Alterations In Neuroblastoma Research Articles

Construction of methylation driver gene-related prognostic signature and development of a new prognostic stratification strategy in neuroblastoma.

Aberrant DNA methylation is one of the major epigenetic alterations in neuroblastoma. Exploring the prognostic significance of methylation driver genes in neuroblastoma could help to comprehensively assess patient prognosis. After identifying methylation driver genes (MDGs), we used the LASSO algorithm and stepwise Cox regression to construct methylation driver gene-related risk score (MDGRS), and evaluated its predictive performance by multiple methods. By combining risk grouping and MDGRS grouping, we developed a new prognostic stratification strategy and explored the intrinsic differences between the different groupings. We identified 44 stably expressed MDGs in neuroblastoma. MDGRS showed superior predictive performance in both internal and external cohorts and was strongly correlated with immune-related scores. MDGRS can be an independent prognostic factor for neuroblastoma, and we constructed the nomogram to facilitate clinical application. Based on the new prognostic stratification strategy, we divided the patients into three groups and found significant differences in overall prognosis, clinical characteristics, and immune infiltration between the different subgroups. MDGRS was an accurate and promising tool to facilitate comprehensive pre-treatment assessment. And the new prognostic stratification strategy could be helpful for clinical decision making.

Targeting anaplastic lymphoma kinase (ALK) gene alterations in neuroblastoma by using alkylating pyrrole-imidazole polyamides.

Anaplastic lymphoma kinase (ALK) aberration is related to high-risk neuroblastomas and is an important therapeutic target. As acquired resistance to ALK tyrosine kinase inhibitors is inevitable, novel anti-ALK drug development is necessary in order to overcome potential drug resistance against ATP-competitive kinase inhibitors. In this study, to overcome ALK inhibitor resistance, we examined the growth inhibition effects of newly developed ALK-targeting pyrrole-imidazole polyamide CCC-003, which was designed to directly bind and alkylate DNA within the F1174L-mutated ALK gene. CCC-003 suppressed cell proliferation in ALK-mutated neuroblastoma cells. The expression of total and phosphorylated ALK was downregulated by CCC-003 treatment but not by treatment with a mismatch polyamide without any binding motif within the ALK gene region. CCC-003 preferentially bound to the DNA sequence with the F1174L mutation and significantly suppressed tumor progression in a human neuroblastoma xenograft mouse model. Our data suggest that the specific binding of CCC-003 to mutated DNA within the ALK gene exerts its anti-tumor activity through a mode of action that is distinct from those of other ALK inhibitors. In summary, our current study provides evidence for the potential of pyrrole-imidazole polyamide ALK inhibitor CCC-003 for the treatment of neuroblastoma thus offering a possible solution to the problem of tyrosine kinase inhibitor resistance.

Investigation of major genetic alterations in neuroblastoma.

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.

Coexpression network analysis identifies transcriptional modules associated with genomic alterations in neuroblastoma

Neuroblastoma is a highly complex and heterogeneous cancer in children. Acquired genomic alterations including MYCN amplification, 1p deletion and 11q deletion are important risk factors and biomarkers in neuroblastoma. Here, we performed a co-expression-based gene network analysis to study the intrinsic association between specific genomic changes and transcriptome organization. We identified multiple gene coexpression modules which are recurrent in two independent datasets and associated with functional pathways including nervous system development, cell cycle, immune system process and extracellular matrix/space. Our results also indicated that modules involved in nervous system development and cell cycle are highly associated with MYCN amplification and 1p deletion, while modules responding to immune system process are associated with MYCN amplification only. In summary, this integrated analysis provides novel insights into molecular heterogeneity and pathogenesis of neuroblastoma. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.

