Tracking epigenetic plasticity in circulating tumor-derived DNA to monitor drug resistance and guide personalized treatment in cancer patients

Project Information

EpiGuide

Grant agreement ID: 101044243

DOI

10.3030/101044243

EC signature date 19 April 2022

Start date 1 September 2022

End date 31 August 2027

Funded under

• European Research Council (ERC)

Total cost

€ 1 998 625,00

EU contribution

€ 1 998 625,00

Coordinated by

VIB VZW
Belgium

Periodic Reporting for period 1 - EpiGuide (Tracking epigenetic plasticity in circulating tumor-derived DNA to monitor drug resistance and guide personalized treatment in cancer patients)

Reporting period: 2022-09-01 to 2025-02-28

Summary of the context and overall objectives of the project

Personalized therapy has revolutionized cancer care during the past decades, but still suffers from frequent drug resistance and relapse. A better understanding of drug resistance mechanisms and their timely tracking and prevention represent areas of urgent clinical unmet need. While novel or clonally selected genetic lesions including DNA mutations and copy number changes are well known causes of therapy failure, emerging evidence supports a role for non-genetic/epigenetic heterogeneity and plasticity in the selective process to escape the pressure of therapy. In addition to unravelling the mechanisms controlling this epigenetic plasticity to identify new therapeutic strategies, there is a growing need for novel tools to detect and monitor epigenetic heterogeneity and plasticity that currently do not exist. EpiGuide aims to establish a blood-based monitoring tool to trace epigenetic mechanisms driving drug resistance development during treatment. We will develop and optimize the EpiGuide assay, an analytic and computational pipeline that measures and monitors methylation and histone modifications of circulating cell-free DNA that tumor cells shed into the blood plasma. In a next step, the efficacy of the EpiGuide assay to detect epigenetic tumor cell state changes will be validated in mouse models and patient samples. The EpiGuide assay will also explore temporal and spatial dynamics of epigenetic switches related to drug resistance and look for associations with clinical outcome. The EpiGuide project focuses on two tumor entities for which epigenetic switches leading to chemotherapy resistance have been described (epithelial-mesenchymal plasticity in triple-negative breast cancer and adrenergic-mesenchymal switch in high-risk neuroblastoma). The long-term goal is to bring the EpiGuide assay into clinical practice for monitoring in clinical trials and personalized cancer care. Major impact of EpiGuide is expected for guiding patient-tailored and disease state-adapted therapies, with a specific benefit of earlier detection of evolving non-genetic tumor cell states leading to drug resistance.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

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.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

At this point, we cannot report on finalized results beyond the state of the arts. However, in relatively short term, we expect (1) to generate a comprehensive and unique epigenomic EMP cell atlas for triple negative breast cancer and (2) to finalize an in-depth benchmarking for cfDNA methylation deconvolution, where different deconvolution tools, sequencing depths, differential methylated region identification algorithms, reference datasets, amongst others are evaluated.