SF3B1 Mutations Are Detectable in 48.9% of Acute Myeloid Leukemia with Normal Karyotype (AML-NK) and ≥15% Ring Sideroblasts and Are Closely Related to FLT3-ITD and RUNX1 Mutations

Mutations in the spliceosome gene SF3B1 (splicing factor 3b, subunit 1; SF3B1 mut) are frequent in patients with myelodysplastic syndromes (MDS) and ring sideroblasts (RS). In contrast, in AML occurrence of SF3B1mut has been published to be comparatively low (2–5%). However, analysis of SF3B1 mut in AML with RS is lacking. We aimed to determine the frequency of SF3B1 mut in AML patients according to the percentage of RS and the association of SF3B1 mut with other genetic markers.

275 AML patients (115 f/160 m; median age: 71.2 years, range: 20.8 – 89.9 years) were analyzed for SF3B1 mut by Sanger sequencing of the coding region (exon 11 to 16). RS were detectable in 176/275 cases (RS in ≥15% of erythroid precursors: n=106; RS in 1–14%: n=70), 99 cases showed no RS. The cohort comprised 202 de novo AML (FAB: M0 n=27, M1 n=36, M2 n=55, M4 n=32, M5 n=1, M6 n=51), 65 s-AML and 8 t-AML patients. Data on other mutations were available as follows: FLT3-ITD n=242, FLT3-TKD n=173, MLL-PTD n=235, NPM1 n=230, RUNX1 n=199, CEBPA n=152, NRAS n=141, KRAS n=56, ASXL1 n=90, IDH1 n=78, IDH2 n=58, TP53 n=74, and DNMT3A n=52. Chromosome banding analysis (combined with FISH if needed) was performed in 262 cases. According to MRC criteria, favorable karyotypes were found in 6, intermediate in 169, and adverse in 87 cases. 120/262 (45.8%) cases had a normal karyotype (NK-AML).

Overall, in 44/275 (16.0%) patients SF3B1 mut were detected with a median mutation/wildtype ratio of 45% (range: 10 – 50%). The most frequent mutation was Lys700Glu (19/44, 43.2%) followed by Lys666Asn/Arg/Thr (15/44, 34.1%) and Arg625Cys/Leu (3/44, 6.8%) and other mutations found in single cases only. Patients without detectable RS had almost no SF3B1 mut in contrast to cases with RS (3/99, 3.0% vs 41/176, 23.3%, p<0.001). Of note, all three patients with SF3B1 mut without RS were s-AML. SF3B1 mut were significantly more frequent in AML with RS ≥15% as compared to RS 1–14% (33/106, 31.1% vs 8/70, 11.4% p=0.003). The frequency of SF3B1 mut was significantly increasing by higher RS categories: group 1, RS 0–14%: SF3B1 mut in 6.5%; group 2, RS 15–34%: 17.9%; group 3, RS 35–54%: 45.4%, group 4, RS 55–74%: 41.2%, group 5, RS 75–100%: 54.5% (group 1 vs 2: p=0.017; 2 vs 3: p=0.020; comparison of the frequency of SF3B1 mut for all groups: p<0.001). In line, SF3B1 mut had higher percentages of RS vs SF3B1 wt (mean: 37% vs 13%, p<0.001), higher age (mean: 72 vs 69 years, p=0.044) and higher platelet counts (mean: 108 vs 71 x10⁹/L, p=0.014). SF3B1 mut was not detected in any of the analyzed t-AMLs. Within cases with RS ≥15% the frequency of SF3B1 mut was only slightly higher in s-AML vs de novo AML (12/34, 35.3% vs 21/69, 30.4%, p=0.657), and likewise was the percentage of RS (mean: 45% vs 37%, p=0.137). In de novo AML, SF3B1 mut occurred more often in FAB M2 and M4 (M2: 13/55, 23.6%; M4 10/32, 31.3%; M2 and M4 combined vs others 23/87, 26.4% vs 4/115, 3.5%, p<0.001). Frequency was lower in FAB M6 vs others (3/51, 5.9% vs 24/151, 15.9%, p=0.094) and M0 (1/27, 3.7% vs 26/175, 14.9%, p=0.138), whereas SF3B1 mut were mutually exclusive of FAB M1 (0/36, 0% vs 27/166, 16.3%, p=0.005). In intermediate MRC karyotypes frequency of SF3B1 mut was much higher vs all others (38/169, 22.5% vs 4/93, 4.3%, p<0.001). In detail, SF3B1 mut showed high occurrence in NK patients (NK vs aberrant: 28/120, 23.3% vs 14/142, 9.9%, p=0.004) and within this subgroup a very high frequency of 48.9% (23/47) in cases with RS ≥15%. In contrast, SF3B1 mut were nearly mutually exclusive of complex karyotype (complex vs all others: 1/57, 1.8% vs 41/205, 20.0%, p<0.001). Furthermore, SF3B1 mut were associated with FLT3-ITD (7/21, 33.3% vs 30/221, 13.6%, p=0.025) and RUNX1 mutations (19/65, 29.2% vs 12/134, 9.0%, p=0.001).

So far, SF3B1 mut were considered to be mainly relevant for MDS. In this study, SF3B1 mut were found in 31.1% of AML with RS ≥15% and even more striking in 48.9% of AML-NK with RS ≥15%. SF3B1 mut were associated with higher age, AML FAB M2 and M4 subtypes, normal karyotype, FLT3-ITD and RUNX1 mutations. Our study adds both de novo and s-AML with RS ≥15% to the myeloid entities with frequent occurrence of SF3B1 mut and suggests analysis of a possible prognostic impact of SF3B1 mut in AML with increased RS.

Jeromin:MLL Munich Leukemia Laboratory: Employment. Bacher:MLL Munich Leukemia Laboratory: Employment. Bayer:MLL Munich Leukemia Laboratory: Employment. Dicker:MLL Munich Leukemia Laboratory: Employment. Eder:MLL Munich Leukemia Laboratory: Employment. Fasan:MLL Munich Leukemia Laboratory: Employment. Grossmann:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership.