1
|
Aliakbari S, Hasanzadeh L, Sayyah M, Amini N, Pourbadie HG. Induced expression of rabies glycoprotein in the dorsal hippocampus enhances hippocampal dependent memory in a rat model of Alzheimer's disease. J Neurovirol 2024:10.1007/s13365-024-01221-y. [PMID: 38943023 DOI: 10.1007/s13365-024-01221-y] [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: 03/24/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/30/2024]
Abstract
The Rabies virus is a neurotropic virus that manipulates the natural cell death processes of its host to ensure its own survival and replication. Studies have shown that the anti-apoptotic effect of the virus is mediated by one of its protein named, rabies glycoprotein (RVG). Alzheimer's disease (AD) is characterized by the loss of neural cells and memory impairment. We aim to examine whether expression of RVG in the hippocampal cells can shield the detrimental effects induced by Aβ. Oligomeric form of Aβ (oAβ) or vehicle was bilaterally microinjected into the dorsal hippocampus of male Wistar rats. One week later, two μl (108 T.U. /ml) of the lentiviral vector carrying RVG gene was injected into their dorsal hippocampus (post-treatment). In another experiment, the lentiviral vector was microinjected one week before Aβ injection (pre-treatment). One week later, the rat's brain was sliced into cross-sections, and the presence of RVG-expressing neuronal cells was confirmed using fluorescent microscopy. Rats were subjected to assessments of spatial learning and memory as well as passive avoidance using the Morris water maze (MWM) and the Shuttle box apparatuses, respectively. Protein expression of AMPA receptor subunit (GluA1) was determined using western blotting technique. In MWM, Aβ treated rats showed decelerated acquisition of the task and impairment of reference memory. RVG expression in the hippocampus prevented and restored the deficits in both pre- and post- treatment conditions, respectively. It also improved inhibitory memory in the oAβ treated rats. RVG increased the expression level of GluA1 level in the hippocampus. Based on our findings, the expression of RVG in the hippocampus has the potential to enhance both inhibitory and spatial learning abilities, ultimately improving memory performance in an AD rat model. This beneficial effect is likely attributed, at least in part, to the increased expression of GluA1-containing AMPA receptors.
Collapse
Affiliation(s)
- Shayan Aliakbari
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Hasanzadeh
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sayyah
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Niloufar Amini
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | | |
Collapse
|
2
|
Latorraca NR, Sabaat S, Habrian C, Bleier J, Stanley C, Marqusee S, Isacoff EY. Domain coupling in activation of a family C GPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582567. [PMID: 38464305 PMCID: PMC10925283 DOI: 10.1101/2024.02.28.582567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The G protein-coupled metabotropic glutamate receptors form homodimers and heterodimers with highly diverse responses to glutamate and varying physiological function. The molecular basis for this diversity remains poorly delineated. We employ molecular dynamics, single-molecule spectroscopy, and hydrogen-deuterium exchange to dissect the pathway of activation triggered by glutamate. We find that activation entails multiple loosely coupled steps and identify a novel pre-active intermediate whose transition to the active state forms dimer interactions that set signaling efficacy. Such subunit interactions generate functional diversity that differs across homodimers and heterodimers. The agonist-bound receptor is remarkably dynamic, with low occupancy of G protein-coupling conformations, providing considerable headroom for modulation of the landscape by allosteric ligands. Sites of sequence diversity within the dimerization interface and diverse coupling between activation rearrangements may contribute to precise decoding of glutamate signals and transients over broad spatial and temporal scales.
Collapse
Affiliation(s)
- Naomi R. Latorraca
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
| | - Sam Sabaat
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
| | - Chris Habrian
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
| | - Julia Bleier
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
| | - Cherise Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
- Department of Chemistry, University of California, Berkeley, California, 94720 USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720 USA
| | - Ehud Y. Isacoff
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720 USA
- Molecular Biology & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Weill Neurohub, University of California, Berkeley, California, 94720 USA
- Molecular Biology & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| |
Collapse
|
3
|
Guerin N, Childs H, Zhou P, Donald BR. DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579944. [PMID: 38405797 PMCID: PMC10888900 DOI: 10.1101/2024.02.12.579944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan, which enable exponential reductions in the size of the peptide sequence search space. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a new framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead therapeutic candidates. We provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
Collapse
|
4
|
Guerin N, Childs H, Zhou P, Donald BR. DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors. Protein Eng Des Sel 2024; 37:gzae007. [PMID: 38757573 PMCID: PMC11099876 DOI: 10.1093/protein/gzae007] [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: 09/03/2023] [Revised: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
Collapse
Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
| | - Henry Childs
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
- Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, United States
| |
Collapse
|
5
|
Javorsky A, Humbert PO, Kvansakul M. Viral manipulation of cell polarity signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119536. [PMID: 37437846 DOI: 10.1016/j.bbamcr.2023.119536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Cell polarity refers to the asymmetric distribution of biomacromolecules that enable the correct orientation of a cell in a particular direction. It is thus an essential component for appropriate tissue development and function. Viral infections can lead to dysregulation of polarity. This is associated with a poor prognosis due to viral interference with core cell polarity regulatory scaffolding proteins that often feature PDZ (PSD-95, DLG, and ZO-1) domains including Scrib, Dlg, Pals1, PatJ, Par3 and Par6. PDZ domains are also promiscuous, binding to several different partners through their C-terminal region which contain PDZ-binding motifs (PBM). Numerous viruses encode viral effector proteins that target cell polarity regulators for their benefit and include papillomaviruses, flaviviruses and coronaviruses. A better understanding of the mechanisms of action utilised by viral effector proteins to subvert host cell polarity sigalling will provide avenues for future therapeutic intervention, while at the same time enhance our understanding of cell polarity regulation and its role tissue homeostasis.
Collapse
Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia; Department of Biochemistry & Pharmacology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia.
| |
Collapse
|
6
|
Strauss A, Gonzalez-Hernandez AJ, Lee J, Abreu N, Selvakumar P, Salas-Estrada L, Kristt M, Marx DC, Gilliland K, Melancon BJ, Filizola M, Meyerson J, Levitz J. Structural basis of allosteric modulation of metabotropic glutamate receptor activation and desensitization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.13.552748. [PMID: 37645747 PMCID: PMC10461995 DOI: 10.1101/2023.08.13.552748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The metabotropic glutamate receptors (mGluRs) are neuromodulatory family C G protein coupled receptors which assemble as dimers and allosterically couple extracellular ligand binding domains (LBDs) to transmembrane domains (TMDs) to drive intracellular signaling. Pharmacologically, mGluRs can be targeted either at the LBDs by glutamate and synthetic orthosteric compounds or at the TMDs by allosteric modulators. Despite the potential of allosteric TMD-targeting compounds as therapeutics, an understanding of the functional and structural basis of their effects on mGluRs is limited. Here we use a battery of approaches to dissect the distinct functional and structural effects of orthosteric versus allosteric ligands. We find using electrophysiological and live cell imaging assays that both agonists and positive allosteric modulators (PAMs) can drive activation and desensitization of mGluRs. The effects of PAMs are pleiotropic, including both the ability to boost the maximal response to orthosteric agonists and to serve independently as desensitization-biased agonists across mGluR subtypes. Conformational sensors reveal PAM-driven inter-subunit re-arrangements at both the LBD and TMD. Motivated by this, we determine cryo-electron microscopy structures of mGluR3 in the presence of either an agonist or antagonist alone or in combination with a PAM. These structures reveal PAM-driven re-shaping of intra- and inter-subunit conformations and provide evidence for a rolling TMD dimer interface activation pathway that controls G protein and beta-arrestin coupling. Highlights -Agonists and PAMs drive mGluR activation, desensitization, and endocytosis-PAMs are desensitization-biased and synergistic with agonists-Four combinatorial ligand conditions reveal an ensemble of full-length mGluR structures with novel interfaces-Activation and desensitization involve rolling TMD interfaces which are re-shaped by PAM.
Collapse
|
7
|
Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
Collapse
Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| |
Collapse
|
8
|
Kouchi Z, Kojima M. A Structural Network Analysis of Neuronal ArhGAP21/23 Interactors by Computational Modeling. ACS OMEGA 2023; 8:19249-19264. [PMID: 37305272 PMCID: PMC10249030 DOI: 10.1021/acsomega.2c08054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/05/2023] [Indexed: 06/13/2023]
Abstract
RhoGTPase-activating proteins (RhoGAPs) play multiple roles in neuronal development; however, details of their substrate recognition system remain elusive. ArhGAP21 and ArhGAP23 are RhoGAPs that contain N-terminal PDZ and pleckstrin homology domains. In the present study, the RhoGAP domain of these ArhGAPs was computationally modeled by template-based methods and the AlphaFold2 software program, and their intrinsic RhoGTPase recognition mechanism was analyzed from the domain structures using the protein docking programs HADDOCK and HDOCK. ArhGAP21 was predicted to preferentially catalyze Cdc42, RhoA, RhoB, RhoC, and RhoG and to downregulate RhoD and Tc10 activities. Regarding ArhGAP23, RhoA and Cdc42 were deduced to be its substrates, whereas RhoD downregulation was predicted to be less efficient. The PDZ domains of ArhGAP21/23 possess the FTLRXXXVY sequence, and similar globular folding consists of antiparalleled β-sheets and two α-helices that are conserved with PDZ domains of MAST-family proteins. A peptide docking analysis revealed the specific interaction of the ArhGAP23 PDZ domain with the PTEN C-terminus. The pleckstrin homology domain structure of ArhGAP23 was also predicted, and the functional selectivity for the interactors regulated by the folding and disordered domains in ArhGAP21 and ArhGAP23 was examined by an in silico analysis. An interaction analysis of these RhoGAPs revealed the existence of mammalian ArhGAP21/23-specific type I and type III Arf- and RhoGTPase-regulated signaling. Multiple recognition systems of RhoGTPase substrates and selective Arf-dependent localization of ArhGAP21/23 may form the basis of the functional core signaling necessary for synaptic homeostasis and axon/dendritic transport regulated by RhoGAP localization and activities.
