Saturday, May 4, 2024
5/4/2024
Abstract Chromosomal translocations involving the Lysine Methyltransferase 2A (KMT2A) gene are commonly found in high-risk subtypes of acute leukemia and produce potent oncoproteins that occupy the chromatin and cause mis-regulation of developmental genes involved in hematopoiesis. Immunotherapies targeting the cell surface protein CD19 have revolutionized the treatment of B-cell Acute Lymphoblastic Leukemia (B-ALL). However, KMT2A-rearanged (KMT2Ar) B-ALLs frequently convert from a B-ALL to an Acute Myeloid Leukemia (AML) phenotype to downregulate the expression of CD19 and evade targeted therapy. Genome-wide sequencing indicates these B-ALL-to-AML-lineage-switching events can occur in the absence of additional mutations, suggesting that non-genetic changes in tumor regulation contribute to this phenotypic shift. We identified groups of KMT2A oncoprotein target genes that show divergent patterns of transcriptionally active and developmentally repressed chromatin in single cells of the same leukemia (Janssens DH et al Nature Genetics 2021). More recently, I developed single-cell combinatorial indexing CUT&Tag (sciCUT&Tag) and applied this method to profile the chromatin landscapes of thousands of cells from a primary infant KMT2Ar B-ALL as well as the infant KMT2Ar B-ALL derived cell line, KOPN-8. I identified a collection of 18 oncoprotein target genes that show the same divergent regulatory programs across heterogeneous cell types in both the primary infant KMT2Ar B-ALL and the KOPN-8 cell line. These patterns suggest the KMT2A oncoproteins activate distinct groups of target genes in related leukemia cells, providing the first glimpse into how these oncoproteins contribute to the non-genetic heterogeneity of KMT2Ar leukemia. This proposal will (1) address how KMT2A oncoproteins contribute to B-ALL-to-AML-lineage-switching events and (2) identify novel therapeutic approaches to effectively identify and treat KMT2Ar B-ALLs with lineage-switching potential. In the first aim, I leverage the KOPN-8 cell line to identify oncoprotein-regulated genes that promote intra-tumoral heterogeneity of high-risk KMT2Ar B-ALLs. In addition, I will identify clinically available small molecules with the potential to be used in combination with CD19-directed immunotherapies to prevent lineage switching. In the second and third aims, I will apply sciCUT&Tag to characterize the chromatin landscapes of a collection of primary KMT2Ar B-ALLs as well as normal hematopoietic stem and progenitor cell types. Using comparative genomics, I will identify novel biomarkers that label KMT2Ar B-ALL cells with lineage-switching potential and that can potentially be used to target this population via novel immunotherapies. This proposal applies the genomics methods Dr. Derek Janssens developed as a postdoc to identify novel treatment strategies to target high-risk KMT2Ar B-ALLs and will establish long-term collaborations with computational and translational biologists as well as clinical researchers as he transitions to a principal investigator role and establishes an independent research program at a tier one institution.
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