Molecular characterization of neuroblastoma tumors - a basis for personalized medicine.

Abstract

Neuroblastoma is a very heterogeneous tumor, with a clinical course ranging from spontaneous regression to aggressive tumor growth. A proper stratification of the patients into different risk groups is therefore important in order to provide the most suitable treatment for each patient. The primary aim of this thesis was therefore to further characterize the genes and mechanisms important for neuroblastoma development using genome wide copy number data from single nucleotide polymorphism (SNP)-arrays as a starting point for more detailed studies of interesting regions of the genome. Furthermore, we wanted to investigate the clinical usefulness of SNP-arrays, both directly as a prognostic tool, and indirectly as a starting point for the generation of patient-specific assays. As to the genes and mechanisms important for neuroblastoma development, we have identified a chromosomal instability phenotype in the 11q deleted subgroup, possibly caused by the DNA repair gene H2AFX located in the commonly deleted region. Furthermore, we have identified and characterized a small subgroup of neuroblastoma with amplification of two regions on 12q, occasionally accompanied by 11q amplification. Gene expression analysis and siRNA knockdown of the genes included in these amplicons indicate that CDK4 and CCND1 are possible drivers of this subgroup and we therefore suggest that this group of neuroblastoma is characterized by a cell cycle de regulation phenotype. Regarding the clinical usefulness, our results show that SNP-arrays are powerful tools for the stratification of neuroblastoma patients into different treatment groups. Not only is it possible to detect known prognostic markers such as MYCN amplification and 11q deletion, but the genome-wide copy number profile in itself is also important, especially for the identification of patients with a favorable prognosis. Moreover, we show that the array-data can be used for detailed mapping of the rearrangement boundaries, which in combination with a multiplex PCR reaction makes it possible to detect tumor-specific fragments that span the junction of the rearranged DNA. These junction PCR assays were also tested for the detection of minimal residual disease, and were found to be sensitive enough to detect very small amounts of tumor DNA in the blood or bone marrow from patients during treatment or follow-up. To conclude, genome-wide techniques, such as SNP-arrays are useful not only for research purposes but also as a clinical tool. These arrays give valuable information for the risk group stratification of neuroblastoma patients, and provide a robust foundation for the development of a personalized treatment strategy for patients with neuroblastoma.