Fibroblast growth factor receptors as therapeutic targets in neuroblastoma

To identify progression-driving molecular alterations in neuroblastoma, we used DNA deep-sequencing of 213 primary tumors, RNA deep-sequencing of 498 primary tumors, and microarray gene expression analysis of 709 tumors. While a heterogeneous mutation spectrum was observed in general, we identified putatively activating mutations in fibroblast growth factor receptor (FGFR) tyrosine kinase genes in several cases of high-risk neuroblastoma patients. In addition, gene expression data suggest that elevated FGFR expression in neuroblastoma is associated with a poor patient outcome, suggesting that FGFR may represent therapeutic targets in neuroblastoma. We are therefore investigating the effects of the FGFR inhibitors Dovitinib (TKI-258) and NVP-BGJ398, which have shown promising anticancer-activity in other malignancies, on growth characteristics of neuroblastoma cell lines. We observed that FGFR are highly expressed in the majority of the analysed neuroblastoma cell lines. Preliminary results of Dovitinib indicate that FGFR kinases may be suitable as a molecular target in neuroblastoma therapy.

Analysis of genomic alterations in neuroblastoma by multiplex ligation-dependent probe amplification and array comparative genomic hybridization: a comparison of results

In cases of neuroblastoma, recurring genetic alterations--losses of the 1p, 3p, 4p, and 11q and/or gains of 1q, 2p, and 17q chromosome arms--are currently used to define the therapeutic strategy in therapeutic protocols for low- and intermediate-risk patients. Different genome-wide analysis techniques, such as array comparative genomic hybridization (aCGH) or multiplex ligation-dependent probe amplification (MLPA), have been suggested for detecting chromosome segmental abnormalities. In this study, we compared the results of the two technologies in the analyses of the DNA of tumor samples from 91 neuroblastoma patients. Similar results were obtained with the two techniques for 75 samples (82%). In five cases (5.5%), the MLPA results were not interpretable. Discrepancies between the aCGH and MLPA results were observed in 11 cases (12%). Among the discrepancies, a 18q21.2-qter gain and 16p11.2 and 11q14.1-q14.3 losses were detected only by aCGH. The MLPA results showed that the 7p, 7q, and 14q chromosome arms were affected in six cases, while in two cases, 2p and 17q gains were observed; these results were confirmed by neither aCGH nor fluorescence in situ hybridization (FISH) analysis. Because of the higher sensitivity and specificity of genome-wide information, reasonable cost, and shorter time of aCGH analysis, we recommend the aCGH procedure for the analysis of genomic alterations in neuroblastoma.

Accumulation of Segmental Alterations Determines Progression in Neuroblastoma

Neuroblastoma is characterized by two distinct types of genetic profiles, consisting of either numerical or segmental chromosome alterations. The latter are associated with a higher risk of relapse, even when occurring together with numerical alterations. We explored the role of segmental alterations in tumor progression and the possibility of evolution from indolent to aggressive genomic types. Array-based comparative genomic hybridization data of 394 neuroblastoma samples were analyzed and linked to clinical data. Integration of ploidy and genomic data indicated that pseudotriploid tumors with mixed numerical and segmental profiles may be derived from pseudotriploid tumors with numerical alterations only. This was confirmed by the analysis of paired samples, at diagnosis and at relapse, as in tumors with a purely numerical profile at diagnosis additional segmental alterations at relapse were frequently observed. New segmental alterations at relapse were also seen in patients with segmental alterations at diagnosis. This was not linked to secondary effects of cytotoxic treatments since it occurred even in patients treated with surgery alone. A higher number of chromosome breakpoints were correlated with advanced age at diagnosis, advanced stage of disease, with a higher risk of relapse, and a poorer outcome. These data provide further evidence of the role of segmental alterations, suggesting that tumor progression is linked to the accumulation of segmental alterations in neuroblastoma. This possibility of genomic evolution should be taken into account in treatment strategies of low- and intermediate-risk neuroblastoma and should warrant biologic reinvestigation at the time of relapse.

Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma

BackgroundCancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors.ResultsWe tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method on 52 neuroblastoma tumors showed that Multiplex Amplicon Quantification can reliably detect the important genomic aberrations.ConclusionMultiplex Amplicon Quantification is a low-cost and high-throughput PCR-based technique that can reliably detect copy number alterations in regions with prognostic relevance for neuroblastoma.

