Scalable and quantitative chromatin profiling from formalin-fixed paraffin-embedded samples

PROJECT SUMMARYThe development of tools to map the location of histone post-translational modifications (PTMs) genome- wide has ushered in a new era of epigenetic research, placing histone PTMs and associated mechanisms in the spotlight as novel biomarkers and therapeutic targets. Despite this progress, leveraging epigenomics for clinical research has been hindered by a lack of high-performance genomic mapping assays that are compatible with formalin-fixed paraffin-embedded (FFPE) tissue, due to DNA damage that is incurred during the FFPE process. Indeed, existing FFPE sample-compatible genomic mapping assays are either low-throughput and insensitive (requiring large sample inputs), or do not resolve specific chromatin features (e.g., promoters, enhancers, etc.). Therefore, next-generation chromatin profiling assays that are able to resolve specific chromatin features using banked FFPE samples are key to unlock access to the massive collection of banked clinical samples and enable novel biomarker discovery / validation for disease-relevant histone PTM targets. To meet this need, EpiCypher is developing CUTANA-FFPETM, a first-in-class low input genomic mapping solution for the study of FFPE clinical samples. This technology is inspired by EpiCypher’s commercial CUTANA® CUTandTag (Cleavage Under Targets and Tagmentation) assays, and leverages an innovative in vitro transcription-based workflow to mitigate the limitations imposed by FFPE sample processing-induced DNA damage. The goal of this Phase I study is to demonstrate the ability of CUTANA-FFPE assays to reliably map histone PTMs in FFPE tissue samples. In Aim 1, we will develop the CUTANA-FFPE workflow to map histone PTMs in fixed cultured cells. Then, in Aim 2, we will employ CUTANA-FFPE assays in clinical FFPE tissue samples and benchmark our results with genomic maps derived from donor-matched fresh frozen tissue. This study will demonstrate feasibility for CUTANA-FFPE to become a powerful new tool to perform high-value epigenomic research in previously inaccessible banked clinical samples. This technology will be of broad interest to basic researchers and drug developers, unlocking the full potential of epigenomics for clinical applications. In Phase II, we will develop robust CUTANA-FFPE kits and automated assay protocols that are optimized for FFPE tissue using ultra-low sample inputs, which will be key for commercializing CUTANA-FFPE to enable epigenomic studies of FFPE clinical samples.