Splicing factor SF3B1 mutations and ring sideroblasts in myelodysplastic syndromes: a Brazilian cohort screening study

Alteration of SF3B1 and SRSF2 Genes in Myelodysplastic Syndromes Patients in Upper Northern Thailand

Background:

The frequency and pattern of mutation in SF3B1 and SRSF2 RNA splicing machinery genes were found to vary among myelodysplastic syndrome (MDS) patients in different populations. There have been less reports of incidence of these gene mutations in Thailand especially in upper northern Thailand. This study therefore had aims to investigate the frequency and pattern of mutation in mutational hotspot of SF3B1 and SRSF2 genes among MDS patients in upper northern Thailand and to investigate the clinical features associated with the mutations.

Methods:

Fifty-five MDS patients who underwent treatment at Maharaj Nakorn Chiang Mai Hospital participated in this study. The detection of SF3B1 and SRSF2 hotspot mutations was carried out using polymerase chain reaction followed by Sanger sequencing. In addition, clinical features of individual patients with these gene mutations were also investigated.

Results:

SF3B1 mutations (SF3B1^mut) were found in 9 patients (16.4%) including E622D (1/9), R625C (1/9), H662Q (1/9), K700E (5/9), and Q699H co-mutation with K700E (1/9). SRSF2 mutations (SRSF2^mut) were found in 4 patients (7.3%) which included P95H (3/4) and P95L (1/4). The SF3B1^mut was associated with lower hemoglobin levels (p = 0.023) and higher platelet counts (p = 0.047) when compared with MDS patients without SF3B1^mut, while SRSF2^mut tended to occur in patients with a higher percentage of bone marrow blasts (p = 0.074).

Conclusion:

The findings confirmed the difference in frequency of SF3B1 and SRSF2 mutations among different populations. Specifically, we found a co-mutation of Q699H and K700E that has not been previously reported in MDS patients in the COSMIC database. It was also found that SF3B1^mut was strongly associated with low hemoglobin level, and high platelet counts whereas SRSF2^mut was mostly clustered in MDS with excess blasts subsequently increasing the probability of progression to acute myeloid leukemia.

Anti-tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC-dependent vulnerability

The modulation of pre-mRNA splicing is proposed as an attractive anti-neoplastic strategy, especially for the cancers that exhibit aberrant pre-mRNA splicing. Here, we discovered that T-025 functions as an orally available and potent inhibitor of Cdc2-like kinases (CLKs), evolutionally conserved kinases that facilitate exon recognition in the splicing machinery. Treatment with T-025 reduced CLK-dependent phosphorylation, resulting in the induction of skipped exons, cell death, and growth suppression in vitro and in vivo Further, through growth inhibitory characterization, we identified high CLK2 expression or MYC amplification as a sensitive-associated biomarker of T-025. Mechanistically, the level of CLK2 expression correlated with the magnitude of global skipped exons in response to T-025 treatment. MYC activation, which altered pre-mRNA splicing without the transcriptional regulation of CLKs, rendered cancer cells vulnerable to CLK inhibitors with synergistic cell death. Finally, we demonstrated in vivo anti-tumor efficacy of T-025 in an allograft model of spontaneous, MYC-driven breast cancer, at well-tolerated dosage. Collectively, our results suggest that the novel CLK inhibitor could have therapeutic benefits, especially for MYC-driven cancer patients.

The Frequency of SF3B1 Mutations in Thai Patients with Myelodysplastic Syndrome

Genetic mutations in genes encoding critical component of RNA splicing machinery including SF3B1 are frequently identified and recognized as the pathogenesis in the development of myelodysplatic syndrome (MDS). In this study, PCR sequencings specific for SF3B1 exon 13, 14, 15, and 16 were performed to analyse genomic DNA isolated from bone marrow samples of 72 newly diagnosed MDS patients. We found that 10 of 72 (14%) patients harbor SF3B1 missense mutations including E622D (1/72), R625C/G (2/72), H662Q (1/72), K666T (1/72), K700E (4/72) and G740E (1/72), respectively. Mutations were predominantly located on exon 14 and 15 of SF3B1 coding sequence. Interestingly, patients with SF3B1 mutations exhibited higher platelet counts (195×10⁹/L VS. 140×10⁹/L, p-value = 0.025) as well as lower hemoglobin levels (81 g/L VS. 92 g/L, p-value = 0.009) and associated with ring sideroblast phenotype (p-value < 0.001) when compared with patients without the SF3B1 mutation. In summary, we reported the frequency of SF3B1 mutations in Thai patients with different subtypes of MDS. SF3B1 mutations were predominantly occurred in MDS-RS and considered as favourable prognosis value. This study further highlighted the clinical important of SF3B1 mutations analysis for the classification of MDS.