Abstract 1137: Next generation sequencing of the neuroblastoma transcriptome identifies multiple protein disrupting mutations

Abstract Introduction: Neuroblastoma (NB) is one of the small round blue cell tumors of childhood arising in the peripheral nervous system. Fifty percent of patients present with metastatic or high risk disease and despite aggressive multimodal therapy approximately 60% percent of these patients eventually succumb to NB. Currently only a handful of molecular alterations are known to influence prognosis, but no clear mechanism of pathogenesis has been demonstrated. Recently, targeted sequencing efforts identified recurrent single nucleotide variants (SNVs) in the ALK gene in 6.1-15% of NB. In an effort to better understand the biology driving this tumor and to identify new targets for therapy, we sequenced the transcriptomes of 20 stage four tumors, including ten MYCN amplified and ten MYCN non-amplified samples, using massively parallel sequencing technology. Methods: In our analysis pipeline, 50 base nucleotide reads are filtered against a database of rRNA, tRNA, repetitive regions, and adapter sequences. The remaining reads were aligned to the reference human genome (hg 18) and a database of spice junctions. Reads that align were analyzed for: 1) base coverage, 2) transcript expression levels, 3) calling SNVs and 4) determination of which of the SNVs were damaging by Sorting Intolerant From Tolerant (SIFT) analysis Results: Initial analysis of the first six samples, yielded an average of 86.6 million uniquely mapped reads per sample. On average we detected the expression of 6,000 genes to a depth of 10x. The RNA seq expression profile correlated well with expression array data from the same sample (r=0.62), while the sequencing data identified an additional 3,000 genes that were not detected by microarray. Our sequencing method maintains “strandedness” allowing the identification of multiple novel antisense non-coding transcripts. Using the SAMtool, an average of 1,255 nonsynonymous SNVs predicted per sample. Of these nonsynonymous SNVs, 69-160 per sample were predicted by the SIFT algorithm to be damaging. Interestingly, 3 different genes had damaging nonsynonymous SNVs in at least 30% of the samples. Conclusion: Next generation sequencing of transcriptome is a powerful and more sensitive method than microarrays for expression profiling and allows for the identification of novel transcripts including non-coding RNAs. Here we report the most extensive profiling of the neuroblastoma transcriptome to date using this technology. We identified several hundred protein disrupting SNVs, and of these 3 were commonly altered. Ongoing analysis is underway to validate our results. The identification of recurrent genetic alterations in NB will assist in developing a better understanding of the mechanisms of pathogenesis of this pediatric cancer and lead to new therapeutic targets. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1137.

Comparison of different techniques for the detection of genetic risk-identifying chromosomal gains and losses in neuroblastoma

Neuroblastoma (NB) is a pediatric neoplasia that shows complex combinations of acquired genetic aberrations. The specific genes and the molecular mechanisms responsible for development and progression of NB remain poorly understood. Our main objective is to compare the results obtained with different techniques for the detection of genomic data in 20 patients with NB using the information obtained to select the appropriate technique in routine analysis for the therapeutic stratification. The genetic methods used in this study are multiprobe fluorescence in situ hybridization (FISH) assay, metaphasic comparative genomic hybridization (mCGH), array comparative genomic hybridization (aCGH), and the multiplex ligation-dependent probe amplification (MLPA). Genomic copy number abnormalities were used to group the cases in four categories: MYCN amplification cases; 11q deletion tumors; cases with partial chromosome gains or losses and samples with entire chromosome alterations. The data obtained from the multigenomic techniques showed a high degree of concordance and our findings support the hypothesis that NB consists of biologically distinct subgroups that differ by genetic characteristics of prognostic relevance. FISH will be essential for the mandatory study of MYCN status. The use of MLPA as routine technique is an advantage procedure for detecting the implication of the common genetic alterations in NB.

Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma

ArrayCGH is commonly used for high-resolution detection of copy-number alterations in tumours, allowing identification of chromosomal aberrations with prognostic or diagnostic relevance. Currently available arrayCGH platforms are still very expensive for analysis of large sets of samples. For this purpose, we have constructed a dedicated mini-array that is enriched for BAC/PAC clones in the prognostic important regions for neuroblastoma and that only covers a small area on the slide, allowing down-scaling of the labelling and hybridisation reagents and hence reducing the price. The mini-arrays were validated on neuroblastoma samples and comparison with high-resolution whole-genome arrayCGH data yielded complete concordant results.

Oligonucleotide array‐based comparative genomic hybridization (aCGH) of 90 neuroblastomas reveals aberration patterns closely associated with relapse pattern and outcome

The study of genomic alterations in neuroblastoma is of particular importance since several cytogenetic markers proved to be closely associated with the clinical phenotype. To disclose patterns of gains and losses, we performed high-resolution oligonucleotide array-based comparative genomic hybridization (aCGH). A total cohort of 90 patients was classified into 6 subsets according to tumor stage and outcome: Stages 1-3+ (with event), Stage 1-3- (no event), Stage 4+/-, and Stage 4S+/-. The aberration patterns in Stages 1-3- and 4S- tumors differed from all other groups as they were predominantly characterized by losses (3, 4, 14, X) and gains (7, 17) of whole chromosomes. However, 59/65 (91%) tumors of Stages 1-3+ or Stage 4 revealed numerous structural copy number alterations (sCNA). While deletions in chromosomes 1, 3, and 11 discriminated outcome in Stage 4, there were no specific sCNA that distinguished tumor stage within the subgroup of unfavorable tumors. sCNA in 1p, 3p, 11q, 17q, or MYCN amplification (MNA) was seen among 22/24 patients who died, 10/12 with metastatic relapses, and 5/9 with local recurrences. Detailed breakpoint analyses on chromosomes 1, 3, 11, and 17 disclosed preferred breaking areas, although breakpoints were not identical. Amplifications were found in 18 patients and involved 2p24 (MYCN) and other segments of chromosome 2, as well as regions on chromosome arms 6q, 12q, and 17q. One single feature in 21q21.1 (BU678720, without known function yet) attracted particular attention since five patients showed a homozygous loss of this sequence.

Inferring a Tumor Progression Model for Neuroblastoma From Genomic Data

The knowledge of the key genomic events that are causal to cancer development and progression not only is invaluable for our understanding of cancer biology but also may have a direct clinical impact. The task of deciphering a model of tumor progression by requiring that it explains (or at least does not contradict) known clinical and molecular evidence can be very demanding, particularly for cancers with complex patterns of clinical and molecular evidence. We formalize the process of model inference and show how a progression model for neuroblastoma (NB) can be inferred from genomic data. The core idea of our method is to translate the model of clonal cancer evolution to mathematical testable rules of inheritance. Seventy-eight NB samples in stages 1, 4S, and 4 were analyzed with array-based comparative genomic hybridization. The pattern of recurrent genomic alterations in NB is strongly stage dependent and it is possible to identify traces of tumor progression in this type of data. A tumor progression model for neuroblastoma is inferred, which is in agreement with clinical evidence, explains part of the heterogeneity of the clinical behavior observed for NB, and is compatible with existing empirical models of NB progression.

High‐resolution detection and mapping of genomic DNA alterations in neuroblastoma

