Fig. 4: LSD1 inhibition rescues Setd1a deficiency-induced gene expression changes in cultured quiescent adult NSCs.

a, b Sample confocal images of immunostaining of Ki67, GFP and DAPI (a; scale bars: 20 μm) and quantification of percentages of Ki67⁺GFP⁺ active NSCs among total GFP⁺ cells at days 5, 7 and 9 after lentivirus infection to express GFP or Cre-GFP in Setd1a-deficient NSCs at day 2. In b, each dot represents data from one image. Values represent mean ± SEM (n = 3 independent cultures for each condition). c, d Pathway analysis of differentially expressed genes upon Setd1a deletion in adult NSCs. Shown in (c) are heatmaps of GO analysis (biological process) of downregulated and upregulated genes in NSCs from days 4 to 9 with GFP or Cre-GFP expression, indicating dysregulated expression of cell cycle genes and DNA repair genes. Shown in (d) is a heatmap of KEGG pathway analysis of downregulated genes from days 4 to 9, revealing downregulated metabolic pathways. e, f Sample confocal images of immunostaining of Ki67, GFP, and DAPI (e; scale bars: 20 μm) and quantification of percentages of Ki67⁺GFP⁺ proliferating NSCs among total GFP⁺ cells under the treatment of LSD1 inhibitor ORY-1001 or DMSO as control at days 5, 7 and 9 with lentivirus to express GFP or Cre-GFP at day 2 (f). Values represent mean ± SEM (n = 3 independent cultures for each condition). g-j RNA-seq analysis of WT (GFP) and Setd1a-difficient (Cre-GFP) NSCs under the treatment of DMSO (control), or LSD1 inhibitor ORY-1001. Shown in (g) is a PCA plot of biological replicates. Shown in (h) are Volcano plots of differentially expressed genes under different conditions. Shown in (i and j) are Venn diagrams of genes that were dysregulated by Setd1a deletion and were rescued by LSD1 inhibitor treatment (left) and GO analysis (biological process) of these genes (right). Two-tailed Student’s t-test is performed for statistical analysis and P values are listed. Source data are provided as a Source Data file.