1
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Heiman MG, Bülow HE. Dendrite morphogenesis in Caenorhabditis elegans. Genetics 2024; 227:iyae056. [PMID: 38785371 PMCID: PMC11151937 DOI: 10.1093/genetics/iyae056] [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: 12/18/2023] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Since the days of Ramón y Cajal, the vast diversity of neuronal and particularly dendrite morphology has been used to catalog neurons into different classes. Dendrite morphology varies greatly and reflects the different functions performed by different types of neurons. Significant progress has been made in our understanding of how dendrites form and the molecular factors and forces that shape these often elaborately sculpted structures. Here, we review work in the nematode Caenorhabditis elegans that has shed light on the developmental mechanisms that mediate dendrite morphogenesis with a focus on studies investigating ciliated sensory neurons and the highly elaborated dendritic trees of somatosensory neurons. These studies, which combine time-lapse imaging, genetics, and biochemistry, reveal an intricate network of factors that function both intrinsically in dendrites and extrinsically from surrounding tissues. Therefore, dendrite morphogenesis is the result of multiple tissue interactions, which ultimately determine the shape of dendritic arbors.
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Affiliation(s)
- Maxwell G Heiman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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2
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Srivastav S, van der Graaf K, Singh P, Utama AB, Meyer MD, McNew JA, Stern M. Atl (atlastin) regulates mTor signaling and autophagy in Drosophila muscle through alteration of the lysosomal network. Autophagy 2024; 20:131-150. [PMID: 37649246 PMCID: PMC10761077 DOI: 10.1080/15548627.2023.2249794] [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: 03/06/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
ABBREVIATIONS atl atlastin; ALR autophagic lysosome reformation; ER endoplasmic reticulum; GFP green fluorescent protein; HSP hereditary spastic paraplegia; Lamp1 lysosomal associated membrane protein 1 PolyUB polyubiquitin; RFP red fluorescent protein; spin spinster; mTor mechanistic Target of rapamycin; VCP valosin containing protein.
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Affiliation(s)
| | | | - Pratibha Singh
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Matthew D. Meyer
- Shared Equipment Authority, Rice University, Houston, Texas, USA
| | - James A. McNew
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Michael Stern
- Department of BioSciences, Rice University, Houston, Texas, USA
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3
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Loncke J, Luyten T, Ramos AR, Erneux C, Bultynck G. Loss of INPP5K attenuates IP 3-induced Ca 2+ responses in the glioblastoma cell line U-251 MG cells. BBA ADVANCES 2023; 4:100105. [PMID: 37842182 PMCID: PMC10568277 DOI: 10.1016/j.bbadva.2023.100105] [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: 06/03/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
INPP5K (inositol polyphosphate 5-phosphatase K) is an endoplasmic reticulum (ER)-resident enzyme that acts as a phosphoinositide (PI) 5-phosphatase, capable of dephosphorylating various PIs including PI 4,5-bisphosphate (PI(4,5)P2), a key phosphoinositide found in the plasma membrane. Given its ER localization and substrate specificity, INPP5K may play a role in ER-plasma membrane contact sites. Furthermore, PI(4,5)P2 serves as a substrate for phospholipase C, an enzyme activated downstream of extracellular agonists acting on Gq-coupled receptors or tyrosine-kinase receptors, leading to IP3 production and subsequent release of Ca2+ from the ER, the primary intracellular Ca2+ storage organelle. In this study, we investigated the impact of INPP5K on ER Ca2+ dynamics using a previously established INPP5K-knockdown U-251 MG glioblastoma cell model. We here describe that loss of INPP5K impairs agonist-induced, IP3 receptor (IP3R)-mediated Ca2+ mobilization in intact cells, while the ER Ca2+ content and store-operated Ca2+ influx remain unaffected. To further elucidate the underlying mechanisms, we examined Ca2+ release in permeabilized cells stimulated with exogenous IP3. Interestingly, the absence of INPP5K also disrupted IP3-induced Ca2+ release events. These results suggest that INPP5K may directly influence IP3R activity through mechanisms yet to be resolved. The findings from this study point towards role of INPP5K in modulating ER calcium dynamics, particularly in relation to IP3-mediated signaling pathways. However, further work is needed to establish the general nature of our findings and to unravel the exact molecular mechanisms underlying the interplay between INNP5K function and Ca2+ signaling.
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Affiliation(s)
- Jens Loncke
- Laboratory of Molecular and Cellular Signaling, KU Leuven, Leuven, Belgium
| | - Tomas Luyten
- Laboratory of Molecular and Cellular Signaling, KU Leuven, Leuven, Belgium
| | - Ana Raquel Ramos
- ULB, IRIBHM, Campus Erasme, Bâtiment C, 808 Route de Lennik, Bruxelles 1070, Belgium
| | - Christophe Erneux
- ULB, IRIBHM, Campus Erasme, Bâtiment C, 808 Route de Lennik, Bruxelles 1070, Belgium
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, KU Leuven, Leuven, Belgium
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4
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Shukla D, Gural BM, Cauley ES, Battula N, Mowla S, Karas BF, Roberts LE, Cavallo L, Turkalj L, Moody SA, Swan LE, Manzini MC. Duplicated zebrafish (Danio rerio) inositol phosphatases inpp5ka and inpp5kb diverged in expression pattern and function. Dev Genes Evol 2023; 233:25-34. [PMID: 37184573 PMCID: PMC10239392 DOI: 10.1007/s00427-023-00703-z] [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: 08/31/2022] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
One hurdle in the development of zebrafish models of human disease is the presence of multiple zebrafish orthologs resulting from whole genome duplication in teleosts. Mutations in inositol polyphosphate 5-phosphatase K (INPP5K) lead to a syndrome characterized by variable presentation of intellectual disability, brain abnormalities, cataracts, muscle disease, and short stature. INPP5K is a phosphatase acting at position 5 of phosphoinositides to control their homeostasis and is involved in insulin signaling, cytoskeletal regulation, and protein trafficking. Previously, our group and others have replicated the human phenotypes in zebrafish knockdown models by targeting both INPP5K orthologs inpp5ka and inpp5kb. Here, we show that inpp5ka is the more closely related orthologue to human INPP5K. While both inpp5ka and inpp5kb mRNA expression levels follow a similar trend in the developing head, eyes, and tail, inpp5ka is much more abundantly expressed in these tissues than inpp5kb. In situ hybridization revealed a similar trend, also showing unique localization of inpp5kb in the pineal gland and retina indicating different transcriptional regulation. We also found that inpp5kb has lost its catalytic activity against its preferred substrate, PtdIns(4,5)P2. Since most human mutations are missense changes disrupting phosphatase activity, we propose that loss of inpp5ka alone can be targeted to recapitulate the human presentation. In addition, we show that the function of inpp5kb has diverged from inpp5ka and may play a novel role in the zebrafish.
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Affiliation(s)
- Dhyanam Shukla
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Brian M Gural
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Edmund S Cauley
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Namarata Battula
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Shorbon Mowla
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Brittany F Karas
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Llion E Roberts
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Luca Cavallo
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Luka Turkalj
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA
| | - Sally A Moody
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Laura E Swan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - M Chiara Manzini
- Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 89 French Street, CHINJ Rm 3274, New Brunswick, NJ, 08901, USA.
