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Yang Y, Guan W, Sheng XM, Gu HJ. Role of Semaphorin 3A in common psychiatric illnesses such as schizophrenia, depression, and anxiety. Biochem Pharmacol 2024; 226:116358. [PMID: 38857830 DOI: 10.1016/j.bcp.2024.116358] [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: 04/23/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
With societal development and an ageing population, psychiatric disorders have become a common cause of severe and long-term disability and socioeconomic burdens worldwide. Semaphorin 3A (Sema-3A) is a secreted glycoprotein belonging to the semaphorin family. Sema-3A is well known as an axon guidance factor in the neuronal system and a potent immunoregulator at all stages of the immune response. It is reported to have various biological functions and is involved in many human diseases, including autoimmune diseases, angiocardiopathy, osteoporosis, and tumorigenesis. The signals of sema-3A involved in the pathogenesis of these conditions, are transduced through its cognate receptors and diverse downstream signalling pathways. An increasing number of studies show that sema-3A plays important roles in synaptic and dendritic development, which are closely associated with the pathophysiological mechanisms of psychiatric disorders, including schizophrenia, depression, and autism, suggesting the involvement of sema-3A in the pathogenesis of mental diseases. This indicates that mutations in sema-3A and alterations in its receptors and signalling may compromise neurodevelopment and predispose patients to these disorders. However, the role of sema-3A in psychiatric disorders, particularly in regulating neurodevelopment, remains elusive. In this review, we summarise the recent progress in understanding sema-3A in the pathogenesis of mental diseases and highlight sema-3A as a potential target for the prevention and treatment of these diseases.
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Affiliation(s)
- Yang Yang
- Department of Pharmacy, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, China
| | - Wei Guan
- Department of Pharmacology, Pharmacy College, Nantong University, China
| | - Xiao-Ming Sheng
- Department of Trauma Center, Affiliated Hospital of Nantong University, China
| | - Hai-Juan Gu
- Department of Pharmacy, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, China.
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2
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Huang Y, Wang M, Ni H, Zhang J, Li A, Hu B, Junqueira Alves C, Wahane S, Rios de Anda M, Ho L, Li Y, Kang S, Neff R, Kostic A, Buxbaum JD, Crary JF, Brennand KJ, Zhang B, Zou H, Friedel RH. Regulation of cell distancing in peri-plaque glial nets by Plexin-B1 affects glial activation and amyloid compaction in Alzheimer's disease. Nat Neurosci 2024; 27:1489-1504. [PMID: 38802590 DOI: 10.1038/s41593-024-01664-w] [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: 10/13/2021] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
Communication between glial cells has a profound impact on the pathophysiology of Alzheimer's disease (AD). We reveal here that reactive astrocytes control cell distancing in peri-plaque glial nets, which restricts microglial access to amyloid deposits. This process is governed by guidance receptor Plexin-B1 (PLXNB1), a network hub gene in individuals with late-onset AD that is upregulated in plaque-associated astrocytes. Plexin-B1 deletion in a mouse AD model led to reduced number of reactive astrocytes and microglia in peri-plaque glial nets, but higher coverage of plaques by glial processes, along with transcriptional changes signifying reduced neuroinflammation. Additionally, a reduced footprint of glial nets was associated with overall lower plaque burden, a shift toward dense-core-type plaques and reduced neuritic dystrophy. Altogether, our study demonstrates that Plexin-B1 regulates peri-plaque glial net activation in AD. Relaxing glial spacing by targeting guidance receptors may present an alternative strategy to increase plaque compaction and reduce neuroinflammation in AD.
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Affiliation(s)
- Yong Huang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haofei Ni
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- School of Medicine, Tongji University, Shanghai, China
| | - Jinglong Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aiqun Li
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Hu
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chrystian Junqueira Alves
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shalaka Wahane
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mitzy Rios de Anda
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuhuan Li
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Orthopedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'An, China
| | - Sangjo Kang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Neff
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana Kostic
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Crary
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Neuropathology Brain Bank & Research Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Departments of Psychiatry and Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Morelli L, Serra L, Ricciardiello F, Gligora I, Donadio V, Caprini M, Liguori R, Giannoccaro MP. The role of antibodies in small fiber neuropathy: a review of currently available evidence. Rev Neurosci 2024; 0:revneuro-2024-0027. [PMID: 38865989 DOI: 10.1515/revneuro-2024-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/26/2024] [Indexed: 06/14/2024]
Abstract
Small fiber neuropathy (SFN) is a peripheral nerve condition affecting thin myelinated Aδ and unmyelinated C-fibers, characterized by severe neuropathic pain and other sensory and autonomic symptoms. A variety of medical disorders can cause SFN; however, more than 50% of cases are idiopathic (iSFN). Some investigations suggest an autoimmune etiology, backed by evidence of the efficacy of IVIG and plasma exchange. Several studies suggest that autoantibodies directed against nervous system antigens may play a role in the development of neuropathic pain. For instance, patients with CASPR2 and LGI1 antibodies often complain of pain, and in vitro and in vivo studies support their pathogenicity. Other antibodies have been associated with SFN, including those against TS-HDS, FGFR3, and Plexin-D1, and new potential targets have been proposed. Finally, a few studies reported the onset of SFN after COVID-19 infection and vaccination, investigating the presence of potential antibody targets. Despite these overall findings, the pathogenic role has been demonstrated only for some autoantibodies, and the association with specific clinical phenotypes or response to immunotherapy remains to be clarified. The purpose of this review is to summarise known autoantibody targets involved in neuropathic pain, putative attractive autoantibody targets in iSFN patients, their potential as biomarkers of response to immunotherapy and their role in the development of iSFN.
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Affiliation(s)
- Luana Morelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
| | - Lucrezia Serra
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
| | - Fortuna Ricciardiello
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
| | - Ilaria Gligora
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
| | - Vincenzo Donadio
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
| | - Marco Caprini
- Department of Pharmacy and Biotechnology (FaBiT), Laboratory of Human and General Physiology, University of Bologna, Via San Donato, 19/2 - 40126, Bologna, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Via Altura, 3 - 40139, Bologna, Italy
| | - Maria Pia Giannoccaro
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura, 3 - 40139, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Via Altura, 3 - 40139, Bologna, Italy
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Liu ZZ, Liu LY, Zhu LY, Zhu J, Luo JY, Wang YF, Xu HA. Plexin B3 guides axons to cross the midline in vivo. Front Cell Neurosci 2024; 18:1292969. [PMID: 38628398 PMCID: PMC11018898 DOI: 10.3389/fncel.2024.1292969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
During the development of neural circuits, axons are guided by a variety of molecular cues to navigate through the brain and establish precise connections with correct partners at the right time and place. Many axon guidance cues have been identified and they play pleiotropic roles in not only axon guidance but also axon fasciculation, axon pruning, and synaptogenesis as well as cell migration, angiogenesis, and bone formation. In search of receptors for Sema3E in axon guidance, we unexpectedly found that Plexin B3 is highly expressed in retinal ganglion cells of zebrafish embryos when retinal axons are crossing the midline to form the chiasm. Plexin B3 has been characterized to be related to neurodevelopmental disorders. However, the investigation of its pathological mechanisms is hampered by the lack of appropriate animal model. We provide evidence that Plexin B3 is critical for axon guidance in vivo. Plexin B3 might function as a receptor for Sema3E while Neuropilin1 could be a co-receptor. The intracellular domain of Plexin B3 is required for Semaphorin signaling transduction. Our data suggest that zebrafish could be an ideal animal model for investigating the role and mechanisms of Sema3E and Plexin B3 in vivo.
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Affiliation(s)
- Zhi-Zhi Liu
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric diseases, Nanchang, China
| | - Ling-Yan Liu
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric diseases, Nanchang, China
| | - Lou-Yin Zhu
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
| | - Jian Zhu
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
| | - Jia-Yu Luo
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric diseases, Nanchang, China
| | - Ye-Fan Wang
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
| | - Hong A. Xu
- Institute of Biomedical Innovation, Nanchang University, Nanchang, China
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang, China
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric diseases, Nanchang, China
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5
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Pshetitsky Y, Mendelman N, Buck M, Meirovitch E. Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: A Symmetry-Based Perspective. J Phys Chem B 2024; 128:1557-1572. [PMID: 38350034 DOI: 10.1021/acs.jpcb.3c06741] [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: 02/15/2024]
Abstract
We report on a new method for the characterization of local structures in proteins based on extensive molecular dynamics (MD) simulations, here, 1 μs in length. The N-H bond of the Rho GTPase binding domain of plexin-B1 (RBD) serves as a probe and the potential, u(MD), which restricts its internal motion, as a qualifier of the local dynamic structure. u(MD) is derived from the MD trajectory as a function of the polar angles, (θ, φ), which specify the N-H orientation in the protein. u(MD) is statistical in character yielding empirical descriptions. To establish more insightful methodical descriptions, we develop a comprehensive method which approximates u(MD) by combinations of analytical Wigner functions that belong to the D2h point group. These combinations, called u(simulated), make it possible to gain a new perspective of local dynamic structures in proteins based on explicit potentials/free energy surfaces and associated probability densities, entropy, and ordering. A simpler method was developed previously using 100 ns MD simulations. In that case, the traditional "perpendicular N-H ordering" setting centered at Cα-Cα with (θ, φ) = (90, 90) and generally, featuring positive φ, prevailed. u(MD) derived from 1 μs MD simulations is considerably more complex requiring substantial model enhancement. The enhanced method applies to the well-structured sections of the RBD. It only applies partly to its loops where u(MD) extends into the negative-φ region where we detect nonperpendicular N-H ordering. This arrangement requires devising new reference structures and making substantial algorithmic changes, to be performed in future work. Here, we focus on developing the comprehensive method and using it to investigate perpendicular ordering settings. We find that secondary structures (loops) exhibit varying (virtually invariant) potentials with Ag, B2u, and B1u (Ag and B2u) D2h symmetry. Application to RBD dimerization and RBD binding to the GTPase Rac1 is described in the subsequent article. Applications to other probes, proteins, and biological functions, based on explicit local potentials, probability densities, entropy, and ordering, are possible.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Abushalbaq O, Baek J, Yaron A, Tran TS. Balancing act of small GTPases downstream of plexin-A4 signaling motifs promotes dendrite elaboration in mammalian cortical neurons. Sci Signal 2024; 17:eadh7673. [PMID: 38227686 DOI: 10.1126/scisignal.adh7673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
The precise development of neuronal morphologies is crucial to the establishment of synaptic circuits and, ultimately, proper brain function. Signaling by the axon guidance cue semaphorin 3A (Sema3A) and its receptor complex of neuropilin-1 and plexin-A4 has multifunctional outcomes in neuronal morphogenesis. Downstream activation of the RhoGEF FARP2 through interaction with the lysine-arginine-lysine motif of plexin-A4 and consequent activation of the small GTPase Rac1 promotes dendrite arborization, but this pathway is dispensable for axon repulsion. Here, we investigated the interplay of small GTPase signaling mechanisms underlying Sema3A-mediated dendritic elaboration in mouse layer V cortical neurons in vitro and in vivo. Sema3A promoted the binding of the small GTPase Rnd1 to the amino acid motif lysine-valine-serine (LVS) in the cytoplasmic domain of plexin-A4. Rnd1 inhibited the activity of the small GTPase RhoA and the kinase ROCK, thus supporting the activity of the GTPase Rac1, which permitted the growth and branching of dendrites. Overexpression of a dominant-negative RhoA, a constitutively active Rac1, or the pharmacological inhibition of ROCK activity rescued defects in dendritic elaboration in neurons expressing a plexin-A4 mutant lacking the LVS motif. Our findings provide insights into the previously unappreciated balancing act between Rho and Rac signaling downstream of specific motifs in plexin-A4 to mediate Sema3A-dependent dendritic elaboration in mammalian cortical neuron development.
