Transcriptional and chromatin accessibility profiling of neural stem cells differentiating into astrocytes reveal dynamic signatures under homeostatic and inflammatory conditions [RNA-Seq]
Astrocytes arise from multipotent neural stem cells (NSCs) and represent the most abundant cell type of the central nervous system (CNS) playing key roles in the developing and adult brain. Since the differentiation of NSCs towards a gliogenic fate is a precisely timed and regulated process, its perturbation gives rise to dysfunctional astrocytic phenotypes. Inflammation, which often underlies neurological disorders, including neurodevelopmental disorders and brain tumors, disrupts the accurate developmental process of NSCs. However, the specific consequences of an inflammatory environment on the epigenetic and transcriptional programs underlying NSCs differentiation into astrocytes is unexplored yet. Here, we address this gap by profiling glial precursors from neural tissue derived from early embryonic stages along their astrocytic differentiation trajectory in the presence or absence of tumor necrosis factor-alpha (TNF), a master pro-inflammatory cytokine. By using a combination of RNA- and ATAC-sequencing approaches, together with footprint and integrated gene regulatory network analyses, we here identify key differences during the differentiation of NSCs into astrocytes under physiological and inflammatory settings. Notably, in agreement with its role to turn cells resistant to inflammatory challenges, we detect Nrf2 as a master transcription factor supporting the astrocytic differentiation under TNF exposure. Further, under these conditions, we unravel additional transcriptional regulatory hubs, including Stat3, Smad3, Cebpb and Nfkb2, highlighting the interplay between signaling pathways underlying physiological astrocytic developmental processes and those involved in inflammatory responses. Overall, our study reports key transcriptional and epigenetic changes leading to the identification of molecular regulators of the astrocytic differentiation. Furthermore, our analyses provide a valuable resource for understanding inflammation-induced astrocytic phenotypes that might contribute to the development and progression of CNS disorders with an inflammatory component. Overall design: RNA-Seq data at multiple timepoints from developing astrocytes under normal and inflammatory conditions