The protein kinase B-Raf proto-oncogene, serine/threonine kinase (BRAF) is an oncogenic driver and therapeutic target in melanoma. Inhibitors of BRAF (BRAFi) have shown high response rates and extended survival in patients with melanoma who bear tumors that express mutations encoding BRAF proteins mutant at Val600, but a vast majority of these patients develop drug resistance1,2. Here we show that loss of stromal antigen 2 (STAG2) or STAG3, which encode subunits of the cohesin complex, in melanoma cells results in resistance to BRAFi. We identified loss-of-function mutations in STAG2, as well as decreased expression of STAG2 or STAG3 proteins in several tumor samples from patients with acquired resistance to BRAFi and in BRAFi-resistant melanoma cell lines. Knockdown of STAG2 or STAG3 expression decreased sensitivity of BRAFVal600Glu-mutant melanoma cells and xenograft tumors to BRAFi. Loss of STAG2 inhibited CCCTC-binding-factor-mediated expression of dual specificity phosphatase 6 (DUSP6), leading to reactivation of mitogen-activated protein kinase (MAPK) signaling (via the MAPKs ERK1 and ERK2; hereafter referred to as ERK). Our studies unveil a previously unknown genetic mechanism of BRAFi resistance and provide new insights into the tumor suppressor function of STAG2 and STAG3.
Subscribe to Journal
Get full journal access for 1 year
only $18.75 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
European Nucleotide Archive
Ribas, A. & Flaherty, K.T. BRAF-targeted therapy changes the treatment paradigm in melanoma. Nat. Rev. Clin. Oncol. 8, 426–433 (2011).
Holderfield, M., Deuker, M.M., McCormick, F. & McMahon, M. Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond. Nat. Rev. Cancer 14, 455–467 (2014).
Moriceau, G. et al. Tunable-combinatorial mechanisms of acquired resistance limit the efficacy of BRAF–MEK co-targeting but result in melanoma drug addiction. Cancer Cell 27, 240–256 (2015).
Van Allen, E.M. et al. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 4, 94–109 (2014).
Shi, H. et al. Acquired resistance and clonal evolution in melanoma during BRAF inhibitor therapy. Cancer Discov. 4, 80–93 (2014).
Lito, P., Rosen, N. & Solit, D.B. Tumor adaptation and resistance to RAF inhibitors. Nat. Med. 19, 1401–1409 (2013).
Kwong, L.N. et al. Co-clinical assessment identifies patterns of BRAF inhibitor resistance in melanoma. J. Clin. Invest. 125, 1459–1470 (2015).
Wagle, N. et al. MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF–MEK inhibition. Cancer Discov. 4, 61–68 (2014).
Long, G.V. et al. Increased MAPK reactivation in early resistance to dabrafenib–trametinib combination therapy of BRAF-mutant metastatic melanoma. Nat. Commun. 5, 5694 (2014).
Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333–339 (2013).
Solomon, D.A., Kim, J.-S. & Waldman, T. Cohesin gene mutations in tumorigenesis: from discovery to clinical significance. BMB Rep. 47, 299–310 (2014).
Losada, A. Cohesin in cancer: chromosome segregation and beyond. Nat. Rev. Cancer 14, 389–393 (2014).
Solomon, D.A. et al. Mutational inactivation of STAG2 causes aneuploidy in human cancer. Science 333, 1039–1043 (2011).
Balbás-Martínez, C. et al. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat. Genet. 45, 1464–1469 (2013).
Guo, G. et al. Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat. Genet. 45, 1459–1463 (2013).
Weinstein, J.N. et al. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315–322 (2014).
Solomon, D.A. et al. Frequent truncating mutations of STAG2 in bladder cancer. Nat. Genet. 45, 1428–1430 (2013).
Crompton, B.D. et al. The genomic landscape of pediatric Ewing sarcoma. Cancer Discov. 4, 1326–1341 (2014).
Tirode, F. et al. Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations. Cancer Discov. 4, 1342–1353 (2014).
Thol, F. et al. Mutations in the cohesin complex in acute myeloid leukemia: clinical and prognostic implications. Blood 123, 914–920 (2014).
Thota, S. et al. Genetic alterations of the cohesin complex genes in myeloid malignancies. Blood 124, 1790–1798 (2014).
Yoshida, K. et al. The landscape of somatic mutations in Down-syndrome-related myeloid disorders. Nat. Genet. 45, 1293–1299 (2013).
Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059–2074 (2013).
Hodis, E. et al. A landscape of driver mutations in melanoma. Cell 150, 251–263 (2012).
Yuan, P. et al. Phenformin enhances the therapeutic benefit of BRAFV600E inhibition in melanoma. Proc. Natl. Acad. Sci. USA 110, 18226–18231 (2013).
Villanueva, J. et al. Acquired resistance to BRAF inhibitors mediated by a RAF kinase switch in melanoma can be overcome by co-targeting MEK and IGF-1R–PI3K. Cancer Cell 18, 683–695 (2010).
Ong, C.-T. & Corces, V.G. CTCF: an architectural protein bridging genome topology and function. Nat. Rev. Genet. 15, 234–246 (2014).
Xiao, T., Wallace, J. & Felsenfeld, G. Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity. Mol. Cell. Biol. 31, 2174–2183 (2011).
Ziebarth, J.D., Bhattacharya, A. & Cui, Y. CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. Nucleic Acids Res. 41, D188–D194 (2013).
Katainen, R. et al. CTCF–cohesin-binding sites are frequently mutated in cancer. Nat. Genet. 47, 818–821 (2015).
Li, H. & Durbin, R. Fast and accurate short-read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The sequence alignment–map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Koboldt, D.C. et al. VarScan 2: somatic mutation and copy-number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010).
Lin, W.M. et al. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res. 68, 664–673 (2008).
Shen, C.-H. et al. Phosphorylation of BRAF by AMPK impairs BRAF–KSR1 association and cell proliferation. Mol. Cell 52, 161–172 (2013).
Kamata, T. et al. A critical function for BRAF at multiple stages of myelopoiesis. Blood 106, 833–840 (2005).
Zheng, B. et al. Oncogenic BRAF negatively regulates the tumor suppressor LKB1 to promote melanoma cell proliferation. Mol. Cell 33, 237–247 (2009).
We thank K. Swanson, Y. Zhang and G. Zhao for critical comments on the manuscript. We also thank L. Chin (MD Anderson Cancer Center), M. Herlyn (Wistar Institute), C. Pritchard (University of Leicester) and J. Zippin (Weill Cornell Medical College) for providing cell lines. This work is supported by the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (D.E.F.), the V Foundation (B.Z.), the Harry J. Lloyd Charitable Trust (B.Z.), the Melanoma Research Alliance (B.Z.) and the US National Institutes of Health (NIH) grants P01 CA163222 (D.E.F.), R01 AR043369 (D.E.F.), R21 CA175907 (D.E.F.) and R01 CA166717 (B.Z.).
The authors declare no competing financial interests.
About this article
Cite this article
Shen, C., Kim, S., Trousil, S. et al. Loss of cohesin complex components STAG2 or STAG3 confers resistance to BRAF inhibition in melanoma. Nat Med 22, 1056–1061 (2016). https://doi.org/10.1038/nm.4155
Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity
Trends in Cancer (2019)