Spitzoid melanoma is a specific morphologic variant of melanoma that most commonly affects children and adolescents, and ranges on the spectrum of malignancy from low grade to overtly malignant. These tumors are generally driven by fusions of ALK, RET, NTRK1/3, MET, ROS1 and BRAF1,2. However, in approximately 50% of cases no genetic driver has been established2. Clinical whole-genome and transcriptome sequencing (RNA-Seq) of a spitzoid tumor from an adolescent revealed a novel gene fusion of MAP3K8, encoding a serine-threonine kinase that activates MEK3,4. The patient, who had exhausted all other therapeutic options, was treated with a MEK inhibitor and underwent a transient clinical response. We subsequently analyzed spitzoid tumors from 49 patients by RNA-Seq and found in-frame fusions or C-terminal truncations of MAP3K8 in 33% of cases. The fusion transcripts and truncated genes all contained MAP3K8 exons 1–8 but lacked the autoinhibitory final exon. Data mining of RNA-Seq from the Cancer Genome Atlas (TCGA) uncovered analogous MAP3K8 rearrangements in 1.5% of adult melanomas. Thus, MAP3K8 rearrangements—uncovered by comprehensive clinical sequencing of a single case—are the most common genetic event in spitzoid melanoma, are present in adult melanomas and could be amenable to MEK inhibition.
Access optionsAccess options
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.
The raw whole-genome sequencing, exome and RNA-Seq dataset generated for the index patient are available in St. Jude Cloud, https://platform.stjude.cloud/requests/publications?publication_accession=SJC-PB-1018, and have also been deposited in European Genome-Phenome Archive under accession number EGAS00001003430. RNA-Seq data from archival samples are available from the authors upon reasonable request and with permission from the St. Jude Children’s Research Hospital IRB.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Lu, C. et al. The genomic landscape of childhood and adolescent melanoma. J. Invest. Dermatol. 135, 816–823 (2015).
Wiesner, T. et al. Kinase fusions are frequent in Spitz tumours and spitzoid melanomas. Nat. Commun. 5, 3116 (2014).
Salmeron, A. et al. Activation of MEK-1 and SEK-1 by Tpl-2 proto-oncoprotein, a novel MAP kinase kinase kinase. EMBO J. 15, 817–826 (1996).
Hagemann, D., Troppmair, J. & Rapp, U. R. Cot protooncoprotein activates the dual specificity kinases MEK-1 and SEK-1 and induces differentiation of PC12 cells. Oncogene 18, 1391–1400 (1999).
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).
Johannessen, C. M. et al. COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature 468, 968–972 (2010).
Little, A. S. et al. Amplification of the driving oncogene, KRAS or BRAF, underpins acquired resistance to MEK1/2 inhibitors in colorectal cancer cells. Sci. Signal. 4, ra17 (2011).
Gándara, M. L., López, P., Hernando, R., Castaño, J. G. & Alemany, S. The COOH-terminal domain of wild-type Cot regulates its stability and kinase specific activity. Mol. Cell. Biol. 23, 7377–7390 (2003).
Lazova, R. et al. Spitz nevi and spitzoid melanomas - exome sequencing and comparison to conventional melanocytic nevi and melanomas. Mod. Pathol. 30, 640–649 (2017).
Shain, A. H. et al. The genetic evolution of melanoma from precursor lesions. N. Engl. J. Med. 373, 1926–1936 (2015).
Pollock, P. M. et al. High frequency of BRAF mutations in nevi. Nat. Genet. 33, 19–20 (2003).
Cancer Genome Atlas Network. Genomic classification of cutaneous melanoma. Cell 161, 1681–1696 (2015).
Hu, X. et al. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res. 46, D1144–D1149 (2018).
Hayward, N. K. et al. Whole-genome landscapes of major melanoma subtypes. Nature 545, 175–180 (2017).
Forbes, S. A. et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 38, D652–D657 (2010).
Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012).
