Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer

Clare Stirzaker,Melissa Papargiris,Ruth Pidsley,Andrew Ryan,Michelle Richards,Mitchell G. Lawrence,Linda Teng,Susan J. Clark,Renea A. Taylor,Birunthi Niranjan,Sam Norden,Gail P. Risbridger,Brooke A. Pereira,Mark Frydenberg

doi:10.1186/s13148-020-00836-2

Abstract

BackgroundProstate cancer changes the phenotype of cells within the stromal microenvironment, including fibroblasts, which in turn promote tumour progression. Functional changes in prostate cancer-associated fibroblasts (CAFs) coincide with alterations in DNA methylation levels at loci-specific regulatory regions. Yet, it is not clear how these methylation changes compare across CAFs from different patients. Therefore, we examined the consistency and prognostic significance of genome-wide DNA methylation profiles between CAFs from patients with different grades of primary prostate cancer.ResultsWe used Infinium MethylationEPIC BeadChips to evaluate genome-wide DNA methylation profiles from 18 matched CAFs and non-malignant prostate tissue fibroblasts (NPFs) from men with moderate to high grade prostate cancer, as well as five unmatched benign prostate tissue fibroblasts (BPFs) from men with benign prostatic hyperplasia. We identified two sets of differentially methylated regions (DMRs) in patient CAFs. One set of DMRs reproducibly differed between CAFs and fibroblasts from non-malignant tissue (NPFs and BPFs). Indeed, more than 1200 DMRs consistently changed in CAFs from every patient, regardless of tumour grade. The second set of DMRs varied between CAFs according to the severity of the tumour. Notably, hypomethylation of the EDARADD promoter occurred specifically in CAFs from high-grade tumours and correlated with increased transcript abundance and increased EDARADD staining in patient tissue. Across multiple cohorts, tumours with low EDARADD DNA methylation and high EDARADD mRNA expression were consistently associated with adverse clinical features and shorter recurrence free survival.ConclusionsWe identified a large set of DMRs that are commonly shared across CAFs regardless of tumour grade and outcome, demonstrating highly consistent epigenome changes in the prostate tumour microenvironment. Additionally, we found that CAFs from aggressive prostate cancers have discrete methylation differences compared to CAFs from moderate risk prostate cancer. Together, our data demonstrates that the methylome of the tumour microenvironment reflects both the presence and the severity of the prostate cancer and, therefore, may provide diagnostic and prognostic potential.

Highlights

Prostate cancer changes the phenotype of cells within the stromal microenvironment, including fibroblasts, which in turn promote tumour progression
We identified a large set of Differentially methylated region (DMR) that are commonly shared across Cancer-associated fibroblast (CAF) regardless of tumour grade and outcome, demonstrating highly consistent epigenome changes in the prostate tumour microenvironment
Non-malignant prostate tissue fibroblast (NPF) and Benign prostate tissue fibroblast (BPF) have negligible differences in DNA methylation Based on the multidimensional scaling (MDS) plot and EPIC CAF-DMRs (Fig. 1b, d), we found that NPFs are more similar to unmatched BPFs than they are to their patient-matched CAFs

Summary

Introduction

Prostate cancer changes the phenotype of cells within the stromal microenvironment, including fibroblasts, which in turn promote tumour progression. Functional changes in prostate cancer-associated fibroblasts (CAFs) coincide with alterations in DNA methylation levels at loci-specific regulatory regions. Tumour formation changes the composition and phenotype of surrounding tissue This creates the complex tumour microenvironment where different cell types, including cancer-associated fibroblasts (CAFs), interact with cancer epithelial cells [1]. The phenotype of CAFs is enduring and does not rely on continuous interactions with epithelial cancer cells This is demonstrated by primary cultures of patient-derived CAFs, which retain distinctive transcriptomic and proteomic profiles and ability to promote tumour progression, even when cultured without tumour epithelium [8, 10, 22, 23]. Other studies have identified differential methylation of candidate genes and an altered repertoire of transcription factor binding sites in CAFs [6, 26, 27]

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