title: Proteomic analysis of the palmitoyl protein thioesterase 1 interactome in SH-SY5Y human neuroblastoma cells.
abstract: Neuronal ceroid lipofuscinoses (NCL) are a group of inherited progressive childhood disorders, characterized by early accumulation of autofluorescent storage material in lysosomes of neurons or other cells. Clinical symptoms of NCL include: progressive loss of vision, mental and motor deterioration, epileptic seizures and premature death. CLN1 disease (MIM#256730) is caused by mutations in the CLN1 gene, which encodes palmitoyl protein thioesterase 1 (PPT1). In this study, we utilised single step affinity purification coupled to mass spectrometry (AP-MS) to unravel the in vivo substrates of human PPT1 in the brain neuronal cells. Protein complexes were isolated from human PPT1 expressing SH-SY5Y stable cells, subjected to filter-aided sample preparation (FASP) and analysed on a Q Exactive Hybrid Quadrupole-Orbitrap mass spectrometer. A total of 23 PPT1 interacting partners (IP) were identified from label free quantitation of the MS data by SAINT platform. Three of the identified PPT1 IP, namely CRMP1, DBH, and MAP1B are predicted to be palmitoylated. Our proteomic analysis confirmed previously suggested roles of PPT1 in axon guidance and lipid metabolism, yet implicates the enzyme in novel roles including: involvement in neuronal migration and dopamine receptor mediated signalling pathway.
  
  
  CONCLUSIONS
  The significance of this work lies in the unravelling of putative in vivo substrates of human CLN1 or PPT1 in brain neuronal cells. Moreover, the PPT1 IP implicate the enzyme in novel roles including: involvement in neuronal migration and dopamine receptor mediated signalling pathway.
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland; Doctoral Program Brain & Mind, University of Helsinki, Helsinki, Finland. Electronic address: enzo.scifo@helsinki.fi.
authors: Enzo
authors: E
authors: Scifo
authors: Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.
authors: Agnieszka
authors: A
authors: Szwajda
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors: Rabah
authors: R
authors: Soliymani
authors: Department of Neurological and Movement Sciences, University of Verona, Verona, Italy.
authors: Francesco
authors: F
authors: Pezzini
authors: Department of Neurological and Movement Sciences, University of Verona, Verona, Italy; Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
authors: Marzia
authors: M
authors: Bianchi
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors: Arvydas
authors: A
authors: Dapkunas
authors: Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
authors: Janusz
authors: J
authors: Dębski
authors: Folkhälsan Institute of Genetics, Helsinki, Finland; National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland.
authors: Kristiina
authors: K
authors: Uusi-Rauva
authors: Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
authors: Michał
authors: M
authors: Dadlez
authors: Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada.
authors: Anne-Claude
authors: AC
authors: Gingras
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors: Jaana
authors: J
authors: Tyynelä
authors: Department of Neurological and Movement Sciences, University of Verona, Verona, Italy.
authors: Alessandro
authors: A
authors: Simonati
authors: Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland; National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland.
authors: Anu
authors: A
authors: Jalanko
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors: Marc H
authors: MH
authors: Baumann
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland; Folkhälsan Institute of Genetics, Helsinki, Finland. Electronic address: maciej.lalowski@helsinki.fi.
authors: Maciej
authors: M
authors: Lalowski
mesh_terms: D001369:Axons / Q000378:metabolism; D001921:Brain / Q000378:metabolism; D045744:Cell Line, Tumor; D002465:Cell Movement; D004734:Energy Metabolism; D015972:Gene Expression Regulation, Neoplastic; D006031:Glycosylation; D057809:HEK293 Cells; D006801:Humans; D008247:Lysosomes / Q000378:metabolism; D013058:Mass Spectrometry; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D008856:Microscopy, Fluorescence; D008928:Mitochondria / Q000502:physiology; D009154:Mutation; D009447:Neuroblastoma / Q000378:metabolism*; D009472:Neuronal Ceroid-Lipofuscinoses / Q000378:metabolism; D009474:Neurons / Q000378:metabolism; D016366:Open Reading Frames; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction; D013869:Thiolester Hydrolases
chemical_list: D008565:Membrane Proteins; D013869:Thiolester Hydrolases; C416054:PPT1 protein, human
keywords: Affinity purification; CLN1 disease; Interactome; Mass spectrometry; Neuronal ceroid lipofuscinoses; Palmitoyl protein thioesterase 1