RUNX1 isoform disequilibrium promotes the development of trisomy 21–associated myeloid leukemia

Abstract

Gain of chromosome 21 (Hsa21) is among the most frequent aneuploidies in leukemia. However, it remains unclear how partial or complete amplifications of Hsa21 promote leukemogenesis and why children with Down syndrome (i.e. trisomy 21) are particularly at risk of leukemia development. Here, we propose that RUNX1 isoform disequilibrium with RUNX1A bias is key to Down syndrome-associated myeloid leukemia (ML-DS). Starting with Hsa21-focused CRISPR-Cas9 screens, we uncovered a strong and specific RUNX1 dependency in ML-DS cells. Expression of the RUNX1A isoform is elevated in ML-DS patients, and mechanistic studies using murine ML-DS models and patient-derived xenografts (PDXs) revealed that excess RUNX1A synergizes with the pathognomonic Gata1s mutation during leukemogenesis by displacing RUNX1C from its endogenous binding sites and inducing oncogenic programs in complex with the MYC cofactor MAX. These effects were reversed by restoring the RUNX1A:RUNX1C equilibrium in PDXs in vitro and in vivo. Moreover, pharmacological interference with MYC:MAX dimerization using MYCi361 exerted strong anti-leukemic effects. Thus, our study highlights the importance of alternative splicing in leukemogenesis, even on a background of aneuploidy, and paves the way for the development of specific and targeted therapies for ML-DS, as well as for other leukemias with Hsa21 aneuploidy or RUNX1 isoform disequilibrium.

The clinical phenotype of germline RUNX1 mutations in relation to the accompanying somatic variants and RUNX1 isoform expression

“…The RUNX1 isoform disequilibrium observed in our study is in line with previous reports and further argues for its potential role in the development of MM in the context of FPDMM, for instance, by expediting the differentiation of myeloid cells, or a prestage to a MM 10 . Recently, a RUNX1a:RUNX1c disequilibrium was shown to promote trisomy 21‐associated leukemia, and restoration of the isoform balance had strong anti‐leukemic effects, reinforcing a role for RUNX1 isoforms as potential targets in blood cancer 12 …”

“…Previous studies have uncovered a role for RUNX1a expression in myeloid neoplasia 9–12 . However, it is unknown how RUNX1 mutations affect RUNX1 isoform expression patterns.…”

“…Previous studies have uncovered a role for RUNX1a expression in myeloid neoplasia. [9][10][11][12] However, it is unknown how RUNX1 mutations affect RUNX1 isoform expression patterns. Therefore, RUNX1 transcript isoform levels were assessed in the proband and his sister, both of whom carriers of RUNX1 R204* that causes a truncation of the RUNX1 transactivating domain present in isoforms RUNX1b and -c but absent in RUNX1a (Figure 1C).…”

“…Moreover, the RUNX1 isoforms play differential roles in normal hematopoiesis, but their function in hematological disease is unclear 7–10 . Overexpression of RUNX1a has been identified in myeloid malignancy (MM) progression and, recently, in the pathogenesis of trisomy 21‐associated myeloid leukemia 11,12 . However, RUNX1 isoform expression patterns in FPDMM or a role in RUNX1 deficiency remain to be investigated.…”

“…[7][8][9][10] Overexpression of RUNX1a has been identified in myeloid malignancy (MM) progression and, recently, in the pathogenesis of trisomy 21-associated myeloid leukemia. 11,12 However, RUNX1 isoform expression patterns in FPDMM or a role in RUNX1 deficiency remain to be investigated.…”