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Series GSE58538 Query DataSets for GSE58538
Status Public on Feb 26, 2015
Title Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Germ cell tumors (GCT) originate from germ cells at different developmental stages (GCT type I – V) They are thought to inherit their methylation profile from (early embryonic) germ cells which undergo a characteristic epigenetic “reset” during maturation. This study aims to provide insight into the developmental timing and underlying biology of the various subtypes of GCTs and their (embryonic) cells of origin by identifying specific and global methylation differences between GCT subtypes. In total, 91 type I-IV GCTs and four cell lines were profiled using the Illumina HumanMethylation450 BeadChip (450K) platform. The data were pre-processed using a validated pipeline and analyzed using an in-house generated extension of the annotation manifest. Marked methylation differences were identified between GCT subtypes both on the global and local level (i.e. differentially methylated regions, imprinting control regions, promoters, etc). GCT subtypes indeed show major similarities to specific stages of (early) developing embryonic germ cells with regard to their methylation profile. The extended annotation manifest for the Illumina 450K platform and methylation datasets are readily available on GEO (GEO accession: GSE58538, GPL18809), providing an integrated hypothesis generating data source for future research.

File S1. Differentially methylated regions between tumors classes as discussed in Table 1 of the associated publication. All figures. Please investigate using the genomic position as search term.

File S2. Differentially methylated regions between GCT cell lines. DMRforPairs output. Significant results only. Please start from the html file.
Overall design 91 germ cell tumors of various histologies were investigated for their methylation profile. Methylation detection was performed using Illumina’s HumanMethylation450 BeadChip. 14 type I teratomas (TE) were included of which 6 were located sacral (3 male: I.TE.s.m; 3 female: I.TE.s.f), 4 were located in the testis (I.TE.t) and 3 were located in the ovary (I.TE.o). 30 pure embryonal carcinomas (EC) were included as well as 21 mixed non seminomas (mNS). 12 seminomas of the testis (SE) were included as well as 4 dysgerminomas (their couterpart in the ovary). Finally, 4 spermatocytic seminomas (SS) and three dermoid cysts were analyzed. For a detailed overview the histological classification of germ cell tumors please see the publication linked to this data or associated literature [1-3]. Four cell lines were included, al modelling type II GCTs. Cell lines derived from EC include NT2[4-8], NCCIT [5, 9] and 2102EP[4-8]. TCam-2 closely resembles SE [10-12].
1. Oosterhuis, J.W. and L.H. Looijenga, Testicular germ-cell tumours in a broader perspective. Nat Rev Cancer, 2005. 5(3): p. 210-22.
2. Looijenga, L.H., Human testicular (non)seminomatous germ cell tumours: the clinical implications of recent pathobiological insights. J Pathol, 2009. 218(2): p. 146-62.
3. Woodward, P.J., et al., Testicular germ cell tumors, in World Health Organization Classification of Tumours Pathology and Genetics of the Urinary System and Male Genital Organs., J.N. Eble, et al., Editors. 2004, IARC Press: Lyon. p. 17-278.
4. Andrews, P.W., et al., A comparative study of eight cell lines derived from human testicular teratocarcinoma. Int J Cancer, 1980. 26(3): p. 269-80.
5. Andrews, P.W., et al., Comparative analysis of cell surface antigens expressed by cell lines derived from human germ cell tumours. Int J Cancer, 1996. 66(6): p. 806-16.
6. Wang, N., et al., Nonrandom abnormalities in chromosome 1 in human testicular cancers. Cancer Res, 1980. 40(3): p. 796-802.
7. Fogh, J. and G. Trempe, New Human Tumor Cell Lines, in Human Tumor Cells in Vitro, J. Fogh, Editor. 1975, Springer US. p. 115-159.
8. Fogh, J., Cultivation, characterization, and identification of human tumor cells with emphasis on kidney, testis, and bladder tumors. Natl Cancer Inst Monogr, 1978(49): p. 5-9.
9. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.
10. Eckert, D., et al., TCam-2 but not JKT-1 cells resemble seminoma in cell culture. Cell Tissue Res, 2008. 331(2): p. 529-38.
11. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96.
12. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8.
Contributor(s) Rijlaarsdam MA, Gillis AJ, Dorssers LC, Looijenga LH
Citation(s) 26173112, 30739914
Submission date Jun 16, 2014
Last update date Sep 18, 2019
Contact name Martin Anne Rijlaarsdam
Phone 0031645408508
Organization name Erasmus MC
Department Pathology
Lab Laboratory for Experimental Patho-Oncology (LEPO)
Street address Wytemaweg 80
City Rotterdam
ZIP/Postal code 3015 CN
Country Netherlands
Platforms (1)
GPL18809 Illumina HumanMethylation450 BeadChip (v1.2, extended annotation)
Samples (95)
GSM1413056 102133-01_germ cell tumor_EC
GSM1413057 102133-02_germ cell tumor_mNS
GSM1413058 102133-03_germ cell tumor_EC
BioProject PRJNA252902

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 130.3 Mb (ftp)(http) ZIP 220.3 Mb (ftp)(http) ZIP
GSE58538_RAW.tar 160.0 Kb (http)(custom) TAR
GSE58538_S1_S2_supplementaryfiles_README.txt 763 b (ftp)(http) TXT
GSE58538_signals.txt.gz 388.0 Mb (ftp)(http) TXT
GSE58538_supplementary_hidden_markov_model_processed_data.csv.gz 3.1 Mb (ftp)(http) CSV
Processed data included within Sample table
Processed data are available on Series record

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