A distinct spectrum of copy number aberrations in pediatric high-grade gliomas

Abstract

Purpose: As genome-scale technologies begin to unravel the complexity of the equivalent tumors in adults, we can attempt detailed characterization of high-grade gliomas in children, that have until recently been lacking. Toward this end, we sought to validate and extend investigations of the differences between pediatric and adult tumors.

Experimental design: We carried out copy number profiling by array comparative genomic hybridization using a 32K bacterial artificial chromosome platform on 63 formalin-fixed paraffin-embedded cases of high-grade glioma arising in children and young people (<23 years).

Results: The genomic profiles of these tumors could be subclassified into four categories: those with stable genomes, which were associated with a better prognosis; those with aneuploid and those with highly rearranged genomes; and those with an amplifier genotype, which had a significantly worse clinical outcome. Independent of this was a clear segregation of cases with 1q gain (more common in children) from those with concurrent 7 gain/10q loss (a defining feature of adults). Detailed mapping of all the amplification and deletion events revealed numerous low-frequency amplifications, including IGF1R, PDGFRB, PIK3CA, CDK6, CCND1, and CCNE1, and novel homozygous deletions encompassing unknown genes, including those at 5q35, 10q25, and 22q13. Despite this, aberrations targeting the "core signaling pathways" in adult glioblastomas are significantly underrepresented in the pediatric setting.

Conclusions: These data highlight that although there are overlaps in the genomic events driving gliomagenesis of all ages, the pediatric disease harbors a distinct spectrum of copy number aberrations compared with adults.

Figure 1. Paediatric high grade gliomas are comprised of different subtypes of copy number profiles

Sample genome plots are given for (A) “Stable” (B) “Aneuploid” (C) “Rearranged” and (D) “Amplifier” genomes within our sample cohort. Log₂ ratios for each clone (y axis) are plotted according to chromosomal location (x axis). The centromeres are represented by vertical lines. Points are coloured green and red to represent gains and losses, respectively.

Figure 2. Genomic subtypes of paediatric high grade glioma have prognostic relevance

Kaplan-Meier plot for overall survival of paediatric high grade gliomas treated at a single institution stratified according to genomic subtype. The “stable” genome cases showed a trend towards better prognosis when compared with all other cases (p = 0.0755, log-rank test), whilst the samples with an “amplifier” genome had a significantly shorter time to death (p=0.00214, log-rank test)

Figure 3. Summary and significance of genomic aberrations in paediatric high grade glioma

The proportion of tumours in which each clone is gained or lost is plotted in grey (y axis) for each BAC clone according to genomic location (x axis). A measure of the frequency, amplitude and focality of high level events was calculated for each affected clone and was overplotted for amplifications (green) and deletions (red), scaled to the absolute maximum for each.

Figure 4. Novel low-frequency amplifications and fine-mapping focal deletions in paediatric high grade glioma

Chromosome plots for (A) chromosome 15, targeting IGF1R; (B) chromosome 5, targeting PDGFRB/CSF1R; (C) chromosome 10, mapping a deletion at 10q25.2-q25.3; and (D) chromosome 11, resolving a deletion at 11q14 to ODZ4 and hsa-mir-708. Log₂ ratios for each clone are plotted (y axis) for each BAC clone according to location (x axis) along the length of the chromosome, with genes and microRNA within the minimal regions plotted underneath according to positional information from the UCSC Genome Browser (hg18).

Figure 5

FISH validation of low frequency amplifications in paediatric high grade glioma. Specific probes for MYCN, PIK3CA, PDGFRA, SKP2, PDGFRB, MYC, CDK4, MDM2, and IGF1R were labelled with Cy5 (red) and co-hybridised to interphase nuclei on FFPE specimens with chromosome-specific control probes labelled with fluoroscein.

Figure 6. Glioblastoma “core signalling pathways” are dysregulated by copy number changes less frequently in paediatric than adult tumours

Signalling pathway heatmap of interactions defined by the TCGA (1). Genes with amplifications are shown in red, genes with focal deletion are shown in blue. The overall frequency of copy number alteration in paediatric high grade glioma for each pathway is listed, and is significantly lower than in adults (25% RTK/PI3K, 19% p53 and 22% RB versus 59%, 70% and 66% for adult glioblastoma respectively).