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Ngadni MA, Chong SL, Kamarudin MNA, Hazni H, Litaudon M, Supratman U, Awang K. Erythrocarpines IN, new limonoids from the barks of Chisocheton erythrocarpus and their neuroprotective effects against hydrogen peroxide in NG108-15 cells. Fitoterapia 2024; 173:105765. [PMID: 38042506 DOI: 10.1016/j.fitote.2023.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
A phytochemical study on the bark of Chisocheton erythrocarpus Hiern (Meliaceae) has led to the isolation of six new phragmalin-type limonoids named erythrocarpines I - N (1-6) along with one known limonoid, erythrocarpine F (7). Their structures were fully characterized by spectroscopic methods. The pre-treatment of NG108-15 cells with 1-5, 7 (2 h) demonstrated low to good protective effects against H2O2 exposure; 1 (83.77% ± 1.84 at 12.5 μM), 2 (69.07 ± 2.01 at 12.5 μM), 3 (80.38 ± 2.1 at 12.5 μM), 4 (62.33 ± 1.95 at 25 μM),5 (58.67 ± 1.85 at 50 μM) and 7 (66.07 ± 2.03 at 12.5 μM). Interestingly, 1 and 3 demonstrated comparable protective effects to positive control epigallocatechin gallate (EGCG) with similar cell viability capacity (≈ 80%), having achieved that at lower concentration (12.5 μM) than EGCG (50 μM). Collectively, the results suggested the promising use of 1 and 3 as potential neuroprotective agents against hydrogen peroxide-induced cytotoxicity in neuronal model.
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Affiliation(s)
- Muhammad Afiq Ngadni
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Soon-Lim Chong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Hazrina Hazni
- Centre for Natural Products Research and Drug Discovery (CENAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Unang Supratman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Khalijah Awang
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Dixit AB, Sharma D, Tripathi M, Srivastava A, Paul D, Prakash D, Sarkar C, Kumar K, Banerjee J, Chandra PS. Genome-wide DNA Methylation and RNAseq Analyses Identify Aberrant Signalling Pathways in Focal Cortical Dysplasia (FCD) Type II. Sci Rep 2018; 8:17976. [PMID: 30568293 PMCID: PMC6299275 DOI: 10.1038/s41598-018-35892-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/01/2018] [Indexed: 01/26/2023] Open
Abstract
Focal cortical dysplasia (FCD) is one of the most common pathologies associated with drug-resistant epilepsy (DRE). The pharmacological targets remain obscured, as the molecular mechanisms underlying FCD are unclear. Implications of epigenetically modulated aberrant gene expression in disease progression are reported in various DRE pathologies except FCD. Here we performed genome-wide CpG-DNA methylation profiling by methylated DNA immunoprecipitation (MeDIP) microarray and RNA sequencing (RNAseq) on cortical tissues resected from FCD type II patients. A total of 19088 sites showed altered DNA methylation in all the CpG islands. Of these, 5725 sites were present in the promoter regions, of which 176 genes showed an inverse correlation between methylation and gene expression. Many of these 176 genes were found to belong to a cohesive network of physically interacting proteins linked to several cellular functions. Pathway analysis revealed significant enrichment of receptor tyrosine kinases (RTK), EGFR, PDGFRA, NTRK3, and mTOR signalling pathways. This is the first study that investigates the epigenetic signature associated with FCD type II pathology. The candidate genes and pathways identified in this study may play a crucial role in the regulation of the pathogenic mechanisms of epileptogenesis associated with FCD type II pathologies.
