Biologic and Therapeutic Consequences of Distinct Hotspot SF3B1 Mutations in MDS

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Project Summary The myelodysplastic syndromes (MDS) are the most common clonal blood disorders, characterized by dominance of the bone marrow by abnormal stem cells and impairment of blood cell production. Patients with MDS suffer from combinations of anemia, infection, bleeding, and multiorgan failure from progressive disease. Outcomes are poor, and treatments are inadequate. Key to developing new treatments is better understanding of the mutations which create these diseases. Roughly half of MDS patients have mutations in spliceosome genes, and of these, SF3B1 is the most commonly mutated. Mutant SF3B1 is neomorphic, disrupting RNA splicing to create what we refer to as JEMs (splice Junctions Enriched in Mutant-spliceosome cells), though how JEMs produce MDS phenotypes is unknown. SF3B1 mutation is regarded as a favorable prognostic marker in MDS. Yet, there is considerable heterogeneity in the pathologic features and clinical outcomes of SF3B1-mutant MDS that remains unexplained. As this heterogeneity beguiles effective disease management, its causes need to be better understood. The premise of our proposal is that a key to understanding SF3B1-mutant MDS is to study the differences between distinct SF3B1 mutations. This gene is mutated in hotspots affecting multiple amino acids, and our preliminary data show that specific mutations associate with distinct clinical features, RNA splicing patterns, and responses to therapy. We also have data that SF3B1 mutations disrupt metabolism in specific ways that likely affect sideroblastic anemia and metabolic vulnerabilities, and we have developed novel human models of SF3B1-mutant hematopoiesis with which to study these processes. The proposed work combines the expertise of a physician-scientist (Dr. Dalton) who specializes in cell biology, genetics, and human cell modeling of disease with that of a clinical investigator (Dr. DeZern) who specializes in clinical studies of bone marrow failure disorders. Together, we will pursue three aims: 1) Characterize the landscape of private and shared JEMs among hotspot SF3B1 mutations in MDS. We will use RNA-seq of primary MDS samples and isogenic human cell models to map the RNA splicing landscape of different SF3B1 mutations and use this as a ‘way in’ to understanding the pathways they disrupt. 2) Establish the role of distinct SF3B1 mutations in the growth and differentiation of human hematopoietic cells. We will use primary MDS samples and isogenic cells to determine mechanisms of sideroblastic anemia, cell fitness, and metabolic vulnerability in SF3B1-mutant hematopoietic cells. 3) Define the clinicopathologic features of distinct SF3B1 mutations in MDS. Leveraging the high-quality data from the NHLBI National MDS Study, we will determine how distinct hotspot SF3B1 mutations affect pathologic and clinical features of MDS through multivariate analysis. Successful completion of these aims promises to reveal pathophysiologic mechanisms of RNA splicing, redefine disease classification and prognosis, and improve treatment approaches in MDS.