Abstract
We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS. Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas. This activating mutation, the third most frequent in our cohort of sun-exposed melanoma after those of BRAF and NRAS, changes Pro29 to serine (RAC1P29S) in the highly conserved switch I domain. Crystal structures, and biochemical and functional studies of RAC1P29S showed that the alteration releases the conformational restraint conferred by the conserved proline, causes an increased binding of the protein to downstream effectors, and promotes melanocyte proliferation and migration. These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit.
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Acknowledgements
This work was supported by the Yale SPORE in Skin Cancer funded by the National Cancer Institute grant number 1 P50 CA121974 (principal investigator, R.H.), the Melanoma Research Alliance (a Team award to R.H., M.B., M.K. and D.F.S.), The National Library of Medicine Training grant 5T15LM007056 (P.E.), the Department of Dermatology (R.H.), Yale Comprehensive Cancer Center (M.K.), the National Health and Medical Research Council of Australia (N.K.H. and K.D.-R.), Gilead Sciences, Inc. (J.S., M.K., R.H. and T.J.B.) and a generous gift from Roz and Jerry Meyer (R.H., M.S. and H.M.K.). We thank C. Truini, W. Meng, B. Speed, E. Straka, A. Raefski, M. Scallion and S. Levin for technical support, P. Parsons, C. Schmidt and colleagues at the Queensland Institute of Medical Research for generously providing many of the melanoma cell lines, the Yale Center for Genome Analysis and the Northeastern Collaborative Access Team (NE-CAT) facility at the Advanced Photon Source at Argonne National Laboratory.
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M.K., R.H., R.P.L., J.S. and T.J.B. designed and supervised the study. Y.K., P.E., M.C., J.P.M., S. Ma, G.G. and A.C. performed the bioinformatic analyses. A.B., E.C., E.C.H., M.J.D., K.D.-R., K.K.K., N.K.H. and S. Mane collected and analyzed the melanoma samples and performed the sequencing and functional experiments. B.H.H. and T.J.B. performed the crystallographic studies. S.A., D.N., M.B., M.S., H.M.K., M.A.M. and R.S.L. provided the clinical specimens and the clinical annotation. D.E.B. and D.F.S. analyzed sun-related mutations. All authors contributed to the final version of the paper.
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Krauthammer, M., Kong, Y., Ha, B. et al. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet 44, 1006–1014 (2012). https://doi.org/10.1038/ng.2359
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