1
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Chouhan S, Sridaran D, Weimholt C, Luo J, Li T, Hodgson MC, Santos LN, Le Sommer S, Fang B, Koomen JM, Seeliger M, Qu CK, Yart A, Kontaridis MI, Mahajan K, Mahajan NP. SHP2 as a primordial epigenetic enzyme expunges histone H3 pTyr-54 to amend androgen receptor homeostasis. Nat Commun 2024; 15:5629. [PMID: 38965223 PMCID: PMC11224269 DOI: 10.1038/s41467-024-49978-4] [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: 04/05/2023] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Mutations that decrease or increase the activity of the tyrosine phosphatase, SHP2 (encoded by PTPN11), promotes developmental disorders and several malignancies by varying phosphatase activity. We uncovered that SHP2 is a distinct class of an epigenetic enzyme; upon phosphorylation by the kinase ACK1/TNK2, pSHP2 was escorted by androgen receptor (AR) to chromatin, erasing hitherto unidentified pY54-H3 (phosphorylation of histones H3 at Tyr54) epigenetic marks to trigger a transcriptional program of AR. Noonan Syndrome with Multiple Lentigines (NSML) patients, SHP2 knock-in mice, and ACK1 knockout mice presented dramatic increase in pY54-H3, leading to loss of AR transcriptome. In contrast, prostate tumors with high pSHP2 and pACK1 activity exhibited progressive downregulation of pY54-H3 levels and higher AR expression that correlated with disease severity. Overall, pSHP2/pY54-H3 signaling acts as a sentinel of AR homeostasis, explaining not only growth retardation, genital abnormalities and infertility among NSML patients, but also significant AR upregulation in prostate cancer patients.
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Affiliation(s)
- Surbhi Chouhan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Dhivya Sridaran
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Jingqin Luo
- Division of Public Health Sciences, Washington University in St Louis, St Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Myles C Hodgson
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Luana N Santos
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Samantha Le Sommer
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Bin Fang
- Moffitt Cancer Center, SRB3, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - John M Koomen
- Moffitt Cancer Center, SRB3, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Markus Seeliger
- Department of Pharmacological Sciences, Stony Brook University Medical School, BST 7-120, Stony Brook, NY, 11794-8651, USA
| | - Cheng-Kui Qu
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Winship Cancer Institute, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Armelle Yart
- UMR 1301-Inserm 5070-CNRS EFS Univ. P. Sabatier, 4bis Ave Hubert Curien, 31100, Toulouse, France
| | - Maria I Kontaridis
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA.
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, 63110, USA.
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2
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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3
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Adisornkanj P, Chanprasit R, Eliason S, Fons JM, Intachai W, Tongsima S, Olsen B, Arold ST, Ngamphiw C, Amendt BA, Tucker AS, Kantaputra P. Genetic Variants in Protein Tyrosine Phosphatase Non-Receptor Type 23 Are Responsible for Mesiodens Formation. BIOLOGY 2023; 12:393. [PMID: 36979085 PMCID: PMC10045488 DOI: 10.3390/biology12030393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
A mesiodens is a supernumerary tooth located in the midline of the premaxilla. To investigate the genetic cause of mesiodens, clinical and radiographic examination were performed on 23 family members of a two-generation Hmong family. Whole exome sequencing (WES) or Sanger sequencing were performed in 22 family members and two unrelated Thai patients with mesiodens. WES in the Hmong family revealed a missense mutation (c.1807G>A;p.Glu603Lys) in PTPN23 in seven affected members and six unaffected members. The mode of inheritance was autosomal dominance with incomplete penetrance (53.84%). Two additional mutations in PTPN23, c.2248C>G;p.Pro750Ala and c.3298C>T;p.Arg1100Cys were identified in two unrelated patients with mesiodens. PTPN23 is a regulator of endosomal trafficking functioning to move activated membrane receptors, such as EGFR, from the endosomal sorting complex towards the ESCRT-III complex for multivesicular body biogenesis, lysosomal degradation, and subsequent downregulation of receptor signaling. Immunohistochemical study and RNAscope on developing mouse embryos showed broad expression of PTPN23 in oral tissues, while immunofluorescence showed that EGFR was specifically concentrated in the midline epithelium. Importantly, PTPN23 mutant protein was shown to have reduced phosphatase activity. In conclusion, mesiodens were associated with genetic variants in PTPN23, suggesting that mesiodens may form due to defects in endosomal trafficking, leading to disrupted midline signaling.