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Affiliation(s)
- Oday Abushalbaq
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Jiyeon Baek
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Avraham Yaron
- Department of Biomolecular Sciences and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tracy S Tran
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
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Junqueira Alves C, Hannah T, Sadia S, Kolsteeg C, Dixon A, Wiener RJ, Nguyen H, Tipping MJ, Ladeira JS, Franklin PFDC, Dutra de Nigro NDP, Dias RA, Zabala Capriles PV, Rodrigues Furtado de Mendonça JP, Slesinger P, Costa K, Zou H, Friedel RH. Invasion of glioma cells through confined space requires membrane tension regulation and mechano-electrical coupling via Plexin-B2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573660. [PMID: 38313256 PMCID: PMC10836082 DOI: 10.1101/2024.01.02.573660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Glioblastoma (GBM) is a malignant brain tumor with uncontrolled invasive growth. Here, we demonstrate how GBM cells usurp guidance receptor Plexin-B2 to gain biomechanical plasticity for polarized migration through confined space. Using live-cell imaging to track GBM cells negotiating microchannels, we reveal active endocytosis at cell front and filamentous actin assembly at rear to propel GBM cells through constrictions. These two processes are interconnected and governed by Plexin-B2 that orchestrates cortical actin and membrane tension, shown by biomechanical assays. Molecular dynamics simulations predict that balanced membrane and actin tension are required for optimal migratory velocity and consistency. Furthermore, Plexin-B2 mechanosensitive function requires a bendable extracellular ring structure and affects membrane internalization, permeability, phospholipid composition, as well as inner membrane surface charge. Together, our studies unveil a key element of membrane tension and mechanoelectrical coupling via Plexin-B2 that enables GBM cells to adapt to physical constraints and achieve polarized confined migration.
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Jacob TV, Doshi GM. New Promising Routes in Peptic Ulcers: Toll-like Receptors and Semaphorins. Endocr Metab Immune Disord Drug Targets 2024; 24:865-878. [PMID: 37605412 DOI: 10.2174/1871530323666230821102718] [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: 12/03/2022] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 08/23/2023]
Abstract
Peptic ulcers (PU) are one of the commonest yet problematic diseases found to be existing in the majority of the population. Today, drugs from a wide range of therapeutic classes are available for the management of the disease. Still, the complications of the condition are difficult to tackle and the side effect profile is quite a concern. The literature indicates that Toll-like receptors (TLRs) and Semaphorins (SEMAs) have been under study for their various pharmacological actions over the past few decades. Both these signalling pathways are found to regulate immunological and inflammatory responses. Moreover, receptors and signalling molecules from the family of TLRs and SEMAs are found to have bacterial recognition and antibacterial properties which are essential in eradicating Helicobacter pylori (H. pylori), one of the major causative agents of PU. Our understanding of SEMAs, a class of proteins involved in cell signalling, is relatively less developed compared to TLRs, another class of proteins involved in the immune response. SEMAs and TLRs play different roles in biological processes, with SEMAs primarily involved in guiding cell migration and axon guidance during development, while TLRs are responsible for recognizing pathogens and initiating an immune response. Here, in this review, we will discuss in detail the signalling cascade of TLRs and SEMAs and thereby understand its association with PU for future therapeutic targeting. The review also aims at providing an overview of the study that has been into exploring the role of these signalling pathways in the management of PU.
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Affiliation(s)
- Teresa V Jacob
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V.M. Road, Vile Parle (W), Mumbai, 400056, India
| | - Gaurav M Doshi
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V.M. Road, Vile Parle (W), Mumbai, 400056, India
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9
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Garg R, Endzhievskaya S, Williamson M. B-type Plexins promote the GTPase activity of Ran to affect androgen receptor nuclear translocation in prostate cancer. Cancer Gene Ther 2023; 30:1513-1523. [PMID: 37563360 PMCID: PMC10645588 DOI: 10.1038/s41417-023-00655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/10/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Resistance to anti-androgen therapy for metastatic prostate cancer is a major clinical problem. Sema3C promotes resistance to androgen withdrawal via its receptor, PlexinB1. Activation of PlexinB1 promotes the ligand-independent nuclear translocation of the androgen receptor (AR), which may contribute to resistance to androgen deprivation therapy. However, the mechanism by which PlexinB1 promotes nuclear translocation is unclear. We show here that PlexinB1 and B2 regulate nuclear import by acting as GTPase activating proteins (GAPs) for the small RasGTPase Ran, a key regulator of nuclear trafficking. Purified PlexinB1/B2 protein catalyses the hydrolysis of RanGTP, and mutations in the GAP domain of PlexinB1 inhibit this activity. Activation of PlexinB1/B2 with Sema4D decreases the levels of RanGTP, while PlexinB1 or B2 depletion increases the levels of activated Ran in the cell. Ran directly associates with B-type plexins in a GTP-dependent manner. Sema4D is internalised by endocytosis, and PlexinB1 and Ran display overlapping patterns of expression. Furthermore, Sema4D/PlexinB1-induced AR nuclear translocation is dependent on the GAP domain of PlexinB1 and is blocked by the expression of non-functional Ran mutants. Depletion of PlexinB1 decreases the nuclear/cytoplasmic ratio of Ran, indicative of a higher RanGTP/GDP ratio. Plexins may promote the growth of androgen-independent prostate cancer through their activity as RanGAPs.
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Affiliation(s)
- Ritu Garg
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sofia Endzhievskaya
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Magali Williamson
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, UK.
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Meng N, Mao L, Jiang Q, Yuan J, Liu L, Wang L. PLXNC1 interference alleviates the inflammatory injury, apoptosis and extracellular matrix degradation of IL-1β-exposed chondrocytes via suppressing GRP78 expression. J Orthop Surg Res 2023; 18:784. [PMID: 37853395 PMCID: PMC10585743 DOI: 10.1186/s13018-023-04207-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Osteoarthritis (OA) is a frequently encountered debilitating joint disorder. Whether plexin C1 (PLXNC1) is implicated in OA is far from being investigated despite its well-documented pro-inflammatory property in human diseases. The goal of this study is to expound the specific role of PLXNC1 in OA and elaborate the probable action mechanism. METHODS Firstly, PLXNC1 expression in the cartilage tissues of patients with OA was examined with GEO database. In interleukin-1beta (IL-1β)-induced OA cell model, RT-qPCR and western blotting tested the expression of PLXNC1, glucose-regulating protein 78 (GRP78) and extracellular matrix (ECM) degradation-related factors. Cell viability and inflammation were respectively judged by CCK-8 assay and RT-qPCR. TUNEL and western blotting estimated cell apoptosis. The potential binding between PLXNC1 and GRP78 was corroborated by Co-IP assay. Western blotting also tested the expression of endoplasmic reticulum stress (ERS)-associated proteins. RESULTS As it turned out, PLXNC1 expression was elevated in the cartilage tissues of patients with OA and IL-1β-treated chondrocytes. When PLXNC1 was depleted, the viability injury, inflammation, apoptosis and ECM degradation of chondrocytes exposed to IL-1β were obstructed. Besides, GRP78 bond to PLXNC1 in IL-1β-treated chondrocytes. The ascending GRP78 expression in the chondrocytes exposed to IL-1β was depleted after PLXNC1 was silenced. Meanwhile, the impacts of PLXNC1 deficiency on the viability, inflammatory response, apoptosis, ECM degradation as well as ERS in IL-1β-exposed chondrocytes were abolished by GRP78 up-regulation. CONCLUSION In summary, PLXNC1 silencing might interact with and down-regulate GRP78 to mitigate the apoptosis, inflammation, and ECM degradation of IL-1β-insulted chondrocytes in OA.
