epz-5676 and Leukemia

On the basis of a previously identified DOT1L peptide mimetic (compound

Topics: Histone-Lysine N-Methyltransferase; Humans; Leukemia; Methyltransferases; Myeloid-Lymphoid Leukemia Protein; Oncogene Proteins, Fusion; Peptides

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.

Topics: Antineoplastic Agents; Automation, Laboratory; Benzamides; Benzimidazoles; Binding Sites; Cell Line, Tumor; Chromatin; Chromatin Immunoprecipitation Sequencing; Gene Expression Regulation, Leukemic; Histone-Lysine N-Methyltransferase; Histones; Humans; Leukemia; Myeloid-Lymphoid Leukemia Protein; Oncogene Proteins, Fusion; Proto-Oncogene Proteins; Pyrimidines; Single-Cell Analysis; Transcriptional Elongation Factors

Topics: Animals; Antineoplastic Agents; Benzimidazoles; Drugs, Investigational; Enzyme Inhibitors; Histone-Lysine N-Methyltransferase; Humans; Jurkat Cells; K562 Cells; Leukemia; Mice; Treatment Outcome; Tumor Cells, Cultured; Xenograft Model Antitumor Assays

Topics: Animals; Antineoplastic Agents; Benzimidazoles; Breast Neoplasms; Epithelial-Mesenchymal Transition; Female; Histone-Lysine N-Methyltransferase; Histones; Humans; Leukemia; Methylation; Methyltransferases; Mice; Neoplastic Stem Cells; Transcriptional Activation

Rearrangements of the MLL gene define a genetically distinct subset of acute leukemias with poor prognosis. Current treatment options are of limited effectiveness; thus, there is a pressing need for new therapies for this disease. Genetic and small molecule inhibitor studies have demonstrated that the histone methyltransferase DOT1L is required for the development and maintenance of MLL-rearranged leukemia in model systems. Here we describe the characterization of EPZ-5676, a potent and selective aminonucleoside inhibitor of DOT1L histone methyltransferase activity. The compound has an inhibition constant value of 80 pM, and demonstrates 37 000-fold selectivity over all other methyltransferases tested. In cellular studies, EPZ-5676 inhibited H3K79 methylation and MLL-fusion target gene expression and demonstrated potent cell killing that was selective for acute leukemia lines bearing MLL translocations. Continuous IV infusion of EPZ-5676 in a rat xenograft model of MLL-rearranged leukemia caused complete tumor regressions that were sustained well beyond the compound infusion period with no significant weight loss or signs of toxicity. EPZ-5676 is therefore a potential treatment of MLL-rearranged leukemia and is under clinical investigation.

Topics: Animals; Antineoplastic Agents; Benzimidazoles; Cell Line, Tumor; Cell Proliferation; DNA Methylation; Dose-Response Relationship, Drug; Female; Histone Methyltransferases; Histone-Lysine N-Methyltransferase; Histones; Humans; Leukemia; Methyltransferases; Myeloid-Lymphoid Leukemia Protein; Neoplasm Transplantation; Protein Conformation; Rats; Rats, Nude