We used array-based comparative genomic hybridization (aCGH) to measure genomic copy number alterations (CNAs) in 42 neuroblastoma cell lines with known 1p36.3, 2p24 (MYCN), 11q23, and 17q23 allelic status. All cell lines showed CNAs, with an average of 22.0% of the genome of each sample showing evidence of gain (11.6%) or loss (10.4%). MYCN amplification was detected in 81% of cell lines, but other regions with high-level genomic amplification were observed only rarely. Gain of 17q material was present in 75% of the samples, and four discrete genomic regions at 17q23.2-17q25.3 were defined. Novel regions of gain were identified, including a 2.6-Mb subtelomeric region at 5p that includes the telomerase reverse transcriptase gene (TERT), which was found in 45% of the cell lines. Hemizygous deletions were noted at 1p36.23-1p36.32 and 11q23.3-11q25 in 60% and 36%, respectively, of the samples, with other frequent (>25%) regions of deletion localized to 1p32.1, 3p21.31-3p22.1, 5q35.2-5q35.3, 7q31.2, 7q34, 9q22.3-9q24.1, 10q26.11-10q26.12, 16q23.1-16q24.3, 18q21.32-18q23, and 20p11.21-20p11.23. A smallest region of overlap (SRO) for CNAs was mapped across all experiments and in each case was consistent with or refined the published data. A single cell line showed a homozygous deletion at 3p22.3, which was verified, and this location was refined by FISH and PCR. There was outstanding concordance of aCGH with PCR-based CNA detection methods. Several potential cooperating loci were identified, including deletion of 11q23-25, which was highly associated with both regional gain and loss at multiple chromosomal loci but was inversely correlated with the deletion of 1p36. Taking all of this together indicates that aCGH can accurately measure CNAs in the neuroblastoma genome and facilitate gene discovery efforts by high-throughput refinement of candidate loci.

Genetic and epigenetic alterations in neuroblastoma

Neuroblastoma is one of the most common solid tumors of childhood. Despite the most recent advances in combined therapy, the overall survival of patients with disseminated disease has not improved in the last 20 years. On the contrary, the increased knowledge of the genetic and molecular abnormalities that characterize neuroblastoma allowed the identification of several important prognostic factors and possible pathways of neuroblastoma development. Moreover, several other structural and numerical non-random chromosome abnormalities were recognized by comparative genomic hybridization and their role is actively investigated. More recently, it has become evident also that epigenetic factors may alter the pattern of expression of multiple genes whose role in neuroblastoma begins to be understood. It is thus likely that a combination of events that include gene translocation and rearrangement and the altered methylation of crucial genes, contribute to neuroblastoma development and progression and are likely responsible for the clinical heterogeneity of this tumor.

A multiplex PCR assay for routine evaluation of deletion of the short arm of chromosome 1 in neuroblastoma

Deletions of the short arm of chromosome 1 (1p) are frequent alterations in neuroblastoma. Although a consensus region of deletion has been mapped to chromosome subband 1p36, recent studies suggest that several distinct loci on this chromosome may be involved in neuroblastoma. Moreover, different patterns of deletion might be associated with different clinical and biological characteristics of the tumours. These findings emphasise the importance of assessing the localisation and the extent of the deletions in neuroblastoma. We developed a technique which allows analysis of loss of heterozygosity at multiple loci on 1p in a single step, making use of a multiplex PCR method. Primers specific for six microsatellite loci mapped in the different regions of interest on 1p were used for simultaneous amplification of DNA, and loss of heterozygosity was determined after separation of the alleles by denaturing polyacrylamide gel electrophoresis. This technique enables a simple analysis of the position and extent of 1p deletions, and can be used for routine evaluation of 1p status in neuroblastoma.

Dominant and recessive molecular changes in neuroblastomas.

Of all human tumors, neuroblastomas bear the most prominent genetic changes. Amplifications and deletions of chromosomal DNA can be identified by light microscopy on chromosomal spreads of neuroblastoma cells with remarkable frequency and consistency. Consequently, extensive studies have been undertaken to elucidate the molecular basis of these cytogenetic changes. A rich body of information has accumulated on the role played by dominant oncogenes and recessive tumor suppressor genes in the pathogenesis of this disease. Most notably, it was found that amplification of N-myc is responsible for the presence of double minutes and homogeneously staining regions in neuroblastoma chromosomes. It has also been discovered that N-myc amplification is a prognostic sign of malignancy. More recently, recessive genetic alterations in neuroblastoma, such as deletion of putative tumor-suppressing genes have received increasing attention, and considerable efforts are being made to identify such genetic elements. Finally, the susceptibility of neuroblastoma cells to differentiating stimuli has made them a popular in vitro system for neurobiological and pharmacological research. The need for suitable in vivo systems has spurred the development of several animal models employing tumor viruses and transgenic technologies.