Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia [ChIP-seq]

Detailed genomic and epigenomic analyses of MECOM (the MDS1 and EVI1 complex locus) have revealed that inversion or translocation of chromosome 3 at MECOM drive inv(3)/t(3;3) myeloid leukemias and revealed MECOM germline mutations in patients with MECOM-associated bone marrow failure syndromes. Here we identify a novel, previously unannotated oncogenic RNA-splicing derived isoform of EVI1 which is frequently present in inv(3)/t(3;3) AML and directly contributes to leukemic transformation. Expression of this EVI1 splice variant enhanced the self-renewal of hematopoietic stem cells and introduction of mutant SF3B1 in mice bearing the humanized inv(3)(q21;26) allele hastened leukemogenesis in vivo. These data provide a mechanistic basis for the frequent co-occurrence of SF3B1 mutations as well as new insights into the pathogenesis of myeloid leukemias harboring inv(3)/t(3;3). Overall design: One day before sample preparation, 293T cells were transfected with pMIGII_3xHA, pMIGII_3xHA-EVI1-WT, or pMIGII_3xHA-EVI1+18 retroviral vector. Detailed protocols for sample preparation were described at: doi.org/10.1016/j.xpro.2021.100404.