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Affiliation(s)
- Nan Meng
- Department of Orthopedics, The Affiliated People's Hospital with Jiangsu University, 8 Dianli Road, Runzhou District, Zhenjiang City, 212002, Jiangsu Province, China
| | - Lingwei Mao
- Department of Orthopedics, The Affiliated People's Hospital with Jiangsu University, 8 Dianli Road, Runzhou District, Zhenjiang City, 212002, Jiangsu Province, China
| | - Qinyi Jiang
- Department of Orthopedics, The Affiliated People's Hospital with Jiangsu University, 8 Dianli Road, Runzhou District, Zhenjiang City, 212002, Jiangsu Province, China
| | - Jishan Yuan
- Department of Orthopedics, The Affiliated People's Hospital with Jiangsu University, 8 Dianli Road, Runzhou District, Zhenjiang City, 212002, Jiangsu Province, China
| | - Linjuan Liu
- Department of Stomatology, The Affiliated Hospital with Jiangsu University, 8 Jiefang Road, Jingkou District, Zhenjiang City, 212002, Jiangsu Province, China.
| | - Lei Wang
- Department of Orthopedics, The Affiliated People's Hospital with Jiangsu University, 8 Dianli Road, Runzhou District, Zhenjiang City, 212002, Jiangsu Province, China.
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11
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Matrone C, Ferretti G. Semaphorin 3A influences neuronal processes that are altered in patients with autism spectrum disorder: Potential diagnostic and therapeutic implications. Neurosci Biobehav Rev 2023; 153:105338. [PMID: 37524141 DOI: 10.1016/j.neubiorev.2023.105338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Autism spectrum disorder (ASD) is a pervasive disorder that most frequently manifests in early childhood and lasts for their entire lifespan. Several behavioural traits characterise the phenotype of patients with ASD, including difficulties in reciprocal social communication as well as compulsive/repetitive stereotyped verbal and non-verbal behaviours. Although multiple hypotheses have been proposed to explain the aetiology of ASD and many resources have been used to improve our understanding of ASD, several aspects remain largely unexplored. Class 3 semaphorins (SEMA3) are secreted proteins involved in the organisation of structural and functional connectivity in the brain that regulate synaptic and dendritic development. Alterations in brain connectivity and aberrant neuronal development have been described in some patients with ASD. Mutations and polymorphisms in SEMA3A and alterations in its receptors and signalling have been associated with some neurological disorders such as schizophrenia and epilepsy, which are comorbidities in ASD, but also with ASD itself. In addition, SEMA3A is a key regulator of the immune response and neuroinflammatory processes, which have been found to be dysregulated in mothers of children who develop ASD and in affected patients. In this review, we highlight neurodevelopmental-related processes in which SEMA3A is involved, which are altered in ASD, and provide a viewpoint emphasising the development of strategies targeting changes in the SEMA3A signal to identify patterns of anomalies distinctive of ASD or to predict the prognosis of affected patients.
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Affiliation(s)
- Carmela Matrone
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy.
| | - Gabriella Ferretti
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy
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12
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Fard D, Giraudo E, Tamagnone L. Mind the (guidance) signals! Translational relevance of semaphorins, plexins, and neuropilins in pancreatic cancer. Trends Mol Med 2023; 29:817-829. [PMID: 37598000 DOI: 10.1016/j.molmed.2023.07.009] [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: 06/24/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/21/2023]
Abstract
Pancreatic cancer is a major cause of demise worldwide. Although key associated genetic changes have been discovered, disease progression is sustained by pathogenic mechanisms that are poorly understood at the molecular level. In particular, the tissue microenvironment of pancreatic adenocarcinoma (PDAC) is usually characterized by high stromal content, scarce recruitment of immune cells, and the presence of neuronal fibers. Semaphorins and their receptors, plexins and neuropilins, comprise a wide family of regulatory signals that control neurons, endothelial and immune cells, embryo development, and normal tissue homeostasis, as well as the microenvironment of human tumors. We focus on the role of these molecular signals in pancreatic cancer progression, as revealed by experimental research and clinical studies, including novel approaches for cancer treatment.
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Affiliation(s)
- Damon Fard
- Università Cattolica del Sacro Cuore, Department of Life Sciences and Public Health, Rome, Italy
| | - Enrico Giraudo
- Department of Science and Drug Technology, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO IRCCS, Candiolo, Turin, Italy
| | - Luca Tamagnone
- Università Cattolica del Sacro Cuore, Department of Life Sciences and Public Health, Rome, Italy; Fondazione Policlinico Gemelli, IRCCS, Rome, Italy.
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13
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Toledano S, Neufeld G. Plexins as Regulators of Cancer Cell Proliferation, Migration, and Invasivity. Cancers (Basel) 2023; 15:4046. [PMID: 37627074 PMCID: PMC10452846 DOI: 10.3390/cancers15164046] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Plexins are a family of nine single-pass transmembrane receptors with a conserved GTPase activating protein (GAP) domain. The plexin family is divided into four subfamilies: Type-A, type-B, type-C, and type-D plexins. Plexins function as receptors for axon guidance factors of the semaphorin family. The semaphorin gene family contains 22 genes that are divided into eight subclasses of which subclasses three to seven represent vertebrate semaphorins. The plexins and their semaphorin ligands have important roles as regulators of angiogenesis, cancer proliferation, and metastasis. Class 3 semaphorins, with the exception of sema3E, are the only semaphorins that do not bind directly to plexins. In order to transduce their signals, they bind instead to complexes consisting of receptors of the neuropilin family and various plexins. Some plexins also form complexes with tyrosine-kinase receptors such as the epidermal growth factor receptor ErbB2, the mesenchymal epithelial transition factor receptor (MET), and the Vascular endothelial growth factor receptor 2 (VEGFR2) and, as a result, can modulate cell proliferation and tumor progression. This review focuses on the roles of the different plexins in the control of cancer cell proliferation and invasiveness. Plexins also affect tumor progression and tumor metastasis by indirect mechanisms, such as modulation of angiogenesis and immune responses. However, these topics are not covered in the present review.
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Affiliation(s)
| | - Gera Neufeld
- The Cancer Research Center, The Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109602, Israel;
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14
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Bica C, Tirpe A, Nutu A, Ciocan C, Chira S, Gurzau ES, Braicu C, Berindan-Neagoe I. Emerging roles and mechanisms of semaphorins activity in cancer. Life Sci 2023; 318:121499. [PMID: 36775114 DOI: 10.1016/j.lfs.2023.121499] [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: 11/28/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Semaphorins are regulatory molecules that are linked to the modulation of several cancer processes, such as angiogenesis, cancer cell invasiveness and metastasis, tumor growth, as well as cancer cell survival. Semaphorin (SEMA) activity depends on the cancer histotypes and their particularities. In broad terms, the effects of SEMAs result from their interaction with specific receptors/co-receptors - Plexins, Neuropilins and Integrins - and the subsequent effects upon the downstream effectors (e.g. PI3K/AKT, MAPK/ERK). The present article serves as an integrative review work, discussing the broad implications of semaphorins in cancer, focusing on cell proliferation/survival, angiogenesis, invasion, metastasis, stemness, and chemo-resistance/response whilst highlighting their heterogeneity as a family. Herein, we emphasized that semaphorins are largely implicated in cancer progression, interacting with the tumor microenvironment components. Whilst some SEMAs (e.g. SEMA3A, SEMA3B) function widely as tumor suppressors, others (e.g. SEMA3C) act as pro-tumor semaphorins. The differences observed in terms of the biological structure of SEMAs and the particularities of each cancer histotypes require that each semaphorin be viewed as a unique entity, and its roles must be researched accordingly. A more in-depth and comprehensive view of the molecular mechanisms that promote and sustain the malignant behavior of cancer cells is of utmost importance.
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Affiliation(s)
- Cecilia Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Alexandru Tirpe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania; Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes Street, 400012 Cluj-Napoca, Romania.
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Cristina Ciocan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Sergiu Chira
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Eugen S Gurzau
- Cluj School of Public Health, College of Political, Administrative and Communication Sciences, Babes-Bolyai University, 7 Pandurilor Street, Cluj-Napoca, Romania; Environmental Health Center, 58 Busuiocului Street, 400240 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
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15
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Zheng B, Lyu L, Wang X, Wen H, Li Y, Li J, Yao Y, Zuo C, Yan S, Xie S, Qi X. Comparative transcriptomic analysis and genome-wide characterization of the Semaphorin family reveal the potential mechanism of angiogenesis around embryo in ovoviviparous black rockfish (Sebastes schlegelii). Gen Comp Endocrinol 2023; 338:114275. [PMID: 36940835 DOI: 10.1016/j.ygcen.2023.114275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023]
Abstract
To guarantee the quality and survival rate of their offspring, ovoviviparous teleost evolved special characteristics of in vivo fertilization and embryo development. Maternal black rockfish, having over 50 thousand embryos developing within the ovary simultaneously, provided around 40% nutrition throughout oocyte development, while the capillaries around each embryo contributed the rest 60% during pregnancy. Since fertilization, capillaries started to proliferate and developed into a placenta-like structure that covered over half of each embryo. Aimed to characterize the potential mechanism behind, comparative transcriptome analysis of samples collected according to the process of pregnancy. Three important time point in the process, including mature oocyte stage, fertilization and sarcomere period, were chosen for the transcriptome sequencing. Our study identified key pathways and genes involved in the cell cycle as well as DNA replication and repair, cell migration and adhesion, immune, and metabolic functions. Notably, several of the semaphoring gene family members were differently expressed. To confirm the accuracy of these genes, total of 32 sema genes were identified from the whole genome and distinct expression pattern of sema genes was observed in different pregnant stages. Our results revealed a novel insight for further investigating the functions of sema genes in reproduction physiology and embryo processes in ovoviviparous teleost.
