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

Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N - Br. J. Cancer (2009)

Bottom Line: 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).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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pediatrics and Human Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal H3Z 2Z3, Canada. nada.jabado@mcgill.ca

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.

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Duplication of 7q34 visualised using BeadStudio. (A) Chromosome-wide data showing duplication at 7q34 through the increase in the log R ratio values (top) and split in the B allele frequencies (bottom) plotted for each SNP for one JPA sample (Patient 10; Table 1). (B) Zoom-in showing genes included within the region of interest. (C) Detailed view of the 7q34 locus amplified in each of the 20 JPA samples. Genes within and outside the region of interest are shown on the left. Genes we further used to validate duplication within this dataset and an additional dataset of 35 tumours are bolded.
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fig1: Duplication of 7q34 visualised using BeadStudio. (A) Chromosome-wide data showing duplication at 7q34 through the increase in the log R ratio values (top) and split in the B allele frequencies (bottom) plotted for each SNP for one JPA sample (Patient 10; Table 1). (B) Zoom-in showing genes included within the region of interest. (C) Detailed view of the 7q34 locus amplified in each of the 20 JPA samples. Genes within and outside the region of interest are shown on the left. Genes we further used to validate duplication within this dataset and an additional dataset of 35 tumours are bolded.

Mentions: To chart genomic alterations in our sample set, we first performed a high-resolution genome-wide screen of the samples using the SNP arrays. The copy number variant (CNV) analysis of the resulting dataset generated on the Human Hap300-Duo and 610-Qad arrays gave similar results for both platforms. All samples had at least one CNV and the overall frequency of CNVs according to the chromosomal position showed that most tumours had only focal abnormalities, some of them previously reported. Most LGA did not have chromosome-wide gains or deletions, with the exception of two JPA samples, which had gains of the whole chromosome 7 (Supplementary Table 2). Regions with loss-of-heterozygosity were rarely found in LGA. We found a single region showing recurrent gain of 7q34 in 20 of 40 (50%) samples (minimal common region of gain for all tumours on chromosome 7:138380901–140119915, NCBI Build 36.3; Figure 1). The gain specifically corresponds to a chromosomal duplication, according to the Illumina Plots. A total copy number of 3 was inferred based of the logR ratio plot that is characterised by an upward deflection from 0 to 0.35 and by a split in the heterozygous allele frequencies (B-allele frequency measure) into two populations, one located at 0.67 (2 : 1 ratio) and the other at 0.33 (1 : 2 ratio; Figure 1). This gain in 7q34 is a somatic event as it was present in the tumour and not in DNA from peripheral blood taken from the same patients (n=7), thus excluding a germ-line segmental duplication (data not shown). It was not found in a set of 1363 control DNA analysed with the Illumina Human-Hap 300K platform (Hakonarson et al, 2007) or in the 25 HGA included in this study.


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

Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N - Br. J. Cancer (2009)

Duplication of 7q34 visualised using BeadStudio. (A) Chromosome-wide data showing duplication at 7q34 through the increase in the log R ratio values (top) and split in the B allele frequencies (bottom) plotted for each SNP for one JPA sample (Patient 10; Table 1). (B) Zoom-in showing genes included within the region of interest. (C) Detailed view of the 7q34 locus amplified in each of the 20 JPA samples. Genes within and outside the region of interest are shown on the left. Genes we further used to validate duplication within this dataset and an additional dataset of 35 tumours are bolded.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2736806&req=5

fig1: Duplication of 7q34 visualised using BeadStudio. (A) Chromosome-wide data showing duplication at 7q34 through the increase in the log R ratio values (top) and split in the B allele frequencies (bottom) plotted for each SNP for one JPA sample (Patient 10; Table 1). (B) Zoom-in showing genes included within the region of interest. (C) Detailed view of the 7q34 locus amplified in each of the 20 JPA samples. Genes within and outside the region of interest are shown on the left. Genes we further used to validate duplication within this dataset and an additional dataset of 35 tumours are bolded.
Mentions: To chart genomic alterations in our sample set, we first performed a high-resolution genome-wide screen of the samples using the SNP arrays. The copy number variant (CNV) analysis of the resulting dataset generated on the Human Hap300-Duo and 610-Qad arrays gave similar results for both platforms. All samples had at least one CNV and the overall frequency of CNVs according to the chromosomal position showed that most tumours had only focal abnormalities, some of them previously reported. Most LGA did not have chromosome-wide gains or deletions, with the exception of two JPA samples, which had gains of the whole chromosome 7 (Supplementary Table 2). Regions with loss-of-heterozygosity were rarely found in LGA. We found a single region showing recurrent gain of 7q34 in 20 of 40 (50%) samples (minimal common region of gain for all tumours on chromosome 7:138380901–140119915, NCBI Build 36.3; Figure 1). The gain specifically corresponds to a chromosomal duplication, according to the Illumina Plots. A total copy number of 3 was inferred based of the logR ratio plot that is characterised by an upward deflection from 0 to 0.35 and by a split in the heterozygous allele frequencies (B-allele frequency measure) into two populations, one located at 0.67 (2 : 1 ratio) and the other at 0.33 (1 : 2 ratio; Figure 1). This gain in 7q34 is a somatic event as it was present in the tumour and not in DNA from peripheral blood taken from the same patients (n=7), thus excluding a germ-line segmental duplication (data not shown). It was not found in a set of 1363 control DNA analysed with the Illumina Human-Hap 300K platform (Hakonarson et al, 2007) or in the 25 HGA included in this study.

Bottom Line: 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).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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pediatrics and Human Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal H3Z 2Z3, Canada. nada.jabado@mcgill.ca

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.

Show MeSH
Related in: MedlinePlus