Acta Neuropathologica

, Volume 121, Issue 6, pp 763–774 | Cite as

Oncogenic FAM131B–BRAF fusion resulting from 7q34 deletion comprises an alternative mechanism of MAPK pathway activation in pilocytic astrocytoma

  • Huriye Cin
  • Claus Meyer
  • Ricarda Herr
  • Wibke G. Janzarik
  • Sally Lambert
  • David T. W. Jones
  • Karine Jacob
  • Axel Benner
  • Hendrik Witt
  • Marc Remke
  • Sebastian Bender
  • Fabian Falkenstein
  • Ton Nu Van Anh
  • Heike Olbrich
  • Andreas von Deimling
  • Arnulf Pekrun
  • Andreas E. Kulozik
  • Astrid Gnekow
  • Wolfram Scheurlen
  • Olaf Witt
  • Heymut Omran
  • Nada Jabado
  • V. Peter Collins
  • Tilman Brummer
  • Rolf Marschalek
  • Peter Lichter
  • Andrey Korshunov
  • Stefan M. Pfister
Original Paper

Abstract

Activation of the MAPK signaling pathway has been shown to be a unifying molecular feature in pilocytic astrocytoma (PA). Genetically, tandem duplications at chromosome 7q34 resulting in KIAA1549BRAF fusion genes constitute the most common mechanism identified to date. To elucidate alternative mechanisms of aberrant MAPK activation in PA, we screened 125 primary tumors for RAF fusion genes and mutations in KRAS, NRAS, HRAS, PTPN11, BRAF and RAF1. Using microarray-based comparative genomic hybridization (aCGH), we identified in three cases an interstitial deletion of ~2.5 Mb as a novel recurrent mechanism forming BRAF gene fusions with FAM131B, a currently uncharacterized gene on chromosome 7q34. This deletion removes the BRAF N-terminal inhibitory domains, giving a constitutively active BRAF kinase. Functional characterization of the novel FAM131B–BRAF fusion demonstrated constitutive MEK phosphorylation potential and transforming activity in vitro. In addition, our study confirmed previously reported BRAF and RAF1 fusion variants in 72% (90/125) of PA. Mutations in BRAF (8/125), KRAS (2/125) and NF1 (4/125) and the rare RAF1 gene fusions (2/125) were mutually exclusive with BRAF rearrangements, with the exception of two cases in our series that concomitantly harbored more than one hit in the MAPK pathway. In summary, our findings further underline the fundamental role of RAF kinase fusion products as a tumor-specific marker and an ideally suited drug target for PA.

Supplementary material

401_2011_817_MOESM1_ESM.eps (3.6 mb)
Supplementary material 1 (Online Resource Fig. 1 Identification of FAM131B-BRAF fusion genes. Sequence trace of the breakpoints in (a) first case 2A23, (b) and (c) in the second case (PA60) of both FAM131B-BRAF splice variants and (d) in BT-005. (e) Amplification of the breakpoint of both splice variant fusion genes in sample PA60)
401_2011_817_MOESM2_ESM.eps (1.2 mb)
Supplementary material 2 (Online Resource Fig.2 Kaplan–Meier survival estimates for progression-free survival (a) comparing patients after gross total tumor resection versus subtotal resection, and (b) patients 1 year of age or younger versus patients above 1 year of age)
401_2011_817_MOESM3_ESM.doc (276 kb)
Supplementary material 3 (DOC 275 kb)
401_2011_817_MOESM4_ESM.doc (22 kb)
Supplementary material 4 (DOC 22 kb)

