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Wang S, Xing X, Ma J, Zheng S, Song Q, Zhang P. Deacylases-structure, function, and relationship to diseases. FEBS Lett 2024; 598:959-977. [PMID: 38644468 DOI: 10.1002/1873-3468.14885] [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: 11/19/2023] [Revised: 01/28/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Reversible S-acylation plays a pivotal role in various biological processes, modulating protein functions such as subcellular localization, protein stability/activity, and protein-protein interactions. These modifications are mediated by acyltransferases and deacylases, among which the most abundant modification is S-palmitoylation. Growing evidence has shown that this rivalrous pair of modifications, occurring in a reversible cycle, is essential for various biological functions. Aberrations in this process have been associated with various diseases, including cancer, neurological disorders, and immune diseases. This underscores the importance of studying enzymes involved in acylation and deacylation to gain further insights into disease pathogenesis and provide novel strategies for disease treatment. In this Review, we summarize our current understanding of the structure and physiological function of deacylases, highlighting their pivotal roles in pathology. Our aim is to provide insights for further clinical applications.
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Affiliation(s)
- Shuxian Wang
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Xiaoke Xing
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Jialin Ma
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Sihao Zheng
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, China
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2
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Gammaldi N, Pezzini F, Michelucci E, Di Giorgi N, Simonati A, Rocchiccioli S, Santorelli FM, Doccini S. Integrative human and murine multi-omics: Highlighting shared biomarkers in the neuronal ceroid lipofuscinoses. Neurobiol Dis 2023; 189:106349. [PMID: 37952681 DOI: 10.1016/j.nbd.2023.106349] [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: 10/03/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL) is a group of neurodegenerative disorders whose molecular mechanisms remain largely unknown. Omics approaches are among the methods that generate new information on modifying factors and molecular signatures. Moreover, omics data integration can address the need to progressively expand knowledge around the disease and pinpoint specific proteins to promote as candidate biomarkers. In this work, we integrated a total of 62 proteomic and transcriptomic datasets originating from humans and mice, employing a new approach able to define dysregulated processes across species, stages and NCL forms. Moreover, we selected a pool of differentially expressed proteins and genes as species- and form-related biomarkers of disease status/progression and evaluated local and spatial differences in most affected brain regions. Our results offer promising targets for potential new therapeutic strategies and reinforce the hypothesis of a connection between NCLs and other forms of dementia, particularly Alzheimer's disease.
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Affiliation(s)
- N Gammaldi
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy; Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation - Pisa, Italy
| | - F Pezzini
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, Verona, Italy
| | - E Michelucci
- Clinical Physiology-National Research Council (IFC-CNR), Pisa, Italy
| | - N Di Giorgi
- Clinical Physiology-National Research Council (IFC-CNR), Pisa, Italy
| | - A Simonati
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, Verona, Italy
| | - S Rocchiccioli
- Clinical Physiology-National Research Council (IFC-CNR), Pisa, Italy
| | - F M Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation - Pisa, Italy
| | - S Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation - Pisa, Italy.
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3
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Li W, Cologna SM. Mass spectrometry-based proteomics in neurodegenerative lysosomal storage disorders. Mol Omics 2022; 18:256-278. [PMID: 35343995 PMCID: PMC9098683 DOI: 10.1039/d2mo00004k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The major function of the lysosome is to degrade unwanted materials such as lipids, proteins, and nucleic acids; therefore, deficits of the lysosomal system can result in improper degradation and trafficking of these biomolecules. Diseases associated with lysosomal failure can be lethal and are termed lysosomal storage disorders (LSDs), which affect 1 in 5000 live births collectively. LSDs are inherited metabolic diseases caused by mutations in single lysosomal and non-lysosomal proteins and resulting in the subsequent accumulation of macromolecules within. Most LSD patients present with neurodegenerative clinical symptoms, as well as damage in other organs. The discovery of new biomarkers is necessary to understand and monitor these diseases and to track therapeutic progress. Over the past ten years, mass spectrometry (MS)-based proteomics has flourished in the biomarker studies in many diseases, including neurodegenerative, and more specifically, LSDs. In this review, biomarkers of disease pathophysiology and monitoring of LSDs revealed by MS-based proteomics are discussed, including examples from Niemann-Pick disease type C, Fabry disease, neuronal ceroid-lipofuscinoses, mucopolysaccharidosis, Krabbe disease, mucolipidosis, and Gaucher disease.
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Affiliation(s)
- Wenping Li
- Department of Chemistry, University of Illinois at Chicago, USA.
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4
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Hou Y, Gao Y, Guo S, Zhang Z, Chen R, Zhang X. Applications of spatially resolved omics in the field of endocrine tumors. Front Endocrinol (Lausanne) 2022; 13:993081. [PMID: 36704039 PMCID: PMC9873308 DOI: 10.3389/fendo.2022.993081] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.
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Affiliation(s)
- Yinuo Hou
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Shudi Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zhibin Zhang
- General Surgery, Tianjin First Center Hospital, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
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5
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Schnackenberg LK, Thorn DA, Barnette D, Jones EE. MALDI imaging mass spectrometry: an emerging tool in neurology. Metab Brain Dis 2022; 37:105-121. [PMID: 34347208 DOI: 10.1007/s11011-021-00797-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/11/2021] [Indexed: 12/24/2022]
Abstract
Neurological disease and disorders remain a large public health threat. Thus, research to improve early detection and/or develop more effective treatment approaches are necessary. Although there are many common techniques and imaging modalities utilized to study these diseases, existing approaches often require a label which can be costly and time consuming. Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a label-free, innovative and emerging technique that produces 2D ion density maps representing the distribution of an analyte(s) across a tissue section in relation to tissue histopathology. One main advantage of MALDI IMS over other imaging modalities is its ability to determine the spatial distribution of hundreds of analytes within a single imaging run, without the need for a label or any a priori knowledge. Within the field of neurology and disease there have been several impactful studies in which MALDI IMS has been utilized to better understand the cellular pathology of the disease and or severity. Furthermore, MALDI IMS has made it possible to map specific classes of analytes to regions of the brain that otherwise may have been lost using more traditional methods. This review will highlight key studies that demonstrate the potential of this technology to elucidate previously unknown phenomenon in neurological disease.
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Affiliation(s)
- Laura K Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - David A Thorn
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - Dustyn Barnette
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - E Ellen Jones
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA.
