Comparison of Clinicopathological Features of Patients with Two Spliceosome Gene Co-Mutations

Introduction

Spliceosome genes (SF3B1, SRSF2, ZRSR2, or U2AF1) are involved in mRNA splicing and their mutations could result in many cancers including hematologic malignancies, making them appealing therapeutic targets. So far, they have been reported to be mutually exclusive due to their synthetic lethality. However, co-mutations of these genes have been reported, the largest study so far including 16 patients with two spliceosome genes mutated and reporting no clinical impact.

In this study, which is likely the largest cohort study reported, we collected and compared 154 patients with two co-mutated spliceosome genes.

Methods

This study is approved by institute IRB protocol. All the patients with mutations in two of spliceosome genes (SF3B1, SRSF2, ZRSR2, or U2AF1) were collected from our NextGen sequencing database (a 96 gene panel) with 10301 tested patients and their clinicopathological findings were collected. The overall survival was calculated from the sequencing date to the death or last contact date. Fisher’s exact test was used for categorical variables, Mann-Whitney U-test for numerical variables, and Kaplan-Meier analysis for survival curves.

Results

Out of our database of 10301 patients with NextGen sequencing results, a total of 154 patients with spliceosome co-mutations were collected (1.5%), including SF3B1/ZRSR2 (35 patients, 22.73%), SRSF2/ZRSR2 (35 patients, 22.73%), SF3B1/SRSF2 (31 patients, 20.13%), ZRSR2/U2AF1 (25 patients, 16.23%), SRSF2/U2AF1 (15 patients, 9.74%), and SF3B1/U2AF1 (13, 8.44%). The male/female ratio of patients with ZRSR2/U2AF1 co-mutations (7.33) was significantly higher than patients with SF3B1/ZRSR2 co-mutations (1.06) (p value 0.0045).

The most frequent morphologic diagnosis for patients with SF3B1 mutations (SF3B1/SRSF2 45.2%, SF3B1/U2AF1 61.54%, and SF3B1/ZRSR2 41.2%) was myelodysplastic syndrome (MDS), with SRSF2/ZRSR2 (51.4%) or ZRSR2/U2AF1 (44%) co-mutations was acute myeloid leukemia (AML), while the SRSF2/U2AF1 co-mutations was MDS/MPN. In patient with MDS, SF3B1/U2AF1 co-mutations (61.54%) were significantly more frequent than SRSF2/U2AF1 co-mutations (13.3%) (p value 0.0163). In MPN patients, SRSF2/U2AF1 co-mutations (26.7%) were significantly more common than SF3B1/SRSF2 co-mutations (0%) (p value 0.0084).

Patients with SF3B1/U2AF1 co-mutations showed significantly lower median WBC (2 k/uL) than patients with SRSF2/U2AF1 (5 k/uL) co-mutations (p value <0.05), while the median platelet levels of patients with ZRSR2/U2AF co-mutations (70 k/uL) or SRSF2/ZRSR2 co-mutations (71 /uL) were significantly lower than the patients with SF3B1/ZRSR2 co-mutations (187 /uL) (p values 0.0009 and 00046, respectively).

Patients with ZRSR2/U2AF1 co-mutations were less likely to have normal karyotype or good cytogenetic profile (25%) than patients with SF3B1/SRSF2 (59.1%, p value 0.03344) or SRSF2/ZRSR2 (57.7%, p value 0.0375) co-mutations, and more likely to have poor cytogenetic profile (40%) than patient with SRSF2/U2AF1 co-mutations (0%, p value 0.02888). The median percentage of peripheral blood blasts in patients with SRSF2/U2AF1 co-mutations was significantly higher (1.5%) than patients with other co-mutations (0 or 1%) (p value <0.05). The median percentage of bone marrow blasts of patient with ZRSR2/U2AF1 (15%) was significantly higher than patients with SF3B1/ZRSR2 co-mutations (1.8%) (p value 0.00386).

No statistically significant difference was found in age, median hemoglobin level, median overall survival time, median percentages of ring-sideroblasts, or degree of fibrosis.

Finally and importantly, no statistical significance was found in the Kaplan-Meier survival curves of these co-mutations.

Discussion

The patients with two spliceosome gene mutations are not as rare as previously expected. The patient with these co-mutations show some difference in male/female ratio, morphological diagnosis, bone marrow cellularity, cytogenetic results, peripheral blood and bone marrow blast percentages, WBC, and platelet counts, and no significant difference in age, median hemoglobin level, median overall survival time, median percentages of ring-sideroblasts, or degree of fibrosis. Importantly, no statistical significance was found in the Kaplan-Meier survival curves. However, larger cohort studies are needed to conform these results or detect more subtle differences.