Abstract
The SH-SY5Y culture system is a convenient neuronal model with the potential to elaborate human/primate-specific transcription networks and pathways related to human cognitive disorders. While this system allows for the exploration of specialized features in the human genome, there is still significant debate about how this model should be implemented, and its appropriateness for answering complex functional questions related to human neural architecture. In view of these questions we sought to characterize the posttranscriptional regulatory structure of the two-stage ATRA differentiation, BDNF maturation protocol proposed by Encinas et al. (2000) using integrative whole-genome gene and microRNA (miRNA) expression analysis. We report that ATRA-BDNF induced significant increases in expression of key synaptic genes, brain-specific miRNA and miRNA biogenesis machinery, and in AChE activity, compared with ATRA alone. Functional annotation clustering associated BDNF more significantly with neuronal terms, and with synaptic terms not found in ATRA-only clusters. While our results support use of SH-SY5Y as a neuronal model, we advocate considered selection of the differentiation agent/s relative to the system being modeled.
Highlights
The nervous system, and in particular the brain, arguably represents the most complex area of human biology
Polysome profiling of active translation conducted by Schratt and colleagues demonstrated that brain-derived neurotrophic factor (BDNF) is required to stimulate local translation of key synaptic components such as CamKII, NMDA receptors NR1, and NR3, PSD93 and LIMK-1 (Schratt et al, 2004). These findings suggest the employment of BDNF for in vitro neuronal maturation may produce cells more closely matching the phenotype and, importantly, gene expression profile of neurons in vivo
Our results presented here suggest that the sequential ATRA differentiation-BDNF maturation program yields a cell www.frontiersin.org www.frontiersin.org
Summary
The nervous system, and in particular the brain, arguably represents the most complex area of human biology. Polysome profiling of active translation conducted by Schratt and colleagues demonstrated that BDNF is required to stimulate local translation of key synaptic components such as CamKII, NMDA receptors NR1, and NR3, PSD93 and LIMK-1 (Schratt et al, 2004) These findings suggest the employment of BDNF for in vitro neuronal maturation may produce cells more closely matching the phenotype and, importantly, gene expression profile of neurons in vivo. When compared with both control and ATRA-treated cohorts, BDNF-matured samples were strikingly enriched for neuronally relevant clusters including “neuron projection” (ES = 4.83, corrected p = 0.00027) and “synaptic transmission” (ES = 2.33, corrected p = 0.03) Some of these terms were present in the ATRA results, they were not significant (Table 1B). The magnitude of the response increased with ATRA concentration used to induce differentiation (Supplementary Figure S3), possibly due to the expression of more BDNF receptors at higher ATRA concentrations
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