Gutman, D. A. et al. The digital slide archive: a software platform for management, integration, and analysis of histology for cancer research. Cancer Res. 77, e75–e78 (2017).
Liang, W. S. et al. Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. Genome Res. 27, 524–532 (2017).
Gruosso, T. et al. MAP3K8/TPL-2/COT is a potential predictive marker for MEK inhibitor treatment in high-grade serous ovarian carcinomas. Nat. Commun. 6, 8583 (2015).
Sourvinos, G., Tsatsanis, C. & Spandidos, D. A. Overexpression of the Tpl-2/Cot oncogene in human breast cancer. Oncogene 18, 4968–4973 (1999).
Clark, A. M., Reynolds, S. H., Anderson, M. & Wiest, J. S. Mutational activation of the MAP3K8 protooncogene in lung cancer. Genes Chromosomes Cancer 41, 99–108 (2004).
Lee, J.-H. et al. TPL2 is an oncogenic driver in keratocanthoma and squamous cell carcinoma. Cancer Res. 76, 6712–6722 (2016).
Ceci, J. D. et al. Tpl-2 is an oncogenic kinase that is activated by carboxy-terminal truncation. Genes Dev. 11, 688–700 (1997).
Patriotis, C., Makris, A., Bear, S. E. & Tsichlis, P. N. Tumor progression locus 2 (Tpl-2) encodes a protein kinase involved in the progression of rodent T-cell lymphomas and in T-cell activation. Proc. Natl Acad. Sci. USA 90, 2251–2255 (1993).
Erny, K. M., Peli, J., Lambert, J. F., Muller, V. & Diggelmann, H. Involvement of the Tpl-2/cot oncogene in MMTV tumorigenesis. Oncogene 13, 2015–2020 (1996).
Poulikakos, P. I. & Solit, D. B. Resistance to MEK inhibitors: should we co-target upstream? Sci. Signal. 4, pe16 (2011).
Samatar, A. A. & Poulikakos, P. I. Targeting RAS-ERK signalling in cancer: promises and challenges. Nat. Rev. Drug Discov. 13, 928–942 (2014).
Kim, K. B. et al. Phase II study of the MEK1/MEK2 inhibitor trametinib in patients with metastatic BRAF-mutant cutaneous melanoma previously treated with or without a BRAF inhibitor. J. Clin. Oncol. 31, 482–489 (2013).
Flaherty, K. T. et al. Improved survival with MEK inhibition in BRAF-mutated melanoma. N. Engl. J. Med. 367, 107–114 (2012).
Ascierto, P. A. et al. MEK162 for patients with advanced melanoma harbouring NRAS or Val600 BRAF mutations: a non-randomised, open-label phase 2 study. Lancet Oncol. 14, 249–256 (2013).
Ranzani, M. et al. BRAF/NRAS wild-type melanoma, NF1 status and sensitivity to trametinib. Pigment Cell Melanoma Res. 28, 117–119 (2015).
Zhou, X. et al. Exploring genomic alteration in pediatric cancer using ProteinPaint. Nat. Genet. 48, 4–6 (2016).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotech. 29, 24–26 (2011).
Lee, S. et al. TERT promoter mutations are predictive of aggressive clinical behavior in patients with spitzoid melanocytic neoplasms. Sci. Rep. 5, 11200 (2015).
Rusch, M. et al. Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. Nat. Commun. 9, 3962 (2018).
Wu, G. et al. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat. Genet. 46, 444–450 (2014).
Roberts, K. G. et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N. Engl. J. Med. 371, 1005–1015 (2014).
Anders, S., Pyl, P. T. & Huber, W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Blokzijl, F., Janssen, R., van Boxtel, R. & Cuppen, E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med. 10, 33 (2018).
McPherson, A. et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol. 7, e1001138 (2011).
Seynnaeve, B. et al. Genetic and epigenetic alterations of TERT are associated with inferior outcome in adolescent and young adult patients with melanoma. Sci. Rep. 7, 45704 (2017).
