Differential enhancer activity in KMT2A::AFF1 patients drives oncogene specific expression such as at MEIS1 and RUNX2. (A) UMAP of single-nucleus gene expression (snGEX) for 4 KMT2A::AFF1 blast samples (chALL1, iALL3-5; VIVO Biobank, United Kingdom) and 3 single-cell GEX (scGEX) samples (EGAS00001003986). (B) Dot plot of marker gene analysis between 7 KMT2A::AFF1 blast samples, showing the top 5 marker genes per sample. (C) Normalized MEIS1 (left) and RUNX2 (right) expression in KM2TA::AFF1 sn/scGEX samples. (D) TOPmentation for H3K27ac and the N terminus of KMT2A (KMT2A-N) in KMT2A::AFF1 blast samples (VIVO Biobank, United Kingdom) at the MEIS1 locus. The chALL1 unique enhancer region downstream of MEIS1 is highlighted in red. (E) TOPmentation for H3K27ac and KMT2A-N in KMT2A::AFF1 blast samples at the RUNX2 locus. The chALL1- and iALL2-specific enhancer region upstream of RUNX2 is highlighted in red. (F) Survival curve comparing high (red) and low (green) MEIS1 expression in B-ALL. Data analyzed from COG P9906 childhood B-ALL clinical trial. (G) Survival curve comparing high (red) and low (green) RUNX2 expression in B-ALL. Data analyzed from the Eastern Cooperative Oncology Group E2993 adult B-ALL clinical trial. UMAP, uniform manifold approximation and projection.