References

  1. 1.
    Brummer T, Martin P, Herzog S, Misawa Y, Daly RJ, Reth M (2006) Functional analysis of the regulatory requirements of B-Raf and the B-Raf(V600E) oncoprotein. Oncogene 25:6262–6276PubMedCrossRefGoogle Scholar
  2. 2.
    Ciampi R, Knauf JA, Rabes HM, Fagin JA, Nikiforov YE (2005) BRAF kinase activation via chromosomal rearrangement in radiation-induced and sporadic thyroid cancer. Cell Cycle 4:547–548PubMedCrossRefGoogle Scholar
  3. 3.
    Dessars B, De Raeve LE, Housni HE, Debouck CJ, Sidon PJ, Morandini R, Roseeuw D, Ghanem GE, Vassart G, Heimann P (2007) Chromosomal translocations as a mechanism of BRAF activation in two cases of large congenital melanocytic nevi. J Invest Dermatol 127:1468–1470PubMedCrossRefGoogle Scholar
  4. 4.
    Dibb NJ, Dilworth SM, Mol CD (2004) Switching on kinases: oncogenic activation of BRAF and the PDGFR family. Nat Rev Cancer 4:718–727PubMedCrossRefGoogle Scholar
  5. 5.
    Eisenhardt AE, Olbrich H, Röring M, Janzarik W, Van Anh TN, Cin H, Remke M, Witt H, Korshunov A, Pfister SM, Omran H, Brummer T (2010) Functional characterization of a BRAF insertion mutant associated with pilocytic astrocytoma. Int J Cancer [Epub ahead of print]Google Scholar
  6. 6.
    Emuss V, Garnett M, Mason C, Marais R (2005) Mutations of C-RAF are rare in human cancer because C-RAF has a low basal kinase activity compared with B-RAF. Cancer Res 65:9719–9726PubMedCrossRefGoogle Scholar
  7. 7.
    Forshew T, Tatevossian R, Lawson A, Ma J, Neale G, Ogunkolade B, Jones T, Aarum J, Dalton J, Bailey S, Chaplin T, Carter R, Gajjar A, Broniscer A, Young B, Ellison D, Sheer D (2009) Activation of the ERK/MAPK pathway: a signature genetic defect in posterior fossa pilocytic astrocytomas. J Pathol 218:172–181PubMedCrossRefGoogle Scholar
  8. 8.
    Gajjar A, Sanford RA, Heideman R, Jenkins JJ, Walter A, Li Y, Langston JW, Muhlbauer M, Boyett JM, Kun LE (1997) Low-grade astrocytoma: a decade of experience at St. Jude Children’s Research Hospital. J Clin Oncol 15:2792–2799PubMedGoogle Scholar
  9. 9.
    Horbinski C, Hamilton R, Nikiforov Y, Pollack I (2010) Association of molecular alterations, including BRAF, with biology and outcome in pilocytic astrocytomas. Acta Neuropathol 119:641–649PubMedCrossRefGoogle Scholar
  10. 10.
    Ichimura K, Ohgaki H, Kleihues P, Collins VP (2004) Molecular pathogenesis of astrocytic tumours. J Neurooncol 70:137–160PubMedCrossRefGoogle Scholar
  11. 11.
    Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N (2009) Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours. Br J Cancer 101:722–733PubMedCrossRefGoogle Scholar
  12. 12.
    Janzarik W, Kratz C, Loges N, Olbrich H, Klein C, Schaefer T, Scheurlen W, Roggendorf W, Weiller C, Niemeyer C, Korinthenberg R, Pfister S, Omran H (2007) Further evidence for a somatic KRAS mutation in a low-grade astrocytoma. Neuropediatrics 38:1–3CrossRefGoogle Scholar
  13. 13.
    Jones D, Ichimura K, Liu L, Pearson D, Plant K, Collins V (2006) Genomic analysis of pilocytic astrocytomas at 0.97 Mb resolution shows an increasing tendency toward chromosomal copy number change with age. J Neuropathol Exp Neurol 65:1049–1058PubMedCrossRefGoogle Scholar
  14. 14.
    Jones DTW, Kocialkowski S, Liu L, Pearson DM, Backlund LM, Ichimura K, Collins VP (2008) Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res 68:8673–8677PubMedCrossRefGoogle Scholar
  15. 15.
    Jones DTW, Kocialkowski S, Liu L, Pearson DM, Ichimura K, Collins VP (2009) Oncogenic RAF1 rearrangement and a novel BRAF mutation as alternatives to KIAA1549:BRAF fusion in activating the MAPK pathway in pilocytic astrocytoma. Oncogene 28:2119–2123PubMedCrossRefGoogle Scholar
  16. 16.
    Kaatsch P (2010) Epidemiology of childhood cancer. Cancer Treat Rev 36:277–285PubMedCrossRefGoogle Scholar
  17. 17.
    Korn EL (1986) Censoring distributions as a measure of follow-up in survival analysis. Stat Med 5:255–260PubMedCrossRefGoogle Scholar
