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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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2
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Gorenberg EL, Massaro Tieze S, Yücel B, Zhao HR, Chou V, Wirak GS, Tomita S, Lam TT, Chandra SS. Identification of substrates of palmitoyl protein thioesterase 1 highlights roles of depalmitoylation in disulfide bond formation and synaptic function. PLoS Biol 2022; 20:e3001590. [PMID: 35358180 PMCID: PMC9004782 DOI: 10.1371/journal.pbio.3001590] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/12/2022] [Accepted: 03/02/2022] [Indexed: 12/30/2022] Open
Abstract
Loss-of-function mutations in the depalmitoylating enzyme palmitoyl protein thioesterase 1 (PPT1) cause neuronal ceroid lipofuscinosis (NCL), a devastating neurodegenerative disease. The substrates of PPT1 are largely undescribed, posing a limitation on molecular dissection of disease mechanisms and therapeutic development. Here, we provide a resource identifying >100 novel PPT1 substrates. We utilized Acyl Resin-Assisted Capture (Acyl RAC) and mass spectrometry to identify proteins with increased in vivo palmitoylation in PPT1 knockout (KO) mouse brains. We then validated putative substrates through direct depalmitoylation with recombinant PPT1. This stringent screen elucidated diverse PPT1 substrates at the synapse, including channels and transporters, G-protein–associated molecules, endo/exocytic components, synaptic adhesion molecules, and mitochondrial proteins. Cysteine depalmitoylation sites in transmembrane PPT1 substrates frequently participate in disulfide bonds in the mature protein. We confirmed that depalmitoylation plays a role in disulfide bond formation in a tertiary screen analyzing posttranslational modifications (PTMs). Collectively, these data highlight the role of PPT1 in mediating synapse functions, implicate molecular pathways in the etiology of NCL and other neurodegenerative diseases, and advance our basic understanding of the purpose of depalmitoylation.
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Affiliation(s)
- Erica L. Gorenberg
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
- Interdepartmental Neuroscience Program, Yale University, New Haven, Connecticut, United States of America
| | - Sofia Massaro Tieze
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
- Interdepartmental Neuroscience Program, Yale University, New Haven, Connecticut, United States of America
| | - Betül Yücel
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
| | - Helen R. Zhao
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
| | - Vicky Chou
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
| | - Gregory S. Wirak
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
| | - Susumu Tomita
- Departments of Neuroscience and of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, United States of America
| | - TuKiet T. Lam
- Departments of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Keck MS & Proteomics Resource, WM Keck Biotechnology Resource Laboratory, New Haven, Connecticut, United States of America
| | - Sreeganga S. Chandra
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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3
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Qu M, Zhou X, Wang X, Li H. Lipid-induced S-palmitoylation as a Vital Regulator of Cell Signaling and Disease Development. Int J Biol Sci 2021; 17:4223-4237. [PMID: 34803494 PMCID: PMC8579454 DOI: 10.7150/ijbs.64046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/20/2021] [Indexed: 12/29/2022] Open
Abstract
Lipid metabolites are emerging as pivotal regulators of protein function and cell signaling. The availability of intracellular fatty acid is tightly regulated by glycolipid metabolism and may affect human body through many biological mechanisms. Recent studies have demonstrated palmitate, either from exogenous fatty acid uptake or de novo fatty acid synthesis, may serve as the substrate for protein palmitoylation and regulate protein function via palmitoylation. Palmitoylation, the most-studied protein lipidation, encompasses the reversible covalent attachment of palmitate moieties to protein cysteine residues. It controls various cellular physiological processes and alters protein stability, conformation, localization, membrane association and interaction with other effectors. Dysregulation of palmitoylation has been implicated in a plethora of diseases, such as metabolic syndrome, cancers, neurological disorders and infections. Accordingly, it could be one of the molecular mechanisms underlying the impact of palmitate metabolite on cellular homeostasis and human diseases. Herein, we explore the relationship between lipid metabolites and the regulation of protein function through palmitoylation. We review the current progress made on the putative role of palmitate in altering the palmitoylation of key proteins and thus contributing to the pathogenesis of various diseases, among which we focus on metabolic disorders, cancers, inflammation and infections, neurodegenerative diseases. We also highlight the opportunities and new therapeutics to target palmitoylation in disease development.
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Affiliation(s)
- Mengyuan Qu
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Zhou
- National Clinical Research Center for Infectious Disease; Department of liver Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xiaotong Wang
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Honggang Li
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
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4
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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5
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Ji B, Skup M. Roles of palmitoylation in structural long-term synaptic plasticity. Mol Brain 2021; 14:8. [PMID: 33430908 PMCID: PMC7802216 DOI: 10.1186/s13041-020-00717-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
Long-term potentiation (LTP) and long-term depression (LTD) are important cellular mechanisms underlying learning and memory processes. N-Methyl-d-aspartate receptor (NMDAR)-dependent LTP and LTD play especially crucial roles in these functions, and their expression depends on changes in the number and single channel conductance of the major ionotropic glutamate receptor α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) located on the postsynaptic membrane. Structural changes in dendritic spines comprise the morphological platform and support for molecular changes in the execution of synaptic plasticity and memory storage. At the molecular level, spine morphology is directly determined by actin cytoskeleton organization within the spine and indirectly stabilized and consolidated by scaffold proteins at the spine head. Palmitoylation, as a uniquely reversible lipid modification with the ability to regulate protein membrane localization and trafficking, plays significant roles in the structural and functional regulation of LTP and LTD. Altered structural plasticity of dendritic spines is also considered a hallmark of neurodevelopmental disorders, while genetic evidence strongly links abnormal brain function to impaired palmitoylation. Numerous studies have indicated that palmitoylation contributes to morphological spine modifications. In this review, we have gathered data showing that the regulatory proteins that modulate the actin network and scaffold proteins related to AMPAR-mediated neurotransmission also undergo palmitoylation and play roles in modifying spine architecture during structural plasticity.
