Extended Data Fig. 6: Acquired DNMT3 overexpression in resistance to valemetostat.
From: Mechanisms of action and resistance in histone methylation-targeted therapy
a, Characteristics of clinically resistant clones based on single-cell analysis and genomic profiling. b, Chronological transition of normalized VAF values for somatic mutations in Pt2 in relation to treatment with valemetostat. c, tSNE projection for Pt2 scRNA-seq data. DNMT3A expression was upregulated in the recurrent clone (P < 10−9). d, scATAC-seq and ChIP-seq tracks at DNMT3A locus. e, Venn diagram depicts overlapped chromatin-condensed inactivated genes (Promoter sum <0.01) in Pt2 tumor cells at Pre, CR, and PD (DNMT3A expression). f, Scatter plots show all gene promoter activities in recurrent clones (y-axis) in Pt2 (left) and Pt3 (right) versus corresponding normal cells (x-axis). The gene loci with decreased copy numbers as defined from the WGS data are indicated in dark purple. g, Histogram shows differentially methylated (ΔmCpG <−10%, or >10%) probes in Pt2 resistant tumor at PD (135 weeks) versus pre-treatment tumor. h, i, Boxplots summarize normalized log2 fold changes of scATAC-seq promoter activities (h) and scRNA-seq gene expression (i) in relation to treatment-associated mCpG gain in Pt2. The genes for which integrated data were available were evaluated. Statistical significance is provided only for main combinations. j, Normalized log2 fold changes of scATAC-seq promoter activities of tumor suppressor genes (TSG) in relation to treatment-associated mCpG gain in Pt2. The genes for which integrated data were available were evaluated. Statistical significance is provided only for main combinations. k, Pt2-derived resistant cell line was successfully established. The same clonal origin and the absence of PRC2 mutations were confirmed by targeted sequencing. Bar graph shows relative RNA levels of DNMT family and PRC2 genes. l, Table summarizes characteristics of ATL cell lines. Pt2_PD cells showed low sensitivity to valemetostat. m, Knockdown and DNMT family and PRC2 genes were induced by lentivirus-mediated shRNA. After lentivirus infection, growth cell numbers for 6 days were calculated. The middle lines within box plots correspond to the medians; lower and upper hinges correspond to the first and third quartiles. The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR. The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR. Statistics and reproducibility are described in Methods.
