Detection and targeting of splicing deregulation in pediatric acute myeloid leukemia stem cells

• Published in: Cell reports. Medicine 2023-03, Vol.4 (3), p.100962-100962, Article 100962
• Main Authors: van der Werf, Inge, Mondala, Phoebe K., Steel, S. Kathleen, Balaian, Larisa, Ladel, Luisa, Mason, Cayla N., Diep, Raymond H., Pham, Jessica, Cloos, Jacqueline, Kaspers, Gertjan J.L., Chan, Warren C., Mark, Adam, La Clair, James J., Wentworth, Peggy, Fisch, Kathleen M., Crews, Leslie A., Whisenant, Thomas C., Burkart, Michael D., Donohoe, Mary E., Jamieson, Catriona H.M.
• Format: Article
• Language: English
• Subjects: Adult; CD47; Child; embryonic stem cells; hematopoietic stem cells; Humans; Leukemia, Myeloid, Acute - drug therapy; Leukemia, Myeloid, Acute - genetics; Mutation; pediatric AML; pre-mRNA splicing; Protein Isoforms - genetics; RBFOX2; Repressor Proteins - genetics; RNA Splicing - genetics; RNA Splicing Factors - genetics; SF3B1; splicing modulation; Stem Cells
• ISSN: 2666-3791; 2666-3791
• DOI: 10.1016/j.xcrm.2023.100962

Pediatric acute myeloid leukemia (pAML) is typified by high relapse rates and a relative paucity of somatic DNA mutations. Although seminal studies show that splicing factor mutations and mis-splicing fuel therapy-resistant leukemia stem cell (LSC) generation in adults, splicing deregulation has not been extensively studied in pAML. Herein, we describe single-cell proteogenomics analyses, transcriptome-wide analyses of FACS-purified hematopoietic stem and progenitor cells followed by differential splicing analyses, dual-fluorescence lentiviral splicing reporter assays, and the potential of a selective splicing modulator, Rebecsinib, in pAML. Using these methods, we discover transcriptomic splicing deregulation typified by differential exon usage. In addition, we discover downregulation of splicing regulator RBFOX2 and CD47 splice isoform upregulation. Importantly, splicing deregulation in pAML induces a therapeutic vulnerability to Rebecsinib in survival, self-renewal, and lentiviral splicing reporter assays. Taken together, the detection and targeting of splicing deregulation represent a potentially clinically tractable strategy for pAML therapy. [Display omitted] •Pediatric acute myeloid leukemia stem cells harbor increased exon skipping events•Decreased RBFOX2 induces embryonic splicing and CD47 splice isoform upregulation•Lentiviral splicing reporter studies show exon skipping reversal with Rebecsinib•Rebecsinib inhibits pediatric acute myeloid leukemia stem cell propagation Pediatric acute myeloid leukemia stem cells (LSCs) harbor increased exon skipping events and decreased RBFOX2 expression, which is linked to embryonic splicing patterns and CD47 splice isoform upregulation. van der Werf et al. show that the reversal of malignant exon skipping with Rebecsinib, a selective splicing modulator, prevents pediatric LSC propagation.