Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. This malignancy shows a wide spectrum of clinical outcome and its prognosis is conditioned by manifold biological and genetic factors. We investigated the tumor genetic profile and clinical data of 29 patients with NB by multiplex ligation-dependent probe amplification (MLPA) to assess therapeutic risk. In 18 of these tumors, MYCN status was assessed by fluorescence in situ hybridization (FISH). Copy number variation was also determined for confirming MLPA findings in two 6p loci. We found 2p, 7q and 17q gains, and 1p and 11q losses as the most frequent chromosome alterations in this cohort. FISH confirmed all cases of MYCN amplification detected by MLPA. In view of unexpected 6p imbalance, copy number variation of two 6p loci was assessed for validating MLPA findings. Based on clinical data and genetic profiles, patients were stratified in pretreatment risk groups according to international consensus. MLPA proved to be effective for detecting multiple genetic alterations in all chromosome regions as requested by the International Neuroblastoma Risk Group (INRG) for therapeutic stratification. Moreover, this technique proved to be cost effective, reliable, only requiring standard PCR equipment, and attractive for routine analysis. However, the observed 6p imbalances made PKHD1 and DCDC2 inadequate for control loci. This must be considered when designing commercial MLPA kits for NB. Finally, four patients showed a normal MLPA profile, suggesting that NB might have a more complex genetic pattern than the one assessed by presently available MLPA kits.
Similar content being viewed by others
References
Maris JM, Hogarty MD, Bagatell R, Cohn SL (2007) Neuroblastoma. Lancet 369:2106–2120. https://doi.org/10.1016/S0140-6736(07)60983-0
Heck JE, Ritz B, Hung RJ et al (2009) The epidemiology of neuroblastoma: a review. Paediatr Perinat Epidemiol 23:125–143. https://doi.org/10.1111/j.1365-3016.2008.00983.x
de Camargo B, de Oliveira Ferreira JM, de Souza Reis R et al (2011) Socioeconomic status and the incidence of non-central nervous system childhood embryonic tumours in Brazil. BMC Cancer 11:160. https://doi.org/10.1186/1471-2407-11-160
Irwin MS, Park JR (2015) Neuroblastoma: paradigm for precision medicine. Pediatr Clin North Am 62:225–256. https://doi.org/10.1016/j.pcl.2014.09.015
Brodeur GM, Iyer R, Croucher JL et al (2014) Therapeutic targets for neuroblastomas. Expert Opin Ther Targets 18:277–292. https://doi.org/10.1517/14728222.2014.867946
Abel F, Dalevi D, Nethander M et al (2011) A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int 11:9. https://doi.org/10.1186/1475-2867-11-9
Cheung N-KV, Dyer M (2013) Neuroblastoma: developmental biology, cancer genomics and immunotherapy. Nat Rev Cancer 13:397–411. https://doi.org/10.1038/nrc3526
Maris JM, Mosse YP, Bradfield JP et al (2008) Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. N Engl J Med 358:2585–2593. https://doi.org/10.1056/NEJMoa0708698
Nguyễn LB, Diskin SJ, Capasso M et al (2011) Phenotype restricted genome-wide association study using a gene-centric approach identifies three low-risk neuroblastoma susceptibility loci. PLoS Genet. https://doi.org/10.1371/journal.pgen.1002026
Diskin SJ, Capasso M, Diamond M et al (2014) Rare variants in TP53 and susceptibility to neuroblastoma. J Natl Cancer Inst 106:7–10. https://doi.org/10.1093/jnci/dju047
Matthay KK, Maris JM, Schleiermacher G et al (2016) Neuroblastoma. Nat Rev Dis Primers 2:16078. https://doi.org/10.1038/nrdp.2016.78
Schleiermacher G, Janoueix-Lerosey I, Delattre O (2014) Recent insights into the biology of neuroblastoma. Int J Cancer 135:2249–2261. https://doi.org/10.1002/ijc.29077