Collapse
Affiliation(s)
- Zen Kouchi
- Department
of Genetics, Institute for Developmental
Research, Aichi Developmental Disability Center, 713-8 Kamiya-cho, Kasugai-city 480-0392 Aichi, Japan
| | - Masaki Kojima
- Laboratory
of Bioinformatics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji 192-0392, Japan
| |
Collapse
|
9
|
Mihalič F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Peters MBA, Benz C, Kassa E, Badgujar D, Inturi R, Ali M, Krystkowiak I, Sayadi A, Andersson E, Aronsson H, Söderberg O, Dobritzsch D, Petsalaki E, Överby AK, Jemth P, Davey NE, Ivarsson Y. Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs. Nat Commun 2023; 14:2409. [PMID: 37100772 PMCID: PMC10132805 DOI: 10.1038/s41467-023-38015-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.
Collapse
Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Girolamo Giudice
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Marie Rubin Sander
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Marie Berit Akpiroro Peters
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dilip Badgujar
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Izabella Krystkowiak
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
| |
Collapse
|
10
|
Langdon CG. Nuclear PTEN's Functions in Suppressing Tumorigenesis: Implications for Rare Cancers. Biomolecules 2023; 13:biom13020259. [PMID: 36830628 PMCID: PMC9953540 DOI: 10.3390/biom13020259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Phosphatase and tensin homolog (PTEN) encodes a tumor-suppressive phosphatase with both lipid and protein phosphatase activity. The tumor-suppressive functions of PTEN are lost through a variety of mechanisms across a wide spectrum of human malignancies, including several rare cancers that affect pediatric and adult populations. Originally discovered and characterized as a negative regulator of the cytoplasmic, pro-oncogenic phosphoinositide-3-kinase (PI3K) pathway, PTEN is also localized to the nucleus where it can exert tumor-suppressive functions in a PI3K pathway-independent manner. Cancers can usurp the tumor-suppressive functions of PTEN to promote oncogenesis by disrupting homeostatic subcellular PTEN localization. The objective of this review is to describe the changes seen in PTEN subcellular localization during tumorigenesis, how PTEN enters the nucleus, and the spectrum of impacts and consequences arising from disrupted PTEN nuclear localization on tumor promotion. This review will highlight the immediate need in understanding not only the cytoplasmic but also the nuclear functions of PTEN to gain more complete insights into how important PTEN is in preventing human cancers.
Collapse
Affiliation(s)
- Casey G. Langdon
- Department of Pediatrics, Darby Children’s Research Institute, Medical University of South Carolina, Charleston, SC 29425, USA; ; Tel.: +1-(843)-792-9289
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| |
Collapse
|
11
|
Zhang X, Xiao N, Cao Y, Peng Y, Lian A, Chen Y, Wang P, Gu W, Xiao B, Yu J, Wang H, Shu L. De novo variants in MAST4 related to neurodevelopmental disorders with developmental delay and infantile spasms: Genotype-phenotype association. Front Mol Neurosci 2023; 16:1097553. [PMID: 36910266 PMCID: PMC9992645 DOI: 10.3389/fnmol.2023.1097553] [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: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Objective This study aims to prove that the de novo variants in MAST4 gene are associated with neurodevelopmental disorders (NDD) with developmental delay (DD) and infantile spasm (IS) and to determine the genotype-phenotype correlations. Methods Trio-based exome sequencing (ES) was performed on the four families enrolled in this study. We collected and systematically reviewed the four probands' clinical data, magnetic resonance images (MRI), and electroencephalography (EEG). We also carried out bioinformatics analysis by integrating published exome/genome sequencing data and human brain transcriptomic data. Results We described four patients whose median age of seizure onset was 5 months. The primary manifestation was infantile spasms with typical hypsarrhythmia on EEG. Developmental delays or intellectual disabilities varied among the four individuals. Three de novo missense variants in MAST4 gene were identified from four families, including chr5:66438324 (c.2693T > C: p.Ile898Thr) z, chr5:66459419 (c.4412C > T: p.Thr1471Ile), and chr5:66462662 (c.7655C > G:p.Ser2552Trp). The missense variant p.Ile898Thr is mapped to the AGC-kinase C-terminal with phosphatase activity. The other variant p.Ser2552Trp is located in a phosphoserine-modified residue which may affect cell membrane stability and signal transduction. Besides, the variant p.Thr1471Ile is a recurrent site screened out in two unrelated patients. Compared to private mutations (found only in a single family or a small population) of MAST4 in the gnomAD non-neuro subset, all de novo variants were predicted to be damaging or probably damaging through different bioinformatic analyses. Significantly higher CADD scores of the variant p.Thr1471Ile indicate more deleteriousness of the recurrent site. And the affected amino acids are highly conserved across multiple species. According to the Brainspan Atlas database, MAST4 is expressed primarily in the mediodorsal nucleus of the thalamus and medial prefrontal cortex during the prenatal period, potentially contributing to embryonic brain development. Conclusion Our results revealed that the variants of MAST4 gene might lead to neurodevelopmental disorders with developmental delay and infantile spasm. Thus, MAST4 variants should be considered the potential candidate gene in patients with neurodevelopmental disorders clinically marked by infantile spasms.
Collapse
Affiliation(s)
- Xi Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Neng Xiao
- Department of Pediatric Neurology, Chenzhou First People's Hospital, Chenzhou, China
| | - Yang Cao
- Department of Radiology, Chenzhou First People's Hospital, Chenzhou, China
| | - Ying Peng
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Aojie Lian
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Clinical Research Center for Placental Medicine in Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Yuanlu Chen
- Department of Pharmacy, Chenzhou First People's Hospital, Chenzhou, China
| | - Pengchao Wang
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, China
| | - Weiyue Gu
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Yu
- Department of Neurology, Children's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, China
| | - Li Shu
- Department of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
12
|
Yang Y, Shuai P, Li X, Sun K, Jiang X, Liu W, Le W, Jiang H, Liu Y, Zhu X. Mettl14-mediated m6A modification is essential for visual function and retinal photoreceptor survival. BMC Biol 2022; 20:140. [PMID: 35698136 PMCID: PMC9195452 DOI: 10.1186/s12915-022-01335-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
Background As the most abundant epigenetic modification of eukaryotic mRNA, N6-methyladenosine (m6A) modification has been shown to play a role in mammalian nervous system development and function by regulating mRNA synthesis and degeneration. However, the role of m6A modification in retinal photoreceptors remains unknown. Results We generated the first retina-specific Mettl14-knockout mouse models using the Rho-Cre and HRGP-Cre lines and investigated the functions of Mettl14 in retinal rod and cone photoreceptors. Our data showed that loss of Mettl14 in rod cells causes a weakened scotopic photoresponse and rod degeneration. Further study revealed the ectopic accumulation of multiple outer segment (OS) proteins in the inner segment (IS). Deficiency of Mettl14 in cone cells led to the mislocalization of cone opsin proteins and the progressive death of cone cells. Moreover, Mettl14 depletion resulted in drastic decreases in METTL3/WTAP levels and reduced m6A methylation levels. Mechanistically, transcriptomic analyses in combination with MeRIP-seq illustrated that m6A depletion via inactivation of Mettl14 resulted in reduced expression levels of multiple phototransduction- and cilium-associated genes, which subsequently led to compromised ciliogenesis and impaired synthesis and transport of OS-residing proteins in rod cells. Conclusions Our data demonstrate that Mettl14 plays an important role in regulating phototransduction and ciliogenesis events and is essential for photoreceptor function and survival, highlighting the importance of m6A modification in visual function. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01335-x.
Collapse
Affiliation(s)
- Yeming Yang
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China.,Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, Qinghai, China
| | - Ping Shuai
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
| | - Xiao Li
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
| | - Kuanxiang Sun
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China
| | - Xiaoyan Jiang
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China
| | - Wenjing Liu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China
| | - Weidong Le
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China.,Department of Neurology, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Haisong Jiang
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China. .,Department of Neurology, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.
| | - Yuping Liu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.
| | - Xianjun Zhu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China. .,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China. .,Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, Qinghai, China. .,Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 610072, Sichuan, China. .,Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China.
| |
Collapse
|
13
|
Role of the glycoprotein thorns in anxious effects of rabies virus: Evidence from an animal study. Brain Res Bull 2022; 185:107-116. [DOI: 10.1016/j.brainresbull.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/11/2022] [Accepted: 05/03/2022] [Indexed: 12/17/2022]
|
14
|
Zhu Y, Alvarez F, Wolff N, Mechaly A, Brûlé S, Neitthoffer B, Etienne-Manneville S, Haouz A, Boëda B, Caillet-Saguy C. Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins. Front Microbiol 2022; 13:829094. [PMID: 35283834 PMCID: PMC8909127 DOI: 10.3389/fmicb.2022.829094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022] Open
Abstract
The C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein E contains a PBM (PDZ-binding motif) targeting PDZ (PSD-95/Dlg/ZO-1) domains, which is identical to the PBM of SARS-CoV. The latter is involved in the pathogenicity of the virus. Recently, we identified 10 human PDZ-containing proteins showing significant interactions with SARS-CoV-2 protein E PBM. We selected several of them involved in cellular junctions and cell polarity (TJP1, PARD3, MLLT4, and LNX2) and MPP5/PALS1 previously shown to interact with SARS-CoV E PBM. Targeting cellular junctions and polarity components is a common strategy by viruses to hijack cell machinery to their advantage. In this study, we showed that these host PDZ domains TJP1, PARD3, MLLT4, LNX2, and MPP5/PALS1 interact in a PBM-dependent manner in vitro and colocalize with the full-length E protein in cellulo, sequestrating the PDZ domains to the Golgi compartment. We solved three crystal structures of complexes between human LNX2, MLLT4, and MPP5 PDZs and SARS-CoV-2 E PBM highlighting its binding preferences for several cellular targets. Finally, we showed different affinities for the PDZ domains with the original SARS-CoV-2 C-terminal sequence containing the PBM and the one of the beta variant that contains a mutation close to the PBM. The acquired mutations in the E protein localized near the PBM might have important effects both on the structure and the ion-channel activity of the E protein and on the host machinery targeted by the variants during the infection.
