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Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

Nature Medicine volume 16, pages 793–798 (2010)Cite this article

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Abstract

Although recurrent gene fusions involving erythroblastosis virus E26 transformation-specific (ETS) family transcription factors are common in prostate cancer, their products are considered 'undruggable' by conventional approaches. Recently, rare targetable gene fusions involving the anaplastic lymphoma receptor tyrosine kinase (ALK) gene, have been identified in 1–5% of lung cancers1, suggesting that similar rare gene fusions may occur in other common epithelial cancers, including prostate cancer. Here we used paired-end transcriptome sequencing to screen ETS rearrangement–negative prostate cancers for targetable gene fusions and identified the SLC45A3-BRAF (solute carrier family 45, member 3–v-raf murine sarcoma viral oncogene homolog B1) and ESRP1-RAF1 (epithelial splicing regulatory protein-1–v-raf-1 murine leukemia viral oncogene homolog-1) gene fusions. Expression of SLC45A3-BRAF or ESRP1-RAF1 in prostate cells induced a neoplastic phenotype that was sensitive to RAF and mitogen-activated protein kinase kinase (MAP2K1) inhibitors. Screening a large cohort of patients, we found that, although rare, recurrent rearrangements in the RAF pathway tend to occur in advanced prostate cancers, gastric cancers and melanoma. Taken together, our results emphasize the key role of RAF family gene rearrangements in cancer, suggest that RAF and MEK inhibitors may be useful in a subset of gene fusion–harboring solid tumors and demonstrate that sequencing of tumor transcriptomes and genomes may lead to the identification of rare targetable fusions across cancer types.

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Figure 1: Discovery of the SLC45A3-BRAF and ESRP1-RAF1 gene fusions in prostate cancer by paired-end transcriptome sequencing.
Figure 2: Experimental validation of the SLC45A3-BRAF, ESRP1-RAF1 and RAF1-ESRP1 and AGTRAP-BRAF gene fusions in the prostate tumor samples and prostate cancer cell lines (DU145, VCaP, LnCaP and 22RV1) and RWPE as negative controls.
Figure 3: Oncogenic properties of SLC45A3-BRAF and ESRP1-RAF1 gene fusions.
Figure 4: RAF and MEK inhibitors block SLC45A3-BRAF or ESRP1-RAF1 gene fusion–mediated oncogenic phenotypes.

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Acknowledgements

We thank R.B. Jenkins (Mayo Clinic) for providing prostate cancer tissues with BRAF overexpression for FISH evaluation, R. Morey for assistance in paired-end sequencing and Illumina for technical support. We thank T. Barrette, R. Lonigro, M. Quist, C. Quist and S. Begley for hardware support, sample database maintenance, data curation and maintenance of paired-end sequence data and useful discussions; D. Sanders and M.Vinco for their assistance in procuring gastric cancer samples; and D. Kim, R. Mehra and R. Varambally for providing prostate and melanoma tissue microarray and clinical information from the University of Michigan cohort. We thank D.F. Fries, X. Jiang, L. Wang, R. Jagirdar, N. Kitabayashi and X. Jing for technical assistance, K. Giles for critical reading of the manuscript and A.K. Tewari, Biobank, Weill Cornell Medical College, for providing prostate cancer samples for mutation analysis. This work was supported in part by the US National Institutes of Health (R01CA132874), Early Detection Research Network grant UO1 CA111275, Prostate SPORE grant P50CA69568, the National Center for Integrative Bioinformatics (U54 DA21519-01A1), the National Center for Functional Genomics supported by the Department of Defense (A.M.C.) and R01 CA125612-01 (M.A.R. and F.D.). S.A.T. is supported by a Young Investigator Award from the Prostate Cancer Foundation. A.M.C. is supported by the Doris Duke Charitable Foundation Clinical Scientist Award, a Burroughs Welcome Foundation Award in Clinical Translational Research and the Prostate Cancer Foundation. A.M.C. is an American Cancer Society Research Professor. N.P. is supported by the development award from the Melanoma Research Alliance. C.A.M. currently derives support from the American Association of Cancer Research Amgen Fellowship in Clinical/Translational Research, the Canary Foundation and American Cancer Society Early Detection Postdoctoral Fellowship, and a Prostate Cancer Foundation Young Investigator Award. B.A. is supported by a Genentech Foundation Postdoctoral Fellowship and Young Investigator Award from Expedition Inspiration. T.A.B. is supported by funding from the Prostate Cancer Foundation, a Young Investigator Award and the Canadian Institute of Health Research.