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Affiliation(s)
- Aparna Banerjee Dixit
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India. .,Dr. B R Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
| | - Devina Sharma
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India.,Department of Neurosurgery, AIIMS, New Delhi, India
| | - Manjari Tripathi
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India.,Department of Neurology, AIIMS, New Delhi, India
| | | | - Debasmita Paul
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India.,Department of Neurosurgery, AIIMS, New Delhi, India
| | - Deepak Prakash
- Department of Forensic Medicine and Toxicology, AIIMS, New Delhi, India
| | | | - Krishan Kumar
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India.,Department of Neurosurgery, AIIMS, New Delhi, India
| | - Jyotirmoy Banerjee
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India.,Department of Biophysics, AIIMS, New Delhi, India
| | - P Sarat Chandra
- Center of Excellence for Epilepsy, A joint NBRC-AIIMS collaboration, NBRC, Manesar, India. .,Department of Neurosurgery, AIIMS, New Delhi, India.
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Yu J, Mu J, Guo Q, Yang L, Zhang J, Liu Z, Yu B, Zhang T, Xie J. Transcriptomic profile analysis of mouse neural tube development by RNA-Seq. IUBMB Life 2017; 69:706-719. [PMID: 28691208 DOI: 10.1002/iub.1653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 12/12/2022]
Abstract
The neural tube is the primordium of the central nervous system (CNS) in which its development is not entirely clear. Understanding the cellular and molecular basis of neural tube development could, therefore, provide vital clues to the mechanism of neural tube defects (NTDs). Here, we investigated the gene expression profiles of three different time points (embryonic day (E) 8.5, 9.5 and 10.5) of mouse neural tube by using RNA-seq approach. About 391 differentially expressed genes (DEGs) were screened during mouse neural tube development, including 45 DEGs involved in CNS development, among which Bmp2, Ascl1, Olig2, Lhx1, Wnt7b and Eomes might play the important roles. Of 45 DEGs, Foxp2, Eomes, Hoxb3, Gpr56, Hap1, Nkx2-1, Sez6l2, Wnt7b, Tbx20, Nfib, Cntn1 and Dcx had different isoforms, and the opposite expression pattern of different isoforms was observed for Gpr56, Nkx2-1 and Sez6l2. In addition, alternative splicing, such as mutually exclusive exon, retained intron, skipped exon and alternative 3' splice site was identified in 10 neural related differentially splicing genes, including Ngrn, Ddr1, Dctn1, Dnmt3b, Ect2, Map2, Mbnl1, Meis2, Vcan and App. Moreover, seven neural splicing factors, such as Nova1/2, nSR100/Srrm4, Elavl3/4, Celf3 and Rbfox1 were differentially expressed during mouse neural tube development. Interestingly, nine DEGs identified above were dysregulated in retinoic acid-induced NTDs model, indicating the possible important role of these genes in NTDs. Taken together, our study provides more comprehensive information on mouse neural tube development, which might provide new insights on NTDs occurrence. © 2017 IUBMB Life, 69(9):706-719, 2017.
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Affiliation(s)
- Juan Yu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Qian Guo
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Lihong Yang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Baofeng Yu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
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Fusco L, Lefort R, Smith K, Benmansour F, Gonzalez G, Barillari C, Rinn B, Fleuret F, Fua P, Pertz O. Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling. J Cell Biol 2016; 212:91-111. [PMID: 26728857 PMCID: PMC4700477 DOI: 10.1083/jcb.201506018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
NeuriteTracker is a computer vision approach used to analyze neuronal morphodynamics and to examine spatiotemporal Rho GTPase signaling networks regulating neurite outgrowth. Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth.