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Affiliation(s)
- Benjun Ji
- Nencki Institute of Experimental Biology, 02-093, Warsaw, Poland.
| | - Małgorzata Skup
- Nencki Institute of Experimental Biology, 02-093, Warsaw, Poland.
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6
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Li W, Fan X, Zhang Y, Huang L, Jiang T, Qin Z, Su J, Luo J, Yi S, Zhang S, Shen Y. A novel pathogenic frameshift variant unmasked by a large de novo deletion at 13q21.33-q31.1 in a Chinese patient with neuronal ceroid lipofuscinosis type 5. BMC MEDICAL GENETICS 2020; 21:100. [PMID: 32393339 PMCID: PMC7216669 DOI: 10.1186/s12881-020-01039-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/29/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Neuronal ceroid lipofuscinosis type 5 (CLN5) is a rare form of neuronal ceroid lipofuscinoses (NCLs) which are a group of inherited neurodegenerative diseases characterized by progressive intellectual and motor deterioration, visual failure, seizures, behavioral changes and premature death. CLN5 was initially named Finnish variant late infantile NCL, it is now known to be present in other ethnic populations and with variable age of onset. Few CLN5 patients had been reported in Chinese population. CASE PRESENTATION In this paper, we report the symptoms of a Chinese patient who suffer from developmental regression and grand mal epilepsy for several years. The DNA was extracted from peripheral blood of proband and both parents, and then whole exome sequencing was performed using genomic DNA. Both sequence variants and copy number variants (CNVs) were analyzed and classified according to guidelines. As the result, a novel frameshift mutation c.718_719delAT/p.Met240fs in CLN5 and a de novo large deletion at 13q21.33-q31.1 which unmasked the frameshift mutation were identified in the proband. Despite the large de novo deletion, which can be classified as a pathogenic copy number variant (CNV), the patient's clinical presentation is mostly consistent with that of CLN5, except for early developmental delay which is believed due to the large deletion. Both variants were detected simultaneously by exome sequencing. CONCLUSIONS This is the first report of whole gene deletion in combination with a novel pathogenic sequence variant in a CLN5 patient. The two mutations detected with whole exome sequencing simultaneously proved the advantage of the sequencing technology for genetic diagnostics.
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Affiliation(s)
- Wei Li
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Xin Fan
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Yue Zhang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Limei Huang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Tingting Jiang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Zailong Qin
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Jiasun Su
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Jingrong Luo
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Shang Yi
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Shujie Zhang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China.
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA.
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7
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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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8
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Mice deficient in the lysosomal enzyme palmitoyl-protein thioesterase 1 (PPT1) display a complex retinal phenotype. Sci Rep 2019; 9:14185. [PMID: 31578378 PMCID: PMC6775149 DOI: 10.1038/s41598-019-50726-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/13/2019] [Indexed: 01/09/2023] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL) type 1 (CLN1) is a neurodegenerative storage disorder caused by mutations in the gene encoding the lysosomal enzyme palmitoyl-protein thioesterase 1 (PPT1). CLN1 patients suffer from brain atrophy, mental and motor retardation, seizures, and retinal degeneration ultimately resulting in blindness. Here, we performed an in-depth analysis of the retinal phenotype of a PPT1-deficient mouse, an animal model of this condition. Reactive astrogliosis and microgliosis were evident in mutant retinas prior to the onset of retinal cell loss. Progressive accumulation of storage material, a pronounced dysregulation of various lysosomal proteins, and accumulation of sequestosome/p62-positive aggregates in the inner nuclear layer also preceded retinal degeneration. At advanced stages of the disease, the mutant retina was characterized by a significant loss of ganglion cells, rod and cone photoreceptor cells, and rod and cone bipolar cells. Results demonstrate that PPT1 dysfunction results in early-onset pathological alterations in the mutant retina, followed by a progressive degeneration of various retinal cell types at relatively late stages of the disease. Data will serve as a reference for future work aimed at developing therapeutic strategies for the treatment of retinal degeneration in CLN1 disease.
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9
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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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10
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Sapir T, Segal M, Grigoryan G, Hansson KM, James P, Segal M, Reiner O. The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function. Front Cell Neurosci 2019; 13:92. [PMID: 30918483 PMCID: PMC6424868 DOI: 10.3389/fncel.2019.00092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/25/2019] [Indexed: 12/12/2022] Open
Abstract
Palmitoyl-protein thioesterase 1 (PPT1) is a depalmitoylation enzyme that is mutated in cases of neuronal ceroid lipofuscinosis (NCL). The hallmarks of the disease include progressive neurodegeneration and blindness, as well as seizures. In the current study, we identified 62 high-confident PPT1-binding proteins. These proteins included a self-interaction of PPT1, two V-type ATPases, calcium voltage-gated channels, cytoskeletal proteins and others. Pathway analysis suggested their involvement in seizures and neuronal morphology. We then proceeded to demonstrate that hippocampal neurons from Ppt1−/− mice exhibit structural deficits, and further investigated electrophysiology parameters in the hippocampi of mutant mice, both in brain slices and dissociated postnatal primary cultures. Our studies reveal new mechanistic features involved in the pathophysiology of this devastating neurodegenerative disease.
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Affiliation(s)
- Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Segal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gayane Grigoryan
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Karin M Hansson
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Peter James
- Department of Immunotechnology, Lund University, Lund, Sweden.,Turku Centre for Biotechnology (BTK), University of Turku, Turku, Finland
| | - Menahem Segal
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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11
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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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