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6
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Augustine EF, Adams HR, de Los Reyes E, Drago K, Frazier M, Guelbert N, Laine M, Levin T, Mink JW, Nickel M, Peifer D, Schulz A, Simonati A, Topcu M, Turunen JA, Williams R, Wirrell EC, King S. Management of CLN1 Disease: International Clinical Consensus. Pediatr Neurol 2021; 120:38-51. [PMID: 34000449 DOI: 10.1016/j.pediatrneurol.2021.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND CLN1 disease (neuronal ceroid lipofuscinosis type 1) is a rare, genetic, neurodegenerative lysosomal storage disorder caused by palmitoyl-protein thioesterase 1 (PPT1) enzyme deficiency. Clinical features include developmental delay, psychomotor regression, seizures, ataxia, movement disorders, visual impairment, and early death. In general, the later the age at symptom onset, the more protracted the disease course. We sought to evaluate current evidence and to develop expert practice consensus to support clinicians who have not previously encountered patients with this rare disease. METHODS We searched the literature for guidelines and evidence to support clinical practice recommendations. We surveyed CLN1 disease experts and caregivers regarding their experiences and recommendations, and a meeting of experts was conducted to ascertain points of consensus and clinical practice differences. RESULTS We found a limited evidence base for treatment and no clinical management guidelines specific to CLN1 disease. Fifteen CLN1 disease experts and 39 caregivers responded to the surveys, and 14 experts met to develop consensus-based recommendations. The resulting management recommendations are uniquely informed by family perspectives, due to the inclusion of caregiver and advocate perspectives. A family-centered approach is supported, and individualized, multidisciplinary care is emphasized in the recommendations. Ascertainment of the specific CLN1 disease phenotype (infantile-, late infantile-, juvenile-, or adult-onset) is of key importance in informing the anticipated clinical course, prognosis, and care needs. Goals and strategies should be periodically reevaluated and adapted to patients' current needs, with a primary aim of optimizing patient and family quality of life.
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Affiliation(s)
- Erika F Augustine
- Department of Neurology and Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland; Departments of Neurology and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York.
| | - Heather R Adams
- Departments of Neurology and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Emily de Los Reyes
- Department of Pediatrics and Neurology, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio
| | | | | | - Norberto Guelbert
- Metabolic Diseases Section, Children's Hospital of Cordoba, Cordoba, Argentina
| | - Minna Laine
- Department of Pediatric Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tanya Levin
- Medical Writing Consultant, Atlanta, Georgia
| | - Jonathan W Mink
- Departments of Neurology, Neuroscience, and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Miriam Nickel
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Angela Schulz
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Simonati
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona School of Medicine, Verona, Italy
| | - Meral Topcu
- Professor Emeritus, Department of Pediatric Neurology, Hacettepe University, Ankara, Turkey
| | - Joni A Turunen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ruth Williams
- Children's Neurosciences Centre, Evelina London Children's Hospital, London, United Kingdom
| | - Elaine C Wirrell
- Divisions of Epilepsy and Child and Adolescent Neurology, Department of Neurology, Mayo Clinic, Rochester, Minnesota
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7
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Casarotto PC, Girych M, Fred SM, Kovaleva V, Moliner R, Enkavi G, Biojone C, Cannarozzo C, Sahu MP, Kaurinkoski K, Brunello CA, Steinzeig A, Winkel F, Patil S, Vestring S, Serchov T, Diniz CRAF, Laukkanen L, Cardon I, Antila H, Rog T, Piepponen TP, Bramham CR, Normann C, Lauri SE, Saarma M, Vattulainen I, Castrén E. Antidepressant drugs act by directly binding to TRKB neurotrophin receptors. Cell 2021; 184:1299-1313.e19. [PMID: 33606976 PMCID: PMC7938888 DOI: 10.1016/j.cell.2021.01.034] [Citation(s) in RCA: 330] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 12/22/2020] [Accepted: 01/21/2021] [Indexed: 12/11/2022]
Abstract
It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical antidepressant effect. We discovered that the transmembrane domain of tyrosine kinase receptor 2 (TRKB), the brain-derived neurotrophic factor (BDNF) receptor that promotes neuronal plasticity and antidepressant responses, has a cholesterol-sensing function that mediates synaptic effects of cholesterol. We then found that both typical and fast-acting antidepressants directly bind to TRKB, thereby facilitating synaptic localization of TRKB and its activation by BDNF. Extensive computational approaches including atomistic molecular dynamics simulations revealed a binding site at the transmembrane region of TRKB dimers. Mutation of the TRKB antidepressant-binding motif impaired cellular, behavioral, and plasticity-promoting responses to antidepressants in vitro and in vivo. We suggest that binding to TRKB and allosteric facilitation of BDNF signaling is the common mechanism for antidepressant action, which may explain why typical antidepressants act slowly and how molecular effects of antidepressants are translated into clinical mood recovery.
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Affiliation(s)
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Senem M Fred
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Vera Kovaleva
- Institute of Biotechnology-HILIFE, University of Helsinki, Helsinki, Finland
| | - Rafael Moliner
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Caroline Biojone
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | | | | | - Katja Kaurinkoski
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | | | - Anna Steinzeig
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Frederike Winkel
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Sudarshan Patil
- Department of Biomedicine and KG Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Stefan Vestring
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tsvetan Serchov
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cassiano R A F Diniz
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, São Paul, Brazil
| | - Liina Laukkanen
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Iseline Cardon
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Brain Master Program, Faculty of Science, Aix-Marseille Université, Marseille, France; Department of Psychiatry, University of Regensburg, Regenburg, Germany
| | - Hanna Antila
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tomasz Rog
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Timo Petteri Piepponen
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Clive R Bramham
- Department of Biomedicine and KG Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Claus Normann
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModul Basics), University of Freiburg, Freiburg, Germany
| | - Sari E Lauri
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Mart Saarma
- Institute of Biotechnology-HILIFE, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland; Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Eero Castrén
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland.
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8
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Demontis GC, Pezzini F, Margari E, Bianchi M, Longoni B, Doccini S, Lalowski MM, Santorelli FM, Simonati A. Electrophysiological Profile Remodeling via Selective Suppression of Voltage-Gated Currents by CLN1/PPT1 Overexpression in Human Neuronal-Like Cells. Front Cell Neurosci 2020; 14:569598. [PMID: 33390903 PMCID: PMC7772423 DOI: 10.3389/fncel.2020.569598] [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: 06/04/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022] Open
Abstract
CLN1 disease (OMIM #256730) is an inherited neurological disorder of early childhood with epileptic seizures and premature death. It is associated with mutations in CLN1 coding for Palmitoyl-Protein Thioesterase 1 (PPT1), a lysosomal enzyme which affects the recycling and degradation of lipid-modified (S-acylated) proteins by removing palmitate residues. Transcriptomic evidence from a neuronal-like cellular model derived from differentiated SH-SY5Y cells disclosed the potential negative roles of CLN1 overexpression, affecting the elongation of neuronal processes and the expression of selected proteins of the synaptic region. Bioinformatic inquiries of transcriptomic data pinpointed a dysregulated expression of several genes coding for proteins related to voltage-gated ion channels, including subunits of calcium and potassium channels (VGCC and VGKC). In SH-SY5Y cells overexpressing CLN1 (SH-CLN1 cells), the resting potential and the membrane conductance in the range of voltages close to the resting potential were not affected. However, patch-clamp recordings indicated a reduction of Ba2+ currents through VGCC of SH-CLN1 cells; Ca2+ imaging revealed reduced Ca2+ influx in the same cellular setting. The results of the biochemical and morphological investigations of CACNA2D2/α2δ-2, an accessory subunit of VGCC, were in accordance with the downregulation of the corresponding gene and consistent with the hypothesis that a lower number of functional channels may reach the plasma membrane. The combined use of 4-AP and NS-1643, two drugs with opposing effects on Kv11 and Kv12 subfamilies of VGKC coded by the KCNH gene family, provides evidence for reduced functional Kv12 channels in SH-CLN1 cells, consistent with transcriptomic data indicating the downregulation of KCNH4. The lack of compelling evidence supporting the palmitoylation of many ion channels subunits investigated in this study stimulates inquiries about the role of PPT1 in the trafficking of channels to the plasma membrane. Altogether, these results indicate a reduction of functional voltage-gated ion channels in response to CLN1/PPT1 overexpression in differentiated SH-SY5Y cells and provide new insights into the altered neuronal excitability which may underlie the severe epileptic phenotype of CLN1 disease. It remains to be shown if remodeling of such functional channels on plasma membrane can occur as a downstream effect of CLN1 disease.
