Abstract 3494: Epigenetic landscape and gene regulation in embryonal brain tumors with multilayered rosettes

Abstract Embryonal tumors with multilayered rosettes (ETMRs) are relatively rare but highly aggressive pediatric brain tumors that mainly affect children under four years of age and are generally associated with poor clinical outcomes. Around 90% of ETMRs harbor amplification of the chromosome 19 miRNA cluster (C19MC), in most cases fused to the TTHY1 gene. The second most recurrent aberration, present in about half of the C19MC-negative cases, are bi-allelic mutations in DICER1. C19MC amplification and positive LIN28A immunostaining are key diagnostic markers for ETMRs. ETMRs also exhibited a distinct DNA methylation profile compared with other embryonal brain tumors such as medulloblastomas (MBs) and atypical teratoid/rhabdoid tumors (ATRTs). However, the detailed epigenetic landscape defined by DNA methylation and histone modifications, its effects on transcriptional regulation in ETMRs, and how these associations differ from MBs, ATRTs, and normal brain tissues remain largely unexplored. To decode the ETMR epigenome, we generated, collected, and integrated whole genome bisulfite sequencing (WGBS), chromatin immunoprecipitation sequencing (ChIP-seq) of various histone marks and epigenetic regulators, RNA sequencing (RNA-seq), and ribosome profiling (Ribo-seq) data from a series of ETMRs, similar data from a series of MBs and ATRTs covering all molecular subtypes, and normal brain tissues for comparison reasons. Through integrative multi-omics analyses, we delineated chromatin states and DNA methylation-defined genomic segments of ETMRs for the first time. ETMR genomes are globally hypomethylated, with wider distributions of unmethylated regions (UMRs) and DNA methylation valleys (DMVs) on its genome compared with MBs, ATRTs, and normal brain tissues. These regions are associated with genes involved in embryonal brain development, essential cellular processes, and oncogenic pathways. Low methylated regions (LMRs) are enriched for transcription factor binding motifs such as CTCF and SOX2, and also act as potential enhancers that modulate several transcriptional and epigenetic regulators. Partially methylated domains are correlated with transcriptional repression in ETMRs, consistent with observations in other biological systems. Moreover, TET enzymes are highly expressed in ETMRs, potentially regulated by BET family proteins such as BRD4. Pharmacological inhibition of TETs and BRDs reduced ETMR cell viability. In summary, our study provides a comprehensive epigenetic landscape of ETMR and its relationship to transcriptional regulation, revealing distinct regulatory mechanisms that enhance understanding of ETMR biology, and identifying potential therapeutic targets for experimental and preclinical validations in this lethal tumor type. Citation Format: Shanzheng Wang, Sander Lambo, Monika Mauermann, Phylicia Stathi, Robert Autry, Natalie Jäger, Stefan M. Pfister, Marcel Kool. Epigenetic landscape and gene regulation in embryonal brain tumors with multilayered rosettes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3494.