Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes

Myelodysplastic syndromes (MDS) are clonal stem cell disorders driven by heterogeneous genetic alterations leading to variable clinical course. MDS with splicing factor SF3B1 mutations is a distinct subtype with a favorable outcome. However, selected co-mutations induce poor prognosis and how these genetic lesions cooperate in human hematopoietic stem and progenitor cells (HSPCs) during disease progression is still unclear. Here, we integrated clinical and molecular profiling of patients with SF3B1 mutations with gene editing of primary and iPSC-derived human HSPCs to show that high-risk co-mutations impart distinct effects on lineage programs of SF3B1-mutant HSPCs. Secondary RUNX1 or STAG2 mutations were clinically associated with advanced disease and reduced survival. However, RUNX1 and STAG2 mutations induced opposing regulation of myeloid transcriptional programs and differentiation in SF3B1-mutant HSPCs. Moreover, high-risk RUNX1 and STAG2, but not low-risk TET2, mutations expanded distinct SF3B1-mutant HSPC subpopulations. These findings provide evidence that progression from low- to high-risk MDS involves distinct molecular and cellular routes depending on co-mutation patterns. Overall design: RNA-seq was performed on FACS-sorted gene edited 5F-HPCs with SF3B1 mutation or wild-type SF3B1, and clonally derived K562 cells. For SF3B1 mutant or wild-type 5F-HPCs, gene expression of RUNX1 or STAG2 edited cells was compared to AAVS1 gene edited controls. For clonally derived K562 cells, splicing profiles of SF3B1 mutant lines with AAVS1, RUNX1 or STAG2 editing was compared to SF3B1 wild-type control edited cells. Raw and processed data for SF3B1 wild-type and single-mutant cells were previously deposited under accession number GSE263299 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263299). *************************************************************** The table below lists GEO accessions reused/reanalyzed for this study. ***************************************************************