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

Abstract

The transcription factors PAX5, IKZF1, and EBF1 are frequently mutated in B cell acute lymphoblastic leukemia (B-ALL). We demonstrate that compound heterozygous loss of multiple genes critical for B and T cell development drives transformation, including Pax5+/−xEbf1+/−, Pax5+/−xIkzf1+/−, and Ebf1+/−xIkzf1+/− mice for B-ALL, or Tcf7+/−xIkzf1+/− mice for T-ALL. 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 Stat5b (~65%) and Jak1 (~68%), or loss-of-function mutations in Cblb (61%) and Myb (32%). These findings underscore the role of JAK/STAT5B signaling in B cell transformation and demonstrate roles for loss-of-function mutations in Cblb and Myb in transformation. RNA-Seq studies demonstrated upregulation of a PDK1>SGK3>MYC pathway; treatment of Pax5+/−xEbf1+/− leukemia cells with PDK1 inhibitors blocked proliferation in vitro. In addition, we identified a conserved transcriptional gene signature between human and murine leukemias characterized by upregulation of myeloid genes, most notably involving the GM-CSF pathway, that resemble a B cell/myeloid mixed-lineage leukemia. Thus, our findings identify multiple mechanisms that cooperate with defects in B cell transcription factors to generate either progenitor B cell or mixed B/myeloid-like leukemias.

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Fig. 1: Compound haploinsufficiency for transcription factor genes drives B cell or T cell leukemia.
Fig. 2: Sleeping Beauty mutagenesis screen to identify genes that cooperate with Pax5 and Ebf1 heterozygosity to induce leukemia.
Fig. 3: Increased Expression of Stat5b in leukemia.
Fig. 4: Loss of Cblb accelerates the onset of B cell ALL.
Fig. 5: Loss of MYB expression results in worse outcome in ALL.
Fig. 6: Inhibition of PDK1 blocks leukemic proliferation.
Fig. 7: Transcriptome profiles from leukemic progenitor B cells show common inter-leukemic transcriptional variation across human and mouse samples.
Fig. 8: Leukemias with a myeloid gene signature.

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Acknowledgements

We thank A. Rost, for technical assistance with mouse breeding; the University of Minnesota’s Supercomputing Institute for providing computing and bioinformatic resources; Dr. Meinrad Busslinger (Pax5+/−), Dr. Rudolf Grosschedl (Ebf1−/−), Dr. Peter Johnson (Cebpa−/−), Dr. Andrew Wells (Ikzf1−/−) and Dr. David Largaespada (Rosa26LSL-SB11T2/OncxRosa26LSL-SB11) for providing the indicated mouse strains. The results published here are in part based upon data generated by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative, phs000218, managed by the NCI. This work was supported by a Cancer Research Institute Investigator award, a Leukemia and Lymphoma Society Scholar award, funding from the UMN Masonic Cancer center and grants from the NIH (RO1 CA232317) to MAF. TKS was supported by grants from the Randy Shaver Cancer Research and Community Fund, NIH NCI (R21 CA216652), and the Masonic Cancer Center. ALS was supported by NCI (CA211249) and Masonic Cancer Center Support Grant (CA077598). SMK was supported by CPRIT MIRA RP 160693 and NIH/NCI P50 CA100632-09.

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Conception and design: L. Heltemes-Harris and M. Farrar. Development of Methodology: L. Heltemes-Harris, A. Sarver, S. Kornblau and M. Farrar. Acquisition of data (provided animals, acquired and managed patients, provided facilities, etc.) L. Heltemes-Harris, G. Hubbard, A. Sarver, S. Kornblau and M. Farrar. Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis): L. Heltemes-Harris, G. Hubbard, R. LaRue, T. Starr, S. Munro, Henzler, A. R. Yang, A. Sarver, S. Kornblau and M. Farrar. Writing, review, and/or revision of the manuscript: L. Heltemes-Harris, G. Hubbard, R. LaRue, T. Starr, S. Munro, C. Henzler, R. Yang, A. Sarver, S. Kornblau and M. Farrar. Administrative, technical, or material support (i.e., reporting or organizing data, constructing databases): L. Heltemes-Harris. Study Supervision: L. Heltemes-Harris, M. Farrar.

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Correspondence to Michael A. Farrar.

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Heltemes-Harris, L.M., Hubbard, G.K., LaRue, R.S. et al. Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia. Oncogene 40, 6166–6179 (2021). https://doi.org/10.1038/s41388-021-02012-z

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