title: Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease.
abstract: BACKGROUND
  The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's disease (PD) and other neurodegenerative diseases has not yet been systematically evaluated.
  
  
  RESULTS
  We have used a systems genomics approach to characterize the SH-SY5Y cell line using whole-genome sequencing to determine the genetic content of the cell line and used transcriptomics and proteomics data to determine molecular correlations. Further, we integrated genomic variants using a network analysis approach to evaluate the suitability of the SH-SY5Y cell line for perturbation experiments in the context of neurodegenerative diseases, including PD.
  
  
  CONCLUSIONS
  The systems genomics approach showed consistency across different biological levels (DNA, RNA and protein concentrations). Most of the genes belonging to the major Parkinson's disease pathways and modules were intact in the SH-SY5Y genome. Specifically, each analysed gene related to PD has at least one intact copy in SH-SY5Y. The disease-specific network analysis approach ranked the genetic integrity of SH-SY5Y as higher for PD than for Alzheimer's disease but lower than for Huntington's disease and Amyotrophic Lateral Sclerosis for loss of function perturbation experiments.
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg. abhimanyu.krishna@uni.lu.
authors.forename: Abhimanyu
authors.initials: A
authors.lastname: Krishna
authors.forename: Maria
authors.initials: M
authors.lastname: Biryukov
authors.forename: Christophe
authors.initials: C
authors.lastname: Trefois
authors.forename: Paul M A
authors.initials: PM
authors.lastname: Antony
authors.forename: Rene
authors.initials: R
authors.lastname: Hussong
authors.forename: Jake
authors.initials: J
authors.lastname: Lin
authors.forename: Merja
authors.initials: M
authors.lastname: Heinäniemi
authors.forename: Gustavo
authors.initials: G
authors.lastname: Glusman
authors.forename: Sandra
authors.initials: S
authors.lastname: Köglsberger
authors.forename: Olga
authors.initials: O
authors.lastname: Boyd
authors.forename: Bart H J
authors.initials: BH
authors.lastname: van den Berg
authors.forename: Dennis
authors.initials: D
authors.lastname: Linke
authors.forename: David
authors.initials: D
authors.lastname: Huang
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Andreas
authors.initials: A
authors.lastname: Tholey
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schneider
authors.forename: David J
authors.initials: DJ
authors.lastname: Galas
authors.forename: Rudi
authors.initials: R
authors.lastname: Balling
authors.forename: Patrick
authors.initials: P
authors.lastname: May
mesh_terms: D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D004251:DNA Transposable Elements / Q000235:genetics; D020869:Gene Expression Profiling; D014644:Genetic Variation; D023281:Genomics; D006801:Humans; D054643:INDEL Mutation; D009447:Neuroblastoma / Q000473:pathology*; D010300:Parkinson Disease / Q000235:genetics*; D040901:Proteomics
chemical_list: D004251:DNA Transposable Elements