurrently, STAT1 induced GRP synthesis to enforce the GRP/GRPR/STAT1 positive feedback loop. Importantly, targeting GRPR by lentivirus-packaged small hairpin RNA or by treatment with a novel GRPR antagonist RH-1402 was able to inhibit cisplatin-induced AKI. In conclusion, GRPR is pathogenic in AKI and mediates AKI via the STAT1-dependent mechanism. Thus, targeting GRPR may be a novel therapeutic strategy for AKI.
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Affiliation(s)
- Chao Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Qiu-Ying Ma
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Anhui Public Health Clinical Center, No. 100 Huaihai Road, Hefei 230012, China
| | - Xue-Qi Liu
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Hai-di Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ming-Jun Yu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shuai-Shuai Xie
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Wen-Xian Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ying Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Jia-Nan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ruo-Bing He
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - He-Ge Bian
- Department of Pharmacology, School of Basic Medical Sciences, Key Laboratory of Anti-inflammatory and Immunopharmacology, Ministry of Education, Anhui Medical University, Hefei 230032, China
| | - Yuan He
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Li Gao
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Sheng-Song Deng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hong-Mei Zang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Qian Gong
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ming-Ming Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Chen Yang
- Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 57 Renmin Road, Zhanjiang 524001, China
| | - Hai-Yong Chen
- Department of Chinese Medicine, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Shenzhen 518009, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Liu Che Woo Institute of Innovative Medicine, Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Juan Jin
- Department of Pharmacology, School of Basic Medical Sciences, Key Laboratory of Anti-inflammatory and Immunopharmacology, Ministry of Education, Anhui Medical University, Hefei 230032, China.
| | - Ri-Sheng Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China.
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18
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Goldtzvik Y, Sen N, Lam SD, Orengo C. Protein diversification through post-translational modifications, alternative splicing, and gene duplication. Curr Opin Struct Biol 2023; 81:102640. [PMID: 37354790 DOI: 10.1016/j.sbi.2023.102640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/26/2023]
Abstract
Proteins provide the basis for cellular function. Having multiple versions of the same protein within a single organism provides a way of regulating its activity or developing novel functions. Post-translational modifications of proteins, by means of adding/removing chemical groups to amino acids, allow for a well-regulated and controlled way of generating functionally distinct protein species. Alternative splicing is another method with which organisms possibly generate new isoforms. Additionally, gene duplication events throughout evolution generate multiple paralogs of the same genes, resulting in multiple versions of the same protein within an organism. In this review, we discuss recent advancements in the study of these three methods of protein diversification and provide illustrative examples of how they affect protein structure and function.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Neeladri Sen
- Department of Structural and Molecular Biology, University College London, London, United Kingdom. https://twitter.com/@NeeladriSen
| | - Su Datt Lam
- Department of Structural and Molecular Biology, University College London, London, United Kingdom; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London, London, United Kingdom.
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19
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Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE. The computational capabilities of many-to-many protein interaction networks. Cell Syst 2023; 14:430-446. [PMID: 37348461 PMCID: PMC10318606 DOI: 10.1016/j.cels.2023.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.
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Affiliation(s)
- Heidi E Klumpe
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Yaron E Antebi
- Department of Molecular Genetics, Weizmann Institute of Science 76100, Rehovot, Israel.
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20
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Mathy CJP, Kortemme T. Emerging maps of allosteric regulation in cellular networks. Curr Opin Struct Biol 2023; 80:102602. [PMID: 37150039 PMCID: PMC10960510 DOI: 10.1016/j.sbi.2023.102602] [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: 12/29/2022] [Revised: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Allosteric regulation is classically defined as action at a distance, where a perturbation outside of a protein active site affects function. While this definition has motivated many studies of allosteric mechanisms at the level of protein structure, translating these insights to the allosteric regulation of entire cellular processes - and their crosstalk - has received less attention, despite the broad importance of allostery for cellular regulation foreseen by Jacob and Monod. Here, we revisit an evolutionary model for the widespread emergence of allosteric regulation in colocalized proteins, describe supporting evidence, and discuss emerging advances in mapping allostery in cellular networks that link precise and often allosteric perturbations at the molecular level to functional changes at the pathway and systems levels.
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Affiliation(s)
- Christopher J P Mathy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, CA, 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, 94158, USA.
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, CA, 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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21
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Im DS. Recent advances in GPR35 pharmacology; 5-HIAA serotonin metabolite becomes a ligand. Arch Pharm Res 2023:10.1007/s12272-023-01449-y. [PMID: 37227682 DOI: 10.1007/s12272-023-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
GPR35, an orphan receptor, has been waiting for its ligand since its cloning in 1998. Many endogenous and exogenous molecules have been suggested to act as agonists of GPR35 including kynurenic acid, zaprinast, lysophosphatidic acid, and CXCL17. However, complex and controversial responses to ligands among species have become a huge hurdle in the development of therapeutics in addition to the orphan state. Recently, a serotonin metabolite, 5-hydroxyindoleacetic acid (5-HIAA), is reported to be a high potency ligand for GPR35 by investigating the increased expression of GPR35 in neutrophils. In addition, a transgenic knock-in mouse line is developed, in which GPR35 was replaced with a human ortholog, making it possible not only to overcome the different selectivity of agonists among species but also to conduct therapeutic experiments on human GPR35 in mouse models. In the present article, I review the recent advances and prospective therapeutic directions in GPR35 research. Especially, I'd like to draw attention of readers to the finding of 5-HIAA as a ligand of GPR35 and lead to apply the 5-HIAA and human GPR35 knock-in mice to their research fields in a variety of pathophysiological conditions.
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Affiliation(s)
- Dong-Soon Im
- Department of Biomedical and Pharmaceutical Sciences and Department of Fundamental Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, 02446, Republic of Korea.
- Laboratory of Pharmacology, College of Pharmacy, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
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22
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Mincarelli L, Uzun V, Wright D, Scoones A, Rushworth SA, Haerty W, Macaulay IC. Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells. Commun Biol 2023; 6:558. [PMID: 37225862 PMCID: PMC10209181 DOI: 10.1038/s42003-023-04936-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor, marked by changes in gene expression. However, many of these approaches neglect isoform-level information and thus do not capture the extent of alternative splicing within the system. Here, we present an integrated short- and long-read single-cell RNA-seq analysis of haematopoietic stem and progenitor cells. We demonstrate that over half of genes detected in standard short-read single-cell analyses are expressed as multiple, often functionally distinct, isoforms, including many transcription factors and key cytokine receptors. We observe global and HSC-specific changes in gene expression with ageing but limited impact of ageing on isoform usage. Integrating single-cell and cell-type-specific isoform landscape in haematopoiesis thus provides a new reference for comprehensive molecular profiling of heterogeneous tissues, as well as novel insights into transcriptional complexity, cell-type-specific splicing events and consequences of ageing.
