Aberrant splicing of MBD1 reshapes the epigenome to drive convergent myeloerythroid defects in MDS

Abstract Myelodysplastic neoplasms (MDS) feature hematopoietic deficits driven in part by transcript splicing abnormalities. Thus far, such disease-driving transcripts have been identified in association with specific splicing factor mutations. However, it remains unclear whether there also exists a set of disease-wide conserved pathological transcripts, which drive MDS independently of mutational status. Here, we characterize an MDS-associated long isoform of MBD1 (MBD1-L) as the first described member of this class of transcripts. Overexpression of MBD1-L in healthy human HSPCs recapitulates archetypal defects of MDS including deficits in erythroid differentiation and reconstitution capacity. These defects arise from an isoform-specific switching of MBD1’s binding behavior, refocusing its heterochromatin-promoting activity from methylated to unmethylated CpGs and enacting broad downregulation of CpG-rich promoters as well as secondary epigenetic effects mediated by its downstream target BCOR . Remarkably, we also find that directly reversing abnormal MBD1 splicing in primary human MDS using nanoparticle-encapsulated ASOs enhances erythroid differentiation. Key points Global mis-splicing of MBD1 represents a novel gain-of-function epigenetic axis driving erythropoietic and proliferative defects in MDS. ASO based depletion of pathogenic MBD1 transcripts restores erythroid differentiation, advancing RNA-based therapies for MDS.