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Affiliation(s)
- Ludovico Fusco
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Riwal Lefort
- Institut Dalla Molle d'Intelligence Artificielle Perceptive (IDIAP Research Institute), 1920 Martigny, Switzerland
| | - Kevin Smith
- Computer Vision Laboratory, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Fethallah Benmansour
- Computer Vision Laboratory, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - German Gonzalez
- Computer Vision Laboratory, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Caterina Barillari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule, 4058 Basel, Switzerland
| | - Bernd Rinn
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule, 4058 Basel, Switzerland
| | - Francois Fleuret
- Institut Dalla Molle d'Intelligence Artificielle Perceptive (IDIAP Research Institute), 1920 Martigny, Switzerland
| | - Pascal Fua
- Computer Vision Laboratory, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Olivier Pertz
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
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Iseppon F, Napolitano LMR, Torre V, Cojoc D. Cdc42 and RhoA reveal different spatio-temporal dynamics upon local stimulation with Semaphorin-3A. Front Cell Neurosci 2015; 9:333. [PMID: 26379503 PMCID: PMC4549648 DOI: 10.3389/fncel.2015.00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/10/2015] [Indexed: 12/24/2022] Open
Abstract
Small RhoGTPases, such as Cdc42 and RhoA, are key players in integrating external cues and intracellular signaling pathways that regulate growth cone (GC) motility. Indeed, Cdc42 is involved in actin polymerization and filopodia formation, whereas RhoA induces GC collapse and neurite retraction through actomyosin contraction. In this study we employed Förster Resonance Energy Transfer (FRET) microscopy to study the spatio-temporal dynamics of Cdc42 and RhoA in GCs in response to local Semaphorin-3A (Sema3A) stimulation obtained with lipid vesicles filled with Sema3A and positioned near the selected GC using optical tweezers. We found that Cdc42 and RhoA were activated at the leading edge of NG108-15 neuroblastoma cells during spontaneous cycles of protrusion and retraction, respectively. The release of Sema3A brought to a progressive activation of RhoA within 30 s from the stimulus in the central region of the GC that collapsed and retracted. In contrast, the same stimulation evoked waves of Cdc42 activation propagating away from the stimulated region. A more localized stimulation obtained with Sema3A coated beads placed on the GC, led to Cdc42 active waves that propagated in a retrograde manner with a mean period of 70 s, and followed by GC retraction. Therefore, Sema3A activates both Cdc42 and RhoA with a complex and different spatial-temporal dynamics.
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Affiliation(s)
- Federico Iseppon
- Neurobiology Sector, International School for Advanced Studies Trieste, Italy
| | - Luisa M R Napolitano
- Neurobiology Sector, International School for Advanced Studies Trieste, Italy ; Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A. Trieste, Italy
| | - Vincent Torre
- Neurobiology Sector, International School for Advanced Studies Trieste, Italy
| | - Dan Cojoc
- Institute of Materials - National Research Council Trieste, Italy
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Diaper DC, Hirth F. Immunostaining of the developing embryonic and larval Drosophila brain. Methods Mol Biol 2013; 1082:3-17. [PMID: 24048923 DOI: 10.1007/978-1-62703-655-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Immunostaining is used to visualize the spatiotemporal expression pattern of developmental control genes that regulate the genesis and specification of the embryonic and larval brain of Drosophila. Immunostaining uses specific antibodies to mark expressed proteins and allows their localization to be traced throughout development. This method reveals insights into gene regulation, cell-type specification, neuron and glial differentiation, and posttranslational protein modifications underlying the patterning and specification of the maturing brain. Depending on the targeted protein, it is possible to visualize a multitude of regions of the Drosophila brain, such as small groups of neurons or glia, defined subcomponents of the brain's axon scaffold, or pre- and postsynaptic structures of neurons. Thus, antibody probes that recognize defined tissues, cells, or subcellular structures like axons or synaptic terminals can be used as markers to identify and analyze phenotypes in mutant embryos and larvae. Several antibodies, combined with different labels, can be used concurrently to examine protein co-localization. This protocol spans over 3-4 days.
