Transcriptomic analysis of CNTF-treated mouse subventricular zone-derived neurosphere culture reveals key transcription factor genes related to adult neurogenesis

Neural Stem Progenitor Cells (NSPCs) maintenance and neuronal cell differentiation are the two key aspects of sustained neurogenesis in the adult mammalian brain. Transcription factors (TFs) are known to regulate these biological processes under the influence of various neurotrophic factors. Understanding the role of key TF genes in regulating adult neurogenesis is essential for determining the functional complexity and neuronal diversity seen in the adult mammalian brain. Although several molecular mechanisms leading to adult neurogenesis have been reported, details on its transcriptional regulation are still limited. Our initial results showed that Ciliary Neurotrophic Factor (CNTF) induced neuronal differentiation in SVZ-derived NSPC cultures. To investigate further the role of CNTF in inducing the expression of TF genes related to adult neurogenesis and the potential pathways involved, whole transcriptome RNA-sequencing (RNA-seq) analysis was done in CNTF-treated Sub-ventricular Zone derived neurosphere cultures from the mouse brain. The study revealed 483 differentially expressed genes (DEGs), among which 33 DEGs were identified as coding for transcription factors (TFs). Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis revealed MAPK, PI3K-Akt, and FoxO as the significantly enriched signaling pathways. Gene co-expression network analysis identified five upregulated TF genes related to adult neurogenesis (Runx1, Hmga2, Fos, ID2, and Prrx1) in a single cluster, interacting with each other, and was also validated by quantitative PCR. Our data suggest several potential TFs that may act as critical regulators in the intrinsic transcriptional networks driving the adult neurogenesis process. Further investigation into these molecular regulators may yield a homogeneous population of neuronal progenitors for translational stem cell studies in the future.