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Chronic Lymphocytic Leukemia

The impact of SF3B1 mutations in CLL on the DNA-damage response

Abstract

Mutations or deletions in TP53 or ATM are well-known determinants of poor prognosis in chronic lymphocytic leukemia (CLL), but only account for approximately 40% of chemo-resistant patients. Genome-wide sequencing has uncovered novel mutations in the splicing factor sf3b1, that were in part associated with ATM aberrations, suggesting functional synergy. We first performed detailed genetic analyses in a CLL cohort (n=110) containing ATM, SF3B1 and TP53 gene defects. Next, we applied a newly developed multiplex assay for p53/ATM target gene induction and measured apoptotic responses to DNA damage. Interestingly, SF3B1 mutated samples without concurrent ATM and TP53 aberrations (sole SF3B1) displayed partially defective ATM/p53 transcriptional and apoptotic responses to various DNA-damaging regimens. In contrast, NOTCH1 or K/N-RAS mutated CLL displayed normal responses in p53/ATM target gene induction and apoptosis. In sole SF3B1 mutated cases, ATM kinase function remained intact, and γH2AX formation, a marker for DNA damage, was increased at baseline and upon irradiation. Our data demonstrate that single mutations in sf3b1 are associated with increased DNA damage and/or an aberrant response to DNA damage. Together, our observations may offer an explanation for the poor prognosis associated with SF3B1 mutations.

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Acknowledgements

We would like to thank all patients for blood donations and participating doctors for recruiting patients. We would like to thank J Guikema and JP Medema for their helpful discussions and R Thijssen for performing the experiments on γH2AX using immunofluorescence. APK is sponsored by clinical fellowship UVA 2001-5097 from the Dutch Cancer Society. Part of this work sponsored by grants NT13519-4 and CZ.1.05/1.1.00/02.0068 from the Ministry of Health of the Czech Republic.

Author Contributions

GDR designed and performed experiments, analyzed data and wrote the paper; IAMD, JL, CO and HM performed experiments; VN performed experiments and analyzed data; AS, JH and AJ performed experiments and analyzed data; PDM performed data analysis; JM and MT analyzed data; ML coordinated the development of the RT-MLPA probe mix; CG managed patient cohorts; TZ supervised 454 sequencing and analyzed data; SP and TS reviewed the manuscript and contributed to the design of experiments; MHO and APK managed patient cohorts and contributed to the design of experiments; EE designed the study, performed data analysis and wrote the paper. All authors reviewed and corrected the manuscript.

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Correspondence to E Eldering.

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te Raa, G., Derks, I., Navrkalova, V. et al. The impact of SF3B1 mutations in CLL on the DNA-damage response. Leukemia 29, 1133–1142 (2015). https://doi.org/10.1038/leu.2014.318

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