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Affiliation(s)
- Laura Mincarelli
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
| | - Vladimir Uzun
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - David Wright
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Anita Scoones
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Stuart A Rushworth
- Norwich Medical School, The University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
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23
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Chen G, Obal D. Detecting and measuring of GPCR signaling - comparison of human induced pluripotent stem cells and immortal cell lines. Front Endocrinol (Lausanne) 2023; 14:1179600. [PMID: 37293485 PMCID: PMC10244570 DOI: 10.3389/fendo.2023.1179600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/12/2023] [Indexed: 06/10/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family of transmembrane proteins that play a major role in many physiological processes, and thus GPCR-targeted drug development has been widely promoted. Although research findings generated in immortal cell lines have contributed to the advancement of the GPCR field, the homogenous genetic backgrounds, and the overexpression of GPCRs in these cell lines make it difficult to correlate the results with clinical patients. Human induced pluripotent stem cells (hiPSCs) have the potential to overcome these limitations, because they contain patient specific genetic information and can differentiate into numerous cell types. To detect GPCRs in hiPSCs, highly selective labeling and sensitive imaging techniques are required. This review summarizes existing resonance energy transfer and protein complementation assay technologies, as well as existing and new labeling methods. The difficulties of extending existing detection methods to hiPSCs are discussed, as well as the potential of hiPSCs to expand GPCR research towards personalized medicine.
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Affiliation(s)
- Gaoxian Chen
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - Detlef Obal
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, United States
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24
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Mészáros B, Park E, Malinverni D, Sejdiu BI, Immadisetty K, Sandhu M, Lang B, Babu MM. Recent breakthroughs in computational structural biology harnessing the power of sequences and structures. Curr Opin Struct Biol 2023; 80:102608. [PMID: 37182396 DOI: 10.1016/j.sbi.2023.102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
Recent advances in computational approaches and their integration into structural biology enable tackling increasingly complex questions. Here, we discuss several key areas, highlighting breakthroughs and remaining challenges. Theoretical modeling has provided tools to accurately predict and design protein structures on a scale currently difficult to achieve using experimental approaches. Molecular Dynamics simulations have become faster and more precise, delivering actionable information inaccessible by current experimental methods. Virtual screening workflows allow a high-throughput approach to discover ligands that bind and modulate protein function, while Machine Learning methods enable the design of proteins with new functionalities. Integrative structural biology combines several of these approaches, pushing the frontiers of structural and functional characterization to ever larger systems, advancing towards a complete understanding of the living cell. These breakthroughs will accelerate and significantly impact diverse areas of science.
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Affiliation(s)
- Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Electa Park
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Duccio Malinverni
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/DucMalinverni
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/bisejdiu
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation & Cellular Therapy, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/k_immadisetty
| | - Manbir Sandhu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/M5andhu
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/langbnj
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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25
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Milligan G. GPR35: from enigma to therapeutic target. Trends Pharmacol Sci 2023; 44:263-273. [PMID: 37002007 DOI: 10.1016/j.tips.2023.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 04/16/2023]
Abstract
The orphan G-protein-coupled receptor 35 (GPR35), although poorly characterised, is attracting considerable interest as a therapeutic target. Marked differences in pharmacology between human and rodent orthologues of the receptor and a dearth of antagonists with affinity for mouse and rat GPR35 have previously restricted the use of preclinical disease models. The development of improved ligands, novel transgenic knock-in mouse lines, and detailed analysis of the disease relevance of single-nucleotide polymorphisms (SNPs) have greatly enhanced understanding of the key roles of GPR35 and have stimulated efforts towards disease-targeted proof-of-concept studies. In this opinion article, new information on the biology of the receptor is considered, whilst insight into how GPR35 is currently being assessed for therapeutic utility - in areas ranging from inflammatory bowel diseases to nonalcoholic steatohepatitis and various cancers - is also provided.
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Affiliation(s)
- Graeme Milligan
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
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26
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Cheng Y, Kang XZ, Chan P, Cheung PHH, Cheng T, Ye ZW, Chan CP, Yu CH, Jin DY. FACI is a novel clathrin adaptor protein 2-binding protein that facilitates low-density lipoprotein endocytosis. Cell Biosci 2023; 13:74. [PMID: 37072871 PMCID: PMC10114425 DOI: 10.1186/s13578-023-01023-5] [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: 12/19/2022] [Accepted: 03/27/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Cholesterol plays a vital role in multiple physiological processes. Cellular uptake of cholesterol is mediated primarily through endocytosis of low-density lipoprotein (LDL) receptor. New modifiers of this process remain to be characterized. Particularly, the role of fasting- and CREB-H-induced (FACI) protein in cholesterol homeostasis merits further investigation. METHODS Interactome profiling by proximity labeling and affinity purification - mass spectrometry was performed. Total internal reflection fluorescence microscopy and confocal immunofluorescence microscopy were used to analyze protein co-localization and interaction. Mutational analysis was carried out to define the domain and residues required for FACI localization and function. Endocytosis was traced by fluorescent cargos. LDL uptake in cultured cells and diet-induced hypercholesterolemia in mice were assessed. RESULTS FACI interacted with proteins critically involved in clathrin-mediated endocytosis, vesicle trafficking, and membrane cytoskeleton. FACI localized to clathrin-coated pits (CCP) on plasma membranes. FACI contains a conserved DxxxLI motif, which mediates its binding with the adaptor protein 2 (AP2) complex. Disruption of this motif of FACI abolished its CCP localization but didn't affect its association with plasma membrane. Cholesterol was found to facilitate FACI transport from plasma membrane to endocytic recycling compartment in a clathrin- and cytoskeleton-dependent manner. LDL endocytosis was enhanced in FACI-overexpressed AML12 cells but impaired in FACI-depleted HeLa cells. In vivo study indicated that hepatic FACI overexpression alleviated diet-induced hypercholesterolemia in mice. CONCLUSIONS FACI facilitates LDL endocytosis through its interaction with the AP2 complex.