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Affiliation(s)
| | - Francesco Pezzini
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Elisa Margari
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Marzia Bianchi
- Research Unit for Multi-factorial Diseases, Obesity and Diabetes, Bambino Gesù Children's Hospital Istituto di Ricerca e Cura a Carattere Scientifico, Rome, Italy
| | - Biancamaria Longoni
- Department of Translational Research and New Technology in Medicine, University of Pisa, Pisa, Italy
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Istituto di Ricerca e Cura a Carattere Scientifico Stella Maris Foundation, Pisa, Italy
| | - Maciej Maurycy Lalowski
- Medicum, Biochemistry/Developmental Biology and HiLIFE-Helsinki Institute of Life Science, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Filippo Maria Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Istituto di Ricerca e Cura a Carattere Scientifico Stella Maris Foundation, Pisa, Italy
| | - Alessandro Simonati
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
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9
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Nelvagal HR, Hurtado ML, Eaton SL, Kline RA, Lamont DJ, Sands MS, Wishart TM, Cooper JD. Comparative proteomic profiling reveals mechanisms for early spinal cord vulnerability in CLN1 disease. Sci Rep 2020; 10:15157. [PMID: 32938982 PMCID: PMC7495486 DOI: 10.1038/s41598-020-72075-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/26/2020] [Indexed: 01/11/2023] Open
Abstract
CLN1 disease is a fatal inherited neurodegenerative lysosomal storage disease of early childhood, caused by mutations in the CLN1 gene, which encodes the enzyme Palmitoyl protein thioesterase-1 (PPT-1). We recently found significant spinal pathology in Ppt1-deficient (Ppt1−/−) mice and human CLN1 disease that contributes to clinical outcome and precedes the onset of brain pathology. Here, we quantified this spinal pathology at 3 and 7 months of age revealing significant and progressive glial activation and vulnerability of spinal interneurons. Tandem mass tagged proteomic analysis of the spinal cord of Ppt1−/−and control mice at these timepoints revealed a significant neuroimmune response and changes in mitochondrial function, cell-signalling pathways and developmental processes. Comparing proteomic changes in the spinal cord and cortex at 3 months revealed many similarly affected processes, except the inflammatory response. These proteomic and pathological data from this largely unexplored region of the CNS may help explain the limited success of previous brain-directed therapies. These data also fundamentally change our understanding of the progressive, site-specific nature of CLN1 disease pathogenesis, and highlight the importance of the neuroimmune response. This should greatly impact our approach to the timing and targeting of future therapeutic trials for this and similar disorders.
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Affiliation(s)
- Hemanth R Nelvagal
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St Louis, School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Maica Llavero Hurtado
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Samantha L Eaton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Rachel A Kline
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Douglas J Lamont
- FingerPrints Proteomics Facility, College of Life Sciences, University of Dundee, Dundee, UK
| | - Mark S Sands
- Department of Genetics, Washington University in St Louis, School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA.,Department of Medicine, Washington University in St Louis, School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA
| | - Thomas M Wishart
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Jonathan D Cooper
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St Louis, School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA. .,Department of Genetics, Washington University in St Louis, School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA. .,Department of Neurology, Washington University in St Louis, School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA. .,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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10
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Wang K, Donnarumma F, Pettit ME, Szot CW, Solouki T, Murray KK. MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4475. [PMID: 31726477 DOI: 10.1002/jms.4475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
A multimodal workflow for mass spectrometry imaging was developed that combines MALDI imaging with protein identification and quantification by liquid chromatography tandem mass spectrometry (LC-MS/MS). Thin tissue sections were analyzed by MALDI imaging, and the regions of interest (ROI) were identified using a smoothing and edge detection procedure. A midinfrared laser at 3-μm wavelength was used to remove the ROI from the brain tissue section after MALDI mass spectrometry imaging (MALDI MSI). The captured material was processed using a single-pot solid-phase-enhanced sample preparation (SP3) method and analyzed by LC-MS/MS using ion mobility (IM) enhanced data independent acquisition (DIA) to identify and quantify proteins; more than 600 proteins were identified. Using a modified database that included isoform and the post-translational modifications chain, loss of the initial methionine, and acetylation, 14 MALDI MSI peaks were identified. Comparison of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the identified proteins was achieved through an evolutionary relationships classification system.
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Affiliation(s)
- Kelin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Michael E Pettit
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, United States
| | - Carson W Szot
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
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11
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Doccini S, Morani F, Nesti C, Pezzini F, Calza G, Soliymani R, Signore G, Rocchiccioli S, Kanninen KM, Huuskonen MT, Baumann MH, Simonati A, Lalowski MM, Santorelli FM. Proteomic and functional analyses in disease models reveal CLN5 protein involvement in mitochondrial dysfunction. Cell Death Discov 2020; 6:18. [PMID: 32257390 PMCID: PMC7105465 DOI: 10.1038/s41420-020-0250-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/27/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
CLN5 disease is a rare form of late-infantile neuronal ceroid lipofuscinosis (NCL) caused by mutations in the CLN5 gene that encodes a protein whose primary function and physiological roles remains unresolved. Emerging lines of evidence point to mitochondrial dysfunction in the onset and progression of several forms of NCL, offering new insights into putative biomarkers and shared biological processes. In this work, we employed cellular and murine models of the disease, in an effort to clarify disease pathways associated with CLN5 depletion. A mitochondria-focused quantitative proteomics approach followed by functional validations using cell biology and immunofluorescence assays revealed an impairment of mitochondrial functions in different CLN5 KO cell models and in Cln5 - /- cerebral cortex, which well correlated with disease progression. A visible impairment of autophagy machinery coupled with alterations of key parameters of mitophagy activation process functionally linked CLN5 protein to the process of neuronal injury. The functional link between impaired cellular respiration and activation of mitophagy pathways in the human CLN5 disease condition was corroborated by translating organelle-specific proteome findings to CLN5 patients' fibroblasts. Our study highlights the involvement of CLN5 in activation of mitophagy and mitochondrial homeostasis offering new insights into alternative strategies towards the CLN5 disease treatment.
