Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia

Abstract The transcription factors EBF1 and PAX5 are frequently mutated in B cell acute lymphoblastic leukemia (B-ALL). We demonstrate that Pax5 +/- x Ebf1 +/- compound heterozygous mice develop highly penetrant leukemia. Similar results were seen in Pax5 +/- x Ikzf1 +/- and Ebf1 +/- x Ikzf1 +/- mice for B-ALL, or in Tcf7 +/- x Ikzf1 +/- mice for T cell leukemia. To identify genetic defects that cooperate with Pax5 and Ebf1 compound heterozygosity to initiate leukemia, we performed a Sleeping Beauty (SB) transposon screen that identified cooperating partners including gain-of-function mutations in Stat5 (∼65%) and Jak1(∼68%) , or loss-of-function mutations in Cblb (61%) and Myb (32%) . These findings underscore the role of JAK/STAT5 signaling in B cell transformation and demonstrate unexpected roles for loss-of-function mutations in Cblb and Myb in leukemic transformation. RNA-Seq studies demonstrated upregulation of a PDK1>SGK3>MYC pathway; treatment of Pax5 +/- x Ebf1 +/- leukemia cells with PDK1 inhibitors blocked proliferation in vitro. Finally, we identified conserved transcriptional variation in a subset of genes between human leukemias and our mouse B-ALL models. Thus, compound haploinsufficiency for B cell transcription factors likely plays a critical role in transformation of human B cells and suggest that PDK1 inhibitors may be effective for treating patients with such defects.