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Affiliation(s)
- Yun Cheng
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
| | - Xiao-Zhuo Kang
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Pearl Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Pak-Hin Hinson Cheung
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Tao Cheng
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Zi-Wei Ye
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Cheng-Han Yu
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
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27
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Heng J, Hu Y, Pérez-Hernández G, Inoue A, Zhao J, Ma X, Sun X, Kawakami K, Ikuta T, Ding J, Yang Y, Zhang L, Peng S, Niu X, Li H, Guixà-González R, Jin C, Hildebrand PW, Chen C, Kobilka BK. Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor. Nat Commun 2023; 14:2005. [PMID: 37037825 PMCID: PMC10085991 DOI: 10.1038/s41467-023-37233-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
Advances in structural biology have provided important mechanistic insights into signaling by the transmembrane core of G-protein coupled receptors (GPCRs); however, much less is known about intrinsically disordered regions such as the carboxyl terminus (CT), which is highly flexible and not visible in GPCR structures. The β2 adrenergic receptor's (β2AR) 71 amino acid CT is a substrate for GPCR kinases and binds β-arrestins to regulate signaling. Here we show that the β2AR CT directly inhibits basal and agonist-stimulated signaling in cell lines lacking β-arrestins. Combining single-molecule fluorescence resonance energy transfer (FRET), NMR spectroscopy, and molecular dynamics simulations, we reveal that the negatively charged β2AR-CT serves as an autoinhibitory factor via interacting with the positively charged cytoplasmic surface of the receptor to limit access to G-proteins. The stability of this interaction is influenced by agonists and allosteric modulators, emphasizing that the CT plays important role in allosterically regulating GPCR activation.
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Affiliation(s)
- Jie Heng
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
| | - Guillermo Pérez-Hernández
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Charitéplatz 1, 10117, Berlin, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Jiawei Zhao
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiuyan Ma
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xiaoou Sun
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Tatsuya Ikuta
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yujie Yang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lujia Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Sijia Peng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hongwei Li
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232, Villigen, PSI, Switzerland
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peter W Hildebrand
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Medical Physics and Biophysics, University Leipzig, 04107, Leipzig, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Krohl PJ, Fine J, Yang H, VanDyke D, Ang Z, Kim KB, Thomas-Tikhonenko A, Spangler JB. Discovery of antibodies targeting multipass transmembrane proteins using a suspension cell-based evolutionary approach. CELL REPORTS METHODS 2023; 3:100429. [PMID: 37056366 PMCID: PMC10088246 DOI: 10.1016/j.crmeth.2023.100429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/06/2023] [Accepted: 02/21/2023] [Indexed: 04/15/2023]
Abstract
Due to their critical functions in cell sensing and signal processing, membrane proteins are highly preferred as pharmacological targets, and antibody drugs constitute the fastest growing category of therapeutic agents on the pharmaceutical market. However, major limitations exist in developing antibodies that recognize complex, multipass transmembrane proteins, such as G-protein-coupled receptors (GPCRs). These challenges, largely due to difficulties with recombinant expression of multipass transmembrane proteins, can be overcome using whole-cell screening techniques, which enable presentation of the functional antigen in its native conformation. Here, we developed suspension cell-based whole-cell panning methodologies to screen for specific binders against GPCRs within a naive yeast-displayed antibody library. We implemented our strategy to discover high-affinity antibodies against four distinct GPCR target proteins, demonstrating the potential for our cell-based screening workflow to advance the discovery of antibody therapeutics targeting membrane proteins.
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Affiliation(s)
- Patrick J. Krohl
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Justyn Fine
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Huilin Yang
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Derek VanDyke
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Zhiwei Ang
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kook Bum Kim
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie B. Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21208, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21208, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University Baltimore, MD 21231, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21287, USA
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29
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A multi-dimensional view of context-dependent G protein-coupled receptor function. Biochem Soc Trans 2023; 51:13-20. [PMID: 36688421 PMCID: PMC9987931 DOI: 10.1042/bst20210650] [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: 12/05/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/24/2023]
Abstract
G protein-coupled receptor (GPCR) family members can sense an extraordinary variety of biomolecules to activate intracellular signalling cascades that modulate key aspects of cell physiology. Apart from their crucial role in maintaining cell homeostasis, these critical sensory and modulatory properties have made GPCRs the most successful drug target class to date. However, establishing direct links between receptor activation of specific intracellular partners and individual physiological outcomes is still an ongoing challenge. By studying this receptor signalling complexity at increasing resolution through the development of novel biosensors and high-throughput techniques, a growing number of studies are revealing how receptor function can be diversified in a spatial, temporal or cell-specific manner. This mini-review will introduce recent examples of this context-dependent receptor signalling and discuss how it can impact our understanding of receptor function in health and disease, and contribute to the search of more selective, efficacious and safer GPCR drug candidates.
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30
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Rahman SN, McNaught-Flores DA, Huppelschoten Y, da Costa Pereira D, Christopoulos A, Leurs R, Langmead CJ. Structural and Molecular Determinants for Isoform Bias at Human Histamine H 3 Receptor Isoforms. ACS Chem Neurosci 2023; 14:645-656. [PMID: 36702158 DOI: 10.1021/acschemneuro.2c00425] [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] [Indexed: 01/28/2023] Open
Abstract
The human histamine H3 receptor (hH3R) is predominantly expressed in the CNS, where it regulates the synthesis and release of histamine and other neurotransmitters. Due to its neuromodulatory role, the hH3R has been associated with various CNS disorders, including Alzheimer's and Parkinson's disease. Markedly, the hH3R gene undergoes extensive splicing, resulting in 20 isoforms, of which 7TM isoforms exhibit variations in the intracellular loop 3 (IL3) and/or C-terminal tail. Particularly, hH3R isoforms that display variations in IL3 (e.g., hH3R-365) are shown to differentially signal via Gαi-dependent pathways upon binding of biased agonists (e.g., immepip, proxifan, imetit). Nevertheless, the mechanisms underlying biased agonism at hH3R isoforms remain unknown. Using a structure-function relationship study with a broad range of H3R agonists, we thereby explored determinants underlying isoform bias at hH3R isoforms that exhibit variations in IL3 (i.e., hH3R-445, -415, -365, and -329) in a Gαi-dependent pathway (cAMP inhibition). Hence, we systematically characterized hH3R isoforms on isoform bias by comparing various ligand properties (i.e., structural and molecular) to the degree of isoform bias. Importantly, our study provides novel insights into the structural and molecular basis of receptor isoform bias, highlighting the importance to study GPCRs with multiple isoforms to better tailor drugs.