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Affiliation(s)
- Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Federica Morani
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Claudia Nesti
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Francesco Pezzini
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Giulio Calza
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Rabah Soliymani
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Giovanni Signore
- NEST, Scuola Normale Superiore, Pisa, Italy
- Fondazione Pisana per la Scienza, Pisa, Italy
| | | | - Katja M. Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mikko T. Huuskonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marc H. Baumann
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Alessandro Simonati
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Maciej M. Lalowski
- Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Filippo M. Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
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12
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Barreto G, Soliymani R, Baumann M, Waris E, Eklund KK, Zenobi-Wong M, Lalowski M. Functional analysis of synovial fluid from osteoarthritic knee and carpometacarpal joints unravels different molecular profiles. Rheumatology (Oxford) 2020; 58:897-907. [PMID: 30085131 DOI: 10.1093/rheumatology/key232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/25/2018] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE In this work, we aimed to elucidate the molecular mechanisms driving primary OA. By studying the dynamics of protein expression in two different types of OA joints we searched for similarities and disparities to identify key molecular mechanisms driving OA. METHODS For this purpose, human SF samples were obtained from CMC-I OA and knee joint of OA patients. SF samples were analysed by label-free quantitative liquid chromatography mass spectrometry. Disease-relevant proteins identified in proteomics studies, such as clusterin, paraoxonase/arylesterase 1 (PON1) and transthyretin were validated by enzyme-linked immunosorbent assays, and on the mRNA level by droplet digital PCR. Functional studies were performed in vitro using primary chondrocytes. RESULTS Differential proteomic changes were observed in the concentration of 40 proteins including clusterin, PON1 and transthyretin. Immunoassay analyses of clusterin, PON1, transthyretin and other inflammatory cytokines confirmed significant differences in protein concentration in SF of CMC-I and knee OA patients, with primarily lower protein expression levels in CMC-I. Functional studies on chondrocytes unequivocally demonstrated that stimulation with SF obtained from knee OA, in contrast to CMC-I OA joint, caused a significant upregulation in pro-inflammatory response, cell death and hypertrophy. CONCLUSION This study demonstrates that differential expression of molecular players in SF from different OA joints evokes diverse effects on primary chondrocytes. The pathomolecular mechanisms of OA may significantly differ in various joints, a finding that brings a new dimension into the pathogenesis of primary OA.
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Affiliation(s)
- Goncalo Barreto
- Tissue Engineering + Biofabrication, ETH Zürich, Zürich, Switzerland
| | - Rabah Soliymani
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
| | - Marc Baumann
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
| | - Eero Waris
- Department of Hand Surgery, University of Helsinki and Helsinki University Central Hospital, Finland
| | - Kari K Eklund
- Rheumatology, University of Helsinki and Helsinki University Central Hospital, Finland.,Orton Orthopaedic Hospital and Research Institute, Invalid Foundation, Helsinki, Finland
| | - Marcy Zenobi-Wong
- Tissue Engineering + Biofabrication, ETH Zürich, Zürich, Switzerland
| | - Maciej Lalowski
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
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13
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Huber RJ, Hughes SM, Liu W, Morgan A, Tuxworth RI, Russell C. The contribution of multicellular model organisms to neuronal ceroid lipofuscinosis research. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165614. [PMID: 31783156 DOI: 10.1016/j.bbadis.2019.165614] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023]
Abstract
The NCLs (neuronal ceroid lipofuscinosis) are forms of neurodegenerative disease that affect people of all ages and ethnicities but are most prevalent in children. Commonly known as Batten disease, this debilitating neurological disorder is comprised of 13 different subtypes that are categorized based on the particular gene that is mutated (CLN1-8, CLN10-14). The pathological mechanisms underlying the NCLs are not well understood due to our poor understanding of the functions of NCL proteins. Only one specific treatment (enzyme replacement therapy) is approved, which is for the treating the brain in CLN2 disease. Hence there remains a desperate need for further research into disease-modifying treatments. In this review, we present and evaluate the genes, proteins and studies performed in the social amoeba, nematode, fruit fly, zebrafish, mouse and large animals pertinent to NCL. In particular, we highlight the use of multicellular model organisms to study NCL protein function, pathology and pathomechanisms. Their use in testing novel therapeutic approaches is also presented. With this information, we highlight how future research in these systems may be able to provide new insight into NCL protein functions in human cells and aid in the development of new therapies.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Stephanie M Hughes
- Department of Biochemistry, School of Biomedical Sciences, Brain Health Research Centre and Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Wenfei Liu
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Alan Morgan
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown St., Liverpool L69 3BX, UK
| | - Richard I Tuxworth
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Claire Russell
- Dept. Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London NW1 0TU, UK.
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14
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Sleat DE, Wiseman JA, El-Banna M, Zheng H, Zhao C, Soherwardy A, Moore DF, Lobel P. Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome. Mol Cell Proteomics 2019; 18:2244-2261. [PMID: 31501224 PMCID: PMC6823856 DOI: 10.1074/mcp.ra119.001587] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/06/2019] [Indexed: 01/06/2023] Open
Abstract
Treatments are emerging for the neuronal ceroid lipofuscinoses (NCLs), a group of similar but genetically distinct lysosomal storage diseases. Clinical ratings scales measure long-term disease progression and response to treatment but clinically useful biomarkers have yet to be identified in these diseases. We have conducted proteomic analyses of brain and cerebrospinal fluid (CSF) from mouse models of the most frequently diagnosed NCL diseases: CLN1 (infantile NCL), CLN2 (classical late infantile NCL) and CLN3 (juvenile NCL). Samples were obtained at different stages of disease progression and proteins quantified using isobaric labeling. In total, 8303 and 4905 proteins were identified from brain and CSF, respectively. We also conduced label-free analyses of brain proteins that contained the mannose 6-phosphate lysosomal targeting modification. In general, we detect few changes at presymptomatic timepoints but later in disease, we detect multiple proteins whose expression is significantly altered in both brain and CSF of CLN1 and CLN2 animals. Many of these proteins are lysosomal in origin or are markers of neuroinflammation, potentially providing clues to underlying pathogenesis and providing promising candidates for further validation.
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Affiliation(s)
- David E Sleat
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854; Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, NJ 08854.
| | | | - Mukarram El-Banna
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Amenah Soherwardy
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854; Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, NJ 08854.
