In this work, we sought to establish an endogenous reporter system enabling real-time monitoring of HOXA9 expression in conjunction with high-throughput CRISPR/Cas9 screening in a human B-ALL MLLr t(4;11) cell line SEM and a AML MLLr t(6;11) cell line OCI-AML2 equipped with an endogenous HOXA9P2A-mCherry reporter allele. Here, RUNX3 is linked to acute myeloid leukemia.