title: Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules.
abstract: Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural features and biochemical compositions. The molecular mechanisms causing progressive neurodegeneration and common molecular pathways linking expression of different NCL genes are largely unknown. We analyzed proteome alterations in the brains of a mouse model of human infantile CLN1 disease-palmitoyl-protein thioesterase 1 (Ppt1) gene knockout and its wild-type age-matched counterpart at different stages: pre-symptomatic, symptomatic and advanced. For this purpose, we utilized a combination of laser capture microdissection-based quantitative liquid chromatography tandem mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight MS imaging to quantify/visualize the changes in protein expression in disease-affected brain thalamus and cerebral cortex tissue slices, respectively. Proteomic profiling of the pre-symptomatic stage thalamus revealed alterations mostly in metabolic processes and inhibition of various neuronal functions, i.e., neuritogenesis. Down-regulation in dynamics associated with growth of plasma projections and cellular protrusions was further corroborated by findings from RNA sequencing of CLN1 patients' fibroblasts. Changes detected at the symptomatic stage included: mitochondrial functions, synaptic vesicle transport, myelin proteome and signaling cascades, such as RhoA signaling. Considerable dysregulation of processes related to mitochondrial cell death, RhoA/Huntington's disease signaling and myelin sheath breakdown were observed at the advanced stage of the disease. The identified changes in protein levels were further substantiated by bioinformatics and network approaches, immunohistochemistry on brain tissues and literature knowledge, thus identifying various functional modules affected in the CLN1 childhood encephalopathy.
authors.affiliation: Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.|Folkhälsan Institute of Genetics, 00014, Helsinki, Finland.
authors.forename: Saara
authors.initials: S
authors.lastname: Tikka
authors.affiliation: Folkhälsan Institute of Genetics, 00014, Helsinki, Finland.|Joint Research Centre, Directorate D-Institute for Reference Materials and Measurements, Standards for Innovation and Sustainable Development, Geel, Belgium.
authors.forename: Evanthia
authors.initials: E
authors.lastname: Monogioudi
authors.affiliation: Brain and Mind Laboratory, Department of Biomedical Engineering and Computational Science (BECS), Aalto University School of Science, 02150, Espoo, Finland.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Gotsopoulos
authors.affiliation: Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.
authors.forename: Rabah
authors.initials: R
authors.lastname: Soliymani
authors.affiliation: Department of Neurological and Movement Sciences, University of Verona, 37134, Verona, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Pezzini
authors.affiliation: Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.|Doctoral Program Brain & Mind, University of Helsinki, Helsinki, Finland.|Campbell Family Mental Health Research Institute, CAMH, University of Toronto, Toronto, Canada.
authors.forename: Enzo
authors.initials: E
authors.lastname: Scifo
authors.affiliation: Folkhälsan Institute of Genetics, 00014, Helsinki, Finland.|Genomics and Biomarkers, National Institute for Health and Welfare (THL), P.O. Box 30, 00271, Helsinki, Finland.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Uusi-Rauva
authors.affiliation: Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.
authors.forename: Jaana
authors.initials: J
authors.lastname: Tyynelä
authors.affiliation: Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.
authors.forename: Marc
authors.initials: M
authors.lastname: Baumann
authors.affiliation: Institute for Molecular Medicine (FIMM), University of Helsinki, 00014, Helsinki, Finland.|Genomics and Biomarkers, National Institute for Health and Welfare (THL), P.O. Box 30, 00271, Helsinki, Finland.
authors.forename: Anu
authors.initials: A
authors.lastname: Jalanko
authors.affiliation: Department of Neurological and Movement Sciences, University of Verona, 37134, Verona, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Simonati
authors.affiliation: Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland. maciej.lalowski@helsinki.fi.|Folkhälsan Institute of Genetics, 00014, Helsinki, Finland. maciej.lalowski@helsinki.fi.
authors.forename: Maciej
authors.identifier: http://orcid.org/0000-0002-3683-4096
authors.initials: M
authors.lastname: Lalowski
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D002540:Cerebral Cortex / Q000378:metabolism* / Q000473:pathology / Q000503:physiopathology; D004195:Disease Models, Animal; D018450:Disease Progression; D005347:Fibroblasts / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D061346:Laser Capture Microdissection; D008297:Male; D051379:Mice; D008928:Mitochondria; D008959:Models, Neurological; D009186:Myelin Sheath / Q000473:pathology; D009419:Nerve Tissue Proteins / Q000096:biosynthesis* / Q000235:genetics; D016501:Neurites / Q000473:pathology; D009472:Neuronal Ceroid-Lipofuscinoses / Q000235:genetics / Q000378:metabolism* / Q000473:pathology / Q000503:physiopathology; D040901:Proteomics; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013788:Thalamus / Q000378:metabolism* / Q000473:pathology / Q000503:physiopathology; D013869:Thiolester Hydrolases / Q000172:deficiency / Q000235:genetics
chemical_list: D009419:Nerve Tissue Proteins; D013869:Thiolester Hydrolases; C095299:palmitoyl-protein thioesterase
keywords: Classic infantile NCL; LC-MSE, lysosomal storage disorders; Laser capture microdissection; MALDI-MSI; PPT1—palmitoyl-protein thioesterase 1; RNA sequence analysis