Borowicz, S. et al. The soft agar colony formation assay. J. Vis. Exp., e51998. https://doi.org/10.3791/51998 (2014).
Chen, X. et al. CONSERTING: integrating copy-number analysis with structural-variation detection. Nat. Methods 12, 527–530 (2015).
Dinkel, H. et al. ELM 2016–data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Res. 44, D294–D300 (2016).
Sharrocks, A. D., Yang, S. H. & Galanis, A. Docking domains and substrate-specificity determination for MAP kinases. Trends Biochem. Sci. 25, 448–453 (2000).
We thank S. Brady for critical review of the manuscript. This work was funded by the American Lebanese Syrian Associated Charities of St. Jude Children’s Research Hospital.
Timeline of the clinical course imaging, and treatment regimens, are shown as colored rectangles along the horizontal timeline. For treatments, HLP is hyperthermic limb perfusion, TVEC is talimogene laherparaepvec and LTT462 is an ERK inhibitor. Subsequent Figures within this manuscript showing specimens or images from this timeline are indicated.
a, Copy number segments from CONSERTING43; red shows a gain in copy number, blue a loss. b, Scatterplot of normalized sequencing coverage from whole-genome sequencing confirms a 75 kb region of neutral copy number encompassing the TERT locus flanked by deletions. c, Structural variant junctions are shown in blue for junctions within the same chromosome and red for junctions linking different chromosomes; the genome position of the partner locus is shown inline. d, RefSeq gene model showing the position of TERT. e, RNA-Seq coverage shows that TERT is expressed. We inspected RNA-Seq coverage at this locus for our 49 additional patient samples and found TERT expression to be absent. f, Splice junctions detected in RNA-Seq and quantified according to the y axis. Canonical splices are shown in blue and non-canonical splices are in red. g, An image of break-apart FISH for TERT performed on the primary tumor from the index case showing split red and green signals, consistent with TERT rearrangement. We performed FISH on 5 additional tumors and found this locus not to be rearranged. All FISH images are at ×100 magnification.
a, Chromosome 10 and b, chromosome 14 copy number profile from CONSERTING. Gray scatterplot represents normalized whole-genome sequencing read depth arranged by genome position on the x axis. Changes in copy number are evident as segmental shifts on the y axis. Although a deletion is evident at the start of 14q, no copy number changes are present at the MAP3K8 (chr10:30,720,950-30,752,762) or GNG2 (chr14:52,325,022-52,438,518) loci in the initial tumor sample (black arrows represent the locations of MAP3K8 and GNG2) on chromosomes 10 and 14, respectively. In the relapsed sample, the copy number of both loci is increased. c, RNA-Seq coverage with the initial tumor sample’s MAP3K8 and GNG2 loci in the upper panels and the relapsed tumor below. MAP3K8 and GNG2 expression are increased approximately threefold in the relapsed sample.
ProteinPaint32 representation of MAP3K8 mutations found over 226 studies housed within cBioPortal16. Specific amino acid changes are shown as lollipops with a size proportional to their frequency in the cohort. The most frequently mutated tumor types were uterine endometrioid carcinoma (n = 25), colorectal adenocarcinoma (n = 21) and cutaneous melanoma (n = 20). A hotspot at R442 is indicated by the black arrow. According to ELM44 (http://elm.eu.org/), Arg442 is part of the sequence KRQRSLYIDL described previously as a MAPK docking site in MAP kinase substrates45. Interestingly, because the MAP3K8 truncation in SJMEL054992_D1 is at codon R440, only R442 is excluded from the truncated MAP3K8.
RNA-Seq coverage overlapping the MAP3K8 locus is shown in the blue histograms. Each histogram is scaled according to the corresponding y axis. Black arrows indicate the positions of fusions or truncations as outlined in Supplementary Table 6. The MAP3K8 locus of all seven rearranged samples is shown.
Unprocessed Western blot image
About this article
Reactions Weekly (2019)