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5
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Foronda H, Fu Y, Covarrubias-Pinto A, Bocker HT, González A, Seemann E, Franzka P, Bock A, Bhaskara RM, Liebmann L, Hoffmann ME, Katona I, Koch N, Weis J, Kurth I, Gleeson JG, Reggiori F, Hummer G, Kessels MM, Qualmann B, Mari M, Dikić I, Hübner CA. Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature 2023:10.1038/s41586-023-06090-9. [PMID: 37225994 DOI: 10.1038/s41586-023-06090-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/17/2023] [Indexed: 05/26/2023]
Abstract
Membrane-shaping proteins characterized by reticulon homology domains play an important part in the dynamic remodelling of the endoplasmic reticulum (ER). An example of such a protein is FAM134B, which can bind LC3 proteins and mediate the degradation of ER sheets through selective autophagy (ER-phagy)1. Mutations in FAM134B result in a neurodegenerative disorder in humans that mainly affects sensory and autonomic neurons2. Here we report that ARL6IP1, another ER-shaping protein that contains a reticulon homology domain and is associated with sensory loss3, interacts with FAM134B and participates in the formation of heteromeric multi-protein clusters required for ER-phagy. Moreover, ubiquitination of ARL6IP1 promotes this process. Accordingly, disruption of Arl6ip1 in mice causes an expansion of ER sheets in sensory neurons that degenerate over time. Primary cells obtained from Arl6ip1-deficient mice or from patients display incomplete budding of ER membranes and severe impairment of ER-phagy flux. Therefore, we propose that the clustering of ubiquitinated ER-shaping proteins facilitates the dynamic remodelling of the ER during ER-phagy and is important for neuronal maintenance.
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Affiliation(s)
- Hector Foronda
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Yangxue Fu
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | | | - Hartmut T Bocker
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Blink AG, Jena, Germany
| | - Alexis González
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | - Eric Seemann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Patricia Franzka
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Andrea Bock
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Lutz Liebmann
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marina E Hoffmann
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | - Istvan Katona
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Nicole Koch
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Joseph G Gleeson
- Department of Neurosciences, Rady Children's Institute for Genomic Medicine Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael M Kessels
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Britta Qualmann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Ivan Dikić
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
- Center for Rare Diseases, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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6
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Xiang Y, Lyu R, Hu J. Oligomeric scaffolding for curvature generation by ER tubule-forming proteins. Nat Commun 2023; 14:2617. [PMID: 37147312 PMCID: PMC10162974 DOI: 10.1038/s41467-023-38294-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
The reticulons and receptor expression-enhancing proteins (REEPs) in the endoplasmic reticulum (ER) are necessary and sufficient for generating ER tubules. However, the mechanism of curvature generation remains elusive. Here, we systematically analyze components of the REEP family based on AI-predicted structures. In yeast REEP Yop1p, TM1/2 and TM3/4 form hairpins and TM2-4 exist as a bundle. Site-directed cross-linking reveals that TM2 and TM4 individually mediate homotypic dimerization, allowing further assembly into a curved shape. Truncated Yop1p lacking TM1 (equivalent to REEP1) retains the curvature-generating capability, undermining the role of the intrinsic wedge. Unexpectedly, both REEP1 and REEP5 fail to replace Yop1p in the maintenance of ER morphology, mostly due to a subtle difference in oligomerization tendency, which involves not only the TM domains, but also the TM-connecting cytosolic loop and previously neglected C-terminal helix. Several hereditary spastic paraplegia-causing mutations in REEP1 appear at the oligomeric interfaces identified here, suggesting compromised self-association of REEP as a pathogenic mechanism. These results indicate that membrane curvature stabilization by integral membrane proteins is dominantly achieved by curved, oligomeric scaffolding.
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Affiliation(s)
- Yun Xiang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Rui Lyu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Junjie Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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7
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Fuentes LA, Marin Z, Tyson J, Baddeley D, Bewersdorf J. The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525608. [PMID: 36747764 PMCID: PMC9900957 DOI: 10.1101/2023.01.26.525608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
UNLABELLED The endoplasmic reticulum’s (ER) structure is directly linked to the many functions of the ER but its formation is not fully understood. We investigate how the ER-membrane curving protein reticulon 4 (Rtn4) localizes to and organizes in the membrane and how that affects local ER structure. We show a strong correlation between the local Rtn4 density and the local ER membrane curvature. Our data further reveal that the typical ER tubule possesses an elliptical cross-section with Rtn4 enriched at either end of the major axis. Rtn4 oligomers are linear-shaped, contain about five copies of the protein, and preferentially orient parallel to the tubule axis. Our observations support a mechanism in which oligomerization leads to an increase of the local Rtn4 concentration with each molecule increasing membrane curvature through a hairpin wedging mechanism. This quantitative analysis of Rtn4 and its effects on the ER membrane result in a new model of tubule shape as it relates to Rtn4. SUMMARY Rtn4 forms linear-shaped oligomers that contain an average of five Rtn4 proteins, localize to the sides of elliptical tubules, prefer orientations near parallel to the tubule axis, and increase local curvature of the ER membrane by increasing local Rtn4 density.
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Affiliation(s)
- Lukas A. Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jonathan Tyson
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
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8
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Du Y, Chang W, Gao L, Deng L, Ji WK. Tex2 is required for lysosomal functions at TMEM55-dependent ER membrane contact sites. J Cell Biol 2023; 222:213838. [PMID: 36705603 PMCID: PMC9930140 DOI: 10.1083/jcb.202205133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/17/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023] Open
Abstract
ER tubules form and maintain membrane contact sites (MCSs) with late endosomes/lysosomes (LE/lys). The molecular composition and cellular functions of these MCSs are poorly understood. Here, we find that Tex2, an SMP domain-containing lipid transfer protein conserved in metazoan and yeast, is a tubular ER protein and is recruited to ER-LE/lys MCSs by TMEM55, phosphatases that convert PI(4,5)P2 to PI5P on LE/lys. We show that the Tex2-TMEM55 interaction occurs between an N-terminal region of Tex2 and a catalytic motif in the PTase domain of TMEM55. The Tex2-TMEM55 interaction can be regulated by endosome-resident type 2 PI4K activities. Functionally, Tex2 knockout results in defects in lysosomal trafficking, digestive capacity, and lipid composition of LE/lys membranes. Together, our data identify Tex2 as a tubular ER protein that resides at TMEM55-dependent ER-LE/lys MCSs required for lysosomal functions.
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Affiliation(s)
- Yuanjiao Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Wuhan, China,https://ror.org/00p991c53Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China,https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China
| | - Weiping Chang
- https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China
| | - Lei Gao
- https://ror.org/05hfa4n20Microscopy Core Facility, Westlake University, Hangzhou, Zhejiang, China
| | - Lin Deng
- https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Wuhan, China,https://ror.org/00p991c53Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China,https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China,Correspondence to Wei-Ke Ji:
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9
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Blood leukocyte transcriptional modules and differentially expressed genes associated with disease severity and age in COVID-19 patients. Sci Rep 2023; 13:898. [PMID: 36650374 PMCID: PMC9844197 DOI: 10.1038/s41598-023-28227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Since the molecular mechanisms determining COVID-19 severity are not yet well understood, there is a demand for biomarkers derived from comparative transcriptome analyses of mild and severe cases, combined with patients' clinico-demographic and laboratory data. Here the transcriptomic response of human leukocytes to SARS-CoV-2 infection was investigated by focusing on the differences between mild and severe cases and between age subgroups (younger and older adults). Three transcriptional modules correlated with these traits were functionally characterized, as well as 23 differentially expressed genes (DEGs) associated to disease severity. One module, correlated with severe cases and older patients, had an overrepresentation of genes involved in innate immune response and in neutrophil activation, whereas two other modules, correlated with disease severity and younger patients, harbored genes involved in the innate immune response to viral infections, and in the regulation of this response. This transcriptomic mechanism could be related to the better outcome observed in younger COVID-19 patients. The DEGs, all hyper-expressed in the group of severe cases, were mostly involved in neutrophil activation and in the p53 pathway, therefore related to inflammation and lymphopenia. These biomarkers may be useful for getting a better stratification of risk factors in COVID-19.
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10
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Kontou A, Herman EK, Field MC, Dacks JB, Koumandou VL. Evolution of factors shaping the endoplasmic reticulum. Traffic 2022; 23:462-473. [PMID: 36040076 PMCID: PMC9804665 DOI: 10.1111/tra.12863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 01/09/2023]
Abstract
Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.
