This unbiased genome-wide study of predominantly pretreated childhood and adolescent pHGG provides further biological insight into this devastating tumor.
Homozygous loss at 8p12 was seen in 16% of pHGG and has not been previously found in adult HGG or pHGG in high-resolution studies using the Affymetrix SNP platforms.16,17
This is likely due to the lack of probes for this particular gene on the Affymetrix 500 and 250 K platforms. The minimal deleted region is of the gene ADAM3A
. The ADAM
family of genes are widely expressed and have many potential functions relating to cell-to-cell communication and adhesion. Little is known about ADAM3A
However, several members of the ADAM
gene family have been implicated in cancer. Notable examples include overexpression of ADAM28
in lung and breast carcinomas22
and loss of expression of ADAM23
in breast tumors correlating with increasing grade.23,24 ADAM17
has been shown to be involved in EGFR regulation, and overexpression of ADAM17
in astrocytes promotes an increase in cell proliferation and invasion.25
This novel homozygous deletion of ADAM3A
therefore merits further study.
Deletion of CDKN2A
in 19% of pHGG has been recently reported.16
In this study, deletion of CDKN2A
was seen in 10% of samples by aCGH and 13% of samples by FISH. Interestingly, none of the DIPGs or infratentorial tumors showed deletion at 9p21 by aCGH or FISH, and all deletions were seen in supratentorial GBMs. Zarghooni et al.26
also noted loss of 9p in supratentorial tumors but did not define specific loss of CDKN2A/CDKN2B
. Loss of CDKN2A
has previously been reported in another supratentorial high-grade malignancy.27
The differential loss of CDKN2A
depending on tumor location may point to a cell of origin effect as seen in ependymoma.28
is a proto-oncogene and part of the MYC transcription factor family.29
It is highly amplified in aggressive neuroblastoma (a sympathetic nervoussystem–derived tumor) and has been reported in primitive neuroectodermal tumors of the central nervous system (CNS PNETs), medulloblastoma, and pHGG.16,30,31
amplification was detected in 5% of both brainstem and supratentorial HGG. Correlation of MYCN
amplification with histological grade revealed that MYCN
amplification is significantly associated with AAs. The relevance and clinical significance of this finding need further study in a larger cohort.
Loss of 17p was seen in 4 of 13 (31%) DIPGs and just 1 of 25 (4%) nonbrainstem tumors. Region 17p is the site of the well-characterized tumor suppressor gene p53
, which has been widely implicated in cancer.32
Mutation of p53
has been reported in adult HGG, but less so in pHGG.16
The high frequency of loss of 17p in DIPG suggests that the loss of the 17p arm is the mechanism for the loss of p53
in this subset of tumors. Zarghooni et al.26
also reported 17p loss associated with pediatric DIPG compared with nonbrainstem HGGs. Combining data from this study and that of Zarghooni et al. reveals 11 of 24 (46%) DIPGs had loss of 17p, while only 3 of 36 (8%) nonbrainstem tumors had loss of 17p, which is statistically significant (P
= 0.02). This site-related difference in the inactivation of the TP53
tumor suppressor gene deserves further study.
Loss of 14q was is seen in 4 of 13 (31%) DIPGs, but only 1 supratentorial pHGG (4%); however, we were not able to identify a focal region of loss. Zarghooni et al.26
also identified 14q loss as being more common in DIPG.
We report an increased frequency gain of 1q in pHGG compared with adult tumors.21
In this study 21% of pHGG demonstrated gain of 1q by aCGH, while only 9% of adult HGG have been reported to have 1q gain.16,33
A recent study by Bax et al.34
found gain of 1q in 12 of 63 (19%) pHGG samples. Combining data from this study with those of Bax et al. reveals 20 of 101 (20%) pHGGs have gain of 1q compared with 17 of 189 (9%) adult tumors. This is statistically significant (P
= 0.03). Gain of 1q is commonly seen in pediatric brain tumors, including CNS PNETs, ependymoma, and HGG, in addition to other pediatric malignancies.16,35
We have recently shown a significant association between 1q gain and decreased survival, as found in some other pediatric malignancies.16,35
Nearly 25% of DIPGs have gain of the whole long arm of chromosome 1, which is comparable to the level of gain seen in other pHGG. In the recent study by Zarghooni et al.,24 PARP-1
, which is located at 1q41–42, was highlighted as gained in 3 of 11 (27%) DIPGs but in only 1 of the 2 pretreatment cases. PARP-1
is involved in repairing DNA damage, and overexpression of PARP-1
could be responsible for resistance to chemotherapy and radiotherapy, making it an attractive potential target for therapy. While focal gains were identified on 1q in this cohort, this did not include the PARP-1
locus at 1q41–42. Further assessment of the frequency of PARP-1
involvement in DIPG is needed.
