Abstract 872: DNA methylation patterns distinguish histologic subtypes of pediatric germ cell tumors

Abstract

Abstract Introduction Pediatric malignant germ cell tumors (GCTs) represent approximately 3% of childhood cancers. GCTs are heterogeneous and grouped together due to the presumed common cell of origin, the primordial germ cell (PGC). Generally, GCTs are grouped into two broad classes based on degree of differentiation: the germinomas, comprised of testicular seminomas and ovarian dysgerminomas, and the nonseminomas, comprised of yolk sac tumors, embryonal carcinomas, choriocarcinomas and teratomas. Aberrant DNA methylation has been implicated in cancer etiology, and may be especially relevant in GCTs due to the extensive epigenetic reprogramming that occurs in the germ line and early embryo during normal development. Methods We evaluated DNA methylation in 52 pediatric GCTs, including 10 yolk sac tumors, 7 dysgerminomas, 28 teratomas, and 8 tumors with mixed tumor histology, obtained from the Cooperative Human Tissue Network (CHTN). DNA methylation was evaluated using the Illumina GoldenGate Cancer Methylation Panel (Illumina, Inc.), which includes 1,505 CpG loci selected from 807 genes with cancer-related potential. Methylation differences in the three main histologic subtypes (yolk sac tumors, dysgerminomas, and teratomas) were evaluated using unsupervised hierarchical clustering with the Manhattan metric and average linkage. We then used a locus by locus approach to identify genes that were differentially methylated by tumor histology using a generalized linear model and accounted for multiple testing by controlling the false-discovery rate (FDR). Ingenuity Pathway Analysis (IPA; Ingenuity Systems) was used to identify pathways that were enriched in this dataset. Results Methylation patterns differed by tumor histology, with all yolk sac tumors forming a distinct cluster. In comparisons of yolk sac tumors with other histologic types, we identified 639 CpG sites with statistically significant differences in methylation (q value < 0.05). Twenty-two CpG loci with the most significant q values also had an adjusted fold change in β > 3, indicating that yolk sac tumors had methylation levels > 3 times higher than tumors of other histologic types at these loci. Three pathways showed significant enrichment in a comparison of yolk sac tumors with other histologic types, with the most significant pathway including genes involved in human embryonic stem cell pluripotency. Conclusion These results support data from a previous study showing that yolk sac tumors exhibit abnormal epigenetic reprogramming (1). Understanding methylation patterns in pediatric GCTs, overall and by histologic type, may identify the developmental stage at which the tumor arose. This knowledge in turn may identify the at-risk period when environmental exposures are most harmful. 1. S. Furukawa et al., Cancer Sci 100, 698 (Apr, 2009). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 872. doi:10.1158/1538-7445.AM2011-872