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Affiliation(s)
- Aspasia Kontou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
| | - Emily K. Herman
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Present address:
Department of Agricultural, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeDundeeUK,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and EnvironmentUniversity College of LondonLondonUK
| | - V. Lila Koumandou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
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11
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Lischka A, Lassuthova P, Çakar A, Record CJ, Van Lent J, Baets J, Dohrn MF, Senderek J, Lampert A, Bennett DL, Wood JN, Timmerman V, Hornemann T, Auer-Grumbach M, Parman Y, Hübner CA, Elbracht M, Eggermann K, Geoffrey Woods C, Cox JJ, Reilly MM, Kurth I. Genetic pain loss disorders. Nat Rev Dis Primers 2022; 8:41. [PMID: 35710757 DOI: 10.1038/s41572-022-00365-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/05/2023]
Abstract
Genetic pain loss includes congenital insensitivity to pain (CIP), hereditary sensory neuropathies and, if autonomic nerves are involved, hereditary sensory and autonomic neuropathy (HSAN). This heterogeneous group of disorders highlights the essential role of nociception in protecting against tissue damage. Patients with genetic pain loss have recurrent injuries, burns and poorly healing wounds as disease hallmarks. CIP and HSAN are caused by pathogenic genetic variants in >20 genes that lead to developmental defects, neurodegeneration or altered neuronal excitability of peripheral damage-sensing neurons. These genetic variants lead to hyperactivity of sodium channels, disturbed haem metabolism, altered clathrin-mediated transport and impaired gene regulatory mechanisms affecting epigenetic marks, long non-coding RNAs and repetitive elements. Therapies for pain loss disorders are mainly symptomatic but the first targeted therapies are being tested. Conversely, chronic pain remains one of the greatest unresolved medical challenges, and the genes and mechanisms associated with pain loss offer new targets for analgesics. Given the progress that has been made, the coming years are promising both in terms of targeted treatments for pain loss disorders and the development of innovative pain medicines based on knowledge of these genetic diseases.
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Affiliation(s)
- Annette Lischka
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Petra Lassuthova
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Christopher J Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Jonathan Baets
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jan Senderek
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Katja Eggermann
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.
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12
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Byrne DJ, Garcia-Pardo ME, Cole NB, Batnasan B, Heneghan S, Sohail A, Blackstone C, O'Sullivan NC. Liver X receptor-agonist treatment rescues degeneration in a Drosophila model of hereditary spastic paraplegia. Acta Neuropathol Commun 2022; 10:40. [PMID: 35346366 PMCID: PMC8961908 DOI: 10.1186/s40478-022-01343-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022] Open
Abstract
Hereditary spastic paraplegias (HSPs) are a group of inherited, progressive neurodegenerative conditions characterised by prominent lower-limb spasticity and weakness, caused by a length-dependent degeneration of the longest corticospinal upper motor neurons. While more than 80 spastic paraplegia genes (SPGs) have been identified, many cases arise from mutations in genes encoding proteins which generate and maintain tubular endoplasmic reticulum (ER) membrane organisation. The ER-shaping proteins are essential for the health and survival of long motor neurons, however the mechanisms by which mutations in these genes cause the axonopathy observed in HSP have not been elucidated. To further develop our understanding of the ER-shaping proteins, this study outlines the generation of novel in vivo and in vitro models, using CRISPR/Cas9-mediated gene editing to knockout the ER-shaping protein ADP-ribosylation factor-like 6 interacting protein 1 (ARL6IP1), mutations in which give rise to the HSP subtype SPG61. Loss of Arl6IP1 in Drosophila results in progressive locomotor deficits, emulating a key aspect of HSP in patients. ARL6IP1 interacts with ER-shaping proteins and is required for regulating the organisation of ER tubules, particularly within long motor neuron axons. Unexpectedly, we identified physical and functional interactions between ARL6IP1 and the phospholipid transporter oxysterol-binding protein-related protein 8 in both human and Drosophila model systems, pointing to a conserved role for ARL6IP1 in lipid homeostasis. Furthermore, loss of Arl6IP1 from Drosophila neurons results in a cell non-autonomous accumulation of lipid droplets in axonal glia. Importantly, treatment with lipid regulating liver X receptor-agonists blocked lipid droplet accumulation, restored axonal ER organisation, and improved locomotor function in Arl6IP1 knockout Drosophila. Our findings indicate that disrupted lipid homeostasis contributes to neurodegeneration in HSP, identifying a potential novel therapeutic avenue for the treatment of this disorder.
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Affiliation(s)
- Dwayne J Byrne
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M Elena Garcia-Pardo
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Nelson B Cole
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Belguun Batnasan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sophia Heneghan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Anood Sohail
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Niamh C O'Sullivan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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13
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Bishayee K, Habib K, Nazim UM, Kang J, Szabo A, Huh SO, Sadra A. RNA binding protein HuD promotes autophagy and tumor stress survival by suppressing mTORC1 activity and augmenting ARL6IP1 levels. J Exp Clin Cancer Res 2022; 41:18. [PMID: 35012594 PMCID: PMC8744261 DOI: 10.1186/s13046-021-02203-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Neuronal-origin HuD (ELAVL4) is an RNA binding protein overexpressed in neuroblastoma (NB) and certain other cancers. The RNA targets of this RNA binding protein in neuroblastoma cells and their role in promoting cancer survival have been unexplored. In the study of modulators of mTORC1 activity under the conditions of optimal cell growth and starvation, the role of HuD and its two substrates were studied. Methods RNA immunoprecipitation/sequencing (RIP-SEQ) coupled with quantitative real-time PCR were used to identify substrates of HuD in NB cells. Validation of the two RNA targets of HuD was via reverse capture of HuD by synthetic RNA oligoes from cell lysates and binding of RNA to recombinant forms of HuD in the cell and outside of the cell. Further analysis was via RNA transcriptome analysis of HuD silencing in the test cells. Results In response to stress, HuD was found to dampen mTORC1 activity and allow the cell to upregulate its autophagy levels by suppressing mTORC1 activity. Among mRNA substrates regulated cell-wide by HuD, GRB-10 and ARL6IP1 were found to carry out critical functions for survival of the cells under stress. GRB-10 was involved in blocking mTORC1 activity by disrupting Raptor-mTOR kinase interaction. Reduced mTORC1 activity allowed lifting of autophagy levels in the cells required for increased survival. In addition, ARL6IP1, an apoptotic regulator in the ER membrane, was found to promote cell survival by negative regulation of apoptosis. As a therapeutic target, knockdown of HuD in two xenograft models of NB led to a block in tumor growth, confirming its importance for viability of the tumor cells. Cell-wide RNA messages of these two HuD substrates and HuD and mTORC1 marker of activity significantly correlated in NB patient populations and in mouse xenografts. Conclusions HuD is seen as a novel means of promoting stress survival in this cancer type by downregulating mTORC1 activity and negatively regulating apoptosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02203-2.
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Affiliation(s)
- Kausik Bishayee
- Department of Pharmacology, College of Medicine, Institute of Natural Medicine, Hallym University, Chuncheon, South Korea
| | - Khadija Habib
- Department of Pharmacology, College of Medicine, Institute of Natural Medicine, Hallym University, Chuncheon, South Korea
| | - Uddin Md Nazim
- Department of Pharmacology, College of Medicine, Institute of Natural Medicine, Hallym University, Chuncheon, South Korea
| | - Jieun Kang
- Department of Pharmacology, College of Medicine, Institute of Natural Medicine, Hallym University, Chuncheon, South Korea
| | - Aniko Szabo
- Department of Anatomy, Alfaisal University, College of Medicine, Riyadh, Kingdom of Saudi Arabia
| | - Sung-Oh Huh
- Department of Pharmacology, College of Medicine, Institute of Natural Medicine, Hallym University, Chuncheon, South Korea.
| | - Ali Sadra
- Department of Pharmacology, College of Medicine, Institute of Natural Medicine, Hallym University, Chuncheon, South Korea.