Collapse
Affiliation(s)
- Yanlei Zhu
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Flavio Alvarez
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Nicolas Wolff
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Benoit Neitthoffer
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Célia Caillet-Saguy
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| |
Collapse
|
15
|
Huang H, Li Y, Wang L, Song Y, Zhang G. Membrane proteomic analysis identifies the polarity protein PARD3 as a novel antiviral protein against PEDV infection. J Proteomics 2021; 253:104462. [PMID: 34954106 PMCID: PMC8695312 DOI: 10.1016/j.jprot.2021.104462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/01/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus causing lethal watery diarrhea in suckling piglets. PEDV could remodel host membrane structures for their replication, assembly and escape from host cells. However, little is known about the host membrane proteins of PEDV infection. In this study, we analyzed differentially abundant proteins (DAPs) between PEDV infection group and control group and identified the polarity protein PARD3 as one of the most significantly DAPs. PARD3 is implicated in the formation of tight junctions at epithelial cell-cell contacts. Then, we found that PEDV infection promoted the degradation of PARD3 via the ubiquitin proteasome pathway. Moreover, knockdown of PARD3 promoted the proliferation of PEDV. Further study showed that the downregulation of PARD3 altered the normal morphology of the tight junction proteins and promoted apical and basolateral virus proliferation. Tight junctions enable epithelial cells to form physical barriers, which act as an innate immune mechanism that can impede viral infection and PEDV affected the barrier functions by causing degradation of PARD3. Taken together, this work is the first time to investigate the membrane protein profile of PEDV-infected cells using quantitative proteomics and suggests that PARD3 could be a potential novel antiviral protein against PEDV infection. Significance Membrane proteins are involved in various physiological and biochemical functions critical for cellular function. It is also dynamic in nature, where many proteins are changed during in response to environmental stress. However, membrane proteins are difficult to study because of their hydrophobicity. Membrane proteomic methods using mass spectrometry analysis have been developed and applied for the characterization of the plasma membrane and subcellular organelles of various virus infected cells. Porcine epidemic diarrhea virus (PEDV) is an enteric pathogen of importance to the swine industry, causing high mortality in neonatal piglets. Because PEDV infected Vero cells can lead to significant changes in cell membrane morphology and form syncytial lesions. Here, we isolated the membrane proteins of PEDV infected and control cells and applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantitatively identify the differentially abundant proteins (DAPs) in PEDV-infected Vero cells and confirmed the DAPs by performing RT-qPCR and Western blot analysis. Among these differential proteins, we focused on a down-regulated protein PARD3 which is important for cell tight junction and cell polarity. Loss of PARD3 can destroy the tight junction of cells and promote the proliferation of PEDV in the apical and basolateral sides. These findings will provide valuable information to better understand the mechanisms underlying the host defense responses to PEDV infection.
Collapse
Affiliation(s)
- Huimin Huang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Li Wang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Huayuan Road No. 116, Zhengzhou 450002, China
| | - Yapeng Song
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Huayuan Road No. 116, Zhengzhou 450002, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
| |
Collapse
|
16
|
Caillet-Saguy C, Wolff N. PDZ-Containing Proteins Targeted by the ACE2 Receptor. Viruses 2021; 13:2281. [PMID: 34835087 PMCID: PMC8624105 DOI: 10.3390/v13112281] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/28/2022] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is a main receptor for SARS-CoV-2 entry to the host cell. Indeed, the first step in viral entry is the binding of the viral trimeric spike (S) protein to ACE2. Abundantly present in human epithelial cells of many organs, ACE2 is also expressed in the human brain. ACE2 is a type I membrane protein with an extracellular N-terminal peptidase domain and a C-terminal collectrin-like domain that ends with a single transmembrane helix and an intracellular 44-residue segment. This C-terminal segment contains a PDZ-binding motif (PBM) targeting protein-interacting domains called PSD-95/Dlg/ZO-1 (PDZ). Here, we identified the human PDZ specificity profile of the ACE2 PBM using the high-throughput holdup assay and measuring the binding intensities of the PBM of ACE2 against the full human PDZome. We discovered 14 human PDZ binders of ACE2 showing significant binding with dissociation constants' values ranging from 3 to 81 μM. NHERF, SHANK, and SNX27 proteins found in this study are involved in protein trafficking. The PDZ/PBM interactions with ACE2 could play a role in ACE2 internalization and recycling that could be of benefit for the virus entry. Interestingly, most of the ACE2 partners we identified are expressed in neuronal cells, such as SHANK and MAST families, and modifications of the interactions between ACE2 and these neuronal proteins may be involved in the neurological symptoms of COVID-19.
Collapse
Affiliation(s)
- Célia Caillet-Saguy
- Unité Récepteurs-Canaux, Institut Pasteur, UMR CNRS 3571, 75015 Paris, France
| | - Nicolas Wolff
- Unité Récepteurs-Canaux, Institut Pasteur, UMR CNRS 3571, 75015 Paris, France
| |
Collapse
|
17
|
Zhao Z, Xu Q, Wei R, Huang L, Wang W, Wei G, Ni T. Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers. Nucleic Acids Res 2021; 49:10369-10381. [PMID: 34508351 PMCID: PMC8501991 DOI: 10.1093/nar/gkab772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. While somatic SNVs near canonical splice sites have been reported to cause abnormal splicing of cancer-related genes, whether these SNVs can affect gene expression through other mechanisms remains an open question. Here, we analyzed RNA sequencing and exome data from 4,998 cancer patients covering ten cancer types and identified 152 somatic SNVs near splice sites that were associated with abnormal intronic polyadenylation (IPA). IPA-associated somatic variants favored the localization near the donor splice sites compared to the acceptor splice sites. A proportion of SNV-associated IPA events overlapped with premature cleavage and polyadenylation events triggered by U1 small nuclear ribonucleoproteins (snRNP) inhibition. GC content, intron length and polyadenylation signal were three genomic features that differentiated between SNV-associated IPA and intron retention. Notably, IPA-associated SNVs were enriched in tumor suppressor genes (TSGs), including the well-known TSGs such as PTEN and CDH1 with recurrent SNV-associated IPA events. Minigene assay confirmed that SNVs from PTEN, CDH1, VEGFA, GRHL2, CUL3 and WWC2 could lead to IPA. This work reveals that IPA acts as a novel mechanism explaining the functional consequence of somatic SNVs in human cancer.
Collapse
Affiliation(s)
- Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Qiushi Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Ran Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Leihuan Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| |
Collapse
|
18
|
Cobos ES, Sánchez IE, Chemes LB, Martinez JC, Murciano-Calles J. A Thermodynamic Analysis of the Binding Specificity between Four Human PDZ Domains and Eight Host, Viral and Designed Ligands. Biomolecules 2021; 11:biom11081071. [PMID: 34439737 PMCID: PMC8393326 DOI: 10.3390/biom11081071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 02/01/2023] Open
Abstract
PDZ domains are binding modules mostly involved in cell signaling and cell–cell junctions. These domains are able to recognize a wide variety of natural targets and, among the PDZ partners, viruses have been discovered to interact with their host via a PDZ domain. With such an array of relevant and diverse interactions, PDZ binding specificity has been thoroughly studied and a traditional classification has grouped PDZ domains in three major specificity classes. In this work, we have selected four human PDZ domains covering the three canonical specificity-class binding mode and a set of their corresponding binders, including host/natural, viral and designed PDZ motifs. Through calorimetric techniques, we have covered the entire cross interactions between the selected PDZ domains and partners. The results indicate a rather basic specificity in each PDZ domain, with two of the domains that bind their cognate and some non-cognate ligands and the two other domains that basically bind their cognate partners. On the other hand, the host partners mostly bind their corresponding PDZ domain and, interestingly, the viral ligands are able to bind most of the studied PDZ domains, even those not previously described. Some viruses may have evolved to use of the ability of the PDZ fold to bind multiple targets, with resulting affinities for the virus–host interactions that are, in some cases, higher than for host–host interactions.
Collapse
Affiliation(s)
- Eva S. Cobos
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Ignacio E. Sánchez
- Laboratorio de Fisiología de Proteínas, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, 1428 Buenos Aires, Argentina;
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, 1650 Buenos Aires, Argentina;
| | - Jose C. Martinez
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Javier Murciano-Calles
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
- Correspondence:
| |
Collapse
|
19
|
Abstract
Viruses are obligatory intracellular parasites that use cell proteins to take the control of the cell functions in order to accomplish their life cycle. Studying the viral-host interactions would increase our knowledge of the viral biology and mechanisms of pathogenesis. Studies on pathogenesis mechanisms of lyssaviruses, which are the causative agents of rabies, have revealed some important host protein partners for viral proteins, especially for most studied species, i.e. RABV. In this review article, the key physical lyssavirus-host protein interactions, their contributions to rabies infection, and their exploitation are discussed to improve the knowledge about rabies pathogenesis.
Collapse
|
20
|
Caillet-Saguy C, Durbesson F, Rezelj VV, Gogl G, Tran QD, Twizere JC, Vignuzzi M, Vincentelli R, Wolff N. Host PDZ-containing proteins targeted by SARS-CoV-2. FEBS J 2021; 288:5148-5162. [PMID: 33864728 PMCID: PMC8250131 DOI: 10.1111/febs.15881] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022]
Abstract
Small linear motifs targeting protein interacting domains called PSD‐95/Dlg/ZO‐1 (PDZ) have been identified at the C terminus of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) proteins E, 3a, and N. Using a high‐throughput approach of affinity‐profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS‐CoV‐2 proteins E, 3A, and N showing significant interactions with dissociation constants values ranging from 3 to 82 μm. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS‐CoV while three (NHERF1, MAST2, RADIL) are specific to SARS‐CoV‐2 E protein. Most of these SARS‐CoV‐2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Among the binders of the SARS‐CoV‐2 proteins E, 3a, or N, seven significantly affect viral replication under knock down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS‐CoV‐2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti‐coronaviral agents for therapeutic purposes.
