Sensitivity to ATR–CHK1 pathway inhibition in MDS/AML is enhanced by SRSF2 mutations and reduced by RUNX1 loss

Abstract

SRSF2 mutations occur in 5–15% of acute myeloid leukemia (AML) and ~15% of myelodysplastic neoplasms (MDS), are enriched in elderly/secondary AML, and lack mutation-directed therapy. We aimed to identify vulnerabilities in MDS/AML with SRSF2 mutations. Ex vivo drug-sensitivity testing of bone marrow cells from AML patients and controls showed that SRSF2-mutant cells are sensitive to CHK1 and WEE1 inhibitors. To test causality, we engineered isogenic K562 cell line clones expressing SRSF2P95H/L/R mutations. RNA sequencing confirmed splicing aberrations characteristic of MDS/AML in these clones. We found that SRSF2P95H/L/R sensitizes cells to ATR–CHK1–WEE1 inhibition. Bone marrow progenitors from Srsf2P95H knock-in mice showed heightened sensitivity to CHK1 inhibition, corroborating the human SRSF2-mutant data. U2af1S34F knock-in mouse progenitors extended this vulnerability to another spliceosome-mutant context. In contrast, RUNX1 mutations were linked to resistance to CHK1 and WEE1 inhibition in SRSF2-mutant AML samples. Runx1 disruption also caused resistance to CHK1 inhibitors in knock-in mouse progenitors harboring Srsf2P95H or U2af1S34F, indicating that RUNX1 loss of function is a mechanism of resistance. In conclusion, SRSF2 and U2AF1 mutations are biomarkers of sensitivity to ATR–CHK1 pathway inhibitors, while RUNX1 mutations cause resistance in splicing factor-mutant cells. These biomarkers can support patient stratification in MDS/AML.