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

Myelodysplastic neoplasms (MDS) feature hematopoietic deficits driven, in part, by transcript splicing abnormalities. To date, such disease-driving transcripts have been identified in association with specific splicing factor mutations. However, conserved aberrant splicing-derived transcripts that drive MDS independently of mutational status remain poorly studied, despite representing global therapeutic targets. In this study, we characterize an MDS-associated isoform of methyl-binding-domain 1 (MBD1; MBD1-L) as a novel member of this class of transcripts. Rather than originating from a mutant splicing factor, the abnormal production of MBD1-L is driven by reduced WTAP expression in MDS. Overexpression of MBD1-L in healthy human hematopoietic stem and progenitor cells recapitulated archetypal MDS defects, including reduced terminal glycophorin A+ erythroid differentiation, suppressed cell cycling, and impaired in vivo reconstitution capacity during increased hematopoietic demand in xenotransplantation assays. An integrated multiomics approach assessing DNA binding of MBD1 isoforms, and the resulting changes in chromatin accessibility, histone mark deposition, and transcriptional changes, revealed that these defects arise from an isoform-specific switch in MBD1 binding behavior. The MBD1-L isoform refocuses heterochromatin-promoting activity of MBD1-L from methylated to unmethylated CpGs, thus enacting broad downregulation of CpG-rich promoters and secondary epigenetic effects mediated through its downstream target, BCOR. Remarkably, we also found that directly reversing abnormal MBD1 splicing across a broad range of primary human MDS samples using nanoparticle-encapsulated antisense RNA oligonucleotides (ASO) enhanced in vitro erythroid differentiation, supporting the therapeutic use of ASO-based therapies for MDS treatment. Thus, our findings demonstrate MBD1-L to be a global disease-driving splice variant in MDS and illustrate the potential of RNA-based therapies for the broad treatment of MDS.