iPSC Model of Stepwise Leukemia Development in Congenital Neutropenia Reveals BAALC as a Key Mediator of Leukemogenesis

Recently, we reported a high frequency of cooperating RUNX1 and CSF3R mutations in CN patients that developed AML or MDS. We established a model for step-wise leukemia progression in CN using iPSC-based hematopoietic differentiation in combination with CRISPR/Cas9-mediated gene editing of iPSCs. Using this model, we confirmed that co-acquisition of CSF3R and RUNX1 mutations is sufficient to induce leukemia in CN. In addition, we identified BAALC (brain and acute leukemia, cytoplasmic) upregulation as a key leukemogenic event downstream of RUNX1 and CSF3R mutations. BAALC mRNA was upregulated in primary CN/AML blasts (n = 5) and in CD34+ HSPCs generated from CN/AML iPSCs of two patients. Importantly, CRISPR/Cas9-mediated knockout of BAALC in CN/AML-iPSCs inhibited proliferation and induced myeloid differentiation of CN/AML blasts. Using connectivity Map analysis of RNA-Seq data of iPSC-derived CD34+ cells, we identified a p38 MAPK/MK2 inhibitor that could possibly reverse BAALC-mediated leukemogenic gene expression signature. Proliferation of primary CN/AML blasts, CN/AML-iPSC-derived CD34+ cells and BAALC-expressing de novo AML blasts was decreased upon treatment with this inhibitor.