The Effect of SF3B1 Mutation on the DNA Damage Response and Nonsense-Mediated mRNA Decay in Cancer.

Alexander C Leeksma,Laura M Faber,Omar Abdel-Wahab,Sarka Pospisilova,M Haidar Kasem,Arjan A Van De Loosdrecht,Alexander Egle,Annelies De Klein,Eric Eldering,Joop H Jansen,Thorsten Zenz,Ingrid A M Derks,Arnon P Kater,Nadja Zaborsky,Martine J Jager,Veronika Navrkalova,Emine Kilic

doi:10.3389/fonc.2020.609409

Abstract

Recurrent mutations in splicing factor 3B subunit 1 (SF3B1) have been identified in several malignancies and are associated with an increased expression of 3’ cryptic transcripts as a result of alternative branchpoint recognition. A large fraction of cryptic transcripts associated with SF3B1 mutations is expected to be sensitive for RNA degradation via nonsense-mediated mRNA decay (NMD). Several studies indicated alterations in various signaling pathways in SF3B1-mutated cells, including an impaired DNA damage response (DDR) in chronic lymphocytic leukemia (CLL). In this study, we investigated isogenic cell lines and treatment naïve primary CLL samples without any TP53 and/or ATM defect, and found no significant effects of SF3B1 mutations on the ATM/p53 response, phosphorylation of H2AX and sensitivity to fludarabine. Cryptic transcripts associated with SF3B1 mutation status were observed at relatively low levels compared to the canonical transcripts and were validated as target for mRNA degradation via NMD. Expression of cryptic transcripts increased after NMD inhibition. In conclusion, our results confirm involvement of NMD in the biological effects of SF3B1 mutations. Further studies may elucidate whether SF3B1-mutant patients could benefit from NMD modulatory agents.

Highlights

Splicing factor 3B subunit 1 (SF3B1) is frequently mutated in different malignancies
Confirmation of altered SF3B1 function in three SF3B1-mutated NALM-6 cell lines against their parental cell line was obtained through increased expression of the SF3B1-associated cryptic transcripts of ATM, FOXP1 and TTI1 (Supplemental Figure S1A).These transcripts were previously reported to be increased in SF3B1 mutated cells [12, 23, 25], and were considered as signature genes that might be linked with pathobiological consequences
Various clinical trials have reported a negative effect of SF3B1 mutations on survival in chemotherapy-treated chronic lymphocytic leukemia (CLL) patients

Summary

Introduction

Splicing factor 3B subunit 1 (SF3B1) is frequently mutated in different malignancies. SF3B1 mutations cause altered splice branchpoint recognition which results in increased 3’ cryptic splicing, and concomitant frameshifts [11, 12]. The enhanced sensitivity of SF3B1-mutated cells to the splicing inhibitor H3B-8800 which is currently tested in phase I clinical trials [16] is in agreement with a therapeutic window of splicing factor inhibitors. Various studies have described the effects of SF3B1 mutations on alternative branchpoint recognition and indicated alterations in several signaling pathways including the DNA damage response [17,18,19], telomere maintenance [18], NF-kB [15, 20], NOTCH1 [18] and MYC signaling [21], but there is no clear view or consensus on the resulting pathological mechanism(s)

Methods

Results

Conclusion