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Affiliation(s)
- Ploy Adisornkanj
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rajit Chanprasit
- Dental Department, Wiang Kaen Hospital, Wiang Kaen, Chiang Rai 57310, Thailand
| | - Steven Eliason
- Department of Anatomy and Cell Biology and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Juan M. Fons
- Centre for Craniofacial and Regenerative Biology, King’s College London, Floor 27 Guy’ Hospital, London Bridge, London SE1 9RT, UK
| | - Worrachet Intachai
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Bjorn Olsen
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard University, Boston, MA 02115, USA
| | - Stefan T. Arold
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Structural Biology, National Institute of Health and Medical Research, National Centre for Scientific Research, University of Montpellier, 34090 Montpellier, France
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Brad A. Amendt
- Department of Anatomy and Cell Biology and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52242, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA 52242, USA
| | - Abigail S. Tucker
- Centre for Craniofacial and Regenerative Biology, King’s College London, Floor 27 Guy’ Hospital, London Bridge, London SE1 9RT, UK
| | - Piranit Kantaputra
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
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4
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Riboldi GM, Faravelli I, Rinchetti P, Lotti F. SMN post-translational modifications in spinal muscular atrophy. Front Cell Neurosci 2023; 17:1092488. [PMID: 36874214 PMCID: PMC9981653 DOI: 10.3389/fncel.2023.1092488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023] Open
Abstract
Since its first identification as the gene responsible for spinal muscular atrophy (SMA), the range of survival motor neuron (SMN) protein functions has increasingly expanded. This multimeric complex plays a crucial role in a variety of RNA processing pathways. While its most characterized function is in the biogenesis of ribonucleoproteins, several studies have highlighted the SMN complex as an important contributor to mRNA trafficking and translation, axonal transport, endocytosis, and mitochondria metabolism. All these multiple functions need to be selectively and finely modulated to maintain cellular homeostasis. SMN has distinct functional domains that play a crucial role in complex stability, function, and subcellular distribution. Many different processes were reported as modulators of the SMN complex activities, although their contribution to SMN biology still needs to be elucidated. Recent evidence has identified post-translational modifications (PTMs) as a way to regulate the pleiotropic functions of the SMN complex. These modifications include phosphorylation, methylation, ubiquitination, acetylation, sumoylation, and many other types. PTMs can broaden the range of protein functions by binding chemical moieties to specific amino acids, thus modulating several cellular processes. Here, we provide an overview of the main PTMs involved in the regulation of the SMN complex with a major focus on the functions that have been linked to SMA pathogenesis.
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Affiliation(s)
| | | | | | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY, United States
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5
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Detering NT, Schüning T, Hensel N, Claus P. The phospho-landscape of the survival of motoneuron protein (SMN) protein: relevance for spinal muscular atrophy (SMA). Cell Mol Life Sci 2022; 79:497. [PMID: 36006469 PMCID: PMC11071818 DOI: 10.1007/s00018-022-04522-9] [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: 03/21/2022] [Revised: 07/27/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
Spinal muscular atrophy (SMA) is caused by low levels of the survival of motoneuron (SMN) Protein leading to preferential degeneration of lower motoneurons in the ventral horn of the spinal cord and brain stem. However, the SMN protein is ubiquitously expressed and there is growing evidence of a multisystem phenotype in SMA. Since a loss of SMN function is critical, it is important to decipher the regulatory mechanisms of SMN function starting on the level of the SMN protein itself. Posttranslational modifications (PTMs) of proteins regulate multiple functions and processes, including activity, cellular trafficking, and stability. Several PTM sites have been identified within the SMN sequence. Here, we map the identified SMN PTMs highlighting phosphorylation as a key regulator affecting localization, stability and functions of SMN. Furthermore, we propose SMN phosphorylation as a crucial factor for intracellular interaction and cellular distribution of SMN. We outline the relevance of phosphorylation of the spinal muscular atrophy (SMA) gene product SMN with regard to basic housekeeping functions of SMN impaired in this neurodegenerative disease. Finally, we compare SMA patient mutations with putative and verified phosphorylation sites. Thus, we emphasize the importance of phosphorylation as a cellular modulator in a clinical perspective as a potential additional target for combinatorial SMA treatment strategies.
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Affiliation(s)
- Nora Tula Detering
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Tobias Schüning
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Niko Hensel
- Ottawa Hospital Research Institute (OHRI), Ottawa, Canada
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany.
- Center for Systems Neuroscience (ZSN), Hannover, Germany.
