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.

Center of Molecular Biology and Gene Therapy Department of Internal Medicine Hematology and Oncology University Hospital Brno and Center of Molecular Medicine CEITEC Masaryk University Brno Czechia

Department of Experimental Immunology Amsterdam University Medical Centers Location AMC University of Amsterdam Amsterdam Netherlands

Department of Hematology Amsterdam University Medical Centers Location AMC University of Amsterdam Amsterdam Netherlands

Department of Hematology Amsterdam University Medical Centers Location VUMC Amsterdam Netherlands

Department of Internal Medicine 3 with Haematology Cancer Cluster Salzburg Salzburg Austria

Department of Internal Medicine 3 with Haematology Medical Oncology Haemostaseology Infectiology and Rheumatology Oncologic Center Paracelsus Medical University Salzburg Austria

Department of Internal Medicine 3 with Haematology Salzburg Cancer Research Institute Laboratory for Immunological and Molecular Cancer Research Salzburg Austria

Department of Internal Medicine Rode Kruis Ziekenhuis Beverwijk Netherlands

Department of Oncology and Haematology University Hospital and University of Zurich Zurich Switzerland

Department of Ophthalmology and Clinical Genetics Erasmus MC Rotterdam Netherlands

Department of Ophthalmology LUMC Leiden Netherlands

Human Oncology and Pathogenesis Program and Leukemia Service Department of Medicine Memorial Sloan Kettering Cancer Center New York NY United States

Laboratory of Hematology Department Laboratory Medicine Radboud University Medical Center Nijmegen Netherlands

Lymphoma and Myeloma Center Amsterdam Amsterdam Netherlands

Translational Functional Cancer Genomics National Center for Tumor Diseases Heidelberg Germany

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