The Cell-Free DNA Methylome Captures Distinctions Between Localized and Metastatic Prostate Tumors

Metastatic lesions of prostate cancer are highly heterogeneous, difficult to biopsy, and usually lethal. Liquid biopsy can provide a more holistic view of the disseminated disease by analyzing cells and biomolecules released into circulation by the tumors. With a technology called cell-free methylated DNA immunoprecipitation coupled with next-generation sequencing (cfMeDIP-seq), we enrich and sequence the methylated DNA in patient plasma using an anti-5-methylcytosine (5mC) antibody. This approach allows us to perform genome-wide analysis of the methylated sites.

This genome-wide methylome analysis strategy showed many advantages. It is not limited to pre-selected regions and captures changes beyond the tumor. Only 3.45% of the informative regions show strong correlation with tumor burden as measured by ctDNA percentage. Regions associated with tumor burden are distributed differently across the genome than uncorrelated ones, which are depleted from CpG islands and promoters and likely underrepresented by pre-selected panel analysis. Additionally, with this data we can infer copy number alterations and fragment length of the template circulating DNA, providing an opportunity for multi-modality analysis. In general, a progressive shortening of fragment length was observed from healthy control to localized metastatic diseases, coupled with an increase of variation in fragmentation profiles.

By analyzing the genome-wide methylome of patients with metastatic castration resistant prostate cancer (mCRPC) from three independent cohorts, we captured common characteristics and created a classifier that can distinguish them from localized disease with high accuracy. Such distinction is applicable for mCRPC patients with very low to not detectable blood tumor burden, providing implications for clinical application such as the early detection of oligometastasis. Oligometastatic prostate cancer is a state characterized by a lower number (usually less than 5) of metastatic sites and represents a transition from localized to widespread metastasis, for which early diagnosis is likely to provide a therapeutic window.

Together, in this study we provide a comprehensive cell-free methylation landscape for patients with localized and mCRPC disease, capture changes beyond the coding region and the tumor itself, identify common features that can distinguish different disease status with high accuracy and consistency, and present a rich resource for the community.

Written by: Sujun Chen^1,2,3 and Housheng Hansen He^1,2

Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
West China School of Public Health, West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University

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