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Affiliation(s)
- Sabrina N Rahman
- Amsterdam Institute for Molecular Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZAmsterdam, The Netherlands.,Drug Discovery Biology and Neuromedicines Discovery Centre, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, Melbourne, 3052VIC, Australia
| | - Daniel A McNaught-Flores
- Amsterdam Institute for Molecular Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZAmsterdam, The Netherlands
| | - Yara Huppelschoten
- Amsterdam Institute for Molecular Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZAmsterdam, The Netherlands
| | - Daniel da Costa Pereira
- Amsterdam Institute for Molecular Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZAmsterdam, The Netherlands
| | - Arthur Christopoulos
- Drug Discovery Biology and Neuromedicines Discovery Centre, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, Melbourne, 3052VIC, Australia
| | - Rob Leurs
- Amsterdam Institute for Molecular Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZAmsterdam, The Netherlands
| | - Christopher J Langmead
- Drug Discovery Biology and Neuromedicines Discovery Centre, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, Melbourne, 3052VIC, Australia
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31
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Ullo MF, Case LB. How cells sense and integrate information from different sources. WIREs Mech Dis 2023:e1604. [PMID: 36781396 DOI: 10.1002/wsbm.1604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
Cell signaling is a fundamental cellular process that enables cells to sense and respond to information in their surroundings. At the molecular level, signaling is primarily carried out by transmembrane protein receptors that can initiate complex downstream signal transduction cascades to alter cellular behavior. In the human body, different cells can be exposed to a wide variety of environmental conditions, and cells express diverse classes of receptors capable of sensing and integrating different signals. Furthermore, different receptors and signaling pathways can crosstalk with each other to calibrate the cellular response. Crosstalk occurs through multiple mechanisms at different levels of signaling pathways. In this review, we discuss how cells sense and integrate different chemical, mechanical, and spatial signals as well as the mechanisms of crosstalk between pathways. To illustrate these concepts, we use a few well-studied signaling pathways, including receptor tyrosine kinases and integrin receptors. Finally, we discuss the implications of dysregulated cellular sensing on driving diseases such as cancer. This article is categorized under: Cancer > Molecular and Cellular Physiology Metabolic Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Maria F Ullo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Pándy-Szekeres G, Caroli J, Mamyrbekov A, Kermani AA, Keserű G, Kooistra A, Gloriam DE. GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources. Nucleic Acids Res 2023; 51:D395-D402. [PMID: 36395823 PMCID: PMC9825476 DOI: 10.1093/nar/gkac1013] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/15/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are physiologically abundant signaling hubs routing hundreds of extracellular signal substances and drugs into intracellular pathways. The GPCR database, GPCRdb supports >5000 interdisciplinary researchers every month with reference data, analysis, visualization, experiment design and dissemination. Here, we present our fifth major GPCRdb release setting out with an overview of the many resources for receptor sequences, structures, and ligands. This includes recently published additions of class D generic residue numbers, a comparative structure analysis tool to identify functional determinants, trees clustering GPCR structures by 3D conformation, and mutations stabilizing inactive/active states. We provide new state-specific structure models of all human non-olfactory GPCRs built using AlphaFold2-MultiState. We also provide a new resource of endogenous ligands along with a larger number of surrogate ligands with bioactivity, vendor, and physiochemical descriptor data. The one-stop-shop ligand resources integrate ligands/data from the ChEMBL, Guide to Pharmacology, PDSP Ki and PubChem database. The GPCRdb is available at https://gpcrdb.org.
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Affiliation(s)
- Gáspár Pándy-Szekeres
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest H-1117, Hungary
| | - Jimmy Caroli
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Alibek Mamyrbekov
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest H-1117, Hungary
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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33
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Hillman T. A Predictive Model for Identifying the Most Effective Anti-CCR5 Monoclonal Antibody. ARCHIVES OF PHARMACY PRACTICE 2023. [DOI: 10.51847/d9m2zufqr4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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34
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Karakulak T, Szklarczyk D, Saylan CC, Moch H, von Mering C, Kahraman A. CanIsoNet: a database to study the functional impact of isoform switching events in diseases. BIOINFORMATICS ADVANCES 2023; 3:vbad050. [PMID: 37123454 PMCID: PMC10133402 DOI: 10.1093/bioadv/vbad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 05/02/2023]
Abstract
Motivation Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases. Results Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks. Availability and implementation CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tülay Karakulak
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Cemil Can Saylan
- Computational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Reşitpaşa, İTÜ Ayazağa Kampüsü, Istanbul, 34467, Türkiye
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, 8006, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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35
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Soutar MPM, Melandri D, O’Callaghan B, Annuario E, Monaghan AE, Welsh NJ, D’Sa K, Guelfi S, Zhang D, Pittman A, Trabzuni D, Verboven AHA, Pan KS, Kia DA, Bictash M, Gandhi S, Houlden H, Cookson MR, Kasri NN, Wood NW, Singleton AB, Hardy J, Whiting PJ, Blauwendraat C, Whitworth AJ, Manzoni C, Ryten M, Lewis PA, Plun-Favreau H. Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson's disease at 16q11.2 and MAPT H1 loci. Brain 2022; 145:4349-4367. [PMID: 36074904 PMCID: PMC9762952 DOI: 10.1093/brain/awac325] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 02/02/2023] Open
Abstract
Parkinson's disease is a common incurable neurodegenerative disease. The identification of genetic variants via genome-wide association studies has considerably advanced our understanding of the Parkinson's disease genetic risk. Understanding the functional significance of the risk loci is now a critical step towards translating these genetic advances into an enhanced biological understanding of the disease. Impaired mitophagy is a key causative pathway in familial Parkinson's disease, but its relevance to idiopathic Parkinson's disease is unclear. We used a mitophagy screening assay to evaluate the functional significance of risk genes identified through genome-wide association studies. We identified two new regulators of PINK1-dependent mitophagy initiation, KAT8 and KANSL1, previously shown to modulate lysine acetylation. These findings suggest PINK1-mitophagy is a contributing factor to idiopathic Parkinson's disease. KANSL1 is located on chromosome 17q21 where the risk associated gene has long been considered to be MAPT. While our data do not exclude a possible association between the MAPT gene and Parkinson's disease, they provide strong evidence that KANSL1 plays a crucial role in the disease. Finally, these results enrich our understanding of physiological events regulating mitophagy and establish a novel pathway for drug targeting in neurodegeneration.
