Integrated epigenomic and transcriptomic analysis reveals multiple coexisting changes associated with venetoclax resistance in t(11;14) MM. (A) UMAP projection showing the distribution of CD138⁺ cells (n = 8679 cells) identified in the t(11;14) patient PM01 using the scATAC-seq and scRNA-seq data in the LSI space (left). Each point represents 1 cell. The cells are marked with color codes based on the different subclusters. The alluvial plot (right) shows the distribution of the cells among the prevenetoclax and postvenetoclax samples for each subcluster identified in the UMAP. (B) Violin plots of the NES obtained in each identified subcluster. These data were generated on the integrated scRNA-seq counts using the msigdb for BM PsC (left) (C8, HAY_BONE_MARROW_PLASMA_CELL) and B cells (right) (C8, HAY_BONE_MARROW_FOLLICULAR_B_CELL). Subclusters from the prevenetoclax sample are highlighted in blue, whereas those from the postvenetoclax sample are in purple. (C) On the left, immunoblotting of parental (wild-type [WT]) and KMS12BM-RUNX1 overexpressing cells for RUNX1 and BCL2, in the presence or absence of venetoclax 200 nM for 3 hours. The bar plot (right) indicates the effect of RUNX1 on NF-kB activation in the KMS12BM overexpressing RUNX1 when compared with parental cells (WT). (D) Bar plot showing the percentage of cell death observed in parental (WT) vs RUNX1-KMS12BM cells after 24 hours of exposure to venetoclax 200 and 500 nM. The data presented are the mean ± standard error of 3 independent experiments. The adjusted P values associated are shown at the top of each bar plot. (E) UMAP projection showing the distribution of CD138⁺ cells (n = 11 811 cells) identified in the t(11;14) patient PM07 using the scATAC-seq and scRNA-seq data in the LSI space (left). Each point represents 1 cell. The cells are marked with color codes based on the different subclusters. The alluvial plot (right) shows the distribution of the cells among the prevenetoclax and postvenetoclax samples for each subcluster identified in the UMAP. (F) Violin plots of the NES obtained in each identified subcluster. These data were generated on the integrated scRNA-seq counts using the msigdb for BM PCs (left) (C8, HAY_BONE_MARROW_PLASMA_CELL) and B cells (right) (C8, HAY_BONE_MARROW_FOLLICULAR_B_CELL). Subclusters from the prevenetoclax sample are highlighted in blue, whereas those from the postvenetoclax sample are in purple. (G) Dot plot representing the scRNA-seq integrated expression of key genes involved in MM biology (CCND1, CCND2, CCND3, FGFR3, and NSD2) and BCL2 family members BCL2, BCL2L1 (BCLXL), BCL2L2 (BCLW), MCL1, BCL2A1, BCL2L11 (BIM), BID, BAX, BAK, BOK, BAD, BMF, BBC3 (PUMA), and PMAIP1 (NOXA) in PM07 subclusters. Subclusters from the prevenetoclax sample are highlighted in blue, whereas the ones from the postvenetoclax sample are in purple. The dot size represents the percentage of cells with values detected in each patient. The color represents the average gene expression in each subcluster. The dark blue indicates a lower gene expression count, and light red a higher count. Note that the average expression scales differ for CCND1 vs the other genes. (H) UMAP projection showing the distribution of CD138⁺ cells (n = 11 811 cells) collected from patient PM07 based on the scATAC-seq and scRNA-seq data in the LSI space. Each point represents 1 cell. The cells are marked with color codes based on the MCL1 amplification. The black color indicates the cells harboring the amplification of MCL1, whereas the gray or light gray indicates the cells without the amplification or with unknown information, respectively.