Epco-07. A Whole Genome Dna Methylation Analysis Revealed Distinct Mechanisms of Development in Diverse Types of Central Nervous System Germ Cell Tumors

Central nervous system germ cell tumors (CNSGCTs) are the most enigmatic brain tumors. They consist of several histologically distinct types of tumors, which are generally sub-grouped into germinomas or non-germinomatous germ cell tumors (NGGCTs). While germinomas are characterized by alterations in the MAPK/PI3K-pathway genes and global hypomethylation, pathogenesis of NGGCTs is largely unknown. To investigate genetic and epigenetic mechanisms of CNSGCT development, 33 CNSGCTs including 7 germinomas and 26 NGGCTs of various histology collected through the Intracranial Germ Cell Tumor Genome Analysis Consortium and Japan Children’s Cancer Group, together with their matched normal DNA, were subjected to a long-read whole genome sequencing using the PromethION system from Oxford Nanopore Technologies. The mean reading depth was 39X for tumor specimen and 31x for blood DNA. The mean N50 value was 9,565 bp. The mean/median number of structural abnormalities was 16.6/16 for germinomas and 27.9/10.5 for NGGCTs, which was not statistically significantly different. A 2 kb deletion involving an exon of USP28 was observed in a single mixed-germ cell tumor case. Deletions involving PRKN were observed in 4 cases. The mean number of ectopic somatic insertions of the LINE-1 element was 1.8 per case. A single mixed GCT had 21 LINE-1 insertions, one of which was located within an intron of NTRK2. The mean of the whole genome DNA methylation level was 38.2% in germinomas and 75.9% in NGGCTs (p=0.0005). Germinomas mostly had biallelic DNA hypomethylation in the imprinted genes, consistent with their presumed primordial germ cell (PGC) origin. On the other hand, NGGCTs showed various levels of methylation in the imprinted genes, suggesting that they may also have originated from PGCs, however at different stages from that of germinomas. Taken together, our whole genome DNA methylation haplotyping provided a new clue to elucidate the pathogenesis of NGGCTs.