1
|
Bannell TAK, Cockburn JJB. The molecular structure and function of fibrocystin, the key gene product implicated in autosomal recessive polycystic kidney disease (ARPKD). Ann Hum Genet 2024; 88:58-75. [PMID: 37905714 DOI: 10.1111/ahg.12535] [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: 07/11/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Autosomal recessive polycystic kidney disease is an early onset inherited hepatorenal disorder affecting around 1 in 20,000 births with no approved specific therapies. The disease is almost always caused by variations in the polycystic kidney and hepatic disease 1 gene, which encodes fibrocystin (FC), a very large, single-pass transmembrane glycoprotein found in primary cilia, urine and urinary exosomes. By comparison to proteins involved in autosomal dominant PKD, our structural and molecular understanding of FC has lagged far behind such that there are no published experimentally determined structures of any part of the protein. Bioinformatics analyses predict that the ectodomain contains a long chain of immunoglobulin-like plexin-transcription factor domains, a protective antigen 14 domain, a tandem G8-TMEM2 homology region and a sperm protein, enterokinase and agrin domain. Here we review current knowledge on the molecular function of the protein from a structural perspective.
Collapse
Affiliation(s)
- Travis A K Bannell
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joseph J B Cockburn
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| |
Collapse
|
2
|
De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function. Structure 2022; 30:1411-1423.e4. [PMID: 35981535 DOI: 10.1016/j.str.2022.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 06/26/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022]
Abstract
Signaling by single-pass transmembrane receptors often involves a formation of ligand-induced receptor dimers with particular conformation, and bivalent receptor binders can modulate receptor functions by inducing different receptor dimer conformations, although such agents are difficult to design. Here, we describe the generation of both antagonistic and agonistic receptor dimerizers toward PlexinB1 (PlxnB1), a receptor for semaphorin 4D (Sema4D), by grafting two different PlxnB1-binding peptides onto the human immunoglobulin G1 (IgG1) Fc protein. The function-modulating activity of a peptide Fc was strongly dependent on the type of the peptide as well as the grafting site, with the best variants showing activity at an nM concentration range. Structural analysis of each peptide-PlxnB1 complex revealed that the agonistic Fc dimerizes PlxnB1 in a face-to-face fashion similar to that induced by Sema4D, whereas antagonistic Fc would induce signaling-incompetent PlxnB1 dimer conformation, enforcing the idea that plexin activation is primarily controlled by the receptor orientation within the dimer.
Collapse
|
3
|
Schardt JS, Jhajj HS, O’Meara RL, Lwo TS, Smith MD, Tessier PM. Agonist antibody discovery: Experimental, computational, and rational engineering approaches. Drug Discov Today 2022; 27:31-48. [PMID: 34571277 PMCID: PMC8714685 DOI: 10.1016/j.drudis.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Agonist antibodies that activate cellular signaling have emerged as promising therapeutics for treating myriad pathologies. Unfortunately, the discovery of rare antibodies with the desired agonist functions is a major bottleneck during drug development. Nevertheless, there has been important recent progress in discovering and optimizing agonist antibodies against a variety of therapeutic targets that are activated by diverse signaling mechanisms. Herein, we review emerging high-throughput experimental and computational methods for agonist antibody discovery as well as rational molecular engineering methods for optimizing their agonist activity.
Collapse
Affiliation(s)
- John S. Schardt
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harkamal S. Jhajj
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryen L. O’Meara
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Timon S. Lwo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
4
|
Plexin-B2 orchestrates collective stem cell dynamics via actomyosin contractility, cytoskeletal tension and adhesion. Nat Commun 2021; 12:6019. [PMID: 34650052 PMCID: PMC8517024 DOI: 10.1038/s41467-021-26296-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 09/29/2021] [Indexed: 11/08/2022] Open
Abstract
During morphogenesis, molecular mechanisms that orchestrate biomechanical dynamics across cells remain unclear. Here, we show a role of guidance receptor Plexin-B2 in organizing actomyosin network and adhesion complexes during multicellular development of human embryonic stem cells and neuroprogenitor cells. Plexin-B2 manipulations affect actomyosin contractility, leading to changes in cell stiffness and cytoskeletal tension, as well as cell-cell and cell-matrix adhesion. We have delineated the functional domains of Plexin-B2, RAP1/2 effectors, and the signaling association with ERK1/2, calcium activation, and YAP mechanosensor, thus providing a mechanistic link between Plexin-B2-mediated cytoskeletal tension and stem cell physiology. Plexin-B2-deficient stem cells exhibit premature lineage commitment, and a balanced level of Plexin-B2 activity is critical for maintaining cytoarchitectural integrity of the developing neuroepithelium, as modeled in cerebral organoids. Our studies thus establish a significant function of Plexin-B2 in orchestrating cytoskeletal tension and cell-cell/cell-matrix adhesion, therefore solidifying the importance of collective cell mechanics in governing stem cell physiology and tissue morphogenesis.
