Aberrant hypermethylation of the major breakpoint cluster region in 17p11.2 in medulloblastomas but not supratentorial PNETs

Deletions of 17p have been consistently reported in up to 50% of medulloblastomas (MBs), and the major breakpoint interval has been localized to chromosome segment 17p11.2. Based on several reports linking aberrant DNA methylation and chromosomal disruption, we examined the methylation pattern in this region by employing restriction landmark genomic scanning (RLGS). Several CpG islands located in the major breakpoint cluster region were identified using a bacterial artificial chromosome (BAC) contig of the breakpoint region. A long-range methylation map was established for 20 MBs and 5 supratentorial primitive neuroectodermal tumors (stPNETs). Selected CpG islands were examined using Southern and bisulfite sequencing analysis. Aberrantly hypermethylated CpG islands in 17p11. 2 were found in 33% of MBs. Interestingly, one CpG island was methylated in MBs, but not in any of the examined stPNETs. A BAC clone covering three of the methylated CpG islands was partially sequenced in the search for a potential tumor suppressor gene. None of the expressed sequence tag sequences and full-length mouse/human cDNAs that were associated with aberrant methylation showed a change in expression levels due to methylation. The potential link between chromosomal instability in 17p11.2 and hypermethylation in this region is discussed.

Gene amplification in PNETs/medulloblastomas: mapping of a novel amplified gene within the MYCN amplicon

OBJECTIVES

The pathological entity of primitive neuroectodermal tumour/medulloblastoma (PNET/MB) comprises a very heterogeneous group of neoplasms on a clinical as well as on a molecular level. We evaluated the importance of DNA amplification in medulloblastomas and other primitive neuroectodermal tumours (PNETs) of the CNS.

METHOD

Restriction landmark genomic scanning (RLGS), a method that allows the detection of low level amplification, was used. RLGS provides direct access to DNA sequences circumventing positional cloning efforts. Furthermore, we analysed several samples by CGH.

DESIGN

Twenty primary medulloblastomas, five supratentorial PNETs, and five medulloblastoma cell lines were studied.

RESULTS

Although our analysis confirms that gene amplification is generally a rare event in childhood PNET/MB, we found a total of 17 DNA fragments that were amplified in seven different tumours. Cloning and sequencing of several of these fragments confirmed the previous finding of MYC amplification in the cell line D341 Med and identified novel DNA sequences amplified in PNET/MB. We describe for the first time amplification of the novel gene, NAG, in a subset of PNET/MB. Despite genomic amplification, NAG was not overexpressed in the tumours studied. We have determined that NAG maps less than 50 kb 5' of DDX1 and approximately 400 kb telomeric of MYCN on chromosome 2p24.

CONCLUSION

We found a similar but slightly higher frequency of amplification than previously reported. We present several DNA fragments that may belong to the CpG islands of novel genes amplified in a small subset of PNET/MB. As an example we describe for the first time the amplification of NAG in the MYCN amplicon in PNET/MB.

Aberrant CpG-island methylation has non-random and tumour-type-specific patterns

CpG islands frequently contain gene promoters or exons and are usually unmethylated in normal cells. Methylation of CpG islands is associated with delayed replication, condensed chromatin and inhibition of transcription initiation. The investigation of aberrant CpG-island methylation in human cancer has primarily taken a candidate gene approach, and has focused on less than 15 of the estimated 45,000 CpG islands in the genome. Here we report a global analysis of the methylation status of 1,184 unselected CpG islands in each of 98 primary human tumours using restriction landmark genomic scanning (RLGS). We estimate that an average of 600 CpG islands (range of 0 to 4,500) of the 45,000 in the genome were aberrantly methylated in the tumours, including early stage tumours. We identified patterns of CpG-island methylation that were shared within each tumour type, together with patterns and targets that displayed distinct tumour-type specificity. The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. Thus, the methylation of particular subsets of CpG islands may have consequences for specific tumour types.

Evaluation of microcytosis in 18 Shibas

OBJECTIVE

To determine whether microcytosis is a typical finding in Shibas.

DESIGN

Prospective study.

ANIMALS

18 Shibas.

PROCEDURE

Blood and serum samples were obtained for automated hematologic analyses (18 dogs) and for determination of ferritin concentration, using ELISA (14 dogs). Blood samples from 30 clinically normal dogs of various other breeds was analyzed to establish a reference range for ferritin concentration.

RESULTS

Erythrocyte mean corpuscular volume in Shibas ranged from 55.6 to 69.1 fl (mean+/-SD, 61.2+/-4.3 fl; median, 60.6 fl; reference range, 63 to 73 fl). Microcytosis was identified in 12 of 18 dogs. Males and females were affected equally. Mean corpuscular hemoglobin concentration was slightly low (range, 32.0 to 33.9%; reference range, 34 to 38%) in 6 dogs, 4 of which had microcytic RBC. Serum ferritin concentrations ranged from 61.2 to 277.0 ng/ml (mean+/-SD, 110.6+/-51.4 ng/ml; median, 106 ng/ml). Reference range for serum ferritin concentration was 50.7 to 440.0 ng/ml (mean+/-SD, 121.2+/-67.1 ng/ml; median, 111.5 ng/ml). Thrombocytopenia (range, 110,000 to 196,000 platelets; reference range, 200,000 to 450,000 platelets) was found in 7 dogs, 6 of which also had microcytic RBC.

CLINICAL IMPLICATIONS

Microcytosis can be a typical finding in Shibas. Common origin of Shibas and Akitas, a breed predisposed to microcytosis, suggests a hereditary basis for this finding.