Louis CU, Shohet JM (2015) Neuroblastoma: molecular pathogenesis and therapy. Annu Rev Med 66:49–63. https://doi.org/10.1146/annurev-med-011514
Barbosa RH, Aguiar FCC, Silva MFL et al (2013) Screening of RB1 alterations in Brazilian patients with retinoblastoma and relatives with retinoma: phenotypic and genotypic associations. Invest Ophthalmol Vis Sci 54:3184–3194. https://doi.org/10.1167/iovs.13-11686
Ambros IM, Brunner B, Aigner G et al (2011) A multilocus technique for risk evaluation of patients with neuroblastoma. Clin Cancer Res 17:792–804. https://doi.org/10.1158/1078-0432.CCR-10-0830
Ambros PF, Ambros IM, Brodeur GM et al (2009) International consensus for neuroblastoma molecular diagnostics: report from the International Neuroblastoma Risk Group (INRG) Biology Committee. Br J Cancer 100:1471–1482. https://doi.org/10.1038/sj.bjc.6605014
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2^-∆∆CT Method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Cohn SL, Pearson ADJ, London WB et al (2009) The International Neuroblastoma Risk Group (INRG) classification system: an INRG task force report. J Clin Oncol 27:289–297. https://doi.org/10.1200/JCO.2008.16.6785
Bown N, Cotterill S, Lastowska M et al (1999) Gain of chromosome arm 17q and adverse outcome in patients with neuroblastoma. N Engl J Med 340:1954–1961. https://doi.org/10.1056/nejm199906243402504
Theissen J, Oberthuer A, Hombach A et al (2014) Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma. Genes Chromosom Cancer 53:639–649. https://doi.org/10.1002/gcc.22174
Kuzyk A, Booth S, Righolt C et al (2015) MYCN overexpression is associated with unbalanced copy number gain, altered nuclear location, and overexpression of chromosome arm 17q genes in neuroblastoma tumors and cell lines. Genes Chromosom Cancer 54:616–628. https://doi.org/10.1002/gcc.22273
Mandriota SJ, Valentijn LJ, Lesne L et al (2015) Ataxia-telangiectasia mutated (ATM) silencing promotes neuroblastoma progression through a MYCN independent mechanism. Oncotarget 6:18558–18576. https://doi.org/10.18632/oncotarget.4061
Hagenbuchner J, Kuznetsov AV, Obexer P, Ausserlechner MJ (2013) BIRC5/Survivin enhances aerobic glycolysis and drug resistance by altered regulation of the mitochondrial fusion/fission machinery. Oncogene 32:4748–4757. https://doi.org/10.1038/onc.2012.500
Hagenbuchner J, Kiechl-Kohlendorfer U, Obexer P, Ausserlechner MJ (2015) BIRC5/Survivin as a target for glycolysis inhibition in high-stage neuroblastoma. Oncogene 35:1–10. https://doi.org/10.1038/onc.2015.264
Huang M, Weiss WA (2013) Neuroblastoma and MYCN. Cold Spring Harb Perspect Med. https://doi.org/10.1101/cshperspect.a014415
Speleman F, Park JR, Henderson TO (2016) Neuroblastoma: a tough nut to crack. Am Soc Clin Oncol Educ Book 35:e548–e557. https://doi.org/10.14694/EDBK_159169
Villamón E, Berbegall AP, Piqueras M et al (2013) Genetic instability and intratumoral heterogeneity in neuroblastoma with MYCN amplification plus 11q deletion. PLoS ONE. https://doi.org/10.1371/journal.pone.0053740
Michels E, Vandesompele J, De Preter K et al (2007) ArrayCGH-based classification of neuroblastoma into genomic subgroups. Genes Chromosom Cancer 46:1098–1108. https://doi.org/10.1002/gcc.20496
Mazzocco K, Defferrari R, Sementa AR et al (2015) Genetic abnormalities in adolescents and young adults with neuroblastoma: a report from the Italian Neuroblastoma group. Pediatr Blood Cancer 62:1725–1732. https://doi.org/10.1002/pbc.25552
Nicholson RI, Gee JM, Harper ME (2001) EGFR and cancer prognosis. Eur J Cancer 37(Suppl 4):S9–S15. https://doi.org/10.1016/S0959-8049(01)00231-3