Collapse
|
5
|
Lu D, Shang G, He X, Bai XC, Zhang X. Architecture of the Sema3A/PlexinA4/Neuropilin tripartite complex. Nat Commun 2021; 12:3172. [PMID: 34039996 PMCID: PMC8155012 DOI: 10.1038/s41467-021-23541-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/30/2021] [Indexed: 02/04/2023] Open
Abstract
Secreted class 3 semaphorins (Sema3s) form tripartite complexes with the plexin receptor and neuropilin coreceptor, which are both transmembrane proteins that together mediate semaphorin signal for neuronal axon guidance and other processes. Despite extensive investigations, the overall architecture of and the molecular interactions in the Sema3/plexin/neuropilin complex are incompletely understood. Here we present the cryo-EM structure of a near intact extracellular region complex of Sema3A, PlexinA4 and Neuropilin 1 (Nrp1) at 3.7 Å resolution. The structure shows a large symmetric 2:2:2 assembly in which each subunit makes multiple interactions with others. The two PlexinA4 molecules in the complex do not interact directly, but their membrane proximal regions are close to each other and poised to promote the formation of the intracellular active dimer for signaling. The structure reveals a previously unknown interface between the a2b1b2 module in Nrp1 and the Sema domain of Sema3A. This interaction places the a2b1b2 module at the top of the complex, far away from the plasma membrane where the transmembrane regions of Nrp1 and PlexinA4 embed. As a result, the region following the a2b1b2 module in Nrp1 must span a large distance to allow the connection to the transmembrane region, suggesting an essential role for the long non-conserved linkers and the MAM domain in neuropilin in the semaphorin/plexin/neuropilin complex.
Collapse
Affiliation(s)
- Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
6
|
State of the structure address on MET receptor activation by HGF. Biochem Soc Trans 2021; 49:645-661. [PMID: 33860789 DOI: 10.1042/bst20200394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
The MET receptor tyrosine kinase (RTK) and its cognate ligand hepatocyte growth factor (HGF) comprise a signaling axis essential for development, wound healing and tissue homeostasis. Aberrant HGF/MET signaling is a driver of many cancers and contributes to drug resistance to several approved therapeutics targeting other RTKs, making MET itself an important drug target. In RTKs, homeostatic receptor signaling is dependent on autoinhibition in the absence of ligand binding and orchestrated set of conformational changes induced by ligand-mediated receptor dimerization that result in activation of the intracellular kinase domains. A fundamental understanding of these mechanisms in the MET receptor remains incomplete, despite decades of research. This is due in part to the complex structure of the HGF ligand, which remains unknown in its full-length form, and a lack of high-resolution structures of the complete MET extracellular portion in an apo or ligand-bound state. A current view of HGF-dependent MET activation has evolved from biochemical and structural studies of HGF and MET fragments and here we review what these findings have thus far revealed.
Collapse
|
7
|
Mechanochemical control of epidermal stem cell divisions by B-plexins. Nat Commun 2021; 12:1308. [PMID: 33637728 PMCID: PMC7910479 DOI: 10.1038/s41467-021-21513-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
The precise spatiotemporal control of cell proliferation is key to the morphogenesis of epithelial tissues. Epithelial cell divisions lead to tissue crowding and local changes in force distribution, which in turn suppress the rate of cell divisions. However, the molecular mechanisms underlying this mechanical feedback are largely unclear. Here, we identify a critical requirement of B-plexin transmembrane receptors in the response to crowding-induced mechanical forces during embryonic skin development. Epidermal stem cells lacking B-plexins fail to sense mechanical compression, resulting in disinhibition of the transcriptional coactivator YAP, hyperproliferation, and tissue overgrowth. Mechanistically, we show that B-plexins mediate mechanoresponses to crowding through stabilization of adhesive cell junctions and lowering of cortical stiffness. Finally, we provide evidence that the B-plexin-dependent mechanochemical feedback is also pathophysiologically relevant to limit tumor growth in basal cell carcinoma, the most common type of skin cancer. Our data define a central role of B-plexins in mechanosensation to couple cell density and cell division in development and disease.
