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Ren Y, Liao H, Yan J, Lu H, Mao X, Wang C, Li YF, Liu Y, Chen C, Chen L, Wang X, Zhou KY, Liu HM, Liu Y, Hua YM, Yu L, Xue Z. Capture of RNA-binding proteins across mouse tissues using HARD-AP. Nat Commun 2024; 15:8421. [PMID: 39341811 PMCID: PMC11438895 DOI: 10.1038/s41467-024-52765-w] [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: 11/26/2023] [Accepted: 09/20/2024] [Indexed: 10/01/2024] Open
Abstract
RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly associated RNA regulatory complexes from cultured cells and fresh tissues. We successfully use HARD-AP to establish a comprehensive atlas of RBPs across mouse primary organs. We then systematically map RNA-binding sites of these RBPs using machine learning-based modeling. Notably, the modeling reveals that the LIM domain as an RNA-binding domain in many RBPs. We validate the LIM-domain-only protein Csrp1 as a tissue-dependent RNA binding protein. Taken together, HARD-AP is a powerful approach that can be used to identify RBPomes from any type of sample, allowing comprehensive and physiologically relevant networks of RNA-protein interactions.
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Affiliation(s)
- Yijia Ren
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hongyu Liao
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jun Yan
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Hongyu Lu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaowei Mao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
- Shimmer Center, Tianfu Jiangxi Laboratory, Chengdu, Sichuan, 641419, China
| | - Chuan Wang
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi-Fei Li
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chong Chen
- Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiangfeng Wang
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Kai-Yu Zhou
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Han-Min Liu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yi-Min Hua
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Lin Yu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Zhihong Xue
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610041, China.
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Gomila Pelegri N, Stanczak AM, Bottomley AL, Milthorpe BK, Gorrie CA, Padula MP, Santos J. Adipose-Derived Stem Cells Spontaneously Express Neural Markers When Grown in a PEG-Based 3D Matrix. Int J Mol Sci 2023; 24:12139. [PMID: 37569515 PMCID: PMC10418654 DOI: 10.3390/ijms241512139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Neurological diseases are among the leading causes of disability and death worldwide and remain difficult to treat. Tissue engineering offers avenues to test potential treatments; however, the development of biologically accurate models of brain tissues remains challenging. Given their neurogenic potential and availability, adipose-derived stem cells (ADSCs) are of interest for creating neural models. While progress has been made in differentiating ADSCs into neural cells, their differentiation in 3D environments, which are more representative of the in vivo physiological conditions of the nervous system, is crucial. This can be achieved by modulating the 3D matrix composition and stiffness. Human ADSCs were cultured for 14 days in a 1.1 kPa polyethylene glycol-based 3D hydrogel matrix to assess effects on cell morphology, cell viability, proteome changes and spontaneous neural differentiation. Results showed that cells continued to proliferate over the 14-day period and presented a different morphology to 2D cultures, with the cells elongating and aligning with one another. The proteome analysis revealed 439 proteins changed in abundance by >1.5 fold. Cyclic nucleotide 3'-phosphodiesterase (CNPase) markers were identified using immunocytochemistry and confirmed with proteomics. Findings indicate that ADSCs spontaneously increase neural marker expression when grown in an environment with similar mechanical properties to the central nervous system.
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Affiliation(s)
- Neus Gomila Pelegri
- Advanced Tissue Engineering and Stem Cell Biology Group, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.G.P.); (B.K.M.)
- Neural Injury Research Unit, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Aleksandra M. Stanczak
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (A.M.S.); (M.P.P.)
| | - Amy L. Bottomley
- Microbial Imaging Facility, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Bruce K. Milthorpe
- Advanced Tissue Engineering and Stem Cell Biology Group, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.G.P.); (B.K.M.)
| | - Catherine A. Gorrie
- Neural Injury Research Unit, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Matthew P. Padula
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (A.M.S.); (M.P.P.)
| | - Jerran Santos
- Advanced Tissue Engineering and Stem Cell Biology Group, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.G.P.); (B.K.M.)
