Fig. 2: Inhibition of KDM1A regulates liver-TEs and impedes HCC cell growth.
a Analysis of the enrichment level of transcription regulatory (TR) proteins on liver-TE elements using ReMapEnrich software, which employed a two-sided binomial test, with p-values adjusted for multiple comparisons using the Benjamini–Yekutieli (BY) method. x: The number of overlaps/total number of liver-TEs, y: Log2 (No. Peaks overlapped with liver-TEs/No. Peaks overlapped with shuffled regions). The exact significance value for each TR was provided in Supplementary Data 4. b Heatmap showing the ChIP-seq profiles of KDM1A within the liver-TE ± 3 kb regions. The control is a set of randomly shuffled regions of the same length as the liver-TEs. c Ngsplot shows the ATAC-seq signal intensity within liver-TEs and the ±10 kb regions in HepG2 cells with downregulated KDM1A. The signal intensity within randomly shuffled TEs was used as control. d CUT&Tag-seq experiments for H3K4me1, H3K4me2, H3K9me2, and H3K27ac were performed in KDM1A downregulated HepG2 cells. Ngsplot was utilized to illustrate changes in histone modifications in liver-TEs and the ±10 kb regions. The signal intensity within randomly shuffled TEs was used as control. e Venn plot shows the liver-TE-associated genes targeted by KDM1A. f RNA-seq experiment and GSEA analysis show the effect of knocking down KDM1A on the expression of a single set of liver-TE-associated genes. The two-sided GSEA analysis was performed without p-value adjustment. g Colony formation assay was performed to assess the growth-inhibitory effects of KDM1A knockdown on liver cancer cells, n = 3 biological replicates. Statistical analyses were performed using a two-sided t-test, and mean ± SD was shown. h, i Nude mice harboring HCC-PDX (approximately 163 mm3) were randomly divided into 2 groups: one group received intraperitoneal injection of 10 μl/g vehicle (10% DMSO, 90% corn oil), and another group received SP2509 treatment (i.p., 10 μl/g, 25 mg/kg, twice a week for 3 weeks). Subsequently, tumor xenograft volumes and mice body weights were measured every three days for three weeks. Statistical analyses were performed using two-sided ANOVA, n = 6 biological replicates, and mean ± SEM was shown (h). After the mice were euthanized, HCC-PDX tumor tissues were tested by CUT&Tag-seq assays using H3K4me1 antibody, showing an increase of H3K4me1 modification within liver-TEs upon SP2509 treatment (i). j SP2509 treatment reduced the organoid formation ability of primary HCC cells, n = 3 biological replicates. Significance was examined by a two-sided t-test, and mean ± SD was shown. Bar = 100 μm. Source data are provided as a Source Data file.