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14
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Nourbakhsh K, Ferreccio AA, Bernard MJ, Yadav S. TAOK2 is an ER-localized kinase that catalyzes the dynamic tethering of ER to microtubules. Dev Cell 2021; 56:3321-3333.e5. [PMID: 34879262 PMCID: PMC8699727 DOI: 10.1016/j.devcel.2021.11.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/17/2021] [Accepted: 11/15/2021] [Indexed: 01/07/2023]
Abstract
The endoplasmic reticulum (ER) depends on extensive association with the microtubule (MT) cytoskeleton for its structure and mitotic inheritance. However, mechanisms that underlie coupling of ER membranes to MTs are poorly understood. We have identified thousand and one amino acid kinase 2 (TAOK2) as a pleiotropic protein kinase that mediates tethering of ER to MTs. In human cells, TAOK2 localizes in distinct ER subdomains via transmembrane helices and an adjacent amphipathic region. Through its C-terminal tail, TAOK2 directly binds MTs, coupling ER membranes to the MT cytoskeleton. In TAOK2 knockout cells, although ER-membrane dynamics are increased, movement of ER along growing MT plus ends is disrupted. ER-MT tethering is tightly regulated by catalytic activity of TAOK2, perturbation of which leads to defects in ER morphology, association with MTs, and cell division. Our study identifies TAOK2 as an ER-MT tether and reveals a kinase-regulated mechanism for control of ER dynamics.
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Affiliation(s)
- Kimya Nourbakhsh
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Amy A Ferreccio
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Matthew J Bernard
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Smita Yadav
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Institute of Stem Cell and Regenerative Medicine, Seattle, WA 98109, USA.
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15
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Jeyasimman D, Ercan B, Dharmawan D, Naito T, Sun J, Saheki Y. PDZD-8 and TEX-2 regulate endosomal PI(4,5)P 2 homeostasis via lipid transport to promote embryogenesis in C. elegans. Nat Commun 2021; 12:6065. [PMID: 34663803 PMCID: PMC8523718 DOI: 10.1038/s41467-021-26177-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
Different types of cellular membranes have unique lipid compositions that are important for their functional identity. PI(4,5)P2 is enriched in the plasma membrane where it contributes to local activation of key cellular events, including actomyosin contraction and cytokinesis. However, how cells prevent PI(4,5)P2 from accumulating in intracellular membrane compartments, despite constant intermixing and exchange of lipid membranes, is poorly understood. Using the C. elegans early embryo as our model system, we show that the evolutionarily conserved lipid transfer proteins, PDZD-8 and TEX-2, act together with the PI(4,5)P2 phosphatases, OCRL-1 and UNC-26/synaptojanin, to prevent the build-up of PI(4,5)P2 on endosomal membranes. In the absence of these four proteins, large amounts of PI(4,5)P2 accumulate on endosomes, leading to embryonic lethality due to ectopic recruitment of proteins involved in actomyosin contractility. PDZD-8 localizes to the endoplasmic reticulum and regulates endosomal PI(4,5)P2 levels via its lipid harboring SMP domain. Accumulation of PI(4,5)P2 on endosomes is accompanied by impairment of their degradative capacity. Thus, cells use multiple redundant systems to maintain endosomal PI(4,5)P2 homeostasis.
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Affiliation(s)
- Darshini Jeyasimman
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Bilge Ercan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Dennis Dharmawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Tomoki Naito
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Jingbo Sun
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
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16
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Sun J, Harion R, Naito T, Saheki Y. INPP5K and Atlastin-1 maintain the nonuniform distribution of ER-plasma membrane contacts in neurons. Life Sci Alliance 2021; 4:4/11/e202101092. [PMID: 34556534 PMCID: PMC8507493 DOI: 10.26508/lsa.202101092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/03/2021] [Accepted: 09/11/2021] [Indexed: 02/04/2023] Open
Abstract
In neurons, the ER extends throughout all cellular processes, forming multiple contacts with the plasma membrane (PM) to fine-tune neuronal physiology. However, the mechanisms that regulate the distribution of neuronal ER-PM contacts are not known. Here, we used the Caenorhabditis elegans DA9 motor neuron as our model system and found that neuronal ER-PM contacts are enriched in soma and dendrite and mostly absent in axons. Using forward genetic screen, we identified that the inositol 5-phosphatase, CIL-1 (human INPP5K), and the dynamin-like GTPase, ATLN-1 (human Atlastin-1), help to maintain the non-uniform, somatodendritic enrichment of neuronal ER-PM contacts. Mechanistically, CIL-1 acts upstream of ATLN-1 to maintain the balance between ER tubules and sheets. In mutants of CIL-1 or ATLN-1, ER sheets expand and invade into the axon. This is accompanied by the ectopic formation of axonal ER-PM contacts and defects in axon regeneration following laser-induced axotomy. As INPP5K and Atlastin-1 have been linked to neurological disorders, the unique distribution of neuronal ER-PM contacts maintained by these proteins may support neuronal resilience during the onset and progression of these diseases.
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Affiliation(s)
- Jingbo Sun
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Raihanah Harion
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tomoki Naito
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore .,Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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17
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McGrath MJ, Eramo MJ, Gurung R, Sriratana A, Gehrig SM, Lynch GS, Lourdes SR, Koentgen F, Feeney SJ, Lazarou M, McLean CA, Mitchell CA. Defective lysosome reformation during autophagy causes skeletal muscle disease. J Clin Invest 2021; 131:135124. [PMID: 33119550 PMCID: PMC7773396 DOI: 10.1172/jci135124] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
The regulation of autophagy-dependent lysosome homeostasis in vivo is unclear. We showed that the inositol polyphosphate 5-phosphatase INPP5K regulates autophagic lysosome reformation (ALR), a lysosome recycling pathway, in muscle. INPP5K hydrolyzes phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] to phosphatidylinositol 4-phosphate [PI(4)P], and INPP5K mutations cause muscular dystrophy by unknown mechanisms. We report that loss of INPP5K in muscle caused severe disease, autophagy inhibition, and lysosome depletion. Reduced PI(4,5)P2 turnover on autolysosomes in Inpp5k–/– muscle suppressed autophagy and lysosome repopulation via ALR inhibition. Defective ALR in Inpp5k–/– myoblasts was characterized by enlarged autolysosomes and the persistence of hyperextended reformation tubules, structures that participate in membrane recycling to form lysosomes. Reduced disengagement of the PI(4,5)P2 effector clathrin was observed on reformation tubules, which we propose interfered with ALR completion. Inhibition of PI(4,5)P2 synthesis or expression of WT INPP5K but not INPP5K disease mutants in INPP5K-depleted myoblasts restored lysosomal homeostasis. Therefore, bidirectional interconversion of PI(4)P/PI(4,5)P2 on autolysosomes was integral to lysosome replenishment and autophagy function in muscle. Activation of TFEB-dependent de novo lysosome biogenesis did not compensate for loss of ALR in Inpp5k–/– muscle, revealing a dependence on this lysosome recycling pathway. Therefore, in muscle, ALR is indispensable for lysosome homeostasis during autophagy and when defective is associated with muscular dystrophy.
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Affiliation(s)
- Meagan J McGrath
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Matthew J Eramo
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Rajendra Gurung
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Absorn Sriratana
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Stefan M Gehrig
- Centre for Muscle Research, Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sonia Raveena Lourdes
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Frank Koentgen
- Ozgene Pty Ltd, Bentley, Perth, Western Australia, Australia
| | - Sandra J Feeney
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Michael Lazarou
- Neuroscience Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Catriona A McLean
- Department of Anatomical Pathology, Alfred Hospital, Prahran, Melbourne, Victoria, Australia
| | - Christina A Mitchell
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
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18
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Hathazi D, Cox D, D'Amico A, Tasca G, Charlton R, Carlier RY, Baumann J, Kollipara L, Zahedi RP, Feldmann I, Deleuze JF, Torella A, Cohn R, Robinson E, Ricci F, Jungbluth H, Fattori F, Boland A, O’Connor E, Horvath R, Barresi R, Lochmüller H, Urtizberea A, Jacquemont ML, Nelson I, Swan L, Bonne G, Roos A. INPP5K and SIL1 associated pathologies with overlapping clinical phenotypes converge through dysregulation of PHGDH. Brain 2021; 144:2427-2442. [PMID: 33792664 PMCID: PMC8418339 DOI: 10.1093/brain/awab133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/12/2021] [Accepted: 01/30/2021] [Indexed: 12/22/2022] Open
Abstract
Marinesco-Sjögren syndrome is a rare human disorder caused by biallelic mutations in SIL1 characterized by cataracts in infancy, myopathy and ataxia, symptoms which are also associated with a novel disorder caused by mutations in INPP5K. While these phenotypic similarities may suggest commonalties at a molecular level, an overlapping pathomechanism has not been established yet. In this study, we present six new INPP5K patients and expand the current mutational and phenotypical spectrum of the disease showing the clinical overlap between Marinesco-Sjögren syndrome and the INPP5K phenotype. We applied unbiased proteomic profiling on cells derived from Marinesco-Sjögren syndrome and INPP5K patients and identified alterations in d-3-PHGDH as a common molecular feature. d-3-PHGDH modulates the production of l-serine and mutations in this enzyme were previously associated with a neurological phenotype, which clinically overlaps with Marinesco-Sjögren syndrome and INPP5K disease. As l-serine administration represents a promising therapeutic strategy for d-3-PHGDH patients, we tested the effect of l-serine in generated sil1, phgdh and inpp5k a+b zebrafish models, which showed an improvement in their neuronal phenotype. Thus, our study defines a core phenotypical feature underpinning a key common molecular mechanism in three rare diseases and reveals a common and novel therapeutic target for these patients.