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Affiliation(s)
- Bingyan Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Likang Lyu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xiaojie Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Jianshuang Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yijia Yao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Chenpeng Zuo
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Shaojing Yan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Songyang Xie
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xin Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
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16
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Tanaka T, Ekimoto T, Nagatomo M, Neyazaki M, Shimoji E, Yamane T, Kanagawa S, Oi R, Mihara E, Takagi J, Akashi S, Ikeguchi M, Nogi T. Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D. Protein Sci 2022; 31:e4452. [PMID: 36156831 PMCID: PMC9601788 DOI: 10.1002/pro.4452] [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: 07/09/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
Semaphorins constitute a large family of secreted and membrane-bound proteins that signal through cell-surface receptors, plexins. Semaphorins generally use low-affinity protein-protein interactions to bind with their specific plexin(s) and regulate distinct cellular processes such as neurogenesis, immune response, and organogenesis. Sema6D is a membrane-bound semaphorin that interacts with class A plexins. Sema6D exhibited differential binding affinities to class A plexins in prior cell-based assays, but the molecular mechanism underlying this selectivity is not well understood. Therefore, we performed hybrid in vitro/in silico analysis to examine the binding mode of Sema6D to class A plexins and to identify residues that give rise to the differential affinities and thus contribute to the selectivity within the same class of semaphorins. Our biophysical binding analysis indeed confirmed that Sema6D has a higher affinity for Plexin-A1 than for other class A plexins, consistent with the binding selectivity observed in the previous cell-based assays. Unexpectedly, our present crystallographic analysis of the Sema6D-Plexin-A1 complex showed that the pattern of polar interactions is not interaction-specific because it matches the pattern in the prior structure of the Sema6A-Plexin-A2 complex. Thus, we performed in silico alanine scanning analysis and discovered hotspot residues that selectively stabilized the Sema6D-Plexin-A1 pair via Van der Waals interactions. We then validated the contribution of these hotspot residues to the variation in binding affinity with biophysical binding analysis and molecular dynamics simulations on the mutants. Ultimately, our present results suggest that shape complementarity in the binding interfaces is a determinant for binding selectivity.
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Affiliation(s)
- Tsubasa Tanaka
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Toru Ekimoto
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Meri Nagatomo
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Makiko Neyazaki
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Erena Shimoji
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Tsutomu Yamane
- Center for Computational Science, RIKENYokohamaKanagawaJapan
| | - Sakura Kanagawa
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Rika Oi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Emiko Mihara
- Institute for Protein Research, Osaka UniversitySuitaOsakaJapan
| | - Junichi Takagi
- Institute for Protein Research, Osaka UniversitySuitaOsakaJapan
| | - Satoko Akashi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
- Center for Computational Science, RIKENYokohamaKanagawaJapan
| | - Terukazu Nogi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
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17
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Yin Z, Zhang J, Xu S, Liu J, Xu Y, Yu J, Zhao M, Pan W, Wang M, Wan J. The role of semaphorins in cardiovascular diseases: Potential therapeutic targets and novel biomarkers. FASEB J 2022; 36:e22509. [PMID: 36063107 DOI: 10.1096/fj.202200844r] [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: 06/03/2022] [Revised: 07/24/2022] [Accepted: 08/09/2022] [Indexed: 12/17/2022]
Abstract
Semaphorins (Semas), which belongs to the axonal guidance molecules, include 8 classes and could affect axon growth in the nervous system. Recently, semaphorins were found to regulate other pathophysiological processes, such as immune response, oncogenesis, tumor angiogenesis, and bone homeostasis, through binding with their plexin and neuropilin receptors. In this review, we summarized the detailed role of semaphorins and their receptors in the pathological progression of various cardiovascular diseases (CVDs), highlighting that semaphorins may be potential therapeutic targets and novel biomarkers for CVDs.
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Affiliation(s)
- Zheng Yin
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jishou Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Shuwan Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jianfang Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Yao Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Junping Yu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Mengmeng Zhao
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Wei Pan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Menglong Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jun Wan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
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18
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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19
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Pshetitsky Y, Mendelman N, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: N-H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry. J Phys Chem B 2022; 126:6396-6407. [PMID: 35980340 DOI: 10.1021/acs.jpcb.2c03431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Amide-bond equilibrium probability density, Peq = exp(-u) (u, local potential), and associated conformational entropy, Sk = -∫Peq (ln Peq) dΩ ─ln ∫dΩ, are derived for the Rho GTPase binding domain of Plexin-B1 (RBD) as monomer and dimer from 1 μs MD simulations. The objective is to elucidate the effect of dimerization on the dynamic structure of the RBD. Dispersed (peaked) Peq functions indicate "flexibility" ("rigidity"; the respective concepts are used below in this context). The L1 and L3 loops are throughout highly flexible, the L2 loop and the secondary structure elements are generally rigid, and the L4 loop is flexible in the monomer and rigid in the dimer. Overall, many residues are more flexible in the dimer. These features, and their implications, are discussed. Unexpectedly, we find that monomer unit 1 of the dimer (in short, d1) is unusually flexible, whereas monomer unit 2 (in short, d2) is as rigid as the RBD monomer. This is revealed due to their engagement in slow-to-intermediate conformational exchange detected previously by 15N relaxation experiments. Such motions occur with rates on the order of 103-104 s-1; hence, they cannot be completely sampled over the course of 1 μs simulation. However, the extent to which rigid d2 is affected is small enough to enable physically relevant analysis. The entropy difference between d2 and the monomer yields an entropic contribution of -7 ± 0.7 kJ/mol to the free energy of RBD dimerization. In previous work aimed at similar objectives we used 50-100 ns MD simulations. Those results and the present result differ considerably. In summary, bond-vector Peq functions derived directly from long MD simulations are useful descriptors of protein structural dynamics and provide accurate conformational entropy. Within the scope of slow conformational exchange, they can be useful, even in the presence of incomplete sampling.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhenlu Li
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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20
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Mendelman N, Pshetitsky Y, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in Ligand-Free, Rac1-Bound, and Dimer RBD. J Phys Chem B 2022; 126:6408-6418. [PMID: 35976064 DOI: 10.1021/acs.jpcb.2c03435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orientational probability densities, Peq = exp(-u) (u, local potential), of bond-vectors in proteins provide information on structural flexibility. The related conformational entropy, Sk = -∫Peq(ln Peq)dΩ - ln ∫dΩ, provides the entropic contribution to the free energy of the physical/biological process studied. We have developed a new method for deriving Peq and Sk from MD simulations, using the N-H bond as probe. Recently we used it to study the dimerization of the Rho GTPase binding domain of Plexin-B1 (RBD). Here we use it to study RBD binding to the small GTPase Rac1. In both cases 1 μs MD simulations have been employed. The RBD has the ubiquitin fold with four mostly long loops. L3 is associated with GTPase binding, L4 with RBD dimerization, L2 participates in interdomain interactions, and L1 has not been associated with function. We find that RBD-Rac1 binding renders L1, L3, and L4 more rigid and the turns β2/α1 and α2/β5 more flexible. By comparison, RBD dimerization renders L4 more rigid, and the α-helices, the β-strands, and L2 more flexible. The rigidity of L1 in RBDRAC is consistent with L1-L3 contacts seen in previous MD simulations. The analysis of the L3-loop reveals two states of distinct flexibility which we associate with involvement in slow conformational exchange processes differing in their rates. Overall, the N-H bonds make an unfavorable entropic contribution of (5.9 ± 0.9) kJ/mol to the free energy of RBD-Rac1 binding; they were found to make a favorably contribution of (-7.0 ± 0.7) kJ/mol to the free energy of RBD dimerization. In summary, the present study provides a new perspective on the impact of Rac1 binding and dimerization on the flexibility characteristics of the RBD. Further studies are stimulated by the results of this work.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhenlu Li
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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21
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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.
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22
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Szczurkowska J, Guo A, Martin J, Lee SI, Martinez E, Chien CT, Khan TA, Singh R, Dadson D, Tran TS, Pautot S, Shelly M. Semaphorin3A/PlexinA3 association with the Scribble scaffold for cGMP increase is required for apical dendrite development. Cell Rep 2022; 38:110483. [PMID: 35294878 PMCID: PMC8994670 DOI: 10.1016/j.celrep.2022.110483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 10/03/2021] [Accepted: 02/12/2022] [Indexed: 11/30/2022] Open
Abstract
The development of the apical dendrite from the leading process of the bipolar pyramidal neuron might be directed by spatially organized extrinsic cues acting on localized intrinsic determinants. The extracellular cues regulating apical dendrite polarization remain elusive. We show that leading process and apical dendrite development are directed by class III Semaphorins and mediated by a localized cGMP-synthesizing complex. The scaffolding protein Scribble that associates with the cGMP-synthesizing enzyme soluble guanylate cyclase (sGC) also associates with the Semaphorin3A (Sema3A) co-receptor PlexinA3. Deletion or knockdown of PlexinA3 and Sema3A or disruption of PlexinA3-Scribble association prevents Sema3A-mediated cGMP increase and causes defects in apical dendrite development. These manipulations also impair bipolar polarity and leading process establishment. Local cGMP elevation or sGC expression rescues the effects of PlexinA3 knockdown or PlexinA3-Scribble complex disruption. During neuronal polarization, leading process and apical dendrite development are directed by a scaffold that links Semaphorin cue to cGMP increase. Szczurkowska et al. show that spatially directed Sema3A may promote development of the leading process and the apical dendrite via the co-receptor PlexinA3 by orchestrating localized cGMP increase on the scaffold protein, Scribble, at the leading edge of developing pyramidal neurons.
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Affiliation(s)
- Joanna Szczurkowska
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Alan Guo
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jacqueline Martin
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Seong-Il Lee
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Edward Martinez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Chia Te Chien
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tamor A Khan
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ravnit Singh
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Doreen Dadson
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tracy S Tran
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | | | - Maya Shelly
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA.
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23
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Chen MZ, Su LY, Ko PH, Hsu MH, Chuang LL, Chen LH, Lu TP, Chuang EY, Chow LP, Tsai MH, Hsu HH, Lai LC. Extracellular domain of semaphorin 5A serves a tumor‑suppressing role by activating interferon signaling pathways in lung adenocarcinoma cells. Int J Oncol 2022; 60:21. [PMID: 35059729 DOI: 10.3892/ijo.2022.5311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
Semaphorin 5A (SEMA5A), which was originally identified as an axon guidance molecule in the nervous system, has been subsequently identified as a prognostic biomarker for lung cancer in nonsmoking women. SEMA5A acts as a tumor suppressor by inhibiting the proliferation and migration of lung cancer cells. However, the regulatory mechanism of SEMA5A is not clear. Therefore, the purpose of the present study was to explore the roles of different domains of SEMA5A in its tumor‑suppressive effects in lung adenocarcinoma cell lines. First, it was revealed that overexpression of full length SEMA5A or its extracellular domain significantly inhibited the proliferation and migration of both A549 and H1299 cells using MTT, colony formation and gap closure assays. Next, microarray analyses were performed to identify genes regulated by different domains of SEMA5A. Among the differentially expressed genes, the most significant function of these genes that were enriched was the 'Interferon Signaling' pathway according to Ingenuity Pathway Analysis. The activation of the 'Interferon Signaling' pathway was validated by reverse transcription‑quantitative PCR and western blotting. In summary, the present study demonstrated that the extracellular domain of SEMA5A could upregulate genes in interferon signaling pathways, resulting in suppressive effects in lung adenocarcinoma cells.