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6
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Schmitz K, Cox J, Esser LM, Voss M, Sander K, Löffler A, Hillebrand F, Erkelenz S, Schaal H, Kähne T, Klinker S, Zhang T, Nagel-Steger L, Willbold D, Seggewiß S, Schlütermann D, Stork B, Grimmler M, Wesselborg S, Peter C. An essential role of the autophagy activating kinase ULK1 in snRNP biogenesis. Nucleic Acids Res 2021; 49:6437-6455. [PMID: 34096600 PMCID: PMC8216288 DOI: 10.1093/nar/gkab452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 01/31/2023] Open
Abstract
The biogenesis of small uridine-rich nuclear ribonucleoproteins (UsnRNPs) depends on the methylation of Sm proteins catalyzed by the methylosome and the subsequent action of the SMN complex, which assembles the heptameric Sm protein ring onto small nuclear RNAs (snRNAs). In this sophisticated process, the methylosome subunit pICln (chloride conductance regulatory protein) is attributed to an exceptional key position as an ‘assembly chaperone’ by building up a stable precursor Sm protein ring structure. Here, we show that—apart from its autophagic role—the Ser/Thr kinase ULK1 (Uncoordinated [unc-51] Like Kinase 1) functions as a novel key regulator in UsnRNP biogenesis by phosphorylation of the C-terminus of pICln. As a consequence, phosphorylated pICln is no longer capable to hold up the precursor Sm ring structure. Consequently, inhibition of ULK1 results in a reduction of efficient UsnRNP core assembly. Thus ULK1, depending on its complex formation, exerts different functions in autophagy or snRNP biosynthesis.
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Affiliation(s)
- Katharina Schmitz
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Cox
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lea Marie Esser
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martin Voss
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Katja Sander
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antje Löffler
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Frank Hillebrand
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany.,Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Thilo Kähne
- Insitute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Stefan Klinker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Sabine Seggewiß
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Schlütermann
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matthias Grimmler
- Hochschule Fresenius, Idstein, Germany.,DiaSys Diagnostic Systems GmbH, Alte Strasse 9, 65558 Holzheim, Germany
| | - Sebastian Wesselborg
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph Peter
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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7
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Schilling M, Prusty AB, Boysen B, Oppermann FS, Riedel YL, Husedzinovic A, Rasouli H, König A, Ramanathan P, Reymann J, Erfle H, Daub H, Fischer U, Gruss OJ. TOR signaling regulates liquid phase separation of the SMN complex governing snRNP biogenesis. Cell Rep 2021; 35:109277. [PMID: 34161763 DOI: 10.1016/j.celrep.2021.109277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/23/2021] [Accepted: 05/27/2021] [Indexed: 01/10/2023] Open
Abstract
The activity of the SMN complex in promoting the assembly of pre-mRNA processing UsnRNPs correlates with condensation of the complex in nuclear Cajal bodies. While mechanistic details of its activity have been elucidated, the molecular basis for condensation remains unclear. High SMN complex phosphorylation suggests extensive regulation. Here, we report on systematic siRNA-based screening for modulators of the capacity of SMN to condense in Cajal bodies and identify mTOR and ribosomal protein S6 kinase β-1 as key regulators. Proteomic analysis reveals TOR-dependent phosphorylations in SMN complex subunits. Using stably expressed or optogenetically controlled phospho mutants, we demonstrate that serine 49 and 63 phosphorylation of human SMN controls the capacity of the complex to condense in Cajal bodies via liquid-liquid phase separation. Our findings link SMN complex condensation and UsnRNP biogenesis to cellular energy levels and suggest modulation of TOR signaling as a rational concept for therapy of the SMN-linked neuromuscular disorder spinal muscular atrophy.