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Affiliation(s)
- Marc P M Soutar
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Daniela Melandri
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Benjamin O’Callaghan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Emily Annuario
- Department of Basic and Clinical Neuroscience, King’s College, London, UK
| | - Amy E Monaghan
- UCL Alzheimer’s Research UK, Drug Discovery Institute, London, UK
- UCL Dementia Research Institute, London, UK
| | - Natalie J Welsh
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Karishma D’Sa
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Francis Crick Institute, London, UK
| | - Sebastian Guelfi
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David Zhang
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Alan Pittman
- Genetics Research Centre, Molecular and Clinical Sciences, St Georges University, London, UK
| | - Daniah Trabzuni
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Anouk H A Verboven
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Kylie S Pan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Demis A Kia
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Magda Bictash
- UCL Alzheimer’s Research UK, Drug Discovery Institute, London, UK
- UCL Dementia Research Institute, London, UK
| | - Sonia Gandhi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Francis Crick Institute, London, UK
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Nicholas W Wood
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- UCL Dementia Research Institute, London, UK
| | - Paul J Whiting
- UCL Alzheimer’s Research UK, Drug Discovery Institute, London, UK
- UCL Dementia Research Institute, London, UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Claudia Manzoni
- Department of Pharmacology, UCL School of Pharmacy, London, UK
| | - Mina Ryten
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Patrick A Lewis
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Comparative Biomedical Sciences, Royal Veterinary College, LondonUK
| | - Hélène Plun-Favreau
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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36
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Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol 2022; 12:1051487. [PMID: 36505834 PMCID: PMC9730332 DOI: 10.3389/fonc.2022.1051487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer-specific alternatively spliced events (ASE) play a role in cancer pathogenesis and can be targeted by immunotherapy, oligonucleotide therapy, and small molecule inhibition. However, identifying actionable ASE targets remains challenging due to the uncertainty of its protein product, structure impact, and proteoform (protein isoform) function. Here we argue that an integrated multi-omics profiling strategy can overcome these challenges, allowing us to mine this untapped source of targets for therapeutic development. In this review, we will provide an overview of current multi-omics strategies in characterizing ASEs by utilizing the transcriptome, proteome, and state-of-art algorithms for protein structure prediction. We will discuss limitations and knowledge gaps associated with each technology and informatics analytics. Finally, we will discuss future directions that will enable the full integration of multi-omics data for ASE target discovery.
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Affiliation(s)
- Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States,*Correspondence: Timothy I. Shaw,
| | - Bi Zhao
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Brandon Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Aleksandra Karolak
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
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37
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Tasma Z, Siow A, Harris PWR, Brimble MA, O’Carroll SJ, Hay DL, Walker CS. PAC 1, VPAC 1, and VPAC 2 Receptor Expression in Rat and Human Trigeminal Ganglia: Characterization of PACAP-Responsive Receptor Antibodies. Int J Mol Sci 2022; 23:ijms232213797. [PMID: 36430275 PMCID: PMC9697343 DOI: 10.3390/ijms232213797] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
Pituitary adenylate cyclase-activating peptide (PACAP) is a neuropeptide expressed in the trigeminal ganglia (TG). The TG conducts nociceptive signals in the head and may play roles in migraine. PACAP infusion provokes headaches in healthy individuals and migraine-like attacks in patients; however, it is not clear whether targeting this system could be therapeutically efficacious. To effectively target the PACAP system, an understanding of PACAP receptor distribution is required. Therefore, this study aimed to characterize commercially available antibodies and use these to detect PACAP-responsive receptors in the TG. Antibodies were initially validated in receptor transfected cell models and then used to explore receptor expression in rat and human TG. Antibodies were identified that could detect PACAP-responsive receptors, including the first antibody to differentiate between the PAC1n and PAC1s receptor splice variants. PAC1, VPAC1, and VPAC2 receptor-like immunoreactivity were observed in subpopulations of both neuronal and glial-like cells in the TG. In this study, PAC1, VPAC1, and VPAC2 receptors were detected in the TG, suggesting they are all potential targets to treat migraine. These antibodies may be useful tools to help elucidate PACAP-responsive receptor expression in tissues. However, most antibodies exhibited limitations, requiring the use of multiple methodologies and the careful inclusion of controls.
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Affiliation(s)
- Zoe Tasma
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Andrew Siow
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Paul W. R. Harris
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Margaret A. Brimble
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Simon J. O’Carroll
- Department of Anatomy and Medical Imaging, and Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, Auckland 1023, New Zealand
| | - Debbie L. Hay
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Department of Pharmacology and Toxicology, The University of Otago, Dunedin 9016, New Zealand
| | - Christopher S. Walker
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Correspondence:
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38
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Zaręba P, Partyka A, Latacz G, Satała G, Zajdel P, Jaśkowska J. New, Eco-Friendly Method for Synthesis of 3-Chlorophenyl and 1,1'-Biphenyl Piperazinylhexyl Trazodone Analogues with Dual 5-HT 1A/5-HT 7 Affinity and Its Antidepressant-like Activity. Molecules 2022; 27:7270. [PMID: 36364104 PMCID: PMC9658223 DOI: 10.3390/molecules27217270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 07/25/2023] Open
Abstract
Serotonin 5-HT1A and 5-HT7 receptors play an important role in the pathogenesis and pharmacotherapy of depression. Previously identified N-hexyl trazodone derivatives, 2-(6-(4-(3-chlorophenyl)piperazin-1-yl)hexyl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one hydrochloride (7a·HCl), with high affinity for 5-HT1AR and 2-(6-(4-([1,1'-biphenyl]-2-yl)piperazin-1-yl)hexyl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one hydrochloride (7b·HCl), a dual-acting 5-HT1A/5-HT7 receptor ligand, were prepared with a new microwave-assisted method. The protocol for the synthesis of 7a and 7b involved reductive alkylation under a mild reducing agent. We produced the final compounds with yield of 56-63% using ethanol or 51-56% in solvent-free conditions in 4 min. We then determined the 5-HT7R binding mode for compounds 7a and 7b using in silico methods and assessed the preliminary ADME and safety properties (hepatotoxicity and CYP3A4 inhibition) using in vitro methods for 7a·HCl and 7b·HCl. Furthermore, we evaluated antidepressant-like activity of the dual antagonist of 5-HT1A/5-HT7 receptors (7b·HCl) in the forced swim test (FST) in mice. The 5-HT1AR ligand (7a·HCl) with a much lower affinity for 5-HT7R compared to that of 7b·HCl was tested comparatively. Both compounds showed antidepressant activity, while 5-HT1A/5-HT7 double antagonist 7b·HCl showed a stronger and more specific response.