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3
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Mgrditchian T, Brown-Clay J, Hoffmann C, Müller T, Filali L, Ockfen E, Mao X, Moreau F, Casellas CP, Kaoma T, Mittelbronn M, Thomas C. Actin cytoskeleton depolymerization increases matrix metalloproteinase gene expression in breast cancer cells by promoting translocation of cysteine-rich protein 2 to the nucleus. Front Cell Dev Biol 2023; 11:1100938. [PMID: 37266453 PMCID: PMC10229898 DOI: 10.3389/fcell.2023.1100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/21/2023] [Indexed: 06/03/2023] Open
Abstract
The actin cytoskeleton plays a critical role in cancer cell invasion and metastasis; however, the coordination of its multiple functions remains unclear. Actin dynamics in the cytoplasm control the formation of invadopodia, which are membrane protrusions that facilitate cancer cell invasion by focusing the secretion of extracellular matrix-degrading enzymes, including matrix metalloproteinases (MMPs). In this study, we investigated the nuclear role of cysteine-rich protein 2 (CRP2), a two LIM domain-containing F-actin-binding protein that we previously identified as a cytoskeletal component of invadopodia, in breast cancer cells. We found that F-actin depolymerization stimulates the translocation of CRP2 into the nucleus, resulting in an increase in the transcript levels of pro-invasive and pro-metastatic genes, including several members of the MMP gene family. We demonstrate that in the nucleus, CRP2 interacts with the transcription factor serum response factor (SRF), which is crucial for the expression of MMP-9 and MMP-13. Our data suggest that CRP2 and SRF cooperate to modulate of MMP expression levels. Furthermore, Kaplan-Meier analysis revealed a significant association between high-level expression of SRF and shorter overall survival and distant metastasis-free survival in breast cancer patients with a high CRP2 expression profile. Our findings suggest a model in which CRP2 mediates the coordination of cytoplasmic and nuclear processes driven by actin dynamics, ultimately resulting in the induction of invasive and metastatic behavior in breast cancer cells.
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Affiliation(s)
- Takouhie Mgrditchian
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Joshua Brown-Clay
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Céline Hoffmann
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tanja Müller
- Department of Cancer Research, Luxembourg Centre of Neuropathology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Liza Filali
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Elena Ockfen
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Xianqing Mao
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Flora Moreau
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Carla Pou Casellas
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Cancer Research, Luxembourg Centre of Neuropathology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-surAlzette, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-surAlzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-surAlzette, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
| | - Clément Thomas
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
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4
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Ang MJ, Kang S, Moon C. Melatonin alters neuronal architecture and increases cysteine-rich protein 1 signaling in the male mouse hippocampus. J Neurosci Res 2020; 98:2333-2348. [PMID: 32754943 DOI: 10.1002/jnr.24708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 01/10/2023]
Abstract
Neuronal plasticity describes changes in structure, function, and connections of neurons. The hippocampus, in particular, has been shown to exhibit considerable plasticity regarding both physiological and morphological functions. Melatonin, a hormone released by the pineal gland, promotes cell survival and dendrite maturation of neurons in the newborn brain and protects against neurological disorders. In this study, we investigated the effect of exogenous melatonin on neuronal architecture and its possible mechanism in the hippocampus of adult male C57BL/6 mice. Melatonin treatment significantly increased the total length and complexity of dendrites in the apical and basal cornu ammonis (CA) 1 and in the dentate gyrus in mouse hippocampi. Spine density in CA1 apical dendrites was increased, but no significant differences in other subregions were observed. In primary cultured hippocampal neurons, the length and arborization of neurites were significantly augmented by melatonin treatment. Additionally, western blot and immunohistochemical analyses in both in vivo and in vitro systems revealed significant increases in the level of cysteine-rich protein 1 (crp-1) protein, which is known to be involved in dendritic branching in mouse hippocampal neurons after melatonin treatment. Our results suggest that exogenous melatonin leads to significant alterations of neuronal micromorphometry in the adult hippocampus, possibly via crp-1 signaling.