Collapse
|
8
|
Junqueira Alves C, Silva Ladeira J, Hannah T, Pedroso Dias RJ, Zabala Capriles PV, Yotoko K, Zou H, Friedel RH. Evolution and Diversity of Semaphorins and Plexins in Choanoflagellates. Genome Biol Evol 2021; 13:6149127. [PMID: 33624753 PMCID: PMC8011033 DOI: 10.1093/gbe/evab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2021] [Indexed: 12/22/2022] Open
Abstract
Semaphorins and plexins are cell surface ligand/receptor proteins that affect cytoskeletal dynamics in metazoan cells. Interestingly, they are also present in Choanoflagellata, a class of unicellular heterotrophic flagellates that forms the phylogenetic sister group to Metazoa. Several members of choanoflagellates are capable of forming transient colonies, whereas others reside solitary inside exoskeletons; their molecular diversity is only beginning to emerge. Here, we surveyed genomics data from 22 choanoflagellate species and detected semaphorin/plexin pairs in 16 species. Choanoflagellate semaphorins (Sema-FN1) contain several domain features distinct from metazoan semaphorins, including an N-terminal Reeler domain that may facilitate dimer stabilization, an array of fibronectin type III domains, a variable serine/threonine-rich domain that is a potential site for O-linked glycosylation, and a SEA domain that can undergo autoproteolysis. In contrast, choanoflagellate plexins (Plexin-1) harbor a domain arrangement that is largely identical to metazoan plexins. Both Sema-FN1 and Plexin-1 also contain a short homologous motif near the C-terminus, likely associated with a shared function. Three-dimensional molecular models revealed a highly conserved structural architecture of choanoflagellate Plexin-1 as compared to metazoan plexins, including similar predicted conformational changes in a segment that is involved in the activation of the intracellular Ras-GAP domain. The absence of semaphorins and plexins in several choanoflagellate species did not appear to correlate with unicellular versus colonial lifestyle or ecological factors such as fresh versus salt water environment. Together, our findings support a conserved mechanism of semaphorin/plexin proteins in regulating cytoskeletal dynamics in unicellular and multicellular organisms.
Collapse
Affiliation(s)
- Chrystian Junqueira Alves
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Júlia Silva Ladeira
- Programa de Pós-graduação em Modelagem Computacional, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Theodore Hannah
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roberto J Pedroso Dias
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Priscila V Zabala Capriles
- Programa de Pós-graduação em Modelagem Computacional, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Karla Yotoko
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Hongyan Zou
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roland H Friedel
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
9
|
Rozbesky D, Verhagen MG, Karia D, Nagy GN, Alvarez L, Robinson RA, Harlos K, Padilla‐Parra S, Pasterkamp RJ, Jones EY. Structural basis of semaphorin-plexin cis interaction. EMBO J 2020; 39:e102926. [PMID: 32500924 PMCID: PMC7327498 DOI: 10.15252/embj.2019102926] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/05/2023] Open
Abstract
Semaphorin ligands interact with plexin receptors to contribute to functions in the development of myriad tissues including neurite guidance and synaptic organisation within the nervous system. Cell-attached semaphorins interact in trans with plexins on opposing cells, but also in cis on the same cell. The interplay between trans and cis interactions is crucial for the regulated development of complex neural circuitry, but the underlying molecular mechanisms are uncharacterised. We have discovered a distinct mode of interaction through which the Drosophila semaphorin Sema1b and mouse Sema6A mediate binding in cis to their cognate plexin receptors. Our high-resolution structural, biophysical and in vitro analyses demonstrate that monomeric semaphorins can mediate a distinctive plexin binding mode. These findings suggest the interplay between monomeric vs dimeric states has a hereto unappreciated role in semaphorin biology, providing a mechanism by which Sema6s may balance cis and trans functionalities.