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Affiliation(s)
- Przemysław Zaręba
- Faculty of Chemical Engineering and Technology, Department of Chemical Technology and Environmental Analytics, Cracow University of Technology, 24 Warszawska Street, 31-155 Cracow, Poland
| | - Anna Partyka
- Department of Clinical Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Cracow, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Cracow, Poland
| | - Grzegorz Satała
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343 Kraków, Poland
| | - Paweł Zajdel
- Department of Organic Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Cracow, Poland
| | - Jolanta Jaśkowska
- Faculty of Chemical Engineering and Technology, Department of Organic Chemistry and Technology, Cracow University of Technology, 24 Warszawska Street, 31-155 Cracow, Poland
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39
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Kumar GA, Puthenveedu MA. Diversity and specificity in location-based signaling outputs of neuronal GPCRs. Curr Opin Neurobiol 2022; 76:102601. [DOI: 10.1016/j.conb.2022.102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
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40
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Schihada H, Klompstra TM, Humphrys LJ, Cervenka I, Dadvar S, Kolb P, Ruas JL, Schulte G. Isoforms of GPR35 have distinct extracellular N-termini that allosterically modify receptor-transducer coupling and mediate intracellular pathway bias. J Biol Chem 2022; 298:102328. [PMID: 35933013 PMCID: PMC9450150 DOI: 10.1016/j.jbc.2022.102328] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022] Open
Abstract
Within the intestine, the human G protein–coupled receptor (GPCR) GPR35 is involved in oncogenic signaling, bacterial infections, and inflammatory bowel disease. GPR35 is known to be expressed as two distinct isoforms that differ only in the length of their extracellular N-termini by 31 amino acids, but detailed insights into their functional differences are lacking. Through gene expression analysis in immune and gastrointestinal cells, we show that these isoforms emerge from distinct promoter usage and alternative splicing. Additionally, we employed optical assays in living cells to thoroughly profile both GPR35 isoforms for constitutive and ligand-induced activation and signaling of 10 different heterotrimeric G proteins, ligand-induced arrestin recruitment, and receptor internalization. Our results reveal that the extended N-terminus of the long isoform limits G protein activation yet elevates receptor–β-arrestin interaction. To better understand the structural basis for this bias, we examined structural models of GPR35 and conducted experiments with mutants of both isoforms. We found that a proposed disulfide bridge between the N-terminus and extracellular loop 3, present in both isoforms, is crucial for constitutive G13 activation, while an additional cysteine contributed by the extended N-terminus of the long GPR35 isoform limits the extent of agonist-induced receptor–β-arrestin2 interaction. The pharmacological profiles and mechanistic insights of our study provide clues for the future design of isoform-specific GPR35 ligands that selectively modulate GPR35–transducer interactions and allow for mechanism-based therapies against, for example, inflammatory bowel disease or bacterial infections of the gastrointestinal system.
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Affiliation(s)
- Hannes Schihada
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Thomas M Klompstra
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Laura J Humphrys
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - Igor Cervenka
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Shamim Dadvar
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Schulte
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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41
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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42
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McKay K, Hamilton NB, Remington JM, Schneebeli ST, Li J. Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery. Front Mol Biosci 2022; 9:879212. [PMID: 35847975 PMCID: PMC9277106 DOI: 10.3389/fmolb.2022.879212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022] Open
Abstract
The lack of biologically relevant protein structures can hinder rational design of small molecules to target G protein-coupled receptors (GPCRs). While ensemble docking using multiple models of the protein target is a promising technique for structure-based drug discovery, model clustering and selection still need further investigations to achieve both high accuracy and efficiency. In this work, we have developed an original ensemble docking approach, which identifies the most relevant conformations based on the essential dynamics of the protein pocket. This approach is applied to the study of small-molecule antagonists for the PAC1 receptor, a class B GPCR and a regulator of stress. As few as four representative PAC1 models are selected from simulations of a homology model and then used to screen three million compounds from the ZINC database and 23 experimentally validated compounds for PAC1 targeting. Our essential dynamics ensemble docking (EDED) approach can effectively reduce the number of false negatives in virtual screening and improve the accuracy to seek potent compounds. Given the cost and difficulties to determine membrane protein structures for all the relevant states, our methodology can be useful for future discovery of small molecules to target more other GPCRs, either with or without experimental structures.
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43
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Kühnen P, Biebermann H, Wiegand S. Pharmacotherapy in Childhood Obesity. Horm Res Paediatr 2022; 95:177-192. [PMID: 34351307 DOI: 10.1159/000518432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The increasing number of obese children and adolescence is a major problem in health-care systems. Currently, the gold standard for the treatment of these patients with obesity is a multicomponent lifestyle intervention. Unfortunately, this strategy is not leading to a substantial and long-lasting weight loss in the majority of patients. This is the reason why there is an urgent need to establish new treatment strategies for children and adolescents with obesity to reduce the risk for the development of any comorbidities like cardiovascular diseases or diabetes mellitus type 2. SUMMARY In this review, we outline available pharmacological therapeutic options for children and compare the available study data with the outcome of conservative treatment approaches. KEY MESSAGES We discussed, in detail, how knowledge about underlying molecular mechanisms might support the identification of effective antiobesity drugs in the future and in which way this might modulate current treatment strategies to support children and adolescence with obesity to lose body weight.
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Affiliation(s)
- Peter Kühnen
- Institute for Experimental Pediatric Endocrinology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Heike Biebermann
- Institute for Experimental Pediatric Endocrinology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Susanna Wiegand
- Center for Social-Pediatric Care/Pediatric Endocrinology and Diabetology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
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44
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Lengger B, Hoch-Schneider EE, Jensen CN, Jakočiu̅nas T, Petersen AA, Frimurer TM, Jensen ED, Jensen MK. Serotonin G Protein-Coupled Receptor-Based Biosensing Modalities in Yeast. ACS Sens 2022; 7:1323-1335. [PMID: 35452231 PMCID: PMC9150182 DOI: 10.1021/acssensors.1c02061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/17/2022] [Indexed: 11/29/2022]
Abstract
Serotonin is a key neurotransmitter involved in numerous physiological processes and serves as an important precursor for manufacturing bioactive indoleamines and alkaloids used in the treatment of human pathologies. In humans, serotonin sensing and signaling can occur by 12 G protein-coupled receptors (GPCRs) coupled to Gα proteins. In yeast, human serotonin GPCRs coupled to Gα proteins have previously been shown to function as whole-cell biosensors of serotonin. However, systematic characterization of serotonin biosensing modalities between variant serotonin GPCRs and application thereof for high-resolution serotonin quantification is still awaiting. To systematically assess GPCR signaling in response to serotonin, we characterized reporter gene expression at two different pHs of a 144-sized library encoding all 12 human serotonin GPCRs in combination with 12 different Gα proteins engineered in yeast. From this screen, we observed changes in the biosensor sensitivities of >4 orders of magnitude. Furthermore, adopting optimal biosensing designs and pH conditions enabled high-resolution high-performance liquid chromatography-validated sensing of serotonin produced in yeast. Lastly, we used the yeast platform to characterize 19 serotonin GPCR polymorphisms found in human populations. While major differences in signaling were observed among the individual polymorphisms when studied in yeast, a cross-comparison of selected variants in mammalian cells showed both similar and disparate results. Taken together, our study highlights serotonin biosensing modalities of relevance to both biotechnological and potential human health applications.