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Affiliation(s)
- Mary Jasmin Ang
- Department of Veterinary Anatomy and Animal Behavior, College of Veterinary Medicine and BK21 Plus Project Team, Chonnam National University, Gwangju, South Korea
| | - Sohi Kang
- Department of Veterinary Anatomy and Animal Behavior, College of Veterinary Medicine and BK21 Plus Project Team, Chonnam National University, Gwangju, South Korea
| | - Changjong Moon
- Department of Veterinary Anatomy and Animal Behavior, College of Veterinary Medicine and BK21 Plus Project Team, Chonnam National University, Gwangju, South Korea
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5
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Dong Z, Haines S, Coates D. Proteomic Profiling of Stem Cell Tissues during Regeneration of Deer Antler: A Model of Mammalian Organ Regeneration. J Proteome Res 2020; 19:1760-1775. [DOI: 10.1021/acs.jproteome.0c00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Stephen Haines
- Proteins & Metabolites, AgResearch Lincoln Research Centre, Lincoln, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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6
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Levin E, Leibinger M, Gobrecht P, Hilla A, Andreadaki A, Fischer D. Muscle LIM Protein Is Expressed in the Injured Adult CNS and Promotes Axon Regeneration. Cell Rep 2020; 26:1021-1032.e6. [PMID: 30673598 DOI: 10.1016/j.celrep.2018.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 09/05/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023] Open
Abstract
Muscle LIM protein (MLP) has long been regarded as a muscle-specific protein. Here, we report that MLP expression is induced in adult rat retinal ganglion cells (RGCs) upon axotomy, and its expression is correlated with their ability to regenerate injured axons. Specific knockdown of MLP in RGCs compromises axon regeneration, while overexpression in vivo facilitates optic nerve regeneration and regrowth of sensory neurons without affecting neuronal survival. MLP accumulates in the cell body, the nucleus, and in axonal growth cones, which are significantly enlarged by its overexpression. Only the MLP fraction in growth cones is relevant for promoting axon extension. Additional data suggest that MLP acts as an actin cross-linker, thereby facilitating filopodia formation and increasing growth cone motility. Thus, MLP-mediated effects on actin could become a therapeutic strategy for promoting nerve repair.
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Affiliation(s)
- Evgeny Levin
- Division of Experimental Neurology, Medical Faculty, Heinrich Heine University, Merowingerplatz 1a, 40225 Düsseldorf, Germany
| | - Marco Leibinger
- Department of Cell Physiology, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany; Division of Experimental Neurology, Medical Faculty, Heinrich Heine University, Merowingerplatz 1a, 40225 Düsseldorf, Germany
| | - Philipp Gobrecht
- Department of Cell Physiology, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany; Division of Experimental Neurology, Medical Faculty, Heinrich Heine University, Merowingerplatz 1a, 40225 Düsseldorf, Germany
| | - Alexander Hilla
- Department of Cell Physiology, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany; Division of Experimental Neurology, Medical Faculty, Heinrich Heine University, Merowingerplatz 1a, 40225 Düsseldorf, Germany
| | - Anastasia Andreadaki
- Department of Cell Physiology, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany; Division of Experimental Neurology, Medical Faculty, Heinrich Heine University, Merowingerplatz 1a, 40225 Düsseldorf, Germany
| | - Dietmar Fischer
- Department of Cell Physiology, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany; Division of Experimental Neurology, Medical Faculty, Heinrich Heine University, Merowingerplatz 1a, 40225 Düsseldorf, Germany.
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7
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Impairments in dendrite morphogenesis as etiology for neurodevelopmental disorders and implications for therapeutic treatments. Neurosci Biobehav Rev 2016; 68:946-978. [PMID: 27143622 DOI: 10.1016/j.neubiorev.2016.04.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/13/2016] [Accepted: 04/13/2016] [Indexed: 02/08/2023]
Abstract
Dendrite morphology is pivotal for neural circuitry functioning. While the causative relationship between small-scale dendrite morphological abnormalities (shape, density of dendritic spines) and neurodevelopmental disorders is well established, such relationship remains elusive for larger-scale dendrite morphological impairments (size, shape, branching pattern of dendritic trees). Here, we summarize published data on dendrite morphological irregularities in human patients and animal models for neurodevelopmental disorders, with focus on autism and schizophrenia. We next discuss high-risk genes for these disorders and their role in dendrite morphogenesis. We finally overview recent developments in therapeutic attempts and we discuss how they relate to dendrite morphology. We find that both autism and schizophrenia are accompanied by dendritic arbor morphological irregularities, and that majority of their high-risk genes regulate dendrite morphogenesis. Thus, we present a compelling argument that, along with smaller-scale morphological impairments in dendrites (spines and synapse), irregularities in larger-scale dendrite morphology (arbor shape, size) may be an important part of neurodevelopmental disorders' etiology. We suggest that this should not be ignored when developing future therapeutic treatments.