Collapse
Affiliation(s)
- Daniel Rozbesky
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Marieke G Verhagen
- Department of Translational NeuroscienceUMC Utrecht Brain CenterUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Dimple Karia
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Gergely N Nagy
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Luis Alvarez
- Cellular ImagingWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ross A Robinson
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
- Present address:
Immunocore LtdAbingdonUK
| | - Karl Harlos
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Sergi Padilla‐Parra
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
- Cellular ImagingWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
- Present address:
Department of Infectious DiseasesFaculty of Life Sciences & MedicineKing's College LondonLondonUK
- Present address:
Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - R Jeroen Pasterkamp
- Department of Translational NeuroscienceUMC Utrecht Brain CenterUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Edith Yvonne Jones
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| |
Collapse
|
10
|
Kuo YC, Chen H, Shang G, Uchikawa E, Tian H, Bai XC, Zhang X. Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation. Nat Commun 2020; 11:1953. [PMID: 32327662 PMCID: PMC7181871 DOI: 10.1038/s41467-020-15862-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/01/2020] [Indexed: 11/09/2022] Open
Abstract
Plexins are receptors for semaphorins that transduce signals for regulating neuronal development and other processes. Plexins are single-pass transmembrane proteins with multiple domains in both the extracellular and intracellular regions. Semaphorin activates plexin by binding to its extracellular N-terminal Sema domain, inducing the active dimer of the plexin intracellular region. The mechanism underlying this activation process of plexin is incompletely understood. We present cryo-electron microscopic structure of full-length human PlexinC1 in complex with the viral semaphorin mimic A39R. The structure shows that A39R induces a specific dimer of PlexinC1 where the membrane-proximal domains from the two PlexinC1 protomers are placed close to each other, poised to promote the active dimer of the intracellular region. This configuration is imposed by a distinct conformation of the PlexinC1 extracellular region, stabilized by inter-domain interactions among the Sema and membrane-proximal domains. Our mutational analyses support the critical role of this conformation in PlexinC1 activation. Plexins are the receptors for the guidance molecules semaphorins and regulate immunity and the development of the nervous and cardiovascular systems. Here authors present a structure of full-length human PlexinC1 in complex with its ligand A39R, which reveals how inter-domain interactions couple extracellular ligand binding to receptor activation and signaling.
Collapse
Affiliation(s)
- Yi-Chun Kuo
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emiko Uchikawa
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hui Tian
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
11
|
Mehta V, Pang KL, Rozbesky D, Nather K, Keen A, Lachowski D, Kong Y, Karia D, Ameismeier M, Huang J, Fang Y, Del Rio Hernandez A, Reader JS, Jones EY, Tzima E. The guidance receptor plexin D1 is a mechanosensor in endothelial cells. Nature 2020; 578:290-295. [PMID: 32025034 PMCID: PMC7025890 DOI: 10.1038/s41586-020-1979-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/05/2019] [Indexed: 01/09/2023]
Abstract
Shear stress on arteries produced by blood flow is important for vascular development and homeostasis but can also initiate atherosclerosis1. Endothelial cells that line the vasculature use molecular mechanosensors to directly detect shear stress profiles that will ultimately lead to atheroprotective or atherogenic responses2. Plexins are key cell-surface receptors of the semaphorin family of cell-guidance signalling proteins and can regulate cellular patterning by modulating the cytoskeleton and focal adhesion structures3-5. However, a role for plexin proteins in mechanotransduction has not been examined. Here we show that plexin D1 (PLXND1) has a role in mechanosensation and mechanically induced disease pathogenesis. PLXND1 is required for the response of endothelial cells to shear stress in vitro and in vivo and regulates the site-specific distribution of atherosclerotic lesions. In endothelial cells, PLXND1 is a direct force sensor and forms a mechanocomplex with neuropilin-1 and VEGFR2 that is necessary and sufficient for conferring mechanosensitivity upstream of the junctional complex and integrins. PLXND1 achieves its binary functions as either a ligand or a force receptor by adopting two distinct molecular conformations. Our results establish a previously undescribed mechanosensor in endothelial cells that regulates cardiovascular pathophysiology, and provide a mechanism by which a single receptor can exhibit a binary biochemical nature.