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Affiliation(s)
- Maximilian Schilling
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany
| | - Archana B Prusty
- Theodor Boveri Institute, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Björn Boysen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Yannick L Riedel
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany
| | - Alma Husedzinovic
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Homa Rasouli
- Evotec SE, Am Klopferspitz 19a, 82152 Martinsried, Germany
| | - Angelika König
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany
| | - Pradhipa Ramanathan
- Theodor Boveri Institute, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Jürgen Reymann
- Advanced Biological Screening Facility, BioQuant Centre, Universität Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Holger Erfle
- Advanced Biological Screening Facility, BioQuant Centre, Universität Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Henrik Daub
- Evotec SE, Am Klopferspitz 19a, 82152 Martinsried, Germany
| | - Utz Fischer
- Theodor Boveri Institute, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Oliver J Gruss
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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8
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Khalaf-Nazzal R, Fasham J, Ubeyratna N, Evans DJ, Leslie JS, Warner TT, Al-Hijawi F, Alshaer S, Baker W, Turnpenny PD, Baple EL, Crosby AH. Final Exon Frameshift Biallelic PTPN23 Variants Are Associated with Microcephalic Complex Hereditary Spastic Paraplegia. Brain Sci 2021; 11:614. [PMID: 34064836 PMCID: PMC8151426 DOI: 10.3390/brainsci11050614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
The hereditary spastic paraplegias (HSPs) are a large clinically heterogeneous group of genetic disorders classified as 'pure' when the cardinal feature of progressive lower limb spasticity and weakness occurs in isolation and 'complex' when associated with other clinical signs. Here, we identify a homozygous frameshift alteration occurring in the last coding exon of the protein tyrosine phosphatase type 23 (PTPN23) gene in an extended Palestinian family associated with autosomal recessive complex HSP. PTPN23 encodes a catalytically inert non-receptor protein tyrosine phosphatase that has been proposed to interact with the endosomal sorting complex required for transport (ESCRT) complex, involved in the sorting of ubiquitinated cargos for fusion with lysosomes. In view of our data, we reviewed previously published candidate pathogenic PTPN23 variants to clarify clinical outcomes associated with pathogenic gene variants. This determined that a number of previously proposed candidate PTPN23 alterations are likely benign and revealed that pathogenic biallelic PTPN23 alterations cause a varied clinical spectrum comprising of complex HSP associated with microcephaly, which may occur without intellectual impairment or involve more severe neurological disease. Together, these findings highlight the importance of the inclusion of the PTPN23 gene on HSP gene testing panels globally.
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Affiliation(s)
- Reham Khalaf-Nazzal
- Biomedical Sciences Department, Faculty of Medicine, Arab American University of Palestine, Jenin P227, Palestine
| | - James Fasham
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Nishanka Ubeyratna
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
| | - David J. Evans
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK;
| | - Joseph S. Leslie
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
| | - Thomas T. Warner
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK;
| | - Fida’ Al-Hijawi
- Paediatrics’ Community Outpatient Clinics, Palestinian Ministry of Health, Jenin P200, Palestine;
| | - Shurouq Alshaer
- Faculty of Graduate Studies, Arab American University, Ramallah P622, Palestine;
| | - Wisam Baker
- Paediatrics Department, Dr. Khalil Suleiman Government Hospital, Jenin P200, Palestine;
| | - Peter D. Turnpenny
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Emma L. Baple
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Andrew H. Crosby
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
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9
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Wang JC, Ramaswami G, Geschwind DH. Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility. Sci Rep 2021; 11:5748. [PMID: 33707641 PMCID: PMC7970949 DOI: 10.1038/s41598-021-85061-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this latter module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.
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Affiliation(s)
- Jerry C Wang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gokul Ramaswami
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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10
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Rademacher S, Detering NT, Schüning T, Lindner R, Santonicola P, Wefel IM, Dehus J, Walter LM, Brinkmann H, Niewienda A, Janek K, Varela MA, Bowerman M, Di Schiavi E, Claus P. A Single Amino Acid Residue Regulates PTEN-Binding and Stability of the Spinal Muscular Atrophy Protein SMN. Cells 2020; 9:cells9112405. [PMID: 33153033 PMCID: PMC7692393 DOI: 10.3390/cells9112405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disease caused by decreased levels of the survival of motoneuron (SMN) protein. Post-translational mechanisms for regulation of its stability are still elusive. Thus, we aimed to identify regulatory phosphorylation sites that modulate function and stability. Our results show that SMN residues S290 and S292 are phosphorylated, of which SMN pS290 has a detrimental effect on protein stability and nuclear localization. Furthermore, we propose that phosphatase and tensin homolog (PTEN), a novel phosphatase for SMN, counteracts this effect. In light of recent advancements in SMA therapies, a significant need for additional approaches has become apparent. Our study demonstrates S290 as a novel molecular target site to increase the stability of SMN. Characterization of relevant kinases and phosphatases provides not only a new understanding of SMN function, but also constitutes a novel strategy for combinatorial therapeutic approaches to increase the level of SMN in SMA.
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Affiliation(s)
- Sebastian Rademacher
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Nora T. Detering
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Tobias Schüning
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Robert Lindner
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Pamela Santonicola
- Institute of Biosciences and Bioresources, National Research Council of Italy, 80131 Naples, Italy; (P.S.); (E.D.S.)
| | - Inga-Maria Wefel
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Janina Dehus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Lisa M. Walter
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Hella Brinkmann
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Agathe Niewienda
- Shared Facility for Mass Spectrometry, Institute of Biochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (A.N.); (K.J.)
| | - Katharina Janek
- Shared Facility for Mass Spectrometry, Institute of Biochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (A.N.); (K.J.)
| | - Miguel A. Varela
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; (M.A.V.); (M.B.)