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15
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Tarczyluk-Wells MA, Salzlechner C, Najafi AR, Lim MJ, Smith D, Platt FM, Williams BP, Cooper JD. Combined Anti-inflammatory and Neuroprotective Treatments Have the Potential to Impact Disease Phenotypes in Cln3 -/- Mice. Front Neurol 2019; 10:963. [PMID: 31572287 PMCID: PMC6749847 DOI: 10.3389/fneur.2019.00963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Batten disease, or juvenile NCL, is a fatal neurodegenerative disorder that occurs due to mutations in the CLN3 gene. Because the function of CLN3 remains unclear, experimental therapies for JNCL have largely concentrated upon the targeting of downstream pathomechanisms. Neuron loss is preceded by localized glial activation, and in this proof-of-concept study we have investigated whether targeting this innate immune response with ibuprofen in combination with the neuroprotective agent lamotrigine improves the previously documented beneficial effects of immunosuppressants alone. Drugs were administered daily to symptomatic Cln3 -/- mice over a 3 month period, starting at 6 months of age, and their impact was assessed using both behavioral and neuropathological outcome measures. During the treatment period, the combination of ibuprofen and lamotrigine significantly improved the performance of Cln3 -/- mice on the vertical pole test, slowing the disease-associated decline, but had less of an impact upon their rotarod performance. There were also moderate and regionally dependent effects upon astrocyte activation that were most pronounced for ibuprofen alone, but there was no overt effect upon microglial activation. Administering such treatments for longer periods will enable testing for any impact upon the neuron loss that occurs later in disease progression. Given the partial efficacy of these treatments, it will be important to test further drugs of this type in order to find more effective combinations.
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Affiliation(s)
- Marta A. Tarczyluk-Wells
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Christoph Salzlechner
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Allison R. Najafi
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Ming J. Lim
- Guy's and St. Thomas' NHS Foundation Trust, King's Health Partners Academic Health Science Centre, Evelina London Children's Hospital, London, United Kingdom
- Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Smith
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Frances M. Platt
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Brenda P. Williams
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Jonathan D. Cooper
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
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16
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Koster KP, Yoshii A. Depalmitoylation by Palmitoyl-Protein Thioesterase 1 in Neuronal Health and Degeneration. Front Synaptic Neurosci 2019; 11:25. [PMID: 31555119 PMCID: PMC6727029 DOI: 10.3389/fnsyn.2019.00025] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
Protein palmitoylation is the post-translational, reversible addition of a 16-carbon fatty acid, palmitate, to proteins. Protein palmitoylation has recently garnered much attention, as it robustly modifies the localization and function of canonical signaling molecules and receptors. Protein depalmitoylation, on the other hand, is the process by which palmitic acid is removed from modified proteins and contributes, therefore, comparably to palmitoylated-protein dynamics. Palmitoylated proteins also require depalmitoylation prior to lysosomal degradation, demonstrating the significance of this process in protein sorting and turnover. Palmitoylation and depalmitoylation serve as particularly crucial regulators of protein function in neurons, where a specialized molecular architecture and cholesterol-rich membrane microdomains contribute to synaptic transmission. Three classes of depalmitoylating enzymes are currently recognized, the acyl protein thioesterases, α/β hydrolase domain-containing 17 proteins (ABHD17s), and the palmitoyl-protein thioesterases (PPTs). However, a clear picture of depalmitoylation has not yet emerged, in part because the enzyme-substrate relationships and specific functions of depalmitoylation are only beginning to be uncovered. Further, despite the finding that loss-of-function mutations affecting palmitoyl-protein thioesterase 1 (PPT1) function cause a severe pediatric neurodegenerative disease, the role of PPT1 as a depalmitoylase has attracted relatively little attention. Understanding the role of depalmitoylation by PPT1 in neuronal function is a fertile area for ongoing basic science and translational research that may have broader therapeutic implications for neurodegeneration. Here, we will briefly introduce the rapidly growing field surrounding protein palmitoylation and depalmitoylation, then will focus on the role of PPT1 in development, health, and neurological disease.
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Affiliation(s)
- Kevin P Koster
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States
| | - Akira Yoshii
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States.,Department of Pediatrics, University of Illinois at Chicago, Chicago, IL, United States.,Department of Neurology, University of Illinois at Chicago, Chicago, IL, United States
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17
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Kline RA, Wishart TM, Mills K, Heywood WE. Applying modern Omic technologies to the Neuronal Ceroid Lipofuscinoses. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165498. [PMID: 31207290 DOI: 10.1016/j.bbadis.2019.06.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/27/2022]
Abstract
The Neuronal Ceroid Lipofuscinoses are a group of severe and progressive neurodegenerative disorders, which generally present during childhood. With new treatments emerging on the horizon, there is a growing need to understand the specific disease mechanisms as well as identify prospective biomarkers for use to stratify patients and monitor treatment. The use of Omics technologies to NCLs has the potential to address this need. We discuss the recent use and outcomes of Omics to various forms of NCL including identification of interactomes, affected biological pathways and potential biomarker candidates. We also identify common pathways affected in NCL across the reviewed studies.
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Affiliation(s)
- Rachel A Kline
- Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
| | - Thomas M Wishart
- Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
| | - Kevin Mills
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Biomedical Research Centre, Great Ormond Street Hospital, UCL Great Ormond Street Institute of Child Health, UK
| | - Wendy E Heywood
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Biomedical Research Centre, Great Ormond Street Hospital, UCL Great Ormond Street Institute of Child Health, UK.
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18
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Siedlarska M, Jamsheer A, Ciaston M, Strzelecka J, Jozwiak S. Rapidly Progressing Brain Atrophy in a Child With Developmental Regression. Pediatr Neurol 2019; 94:80-81. [PMID: 30635150 DOI: 10.1016/j.pediatrneurol.2018.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 10/27/2022]
Affiliation(s)
| | | | - Michal Ciaston
- Department of Radiology, Medical University of Warsaw, Warsaw, Poland
| | - Jolanta Strzelecka
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Sergiusz Jozwiak
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
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19
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What if? Mouse proteomics after gene inactivation. J Proteomics 2019; 199:102-122. [DOI: 10.1016/j.jprot.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022]
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20
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Lalowski MM, Björk S, Finckenberg P, Soliymani R, Tarkia M, Calza G, Blokhina D, Tulokas S, Kankainen M, Lakkisto P, Baumann M, Kankuri E, Mervaala E. Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach. Front Physiol 2018; 9:365. [PMID: 29695975 PMCID: PMC5904546 DOI: 10.3389/fphys.2018.00365] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/26/2018] [Indexed: 01/19/2023] Open
Abstract
The heart of a newborn mouse has an exceptional capacity to regenerate from myocardial injury that is lost within the first week of its life. In order to elucidate the molecular mechanisms taking place in the mouse heart during this critical period we applied an untargeted combinatory multiomics approach using large-scale mass spectrometry-based quantitative proteomics, metabolomics and mRNA sequencing on hearts from 1-day-old and 7-day-old mice. As a result, we quantified 1.937 proteins (366 differentially expressed), 612 metabolites (263 differentially regulated) and revealed 2.586 differentially expressed gene loci (2.175 annotated genes). The analyses pinpointed the fructose-induced glycolysis-pathway to be markedly active in 1-day-old neonatal mice. Integrated analysis of the data convincingly demonstrated cardiac metabolic reprogramming from glycolysis to oxidative phosphorylation in 7-days old mice, with increases of key enzymes and metabolites in fatty acid transport (acylcarnitines) and β-oxidation. An upsurge in the formation of reactive oxygen species and an increase in oxidative stress markers, e.g., lipid peroxidation, altered sphingolipid and plasmalogen metabolism were also evident in 7-days mice. In vitro maintenance of physiological fetal hypoxic conditions retained the proliferative capacity of cardiomyocytes isolated from newborn mice hearts. In summary, we provide here a holistic, multiomics view toward early postnatal changes associated with loss of a tissue regenerative capacity in the neonatal mouse heart. These results may provide insight into mechanisms of human cardiac diseases associated with tissue regenerative incapacity at the molecular level, and offer a prospect to discovery of novel therapeutic targets.
