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

Abstract

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.

RA Differentiation Enhances Dopaminergic Features, Changes Redox Parameters, and Increases Dopamine Transporter Dependency in 6-Hydroxydopamine-Induced Neurotoxicity in SH-SY5Y Cells

“…There are many lines of evidence showing the effect of RA-differentiation in SH-SY5Y regarding the evaluation of proliferation rates (Ross 1996;Pezzini et al 2016;Kunzler et al 2016). Previous studies have demonstrated that RAinduced differentiation can cause cell cycle arrest either in G1/G0 phase or in G2/M phase and a decrease in proliferation rates, which leads to terminal differentiation of neuroblastoma cells (Qiao et al 2012;Hämmerle et al 2013).…”

The Networks of Genes Encoding Palmitoylated Proteins in Axonal and Synaptic Compartments Are Affected in PPT1 Overexpressing Neuronal-Like Cells

“…Human neuroblastoma SH-SY5Y cells (catalog number #94030304 European Collection of Cell Cultures) were cultured in DMEM-High glucose medium supplemented with 15% Foetal Bovine Serum (FBS), 2 mM L-glutamine and 1% non-essential amino acids (all from Euroclone), at 37°C in humified atmosphere with 5% CO 2 , as described (Pezzini et al, 2017 ).…”

“…The aim of this study was to recognize molecular signatures and functional modules connected with overexpressed CLN1 in human neuronal cellular system. We utilized SH-SY5Y neuroblastoma cells (differentiated into a neuronal-like phenotype, Pezzini et al, 2017 ) to overexpress wt CLN1 and a selection of disease related mutations previously detected in CLN1-affected children. The differentiated cell lines underwent whole transcriptomic profiling by RNA-seq, to identify differentially expressed genes (DEGs) which are functionally related to the overexpression of wild-type or mutated PPT1.…”

Translation of upstream open reading frames in a model of neuronal differentiation

“…Treatment of human neuroblastoma cells with retinoic acid triggers their exit from the cell cycle and their differentiation into a neuron-like cell type (Sidell 1982, Pahlman, Ruusala et al 1984. While many studies have sought to understand genetic changes underlying this process, most have focused on transcript-level changes, with evaluation of shifts in protein abundance only studied on a case-by-case basis (Hanada, Krajewski et al 1993, Kaplan, Matsumoto et al 1993, Korecka, van Kesteren et al 2013, Pezzini, Bettinetti et al 2017). Here we used RP in this simple model system to study the role of uORF activity in regulating protein translation during neuronal differentiation.…”