RUNX1 deficiency cooperates with SRSF2 mutation to induce multilineage hematopoietic defects characteristic of MDS

Abstract

Myelodysplastic syndromes (MDS) are a heterogeneous group of hematologic malignancies with propensity to progress to acute myeloid leukemia (AML). Causal mutations in multiple classes of genes have been identified in MDS patients with some patients harboring more than one mutation. Interestingly, double mutations tend to occur in different classes, rather than the same class of genes, as exemplified by frequent co-occurring mutations in the transcription factor RUNX1 and the splicing factor SRSF2. This prototypic double mutant provides an opportunity to understand how their divergent functions in transcription and post-transcriptional regulation may be altered to jointly promote MDS. Here we report a mouse model in which Runx1 knockout was combined with the Srsf2 P95H mutation to cause multi-lineage hematopoietic defects. Besides their additive and synergistic effects, we also unexpectedly noted a degree of antagonizing activity of single mutations in specific hematopoietic progenitors. To uncover the mechanism, we further developed a cellular model using human K562 cells and performed parallel gene expression and splicing analyses in both human and murine contexts. Strikingly, while RUNX1 deficiency was responsible for altered transcription in both single and double mutants, it also induced dramatic changes in global splicing, as seen with mutant SRSF2, and only their combination induced mis-splicing of genes selectively enriched in the DNA damage response and cell cycle checkpoint pathways. Collectively, these data reveal the convergent impact of a prototypic MDS-associated double mutant on RNA processing and suggest that aberrant DNA damage repair and cell cycle regulation critically contribute to MDS development.

RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks

“…To elucidate how RUNX1 R320∗ may alter transcription differently than RUNX1 RHD loss-of-function mutants, we compared RUNX1 R320∗ dysregulated genes with our previously generated RUNX1 knockdown RNA-seq data set in K562 cells 35 ( Figure 3 C; supplemental Figure 2 A). Remarkably, most (74.63%) genes dysregulated in RUNX1 R320 ∗ were unique and not perturbed in RUNX1-depleted cells.…”

Impact of Next-Generation Sequencing in Diagnosis, Prognosis and Therapeutic Management of Acute Myeloid Leukemia/Myelodysplastic Neoplasms

“…The Serine and Arginine Rich Splicing Factor 2 (SRSF2) is a splicing factor in which mutations occur in up to 20% of AML/MDS and is frequently associated with mtRUNX1, conferring a particularly poor prognosis [ 24 ]. The reasons why the mtSRSF2/mtRUNX1 association is so deleterious have been analyzed [ 25 ]. Very interestingly, this co-mutation induces mis-splicing of a series of genes involved in the DNA damage response and in the cell-cycle checkpoint pathways (Fanconi anemia of complementation group J gene/ BRIP1 , NABP1 , TBRG4 and AKAP8L ).…”

The eukaryotic translation initiation factor eIF4E unexpectedly acts in splicing thereby coupling mRNA processing with translation

“…[ 72 , 83 , 84 ] Additionally, mutation of other AML‐associated proteins such as RUNX1, while rare, are associated with altered splicing in MDS and AML. [ 85 ] Importantly, AML is characterized by disrupted splicing far more frequently than SF or RUNX mutation occur in patients. [ 12 ]…”