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Fig. 5 | Genome Medicine

Fig. 5

From: Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

Fig. 5

TF activity in E/R+ leukemic cells. a Regulon activity is visualized as a heatmap as in Fig. 2a comparing E/R+ cells and normal BM cells. Cell cycle stage C: S/G2/M, G1: G1. Annotated functional category: CM, chromatin modifier; CR, coregulator; TF, transcription factor; ST, splicing/transcription complex. b Bulk mRNA expression data for ELK3 and SP4 from Hemap is shown on a t-SNE map comparing transcriptomes across hematologic malignancies (ALL, acute lymphoblastic leukemia; BCL/TCL, B/T cell lymphoma; CLL, chronic lymphocytic leukemia; MM, multiple myeloma; CML/AML, chronic/acute myeloid leukemia). The location of pre-B-ALL and E/R+ samples is indicated on the plot. Red color tones indicate high expression. c Bulk GRO- and RNA-seq data is shown at the ELK3 locus. GRO-seq tracks correspond to E/R+ REH cell line and two primary E/R+ bone marrows. Representative RNA-seq signal (coverage) and splicing pattern (Sashimi plot, +strand splicing corresponding to min 10 junction spanning reads) are shown from ALL10. d Distributions of expression level at diagnosis and day 15 post-treatment are shown as violin plots for a set of TFs with significant expression change (refer to Additional file 4: Table S3). Y-axis corresponds to normalized expression level. The differentiation marker MS4A1 (mRNA) and CD20 (corresponding protein) level is shown for comparison. e The luminescence signal from MTS assay (above) and relative cell counts (viable cells in colored bars, total cell count indicated without fill) at different drug concentrations are shown. TK, TK216; XR, XRP44X). f Schematic summary of repressed pathway gene expression upon ETS-inhibition in REH cells (refer to Additional file 4: Table S3). g Distributions of mRNA expression level of TERF2 and HLA-E comparing XRP44X treatment to control are shown based on scRNA-seq data in REH

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