Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells

Abstract

The splicing factor SF3B1 is the most commonly mutated gene in the myelodysplastic syndrome (MDS), particularly in patients with refractory anemia with ring sideroblasts (RARS). We investigated the functional effects of SF3B1 disruption in myeloid cell lines: SF3B1 knockdown resulted in growth inhibition, cell cycle arrest and impaired erythroid differentiation and deregulation of many genes and pathways, including cell cycle regulation and RNA processing. MDS is a disorder of the hematopoietic stem cell and we thus studied the transcriptome of CD34+ cells from MDS patients with SF3B1 mutations using RNA sequencing. Genes significantly differentially expressed at the transcript and/or exon level in SF3B1 mutant compared with wild-type cases include genes that are involved in MDS pathogenesis (ASXL1 and CBL), iron homeostasis and mitochondrial metabolism (ALAS2, ABCB7 and SLC25A37) and RNA splicing/processing (PRPF8 and HNRNPD). Many genes regulated by a DNA damage-induced BRCA1–BCLAF1–SF3B1 protein complex showed differential expression/splicing in SF3B1 mutant cases. This is the first study to determine the target genes of SF3B1 mutation in MDS CD34+ cells. Our data indicate that SF3B1 has a critical role in MDS by affecting the expression and splicing of genes involved in specific cellular processes/pathways, many of which are relevant to the known RARS pathophysiology, suggesting a causal link.

Mutations of myelodysplastic syndromes (MDS): An update

“…The protein complex regulates pre-mRNA splicing of genes involved in DNA damage signaling and repair, and thus the altered activity of this complex results in impaired DNA repair and genetic instability. In MDS patients with SF3B1 mutations, such impaired function of this complex is demonstrated to be associated with possible downstream effects of its DNA repair potential [43,44].…”

Distinct splicing signatures affect converged pathways in myelodysplastic syndrome patients carrying mutations in different splicing regulators

“…The observation that splicing factor mutations in MDS are largely mutually exclusive suggests that these mutant splicing factors may induce a shared set of mRNA isoforms that may contribute to the development and progression of MDS. Several studies utilizing deep sequencing examined the splicing patterns associated with these mutations (Przychodzen et al 2013;Dolatshad et al 2015). However, it has been technically challenging to obtain quantitative data from the large number of patient samples to deduce potential disease mechanisms imposed by specific genetic lesions.…”

Splicing factor mutations in MDS RARS and MDS/MPN-RS-T

“…These results also raise another possibility that other deregulated genes, alone or in combination with ABCB7 downregulation, are responsible for the formation of RS. To this end, Mupo et al examined expression of Tmem14c, Alas2, and Slc25a37 (mitochondrial iron importer) as well as Abcb7 in their Sf3b1 K700E/WT KI mice [60]. However, no altered expression of these genes was detected in LSK cells in this model [46].…”