Abstract 3223: Chromatin profiling from formalin-fixed paraffin-embedded samples for biomarker discovery

Abstract As the oncology field moves towards a precision medicine model of patient care, understanding and profiling the epigenetic landscape is increasingly important. Gene expression and cell function are regulated by epigenomic features, including histone post-translational modifications (PTMs), transcription factors, and other chromatin proteins. Mapping the location of these features provides a powerful approach to study chromatin mechanisms driving disease and can be leveraged for biomarker and drug development. Formalin-fixed paraffin-embedded (FFPE) tissues banked from cancer clinical trials could be a rich resource for retrospective biomarker studies, due to their association with drug response and disease progression data. However, using FFPE tissues for genomic mapping assays has been technically challenging for multiple reasons. For instance, the removal of paraffin, heavy cross-linking conditions, and degraded nucleic acids can make FFPE samples unsuitable for standard transcriptomic and epigenomic mapping assays (RNA-seq, ATAC-seq, ChIP-seq). To better leverage chromatin profiling for translational research, we developed a modified CUT Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3223.