Loss of 10q is seen in 6 of 38 (16%) of all pHGG samples and only 1 of 13 DIPGs in this study, which is notably lower than the 35% loss of 10q previously reported in pHGG.16
Loss of 10q is the most common whole-arm aberration in adult GBM (~80%), which includes loss of PTEN
The difference between the frequency of 10q loss in pHGG in this study (6/38) compared with adult HGG (152/189) is statistically significant (P
= 0.0001).33 PTEN
is a tumor suppressor gene that negatively regulates the Akt signaling pathway, and PTEN
loss or mutation is seen in a number of different cancers.1
The lack of 10q loss in this DIPG cohort may indicate a different mechanism of Akt signaling pathway activation or that different pathways are involved in these pediatric tumors. However, a recent study by Zarghooni et al.26
loss in 27% of both DIPG and nonbrainstem pHGG. An increased sample cohort is needed to determine whether 10q loss is a predominant feature of supratentorial tumors.
Expression of platelet-derived growth factor receptor-α (PDGFRA) correlates with malignant grade in pHGG, with high expression being associated with malignant histology (WHO Grades II and IV).37
We have recently reported amplification of PDGFRA
in 12% of Grade III and 17% of Grade IV pHGG tumors in a large recent series based on high-resolution copy number and expression profiling.16
Similar levels of focal amplification are reported in this series based on aCGH data and IHC. In this same collaborative study, amplification of PDGFRA
was found at a significantly higher frequency (50%) in irradiation-induced childhood and adolescent HGG.16
This later finding might explain the relatively high frequency of PDGFRA expression reported by Zarghooni et al., as 82% of their cohort was analyzed posttreatment.26
Consistent with this possibility is that amplification of PDGFRA
in adult tumors is associated with a secondary GBM,38
although the time course for the latter is likely longer. Further studies of the role of PDGFRA in childhood and adolescent HGG are needed to understand the influence of treatment on PDGFRA
amplification and to determine whether this tyrosine kinase receptor is a conditional target for therapy in the subset of pHGG with PDGFRA
amplification, the most common focal amplification in adult HGG,1,36,39
does not appear to be a feature of pHGG; indeed, no amplification of EGFR
was seen in the 38 pHGG samples in our cohort.
The findings in this study have shown that pediatric and adult HGG represent 2 different genetic entities that are distinguished by differences in copy number changes. Overall there are marked differences in the degree of genomic imbalance between adult and childhood/adolescent HGG. Four focal regions of amplification were seen across this data set compared with 27 different sites of amplification identified in a dataset of 97 adult HGG samples by metaphase CGH.36
Moreover, a subgroup of pHGG tumors (13%) have balanced genomes by aCGH analysis. This has also been seen in other pediatric brain tumors, including ependymoma and CNS PNETs.40,41
In our series of pHGG, this was not defined by young age at diagnosis as for ependymoma.40
This important difference in the number of genomic imbalances and regions of amplification in adults and children may reflect the development of the tumor in a narrower time frame/developmental window. It might also be that other mechanisms are important in the pathogenesis of these tumors and suggests that relatively fewer mutations may be required to initiate the disease if these arise within a specific developmental period. We are currently undertaking genome-wide methylation analysis to determine whether epigenetic mechanisms may play a role in these cases.
Zarghooni et al.26
identified a number of genes involved in DNA repair pathways as being lost in DIPG. Loss of some of these DNA repair pathway genes was seen in this study as part of whole-arm deletions, such as 17p (RPA1
), 14q (MNAT1
), and 1p (MSH4
). However, losses of other DNA repair pathway genes identified by Zarghooni were not seen in this study (GTF2H3
, and PMS1
Importantly their cohort included just 2 pretreatment samples compared with 10 pretreatment samples in this study, suggesting that treatment with DNA-damaging agents such as radiotherapy and temozolomide may be responsible for the loss of DNA repair pathway genes and possibly other genetic aberrations. We have previously shown that diagnostic biopsy of diffuse brain stem glioma is relatively safe10
and can now demonstrate that pretreatment tumor tissue can generate high-quality biological information on which to base future strategies.
This study adds to the body of knowledge regarding this poor prognosis tumor, providing further insight into underlying biology, and highlights potential therapeutic possibilities. Overall, pediatric DIPGs share many genetic changes with supratentorial pHGG. However, the frequency of aberrations differs in some instances, notably the low occurrence of 10q loss, the lack of any CDKN2A/CDKN2B loss in DIPG, and the high frequency of 14q and 17p loss in DIPG relative to their supratentorial counterpart. Larger studies need to be done on pretreatment DIPG based on tumor biopsies at diagnosis to comprehensively map the genetics of these tumors.
We also report the novel homozygous deletion of ADAM3A, one of the ADAM family of genes that are thought to play a role in cancer, confirm and extend the database of genetic aberrations that have been previously reported in pHGG, such as amplification of PDGFRA, MYCN, and cyclin D1, and raise the association between MYCN amplification and AA.