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| Status |
Public on Jun 01, 2014 |
| Title |
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines (methylation data). |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Background: Germ Cell Cancers (GCC), originating from Primordial Germ Cells /gonocytes, are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS, stem cell component: embryonal carcinoma (EC)). Somatic mutations are rarely found in GCC. It has been proposed that disruption of the epigenetic constitution, either primarily or secondary (e.g. environmental influences), is involved in cancer, and specifically in GCC.
Results: This study aims at identifying epigenetic footprints of SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in GCC and related disruption of germ cell maturation. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data was acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP sequencing (activating histone modifications (H3K4me3, H3K27ac)). The data show that known germ cell markers are not only present and differentiating between SE and NS at the expression level, but also in the epigenetic landscape.
Conclusion: The overall similarity between TCam-2 / NCCIT supports an erased embryonic gem cell arrested in early gonadal development as common origin. Subtle difference in the (integrated) epigenetic and expression profiles indicated TCam-2 to exhibit a more germ cell like profile (enrichment Androgen regulation) while NCCIT proved more pluripotent. The results provide insight into an integrated analysis of the functional genome in GCC cell lines.
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| Overall design |
Two wildtype germ cell cancer (type II germ cell tumor) cell lines were analyzed. TCam-2 (representative for the seminomatous subtype of germ cell cancer) , [1, 2]) and NCCIT (representative of the non-seminomatous (embryonal carcinoma) subtype of germ cell cancer, [3]). 1. 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. 2. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96. 3. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.
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| Contributor(s) |
van der Zwan YG, Rijlaarsdam MA, Gillis AJ, Dorssers LC, Looijenga LH |
| Citation(s) |
24887064 |
| Submission date |
Mar 31, 2014 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Martin Anne Rijlaarsdam |
| E-mail(s) |
m.a.rijlaarsdam@gmail.com
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| Phone |
0031645408508
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| Organization name |
Erasmus MC
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| Department |
Pathology
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| Lab |
Laboratory for Experimental Patho-Oncology (LEPO)
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| Street address |
Wytemaweg 80
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| City |
Rotterdam |
| ZIP/Postal code |
3015 CN |
| Country |
Netherlands |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE56454 |
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines |
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| Relations |
| BioProject |
PRJNA243358 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56382_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| GSE56382_raw_signal.intensities.txt.gz |
9.7 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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