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Sensitivity of splicing factor mutant hematopoietic cells to GSK-3 inhibition

ABSTRACT: Recurrent mutations in the splicing factors SRSF2 and SF3B1 are common in myelodysplasia (MDS) and acute myeloid leukemia (AML). These mutations are invariably heterozygous, as cells with splicing factor mutations nevertheless depend on wild-type splicing activity. Disrupting splicing further is lethal, suggesting a therapeutic vulnerability for splicing factor mutant hematopoietic neoplasms. Glycogen synthase kinase-3 (GSK-3) phosphorylates multiple splicing factors, including SRSF2 and SF3B1, and regulates the splicing of a broad range of mRNAs in human cells. Inhibition of GSK-3 disrupts splicing and promotes cell death in hematopoietic cells with heterozygous mutations in SRSF2 or SF3B1 and not in cells with wild-type splicing factors. To characterize how GSK-3 inhibition alters splicing and leads to cell death in SRSF2P95H/+ and SF3B1K700E/+ cells, we have performed deep RNA sequencing on K562 cells with SRSF2P95H/+ or SF3B1K700E/+ knocked into the endogenous locus (provided by Omar Abdel-Wahab (Wang et al; PMID 30799057) and treated with the GSK-3 inhibitor CHIR99021. Parental cells with wild-type splicing factors were included as controls. RNA-Seq data were further analyzed through the rMATS pipeline to assess changes in mRNA splicing (Liu et al, 2023).

ORGANISM(S): Homo sapiens

PROVIDER: GSE235600 | GEO | 2023/06/28

REPOSITORIES: GEO

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Project description:Mutations in spliceosomal genes are commonly found in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations occur at highly restricted amino acid residues and perturb normal splice site and exon recognition. Spliceosomal mutations are always heterozygous and rarely co-occur with one another, suggesting that cells may only tolerate a partial deviation from normal splicing activity. To test this hypothesis, we generated mice with inducible hemizygous expression of the commonly occurring SRSF2P95H mutation in the hematopoietic system. These mice rapidly developed lethal bone marrow failure upon activation of the Srsf2P95H mutation with concomitant deletion of the wildtype Srsf2 allele, demonstrating that Srsf2-mutant cells depend on the wildtype Srsf2 allele for survival. We next tested whether spliceosomal-mutant leukemias display greater sensitivity to pharmacologic splicing inhibition induced by the small molecule E7107. Treatment of isogenic murine leukemias as well as patient-derived xenograft (PDX) AMLs showed significant reductions in leukemic burden specifically in samples carrying spliceosomal mutations. Collectively, these data provide genetic and pharmacologic evidence that leukemias with spliceosomal mutations are preferentially susceptible to additional splicing perturbations in vivo compared with wildtype counterparts. Modulation of spliceosome function may provide a novel therapeutic avenue in genetically defined subsets of MDS/AML patients. We created an isogenic murine leukemia model by retroviral overexpression of the MLL-AF9 fusion oncogene in Vav-Cre Srsf2+/+ or Vav-Cre Srsf2P95H/+ BM cells followed by transplantation into lethally irradiated recipient mice. In order to determine the mechanistic origins of the Srsf2 mutant-selective effects of E7107, we analyzed transcriptional changes after five consecutive days of E7107 or vehicle treatment in vivo. GFP+ Cd11b+ cells were purified from the BM of recipient mice exactly three hours after the last dose of E7107 and were subjected to paired-end 2x50bp RNA-seq. For the knock-in/knock-out experiments, we generated inducible, hemizygous Srsf2P95H mice to study the effects of wildtype Srsf2 deletion with concomitant activation of the Srsf2P95H allele. Mx1-cre Srsf2fl/+ mice were crossed to Srsf2P95H/+ mice to generate Srsf2 wildtype (Mx1-cre Srsf2+/+), Srsf2 heterozygous knockout (Mx1-Cre Srsf2+/-), Srsf2 heterozygous P95H mutant (Mx1-Cre Srsf2P95H/+), and Srsf2 hemizygous P95H mutant (Mx1-Cre Srsf2P95H/-) mice, which were subjected to single-end 101bp RNA-seq.

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Sensitivity of splicing factor mutant hematopoietic cells to GSK-3 inhibition

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