| 1. |
- Carén, Helena, 1979, et al.
(author)
-
High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset.
- 2010
-
In: PNAS. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 107:9, s. 4323-4328
-
Journal article (peer-reviewed)abstract
- Analysis of chromosomal aberrations is used to determine the prognosis of neuroblastomas (NBs) and to aid treatment decisions. MYCN amplification (MNA) alone is an incomplete poor prognostic factor, and chromosome 11q status has recently been included in risk classification. We analyzed 165 NB tumors using high-density SNP microarrays and specifically compared the high-risk groups defined by MNA (n = 37) and 11q-deletion (n = 21). Median patient age at diagnosis was 21 months for MNA tumors and 42 months for 11q-deletion tumors, and median survival time after diagnosis was 16 months for MNA and 40 months for 11q deletion. Overall survival (at 8 years) was approximately 35% in both groups. MNA and 11q deletion were almost mutually exclusive; only one case harbored both aberrations. The numbers of segmental aberrations differed significantly; the MNA group had a median of four aberrations, whereas the 11q-deletion group had 12. The high frequency of chromosomal breaks in the 11q-deletion group is suggestive of a chromosomal instability phenotype gene located in 11q; one such gene, H2AFX, is located in 11q23.3 (within the 11q-deletion region). Furthermore, in the groups with segmental aberrations without MNA or 11q deletion, the tumors with 17q gain have worse prognosis than those with segmental aberrations without 17q gain, which have a favorable outcome. This study has implications for therapy in different risk groups and stresses that genome-wide microarray analyses should be included in clinical management to fully evaluate risk, aid diagnosis, and guide treatment.
|
|
| 2. |
|
|
| 3. |
- Kryh, Hanna, 1983, et al.
(author)
-
Comprehensive SNP array study of frequently used neuroblastoma cell lines; copy neutral loss of heterozygosity is common in the cell lines but uncommon in primary tumors.
- 2011
-
In: BMC genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 12:1
-
Journal article (peer-reviewed)abstract
- ABSTRACT: BACKGROUND: Copy neutral loss of heterozygosity (CN-LOH) refers to a special case of LOH occurring without any resulting loss in copy number. These alterations is sometimes seen in tumors as a way to inactivate a tumor suppressor gene and have been found to be important in several types of cancer. RESULTS: We have used high density single nucleotide polymorphism arrays in order to investigate the frequency and distribution of CN-LOH and other allelic imbalances in neuroblastoma (NB) tumors and cell lines. Our results show that the frequency of these near-CN-LOH events is significantly higher in the cell lines compared to the primary tumors and that the types of CN-LOH differ between the groups. We also show that the low-risk neuroblastomas that are generally considered to have a "triploid karyotype" often present with a complex numerical karyotype (no segmental changes) with 2-5 copies of each chromosome. Furthermore a comparison has been made between the three related cell lines SK-N-SH, SH-EP and SH-SY5Y with respect to overall genetic aberrations, and several aberrations unique to each of the cell lines has been found. CONCLUSIONS: We have shown that the NB tumors analyzed contain several interesting allelic imbalances that would either go unnoticed or be misinterpreted using other genome-wide techniques. These findings indicate that the genetics underlying NB might be even more complex than previously known and that SNP arrays are important analysis tools. We have also showed that these near-CN-LOH events are more frequently seen in NB cell lines compared to NB tumors and that a set of highly related cell lines have continued to evolve secondary to the subcloning event. Taken together our analysis highlights that cell lines in many cases differ substantially from the primary tumors they are thought to represent, and that caution should be taken when drawing conclusions from cell line-based studies.
|
|
| 4. |
- Kryh, Hanna, 1983
(author)
-
Molecular characterization of neuroblastoma tumors - a basis for personalized medicine.
- 2012
-
Doctoral thesis (other academic/artistic)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.
|
|
| 5. |
- Kryh, Hanna, 1983, et al.
(author)
-
MYCN amplicon junctions as tumor-specific targets for minimal residual disease detection in neuroblastoma
- 2011
-
In: International Journal of Oncology. - : Spandidos Publications. - 1019-6439 .- 1791-2423. ; 39:5, s. 1063-1071
-
Journal article (peer-reviewed)abstract
- The MYCN gene is frequently amplified in unfavorable neuroblastoma tumors. Therefore, this study aimed at characterizing the novel junctions connecting the amplified DNA segments (amplicons) and obtaining tumor-specific PCR fragments for use in detecting minimal residual disease (MRD). High-density SNP arrays were used to map the end-points of the MYCN amplicons in a subset of neuroblastoma tumors. Primers were designed to give rise to a tumor-specific PCR product and were examined for MRD in the blood and bone marrow using quantitative PCR. Tumor-specific junction fragments were detected in all cases, confirming a head-to-tail tandem orientation of the amplicons and revealing microhomology at the amplicon junctions, thus suggesting a rolling circle caused by microhomology-mediated break-induced replication (MMBIR) as a possible mechanism initiating the MYCN amplification. We also evaluated the use of these junctions as tumor-specific targets for detecting MRD and observed that tumor DNA could be readily detected and quantified in either blood or bone marrow at a sensitivity of 1/10(6) tumor/control DNA. This study provides new information on the mechanisms of oncogene amplification and envisages means of rapidly obtaining highly sensitive PCR-based tools for tumor/patient-specific monitoring of treatment response and the early detection of relapse in patients with neuroblastoma.
|
|
| 6. |
- Martinez-Monleon, Angela, et al.
(author)
-
Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup
- 2022
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
-
Journal article (peer-reviewed)abstract
- In neuroblastoma, MYCN amplification and 11q-deletion are important, although incomplete, markers of high-risk disease. It is therefore relevant to characterize additional alterations that can function as prognostic and/or predictive markers. Using SNP-microarrays, a group of neuroblastoma patients showing amplification of one or multiple 12q loci was identified. Two loci containing CDK4 and MDM2 were commonly co-amplified, although amplification of either locus in the absence of the other was observed. Pharmacological inhibition of CDK4/6 with ribociclib or abemaciclib decreased proliferation in a broad set of neuroblastoma cell lines, including CDK4/MDM2-amplified, whereas MDM2 inhibition by Nutlin-3a was only effective in p53(wild-type) cells. Combined CDK4/MDM2 targeting had an additive effect in p53(wild-type) cell lines, while no or negative additive effect was observed in p53(mutated) cells. Most 12q-amplified primary tumors were of abdominal origin, including those of intrarenal origin initially suspected of being Wilms' tumor. An atypical metastatic pattern was also observed with low degree of bone marrow involvement, favoring other sites such as the lungs. Here we present detailed biological data of an aggressive neuroblastoma subgroup hallmarked by 12q amplification and atypical clinical presentation for which our in vitro studies indicate that CDK4 and/or MDM2 inhibition also could be beneficial.
|
|
