SF3B1 mutations in chronic lymphocytic leukemia

Abstract

SF3B1 is a critical component of the splicing machinery, which catalyzes the removal of introns from precursor messenger RNA (mRNA). Next-generation sequencing studies have identified mutations in SF3B1 in chronic lymphocytic leukemia (CLL) at high frequency. In CLL, SF3B1 mutation is associated with more aggressive disease and shorter survival, and recent studies suggest that it can be incorporated into prognostic schema to improve the prediction of disease progression. Mutations in SF3B1 are predominantly subclonal genetic events in CLL, and hence are likely later events in the progression of CLL. Evidence of altered pre-mRNA splicing has been detected in CLL cases with SF3B1 mutations. Although the causative link between SF3B1 mutation and CLL pathogenesis remains unclear, several lines of evidence suggest SF3B1 mutation might be linked to genomic stability and epigenetic modification.

Figure 1

Distribution of mutations in SF3B1. Mutations in SF3B1 predominantly localize to its C-terminal domain between the fifth and eighth HEAT repeats (exons 14-16). (A) The accumulated mutation sites and frequencies from 5 published CLL sequencing studies. (B) The mutation sites and frequencies reported from other types of cancers (retrieved from COSMIC [version 62]). Rare mutations outside of the fifth to eighth HEAT repeats are not shown.

Figure 2

SF3B1 expression and methylation in normal and CLL cells. (A) SF3B1 relative expression in different human tissues. (B) SF3B1 relative expression in normal B-cell subpopulations and CLL samples. CB, centroblast; CC, centrocyte. Data generated from Affymetrix HG-U133Plus2 arrays. (C) DNA methylation on SF3B1 in CLL samples with or without SF3B1 mutation and normal B cells. (D) Targeted pyrosequencing of a SF3B1 K700E site of cDNA from normal peripheral blood mononuclear cells (top, NL PBMC) compared with cDNA from a CLL sample with known K700E mutation in SF3B1 (bottom). K700E mutation is generated from an A2098G transition on the sense strand; this pyrosequencing assay was designed to detect the T to C transition at the corresponding site on the antisense strand. cDNA, complementary DNA. Panel A adapted from the Novartis Gene Atlas with permission. Panel B adapted from Rossi et al with permission. Panel C adapted from Kulis et al with permission.

Figure 3

SF3B1 mutation is a predominantly subclonal event in CLL. (A) Percentage of the mutations classified as clonal (orange) and subclonal (blue) for each putative CLL driver, within a cohort of 149 CLL cases. The number of cases (n) affected by each genetic alteration is shown (*Drivers with q value < 0.1 for a higher proportion of clonal mutations compared with the entire CLL drivers set). (B) Analysis of co-occurrence of the 19 SF3B1 mutations within 149 CLL cases with other driver alterations. Top bar shows the color representation of CCF. (C) Joint distributions of CCF values across 2 time points using clustering analysis (see Landau et al for method). Red denotes a mutation that had an increase in CCF of >0.2 (with probability >0.5). The dotted diagonal line represents CCF values that were identical across the 2 time points. The dotted parallel lines denote the 0.2 CCF interval on either side. Panel A adapted from Landau et al with permission.

Figure 4

SF3B1 is an essential component in U2 snRNP and crucial for RNA splicing. (A) SF3B1 lies within the U2 snRNP and interacts with the 5′ and 3′ adjacent sites of the BPS, a critical splice site motif. PY tract, polypyrimidine tract. (B) A schematic of the stepwise process of pre-mRNA splicing.

Figure 5

The potential impact of mutated SF3B1 on the pathobiology of CLL.