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Dong C, Liu W, Zhang Y, Song Y, Du J, Huang Z, Wang T, Yu Z, Ma X. Identification of Common Hub Genes in Human Dermal Fibroblasts Stimulated by Mechanical Stretch at Both the Early and Late Stages. Front Surg 2022; 9:846161. [PMID: 35510126 PMCID: PMC9058084 DOI: 10.3389/fsurg.2022.846161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/16/2022] [Indexed: 11/25/2022] Open
Abstract
Background Mechanical stretch is vital for soft tissue regeneration and development and is utilized by plastic surgeons for tissue expansion. Identifying the common hub genes in human dermal fibroblasts (HDFs) stimulated by mechanical stretch at different stages will help elucidate the mechanisms involved and improve the efficiency of tissue expansion. Methods A gene expression dataset (GSE58389) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in HDFs between cyclic mechanical stretching and static samples were identified at 5 and 24 h. Common DEGs overlapped in both the 5 h and 24 h groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to determine the functions of the DEGs. Protein-protein interaction networks were constructed using the STRING database. The top 10 hub genes were selected using the plug-in Cytohubba within Cytoscape. The regulatory network of hub genes was predicted using NetworkAnalyst. Results A total of 669 and 249 DEGs were identified at the early (5 h) and late stages (24 h), respectively. Of these, 152 were present at both stages and were designated as common DEGs. The top enriched GO terms were “regulation of autophagy” at the early stage, and “sterol biosynthetic processes” at the late stage. The top KEGG terms were “pyrimidine metabolism” and “synaptic vesicle cycle” at the early and late stages, respectively. Seven common DEGs [DEAD-box helicase 17 (DDX17), exocyst complex component 7 (EXOC7), CASK interacting protein 1 (CASKIN1), ribonucleoprotein PTB-binding 1 (RAVER1), late cornified envelope 1D (LCE1D), LCE1C, and polycystin 1, transient receptor potential channel interacting (PKD1)] and three common DEGs [5′-3′ exoribonuclease 2 (XRN2), T-complex protein 1 (TCP1), and syntaxin 3 (STX3)] were shown to be upregulated and downregulated hub genes, respectively. The GO terms of the common hub genes were “skin development” and “mRNA processing.” After constructing the regulatory network, hsa-mir-92a-3p, hsa-mir-193b-3p, RNA polymerase II subunit A (POLR2A), SMAD family member 5 (SMAD5), and MYC-associated zinc finger protein (MAZ) were predicted as potential targets in both stages. Conclusion At the early stage, there were clear changes in gene expression related to DNA and chromatin alterations; at late stages, gene expression associated with cholesterol metabolism was suppressed. Common DEGs related to skin development, transcriptional regulation, and cytoskeleton rearrangement identified in both stages were found to be potential targets for promoting HDF growth and alignment under mechanical stretch.
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Novel Roles of SH2 and SH3 Domains in Lipid Binding. Cells 2021; 10:cells10051191. [PMID: 34068055 PMCID: PMC8152464 DOI: 10.3390/cells10051191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
Signal transduction, the ability of cells to perceive information from the surroundings and alter behavior in response, is an essential property of life. Studies on tyrosine kinase action fundamentally changed our concept of cellular regulation. The induced assembly of subcellular hubs via the recognition of local protein or lipid modifications by modular protein interactions is now a central paradigm in signaling. Such molecular interactions are mediated by specific protein interaction domains. The first such domain identified was the SH2 domain, which was postulated to be a reader capable of finding and binding protein partners displaying phosphorylated tyrosine side chains. The SH3 domain was found to be involved in the formation of stable protein sub-complexes by constitutively attaching to proline-rich surfaces on its binding partners. The SH2 and SH3 domains have thus served as the prototypes for a diverse collection of interaction domains that recognize not only proteins but also lipids, nucleic acids, and small molecules. It has also been found that particular SH2 and SH3 domains themselves might also bind to and rely on lipids to modulate complex assembly. Some lipid-binding properties of SH2 and SH3 domains are reviewed here.
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Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding. Cells 2021; 10:cells10010173. [PMID: 33467043 PMCID: PMC7830187 DOI: 10.3390/cells10010173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Abstract
SH3 domains constitute an important class of protein modules involved in a variety of cellular functions. They participate in protein-protein interactions via their canonical ligand binding interfaces composed of several evolutionarily conserved aromatic residues forming binding grooves for typical (PxxP) and atypical (PxxxPR, RxxK, RKxxY) binding motifs. The calcium/calmodulin-dependent serine protein kinase (CASK)-interacting protein 1, or Caskin1, a multidomain scaffold protein regulating the cortical actin filaments, is enriched in neural synapses in mammals. Based on its known interaction partners and knock-out animal studies, Caskin1 may play various roles in neural function and it is thought to participate in several pathological processes of the brain. Caskin1 has a single, atypical SH3 domain in which key aromatic residues are missing from the canonical binding groove. No protein interacting partner for this SH3 domain has been identified yet. Nevertheless, we have recently demonstrated the specific binding of this SH3 domain to the signaling lipid mediator lysophospatidic acid (LPA) in vitro. Here we report the solution NMR structure of the human Caskin1 SH3 domain and analyze its structural features in comparison with other SH3 domains exemplifying different strategies in target selectivity. The key differences revealed by our structural study show that the canonical binding groove found in typical SH3 domains accommodating proline-rich motifs is missing in Caskin1 SH3, most likely excluding a bona fide protein target for the domain. The LPA binding site is distinct from the altered protein binding groove. We conclude that the SH3 domain of Caskin1 might mediate the association of Caskin1 with membrane surfaces with locally elevated LPA content.