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8
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Menon S, Gupton SL. Building Blocks of Functioning Brain: Cytoskeletal Dynamics in Neuronal Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 322:183-245. [PMID: 26940519 PMCID: PMC4809367 DOI: 10.1016/bs.ircmb.2015.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neural connectivity requires proper polarization of neurons, guidance to appropriate target locations, and establishment of synaptic connections. From when neurons are born to when they finally reach their synaptic partners, neurons undergo constant rearrangment of the cytoskeleton to achieve appropriate shape and polarity. Of particular importance to neuronal guidance to target locations is the growth cone at the tip of the axon. Growth-cone steering is also dictated by the underlying cytoskeleton. All these changes require spatiotemporal control of the cytoskeletal machinery. This review summarizes the proteins that are involved in modulating the actin and microtubule cytoskeleton during the various stages of neuronal development.
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Affiliation(s)
- Shalini Menon
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Stephanie L Gupton
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, United States of America; Neuroscience Center and Curriculum in Neurobiology, University of North Carolina, Chapel Hill, NC, United States of America; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States of America.
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9
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Copf T. Importance of gene dosage in controlling dendritic arbor formation during development. Eur J Neurosci 2015; 42:2234-49. [PMID: 26108333 DOI: 10.1111/ejn.13002] [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: 02/11/2015] [Revised: 06/05/2015] [Accepted: 06/18/2015] [Indexed: 12/11/2022]
Abstract
Proper dendrite morphology is crucial for normal nervous system functioning. While a number of genes have been implicated in dendrite morphogenesis in both invertebrates and mammals, it remains unclear how developing dendrites respond to changes in gene dosage and what type of patterns their responses may follow. To understand this, I review here evidence from the recent literature, focusing on the genetic studies performed in the Drosophila larval dendritic arborization class IV neuron, an excellent cell type to understand dendrite morphogenesis. I summarize how class IV arbors change morphology in response to developmental fluctuations in the expression levels of 47 genes, studied by means of genetic manipulations such as loss-of-function and gain-of-function, and for which sufficient information is available. I find that arbors can respond to changing gene dosage in several distinct ways, each characterized by a singular dose-response curve. Interestingly, in 72% of cases arbors are sensitive, and thus adjust their morphology, in response to both decreases and increases in the expression of a given gene, indicating that dendrite morphogenesis is a process particularly sensitive to gene dosage. By summarizing the parallels between Drosophila and mammals, I show that many Drosophila dendrite morphogenesis genes have orthologs in mammals, and that some of these are associated with mammalian dendrite outgrowth and human neurodevelopmental disorders. One notable disease-related molecule is kinase Dyrk1A, thought to be a causative factor in Down syndrome. Both increases and decreases in Dyrk1A gene dosage lead to impaired dendrite morphogenesis, which may contribute to Down syndrome pathoetiology.
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Affiliation(s)
- Tijana Copf
- Institute of Molecular Biology and Biotechnology, Nikolaou Plastira 100, PO Box 1385, Heraklion, GR-70013, Crete, Greece
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10
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Trip6 promotes dendritic morphogenesis through dephosphorylated GRIP1-dependent myosin VI and F-actin organization. J Neurosci 2015; 35:2559-71. [PMID: 25673849 DOI: 10.1523/jneurosci.2125-14.2015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Thyroid receptor-interacting protein 6 (Trip6), a multifunctional protein belonging to the zyxin family of LIM proteins, is involved in various physiological and pathological processes, including cell migration and tumorigenesis. However, the role of Trip6 in neurons remains unknown. Here, we show that Trip6 is expressed in mouse hippocampal neurons and promotes dendritic morphogenesis. Through interaction with the glutamate receptor-interacting protein 1 (GRIP1) and myosin VI, Trip6 is crucial for the total dendritic length and the number of primary dendrites in cultured hippocampal neurons. Trip6 depletion reduces F-actin content and impairs dendritic morphology, and this phenocopies GRIP1 or myosin VI knockdown. Furthermore, phosphorylation of GRIP1(956T) by AKT1 inhibits the interaction between GRIP1 and myosin VI, but facilitates GRIP1 binding to 14-3-3 protein, which is required for regulating F-actin organization and dendritic morphogenesis. Thus, the Trip6-GRIP1-myosin VI interaction and its regulation on F-actin network play a significant role in dendritic morphogenesis.