Collapse
Affiliation(s)
- Vedanta Mehta
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kar-Lai Pang
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniel Rozbesky
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katrin Nather
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam Keen
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dariusz Lachowski
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK
| | - Youxin Kong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dimple Karia
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michael Ameismeier
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jianhua Huang
- Department of Medicine, Duke University, Durham, NC, USA
| | - Yun Fang
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Armando Del Rio Hernandez
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK
| | - John S Reader
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - E Yvonne Jones
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ellie Tzima
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
12
|
Rozbesky D, Robinson RA, Jain V, Renner M, Malinauskas T, Harlos K, Siebold C, Jones EY. Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning. Nat Commun 2019; 10:3691. [PMID: 31417095 PMCID: PMC6695400 DOI: 10.1038/s41467-019-11683-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Semaphorin ligands and their plexin receptors are one of the major cell guidance factors that trigger localised changes in the cytoskeleton. Binding of semaphorin homodimer to plexin brings two plexins in close proximity which is a prerequisite for plexin signalling. This model appears to be too simplistic to explain the complexity and functional versatility of these molecules. Here, we determine crystal structures for all members of Drosophila class 1 and 2 semaphorins. Unlike previously reported semaphorin structures, Sema1a, Sema2a and Sema2b show stabilisation of sema domain dimer formation via a disulfide bond. Unexpectedly, our structural and biophysical data show Sema1b is a monomer suggesting that semaphorin function may not be restricted to dimers. We demonstrate that semaphorins can form heterodimers with members of the same semaphorin class. This heterodimerization provides a potential mechanism for cross-talk between different plexins and co-receptors to allow fine-tuning of cell signalling.
Collapse
Affiliation(s)
- Daniel Rozbesky
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Ross A Robinson
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Immunocore Ltd, Milton Park, Abingdon, OX14 4RY, UK
| | - Vitul Jain
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| |
Collapse
|
13
|
Kodama T, Kochi Y, Nakai W, Mizuno H, Baba T, Habu K, Sawada N, Tsunoda H, Shima T, Miyawaki K, Kikushige Y, Mori Y, Miyamoto T, Maeda T, Akashi K. Anti-GPRC5D/CD3 Bispecific T-Cell-Redirecting Antibody for the Treatment of Multiple Myeloma. Mol Cancer Ther 2019; 18:1555-1564. [PMID: 31270154 DOI: 10.1158/1535-7163.mct-18-1216] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/29/2019] [Accepted: 06/28/2019] [Indexed: 11/16/2022]
Abstract
Although treatment advances over recent decades have significantly improved survival of patients with multiple myeloma, there is still an unmet medical need for more effective treatments. In this study, we identified G-protein-coupled receptor family C group 5 member D (GPRC5D) expression on the surface of malignant cells involved in multiple myeloma, but except for plasma cells and B cells, not at appreciable levels on normal hematopoietic cells and bone marrow progenitors, including hematopoietic stem cells. In addition, we constructed IgG-based anti-GPRC5D/CD3 bispecific T-cell-redirecting antibodies (GPRC5D TRAB), which suppressed the tumor growth of GPRC5D-positive myeloma cells through the activation of T cells in vitro and in vivo in xenograft models. Collectively, these findings suggest that GPRC5D is an antigen specific to multiple myeloma and a potential target of TRAB therapy.
Collapse
Affiliation(s)
- Tatsushi Kodama
- Chugai Pharmabody Research Pte. Ltd., Singapore. .,Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Yu Kochi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Waka Nakai
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Hideaki Mizuno
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Takeshi Baba
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Kiyoshi Habu
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Noriaki Sawada
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Hiroyuki Tsunoda
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Takahiro Shima
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yoshikane Kikushige
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yasuo Mori
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takahiro Maeda
- Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.,Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| |
Collapse
|
14
|
Tanaka H, Arima Y, Kamimura D, Tanaka Y, Takahashi N, Uehata T, Maeda K, Satoh T, Murakami M, Akira S. Phosphorylation-dependent Regnase-1 release from endoplasmic reticulum is critical in IL-17 response. J Exp Med 2019; 216:1431-1449. [PMID: 31072819 PMCID: PMC6547859 DOI: 10.1084/jem.20181078] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 03/07/2019] [Accepted: 04/12/2019] [Indexed: 12/21/2022] Open
Abstract
The endoribonuclease Regnase-1 suppresses inflammation through RNA degradation. Here, we show that Regnase-1 is phosphorylated and inactivated by the Act1-TBK1-IKKi axis during IL-17 stimulation. Moreover, this phosphorylation substantially contributes to the mRNA stabilization needed for amplification of TH17-cell–mediated inflammation. Regnase-1 (also known as Zc3h12a or MCPIP-1) is an endoribonuclease involved in mRNA degradation of inflammation-associated genes. Regnase-1 is inactivated in response to external stimuli through post-translational modifications including phosphorylation, yet the precise role of phosphorylation remains unknown. Here, we demonstrate that interleukin (IL)-17 induces phosphorylation of Regnase-1 in an Act1-TBK1/IKKi–dependent manner, especially in nonhematopoietic cells. Phosphorylated Regnase-1 is released from the endoplasmic reticulum (ER) into the cytosol, thereby losing its mRNA degradation function, which leads to expression of IL-17 target genes. By using CRISPR/Cas-9 technology, we generated Regnase-1 mutant mice, in which IL-17–induced Regnase-1 phosphorylation is completely blocked. Mutant mice (Regnase-1AA/AA and Regnase-1ΔCTD/ΔCTD) were resistant to the IL-17–mediated inflammation caused by T helper 17 (Th17) cells in vivo. Thus, Regnase-1 plays a critical role in the development of IL-17–mediated inflammatory diseases via the Act1-TBK1-IKKi axis, and blockade of Regnase-1 phosphorylation sites may be promising for treatment of Th17-associated diseases.