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Affiliation(s)
- Denisa Hathazi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Dan Cox
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Adele D'Amico
- Laboratory of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Richard Charlton
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Robert-Yves Carlier
- AP-HP, Service d’Imagerie Médicale, Raymond Poincaré Hospital, 92380 Garches, France
- Inserm U 1179, University of Versailles Saint-Quentin-en-Yvelines (UVSQ), 78180 Versailles, France
| | - Jennifer Baumann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | | | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - Ingo Feldmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH) (A.B., J.F.D.), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91000 Evry, France
| | - Annalaura Torella
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Ronald Cohn
- SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Emily Robinson
- Department of molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Francesco Ricci
- Department of molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Heinz Jungbluth
- Guy’s and St Thomas’ NHS Trust, King’s College London, London, SE1 7EH, UK
| | - Fabiana Fattori
- Laboratory of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH) (A.B., J.F.D.), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91000 Evry, France
| | - Emily O’Connor
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 5B2, Canada
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Rita Barresi
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Hanns Lochmüller
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 5B2, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center—University of Freiburg, Faculty of Medicine, 79095 Freiburg, Germany
| | | | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pôle Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, 97410 La Réunion, France
| | - Isabelle Nelson
- Sorbonne Université, Inserm UMRS974, Centre de Recherche en Myologie, Institut de Myologie, 75013 Paris, France
| | - Laura Swan
- Department of molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Gisèle Bonne
- Sorbonne Université, Inserm UMRS974, Centre de Recherche en Myologie, Institut de Myologie, 75013 Paris, France
| | - Andreas Roos
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 5B2, Canada
- Department of Pediatric Neurology, University Hospital Essen, University of Duisburg-Essen, Faculty of Medicine, 45147 Essen, Germany
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19
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Nakatsu F, Kawasaki A. Functions of Oxysterol-Binding Proteins at Membrane Contact Sites and Their Control by Phosphoinositide Metabolism. Front Cell Dev Biol 2021; 9:664788. [PMID: 34249917 PMCID: PMC8264513 DOI: 10.3389/fcell.2021.664788] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/06/2021] [Indexed: 01/10/2023] Open
Abstract
Lipids must be correctly transported within the cell to the right place at the right time in order to be fully functional. Non-vesicular lipid transport is mediated by so-called lipid transfer proteins (LTPs), which contain a hydrophobic cavity that sequesters lipid molecules. Oxysterol-binding protein (OSBP)-related proteins (ORPs) are a family of LTPs known to harbor lipid ligands, such as cholesterol and phospholipids. ORPs act as a sensor or transporter of those lipid ligands at membrane contact sites (MCSs) where two different cellular membranes are closely apposed. In particular, a characteristic functional property of ORPs is their role as a lipid exchanger. ORPs mediate counter-directional transport of two different lipid ligands at MCSs. Several, but not all, ORPs transport their lipid ligand from the endoplasmic reticulum (ER) in exchange for phosphatidylinositol 4-phosphate (PI4P), the other ligand, on apposed membranes. This ORP-mediated lipid “countertransport” is driven by the concentration gradient of PI4P between membranes, which is generated by its kinases and phosphatases. In this review, we will discuss how ORP function is tightly coupled to metabolism of phosphoinositides such as PI4P. Recent progress on the role of ORP-mediated lipid transport/countertransport at multiple MCSs in cellular functions will be also discussed.
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Affiliation(s)
- Fubito Nakatsu
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata, Japan
| | - Asami Kawasaki
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata, Japan
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20
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Wang Q, Cao Z, Du B, Zhang Q, Chen L, Wang X, Yuan Z, Wang P, He R, Shan J, Zhao Y, Miao L. Membrane contact site-dependent cholesterol transport regulates Na +/K +-ATPase polarization and spermiogenesis in Caenorhabditis elegans. Dev Cell 2021; 56:1631-1645.e7. [PMID: 34051143 DOI: 10.1016/j.devcel.2021.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 03/08/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
Spermiogenesis in nematodes is a process whereby round and quiescent spermatids differentiate into asymmetric and crawling spermatozoa. The molecular mechanism underlying this symmetry breaking remains uncharacterized. In this study, we revealed that sperm-specific Na+/K+-ATPase (NKA) is evenly distributed on the plasma membrane (PM) of Caenorhabditis elegans spermatids but is translocated to and subsequently enters the invaginated membrane of the spermatozoa cell body during sperm activation. The polarization of NKA depends on the transport of cholesterol from the PM to membranous organelles (MOs) via membrane contact sites (MCSs). The inositol 5-phosphatase CIL-1 and the MO-localized PI4P phosphatase SAC-1 may mediate PI4P metabolism to drive cholesterol countertransport via sterol/lipid transport proteins through MCSs. Furthermore, the NKA function is required for C. elegans sperm motility and reproductive success. Our data imply that the lipid dynamics mediated by MCSs might play crucial roles in the establishment of cell polarity. eGraphical abstract.
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Affiliation(s)
- Qiushi Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Cao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Baochen Du
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lianwan Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiheng Yuan
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun He
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin Shan
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmei Zhao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Long Miao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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21
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Sicking M, Lang S, Bochen F, Roos A, Drenth JPH, Zakaria M, Zimmermann R, Linxweiler M. Complexity and Specificity of Sec61-Channelopathies: Human Diseases Affecting Gating of the Sec61 Complex. Cells 2021; 10:1036. [PMID: 33925740 PMCID: PMC8147068 DOI: 10.3390/cells10051036] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/14/2022] Open
Abstract
The rough endoplasmic reticulum (ER) of nucleated human cells has crucial functions in protein biogenesis, calcium (Ca2+) homeostasis, and signal transduction. Among the roughly one hundred components, which are involved in protein import and protein folding or assembly, two components stand out: The Sec61 complex and BiP. The Sec61 complex in the ER membrane represents the major entry point for precursor polypeptides into the membrane or lumen of the ER and provides a conduit for Ca2+ ions from the ER lumen to the cytosol. The second component, the Hsp70-type molecular chaperone immunoglobulin heavy chain binding protein, short BiP, plays central roles in protein folding and assembly (hence its name), protein import, cellular Ca2+ homeostasis, and various intracellular signal transduction pathways. For the purpose of this review, we focus on these two components, their relevant allosteric effectors and on the question of how their respective functional cycles are linked in order to reconcile the apparently contradictory features of the ER membrane, selective permeability for precursor polypeptides, and impermeability for Ca2+. The key issues are that the Sec61 complex exists in two conformations: An open and a closed state that are in a dynamic equilibrium with each other, and that BiP contributes to its gating in both directions in cooperation with different co-chaperones. While the open Sec61 complex forms an aqueous polypeptide-conducting- and transiently Ca2+-permeable channel, the closed complex is impermeable even to Ca2+. Therefore, we discuss the human hereditary and tumor diseases that are linked to Sec61 channel gating, termed Sec61-channelopathies, as disturbances of selective polypeptide-impermeability and/or aberrant Ca2+-permeability.
