title: Drafting the CLN3 protein interactome in SH-SY5Y human neuroblastoma cells: a label-free quantitative proteomics approach.
abstract: Neuronal ceroid lipofuscinoses (NCL) are the most common inherited progressive encephalopathies of childhood. One of the most prevalent forms of NCL, Juvenile neuronal ceroid lipofuscinosis (JNCL) or CLN3 disease (OMIM: 204200), is caused by mutations in the CLN3 gene on chromosome 16p12.1. Despite progress in the NCL field, the primary function of ceroid-lipofuscinosis neuronal protein 3 (CLN3) remains elusive. In this study, we aimed to clarify the role of human CLN3 in the brain by identifying CLN3-associated proteins using a Tandem Affinity Purification coupled to Mass Spectrometry (TAP-MS) strategy combined with Significance Analysis of Interactome (SAINT). Human SH-SY5Y-NTAP-CLN3 stable cells were used to isolate native protein complexes for subsequent TAP-MS. Bioinformatic analyses of isolated complexes yielded 58 CLN3 interacting partners (IP) including 42 novel CLN3 IP, as well as 16 CLN3 high confidence interacting partners (HCIP) previously identified in another high-throughput study by Behrends et al., 2010. Moreover, 31 IP of ceroid-lipofuscinosis neuronal protein 5 (CLN5) were identified (18 of which were in common with the CLN3 bait). Our findings support previously suggested involvement of CLN3 in transmembrane transport, lipid homeostasis and neuronal excitability, as well as link it to G-protein signaling and protein folding/sorting in the ER.
authors: Meilahti Clinical Proteomics Core Facility, Institute of Biomedicine/Anatomy, and Finnish Graduate School of Neuroscience, University of Helsinki, Helsinki, Finland. enzo.scifo@helsinki.fi
authors: Enzo
authors: E
authors: Scifo
authors: Agnieszka
authors: A
authors: Szwajda
authors: Janusz
authors: J
authors: Dębski
authors: Kristiina
authors: K
authors: Uusi-Rauva
authors: Tapio
authors: T
authors: Kesti
authors: Michał
authors: M
authors: Dadlez
authors: Anne-Claude
authors: AC
authors: Gingras
authors: Jaana
authors: J
authors: Tyynelä
authors: Marc H
authors: MH
authors: Baumann
authors: Anu
authors: A
authors: Jalanko
authors: Maciej
authors: M
authors: Lalowski
mesh_terms: D045744:Cell Line, Tumor; D002846:Chromatography, Affinity; D057809:HEK293 Cells; D006801:Humans; D047468:Immunoprecipitation; D008562:Membrane Glycoproteins / Q000378:metabolism*; D018832:Molecular Chaperones / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D009447:Neuroblastoma; D009472:Neuronal Ceroid-Lipofuscinoses / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D021381:Protein Transport; D020543:Proteome / Q000302:isolation & purification / Q000378:metabolism*; D040901:Proteomics; D021241:Spectrometry, Mass, Electrospray Ionization; D053719:Tandem Mass Spectrometry
chemical_list: C105199:CLN3 protein, human; D008562:Membrane Glycoproteins; D018832:Molecular Chaperones; D020543:Proteome