Wednesday, April 2, 2025
4/2/2025
Molecular mechanisms of splicing dependency in cohesin-mutant myelodysplasia - Project Summary There is a fundamental gap in our understanding of how mutations in the cohesin complex, a multimeric protein complex essential for sister chromatid cohesion, chromatin organization into loops and gene regulation, cause myelodysplastic syndromes (MDS). Continued existence of this gap represents an important problem because despite the high frequency of cohesin mutations in MDS and its association with high risk of disease and poor outcomes, there are currently no treatment strategies to specifically target cohesin-mutant cells in MDS. STAG2 mutations are mutually exclusive with mutations in the splicing factor SF3B1, the most commonly mutated gene in MDS. Furthermore, cohesin proteins have been shown to bind SF3 splicing factors and RNA binding proteins (RBPs) and are dependent on normal spliceosome function for their survival. New genetically engineered models of cohesin-mutant MDS offer a unique opportunity to test the contribution of disease alleles to splicing abnormalities and therapeutic response, and to dissect the interaction between the cohesin and splicing complexes. The long-term goal is to improve outcomes in cohesin-mutant MDS by deeper mechanistic understanding of disease biology. The overall objective of this application is to determine why splicing is a genetic dependency in cohesin-mutant MDS. The central hypothesis is that an RNA-mediated interaction between cohesin and splicing complexes is disrupted in cohesin-mutant MDS and leads to splicing deregulation and dependency of cohesin-mutant cells on proper splicing, which can be exploited therapeutically. Guided by strong preliminary data from the applicant’s laboratory, the hypothesis will be tested by pursuing two specific aims: 1) Determine the splicing changes and the effect of splicing modulation on STAG2-mutant MDS; and 2) Dissect the interaction between the cohesin complex and the SF3B splicing complex. Under the first Aim, the applicant will characterize transcriptional and splicing changes in hematopoietic stem and progenitor cells of a novel genetic murine model of progression from Tet2-mutant clonal hematopoiesis of indeterminate potential (CHIP) to Tet2/Stag2-mutant MDS. They will also test the effect of splicing modulation on MDS progression in vivo and using cohesin-mutant MDS patient samples. Under the second Aim, a combination of transcriptomic and cross- linking and immunoprecipitation experiments will be used in several well established in vitro models to identify specific RNA species that mediate the interaction between the cohesin and splicing complexes. The approach is innovative through the application of novel murine models. The downstream effects of the interaction between cohesin and splicing and its disruption in cohesin-mutant MDS have not been clarified, and the mechanisms driving splicing dependency in cohesin-mutant cells are unknown. The proposed research is significant, because it is expected to define the biological role of cohesin mutations in a high-risk subset of MDS associated with poor outcomes. The expected output for the proposed research is that the knowledge gained will be immediately clinically significant for patients with cohesin-mutant MDS and inform new treatment strategies.
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