Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness

Abstract

The genetic lesions identified in chronic lymphocytic leukemia (CLL) do not entirely recapitulate the disease pathogenesis and the development of serious complications, such as chemorefractoriness. While investigating the coding genome of fludarabine-refractory CLL, we observed that mutations of SF3B1, encoding a splicing factor and representing a critical component of the cell spliceosome, were recurrent in 10 of 59 (17%) fludarabine-refractory cases, with a frequency significantly greater than that observed in a consecutive CLL cohort sampled at diagnosis (17/301, 5%; P = .002). Mutations were somatically acquired, were generally represented by missense nucleotide changes, clustered in selected HEAT repeats of the SF3B1 protein, recurrently targeted 3 hotspots (codons 662, 666, and 700), and were predictive of a poor prognosis. In fludarabine-refractory CLL, SF3B1 mutations and TP53 disruption distributed in a mutually exclusive fashion (P = .046). The identification of SF3B1 mutations points to splicing regulation as a novel pathogenetic mechanism of potential clinical relevance in CLL.

Figure 1

SF3B1 mutations in CLL and RS. Schematic diagram of the human SF3B1 gene (top) and protein (bottom) with its functional domains (PPP1R8 binding domain and HEAT repeats), and multiple alignment of the HEAT3, HEAT4, and HEAT5 amino acid sequences of the human SF3B1 protein with orthologous SF3B1 proteins (n = 15). Amino acids conserved among species are highlighted. Color-coded shapes indicate the position of the mutations found in CLL at diagnosis, in fludarabine-refractory CLL, and in RS.

Figure 2

Prevalence, mutual relationship with other genetic lesions, and clinical impact of SF3B1 mutations in CLL. (A) Prevalence of SF3B1 mutations in CLL at diagnosis, in fludarabine-refractory CLL, and in RS; numbers on top indicate the actual number of mutated samples over the total number analyzed. (B) Mutual relationship of SF3B1 mutations with other genetic lesions in CLL at diagnosis and in fludarabine-refractory CLL. In the heat map, rows correspond to identical genes, and columns represent individual patients color-coded based on the gene status (white: wild type; red: mutations of SF3B1, mutations of NOTCH1, mutations and/or deletion of TP53, deletion of ATM). (C) Kaplan-Meier estimates of treatment-free survival (TFS) and overall survival (OS) from diagnosis in the consecutive series of newly diagnosed and previously untreated CLL (n = 301). SF3B1 wild-type (SF3B1 wt) are represented by the blue line. SF3B1 mutated cases (SF3B1 M) are represented by the red line. (D) Gene expression levels of BCL6, AICDA, BCL2, IRF4, and SF3B1 in normal B-cell subpopulations (Naive; centroblasts, CB; centrocytes, CC; memory) and CLL samples. Relative levels of gene expression are depicted with a color scale: red represents the greatest level of expression and blue represents the lowest level.