Collapse
Affiliation(s)
| | | | - Veronica V Rezelj
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France
| | - Gergö Gogl
- IGBMC, INSERM U1258/UMR CNRS 7104, Illkirch, France
| | - Quang Dinh Tran
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France.,École doctorale BioSPC, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Jean-Claude Twizere
- GIGA Institute, Molecular Biology of Diseases, Viral Interactomes laboratory, University of Liege, Belgium
| | - Marco Vignuzzi
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France
| | | | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, UMR CNRS 3571, Paris, France
| |
Collapse
|
21
|
A rare coding mutation in the MAST2 gene causes venous thrombosis in a French family with unexplained thrombophilia: The Breizh MAST2 Arg89Gln variant. PLoS Genet 2021; 17:e1009284. [PMID: 33465109 PMCID: PMC7846112 DOI: 10.1371/journal.pgen.1009284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/29/2021] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
Rare variants outside the classical coagulation cascade might cause inherited thrombosis. We aimed to identify the variant(s) causing venous thromboembolism (VTE) in a family with multiple relatives affected with unprovoked VTE and no thrombophilia defects. We identified by whole exome sequencing an extremely rare Arg to Gln variant (Arg89Gln) in the Microtubule Associated Serine/Threonine Kinase 2 (MAST2) gene that segregates with VTE in the family. Free-tissue factor pathway inhibitor (f-TFPI) plasma levels were significantly decreased in affected family members compared to healthy relatives. Conversely, plasminogen activator inhibitor-1 (PAI-1) levels were significantly higher in affected members than in healthy relatives. RNA sequencing analysis of RNA interference experimental data conducted in endothelial cells revealed that, of the 13,387 detected expressed genes, 2,354 have their level of expression modified by MAST2 knockdown, including SERPINE1 coding for PAI-1 and TFPI. In HEK293 cells overexpressing the MAST2 Gln89 variant, TFPI and SERPINE1 promoter activities were respectively lower and higher than in cells overexpressing the MAST2 wild type. This study identifies a novel thrombophilia-causing Arg89Gln variant in the MAST2 gene that is here proposed as a new molecular player in the etiology of VTE by interfering with hemostatic balance of endothelial cells.
Collapse
|
22
|
Genera M, Quioc-Salomon B, Nourisson A, Colcombet-Cazenave B, Haouz A, Mechaly A, Matondo M, Duchateau M, König A, Windisch MP, Neuveut C, Wolff N, Caillet-Saguy C. Molecular basis of the interaction of the human tyrosine phosphatase PTPN3 with the hepatitis B virus core protein. Sci Rep 2021; 11:944. [PMID: 33441627 PMCID: PMC7806630 DOI: 10.1038/s41598-020-79580-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
Interactions between the hepatitis B virus core protein (HBc) and host cell proteins are poorly understood, although they may be essential for the propagation of the virus and its pathogenicity. HBc has a C-terminal PDZ (PSD-95, Dlg1, ZO-1)-binding motif (PBM) that is responsible for interactions with host PDZ domain-containing proteins. In this work, we focused on the human protein tyrosine phosphatase non-receptor type 3 (PTPN3) and its interaction with HBc. We solved the crystal structure of the PDZ domain of PTPN3 in complex with the PBM of HBc, revealing a network of interactions specific to class I PDZ domains despite the presence of a C-terminal cysteine in this atypical PBM. We further showed that PTPN3 binds the HBc protein within capsids or as a homodimer. We demonstrate that overexpression of PTPN3 significantly affects HBV infection in HepG2 NTCP cells. Finally, we performed proteomics studies on both sides by pull-down assays and screening of a human PDZ domain library. We identified a pool of human PBM-containing proteins that might interact with PTPN3 in cells and that could be in competition with the HBc PBM during infection, and we also identified potential cellular partners of HBc through PDZ-PBM interactions. This study opens up many avenues of future investigations into the pathophysiology of HBV.
Collapse
Affiliation(s)
- Mariano Genera
- Channel-Receptors Unit, UMR 3571, CNRS, Institut Pasteur, 75015, Paris, France.,Complexité du Vivant, Sorbonne Université, 75005, Paris, France
| | - Barbara Quioc-Salomon
- UMR 3569, CNRS, 75015, Paris, France.,Department of Virology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Antonin Nourisson
- Channel-Receptors Unit, UMR 3571, CNRS, Institut Pasteur, 75015, Paris, France
| | - Baptiste Colcombet-Cazenave
- Channel-Receptors Unit, UMR 3571, CNRS, Institut Pasteur, 75015, Paris, France.,Complexité du Vivant, Sorbonne Université, 75005, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, Department of Structural Biology and Chemistry, CNRS, UMR-3528, Institut Pasteur, 75015, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, Department of Structural Biology and Chemistry, CNRS, UMR-3528, Institut Pasteur, 75015, Paris, France
| | - Mariette Matondo
- Proteomics Platform, Mass Spectrometry for Biology Utechs (MSBio), USR 2000, CNRS, Institut Pasteur, 75724, Paris, France
| | - Magalie Duchateau
- Proteomics Platform, Mass Spectrometry for Biology Utechs (MSBio), USR 2000, CNRS, Institut Pasteur, 75724, Paris, France
| | - Alexander König
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Marc P Windisch
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Christine Neuveut
- UMR 3569, CNRS, 75015, Paris, France.,Department of Virology, Institut Pasteur, Paris, France.,Institute of Human Genetics, 141 rue de la Cardonille, 34090, Montpellier, France
| | - Nicolas Wolff
- Channel-Receptors Unit, UMR 3571, CNRS, Institut Pasteur, 75015, Paris, France
| | - Célia Caillet-Saguy
- Channel-Receptors Unit, UMR 3571, CNRS, Institut Pasteur, 75015, Paris, France.
| |
Collapse
|
23
|
Viral PDZ Binding Motifs Influence Cell Behavior Through the Interaction with Cellular Proteins Containing PDZ Domains. Methods Mol Biol 2021; 2256:217-236. [PMID: 34014525 DOI: 10.1007/978-1-0716-1166-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Viruses have evolved to interact with their hosts. Some viruses such as human papilloma virus, dengue virus, SARS-CoV, or influenza virus encode proteins including a PBM that interact with cellular proteins containing PDZ domains. There are more than 400 cellular protein isoforms with these domains in the human genome, indicating that viral PBMs have a high potential to influence the behavior of the cell. In this review we analyze the most relevant cellular processes known to be affected by viral PBM-cellular PDZ interactions including the establishment of cell-cell interactions and cell polarity, the regulation of cell survival and apoptosis and the activation of the immune system. Special attention has been provided to coronavirus PBM conservation throughout evolution and to the role of the PBMs of human coronaviruses SARS-CoV and MERS-CoV in pathogenesis.
Collapse
|
24
|
Caillet-Saguy C, Brûlé S, Wolff N, Raynal B. PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations. Methods Mol Biol 2021; 2256:89-124. [PMID: 34014518 DOI: 10.1007/978-1-0716-1166-1_6] [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] [Indexed: 06/12/2023]
Abstract
PDZ domains are small globular domains involved in protein-protein interactions. They participate in a wide range of critical cellular processes. These domains, very abundant in the human proteome, are widely studied by high-throughput interactomics approaches and by biophysical and structural methods. However, the quality of the results is strongly related to the optimal folding and solubility of the domains. We provide here a detailed description of protocols for a strict quality assessment of the PDZ constructs. We describe appropriate experimental approaches that have been selected to overcome the small size of such domains to check the purity, identity, homogeneity, stability, and folding of samples.
Collapse
Affiliation(s)
| | - Sébastien Brûlé
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS UMR 3571, Paris, France.
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
| |
Collapse
|
25
|
Jané P, Gógl G, Kostmann C, Bich G, Girault V, Caillet-Saguy C, Eberling P, Vincentelli R, Wolff N, Travé G, Nominé Y. Interactomic affinity profiling by holdup assay: Acetylation and distal residues impact the PDZome-binding specificity of PTEN phosphatase. PLoS One 2020; 15:e0244613. [PMID: 33382810 PMCID: PMC7774954 DOI: 10.1371/journal.pone.0244613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/12/2020] [Indexed: 12/15/2022] Open
Abstract
Protein domains often recognize short linear protein motifs composed of a core conserved consensus sequence surrounded by less critical, modulatory positions. PTEN, a lipid phosphatase involved in phosphatidylinositol 3-kinase (PI3K) pathway, contains such a short motif located at the extreme C-terminus capable to recognize PDZ domains. It has been shown that the acetylation of this motif could modulate the interaction with several PDZ domains. Here we used an accurate experimental approach combining high-throughput holdup chromatographic assay and competitive fluorescence polarization technique to measure quantitative binding affinity profiles of the PDZ domain-binding motif (PBM) of PTEN. We substantially extended the previous knowledge towards the 266 known human PDZ domains, generating the full PDZome-binding profile of the PTEN PBM. We confirmed that inclusion of N-terminal flanking residues, acetylation or mutation of a lysine at a modulatory position significantly altered the PDZome-binding profile. A numerical specificity index is also introduced as an attempt to quantify the specificity of a given PBM over the complete PDZome. Our results highlight the impact of modulatory residues and post-translational modifications on PBM interactomes and their specificity.
Collapse
Affiliation(s)
- Pau Jané
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Gergő Gógl
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Camille Kostmann
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Goran Bich
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Virginie Girault
- Unité Récepteurs-canaux, Institut Pasteur, UMR 3571/CNRS, Paris, France
| | | | - Pascal Eberling
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS/Aix-Marseille Université, Marseille, France
| | - Nicolas Wolff
- Unité Récepteurs-canaux, Institut Pasteur, UMR 3571/CNRS, Paris, France
| | - Gilles Travé
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- (Equipe labelisée Ligue, 2015) Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| |
Collapse
|
26
|
Levis NA, Reed EMX, Pfennig DW, Burford Reiskind MO. Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads. Ecol Evol 2020; 10:8976-8988. [PMID: 32884672 PMCID: PMC7452772 DOI: 10.1002/ece3.6602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases-especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an "omnivore" morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a "carnivore" morph that is favored in ephemeral, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with each morph (carnivores vs. omnivores) and loci associated with adaptive phenotypic plasticity (adaptive vs. maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might mediate adaptive plasticity.