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Affiliation(s)
- Bettina Lengger
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Emma E. Hoch-Schneider
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christina N. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tadas Jakočiu̅nas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Anja A. Petersen
- Novo
Nordisk Foundation Center for Basic Metabolic Research, Faculty of
Health and Medical Sciences, University
of Copenhagen, Maersk
Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Thomas M. Frimurer
- Novo
Nordisk Foundation Center for Basic Metabolic Research, Faculty of
Health and Medical Sciences, University
of Copenhagen, Maersk
Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Emil D. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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45
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Matic M, Singh G, Carli F, Oliveira Rosa ND, Miglionico P, Magni L, Gutkind JS, Russell RB, Inoue A, Raimondi F. PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. Nucleic Acids Res 2022; 50:W598-W610. [PMID: 35639758 PMCID: PMC9252787 DOI: 10.1093/nar/gkac426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
In this study we show that protein language models can encode structural and functional information of GPCR sequences that can be used to predict their signaling and functional repertoire. We used the ESM1b protein embeddings as features and the binding information known from publicly available studies to develop PRECOGx, a machine learning predictor to explore GPCR interactions with G protein and β-arrestin, which we made available through a new webserver (https://precogx.bioinfolab.sns.it/). PRECOGx outperformed its predecessor (e.g. PRECOG) in predicting GPCR-transducer couplings, being also able to consider all GPCR classes. The webserver also provides new functionalities, such as the projection of input sequences on a low-dimensional space describing essential features of the human GPCRome, which is used as a reference to track GPCR variants. Additionally, it allows inspection of the sequence and structural determinants responsible for coupling via the analysis of the most important attention maps used by the models as well as through predicted intramolecular contacts. We demonstrate applications of PRECOGx by predicting the impact of disease variants (ClinVar) and alternative splice forms from healthy tissues (GTEX) of human GPCRs, revealing the power to dissect system biasing mechanisms in both health and disease.
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Affiliation(s)
- Marin Matic
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Gurdeep Singh
- Heidelberg University Biochemistry Centre, 69120 Heidelberg, Germany.,BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Francesco Carli
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Natalia De Oliveira Rosa
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Pasquale Miglionico
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Lorenzo Magni
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of CA, San Diego, La Jolla, CA 92093, USA
| | - Robert B Russell
- Heidelberg University Biochemistry Centre, 69120 Heidelberg, Germany.,BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Francesco Raimondi
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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46
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Structure-guided optimization of light-activated chimeric G-protein-coupled receptors. Structure 2022; 30:1075-1087.e4. [PMID: 35588733 DOI: 10.1016/j.str.2022.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/22/2022] [Accepted: 04/22/2022] [Indexed: 01/11/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest human receptor family and involved in virtually every physiological process. One hallmark of their function is specific coupling to selected signaling pathways. The ability to tune this coupling would make development of receptors with new capabilities possible. Complexes of GPCRs and G-proteins have recently been resolved at high resolution, but this information was in only few cases harnessed for rational receptor engineering. Here, we demonstrate structure-guided optimization of light-activated OptoXRs. Our hypothesis was that incorporation of GPCR-Gα contacts would lead to improved coupling. We first evaluated structure-based alignments for chimeric receptor fusion. We then show in a light-activated β2AR that including Gα contacts increased signaling 7- to 20-fold compared with other designs. In turn, contact elimination diminished function. Finally, this platform allowed optimization of a further OptoXR and spectral tuning. Our work exemplifies structure-based OptoXR development for targeted cell and network manipulation.
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47
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Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR. Differential assembly diversifies GABA A receptor structures and signalling. Nature 2022; 604:190-194. [PMID: 35355020 PMCID: PMC7612593 DOI: 10.1038/s41586-022-04517-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/04/2022] [Indexed: 01/07/2023]
Abstract
Type A γ-aminobutyric acid receptors (GABAARs) are pentameric ligand-gated chloride channels that mediate fast inhibitory signalling in neural circuits1,2 and can be modulated by essential medicines including general anaesthetics and benzodiazepines3. Human GABAAR subunits are encoded by 19 paralogous genes that can, in theory, give rise to 495,235 receptor types. However, the principles that govern the formation of pentamers, the permutational landscape of receptors that may emerge from a subunit set and the effect that this has on GABAergic signalling remain largely unknown. Here we use cryogenic electron microscopy to determine the structures of extrasynaptic GABAARs assembled from α4, β3 and δ subunits, and their counterparts incorporating γ2 instead of δ subunits. In each case, we identified two receptor subtypes with distinct stoichiometries and arrangements, all four differing from those previously observed for synaptic, α1-containing receptors4-7. This, in turn, affects receptor responses to physiological and synthetic modulators by creating or eliminating ligand-binding sites at subunit interfaces. We provide structural and functional evidence that selected GABAAR arrangements can act as coincidence detectors, simultaneously responding to two neurotransmitters: GABA and histamine. Using assembly simulations and single-cell RNA sequencing data8,9, we calculated the upper bounds for receptor diversity in recombinant systems and in vivo. We propose that differential assembly is a pervasive mechanism for regulating the physiology and pharmacology of GABAARs.