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Affiliation(s)
- Ming-Zhen Chen
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, R.O.C
| | - Li-Yu Su
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, R.O.C
| | - Pin-Hao Ko
- Department of Traditional Chinese Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 330, Taiwan, R.O.C
| | - Ming-Hsuan Hsu
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, R.O.C
| | - Li-Ling Chuang
- School of Physical Therapy and Graduate Institute of Rehabilitation Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan, R.O.C
| | - Li-Han Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Lu-Ping Chow
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Hsao-Hsun Hsu
- Division of Thoracic Surgery, Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan, R.O.C
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, R.O.C
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24
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Steele JL, Morrow MM, Sarnat HB, Alkhunaizi E, Brandt T, Chitayat DA, DeFilippo CP, Douglas GV, Dubbs HA, Elloumi HZ, Glassford MR, Hannibal MC, Héron B, Kim LE, Marco EJ, Mignot C, Monaghan KG, Myers KA, Parikh S, Quinonez SC, Rajabi F, Shankar SP, Shinawi MS, van de Kamp JJP, Veerapandiyan A, Waldman AT, Graf WD. Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome. Pediatr Neurol 2022; 126:65-73. [PMID: 34740135 DOI: 10.1016/j.pediatrneurol.2021.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Semaphorins and plexins are ligands and cell surface receptors that regulate multiple neurodevelopmental processes such as axonal growth and guidance. PLXNA3 is a plexin gene located on the X chromosome that encodes the most widely expressed plexin receptor in fetal brain, plexin-A3. Plexin-A3 knockout mice demonstrate its role in semaphorin signaling in vivo. The clinical manifestations of semaphorin/plexin neurodevelopmental disorders have been less widely explored. This study describes the neurological and neurodevelopmental phenotypes of boys with maternally inherited hemizygous PLXNA3 variants. METHODS Data-sharing through GeneDx and GeneMatcher allowed identification of individuals with autism or intellectual disabilities (autism/ID) and hemizygous PLXNA3 variants in collaboration with their physicians and genetic counselors, who completed questionnaires about their patients. In silico analyses predicted pathogenicity for each PLXNA3 variant. RESULTS We assessed 14 boys (mean age, 10.7 [range 2 to 25] years) with maternally inherited hemizygous PLXNA3 variants and autism/ID ranging from mild to severe. Other findings included fine motor dyspraxia (92%), attention-deficit/hyperactivity traits, and aggressive behaviors (63%). Six patients (43%) had seizures. Thirteen boys (93%) with PLXNA3 variants showed novel or very low allele frequencies and probable damaging/disease-causing pathogenicity in one or more predictors. We found a genotype-phenotype correlation between PLXNA3 cytoplasmic domain variants (exons 22 to 32) and more severe neurodevelopmental disorder phenotypes (P < 0.05). CONCLUSIONS We report 14 boys with maternally inherited, hemizygous PLXNA3 variants and a range of neurodevelopmental disorders suggesting a novel X-linked intellectual disability syndrome. Greater understanding of PLXNA3 variant pathogenicity in humans will require additional clinical, computational, and experimental validation.
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Affiliation(s)
| | | | - Harvey B Sarnat
- Departments of Paediatrics, Pathology (Neuropathology), and Clinical Neurosciences, University of Calgary Cumming School of Medicine and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Ebba Alkhunaizi
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - David A Chitayat
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Colette P DeFilippo
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, University of California-Davis, Sacramento, California
| | | | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Megan R Glassford
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Mark C Hannibal
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Bénédicte Héron
- Hôpital Armand Trousseau, Service de Neurologie Pédiatrique, Paris, France
| | - Linda E Kim
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Elysa J Marco
- Department of Neurodevelopmental Medicine, CorticaCare, San Diego, California
| | - Cyril Mignot
- Clinical Genetic Department, Pitié Salpétrière University Hospital, Paris, France
| | | | - Kenneth A Myers
- Division of Neurology, Department of Pediatrics, McGill University Health Centre, Montreal, Canada
| | - Sumit Parikh
- Department of Mitochondrial Medicine & Genetics, Cleveland Clinic, Cleveland, Ohio
| | - Shane C Quinonez
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Suma P Shankar
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, University of California-Davis, Sacramento, California
| | - Marwan S Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | | | - Aravindhan Veerapandiyan
- Division of Neurology, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Arkansas
| | - Amy T Waldman
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - William D Graf
- Division of Neurology, Department of Pediatrics, Connecticut Children's, University of Connecticut, Farmington, Connecticut.
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25
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Li S, Hua X, Zheng M, Wu J, Ma Z, Xing X, Ma J, Zhang J, Shan C, Xu J. PLXNA2 knockdown promotes M2 microglia polarization through mTOR/STAT3 signaling to improve functional recovery in rats after cerebral ischemia/reperfusion injury. Exp Neurol 2021; 346:113854. [PMID: 34474008 DOI: 10.1016/j.expneurol.2021.113854] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/08/2021] [Accepted: 08/26/2021] [Indexed: 01/04/2023]
Abstract
Ischemic stroke is an acute cerebrovascular disease characterized by high mortality, morbidity and disability rates. Ischemia/reperfusion is a critical pathophysiological basis of motor and cognitive dysfunction caused by ischemic stroke. Microglia, innate immune cells of the central nervous system, mediate the neuroinflammatory response to ischemia/reperfusion. PlexinA2 (PLXNA2) plays an important role in the regulation of neuronal axon guidance, the immune response and angiogenesis. However, it is not clear whether PLXNA2 regulates microglia polarization in ischemic stroke or the underlying mechanism. In the present study, we investigated the role of PLXNA2 in rats with middle cerebral artery occlusion/reperfusion (MCAO/R) and BV2 microglia cells with oxygen and glucose deprivation/reoxygenation (OGD/R). A battery of behavioral tests, including the beam balance test, forelimb placement test, foot fault test, cylinder test, CatWalk gait analysis and Morris water maze test were performed to evaluate sensorimotor function, locomotor activity and cognitive ability. The expression of M1/M2-specific markers in the ischemic penumbra and BV2 microglia cells was detected using immunofluorescence staining, quantitative real-time PCR analysis and Western blot analysis. Our study showed that PLXNA2 knockdown accelerated the recovery of motor function and cognitive ability after MCAO/R. In addition, PLXNA2 knockdown restrained proinflammatory cytokine release and promoted anti-inflammatory cytokine release, and the mammalian target of rapamycin (mTOR)/signal transducer and activator of transcription 3 (STAT3) pathway was involved in PLXNA2 regulated microglia polarization. Taken together, our results indicate that PLXNA2 knockdown reduces neuroinflammation by switching the microglia phenotype from M1 to M2 in the ischemic penumbra of MCAO/R-injured rats, which may be due to the inhibition of mTOR/STAT3 signaling. Treatments targeting PLXNA2 may be a promising therapeutic strategy for ischemic stroke.
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Affiliation(s)
- Sisi Li
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xuyun Hua
- Department of Traumatology and Orthopedics, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Mouxiong Zheng
- Department of Traumatology and Orthopedics, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Jiajia Wu
- Center of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Zhenzhen Ma
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiangxin Xing
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jie Ma
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Junpeng Zhang
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chunlei Shan
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Center of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China; Engineering Research Center of Traditional Chinese Medicine Intelligent Rehabilitation, Ministry of Education, Shanghai 201203, China
| | - Jianguang Xu
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Traditional Chinese Medicine Intelligent Rehabilitation, Ministry of Education, Shanghai 201203, China.
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26
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Christie SM, Hao J, Tracy E, Buck M, Yu JS, Smith AW. Interactions between semaphorins and plexin-neuropilin receptor complexes in the membranes of live cells. J Biol Chem 2021; 297:100965. [PMID: 34270956 PMCID: PMC8350011 DOI: 10.1016/j.jbc.2021.100965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 11/27/2022] Open
Abstract
Signaling of semaphorin ligands via their plexin-neuropilin receptors is involved in tissue patterning in the developing embryo. These proteins play roles in cell migration and adhesion but are also important in disease etiology, including in cancer angiogenesis and metastasis. While some structures of the soluble domains of these receptors have been determined, the conformations of the full-length receptor complexes are just beginning to be elucidated, especially within the context of the plasma membrane. Pulsed-interleaved excitation fluorescence cross-correlation spectroscopy allows direct insight into the formation of protein-protein interactions in the membranes of live cells. Here, we investigated the homodimerization of neuropilin-1 (Nrp1), plexin A2, plexin A4, and plexin D1 using pulsed-interleaved excitation fluorescence cross-correlation spectroscopy. Consistent with previous studies, we found that Nrp1, plexin A2, and plexin A4 are present as dimers in the absence of exogenous ligand. Plexin D1, on the other hand, was monomeric under similar conditions, which had not been previously reported. We also found that plexin A2 and A4 assemble into a heteromeric complex. Stimulation with semaphorin 3A or semaphorin 3C neither disrupts nor enhances the dimerization of the receptors when expressed alone, suggesting that activation involves a conformational change rather than a shift in the monomer-dimer equilibrium. However, upon stimulation with semaphorin 3C, plexin D1 and Nrp1 form a heteromeric complex. This analysis of interactions provides a complementary approach to the existing structural and biochemical data that will aid in the development of new therapeutic strategies to target these receptors in cancer.
