Epigenomic analysis of cell-free nucleosomes for cancer research

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PROJECT SUMMARY Cell-free DNA (cfDNA) levels are elevated in the blood of individuals with cancer, leading to increased interest in liquid biopsy (LB)-based assays for disease diagnostics and monitoring. Despite this, current cfDNA assays are challenged by limited sensitivity and specificity to differentiate between cell types and disease states. cfDNA is primarily found as cell-free nucleosomes (cfNucs), which consist of histone octamers wrapped in DNA. Nuc features, such as the presence and genomic localization of histone post-translational modifications (PTMs), play important roles in gene regulation and are highly associated with tissue type and disease state. As such, the epigenomic analysis of cfNucs has the potential to deliver a transformative method of research that can provide the specificity required to diagnose and differentiate between diseases that is lacking from current assays. To meet this need, EpiCypher is developing cfNuc-seq, the first commercial platform for the epigenomic analysis of histone PTMs on cfNucs. Previous attempts to develop approaches for analysis of histone PTMs on cfNucs exhibited low sensitivity and were not truly quantitative. The innovation of this proposal is the application of ultra-affinity detection reagents to develop a novel, highly sensitive immunoprecipitation-based workflow to quantitative compare cfNucs across disease states. Our approach will leverage EpiCypher’s novel recombinant DNA-barcoded designer nucleosome spike-in controls to enable normalization and quantitative cross-sample comparison, which is essential due to the low and variable abundance of cfNucs across patients and disease states. The goal of this Phase I study is to perform foundational work towards developing and commercializing the cfNuc-seq platform. Towards this goal, we will first develop optimized assays to profile distinct chromatin compartments (Aim 1). We will then demonstrate the ability of our assay to detect distinct cancer cell signatures in clinical samples (Aim 2), demonstrating strong proof-of-concept for our approach. In subsequent Phase II studies, we will expand target validation and develop and launch high-throughput cfNuc-seq assays and services to enable exciting new biomarker and diagnostics research.