Persistent altered fusion transcript splicing identifies RUNX1‐RUNX1T1+ AML patients likely to relapse

In acute myeloid leukemia (AML) mouse models, the RUNX1‐RUNX1T1 fusion protein has failed to produce leukemia by itself, but alternative splicing of exon 9a of the RUNX1‐RUNX1T1 fusion transcript (FT) has recently been shown to enhance the leukemogenic potential. We have analyzed 138 diagnosis and follow‐up samples from 13 RUNX1‐RUNX1T1+ patients as well as diagnosis samples from 13 RUNX1‐RUNX1T1? AML patients and 26 healthy donors. Levels of native RUNX1T1 mRNA were low in both healthy and RUNX1‐RUNX1T1‐negative AML samples. Likewise, the ratio between RUNX1T1 mRNA harboring exon 9a and lacking exon 9a was low and tightly regulated (0.017–0.11). In contrast, 11/13 RUNX1‐RUNX1T1‐positive AML patients displayed high and variable ratios of FT ranging from 0.05 to 0.46 (P < 0.001, Wilcoxon rank‐sum test), indicating altered exon 9a splicing in these patients. Importantly, patients who remained in continuous complete remission displayed a faster disappearance of the RUNX1‐RUNX1T1 exon 9a splice variant compared to patients bound to relapse (P = 0.02). In conclusion, alternative splicing seems to be part of the leukemogenic process in the majority of RUNX1‐RUNX1T1‐positive AML patients, and splice variant kinetics under cytoreduction may be a predictor for patients prone to relapse.