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Affiliation(s)
- Maciej M Lalowski
- Department of Biochemistry, Department of Developmental Biology, Faculty of Medicine, Helsinki Institute of Life Science (HiLIFE) and Medicum, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Susann Björk
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Piet Finckenberg
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Rabah Soliymani
- Department of Biochemistry, Department of Developmental Biology, Faculty of Medicine, Helsinki Institute of Life Science (HiLIFE) and Medicum, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Miikka Tarkia
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Giulio Calza
- Department of Biochemistry, Department of Developmental Biology, Faculty of Medicine, Helsinki Institute of Life Science (HiLIFE) and Medicum, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Daria Blokhina
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Sari Tulokas
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Päivi Lakkisto
- Medicum, Department of Clinical Chemistry and Hematology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Marc Baumann
- Department of Biochemistry, Department of Developmental Biology, Faculty of Medicine, Helsinki Institute of Life Science (HiLIFE) and Medicum, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, Finland
| | - Esko Kankuri
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
| | - Eero Mervaala
- Medicum, Department of Pharmacology, Faculty of Medicine, PB63, University of Helsinki, Helsinki, Finland
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21
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Maudsley S, Devanarayan V, Martin B, Geerts H. Intelligent and effective informatic deconvolution of “Big Data” and its future impact on the quantitative nature of neurodegenerative disease therapy. Alzheimers Dement 2018; 14:961-975. [DOI: 10.1016/j.jalz.2018.01.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/03/2017] [Accepted: 01/18/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Stuart Maudsley
- Department of Biomedical ResearchUniversity of AntwerpAntwerpBelgium
- VIB Center for Molecular NeurologyAntwerpBelgium
| | | | - Bronwen Martin
- Department of Biomedical ResearchUniversity of AntwerpAntwerpBelgium
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22
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Laakkonen EK, Soliymani R, Karvinen S, Kaprio J, Kujala UM, Baumann M, Sipilä S, Kovanen V, Lalowski M. Estrogenic regulation of skeletal muscle proteome: a study of premenopausal women and postmenopausal MZ cotwins discordant for hormonal therapy. Aging Cell 2017; 16:1276-1287. [PMID: 28884514 PMCID: PMC5676059 DOI: 10.1111/acel.12661] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2017] [Indexed: 12/31/2022] Open
Abstract
Female middle age is characterized by a decline in skeletal muscle mass and performance, predisposing women to sarcopenia, functional limitations, and metabolic dysfunction as they age. Menopausal loss of ovarian function leading to low circulating level of 17β‐estradiol has been suggested as a contributing factor to aging‐related muscle deterioration. However, the underlying molecular mechanisms remain largely unknown and thus far androgens have been considered as a major anabolic hormone for skeletal muscle. We utilized muscle samples from 24 pre‐ and postmenopausal women to establish proteome‐wide profiles, associated with the difference in age (30–34 years old vs. 54–62 years old), menopausal status (premenopausal vs. postmenopausal), and use of hormone replacement therapy (HRT; user vs. nonuser). None of the premenopausal women used hormonal medication while the postmenopausal women were monozygotic (MZ) cotwin pairs of whom the other sister was current HRT user or the other had never used HRT. Label‐free proteomic analyses resulted in the quantification of 797 muscle proteins of which 145 proteins were for the first time associated with female aging using proteomics. Furthermore, we identified 17β‐estradiol as a potential upstream regulator of the observed differences in muscle energy pathways. These findings pinpoint the underlying molecular mechanisms of the metabolic dysfunction accruing upon menopause, thus having implications for understanding the complex functional interactions between female reproductive hormones and health.
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Affiliation(s)
- Eija K. Laakkonen
- Faculty of Sport and Health Sciences Gerontology Research Center University of Jyväskylä Jyväskylä Finland
| | - Rabah Soliymani
- Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core Facility University of Helsinki Helsinki Finland
| | - Sira Karvinen
- Faculty of Sport and Health Sciences Gerontology Research Center University of Jyväskylä Jyväskylä Finland
- Divisions of Rehabilitation Science and Physical Therapy Department of Rehabilitation Medicine Medical School University of Minnesota Minneapolis MN USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM University of Helsinki Helsinki Finland
| | - Urho M. Kujala
- Faculty of Sport and Health Sciences University of Jyväskylä Jyväskylä Finland
| | - Marc Baumann
- Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core Facility University of Helsinki Helsinki Finland
| | - Sarianna Sipilä
- Faculty of Sport and Health Sciences Gerontology Research Center University of Jyväskylä Jyväskylä Finland
| | - Vuokko Kovanen
- Faculty of Sport and Health Sciences University of Jyväskylä Jyväskylä Finland
| | - Maciej Lalowski
- Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core Facility University of Helsinki Helsinki Finland
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23
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Pezzini F, Bianchi M, Benfatto S, Griggio F, Doccini S, Carrozzo R, Dapkunas A, Delledonne M, Santorelli FM, Lalowski MM, Simonati A. The Networks of Genes Encoding Palmitoylated Proteins in Axonal and Synaptic Compartments Are Affected in PPT1 Overexpressing Neuronal-Like Cells. Front Mol Neurosci 2017; 10:266. [PMID: 28878621 PMCID: PMC5572227 DOI: 10.3389/fnmol.2017.00266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/07/2017] [Indexed: 12/13/2022] Open
Abstract
CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product Palmitoyl-Protein Thioesterase 1 (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 expression is also linked to synaptic compartments. The aim of this study was to unravel molecular signatures connected to CLN1. We utilized SH-SY5Y neuroblastoma cells overexpressing wild type CLN1 (SH-p.wtCLN1) and five selected CLN1 patients’ mutations. The cellular distribution of wtPPT1 was consistent with regular processing of endogenous protein, partially detected inside Lysosomal Associated Membrane Protein 2 (LAMP2) positive vesicles, while the mutants displayed more diffuse cytoplasmic pattern. Transcriptomic profiling revealed 802 differentially expressed genes (DEGs) in SH-p.wtCLN1 (as compared to empty-vector transfected cells), whereas the number of DEGs detected in the two mutants (p.L222P and p.M57Nfs*45) was significantly lower. Bioinformatic scrutiny linked DEGs with neurite formation and neuronal transmission. Specifically, neuritogenesis and proliferation of neuronal processes were predicted to be hampered in the wtCLN1 overexpressing cell line, and these findings were corroborated by morphological investigations. Palmitoylation survey identified 113 palmitoylated protein-encoding genes in SH-p.wtCLN1, including 25 ones simultaneously assigned to axonal growth and synaptic compartments. A remarkable decrease in the expression of palmitoylated proteins, functionally related to axonal elongation (GAP43, CRMP1 and NEFM) and of the synaptic marker SNAP25, specifically in SH-p.wtCLN1 cells was confirmed by immunoblotting. Subsequent, bioinformatic network survey of DEGs assigned to the synaptic annotations linked 81 DEGs, including 23 ones encoding for palmitoylated proteins. Results obtained in this experimental setting outlined two affected functional modules (connected to the axonal and synaptic compartments), which can be associated with an altered gene dosage of wtCLN1. Moreover, these modules were interrelated with the pathological effects associated with loss of PPT1 function, similarly as observed in the Ppt1 knockout mice and patients with CLN1 disease.