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Affiliation(s)
| | - Jing Hao
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Erin Tracy
- Department of Chemistry, University of Akron, Akron, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer S Yu
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA; Department of Radiation Oncology, Cleveland Clinic, Cleveland, Ohio, USA; Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, Ohio, USA.
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27
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Li ZL, Buck M. Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2. Biophys J 2021; 120:2828-2837. [PMID: 34087218 PMCID: PMC8169233 DOI: 10.1016/j.bpj.2021.05.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/30/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1-685) and the S2 (res. 686-1273) domains by furin protease. Nrp1 predominantly binds to the C-terminal RRAR amino acid motif (res. 682-685) of the S1 domain. In this study, we firstly modeled the association of an Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640-685) and thereby assists the detachment of S2 N-terminal region (res. 686-700). Without Nrp1 bound, S1 tends to become stretched, whereas the bound Nrp1 stimulates an earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes; thus, Nrp1 likely increases virus infectivity by facilitating the S1 and S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and angiotensin-converting enzyme 2 (ACE2). Understanding of such an Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1-ACE2 targeted combination therapy.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, School of Medicine, Cleveland, Ohio
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Cleveland, Ohio; Department of Pharmacology, School of Medicine, Cleveland, Ohio; Department of Neurosciences, School of Medicine, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, Ohio.
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28
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Modelling and Refining Neuronal Circuits with Guidance Cues: Involvement of Semaphorins. Int J Mol Sci 2021; 22:ijms22116111. [PMID: 34204060 PMCID: PMC8201269 DOI: 10.3390/ijms22116111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/17/2022] Open
Abstract
The establishment of neuronal circuits requires neurons to develop and maintain appropriate connections with cellular partners in and out the central nervous system. These phenomena include elaboration of dendritic arborization and formation of synaptic contacts, initially made in excess. Subsequently, refinement occurs, and pruning takes places both at axonal and synaptic level, defining a homeostatic balance maintained throughout the lifespan. All these events require genetic regulations which happens cell-autonomously and are strongly influenced by environmental factors. This review aims to discuss the involvement of guidance cues from the Semaphorin family.
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29
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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.
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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.
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Chung S, Yang J, Kim HJ, Hwang EM, Lee W, Suh K, Choi H, Mook-Jung I. Plexin-A4 mediates amyloid-β-induced tau pathology in Alzheimer's disease animal model. Prog Neurobiol 2021; 203:102075. [PMID: 34004220 DOI: 10.1016/j.pneurobio.2021.102075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
Amyloid-β (Aβ) and tau are major pathological hallmarks of Alzheimer's disease (AD). Several studies have revealed that Aβ accelerates pathological tau transition and spreading during the disease progression, and that reducing tau can mitigate pathological features of AD. However, molecular links between Aβ and tau pathologies remain elusive. Here, we suggest a novel role for the plexin-A4 as an Aβ receptor that induces aggregated tau pathology. Plexin-A4, previously known as proteins involved in regulating axon guidance and synaptic plasticity, can bound to Aβ with co-receptor, neuropilin-2. Genetic downregulation of plexin-A4 in neurons was sufficient to prevent Aβ-induced activation of CDK5 and reduce tau hyperphosphorylation and aggregation, even in the presence of Aβ. In an AD mouse model that manifests both Aβ and tau pathologies, genetic downregulation of plexin-A4 in the hippocampus reduced tau pathology and ameliorated spatial memory impairment. Collectively, these results indicate that the plexin-A4 is capable of mediating Aβ-induced tau pathology in AD pathogenesis.
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Affiliation(s)
- Sunwoo Chung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Jinhee Yang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; Biorchestra Co., Ltd., Techno 4-ro 17, Daejeon 34013, South Korea.
| | - Haeng Jun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Eun Mi Hwang
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea.
| | - Wonik Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Kyujin Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Hayoung Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Inhee Mook-Jung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
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Carulli D, de Winter F, Verhaagen J. Semaphorins in Adult Nervous System Plasticity and Disease. Front Synaptic Neurosci 2021; 13:672891. [PMID: 34045951 PMCID: PMC8148045 DOI: 10.3389/fnsyn.2021.672891] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Semaphorins, originally discovered as guidance cues for developing axons, are involved in many processes that shape the nervous system during development, from neuronal proliferation and migration to neuritogenesis and synapse formation. Interestingly, the expression of many Semaphorins persists after development. For instance, Semaphorin 3A is a component of perineuronal nets, the extracellular matrix structures enwrapping certain types of neurons in the adult CNS, which contribute to the closure of the critical period for plasticity. Semaphorin 3G and 4C play a crucial role in the control of adult hippocampal connectivity and memory processes, and Semaphorin 5A and 7A regulate adult neurogenesis. This evidence points to a role of Semaphorins in the regulation of adult neuronal plasticity. In this review, we address the distribution of Semaphorins in the adult nervous system and we discuss their function in physiological and pathological processes.
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Affiliation(s)
- Daniela Carulli
- Laboratory for Neuroregeneration, Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, Netherlands
- Department of Neuroscience Rita Levi-Montalcini and Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Turin, Italy
| | - Fred de Winter
- Laboratory for Neuroregeneration, Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, Netherlands
| | - Joost Verhaagen
- Laboratory for Neuroregeneration, Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, Netherlands
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Zhang YF, Zhang Y, Jia DD, Yang HY, Cheng MD, Zhu WX, Xin H, Li PF, Zhang YF. Insights into the regulatory role of Plexin D1 signalling in cardiovascular development and diseases. J Cell Mol Med 2021; 25:4183-4194. [PMID: 33837646 PMCID: PMC8093976 DOI: 10.1111/jcmm.16509] [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: 12/29/2020] [Revised: 03/04/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
Plexin D1 (PLXND1), which was previously thought to mediate semaphorin signalling, belongs to the Plexin family of transmembrane proteins. PLXND1 cooperates mostly with the coreceptor neuropilin and participates in many aspects of axonal guidance. PLXND1 can also act as both a tumour promoter and a tumour suppressor. Emerging evidence suggests that mutations in PLXND1 or Semaphorin 3E, the canonical ligand of PLXND1, can lead to serious cardiovascular diseases, such as congenital heart defects, CHARGE syndrome and systemic sclerosis. Upon ligand binding, PLXND1 can act as a GTPase‐activating protein (GAP) and modulate integrin‐mediated cell adhesion, cytoskeletal dynamics and cell migration. These effects may play regulatory roles in the development of the cardiovascular system and disease. The cardiovascular effects of PLXND1 signalling have gradually been elucidated. PLXND1 was recently shown to detect physical forces and translate them into intracellular biochemical signals in the context of atherosclerosis. Therefore, the role of PLXND1 in cardiovascular development and diseases is gaining research interest because of its potential as a biomarker and therapeutic target. In this review, we describe the cardiac effects, vascular effects and possible molecular mechanisms of PLXND1 signalling.
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Affiliation(s)
- Yi-Fei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dong-Dong Jia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hong-Yu Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Meng-Die Cheng
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wen-Xiu Zhu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Xin
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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33
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Taguchi S, Suga H. Targeting of extracellular protein-protein interactions with macrocyclic peptides. Curr Opin Chem Biol 2021; 62:82-89. [PMID: 33774472 DOI: 10.1016/j.cbpa.2021.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
Targeting of extracellular protein-protein interactions (PPI) is emerging as a major application for de novo discovered macrocyclic peptides. Modern discovery platforms can routinely identify macrocyclic peptide ligands capable of highly selective modulation of extracellular signaling pathways; amenability to chemical synthesis and natural modularity of peptides additionally provides an avenue for their further structural elaboration, while the challenge of cell internalization can be minimized. Here, we discuss the recent progress in targeting extracellular PPIs with macrocyclic peptides by focusing on a number of recent case studies. We analyze the scope and potential limitations of the discovery systems in identifying functional macrocyclic ligands. We also highlight the recent technical advancements allowing for a more streamlined discovery pipeline and our brief perspective in this field.
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Affiliation(s)
- Shota Taguchi
- Department of Advanced Interdisciplinary, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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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.
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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
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Huang Y, Tejero R, Lee VK, Brusco C, Hannah T, Bertucci TB, Junqueira Alves C, Katsyv I, Kluge M, Foty R, Zhang B, Friedel CC, Dai G, Zou H, Friedel RH. Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics. Commun Biol 2021; 4:145. [PMID: 33514835 PMCID: PMC7846610 DOI: 10.1038/s42003-021-01667-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Infiltrative growth is a major cause of high lethality of malignant brain tumors such as glioblastoma (GBM). We show here that GBM cells upregulate guidance receptor Plexin-B2 to gain invasiveness. Deletion of Plexin-B2 in GBM stem cells limited tumor spread and shifted invasion paths from axon fiber tracts to perivascular routes. On a cellular level, Plexin-B2 adjusts cell adhesiveness, migratory responses to different matrix stiffness, and actomyosin dynamics, thus empowering GBM cells to leave stiff tumor bulk and infiltrate softer brain parenchyma. Correspondingly, gene signatures affected by Plexin-B2 were associated with locomotor regulation, matrix interactions, and cellular biomechanics. On a molecular level, the intracellular Ras-GAP domain contributed to Plexin-B2 function, while the signaling relationship with downstream effectors Rap1/2 appeared variable between GBM stem cell lines, reflecting intertumoral heterogeneity. Our studies establish Plexin-B2 as a modulator of cell biomechanics that is usurped by GBM cells to gain invasiveness.