Collapse
Affiliation(s)
- Hiroki Tanaka
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yasunobu Arima
- Division of Molecular Neuroimmunology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Daisuke Kamimura
- Division of Molecular Neuroimmunology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Yuki Tanaka
- Division of Molecular Neuroimmunology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Noriyuki Takahashi
- Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., Kanagawa, Japan
| | - Takuya Uehata
- Department of Host Defense, Research Institute for Microbial Research, Osaka University, Osaka, Japan
| | - Kazuhiko Maeda
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Department of Host Defense, Research Institute for Microbial Research, Osaka University, Osaka, Japan
| | - Takashi Satoh
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Department of Host Defense, Research Institute for Microbial Research, Osaka University, Osaka, Japan
| | - Masaaki Murakami
- Division of Molecular Neuroimmunology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Osaka, Japan .,Department of Host Defense, Research Institute for Microbial Research, Osaka University, Osaka, Japan
| |
Collapse
|
15
|
Brown ZP, Takagi J. Advances in domain and subunit localization technology for electron microscopy. Biophys Rev 2019; 11:149-155. [PMID: 30834502 DOI: 10.1007/s12551-019-00513-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/20/2019] [Indexed: 12/26/2022] Open
Abstract
The award of the 2017 Nobel Prize in chemistry, 'for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution', was recognition that this method, and electron microscopy more generally, represent powerful techniques in the scientific armamentarium for atomic level structural assessment. Technical advances in equipment, software, and sample preparation, have allowed for high-resolution structural determination of a range of complex biological machinery such that the position of individual atoms within these mega-structures can be determined. However, not all targets are amenable to attaining such high-resolution structures and some may only be resolved at so-called intermediate resolutions. In these cases, other tools are needed to correctly characterize the domain or subunit orientation and architecture. In this review, we will outline various methods that can provide additional information to help understand the macro-level organization of proteins/biomolecular complexes when high-resolution structural description is not available. In particular, we will discuss the recent development and use of a novel protein purification approach, known as the the PA tag/NZ-1 antibody system, which provides numberous beneficial properties, when used in electron microscopy experimentation.
Collapse
Affiliation(s)
- Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| |
Collapse
|
16
|
Junqueira Alves C, Yotoko K, Zou H, Friedel RH. Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases. Sci Rep 2019; 9:1970. [PMID: 30760850 PMCID: PMC6374515 DOI: 10.1038/s41598-019-38512-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 12/28/2018] [Indexed: 12/20/2022] Open
Abstract
The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules.
Collapse
Affiliation(s)
- Chrystian Junqueira Alves
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Karla Yotoko
- Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Hongyan Zou
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Department of Neurosurgery, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Roland H Friedel
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA. .,Department of Neurosurgery, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.
| |
Collapse
|
17
|
Bashiruddin NK, Matsunaga Y, Nagano M, Takagi J, Suga H. Facile Synthesis of Dimeric Thioether–Macrocyclic Peptides with Antibody-like Affinity against Plexin-B1. Bioconjug Chem 2018; 29:1847-1851. [DOI: 10.1021/acs.bioconjchem.8b00219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nasir K. Bashiruddin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yukiko Matsunaga
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| |
Collapse
|
18
|
Abstract
The regulation of the guidance receptor plexin is incompletely understood. In this issue, Kong et al. (2016) present crystal structures of the full-length extracellular region of class A plexins, revealing its dual role in both autoinhibition and activation.
Collapse
Affiliation(s)
- Yi-Chun Kuo
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| |
Collapse
|
19
|
Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide. Cell Chem Biol 2016; 23:1341-1350. [DOI: 10.1016/j.chembiol.2016.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/08/2016] [Accepted: 10/10/2016] [Indexed: 02/04/2023]
|