- Department of Paediatrics, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Melissa Bowerman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; (M.A.V.); (M.B.)
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Elia Di Schiavi
- Institute of Biosciences and Bioresources, National Research Council of Italy, 80131 Naples, Italy; (P.S.); (E.D.S.)
| | - Peter Claus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
- Correspondence:
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11
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The ESCRT-II Subunit EAP20/VPS25 and the Bro1 Domain Proteins HD-PTP and BROX Are Individually Dispensable for Herpes Simplex Virus 1 Replication. J Virol 2020; 94:JVI.01641-19. [PMID: 31748394 DOI: 10.1128/jvi.01641-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/14/2019] [Indexed: 12/14/2022] Open
Abstract
Capsid envelopment during assembly of the neurotropic herpesviruses herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV) in the infected cell cytoplasm is thought to involve the late-acting cellular ESCRT (endosomal sorting complex required for transport) components ESCRT-III and VPS4 (vacuolar protein sorting 4). However, HSV-1, unlike members of many other families of enveloped viruses, does not appear to require the ESCRT-I subunit TSG101 or the Bro1 domain-containing protein ALIX (Alg-2-interacting protein X) to recruit and activate ESCRT-III. Alternative cellular factors that are known to be capable of regulating ESCRT-III function include the ESCRT-II complex and other members of the Bro1 family. We therefore used small interfering RNA (siRNA) to knock down the essential ESCRT-II subunit EAP20/VPS25 (ELL-associated protein 20/vacuolar protein sorting 25) and the Bro1 proteins HD-PTP (His domain-containing protein tyrosine phosphatase) and BROX (Bro1 domain and CAAX motif containing). We demonstrated reductions in levels of the targeted proteins by Western blotting and used quantitative microscopic assays to confirm loss of ESCRT-II and HD-PTP function. We found that in single-step replication experiments, the final yields of HSV-1 were unchanged following loss of EAP20, HD-PTP, or BROX.IMPORTANCE HSV-1 is a pathogen of the human nervous system that uses its own virus-encoded proteins and the normal cellular ESCRT machinery to drive the construction of its envelope. How HSV-1 structural proteins interact with ESCRT components and which subsets of cellular ESCRT proteins are utilized by the virus remain largely unknown. Here, we demonstrate that an essential component of the ESCRT-II complex and two ESCRT-associated Bro1 proteins are dispensable for HSV-1 replication.
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12
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Phenotype and mutation expansion of the PTPN23 associated disorder characterized by neurodevelopmental delay and structural brain abnormalities. Eur J Hum Genet 2019; 28:76-87. [PMID: 31395947 PMCID: PMC6906308 DOI: 10.1038/s41431-019-0487-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/25/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
PTPN23 is a His-domain protein-tyrosine phosphatase implicated in ciliogenesis, the endosomal sorting complex required for transport (ESCRT) pathway, and RNA splicing. Until recently, no defined human phenotype had been associated with alterations in this gene. We identified and report a cohort of seven patients with either homozygous or compound heterozygous rare deleterious variants in PTPN23. Combined with four patients previously reported, a total of 11 patients with this disorder have now been identified. We expand the phenotypic and variation spectrum associated with defects in this gene. Patients have strong phenotypic overlap, suggesting a defined autosomal recessive syndrome caused by reduced function of PTPN23. Shared characteristics of affected individuals include developmental delay, brain abnormalities (mainly ventriculomegaly and/or brain atrophy), intellectual disability, spasticity, language disorder, microcephaly, optic atrophy, and seizures. We observe a broad range of variants across patients that are likely strongly reducing the expression or disrupting the function of the protein. However, we do not observe any patients with an allele combination predicted to result in complete loss of function of PTPN23, as this is likely incompatible with life, consistent with reported embryonic lethality in the mouse. None of the observed or reported variants are recurrent, although some have been identified in homozygosis in patients from consanguineous populations. This study expands the phenotypic and molecular spectrum of PTPN23 associated disease and identifies major shared features among patients affected with this disorder, while providing additional support to the important role of PTPN23 in human nervous and visual system development and function.