Collapse
Affiliation(s)
| | - Emily M. X. Reed
- Department of Biological SciencesNorth Carolina State UniversityRaleighNCUSA
| | - David W. Pfennig
- Department of BiologyUniversity of North CarolinaChapel HillNCUSA
| | | |
Collapse
|
27
|
High MAST2 mRNA expression and its role in diagnosis and prognosis of liver cancer. Sci Rep 2019; 9:19865. [PMID: 31882722 PMCID: PMC6934750 DOI: 10.1038/s41598-019-56476-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Liver cancer is a high morbidity and low survival disease all over the world. Chromosomal instability is hallmark of liver cancer. Microtubule-associated serine and threonine kinase 2 (MAST2), as a microtubule associated protein, may involve in tumorous chromosomal instability and plays important roles in cell proliferation and survival. The role of MAST2 in liver cancer has not been well elucidated, which is the aim of our study. In this study, The Cancer Genome Atlas database was used to study the MAST2 mRNA expression in liver cancer, and Chi-squared tests were performed to test the correlation between clinical features and MAST2 expression. ROC curve was performed to examined the diagnostic capacity. The prognostic value of MAST2 in liver cancer was assessed through Kaplan-Meier curves as well as Cox analysis. Our results showed MAST2 was upregulated in liver cancer, and the area under the curve (AUC) was 0.925 and indicated powerful diagnostic capability. High MAST2 expression was associated with advanced clinical status such as histological type (p = 0.0059), histologic grade (p = 0.0142), stage (p = 0.0008), T classification (p = 0.0028), N classification (p = 0.0107), survival status (p = 0.0062), and poor prognosis of patients. Importantly, MAST2 was an independent risk factor for patients' prognosis after adjusting for other risk factors including stage, T classification, and residual tumor. In total, MAST2 is a potential diagnostic and prognostic biomarker of liver cancer.
Collapse
|
28
|
Multifaceted Regulation of PTEN Subcellular Distributions and Biological Functions. Cancers (Basel) 2019; 11:cancers11091247. [PMID: 31454965 PMCID: PMC6770588 DOI: 10.3390/cancers11091247] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/19/2022] Open
Abstract
Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor suppressor gene frequently found to be inactivated in over 30% of human cancers. PTEN encodes a 54-kDa lipid phosphatase that serves as a gatekeeper of the phosphoinositide 3-kinase pathway involved in the promotion of multiple pro-tumorigenic phenotypes. Although the PTEN protein plays a pivotal role in carcinogenesis, cumulative evidence has implicated it as a key signaling molecule in several other diseases as well, such as diabetes, Alzheimer's disease, and autism spectrum disorders. This finding suggests that diverse cell types, especially differentiated cells, express PTEN. At the cellular level, PTEN is widely distributed in all subcellular compartments and organelles. Surprisingly, the cytoplasmic compartment, not the plasma membrane, is the predominant subcellular location of PTEN. More recently, the finding of a secreted 'long' isoform of PTEN and the presence of PTEN in the cell nucleus further revealed unexpected biological functions of this multifaceted molecule. At the regulatory level, PTEN activity, stability, and subcellular distribution are modulated by a fascinating array of post-translational modification events, including phosphorylation, ubiquitination, and sumoylation. Dysregulation of these regulatory mechanisms has been observed in various human diseases. In this review, we provide an up-to-date overview of the knowledge gained in the last decade on how different functional domains of PTEN regulate its biological functions, with special emphasis on its subcellular distribution. This review also highlights the findings of published studies that have reported how mutational alterations in specific PTEN domains can lead to pathogenesis in humans.
Collapse
|
29
|
Khan Z, Terrien E, Delhommel F, Lefebvre-Omar C, Bohl D, Vitry S, Bernard C, Ramirez J, Chaffotte A, Ricquier K, Vincentelli R, Buc H, Prehaud C, Wolff N, Lafon M. Structure-based optimization of a PDZ-binding motif within a viral peptide stimulates neurite outgrowth. J Biol Chem 2019; 294:13755-13768. [PMID: 31346033 DOI: 10.1074/jbc.ra119.008238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/11/2019] [Indexed: 11/06/2022] Open
Abstract
Protection of neuronal homeostasis is a major goal in the management of neurodegenerative diseases. Microtubule-associated Ser/Thr kinase 2 (MAST2) inhibits neurite outgrowth, and its inhibition therefore represents a potential therapeutic strategy. We previously reported that a viral protein (G-protein from rabies virus) capable of interfering with protein-protein interactions between the PDZ domain of MAST2 and the C-terminal moieties of its cellular partners counteracts MAST2-mediated suppression of neurite outgrowth. Here, we designed peptides derived from the native viral protein to increase the affinity of these peptides for the MAST2-PDZ domain. Our strategy involved modifying the length and flexibility of the noninteracting sequence linking the two subsites anchoring the peptide to the PDZ domain. Three peptides, Neurovita1 (NV1), NV2, and NV3, were selected, and we found that they all had increased affinities for the MAST2-PDZ domain, with Kd values decreasing from 1300 to 60 nm, while target selectivity was maintained. A parallel biological assay evaluating neurite extension and branching in cell cultures revealed that the NV peptides gradually improved neural activity, with the efficacies of these peptides for stimulating neurite outgrowth mirroring their affinities for MAST2-PDZ. We also show that NVs can be delivered into the cytoplasm of neurons as a gene or peptide. In summary, our findings indicate that virus-derived peptides targeted to MAST2-PDZ stimulate neurite outgrowth in several neuron types, opening up promising avenues for potentially using NVs in the management of neurodegenerative diseases.
Collapse
Affiliation(s)
- Zakir Khan
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris 75015, France
| | - Elouan Terrien
- Institut Pasteur, Unité de RMN des Biomolécules, UMR 3528, CNRS, Paris 75015, France
| | - Florent Delhommel
- Institut Pasteur, Unité de RMN des Biomolécules, UMR 3528, CNRS, Paris 75015, France
| | - Cynthia Lefebvre-Omar
- Institut du Cerveau et de la Moelle Epinière, ICM, U1127 INSERM, UMR 7225 CNRS, Sorbonne Université, Paris 75013, France
| | - Delphine Bohl
- Institut du Cerveau et de la Moelle Epinière, ICM, U1127 INSERM, UMR 7225 CNRS, Sorbonne Université, Paris 75013, France
| | - Sandrine Vitry
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris 75015, France
| | - Clara Bernard
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris 75015, France
| | - Juan Ramirez
- Institut Pasteur, Unité de RMN des Biomolécules, UMR 3528, CNRS, Paris 75015, France
| | - Alain Chaffotte
- Institut Pasteur, Unité de RMN des Biomolécules, UMR 3528, CNRS, Paris 75015, France
| | - Kevin Ricquier
- Institut Pasteur, Unité de RMN des Biomolécules, UMR 3528, CNRS, Paris 75015, France
| | - Renaud Vincentelli
- Unité Mixte de Recherche 7257, CNRS Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13009, France
| | - Henri Buc
- Institut Pasteur, Paris 75015, France
| | - Christophe Prehaud
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris 75015, France
| | - Nicolas Wolff
- Institut Pasteur, Unité de RMN des Biomolécules, UMR 3528, CNRS, Paris 75015, France
| | - Monique Lafon
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris 75015, France
| |
Collapse
|
30
|
An SWA, Choi E, Hwang W, Son HG, Yang J, Seo K, Nam H, Nguyen NTH, Kim EJE, Suh BK, Kim Y, Nakano S, Ryu Y, Man Ha C, Mori I, Park SK, Yoo J, Kim S, Lee SV. KIN-4/MAST kinase promotes PTEN-mediated longevity of Caenorhabditis elegans via binding through a PDZ domain. Aging Cell 2019; 18:e12906. [PMID: 30773781 PMCID: PMC6516182 DOI: 10.1111/acel.12906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/16/2018] [Accepted: 12/02/2018] [Indexed: 01/09/2023] Open
Abstract
PDZ domain‐containing proteins (PDZ proteins) act as scaffolds for protein–protein interactions and are crucial for a variety of signal transduction processes. However, the role of PDZ proteins in organismal lifespan and aging remains poorly understood. Here, we demonstrate that KIN‐4, a PDZ domain‐containing microtubule‐associated serine‐threonine (MAST) protein kinase, is a key longevity factor acting through binding PTEN phosphatase in Caenorhabditis elegans. Through a targeted genetic screen for PDZ proteins, we find that kin‐4 is required for the long lifespan of daf‐2/insulin/IGF‐1 receptor mutants. We then show that neurons are crucial tissues for the longevity‐promoting role of kin‐4. We find that the PDZ domain of KIN‐4 binds PTEN, a key factor for the longevity of daf‐2 mutants. Moreover, the interaction between KIN‐4 and PTEN is essential for the extended lifespan of daf‐2 mutants. As many aspects of lifespan regulation in C. elegans are evolutionarily conserved, MAST family kinases may regulate aging and/or age‐related diseases in mammals through their interaction with PTEN.
Collapse
Affiliation(s)
- Seon Woo A. An
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Eun‐Seok Choi
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Wooseon Hwang
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Heehwa G. Son
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Jae‐Seong Yang
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Keunhee Seo
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Hyun‐Jun Nam
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Nhung T. H. Nguyen
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Eun Ji E. Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Bo Kyoung Suh
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Youngran Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Shunji Nakano
- Neuroscience Institute, Graduate School of Science Nagoya University Nagoya Japan
| | - Youngjae Ryu
- Research Division Korea Brain Research Institute Daegu South Korea
| | - Chang Man Ha
- Research Division Korea Brain Research Institute Daegu South Korea
| | - Ikue Mori
- Neuroscience Institute, Graduate School of Science Nagoya University Nagoya Japan
| | - Sang Ki Park
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Joo‐Yeon Yoo
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Sanguk Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Seung‐Jae V. Lee
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| |
Collapse
|
31
|
Genera M, Samson D, Raynal B, Haouz A, Baron B, Simenel C, Guerois R, Wolff N, Caillet-Saguy C. Structural and functional characterization of the PDZ domain of the human phosphatase PTPN3 and its interaction with the human papillomavirus E6 oncoprotein. Sci Rep 2019; 9:7438. [PMID: 31092861 PMCID: PMC6520365 DOI: 10.1038/s41598-019-43932-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/27/2019] [Indexed: 02/07/2023] Open
Abstract
The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a PDZ (PSD-95/Dlg/ZO-1) domain-containing phosphatase with a tumor-suppressive or a tumor-promoting role in many cancers. Interestingly, the high-risk genital human papillomavirus (HPV) types 16 and 18 target the PDZ domain of PTPN3. The presence of a PDZ binding motif (PBM) on E6 confers interaction with a number of different cellular PDZ domain-containing proteins and is a marker of high oncogenic potential. Here, we report the molecular basis of interaction between the PDZ domain of PTPN3 and the PBM of the HPV E6 protein. We combined biophysical, NMR and X-ray experiments to investigate the structural and functional properties of the PDZ domain of PTPN3. We showed that the C-terminal sequences from viral proteins encompassing a PBM interact with PTPN3-PDZ with similar affinities to the endogenous PTPN3 ligand MAP kinase p38γ. PBM binding stabilizes the PDZ domain of PTPN3. We solved the X-ray structure of the PDZ domain of PTPN3 in complex with the PBM of the HPV E6 protein. The crystal structure and the NMR chemical shift mapping of the PTPN3-PDZ/peptide complex allowed us to pinpoint the main structural determinants of recognition of the C-terminal sequence of the E6 protein and the long-range perturbations induced upon PBM binding.