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Affiliation(s)
- Danielle C Diaper
- Department of Neuroscience, MRC Centre for Neurodegeneration Research, Institute of Psychiatry, King's College London, London, UK
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7
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Different modes of growth cone collapse in NG 108-15 cells. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:591-605. [PMID: 23644679 PMCID: PMC3705140 DOI: 10.1007/s00249-013-0907-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/27/2013] [Accepted: 04/13/2013] [Indexed: 10/27/2022]
Abstract
In the fundamental process of neuronal path-finding, a growth cone at the tip of every neurite detects and follows multiple guidance cues regulating outgrowth and initiating directional changes. While the main focus of research lies on the cytoskeletal dynamics underlying growth cone advancement, we investigated collapse and retraction mechanisms in NG108-15 growth cones transiently transfected with mCherry-LifeAct and pCS2+/EMTB-3XGFP for filamentous actin and microtubules, respectively. Using fluorescence time lapse microscopy we could identify two distinct modes of growth cone collapse leading either to neurite retraction or to a controlled halt of neurite extension. In the latter case, lateral movement and folding of actin bundles (filopodia) confine microtubule extension and limit microtubule-based expansion processes without the necessity of a constantly engaged actin turnover machinery. We term this previously unreported second type fold collapse and suggest that it marks an intermediate-term mode of growth regulation closing the gap between full retraction and small scale fluctuations.
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8
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Higashida H. A personal view from a long-lasting collaborator on the research strategies of Marshall Nirenberg. Neurochem Int 2012; 61:821-7. [PMID: 22414530 DOI: 10.1016/j.neuint.2012.02.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/19/2012] [Accepted: 02/25/2012] [Indexed: 11/20/2022]
Abstract
In this review, I summarized transition in Dr. Marshall Nirenberg's research interests during 1970s, from a view of a long-lasting collaborator. Nirenberg switched his research filed to neurobiology after his success in deciphering genetic code and being honored with the Nobel Prize in Physiology or Medicine in 1968. His targets were to obtain genetically pure population of neurons, i.e. neuroblastoma clones, to make somatic hydrid cells, to culture neuronal and muscle cells, and to produce monoclonal antibodies against whole retinal or neuroblastoma cells. He studied neurotransmitters, receptors, cyclic nucleotides, cell differentiation, secretion, synapse formation, and chemical recognition. Especially he liked his hypothesis for opiate tolerance and dependency as a model of cellular memory. Through these studies, he seemed to devote all his time of about 50 years from 1960s to decoding brain memory processes.
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Affiliation(s)
- Haruhiro Higashida
- Department of Biophysical Genetics, Kanazawa University Graduate School of Medicine, Kanazawa 920-8640, Japan.
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Tsuji T, Higashida C, Aoki Y, Islam MS, Dohmoto M, Higashida H. Ect2, an ortholog of Drosophila Pebble, regulates formation of growth cones in primary cortical neurons. Neurochem Int 2012; 61:854-8. [PMID: 22366651 DOI: 10.1016/j.neuint.2012.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/23/2012] [Accepted: 02/03/2012] [Indexed: 10/28/2022]
Abstract
In collaboration with Marshall Nirenberg, we performed in vivo RNA interference (RNAi) genome-wide screening in Drosophila embryos. Pebble has been shown to be involved in Drosophila neuronal development. We have also reported that depletion of Ect2, a mammalian ortholog of Pebble, induces differentiation in NG108-15 neuronal cells. However, the precise role of Ect2 in neuronal development has yet to be studied. Here, we confirmed in PC12 pheochromocytoma cells that inhibition of Ect2 expression by RNAi stimulated neurite outgrowth, and in the mouse embryonic cortex that Ect2 was accumulated throughout the ventricular and subventricular zones with neuronal progenitor cells. Next, the effects of Ect2 depletion were studied in primary cultures of mouse embryonic cortical neurons: Loss of Ect2 did not affect the differentiation stages of neuritogenesis, the number of neurites, or axon length, while the numbers of growth cones and growth cone-like structures were increased. Taken together, our results suggest that Ect2 contributes to neuronal morphological differentiation through regulation of growth cone dynamics.
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Affiliation(s)
- Takahiro Tsuji
- Department of Biophysical Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa 920-8640, Japan
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