Our understanding of the genetics of chronic lymphocytic leukemia (CLL) has advanced significantly in the last few years. Recently, somatic mutations in SF3B1, a gene encoding a core component of the RNA splicing machinery, have been detected in tumor samples from variable proportions of CLL patients. Interestingly, mutations of SF3B1 are also found in patients with myelodysplastic syndrome, where they represent founding mutations, are specifically associated with phenotype with ring sideroblasts, and have a favorable prognostic significance.
In this study, we analyzed incidence and clinical significance of SF3B1 mutation in 335 consecutive unselected CLL patients followed between 2000 and 2011. We analyzed 359 tumor samples from 335 patients: 191 were collected at diagnosis, 75 during follow up in untreated patients with stable disease (median time from diagnosis to sampling 24 months, range 8–110), 31 at first progression and before first line therapy (median time from diagnosis to sampling 37 months, range 5–110), and 62 in previously treated patients with active disease (median time from diagnosis to sampling 51 months, range 7–171). The overall median follow-up was 57 months (range 10–225). SF3B1 exons 14, 15 and 16 were screened for mutation by using denaturing high-performance liquid chromatography (DHPLC), and positive samples were then analyzed by Sanger sequencing.
We detected 30 heterozygous missense mutations in 29 patients, with an overall incidence of 8.7% (29/335). Most of mutations were single base substitutions, and the most frequent mutation was K700E in exon 15, found in 40% of mutated patients, followed by G742D in exon 16 (27% of mutants). While SF3B1 (K700E) is the most frequent mutation also in myelodysplastic syndromes, SF3B1 (G742D) is rarely found in these latter disorders.
Mutations frequency was low at diagnosis (6.3%) and in untreated patients with stable disease (5.3%), whereas it increased significantly at progression (9.7%) and in previously treated patients with active disease (16.1%) (P=.027). Of 268 patients evaluated at diagnosis and before progression or treatment, 87% were in Binet stage A and 13% in Binet stage B or C, 40% had unmutated IGHV status, 14% carried del11q or del17p detected by I-FISH, 15% were CD38+ and 25% were ZAP70+. Within this group, SF3B1 mutations were detected in 16/268 (6%) patients, and were associated with advanced Binet stage (B or C) (15% vs 5%, P=.037); there was also a trend for association with unmutated IGHV pattern (P=.053) and CD38 expression (P= .068). Interestingly, of 9 patients carrying IGHV3–21, four were SF3B1 mutated and had a stereotyped HCDR3.
In order to evaluate the impact of SF3B1 mutation on overall survival (OS) and time to first treatment (TTFT), we analyzed 234 untreated patients in Binet stage A (161 evaluated at diagnosis and 73 during follow-up). Also in this subset, SF3B1 mutation (11/234 or 5%) was associated with CD38 expression (P=.007) and unmutated IGHV status (P=.05). Median OS was not reached (9 events so far). In univariate analysis, SF3B1 mutation had no impact on OS, whereas unmutated IGHV, CD38 expression and ZAP70 positivity were associated with worse OS (P=.002, P=.002 and P=.003, respectively).
Seventy-six patients were treated and median TTFT was 40 months (range 1–154). Univariate analysis showed an adverse impact of SF3B1 mutation on TTFT (median TTFT 26 months in mutated vs 109 months in unmutated patients, P=.0009). Unmutated IGHV, CD38 expression and presence of del17p or del11q had a crude association with shorter TTFT as well (P<.0001, P=.0002 and P=.0009, respectively). However, in a Cox multivariable analysis, SF3B1 mutation status lost significance and only IGHV status maintained an independent adverse impact on TTFT.
In 37 CLL patients, serial samples were available for mutation analysis. We identified three SF3B1 mutations that were acquired at follow up, and this occurred in patients who were refractory to or relapsed after at least one line of therapy.
In conclusion, the findings of this study indicate that SF3B1 mutations have a low incidence in early stages of CLL, whereas they occur more frequently in advanced stages. At variance with myelodysplastic syndromes, SF3B1 mutations are unlikely to represent founding or driver mutations in CLL patients. More likely, they occur during clonal evolution of the disease, and may therefore be considered as a molecular marker of disease progression.
No relevant conflicts of interest to declare.
Asterisk with author names denotes non-ASH members.