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13
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Burke MF, McLaurin DM, Logan MK, Hebert MD. Alteration of 28S rRNA 2'- O-methylation by etoposide correlates with decreased SMN phosphorylation and reduced Drosha levels. Biol Open 2019; 8:bio041848. [PMID: 30858166 PMCID: PMC6451326 DOI: 10.1242/bio.041848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
The most common types of modification in human rRNA are pseudouridylation and 2'-O ribose methylation. These modifications are performed by small nucleolar ribonucleoproteins (snoRNPs) which contain a guide RNA (snoRNA) that base pairs at specific sites within the rRNA to direct the modification. rRNA modifications can vary, generating ribosome heterogeneity. One possible method that can be used to regulate rRNA modifications is by controlling snoRNP activity. RNA fragments derived from some small Cajal body-specific RNAs (scaRNA 2, 9 and 17) may influence snoRNP activity. Most scaRNAs accumulate in the Cajal body - a subnuclear domain - where they participate in the biogenesis of small nuclear RNPs, but scaRNA 2, 9 and 17 generate nucleolus-enriched fragments of unclear function, and we hypothesize that these fragments form regulatory RNPs that impact snoRNP activity and modulate rRNA modifications. Our previous work has shown that SMN, Drosha and various stresses, including etoposide treatment, may alter regulatory RNP formation. Here we demonstrate that etoposide treatment decreases the phosphorylation of SMN, reduces Drosha levels and increases the 2'-O-methylation of two sites within 28S rRNA. These findings further support a role for SMN and Drosha in regulating rRNA modification, possibly by affecting snoRNP or regulatory RNP activity.
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Affiliation(s)
- Marilyn F Burke
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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14
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Smigiel R, Landsberg G, Schilling M, Rydzanicz M, Pollak A, Walczak A, Stodolak A, Stawinski P, Mierzewska H, Sasiadek MM, Gruss OJ, Ploski R. Developmental epileptic encephalopathy with hypomyelination and brain atrophy associated with PTPN23 variants affecting the assembly of UsnRNPs. Eur J Hum Genet 2018; 26:1502-1511. [PMID: 29899372 DOI: 10.1038/s41431-018-0179-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/20/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023] Open
Abstract
PTPN23 encodes a ubiquitously expressed non-receptor type, catalytically inactive protein-tyrosine phosphatase found in all cells including neurons. Recently, we have identified PTPN23 in a cellular screen for the systematic identification of novel regulators of survival motor neuron (SMN) function in the assembly of splicing factors (Uridine-rich small nuclear ribonucleoproteins, UsnRNPs). Based on three families, recessive PTPN23 variants have been associated with human disease tentatively, without functional studies. Here, we describe a pediatric proband with severe developmental delay, epilepsy, cortical blindness, hypomyelination and brain atrophy on MRI. Whole exome sequencing and family study showed two novel PTPN23 variants, c.1902C>G (p.(Asn634Lys)) and c.2974delC (p.(Leu992Tyrfs*168)), in compound heterozygous state, which are predicted in silico to be damaging. When studying patient's fibroblasts we found similar expression of SMN but a dramatic reduction of cells displaying SMN accumulation in Cajal bodies (CB). SMN strongly accumulated in CB in more than 50% of unrelated control cell fibroblasts as well as in fibroblasts from the parent carrying only the c.2974delC (p.(Leu992Tyrfs*168)) variant (predicted to cause loss-of-function). In contrast, only 22% of cells showed respective SMN accumulations in patient fibroblasts (p = 1.9-2.5 × 10-7) while showing a higher level of nucleoplasmic SMN. Furthermore, the remaining accumulations in patient cells displayed weaker SMN signals than control or heterozygous wt/c.2974delC (p.(Leu992Tyrfs*168)) fibroblasts. Our report provides the first description of the clinical phenotype of recessive PTPN23 variants with pathogenicity substantiated by a functional study.
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Affiliation(s)
- Robert Smigiel
- Department of Paediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Gerd Landsberg
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Maximilian Schilling
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Anna Stodolak
- Department of Paediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland.,Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Hanna Mierzewska
- Department of Child and Adolescent Neurology, Institute of Mother and Child, Warsaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Oliver J Gruss
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland.
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15
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Lafarga V, Tapia O, Sharma S, Bengoechea R, Stoecklin G, Lafarga M, Berciano MT. CBP-mediated SMN acetylation modulates Cajal body biogenesis and the cytoplasmic targeting of SMN. Cell Mol Life Sci 2018; 75:527-546. [PMID: 28879433 PMCID: PMC11105684 DOI: 10.1007/s00018-017-2638-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/09/2017] [Accepted: 08/29/2017] [Indexed: 01/12/2023]
Abstract
The survival of motor neuron (SMN) protein plays an essential role in the biogenesis of spliceosomal snRNPs and the molecular assembly of Cajal bodies (CBs). Deletion of or mutations in the SMN1 gene cause spinal muscular atrophy (SMA) with degeneration and loss of motor neurons. Reduced SMN levels in SMA lead to deficient snRNP biogenesis with consequent splicing pathology. Here, we demonstrate that SMN is a novel and specific target of the acetyltransferase CBP (CREB-binding protein). Furthermore, we identify lysine (K) 119 as the main acetylation site in SMN. Importantly, SMN acetylation enhances its cytoplasmic localization, causes depletion of CBs, and reduces the accumulation of snRNPs in nuclear speckles. In contrast, the acetylation-deficient SMNK119R mutant promotes formation of CBs and a novel category of promyelocytic leukemia (PML) bodies enriched in this protein. Acetylation increases the half-life of SMN protein, reduces its cytoplasmic diffusion rate and modifies its interactome. Hence, SMN acetylation leads to its dysfunction, which explains the ineffectiveness of HDAC (histone deacetylases) inhibitors in SMA therapy despite their potential to increase SMN levels.