Keller J, Nimnual AS, Varghese MS et al (2016) A novel EGFR extracellular domain mutant, EGFRdelta768, possesses distinct biological and biochemical properties in neuroblastoma. Mol Cancer Res 1–13. https://doi.org/10.1158/1541-7786.MCR-15-0477
Shostak K, Chariot A (2015) EGFR and NF-κB: partners in cancer. Trends Mol Med 21:385–393. https://doi.org/10.1016/j.molmed.2015.04.001
Knuutila S, Björkqvist AM, Autio K et al (1998) DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies. Am J Pathol 152:1107–1123
Santos GC, Zielenska M, Prasad M, Squire JA (2007) Chromosome 6p amplification and cancer progression. J Clin Pathol 60:1–7. https://doi.org/10.1136/jcp.2005.034389
Plantaz D, Mohapatra G, Matthay KK et al (1997) Gain of chromosome 17 is the most frequent abnormality detected in neuroblastoma by comparative genomic hybridization. Am J Pathol 150:81–89
Brodeur GM (2003) Neuroblastoma: biological insights into a clinical enigma. Nat Rev Cancer 3:203–216. https://doi.org/10.1038/nrc1014
Braekeveldt N, Wigerup C, Tadeo I et al (2016) Neuroblastoma patient-derived orthotopic xenografts reflect the microenvironmental hallmarks of aggressive patient tumours. Cancer Lett 375:384–389. https://doi.org/10.1016/j.canlet.2016.02.046
van Eijk R, Eilers PH, Natté R et al (2010) MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification. BMC Bioinf 11:67. https://doi.org/10.1186/1471-2105-11-67
Fischer M, Bauer T, Oberthür a et al (2010) Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q. Oncogene 29:865–875. https://doi.org/10.1038/onc.2009.390
Spitz R, Hero B, Ernestus K, Berthold F (2003) Deletions in chromosome arms 3p and 11q are new prognostic markers in localized and 4 s neuroblastoma. Clin Cancer Res 9:52–58
Carén H, Kryh H, Nethander M et al (2010) High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc Natl Acad Sci USA 107:4323–4328. https://doi.org/10.1073/pnas.0910684107
Cetinkaya C, Martinsson T, Sandgren J et al (2013) Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation. BMC Cancer 13:1. https://doi.org/10.1186/1471-2407-13-231
Owens C, Irwin M (2012) Neuroblastoma: the impact of biology and cooperation leading to personalized treatments. Crit Rev Clin Lab Sci 49:85–115. https://doi.org/10.3109/10408363.2012.683483
Fujita T, Igarashi J, Okawa ER et al (2008) CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas. J Natl Cancer Inst 100:940–949. https://doi.org/10.1093/jnci/djn176
Koyama H, Zhuang T, Light JE et al (2012) Mechanisms of CHD5 inactivation in neuroblastomas. Clin Cancer Res 18:1588–1597. https://doi.org/10.1158/1078-0432.CCR-11-2644
Maris JM, Weiss MJ, Guo C et al (2000) Loss of heterozygosity at 1p36 independently predicts for disease progression but not decreased overall survival probability in neuroblastoma patients: a children’s cancer group study. J Clin Oncol 18:1888–1899. https://doi.org/10.1200/jco.2000.18.9.1888
Attiyeh EF, London WB, Mossé YP et al (2005) Chromosome 1p and 11q deletions and outcome in neuroblastoma. N Engl J Med 353:2243–2253. https://doi.org/10.1056/NEJMoa052399
Kolla V, Zhuang T, Higashi M et al (2014) Role of CHD5 in human cancers: 10 years later. Cancer Res 74:652–658. https://doi.org/10.1158/0008-5472.CAN-13-3056
Acknowledgements
Work supported by Conselho Nacional de Ciência e Tecnologia (CNPq; Grant 573806/2008-0) and Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ; Grant E26/170.026/2008).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that there is no conflict of interest regarding the publication of this article.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Costa, R.A., Seuánez, H. Investigation of major genetic alterations in neuroblastoma. Mol Biol Rep 45, 287–295 (2018). https://doi.org/10.1007/s11033-018-4161-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-018-4161-4