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Detection of mutations in the BRAF gene in patients with KIT and PDGFRA wild-type gastrointestinal stromal tumors

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Abstract

Gastrointestinal stromal tumors (GISTs) are characterized by mutations in exons 9, 11, 13, and 17 of KIT or exons 12, 14, and 18 of PDGFRA gene. However, approximately 10 to 15 % of GISTs lack the mutations in KIT and PDGFRA, and these are referred to as wild-type GISTs which are less sensitive to tyrosine-kinase inhibitors. The aim of this study was to detect BRAF mutations in patients with wild-type GISTs. We applied a sensitive allele-specific PCR, which was optimized using the V600E mutation-harboring cell line RKO, followed by verification of the results by dideoxy sequencing. We selected 149 GIST patients without detectable mutations in KIT and PDGFRA genes from the Slovak national GIST register and analyzed biopsy specimens for the presence of BRAF mutations in exon 15. We identified nine patients with the V600E mutation. The BRAF-driven GISTs were primary gastric (n = 3), small intestinal (n = 3), colon (n = 1), and of uncertain origin (n = 1). We also included a liver metastasis of a patient with a simultaneous KIT exon 11-mutated intra-abdominal metastasis. We conclude that genome analysis of wild-type GISTs for mutations should include the BRAF gene, as its mutation status contributes to understanding of pathogenesis and might be important for decisions on therapy.

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References

  1. Hirota S, Isozaki K, Moriyama Y, Hashimoto K, Nishida T, Ishigur S, Kawano K, Handa M, Kurata A, Takeda M, Tunio GM, Matsuzawa Y, Kanakura Y, Shinomura Y, Kitamura Y (1998) Gain-of function mutations of c-kit in human gastrointestinal stromal tumors. Science 279:577–580. doi:10.1126/science.279.5350.577

    Article  CAS  PubMed  Google Scholar 

  2. Heinrich MC, Corless CL, Duensing A, McGreevey L, Jie Chen C, Joseph N, Singer S, Griffith DJ, Haley A, Town A, Demetri GD, Fletcher CDM, Fletcher JA (2003) PDGFRA activating mutations in gastrointestinal stromal tumors. Science 299:708–710. doi:10.1126/science.1079666

    Article  CAS  PubMed  Google Scholar 

  3. Barnett CM, Corless CL, Heinrich MC (2013) Gastrointestinal stromal tumors: molecular markers and genetic subtypes. Hematol Oncol Clin N Am 27:871–888. doi:10.1016/j.hoc.2013.07.003

    Article  Google Scholar 

  4. Heinrich MC, Owzar K, Corless CL et al (2008) Correlation of kinase genyotype and clinical outcome in the North America intergroup phase III trial of imatinib mesylate for treatment of advanced gastrointestinal stromal tumor: CALGB 150105 Study by Cancer and Leukemia Group B and Southwest Oncology Group. J Clin Oncol 28:5360–5367. doi:10.1200/JCO.2008.17.4284

    Article  Google Scholar 

  5. Gill AJ, Chou A, Vilain R et al (2010) Immunohistochemeistry for SDHB divides gastrointestinal stromal tumors (GISTs) into 2 distinct types. Am J Surg Pathol 3:636–644. doi:10.1097/PAS.0b013e3181d6150d

    Google Scholar 

  6. Pantaleo MA, Astolfi A, Urbini M et al (2014) Analysis of all subunits, SDHA, SDHB, SDHC, SDHD, of the succinate dehydrogenase complex in KIT/PDGFRA wild-type GIST. Eur J Hum Genet 22:32–39. doi:10.1038/ejhg.2013.80

    Article  CAS  PubMed  Google Scholar 

  7. Nannini M, Astolfi A, Urbini M, Indio V, Santini D, Heinrich MC, Corless CL, Ceccarelli C, Saponara M, Mandrioli A, Lolli C, Ercolani G, Brandi G, Biasco G, Pantaleo MA (2014) Integrated genomic study of quadruple-WT GIST (KIT/PDGFRA/SDH/RAS pathway wild-type GIST). BMC Cancer 14:685. doi:10.1186/1471-2407-14-685

    Article  PubMed  PubMed Central  Google Scholar 

  8. Davies H, Bignell GR, Cox C, Stephens P et al (2002) Mutations of the BRAF gene in human cancer. Nature 417:949–954. doi:10.1038/nature00766

    Article  CAS  PubMed  Google Scholar 

  9. Wan PT, Garnett MJ, Roe SM, Lee S, Niculescu-Duvaz D, Good VM, Jones CM, Marshall CJ, Springer CJ, Barford D, Marais R, Cancer Genome Project (2004) Mechanisms of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 116:855–867. doi:10.1016/S0092-8674(04)00215-6

