Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [DRIP-seq]

Myelodysplastic syndromes (MDS) with mutated SF3B1 gene have many features including a favorable outcome that are distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we show that SF3B1-mutated MDS are characterized by a dramatically reduced R-loop formation predominating in gene bodies, which tightly associates with reduced retention of introns specifically found in SF3B1-mutated, but not in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibited augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation, which were recapitulated in murine Sf3b1K700E/+ proerythroblasts. Importantly, R-loop formation was restored by histone deacetylase inhibition using SAHA/vorinostat, which improved Sf3b1K700E/+ erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress is a hallmark of SF3B1- mutated MDS ineffective erythropoiesis, which could be used as a new therapeutic target. Comparative Rloop analysis with DRIP-seq data for CD34+-derived proE/basoE cells, with or without HDACi treatment. Please note that not all samples have been treated with HDACi. Therefore, in fig3A, all SF3B1 WT and all SF3B1 MUT samples have been used, whereas in fig6A, samples labelled WT4, 5 and 6, and MUT3, 4 and 5 were used.