  18. 18.
    Korshunov A, Meyer J, Capper D, Christians A, Remke M, Witt H, Pfister S, von Deimling A, Hartmann C (2009) Combined molecular analysis of BRAF and IDH1 distinguishes pilocytic astrocytoma from diffuse astrocytoma. Acta Neuropathol 118:401–405PubMedCrossRefGoogle Scholar
  19. 19.
    Lawson A, Tatevossian R, Phipps K, Picker S, Michalski A, Sheer D, Jacques T, Forshew T (2010) RAF gene fusions are specific to pilocytic astrocytoma in a broad paediatric brain tumour cohort. Acta Neuropathol 120:271–273PubMedCrossRefGoogle Scholar
  20. 20.
    Lichter P, Cremer T, Borden J, Manuelidis L, Ward D (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80:224–234PubMedCrossRefGoogle Scholar
  21. 21.
    Listernick R, Ferner R, Liu G, Gutmann D (2007) Optic pathway gliomas in neurofibromatosis-1: controversies and recommendations. Ann Neurol 61:189–198PubMedCrossRefGoogle Scholar
  22. 22.
    Louis D, Ohgaki H, Wiestler O, Cavenee W, Burger P, Jouvet A, Scheithauer B, Kleihues P (2007) The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol 114:97–109PubMedCrossRefGoogle Scholar
  23. 23.
    Mendrzyk F, Radlwimmer B, Joos S, Kokocinski F, Benner A, Stange DE, Neben K, Fiegler H, Carter NP, Reifenberger G, Korshunov A, Lichter P (2005) Genomic and protein expression profiling identifies CDK6 as novel independent prognostic marker in medulloblastoma. J Clin Oncol 23:8853–8862PubMedCrossRefGoogle Scholar
  24. 24.
    Meyer C, Schneider B, Reichel M, Angermueller S, Strehl S, Schnittger S, Schoch C, Jansen MWJC, van Dongen JJ, Pieters R, Haas OA, Dingermann T, Klingebiel T, Marschalek R (2005) Diagnostic tool for the identification of MLL rearrangements including unknown partner genes. Proc Natl Acad Sci USA 102:449–454PubMedCrossRefGoogle Scholar
  25. 25.
    Ohgaki H, Kleihues P (2005) Population-based studies on incidence, survival rates, and genetic alterations in astrocytic and oligodendroglial gliomas. J Neuropathol Exp Neurol 64:479–489PubMedGoogle Scholar
  26. 26.
    Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, Shankar S, Han B, Cao Q, Cao X, Suleman K, Kumar-Sinha C, Dhanasekaran SM, Chen Y-b, Esgueva R, Banerjee S, LaFargue CJ, Siddiqui J, Demichelis F, Moeller P, Bismar TA, Kuefer R, Fullen DR, Johnson TM, Greenson JK, Giordano TJ, Tan P, Tomlins SA, Varambally S, Rubin MA, Maher CA, Chinnaiyan AM (2010) Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med 16:793–798PubMedCrossRefGoogle Scholar
  27. 27.
    Pfister S, Janzarik W, Remke M, Ernst A, Werft W, Becker N, Toedt G, Wittmann A, Wittmann A, Kratz C, Olbrich H, Ahmadi R, Thieme B, Joos S, Radlwimmer B, Kulozik A, Pietsch T, Herold-Mende C, Gnekow A, Reifenberger G, Korshunov A, Scheurlen W, Omran H, Lichter P (2008) BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas. J Clin Invest 118(5):1739–1749PubMedCrossRefGoogle Scholar
  28. 28.
    Pfister S, Remke M, Benner A, Mendrzyk F, Toedt G, Felsberg J, Wittmann A, Devens F, Gerber NU, Joos S, Kulozik A, Reifenberger G, Rutkowski S, Wiestler OD, Radlwimmer B, Scheurlen W, Lichter P, Korshunov A (2009) Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci. J Clin Oncol 27:1627–1636PubMedCrossRefGoogle Scholar
  29. 29.
    Pfister S, Witt O (2009) Pediatric gliomas. Recent Results Cancer Res 171:67–81PubMedCrossRefGoogle Scholar
  30. 30.
    Qaddoumi I, Sultan I, Gajjar A (2009) Outcome and prognostic features in pediatric gliomas. Cancer 115:5761–5770PubMedCrossRefGoogle Scholar
  31. 31.
    R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
  32. 32.
    Sharma M, Zehnbauer B, Watson M, Gutmann D (2005) RAS pathway activation and an oncogenic RAS mutation in sporadic pilocytic astrocytoma. Neurology 65:1335–1336PubMedCrossRefGoogle Scholar
  33. 33.
    Sievert A, Fisher M (2009) Pediatric low-grade gliomas. J Child Neurol 24:1397–1408PubMedCrossRefGoogle Scholar
