Somatic PRPF8 Mutations in Myeloid Neoplasia

Somaticmutations in genes of the RNA-splicing machinery are recurrent in myeloid neoplasia. PRPF8 has a central role in the spliceosome assembly and it is required in all tissues. Somatic mutations in PRPF8 have been described in patients with MDS. We previously showed that PRPF8 mutations (PRPF8^MT) are associated with presence of ring sideroblasts (RS) and a distinct myeloid phenotype. However, to date, no comprehensive analysis has been conducted to unravel the clonal architecture of PRPF8^MTpatients.

We took advantage of a large database of patients with bone marrow failure syndromes (BMFS) annotated for molecular and clinical characteristics (n=1700; median follow up 1.0 year, range 1-5 years), median age was 71 years (range, 13-93). Whole exome sequencing and targeted deep sequencing of a panel of 65 genes was applied. Our analyses included somatic mutational patterns, clonal hierarchy, and cross-sectional correlation in the cohort of PRPF8^MT and PRPF8 wild type.

PRPF8 mutations were found in 4% (65/1700) of patients. The mutations were mainly missense but nonsense, frameshift, and splice mutations were also seen. No specific hotspot was identified, although we noted that mutations at D1958 were detected in 7 patients, F1099 in 4 patients and C1594 and V1015 mutations were detected in 3 patients each. 6 mutations (-17/17p-) were consistent with hemizygous configuration of PRPF8^MT.

A total of 368 mutations in the 65 gene panel were detected. Median number of mutations/ patient was 3 (range 1-26). PRPF8^MT cases had a median overall survival (OS) of 26 months (mo) (range 8-110). 48/65 samples were tested for the presence of RS, showing 31% of samples with RS (RS+) and 69% of samples without RS (RS-). PRPF8^MT/RS+ were mainly MDS (47%) and MDS/MPN (27%) while PRPF8^MT/RS- were distributed in MDS (27%), BMFS (AA, PRCA, PNH; 27%), and AML (24%). We found that PRPF8^MT/RS+ had a higher neutrophil counts vs. PRPF8^MT/RS- (3.2±2.2 vs. 1.7±0.02) as well as platelets counts (158±197 vs. 91±150; P=.06) and a mild decreased number of lymphocytes (1.0±0.6 vs. 1.8±2.3, P=.03) perhaps due to a higher proportion of patients with BMFS. PRPF8^MT were mostly normal karyotype (45%) with a low percentage of complex karyotypes (16%)

We dissected the clonal hierarchy of PRPF8^MT and found that 38% (25/65) were ancestral while 62% (40/65) were secondary hits. The most commonly ancestral mutations besides PRPF8 were TET2 (n=3) and SF3B1 (n=3). The most common secondary mutations after PRPF8 were TET2 (n=14) and ASXL1 (n=14). In MDS and AML, PRPF8^MT were either ancestral or secondary, while in MDS/MPN and BMFS, PRPF8^MT was mostly a secondary mutation (71% and 75%, P=.05 and P=.04).

We further analyzed the mutational spectrum of PRPF8^MT patients. Cross-sectional analysis identified that the top mutated genes in PRPF8^MT clustered in epigenetic regulation and histone modification (19%; TET2, DNMT3A, IDH1/2, EZH2, ASXL1, KDM6A), followed by transcriptional regulation (13%; RUNX1, BCOR/L1, PHF6, ETV6, TP53), RNA-splicing (12%; SRSF2, SF3B1, LUC7L2, U2AF1, ZRSR2, DDX41, DHX29), and DNA-repair (7%; CUX1). Unlike other splicing mutations PRPF8 coexisted with other splicing lesions: SF3B1 (12%), SRSF2 (6%), LUC7L2 (9%), U2AF1 (8%), and ZRSR2 (6%). Of note, we found rare cases with triple splicing factor mutations (n=6). When we assessed the impact of the clonal architecture, ancestral PRPF8^MT had a shorter OS than those with secondary mutations (35mo vs. 59mo; P=.04).

In sum,clonal architecture analyses showed that PRPF8^MT are frequently secondary rather than ancestral mutations but when are ancestral hits, they lead to dismal prognosis. Unlike the more common spliceosomal factor mutations (SF3B1, U2AF1, SRSF2) that rarely co-occur, PRPF8^MT often co-occur with other spliceosomal mutations. This may be due to the fact that PRPF8^MT are mostly secondary mutations.