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. 2021 Nov 25;12:6905. doi: 10.1038/s41467-021-27270-z

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a UMAP showing clustering of CD19+ cells from ^CRISPRMLL-AF4+ (light green; black border = proB ALL, no border = preB-ALL) and control (gray) mice with HOXA^lo MLL-AF4 (dark green, n = 11), HOXA^hi MLL-AF4 (purple, n = 20), and MLLwt (blue, n = 9) infant-ALL patient samples from a publicly available dataset²⁷ based on 7041 significantly differentially expressed genes (FDR < 0.05, edgeR glm test) between ^CRISPRMLL-AF4+ ALL, controls, MLL-AF4 infant-ALL, and MLLwt infant-ALL. b Gene set enrichment analysis (GSEA)⁵² showing ^CRISPRMLL-AF4+ ALL is more enriched for genes that are upregulated in MLL-AF4 ALL compared to MLLwt ALL (1000 genes) when compared to CD19+ cells from control mice (p < 0.01). c UMAP showing clustering of ^CRISPRMLL-AF4⁺ (light green; black border = proB ALL, no border = preB-ALL) with HOXA^lo MLL-AF4 (dark green, n = 11) HOXA^hi MLL-AF4 infant-ALL (purple, n = 8), and HOXA^hi MLL-AF4 childhood-ALL (orange, n = 5) from a publicly available patient dataset²³ based on 765 significantly differentially expressed genes (FDR < 0.05; edgeR glm test) between these three patient subsets (Supplementary Data 3). d Expression (TPM) of HOXA9 and IRX1 in HOXA^hi MLL-AF4 infant-ALL (purple, n = 8), HOXA^lo MLL-AF4 infant-ALL (dark green, n = 11) and ^CRISPRMLL-AF4+ ALL (light green; black border = proB ALL, no border = preB ALL). Data are shown as mean ± SEM. Source data are provided as a Source Data file. e Venn diagram showing overlap of MLL-AF4-bound genes (genes with an MLL-AF4 peak in the gene body) in ^CRISPRMLL-AF4+ ALL in a primary recipient mouse, the MLL-AF4+ SEM cell line and a primary MLL-AF4 childhood-ALL (chALL) patient sample. MLL-AF4 peaks = directly overlapping MLL-N and AF4-C peaks. f Representative ChIP-seq tracks at the MLL-AF4 target gene, RUNX1 in ^CRISPRMLL-AF4 + ALL, the SEM cell line and a primary MLL-AF4 childhood-ALL (chALL) patient sample.