  34. 34.
    Sievert A, Jackson E, Gai X, Hakonarson H, Judkins A, Resnick A, Sutton L, Storm P, Shaikh T, Biegel J (2009) Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene. Brain Pathol 19:449–458PubMedCrossRefGoogle Scholar
  35. 35.
    Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399–407PubMedCrossRefGoogle Scholar
  36. 36.
    Wan PTC, Garnett MJ, Roe SM, Lee S, Niculescu-Duvaz D, Good VM, Project CG, Jones CM, Marshall CJ, Springer CJ, Barford D, Marais R (2004) Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 116:855–867PubMedCrossRefGoogle Scholar
  37. 37.
    Weinstock DM, Elliott B, Jasin M (2006) A model of oncogenic rearrangements: differences between chromosomal translocation mechanisms and simple double-strand break repair. Blood 107:777–780PubMedCrossRefGoogle Scholar
  38. 38.
    Yu J, Deshmukh H, Gutmann RJ, Emnett RJ, Rodriguez FJ, Watson MA, Nagarajan R, Gutmann DH (2009) Alterations of BRAF and HIPK2 loci predominate in sporadic pilocytic astrocytoma. Neurology 73:1526–1531PubMedCrossRefGoogle Scholar
  39. 39.
    Zielinski B, Gratias S, Toedt G, Mendrzyk F, Stange DE, Radlwimmer B, Lohmann DR, Lichter P (2005) Detection of chromosomal imbalances in retinoblastoma by matrix-based comparative genomic hybridization. Genes Chromosomes Cancer 43:294–301PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Huriye Cin
    • 1
  • Claus Meyer
    • 2
  • Ricarda Herr
    • 3
  • Wibke G. Janzarik
    • 4
    • 5
  • Sally Lambert
    • 6
  • David T. W. Jones
    • 1
  • Karine Jacob
    • 7
  • Axel Benner
    • 8
  • Hendrik Witt
    • 1
    • 9
  • Marc Remke
    • 1
    • 9
  • Sebastian Bender
    • 1
    • 9
  • Fabian Falkenstein
    • 10
  • Ton Nu Van Anh
    • 5
  • Heike Olbrich
    • 5
    • 11
  • Andreas von Deimling
    • 12
    • 13
  • Arnulf Pekrun
    • 14
  • Andreas E. Kulozik
    • 9
  • Astrid Gnekow
    • 10
  • Wolfram Scheurlen
    • 15
  • Olaf Witt
    • 9
    • 16
  • Heymut Omran
    • 11
  • Nada Jabado
    • 7
    • 17
  • V. Peter Collins
    • 6
  • Tilman Brummer
    • 3
  • Rolf Marschalek
    • 2
  • Peter Lichter
    • 1
  • Andrey Korshunov
    • 12
    • 13
  • Stefan M. Pfister
    • 1
    • 9
  1. 1.Division of Molecular GeneticsGerman Cancer Research CenterHeidelbergGermany
  2. 2.Institute of Pharmaceutical Biology, Diagnostic Center of Acute Leukemia (DCAL)Goethe-UniversityFrankfurtGermany
  3. 3.Centre for Biological Systems Analysis (ZBSA), Centre for Biological Signalling Studies BIOSS, Faculty of BiologyAlbert-Ludwigs-UniversityFreiburgGermany
  4. 4.Department of NeurologyUniversity Hospital FreiburgFreiburgGermany
  5. 5.Department of Pediatric Neurology and Muscle DisordersUniversity Hospital FreiburgFreiburgGermany
  6. 6.Division of Molecular Histopathology, Department of PathologyUniversity of CambridgeCambridgeUK
  7. 7.Department of Human GeneticsMcGill University Health CenterMontrealCanada
  8. 8.Division of BiostatisticsGerman Cancer Research Center (DKFZ)HeidelbergGermany
  9. 9.Department of Pediatric Oncology, Hematology and ImmunologyUniversity HospitalHeidelbergGermany
  10. 10.Department of PediatricsKlinikum AugsburgAugsburgGermany
  11. 11.Clinic and Polyclinic for Pediatrics, Department of General PediatricsUniversity HospitalMuensterGermany
  12. 12.Department of NeuropathologyUniversity HospitalHeidelbergGermany
  13. 13.Clinical Cooperation Unit Neuropathology, German Cancer Research CenterHeidelbergGermany
  14. 14.Klinikum Bremen Mitte gGmbH, Prof-Hess-Kinderklinik, Klinikum Bremen-MitteBremenGermany
  15. 15.Cnopf’sche Kinderklinik, Nürnberg Children’s HospitalNürnbergGermany
  16. 16.Clinical Cooperation Unit Pediatric Oncology, German Cancer Research CenterHeidelbergGermany
  17. 17.Department of PediatricsMontreal Children’s Hospital, McGill University Health CenterMontrealCanada

Personalised recommendations