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Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Sven Lang
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Florian Bochen
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
| | - Andreas Roos
- Department of Neuropediatrics, Essen University Hospital, D-45147 Essen, Germany;
| | - Joost P. H. Drenth
- Department of Molecular Gastroenterology and Hepatology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Muhammad Zakaria
- Department of Genetics, Hazara University, Mansehra 21300, Pakistan;
| | - Richard Zimmermann
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Maximilian Linxweiler
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
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22
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Role of protons in calcium signaling. Biochem J 2021; 478:895-910. [PMID: 33635336 DOI: 10.1042/bcj20200971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023]
Abstract
Thirty-six years after the publication of the important article by Busa and Nuccitelli on the variability of intracellular pH (pHi) and the interdependence of pHi and intracellular Ca2+ concentration ([Ca2+]i), little research has been carried out on pHi and calcium signaling. Moreover, the results appear to be contradictory. Some authors claim that the increase in [Ca2+]i is due to a reduction in pHi, others that it is caused by an increase in pHi. The reasons for these conflicting results have not yet been discussed and clarified in an exhaustive manner. The idea that variations in pHi are insignificant, because cellular buffers quickly stabilize the pHi, may be a limiting and fundamentally wrong concept. In fact, it has been shown that protons can move and react in the cell before they are neutralized. Variations in pHi have a remarkable impact on [Ca2+]i and hence on some of the basic biochemical mechanisms of calcium signaling. This paper focuses on the possible triggering role of protons during their short cellular cycle and it suggests a new hypothesis for an IP3 proton dependent mechanism of action.
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23
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Shang C, Li Y, Wu Z, Han Q, Zhu Y, He T, Guo H. The Prognostic Value of DNA Methylation, Post-Translational Modifications and Correlated with Immune Infiltrates in Gynecologic Cancers. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:39-53. [PMID: 33488112 PMCID: PMC7814251 DOI: 10.2147/pgpm.s293399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/26/2020] [Indexed: 11/23/2022]
Abstract
Background To depict the prognostic landscape of gynecological cancers from the perspective of DNA methylation, alternative splicing (AS) and polyadenylation (APA) events and investigate their correlation with immune infiltrates. Methods Methylation and RNA-seq data and corresponding clinical information regarding gynecologic cancers were used to explore the relationships between changes in DNA methylation, AS and APA events and gynecologic cancer prognosis. QRT-PCR and multiple bioinformatics tools were employed to construct a gene interaction network and explore immune infiltrates. Results Only the mRNA levels of CIRBP and INPP5K were simultaneously significantly decreased in gynecologic cancers and negatively associated with overall survival, which verified by qrt-PCR. We also identified that CIRBP or INPP5K DNA methylation, AS and APA events are prognostic indicators of gynecologic cancers. The activation of T cells might be the main signaling pathway by which these genes modulate cancer progression. CIRBP/INPP5K expression is positively associated with immune infiltration and is a major risk factor of survival, especially among uterine corpus endometrial carcinoma (UCEC) patients. Conclusion According to these findings, the DNA methylation, AS and APA events of CIRBP and INPP5K may serve as important prognostic biomarkers and targets in gynecological cancers by modulating T cell infiltration.
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Affiliation(s)
- Chunliang Shang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Yuan Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Zhangxin Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Qin Han
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Yuan Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Tianhui He
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, People's Republic of China
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24
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Schurmans S, Vande Catsyne CA, Desmet C, Moës B. The phosphoinositide 5-phosphatase INPP5K: From gene structure to in vivo functions. Adv Biol Regul 2021; 79:100760. [PMID: 33060052 DOI: 10.1016/j.jbior.2020.100760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
INPP5K (Inositol Polyphosphate 5-Phosphatase K, or SKIP (for Skeletal muscle and Kidney enriched Inositol Phosphatase) is a member of the phosphoinositide 5-phosphatases family. Its protein structure is comprised of a N-terminal catalytic domain which hydrolyses both PtdIns(4,5)P2 and PtdIns(3,4,5)P3, followed by a SKICH domain at the C-terminus which is responsible for protein-protein interactions and subcellular localization of INPP5K. Strikingly, INPP5K is mostly concentrated in the endoplasmic reticulum, although it is also detected at the plasma membrane, in the cytosol and the nucleus. Recently, mutations in INPP5K have been detected in patients with a rare form of autosomal recessive congenital muscular dystrophy with cataract, short stature and intellectual disability. INPP5K functions extend from control of insulin signaling, endoplasmic reticulum stress response and structural integrity, myoblast differentiation, cytoskeleton organization, cell adhesion and migration, renal osmoregulation, to cancer. The goal of this review is thus to summarize and comment recent and less recent data in the literature on INPP5K, in particular on the structure, expression, intracellular localization, interactions and functions of this specific member of the 5-phosphatases family.
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Affiliation(s)
- Stéphane Schurmans
- Laboratoire de Génétique Fonctionnelle, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium; Secteur de Biochimie Métabolique Vétérinaire, Département des Sciences Fonctionnelles, Faculté de Médecine Vétérinaire, Building B42, Université de Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000-Liège, Belgium.
| | - Charles-Andrew Vande Catsyne
- Laboratoire de Génétique Fonctionnelle, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium
| | - Christophe Desmet
- Laboratory of Cellular and Molecular Immunology, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium
| | - Bastien Moës
- Laboratoire de Génétique Fonctionnelle, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium
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25
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D'Amico A, Fattori F, Nicita F, Barresi S, Tasca G, Verardo M, Pizzi S, Moroni I, De Mitri F, Frongia A, Pane M, Mercuri E, Tartaglia M, Bertini E. A Recurrent Pathogenic Variant of INPP5K Underlies Autosomal Recessive Congenital Muscular Dystrophy With Cataracts and Intellectual Disability: Evidence for a Founder Effect in Southern Italy. Front Genet 2020; 11:565868. [PMID: 33193651 PMCID: PMC7530278 DOI: 10.3389/fgene.2020.565868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/18/2020] [Indexed: 01/04/2023] Open
Abstract
Inositol polyphosphate-5-phosphatase K [INPP5K (MIM: 607875)] acts as a PIP3 5-phosphatase and regulates actin cytoskeleton, insulin, and cell migration. Biallelic pathogenic variants in INPP5K have recently been reported in patients affected by a form of muscular dystrophy with childhood onset. Affected patients have limb girdle muscle weakness, often associated with bilateral cataracts, short stature, and intellectual disability. Here we report four patients affected by INPP5K-related muscle dystrophy, who were apparently unrelated but originated from the same geographical area in South Italy. These patients manifest a recognizable phenotype characterized by early onset muscular dystrophy associated with short stature and intellectual disability. All affected subjects were homozygous or compound heterozygous for the c.67G > A (p.Val23Met) missense change and shared a common haplotype, indicating the occurrence of a founder effect.
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Affiliation(s)
- Adele D'Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Fabiana Fattori
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Margherita Verardo
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Isabella Moroni
- Child Neurology Unit, Foundation IRCCS Neurological Institute "C. Besta", Milan, Italy
| | - Francesca De Mitri
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Annalia Frongia
- Pediatric Neurology Unit, Catholic University and Nemo Center, Rome, Italy
| | - Marika Pane
- Pediatric Neurology Unit, Catholic University and Nemo Center, Rome, Italy
| | - Eugenio Mercuri
- Pediatric Neurology Unit, Catholic University and Nemo Center, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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26
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Hammond GRV, Burke JE. Novel roles of phosphoinositides in signaling, lipid transport, and disease. Curr Opin Cell Biol 2020; 63:57-67. [PMID: 31972475 PMCID: PMC7247936 DOI: 10.1016/j.ceb.2019.12.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 12/22/2022]
Abstract
Phosphoinositides (PPIns) are lipid signaling molecules that act as master regulators of cellular signaling. Recent studies have revealed novel roles of PPIns in myriad cellular processes and multiple human diseases mediated by misregulation of PPIn signaling. This review will present a timely summary of recent discoveries in PPIn biology, specifically their role in regulating unexpected signaling pathways, modification of signaling outcomes downstream of integral membrane proteins, and novel roles in lipid transport. This has revealed new roles of PPIns in regulating membrane trafficking, immunity, cell polarity, and response to extracellular signals. A specific focus will be on novel opportunities to target PPIn metabolism for treatment of human diseases, including cancer, pathogen infection, developmental disorders, and immune disorders.
