Dataset Information

Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours.

ABSTRACT:

Background

Juvenile pilocytic astrocytomas (JPA), a subgroup of low-grade astrocytomas (LGA), are common, heterogeneous and poorly understood subset of brain tumours in children. Chromosomal 7q34 duplication leading to fusion genes formed between KIAA1549 and BRAF and subsequent constitutive activation of BRAF was recently identified in a proportion of LGA, and may be involved in their pathogenesis. Our aim was to investigate additional chromosomal unbalances in LGA and whether incidence of 7q34 duplication is associated with tumour type or location.

Methods and results

Using Illumina-Human-Hap300-Duo and 610-Quad high-resolution-SNP-based arrays and quantitative PCR on genes of interest, we investigated 84 paediatric LGA. We demonstrate that 7q34 duplication is specific to sporadic JPA (35 of 53 - 66%) and does not occur in other LGA subtypes (0 of 27) or NF1-associated-JPA (0 of 4). We also establish that it is site specific as it occurs in the majority of cerebellar JPA (24 of 30 - 80%) followed by brainstem, hypothalamic/optic pathway JPA (10 of 16 - 62.5%) and is rare in hemispheric JPA (1 of 7 - 14%). The MAP-kinase pathway, assessed through ERK phosphorylation, was active in all tumours regardless of 7q34 duplication. Gain of function studies performed on hTERT-immortalised astrocytes show that overexpression of wild-type BRAF does not increase cell proliferation or baseline MAPK signalling even if it sensitises cells to EGFR stimulation.

Conclusions and interpretation

Our results suggest that variants of JPA might arise from a unique site-restricted progenitor cell where 7q34 duplication, a hallmark of this tumour-type in association to MAPK-kinase pathway activation, potentially plays a site-specific role in their pathogenesis. Importantly, gain of function abnormalities in components of MAP-Kinase signalling are potentially present in all JPA making this tumour amenable to therapeutic targeting of this pathway.

SUBMITTER: Jacob K

PROVIDER: S-EPMC2736806 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Juvenile pilocytic astrocytoma (JPA) is one of the most common brain tumors in children. The expression profiles of 21 JPAs, determined using Affymetrix GeneChip U133A, were compared with subjects with normal cerebella. The genes involved in neurogenesis, cell adhesion, synaptic transmission, central nervous system development, potassium ion transport, protein dephosphorylation, and cell differentiation were found to be significantly deregulated in JPA. These 21 JPAs were further clustered into two major groups by unsupervised hierarchical clustering using a set of 848 genes with high covariance (0.5-10). Supervised analysis with Significance Analysis of Microarrays software between these two potential subgroups identified a list of significant differentially expressed genes involved in cell adhesion, regulation of cell growth, cell motility, nerve ensheathment, and angiogenesis. Immunostaining of myelin basic protein on paraffin sections derived from 18 incompletely resected JPAs suggests that JPA without myelin basic protein–positively stained tumor cells may have a higher tendency to progress. Experiment Overall Design: Under an Institutional Review Board–approved protocol, brain tumor tissues were obtained, after informed consent, from patients undergoing tumor resection or other tumor-related neurosurgical procedures at the Texas Children's Hospital, Baylor College of Medicine. Samples of normal cerebellar tissue (n = 2) were isolated from surgically removed tissue adjacent to resected tumor tissue. Portions of the tumors were fixed in 10% formaldehyde and embedded in paraffin for sectioning and pathologic reviews, and the residual tissue samples were snap-frozen in liquid nitrogen and stored at –80°C for RNA extraction. All samples were obtained at initial diagnosis with no prior exposure to chemotherapy or radiation therapy. Normal fetal brain RNA was obtained from Stratagene (La Jolla, CA) and a normal cerebellum RNA was from Ambion, Inc. (Austin, TX). Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) followed by DNase I treatment and clean-up on aRNeasy spin column (Qiagen, Valencia, CA). RNA quality and purity were assessed by agarose gel electrophoresis and absorbance measurement at A260/A280.

Project description:Juvenile pilocytic astrocytoma (JPA) is one of the most common brain tumors in children. The expression profiles of 21 JPAs, determined using Affymetrix GeneChip U133A, were compared with subjects with normal cerebella. The genes involved in neurogenesis, cell adhesion, synaptic transmission, central nervous system development, potassium ion transport, protein dephosphorylation, and cell differentiation were found to be significantly deregulated in JPA. These 21 JPAs were further clustered into two major groups by unsupervised hierarchical clustering using a set of 848 genes with high covariance (0.5-10). Supervised analysis with Significance Analysis of Microarrays software between these two potential subgroups identified a list of significant differentially expressed genes involved in cell adhesion, regulation of cell growth, cell motility, nerve ensheathment, and angiogenesis. Immunostaining of myelin basic protein on paraffin sections derived from 18 incompletely resected JPAs suggests that JPA without myelin basic proteinâpositively stained tumor cells may have a higher tendency to progress. Experiment Overall Design: Under an Institutional Review Boardâapproved protocol, brain tumor tissues were obtained, after informed consent, from patients undergoing tumor resection or other tumor-related neurosurgical procedures at the Texas Children's Hospital, Baylor College of Medicine. Samples of normal cerebellar tissue (n = 2) were isolated from surgically removed tissue adjacent to resected tumor tissue. Portions of the tumors were fixed in 10% formaldehyde and embedded in paraffin for sectioning and pathologic reviews, and the residual tissue samples were snap-frozen in liquid nitrogen and stored at â80Â°C for RNA extraction. All samples were obtained at initial diagnosis with no prior exposure to chemotherapy or radiation therapy. Normal fetal brain RNA was obtained from Stratagene (La Jolla, CA) and a normal cerebellum RNA was from Ambion, Inc. (Austin, TX). Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) followed by DNase I treatment and clean-up on aRNeasy spin column (Qiagen, Valencia, CA). RNA quality and purity were assessed by agarose gel electrophoresis and absorbance measurement at A260/A280.