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

by Selleckchem | Sep 10 2023

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.

Comments:

The passage you provided describes a study that focuses on chromosomal translocations involving the KMT2A gene, which is responsible for encoding the KMT2A lysine methyltransferase enzyme. These translocations often occur in cases of acute myeloid and lymphoid leukemias, resulting in fusion of the KMT2A gene with other chromatin-regulatory proteins.

The researchers aimed to map the specific targets across the genome that are affected by these KMT2A fusion proteins. They used a modified technique called CUT&Tag chromatin profiling, which allows for automated and comprehensive analysis of chromatin regulation. By applying this technique to cell lines and patient samples, the researchers were able to identify both common and tumor-subtype-specific sites where abnormal chromatin regulation occurs due to the presence of KMT2A fusion proteins.

A particular subset of the binding sites for KMT2A fusion proteins was found to exhibit a bivalent chromatin signature, marked by the presence of both H3K4me3 and H3K27me3 modifications. Furthermore, single-cell CUT&Tag profiling revealed that these sites displayed heterogeneity between individual cells, suggesting the potential for lineage plasticity.

The researchers also discovered that the abnormal enrichment of H3K4me3 within gene bodies was sensitive to Menin inhibitors. This finding highlights the usefulness of automated chromatin profiling in identifying potential vulnerabilities and therapeutic targets. By integrating automated and single-cell CUT&Tag techniques, the researchers were able to uncover epigenomic heterogeneity within patient samples and make predictions regarding the sensitivity of these samples to specific therapeutic agents.

In summary, this study demonstrates the power of automated chromatin profiling techniques in understanding the epigenetic changes associated with KMT2A fusion proteins in leukemia. It provides insights into the chromatin regulation patterns, heterogeneity, and potential therapeutic vulnerabilities, thereby contributing to our understanding of the disease and potentially guiding the development of targeted therapies.