Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia

Acute myeloid and lymphoid leukemias often harbor chromosomal translocations involving the KMT2A gene, encoding the KMT2A lysine methyltransferase (also known as mixed-lineage leukemia-1), and produce in-frame fusions of KMT2A to other chromatin-regulatory proteins. Here we map fusion-specific targets across the genome for diverse KMT2A oncofusion proteins in cell lines and patient samples. By modifying CUT&Tag chromatin profiling for full automation, we identify common and tumor-subtype-specific sites of aberrant chromatin regulation induced by KMT2A oncofusion proteins. A subset of KMT2A oncofusion-binding sites are marked by bivalent (H3K4me3 and H3K27me3) chromatin signatures, and single-cell CUT&Tag profiling reveals that these sites display cell-to-cell heterogeneity suggestive of lineage plasticity. In addition, we find that aberrant enrichment of H3K4me3 in gene bodies is sensitive to Menin inhibitors, demonstrating the utility of automated chromatin profiling for identifying therapeutic vulnerabilities. Thus, integration of automated and single-cell CUT&Tag can uncover epigenomic heterogeneity within patient samples and predict sensitivity to therapeutic agents. Automated and single-cell CUT&Tag is used to characterize the effects of KMT2A fusion proteins on chromatin in human primary leukemia samples, identifying oncogenic networks and fusion-specific therapeutic vulnerabilities.

Automated summary

This study maps fusion-specific targets of KMT2A oncofusion proteins across the genome, revealing aberrant chromatin regulation induced by these fusion proteins and cell-to-cell heterogeneity at these sites, which can predict sensitivity to therapeutic agents. Automated and single-cell CUT&Tag profiling characterizes the effects of KMT2A fusion proteins on chromatin in human primary leukemia samples, identifying oncogenic networks and fusion-specific therapeutic vulnerabilities.