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

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.

[1]  S. Chandarlapaty,et al.  Mutant SF3B1 promotes AKT and NF-kB driven mammary tumorigenesis. , 2020, The Journal of clinical investigation.

[2]  L. Pasqualucci,et al.  Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization. , 2020, Cancer discovery.

[3]  J. Alfaro,et al.  Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics , 2020, Cancers.

[4]  A. Krainer,et al.  Recurrent SRSF2 mutations in MDS affect both splicing and NMD , 2020, Genes & development.

[5]  Alexander V Penson,et al.  Spliceosomal disruption of the non-canonical BAF complex in cancer , 2019, Nature.

[6]  Jörg Menche,et al.  Mutational Landscape of the Transcriptome Offers Putative Targets for Immunotherapy of Myeloproliferative Neoplasms. , 2019, Blood.

[7]  Angela N. Brooks,et al.  A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. , 2019, Cancer cell.

[8]  A. Leeksma.  Making sense of genomic complexity and nonsense-RNA in hematologic malignancies , 2019 .

[9]  A. Gavin,et al.  Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations. , 2018, Blood.

[10]  B. Ebert,et al.  Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations. , 2018, Cancer cell.

[11]  K. de Heer,et al.  Clonal diversity predicts adverse outcome in chronic lymphocytic leukemia , 2018, Leukemia.

[12]  M. Warmuth,et al.  H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers , 2018, Nature Medicine.

[13]  Jon C. Aster,et al.  Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. , 2016, Cancer cell.

[14]  Omar Abdel-Wahab,et al.  Therapeutic targeting of splicing in cancer , 2016, Nature Medicine.

[15]  R. Kusec,et al.  Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes , 2016, Leukemia.

[16]  M. Warmuth,et al.  Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3' Splice Site Selection through Use of a Different Branch Point. , 2015, Cell reports.

[17]  Dennis Carson,et al.  Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers , 2015, PLoS Comput. Biol..

[18]  T. Stankovic,et al.  The impact of SF3B1 mutations in CLL on the DNA-damage response , 2014, Leukemia.

[19]  M. Salto‐Tellez,et al.  Identification of a BRCA1-mRNA Splicing Complex Required for Efficient DNA Repair and Maintenance of Genomic Stability , 2014, Molecular cell.

[20]  Alfonso Valencia,et al.  Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia , 2014, Genome research.

[21]  M. Cazzola,et al.  Gene mutations and treatment outcome in chronic lymphocytic leukemia: results from the CLL8 trial. , 2012, Blood.

[22]  David Gentien,et al.  SF3B1 mutations are associated with alternative splicing in uveal melanoma. , 2013, Cancer discovery.

[23]  A. Hinnebusch,et al.  Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 , 2013, Nature Genetics.

[24]  D. Catovsky,et al.  The clinical significance of NOTCH1 and SF3B1 mutations in the UK LRF CLL4 trial. , 2013, Blood.

[25]  A. Bowcock,et al.  Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma , 2013, Nature Genetics.

[26]  A. Gopalsamy,et al.  Identification of pyrimidine derivatives as hSMG-1 inhibitors. , 2012, Bioorganic & medicinal chemistry letters.

[27]  Alexandru Almasan,et al.  Histone H2AX phosphorylation: a marker for DNA damage. , 2012, Methods in molecular biology.

[28]  E. Giné,et al.  Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia , 2011, Nature Genetics.

[29]  L. Pasqualucci,et al.  Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness. , 2011, Blood.

[30]  Peter J Campbell,et al.  Clinical significance of SF3B1 mutations in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms , 2011, Blood.

[31]  M. Stratton,et al.  Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. , 2011, The New England journal of medicine.

[32]  A. Moorman,et al.  Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data , 2009, Nucleic acids research.