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Project 3: RNA Splicing Modulators for MDS/AML

Timothy Graubert, MD, and Matthew Walter, MD

U2AF1 mutations found in individuals with MDS. Missense mutations were detected in codons 34 and 157 of U2AF1. The ZnF1 (zinc finger 1), UHM (U2AF homology motif), ZnF2 (zinc finger 2) and RS (arginine-serine rich) domains are shown.

We and others recently discovered that mutations in several genes that encode core components of the mRNA splicing machinery
(the “spliceosome”) are recurrently mutated in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML).

It is extremely rare for more than one of these genes to be mutated in an individual MDS or
AML patient, suggesting they share a similar
role in perturbing pre-mRNA splicing in
MDS/AML pathogenesis. Although the molecular consequences of these mutations are not yet known, their presence in tumors may provide a vulnerability that can be exploited therapeutically.

Our collaborators have developed potent and selective modulators of the spliceosome. We hypothesize that splicing modulators may represent a novel targeted therapy for patients with MDS or AML harboring spliceosome mutations.

In Project 3, we will test the activity of splicing modulators in preclinical models using human cells (Aim 1). We will use primary human de novo or MDS-derived AML myeloblasts wildtype or mutant for spliceosome genes and test the impact of splicing modulators on growth and viability. In addition, we will test the splicing modulators in xenograft experiments using primary human hematopoietic cells (expressing mutant vs. wildtype alleles of spliceosome genes) and fully transformed human AML myeloblasts (wildtype or mutant for spliceosome genes). We will also identify biomarkers of molecular response to splicing modulators (Aim 2).

We will characterize the pattern of splicing globally in normal human hematopoietic cells by RNA-seq, before and after treatment with splicing modulators to find reproducible changes in mRNA isoforms that are associated with drug exposure. We will take the most promising biomarkers forward and develop assays using a sensitive, high throughput, quantitative digital analysis platform that is suitable for use with clinical samples.

The goal of these studies is to develop a robust assay that can be used to measure the molecular response to splicing modulators and correlate with clinical responses to these agents in future therapeutic trials for patients with MDS or AML.