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Affiliation(s)
- Francesco Pezzini
- Neurology (Neuropathology and Child Neurology), Department of Neuroscience, Biomedicine and Movement, University of VeronaVerona, Italy
| | - Marzia Bianchi
- Unit of Muscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Children's HospitalRome, Italy
| | - Salvatore Benfatto
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | - Francesca Griggio
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | - Stefano Doccini
- Molecular Medicine, IRCCS Stella MarisCalambrone-Pisa, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Children's HospitalRome, Italy
| | - Arvydas Dapkunas
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of HelsinkiHelsinki, Finland
| | - Massimo Delledonne
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Maciej M Lalowski
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of HelsinkiHelsinki, Finland
| | - Alessandro Simonati
- Neurology (Neuropathology and Child Neurology), Department of Neuroscience, Biomedicine and Movement, University of VeronaVerona, Italy
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24
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Simonati A, Williams RE, Nardocci N, Laine M, Battini R, Schulz A, Garavaglia B, Moro F, Pezzini F, Santorelli FM. Phenotype and natural history of variant late infantile ceroid-lipofuscinosis 5. Dev Med Child Neurol 2017; 59:815-821. [PMID: 28542837 DOI: 10.1111/dmcn.13473] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/04/2017] [Indexed: 01/10/2023]
Abstract
AIM To characterize the phenotypic profile of a cohort of children affected with CLN5, a rare form of neuronal ceroid-lipofuscinosis (NCL), and to trace the features of the natural history of the disease. METHOD Records of 15 children (nine males, six females) were obtained from the data sets of the DEM-CHILD International NCL Registry. Disease progression was measured by rating six functional domains at different time points along the disease course. All patients underwent mutation analysis of the CLN5 gene and ultrastructural investigations of peripheral tissues. Expression of the gene product, pCLN5, was characterized in vitro in six patients. RESULTS Disease onset was at 2 to 7 years 6 months of age: impaired learning and cognition were the most common early symptoms. Seizures occurred relatively late (median age 8y) and were the presenting symptoms in two children. Nine mutations were detected in 30 alleles, including six mutations predicting a truncated protein. Mixed cytosomes were observed by electron microscopy. Differences of disease progression were observed in two groups of patients and could be related to their genetic profile. INTERPRETATION Clinical features in a multicentre cohort of patients with CLN5 confirm that cognitive difficulties are early clinical markers of this condition. Severe mutations were associated with a more rapid decline of neurological function.
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Affiliation(s)
- Alessandro Simonati
- Department of Neuroscience, Biomedicine, Movement - Neurology (Child Neurology and Psychiatry, and Neuropathology), University of Verona, Verona, Italy
| | - Ruth E Williams
- Children's Neurosciences Centre, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Nardo Nardocci
- Department of Developmental Neuroscience and Molecular Neurogenetics, IRCCS Foundation Neurological Institute C Besta, Milan, Italy
| | - Minna Laine
- Department of Child Neurology, Helsinki University Central Hospital, Peijas Hospital, HUCH, Helsinki, Finland
| | - Roberta Battini
- Molecular Medicine Unit and Child Neurology, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Angela Schulz
- Department of Paediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Barbara Garavaglia
- Children's Neurosciences Centre, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Francesca Moro
- Molecular Medicine Unit and Child Neurology, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Francesco Pezzini
- Department of Neuroscience, Biomedicine, Movement - Neurology (Child Neurology and Psychiatry, and Neuropathology), University of Verona, Verona, Italy
| | - Filippo M Santorelli
- Molecular Medicine Unit and Child Neurology, IRCCS Fondazione Stella Maris, Pisa, Italy
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25
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Dilillo M, Pellegrini D, Ait-Belkacem R, de Graaf EL, Caleo M, McDonnell LA. Mass Spectrometry Imaging, Laser Capture Microdissection, and LC-MS/MS of the Same Tissue Section. J Proteome Res 2017. [DOI: 10.1021/acs.jproteome.7b00284] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- Department of Chemistry
and Industrial Chemistry, University of Pisa, 56126 Pisa, Italy
| | - Davide Pellegrini
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- NEST, Scuola Normale Superiore di Pisa, 56127 Pisa, Italy
| | | | | | | | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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26
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Scifo E, Calza G, Fuhrmann M, Soliymani R, Baumann M, Lalowski M. Recent advances in applying mass spectrometry and systems biology to determine brain dynamics. Expert Rev Proteomics 2017; 14:545-559. [PMID: 28539064 DOI: 10.1080/14789450.2017.1335200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders. Different proteomics workflows for isolation/enrichment of specific cell populations or brain regions, sample processing; mass spectrometry technologies, for differential proteome quantitation, analysis of post-translational modifications and imaging approaches in the brain are critically deliberated. Future directions, including analysis of cellular sub-compartments, targeted MS platforms (selected/parallel reaction monitoring) and use of mass cytometry are also discussed. Expert commentary: Here, we summarize and evaluate current mass spectrometry based approaches for determining brain dynamics in health and diseases states, with a focus on neurological disorders. Furthermore, we provide insight on current trends and new MS technologies with potential to improve this analysis.
