Cellular and Molecular Neurobiology

, Volume 37, Issue 4, pp 665–682 | Cite as

Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells

  • Francesco Pezzini
  • Laura Bettinetti
  • Francesca Di Leva
  • Marzia Bianchi
  • Elisa Zoratti
  • Rosalba Carrozzo
  • Filippo M. Santorelli
  • Massimo Delledonne
  • Maciej Lalowski
  • Alessandro Simonati
Original Research


Human SH-SY5Y neuroblastoma cells are widely utilized in in vitro studies to dissect out pathogenetic mechanisms of neurodegenerative disorders. These cells are considered as neuronal precursors and differentiate into more mature neuronal phenotypes under selected growth conditions. In this study, in order to decipher the pathways and cellular processes underlying neuroblastoma cell differentiation in vitro, we performed systematic transcriptomic (RNA-seq) and bioinformatic analysis of SH-SY5Y cells differentiated according to a two-step paradigm: retinoic acid treatment followed by enriched neurobasal medium. Categorization of 1989 differentially expressed genes (DEGs) identified in differentiated cells functionally linked them to changes in cell morphology including remodelling of plasma membrane and cytoskeleton, and neuritogenesis. Seventy-three DEGs were assigned to axonal guidance signalling pathway, and the expression of selected gene products such as neurotrophin receptors, the functionally related SLITRK6, and semaphorins, was validated by immunoblotting. Along with these findings, the differentiated cells exhibited an ability to elongate longer axonal process as assessed by the neuronal cytoskeletal markers biochemical characterization and morphometric evaluation. Recognition of molecular events occurring in differentiated SH-SY5Y cells is critical to accurately interpret the cellular responses to specific stimuli in studies on disease pathogenesis.


SH-SY5Y differentiation RNA-seq analysis Axonal guidance signalling Semaphorins Neuronal markers Axonal elongation 



Brain-derived neurotrophic factor


Dibutyryl-cyclic AMP


Differentially expressed gene


Frizzled receptors


Fragments per kilobase per million mapped reads


QIAGEN’s ingenuity® pathway analysis


Log2 fold change (ratio between averaged FPKM of RA-NBM differentiated cells and the averaged FPKM of untreated cells)


Nerve growth factor


Nerve growth factor receptor






Neurotrophic tyrosine kinase receptor type 2


Plexin A4


Phosphorylated heavy-chain neurofilament proteins


Phosphorylated medium-chain neurofilament proteins


All trans retinoic acid


9-day-long differentiation paradigm in which SH-SY5Y cells were pre-differentiated in RA medium (6 days) and subsequently treated with neurobasal medium enriched with neurotrophic factors (3 days)


9-day-long differentiation paradigm in which SH-SY5Y cells were pre-differentiated in RA medium (6 days) and subsequently treated with serum-free medium containing rhBDNF (3 days)




SLIT and NTRK-like family


Synapsin I



Dr. A. Ferrarini and Dr. E. Dal Molin from the Department of Biotechnology of Verona University are fully acknowledged for their experienced support with RNA-seq analysis. We are grateful to the scientists and technicians of the Laboratory of Neuropathology, University of Verona School of Medicine. We also thank Dr. Enzo Scifo (University of Toronto, Canada) for critical comments on the manuscript.

Author contributions

F.P: designed and performed experiments, interpreted data, prepared figures and tables, and wrote the manuscript; L.B.: performed experiments and analysed data; F.DiL.: analysed and interpreted data; M.B.: analysed data; E.Z.: performed experiments and analysed data; R.C.: analysed and interpreted data; M.D.: designed experiments, interpreted data, revised the manuscript; F.M.S.: conceived the study, and revised the manuscript; M.L. designed the study, analysed and interpreted data, prepared figures, revised the manuscript; A.S.: conceived and designed the study, analysed and interpreted data, drafted and revised the manuscript.


This study was funded by European Union Seventh Framework Programme (FP7/2007-2013) under Grant Agreement No 281234.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Neuroscience, Biomedicine and MovementUniversity of VeronaVeronaItaly
  2. 2.Department of BiotechnologiesUniversity of VeronaVeronaItaly
  3. 3.Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineIRCCS Bambino Gesù Children’s HospitalRomeItaly
  4. 4.Applied Research on Cancer-Network (ARC-NET)University of VeronaVeronaItaly
  5. 5.Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineIRCCS Stella MarisCalambrone-PisaItaly
  6. 6.Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core FacilityUniversity of HelsinkiHelsinkiFinland
  7. 7.Aptuit s.r.l.VeronaItaly

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