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Torres M, Rosselló CA, Fernández-García P, Lladó V, Kakhlon O, Escribá PV. The Implications for Cells of the Lipid Switches Driven by Protein-Membrane Interactions and the Development of Membrane Lipid Therapy. Int J Mol Sci 2020; 21:ijms21072322. [PMID: 32230887 PMCID: PMC7177374 DOI: 10.3390/ijms21072322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
The cell membrane contains a variety of receptors that interact with signaling molecules. However, agonist-receptor interactions not always activate a signaling cascade. Amphitropic membrane proteins are required for signal propagation upon ligand-induced receptor activation. These proteins localize to the plasma membrane or internal compartments; however, they are only activated by ligand-receptor complexes when both come into physical contact in membranes. These interactions enable signal propagation. Thus, signals may not propagate into the cell if peripheral proteins do not co-localize with receptors even in the presence of messengers. As the translocation of an amphitropic protein greatly depends on the membrane's lipid composition, regulation of the lipid bilayer emerges as a novel therapeutic strategy. Some of the signals controlled by proteins non-permanently bound to membranes produce dramatic changes in the cell's physiology. Indeed, changes in membrane lipids induce translocation of dozens of peripheral signaling proteins from or to the plasma membrane, which controls how cells behave. We called these changes "lipid switches", as they alter the cell's status (e.g., proliferation, differentiation, death, etc.) in response to the modulation of membrane lipids. Indeed, this discovery enables therapeutic interventions that modify the bilayer's lipids, an approach known as membrane-lipid therapy (MLT) or melitherapy.
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Affiliation(s)
- Manuel Torres
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Ctra. de Valldemossa km 7.5, E-07122 Palma, Spain; (M.T.); (C.A.R.); (P.F.-G.); (V.L.)
- Department of R&D, Laminar Pharmaceuticals SL. ParcBit, Ed. Naorte B, E-07121 Palma, Spain
| | - Catalina Ana Rosselló
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Ctra. de Valldemossa km 7.5, E-07122 Palma, Spain; (M.T.); (C.A.R.); (P.F.-G.); (V.L.)
- Department of R&D, Laminar Pharmaceuticals SL. ParcBit, Ed. Naorte B, E-07121 Palma, Spain
| | - Paula Fernández-García
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Ctra. de Valldemossa km 7.5, E-07122 Palma, Spain; (M.T.); (C.A.R.); (P.F.-G.); (V.L.)
- Department of R&D, Laminar Pharmaceuticals SL. ParcBit, Ed. Naorte B, E-07121 Palma, Spain
| | - Victoria Lladó
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Ctra. de Valldemossa km 7.5, E-07122 Palma, Spain; (M.T.); (C.A.R.); (P.F.-G.); (V.L.)
- Department of R&D, Laminar Pharmaceuticals SL. ParcBit, Ed. Naorte B, E-07121 Palma, Spain
| | - Or Kakhlon
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, 91120 Jerusalem, Israel;
| | - Pablo Vicente Escribá
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Ctra. de Valldemossa km 7.5, E-07122 Palma, Spain; (M.T.); (C.A.R.); (P.F.-G.); (V.L.)
- Correspondence:
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Bencsik N, Pusztai S, Borbély S, Fekete A, Dülk M, Kis V, Pesti S, Vas V, Szűcs A, Buday L, Schlett K. Dendritic spine morphology and memory formation depend on postsynaptic Caskin proteins. Sci Rep 2019; 9:16843. [PMID: 31727973 PMCID: PMC6856520 DOI: 10.1038/s41598-019-53317-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022] Open
Abstract
CASK-interactive proteins, Caskin1 and Caskin2, are multidomain neuronal scaffold proteins. Recent data from Caskin1 knockout animals indicated only a mild role of Caskin1 in anxiety and pain perception. In this work, we show that deletion of both Caskins leads to severe deficits in novelty recognition and spatial memory. Ultrastructural analyses revealed a reduction in synaptic profiles and dendritic spine areas of CA1 hippocampal pyramidal neurons of double knockout mice. Loss of Caskin proteins impaired LTP induction in hippocampal slices, while miniature EPSCs in dissociated hippocampal cultures appeared to be unaffected. In cultured Caskin knockout hippocampal neurons, overexpressed Caskin1 was enriched in dendritic spine heads and increased the amount of mushroom-shaped dendritic spines. Chemically induced LTP (cLTP) mediated enlargement of spine heads was augmented in the knockout mice and was not influenced by Caskin1. Immunocytochemistry and immunoprecipitation confirmed that Shank2, a master scaffold of the postsynaptic density, and Caskin1 co-localized within the same complex. Phosphorylation of AMPA receptors was specifically altered by Caskin deficiency and was not elevated by cLTP treatment further. Taken together, our results prove a previously unnoticed postsynaptic role of Caskin scaffold proteins and indicate that Caskins influence learning abilities via regulating spine morphology and AMPA receptor localisation.