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Affiliation(s)
- Yong Huang
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rut Tejero
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vivian K Lee
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Concetta Brusco
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Theodore Hannah
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Taylor B Bertucci
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Chrystian Junqueira Alves
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ramsey Foty
- Department of Surgery, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guohao Dai
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Hongyan Zou
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Roland H Friedel
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Li ZL, Buck M. Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.06.425627. [PMID: 33442700 PMCID: PMC7805474 DOI: 10.1101/2021.01.06.425627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR amino acid sequence of the S1 domain. In this study, we model the association of a Nrp1 (a2-b1-b2) protein with the Spike protein computationally and analyze the topological constraints in the SARS-CoV-2 Spike protein for binding with Nrp1 and ACE2. Importantly, we study the exit mechanism of S2 from the S1 domain with the assistance of ACE2 as well as Nrp1 by molecular dynamics pulling simulations. In the presence of Nrp1, by binding the S1 more strongly to the host membrane, there is a high probability of S2 being pulled out, rather than S1 being stretched. Thus, Nrp1 binding could stimulate the exit of S2 from the S1 domain, which will likely increase virus infectivity as the liberated S2 domain mediates the fusion of virus and host membranes. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future combination therapy.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
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37
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Insights into the mechanism of vascular endothelial cells on bone biology. Biosci Rep 2021; 41:227494. [PMID: 33403387 PMCID: PMC7816070 DOI: 10.1042/bsr20203258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/25/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
In the skeletal system, blood vessels not only function as a conduit system for transporting gases, nutrients, metabolic waste, or cells but also provide multifunctional signal molecules regulating bone development, regeneration, and remodeling. Endothelial cells (ECs) in bone tissues, unlike in other organ tissues, are in direct contact with the pericytes of blood vessels, resulting in a closer connection with peripheral connective tissues. Close-contact ECs contribute to osteogenesis and osteoclastogenesis by secreting various cytokines in the paracrine or juxtacrine pathways. An increasing number of studies have revealed that extracellular vesicles (EVs) derived from ECs can directly regulate maturation process of osteoblasts and osteoclasts. The different pathways focus on targets at different distances, forming the basis of the intimate spatial and temporal link between bone tissue and blood vessels. Here, we provide a systematic review to elaborate on the function of ECs in bone biology and its underlying mechanisms based on three aspects: paracrine, EVs, and juxtacrine. This review proposes the possibility of a therapeutic strategy targeting blood vessels, as an adjuvant treatment for bone disorders.
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Abstract
In the final stages of apoptosis, apoptotic cells can generate a variety of membrane-bound vesicles known as apoptotic extracellular vesicles (ApoEVs). Apoptotic bodies (ApoBDs), a major subset of ApoEVs, are formed through a process termed apoptotic cell disassembly characterised by a series of tightly regulated morphological steps including plasma membrane blebbing, apoptotic membrane protrusion formation and fragmentation into ApoBDs. To better characterise the properties of ApoBDs and elucidate their function, a number of methods including differential centrifugation, filtration and fluorescence-activated cell sorting were developed to isolate ApoBDs. Furthermore, it has become increasingly clear that ApoBD formation can contribute to various biological processes such as apoptotic cell clearance and intercellular communication. Together, recent literature demonstrates that apoptotic cell disassembly and thus, ApoBD formation, is an important process downstream of apoptotic cell death. In this chapter, we discuss the current understandings of the molecular mechanisms involved in regulating apoptotic cell disassembly, techniques for ApoBD isolation, and the functional roles of ApoBDs in physiological and pathological settings.
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McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
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Mendelman N, Zerbetto M, Buck M, Meirovitch E. Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR Relaxation Theory and Molecular Dynamics Simulation Approaches. J Phys Chem B 2020; 124:9323-9334. [PMID: 32981310 DOI: 10.1021/acs.jpcb.0c05846] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method for determining conformational entropy in proteins is reported. Proteins prevail as conformational ensembles, p ∝ exp(-u). By selecting a bond vector (e.g., N-H) as a conformation representative, molecular dynamics simulations can provide (relative to a reference structure) p as approximate Boltzmann probability density and u as N-H potential of mean force (POMF). The latter is as accurate as implied by the force field but statistical in character; this limits the insights it can provide and its utilization. Conformational entropy is given exclusively by u. Deriving it from POMFs renders it accurate but statistical in character. Previously, we devised explicit (i.e., analytical but not exact) potentials made of Wigner functions, D0KL, with L ≤ 4, which closely resemble the corresponding POMFs in form; hence, they also approach the latter in accuracy. Such potentials can be beneficially characterized/compared in terms of composition, symmetry, and associated order parameters. In this study, we develop a method for deriving conformational entropy from them, which also features the benefits specified above. The method developed is applied to the dimerization of the Rho GTPase-binding domain of plexin-B1. Insights into local ordering, entropy compensation, and features of allostery are gained. In previous work, we developed the slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation from restricted bond vector motion in proteins. SRLS comprises explicit (restricting) potentials of the kind developed here. It also comprises diffusion tensors describing the local motion and related features of local geometry. The complete model fits experimental data. In future work, the explicit potentials developed here will be inserted unchanged in SRLS-based data fitting, thereby improving the picture of structural dynamics. Given that SRLS is unique in featuring potentials that can closely approach the corresponding POMFs in accuracy, the present study is an important step toward generally improving protein dynamics by NMR relaxation.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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41
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Atkin-Smith GK, Miles MA, Tixeira R, Lay FT, Duan M, Hawkins CJ, Phan TK, Paone S, Mathivanan S, Hulett MD, Chen W, Poon IKH. Plexin B2 Is a Regulator of Monocyte Apoptotic Cell Disassembly. Cell Rep 2020; 29:1821-1831.e3. [PMID: 31722200 DOI: 10.1016/j.celrep.2019.10.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/10/2019] [Accepted: 10/03/2019] [Indexed: 12/18/2022] Open
Abstract
Billions of cells undergo apoptosis daily and often fragment into small, membrane-bound extracellular vesicles termed apoptotic bodies (ApoBDs). We demonstrate that apoptotic monocytes undergo a highly coordinated disassembly process and form long, beaded protrusions (coined as beaded apoptopodia), which fragment to release ApoBDs. Here, we find that the protein plexin B2 (PlexB2), a transmembrane receptor that regulates axonal guidance in neurons, is enriched in the ApoBDs of THP1 monocytes and is a caspase 3/7 substrate. To determine whether PlexB2 is involved in the disassembly of apoptotic monocytes, we generate PlexB2-deficient THP1 monocytes and demonstrate that lack of PlexB2 impairs the formation of beaded apoptopodia and ApoBDs. Consequently, the loss of PlexB2 in apoptotic THP1 monocytes impairs their uptake by both professional and non-professional phagocytes. Altogether, these data identify PlexB2 as a positive regulator of apoptotic monocyte disassembly and demonstrate the importance of this process in apoptotic cell clearance.
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Affiliation(s)
- Georgia K Atkin-Smith
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mark A Miles
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Rochelle Tixeira
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Fung T Lay
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mubing Duan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Christine J Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Thanh Kha Phan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Stephanie Paone
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mark D Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Ivan K H Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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Fard D, Tamagnone L. Semaphorins in health and disease. Cytokine Growth Factor Rev 2020; 57:55-63. [PMID: 32900601 DOI: 10.1016/j.cytogfr.2020.05.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 05/12/2020] [Indexed: 11/18/2022]
Abstract
Cell-cell communication is pivotal to guide embryo development, as well as to maintain adult tissues homeostasis and control immune response. Among extracellular factors responsible for this function, are the Semaphorins, a broad family of around 20 different molecular cues conserved in evolution and widely expressed in all tissues. The signaling cascades initiated by semaphorins depend on a family of conserved receptors, called Plexins, and on several additional molecules found in the receptor complexes. Moreover, multiple intracellular pathways have been described to act downstream of semaphorins, highlighting significant diversity in the signaling cascades controlled by this family. Notably, semaphorin expression is altered in many human diseases, such as immunopathologies, neurodegenerative diseases and cancer. This underscores the importance of semaphorins as regulatory factors in the tissue microenvironment and has prompted growing interest for assessing their potential relevance in medicine. This review article surveys the main contexts in which semaphorins have been found to regulate developing and healthy adult tissues, and the signaling cascades implicated in these functions. Vis a vis, we will highlight the main pathological processes in which semaphorins are thought to have a role thereof.
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Affiliation(s)
- Damon Fard
- University of Torino School of Medicine, Torino, Italy
| | - Luca Tamagnone
- Università Cattolica del Sacro Cuore, Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy.
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43
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Zhang X, Shao S, Li L. Characterization of Class-3 Semaphorin Receptors, Neuropilins and Plexins, as Therapeutic Targets in a Pan-Cancer Study. Cancers (Basel) 2020; 12:cancers12071816. [PMID: 32640719 PMCID: PMC7409005 DOI: 10.3390/cancers12071816] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
Class-3 semaphorins (SEMA3s), initially characterized as axon guidance cues, have been recognized as key regulators for immune responses, angiogenesis, tumorigenesis and drug responses. The functions of SEMA3s are attributed to the activation of downstream signaling cascades mainly mediated by cell surface receptors neuropilins (NRPs) and plexins (PLXNs), yet their roles in human cancers are not completely understood. Here, we provided a detailed pan-cancer analysis of NRPs and PLXNs in their expression, and association with key signal transducers, patient survival, tumor microenvironment (TME), and drug responses. The expression of NRPs and PLXNs were dysregulated in many cancer types, and the majority of them were further dysregulated in metastatic tumors, indicating a role in metastatic progression. Importantly, the expression of these genes was frequently associated with key transducers, patient survival, TME, and drug responses; however, the direction of the association varied for the particular gene queried and the specific cancer type/subtype tested. Specifically, NRP1, NRP2, PLXNA1, PLXNA3, PLXNB3, PLXNC1, and PLXND1 were primarily associated with aggressive phenotypes, whereas the rest were more associated with favorable prognosis. These data highlighted the need to study each as a separate entity in a cancer type- and subtype-dependent manner.