Collapse
Affiliation(s)
- Mariano Genera
- Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, F-75724, Paris, France.,Sorbonne Université, Complexité du Vivant, F-75005, Paris, France
| | - Damien Samson
- RMN des biomolécules, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie, Institut Pasteur UMR 3528, CNRS, F-75724, Paris, France
| | - Bruno Baron
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Catherine Simenel
- RMN des biomolécules, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Raphael Guerois
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, Cedex, France
| | - Nicolas Wolff
- Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, F-75724, Paris, France
| | - Célia Caillet-Saguy
- Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, F-75724, Paris, France.
| |
Collapse
|
32
|
Thomas M, Banks L. Upsetting the Balance: When Viruses Manipulate Cell Polarity Control. J Mol Biol 2018; 430:3481-3503. [PMID: 29680664 PMCID: PMC7094317 DOI: 10.1016/j.jmb.2018.04.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/20/2022]
Abstract
The central importance of cell polarity control is emphasized by the frequency with which it is targeted by many diverse viruses. It is clear that in targeting key polarity control proteins, viruses affect not only host cell polarity, but also influence many cellular processes, including transcription, replication, and innate and acquired immunity. Examination of the interactions of different virus proteins with the cell and its polarity controls during the virus life cycles, and in virally-induced cell transformation shows ever more clearly how intimately all cellular processes are linked to the control of cell polarity.
Collapse
|
33
|
Naderali E, Khaki AA, Rad JS, Ali-Hemmati A, Rahmati M, Charoudeh HN. Regulation and modulation of PTEN activity. Mol Biol Rep 2018; 45:2869-2881. [PMID: 30145641 DOI: 10.1007/s11033-018-4321-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/20/2018] [Indexed: 01/04/2023]
Abstract
PTEN (Phosphatase and tensin homolog deleted on chromosome ten) is a tumor suppressor that is frequently mutated in most human cancers. PTEN is a lipid and protein phosphatase that antagonizes PI3K/AKT pathway through lipid phosphatase activity at the plasma membrane. More recent studies showed that, in addition to the putative role of PTEN as a PI(3,4,5)P3 3-phosphatase, it is a PI(3,4)P2 3-phosphatase during stimulation of class I PI3K signaling pathway by growth factor. Although PTEN tumor suppressor function via it's lipid phosphatase activity occurs primarily in the plasma membrane, it can also be found in the nucleus, in cytoplasmic organelles and extracellular space. PTEN has also shown phosphatase independent functions in the nucleus. PTEN can exit from the cell through exosomal export or secretion and has a tumor suppressor function in adjacent cells. PTEN has a critical role in growth, the cell cycle, protein synthesis, survival, DNA repair and migration. Understanding the regulation of PTEN function, activity, stability, localization and its dysregulation outcomes and also the intracellular and extracellular role of PTEN and paracrine role of PTEN-L in tumor cells as an exogenous therapeutic agent can help to improve clinical conceptualization and treatment of cancer.
Collapse
Affiliation(s)
- Elahe Naderali
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Afshin Khaki
- Department of Anatomical sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Soleymani Rad
- Department of Anatomical sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Ali-Hemmati
- Department of Anatomical sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Rahmati
- Department of Clinical Biochemistry Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hojjatollah Nozad Charoudeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Cell Therapy Research Laboratory, Drug Applied Research Center, Tabriz University of Medical Sciences, P.O. Box: 51656-65811, Tabriz, Iran.
| |
Collapse
|
34
|
McLoughlin NM, Mueller C, Grossmann TN. The Therapeutic Potential of PTEN Modulation: Targeting Strategies from Gene to Protein. Cell Chem Biol 2018; 25:19-29. [DOI: 10.1016/j.chembiol.2017.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 01/04/2023]
|
35
|
Malaney P, Uversky VN, Davé V. PTEN proteoforms in biology and disease. Cell Mol Life Sci 2017; 74:2783-2794. [PMID: 28289760 PMCID: PMC11107534 DOI: 10.1007/s00018-017-2500-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 01/30/2023]
Abstract
Proteoforms are specific molecular forms of protein products arising from a single gene that possess different structures and different functions. Therefore, a single gene can produce a large repertoire of proteoforms by means of allelic variations (mutations, indels, SNPs), alternative splicing and other pre-translational mechanisms, post-translational modifications (PTMs), conformational dynamics, and functioning. Resulting proteoforms that have different sizes, alternative splicing patterns, sets of post-translational modifications, protein-protein interactions, and protein-ligand interactions, might dramatically increase the functionality of the encoded protein. Herein, we have interrogated the tumor suppressor PTEN for its proteoforms and find that this protein exists in multiple forms with distinct functions and sub-cellular localizations. Furthermore, the levels of each PTEN proteoform in a given cell may affect its biological function. Indeed, the paradigm of the continuum model of tumor suppression by PTEN can be better explained by the presence of a continuum of PTEN proteoforms, diversity, and levels of which are associated with pathological outcomes than simply by the different roles of mutations in the PTEN gene. Consequently, understanding the mechanisms underlying the dysregulation of PTEN proteoforms by several genomic and non-genomic mechanisms in cancer and other diseases is imperative. We have identified different PTEN proteoforms, which control various aspects of cellular function and grouped them into three categories of intrinsic, function-induced, and inducible proteoforms. A special emphasis is given to the inducible PTEN proteoforms that are produced due to alternative translational initiation. The novel finding that PTEN forms dimers with biological implications supports the notion that PTEN proteoform-proteoform interactions may play hitherto unknown roles in cellular homeostasis and in pathogenic settings, including cancer. These PTEN proteoforms with unique properties and functionalities offer potential novel therapeutic opportunities in the treatment of various cancers and other diseases.
Collapse
Affiliation(s)
- Prerna Malaney
- Department of Pathology and Cell Biology, Morsani College of Medicine, MDC 64, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33612, USA
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave., Saint Petersburg, Russia, 194064
| | - Vrushank Davé
- Department of Pathology and Cell Biology, Morsani College of Medicine, MDC 64, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA.
- Department of Oncological Sciences, Morsani College of Medicine, University of South Florida, Bruce B. Downs Blvd, Tampa, FL, 33612, USA.
| |
Collapse
|
36
|
Seo W, Prehaud C, Khan Z, Sabeta C, Lafon M. Investigation of rabies virus glycoprotein carboxyl terminus as an in vitro predictive tool of neurovirulence. A 3R approach. Microbes Infect 2017; 19:476-484. [PMID: 28602914 DOI: 10.1016/j.micinf.2017.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 03/10/2017] [Accepted: 05/30/2017] [Indexed: 01/29/2023]
Abstract
In the field of live viral vaccines production, there is an unmet need for in vitro tests complying a 3R approach (Refine, Replace and Reduce the use of animal experimentation) to replace the post-licensing safety tests currently assayed in animals. Here, we performed a pilot study evaluating whether virulence of rabies virus, RABV, can be forecast by an in vitro test of neurite outgrowth. The rationale to use neurite outgrowth as a read-out for this test is based on the salient property of the cytoplasmic domain of the G-protein (Cyto-G) of virulent RABV strains - not of attenuated RABV strains - to stimulate neurite outgrowth in vitro. We observed that neurite elongation triggered by the Cyto-Gs encoded by different RABV field isolates correlate with the distinct virulence scores obtained in a mouse model of experimental rabies. Our results cast the idea that it could be feasible to predict RABV virulence by testing the in vitro property of a RABV strain to promote neurite outgrowth without the use of animal experimentation.
Collapse
Affiliation(s)
- Wonhyo Seo
- OIE Rabies Reference Laboratory, ARC-Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort, South Africa; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa; Institut Pasteur, CNRS, Unité de Neuroimmunologie Virale, Département de Virologie, Paris, France
| | - Christophe Prehaud
- Institut Pasteur, CNRS, Unité de Neuroimmunologie Virale, Département de Virologie, Paris, France
| | - Zakir Khan
- Institut Pasteur, CNRS, Unité de Neuroimmunologie Virale, Département de Virologie, Paris, France
| | - Claude Sabeta
- OIE Rabies Reference Laboratory, ARC-Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort, South Africa; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa
| | - Monique Lafon
- Institut Pasteur, CNRS, Unité de Neuroimmunologie Virale, Département de Virologie, Paris, France.
| |
Collapse
|
37
|
Azimzadeh Jamalkandi S, Mozhgani SH, Gholami Pourbadie H, Mirzaie M, Noorbakhsh F, Vaziri B, Gholami A, Ansari-Pour N, Jafari M. Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways. Front Microbiol 2016; 7:1688. [PMID: 27872612 PMCID: PMC5098112 DOI: 10.3389/fmicb.2016.01688] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/07/2016] [Indexed: 12/16/2022] Open
Abstract
The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein–protein interaction network (PPIN) of infected cells to elucidate the rabies-implicated signal transduction network (RISN). To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.
