Abstract 213: Epigenomic dissection of histology-specific drivers of testicular germ cell tumors

Outcomes of testicular germ cell tumors (TGCT), which are the most common malignancies in adolescents and young adult males, are paradoxical; although highly curable with platinum based chemotherapy, testicular cancer is also the cause of the highest number of years of life lost of any adult malignancy. Major barriers to research aiming to uncover novel therapeutic approaches for chemotherapy-resistant TGCTs include its relatively low incidence, histologic diversity (seminoma vs multiple non-seminoma histologies), and the rarity of tissue biopsies in the metastatic setting. As epigenomic alterations play a key role in germ cell development, and there is a paucity of genomic alterations associated with the initiation and development of therapeutic resistance in TGCT, we hypothesized that epigenomic analysis integrated with transcriptomics in a cohort of pre- and post-treatment TGCTs may reveal novel targetable pathways in TGCT. We collected a cohort of 24 TGCT patients with multiple pre- and post-treatment formalin fixed paraffin embedded (FFPE) tissue, and macrodissected histology-specific tumor foci from surrounding stroma. This tissue was subjected to chromatin-immunoprecipitation (ChIP-seq) of the H3K27Ac enhancer chromatin mark and transcriptional profiling (RNA-seq). Histology-specific cell lines were subjected to the same molecular assays. As an initial analysis, we compared differential enhancer marks (ChIP-seq peaks) and transcripts between specific histologies to identify putative drivers of tumor phenotype and tested the function of these candidate drivers in cell lines. Of 52 histology-specific foci dissected from FFPE slides, we generated matched H3K27Ac and RNA data from 19 samples, H3K27Ac data only from 15 samples including two choriocarcinomas, and RNA only data from 3 samples. Principal component analysis demonstrated that epigenomic and transcriptomic profiles clustered by histology rather than by patient. Superenhancer and motif analysis of enhancer marks suggested various histology-specific transcriptional drivers including POU5F1 and NANOG in EC and SEM, E2F in SEM, AP-1 in TER, the HNF and WNT factors in YST, and GRHL2 in choriocarcinoma. A CRISPR-knockout screen in EC cells in the presence of cisplatin and etoposide indicated that POU5F1 and NANOG promote chemotherapy sensitivity in EC cells. Integrated chromatin and transcriptional analyses suggested multiple potential up- and down-stream effectors of WNT signaling in YST, including multiple extracellular matrix proteins. Collectively, our chromatin, transcriptomic and CRISPR assays in TGCT samples have nominated multiple histology-specific drivers of tumor phenotype. Further analysis of pre- vs post- treatment samples and broader validation of these findings is ongoing. Citation Format: Esmé Wheeler,Alok K. Tewari, Anis A. Hamid, Henry Long, Christopher Sweeney, Myles Brown, Eliezer Van Allen. Epigenomic dissection of histology-specific drivers of testicular germ cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 213.