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Affiliation(s)
- Xiaoli Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210, USA;
- Correspondence:
| | - Shuai Shao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43201, USA;
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210, USA;
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Li ZL, Müller-Greven J, Kim S, Tamagnone L, Buck M. Plexin-Bs enhance their GAP activity with a novel activation switch loop generating a cooperative enzyme. Cell Mol Life Sci 2020; 78:1101-1112. [PMID: 32601713 DOI: 10.1007/s00018-020-03571-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/24/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023]
Abstract
Plexins receive guidance cues from semaphorin ligands and transmit their signal through the plasma membrane. This family of proteins is unique amongst single-pass transmembrane receptors as their intracellular regions interact directly with several small GTPases, which regulate cytoskeletal dynamics and cell adhesion. Here, we characterize the GTPase Activating Protein (GAP) function of Plexin-B1 and find that a cooperative GAP activity towards the substrate GTPase, Rap1b, is associated with the N-terminal Juxtamembrane region of Plexin-B1. Importantly, we unveil an activation mechanism of Plexin-B1 by identifying a novel functional loop which partially blocks Rap1b entry into the plexin GAP domain. Consistent with the concept of allokairy developed for other systems, Plexin-B activity is increased by an apparent substrate-mediated cooperative effect. Simulations and mutagenesis suggest the repositioned JM conformation is stabilized by the new activation switch loop when the active site is occupied, giving rise to faster enzymatic turnover and cooperative behavior. The biological implications, essentially those of a threshold behavior for cell migration, are discussed.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Jeannine Müller-Greven
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - SoonJeung Kim
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Luca Tamagnone
- School of Medicine, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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45
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Rintz E, Gaffke L, Podlacha M, Brokowska J, Cyske Z, Węgrzyn G, Pierzynowska K. Transcriptomic Changes Related to Cellular Processes with Particular Emphasis on Cell Activation in Lysosomal Storage Diseases from the Group of Mucopolysaccharidoses. Int J Mol Sci 2020; 21:ijms21093194. [PMID: 32366041 PMCID: PMC7246638 DOI: 10.3390/ijms21093194] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Although mucopolysaccharidoses (MPS), inherited metabolic diseases from the group of lysosomal storage diseases (LSD), are monogenic disorders, recent studies indicated that their molecular mechanisms are complicated. Storage of glycosaminoglycans (GAGs), arising from a deficiency in one of the enzymes involved in the degradation of these compounds, is the primary cause of each MPS type. However, dysfunctions of various cellular organelles and disturbance of cellular processes have been reported which contribute considerably to pathomechanisms of the disease. Here, we present a complex transcriptomic analysis in which all types and subtypes of MPS were investigated, with special emphasis on genes related to cell activation processes. Complex changes in expression of these genes were found in fibroblasts of all MPS types, with number of transcripts revealing higher or lower levels (relative to control fibroblasts) between 19 and over 50, depending on MPS type. Genes in which expression was significantly affected in most MPS types code for proteins involved in following processes, classified according to Gene Ontology knowledge database: cell activation, cell growth, cell recognition, and cell division. Levels of some transcripts (including CD9, CLU, MME and others) were especially significantly changed (over five times relative to controls). Our results are discussed in the light of molecular pathomechanisms of MPS, indicating that secondary and/or tertiary changes, relative to GAG storage, might significantly modulate cellular dysfunctions and contribute to molecular mechanisms of the disease. This may influence the efficacy of various therapies and suggests why various treatments are not fully effective in improving the complex symptoms of MPS.
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46
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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.
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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.
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47
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Rigby MJ, Gomez TM, Puglielli L. Glial Cell-Axonal Growth Cone Interactions in Neurodevelopment and Regeneration. Front Neurosci 2020; 14:203. [PMID: 32210757 PMCID: PMC7076157 DOI: 10.3389/fnins.2020.00203] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
The developing nervous system is a complex yet organized system of neurons, glial support cells, and extracellular matrix that arranges into an elegant, highly structured network. The extracellular and intracellular events that guide axons to their target locations have been well characterized in many regions of the developing nervous system. However, despite extensive work, we have a poor understanding of how axonal growth cones interact with surrounding glial cells to regulate network assembly. Glia-to-growth cone communication is either direct through cellular contacts or indirect through modulation of the local microenvironment via the secretion of factors or signaling molecules. Microglia, oligodendrocytes, astrocytes, Schwann cells, neural progenitor cells, and olfactory ensheathing cells have all been demonstrated to directly impact axon growth and guidance. Expanding our understanding of how different glial cell types directly interact with growing axons throughout neurodevelopment will inform basic and clinical neuroscientists. For example, identifying the key cellular players beyond the axonal growth cone itself may provide translational clues to develop therapeutic interventions to modulate neuron growth during development or regeneration following injury. This review will provide an overview of the current knowledge about glial involvement in development of the nervous system, specifically focusing on how glia directly interact with growing and maturing axons to influence neuronal connectivity. This focus will be applied to the clinically-relevant field of regeneration following spinal cord injury, highlighting how a better understanding of the roles of glia in neurodevelopment can inform strategies to improve axon regeneration after injury.
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Affiliation(s)
- Michael J Rigby
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, United States.,Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Timothy M Gomez
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, United States.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, United States.,Waisman Center, University of Wisconsin-Madison, Madison, WI, United States.,Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, United States
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48
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Huang LJ, Shen Y, Bai J, Wang FX, Feng YD, Chen HL, Peng Y, Zhang R, Li FM, Zhang PH, Lei XR, Xue F, Ma YP, Hu JS, He AL. High Expression Levels of Long Noncoding RNA Small Nucleolar RNA Host Gene 18 and Semaphorin 5A Indicate Poor Prognosis in Multiple Myeloma. Acta Haematol 2019; 143:279-288. [PMID: 31597158 DOI: 10.1159/000502404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND The aim of this study was to detect the expression of long noncoding RNA small nucleolar RNA host gene 18 (SNHG18) andsemaphorin 5A (SEMA5A) genes in multiple myeloma (MM) patients and to explore the correlation of the expression of these genes with the clinical characteristics and prognosis of MM patients. METHODS Forty-seven newly diagnosed MM, 18 complete remission MM, 13 refractory/relapse MM, and 22 iron deficiency anemia (serving as control) samples were extracted at the Department of Hematology, Second Affiliated Hospital of Xian Jiaotong University between January 2015 and December 2016. The clinical features of the MM patients are summarized. Real-time quantitative PCR was performed to analyze the relative expression levels of the SNHG18 and SEMA5Agenes. The clinical characteristics and overall survival (OS) of the MM patients were statistically analyzed while measuring different levels of SNHG18 and SEMA5Agene expression. At the same time, the correlation between the expression of SNHG18 and SEMA5A was also analyzed. RESULTS The analysis confirmed that SNHG18 and its possible target gene SEMA5A were both highly expressed in newly diagnosed MM patients. After analyzing the clinical significance of SNHG18 and SEMA5A in MM patients, we found that the expression of SNHG18 and SEMA5A was related to the Durie-Salmon (DS), International Staging System (ISS), and Revised International Staging System (R-ISS) classification systems, and the Mayo Clinic Risk Stratification for Multiple Myeloma (mSMART; p < 0.05). Moreover, we observed a significant difference in OS between the SNHG18/SEMA5A high expression group and the low expression group. We found a positive correlation between SNHG18 and SEMA5A expression (r = 0.709, p < 0.01). Surprisingly, the expected median OS times of both the SNHG18 and SEMA5Ahigh expression groups were significantly decreased, which was in contrast to those of both the SNHG18 and SEMA5Alow expression groups and the single-gene high expression group (p < 0.05). CONCLUSION High expression of both SNHG18 and SEMA5A is associated with poor prognosis in patients with MM.
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Affiliation(s)
- Ling-Juan Huang
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of General Medicine, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China
- School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Ying Shen
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ju Bai
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Fang-Xia Wang
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuan-Dong Feng
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hong-Li Chen
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yue Peng
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ru Zhang
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Fang-Mei Li
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pei-Hua Zhang
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao-Ru Lei
- Institute of Hematology, Xi'an Central Hospital, Xi'an, China
| | - Feng Xue
- Department of Hematology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China
| | - Yan-Ping Ma
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jin-Song Hu
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Ai-Li He
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China,
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Mendelman N, Zerbetto M, Buck M, Meirovitch E. Local Ordering at the N-H Sites of the Rho GTPase Binding Domain of Plexin-B1: Impact of Dimerization. J Phys Chem B 2019; 123:8019-8033. [PMID: 31469564 DOI: 10.1021/acs.jpcb.9b05905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new molecular dynamics (MD) based method for describing analytically local potentials at mobile N-H sites in proteins. Here we apply it to the monomer and dimer of the Rho GTPase binding domain (RBD) of the transmembrane receptor plexin-B1 to gain insight into dimerization, which can compete with Rho GTPase binding. In our method, the local potential is given by linear combinations, u(DL,K), of the real combinations of the Wigner rotation matrix elements, DL,K, with L = 1-4 and appropriate symmetry. The combination that "fits best" the corresponding MD potential of mean force, u(MD), is the potential we are seeking, u(DL,K - BEST). For practical reasons the fitting process involves probability distributions, Peq ∝ exp(-u), instead of potentials, u. The symmetry of the potential, u(DL,K), may be related to the irreducible representations of the D2h point group. The monomer (dimer) potentials have mostly Ag and B2u (B1u and B2u) symmetry. For the monomer, the associated probability distributions are generally dispersed in space, shallow, and centered at the "reference N-H orientation" (defined in section 3.1. below); for the dimer many are more concentrated, deep and centered away from the "reference N-H orientation". The u(DL,K) functions provide a consistent description of the potential energy landscape at protein N-H sites. The L1-loop of the plexin-B1 RBD is not seen in the crystal structure, and many resonances of the L4 loop are missing in the NMR 15N-1H HSQC spectrum of the dimer; we suggest reasons for these features. An allosteric signal transmission pathway was reported previously for the monomer. We find that it has shallow N-H potentials at its ends, which become deeper as one proceeds toward the middle, complementing structurally the previously derived dynamic picture. Prospects of this study include correlating u(DL,K - BEST) with MD force-fields, and using them without further adjustment in NMR relaxation analysis schemes.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences , University of Padova , Padova 35131 , Italy
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University , Cleveland Ohio 44106 , United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 52900 , Israel
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50
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Tan G. Inhibitory effects of Semaphorin 3F as an alternative candidate to anti-VEGF monoclonal antibody on angiogenesis. In Vitro Cell Dev Biol Anim 2019; 55:756-765. [DOI: 10.1007/s11626-019-00392-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022]
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