Jam3 deficiency before leukemic onset upregulates AP-1/TNF-α transcriptional network in HSPCs. (A) Volcano plot displaying DEGs between L-HSCs isolated from the BM of Jam3–proficient (iMLL Jam3^fl/fl) and Jam3–deficient (iMLL Jam3^ko/ko) leukemic mice (n = 3 per genotype). The vertical axis shows the mean expression value of log₁₀, and the horizontal axis shows the log₂ fold change (FC) value obtained from triplicate experiments. Genes with log₂ FC >1, and adjusted P value <.05, adjusted P value <.05 and log₂ FC >1 are represented in red, blue, and green, respectively. (B) Volcano plot displaying DEGs for L-GMPs. (C) Gene set expression analysis using transcriptomes from L-HSCs shown in panel A. The most significant gene sets are shown. (D) Heat map showing log₂ normalized transcripts per million (tpm) of genes differentially expressed between HSCs isolated from the BM of Jam3–deficient (iMLL Jam3^ko/ko) and Jam3–proficient (iMLL Jam3^fl/fl) leukemic mice (adjusted P < .05). Genes in gray are differentially expressed between Jam3-deficient and Jam3-proficient mice both in L-HSC and L-GMP compartments. (E) Venn diagram showing DEGs identified in this study, in the LSC-17 core signature,²⁴ or in genes defining the CD34⁺/AP-1^High cluster in the single-cell RNA sequencing study by Velten et al.²⁸ FDR, false discovery rate; NES, net enrichment score.