Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q

Abstract

A number of distinct subtypes of neuroblastoma exist with different genetic abnormalities that are predicative of outcome. Whole chromosome gains are usually associated with low stage disease and favourable outcome, whereas loss of 1p, 3p and 11q, unbalanced gain of 17q and MYCN amplification (MNA) are indicative of high stage disease and unfavourable prognosis. Although MNA and loss of 11q appear to represent two distinct genetic subtypes of advanced stage neuroblastoma, a detailed understanding of how these subtypes differ in terms of global gene expression is still lacking. We have used metaphase comparative genomic hybridization (CGH) analysis in combination with oligonucleotide technology to identify patterns of gene expression that correlate with specific genomic imbalances found in primary neuroblastic tumours and cell lines. The tumours analysed in this manner included a ganglioneuroma, along with various ganglioneuroblastoma and neuroblastoma of different stages and histopathological classifications. Oligonucleotide microarray-based gene expression profile analysis was performed with Affymetrix HU133A arrays representing approximately 14 500 unique genes. The oligonucleotide microarray results were subsequently validated by quantitative real-time PCR, immunohistochemical staining, and by comparison of specific gene expression patterns with published results. Hierarchical clustering of gene expression data distinguished tumours on the basis of stage, differentiation and genetic abnormalities. A number of genes were identified whose patterns of expression were highly correlated with 11q loss; supporting the concept that loss of 11q represents a distinct genetic subtype of neuroblastoma. The implications of these results in the process of neuroblastoma development and progression are discussed.

The neuroblastoma and ganglion components of nodular ganglioneuroblastoma are genetically similar: evidence against separate clonal origins

“…Moreover, these regions of gain have also been reported in other array studies on neuroblastoma. 23,24,[28][29][30]38 Thus, although our results suggest there may be a genetic profile characteristic of nodular ganglioneuroblastoma, it would not appear to distinguish this subtype of neuroblastoma from others. In our series, there was no correlation between the total number of copy number alterations or specific gains and losses and histologic prognostic categories (favorable vs unfavorable) or patient outcome.…”

“…28,30 We next examined other regions of the genome for gains and losses using single-nucleotide polymorphism arrays to identify copy number alterations that might be specific to the nodular ganglioneuroblastoma subtype. One potential limitation of our study was that two of the eight cases were post chemotherapy, and chemotherapy might introduce additional genetic changes.…”

“…13,[17][18][19] Neuroblastoma is characterized by multiple chromosomal abnormalities (reviewed in refs 1,3), but whether these are shared by the nodular ganglioneuroblastoma subtype is not known. Genome-wide approaches such as array comparative genomic hybridization [20][21][22][23][24][25] and single-nucleotide polymorphism arrays 26,27 have been used to identify whole chromosome and segmental gains and losses in neuroblastoma; however, only two studies specifically mentioned the inclusion of ganglioneuroblastoma samples 28,29 and results were inconsistent. The neuroblastoma component is thought to have a clonal origin distinct from the ganglioneuromatous part of the tumor.…”

High-Resolution Analysis of Chromosomal Breakpoints and Genomic Instability Identifies PTPRD as a Candidate Tumor Suppressor Gene in Neuroblastoma

“…Loss of 11q and gain of 17q were the sole imbalances detected in one tumor, which supports the notion that these are early events. In addition, expression microarray analysis of 11qÀ neuroblastomas has shown that rare low-stage 11qÀ tumors sometimes have global gene expression profiles that are much more similar to low-stage hyperdiploid tumors than to high-stage 11qÀ tumors, an indication that loss of 11q and gain of 17q are insufficient for the establishment of metastasis (13). It is tempting to speculate that some of the microdeletions and duplications listed in Table 1 contribute to the establishment of metastatic potential in neuroblastoma; however, the possibility that many of them are merely a consequence of global genomic instability cannot be ruled out.…”

“…The abnormalities identified in this study are therefore not representative of the entire neuroblastoma population. Samples from the Our Lady's Hospital for Sick Children and Children's Hospital at Westmead were characterized previously for largescale chromosomal imbalances by metaphase CGH analysis (12)(13)(14)(15), whereas samples from the Children's Oncology Group have been analyzed for loss of 11q by allotyping with several different polymorphic loci (6). MYCN amplification status in each sample was also assessed by either fluorescence in situ hybridization, Southern blotting, or quantitative PCR.…”