The first objective of the project is focused on the development of an analytic and computational pipeline for epigenetic cell state monitoring in liquid biopsies. On the analytic side, we have optimized the cfChIP protocol and successfully generated libraries on mouse plasma samples. In a next phase, we will sequence the libraries and perform quality control. On the computational side, we have built a computational pipeline (NextFlow) for in depth benchmarking of different deconvolution tools and strategies. This tool will be used to evaluate deconvolution of DNA methylation for identification of different cell states in blood plasma.
The second objective of the project is directed towards validation of the EpiGuide assay and studying the dynamics of epigenetic tumor cell state switches in mouse models. During the first 2 years of the project, we have mostly focused on the triple negative breast cancer mouse model. To allow identification of cell states using epigenomic analysis of blood cfDNA, we need a comprehensive epigenomic reference atlas of epithelial-mesenchymal plasticity. To this end, we have successfully isolated mice tumors and sorted different cell state populations. We are currently profiling these samples for different epigenetic layers (RNA-seq for transcriptome analysis, cfRRBS for DNA methylation analysis, CUT&TAG for histone modification profiling and ATAC-seq for open chromatic profiling) and will use these data as reference for the analysis of the data generated on blood plasma.
The third part of the project aims to monitor epigenetic plasticity in liquid biopsies from cancer patients using the EpiGuide assay. For this project part, we have set up collaboration at UZGent and internationally to get access to longitudinally collected liquid biopsy samples of triple negative breast cancer and high-risk neuroblastoma patients.
