Gene-body DNA methylation of ONECUT2 predicts its expression and prostate cancer aggressiveness in needle biopsies

TL;DR

This study shows that DNA methylation in the ONECUT2 gene predicts its expression and the aggressiveness of prostate cancer in biopsies.

Contribution

The study identifies ONECUT2 gene-body methylation as a novel biomarker for prostate cancer aggressiveness and potential therapeutic target.

Findings

ONECUT2 gene-body methylation strongly correlates with its expression and patient survival in prostate cancer datasets.

Hypermethylation of ONECUT2 gene-body distinguishes tumor from normal tissue in biopsies with high accuracy (AUC = 0.86).

ONECUT2 methylation predicts aggressive cancer features like higher Gleason score and lymph node involvement.

Abstract

ONECUT2 is a lineage plasticity driver and therapeutic target in aggressive prostate cancer (PCa). This study investigated whether ONECUT2 gene-body DNA methylation regulates its expression and assessed its potential as a biomarker in clinical specimens.

We analyzed associations between ONECUT2 gene-body methylation, expression, and patient survival across multiple datasets. The effect of DNA methylation on ONECUT2 expression was tested in prostate cancer cell lines using a DNA methyltransferase inhibitor (DNMTi). Validation was further performed in needle biopsy samples by targeted bisulfite sequencing for DNA methylation and RT-PCR for gene expression.

ONECUT2 expression strongly correlated with gene-body DNA methylation and patient survival in multiple datasets. DNMTi treatment confirmed this relationship in prostate cancer cells. In 208 biopsies from prostate cancer patients, hypermethylation of gene-body of ONECUT2 was linked to higher ONECUT2 expression and effectively distinguished tumor from adjacent normal tissue (p < 0.001 and AUC = 0.86). It also predicted aggressive features, including higher Gleason score (p = 0.01 and AUC = 0.68), advanced T stage (p = 0.04 and AUC = 0.65), seminal vesicle invasion (p = 0.0024 and AUC = 0.76), and lymph node involvement (p = 0.0005 and AUC = 0.80).

Assessing ONECUT2 gene-body methylation in biopsies may serve as a surrogate for ONECUT2 expression and provide predictive insights into disease progression before surgery. Furthermore, suppressing ONECUT2 through DNMTi treatment represents a potential therapeutic strategy for aggressive PCa.

The online version contains supplementary material available at 10.1186/s40364-026-00890-7.

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