Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia

Abstract

Detailed genomic and epigenomic analyses of MECOM (the MDS1 and EVI1 complex locus) have revealed that inversion or translocation of chromosome 3 drive inv(3)/t(3;3) myeloid leukemias via structural rearrangement of an enhancer which upregulates transcription of EVI1. 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. This EVI1 isoform is generated by oncogenic mutations in the core RNA splicing factor SF3B1, which is mutated in >30% of inv(3)/t(3;3) myeloid neoplasm patients and thereby represents the single most commonly co-occurring genomic alteration in inv(3)/t(3;3) patients. SF3B1 mutations are statistically uniquely enriched in inv(3)/t(3;3) myeloid neoplasm patients and patient-derived cell lines compared with other forms of AML and promote mis-splicing of EVI1 generating an in-frame insertion of six amino acids at the 3' end of the second Zinc finger domain of EVI1. 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)(q21q26) allele resulted in generation of this novel EVI1 isoform in mice and hastened leukemogenesis in vivo. The mutant SF3B1 spliceosome depends upon an exonic splicing enhancer within EVI1 exon 13 to promote usage of a cryptic branch point and aberrant 3' splice site within intron 12 resulting in the generation of this isoform. 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).

Systematic evaluation of AML-associated antigens identifies anti-U5 SNRNP200 therapeutic antibodies for the treatment of acute myeloid leukemia

“…8a ). Across nine models, expression of U5 snRNP200 was most prominent on AML cells from mice bearing the humanized inversion chromosome 3q21q26 allele (‘inversion 3 mice’) 36 , 37 as well as simultaneous overexpression of fusion gene MLL-AF9 (also known as KMT2A - MLLT3 ) and NRAS G12D cDNA (known as ‘RN2’ cells 38 ). Evaluation of cell surface U5 snRNP200 expression on five EVI1 (also known as MECOM )-rearranged AML patient samples by high-density 36-color spectral flow cytometry as well as on three human EVI1 -rearranged patient-derived AML cell lines (HNT-34, MUTZ-3 and YCU-AML1) revealed clear U5 snRNP200 surface expression on all five EVI1 -rearranged patient samples as well as an overlap with CD33 and CD32A expression (Extended Data Fig.…”

“…The inv(3)(3q21q26) mouse strain 36 (RBRC09508) was provided by RIKEN BRC through the National BioResource Project of the MEXT and AMED, Japan. Male and female Mx1 Cre Sf3b1 K700E/WT inv(3)(q21q26) CD45.2 + cells 37 were serially transplanted into male and female CD45.1 + mice. Mice were bred and maintained in individual ventilated cages and fed with autoclaved food and water at the Memorial Sloan Kettering Animal Facility.…”

<i>EVI1</i> Disruption Post Neuroblastoma Treatment: A Case Analysis of Treatment-Associated Acute Myeloid Leukemia in a Pediatric Patient

“…EVI1 encodes a transcription factor essential for hematopoiesis. It is well-established that prevalent mutations in inv(3)/ t (3; 3) chromosomal rearrangement-induced AML encompass monosomy 7 and genes associated with the RUNX1, IKZF1 , and RAS signaling pathways ( NRAS, KRAS, PTPN11, and NF1 ) [ 14 , 15 ]. SMNs development may arise randomly or due to genetic susceptibility or mutagenic effects of initial cancer treatments.…”

EVI1-mediated Programming of Normal and Malignant Hematopoiesis

“…Mutations in the splicing factor SF3B1 have been found to co‐occur in >30% of t(3;3)/inv(3) cases 81 . The mutated SF3B1 causes alternative splicing of the EVI1 transcript, leading to a novel oncogenic isoform with an addition of 18 base pairs/6 amino acids in the distal zinc finger domain 82 . This EVI1 +18 isoform exhibits altered DNA binding and increased oncogenicity.…”