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Affiliation(s)
- Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada.
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27
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Öztürk Z, O’Kane CJ, Pérez-Moreno JJ. Axonal Endoplasmic Reticulum Dynamics and Its Roles in Neurodegeneration. Front Neurosci 2020; 14:48. [PMID: 32116502 PMCID: PMC7025499 DOI: 10.3389/fnins.2020.00048] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The physical continuity of axons over long cellular distances poses challenges for their maintenance. One organelle that faces this challenge is endoplasmic reticulum (ER); unlike other intracellular organelles, this forms a physically continuous network throughout the cell, with a single membrane and a single lumen. In axons, ER is mainly smooth, forming a tubular network with occasional sheets or cisternae and low amounts of rough ER. It has many potential roles: lipid biosynthesis, glucose homeostasis, a Ca2+ store, protein export, and contacting and regulating other organelles. This tubular network structure is determined by ER-shaping proteins, mutations in some of which are causative for neurodegenerative disorders such as hereditary spastic paraplegia (HSP). While axonal ER shares many features with the tubular ER network in other contexts, these features must be adapted to the long and narrow dimensions of axons. ER appears to be physically continuous throughout axons, over distances that are enormous on a subcellular scale. It is therefore a potential channel for long-distance or regional communication within neurons, independent of action potentials or physical transport of cargos, but involving its physiological roles such as Ca2+ or organelle homeostasis. Despite its apparent stability, axonal ER is highly dynamic, showing features like anterograde and retrograde transport, potentially reflecting continuous fusion and breakage of the network. Here we discuss the transport processes that must contribute to this dynamic behavior of ER. We also discuss the model that these processes underpin a homeostatic process that ensures both enough ER to maintain continuity of the network and repair breaks in it, but not too much ER that might disrupt local cellular physiology. Finally, we discuss how failure of ER organization in axons could lead to axon degenerative diseases, and how a requirement for ER continuity could make distal axons most susceptible to degeneration in conditions that disrupt ER continuity.
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Affiliation(s)
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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28
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Pemberton JG, Kim YJ, Balla T. Integrated regulation of the phosphatidylinositol cycle and phosphoinositide-driven lipid transport at ER-PM contact sites. Traffic 2019; 21:200-219. [PMID: 31650663 DOI: 10.1111/tra.12709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Abstract
Among the structural phospholipids that form the bulk of eukaryotic cell membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the common precursor for low-abundance regulatory lipids, collectively referred to as polyphosphoinositides (PPIn). The metabolic turnover of PPIn species has received immense attention because of the essential functions of these lipids as universal regulators of membrane biology and their dysregulation in numerous human pathologies. The diverse functions of PPIn lipids occur, in part, by orchestrating the spatial organization and conformational dynamics of peripheral or integral membrane proteins within defined subcellular compartments. The emerging role of stable contact sites between adjacent membranes as specialized platforms for the coordinate control of ion exchange, cytoskeletal dynamics, and lipid transport has also revealed important new roles for PPIn species. In this review, we highlight the importance of membrane contact sites formed between the endoplasmic reticulum (ER) and plasma membrane (PM) for the integrated regulation of PPIn metabolism within the PM. Special emphasis will be placed on non-vesicular lipid transport during control of the PtdIns biosynthetic cycle as well as toward balancing the turnover of the signaling PPIn species that define PM identity.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
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29
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Ramos AR, Ghosh S, Suhel T, Chevalier C, Obeng EO, Fafilek B, Krejci P, Beck B, Erneux C. Phosphoinositide 5-phosphatases SKIP and SHIP2 in ruffles, the endoplasmic reticulum and the nucleus: An update. Adv Biol Regul 2019; 75:100660. [PMID: 31628071 DOI: 10.1016/j.jbior.2019.100660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/18/2019] [Accepted: 09/30/2019] [Indexed: 01/22/2023]
Abstract
Phosphoinositides (PIs) are phosphorylated derivatives of phosphatidylinositol. They act as signaling molecules linked to essential cellular mechanisms in eukaryotic cells, such as cytoskeleton organization, mitosis, polarity, migration or invasion. PIs are phosphorylated and dephosphorylated by a large number of PI kinases and PI phosphatases acting at the 5-, 4- and 3- position of the inositol ring. PI 5-phosphatases i.e. OCRL, INPP5B, SHIP1/2, Synaptojanin 1/2, INPP5E, INPP5J, SKIP (INPP5K) are enzymes that dephosphorylate the 5-phosphate position of PIs. Several human genetic diseases such as the Lowe syndrome, some congenital muscular dystrophy and opsismodysplasia are due to mutations in PI phosphatases, resulting in loss-of-function. The PI phosphatases are also up or down regulated in several human cancers such as glioblastoma or breast cancer. Their cellular localization, that is dynamic and varies in response to stimuli, is an important issue to understand function. This is the case for two members of the PI 5-phosphatase SKIP and SHIP2. Both enzymes are in ruffles, plasma membranes, the endoplasmic reticulum, a situation that is unique for SKIP, and the nucleus. Following localization, PI 5-phosphatases act on specific cellular pools of PIs, which in turn interact with target proteins. Nuclear PIs have emerged as regulators of genome functions in different area of cell signaling. They often localize to nuclear speckles, as do several PI metabolizing kinases and phosphatases. We asked whether SKIP and SHIP2 could have an impact on nuclear PI(4,5)P2. In two glioblastoma cell models, lowering SKIP expression had an impact on nuclear PI(4,5)P2. In a model of SHIP2 deletion in MCF-7 cells, no change in nuclear PI(4,5)P2 was observed. Finally, we present evidence of an anti-tumoral role of SKIP in vivo, in xenografts using as model U87shSKIP cells.
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Affiliation(s)
- Ana Raquel Ramos
- IRIBHM, Campus Erasme, ULB Bâtiment C, 808 Route de Lennik, 1070, Bruxelles, Belgium
| | - Somadri Ghosh
- IRIBHM, Campus Erasme, ULB Bâtiment C, 808 Route de Lennik, 1070, Bruxelles, Belgium
| | - Tara Suhel
- IRIBHM, Campus Erasme, ULB Bâtiment C, 808 Route de Lennik, 1070, Bruxelles, Belgium
| | - Clément Chevalier
- Center for Microscopy and Molecular Imaging ULB, 12 Rue des Professeurs Jeener et Brachet, 6041, Charleroi, Belgium
| | - Eric Owusu Obeng
- IRIBHM, Campus Erasme, ULB Bâtiment C, 808 Route de Lennik, 1070, Bruxelles, Belgium; Department of Biomedical Sciences, University of Bologna, Via Irnerio, 48, 40126, Bologna, Italy
| | - Bohumil Fafilek
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Benjamin Beck
- IRIBHM, Campus Erasme, ULB Bâtiment C, 808 Route de Lennik, 1070, Bruxelles, Belgium
| | - Christophe Erneux
- IRIBHM, Campus Erasme, ULB Bâtiment C, 808 Route de Lennik, 1070, Bruxelles, Belgium.
