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Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma [Illumina]

ABSTRACT: The pathogenesis of intracranial germ cell tumors (iGCTs) is not yet fully uncovered despite exhaustive genomic analyses. By means of a genome-wide methylation analysis, we show that pure germinoma is characterized by global DNA low methylation, a unique epigenetic feature distinct from all other subtypes of iGCTs. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, indicating the cells of origin. Unlike PGC, however, hypomethylation extends to LINE1 retrotransposon. Microdissected histologically and epigenetically distinct components of mixed-GCTs shared identical mutations in the MAPK or PI3K pathways, suggesting that the genetic alterations were likely to have occurred at the pre-implantation phase in early embryogenesis. Thus, we propose iGCTs are “Zygotoma”.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70783 | GEO | 2016/04/01

SECONDARY ACCESSION(S): PRJNA289532

REPOSITORIES: GEO

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Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma [Agilent]

Project description:The pathogenesis of intracranial germ cell tumors (iGCTs) is not yet fully uncovered despite exhaustive genomic analyses. By means of a genome-wide methylation analysis, we show that pure germinoma is characterized by global DNA low methylation, a unique epigenetic feature distinct from all other subtypes of iGCTs. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, indicating the cells of origin. Unlike PGC, however, hypomethylation extends to LINE1 retrotransposon. Microdissected histologically and epigenetically distinct components of mixed-GCTs shared identical mutations in the MAPK or PI3K pathways, suggesting that the genetic alterations were likely to have occurred at the pre-implantation phase in early embryogenesis. Thus, we propose iGCTs are âZygotomaâ. Genomic DNA from the 81 GCTs were hybridized to the SurePrint G3 Human CGH 8 Ã 60 K Oligo Microarrays G4450A (Agilent Technologies, Santa Clara, CA).

2016-04-01 | E-GEOD-70782 | biostudies-arrayexpress

Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma [Agilent]

2016-04-01 | GSE70782 | GEO

Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma [Illumina]

Project description:The pathogenesis of intracranial germ cell tumors (iGCTs) is not yet fully uncovered despite exhaustive genomic analyses. By means of a genome-wide methylation analysis, we show that pure germinoma is characterized by global DNA low methylation, a unique epigenetic feature distinct from all other subtypes of iGCTs. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, indicating the cells of origin. Unlike PGC, however, hypomethylation extends to LINE1 retrotransposon. Microdissected histologically and epigenetically distinct components of mixed-GCTs shared identical mutations in the MAPK or PI3K pathways, suggesting that the genetic alterations were likely to have occurred at the pre-implantation phase in early embryogenesis. Thus, we propose iGCTs are âZygotomaâ. Bisulphite converted DNA from 77 samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip

2016-04-01 | E-GEOD-70783 | biostudies-arrayexpress

microRNA expression data from pediatric primary intracranial germ cell tumor

Project description:Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented the first miRNA profile of pediatric primary intracranial GCTs. 12 central nervous system GCT cases with different histological subtypes are subjected to miRNA expression analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma , immature teratoma , mixed GCTs of NGMGCTs category, yolk sac tumor, immature teratoma, and embryonal carcinoma.

2010-05-14 | E-GEOD-19347 | biostudies-arrayexpress

expression data from pediatric primary intracranial germ cell tumor

Project description:Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented a distinct mRNA profile correlating with GCT histological differentiation and prognosis. 13 central nervous system GCT cases with different histological subtypes are subjected to transcriptome analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma , immature teratoma , mixed GCTs of NGMGCTs category, yolk sac tumor, immature teratoma, and embryonal carcinoma.

2010-03-09 | E-GEOD-19348 | biostudies-arrayexpress

microRNA expression data from pediatric primary intracranial germ cell tumor

2010-02-26 | GSE19347 | GEO

expression data from pediatric primary intracranial germ cell tumor

2010-02-26 | GSE19348 | GEO

Genotyping and analysis of chromosome copy number variation (CNV) from pediatric primary intracranial germ cell tumor

Project description:Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented CNVs correlating with GCTs malignancy and clinical risk. 16 central nervous system GCT cases with different histological subtypes are subjected to genotyping and CNVs analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma, immature teratoma, mixed GCTs of NGMGCTs category, yolk sac tumor, immature teratoma, and embryonal carcinoma.

2010-06-24 | E-GEOD-19349 | biostudies-arrayexpress

Genotyping and analysis of chromosome copy number variation (CNV) from pediatric primary intracranial germ cell tumor

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Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma

Project description:Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma

| PRJNA289527 | ENA