Identification of characteristic genes distinguishing neural stem cells from astrocytes

Abstract Background Neural stem cells (NSCs) have unique biological characteristics such as continuous proliferation and multipotential differentiation, providing a possible method for restoration of central nervous system (CNS) function after injury or disease. NSCs and astrocytes share many similar biological properties including cell morphology and molecular expression and can trans-differentiate into each other under certain conditions. However, characteristic genes specifically expressed by NSCs have not been well described. Methods To provide insights into the characteristic expression of NSCs, bioinformatics analysis of two microarrays of mouse NSCs and astrocytes was performed. Compared to astrocytes, the differentially expressed genes (DEGs) in NSCs were identified and annotated by GO, KEGG and GSEA analysis, respectively. Then key genes were screened by protein-protein interaction (PPI) network and modules analysis, and were verified using multiple high-throughput sequencing resources. Finally, the expression difference between the two cell types was confirmed by Real-time Quantitative PCR (qPCR), western blotting and immunochemical analysis. Results In the present study, 282 and 250 NSC-enriched genes from two microarrays were identified and annotated respectively, and the 77 overlapping DEGs were then selected. From the PPI network 24 key genes in three modules were screened out. Importantly, sequencing data of tissues showed that these 24 key genes tended to be highly expressed in NSCs compared with astrocytes. Furthermore, qPCR and western blot analysis of cultured NSCs and astrocytes showed two genes ( KIF2C and TOP2A ) were not only differentially expressed in RNA level but also at the protein level. Importantly, the NSC-specific genes KIF2C and TOP2A were validated by immunohistochemistry in vivo . Conclusion In present study, we identified 2 hub genes ( KIF2C and TOP2A ) that might serve as potential biomarkers for distinguishing NSCs from astrocytes, contributing to our comprehensive understanding of the biological properties and functions of NSCs.