Collapse
Affiliation(s)
| | - Sayed-Hamidreza Mozhgani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences Tehran, Iran
| | | | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences Tehran, Iran
| | - Behrouz Vaziri
- Protein Chemistry and Proteomics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran Tehran, Iran
| | - Alireza Gholami
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran Tehran, Iran
| | - Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of TehranTehran, Iran; Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College LondonLondon, UK
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran Tehran, Iran
| |
Collapse
|
38
|
Zhou L, Bu Y, Liang Y, Zhang F, Zhang H, Li S. Epstein-Barr Virus (EBV)-BamHI-A Rightward Transcript (BART)-6 and Cellular MicroRNA-142 Synergistically Compromise Immune Defense of Host Cells in EBV-Positive Burkitt Lymphoma. Med Sci Monit 2016; 22:4114-4120. [PMID: 27796281 PMCID: PMC5094474 DOI: 10.12659/msm.897306] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background This study was designed to explore the molecular mechanism underlying the effect of cellular miRNAs and EBV miRNA upon the expression of targets such as PTEN, and their involvement in the pathogenesis of Burkitt lymphoma. Material/Methods In this study, we examined several differentially expressed cellular miRNAs in EBV-positive versus EBV-negative Burkett lymphoma tissue samples, and confirmed PTEN as targets of cellular miR-142 by using a bioinformatics tool, luciferase reporter system, oligo transfection, real-time PCR, and Western blot analysis. Results We further confirmed the binding site of miR-142 in the 3′UTR of the target genes, and established the negative regulatory relationship between miRNA and mRNAs with luciferase activity assay. To verify the regulatory relationship between the miRNAs and PTEN, we evaluated the expression of PTEN in the tissue samples, and found that PTEN was downregulated in EBV- positive Burkett lymphoma. Additionally, lymphoma cells were transfected with EBV-BART-6-3p and miR-142 and we found that EBV-BART-6-3p and miR-142 synergistically reduced expression of IL-6R and PTEN. Furthermore, we also examined viability of the cells in each treatment group, and showed that EBV-BART-6-3p and miR-142 synergistically promoted proliferation of the cells. Conclusions These findings improve our knowledge about the role of miR-142/EBV-BART-6-3p and their target, PTEN, in the development of Burkett lymphoma; they could be novel therapeutic targets for the treatment of EBV-positive Burkett lymphoma.
Collapse
Affiliation(s)
- Ling Zhou
- Department of Hematology, The First People's Hospital, Jining, Shandong, China (mainland)
| | - Yunwen Bu
- Department of Hematology, The First People's Hospital, Jining, Shandong, China (mainland)
| | - Yanyan Liang
- Department of Hematology, The First People's Hospital, Jining, Shandong, China (mainland)
| | - Fang Zhang
- Department of Hematology, The First People's Hospital, Jining, Shandong, China (mainland)
| | - Haiguo Zhang
- Department of Hematology, The First People's Hospital, Jining, Shandong, China (mainland)
| | - Shumei Li
- Department of Hematology, The First People's Hospital, Jining, Shandong, China (mainland)
| |
Collapse
|
39
|
Li J, Zhang J, Tang M, Xin J, Xu Y, Volk A, Hao C, Hu C, Sun J, Wei W, Cao Q, Breslin P, Zhang J. Hematopoietic Stem Cell Activity Is Regulated by Pten Phosphorylation Through a Niche-Dependent Mechanism. Stem Cells 2016; 34:2130-44. [PMID: 27096933 DOI: 10.1002/stem.2382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/19/2016] [Accepted: 03/26/2016] [Indexed: 12/21/2022]
Abstract
The phosphorylated form of Pten (p-Pten) is highly expressed in >70% of acute myeloid leukemia samples. However, the role of p-Pten in normal and abnormal hematopoiesis has not been studied. We found that Pten protein levels are comparable among long-term (LT) hematopoietic stem cells (HSCs), short-term (ST) HSCs, and multipotent progenitors (MPPs); however, the levels of p-Pten are elevated during the HSC-to-MPP transition. To study whether p-Pten is involved in regulating self-renewal and differentiation in HSCs, we compared the effects of overexpression of p-Pten and nonphosphorylated Pten (non-p-Pten) on the hematopoietic reconstitutive capacity (HRC) of HSCs. We found that overexpression of non-p-Pten enhances the LT-HRC of HSCs, whereas overexpression of p-Pten promotes myeloid differentiation and compromises the LT-HRC of HSCs. Such phosphorylation-regulated Pten functioning is mediated by repressing the cell:cell contact-induced activation of Fak/p38 signaling independent of Pten's lipid phosphatase activity because both p-Pten and non-p-Pten have comparable activity in repressing PI3K/Akt signaling. Our studies suggest that, in addition to repressing PI3K/Akt/mTor signaling, non-p-Pten maintains HSCs in bone marrow niches via a cell-contact inhibitory mechanism by inhibiting Fak/p38 signaling-mediated proliferation and differentiation. In contrast, p-Pten promotes the proliferation and differentiation of HSCs by enhancing the cell contact-dependent activation of Src/Fak/p38 signaling. Stem Cells 2016;34:2130-2144.
Collapse
Affiliation(s)
- Jing Li
- Department of Biology, College of Life and Environment Science, Shanghai Normal University, Shanghai, People's Republic of China.,Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA
| | - Jun Zhang
- Department of Biology, College of Life and Environment Science, Shanghai Normal University, Shanghai, People's Republic of China.,Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA
| | - Minghui Tang
- Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA
| | - Junping Xin
- Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA
| | - Yan Xu
- Department of Biology, College of Life and Environment Science, Shanghai Normal University, Shanghai, People's Republic of China
| | - Andrew Volk
- Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA
| | - Caiqin Hao
- Department of Biology, College of Life and Environment Science, Shanghai Normal University, Shanghai, People's Republic of China
| | - Chenglong Hu
- Department of Biology, College of Life and Environment Science, Shanghai Normal University, Shanghai, People's Republic of China
| | - Jiewen Sun
- Department of Biology, College of Life and Environment Science, Shanghai Normal University, Shanghai, People's Republic of China
| | - Wei Wei
- Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA
| | - Quichan Cao
- Department of Public Health Sciences, Loyola University Chicago, Chicago, Illinois, USA
| | - Peter Breslin
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA.,Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA.,Department of Molecular and Cellular Physiology, Loyola University Chicago, Chicago, Illinois, USA
| | - Jiwang Zhang
- Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Chicago, Illinois, USA.,Department of Pathology, Loyola University Medical Center, Maywood, Illinois, USA
| |
Collapse
|
40
|
James CD, Roberts S. Viral Interactions with PDZ Domain-Containing Proteins-An Oncogenic Trait? Pathogens 2016; 5:pathogens5010008. [PMID: 26797638 PMCID: PMC4810129 DOI: 10.3390/pathogens5010008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 02/06/2023] Open
Abstract
Many of the human viruses with oncogenic capabilities, either in their natural host or in experimental systems (hepatitis B and C, human T cell leukaemia virus type 1, Kaposi sarcoma herpesvirus, human immunodeficiency virus, high-risk human papillomaviruses and adenovirus type 9), encode in their limited genome the ability to target cellular proteins containing PSD95/ DLG/ZO-1 (PDZ) interaction modules. In many cases (but not always), the viruses have evolved to bind the PDZ domains using the same short linear peptide motifs found in host protein-PDZ interactions, and in some cases regulate the interactions in a similar fashion by phosphorylation. What is striking is that the diverse viruses target a common subset of PDZ proteins that are intimately involved in controlling cell polarity and the structure and function of intercellular junctions, including tight junctions. Cell polarity is fundamental to the control of cell proliferation and cell survival and disruption of polarity and the signal transduction pathways involved is a key event in tumourigenesis. This review focuses on the oncogenic viruses and the role of targeting PDZ proteins in the virus life cycle and the contribution of virus-PDZ protein interactions to virus-mediated oncogenesis. We highlight how many of the viral associations with PDZ proteins lead to deregulation of PI3K/AKT signalling, benefitting virus replication but as a consequence also contributing to oncogenesis.
Collapse
Affiliation(s)
- Claire D James
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK.
- Present address; Virginia Commonwealth University, School of Dentistry, W. Baxter Perkinson Jr. Building, 521 North 11th Street, P.O. Box 980566, Richmond, VA 23298-0566, USA.
| | - Sally Roberts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK.
| |
Collapse
|
41
|
Pulido R. PTEN: a yin-yang master regulator protein in health and disease. Methods 2016; 77-78:3-10. [PMID: 25843297 DOI: 10.1016/j.ymeth.2015.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 01/16/2023] Open
Abstract
The PTEN gene is a tumor suppressor gene frequently mutated in human tumors, which encodes a ubiquitous protein whose major activity is to act as a lipid phosphatase that counteracts the action of the oncogenic PI3K. In addition, PTEN displays protein phosphatase- and catalytically-independent activities. The physiologic control of PTEN function, and its inactivation in cancer and other human diseases, including some neurodevelopmental disorders, is upon the action of multiple regulatory mechanisms. This provides a wide spectrum of potential therapeutic approaches to reconstitute PTEN activity. By contrast, inhibition of PTEN function may be beneficial in a different group of human diseases, such as type 2 diabetes or neuroregeneration-related pathologies. This makes PTEN a functionally dual yin-yang protein with high potential in the clinics. Here, a brief overview on PTEN and its relation with human disease is presented.
Collapse
Affiliation(s)
- Rafael Pulido
- BioCruces Health Research Institute, Barakaldo, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
| |
Collapse
|
42
|
Deciphering the unconventional peptide binding to the PDZ domain of MAST2. Biochem J 2015; 469:159-68. [DOI: 10.1042/bj20141198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 05/05/2015] [Indexed: 11/17/2022]
Abstract
Peptide binding on to microtubule-associated serine threonine kinase 2 (MAST2)—PDZ (PSD-95, Dlg1, Zo-1) prevents dimerization of the domain without directly competing with the monomer interface. Peptide binding affects positions distal from the binding groove through a network of residues undergoing subtle changes of conformation and dynamics.
Collapse
|
43
|
PTEN–PDZ domain interactions: Binding of PTEN to PDZ domains of PTPN13. Methods 2015; 77-78:147-56. [DOI: 10.1016/j.ymeth.2014.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023] Open
|
44
|
Geng X, Sha J, Liu S, Bao L, Zhang J, Wang R, Yao J, Li C, Feng J, Sun F, Sun L, Jiang C, Zhang Y, Chen A, Dunham R, Zhi D, Liu Z. A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance. BMC Genomics 2015; 16:196. [PMID: 25888203 PMCID: PMC4372039 DOI: 10.1186/s12864-015-1409-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/27/2015] [Indexed: 11/16/2022] Open
Abstract
Background Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus). Results A genomic region on linkage group 7 was found to be significantly associated with columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host. Conclusion The GWAS revealed four QTLs associated with columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for columnaris resistance.