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11
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Human muscle LIM protein dimerizes along the actin cytoskeleton and cross-links actin filaments. Mol Cell Biol 2014; 34:3053-65. [PMID: 24934443 DOI: 10.1128/mcb.00651-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The muscle LIM protein (MLP) is a nucleocytoplasmic shuttling protein playing important roles in the regulation of myocyte remodeling and adaptation to hypertrophic stimuli. Missense mutations in human MLP or its ablation in transgenic mice promotes cardiomyopathy and heart failure. The exact function(s) of MLP in the cytoplasmic compartment and the underlying molecular mechanisms remain largely unknown. Here, we provide evidence that MLP autonomously binds to, stabilizes, and bundles actin filaments (AFs) independently of calcium and pH. Using total internal reflection fluorescence microscopy, we have shown how MLP cross-links actin filaments into both unipolar and mixed-polarity bundles. Quantitative analysis of the actin cytoskeleton configuration confirmed that MLP substantially promotes actin bundling in live myoblasts. In addition, bimolecular fluorescence complementation (BiFC) assays revealed MLP self-association. Remarkably, BiFC complexes mostly localize along actin filament-rich structures, such as stress fibers and sarcomeres, supporting a functional link between MLP self-association and actin cross-linking. Finally, we have demonstrated that MLP self-associates through its N-terminal LIM domain, whereas it binds to AFs through its C-terminal LIM domain. Together our data support that MLP contributes to the maintenance of cardiomyocyte cytoarchitecture by a mechanism involving its self-association and actin filament cross-linking.
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12
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Hoffmann C, Moes D, Dieterle M, Neumann K, Moreau F, Tavares Furtado A, Dumas D, Steinmetz A, Thomas C. Live cell imaging reveals actin-cytoskeleton-induced self-association of the actin-bundling protein WLIM1. J Cell Sci 2014; 127:583-98. [PMID: 24284066 DOI: 10.1242/jcs.134536] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crosslinking of actin filaments into bundles is essential for the assembly and stabilization of specific cytoskeletal structures. However, relatively little is known about the molecular mechanisms underlying actin bundle formation. The two LIM-domain-containing proteins define a novel and evolutionarily conserved family of actin-bundling proteins whose actin-binding and -crosslinking activities primarily rely on their LIM domains. Using TIRF microscopy, we describe real-time formation of actin bundles induced by tobacco NtWLIM1 in vitro. We show that NtWLIM1 binds to single filaments and subsequently promotes their interaction and zippering into tight bundles of mixed polarity. NtWLIM1-induced bundles grew by both elongation of internal filaments and addition of preformed fragments at their extremities. Importantly, these data are highly consistent with the modes of bundle formation and growth observed in transgenic Arabidopsis plants expressing a GFP-fused Arabidopsis AtWLIM1 protein. Using two complementary live cell imaging approaches, a close relationship between NtWLIM1 subcellular localization and self-association was established. Indeed, both BiFC and FLIM-FRET data revealed that, although unstable NtWLIM1 complexes can sporadically form in the cytosol, stable complexes concentrate along the actin cytoskeleton. Remarkably, disruption of the actin cytoskeleton significantly impaired self-association of NtWLIM1. In addition, biochemical analyses support the idea that F-actin facilitates the switch of purified recombinant NtWLIM1 from a monomeric to a di- or oligomeric state. On the basis of our data, we propose a model in which actin binding promotes the formation and stabilization of NtWLIM1 complexes, which in turn might drive the crosslinking of actin filaments.
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Affiliation(s)
- Céline Hoffmann
- Centre de Recherche Public-Santé, 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
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13
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Axonal regeneration after spinal cord injury in zebrafish and mammals: differences, similarities, translation. Neurosci Bull 2013; 29:402-10. [PMID: 23893428 DOI: 10.1007/s12264-013-1361-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/09/2013] [Indexed: 10/26/2022] Open
Abstract
Spinal cord injury (SCI) in mammals results in functional deficits that are mostly permanent due in part to the inability of severed axons to regenerate. Several types of growth-inhibitory molecules expressed at the injury site contribute to this regeneration failure. The responses of axons to these inhibitors vary greatly within and between organisms, reflecting axons' characteristic intrinsic propensity for regeneration. In the zebrafish (Danio rerio) many but not all axons exhibit successful regeneration after SCI. This review presents and compares the intrinsic and extrinsic determinants of axonal regeneration in the injured spinal cord in mammals and zebrafish. A better understanding of the molecules and molecular pathways underlying the remarkable individualism among neurons in mature zebrafish may support the development of therapies for SCI and their translation to the clinic.