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Affiliation(s)
- Vanesa Lafarga
- Laboratory of Genomic Instability, "Centro Nacional de Investigaciones Oncológicas" (CNIO), 28024, Madrid, Spain
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Olga Tapia
- Department of Anatomy and Cell Biology, "Centro de Investigación en Red de Enfermedades Neurodegenerativas" (CIBERNED), University of Cantabria-IDIVAL, 39011, Santander, Spain
| | - Sahil Sharma
- Department of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 68167, Mannheim, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 68167, Mannheim, Germany
| | - Rocio Bengoechea
- Department of Neurology, The Hope Center for Neurological Diseases, School of Medicine of Washington University, St. Louis, 63110, USA
| | - Georg Stoecklin
- Department of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 68167, Mannheim, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 68167, Mannheim, Germany
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology, "Centro de Investigación en Red de Enfermedades Neurodegenerativas" (CIBERNED), University of Cantabria-IDIVAL, 39011, Santander, Spain
| | - Maria T Berciano
- Department of Anatomy and Cell Biology, "Centro de Investigación en Red de Enfermedades Neurodegenerativas" (CIBERNED), University of Cantabria-IDIVAL, 39011, Santander, Spain.
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16
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Myopic (HD-PTP, PTPN23) selectively regulates synaptic neuropeptide release. Proc Natl Acad Sci U S A 2018; 115:1617-1622. [PMID: 29378961 DOI: 10.1073/pnas.1716801115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Neurotransmission is mediated by synaptic exocytosis of neuropeptide-containing dense-core vesicles (DCVs) and small-molecule transmitter-containing small synaptic vesicles (SSVs). Exocytosis of both vesicle types depends on Ca2+ and shared secretory proteins. Here, we show that increasing or decreasing expression of Myopic (mop, HD-PTP, PTPN23), a Bro1 domain-containing pseudophosphatase implicated in neuronal development and neuropeptide gene expression, increases synaptic neuropeptide stores at the Drosophila neuromuscular junction (NMJ). This occurs without altering DCV content or transport, but synaptic DCV number and age are increased. The effect on synaptic neuropeptide stores is accounted for by inhibition of activity-induced Ca2+-dependent neuropeptide release. cAMP-evoked Ca2+-independent synaptic neuropeptide release also requires optimal Myopic expression, showing that Myopic affects the DCV secretory machinery shared by cAMP and Ca2+ pathways. Presynaptic Myopic is abundant at early endosomes, but interaction with the endosomal sorting complex required for transport III (ESCRT III) protein (CHMP4/Shrub) that mediates Myopic's effect on neuron pruning is not required for control of neuropeptide release. Remarkably, in contrast to the effect on DCVs, Myopic does not affect release from SSVs. Therefore, Myopic selectively regulates synaptic DCV exocytosis that mediates peptidergic transmission at the NMJ.
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17
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Sowada N, Hashem MO, Yilmaz R, Hamad M, Kakar N, Thiele H, Arold ST, Bode H, Alkuraya FS, Borck G. Mutations of PTPN23 in developmental and epileptic encephalopathy. Hum Genet 2017; 136:1455-1461. [PMID: 29090338 DOI: 10.1007/s00439-017-1850-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/22/2017] [Indexed: 11/26/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) are a heterogeneous group of neurodevelopmental disorders with poor prognosis. Recent discoveries have greatly expanded the repertoire of genes that are mutated in epileptic encephalopathies and DEE, often in a de novo fashion, but in many patients, the disease remains molecularly uncharacterized. Here, we describe a new form of DEE in patients with likely deleterious biallelic variants in PTPN23. The phenotype is characterized by early onset drug-resistant epilepsy, severe and global developmental delay, microcephaly, and sometimes premature death. PTPN23 encodes a tyrosine phosphatase with strong brain expression, and its knockout in mouse is embryonically lethal. Structural modeling supports a deleterious effect of the identified alleles. Our data suggest that PTPN23 mutations cause a rare severe form of autosomal-recessive DEE in humans, a finding that requires confirmation.
