The role of splicing and microenvironmental aberrancies as drivers of disease in myelodysplastic neoplasms

Abstract

Myelodysplastic neoplasms (MDS) feature recurrent aberrations in alternative splicing (AS). Many such abnormalities are associated with specific splicing factor (SF) mutations, and result in pathological transcript isoforms that drive disease. However, little is known about about the subset of AS events that are not associated with SF mutations. Our work identifies and characterizes splicing events that are shared between SF mutant and SF-wildtype MDS. We find that a sizeable overlap of AS events exists between MDS mutational subtypes, with an enrichment of gain-of-function consequences. We describe the AS of Methyl-binding-domain 1 MBD1 as one such disease-wide pathological event, which drives defective erythropoiesis via the preferential production of a long MBD1 isoform, altering MBD1’s DNA-binding function. This leads to broad repression of hypomethylated CpG-rich promoter sites, producing impairment of erythropoiesis and cell cycling. Conversely, the reversal of excess MBD1-L ameliorates erythroid differentiation in MDS. In addition, we performed RNAi screening of the remaining set of MDS-wide AS events, identifying potential survival dependencies including the transcription factor MLX, demonstrating that mutation-independent AS events contain therapeutic vulnerabilities. Finally, we show that defective stroma from MDS patients can impair erythropoiesis in otherwise healthy HSPCs, and aggravate malignant phenotypes in SRSF2- mutant HSPCs, implicating microenvironmental disruptions in the evolution and maintenance of the MDS state.