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Gallo G. Mechanisms underlying the initiation and dynamics of neuronal filopodia: from neurite formation to synaptogenesis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 301:95-156. [PMID: 23317818 DOI: 10.1016/b978-0-12-407704-1.00003-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Filopodia are finger-like cellular protrusions found throughout the metazoan kingdom and perform fundamental cellular functions during development and cell migration. Neurons exhibit a wide variety of extremely complex morphologies. In the nervous system, filopodia underlie many major morphogenetic events. Filopodia have roles spanning the initiation and guidance of neuronal processes, axons and dendrites to the formation of synaptic connections. This chapter addresses the mechanisms of the formation and dynamics of neuronal filopodia. Some of the major lessons learned from the study of neuronal filopodia are (1) there are multiple mechanisms that can regulate filopodia in a context-dependent manner, (2) that filopodia are specialized subcellular domains, (3) that filopodia exhibit dynamic membrane recycling which also controls aspects of filopodial dynamics, (4) that neuronal filopodia contain machinery for the orchestration of the actin and microtubule cytoskeleton, and (5) localized protein synthesis contributes to neuronal filopodial dynamics.
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Affiliation(s)
- Gianluca Gallo
- Shriners Hospitals Pediatric Research Center, Center for Neural Repair and Rehabilitation, Department of Anatomy and Cell Biology, Temple University, Philadelphia, PA, USA.
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15
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Arikkath J. Molecular mechanisms of dendrite morphogenesis. Front Cell Neurosci 2012; 6:61. [PMID: 23293584 PMCID: PMC3531598 DOI: 10.3389/fncel.2012.00061] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/08/2012] [Indexed: 01/28/2023] Open
Abstract
Dendrites are key integrators of synaptic information in neurons and play vital roles in neuronal plasticity. Hence, it is necessary that dendrite arborization is precisely controlled and coordinated with synaptic activity to ensure appropriate functional neural network integrity. In the past several years, it has become increasingly clear that several cell intrinsic and extrinsic mechanisms contribute to dendritic arborization. In this review, we will discuss some of the molecular mechanisms that regulate dendrite morphogenesis, particularly in cortical and hippocampal pyramidal neurons and some of the implications of aberrant dendritic morphology for human disease. Finally, we will discuss the current challenges and future directions in the field.
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Affiliation(s)
- Jyothi Arikkath
- Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center Omaha, NE, USA
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Ma L, Yu YM, Guo Y, Hart RP, Schachner M. Cysteine- and glycine-rich protein 1a is involved in spinal cord regeneration in adult zebrafish. Eur J Neurosci 2012; 35:353-65. [PMID: 22288476 DOI: 10.1111/j.1460-9568.2011.07958.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to mammals, adult zebrafish have the ability to regrow descending axons and gain locomotor recovery after spinal cord injury (SCI). In zebrafish, a decisive factor for successful spinal cord regeneration is the inherent ability of some neurons to regrow their axons via (re)expressing growth-associated genes during the regeneration period. The nucleus of the medial longitudinal fascicle (NMLF) is one of the nuclei capable of regenerative response after SCI. Using microarray analysis with laser capture microdissected NMLF, we show that cysteine- and glycine-rich protein (CRP)1a (encoded by the csrp1a gene in zebrafish), the function of which is largely unknown in the nervous system, was upregulated after SCI. In situ hybridization confirmed the upregulation of csrp1a expression in neurons during the axon growth phase after SCI, not only in the NMLF, but also in other nuclei capable of regeneration, such as the intermediate reticular formation and superior reticular formation. The upregulation of csrp1a expression in regenerating nuclei started at 3 days after SCI and continued to 21 days post-injury, the longest time point studied. In vivo knockdown of CRP1a expression using two different antisense morpholino oligonucleotides impaired axon regeneration and locomotor recovery when compared with a control morpholino, demonstrating that CRP1a upregulation is an important part of the innate regeneration capability in injured neurons of adult zebrafish. This study is the first to demonstrate the requirement of CRP1a for zebrafish spinal cord regeneration.
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Affiliation(s)
- Liping Ma
- W. M. Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA
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