Fig. 7: Transcriptomic changes upon partial KMT2A inhibition and gemcitabine treatment in PCSCs.

a Schematic illustration of the workflow for RNA-seq analysis in ABCG2⁺ L3.6pl cells treated with MM-102 (50 µM) for 5 days and gemcitabine (100 nm) for 24 h. The schematic illustration was created with Biorender scientific illustration software. b Principal component analysis (PCA) of normalized RNA-seq data of ABCG2⁺ L3.6pl cells treated with DMSO (control), MM-102 (50 µM), gemcitabine (100 nm), and combined MM-102 (50 µM) and gemcitabine (100 nm), demonstrating the clustering of RNA-seq samples by treatment. Each treatment group consists of 3 biological replicates. PC1 and PC2 account for 80.04% and 7.03% of data variability, respectively. c–e Volcano scatter plots demonstrating significantly upregulated (red) and significantly downregulated (green) genes in ABCG2⁺ L3.6pl cells treated with MM-102 (c), gemcitabine (d), and combined MM-102 and gemcitabine (e) as compared to the DMSO-treated (control) group (n = 3 biologically independent experiments). The top 20 significantly downregulated and upregulated genes are annotated. Significant differential gene expression was defined as |log2 Fold change| > 1 for upregulated genes and <−1 for downregulated genes at an adjusted p-value < 0.05. The statistical test used was two-sided. The effect size was shrunk using the ashr method and p-values were adjusted using the independent hypothesis weighting (IHW) method. f–h WikiPathway enrichment analyses of significantly DEGs in ABCG2⁺ L3.6pl cells treated with MM-102 as a single agent (f), gemcitabine (g), and combined MM-102 and gemcitabine (h) as compared to the DMSO-treated (control) group (n = 3 biologically independent experiments). The size and color of the dots represent the number of genes enriched in the pathway of interest and the significance of enrichment, respectively. The statistical test was performed using the method provided by g:GOSt which uses the well-proven cumulative hypergeometric test. The multiple testing correction was performed using the default g:SCS (Set Counts and Sizes) correction method. i–k Bar charts illustrating log2(fold change) of expression levels of significantly DEGs involved in the regulation of self-renewal and pluripotency in ABCG2⁺ L3.6pl cells treated with MM-102 (i), gemcitabine (j), and combined MM-102 and gemcitabine (k) versus DMSO-treated (control) group (n = 3 biologically independent experiments). Significant differential gene expression was defined as |log2 Fold change| > 1 for upregulated genes and <− 1 for downregulated genes at an adjusted p-value < 0.05.