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Myelodysplastic syndrome

SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells

Leukemia volume 32, pages 2659–2671 (2018)Cite this article

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Abstract

Recurrent mutations in the splicing factor SRSF2 are associated with poor clinical outcomes in myelodysplastic syndromes (MDS). Their high frequency suggests these mutations drive oncogenesis, yet the molecular explanation for this process is unclear. SRSF2 mutations could directly affect pre-mRNA splicing of a vital gene product; alternatively, a whole network of gene products could be affected. Here we determine how SRSF2 mutations globally affect RNA binding and splicing in vivo using HITS-CLIP. Remarkably, the majority of differential binding events do not translate into alternative splicing of exons with SRSF2P95H binding sites. Alternative splice alterations appear to be dominated by indirect effects. Importantly, SRSF2P95H targets are enriched in RNA processing and splicing genes, including several members of the hnRNP and SR families of proteins, suggesting a “splicing-cascade” phenotype wherein mutation of a single splicing factor leads to widespread modifications in multiple RNA processing and splicing proteins. We show that splice alteration of HNRNPA2B1, a splicing factor differentially bound and spliced by SRSF2P95H, impairs hematopoietic differentiation in vivo. Our data suggests a model whereby the recurrent mutations in splicing factors set off a cascade of gene regulatory events that together affect hematopoiesis and drive cancer.

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Acknowledgements

We thank all our patients. We thank all clinicians and clinical staff for their help with patient recruitment. Work was funded in part by the Edward P. Evans Foundation, by the NIH/NIDDK R01DK102792, departmental funds from the Yale Comprehensive Cancer Center (YCCC), and a YCCC pilot grant (to SH). This material is based in part upon work supported by the State of Connecticut under the Regenerative Medicine Research Fund (GS, SH). Its contents are solelythe responsibility of the authors and do not necessarily represent the official views of the State ofConnecticut or Connecticut Innovations, Incorporated. Research reported in this publication was in part supported by the NIDDK under Grant U54DK106857. YL was partially supported by the National Natural Science Foundation of China (Grant No. 81660682). We thank Diane Krause, Manoj Pillai, and Karla Neugebauer (Yale University) for helpful suggestions. We thank the Yale Stem Cell Center Genomics Core and the Yale Center for Genome Analysis (YCGA) for high-throughput sequencing and the Yale University High Performance Computing Center for use of clusters to run bioinformatics analysis. We thank Dr. Tomoyuki Yamaguchi at the Japan Science and Technology Agency for the kind gift of the CS-TRE-Ubc-tTA-I2G plasmid [56]. We also thank Didier Trono for the psPAX2 plasmid (Addgene plasmid # 12260) and Tannishtha Reya for the pCMV-VSVG plasmid (Addgene plasmid # 14888).

Author contributions

:TT analyzed next-generation sequencing data and wrote the manuscript. YL, KR, PJ, and GS performed experiments, analyzed the data, and wrote the manuscript. AT, YS, JM, KB, RV, AA, and AD performed experiments. AQ provided essential input for the manuscript. SH initiated the study, performed experiments, analyzed the data, provided supervision and wrote the manuscript with input from the other authors.

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  1. Yang Liang

    Present address: Department of Ecology and Evolutionary Biology, Yale University School of Medicine, New Haven, CT, 06511, USA

Authors and Affiliations

  1. Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06511, USA

    Yang Liang, Toma Tebaldi, Kai Rejeski, Poorval Joshi, Ashley Taylor, Yuanbin Song, Radovan Vasic, Jamie Maziarz, Kunthavai Balasubramanian, Anastasia Ardasheva, Alicia Ding & Stephanie Halene

  2. Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China

    Yang Liang

  3. Laboratory of Translational Genomics, Centre for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy

    Toma Tebaldi & Alessandro Quattrone

  4. Division of Hematology, Oncology and Stem Cell Transplantation, Department of Internal Medicine, University of Freiburg Medical Center, Hugstetter Str. 55, 79106, Freiburg, Germany

    Kai Rejeski

  5. Centre for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy

    Giovanni Stefani

  6. Department of Ecology and Evolutionary Biology, Yale University School of Medicine, New Haven, CT, 06511, USA

    Jamie Maziarz

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These authors contributed equally: Yang Liang, Toma Tebaldi, Kai Rejeski, Poorval Joshi, Giovanni Stefani.

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Liang, Y., Tebaldi, T., Rejeski, K. et al. SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells. Leukemia 32, 2659–2671 (2018). https://doi.org/10.1038/s41375-018-0152-7

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