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Affiliation(s)
- Norbert Bencsik
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - Szilvia Pusztai
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - Sándor Borbély
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary.,Institute of Cognitive Neuroscience and Psychology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anna Fekete
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Metta Dülk
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Viktor Kis
- Department Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Szabolcs Pesti
- Department Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Virág Vas
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Attila Szűcs
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Department Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Katalin Schlett
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary.
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Kursula P. Shanks — multidomain molecular scaffolds of the postsynaptic density. Curr Opin Struct Biol 2019; 54:122-128. [DOI: 10.1016/j.sbi.2019.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/24/2018] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
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Katano T, Takao K, Abe M, Yamazaki M, Watanabe M, Miyakawa T, Sakimura K, Ito S. Distribution of Caskin1 protein and phenotypic characterization of its knockout mice using a comprehensive behavioral test battery. Mol Brain 2018; 11:63. [PMID: 30359304 PMCID: PMC6202847 DOI: 10.1186/s13041-018-0407-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/14/2018] [Indexed: 01/17/2023] Open
Abstract
Calcium/calmodulin-dependent serine protein kinase (CASK)-interacting protein 1 (Caskin1) is a direct binding partner of the synaptic adaptor protein CASK. Because Caskin1 forms homo-multimers and binds not only CASK but also other neuronal proteins in vitro, it is anticipated to have neural functions; but its exact role in mammals remains unclear. Previously, we showed that the concentration of Caskin1 in the spinal dorsal horn increases under chronic pain. To characterize this protein, we generated Caskin1-knockout (Caskin1-KO) mice and specific anti-Caskin1 antibodies. Biochemical and immunohistochemical analyses demonstrated that Caskin1 was broadly distributed in the whole brain and spinal cord, and that it primarily localized at synapses. To elucidate the neural function of Caskin1 in vivo, we subjected Caskin1-KO mice to comprehensive behavioral analysis. The mutant mice exhibited differences in gait, enhanced nociception, and anxiety-like behavior relative to their wild-type littermates. In addition, the knockouts exhibited strong freezing responses, with or without a cue tone, in contextual and cued-fear conditioning tests as well as low memory retention in the Barnes Maze test. Taken together, these results suggest that Caskin1 contributes to a wide spectrum of behavioral phenotypes, including gait, nociception, memory, and stress response, in broad regions of the central nervous system.
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Affiliation(s)
- Tayo Katano
- Department of Medical Chemistry, Kansai Medical University, Hirakata, 573-1010 Japan
| | - Keizo Takao
- Section of Behavior Patterns, National Institute of Physiological Sciences NINS, Okazaki, Aichi 444-8585 Japan
- Division of Experimental Animal Resource and Development, Life Science Research Center, University of Toyama, Toyama, 930-0194 Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585 Japan
| | - Maya Yamazaki
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585 Japan
- Department of Neurology, University of California, San Francisco, 94158 USA
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University School of Medicine, Sapporo, 060-8638 Japan
| | - Tsuyoshi Miyakawa
- Section of Behavior Patterns, National Institute of Physiological Sciences NINS, Okazaki, Aichi 444-8585 Japan
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192 Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585 Japan
| | - Seiji Ito
- Department of Medical Chemistry, Kansai Medical University, Hirakata, 573-1010 Japan
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The lipid mediator lysophosphatidic acid induces folding of disordered peptides with basic amphipathic character into rare conformations. Sci Rep 2018; 8:14499. [PMID: 30266943 PMCID: PMC6162328 DOI: 10.1038/s41598-018-32786-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
Membrane-active, basic amphipathic peptides represent a class of biomolecules with diverse functions. Sequentially close protein segments also show similar behaviour in several ways. Here we investigated the effect of the lipid mediator lysophosphatidic acid (LPA) on the conformation of structurally disordered peptides including extracellular antimicrobial peptides (AMPs), and calmodulin-binding motifs derived from cytosolic and membrane target proteins. The interaction with associated LPA resulted in gain of ordered secondary structure elements, which for most cases were previously uncharacteristic of the particular peptide. Results revealed mechanism of the LPA-peptide interactions with regulation of the lipid on peptide conformation and oligomerization in a concentration-dependent manner involving (1) relocation of tryptophan residues into the lipid cluster, (2) multiple contacts between the binding partners dictated by complex driving forces, (3) multiple peptide binding to LPA associates with an affinity in the low micromolar range, and (4) selectivity for LPA compared with structurally related lipids. In line with recent findings showing endogenous molecules inducing structural changes in AMPs, we propose that accumulation of LPA in signalling or pathological processes might modulate host-defense activity or trigger certain processes by direct interaction with cationic amphipathic peptide sequences.
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