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Author notes

  1. Nallasivam Palanisamy, Bushra Ateeq and Shanker Kalyana-Sundaram: These authors contributed equally to this work.

Authors and Affiliations

  1. Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA

    Nallasivam Palanisamy, Bushra Ateeq, Shanker Kalyana-Sundaram, Kalpana Ramnarayanan, Sunita Shankar, Bo Han, Qi Cao, Xuhong Cao, Khalid Suleman, Chandan Kumar-Sinha, Saravana M Dhanasekaran, Javed Siddiqui, Scott A Tomlins, Sooryanarayana Varambally, Christopher A Maher & Arul M Chinnaiyan

  2. Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA

    Nallasivam Palanisamy, Bushra Ateeq, Shanker Kalyana-Sundaram, Kalpana Ramnarayanan, Sunita Shankar, Bo Han, Qi Cao, Khalid Suleman, Chandan Kumar-Sinha, Saravana M Dhanasekaran, Javed Siddiqui, Douglas R Fullen, Joel K Greenson, Thomas J Giordano, Scott A Tomlins, Sooryanarayana Varambally, Christopher A Maher & Arul M Chinnaiyan

  3. Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA

    Nallasivam Palanisamy, Shanker Kalyana-Sundaram, Sooryanarayana Varambally & Arul M Chinnaiyan

  4. Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA

    Dorothee Pflueger, Ying-bei Chen, Raquel Esgueva, Christopher J LaFargue, Francesca Demichelis & Mark A Rubin

  5. Department of Urology, University Hospital Ulm, Ulm, Germany

    Dorothee Pflueger & Rainer Kuefer

  6. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA

    Xuhong Cao & Arul M Chinnaiyan

  7. Department of Public Health, Weill Cornell Medical College, New York, New York, USA

    Samprit Banerjee

  8. Department of Urology, University of Michigan, Ann Arbor, Michigan, USA

    Javed Siddiqui & Arul M Chinnaiyan

  9. Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA

    Francesca Demichelis

  10. Department of Pathology, University Hospital Ulm, Ulm, Germany

    Peter Moeller

  11. Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, Canada

    Tarek A Bismar

  12. Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA

    Douglas R Fullen & Timothy M Johnson

  13. Duke-National University of Singapore Graduate Medical School, Singapore

    Patrick Tan

  14. Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, USA

    Christopher A Maher

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Contributions

N.P., B.A., S.A.T., C.A.M. and A.M.C. designed experiments and wrote the manuscript. N.P. performed paired-end transcriptome library preparation and FISH probe design, preparation and analysis. S.K.-S. and C.A.M. performed bioinformatics analysis for gene fusion nominations. B.A., K.R., S.S., Q.C., S.M.D., S.V. and S.A.T. conducted experiments including design and generation of expression constructs, in vitro assays, western blotting, qRT PCR validation and data analysis and interpretation. B.A. performed in vivo experiments. N.P., B.H., K.S. and D.P. performed FISH assays on cancer tissue microarrays. X.C. performed sequencing. C.K.-S. performed BRAF mutation analysis by pyrosequencing. Y.-b.C., R.E., S.B., C.J.L., J.S., F.D., P.M., T.A.B., R.K. and M.A.R. provided prostate cancer specimens and performed FISH assays. D.R.F. and T.M.J. provided melanoma tissue microarrays. T.J.G. and J.K.G. provided gastric cancer tissue microarrays. P.T. provided gastric cancer tissues and RNAs. A.M.C. directed the study.

Corresponding author

Correspondence to Arul M Chinnaiyan.

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The authors declare no competing financial interests.

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Palanisamy, N., Ateeq, B., Kalyana-Sundaram, S. et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med 16, 793–798 (2010). https://doi.org/10.1038/nm.2166

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