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Affiliation(s)
- Nadine Sowada
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Mais Omar Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rüstem Yilmaz
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Muddathir Hamad
- Department of Pediatrics, King Khalid University Hospital, Riyadh, Saudi Arabia
| | - Naseebullah Kakar
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Harald Bode
- Division of Pediatric Neurology, Children's Hospital, University of Ulm, Ulm, Germany
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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18
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Gruss OJ, Meduri R, Schilling M, Fischer U. UsnRNP biogenesis: mechanisms and regulation. Chromosoma 2017; 126:577-593. [PMID: 28766049 DOI: 10.1007/s00412-017-0637-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 12/24/2022]
Abstract
Macromolecular complexes composed of proteins or proteins and nucleic acids rather than individual macromolecules mediate many cellular activities. Maintenance of these activities is essential for cell viability and requires the coordinated production of the individual complex components as well as their faithful incorporation into functional entities. Failure of complex assembly may have fatal consequences and can cause severe diseases. While many macromolecular complexes can form spontaneously in vitro, they often require aid from assembly factors including assembly chaperones in the crowded cellular environment. The assembly of RNA protein complexes implicated in the maturation of pre-mRNAs (termed UsnRNPs) has proven to be a paradigm to understand the action of assembly factors and chaperones. UsnRNPs are assembled by factors united in protein arginine methyltransferase 5 (PRMT5)- and survival motor neuron (SMN)-complexes, which act sequentially in the UsnRNP production line. While the PRMT5-complex pre-arranges specific sets of proteins into stable intermediates, the SMN complex displaces assembly factors from these intermediates and unites them with UsnRNA to form the assembled RNP. Despite advanced mechanistic understanding of UsnRNP assembly, our knowledge of regulatory features of this essential and ubiquitous cellular function remains remarkably incomplete. One may argue that the process operates as a default biosynthesis pathway and does not require sophisticated regulatory cues. Simple theoretical considerations and a number of experimental data, however, indicate that regulation of UsnRNP assembly most likely happens at multiple levels. This review will not only summarize how individual components of this assembly line act mechanistically but also why, how, and when the UsnRNP workflow might be regulated by means of posttranslational modification in response to cellular signaling cues.
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Affiliation(s)
- Oliver J Gruss
- Department of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Karlrobert-Kreiten-Str. 13, 53115, Bonn, Germany.
| | - Rajyalakshmi Meduri
- Department of Biochemistry, University of Würzburg, Biozentrum, Am Hubland, D-97074, Würzburg, Germany
| | - Maximilian Schilling
- Department of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Karlrobert-Kreiten-Str. 13, 53115, Bonn, Germany
| | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Biozentrum, Am Hubland, D-97074, Würzburg, Germany.
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Hebert MD, Poole AR. Towards an understanding of regulating Cajal body activity by protein modification. RNA Biol 2016; 14:761-778. [PMID: 27819531 DOI: 10.1080/15476286.2016.1243649] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The biogenesis of small nuclear ribonucleoproteins (snRNPs), small Cajal body-specific RNPs (scaRNPs), small nucleolar RNPs (snoRNPs) and the telomerase RNP involves Cajal bodies (CBs). Although many components enriched in the CB contain post-translational modifications (PTMs), little is known about how these modifications impact individual protein function within the CB and, in concert with other modified factors, collectively regulate CB activity. Since all components of the CB also reside in other cellular locations, it is also important that we understand how PTMs affect the subcellular localization of CB components. In this review, we explore the current knowledge of PTMs on the activity of proteins known to enrich in CBs in an effort to highlight current progress as well as illuminate paths for future investigation.
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Affiliation(s)
- Michael D Hebert
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Aaron R Poole
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
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Post-Translational Modifications and RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:297-317. [PMID: 27256391 DOI: 10.1007/978-3-319-29073-7_12] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins affect cellular metabolic programs through development and in response to cellular stimuli. Though much work has been done to elucidate the roles of a handful of RNA-binding proteins and their effect on RNA metabolism, the progress of studies to understand the effects of post-translational modifications of this class of proteins is far from complete. This chapter summarizes the work that has been done to identify the consequence of post-translational modifications to some RNA-binding proteins. The effects of these modifications have been shown to increase the panoply of functions that a given RNA-binding protein can assume. We will survey the experimental methods that are used to identify the presence of several protein modifications and methods that attempt to discern the consequence of these modifications.
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