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

SRSF2 mutations occur in up to 25% of acute myeloid leukemia (AML) and 17% of myelodysplastic syndrome (MDS) cases and are associated with poor prognosis, yet no mutation-directed therapy exists.

Here, we aimed to identify therapeutically targetable vulnerabilities in MDS/AML with SRSF2 mutations. Ex vivo drug-sensitivity testing of bone marrow cells from AML patients and healthy donors showed that SRSF2 -mutant cells are sensitive to inhibitors of CHK1, and WEE1 DNA damage response (DDR) kinases.

To test causality, we engineered isogenic K562 cell line clones expressing SRSF2 ^P95H/L/R mutations. RNA sequencing confirmed splicing aberrations characteristic of MDS/AML in these clones. We found that SRSF2 ^P95H/L/R sensitize leukemia cells to ATR–CHK1–WEE1 inhibition. Bone marrow progenitors from Srsf2 ^P95H and U2AF1 ^S34F knock-in mice showed heightened sensitivity to CHK1 inhibition, corroborating the human data.

In contrast, RUNX1 mutations were linked to resistance against CHK1 and WEE1 inhibition in SRSF2 -mutant AML samples. Runx1 loss also caused resistance to CHK1 inhibitors in knock-in mouse progenitors harboring Srsf2 ^P95H or U2AF1 ^S34F , indicating that RUNX1 loss 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. These biomarkers can support patient stratification in MDS/AML.