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Affiliation(s)
- Enzo Scifo
- a Department of Psychiatry, and of Pharmacology and Toxicology , University of Toronto, Campbell Family Mental Health Research Institute of CAMH , Toronto , Canada
| | - Giulio Calza
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Martin Fuhrmann
- c Neuroimmunology and Imaging Group , German Center for Neurodegenerative Diseases (DZNE) , Bonn , Germany
| | - Rabah Soliymani
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Marc Baumann
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Maciej Lalowski
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
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27
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Salvalaio M, D'Avanzo F, Rigon L, Zanetti A, D'Angelo M, Valle G, Scarpa M, Tomanin R. Brain RNA-Seq Profiling of the Mucopolysaccharidosis Type II Mouse Model. Int J Mol Sci 2017; 18:ijms18051072. [PMID: 28513549 PMCID: PMC5454982 DOI: 10.3390/ijms18051072] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage disorders (LSDs) are a group of about 50 genetic metabolic disorders, mainly affecting children, sharing the inability to degrade specific endolysosomal substrates. This results in failure of cellular functions in many organs, including brain that in most patients may go through progressive neurodegeneration. In this study, we analyzed the brain of the mouse model for Hunter syndrome, a LSD mostly presenting with neurological involvement. Whole transcriptome analysis of the cerebral cortex and midbrain/diencephalon/hippocampus areas was performed through RNA-seq. Genes known to be involved in several neurological functions showed a significant differential expression in the animal model for the disease compared to wild type. Among the pathways altered in both areas, axon guidance, calcium homeostasis, synapse and neuroactive ligand-receptor interaction, circadian rhythm, neuroinflammation and Wnt signaling were the most significant. Application of RNA sequencing to dissect pathogenic alterations of complex syndromes allows to photograph perturbations, both determining and determined by these disorders, which could simultaneously occur in several metabolic and biochemical pathways. Results also emphasize the common, altered pathways between neurodegenerative disorders affecting elderly and those associated with pediatric diseases of genetic origin, perhaps pointing out a general common course for neurodegeneration, independent from the primary triggering cause.
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Affiliation(s)
- Marika Salvalaio
- Women's and Children's Health Department, University of Padova, Via Giustiniani 3, 35128 Padova, Italy.
- Pediatric Research Institute-Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy.
| | - Francesca D'Avanzo
- Women's and Children's Health Department, University of Padova, Via Giustiniani 3, 35128 Padova, Italy.
- Pediatric Research Institute-Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy.
| | - Laura Rigon
- Women's and Children's Health Department, University of Padova, Via Giustiniani 3, 35128 Padova, Italy.
- Pediatric Research Institute-Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy.
| | - Alessandra Zanetti
- Women's and Children's Health Department, University of Padova, Via Giustiniani 3, 35128 Padova, Italy.
- Pediatric Research Institute-Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy.
| | - Michela D'Angelo
- CRIBI Biotechnology Center, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
| | - Giorgio Valle
- CRIBI Biotechnology Center, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
| | - Maurizio Scarpa
- Women's and Children's Health Department, University of Padova, Via Giustiniani 3, 35128 Padova, Italy.
- Pediatric Research Institute-Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy.
- Brains for Brain Foundation, Via Giustiniani 3, 35128 Padova, Italy.
| | - Rosella Tomanin
- Women's and Children's Health Department, University of Padova, Via Giustiniani 3, 35128 Padova, Italy.
- Pediatric Research Institute-Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy.
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28
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Widespread Expression of a Membrane-Tethered Version of the Soluble Lysosomal Enzyme Palmitoyl Protein Thioesterase-1. JIMD Rep 2017; 36:85-92. [PMID: 28213849 DOI: 10.1007/8904_2017_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/13/2016] [Accepted: 12/29/2016] [Indexed: 12/13/2022] Open
Abstract
"Cross-correction," the transfer of soluble lysosomal enzymes between neighboring cells, forms the foundation for therapeutics of lysosomal storage disorders (LSDs). However, "cross-correction" poses a significant barrier to studying the role of specific cell types in LSD pathogenesis. By expressing the native enzyme in only one cell type, neighboring cell types are invariably corrected. In this study, we present a strategy to limit "cross-correction" of palmitoyl-protein thioesterase-1(PPT1), a lysosomal hydrolase deficient in Infantile Neuronal Ceroid Lipofuscinosis (INCL, Infantile Batten disease) to the lysosomal membrane via the C-terminus of lysosomal associated membrane protein-1 (LAMP1). Tethering PPT1 to the lysosomal membrane prevented "cross-correction" while allowing PPT1 to retain its enzymatic function and localization in vitro. A transgenic line harboring the lysosomal membrane-tethered PPT1 was then generated. We show that expression of lysosome-restricted PPT1 in vivo largely rescues the INCL biochemical, histological, and functional phenotype. These data suggest that lysosomal tethering of PPT1 via the C-terminus of LAMP1 is a viable strategy and that this general approach can be used to study the role of specific cell types in INCL pathogenesis, as well as other LSDs. Ultimately, understanding the role of specific cell types in the disease progression of LSDs will help guide the development of more targeted therapeutics. One Sentence Synopsis: Tethering PPT1 to the lysosomal membrane is a viable strategy to prevent "cross-correction" and will allow for the study of specific cellular contributions in INCL pathogenesis.
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29
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Meyer M, Kovács AD, Pearce DA. Decreased sensitivity of palmitoyl protein thioesterase 1-deficient neurons to chemical anoxia. Metab Brain Dis 2017; 32:275-279. [PMID: 27722792 PMCID: PMC5335868 DOI: 10.1007/s11011-016-9919-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/03/2016] [Indexed: 01/12/2023]
Abstract
Infantile CLN1 disease, also known as infantile neuronal ceroid lipofuscinosis, is a fatal childhood neurodegenerative disorder caused by mutations in the CLN1 gene. CLN1 encodes a soluble lysosomal enzyme, palmitoyl protein thioesterase 1 (PPT1), and it is still unclear why neurons are selectively vulnerable to the loss of PPT1 enzyme activity in infantile CLN1 disease. To examine the effects of PPT1 deficiency on several well-defined neuronal signaling and cell death pathways, different toxic insults were applied in cerebellar granule neuron cultures prepared from wild type (WT) and palmitoyl protein thioesterase 1-deficient (Ppt1 -/- ) mice, a model of infantile CLN1 disease. Glutamate uptake inhibition by t-PDC (L-trans-pyrrolidine-2,4-dicarboxylic acid) or Zn2+-induced general mitochondrial dysfunction caused similar toxicity in WT and Ppt1 -/- cultures. Ppt1 -/- neurons, however, were more sensitive to mitochondrial complex I inhibition by MPP+ (1-methyl-4-phenylpyridinium), and had significantly decreased sensitivity to chemical anoxia induced by the mitochondrial complex IV inhibitor, sodium azide. Our results indicate that PPT1 deficiency causes alterations in the mitochondrial respiratory chain.
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Affiliation(s)
- Meredith Meyer
- Sanford Children's Health Research Center, Sanford Research, 2301 E. 60th Street, Sioux Falls, SD, 57104, USA
| | - Attila D Kovács
- Sanford Children's Health Research Center, Sanford Research, 2301 E. 60th Street, Sioux Falls, SD, 57104, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota Sioux Falls, Sioux Falls, SD, 57104, USA
| | - David A Pearce
- Sanford Children's Health Research Center, Sanford Research, 2301 E. 60th Street, Sioux Falls, SD, 57104, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota Sioux Falls, Sioux Falls, SD, 57104, USA.
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