Genomewide analysis of S6K1-depleted human dorsal forebrain organoids [RNA-seq]

To elucidate the role of S6K1 in human brain development, we performed next-generation sequencing-based genomweide analysis of S6K1 knockout (KO) human embryonic stem cells (ESCs) and brain organoids. Development/differentiation-related genes were highly enriched in DEGs of S6K1 KO hESCs compared to WT hESCs. Single cell transcriptomic analysis showed unusual retinal cell development in S6K1-depleted brain organoids, thereby reducing neural populations. Furthermore, we generated brain organoids containing both WT and S6K1 KO cells and then isolated them after completing differentiation to compare the feature of each portion grown in mixed condition. ATAC sequencing analysis of each portion in mixed brain organoids displayed no significant differences in retinal cell marker gene transcriptomes between WT and S6K1 KO portions, while chromatin accessibility of neural-specific genes were lower in S6K1 KO portion than WT. Collectively, this study revealed that S6K1 plays dual role in human brain development; suppression of retinal lineage specification and production of mature neurons through non-cell autonomous and cell autonomous action, respectively. Bulk RNA sequencing of three replicates of WT and three replicates of S6K1-depleted human embryonic stem cells line (H7)