    Article  CAS  PubMed  Google Scholar 

  10. Agaram NP, Wong GC, Guo T, Maki RG, Singer S, Dematteo RP, Besmer P, Antonescu CR (2008) Novel V600E mutations in imatinib naïve and imatinib resistant gastrointestinal stromal tumors. Genes Chromosomes Cancer 47:853–859. doi:10.1002/gcc.20589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Agaimy A, Terracciano LM, Dirnhofer S, Tornillo L, Foester A, Hartmann A, Bihl MP (2009) V600E BRAF mutations are alternative early molecular events in a subset of KIT/PDGFRA wild-Tye gastrointestinal stromal tumours. J Clin Pathol 62:613–616. doi:10.1136/jcp.2009.064550

    Article  CAS  PubMed  Google Scholar 

  12. Martinho O, Gouveia A, Viana-Pereira M, Silva P, Pimenta A, Reis RM, Lopes JM (2009) Low frequency of MAP kinase pathway alterations in KIT and PDFGRA wild-type GISTs. Histopathology 55:53–62. doi:10.1111/j.1365-2559.2009.03323.x

    Article  PubMed  Google Scholar 

  13. Hostein I, Faur N, Primois C, Boury F, Denard J, Emile JF, Bringuier PP, Scoazec JY, Coindre JM (2010) BRAF mutation status in gastrointestinal stromal tumors. Am J Clin Pathol 133:141–148. doi:10.1309/AJCPPCKGA2QGBJ1R

    Article  CAS  PubMed  Google Scholar 

  14. Debiec-Rychter M, Sciot R, Cesne A, Schlemmer M, Hohenberger P, Oosterom AT, Blay JY, Leyvraz S, Stul M, Casali PG, Zalcberg J, Verweij J, Glabbeke M, Hagemeijer A, Judson I KIT mutations and dose selection for imatinib in patients with advanced gastrointestinal stromal tumours. Eur J Cancer 42:1093–1103. doi:10.1016/j.ejca.2006.01.030

  15. Miranda C, Nucifora M, Molinari F, Conca E, Anania MC, Bordoni A, Saletti P, Mazzucchelli L, Pilotti S, Pierotti MA, Tamborini E, Greco A, Frattini M (2012) KRAS and BRAF mutations predict primary resistance to imatinib in gastrointestinal stromal tumors. Clin Cancer Res 18:1769–1776. doi:10.1158/1078-0432.CCR-11-2230

    Article  CAS  PubMed  Google Scholar 

  16. Falchook GS, Trent JC, Heinrich MC, Beadling C, Patterson J, Bastida CC, Blackman SC, Kurzrock R (2013) BRAF mutant gastrointestinal stromal tumor: first report of regression with BRAF inhibitor dabrafenib (GSK2118436) and whole exomix sequencing analysis for acquired resistance. Oncotarget 4:310–315. doi:10.18632/oncotarget.864

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Daniels M, Lurkin I, Pauli R, Erbstosser E et al (2011) Spectrum of KIT/PDGFRA/BRAF mutations and phosphatidylinositol −3-kinase pathway gene alterations in gastrointestinal stromal tumors (GIST). Cancer Lett 312:43–54. doi:10.1016/j.canlet.2011.07.029

    Article  CAS  PubMed  Google Scholar 

  18. Joensuu H, Vehtari A, Riihimäki J, Nishida T, Steigen SE, Brabec P, Plank L, Nilsson B, Cirilli C, Braconi C, Bordoni A, Magnusson MK, Linke Z, Sufliarsky J, Federico M, Jonasson JG, Tos AP, Rutkowski P (2012) Risk of recurrence of gastrointestinal stromal tumors after surgery: an analysis of pooled population-based cohorts. Lancet Oncol 121:539–549. doi:10.1016/S1470-2045(11)70299-6

    Google Scholar 

  19. Minarik G, Plank L, Lasabova Z, Szemes T, Burjanivova T, Szepe P, Buzalkova V, Porubsky D, Sufliarsky J (2013) Spectrum of mutations in gastrointestinal stromal tumor patients – a population based study from Slovakia. APMIS 121:539–548. doi:10.1111/apm.12019

    Article  CAS  PubMed  Google Scholar 

  20. Liegl-Atzwanger B, Fletcher JA, Fletcher CDM (2010) Gastrointestinal stromal tumors. Virchows Arch 456:111–127. doi:10.1007/s00428-008-0875-y

