Seminoma and Embryonal Carcinoma Footprints Identified by Analysis of Integrated Genome-Wide Epigenetic and Expression Profiles of Germ Cell Cancer Cell Lines

Abstract

BackgroundOriginating from Primordial Germ Cells/gonocytes and developing via a precursor lesion called Carcinoma In Situ (CIS), Germ Cell Cancers (GCC) are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS). During physiological germ cell formation/maturation, epigenetic processes guard homeostasis by regulating the accessibility of the DNA to facilitate transcription. Epigenetic deregulation through genetic and environmental parameters (i.e. genvironment) could disrupt embryonic germ cell development, resulting in delayed or blocked maturation. This potentially facilitates the formation of CIS and progression to invasive GCC. Therefore, determining the epigenetic and functional genomic landscape in GCC cell lines could provide insight into the pathophysiology and etiology of GCC and provide guidance for targeted functional experiments.ResultsThis study aims at identifying epigenetic footprints in 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 the pathophysiology and etiology of GCC. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data were acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP-sequencing (activating histone modifications (H3K4me3, H3K27ac)). Results indicate known germ cell markers not only to be differentiating between SE and NS at the expression level, but also in the epigenetic landscape.ConclusionThe overall similarity between TCam-2/NCCIT support an erased embryonic germ cell arrested in early gonadal development as common cell of origin although the exact developmental stage from which the tumor cells are derived might differ. Indeed, subtle difference in the (integrated) epigenetic and expression profiles indicate TCam-2 to exhibit a more germ cell-like profile, whereas NCCIT shows a more pluripotent phenotype. The results provide insight into the functional genome in GCC cell lines.

An oncofetal and developmental perspective on testicular germ cell cancer

“…In a recent investigation of whole genome methylation profiling, we confirmed these global findings and relate TGCC to PGCs and early gonocytes based on methylation of specific functional regions (e.g. imprinting control regions) (Rijlaarsdam et al, 2014, submitted for publication) (Fig. 1).…”

“…Chromosomal constitution, as well as cell cycle control and DNA repair have also been shown to work analogous to pre-meiotic germ cells in TGCC (the latter two are reviewed below and in [73,74]). With regard to their epigenetic status there are strong similarities between TGCC and PGCs [57,[92][93][94][95]. Specifically, SE mirror the methylation profile of their hypomethylated progenitor CIS [96], which in turn reflects the generally hypomethylated state of PGCs [49,51].…”

Epigenetic treatment combinations to effectively target cisplatin‐resistant germ cell tumors: past, present, and future considerations

“…Methylation of cytosine residues is mediated by three different DNA methyl transferase, of which DNA methyltransferase 1 (DNMT1) maintains methylation patterns during mitosis and DNMT3A and DNMT3B promote de novo methylation (Jones & Liang, 2009). Different DNA methylation patterns are found in the different GCT subtypes reflecting distinct developmental switches and clearly distinguish seminomas from non-seminomas (van der Zwan et al, 2014). The PGC-like seminomas and the GCT precursor GCNIS commonly harbor a hypomethylated genome, whereas embryonal carcinomas, choriocarcinomas, and yolk-sac tumors, representing a pluripotent and undifferentiated phenotype (embryonal carcinoma) or extra-embryonic (yolk-sac tumors, choriocarcinomas) differentiation phenotype contain moderate DNA methylation levels, and finally, the mature teratomas, representing tissues of all three germ layers, display a heavily methylated genome ( Fig.…”

N6‐Methyladenosine detected in RNA of testicular germ cell tumors is controlled by METTL3, ALKBH5, YTHDC1/F1/F2, and HNRNPC as writers, erasers, and readers

“…GCNIS is the result of a defective (primordial) germ cell development (Oosterhuis & Looijenga, ; Sonne et al ., ; Almstrup et al ., ). Seminomas are highly similar to GCNIS in terms of DNA methylation levels, gene expression, and histology, while the stem cell population of the non‐seminomas, the embryonal carcinoma (EC) is often described as a malignant counterpart of embryonic stem cells (Almstrup et al ., ; Oosterhuis & Looijenga, ; Biermann et al ., ; Wermann et al ., ; Kristensen et al ., ; Van Der Zwan et al ., , ). Thus, ECs show the characteristics of pluri‐ to totipotency and are able to differentiate into cells of all germ layers (teratoma) and extra‐embryonic tissues (choriocarcinoma, yolk‐sac tumor; Oosterhuis & Looijenga, ).…”