Collapse
Affiliation(s)
- Xin Geng
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Jin Sha
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Shikai Liu
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Lisui Bao
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Jiaren Zhang
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Ruijia Wang
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Jun Yao
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Chao Li
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Jianbin Feng
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Fanyue Sun
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Luyang Sun
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Chen Jiang
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Yu Zhang
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Ailu Chen
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Rex Dunham
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| | - Degui Zhi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Zhanjiang Liu
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA.
| |
Collapse
|
45
|
Caillet-Saguy C, Maisonneuve P, Delhommel F, Terrien E, Babault N, Lafon M, Cordier F, Wolff N. Strategies to interfere with PDZ-mediated interactions in neurons: What we can learn from the rabies virus. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:53-9. [PMID: 25748547 DOI: 10.1016/j.pbiomolbio.2015.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/19/2015] [Accepted: 02/24/2015] [Indexed: 11/29/2022]
Abstract
PDZ (PSD-95/Dlg/ZO-1) domains play a major role in neuronal homeostasis in which they act as scaffold domains regulating cellular trafficking, self-association and catalytic activity of essential proteins such as kinases and phosphatases. Because of their central role in cell signaling, cellular PDZ-containing proteins are preferential targets of viruses to hijack cellular function to their advantage. Here, we describe how the viral G protein of the rabies virus specifically targets the PDZ domain of neuronal enzymes during viral infection. By disrupting the complexes formed by cellular enzymes and their ligands, the virus triggers drastic effect on cell signaling and commitment of the cell to either survival (virulent strains) or death (vaccinal strains). We provide structural and biological evidences that the viral proteins act as competitors endowed with specificity and affinity in an essential cellular process by mimicking PDZ binding motif of cellular partners. Disruption of critical endogenous protein-protein interactions by viral protein drastically alters intracellular protein trafficking and catalytic activity of cellular proteins that control cell homeostasis. This work opens up many perspectives to mimic viral sequences and developing innovative therapies to manipulate cellular homeostasis.
Collapse
Affiliation(s)
- Célia Caillet-Saguy
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Pierre Maisonneuve
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Florent Delhommel
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Docteur Roux, 75015 Paris, France
| | - Elouan Terrien
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Nicolas Babault
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Monique Lafon
- Unité de Neuroimmunologie Virale, Département de Virologie, Institut Pasteur, Paris, France
| | - Florence Cordier
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Nicolas Wolff
- Unité de RMN des Biomolécules (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France.
| |
Collapse
|
46
|
Milella M, Falcone I, Conciatori F, Cesta Incani U, Del Curatolo A, Inzerilli N, Nuzzo CMA, Vaccaro V, Vari S, Cognetti F, Ciuffreda L. PTEN: Multiple Functions in Human Malignant Tumors. Front Oncol 2015; 5:24. [PMID: 25763354 PMCID: PMC4329810 DOI: 10.3389/fonc.2015.00024] [Citation(s) in RCA: 323] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/22/2015] [Indexed: 12/16/2022] Open
Abstract
PTEN is the most important negative regulator of the PI3K signaling pathway. In addition to its canonical, PI3K inhibition-dependent functions, PTEN can also function as a tumor suppressor in a PI3K-independent manner. Indeed, the PTEN network regulates a broad spectrum of biological functions, modulating the flow of information from membrane-bound growth factor receptors to nuclear transcription factors, occurring in concert with other tumor suppressors and oncogenic signaling pathways. PTEN acts through its lipid and protein phosphatase activity and other non-enzymatic mechanisms. Studies conducted over the past 10 years have expanded our understanding of the biological role of PTEN, showing that in addition to its ability to regulate proliferation and cell survival, it also plays an intriguing role in regulating genomic stability, cell migration, stem cell self-renewal, and tumor microenvironment. Changes in PTEN protein levels, location, and enzymatic activity through various molecular mechanisms can generate a continuum of functional PTEN levels in inherited syndromes, sporadic cancers, and other diseases. PTEN activity can indeed, be modulated by mutations, epigenetic silencing, transcriptional repression, aberrant protein localization, and post-translational modifications. This review will discuss our current understanding of the biological role of PTEN, how PTEN expression and activity are regulated, and the consequences of PTEN dysregulation in human malignant tumors.
Collapse
Affiliation(s)
- Michele Milella
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Italia Falcone
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Fabiana Conciatori
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Ursula Cesta Incani
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Anais Del Curatolo
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Nicola Inzerilli
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Carmen M A Nuzzo
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Vanja Vaccaro
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Sabrina Vari
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Francesco Cognetti
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| | - Ludovica Ciuffreda
- Division of Medical Oncology A, Regina Elena National Cancer Institute , Rome , Italy
| |
Collapse
|
47
|
Abstract
The importance of PTEN in cellular function is underscored by the frequency of its deregulation in cancer. PTEN tumor-suppressor activity depends largely on its lipid phosphatase activity, which opposes PI3K/AKT activation. As such, PTEN regulates many cellular processes, including proliferation, survival, energy metabolism, cellular architecture, and motility. More than a decade of research has expanded our knowledge about how PTEN is controlled at the transcriptional level as well as by numerous posttranscriptional modifications that regulate its enzymatic activity, protein stability, and cellular location. Although the role of PTEN in cancers has long been appreciated, it is also emerging as an important factor in other diseases, such as diabetes and autism spectrum disorders. Our understanding of PTEN function and regulation will hopefully translate into improved prognosis and treatment for patients suffering from these ailments.
Collapse
Affiliation(s)
- Carolyn A Worby
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721;
| | | |
Collapse
|
48
|
Characterization of nuclear PTEN and its post translational modifications. Methods 2015; 77-78:104-11. [PMID: 25616216 DOI: 10.1016/j.ymeth.2015.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 11/21/2022] Open
Abstract
Somatic loss-of-function mutations of PTEN are found in a variety of human malignancies. Our recent work demonstrated that the nuclear function of PTEN is implicated in the maintenance of genome integrity. Proper subcellular localization of PTEN following genotoxic stress is coordinated by a cellular mechanism that involves post-translational modification by SUMOylation and ATM-mediated phosphorylation. Here we summarize biochemical and cell-based methodologies that can be used to characterize the SUMOylation and phosphorylation state of nuclear PTEN in the context of DNA damage. In addition, we describe assays to determine the biological function of SUMO-PTEN in homologous recombination DNA repair. These methods will help elucidate the precise molecular mechanisms of PTEN's role in the maintenance of genomic stability.
Collapse
|
49
|
Erlendsson S, Rathje M, Heidarsson PO, Poulsen FM, Madsen KL, Teilum K, Gether U. Protein interacting with C-kinase 1 (PICK1) binding promiscuity relies on unconventional PSD-95/discs-large/ZO-1 homology (PDZ) binding modes for nonclass II PDZ ligands. J Biol Chem 2014; 289:25327-40. [PMID: 25023278 DOI: 10.1074/jbc.m114.548743] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PDZ domain proteins control multiple cellular functions by governing assembly of protein complexes. It remains unknown why individual PDZ domains can bind the extreme C terminus of very diverse binding partners and maintain selectivity. By employing NMR spectroscopy, together with molecular modeling, mutational analysis, and fluorescent polarization binding experiments, we identify here three structural mechanisms explaining why the PDZ domain of PICK1 selectively binds >30 receptors, transporters, and kinases. Class II ligands, including the dopamine transporter, adopt a canonical binding mode with promiscuity obtained via differential packing in the binding groove. Class I ligands, such as protein kinase Cα, depend on residues upstream from the canonical binding sequence that are likely to interact with flexible loop residues of the PDZ domain. Finally, we obtain evidence that the unconventional ligand ASIC1a has a dual binding mode involving a canonical insertion and a noncanonical internal insertion with the two C-terminal residues forming interactions outside the groove. Together with an evolutionary analysis, the data show how unconventional binding modes might evolve for a protein recognition domain to expand the repertoire of functionally important interactions.
Collapse
Affiliation(s)
- Simon Erlendsson
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Mette Rathje
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and
| | - Pétur O Heidarsson
- the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Flemming M Poulsen
- the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kenneth L Madsen
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and
| | - Kaare Teilum
- the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ulrik Gether
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and
| |
Collapse
|
50
|
Kreis P, Leondaritis G, Lieberam I, Eickholt BJ. Subcellular targeting and dynamic regulation of PTEN: implications for neuronal cells and neurological disorders. Front Mol Neurosci 2014; 7:23. [PMID: 24744697 PMCID: PMC3978343 DOI: 10.3389/fnmol.2014.00023] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/12/2014] [Indexed: 01/13/2023] Open
Abstract
PTEN is a lipid and protein phosphatase that regulates a diverse range of cellular mechanisms. PTEN is mainly present in the cytosol and transiently associates with the plasma membrane to dephosphorylate PI(3,4,5)P3, thereby antagonizing the PI3-Kinase signaling pathway. Recently, PTEN has been shown to associate also with organelles such as the endoplasmic reticulum (ER), the mitochondria, or the nucleus, and to be secreted outside of the cell. In addition, PTEN dynamically localizes to specialized sub-cellular compartments such as the neuronal growth cone or dendritic spines. The diverse localizations of PTEN imply a tight temporal and spatial regulation, orchestrated by mechanisms such as posttranslational modifications, formation of distinct protein–protein interactions, or the activation/recruitment of PTEN downstream of external cues. The regulation of PTEN function is thus not only important at the enzymatic activity level, but is also associated to its spatial distribution. In this review we will summarize (i) recent findings that highlight mechanisms controlling PTEN movement and sub-cellular localization, and (ii) current understanding of how PTEN localization is achieved by mechanisms controlling posttranslational modification, by association with binding partners and by PTEN structural or activity requirements. Finally, we will discuss the possible roles of compartmentalized PTEN in developing and mature neurons in health and disease.
Collapse
Affiliation(s)
- Patricia Kreis
- MRC Centre for Developmental Neurobiology, King's College London London, UK
| | - George Leondaritis
- MRC Centre for Developmental Neurobiology, King's College London London, UK ; Institute of Biochemistry, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Ivo Lieberam
- MRC Centre for Developmental Neurobiology, King's College London London, UK
| | - Britta J Eickholt
- MRC Centre for Developmental Neurobiology, King's College London London, UK ; Institute of Biochemistry, Charité - Universitätsmedizin Berlin Berlin, Germany
| |
Collapse
|