    Article  PubMed  Google Scholar 

  21. Fletcher C, Bridge J, Hogendoorn P, Mertens F (eds) (2013) ISBN-10 9283224345 World Health Organization classification of tumours of soft tissue and bone: pathology and genetics of tumours of soft tissue and bone, 4th edn. IARC Press, Lyon, France

    Google Scholar 

  22. Van Krieken JH, Jung A, Kirchner T et al (2008) KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for an European quality assurance program. Virchows Arch 453:417–431. doi:10.1007/s00428-008-0665-y

    Article  CAS  PubMed  Google Scholar 

  23. Haller F, Schulten HJ, Armbrust T et al (2007) Multicentric sporadic gastrointestinal stromal tumors (GISTs) of the stomach with distinct clonal origin: differential diagnosis to familial and syndromal GIST variants and peritoneal metastasis. Am J Surg Pathol 31:933–937. doi:10.1097/01.pas.0000213440.78407.27

    Article  PubMed  Google Scholar 

  24. Kang DY, Park CH, Choi JS et al (2007) Multiple gastrointestinal stromal tumors: clinicopathological and genetic analysis of 12 patients. Am J Surg Pathol 31:224–232. doi:10.1097/01.pas.0000213318.66800.94

    Article  PubMed  Google Scholar 

  25. Gasparotto D, Rossi S, Bearz I et al (2008) Multiple primary sporadic gastrointestinal stromal tumors in the adult: an underestimate entity. Clin Cancer Res 14:5715–5721. doi:10.1158/1078-0432.CCR-12-3863

    Article  CAS  PubMed  Google Scholar 

  26. Curtin JA, Busam K, Pinkel D, Bastian BC (2006) Somatic activation of KIT in distinct sunbtypes of melanoma. J Clin Oncol 10:4340–4346. doi:10.1200/JCO.2006.06.2984

    Article  Google Scholar 

  27. Lamy A, Blanchard F, LePessot F, Sesboué R, DiFiore F, Bossut J, Fiant E, Frébourg T, Sabourin JC Metastatic colorectal cancer KRAS genotyping in routine practice: results and pitfalls. Mod Pathol 24:1090–1100. doi:10.1038/modpathol.2011.60

  28. Mao C, Wu XY, Yang ZY, Threapleton DE, Yuan JQ, Yu YY, Tang JL (2015) Concordant analysis of KRAS, BRAF, PIK3CA mutations, and PTEN expression between primary colorectal cancer and matched metastases. Sci Rep 5:8065. doi:10.1038/srep08065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Schoppmann SF, Vinatzer U, Popitsch N, Mittlbock M, Leibman-Reindl S, Jomrich G, Streubel B, Bimer P (2013) Novel clinically relevant genes in gastrointestinal stromal tumors indetified by exome sequencing. Clin Canc Res 19:5329–5339. doi:10.1158/1078-0432.CCR-12-3863

    Article  CAS  Google Scholar 

  30. Gleeson FC, Kipp BR, Kerr SE, Voss JS, Graham RP, Campion MB, Minot DM, Tu ZJ, Klee EW, Lazaridis KN, Henry MR, Levy MJ (2015) Kinase genotype analysis of gastric gastrointestinal stromal tumor cytology samples using targeted next-generation sequencing. Clin Gastroenterol Hepatol 13:202–206. doi:10.1016/j.cgh.2014.06.024

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This study was supported by the grant of Novartis Slovakia Ltd., s,r,o, by the project CEPV II (ITMS 26220120036) as well as by the project of Slovak Research and Development Agency no. APVV-14-0273. We thank Mrs. A. Vanochova for her excellent technical assistance.

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Authors and Affiliations

  1. Department of Pathological Anatomy, Jessenius Faculty of Medicine and University Hospital in Martin, Comenius University in Bratislava, Kollarova 2, 03601, Martin, Slovakia

    Karin Jasek, Veronika Buzalkova, Andrea Stanclova, Peter Szepe & Lukas Plank

  2. Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Malá hora 4C, 03601, Martin, Slovakia

    Karin Jasek & Zora Lasabova

  3. Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108, Bratislava, Slovakia

    Gabriel Minarik

  4. Department of Molecular Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 03601, Martin, Slovakia

    Zora Lasabova

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  1. Karin Jasek
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  2. Veronika Buzalkova
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Correspondence to Zora Lasabova.

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The study is in compliance with ethical standards.

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Lukas Plank and Zora Lasabova senior co-authors

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Jasek, K., Buzalkova, V., Minarik, G. et al. Detection of mutations in the BRAF gene in patients with KIT and PDGFRA wild-type gastrointestinal stromal tumors. Virchows Arch 470, 29–36 (2017). https://doi.org/10.1007/s00428-016-2044-4

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  • DOI: https://doi.org/10.1007/s00428-016-2044-4

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