Derek H. Janssens, PhD
Fred Hutchinson Cancer Research Center, Washington, United States
Single cell genomic technologies have been extremely useful to understand how differences in the mutational landscapes (genetic heterogeneity) as well as the metabolic, cell signaling and gene regulatory states (non-genetic heterogeneity) of tumor cells can result in different responses to therapeutic intervention. Many recurring oncogenic mutations are found in genes that encode chromatin regulatory proteins. In this talk, I will discuss how the CUT&RUN and CUT&Tag chromatin profiling methods can be used to examine chromatin associated oncoproteins and the regulation of non-genetic tumor heterogeneity.
Chromosomal translocations that produce in-frame fusion proteins involving the chromatin modifying enzyme Lysine Methyl-Transferase 2A (KMT2A; also referred to as Mixed Lineage Leukemia-1) are found in approximately 10% of new acute leukemia cases each year. Despite bearing related mutations, KMT2A-rearranged (KMT2Ar) leukemias are extremely heterogeneous and can present as pro-B-cell acute lymphoblastic leukemia (B-ALL) acute myeloid leukemia (AML) and mixed phenotype acute leukemia. In addition, high-risk KMT2Ar leukemia subtypes are associated with an unusual degree of lineage plasticity, and occasionally undergo a B-ALL-to-AML phenotypic shift to evade targeted therapies. We used automated CUT&RUN and CUT&Tag in combination with single-cell CUT&Tag to characterize the chromatin landscapes of a diverse panel of KMT2Ar leukemia cell lines and patient samples. We identified a subset of KMT2A oncoprotein binding sites that are marked by both the active chromatin modification H3K4me3 as well as repressive chromatin modification H3K27me3. Strikingly, we identified groups of oncoprotein target genes that show divergent patterns of active and repressive chromatin in the same leukemia, suggesting the KMT2A oncoproteins contribute to lineage plasticity by activating multiple different oncogenic networks. Recently, several multi-modal single cell CUT&Tag methods have been developed in the lab, and I will also discuss novel applications of these single cell datatypes.