Human Cancer-Associated Mutations of SF3B1 Lead to a Splicing Modification of Its Own RNA.

Tiffany Bergot,Delphine G Bernard,Nathalie Douet-Guilbert,Eric Lippert,Séverine Commet,Laurent Corcos

doi:10.3390/cancers12030652

Abstract

Deregulation of pre-mRNA splicing is observed in many cancers and hematological malignancies. Genes encoding splicing factors are frequently mutated in myelodysplastic syndromes, in which SF3B1 mutations are the most frequent. SF3B1 is an essential component of the U2 small nuclear ribonucleoprotein particle that interacts with branch point sequences close to the 3’ splice site during pre-mRNA splicing. SF3B1 mutations mostly lead to substitutions at restricted sites in the highly conserved HEAT domain, causing a modification of its function. We found that SF3B1 was aberrantly spliced in various neoplasms carrying an SF3B1 mutation, by exploring publicly available RNA sequencing raw data. We aimed to characterize this novel SF3B1 transcript, which is expected to encode a protein with an insertion of eight amino acids in the H3 repeat of the HEAT domain. We investigated the splicing proficiency of this SF3B1 protein isoform, in association with the most frequent mutation (K700E), through functional complementation assays in two myeloid cell lines stably expressing distinct SF3B1 variants. The yeast Schizosaccharomyces pombe was also used as an alternative model. Insertion of these eight amino acids in wild-type or mutant SF3B1 (K700E) abolished SF3B1 essential function, highlighting the crucial role of the H3 repeat in the splicing function of SF3B1.

Highlights

About 95% of coding genes in humans are subjected to alternative splicing, a highly regulated and complex mechanism that diversifies the proteome by creating multiple proteins from the same gene.Deregulation of splicing is observed in many cancers and hematological diseases [1,2]
By exploring publicly available RNA-seq raw data obtained from patients with SF3B1 mutations, we identified a transcript of SF3B1 that was solely detected in SF3B1 mutated samples in various neoplasms, including breast cancer [16], uveal melanoma [19] and recently in myelodysplastic syndromes (MDS) [28]
We first examined whether SF3B1ins transcript was effectively detected in a series of bone marrow mononuclear cell samples derived from 11 MDS-ring sideroblasts (RS) patients, in comparison to patients with Idiopathic Cytopenia of Undetermined Significance (n = 4) or from MDS

Summary

Introduction

About 95% of coding genes in humans are subjected to alternative splicing, a highly regulated and complex mechanism that diversifies the proteome by creating multiple proteins from the same gene.Deregulation of splicing is observed in many cancers and hematological diseases [1,2]. Recent massive sequencing of many cancer genomes allowed the identification of recurrent mutations in genes encoding splicing factors, including SF3B1 (Splicing Factor 3B subunit 1), SRFS2 (Serine and arginine rich splicing factor 2), U2AF1 (U2 small nuclear RNA auxiliary factor 1), and ZRSR2 CCCH-type, RNA binding motif and Serine/Arginine Rich 2), suggesting that somatic alterations of genes involved in splicing are common in cancer [2,3]. MDS are complex and heterogeneous acquired pathologies of the bone marrow, characterized by a clonal and ineffective hematopoiesis, resulting in a deficit of mature myeloid blood cells and a risk of clonal progression including evolution to acute myeloid leukemia. Mutations in genes involved in epigenetic regulation are frequently present in MDS.

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