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30
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Volpatti JR, Al-Maawali A, Smith L, Al-Hashim A, Brill JA, Dowling JJ. The expanding spectrum of neurological disorders of phosphoinositide metabolism. Dis Model Mech 2019; 12:12/8/dmm038174. [PMID: 31413155 PMCID: PMC6737944 DOI: 10.1242/dmm.038174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phosphoinositides (PIPs) are a ubiquitous group of seven low-abundance phospholipids that play a crucial role in defining localized membrane properties and that regulate myriad cellular processes, including cytoskeletal remodeling, cell signaling cascades, ion channel activity and membrane traffic. PIP homeostasis is tightly regulated by numerous inositol kinases and phosphatases, which phosphorylate and dephosphorylate distinct PIP species. The importance of these phospholipids, and of the enzymes that regulate them, is increasingly being recognized, with the identification of human neurological disorders that are caused by mutations in PIP-modulating enzymes. Genetic disorders of PIP metabolism include forms of epilepsy, neurodegenerative disease, brain malformation syndromes, peripheral neuropathy and congenital myopathy. In this Review, we provide an overview of PIP function and regulation, delineate the disorders associated with mutations in genes that modulate or utilize PIPs, and discuss what is understood about gene function and disease pathogenesis as established through animal models of these diseases. Summary: This Review highlights the intersection between phosphoinositides and the enzymes that regulate their metabolism, which together are crucial regulators of myriad cellular processes and neurological disorders.
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Affiliation(s)
- Jonathan R Volpatti
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Almundher Al-Maawali
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman
| | - Lindsay Smith
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aqeela Al-Hashim
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Neuroscience, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Julie A Brill
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James J Dowling
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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31
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Ijuin T. Phosphoinositide phosphatases in cancer cell dynamics-Beyond PI3K and PTEN. Semin Cancer Biol 2019; 59:50-65. [PMID: 30922959 DOI: 10.1016/j.semcancer.2019.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
Phosphoinositides are a group of lipids that regulate intracellular signaling and subcellular biological events. The signaling by phosphatidylinositol-3,4,5-trisphosphate and Akt mediates the action of growth factors that are essential for cell proliferation, gene transcription, cell migration, and polarity. The hyperactivation of this signaling has been identified in different cancer cells; and, it has been implicated in oncogenic transformation and cancer cell malignancy. Recent studies have argued the role of phosphoinositides in cancer cell dynamics, including actin cytoskeletal rearrangement at the plasma membrane and the organization of intracellular compartments. The focus of this review is to summarize the impact of the activities of phosphoinositide phosphatases on intracellular signaling related to cancer cell dynamics and to discuss how the abnormalities in the activities of the enzymes alter the levels of phosphoinositides in cancer cells.
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Affiliation(s)
- Takeshi Ijuin
- Division of Biochemistry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chu-o, Kobe 650-0017, Japan.
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32
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Ramos AR, Ghosh S, Dedobbeleer M, Robe PA, Rogister B, Erneux C. Lipid phosphatases SKIP and SHIP2 regulate fibronectin-dependent cell migration in glioblastoma. FEBS J 2019; 286:1120-1135. [PMID: 30695232 DOI: 10.1111/febs.14769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/08/2018] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
Abstract
Cell migration is an important process that occurs during development and has also been linked to the motility of cancer cells. Cytoskeleton reorganization takes place in the migration process leading to lamellipodia formation. Understanding the molecular underpinnings of cell migration is particularly important in studies of glioblastoma, a highly invasive and aggressive cancer type. Two members of the phosphoinositide 5-phosphatase family, SKIP and SHIP2, have been associated with cell migration in glioblastoma; however, the precise role these enzymes play in the process-and whether they work in concert-remains unclear. Here, we compared phosphoinositide 5-phosphatases expression in glioblastoma primary cells and cell lines and showed that SHIP2 and SKIP expression greatly varies between different cell types, while OCRL, another phosphoinositide 5-phosphatase, is constitutively expressed. Upon adhesion of U-251 MG cells to fibronectin, SHIP2, SKIP, and PI(4,5)P2 colocalized in membrane ruffles. Upregulation of PI(4,5)P2 was observed in SKIP-depleted U-251 MG cells compared to control cells, but only when cells were adhered to fibronectin. Both PTEN-deficient (U-251) and PTEN-containing (LN229) glioblastoma cells showed a decrease in cell migration velocity in response to SKIP downregulation. Moreover, a SHIP2 catalytic inhibitor lowered cell migration velocity in the U-251 MG cell line. We conclude that integrin activation in U-251 cells leads to colocalization of both SKIP and SHIP2 in ruffles, where they act as potential drivers of cell migration. Depending on their expression levels in glioblastoma, phosphoinositide 5-phosphatases could cooperate and synergize in the regulation of cell migration and adhesion.
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Affiliation(s)
| | | | | | - Pierre A Robe
- Department of Neurology and Neurosurgery, Utrecht University Medical Center, The Netherlands
| | - Bernard Rogister
- GIGA-Neurosciences Research Center, Université de Liège, Belgium
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33
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Wang N, Rapoport TA. Reconstituting the reticular ER network - mechanistic implications and open questions. J Cell Sci 2019; 132:132/4/jcs227611. [PMID: 30670475 DOI: 10.1242/jcs.227611] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The endoplasmic reticulum (ER) is a major membrane-bound organelle in all eukaryotic cells. This organelle comprises morphologically distinct domains, including the nuclear envelope and peripheral sheets and tubules. The tubules are connected by three-way junctions into a network. Several membrane proteins have been implicated in network formation; curvature-stabilizing proteins generate the tubules themselves, and membrane-anchored GTPases fuse tubules into a network. Recent experiments have shown that a tubular network can be formed with reconstituted proteoliposomes containing the yeast membrane-fusing GTPase Sey1 and a curvature-stabilizing protein of either the reticulon or REEP protein families. The network forms in the presence of GTP and is rapidly disassembled when GTP hydrolysis of Sey1 is inhibited, indicating that continuous membrane fusion is required for its maintenance. Atlastin, the ortholog of Sey1 in metazoans, forms a network on its own, serving both as a fusion and curvature-stabilizing protein. These results show that the reticular ER can be generated by a surprisingly small set of proteins, and represents an energy-dependent steady state between formation and disassembly. Models for the molecular mechanism by which curvature-stabilizing proteins cooperate with fusion GTPases to form a reticular network have been proposed, but many aspects remain speculative, including the function of additional proteins, such as the lunapark protein, and the mechanism by which the ER interacts with the cytoskeleton. How the nuclear envelope and peripheral ER sheets are formed remain major unresolved questions in the field. Here, we review reconstitution experiments with purified curvature-stabilizing proteins and fusion GTPases, discuss mechanistic implications and point out open questions.
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Affiliation(s)
- Ning Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
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34
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Ramos AR, Ghosh S, Erneux C. The impact of phosphoinositide 5-phosphatases on phosphoinositides in cell function and human disease. J Lipid Res 2018; 60:276-286. [PMID: 30194087 DOI: 10.1194/jlr.r087908] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/01/2018] [Indexed: 02/06/2023] Open
Abstract
Phosphoinositides (PIs) are recognized as major signaling molecules in many different functions of eukaryotic cells. PIs can be dephosphorylated by multiple phosphatase activities at the 5-, 4-, and 3- positions. Human PI 5-phosphatases belong to a family of 10 members. Except for inositol polyphosphate 5-phosphatase A, they all catalyze the dephosphorylation of PI(4,5)P2 and/or PI(3,4,5)P3 at the 5- position. PI 5-phosphatases thus directly control the levels of PI(3,4,5)P3 and participate in the fine-tuning regulatory mechanisms of PI(3,4)P2 and PI(4,5)P2 Second messenger functions have been demonstrated for PI(3,4)P2 in invadopodium maturation and lamellipodia formation. PI 5-phosphatases can use several substrates on isolated enzymes, and it has been challenging to establish their real substrate in vivo. PI(4,5)P2 has multiple functions in signaling, including interacting with scaffold proteins, ion channels, and cytoskeleton proteins. PI 5-phosphatase isoenzymes have been individually implicated in human diseases, such as the oculocerebrorenal syndrome of Lowe, through mechanisms that include lipid control. Oncogenic and tumor-suppressive functions of PI 5-phosphatases have also been reported in different cell contexts. The mechanisms responsible for genetic diseases and for oncogenic or tumor-suppressive functions are not fully understood. The regulation of PI 5-phosphatases is thus crucial in understanding cell functions.
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Affiliation(s)
- Ana Raquel Ramos
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Somadri Ghosh
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Christophe Erneux
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium
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