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Affiliation(s)
| | - Rooma Desai
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Youssef Jounaidi
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Xiaojuan Zhou
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Simonas Masiulis
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, Eindhoven, Netherlands
| | | | | | - Keith W Miller
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Pearce A, Redfern-Nichols T, Harris M, Poyner DR, Wigglesworth M, Ladds G. Determining the Effects of Differential Expression of GRKs and β-arrestins on CLR-RAMP Agonist Bias. Front Physiol 2022; 13:840763. [PMID: 35422711 PMCID: PMC9001978 DOI: 10.3389/fphys.2022.840763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
Signalling of the calcitonin-like receptor (CLR) is multifaceted, due to its interaction with receptor activity modifying proteins (RAMPs), and three endogenous peptide agonists. Previous studies have focused on the bias of G protein signalling mediated by the receptor and receptor internalisation of the CLR-RAMP complex has been assumed to follow the same pattern as other Class B1 G Protein-Coupled Receptors (GPCRs). Here we sought to measure desensitisation of the three CLR-RAMP complexes in response to the three peptide agonists, through the measurement of β-arrestin recruitment and internalisation. We then delved further into the mechanism of desensitisation through modulation of β-arrestin activity and the expression of GPCR kinases (GRKs), a key component of homologous GPCR desensitisation. First, we have shown that CLR-RAMP1 is capable of potently recruiting β-arrestin1 and 2, subsequently undergoing rapid endocytosis, and that CLR-RAMP2 and -RAMP3 also utilise these pathways, although to a lesser extent. Following this we have shown that agonist-dependent internalisation of CLR is β-arrestin dependent, but not required for full agonism. Overexpression of GRK2-6 was then found to decrease receptor signalling, due to an agonist-independent reduction in surface expression of the CLR-RAMP complex. These results represent the first systematic analysis of the importance of β-arrestins and GRKs in CLR-RAMP signal transduction and pave the way for further investigation regarding other Class B1 GPCRs.
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Affiliation(s)
- Abigail Pearce
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | | | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - David R. Poyner
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - Mark Wigglesworth
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, London, United Kingdom
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Graham Ladds,
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Narci K, Kahraman DC, Koyas A, Ersahin T, Tuncbag N, Atalay RC. Context dependent isoform specific PI3K inhibition confers drug resistance in hepatocellular carcinoma cells. BMC Cancer 2022; 22:320. [PMID: 35331184 PMCID: PMC8953069 DOI: 10.1186/s12885-022-09357-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Targeted therapies for Primary liver cancer (HCC) is limited to the multi-kinase inhibitors, and not fully effective due to the resistance to these agents because of the heterogeneous molecular nature of HCC developed during chronic liver disease stages and cirrhosis. Although combinatorial therapy can increase the efficiency of targeted therapies through synergistic activities, isoform specific effects of the inhibitors are usually ignored. This study concentrated on PI3K/Akt/mTOR pathway and the differential combinatory bioactivities of isoform specific PI3K-α inhibitor (PIK-75) or PI3K-β inhibitor (TGX-221) with Sorafenib dependent on PTEN context. METHODS The bioactivities of inhibitors on PTEN adequate Huh7 and deficient Mahlavu cells were investigated with real time cell growth, cell cycle and cell migration assays. Differentially expressed genes from RNA-Seq were identified by edgeR tool. Systems level network analysis of treatment specific pathways were performed with Prize Collecting Steiner Tree (PCST) on human interactome and enriched networks were visualized with Cytoscape platform. RESULTS Our data from combinatory treatment of Sorafenib and PIK-75 and TGX-221 showed opposite effects; while PIK-75 displays synergistic effects on Huh7 cells leading to apoptotic cell death, Sorafenib with TGX-221 display antagonistic effects and significantly promotes cell growth in PTEN deficient Mahlavu cells. Signaling pathways were reconstructed and analyzed in-depth from RNA-Seq data to understand mechanism of differential synergistic or antagonistic effects of PI3K-α (PIK-75) and PI3K-β (TGX-221) inhibitors with Sorafenib. PCST allowed as to identify AOX1 and AGER as targets in PI3K/Akt/mTOR pathway for this combinatory effect. The siRNA knockdown of AOX1 and AGER significantly reduced cell proliferation in HCC cells. CONCLUSIONS Simultaneously constructed and analyzed differentially expressed cellular networks presented in this study, revealed distinct consequences of isoform specific PI3K inhibition in PTEN adequate and deficient liver cancer cells. We demonstrated the importance of context dependent and isoform specific PI3K/Akt/mTOR signaling inhibition in drug resistance during combination therapies. ( https://github.com/cansyl/Isoform-spesific-PI3K-inhibitor-analysis ).
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Affiliation(s)
- Kubra Narci
- Cancer System Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Deniz Cansen Kahraman
- Cancer System Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Altay Koyas
- Cancer System Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Tulin Ersahin
- Cancer System Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Nurcan Tuncbag
- Cancer System Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Rengul Cetin Atalay
- Cancer System Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey.
- Present Address: Section of Pulmonary and Critical Care Medicine, the University of Chicago, Chicago, IL, 60637, USA.
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Johansen OS, Ma T, Gerhart-Hines Z. Leveraging GPCR signaling in thermogenic fat to counteract metabolic diseases. Mol Metab 2022; 60:101474. [PMID: 35339729 PMCID: PMC9046952 DOI: 10.1016/j.molmet.2022.101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 11/05/2022] Open
Abstract
Background Thermogenic brown and beige adipocytes are recognized for their unique capacity to consume extraordinary levels of metabolites and lipids from the blood to fuel heat-producing catabolic processes [[1], [2], [3], [4], [5], [6], [7]]. In humans, the functions of thermogenic adipocytes are associated with cardiometabolic protection and improved glycemic control [[8], [9], [10], [11], [12], [13]]. Consequently, engaging these macronutrient-consuming and energy-dissipating activities has gained attention as a promising therapeutic strategy for counteracting metabolic diseases, such as obesity and diabetes. Scope of review In this review, we highlight new advances in our understanding of the physiological role of G protein-coupled receptors (GPCRs) in controlling thermogenic adipocyte biology. We further extend our discussion to the opportunities and challenges posed by pharmacologically targeting different elements of GPCR signaling in these highly specialized fat cells. Major conclusions GPCRs represent appealing candidates through which to harness adipose thermogenesis. Yet safely and effectively targeting these druggable receptors on brown and beige adipocytes has thus far proven challenging. Therefore, continued interrogation across the GPCR landscape is necessary for future leaps within the field of thermogenic fat biology to unlock the therapeutic potential of adipocyte catabolism. Brown and beige thermogenic adipocytes robustly consume and catabolize macronutrients. The catabolic activity of thermogenic adipocytes promotes organismal energy balance. Thermogenic adipocyte functions are tightly controlled by G protein-coupled receptors (GPCRs). GPCRs can be potentially targeted at multiple levels to therapeutically harness thermogenic activity.
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Affiliation(s)
- Olivia Sveidahl Johansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, DK
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, DK; Embark Biotech ApS, Copenhagen, DK
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, DK; Embark Biotech ApS, Copenhagen, DK; Center for Adipocyte Signaling, Odense, DK.
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