Fig. 3. The transcriptome of the pre-BCR-dependent expansion stage is governed by MYC-associated gene expression networks and requires repression of Ebf1 expression.

a Highlighted population of the pre-BCR-dependent cluster (left) and feature plots for the pre-BCR-dependent markers highly expressed during this stage (right). b Violin plot of B-lymphoid transcription-factor expression, including Ebf1, Pax5, and Ikzf1 across B-cell development. c Violin plot of additional genes that are downregulated during pre-BCR-dependent proliferation, which includes Il7r, and EBF1-target genes such as Cd79a and Cd79b. d Landscape In silico Deletion Analysis (LISA) to predict the transcriptional regulator of the top 100 differentially upregulated genes during pre-BCR-dependent proliferation (left table). Gene-set enrichment analysis was performed to identify gene sets from the Molecular Signature Database that were enriched in the pre-BCR-dependent cells. Comparison between the pre-BCR-independent cells (left side) and the pre-BCR-dependent cells was performed (right side). Statistical significance was calculated using one-sided Wilcoxon rank-sum test. e EBF1-binding sites at the promoters of Nrgn, Slc7a5 and Slc3a2 with indicated MACS peak calls²⁰. Data were obtained from GSM2863146. f Log2-transformed FPKM expression values obtained from RNA-seq of wild-type and Pax5^+/− × Ebf1^+/− (PE) leukemic progenitor B cells. Progenitor B cells were obtained via negative selection of CD11c, TER119, Ly6G, Ig Kappa, and Ig Lambda and positive selection of CD19. Statistical significance was determined using a two-tailed unpaired student t-test for Ybx3 (P = 0.0024) and Slc7a5 (P = 0.0001). RNA-seq data were obtained from GSE148680. A two-tailed Mann–Whitney test was performed for Slc3a2 (P = 0.0083) due to non-normal distribution. n = 7 biologically independent samples over one independent experiment. Color scales in a, b, and c represent natural log-transformed SCTransform-corrected counts.